1
|
Subramanian DL, Miller AMP, Smith DM. A comparison of hippocampal and retrosplenial cortical spatial and contextual firing patterns. Hippocampus 2024. [PMID: 38770779 DOI: 10.1002/hipo.23610] [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] [Received: 10/16/2023] [Revised: 03/22/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
The hippocampus (HPC) and retrosplenial cortex (RSC) are key components of the brain's memory and navigation systems. Lesions of either region produce profound deficits in spatial cognition and HPC neurons exhibit well-known spatial firing patterns (place fields). Recent studies have also identified an array of navigation-related firing patterns in the RSC. However, there has been little work comparing the response properties and information coding mechanisms of these two brain regions. In the present study, we examined the firing patterns of HPC and RSC neurons in two tasks which are commonly used to study spatial cognition in rodents, open field foraging with an environmental context manipulation and continuous T-maze alternation. We found striking similarities in the kinds of spatial and contextual information encoded by these two brain regions. Neurons in both regions carried information about the rat's current spatial location, trajectories and goal locations, and both regions reliably differentiated the contexts. However, we also found several key differences. For example, information about head direction was a prominent component of RSC representations but was only weakly encoded in the HPC. The two regions also used different coding schemes, even when they encoded the same kind of information. As expected, the HPC employed a sparse coding scheme characterized by compact, high contrast place fields, and information about spatial location was the dominant component of HPC representations. RSC firing patterns were more consistent with a distributed coding scheme. Instead of compact place fields, RSC neurons exhibited broad, but reliable, spatial and directional tuning, and they typically carried information about multiple navigational variables. The observed similarities highlight the closely related functions of the HPC and RSC, whereas the differences in information types and coding schemes suggest that these two regions likely make somewhat different contributions to spatial cognition.
Collapse
Affiliation(s)
| | - Adam M P Miller
- Department of Psychology, Cornell University, Ithaca, New York, USA
| | - David M Smith
- Department of Psychology, Cornell University, Ithaca, New York, USA
| |
Collapse
|
2
|
Harris D, Delcher C. Geo spatial Imprecision With Constraints for Precision Public Health: Algorithm Development and Validation. Online J Public Health Inform 2024; 16:e54958. [PMID: 38772021 DOI: 10.2196/54958] [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: 11/30/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Location and environmental social determinants of health are increasingly important factors in both an individual's health and the monitoring of community-level public health issues. OBJECTIVE We aimed to measure the extent to which location obfuscation techniques, designed to protect an individual's privacy, can unintentionally shift geographical coordinates into neighborhoods with significantly different socioeconomic demographics, which limits the precision of findings for public health stakeholders. METHODS Point obfuscation techniques intentionally blur geographic coordinates to conceal the original location. The pinwheel obfuscation method is an existing technique in which a point is moved along a pinwheel-like path given a randomly chosen angle and a maximum radius; we evaluate the impact of this technique using 2 data sets by comparing the demographics of the original point and the resulting shifted point by cross-referencing data from the United States Census Bureau. RESULTS Using poverty measures showed that points from regions of low poverty may be shifted to regions of high poverty; similarly, points in regions with high poverty may be shifted into regions of low poverty. We varied the maximum allowable obfuscation radius; the mean difference in poverty rate before and after obfuscation ranged from 6.5% to 11.7%. Additionally, obfuscation inadvertently caused false hot spots for deaths by suicide in Cook County, Illinois. CONCLUSIONS Privacy concerns require patient locations to be imprecise to protect against risk of identification; precision public health requires accuracy. We propose a modified obfuscation technique that is constrained to generate a new point within a specified census-designated region to preserve both privacy and analytical accuracy by avoiding demographic shifts.
Collapse
Affiliation(s)
- Daniel Harris
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, United States
| | - Chris Delcher
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| |
Collapse
|
3
|
Rahimzadeh N, Srinivasan SS, Zhang J, Swarup V. Gene networks and systems biology in Alzheimer's disease: Insights from multi-omics approaches. Alzheimers Dement 2024; 20:3587-3605. [PMID: 38534018 PMCID: PMC11095483 DOI: 10.1002/alz.13790] [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: 10/20/2023] [Revised: 01/25/2024] [Accepted: 02/17/2024] [Indexed: 03/28/2024]
Abstract
Despite numerous studies in the field of dementia and Alzheimer's disease (AD), a comprehensive understanding of this devastating disease remains elusive. Bulk transcriptomics have provided insights into the underlying genetic factors at a high level. Subsequent technological advancements have focused on single-cell omics, encompassing techniques such as single-cell RNA sequencing and epigenomics, enabling the capture of RNA transcripts and chromatin states at a single cell or nucleus resolution. Furthermore, the emergence of spatial omics has allowed the study of gene responses in the vicinity of amyloid beta plaques or across various brain regions. With the vast amount of data generated, utilizing gene regulatory networks to comprehensively study this disease has become essential. This review delves into some techniques employed in the field of AD, explores the discoveries made using these techniques, and provides insights into the future of the field.
Collapse
Affiliation(s)
- Negin Rahimzadeh
- Mathematical, Computational, and Systems Biology (MCSB) ProgramUniversity of California IrvineIrvineCaliforniaUSA
| | - Shushrruth Sai Srinivasan
- Mathematical, Computational, and Systems Biology (MCSB) ProgramUniversity of California IrvineIrvineCaliforniaUSA
| | - Jing Zhang
- Department of Computer ScienceUniversity of CaliforniaIrvineCaliforniaUSA
| | - Vivek Swarup
- Department of Neurobiology and BehaviorUniversity of California IrvineIrvineCaliforniaUSA
- Institute for Memory Impairments and Neurological Disorders (MIND)University of California IrvineIrvineCaliforniaUSA
| |
Collapse
|
4
|
Ramirez Flores RO, Schäfer PSL, Küchenhoff L, Saez-Rodriguez J. Complementing Cell Taxonomies with a Multicellular Analysis of Tissues. Physiology (Bethesda) 2024; 39:0. [PMID: 38319138 DOI: 10.1152/physiol.00001.2024] [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: 01/03/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting of cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of single-cell dynamics upon shared external queues and spatial organizations. However, little is known about the relationship between single-cell heterogeneity and the emergence and maintenance of robust multicellular processes in developed tissues and its role in (patho)physiology. Here, we present emerging computational modeling strategies that use increasingly available large-scale cross-condition single-cell and spatial datasets to study multicellular organization in tissues and complement cell taxonomies. This perspective should enable us to better understand how cells within tissues collectively process information and adapt synchronized responses in disease contexts and to bridge the gap between structural changes and functions in tissues.
