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Rosenman ETR, Basse G, Owen AB, Baiocchi M. Combining observational and experimental datasets using shrinkage estimators. Biometrics 2023; 79:2961-2973. [PMID: 36629736 DOI: 10.1111/biom.13827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 01/04/2023] [Indexed: 01/12/2023]
Abstract
We consider the problem of combining data from observational and experimental sources to draw causal conclusions. To derive combined estimators with desirable properties, we extend results from the Stein shrinkage literature. Our contributions are threefold. First, we propose a generic procedure for deriving shrinkage estimators in this setting, making use of a generalized unbiased risk estimate. Second, we develop two new estimators, prove finite sample conditions under which they have lower risk than an estimator using only experimental data, and show that each achieves a notion of asymptotic optimality. Third, we draw connections between our approach and results in sensitivity analysis, including proposing a method for evaluating the feasibility of our estimators.
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Linero AR. Prior and posterior checking of implicit causal assumptions. Biometrics 2023; 79:3153-3164. [PMID: 37325868 DOI: 10.1111/biom.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/18/2023] [Indexed: 06/17/2023]
Abstract
Causal inference practitioners have increasingly adopted machine learning techniques with the aim of producing principled uncertainty quantification for causal effects while minimizing the risk of model misspecification. Bayesian nonparametric approaches have attracted attention as well, both for their flexibility and their promise of providing natural uncertainty quantification. Priors on high-dimensional or nonparametric spaces, however, can often unintentionally encode prior information that is at odds with substantive knowledge in causal inference-specifically, the regularization required for high-dimensional Bayesian models to work can indirectly imply that the magnitude of the confounding is negligible. In this paper, we explain this problem and provide tools for (i) verifying that the prior distribution does not encode an inductive bias away from confounded models and (ii) verifying that the posterior distribution contains sufficient information to overcome this issue if it exists. We provide a proof-of-concept on simulated data from a high-dimensional probit-ridge regression model, and illustrate on a Bayesian nonparametric decision tree ensemble applied to a large medical expenditure survey.
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Yang Y, Lubin M, Zhou Z, Niu K. An Analysis of Honeybee Population Dynamics. Stud Health Technol Inform 2023; 308:76-85. [PMID: 38007728 DOI: 10.3233/shti230827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
Colony Collapse disorder (the CCD) is the term used to describe the global decline in bee populations. The research mission of this article is to identify which factors contribute to the CCD and understand how these factors contribute to the decline of bee populations, which may provide methods for restoring global bee populations. Two parts of the study will be mentioned in this article. The first half of our study was to understand such collective intelligence (and habits such as seasonal behavioral change) and use a mathematical model to simulate it. We then input the variables that we used to simulate honeybee collective intelligence into a time-dependent model to predict the population of a honey colony over time. In this model, we excluded the factors that might cause the CCD on purpose, so we could use it as a controlled set of honeybee natural population dynamics. We compared the results of this population model to experimental data we found, and they matched within certain degrees. The second half of our study was to perform a sensitivity analysis by introducing back the three factors that might cause the CCD to the population model including climate change, pesticides, and habitat destruction. The paper further discussed the strength and weaknesses of the mathematical model and used this model to predict how many honeybee hives were needed to support the pollination of a 20-acre parcel of land containing crops that benefit from pollination. Additionally, an infographic of our method was illustrated.
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Borgiani E, Nasello G, Ory L, Herpelinck T, Groeneveldt L, Bucher CH, Schmidt-Bleek K, Geris L. COMMBINI: an experimentally-informed COmputational Model of Macrophage dynamics in the Bone INjury Immunoresponse. Front Immunol 2023; 14:1231329. [PMID: 38130715 PMCID: PMC10733790 DOI: 10.3389/fimmu.2023.1231329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bone fracture healing is a well-orchestrated but complex process that involves numerous regulations at different scales. This complexity becomes particularly evident during the inflammatory stage, as immune cells invade the healing region and trigger a cascade of signals to promote a favorable regenerative environment. Thus, the emergence of criticalities during this stage might hinder the rest of the process. Therefore, the investigation of the many interactions that regulate the inflammation has a primary importance on the exploration of the overall healing progression. In this context, an in silico model named COMMBINI (COmputational Model of Macrophage dynamics in the Bone INjury Immunoresponse) has been developed to investigate the mechano-biological interactions during the early inflammatory stage at the tissue, cellular and molecular levels. An agent-based model is employed to simulate the behavior of immune cells, inflammatory cytokines and fracture debris as well as their reciprocal multiscale biological interactions during the development of the early inflammation (up to 5 days post-injury). The strength of the computational approach is the capacity of the in silico model to simulate the overall healing process by taking into account the numerous hidden events that contribute to its success. To calibrate the model, we present an in silico immunofluorescence method that enables a direct comparison at the cellular level between the model output and experimental immunofluorescent images. The combination of sensitivity analysis and a Genetic Algorithm allows dynamic cooperation between these techniques, enabling faster identification of the most accurate parameter values, reducing the disparity between computer simulation and histological data. The sensitivity analysis showed a higher sensibility of the computer model to the macrophage recruitment ratio during the early inflammation and to proliferation in the late stage. Furthermore, the Genetic Algorithm highlighted an underestimation of macrophage proliferation by in vitro experiments. Further experiments were conducted using another externally fixated murine model, providing an independent validation dataset. The validated COMMBINI platform serves as a novel tool to deepen the understanding of the intricacies of the early bone regeneration phases. COMMBINI aims to contribute to designing novel treatment strategies in both the biological and mechanical domains.
