1
|
Han SJ, Kim H, Ku SY, Suh CS. Comparison of resumption of ovulation after cessation of oral contraceptives and medroxyprogesterone acetate in women with polycystic ovary syndrome. Gynecol Endocrinol 2024; 40:2309349. [PMID: 38306179 DOI: 10.1080/09513590.2024.2309349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/17/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVE Both oral contraceptive pills (OCPs) and cyclic medroxyprogesterone acetate (MPA) are widely used to control menstrual abnormalities in women with polycystic ovary syndrome (PCOS). We aimed to evaluate the chance of ovulation resumption after cessation of OCPs and MPA in women with PCOS. METHODS A retrospective study was conducted of women with PCOS who were treated with OCPs or cyclic MPA from September 2015 to March 2019. After cessation of medication, ovulation was assessed using basal body temperature and/or measurement of serum progesterone. The odds ratio for ovulation resumption was assessed with multivariable logistic regression. Additionally, doubly robust analysis was performed with inverse-probability-weighted analysis and regression adjustment based on the covariate balancing propensity score to adjust for the effect of covariates on the treatment assignment. RESULTS Among 272 women with PCOS, 136 were prescribed OCPs and 136 were prescribed cyclic MPA. Ovulation resumed in 18.4% of women (n = 25) after cessation of MPA and in 24.3% of women (n = 33) after cessation of OCPs. The odds of ovulation resumption in MPA users were comparable with those in OCP users (adjusted odds ratio (aOR) 1.00, 95% confidence interval (CI) 0.89-1.12). After multiple imputation due to missing values, the results did not change substantially (aOR 0.99, 95% CI 0.89-1.10). CONCLUSIONS Among women with PCOS, MPA users have a similar chance of ovulation resumption as OCP users after cessation of medication. Cyclic MPA can be a good alternative to OCPs in women for whom OCPs are contraindicated or who decline to take OCPs.
Collapse
Affiliation(s)
- Soo Jin Han
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Hoon Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Seung-Yup Ku
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| | - Chang Suk Suh
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Korea
| |
Collapse
|
2
|
Cheng X, Meng X, Chen R, Song Z, Li S, Wei S, Lv H, Zhang S, Tang H, Jiang Y, Zhang R. The molecular subtypes of autoimmune diseases. Comput Struct Biotechnol J 2024; 23:1348-1363. [PMID: 38596313 PMCID: PMC11001648 DOI: 10.1016/j.csbj.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Autoimmune diseases (ADs) are characterized by their complexity and a wide range of clinical differences. Despite patients presenting with similar symptoms and disease patterns, their reactions to treatments may vary. The current approach of personalized medicine, which relies on molecular data, is seen as an effective method to address the variability in these diseases. This review examined the pathologic classification of ADs, such as multiple sclerosis and lupus nephritis, over time. Acknowledging the limitations inherent in pathologic classification, the focus shifted to molecular classification to achieve a deeper insight into disease heterogeneity. The study outlined the established methods and findings from the molecular classification of ADs, categorizing systemic lupus erythematosus (SLE) into four subtypes, inflammatory bowel disease (IBD) into two, rheumatoid arthritis (RA) into three, and multiple sclerosis (MS) into a single subtype. It was observed that the high inflammation subtype of IBD, the RA inflammation subtype, and the MS "inflammation & EGF" subtype share similarities. These subtypes all display a consistent pattern of inflammation that is primarily driven by the activation of the JAK-STAT pathway, with the effective drugs being those that target this signaling pathway. Additionally, by identifying markers that are uniquely associated with the various subtypes within the same disease, the study was able to describe the differences between subtypes in detail. The findings are expected to contribute to the development of personalized treatment plans for patients and establish a strong basis for tailored approaches to treating autoimmune diseases.
Collapse
Affiliation(s)
| | | | | | - Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuhao Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hao Tang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| |
Collapse
|
3
|
Gong B, Qu T, Zhang J, Jia Y, Song Z, Chen C, Yang J, Wang C, Liu Y, Jin Y, Cao W, Zhao Q. Downregulation of ABLIM3 confers to the metastasis of neuroblastoma via regulating the cell adhesion molecules pathway. Comput Struct Biotechnol J 2024; 23:1547-1561. [PMID: 38645433 PMCID: PMC11031727 DOI: 10.1016/j.csbj.2024.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/30/2024] [Accepted: 04/07/2024] [Indexed: 04/23/2024] Open
Abstract
Neuroblastoma (NB) is the most prevalent extracranial solid tumor in pediatric patients, and its treatment failure often associated with metastasis. In this study, LASSO, SVM-RFE, and random forest tree algorithms, was used to identify the pivotal gene involved in NB metastasis. NB cell lines (SK-N-AS and SK-N-BE2), in conjunction with NB tissue were used for further study. ABLIM3 was identified as the hub gene and can be an independent prognostic factor for patients with NB. The immunohistochemical analysis revealed that ABLIM3 is negatively correlated with the metastasis of NB. Patients with low expression of ABLIM3 had a poor prognosis. High ABLIM3 expression correlated with APC co-stimulation and Type1 IFN response, and TIDE analysis indicated that patients with low ABLIM3 expression exhibited enhanced responses to immunotherapy. Downregulation of ABLIM3 by shRNA transfection increased the migration and invasion ability of NB cells. Gene Set Enrichment Analysis (GSEA) revealed that genes associated with ABLIM3 were primarily enriched in the cell adhesion molecules (CAMs) pathway. RT-qPCR and western blot analyses demonstrated that downregulation of ABLIM3 led to decreased expression of ITGA3, ITGA8, and KRT19, the key components of CAMs. This study indicated that ABLIM3 can be an independent prognostic factor for NB patients, and CAMs may mediate the effect of ABLIM3 on the metastasis of NB, suggesting that ABLIM3 is a potential therapeutic target for NB metastasis, which provides a novel strategy for future research and treatment strategies for NB patients.
Collapse
Affiliation(s)
- Baocheng Gong
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Tongyuan Qu
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Jiaojiao Zhang
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yubin Jia
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Zian Song
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Chong Chen
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jiaxing Yang
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Chaoyu Wang
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yun Liu
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yan Jin
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Wenfeng Cao
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Qiang Zhao
- Department of Pediatric Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| |
Collapse
|
4
|
Han X, Li C, Yuan X, Cui J, Han Z, Meng J, Zhao W, Xie F, Wang K, Liu Y, Muo G, Xi N, Zheng M, Wang R, Xiao K, Chen W, Xiong J, Zhao D, Zhang X, Han X, Cheng H, Yu Z, Shi Y, Xie W, Xie L. Associations of nirmatrelvir-ritonavir treatment with death and clinical improvement in hospitalized patients with COVID-19 during the Omicron wave in Beijing, China: a multicentre, retrospective cohort study. Ann Med 2024; 56:2313062. [PMID: 38354691 PMCID: PMC10868413 DOI: 10.1080/07853890.2024.2313062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND The effectiveness of nirmatrelvir-ritonavir has mainly been shown in non-hospitalized patients with mild-to-moderate coronavirus disease 2019 (COVID-19). The real-world effectiveness of nirmatrelvir-ritonavir urgently needs to be determined using representative in-hospital patients with COVID-19 during the Omicron wave of the pandemic. METHODS We performed a multicentre, retrospective study in five Chinese PLA General Hospital medical centers in Beijing, China. Patients hospitalized with COVID-19 from 10 December 2022 to 20 February 2023 were eligible for inclusion. A 1:1 propensity score matching was performed between the nirmatrelvir-ritonavir group and the control group. RESULTS 1010 recipients of nirmatrelvir-ritonavir and 1010 matched controls were finally analyzed after matching. Compared with matched controls, the nirmatrelvir-ritonavir group had a lower incidence rate of all-cause death (4.6/1000 vs. 6.3/1000 person-days, p = 0.013) and a higher incidence rate of clinical improvement (47.6/1000 vs. 45.8/1000 person-days, p = 0.012). Nirmatrelvir-ritonavir was associated with a 22% lower all-cause mortality and a 14% higher incidence of clinical improvement. Initiation of nirmatrelvir-ritonavir within 5 days after symptom onset was associated with a 50% lower mortality and a 26% higher clinical improvement rate. By contrast, no significant associations were identified among patients receiving nirmatrelvir-ritonavir treatment more than 5 days after symptom onset. Nirmatrelvir-ritonavir was also associated with a 50% increase in survival days and a 12% decrease in days to clinical improvement. CONCLUSION Among hospitalized patients with COVID-19 during the Omicron wave in Beijing, China, the early initiation of nirmatrelvir-ritonavir was associated with clinical benefits of lowering mortality and improving clinical recovery.
Collapse
Affiliation(s)
- Xiaobo Han
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Chenglong Li
- National Institute of Health Data Science, Peking University, Beijing, China
- Institute of Medical Technology, Health Science Center of Peking University, Beijing, China
| | - Xin Yuan
- Pulmonary and Critical Care Medicine Department, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Junchang Cui
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Zhihai Han
- Pulmonary and Critical Care Medicine Department, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jiguang Meng
- Pulmonary and Critical Care Medicine Department, The Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
- Naval Clinical College, Anhui Medical University, Hefei, China
| | - Weiguo Zhao
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fei Xie
- Pulmonary and Critical Care Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Kaifei Wang
- Pulmonary and Critical Care Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yuhong Liu
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Guoxin Muo
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Na Xi
- Pharmacy Department, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Mengli Zheng
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Rentao Wang
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Kun Xiao
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Wei Chen
- Pulmonary and Critical Care Medicine Department, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Junchen Xiong
- Pulmonary and Critical Care Medicine Department, The Sixth Medical Center, Chinese PLA General Hospital, Beijing, China
- Pulmonary and Critical Care Medicine Department, The Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Dahui Zhao
- Pulmonary and Critical Care Medicine Department, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xinxin Zhang
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xinjie Han
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Haibo Cheng
- Shandong Future Network Research Institute, Jiangsu Future Network Group Co., Ltd., Jiangsu, China
| | - Zhongkuo Yu
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Yinghan Shi
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| | - Wuxiang Xie
- Peking University Clinical Research Institute, Peking University First Hospital, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, Beijing, China
| | - Lixin Xie
- College of Pulmonary and Critical Care Medicine, The Eighth Medical Center, Chinese PLA General Hospital, Beijing, China
- Chinese PLA Medical School, Beijing, China
| |
Collapse
|
5
|
Ali W, Overton CE, Wilkinson RR, Sharkey KJ. Deterministic epidemic models overestimate the basic reproduction number of observed outbreaks. Infect Dis Model 2024; 9:680-688. [PMID: 38638338 PMCID: PMC11024615 DOI: 10.1016/j.idm.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 04/20/2024] Open
Abstract
The basic reproduction number, R0, is a well-known quantifier of epidemic spread. However, a class of existing methods for estimating R0 from incidence data early in the epidemic can lead to an over-estimation of this quantity. In particular, when fitting deterministic models to estimate the rate of spread, we do not account for the stochastic nature of epidemics and that, given the same system, some outbreaks may lead to epidemics and some may not. Typically, an observed epidemic that we wish to control is a major outbreak. This amounts to implicit selection for major outbreaks which leads to the over-estimation problem. We formally characterised the split between major and minor outbreaks by using Otsu's method which provides us with a working definition. We show that by conditioning a 'deterministic' model on major outbreaks, we can more reliably estimate the basic reproduction number from an observed epidemic trajectory.
Collapse
Affiliation(s)
- Wajid Ali
- Department of Mathematical Sciences, University of Liverpool, Peach Street, Liverpool, L69 7ZX, England, United Kingdom
| | - Christopher E. Overton
- Department of Mathematical Sciences, University of Liverpool, Peach Street, Liverpool, L69 7ZX, England, United Kingdom
| | - Robert R. Wilkinson
- Department of Applied Mathematics, Liverpool John Moores University, Byrom Street, Liverpool, L3 5UX, England, United Kingdom
| | - Kieran J. Sharkey
- Department of Mathematical Sciences, University of Liverpool, Peach Street, Liverpool, L69 7ZX, England, United Kingdom
| |
Collapse
|
6
|
Park S, Kim J, Wang X, Lim J. Variable Selection in Bayesian Multiple Instance Regression using Shotgun Stochastic Search. Comput Stat Data Anal 2024; 196:107954. [PMID: 38646418 PMCID: PMC11027161 DOI: 10.1016/j.csda.2024.107954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
In multiple instance learning (MIL), a bag represents a sample that has a set of instances, each of which is described by a vector of explanatory variables, but the entire bag only has one label/response. Though many methods for MIL have been developed to date, few have paid attention to interpretability of models and results. The proposed Bayesian regression model stands on two levels of hierarchy, which transparently show how explanatory variables explain and instances contribute to bag responses. Moreover, two selection problems are simultaneously addressed; the instance selection to find out the instances in each bag responsible for the bag response, and the variable selection to search for the important covariates. To explore a joint discrete space of indicator variables created for selection of both explanatory variables and instances, the shotgun stochastic search algorithm is modified to fit in the MIL context. Also, the proposed model offers a natural and rigorous way to quantify uncertainty in coefficient estimation and outcome prediction, which many modern MIL applications call for. The simulation study shows the proposed regression model can select variables and instances with high performance (AUC greater than 0.86), thus predicting responses well. The proposed method is applied to the musk data for prediction of binding strengths (labels) between molecules (bags) with different conformations (instances) and target receptors. It outperforms all existing methods, and can identify variables relevant in modeling responses.