Collapse
Affiliation(s)
- Ricardo Omar Ramirez Flores
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Philipp Sven Lars Schäfer
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Leonie Küchenhoff
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Heidelberg University and Institute for Computational Biomedicine, Heidelberg University Hospital, Heidelberg, Germany
| |
Collapse
|
5
|
Belfrage E, Ek S, Johansson Å, Brauner H, Sonesson A, Drott K. Predictive and Prognostic Biomarkers in Patients With Mycosis Fungoides and Sézary Syndrome (BIO-MUSE): Protocol for a Translational Study. JMIR Res Protoc 2024; 13:e55723. [PMID: 38436589 PMCID: PMC11027051 DOI: 10.2196/55723] [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: 12/21/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Cutaneous T-cell lymphoma (CTCL) is a rare group of lymphomas that primarily affects the skin. Mycosis fungoides (MF) is the most common form of CTCL and Sézary syndrome (SS) is more infrequent. Early stages (IA-IIA) have a favorable prognosis, while advanced stages (IIB-IVB) have a worse prognosis. Around 25% of patients with early stages of the disease will progress to advanced stages. Malignant skin-infiltrating T-cells in CTCL are accompanied by infiltrates of nonmalignant T-cells and other immune cells that produce cytokines that modulate the inflammation. Skin infection, often with Staphylococcus aureus, is frequent in advanced stages and can lead to sepsis and death. S. aureus has also been reported to contribute to the progression of the disease. Previous reports indicate a shift from Th1 to Th2 cytokine production and dysfunction of the skin barrier in CTCL. Treatment response is highly variable and often unpredictable, and there is a need for new predictive and prognostic biomarkers. OBJECTIVE This prospective translational study aims to identify prognostic biomarkers in the blood and skin of patients with MF and SS. METHODS The Predictive and Prognostic Biomarkers in Patients With MF and SS (BIO-MUSE) study aims to recruit 120 adult patients with MF or SS and a control group of 20 healthy volunteers. The treatments will be given according to clinical routine. The sampling of each patient will be performed every 3 months for 3 years. The blood samples will be analyzed for lactate dehydrogenase, immunoglobulin E, interleukins, thymus and activation-regulated chemokine, and lymphocyte subpopulations. The lymphoma microenvironment will be investigated through digital spatial profiling and single-cell RNA sequencing. Microbiological sampling and analysis of skin barrier function will be performed. The life quality parameters will be evaluated. The results will be evaluated by the stage of the disease. RESULTS Patient inclusion started in 2021 and is still ongoing in 2023, with 18 patients and 20 healthy controls enrolled. The publication of selected translational findings before the publication of the main results of the trial is accepted. CONCLUSIONS This study aims to investigate blood and skin with a focus on immune cells and the microbiological environment to identify potential new prognostic biomarkers in MF and SS. TRIAL REGISTRATION ClinicalTrials.gov NCT04904146; https://www.clinicaltrials.gov/study/NCT04904146. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/55723.
Collapse
Affiliation(s)
- Emma Belfrage
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund, Sweden
| | - Sara Ek
- Department of Immunotechnology, Faculty of Engineering, Lund University, Lund, Sweden
| | - Åsa Johansson
- Clinical Genetics and Pathology, Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Skåne University Hospital, Lund, Sweden
| | - Hanna Brauner
- Division of Dermatology and Venereology, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Dermatology and Venereology, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Sonesson
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund, Sweden
| | - Kristina Drott
- Department of Hematology and Transfusion Medicine, Skåne University Hospital, Lund, Sweden
| |
Collapse
|
6
|
Tesfaye S, Regassa F, Beyene G, Leta S, Paeshuyse J. Spatiotemporal analysis and forecasting of lumpy skin disease outbreaks in Ethiopia based on retrospective outbreak reports. Front Vet Sci 2024; 11:1277007. [PMID: 38532795 PMCID: PMC10964905 DOI: 10.3389/fvets.2024.1277007] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Introduction Lumpy skin disease is a viral disease that affects cattle belonging to genus Capripoxvirus (Poxviridae) and lead to significant economic losses. Objective The objective of this study was to evaluate the distribution of lumpy skin disease (LSD) outbreaks and predict future patterns based on retrospective outbreak reports in Ethiopia. Methods Data were collected through direct communication with regional laboratories and a hierarchical reporting system from the Peasant Associations to Ministry of Agriculture. Time-series data for the LSD outbreaks were analyzed using classical additive time-series decomposition and STL decomposition. Four models (ARIMA, SARIMA, ETS, STLF) were also used to forecast the number of LSD outbreaks that occurred each month for the years (2021-2025) after the models' accuracy test was performed. Additionally, the space-time permutation model (STP) were also used to study retrospective space-time cluster analysis of LSD outbreaks in Ethiopia. Results This study examined the geographical and temporal distribution of LSD outbreaks in Ethiopia from 2008 to 2020, reporting a total of 3,256 LSD outbreaks, 14,754 LSD-positive cases, 7,758 deaths, and 289 slaughters. It also covered approximately 68% of Ethiopia's districts, with Oromia reporting the highest LSD outbreaks. In the LSD's temporal distribution, the highest peak was reported following the rainy season in September to December and its lowest peak in the dry months of April and May. Out of the four models tested for forecasting, the SARIMA (3, 0, 0) (2, 1, 0) [12] model performed well for the validation data, while the STLF+Random Walk had a robust prediction for the training data. Thus, the SARIMA and STLF+Random Walk models produced a more accurate forecast of LSD outbreaks between 2020 and 2025. From retrospective Space-Time Cluster Analysis of LSD, eight possible clusters were also identified, with five of them located in central part of Ethiopia. Conclusion The study's time series and ST-cluster analysis of LSD outbreak data provide valuable insights into the spatial and temporal dynamics of the disease in Ethiopia. These insights can aid in the development of effective strategies to control and prevent the spread of the disease and holds great potential for improving efforts to combat LSD in the country.
Collapse
Affiliation(s)
- Shimels Tesfaye
- Laboratory of Host–Pathogen Interaction, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, Leuven, Belgium
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Addis Ababa, Ethiopia
| | - Fikru Regassa
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Addis Ababa, Ethiopia
- Ministry of Agriculture, Livestock and Fisheries, Addis Ababa, Ethiopia
| | - Gashaw Beyene
- Ministry of Agriculture, Livestock and Fisheries, Addis Ababa, Ethiopia
- Epidemiology Directorate, Ministry of Agriculture, Livestock and Fisheries, Addis Ababa, Ethiopia
| | - Samson Leta
- Laboratory of Host–Pathogen Interaction, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, Leuven, Belgium
- College of Veterinary Medicine and Agriculture, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jan Paeshuyse
- Laboratory of Host–Pathogen Interaction, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, Leuven, Belgium
| |
Collapse
|
7
|
John P, Varga C, Cooke M, Majowicz SE. Temporal, spatial and space-time distribution of infections caused by five major enteric pathogens, Ontario, Canada, 2010-2017. Zoonoses Public Health 2024; 71:178-190. [PMID: 37990481 DOI: 10.1111/zph.13096] [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: 05/22/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
AIMS In Canada, enteric diseases pose substantial health and economic burdens. The distribution of these diseases is uneven across both geography and time and understanding these patterns is therefore important for the prevention of future outbreaks. We evaluated temporal, spatial and space-time clustering of laboratory-confirmed cases of Campylobacter spp. (n = 28,728), non-typhoidal Salmonella spp. (n = 22,640), Shiga toxin-producing Escherichia coli (STEC; n = 1340), Yersinia spp. (n = 1674) and Listeria monocytogenes (n = 471) infections, reported between 2010 and 2017 inclusive in Ontario, the most populous province in Canada (population ~ 13,500,000 in 2016). METHODS AND RESULTS For each enteric pathogen, we calculated the mean incidence rates (IRs) for Ontario's 35 public health unit (PHU) areas and visualized them using choropleth maps. We identified temporal, spatial and space-time high infection rate clusters using retrospective Poisson scan statistics. Campylobacter and Salmonella infections had the highest IRs, while Listeria infections had the lowest. Campylobacter, Salmonella, STEC and Listeria mostly clustered temporally in the spring/summer and sometimes extended into fall, while Yersinia showed a less clear seasonal pattern. The IR visualizations and spatial and space-time scan statistics showed geographic heterogeneity of infection rates with high infection rate clusters detected mainly in PHUs across the southwestern and central-western regions of Ontario for Campylobacter, Salmonella and STEC infections, and mainly in PHUs located in the central-eastern regions for Yersinia and Listeria. A high proportion of cases in some of the significant Salmonella, STEC and Listeria infection clusters were linked to disease outbreaks. CONCLUSIONS Results from this study will inform heightened public health surveillance, and prevention and control programmes, in populations and regions of high infection rates. Further research is needed to determine the pathogen-specific socioeconomic, environmental and agricultural risk factors that may be related to the temporal and spatial disease patterns we observed in our study.