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Leppälä K. Sensitivity Analysis on Odds Ratios. Am J Epidemiol 2023; 192:1882-1886. [PMID: 37312597 PMCID: PMC10631298 DOI: 10.1093/aje/kwad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
The classical Cornfield inequalities state that if a third confounding variable is fully responsible for an observed association between the exposure and the outcome variables, then the association between both the exposure and the confounder, and the confounder and the outcome, must be at least as strong as the association between the exposure and the outcome, as measured by the risk ratio. The work of Ding and VanderWeele on assumption-free sensitivity analysis sharpens this bound to a bivariate function of the 2 risk ratios involving the confounder. Analogous results are nonexistent for the odds ratio, even though the conversion from odds ratios to risk ratios can sometimes be problematic. We present a version of the classical Cornfield inequalities for the odds ratio. The proof is based on the mediant inequality, dating back to ancient Alexandria. We also develop several sharp bivariate bounds of the observed association, where the 2 variables are either risk ratios or odds ratios involving the confounder.
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Mizutani S, Zhou Y, Tian YS, Takagi T, Ohkubo T, Hattori S. DTAmetasa: An R shiny application for meta-analysis of diagnostic test accuracy and sensitivity analysis of publication bias. Res Synth Methods 2023; 14:916-925. [PMID: 37640914 DOI: 10.1002/jrsm.1666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 07/12/2023] [Accepted: 08/15/2023] [Indexed: 08/31/2023]
Abstract
Meta-analysis of diagnostic test accuracy (DTA) is a powerful statistical method for synthesizing and evaluating the diagnostic capacity of medical tests and has been extensively used by clinical physicians and healthcare decision-makers. However, publication bias (PB) threatens the validity of meta-analysis of DTA. Some statistical methods have been developed to deal with PB in meta-analysis of DTA, but implementing these methods requires high-level statistical knowledge and programming skill. To assist non-technical users in running most routines in meta-analysis of DTA and handling with PB, we developed an interactive application, DTAmetasa. DTAmetasa is developed as a web-based graphical user interface based on the R shiny framework. It allows users to upload data and conduct meta-analysis of DTA by "point and click" operations. Moreover, DTAmetasa provides the sensitivity analysis of PB and presents the graphical results to evaluate the magnitude of the PB under various publication mechanisms. In this study, we introduce the functionalities of DTAmetasa and use the real-world meta-analysis to show its capacity for dealing with PB.
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Tai YC, Wang W, Wells MT. Two-sample inference procedures under nonproportional hazards. Pharm Stat 2023; 22:1016-1030. [PMID: 37429738 DOI: 10.1002/pst.2324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/11/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
We introduce a new two-sample inference procedure to assess the relative performance of two groups over time. Our model-free method does not assume proportional hazards, making it suitable for scenarios where nonproportional hazards may exist. Our procedure includes a diagnostic tau plot to identify changes in hazard timing and a formal inference procedure. The tau-based measures we develop are clinically meaningful and provide interpretable estimands to summarize the treatment effect over time. Our proposed statistic is a U-statistic and exhibits a martingale structure, allowing us to construct confidence intervals and perform hypothesis testing. Our approach is robust with respect to the censoring distribution. We also demonstrate how our method can be applied for sensitivity analysis in scenarios with missing tail information due to insufficient follow-up. Without censoring, Kendall's tau estimator we propose reduces to the Wilcoxon-Mann-Whitney statistic. We evaluate our method using simulations to compare its performance with the restricted mean survival time and log-rank statistics. We also apply our approach to data from several published oncology clinical trials where nonproportional hazards may exist.