Collapse
Affiliation(s)
- Seongoh Park
- School of Mathematics, Statistics and Data Science, Sungshin Women’s University, Seoul, Korea
- Data Science Center, Sungshin Women’s University, Seoul, Korea
| | - Joungyoun Kim
- Department of Artificial Intelligence, University of Seoul, Seoul, Korea
| | - Xinlei Wang
- Center for Data Science Research and Education, College of Science, University of Texas at Arlington, Arlington, TX, USA
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, USA
| | - Johan Lim
- Department of Statistics, Seoul National University, Seoul, 08826, Korea
| |
Collapse
|
7
|
Yamasaki Y, Nakamura K, Kashiwabara N, Chiba S, Akiyama H, Tsutsumi T. Development of a processing factor prediction model for pesticides in processed tomato foods using elastic net regularization. Food Chem 2024; 447:138943. [PMID: 38489881 DOI: 10.1016/j.foodchem.2024.138943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/09/2024] [Accepted: 03/02/2024] [Indexed: 03/17/2024]
Abstract
A novel regularized elastic net regression model was developed to predict processing factor (PF) for pesticide residues, which represents a change in the residue levels during food processing. The PF values for tomato juice, wet pomace and dry pomace in the evaluations and reports published by the Joint FAO/WHO Meeting on Pesticide Residues significantly correlated with the physicochemical properties of pesticides, and subsequently the correlation was observed in the present tomato processing study. The elastic net regression model predicted the PF values using the physicochemical properties as predictor variables for both training and test data within a 2-fold range for 80-100% of the pesticides tested in the tomato processing study while overcoming multicollinearity. These results suggest that the PF values are predictable at a certain degree of accuracy from the unique sets of physicochemical properties of pesticides using the developed model based on a processing study with representative pesticides.
Collapse
Affiliation(s)
- Yuki Yamasaki
- Division of Foods, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Kosuke Nakamura
- Division of Foods, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan.
| | - Nao Kashiwabara
- Division of Foods, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Shinji Chiba
- Division of Foods, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Hiroshi Akiyama
- Division of Foods, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan; Department of Analytical Chemistry, School of Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-Ku, Tokyo 142-8501, Japan
| | - Tomoaki Tsutsumi
- Division of Foods, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| |
Collapse
|
8
|
Qin X, Hu J, Ma S, Wu M. Estimation of multiple networks with common structures in heterogeneous subgroups. J MULTIVARIATE ANAL 2024; 202:105298. [PMID: 38433779 PMCID: PMC10907012 DOI: 10.1016/j.jmva.2024.105298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Network estimation has been a critical component of high-dimensional data analysis and can provide an understanding of the underlying complex dependence structures. Among the existing studies, Gaussian graphical models have been highly popular. However, they still have limitations due to the homogeneous distribution assumption and the fact that they are only applicable to small-scale data. For example, cancers have various levels of unknown heterogeneity, and biological networks, which include thousands of molecular components, often differ across subgroups while also sharing some commonalities. In this article, we propose a new joint estimation approach for multiple networks with unknown sample heterogeneity, by decomposing the Gaussian graphical model (GGM) into a collection of sparse regression problems. A reparameterization technique and a composite minimax concave penalty are introduced to effectively accommodate the specific and common information across the networks of multiple subgroups, making the proposed estimator significantly advancing from the existing heterogeneity network analysis based on the regularized likelihood of GGM directly and enjoying scale-invariant, tuning-insensitive, and optimization convexity properties. The proposed analysis can be effectively realized using parallel computing. The estimation and selection consistency properties are rigorously established. The proposed approach allows the theoretical studies to focus on independent network estimation only and has the significant advantage of being both theoretically and computationally applicable to large-scale data. Extensive numerical experiments with simulated data and the TCGA breast cancer data demonstrate the prominent performance of the proposed approach in both subgroup and network identifications.
Collapse
Affiliation(s)
- Xing Qin
- School of Statistics and Information, Shanghai University of International Business and Economics, Shanghai, China
| | - Jianhua Hu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
| | - Shuangge Ma
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
| | - Mengyun Wu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
| |
Collapse
|
9
|
Sampedro-Piquero P, Buades-Sitjar F, Capilla A, Zancada-Menéndez C, González-Baeza A, Moreno-Fernández RD. Risky alcohol use during youth: Impact on emotion, cognitive networks, and resting-state EEG activity. Prog Neuropsychopharmacol Biol Psychiatry 2024; 132:110994. [PMID: 38514039 DOI: 10.1016/j.pnpbp.2024.110994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024]
Abstract
The identification of the risk factors of alcohol consumption in youths is crucial for early interventions focused on reducing harmful alcohol use. In our study, 82 college students (40 healthy control (CO group) and 42 with risky alcohol use (RAU group) determined by AUDIT questionnaire) between the ages of 18 and 25 years underwent a comprehensive neuropsychological assessment covering emotional and cognitive functioning. Their resting-state activity was also recorded with an EEG for 10 min with their eyes open (EO) and 10 min with their eyes closed (EC) and analyzed using the Fitting Oscillations & One-Over-F (FOOOF) paradigm. After adjusting for sex, those in the RAU group had higher emotional dysregulation and impulsivity traits. The RAU girls presented more emotional regulation problems, such as dysregulation and negative urgency compared with the RAU boys. The RAU youths had significantly worse functioning in several cognitive domains, such as sustained attention, verbal memory, and executive functions. Cognitive network analysis revealed a different pattern of connections in each group showing that in the RAU group, the verbal memory domain had the highest connection with other cognitive functions. The EEG analyses did not reveal any significant differences between the CO and the RAU groups. However, we observed only in the EO condition that boys the from the RAU group displayed a higher theta/beta ratio than the RAU girls, whereas these differences were not observed within the CO group. Our findings highlight the need to explore more deeply the emotional, cognitive and brain changes underlying the RAU in young people.
Collapse
Affiliation(s)
- P Sampedro-Piquero
- Departamento de Psicología Biológica y de la Salud, Facultad de Psicología, Universidad Autónoma de Madrid, Spain.
| | - F Buades-Sitjar
- Departamento de Psicología Biológica y de la Salud, Facultad de Psicología, Universidad Autónoma de Madrid, Spain
| | - A Capilla
- Departamento de Psicología Biológica y de la Salud, Facultad de Psicología, Universidad Autónoma de Madrid, Spain
| | - C Zancada-Menéndez
- Facultad de Ciencias de la Salud, Universidad Internacional de La Rioja (UNIR), Logroño, Spain
| | - A González-Baeza
- Departamento de Psicología Biológica y de la Salud, Facultad de Psicología, Universidad Autónoma de Madrid, Spain
| | | |
Collapse
|
10
|
Khoraminejad B, Sakowitz S, Gao Z, Chervu N, Curry J, Ali K, Bakhtiyar SS, Benharash P. Association of substance-use disorder with outcomes of major elective abdominal operations: A contemporary national analysis. Surg Open Sci 2024; 19:44-49. [PMID: 38585038 PMCID: PMC10995883 DOI: 10.1016/j.sopen.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 03/15/2024] [Indexed: 04/09/2024] Open
Abstract
Background Affecting >20million people in the U.S., including 4 % of all hospitalized patients, substance use disorder (SUD) represents a growing public health crisis. Evaluating a national cohort, we aimed to characterize the association of concurrent SUD with perioperative outcomes and resource utilization following elective abdominal operations. Methods All adult hospitalizations entailing elective colectomy, gastrectomy, esophagectomy, hepatectomy, and pancreatectomy were tabulated from the 2016-2020 National Inpatient Sample. Patients with concurrent substance use disorder, comprising alcohol, opioid, marijuana, sedative, cocaine, inhalant, hallucinogen, or other psychoactive/stimulant use, were considered the SUD cohort (others: nSUD). Multivariable regression models were constructed to evaluate the independent association between SUD and key outcomes. Results Of ∼1,088,145 patients, 32,865 (3.0 %) comprised the SUD cohort. On average, SUD patients were younger, more commonly male, of lowest quartile income, and of Black race. SUD patients less frequently underwent colectomy, but more often pancreatectomy, relative to nSUD.Following risk adjustment and with nSUD as reference, SUD demonstrated similar likelihood of in-hospital mortality, but remained associated with increased odds of any perioperative complication (Adjusted Odds Ratio [AOR] 1.17, CI 1.09-1.25). Further, SUD was linked with incremental increases in adjusted length of stay (β + 0.90 days, CI +0.68-1.12) and costs (β + $3630, CI +2650-4610), as well as greater likelihood of non-home discharge (AOR 1.54, CI 1.40-1.70). Conclusions Concurrent substance use disorder was associated with increased complications, resource utilization, and non-home discharge following major elective abdominal operations. Novel interventions are warranted to address increased risk among this vulnerable population and address significant disparities in postoperative outcomes.
Collapse
Affiliation(s)
- Baran Khoraminejad
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
- Boston University, Boston, MA, United States of America
| | - Sara Sakowitz
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Zihan Gao
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Nikhil Chervu
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Joanna Curry
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Konmal Ali
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Syed Shahyan Bakhtiyar
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, University of Colorado, Denver, Aurora, CO, United States of America
| | - Peyman Benharash
- CORELAB, Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
- Department of Surgery, University of California, Los Angeles, Los Angeles, CA, United States of America
| |
Collapse
|
11
|
Wang Z, Rowe DB, Li X, Brown DA. A fully Bayesian approach for comprehensive mapping of magnitude and phase brain activation in complex-valued fMRI data. Magn Reson Imaging 2024; 109:271-285. [PMID: 38537891 DOI: 10.1016/j.mri.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/03/2024] [Accepted: 03/19/2024] [Indexed: 04/01/2024]
Abstract
Functional magnetic resonance imaging (fMRI) plays a crucial role in neuroimaging, enabling the exploration of brain activity through complex-valued signals. These signals, composed of magnitude and phase, offer a rich source of information for understanding brain functions. Traditional fMRI analyses have largely focused on magnitude information, often overlooking the potential insights offered by phase data. In this paper, we propose a novel fully Bayesian model designed for analyzing single-subject complex-valued fMRI (cv-fMRI) data. Our model, which we refer to as the CV-M&P model, is distinctive in its comprehensive utilization of both magnitude and phase information in fMRI signals, allowing for independent prediction of different types of activation maps. We incorporate Gaussian Markov random fields (GMRFs) to capture spatial correlations within the data, and employ image partitioning and parallel computation to enhance computational efficiency. Our model is rigorously tested through simulation studies, and then applied to a real dataset from a unilateral finger-tapping experiment. The results demonstrate the model's effectiveness in accurately identifying brain regions activated in response to specific tasks, distinguishing between magnitude and phase activation.
Collapse
Affiliation(s)
- Zhengxin Wang
- School of Mathematical and Statistical Sciences, Clemson University, Clemson 29634, SC, USA
| | - Daniel B Rowe
- Department of Mathematical and Statistical Sciences, Marquette University, Milwaukee 53233, WI, USA
| | - Xinyi Li
- School of Mathematical and Statistical Sciences, Clemson University, Clemson 29634, SC, USA
| | - D Andrew Brown
- School of Mathematical and Statistical Sciences, Clemson University, Clemson 29634, SC, USA.
| |
Collapse
|
12
|
Westberry BP, Rio M, Waterland MR, Williams MAK. On the origin of optical rotation changes during the κ-carrageenan disorder-to-order transition. Carbohydr Polym 2024; 333:121975. [PMID: 38494229 DOI: 10.1016/j.carbpol.2024.121975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/19/2024]
Abstract
It is well established that solutions of both polymeric and oligomeric κ-carrageenan exhibit a clear change in optical rotation (OR), in concert with gel-formation for polymeric samples, as the solution is cooled in the presence of certain ions. The canonical interpretation - that this OR change reflects a 'coil-to-helix transition' in single chains - has seemed unambiguous; the solution- or 'disordered'-state structure has ubiquitously been assumed to be a 'random coil', and the helical nature of carrageenan in the solid-state was settled in the 1970s. However, recent work has found that κ-carrageenan contains substantial helical secondary structure elements in the disordered-state, raising doubts over the validity of this interpretation. To investigate the origins of the OR, density-functional theory calculations were conducted using atomic models of κ-carrageenan oligomers. Changes were found to occur in the predicted OR owing purely to dimerization of chains, and - together with the additional effects of slight changes in conformation that occur when separated helical chains form double-helices - the predicted OR changes are qualitatively consistent with experimental results. These findings contribute to a growing body of evidence that the carrageenan 'disorder-to-order' transition is a cooperative process, and have further implications for the interpretation of OR changes demonstrated by macromolecules in general.
Collapse
Affiliation(s)
- B P Westberry
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand; Fonterra Research and Development Centre, Private Bag 11029, Dairy Farm Road, Palmerston North, New Zealand.
| | - M Rio
- National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand; Science Infrastructure (NeSI), Auckland, New Zealand
| | - M R Waterland
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - M A K Williams
- School of Natural Sciences, Massey University, Palmerston North, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| |
Collapse
|
13
|
Flaig J, Houy N. Disease X epidemic control using a stochastic model and a deterministic approximation: Performance comparison with and without parameter uncertainties. Comput Methods Programs Biomed 2024; 249:108136. [PMID: 38537494 DOI: 10.1016/j.cmpb.2024.108136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/21/2024]
Abstract
BACKGROUND The spread of infectious diseases can be modeled using deterministic or stochastic models. A deterministic approximation of a stochastic model can be appropriate under some conditions, but is unable to capture the discrete nature of populations. We look into the choice of a model from the perspective of decision making. METHOD We consider an emerging disease (Disease X) in a closed population modeled by a stochastic SIR model or its deterministic approximation. The objective of the decision maker is to minimize the cumulative number of symptomatic infected-days over the course of the epidemic by picking a vaccination policy. We consider four decision making scenarios: based on the stochastic model or the deterministic model, and with or without parameter uncertainty. We also consider different sample sizes for uncertain parameter draws and stochastic model runs. We estimate the average performance of decision making in each scenario and for each sample size. RESULTS The model used for decision making has an influence on the picked policies. The best achievable performance is obtained with the stochastic model, knowing parameter values, and for a large sample size. For small sample sizes, the deterministic model can outperform the stochastic model due to stochastic effects. Resolving uncertainties may bring more benefit than switching to the stochastic model in our example. CONCLUSION This article illustrates the interplay between the choice of a type of model, parameter uncertainties, and sample sizes. It points to issues to be considered when optimizing a stochastic model.