Collapse
Affiliation(s)
- Patience John
- School of Public Health Sciences, University of Waterloo, Waterloo, Ontario, Canada
| | - Csaba Varga
- School of Public Health Sciences, University of Waterloo, Waterloo, Ontario, Canada
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Martin Cooke
- School of Public Health Sciences, University of Waterloo, Waterloo, Ontario, Canada
- Department of Sociology and Legal Studies, University of Waterloo, Waterloo, Ontario, Canada
| | - Shannon E Majowicz
- School of Public Health Sciences, University of Waterloo, Waterloo, Ontario, Canada
| |
Collapse
|
8
|
Aung TN, Bates KM, Rimm DL. High-Plex Assessment of Biomarkers in Tumors. Mod Pathol 2024; 37:100425. [PMID: 38219953 DOI: 10.1016/j.modpat.2024.100425] [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: 08/30/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
The assessment of biomarkers plays a critical role in the diagnosis and treatment of many cancers. Biomarkers not only provide diagnostic, prognostic, or predictive information but also can act as effective targets for new pharmaceutical therapies. As the utility of biomarkers increases, it becomes more important to utilize accurate and efficient methods for biomarker discovery and, ultimately, clinical assessment. High-plex imaging studies, defined here as assessment of 8 or more biomarkers on a single slide, have become the method of choice for biomarker discovery and assessment of biomarker spatial context. In this review, we discuss methods of measuring biomarkers in slide-mounted tissue samples, detail the various high-plex methods that allow for the simultaneous assessment of multiple biomarkers in situ, and describe the impact of high-plex biomarker assessment on the future of anatomic pathology.
Collapse
Affiliation(s)
- Thazin N Aung
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Katherine M Bates
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut; Department of Internal Medicine (Medical Oncology), Yale University School of Medicine, New Haven, Connecticut.
| |
Collapse
|
9
|
Winkler I, Tolkachov A, Lammers F, Lacour P, Daugelaite K, Schneider N, Koch ML, Panten J, Grünschläger F, Poth T, Ávila BMD, Schneider A, Haas S, Odom DT, Gonçalves Â. The cycling and aging mouse female reproductive tract at single-cell resolution. Cell 2024; 187:981-998.e25. [PMID: 38325365 DOI: 10.1016/j.cell.2024.01.021] [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: 07/25/2022] [Revised: 04/21/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024]
Abstract
The female reproductive tract (FRT) undergoes extensive remodeling during reproductive cycling. This recurrent remodeling and how it shapes organ-specific aging remains poorly explored. Using single-cell and spatial transcriptomics, we systematically characterized morphological and gene expression changes occurring in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrous cycle, during decidualization, and into aging. These analyses reveal that fibroblasts play central-and highly organ-specific-roles in FRT remodeling by orchestrating extracellular matrix (ECM) reorganization and inflammation. Our results suggest a model wherein recurrent FRT remodeling over reproductive lifespan drives the gradual, age-related development of fibrosis and chronic inflammation. This hypothesis was directly tested using chemical ablation of cycling, which reduced fibrotic accumulation during aging. Our atlas provides extensive detail into how estrus, pregnancy, and aging shape the organs of the female reproductive tract and reveals the unexpected cost of the recurrent remodeling required for reproduction.
Collapse
Affiliation(s)
- Ivana Winkler
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany
| | - Alexander Tolkachov
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Fritjof Lammers
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Perrine Lacour
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Klaudija Daugelaite
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany
| | - Nina Schneider
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany
| | - Marie-Luise Koch
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany
| | - Jasper Panten
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany; German Cancer Research Center (DKFZ), Division of Computational Genomics and Systems Genetics, 69120 Heidelberg, Germany
| | - Florian Grünschläger
- Heidelberg University, Faculty of Biosciences, 69117 Heidelberg, Germany; German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Division of Stem Cells and Cancer, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | - Tanja Poth
- CMCP - Center for Model System and Comparative Pathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | | | - Augusto Schneider
- Universidade Federal de Pelotas, Faculdade de Nutrição, 96010-610 Pelotas, RS, Brazil
| | - Simon Haas
- German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Division of Stem Cells and Cancer, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Charité - Universitätsmedizin Berlin, Department of Hematology, Oncology and Cancer Immunology, 10115 Berlin, Germany
| | - Duncan T Odom
- German Cancer Research Center (DKFZ), Division of Regulatory Genomics and Cancer Evolution, 69120 Heidelberg, Germany; Cancer Research UK - Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Ângela Gonçalves
- German Cancer Research Center (DKFZ), Division of Somatic Evolution and Early Detection, 69120 Heidelberg, Germany.
| |
Collapse
|
10
|
Drechsler M. Flexibility trade-offs in conservation offsets. Conserv Biol 2024; 38:e14144. [PMID: 37424366 DOI: 10.1111/cobi.14144] [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: 11/21/2022] [Revised: 05/24/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
Conservation offsets promise cost-effective conservation of biodiversity, especially under economic and environmental change, because they represent a more flexible approach to biodiversity conservation, allowing for the economic development of ecologically valuable land provided that this development is offset by restoration of previously developed areas. The level of flexibility is determined by the trading rules. Lax rules allow for more flexibility, which promises cost savings, but will likely lead to unintended loss of biodiversity. I analyzed the trade-off between economic costs and ecological benefits (biodiversity conservation) in biodiversity offsetting with an ecological-economic model that considered the three main types of offset flexibility: spatial, temporal, and ecosystem type. I sought to examine the influence of ecological and economic conditions on offset flexibility trade-offs. Large variation in the conservation costs and small costs of habitat restoration strongly increased trading activity and reduced the ecological benefit. The ecological benefit was most sensitive to spatial flexibility when a short range of ecological interaction was considered. At a large interaction range, spatial flexibility delivered large cost savings without overly reducing the ecological benefit. Risks and time lags associated with habitat restoration favored an offsetting scheme in which credits are awarded with the initiation of restoration projects rather than their successful completion-given appropriate offsetting multipliers were chosen. Altogether, under scarce resources, the level of flexibility in an offsetting scheme should be chosen by carefully balancing ecological benefits and economic costs.
Collapse
Affiliation(s)
- Martin Drechsler
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Brandenburg University of Technology Cottbus-Senftenberg Erich-Weinert-Straße 1, Cottbus, Germany
| |
Collapse
|
11
|
Vandermeer J, Perfecto I. Combining intransitive and higher-order effects in a coupled oscillator framework: A case study of an ant community. Ecology 2024; 105:e4218. [PMID: 38032663 DOI: 10.1002/ecy.4218] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/19/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
A growing body of literature recognizes that pairwise species interactions are not necessarily an appropriate metaphorical molecule of community ecology. Two examples are intransitive competition and nonlinear higher-order effects. While these two processes have been discussed extensively, the explicit analysis of how the two of them behave when simultaneously part of the same dynamic system has not yet been explored theoretically. A concrete situation exists on coffee farms in Puerto Rico in which three ant species form an intransitive competitive triplet, and that triplet is strongly influenced, nonlinearly, by a fly parasitoid that modifies the competitive ability of one of the species. Using this arrangement as a template, we explore the dynamical consequences with a simple ordinary differential equation (ODE) model. Results are complicated and include alternative periodic and chaotic attractors. The qualitative structures of those complications, however, may be approximately retrieved from the basic natural history of the system.