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Vitullo P, Cicci L, Possenti L, Coclite A, Costantino ML, Zunino P. Sensitivity analysis of a multi-physics model for the vascular microenvironment. INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING 2023; 39:e3752. [PMID: 37455669 DOI: 10.1002/cnm.3752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/17/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023]
Abstract
The vascular microenvironment is the scale at which microvascular transport, interstitial tissue properties and cell metabolism interact. The vascular microenvironment has been widely studied by means of quantitative approaches, including multi-physics mathematical models as it is a central system for the pathophysiology of many diseases, such as cancer. The microvascular architecture is a key factor for fluid balance and mass transfer in the vascular microenvironment, together with the physical parameters characterizing the vascular wall and the interstitial tissue. The scientific literature of this field has witnessed a long debate about which factor of this multifaceted system is the most relevant. The purpose of this work is to combine the interpretative power of an advanced multi-physics model of the vascular microenvironment with state of the art and robust sensitivity analysis methods, in order to determine the factors that most significantly impact quantities of interest, related in particular to cancer treatment. We are particularly interested in comparing the factors related to the microvascular architecture with the ones affecting the physics of microvascular transport. Ultimately, this work will provide further insight into how the vascular microenvironment affects cancer therapies, such as chemotherapy, radiotherapy or immunotherapy.
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Ng WH, Myers CR, McArt S, Ellner SP. A Time for Every Purpose: Using Time-Dependent Sensitivity Analysis to Help Understand and Manage Dynamic Ecological Systems. Am Nat 2023; 202:630-654. [PMID: 37963117 DOI: 10.1086/726143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
AbstractSensitivity analysis is often used to help understand and manage ecological systems by assessing how a constant change in vital rates or other model parameters might affect the management outcome. This allows the manager to identify the most favorable course of action. However, realistic changes are often localized in time-for example, a short period of culling leads to a temporary increase in the mortality rate over the period. Hence, knowing when to act may be just as important as knowing what to act on. In this article, we introduce the method of time-dependent sensitivity analysis (TDSA) that simultaneously addresses both questions. We illustrate TDSA using three case studies: transient dynamics in static disease transmission networks, disease dynamics in a reservoir species with seasonal life history events, and endogenously driven population cycles in herbivorous invertebrate forest pests. We demonstrate how TDSA often provides useful biological insights, which are understandable on hindsight but would not have been easily discovered without the help of TDSA. However, as a caution, we also show how TDSA can produce results that mainly reflect uncertain modeling choices and are therefore potentially misleading. We provide guidelines to help users maximize the utility of TDSA while avoiding pitfalls.
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Salikhanov I, Kunirova G, Aitbaeva A, Crape B, Wieser S, Katapodi M. Cost-Effectiveness of Hospice Palliative Care for Patients With Cancer and Family Caregivers: A Multicenter Study in Kazakhstan. Value Health Reg Issues 2023; 38:69-76. [PMID: 37586226 DOI: 10.1016/j.vhri.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
OBJECTIVES In Kazakhstan, palliative care is offered through hospices, cancer centers, general hospitals, and mobile teams to approximately 107 000 patients in need. As a country with a transitional economy and a newly implemented social healthcare insurance system, Kazakhstan seeks a cost-effective allocation of limited resources for end-of-life care. This study aimed to assess cost-effectiveness of hospice-based palliative care for patients with cancer compared with the current standard of care provided in cancer centers across the country and, thereby, provide a better understanding for policy making regarding palliative care. METHODS A total of 182 family caregivers were recruited, 104 from 3 hospices and 78 from 3 palliative care units of cancer centers. Patients' state of health and family caregivers' burden were assessed with the Palliative Outcome Scale and the Zarit Burden Interview. Direct medical and nonmedical costs and family caregivers' out-of-pocket expenses associated with palliative care were collected. One-way and probabilistic sensitivity analysis was conducted by generating 1000 resamples using bootstrapping with Monte-Carlo simulation. RESULTS After 14 days of inpatient palliative care, patients' mean Palliative Outcome Scale score was 2.5 points better in the hospice group than the cancer center group. Family caregiver burden was 4.5 points better in the hospice group. Mean treatment costs were $31 lower for the hospice group. There was a statistically significant correlation between the total cost of treatment and patients' quality of life (r = 0.58). Probabilistic sensitivity analysis showed that hospice-based care has better outcomes and lower costs than care provided in cancer centers in 80% of tested scenarios. CONCLUSION Hospice-based palliative care is cost-effective compared with the care provided in palliative units of cancer centers in resource-limited settings in Kazakhstan.