Collapse
Affiliation(s)
- Julien Flaig
- Epidemiology and Modelling of Infectious Diseases (EPIMOD), F-69002 Lyon, France.
| | - Nicolas Houy
- University of Lyon, Lyon, F-69007, France; CNRS, GATE Lyon Saint-Etienne, F-69130, France.
| |
Collapse
|
14
|
Räike A, Taskinen A, Härkönen LH, Kortelainen P, Lepistö A. Browning from headwaters to coastal areas in the boreal region: Trends and drivers. Sci Total Environ 2024; 927:171959. [PMID: 38537816 DOI: 10.1016/j.scitotenv.2024.171959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/05/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024]
Abstract
Browning of freshwaters, mainly caused by increased terrestrial organic carbon loading, has been widely studied during the last decades. However, there are still uncertainties regarding both the extent of browning in different aquatic ecosystems and the actual importance of different driving forces and mechanisms. To refine understanding of the extent and causes of browning and its temporal variation, we gathered a comprehensive dataset including 746 Finnish water quality monitoring stations representing various waterbody types: streams, rivers, lakes, and coastal waters. Monotonic trend analyses revealed that TOC concentrations increased in all waterbody types during the study period from 1990 to 2020, whereas non-linear trends indicated that upward trends in TOC concentrations have substantially decreased since the mid-2000s. However, despite the upward trends levelling off, non-linear analyses also indicated decreases in TOC concentrations at only a few stations. As a result, the TOC contents of the majority of Finnish waterbody types in 2020 were at a higher level than in 1990. To examine the driving forces of increasing TOC concentrations, we selected 100 riverine catchments and linked the detected trends to 24 different drivers, including both hydrometeorological and catchment characteristics. The increased TOC concentrations in surface waters could be connected to diverse human impacts: hydrometeorological variables impacted by climate change, decreased acidic deposition, and land use in terms of peatland drainage. The importance of increased temperatures was emphasized, and its role as a driver of increased leaching of organic carbon in the forthcoming years is expected to grow with climate change.
Collapse
Affiliation(s)
- Antti Räike
- Finnish Environment Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland.
| | - Antti Taskinen
- Finnish Environment Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Laura H Härkönen
- Finnish Environment Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Pirkko Kortelainen
- Finnish Environment Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Ahti Lepistö
- Finnish Environment Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| |
Collapse
|
15
|
Csordas A, Sipos B, Kurucova T, Volfova A, Zamola F, Tichy B, Hicks DG. Cell Tree Rings: the structure of somatic evolution as a human aging timer. GeroScience 2024; 46:3005-3019. [PMID: 38172489 PMCID: PMC11009167 DOI: 10.1007/s11357-023-01053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Biological age is typically estimated using biomarkers whose states have been observed to correlate with chronological age. A persistent limitation of such aging clocks is that it is difficult to establish how the biomarker states are related to the mechanisms of aging. Somatic mutations could potentially form the basis for a more fundamental aging clock since the mutations are both markers and drivers of aging and have a natural timescale. Cell lineage trees inferred from these mutations reflect the somatic evolutionary process, and thus, it has been conjectured, the aging status of the body. Such a timer has been impractical thus far, however, because detection of somatic variants in single cells presents a significant technological challenge. Here, we show that somatic mutations detected using single-cell RNA sequencing (scRNA-seq) from thousands of cells can be used to construct a cell lineage tree whose structure correlates with chronological age. De novo single-nucleotide variants (SNVs) are detected in human peripheral blood mononuclear cells using a modified protocol. A default model based on penalized multiple regression of chronological age on 31 metrics characterizing the phylogenetic tree gives a Pearson correlation of 0.81 and a median absolute error of ~4 years between predicted and chronological ages. Testing of the model on a public scRNA-seq dataset yields a Pearson correlation of 0.85. In addition, cell tree age predictions are found to be better predictors of certain clinical biomarkers than chronological age alone, for instance glucose, albumin levels, and leukocyte count. The geometry of the cell lineage tree records the structure of somatic evolution in the individual and represents a new modality of aging timer. In addition to providing a numerical estimate of "cell tree age," it unveils a temporal history of the aging process, revealing how clonal structure evolves over life span. Cell Tree Rings complements existing aging clocks and may help reduce the current uncertainty in the assessment of geroprotective trials.
Collapse
Affiliation(s)
- Attila Csordas
- AgeCurve Limited, Cambridge, CB2 1SD, UK.
- Doctoral School of Clinical Medicine, University of Szeged, Szeged, H-6720, Hungary.
| | | | - Terezia Kurucova
- CEITEC - Central European Institute of Technology, Masaryk University, 62500, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, 62500, Brno, Czechia
| | - Andrea Volfova
- HealthyLongevity.clinic Inc, 540 University Ave, Palo Alto, CA, 94301, USA
| | - Frantisek Zamola
- HealthyLongevity.clinic Inc, 540 University Ave, Palo Alto, CA, 94301, USA
| | - Boris Tichy
- CEITEC - Central European Institute of Technology, Masaryk University, 62500, Brno, Czechia
| | - Damien G Hicks
- AgeCurve Limited, Cambridge, CB2 1SD, UK
- Swinburne University of Technology, Hawthorn, VIC, 3122, Australia
| |
Collapse
|
16
|
She Z, Liu Z, Cai H, Liu H, Song Y, Li B, Lan X, Jiang T. A framework to evaluate the impact of a hazard chain and geographical covariates on spatial extreme water levels: A case study in the Pearl River Delta. Sci Total Environ 2024; 926:172066. [PMID: 38556022 DOI: 10.1016/j.scitotenv.2024.172066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
The interactions and collective impacts of different types of hazards within a compound hazard system, along with the influence of geographical covariates on flooding are presently unclear. Understanding these relationships is crucial for comprehending the formation and dynamic processes of the hazard chain and improving the ability to identify flood warning signals in complex hazard scenarios. In this study, we presented a multivariate spatial extreme value hierarchical (MSEVH) framework to assess the spatial extreme water levels (EWL) at different return levels under the influence of a hazard chain and geographical covariates. The Pearl River Delta (PRD) was selected as a research example to assess the effectiveness of the MSEVH framework. Firstly, we identified a hazard chain (extreme streamflow from the Xijiang River (XR) - extreme streamflow from the Beijiang River (BR) - extreme sea level) and three geographical covariates influencing EWL in the PRD. Then, we compared four hazard scenarios in the MSEVH framework to evaluate the spatial EWL at different return levels under the influence of the hazard chain in the PRD. The final step involves assessing spatial EWL with the effect of the hazard chain and geographical covariates. The results indicate that when extreme streamflow from XR and BR occurs concurrently, the extreme streamflow from BR weakens the influence of extreme streamflow from XR on EWL in the PRD. However, it cannot fully offset the overall impact of extreme streamflow from XR on EWL. In addition, when extreme streamflow from XR, extreme streamflow from BR, and extreme sea level occur simultaneously, the extreme sea level enhances the influence of concurrent extreme streamflow from XR and BR on EWL in the PRD. The proposed MSEVH is not only applicable to the PRD but also shows promising potential for evaluating extreme hydrometeorological variables under the influence of other hazard chains.
Collapse
Affiliation(s)
- Zhenyan She
- Institute of Estuarine and Coastal Research, School of Ocean Engineering and Technology, Sun Yat-sen University, 519082 Zhuhai, China
| | - Zhiyong Liu
- Center for Water Resources and Environment, School of Civil Engineering, Sun Yat-sen University, Guangzhou 510275, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519082 Zhuhai, China.
| | - Huayang Cai
- Institute of Estuarine and Coastal Research, School of Ocean Engineering and Technology, Sun Yat-sen University, 519082 Zhuhai, China.
| | - Haibo Liu
- Powerchina Eco-environmental Group Co., Ltd., Shenzhen 518101, China
| | - Yunlong Song
- VAST Institute of Water Ecology and Environment, Shenzhen 518101, China
| | - Bo Li
- Institute of Estuarine and Coastal Research, School of Ocean Engineering and Technology, Sun Yat-sen University, 519082 Zhuhai, China
| | - Xin Lan
- Center for Water Resources and Environment, School of Civil Engineering, Sun Yat-sen University, Guangzhou 510275, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519082 Zhuhai, China
| | - Tao Jiang
- School of Geography and Planning, Sun Yat-Sen University, Guangzhou 510006, China
| |
Collapse
|
17
|
Song Y, Han H, Fu L, Wang T. Penalized weighted smoothed quantile regression for high-dimensional longitudinal data. Stat Med 2024; 43:2007-2042. [PMID: 38634309 DOI: 10.1002/sim.10056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/30/2024] [Accepted: 02/25/2024] [Indexed: 04/19/2024]
Abstract
Quantile regression, known as a robust alternative to linear regression, has been widely used in statistical modeling and inference. In this paper, we propose a penalized weighted convolution-type smoothed method for variable selection and robust parameter estimation of the quantile regression with high dimensional longitudinal data. The proposed method utilizes a twice-differentiable and smoothed loss function instead of the check function in quantile regression without penalty, and can select the important covariates consistently using the efficient gradient-based iterative algorithms when the dimension of covariates is larger than the sample size. Moreover, the proposed method can circumvent the influence of outliers in the response variable and/or the covariates. To incorporate the correlation within each subject and enhance the accuracy of the parameter estimation, a two-step weighted estimation method is also established. Furthermore, we prove the oracle properties of the proposed method under some regularity conditions. Finally, the performance of the proposed method is demonstrated by simulation studies and two real examples.
Collapse
Affiliation(s)
- Yanan Song
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, China
| | - Haohui Han
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, China
| | - Liya Fu
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, China
| | - Ting Wang
- Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
18
|
Munko M, Ditzhaus M, Dobler D, Genuneit J. RMST-based multiple contrast tests in general factorial designs. Stat Med 2024; 43:1849-1866. [PMID: 38402907 DOI: 10.1002/sim.10017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/13/2023] [Accepted: 01/06/2024] [Indexed: 02/27/2024]
Abstract
Several methods in survival analysis are based on the proportional hazards assumption. However, this assumption is very restrictive and often not justifiable in practice. Therefore, effect estimands that do not rely on the proportional hazards assumption are highly desirable in practical applications. One popular example for this is the restricted mean survival time (RMST). It is defined as the area under the survival curve up to a prespecified time point and, thus, summarizes the survival curve into a meaningful estimand. For two-sample comparisons based on the RMST, previous research found the inflation of the type I error of the asymptotic test for small samples and, therefore, a two-sample permutation test has already been developed. The first goal of the present paper is to further extend the permutation test for general factorial designs and general contrast hypotheses by considering a Wald-type test statistic and its asymptotic behavior. Additionally, a groupwise bootstrap approach is considered. Moreover, when a global test detects a significant difference by comparing the RMSTs of more than two groups, it is of interest which specific RMST differences cause the result. However, global tests do not provide this information. Therefore, multiple tests for the RMST are developed in a second step to infer several null hypotheses simultaneously. Hereby, the asymptotically exact dependence structure between the local test statistics is incorporated to gain more power. Finally, the small sample performance of the proposed global and multiple testing procedures is analyzed in simulations and illustrated in a real data example.
Collapse
Affiliation(s)
- Merle Munko
- Department of Mathematics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Marc Ditzhaus
- Department of Mathematics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Dennis Dobler
- Department of Mathematics, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jon Genuneit
- Department of Pediatrics, Leipzig University, Leipzig, Germany
| |
Collapse
|
19
|
Cao W, Chu H, Hanson T, Siegel L. A Bayesian nonparametric meta-analysis model for estimating the reference interval. Stat Med 2024; 43:1905-1919. [PMID: 38409859 DOI: 10.1002/sim.10001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 10/24/2023] [Accepted: 12/17/2023] [Indexed: 02/28/2024]
Abstract
A reference interval represents the normative range for measurements from a healthy population. It plays an important role in laboratory testing, as well as in differentiating healthy from diseased patients. The reference interval based on a single study might not be applicable to a broader population. Meta-analysis can provide a more generalizable reference interval based on the combined population by synthesizing results from multiple studies. However, the assumptions of normally distributed underlying study-specific means and equal within-study variances, which are commonly used in existing methods, are strong and may not hold in practice. We propose a Bayesian nonparametric model with more flexible assumptions to extend random effects meta-analysis for estimating reference intervals. We illustrate through simulation studies and two real data examples the performance of our proposed approach when the assumptions of normally distributed study means and equal within-study variances do not hold.
Collapse
Affiliation(s)
- Wenhao Cao
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Haitao Chu
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, USA
- Statistical Research and Data Science Center, Pfizer Inc., New York, New York, USA
| | - Timothy Hanson
- Enterprise CRMS, Medtronic Plc, Mounds View, Minnesota, USA
| | - Lianne Siegel
- Division of Biostatistics and Health Data Science, University of Minnesota, Minneapolis, Minnesota, USA
| |
Collapse
|
20
|
de Oliveira ACP, Nunes A, Oliveira MA, Oliveira RS, Rodrigues RG, Branquinho C. Shifts in plant functional groups along an aridity gradient in a tropical dry forest. Sci Total Environ 2024; 924:171695. [PMID: 38485025 DOI: 10.1016/j.scitotenv.2024.171695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
Increasing aridity associated with climate change may lead to the crossing of critical ecosystem thresholds in drylands, compromising ecosystem services for millions of people. In this context, finding tools to detect at early stages the effects of increasing aridity on ecosystems is extremely urgent to avoid irreversible damage. Here, we assess shifts in plant community functional structure along a spatial aridity gradient in tropical dryland (Brazilian Caatinga), to select the most appropriate plant functional groups as ecological indicators likely useful to predict temporal ecosystem trajectories in response to aridity. We identified seven plant functional groups based on 13 functional traits associated with plant establishment, defense, regeneration, and dispersal, whose relative abundances changed, linearly and non-linearly, with increasing aridity, showing either increasing or decreasing trends. Of particular importance is the increase in abundance of plants with high chemical defense and Crassulacean Acid Metabolism (CAM) photosynthetic pathway, with increasing aridity. We propose the use of these functional groups as early warning indicators to detect aridity impacts on these dryland ecosystems and shifts in ecosystem functioning. This information can also be used in the elaboration of mitigation and ecological restoration measures to prevent and revert current and future climate change impacts on tropical dry forests.