Collapse
Affiliation(s)
- John Vandermeer
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- School of Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
| | - Ivette Perfecto
- School of Environment and Sustainability, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
12
|
Rizza A, Pedale T, Mastroberardino S, Olivetti Belardinelli M, Van der Lubbe RHJ, Spence C, Santangelo V. Working Memory Maintenance of Visual and Auditory Spatial Information Relies on Supramodal Neural Codes in the Dorsal Frontoparietal Cortex. Brain Sci 2024; 14:123. [PMID: 38391698 PMCID: PMC10886761 DOI: 10.3390/brainsci14020123] [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: 12/18/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 02/24/2024] Open
Abstract
The frontoparietal attention network plays a pivotal role during working memory (WM) maintenance, especially under high-load conditions. Nevertheless, there is ongoing debate regarding whether this network relies on supramodal or modality-specific neural signatures. In this study, we used multi-voxel pattern analysis (MVPA) to evaluate the neural representation of visual versus auditory information during WM maintenance. During fMRI scanning, participants maintained small or large spatial configurations (low- or high-load trials) of either colour shades or sound pitches in WM for later retrieval. Participants were less accurate in retrieving high- vs. low-load trials, demonstrating an effective manipulation of WM load, irrespective of the sensory modality. The frontoparietal regions involved in maintaining high- vs. low-load spatial maps in either sensory modality were highlighted using a conjunction analysis. Widespread activity was found across the dorsal frontoparietal network, peaking on the frontal eye fields and the superior parietal lobule, bilaterally. Within these regions, MVPAs were performed to quantify the pattern of distinctness of visual vs. auditory neural codes during WM maintenance. These analyses failed to reveal distinguishable patterns in the dorsal frontoparietal regions, thus providing support for a common, supramodal neural code associated with the retention of either visual or auditory spatial configurations.
Collapse
Affiliation(s)
- Aurora Rizza
- Department of Psychology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Tiziana Pedale
- Functional Neuroimaging Laboratory, IRCCS Santa Lucia Foundation, Via Ardeatina 306, 00179 Rome, Italy
| | - Serena Mastroberardino
- Department of Philosophy, Social Sciences & Education, University of Perugia, Piazza G. Ermini 1, 06123 Perugia, Italy
| | - Marta Olivetti Belardinelli
- Department of Psychology, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
- ECONA, Interuniversity Centre for Research on Cognitive Processing in Natural and Artificial Systems, Sapienza University of Rome, Via dei Marsi 78, 00185 Rome, Italy
| | - Rob H J Van der Lubbe
- Cognition, Data and Education, University of Twente, Drienerlolaan 5, 7522 NB Enschede, The Netherlands
- Laboratory of Vision Science and Optometry, Adam Mickiewicz University, Wieniawskiego 1, 61-712 Poznan, Poland
| | - Charles Spence
- Department of Experimental Psychology, University of Oxford, Anna Watts Building, Oxford OX2 6BW, UK
| | - Valerio Santangelo
- Functional Neuroimaging Laboratory, IRCCS Santa Lucia Foundation, Via Ardeatina 306, 00179 Rome, Italy
- Department of Philosophy, Social Sciences & Education, University of Perugia, Piazza G. Ermini 1, 06123 Perugia, Italy
| |
Collapse
|
13
|
Ahluwalia P, Ballur K, Leeman T, Vashisht A, Singh H, Omar N, Mondal AK, Vaibhav K, Baban B, Kolhe R. Incorporating Novel Technologies in Precision Oncology for Colorectal Cancer: Advancing Personalized Medicine. Cancers (Basel) 2024; 16:480. [PMID: 38339232 PMCID: PMC10854941 DOI: 10.3390/cancers16030480] [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] [Received: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 02/12/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most heterogeneous and deadly diseases, with a global incidence of 1.5 million cases per year. Genomics has revolutionized the clinical management of CRC by enabling comprehensive molecular profiling of cancer. However, a deeper understanding of the molecular factors is needed to identify new prognostic and predictive markers that can assist in designing more effective therapeutic regimens for the improved management of CRC. Recent breakthroughs in single-cell analysis have identified new cell subtypes that play a critical role in tumor progression and could serve as potential therapeutic targets. Spatial analysis of the transcriptome and proteome holds the key to unlocking pathogenic cellular interactions, while liquid biopsy profiling of molecular variables from serum holds great potential for monitoring therapy resistance. Furthermore, gene expression signatures from various pathways have emerged as promising prognostic indicators in colorectal cancer and have the potential to enhance the development of equitable medicine. The advancement of these technologies for identifying new markers, particularly in the domain of predictive and personalized medicine, has the potential to improve the management of patients with CRC. Further investigations utilizing similar methods could uncover molecular subtypes specific to emerging therapies, potentially strengthening the development of personalized medicine for CRC patients.
Collapse
Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kalyani Ballur
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Tiffanie Leeman
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Nivin Omar
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kumar Vaibhav
- Department of Neurosurgery, Augusta University, Augusta, GA 30912, USA;
| | - Babak Baban
- Departments of Neurology and Surgery, Augusta University, Augusta, GA 30912, USA;
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| |
Collapse
|
14
|
Mogano K, Sabeta CT, Suzuki T, Makita K, Chirima GJ. Patterns of Animal Rabies Prevalence in Northern South Africa between 1998 and 2022. Trop Med Infect Dis 2024; 9:27. [PMID: 38276638 PMCID: PMC10819520 DOI: 10.3390/tropicalmed9010027] [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] [Received: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Rabies is endemic in South Africa and rabies cycles are maintained in both domestic and wildlife species. The significant number of canine rabies cases reported by the World Organization for Animal Health Reference Laboratory for Rabies at Onderstepoort suggests the need for increased research and mass dog vaccinations on specific targeted foci in the country. This study aimed to investigate the spatiotemporal distribution of animal rabies cases from 1998 to 2017 in northern South Africa and environmental factors associated with highly enzootic municipalities. A descriptive analysis was used to investigate temporal patterns. The Getis-Ord Gi statistical tool was used to exhibit low and high clusters. Logistic regression was used to examine the association between the predictor variables and highly enzootic municipalities. A total of 9580 specimens were submitted for rabies diagnosis between 1998 and 2022. The highest positive case rates were from companion animals (1733 cases, 59.71%), followed by livestock (635 cases, 21.88%) and wildlife (621 cases, 21.39%). Rabies cases were reported throughout the year, with the majority occurring in the mid-dry season. Hot spots were frequently in the northern and eastern parts of Limpopo and Mpumalanga. Thicket bush and grassland were associated with rabies between 1998 and 2002. However, between 2008 and 2012, cultivated commercial crops and waterbodies were associated with rabies occurrence. In the last period, plantations and woodlands were associated with animal rabies. Of the total number of municipalities, five consistently and repeatedly had the highest rabies prevalence rates. These findings suggest that authorities should prioritize resources for those municipalities for rabies elimination and management.