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Zheng Z, Zhang Z. Circumferential Damage Monitoring of Steel Pipe Using a Radar Map Based on Torsional Guided Waves. SENSORS (BASEL, SWITZERLAND) 2023; 23:8734. [PMID: 37960434 PMCID: PMC10647777 DOI: 10.3390/s23218734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Ultrasonic guided wave technology has been successfully applied to detect multiple types of defects in pipes. However, the circumferential location and coverage of a defect are less studied because it is difficult to determine. In this study, the fundamental torsional mode T (0, 1) is selected to conduct monitoring of the circumferential defect in pipelines because of its almost non-dispersive property. A radar map of the peak wave signals at 30 circumferential positions is proposed to detect the damage. The circumferential defect of a steel pipe is thoroughly investigated using numerical simulation. First, the circumferential positioning of defects in various areas of the pipe is studied. Second, the results are compared to those based on longitudinal guide waves. Finally, the circumferential coverage of a defect in the pipeline is determined. The waves are excited and received using the pitch-catch approach, and the collected monitoring signals are processed using the Hilbert transformation. According to the findings, the circumferential defect in the pipe can be effectively identified from a 'T' shape in the radar image, and the monitoring method by the torsional guided wave is superior to the longitudinal wave method. The results clearly demonstrate the advantages of torsional guided waves in defect monitoring. The proposed method is expected to provide a promising solution to circumferential damage identification in pipelines.
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van Leeuwen JL, Kier WM. Predicting the effects of spatiotemporal modifications of muscle activation on the tentacle extension in squid. Front Bioeng Biotechnol 2023; 11:1193409. [PMID: 37929190 PMCID: PMC10620692 DOI: 10.3389/fbioe.2023.1193409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023] Open
Abstract
Squid use eight arms and two slender tentacles to capture prey. The muscular stalks of the tentacles are elongated approximately 80% in 20-40 ms towards the prey, which is adhered to the terminal clubs by arrays of suckers. Using a previously developed forward dynamics model of the extension of the tentacles of the squid Doryteuthis pealeii (formerly Loligo pealeii), we predict how spatial muscle-activation patterns result in a distribution of muscular power, muscle work, and kinetic and elastic energy along the tentacle. The simulated peak extension speed of the tentacles is remarkably insensitive to delays of activation along the stalk, as well as to random variations in the activation onset. A delay along the tentacle of 50% of the extension time has only a small effect on the peak extension velocity of the tentacle compared with a zero-delay pattern. A slight delay of the distal portion relative to the proximal has a small positive effect on peak extension velocity, whereas negative delays (delay reversed along stalk) always reduce extension performance. In addition, tentacular extension is relatively insensitive to superimposed random variations in the prescribed delays along the stalk. This holds in particular for small positive delays that are similar to delays predicted from measured axonal diameters of motor neurons. This robustness against variation in the activation distribution reduces the accuracy requirements of the neuronal control and is likely due to the non-linear mechanical properties of the muscular tissue in the tentacle.
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Vancak V, Sjölander A. Sensitivity analysis of G-estimators to invalid instrumental variables. Stat Med 2023; 42:4257-4281. [PMID: 37497859 DOI: 10.1002/sim.9859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 06/05/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
Instrumental variables regression is a tool that is commonly used in the analysis of observational data. The instrumental variables are used to make causal inference about the effect of a certain exposure in the presence of unmeasured confounders. A valid instrumental variable is a variable that is associated with the exposure, affects the outcome only through the exposure (exclusion), and is not confounded with the outcome (exogeneity). Unlike the first assumption, the other two are generally untestable and rely on subject-matter knowledge. Therefore, a sensitivity analysis is desirable to assess the impact of assumptions' violation on the estimated parameters. In this paper, we propose and demonstrate a new method of sensitivity analysis for G-estimators in causal linear and non-linear models. We introduce two novel aspects of sensitivity analysis in instrumental variables studies. The first is a single sensitivity parameter that captures violations of exclusion and exogeneity assumptions. The second is an application of the method to non-linear models. The introduced framework is theoretically justified and is illustrated via a simulation study. Finally, we illustrate the method by application to real-world data and provide guidelines on conducting sensitivity analysis.