Collapse
Affiliation(s)
- Ana Cláudia Pereira de Oliveira
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Institute for Global Change and Sustainability, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Alice Nunes
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Institute for Global Change and Sustainability, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
| | - Maria Alexandra Oliveira
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Institute for Global Change and Sustainability, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Rafael S Oliveira
- Department of Plant Biology, Universidade de Campinas, Campinas, São Paulo, Brazil
| | - Renato Garcia Rodrigues
- Centre for Ecology and Environmental Monitoring, Universidade Federal do Vale do São Francisco, Petrolina, Pernambuco, Brazil
| | - Cristina Branquinho
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Institute for Global Change and Sustainability, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| |
Collapse
|
21
|
Ayotte SH, Allen CR, Parker A, Stein OR, Lauchnor EG. Greenhouse gas production from an intermittently dosed cold-climate wastewater treatment wetland. Sci Total Environ 2024; 924:171484. [PMID: 38462002 DOI: 10.1016/j.scitotenv.2024.171484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/23/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024]
Abstract
This study explores the greenhouse gas (GHG) fluxes of nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) from a two-stage, cold-climate vertical-flow treatment wetland (TW) treating ski area wastewater at 3 °C average water temperature. The system is designed like a modified Ludzack-Ettinger process with the first stage a partially saturated, denitrifying TW followed by an unsaturated nitrifying TW and recycle of nitrified effluent. An intermittent wastewater dosing scheme was established for both stages, with alternating carbon-rich wastewater and nitrate-rich recycle to the first stage. The system has demonstrated effective chemical oxygen demand (COD) and total inorganic nitrogen (TIN) removal in high-strength wastewater over seven years of winter operation. Following two closed-loop, intensive GHG winter sampling campaigns at the TW, the magnitude of N2O flux was 2.2 times higher for denitrification than nitrification. CH4 and N2O emissions were strongly correlated with hydraulic loading, whereas CO2 was correlated with surface temperature. GHG fluxes from each stage were related to both microbial activity and off-gassing of dissolved species during wastewater dosing, thus the time of sampling relative to dosing strongly influenced observed fluxes. These results suggest that estimates of GHG fluxes from TWs may be biased if mass transfer and mechanisms of wastewater application are not considered. Emission factors for N2O and CH4 were 0.27 % as kg-N2O-N/kg-TINremoved and 0.04 % kg-CH4-C/kg-CODremoved, respectively. The system had observed seasonal emissions of 600.5 kg CO2 equivalent of GHGs estimated over 130-days of operation. These results indicate a need for wastewater treatment processes to mitigate GHGs.
Collapse
Affiliation(s)
- S H Ayotte
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; Department of Civil Engineering, Montana State University, Bozeman, MT 59717, USA; Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA
| | - C R Allen
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; Department of Civil Engineering, Montana State University, Bozeman, MT 59717, USA
| | - A Parker
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; Department of Mathematical Sciences, Montana State University, Bozeman, MT 59717, USA
| | - O R Stein
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; Department of Civil Engineering, Montana State University, Bozeman, MT 59717, USA
| | - E G Lauchnor
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA; Department of Civil Engineering, Montana State University, Bozeman, MT 59717, USA; Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
| |
Collapse
|
22
|
Huang J, Morsomme R, Dunson D, Xu J. Detecting changes in the transmission rate of a stochastic epidemic model. Stat Med 2024; 43:1867-1882. [PMID: 38409877 DOI: 10.1002/sim.10050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 10/26/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
Throughout the course of an epidemic, the rate at which disease spreads varies with behavioral changes, the emergence of new disease variants, and the introduction of mitigation policies. Estimating such changes in transmission rates can help us better model and predict the dynamics of an epidemic, and provide insight into the efficacy of control and intervention strategies. We present a method for likelihood-based estimation of parameters in the stochastic susceptible-infected-removed model under a time-inhomogeneous transmission rate comprised of piecewise constant components. In doing so, our method simultaneously learns change points in the transmission rate via a Markov chain Monte Carlo algorithm. The method targets the exact model posterior in a difficult missing data setting given only partially observed case counts over time. We validate performance on simulated data before applying our approach to data from an Ebola outbreak in Western Africa and COVID-19 outbreak on a university campus.
Collapse
Affiliation(s)
- Jenny Huang
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Raphaël Morsomme
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - David Dunson
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Jason Xu
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| |
Collapse
|
23
|
Weiß M, Gutzeit J, Appel KS, Bahmer T, Beutel M, Deckert J, Fricke J, Hanß S, Hettich-Damm N, Heuschmann PU, Horn A, Jauch-Chara K, Kohls M, Krist L, Lorenz-Depiereux B, Otte C, Pape D, Reese JP, Schreiber S, Störk S, Vehreschild JJ, Hein G. Depression and fatigue six months post-COVID-19 disease are associated with overlapping symptom constellations: A prospective, multi-center, population-based cohort study. J Affect Disord 2024; 352:296-305. [PMID: 38360365 DOI: 10.1016/j.jad.2024.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Depression and fatigue are commonly observed sequelae following viral diseases such as COVID-19. Identifying symptom constellations that differentially classify post-COVID depression and fatigue may be helpful to individualize treatment strategies. Here, we investigated whether self-reported post-COVID depression and post-COVID fatigue are associated with the same or different symptom constellations. METHODS To address this question, we used data from COVIDOM, a population-based cohort study conducted as part of the NAPKON-POP platform. Data were collected in three different German regions (Kiel, Berlin, Würzburg). We analyzed data from >2000 individuals at least six months past a PCR-confirmed COVID-19 disease, using elastic net regression and cluster analysis. The regression model was developed in the Kiel data set, and externally validated using data sets from Berlin and Würzburg. RESULTS Our results revealed that post-COVID depression and fatigue are associated with overlapping symptom constellations consisting of difficulties with daily activities, perceived health-related quality of life, chronic exhaustion, unrestful sleep, and impaired concentration. Confirming the overlap in symptom constellations, a follow-up cluster analysis could categorize individuals as scoring high or low on depression and fatigue but could not differentiate between both dimensions. LIMITATIONS The data presented are cross-sectional, consisting primarily of self-reported questionnaire or medical records rather than biometric data. CONCLUSIONS In summary, our results suggest a strong link between post-COVID depression and fatigue, highlighting the need for integrative treatment approaches.
Collapse
Affiliation(s)
- Martin Weiß
- University Hospital Würzburg, Center of Mental Health, Department of Psychiatry, Psychosomatic and Psychotherapy, Margarete-Höppel-Platz 1, 97080 Würzburg, Germany.
| | - Julian Gutzeit
- University Hospital Würzburg, Center of Mental Health, Department of Psychiatry, Psychosomatic and Psychotherapy, Margarete-Höppel-Platz 1, 97080 Würzburg, Germany
| | - Katharina S Appel
- Goethe University Frankfurt, University Hospital, Center for Internal Medicine, Medical Department 2 (Hematology/Oncology and Infectious Diseases), Frankfurt, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I for Internal Medicine, Cologne, Germany
| | - Thomas Bahmer
- Department I of Internal Medicine, UKSH Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany; Airway Research Center North (ARCN), German Center for Lung Research (DZL), Wöhrendamm 80, 22927 Großhansdorf, Germany
| | - Manfred Beutel
- Department for Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg University Mainz, Untere Zahlbacher Str. 8, 55131 Mainz, Germany
| | - Jürgen Deckert
- University Hospital Würzburg, Center of Mental Health, Department of Psychiatry, Psychosomatic and Psychotherapy, Margarete-Höppel-Platz 1, 97080 Würzburg, Germany
| | - Julia Fricke
- Institute of Social Medicine, Epidemiology and Health Economics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Sabine Hanß
- Department of Medical Informatics, University Medical Center Göttingen, Göttingen, Germany
| | - Nora Hettich-Damm
- Department for Psychosomatic Medicine and Psychotherapy, University Medical Center of the Johannes Gutenberg University Mainz, Untere Zahlbacher Str. 8, 55131 Mainz, Germany
| | - Peter U Heuschmann
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany; Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center, Department of Internal Medicine I, University Hospital Würzburg, Am Schwarzenberg 15, 97078 Würzburg, Germany; Clinical Trial Center Würzburg (CTC/ZKS), University Hospital Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany; Institute of Medical Data Science, University Hospital Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Anna Horn
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany; Institute of Medical Data Science, University Hospital Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Kamila Jauch-Chara
- Department of Psychiatry and Psychotherapy, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Mirjam Kohls
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Lilian Krist
- Institute of Social Medicine, Epidemiology and Health Economics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | | | - Christian Otte
- Charité - Universitätsmedizin Berlin, Department of Psychiatry and Neurosciences, Campus Benjamin Franklin, Berlin, Germany
| | - Daniel Pape
- Department I of Internal Medicine, UKSH Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Jens-Peter Reese
- Institute of Clinical Epidemiology and Biometry, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany; Institute of Medical Data Science, University Hospital Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Stefan Schreiber
- Department I of Internal Medicine, UKSH Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Stefan Störk
- Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center, Department of Internal Medicine I, University Hospital Würzburg, Am Schwarzenberg 15, 97078 Würzburg, Germany
| | - Jörg Janne Vehreschild
- Goethe University Frankfurt, University Hospital, Center for Internal Medicine, Medical Department 2 (Hematology/Oncology and Infectious Diseases), Frankfurt, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I for Internal Medicine, Cologne, Germany; German Centre for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Grit Hein
- University Hospital Würzburg, Center of Mental Health, Department of Psychiatry, Psychosomatic and Psychotherapy, Margarete-Höppel-Platz 1, 97080 Würzburg, Germany
| |
Collapse
|
24
|
Rana D, Westrop S, Jaiswal N, Germeni E, McGarty A, Ells L, Lally P, McEwan M, Melville C, Harris L, Wu O. Lifestyle modification interventions for adults with intellectual disabilities: systematic review and meta-analysis at intervention and component levels. J Intellect Disabil Res 2024; 68:387-445. [PMID: 38414293 DOI: 10.1111/jir.13098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 02/29/2024]
Abstract
BACKGROUND Adults with intellectual disabilities (IDs) are susceptible to multiple health risk behaviours such as alcohol consumption, smoking, low physical activity, sedentary behaviour and poor diet. Lifestyle modification interventions can prevent or reduce negative health consequences caused by these behaviours. We aim to determine the effectiveness of lifestyle modification interventions and their components in targeting health risk behaviours in adults with IDs. METHODS A systematic review and meta-analysis were conducted. Electronic databases, clinical trial registries, grey literature and citations of systematic reviews and included studies were searched in January 2021 (updated February 2022). Randomised controlled trials and non-randomised controlled trials targeting alcohol consumption, smoking, low physical activity, sedentary behaviours and poor diet in adults (aged ≥ 18 years) with ID were included. Meta-analysis was conducted at the intervention level (pairwise and network meta-analysis) and the component-level (component network meta-analysis). Studies were coded using Michie's 19-item theory coding scheme and 94-item behaviour change taxonomies. Risk of bias was assessed using the Cochrane Risk of Bias (ROB) Version 2 and Risk of Bias in Non-randomised Studies of Interventions (ROBINS-I). The study involved a patient and public involvement (PPI) group, including people with lived experience, who contributed extensively by shaping the methodology, providing valuable insights in interpreting results and organising of dissemination events. RESULTS Our literature search identified 12 180 articles, of which 80 studies with 4805 participants were included in the review. The complexity of lifestyle modification intervention was dismantled by identifying six core components that influenced outcomes. Interventions targeting single or multiple health risk behaviours could have a single or combination of multiple core-components. Interventions (2 RCTS; 4 non-RCTs; 228 participants) targeting alcohol consumption and smoking behaviour were effective but based on limited evidence. Similarly, interventions targeting low physical activity only (16 RCTs; 17 non-RCTs; 1413 participants) or multiple behaviours (low physical activity only, sedentary behaviours and poor diet) (17 RCTs; 24 non-RCTs; 3164 participants) yielded mixed effectiveness in outcomes. Most interventions targeting low physical activity only or multiple behaviours generated positive effects on various outcomes while some interventions led to no change or worsened outcomes, which could be attributed to the presence of a single core-component or a combination of similar core components in interventions. The intervention-level meta-analysis for weight management outcomes showed that none of the interventions were associated with a statistically significant change in outcomes when compared with treatment-as-usual and each other. Interventions with core-components combination of energy deficit diet, aerobic exercise and behaviour change techniques showed the highest weight loss [mean difference (MD) = -3.61, 95% credible interval (CrI) -9.68 to 1.95] and those with core-components combination dietary advice and aerobic exercise showed a weight gain (MD 0.94, 95% CrI -3.93 to 4.91). Similar findings were found with the component network meta-analysis for which additional components were identified. Most studies had a high and moderate risk of bias. Various theories and behaviour change techniques were used in intervention development and adaptation. CONCLUSION Our systematic review is the first to comprehensively explore lifestyle modification interventions targeting a range of single and multiple health risk behaviours in adults with ID, co-produced with people with lived experience. It has practical implications for future research as it highlights the importance of mixed-methods research in understanding lifestyle modification interventions and the need for population-specific improvements in the field (e.g., tailored interventions, development of evaluation instruments or tools, use of rigorous research methodologies and comprehensive reporting frameworks). Wide dissemination of related knowledge and the involvement of PPI groups, including people with lived experience, will help future researchers design interventions that consider the unique needs, desires and abilities of people with ID.