Collapse
Affiliation(s)
- Kgaogelo Mogano
- Agricultural Research Council, GeoInformatics Division, Natural Resources and Engineering, 600 Belvedere St., Pretoria 0083, South Africa
- Department of Geography, Geoinformatics and Meteorology, University of Pretoria, Pretoria 0028, South Africa
| | - Claude Taurai Sabeta
- Veterinary Tropical Diseases Department, University of Pretoria, Pretoria 0110, South Africa
- World Organisation for Animal Health (WOAH) Rabies Reference Laboratory, Agricultural Research Council (Onderstepoort Veterinary Research), Onderstepoort, Pretoria 0110, South Africa
| | - Toru Suzuki
- Department of Environmental and Symbiotic Sciences, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - Kohei Makita
- Department of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan
| | - George Johannes Chirima
- Agricultural Research Council, GeoInformatics Division, Natural Resources and Engineering, 600 Belvedere St., Pretoria 0083, South Africa
- Department of Geography, Geoinformatics and Meteorology, University of Pretoria, Pretoria 0028, South Africa
| |
Collapse
|
15
|
Suwatthanarak T, Thanormjit K, Suwatthanarak T, Acharayothin O, Methasate A, Chinswangwatanakul V, Tanjak P. Spatial Transcriptomic Profiling of Tetraspanins in Stage 4 Colon Cancer from Primary Tumor and Liver Metastasis. Life (Basel) 2024; 14:126. [PMID: 38255741 PMCID: PMC10817616 DOI: 10.3390/life14010126] [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] [Received: 12/06/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Stage 4 colon cancer (CC) presents a significant global health challenge due to its poor prognosis and limited treatment options. Tetraspanins, the transmembrane proteins involved in crucial cancer processes, have recently gained attention as diagnostic markers and therapeutic targets. However, their spatial expression and potential roles in stage 4 CC tissues remain unknown. Using the GeoMx digital spatial profiler, we profiled all 33 human tetraspanin genes in 48 areas within stage 4 CC tissues, segmented into immune, fibroblast, and tumor compartments. Our results unveiled diverse gene expression patterns across different primary tumor sub-regions. CD53 exhibited distinct overexpression in the immune compartment, hinting at a potential role in immune modulation. TSPAN9 was specifically overexpressed in the fibroblast compartment, suggesting involvement in tumor invasion and metastasis. CD9, CD151, TSPAN1, TSPAN3, TSPAN8, and TSPAN13 displayed specific overexpression in the tumor compartment, indicating potential roles in tumor growth. Furthermore, our differential analysis revealed significant spatial changes in tetraspanin expression between patient-matched stage 4 primary CC and metastatic liver tissues. These findings provide spatially resolved insights into the expression and potential roles of tetraspanins in stage 4 CC progression, proposing their utility as diagnostic markers and therapeutic targets. Understanding this landscape is beneficial for tailoring therapeutic strategies to specific sub-tumor regions in the context of stage 4 CC and liver metastasis.
Collapse
Affiliation(s)
- Thanawat Suwatthanarak
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (K.T.); (V.C.)
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (O.A.); (A.M.)
| | - Kullanist Thanormjit
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (K.T.); (V.C.)
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (O.A.); (A.M.)
| | - Tharathorn Suwatthanarak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (O.A.); (A.M.)
| | - Onchira Acharayothin
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (O.A.); (A.M.)
| | - Asada Methasate
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (O.A.); (A.M.)
| | - Vitoon Chinswangwatanakul
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (K.T.); (V.C.)
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (O.A.); (A.M.)
| | - Pariyada Tanjak
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (K.T.); (V.C.)
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (T.S.); (O.A.); (A.M.)
| |
Collapse
|
16
|
Kam NW, Lo AWI, Hung DTY, Ko H, Wu KC, Kwong DLW, Lam KO, Leung TW, Che CM, Lee VHF. Shift in Tissue-Specific Immune Niches and CD137 Expression in Tuberculoma of Pembrolizumab-Treated Nasopharyngeal Carcinoma Patients. Cancers (Basel) 2024; 16:268. [PMID: 38254759 PMCID: PMC10813936 DOI: 10.3390/cancers16020268] [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] [Received: 12/07/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
The use of immune checkpoint inhibitors (ICIs) in cancer treatment has shown promise but can also have unintended consequences, such as reactivating latent tuberculosis (TB). To develop treatments that address ICIs-related adverse events, it is essential to understand cellular heterogeneity across healthy and pathological tissues. We performed cross-tissue multiplexed staining analysis on samples from two patients with TB reactivation during pembrolizumab treatment for metastatic nasopharyngeal carcinoma. CD8+ T cells, rather than CD4+ T cells, accumulated preferentially in the tuberculoma and were associated with increased production of IFNγ and expression of CD137. Additionally, CD137 enrichment played a role in the spatial organization of the tuberculoma, with specific interaction limited to spatial proximal cells between IFNγ+ CD137+ CD8+ T cells and IL12+ CD137+ type-1 macrophages. This unique feature was not observed in non-tumoral or tumoral tissues. Our analysis of public transcriptomic datasets supported the notion that this cellular interaction was more prominent in patients with durable ICI responses compared to those with non-ICI-related TB. We suggest that shifts towards CD137-rich immune niches are correlated with both off-target immune-related adverse events and anti-tumor efficacy. Targeting the tumor microenvironment through conditional activation of anti-CD137 signaling in combination with ICIs can modulate the reactivity of T cells and macrophages for localized tumor killing without the potential off-target immune-related risks associated with ICIs alone.
Collapse
Affiliation(s)
- Ngar Woon Kam
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Laboratory of Synthetic Chemistry and Chemical Biology Limited, Hong Kong 999077, China;
| | | | - Desmond Tae Yang Hung
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
| | - Ho Ko
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China;
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Ka Chun Wu
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Laboratory of Synthetic Chemistry and Chemical Biology Limited, Hong Kong 999077, China;
| | - Dora Lai Wan Kwong
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518000, China
| | - Ka On Lam
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518000, China
| | - To Wai Leung
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
| | - Chi Ming Che
- Laboratory of Synthetic Chemistry and Chemical Biology Limited, Hong Kong 999077, China;
- Department of Chemistry, Faculty of Science, The University of Hong Kong, Hong Kong 999077, China
| | - Victor Ho Fun Lee
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518000, China
| |
Collapse
|
17
|
Curry AR, Ooi L, Matosin N. How spatial omics approaches can be used to map the biological impacts of stress in psychiatric disorders: a perspective, overview and technical guide. Stress 2024; 27:2351394. [PMID: 38752853 DOI: 10.1080/10253890.2024.2351394] [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: 10/17/2023] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
Exposure to significant levels of stress and trauma throughout life is a leading risk factor for the development of major psychiatric disorders. Despite this, we do not have a comprehensive understanding of the mechanisms that explain how stress raises psychiatric disorder risk. Stress in humans is complex and produces variable molecular outcomes depending on the stress type, timing, and duration. Deciphering how stress increases disorder risk has consequently been challenging to address with the traditional single-target experimental approaches primarily utilized to date. Importantly, the molecular processes that occur following stress are not fully understood but are needed to find novel treatment targets. Sequencing-based omics technologies, allowing for an unbiased investigation of physiological changes induced by stress, are rapidly accelerating our knowledge of the molecular sequelae of stress at a single-cell resolution. Spatial multi-omics technologies are now also emerging, allowing for simultaneous analysis of functional molecular layers, from epigenome to proteome, with anatomical context. The technology has immense potential to transform our understanding of how disorders develop, which we believe will significantly propel our understanding of how specific risk factors, such as stress, contribute to disease course. Here, we provide our perspective of how we believe these technologies will transform our understanding of the neurobiology of stress, and also provided a technical guide to assist molecular psychiatry and stress researchers who wish to implement spatial omics approaches in their own research. Finally, we identify potential future directions using multi-omics technology in stress research.