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Runge MC, Shea K, Howerton E, Yan K, Hochheiser H, Rosenstrom E, Probert WJM, Borchering R, Marathe MV, Lewis B, Venkatramanan S, Truelove S, Lessler J, Viboud C. Scenario Design for Infectious Disease Projections: Integrating Concepts from Decision Analysis and Experimental Design. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.11.23296887. [PMID: 37873156 PMCID: PMC10592999 DOI: 10.1101/2023.10.11.23296887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, value of information, situational awareness, horizon scanning, and forecasting) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.
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Nguyen H, Schubert KE, Chang E, Nie Y, Pohling C, Van Buskirk S, Yamamoto V, Zeng Y, Schulte RW, Patel CB. Electric field distributions in realistic 3D rat head models during alternating electric field (AEF) therapy: a computational study. Phys Med Biol 2023; 68:205015. [PMID: 37703902 DOI: 10.1088/1361-6560/acf98d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023]
Abstract
Objective.Application of alternating electrical fields (AEFs) in the kHz range is an established treatment modality for primary and recurrent glioblastoma. Preclinical studies would enable innovations in treatment monitoring and efficacy, which could then be translated to benefit patients. We present a practical translational process converting image-based data into 3D rat head models for AEF simulations and study its sensitivity to parameter choices.Approach.Five rat head models composed of up to 7 different tissue types were created, and relative permittivity and conductivity of individual tissues obtained from the literature were assigned. Finite element analysis was used to model the AEF strength and distribution in the models with different combinations of head tissues, a virtual tumor, and an electrode pair.Main results.The simulations allowed for a sensitivity analysis of the AEF distribution with respect to different tissue combinations and tissue parameter values.Significance.For a single pair of 5 mm diameter electrodes, an average AEF strength inside the tumor exceeded 1.5 V cm-1, expected to be sufficient for a relevant therapeutic outcome. This study illustrates a robust and flexible approach for simulating AEF in different tissue types, suitable for preclinical studies in rodents and translatable to clinical use.
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Hafez MA, Halloran JP. Polynomial chaos expansion based sensitivity analysis of predicted knee reactions-assessing the influence of the primary ligaments in distraction based models. Comput Methods Biomech Biomed Engin 2023; 26:1678-1690. [PMID: 36222456 DOI: 10.1080/10255842.2022.2131401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/11/2022] [Accepted: 09/21/2022] [Indexed: 11/03/2022]
Abstract
Computational knee models have shown that predicted condylar reactions are sensitive to the utilized ligament mechanical parameters. These models, however, are computationally expensive with multiple sources of uncertainty. Traditional uncertainty analysis using Monte-Carlo (MC) inspired methods are costly to perform. The purpose of this study was to use two example calibrated knee models to compare quasi-MC versus polynomial chaos expansion (PCE) sensitivity analyses of predicted condylar reactions that included uncertainty in the mechanical parameters of the ligaments. PCE was practically identical versus quasi-MC with 95% and 98% reductions in model evaluations for analyses with 10 and 6 uncertain variables, respectively.
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Ren B, Lipsitz SR, Weiss RD, Fitzmaurice GM. Multiple imputation for non-monotone missing not at random data using the no self-censoring model. Stat Methods Med Res 2023; 32:1973-1993. [PMID: 37647237 DOI: 10.1177/09622802231188520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Although approaches for handling missing data from longitudinal studies are well-developed when the patterns of missingness are monotone, fewer methods are available for non-monotone missingness. Moreover, the conventional missing at random assumption-a natural benchmark for monotone missingness-does not model realistic beliefs about the non-monotone missingness processes (Robins and Gill, 1997). This has provided the impetus for alternative non-monotone missing not at random mechanisms. The "no self-censoring" model is such a mechanism and assumes the probability an outcome variable is missing is independent of its value when conditioning on all other possibly missing outcome variables and their missingness indicators. As an alternative to "weighting" methods that become computationally demanding with increasing number of outcome variables, we propose a multiple imputation approach under no self-censoring. We focus on the case of binary outcomes and present results of simulation and asymptotic studies to investigate the performance of the proposed imputation approach. We describe a related approach to sensitivity analysis to departure from no self-censoring. We discuss the relationship between missing at random and no self-censoring and prove that one is not a special case of the other. Finally, we discuss extensions to non-binary data settings. The proposed methods are illustrated with application to a substance use disorder clinical trial.