Collapse
Affiliation(s)
- D Rana
- Health Economics and Health Technology Assessment, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - S Westrop
- Health Economics and Health Technology Assessment, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Mental Health and Wellbeing, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - N Jaiswal
- Health Economics and Health Technology Assessment, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - E Germeni
- Health Economics and Health Technology Assessment, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - A McGarty
- Mental Health and Wellbeing, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - L Ells
- School of Clinical and Applied Sciences, Leeds Beckett University, Leeds, UK
| | - P Lally
- UCL Institute of Epidemiology and Health Care, University College London, London, UK
- Department of Psychology, University of Surrey, Guildford, UK
| | - M McEwan
- People First (Scotland), Edinburgh, UK
| | - C Melville
- Mental Health and Wellbeing, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - L Harris
- School of Medicine, Dentistry and Nursing, University of Glasgow, Glasgow, UK
| | - O Wu
- Health Economics and Health Technology Assessment, School of Health and Wellbeing, University of Glasgow, Glasgow, UK
| |
Collapse
|
25
|
Bertinetti C, Härer A, Karagic N, Meyer A, Torres-Dowdall J. Repeated Divergence in Opsin Gene Expression Mirrors Photic Habitat Changes in Rapidly Evolving Crater Lake Cichlid Fishes. Am Nat 2024; 203:604-617. [PMID: 38635367 DOI: 10.1086/729420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
AbstractSelection pressures differ along environmental gradients, and traits tightly linked to fitness (e.g., the visual system) are expected to track such variation. Along gradients, adaptation to local conditions might be due to heritable and nonheritable environmentally induced variation. Disentangling these sources of phenotypic variation requires studying closely related populations in nature and in the laboratory. The Nicaraguan lakes represent an environmental gradient in photic conditions from clear crater lakes to very turbid great lakes. From two old, turbid great lakes, Midas cichlid fish (Amphilophus cf. citrinellus) independently colonized seven isolated crater lakes of varying light conditions, resulting in a small adaptive radiation. We estimated variation in visual sensitivities along this photic gradient by measuring cone opsin gene expression among lake populations. Visual sensitivities observed in all seven derived crater lake populations shifted predictably in direction and magnitude, repeatedly mirroring changes in photic conditions. Comparing wild-caught and laboratory-reared fish revealed that 48% of this phenotypic variation is genetically determined and evolved rapidly. Decreasing intrapopulation variation as environments become spectrally narrower suggests that different selective landscapes operate along the gradient. We conclude that the power to predict phenotypic evolution along gradients depends on both the magnitude of environmental change and the selective landscape shape.
Collapse
|
26
|
Lamp J, Wu Y, Lamp S, Afriyie P, Ashur N, Bilchick K, Breathett K, Kwon Y, Li S, Mehta N, Pena ER, Feng L, Mazimba S. Characterizing advanced heart failure risk and hemodynamic phenotypes using interpretable machine learning. Am Heart J 2024; 271:1-11. [PMID: 38336159 DOI: 10.1016/j.ahj.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND Although previous risk models exist for advanced heart failure with reduced ejection fraction (HFrEF), few integrate invasive hemodynamics or support missing data. This study developed and validated a heart failure (HF) hemodynamic risk and phenotyping score for HFrEF, using Machine Learning (ML). METHODS Prior to modeling, patients in training and validation HF cohorts were assigned to 1 of 5 risk categories based on the composite endpoint of death, left ventricular assist device (LVAD) implantation or transplantation (DeLvTx), and rehospitalization in 6 months of follow-up using unsupervised clustering. The goal of our novel interpretable ML modeling approach, which is robust to missing data, was to predict this risk category (1, 2, 3, 4, or 5) using either invasive hemodynamics alone or a rich and inclusive feature set that included noninvasive hemodynamics (all features). The models were trained using the ESCAPE trial and validated using 4 advanced HF patient cohorts collected from previous trials, then compared with traditional ML models. Prediction accuracy for each of these 5 categories was determined separately for each risk category to generate 5 areas under the curve (AUCs, or C-statistics) for belonging to risk category 1, 2, 3, 4, or 5, respectively. RESULTS Across all outcomes, our models performed well for predicting the risk category for each patient. Accuracies of 5 separate models predicting a patient's risk category ranged from 0.896 +/- 0.074 to 0.969 +/- 0.081 for the invasive hemodynamics feature set and 0.858 +/- 0.067 to 0.997 +/- 0.070 for the all features feature set. CONCLUSION Novel interpretable ML models predicted risk categories with a high degree of accuracy. This approach offers a new paradigm for risk stratification that differs from prediction of a binary outcome. Prospective clinical evaluation of this approach is indicated to determine utility for selecting the best treatment approach for patients based on risk and prognosis.
Collapse
Affiliation(s)
- Josephine Lamp
- Department of Computer Science, University of Virginia, Charlottesville, VA.
| | - Yuxin Wu
- Department of Computer Science, University of California, Los Angeles, CA
| | - Steven Lamp
- Department of Computer Science, University of Virginia, Charlottesville, VA
| | - Prince Afriyie
- Department of Statistics, University of Virginia, Charlottesville, VA
| | - Nicholas Ashur
- Department of Cardiovascular Medicine, University of Virginia, Charlottesville, VA
| | - Kenneth Bilchick
- Department of Cardiovascular Medicine, University of Virginia, Charlottesville, VA
| | - Khadijah Breathett
- Division of Cardiovascular Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Younghoon Kwon
- Department of Cardiovascular Medicine, University of Washington, Seattle, WA
| | - Song Li
- Department of Cardiovascular Medicine, University of Washington, Seattle, WA
| | - Nishaki Mehta
- Department of Cardiology, William Beaumont Oakland University School of Medicine, Royal Oak, MI
| | - Edward Rojas Pena
- Department of Cardiovascular Medicine, University of Virginia, Charlottesville, VA
| | - Lu Feng
- Department of Computer Science, University of Virginia, Charlottesville, VA
| | - Sula Mazimba
- Department of Cardiovascular Medicine, University of Virginia, Charlottesville, VA; Transplant Institute, AdventHealth, Orlando, FL
| |
Collapse
|
27
|
Jeong SH, Lee MG, Kim YS, Chung IW. Change in absolute neutrophil count after COVID-19 infection in patients using clozapine versus other antipsychotics. Int Clin Psychopharmacol 2024; 39:187-194. [PMID: 38261424 DOI: 10.1097/yic.0000000000000506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
It was reported that patients who contracted COVID-19 while taking clozapine exhibited a distinct hematological response. However, the absence of control groups made it difficult to attribute it to clozapine. The changes in absolute neutrophil counts (ANCs) during the 4 weeks after COVID-19 infection were compared between the two groups of patients with severe mental illnesses (SMIs) (49 patients using clozapine and 54 using other antipsychotics) using generalized additive modeling. Although the pattern of a transient drop in ANC followed by gradual recovery could be demonstrated in both groups, it was more pronounced in the clozapine group ( P = 0.00025). Nevertheless, overall ANC remained at a higher level in the clozapine group. The results suggested potential interaction between clozapine and COVID-19 at the level of hematological dynamics. However, it did not necessarily indicate that such interaction is inevitably harmful or dangerous. It was more of a concern that some patients using other antipsychotics exhibited decreased ANC, which did not easily recover. Traditionally, clinicians have been concerned about the worsening of hematological side effects in clozapine patients after COVID-19 infection. However, the obtained result highlighted the necessity of hematological monitoring in patients using any type of antipsychotics for SMIs.
Collapse
Affiliation(s)
- Seong Hoon Jeong
- Department of Psychiatry, Daejeon Eulji Medical Center, Eulji University School of Medicine, Daejeon
| | | | - Yong Sik Kim
- Department of Psychiatry, Nowon-Uiijeongbu Eulji Medical Center, Eulji University School of Medicine, Seoul
- Institute of Clinical Psychopharmacology, Dongguk University School of Medicine, Goyang
| | - In Won Chung
- Department of Psychiatry and Yong-In Psychiatric Institute, Yong-In Mental Hospital, Yongin, Republic of Korea
| |
Collapse
|
28
|
Papazova I, Wunderlich S, Papazov B, Vogelmann U, Keeser D, Karali T, Falkai P, Rospleszcz S, Maurus I, Schmitt A, Hasan A, Malchow B, Stöcklein S. Characterizing cognitive subtypes in schizophrenia using cortical curvature. J Psychiatr Res 2024; 173:131-138. [PMID: 38531143 DOI: 10.1016/j.jpsychires.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 03/11/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024]
Abstract
Cognitive deficits are a core symptom of schizophrenia, but research on their neural underpinnings has been challenged by the heterogeneity in deficits' severity among patients. Here, we address this issue by combining logistic regression and random forest to classify two neuropsychological profiles of patients with high (HighCog) and low (LowCog) cognitive performance in two independent samples. We based our analysis on the cortical features grey matter volume (VOL), cortical thickness (CT), and mean curvature (MC) of N = 57 patients (discovery sample) and validated the classification in an independent sample (N = 52). We investigated which cortical feature would yield the best classification results and expected that the 10 most important features would include frontal and temporal brain regions. The model based on MC had the best performance with area under the curve (AUC) values of 76% and 73%, and identified fronto-temporal and occipital brain regions as the most important features for the classification. Moreover, subsequent comparison analyses could reveal significant differences in MC of single brain regions between the two cognitive profiles. The present study suggests MC as a promising neuroanatomical parameter for characterizing schizophrenia cognitive subtypes.
Collapse
Affiliation(s)
- Irina Papazova
- Psychiatry and Psychotherapy, Faculty of Medicine, University of Augsburg, Geschwister-Schönert-Straße 1, 86156, Augsburg, Germany; Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany; DZPG (German Center for Mental Health), partner site München, Augsburg, Germany.
| | - Stephan Wunderlich
- Department of Radiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany; Department of Interventional Radiology, Technical University of Munich, Munich, Germany
| | - Boris Papazov
- Department of Radiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Ulrike Vogelmann
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Daniel Keeser
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany; Department of Radiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Temmuz Karali
- Department of Radiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany; Max Planck Institute of Psychiatry, Munich, Germany
| | - Susanne Rospleszcz
- Institute of Epidemiology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Munich, Germany; Department of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isabel Maurus
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Andrea Schmitt
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany; Laboratory of Neuroscience (LIM27), Institute of Psychiatry, University of São Paulo (USP), São Paulo, Brazil
| | - Alkomiet Hasan
- Psychiatry and Psychotherapy, Faculty of Medicine, University of Augsburg, Geschwister-Schönert-Straße 1, 86156, Augsburg, Germany; DZPG (German Center for Mental Health), partner site München, Augsburg, Germany
| | - Berend Malchow
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
| | - Sophia Stöcklein
- Department of Radiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| |
Collapse
|
29
|
Lolli L, Bonanno D, Lopez E, Di Salvo V. Night-to-night variability of objective sleep outcomes in youth Middle Eastern football players. Sleep Med 2024; 117:193-200. [PMID: 38564918 DOI: 10.1016/j.sleep.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/19/2024] [Accepted: 03/16/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE To describe components of night-to-night variation in objective measures of sleep. METHODS We conducted a secondary data analysis of consecutive and chronologically ordered actigraphy-based measurements for time in bed (min), time asleep (min), and wake-after-sleep onset (min). This investigation examined 575 individual night-based measures available for a sub-sample of fifty-two, male youth Middle Eastern football players tracked over a 14-day surveillance period (chronological age range: 12.1 to 16 years). Distinct multivariable-adjusted generalized additive models included each objective sleep outcome measure as dependent variable and disaggregated components of variation for night measurement-by-sleep period interaction, week part (weekday or weekend), and study participant random effects from within-subject night-to-night sleep variation. RESULTS The within-subject standard deviation (SD) of ±98 min (95% confidence interval [CI], 92 to 104 min) for time in bed, ±87 min (95%CI, 82 to 93 min) for time asleep, and ±23 min (95%CI, 22 to 25 min) for wake-after-sleep-onset overwhelmed other sources of variability and accounted for ∼44% to 53% of the overall night-to-night variation. The night measurement-by-fragmented sleep period interaction SD was ±83 min (95%CI, 44 to 156 min) for time in bed, ±67 min (95%CI, 34 to 131 min) for time asleep, and ±15 min (95%CI, 7 to 32 min) for wake-after-sleep-onset that accounted for ∼22% to 32% of each sleep outcome measure overall variability. CONCLUSIONS Substantial random night-to-night within-subject variability poses additional challenges for strategies aiming to mitigate problems of insufficient and inconsistent sleep that are detrimental to school learning and youth athlete development processes.