Collapse
Affiliation(s)
- Amber R Curry
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Molecular Horizons, School of Chemistry and Molecular Bioscience, Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Lezanne Ooi
- Molecular Horizons, School of Chemistry and Molecular Bioscience, Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Natalie Matosin
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
- Molecular Horizons, School of Chemistry and Molecular Bioscience, Faculty of Science Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| |
Collapse
|
18
|
Ridnour LA, Cheng RYS, Heinz WF, Pore M, Gonzalez AL, Femino EL, Moffat R, Wink AL, Imtiaz F, Coutinho L, Butcher D, Edmondson EF, Rangel MC, Wong STC, Lipkowitz S, Glynn S, Vitek MP, McVicar DW, Li X, Anderson SK, Paolocci N, Hewitt SM, Ambs S, Billiar TR, Chang JC, Lockett SJ, Wink DA. Spatial analysis of NOS2 and COX2 interaction with T-effector cells reveals immunosuppressive landscapes associated with poor outcome in ER- breast cancer patients. bioRxiv 2023:2023.12.21.572867. [PMID: 38187660 PMCID: PMC10769421 DOI: 10.1101/2023.12.21.572867] [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] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Multiple immunosuppressive mechanisms exist in the tumor microenvironment that drive poor outcomes and decrease treatment efficacy. The co-expression of NOS2 and COX2 is a strong predictor of poor prognosis in ER- breast cancer and other malignancies. Together, they generate pro-oncogenic signals that drive metastasis, drug resistance, cancer stemness, and immune suppression. Using an ER- breast cancer patient cohort, we found that the spatial expression patterns of NOS2 and COX2 with CD3+CD8+PD1- T effector (Teff) cells formed a tumor immune landscape that correlated with poor outcome. NOS2 was primarily associated with the tumor-immune interface, whereas COX2 was associated with immune desert regions of the tumor lacking Teff cells. A higher ratio of NOS2 or COX2 to Teff was highly correlated with poor outcomes. Spatial analysis revealed that regional clustering of NOS2 and COX2 was associated with stromal-restricted Teff, while only COX2 was predominant in immune deserts. Examination of other immunosuppressive elements, such as PDL1/PD1, Treg, B7H4, and IDO1, revealed that PDL1/PD1, Treg, and IDO1 were primarily associated with restricted Teff, whereas B7H4 and COX2 were found in tumor immune deserts. Regardless of the survival outcome, other leukocytes, such as CD4 T cells and macrophages, were primarily in stromal lymphoid aggregates. Finally, in a 4T1 model, COX2 inhibition led to a massive cell infiltration, thus validating the hypothesis that COX2 is an essential component of the Teff exclusion process and, thus, tumor evasion. Our study indicates that NOS2/COX2 expression plays a central role in tumor immunosuppression. Our findings indicate that new strategies combining clinically available NOS2/COX2 inhibitors with various forms of immune therapy may open a new avenue for the treatment of aggressive ER-breast cancers.
Collapse
Affiliation(s)
- Lisa A Ridnour
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Robert Y S Cheng
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Milind Pore
- Imaging Mass Cytometry Frederick National Laboratory for Cancer Research
| | - Ana L Gonzalez
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Elise L Femino
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Rebecca Moffat
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Adelaide L Wink
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Fatima Imtiaz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - Leandro Coutinho
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
- Faculdade de Medicina da Universidade de São Paulo and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Donna Butcher
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
| | - Elijah F Edmondson
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
| | - M Cristina Rangel
- Faculdade de Medicina da Universidade de São Paulo and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
| | | | | | - Sharon Glynn
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
| | | | - Daniel W McVicar
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
| | - Stephen K Anderson
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
- Basic Science Program, Frederick National Laboratory for Cancer Research
| | - Nazareno Paolocci
- Division of Cardiology, Department of Medicine, Johns Hopkins University, and Department of Biomedical Sciences, University of Padova, Italy
- Laboratory of Pathology CCR, NCI, NIH
| | | | - Stefan Ambs
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Timothy R Billiar
- Mary and Ron Neal Cancer Center, Houston Methodist Hospital and Weill Cornell Medicine, Houston, TX
| | - Jenny C Chang
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
- Imaging Mass Cytometry Frederick National Laboratory for Cancer Research
- Faculdade de Medicina da Universidade de São Paulo and Comprehensive Center for Precision Oncology, Universidade de São Paulo, São Paulo, SP, Brazil
- Molecular Histopathology Laboratories, Leidos Biomedical Research Inc. for the National Cancer Institute
- Houston Methodist Weill Cornell Medical College, Houston TX
- Women's Malignancies Branch, CCR, NCI, NIH
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
- (Mike Duke)
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
- Basic Science Program, Frederick National Laboratory for Cancer Research
- Division of Cardiology, Department of Medicine, Johns Hopkins University, and Department of Biomedical Sciences, University of Padova, Italy
- Laboratory of Pathology CCR, NCI, NIH
- Laboratory of Human Carcinogenesis, CCR, NCI, NIH, Bethesda, MD
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA
- Mary and Ron Neal Cancer Center, Houston Methodist Hospital and Weill Cornell Medicine, Houston, TX
| | - Stephen J Lockett
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research; Leidos Biomedical Research Inc. for the National Cancer Institute, Frederick, MD
| | - David A Wink
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| |
Collapse
|
19
|
Mansoori B, Silvestris N, Baradaran B. Editorial: Spatial single-cell sequencing in studying solid cancer development. Front Immunol 2023; 14:1342989. [PMID: 38149241 PMCID: PMC10749922 DOI: 10.3389/fimmu.2023.1342989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023] Open
Affiliation(s)
- Behzad Mansoori
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, United States
| | - Nicola Silvestris
- Department of Human Pathology in Adulthood and Childhood Gaetano Barresi, University of Messina, Messina, Italy
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
20
|
Lu X, Griebsch C, Norris JM, Ward MP. Landscape, Socioeconomic, and Meteorological Risk Factors for Canine Leptospirosis in Urban Sydney (2017-2023): A Spatial and Temporal Study. Vet Sci 2023; 10:697. [PMID: 38133248 PMCID: PMC10747920 DOI: 10.3390/vetsci10120697] [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: 10/30/2023] [Revised: 11/21/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Leptospirosis is a potentially fatal zoonotic disease caused by infection with pathogenic Leptospira spp. We described reported clinical cases of canine leptospirosis in the council areas of the Inner West and the City of Sydney, Australia, from December 2017 to January 2023 and tested the association with urban spatial (landscape and socioeconomic factors, community seroprevalence, and urban heat island effect) and temporal (precipitation and minimum and maximum temperature) factors and the cases using log-transformed Poisson models, spatially stratified population-adjusted conditional logistic models, General Additive Models (GAMs), and Autoregressive Integrated Moving Average (ARIMA) models. The results suggested that canine leptospirosis is now endemic in the study area. A longer distance to the nearest veterinary hospital (RR 0.118, 95% CI -4.205--0.065, p < 0.05) and a mildly compromised Index of Economic Resources (IER) (RR 0.202, 95% CI -3.124--0.079, p < 0.05) were significant protective factors against leptospirosis. In areas proximal to the clinical cases and seropositive samples, the presence of tree cover was a strong risk factor for higher odds of canine leptospirosis (OR 5.80, 95% CI 1.12-30.11, p < 0.05). As the first study exploring risk factors associated with canine leptospirosis in urban Sydney, our findings indicate a potential transmission from urban green spaces and the possibility of higher exposure to Leptospira-or increased case detection and reporting-in areas adjacent to veterinary hospitals.