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Xiong S, Bi Y. A Novel Multi-Step Global Mechanism Scheme for n-Decane Combustion. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1389. [PMID: 37895510 PMCID: PMC10606497 DOI: 10.3390/e25101389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/30/2023] [Accepted: 07/16/2023] [Indexed: 10/29/2023]
Abstract
Based on the directed relation graph with error propagation (DRGEP) reduction method, a detailed mechanism consisting of 119 species and 527 reactions for n-decane was simplified. As a result, a skeletal mechanism comprising 32 species and 73 reactions was derived. Subsequently, the quasi-steady state approximation (QSSA) reduction method was employed to further simplify the skeletal mechanism, resulting in a reduced mechanism with 18 species and 14 global reactions. A comparison between the reduced mechanism, skeletal mechanism, and detailed mechanism revealed that the reduced and skeletal mechanisms successfully replicated the combustion characteristics of the detailed mechanism under a range of initial conditions. These models can be credibly incorporated into large-scale combustion simulation, serving as a solid foundation for enhancing computational efficiency.
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Liu S, Zhang Y, Golm GT, Liu G(F, Yang S. Robust analyzes for longitudinal clinical trials with missing and non-normal continuous outcomes. STATISTICAL THEORY AND RELATED FIELDS 2023; 8:1-14. [PMID: 38800501 PMCID: PMC11115336 DOI: 10.1080/24754269.2023.2261351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 09/16/2023] [Indexed: 05/29/2024]
Abstract
Missing data is unavoidable in longitudinal clinical trials, and outcomes are not always normally distributed. In the presence of outliers or heavy-tailed distributions, the conventional multiple imputation with the mixed model with repeated measures analysis of the average treatment effect (ATE) based on the multivariate normal assumption may produce bias and power loss. Control-based imputation (CBI) is an approach for evaluating the treatment effect under the assumption that participants in both the test and control groups with missing outcome data have a similar outcome profile as those with an identical history in the control group. We develop a robust framework to handle non-normal outcomes under CBI without imposing any parametric modeling assumptions. Under the proposed framework, sequential weighted robust regressions are applied to protect the constructed imputation model against non-normality in the covariates and the response variables. Accompanied by the subsequent mean imputation and robust model analysis, the resulting ATE estimator has good theoretical properties in terms of consistency and asymptotic normality. Moreover, our proposed method guarantees the analysis model robust-ness of the ATE estimation in the sense that its asymptotic results remain intact even when the analysis model is misspecified. The superiority of the proposed robust method is demonstrated by comprehensive simulation studies and an AIDS clinical trial data application.
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Dang LE, Gruber S, Lee H, Dahabreh IJ, Stuart EA, Williamson BD, Wyss R, Díaz I, Ghosh D, Kıcıman E, Alemayehu D, Hoffman KL, Vossen CY, Huml RA, Ravn H, Kvist K, Pratley R, Shih MC, Pennello G, Martin D, Waddy SP, Barr CE, Akacha M, Buse JB, van der Laan M, Petersen M. A causal roadmap for generating high-quality real-world evidence. J Clin Transl Sci 2023; 7:e212. [PMID: 37900353 PMCID: PMC10603361 DOI: 10.1017/cts.2023.635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 10/31/2023] Open
Abstract
Increasing emphasis on the use of real-world evidence (RWE) to support clinical policy and regulatory decision-making has led to a proliferation of guidance, advice, and frameworks from regulatory agencies, academia, professional societies, and industry. A broad spectrum of studies use real-world data (RWD) to produce RWE, ranging from randomized trials with outcomes assessed using RWD to fully observational studies. Yet, many proposals for generating RWE lack sufficient detail, and many analyses of RWD suffer from implausible assumptions, other methodological flaws, or inappropriate interpretations. The Causal Roadmap is an explicit, itemized, iterative process that guides investigators to prespecify study design and analysis plans; it addresses a wide range of guidance within a single framework. By supporting the transparent evaluation of causal assumptions and facilitating objective comparisons of design and analysis choices based on prespecified criteria, the Roadmap can help investigators to evaluate the quality of evidence that a given study is likely to produce, specify a study to generate high-quality RWE, and communicate effectively with regulatory agencies and other stakeholders. This paper aims to disseminate and extend the Causal Roadmap framework for use by clinical and translational researchers; three companion papers demonstrate applications of the Causal Roadmap for specific use cases.