Collapse
Affiliation(s)
- Lorenzo Lolli
- Aspire Academy, Football Performance & Science Department, Doha, Qatar; Department of Sport and Exercise Sciences, Institute of Sport, Manchester Metropolitan University, Manchester, UK.
| | - Daniele Bonanno
- Aspire Academy, Football Performance & Science Department, Doha, Qatar
| | - Emmanuel Lopez
- Aspire Academy, Football Performance & Science Department, Doha, Qatar
| | - Valter Di Salvo
- Aspire Academy, Football Performance & Science Department, Doha, Qatar; Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy
| |
Collapse
|
30
|
Jiang F, Tao Z, Zhang Y, Xie X, Bao Y, Hu Y, Ding J, Wu C. Machine learning combined with single-cell analysis reveals predictive capacity and immunotherapy response of T cell exhaustion-associated lncRNAs in uterine corpus endometrial carcinoma. Cell Signal 2024; 117:111077. [PMID: 38311301 DOI: 10.1016/j.cellsig.2024.111077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/24/2023] [Accepted: 02/01/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND The exhaustion of T-cells is a primary factor contributing to immune dysfunction in cancer. Long non-coding RNAs (lncRNAs) play a significant role in the advancement, survival, and treatment of Uterine Corpus Endometrial Carcinoma (UCEC). Nevertheless, there has been no investigation into the involvement of lncRNAs associated with T-cell exhaustion (TEXLs) in UCEC. The goal of this work is to establish predictive models for TEXLs in UCEC and study their related immune features. METHODS Using transcriptome and single-cell sequencing data from The Cancer Genome Atlas and Gene Expression Omnibus databases, we employed co-expression analysis and univariate Cox regression to identify prognostic-associated TEXLs (pTEXLs). The prognostic model was developed using the Least Absolute Contraction and Selection Operator. The immunotherapy characteristics of the prognostic model risk score were studied. Then molecular subgroups were identified through non-negative Matrix Factorization based on pTEXLs. The identification of co-expressed genes was done using a weighted correlation network analysis. Subsequently, a diagnostic model for UCEC was created. In-depth investigations, both in vitro and in vivo, were carried out to elucidate the molecular mechanism of the key gene within the diagnostic model. RESULTS Receiver operating characteristic curve, calibration curve, and decision curve analysis proved the validity of the predictive models established according to pTEXLs. The subgroup with lower risk scores in the prognostic model has better responses to blocking immune checkpoint therapy. Single-cell analysis suggests that the expression level of MIEN1 is relatively high in immune cells among diagnostic genes. Furthermore, the targeted suppression of MIEN1 via sh-MIEN1 diminishes the proliferative, migratory, and invasive capacities of UCEC cells, potentially associated with CD8+ T cell exhaustion. CONCLUSIONS The association between TEXLs and UCEC was methodically elucidated by our investigation. A stable pTEXLs risk prediction model and a diagnosis model for UCEC were also established.
Collapse
Affiliation(s)
- Feng Jiang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ziyu Tao
- Department of Ultrasound, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yun Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoyan Xie
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yunlei Bao
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yifang Hu
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Jingxin Ding
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Shanghai, China.
| | - Chuyan Wu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| |
Collapse
|
31
|
He Y, Xiao L. Structured Pruning for Deep Convolutional Neural Networks: A Survey. IEEE Trans Pattern Anal Mach Intell 2024; 46:2900-2919. [PMID: 38015707 DOI: 10.1109/tpami.2023.3334614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The remarkable performance of deep Convolutional neural networks (CNNs) is generally attributed to their deeper and wider architectures, which can come with significant computational costs. Pruning neural networks has thus gained interest since it effectively lowers storage and computational costs. In contrast to weight pruning, which results in unstructured models, structured pruning provides the benefit of realistic acceleration by producing models that are friendly to hardware implementation. The special requirements of structured pruning have led to the discovery of numerous new challenges and the development of innovative solutions. This article surveys the recent progress towards structured pruning of deep CNNs. We summarize and compare the state-of-the-art structured pruning techniques with respect to filter ranking methods, regularization methods, dynamic execution, neural architecture search, the lottery ticket hypothesis, and the applications of pruning. While discussing structured pruning algorithms, we briefly introduce the unstructured pruning counterpart to emphasize their differences. Furthermore, we provide insights into potential research opportunities in the field of structured pruning. A curated list of neural network pruning papers can be found at: https://github.com/he-y/Awesome-Pruning. A dedicated website offering a more interactive comparison of structured pruning methods can be found at: https://huggingface.co/spaces/he-yang/Structured-Pruning-Survey.
Collapse
|
32
|
Turk T, Labarile M, Braun DL, Rauch A, Stöckle M, Cavassini M, Hoffmann M, Calmy A, Bernasconi E, Notter J, Pasin C, Günthard HF, Kouyos RD. Characterization and Determinants of Long-Term Immune Recovery Under Suppressive Antiretroviral Therapy. J Acquir Immune Defic Syndr 2024; 96:68-76. [PMID: 38301637 DOI: 10.1097/qai.0000000000003388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
OBJECTIVE We developed a robust characterization of immune recovery trajectories in people living with HIV on antiretroviral treatment (ART) and relate our findings to epidemiological risk factors and bacterial pneumonia. METHODS Using data from the Swiss HIV Cohort Study and the Zurich Primary HIV Infection Cohort Study (n = 5907), we analyzed the long-term trajectories of CD4 cell and CD8 cell counts and their ratio in people living with HIV on ART for at least 8 years by fitting nonlinear mixed-effects models. The determinants of long-term immune recovery were investigated using generalized additive models. In addition, prediction accuracy of the modeled trajectories and their impact on the fit of a model for bacterial pneumonia was assessed. RESULTS Overall, our population showed good immune recovery (median plateau [interquartile range]-CD4: 718 [555-900] cells/μL, CD8: 709 [547-893] cells/μL, CD4/CD8: 1.01 [0.76-1.37]). The following factors were predictive of recovery: age, sex, nadir/zenith value, pre-ART HIV-1 viral load, hepatitis C, ethnicity, acquisition risk, and timing of ART initiation. The fitted models proved to be an accurate and efficient way of predicting future CD4 and CD8 cell recovery dynamics: Compared with carrying forward the last observation, mean squared errors of the fitted values were lower by 1.3%-18.3% across outcomes. When modeling future episodes of bacterial pneumonia, using predictors derived from the recovery dynamics improved most model fits. CONCLUSION We described and validated a method to characterize individual immune recovery trajectories of people living with HIV on suppressive ART. These trajectories accurately predict long-term immune recovery and the occurrence of bacterial pneumonia.
Collapse
Affiliation(s)
- Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marco Labarile
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Matthias Hoffmann
- Clinic for Infectious Diseases, Cantonal Hospital Olten, Olten, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, Geneva University Hospital, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, Lugano, Switzerland
- University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland ; and
| | | | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
33
|
Sun J, Cook T. A simple and robust parametric shared frailty model for recurrent events with the competing risk of death: An application to the Carvedilol Prospective Randomized Cumulative Survival trial. Stat Methods Med Res 2024; 33:765-793. [PMID: 38625756 DOI: 10.1177/09622802241236934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Many non-fatal events can be considered recurrent in that they can occur repeatedly over time, and some researchers may be interested in the trajectory and relative risk of non-fatal events. With the competing risk of death, the treatment effect on the mean number of recurrent events is non-identifiable since the observed mean is a function of both the recurrent event and terminal event processes. In this paper, we assume independence between the non-fatal and the terminal event process, conditional on the shared frailty, to fit a parametric model that recovers the trajectory of, and identifies the effect of treatment on, the non-fatal event process in the presence of the competing risk of death. Simulation studies are conducted to verify the reliability of our estimators. We illustrate the method and perform model diagnostics using the Carvedilol Prospective Randomized Cumulative Survival trial which involves heart-failure events.
Collapse
Affiliation(s)
- Jiren Sun
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas Cook
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
34
|
Bandyopadhyay S, Peddi S, Sarma M, Samanta D. Decoding Autism: Uncovering patterns in brain connectivity through sparsity analysis with rs-fMRI data. J Neurosci Methods 2024; 405:110100. [PMID: 38431227 DOI: 10.1016/j.jneumeth.2024.110100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/11/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND In the realm of neuro-disorders, precise diagnosis and treatment rely heavily on objective imaging-based biomarker identification. This study employs a sparsity approach on resting-state fMRI to discern relevant brain region connectivity for predicting Autism. NEW METHOD The proposed methodology involves four key steps: (1) Utilizing three probabilistic brain atlases to extract functionally homogeneous brain regions from fMRI data. (2) Employing a hybrid approach of Graphical Lasso and Akaike Information Criteria to optimize sparse inverse covariance matrices for representing the brain functional connectivity. (3) Employing statistical techniques to scrutinize functional brain structures in Autism and Control subjects. (4) Implementing both autoencoder-based feature extraction and entire feature-based approach coupled with AI-based learning classifiers to predict Autism. RESULTS The ensemble classifier with the extracted feature set achieves a classification accuracy of 84.7% ± 0.3% using the MSDL atlas. Meanwhile, the 1D-CNN model, employing all features, exhibits superior classification accuracy of 88.6% ± 1.7% with the Smith 2009 (rsn70) atlas. COMPARISON WITH EXISTING METHOD (S) The proposed methodology outperforms the conventional correlation-based functional connectivity approach with a notably high prediction accuracy of more than 88%, whereas considering all direct and noisy indirect region-based functional connectivity, the traditional methods bound the prediction accuracy within 70% to 79%. CONCLUSIONS This study underscores the potential of sparsity-based FC analysis using rs-fMRI data as a prognostic biomarker for detecting Autism.
Collapse
Affiliation(s)
- Soham Bandyopadhyay
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, India.
| | - Santhoshkumar Peddi
- Computer Science and Engineering, Indian Institute of Technology Kharagpur, India
| | - Monalisa Sarma
- Subir Chowdhury School of Quality and Reliability, Indian Institute of Technology Kharagpur, India
| | - Debasis Samanta
- Computer Science and Engineering, Indian Institute of Technology Kharagpur, India
| |
Collapse
|
35
|
Iddrisu AK, Iddrisu WA, Azomyan ASG, Gumedze F. Joint modeling of longitudinal CD4 count data and time to first occurrence of composite outcome. J Clin Tuberc Other Mycobact Dis 2024; 35:100434. [PMID: 38584976 PMCID: PMC10995979 DOI: 10.1016/j.jctube.2024.100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
In this study, we jointly modeled longitudinal CD4 count data and survival outcome (time-to-first occurrence of composite outcome of death, cardiac tamponade or constriction) in other to investigate the effects of Mycobacterium indicus pranii immunotherapy and the CD4 count measurements on the hazard of the composite outcome among patients with HIV and tuberculous (TB) pericarditis. In this joint modeling framework, the models for longitudinal and the survival data are linked by an association structure. The association structure represents the hazard of the event for 1-unit increase in the longitudinal measurement. Models fitting and parameter estimation were carried out using R version 4.2.3. The association structure that represents the strength of the association between the hazard for an event at time point j and the area under the longitudinal trajectory up to the same time j provides the best fit. We found that 1-unit increase in CD4 count results in 2 % significant reduction in the hazard of the composite outcome. Among HIV and TB pericarditis individuals, the hazard of the composite outcome does not differ between of M.indicus pranii versus placebo. Application of joint models to investigate the effect of M.indicus pranii on the hazard of the composite outcome is limited. Hence, this study provides information on the effect of M.indicus pranii on the hazard of the composite outcome among HIV and TB pericarditis patients.
Collapse
Affiliation(s)
- Abdul-Karim Iddrisu
- Department of Mathematics and Statistics, University of Energy and Natural Resources, Ghana
| | | | | | - Freedom Gumedze
- Department of Statistical Sciences, University of Cape Town, South Africa
| |
Collapse
|
36
|
Martinez Boggio G, Monteiro HF, Lima FS, Figueiredo CC, Bisinotto RS, Santos JEP, Mion B, Schenkel FS, Ribeiro ES, Weigel KA, Peñagaricano F. Host and rumen microbiome contributions to feed efficiency traits in Holstein cows. J Dairy Sci 2024; 107:3090-3103. [PMID: 38135048 DOI: 10.3168/jds.2023-23869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h2) and microbiability (m2), respectively. However, if the genome and microbiome are included in the model, then the h2 reflects only the contribution of the direct genetic effects quantified as direct heritability (hd2), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho2). The objectives of this study were to estimate h2, hd2,m2, and ho2 for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd2 estimates were always 10% to 15% lower than h2 estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m2 estimates were moderate for all traits, and up to 26% for milk energy. The ho2 was greater than the sum of hd2 and m2, suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.
Collapse
Affiliation(s)
| | - Hugo F Monteiro
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA 95616
| | - Fabio S Lima
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA 95616
| | - Caio C Figueiredo
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA 99163
| | - Rafael S Bisinotto
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL 32610
| | - José E P Santos
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - Bruna Mion
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Flavio S Schenkel
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Eduardo S Ribeiro
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Kent A Weigel
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706
| |
Collapse
|
37
|
Weng Y, Tian L, Boothroyd D, Lee J, Zhang K, Lu D, Lindan CP, Bollyky J, Huang B, Rutherford GW, Maldonado Y, Desai M. Adjusting Incidence Estimates with Laboratory Test Performances: A Pragmatic Maximum Likelihood Estimation-Based Approach. Epidemiology 2024; 35:295-307. [PMID: 38465940 PMCID: PMC11022996 DOI: 10.1097/ede.0000000000001725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/28/2024] [Indexed: 03/12/2024]
Abstract
Understanding the incidence of disease is often crucial for public policy decision-making, as observed during the COVID-19 pandemic. Estimating incidence is challenging, however, when the definition of incidence relies on tests that imperfectly measure disease, as in the case when assays with variable performance are used to detect the SARS-CoV-2 virus. To our knowledge, there are no pragmatic methods to address the bias introduced by the performance of labs in testing for the virus. In the setting of a longitudinal study, we developed a maximum likelihood estimation-based approach to estimate laboratory performance-adjusted incidence using the expectation-maximization algorithm. We constructed confidence intervals (CIs) using both bootstrapped-based and large-sample interval estimator approaches. We evaluated our methods through extensive simulation and applied them to a real-world study (TrackCOVID), where the primary goal was to determine the incidence of and risk factors for SARS-CoV-2 infection in the San Francisco Bay Area from July 2020 to March 2021. Our simulations demonstrated that our method converged rapidly with accurate estimates under a variety of scenarios. Bootstrapped-based CIs were comparable to the large-sample estimator CIs with a reasonable number of incident cases, shown via a simulation scenario based on the real TrackCOVID study. In more extreme simulated scenarios, the coverage of large-sample interval estimation outperformed the bootstrapped-based approach. Results from the application to the TrackCOVID study suggested that assuming perfect laboratory test performance can lead to an inaccurate inference of the incidence. Our flexible, pragmatic method can be extended to a variety of disease and study settings.