Collapse
Affiliation(s)
| | | | | | - Michael P. Ward
- Sydney School of Veterinary Science, The University of Sydney, Camperdown, NSW 2050, Australia; (X.L.); (C.G.); (J.M.N.)
| |
Collapse
|
21
|
Schambow RA, Hussain S, Antognoli MC, Kreindel S, Reyes R, Perez AM. Epidemiological Assessment of African Swine Fever Spread in the Dominican Republic. Pathogens 2023; 12:1414. [PMID: 38133297 PMCID: PMC10746036 DOI: 10.3390/pathogens12121414] [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] [Received: 11/02/2023] [Revised: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Since African Swine Fever (ASF) was detected in the Dominican Republic in July 2021, it has negatively impacted the country's swine industry. Assessing the epidemiological situation is crucial to helping local authorities and industry stakeholders control the disease. Here, data on 155 reported outbreaks in the Dominican Republic from November 2022 to June 2023 were evaluated. Descriptive spatiotemporal analysis was performed to characterize disease distribution and spread, and between-herd R0 was calculated for the study period. The Knox test and a space-time permutation model were used to evaluate clustering. Data on clinical presentation, biosecurity measures, and suspected reasons for introduction were categorized and summarized. The majority (78%) of outbreaks occurred on backyard farms which generally had low biosecurity. Across farm types, the majority of pigs were still alive at the time of depopulation. Spatiotemporal findings and R0 estimates suggest an endemic pattern of disease geographically located centrally within the country. Clustering was detected even at small temporal and spatial distances due to outbreaks amongst neighboring backyard farms. These results provide critical information on the current state of the ASF epidemic in the Dominican Republic and will aid government officials and swine industry leaders in developing effective ASF control strategies.
Collapse
Affiliation(s)
- Rachel A. Schambow
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (S.H.); (A.M.P.)
| | - Syed Hussain
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (S.H.); (A.M.P.)
| | - Maria C. Antognoli
- International Services Action Programs, Animal Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO 80526, USA; (M.C.A.); (S.K.)
| | - Silvia Kreindel
- International Services Action Programs, Animal Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO 80526, USA; (M.C.A.); (S.K.)
| | - Raysa Reyes
- Instituto del Estudio de las Enfermedades Zoonóticas, Universidad Autónoma de Santo Domingo, Santo Domingo 10904, Dominican Republic;
| | - Andres M. Perez
- Center for Animal Health and Food Safety, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; (S.H.); (A.M.P.)
| |
Collapse
|
22
|
Neale Z, Rudolf VHW. Predation and competition drive trait diversity across space and time. Ecology 2023; 104:e4182. [PMID: 37786267 DOI: 10.1002/ecy.4182] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/24/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Competition should play a key role in shaping community assembly and thereby local and regional biodiversity patterns. However, identifying its relative importance and effects in natural communities is challenging because theory suggests that competition can lead to different and even opposing patterns depending on the underlying mechanisms. Here, we have taken a different approach: rather than attempting to indirectly infer competition from diversity patterns, we compared trait diversity patterns in odonate (dragonfly and damselfly) communities across different spatial and temporal scales along a natural competition-predation gradient. At the local scale (within a community), we found that trait diversity increased with the size of top predators (from invertebrates to fish). This relationship is consistent with differences in taxonomic diversity, suggesting that competition reduces local trait diversity through competitive exclusion. Spatial (across communities) and temporal (within communities over time) trait variation peaked in communities with intermediate predators indicating that both high levels of competition or predation select for trait convergence of communities. This indicates that competition acts as a deterministic force that reduces trait diversity at the local, regional, and temporal scales, which contrasts with patterns at the taxonomic level. Overall, results from this natural experiment reveal how competition and predation interact to shape biodiversity patterns in natural communities across spatial and temporal scales and provide new insights into the underlying mechanisms.
Collapse
Affiliation(s)
- Zoey Neale
- Graduate Program in Ecology and Evolutionary Biology, BioSciences, Rice University, Houston, Texas, USA
| | - Volker H W Rudolf
- Graduate Program in Ecology and Evolutionary Biology, BioSciences, Rice University, Houston, Texas, USA
| |
Collapse
|
23
|
Ramirez Flores RO, Lanzer JD, Dimitrov D, Velten B, Saez-Rodriguez J. Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease. eLife 2023; 12:e93161. [PMID: 37991480 PMCID: PMC10718529 DOI: 10.7554/elife.93161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 10/05/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023] Open
Abstract
Biomedical single-cell atlases describe disease at the cellular level. However, analysis of this data commonly focuses on cell-type-centric pairwise cross-condition comparisons, disregarding the multicellular nature of disease processes. Here, we propose multicellular factor analysis for the unsupervised analysis of samples from cross-condition single-cell atlases and the identification of multicellular programs associated with disease. Our strategy, which repurposes group factor analysis as implemented in multi-omics factor analysis, incorporates the variation of patient samples across cell-types or other tissue-centric features, such as cell compositions or spatial relationships, and enables the joint analysis of multiple patient cohorts, facilitating the integration of atlases. We applied our framework to a collection of acute and chronic human heart failure atlases and described multicellular processes of cardiac remodeling, independent to cellular compositions and their local organization, that were conserved in independent spatial and bulk transcriptomics datasets. In sum, our framework serves as an exploratory tool for unsupervised analysis of cross-condition single-cell atlases and allows for the integration of the measurements of patient cohorts across distinct data modalities.
Collapse
Affiliation(s)
- Ricardo Omar Ramirez Flores
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuantHeidelbergGermany
| | - Jan David Lanzer
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuantHeidelbergGermany
| | - Daniel Dimitrov
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuantHeidelbergGermany
| | - Britta Velten
- Heidelberg University, Centre for Organismal Studies, Centre for Scientific ComputingHeidelbergGermany
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, BioQuantHeidelbergGermany
| |
Collapse
|
24
|
Abstract
Mathematical and computational models of biological systems are increasingly complex, typically comprised of hybrid multi-scale methods such as ordinary differential equations, partial differential equations, agent-based and rule-based models, etc. These mechanistic models concurrently simulate detail at resolutions of whole host, multi-organ, organ, tissue, cellular, molecular, and genomic dynamics. Lacking analytical and numerical methods, solving complex biological models requires iterative parameter sampling-based approaches to establish appropriate ranges of model parameters that capture corresponding experimental datasets. However, these models typically comprise large numbers of parameters and therefore large degrees of freedom. Thus, fitting these models to multiple experimental datasets over time and space presents significant challenges. In this work we undertake the task of reviewing, testing, and advancing calibration practices across models and dataset types to compare methodologies for model calibration. Evaluating the process of calibrating models includes weighing strengths and applicability of each approach as well as standardizing calibration methods. Our work compares the performance of our model agnostic Calibration Protocol (CaliPro) with approximate Bayesian computing (ABC) to highlight strengths, weaknesses, synergies, and differences among these methods. We also present next-generation updates to CaliPro. We explore several model implementations and suggest a decision tree for selecting calibration approaches to match dataset types and modeling constraints.