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Nguyen TT, Lee SB, Kang JJ, Oh SY. Optimal Design of Galvanic Vestibular Stimulation for Patients with Vestibulopathy and Cerebellar Disorders. Brain Sci 2023; 13:1333. [PMID: 37759934 PMCID: PMC10526825 DOI: 10.3390/brainsci13091333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/02/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
OBJECTIVES Galvanic vestibular stimulation (GVS) has shown positive outcomes in various neurological and psychiatric disorders, such as enhancing postural balance and cognitive functions. In order to expedite the practical application of GVS in clinical settings, our objective was to determine the best GVS parameters for patients with vestibulopathy and cerebellar disorders using optimal design calculation. METHODS A total of 31 patients (26 males, mean age 57.03 ± 14.75 years, age range 22-82 years) with either unilateral or bilateral vestibulopathy (n = 18) or cerebellar ataxia (n = 13) were enrolled in the study. The GVS intervention included three parameters, waveform (sinusoidal, direct current [DC], and noisy), amplitude (0.4, 0.8, and 1.2 mA), and duration of stimulation (5 and 30 min), resulting in a total of 18 GVS intervention modes as input variables. To evaluate the effectiveness of GVS, clinical vertigo and gait assessments were conducted using the Dizziness Visual Analogue Scale (D-VAS), Activities-specific Balance Confidence Scale (ABC), and Scale for Assessment and Rating of Ataxia (SARA) as output variables. Optimal design and local sensitivity analysis were employed to determine the most optimal GVS modes. RESULTS Patients with unilateral vestibulopathy experienced the most favorable results with either noisy or sinusoidal GVS at 0.4 mA amplitude for 30 min, followed by DC GVS at 0.8 mA amplitude for 5 min. Noisy GVS at 0.8 or 0.4 mA amplitude for 30 min demonstrated the most beneficial effects in patients with bilateral vestibulopathy. For patients with cerebellar ataxia, the optimal choices were noisy GVS with 0.8 or 0.4 mA amplitude for 5 or 30 min. CONCLUSIONS This study is the first to utilize design optimization methods to identify the GVS stimulation parameters that are tailored to individual-specific characteristics of dizziness and imbalance. A sensitivity analysis was carried out along with the optimal design to offset the constraints of a limited sample size, resulting in the identification of the most efficient GVS modes for patients suffering from vestibular and cerebellar disorders.
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Chien SC, Chang YH, Yen CM, Chen YE, Liu CC, Hsiao YP, Yang PY, Lin HM, Lu XH, Wu IC, Hsu CC, Chiou HY, Chung RH. Predicting Long-Term Care Service Demands for Cancer Patients: A Machine Learning Approach. Cancers (Basel) 2023; 15:4598. [PMID: 37760567 PMCID: PMC10526410 DOI: 10.3390/cancers15184598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Long-term care (LTC) service demands among cancer patients are significantly understudied, leading to gaps in healthcare resource allocation and policymaking. OBJECTIVE This study aimed to predict LTC service demands for cancer patients and identify the crucial factors. METHODS 3333 cases of cancers were included. We further developed two specialized prediction models: a Unified Prediction Model (UPM) and a Category-Specific Prediction Model (CSPM). The UPM offered generalized forecasts by treating all services as identical, while the CSPM built individual predictive models for each specific service type. Sensitivity analysis was also conducted to find optimal usage cutoff points for determining the usage and non-usage cases. RESULTS Service usage differences in lung, liver, brain, and pancreatic cancers were significant. For the UPM, the top 20 performance model cutoff points were adopted, such as through Logistic Regression (LR), Quadratic Discriminant Analysis (QDA), and XGBoost (XGB), achieving an AUROC range of 0.707 to 0.728. The CSPM demonstrated performance with an AUROC ranging from 0.777 to 0.837 for the top five most frequently used services. The most critical predictive factors were the types of cancer, patients' age and female caregivers, and specific health needs. CONCLUSION The results of our study provide valuable information for healthcare decisions, resource allocation optimization, and personalized long-term care usage for cancer patients.