Collapse
Affiliation(s)
- Yingjie Weng
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Lu Tian
- Biomedical Data Science, Department of Medicine, Stanford University, Palo Alto, CA
| | - Derek Boothroyd
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Justin Lee
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Kenny Zhang
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Di Lu
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
| | - Christina P. Lindan
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA
| | - Jenna Bollyky
- Division of Primary Care & Population Health, School of Medicine, Stanford University, Stanford, CA
| | - Beatrice Huang
- Department of Family and Community Medicine, University of California, San Francisco, CA
| | - George W. Rutherford
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA
| | - Yvonne Maldonado
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Manisha Desai
- From the Quantitative Sciences Unit, Department of Medicine, Stanford University, Palo Alto, CA
- Biomedical Data Science, Department of Medicine, Stanford University, Palo Alto, CA
| |
Collapse
|
38
|
Coors A, Lee S, Habeck C, Stern Y. Personality traits and cognitive reserve-High openness benefits cognition in the presence of age-related brain changes. Neurobiol Aging 2024; 137:38-46. [PMID: 38402781 PMCID: PMC10947819 DOI: 10.1016/j.neurobiolaging.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
Cognitive reserve explains differential susceptibility of cognitive performance to neuropathology. We investigated whether certain personality traits underlie cognitive reserve and are accordingly associated with better cognition and less cognitive decline in the presence of age-related brain changes. We included healthy adults aged 19-80 years for cross-sectional (N=399) and longitudinal (N=273, mean follow-up time=5 years, SD=0.7 years) analyses. Assessment of the BIG5 personality traits openness, conscientiousness, extraversion, agreeableness, and neuroticism was questionnaire-based. Each cognitive domain (perceptual speed, memory, fluid reasoning, vocabulary) was measured with up to six tasks. Cognitive domain-specific brain status variables were obtained by combining 77 structural brain measures into single scores using elastic net regularization. These brain status variables explained up to 43.1% of the variance in cognitive performance. We found that higher openness was associated with higher fluid reasoning and better vocabulary after controlling for brain status, age, and sex. Further, lower brain status was associated with a greater decline in perceptual speed only in individuals with low openness. We conclude that high openness benefits cognitive reserve.
Collapse
Affiliation(s)
- Annabell Coors
- Cognitive Neuroscience Division, Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Seonjoo Lee
- Mental Health Data Science, New York State Psychiatric Institute, New York, NY, USA; Department of Psychiatry and Biostatistics, Columbia University, New York, NY, USA
| | - Christian Habeck
- Cognitive Neuroscience Division, Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Taub Institute for Research in Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Yaakov Stern
- Cognitive Neuroscience Division, Department of Neurology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Taub Institute for Research in Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA; Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.
| |
Collapse
|
39
|
Shortall CR, Cook SM, Mauchline AL, Bell JR. Long-term trends in migrating Brassicogethes aeneus in the UK. Pest Manag Sci 2024; 80:2294-2305. [PMID: 37035871 DOI: 10.1002/ps.7501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The pollen beetle (Brassicogethes aeneus) causes significant yield loss in oilseed rape (Brassica napus). Predicting population changes remains a scientific challenge, especially since its phenology and abundance varies dramatically over space and time. We used generalized additive models to investigate the long-term trends in pollen beetle annual, seasonal and monthly counts from Rothamsted 12.2 m suction-traps. We hypothesised that the beetle's abundance is positively related to the area of oilseed rape at a national and regional level. We used random forest models to investigate the inter-generational relationship within years. RESULTS Although Brassicogethes aeneus annual counts and area of oilseed rape grown in the UK both increased by 162% and 113%, respectively, over the time period studied, they were not significantly related. The size of the immigrating pollen beetle population (up to 1 June) can be explained both by the size of the population in the previous summer and prevailing winter temperatures, indicating a positive feedback mechanism. CONCLUSION Currently, pollen beetle numbers continue to increase in the UK, meaning that control issues may persist. However the relationship between counts in spring, during the susceptible phase of the crop, and counts in the previous summer indicates that it may be possible to forecast the counts of the spring migration of Brassicogethes aeneus a few months in advance using suction-trap samples, which could aid decisions on control options. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Collapse
Affiliation(s)
- Chris R Shortall
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| | - Samantha M Cook
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| | - Alice L Mauchline
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - James R Bell
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, UK
| |
Collapse
|
40
|
Wang X, Lee H, Haaland B, Kerrigan K, Puri S, Akerley W, Shen J. A matching-based machine learning approach to estimating optimal dynamic treatment regimes with time-to-event outcomes. Stat Methods Med Res 2024; 33:794-806. [PMID: 38502008 DOI: 10.1177/09622802241236954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Observational data (e.g. electronic health records) has become increasingly important in evidence-based research on dynamic treatment regimes, which tailor treatments over time to patients based on their characteristics and evolving clinical history. It is of great interest for clinicians and statisticians to identify an optimal dynamic treatment regime that can produce the best expected clinical outcome for each individual and thus maximize the treatment benefit over the population. Observational data impose various challenges for using statistical tools to estimate optimal dynamic treatment regimes. Notably, the task becomes more sophisticated when the clinical outcome of primary interest is time-to-event. Here, we propose a matching-based machine learning method to identify the optimal dynamic treatment regime with time-to-event outcomes subject to right-censoring using electronic health record data. In contrast to the established inverse probability weighting-based dynamic treatment regime methods, our proposed approach provides better protection against model misspecification and extreme weights in the context of treatment sequences, effectively addressing a prevalent challenge in the longitudinal analysis of electronic health record data. In simulations, the proposed method demonstrates robust performance across a range of scenarios. In addition, we illustrate the method with an application to estimate optimal dynamic treatment regimes for patients with advanced non-small cell lung cancer using a real-world, nationwide electronic health record database from Flatiron Health.
Collapse
Affiliation(s)
- Xuechen Wang
- Department of Population Health Sciences, Division of Biostatistics, University of Utah, Salt Lake City, UT, USA
| | - Hyejung Lee
- Department of Population Health Sciences, Division of Biostatistics, University of Utah, Salt Lake City, UT, USA
| | - Benjamin Haaland
- Department of Population Health Sciences, Division of Biostatistics, University of Utah, Salt Lake City, UT, USA
| | - Kathleen Kerrigan
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sonam Puri
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Wallace Akerley
- Department of Internal Medicine, Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Jincheng Shen
- Department of Population Health Sciences, Division of Biostatistics, University of Utah, Salt Lake City, UT, USA
| |
Collapse
|
41
|
Wang Y, Fu Y, Sun X. Knockoffs-SPR: Clean Sample Selection in Learning With Noisy Labels. IEEE Trans Pattern Anal Mach Intell 2024; 46:3242-3256. [PMID: 38039178 DOI: 10.1109/tpami.2023.3338268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2023]
Abstract
A noisy training set usually leads to the degradation of the generalization and robustness of neural networks. In this article, we propose a novel theoretically guaranteed clean sample selection framework for learning with noisy labels. Specifically, we first present a Scalable Penalized Regression (SPR) method, to model the linear relation between network features and one-hot labels. In SPR, the clean data are identified by the zero mean-shift parameters solved in the regression model. We theoretically show that SPR can recover clean data under some conditions. Under general scenarios, the conditions may be no longer satisfied; and some noisy data are falsely selected as clean data. To solve this problem, we propose a data-adaptive method for Scalable Penalized Regression with Knockoff filters (Knockoffs-SPR), which is provable to control the False-Selection-Rate (FSR) in the selected clean data. To improve the efficiency, we further present a split algorithm that divides the whole training set into small pieces that can be solved in parallel to make the framework scalable to large datasets. While Knockoffs-SPR can be regarded as a sample selection module for a standard supervised training pipeline, we further combine it with a semi-supervised algorithm to exploit the support of noisy data as unlabeled data. Experimental results on several benchmark datasets and real-world noisy datasets show the effectiveness of our framework and validate the theoretical results of Knockoffs-SPR.
Collapse
|
42
|
Wang WL, Castro LM, Li HJ, Lin TI. Mixtures of t $$ t $$ factor analysers with censored responses and external covariates: An application to educational data from Peru. Br J Math Stat Psychol 2024; 77:316-336. [PMID: 38095333 DOI: 10.1111/bmsp.12329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 10/21/2023] [Accepted: 11/16/2023] [Indexed: 04/10/2024]
Abstract
Analysing data from educational tests allows governments to make decisions for improving the quality of life of individuals in a society. One of the key responsibilities of statisticians is to develop models that provide decision-makers with pertinent information about the latent process that educational tests seek to represent. Mixtures oft $$ t $$ factor analysers (MtFA) have emerged as a powerful device for model-based clustering and classification of high-dimensional data containing one or several groups of observations with fatter tails or anomalous outliers. This paper considers an extension of MtFA for robust clustering of censored data, referred to as the MtFAC model, by incorporating external covariates. The enhanced flexibility of including covariates in MtFAC enables cluster-specific multivariate regression analysis of dependent variables with censored responses arising from upper and/or lower detection limits of experimental equipment. An alternating expectation conditional maximization (AECM) algorithm is developed for maximum likelihood estimation of the proposed model. Two simulation experiments are conducted to examine the effectiveness of the techniques presented. Furthermore, the proposed methodology is applied to Peruvian data from the 2007 Early Grade Reading Assessment, and the results obtained from the analysis provide new insights regarding the reading skills of Peruvian students.
Collapse
Affiliation(s)
- Wan-Lun Wang
- Department of Statistics and Institute of Data Science, National Cheng Kung University, Tainan, Taiwan
| | - Luis M Castro
- Department of Statistics, Pontificia Universidad Católica de Chile, Santiago, Chile
- Center for the Discovery of Structures in Complex Data, Santiago, Chile
| | - Huei-Jyun Li
- Institute of Statistics, National Chung Hsing University, Taichung, Taiwan
| | - Tsung-I Lin
- Institute of Statistics, National Chung Hsing University, Taichung, Taiwan
- Department of Public Health, China Medical University, Taichung, Taiwan
| |
Collapse
|
43
|
Veloy C, Coll M, Pennino MG, Garcia E, Esteban A, García-Ruiz C, Certain G, Vaz S, Jadaud A, González M, Hidalgo M. Understanding the response of the Western Mediterranean cephalopods to environment and fishing in a context of alleged winners of change. Mar Environ Res 2024; 197:106478. [PMID: 38594093 DOI: 10.1016/j.marenvres.2024.106478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/09/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Increasing impacts of both fisheries and climate change have resulted in shifts in the structure and functioning of marine communities. One recurrent observation is the rise of cephalopods as fish recede. This is generally attributed to the removal of main predators and competitors by fishing, while mechanistic evidence is still lacking. In addition, climate change may influence cephalopods due to their high environmental sensitivity. We aim to unveil the effects of different anthropogenic and environmental drivers at different scales focusing on the cephalopod community of the Western Mediterranean Sea. We investigate several ecological indicators offering a wide range of information about their ecology, and statistically relating them with environmental, biotic and fisheries drivers. Our results highlight non-linear changes of indicators along with spatial differences in their responses. Overall, the environment drivers have greater effects than biotic and local human impacts with contrasting effects of temperature across the geographic gradient. We conclude that cephalopods may be impacted by climate change in the future while not necessary through positive warming influence, which should make us cautious when referring to them as generalized winners of current changes.
Collapse
Affiliation(s)
- Carlos Veloy
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de La Barceloneta, Nº 37-49, 08003, Barcelona, Spain.
| | - Marta Coll
- Institute of Marine Science (ICM-CSIC), Passeig Marítim de La Barceloneta, Nº 37-49, 08003, Barcelona, Spain
| | - Maria Grazia Pennino
- Instituto Español de Oceanografía (IEO-CSIC) (Madrid), Calle del Corazón de María, 8, 28002, Madrid, Spain
| | - Encarnación Garcia
- Instituto Español de Oceanografía (IEO-CSIC) (Murcia), Calle el Varadero, 1, 30740, San Pedro del Pinatar, Spain
| | - Antonio Esteban
- Instituto Español de Oceanografía (IEO-CSIC) (Murcia), Calle el Varadero, 1, 30740, San Pedro del Pinatar, Spain
| | - Cristina García-Ruiz
- Instituto Español de Oceanografía (IEO-CSIC) (Málaga), Puerto Pesquero, s/n Aptdo. 285, 29640, Fuengirola, Spain
| | | | - Sandrine Vaz
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, Sète, France
| | | | - María González
- Instituto Español de Oceanografía (IEO-CSIC) (Murcia), Calle el Varadero, 1, 30740, San Pedro del Pinatar, Spain
| | - Manuel Hidalgo
- Instituto Español de Oceanografía (IEO-CSIC) (Baleares), Ecosystem Oceanography Group (GRECO), Moll de Ponent, 07015, Palma, Spain
| |
Collapse
|
44
|
Park SY, Park SY, Seo S, Kwon HS, Kim SH, Kim SH, Park HK, Chang YS, Kim CW, Lee BJ, Park HS, Cho YS, Oh HB, Ostrov DA, Won S, Kim TB. HLA-DRB1 is associated with cefaclor-induced immediate hypersensitivity. World Allergy Organ J 2024; 17:100901. [PMID: 38638799 PMCID: PMC11021981 DOI: 10.1016/j.waojou.2024.100901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
Background Drug-induced hypersensitivity such as anaphylaxis is an important cause of drug-related morbidity and mortality. Cefaclor is a leading cause of drug induced type I hypersensitivity in Korea, but little is yet known about genetic biomarkers to predict this hypersensitivity reaction. We aimed to evaluate the possible involvement of genes in cefaclor induced type I hypersensitivity. Methods Whole exome sequencing (WES) and HLA genotyping were performed in 43 patients with cefaclor induced type I hypersensitivity. In addition, homology modeling was performed to identify the binding forms of cefaclor to HLA site. Results Anaphylaxis was the most common phenotype of cefaclor hypersensitivity (90.69%). WES results show that rs62242177 and rs62242178 located in LIMD1 region were genome-wide significant at the 5 × 10-8 significance level. Cefaclor induced type I hypersensitivity was significantly associated with HLA-DRB1∗04:03 (OR 4.61 [95% CI 1.51-14.09], P < 0.002) and HLA-DRB1∗14:54 (OR 3.86 [95% CI 1.09-13.67], P < 0.002). Conclusion LIMD1, HLA-DRB1∗04:03 and HLA-DRB1∗14:54 may affect susceptibility to cefaclor induced type I hypersensitivity. Further confirmative studies with a larger patient population should be performed to ascertain the role of HLA-DRB1 and LIMD1 in the development of cefaclor induced hypersensitivity.
Collapse
Affiliation(s)
- So-Young Park
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
- Division of Pulmonary, Allergy and Critical Care Medicine, Chung-Ang University Gwangmyeong Hospital, Gwangmyeong, South Korea
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, South Korea
| | - So Young Park
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sujin Seo
- Department of Public Health Science, Seoul National University, Seoul, South Korea
| | - Hyouk-Soo Kwon
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Seung-Hyun Kim
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
| | - Sae-Hoon Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hye-Kyung Park
- Department of Internal Medicine, School of Medicine, Busan National University, Busan, South Korea
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Cheol-Woo Kim
- Department of Internal Medicine, Inha University College of Medicine, Incheon, South Korea
| | - Byung Jae Lee
- Division of Allergy, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Hae-Sim Park
- Department of Allergy and Clinical Immunology, Ajou University School of Medicine, Suwon, South Korea
| | - You Sook Cho
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Heung-Bum Oh
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, USA
| | - Sungho Won
- Department of Public Health Science, Seoul National University, Seoul, South Korea
| | - Tae Bum Kim
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| |
Collapse
|
45
|
Cheek CL, Lindner P, Grigorenko EL. Statistical and Machine Learning Analysis in Brain-Imaging Genetics: A Review of Methods. Behav Genet 2024; 54:233-251. [PMID: 38336922 DOI: 10.1007/s10519-024-10177-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
Brain-imaging-genetic analysis is an emerging field of research that aims at aggregating data from neuroimaging modalities, which characterize brain structure or function, and genetic data, which capture the structure and function of the genome, to explain or predict normal (or abnormal) brain performance. Brain-imaging-genetic studies offer great potential for understanding complex brain-related diseases/disorders of genetic etiology. Still, a combined brain-wide genome-wide analysis is difficult to perform as typical datasets fuse multiple modalities, each with high dimensionality, unique correlational landscapes, and often low statistical signal-to-noise ratios. In this review, we outline the progress in brain-imaging-genetic methodologies starting from early massive univariate to current deep learning approaches, highlighting each approach's strengths and weaknesses and elongating it with the field's development. We conclude by discussing selected remaining challenges and prospects for the field.
Collapse
Affiliation(s)
- Connor L Cheek
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA.
- Department of Physics, University of Houston, Houston, TX, USA.
| | - Peggy Lindner
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA
- Department of Information Science Technology, University of Houston, Houston, TX, USA
| | - Elena L Grigorenko
- Texas Institute for Evaluation, Measurement, and Statistics, University of Houston, Houston, TX, USA
- Department of Psychology, University of Houston, Houston, TX, USA
- Baylor College of Medicine, Houston, TX, USA
- Sirius University of Science and Technology, Sochi, Russia
| |
Collapse
|
46
|
Ing C, Silber JH, Lackraj D, Olfson M, Miles C, Reiter JG, Jain S, Chihuri S, Guo L, Gyamfi-Bannerman C, Wall M, Li G. Behavioural disorders after prenatal exposure to anaesthesia for maternal surgery. Br J Anaesth 2024; 132:899-910. [PMID: 38423824 DOI: 10.1016/j.bja.2024.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/27/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND The association between prenatal exposure to general anaesthesia for maternal surgery during pregnancy and subsequent risk of disruptive or internalising behavioural disorder diagnosis in the child has not been well-defined. METHODS A nationwide sample of pregnant women linked to their liveborn infants was evaluated using the Medicaid Analytic eXtract (MAX, 1999-2013). Multivariate matching was used to match each child prenatally exposed to general anaesthesia owing to maternal appendectomy or cholecystectomy during pregnancy with five unexposed children. The primary outcome was diagnosis of a disruptive or internalising behavioural disorder in children. Secondary outcomes included diagnoses for a range of other neuropsychiatric disorders. RESULTS We matched 34,271 prenatally exposed children with 171,355 unexposed children in the database. Prenatally exposed children were more likely than unexposed children to receive a diagnosis of a disruptive or internalising behavioural disorder (hazard ratio [HR], 1.31; 95% confidence interval [CI], 1.23-1.40). For secondary outcomes, increased hazards of disruptive (HR, 1.32; 95% CI, 1.24-1.41) and internalising (HR, 1.36; 95% CI, 1.20-1.53) behavioural disorders were identified, and also increased hazards of attention-deficit/hyperactivity disorder (HR, 1.32; 95% CI, 1.22-1.43), behavioural disorders (HR, 1.28; 95% CI, 1.14-1.42), developmental speech or language disorders (HR, 1.16; 95% CI, 1.05-1.28), and autism (HR, 1.31; 95% CI, 1.05-1.64). CONCLUSIONS Prenatal exposure to general anaesthesia is associated with a 31% increased risk for a subsequent diagnosis of a disruptive or internalising behavioural disorder in children. Caution is advised when making any clinical decisions regarding care of pregnant women, as avoidance of necessary surgery during pregnancy can have detrimental effects on mothers and their children.
Collapse
Affiliation(s)
- Caleb Ing
- Department of Anesthesiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Epidemiology, Mailman School of Public Health, New York, NY, USA.
| | - Jeffrey H Silber
- Center for Outcomes Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Deven Lackraj
- Department of Anesthesiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Mark Olfson
- Department of Epidemiology, Mailman School of Public Health, New York, NY, USA; Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Caleb Miles
- Department of Biostatistics, Mailman School of Public Health, New York, NY, USA
| | - Joseph G Reiter
- Center for Outcomes Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Siddharth Jain
- Center for Outcomes Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stanford Chihuri
- Department of Anesthesiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ling Guo
- Department of Anesthesiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Cynthia Gyamfi-Bannerman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Melanie Wall
- Department of Psychiatry, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Biostatistics, Mailman School of Public Health, New York, NY, USA
| | - Guohua Li
- Department of Anesthesiology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Epidemiology, Mailman School of Public Health, New York, NY, USA
| |
Collapse
|
47
|
Hopker JG, Griffin JE, Hinoveanu LC, Saugy J, Faiss R. Competitive performance as a discriminator of doping status in elite athletes. Drug Test Anal 2024; 16:473-481. [PMID: 37602904 DOI: 10.1002/dta.3563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023]
Abstract
As the aim of any doping regime is to improve sporting performance, it has been suggested that analysis of athlete competitive results might be informative in identifying those at greater risk of doping. This research study aimed to investigate the utility of a statistical performance model to discriminate between athletes who have a previous anti-doping rule violation (ADRV) and those who do not. We analysed performances of male and female 100 and 800 m runners obtained from the World Athletics database using a Bayesian spline model. Measures of unusual improvement in performance were quantified by comparing the yearly change in athlete's performance (delta excess performance) to quantiles of performance in their age-matched peers from the database population. The discriminative ability of these measures was investigated using the area under the ROC curve (AUC) with the 55%, 75% and 90% quantiles of the population performance. The highest AUC values across age were identified for the model with a 75% quantile (AUC = 0.78-0.80). The results of this study demonstrate that delta excess performance was able to discriminate between athletes with and without ADRVs and therefore could be used to assist in the risk stratification of athletes for anti-doping purposes.
Collapse
Affiliation(s)
- James G Hopker
- School of Sport & Exercise Sciences, University of Kent, Canterbury, Kent, UK
| | - Jim E Griffin
- Department of Statistical Science, University College London, London, UK
| | | | - Jonas Saugy
- Research & Expertise in Antidoping Sciences, University of Lausanne, Lausanne, Switzerland
| | - Raphael Faiss
- Research & Expertise in Antidoping Sciences, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
48
|
Xing Z, Xu H, Ai K, Deng H, Hong Y, Deng P, Wang J, Xiong W, Li Z, Zhu L, Li Y. Gross Hematuria Does not Affect the Selection of Nephrectomy Types for Clinical Stage 1 Clear Cell Renal Cell Carcinoma: A Multicenter, Retrospective Cohort Study. Ann Surg Oncol 2024; 31:3531-3543. [PMID: 38329657 DOI: 10.1245/s10434-024-14958-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
PURPOSE This study aimed to discuss the correlation between gross hematuria and postoperative upstaging (from T1 to T3a) in patients with cT1 clear cell renal cell carcinoma (ccRCC) and to compare oncologic outcomes of partial nephrectomy (PN) and radical nephrectomy (RN) in patients with gross hematuria. METHODS A total of 2145 patients who met the criteria were enrolled in the study (including 363 patients with gross hematuria). The least absolute selection and shrinkage operator logistic regression was used to evaluate the risk factor of postoperative pathological upstaging. The propensity score matching (PSM) and stable inverse probability of treatment weighting (IPTW) analysis were used to balance the confounding factors. The Kaplan-Meier analysis and multivariate Cox proportional risk regression model were used to assess the prognosis. RESULTS Gross hematuria was a risk factor of postoperative pathological upstaging (odds ratio [OR] = 3.96; 95% confidence interval [CI] 2.44-6.42; P < 0.001). After PSM and stable IPTW adjustment, the characteristics were similar in corresponding patients in the PN and RN groups. In the PSM cohort, PN did not have a statistically significant impact on recurrence-free survival (hazard ratio [HR] = 1.48; 95% CI 0.25-8.88; P = 0.67), metastasis-free survival (HR = 1.24; 95% CI 0.33-4.66; P = 0.75), and overall survival (HR = 1.46; 95% CI 0.31-6.73; P = 0.63) compared with RN. The results were confirmed in sensitivity analyses. CONCLUSIONS Although gross hematuria was associated with postoperative pathological upstaging in patients with cT1 ccRCC, PN should still be the preferred treatment for such patients.
Collapse
Affiliation(s)
- Zhuo Xing
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Haozhe Xu
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kai Ai
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haitao Deng
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yulong Hong
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Piye Deng
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jie Wang
- Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- Department of Urology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhi Li
- Department of Urology, The Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, Hunan, China
| | - Lingfei Zhu
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yuan Li
- Department of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| |
Collapse
|
49
|
Daneshvar A, Golalizadeh M. Quantile regression shrinkage and selection via the Lqsso. J Biopharm Stat 2024; 34:297-322. [PMID: 37032487 DOI: 10.1080/10543406.2023.2198593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
Quantile regression has recently received a considerable attention due to its remarkable development in enriching the variety of regression models. Many efforts have been made to blend different penalty and loss function to extend or develop novel regression models that are unique from different perspectives. Bearing in mind that the lasso quantile regression model ignores the randomness of the realizations in the penalty part, we propose a new penalty for the quantile regression models. Similar to the adaptive lasso quantile regression model, the proposed model simultaneously does estimation and variable selection tasks. We call the new model 'lqsso-QR', standing for the least quantile shrinkage and selection operator quantile regression. In this article, we present a sufficient and necessary condition for the variable selection of the lasso quantile regression to enjoy the consistent property. We show that the lqsso-QR follows oracle properties under some mild conditions. From computational perspective, we apply an efficient algorithm, originally developed for the lasso quantile regression. Using simulation studies, we elaborate on the superiority of the proposed model compared with other lasso-type penalties, especially regarding relative prediction error. Also, an application of our method to a real-life data; the rat eye data, is reported.
Collapse
|
50
|
Wang C, Du M. Martingale-residual-based greedy model averaging for high-dimensional current status data. Stat Med 2024; 43:1726-1742. [PMID: 38381059 DOI: 10.1002/sim.10037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/08/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024]
Abstract
Current status data are a type of failure time data that arise when the failure time of study subject cannot be determined precisely but is known only to occur before or after a random monitoring time. Variable selection methods for the failure time data have been discussed extensively in the literature. However, the statistical inference of the model selected based on the variable selection method ignores the uncertainty caused by model selection. To enhance the prediction accuracy for risk quantities such as survival probability, we propose two optimal model averaging methods under semiparametric additive hazards models. Specifically, based on martingale residuals processes, a delete-one cross-validation (CV) process is defined, and two new CV functional criteria are derived for choosing model weights. Furthermore, we present a greedy algorithm for the implementation of the techniques, and the asymptotic optimality of the proposed model averaging approaches is established, along with the convergence of the greedy averaging algorithms. A series of simulation experiments demonstrate the effectiveness and superiority of the proposed methods. Finally, a real-data example is provided as an illustration.
Collapse
Affiliation(s)
- Chang Wang
- School of Mathematics, Jilin University, Changchun, China
| | - Mingyue Du
- School of Mathematics, Jilin University, Changchun, China
| |
Collapse
|