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Serafini E, Corti A, Gallo D, Chiastra C, Li XC, Casarin S. An agent-based model of cardiac allograft vasculopathy: toward a better understanding of chronic rejection dynamics. Front Bioeng Biotechnol 2023; 11:1190409. [PMID: 37771577 PMCID: PMC10523786 DOI: 10.3389/fbioe.2023.1190409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/17/2023] [Indexed: 09/30/2023] Open
Abstract
Cardiac allograft vasculopathy (CAV) is a coronary artery disease affecting 50% of heart transplant (HTx) recipients, and it is the major cause of graft loss. CAV is driven by the interplay of immunological and non-immunological factors, setting off a cascade of events promoting endothelial damage and vascular dysfunction. The etiology and evolution of tissue pathology are largely unknown, making disease management challenging. So far, in vivo models, mostly mouse-based, have been widely used to study CAV, but they are resource-consuming, pose many ethical issues, and allow limited investigation of time points and important biomechanical measurements. Recently, agent-based models (ABMs) proved to be valid computational tools for deciphering mechanobiological mechanisms driving vascular adaptation processes at the cell/tissue level, augmenting cost-effective in vivo lab-based experiments, at the same time guaranteeing richness in observation time points and low consumption of resources. We hypothesize that integrating ABMs with lab-based experiments can aid in vivo research by overcoming those limitations. Accordingly, this work proposes a bidimensional ABM of CAV in a mouse coronary artery cross-section, simulating the arterial wall response to two distinct stimuli: inflammation and hemodynamic disturbances, the latter considered in terms of low wall shear stress (WSS). These stimuli trigger i) inflammatory cell activation and ii) exacerbated vascular cell activities. Moreover, an extensive analysis was performed to investigate the ABM sensitivity to the driving parameters and inputs and gain insights into the ABM working mechanisms. The ABM was able to effectively replicate a 4-week CAV initiation and progression, characterized by lumen area decrease due to progressive intimal thickening in regions exposed to high inflammation and low WSS. Moreover, the parameter and input sensitivity analysis highlighted that the inflammatory-related events rather than the WSS predominantly drive CAV, corroborating the inflammatory nature of the vasculopathy. The proof-of-concept model proposed herein demonstrated its potential in deepening the pathology knowledge and supporting the in vivo analysis of CAV.
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Chung J, Lee K. Credit Card Fraud Detection: An Improved Strategy for High Recall Using KNN, LDA, and Linear Regression. SENSORS (BASEL, SWITZERLAND) 2023; 23:7788. [PMID: 37765845 PMCID: PMC10535547 DOI: 10.3390/s23187788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
Efficiently and accurately identifying fraudulent credit card transactions has emerged as a significant global concern along with the growth of electronic commerce and the proliferation of Internet of Things (IoT) devices. In this regard, this paper proposes an improved algorithm for highly sensitive credit card fraud detection. Our approach leverages three machine learning models: K-nearest neighbor, linear discriminant analysis, and linear regression. Subsequently, we apply additional conditional statements, such as "IF" and "THEN", and operators, such as ">" and "<", to the results. The features extracted using this proposed strategy achieved a recall of 1.0000, 0.9701, 1.0000, and 0.9362 across the four tested fraud datasets. Consequently, this methodology outperforms other approaches employing single machine learning models in terms of recall.
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Zhuang J, Liu M, Wu H, Wang J. Designing an Environmental Wind Tunnel Cooling System for High-Speed Trains with Air Compression Cooling and a Sensitivity Analysis of Design Parameters. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1312. [PMID: 37761611 PMCID: PMC10530046 DOI: 10.3390/e25091312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
Environmental wind tunnels for high-speed trains play a significant role in their development. The cooling system of the wind tunnel poses a challenge as it requires lower temperatures and a higher cooling capacity during operation. The conventional approach to wind tunnel refrigeration uses evaporative cooling, which is less efficient at low temperatures and comes with environmental and safety risks. In this study, we propose an innovative air compression refrigeration method based on the Brayton cycle. This method converts high-pressure air into low-temperature air at atmospheric pressure for wind tunnel refrigeration. The new cooling system has reduced energy usage by 3.72 MW, leading to a 13.15% improvement. The return cooler of the system is modeled using the effective number of heat transfer units and the mean temperature difference design method. Additionally, the turbine within the system is analyzed using one-dimensional flow characteristic analysis and the principle of similarity. This method has been validated by comparing it to other published papers. Subsequently, we perform a thorough sensitivity analysis on the key design parameters of the system. We observe that with a sufficient heat transfer area of the recooler, the cooling efficiency of the system exhibits a gradual decline from 64% to 60% as the mass flow rate of the system rises. For a fixed turbine, the cooling efficiency of the system rises from 20% to 62% and subsequently declines to 37%, with an increase in the mass flow rate. As a result, we conclude that the design parameters of the turbine have a more significant influence on the cooling efficiency of the system than the recooler. Our study will establish a foundation for selecting parameters to optimize the refrigeration system in the future.
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