Collapse
Affiliation(s)
- Pariksheet Nanda
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| |
Collapse
|
25
|
Gray S, Ottensmeier CH. Advancing Understanding of Non-Small Cell Lung Cancer with Multiplexed Antibody-Based Spatial Imaging Technologies. Cancers (Basel) 2023; 15:4797. [PMID: 37835491 PMCID: PMC10571797 DOI: 10.3390/cancers15194797] [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: 08/21/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) remains a cause of significant morbidity and mortality, despite significant advances made in its treatment using immune checkpoint inhibitors (ICIs) over the last decade; while a minority experience prolonged responses with ICIs, benefit is limited for most patients. The development of multiplexed antibody-based (MAB) spatial tissue imaging technologies has revolutionised analysis of the tumour microenvironment (TME), enabling identification of a wide range of cell types and subtypes, and analysis of the spatial relationships and interactions between them. Such study has the potential to translate into a greater understanding of treatment susceptibility and resistance, factors influencing prognosis and recurrence risk, and identification of novel therapeutic approaches and rational treatment combinations to improve patient outcomes in the clinic. Herein we review studies that have leveraged MAB technologies to deliver novel insights into the TME of NSCLC.
Collapse
Affiliation(s)
- Simon Gray
- Department of Molecular and Clinical Cancer Medicine, Faculty of Health and Life Sciences, University of Liverpool, Ashton St., Liverpool L69 3GB, UK
- Department of Medical Oncology, The Clatterbridge Cancer Centre NHS Foundation Trust, Pembroke Pl., Liverpool L7 8YA, UK
| | - Christian H. Ottensmeier
- Department of Molecular and Clinical Cancer Medicine, Faculty of Health and Life Sciences, University of Liverpool, Ashton St., Liverpool L69 3GB, UK
- Department of Medical Oncology, The Clatterbridge Cancer Centre NHS Foundation Trust, Pembroke Pl., Liverpool L7 8YA, UK
| |
Collapse
|
26
|
Rybansky D, Marsalek P, Sotola M, Hroncek J, Drahorad L, Kusnir O, Prokop J. Design and Behavior of Lightweight Flexible Structure with Spatial Pattern Reducing Contact Surface Fraction. Polymers (Basel) 2023; 15:3896. [PMID: 37835945 PMCID: PMC10575436 DOI: 10.3390/polym15193896] [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] [Received: 08/09/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
Flexible structures are increasingly important in biomedical applications, where they can be used to achieve adaptable designs. This paper presents a study of the design and behavior of 3D-printed lightweight flexible structures. In this work, we focus on the design principles and numerical modelling of spatial patterns, as well as their mechanical properties and behavior under various loads. Contact surface fraction was determined as the ratio of the surface area of the printed pattern to the surface area of the entire curved surface. The objective of this work is to design a spatial pattern reducing contact surface fraction and develop a non-linear numerical model evaluating the structure's stiffness; in addition, we aimed to identify the best design pattern with respect to its stiffness:mass ratio. The experimental verification of the numerical model is performed on 3D-printed prototypes prepared using the Selective Laser Sintering (SLS) method and made of Nylon-Polyamide 12. The obtained results provide insights into designing and optimizing lightweight external biomedical applications such as prostheses, orthoses, helmets, or adaptive cushions.
Collapse
Affiliation(s)
- David Rybansky
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VSB—Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Czech Republic
| | - Pavel Marsalek
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VSB—Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Czech Republic
| | - Martin Sotola
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VSB—Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Czech Republic
| | - Juraj Hroncek
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VSB—Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Czech Republic
| | - Lukas Drahorad
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VSB—Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Czech Republic
| | - Ondrej Kusnir
- Department of Applied Mechanics, Faculty of Mechanical Engineering, VSB—Technical University of Ostrava, 17. listopadu 2172/15, 708 00 Ostrava, Czech Republic
| | - Jiri Prokop
- Department of Surgical Studies, Faculty of Medicine, University of Ostrava, Dvorakova 7, 701 03 Ostrava, Czech Republic
- Department of Surgery, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
| |
Collapse
|
27
|
Bartov R, Wagner M, Shvalb N, Hochhauser M. Enhancing Handwriting Performance of Children with Developmental Coordination Disorder (DCD) Using Computerized Visual Feedback. Children (Basel) 2023; 10:1534. [PMID: 37761495 PMCID: PMC10529407 DOI: 10.3390/children10091534] [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: 07/24/2023] [Revised: 08/21/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
Recent studies have analyzed the writing metrics of children with developmental coordination disorder (DCD) using computerized systems. To date, the use of computerized visual feedback to improve handwriting has not been investigated. This study aimed to examine the effects of computerized visual feedback on handwriting performance in time, spatial orientation, and pressure indices for children with DCD. Twenty-seven children aged 7 to 12 years with DCD assessed by the Movement Assessment Battery for Children and the Developmental Coordination Disorder Questionnaire received one weekly intervention session for 8 weeks, during which they twice copied an excerpt onto a tablet. Once, they received visual feedback where the writing color corresponded to the degree of pressure on the writing surface, and once they received no visual feedback. The two conditions were counterbalanced throughout the sessions. Pre-intervention sessions were compared with post-intervention sessions and with new texts for time, spatial orientation, and pressure measures. The findings revealed significantly decreased total and mean letter writing, in-air, and writing time and increased capacity in the visual feedback condition. In the spatial variables, a significant decrease in letter height variance was found. Pressure increased significantly throughout the intervention with visual feedback, whereas it decreased post-test in the writing task in both conditions and was maintained in the new text. Visual feedback intervention can increase the kinesthetic-haptic feedback required to regulate pressure during writing, promoting more efficient feedforward processes and improving output quality and capacity. The training effectiveness was transferable, and the intervention accessibility could increase student autonomy.
Collapse
Affiliation(s)
- Rachel Bartov
- Department of Occupational Therapy, Ariel University, Ariel 40700, Israel;
- Department of Special Education, Orot Israel College, Elkana 4481400, Israel
| | - Michael Wagner
- Department of Industrial Engineering and Management, Ariel University, Ariel 40700, Israel;
| | - Nir Shvalb
- Department of Mechanical Engineering and Mechatronics, Ariel University, Ariel 40700, Israel;
| | - Michal Hochhauser
- Department of Occupational Therapy, Ariel University, Ariel 40700, Israel;
| |
Collapse
|
28
|
Anstee JE, Feehan KT, Opzoomer JW, Dean I, Muller HP, Bahri M, Cheung TS, Liakath-Ali K, Liu Z, Choy D, Caron J, Sosnowska D, Beatson R, Muliaditan T, An Z, Gillett CE, Lan G, Zou X, Watt FM, Ng T, Burchell JM, Kordasti S, Withers DR, Lawrence T, Arnold JN. LYVE-1 + macrophages form a collaborative CCR5-dependent perivascular niche that influences chemotherapy responses in murine breast cancer. Dev Cell 2023; 58:1548-1561.e10. [PMID: 37442140 DOI: 10.1016/j.devcel.2023.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 06/23/2022] [Revised: 04/05/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023]
Abstract
Tumor-associated macrophages (TAMs) are a heterogeneous population of cells that facilitate cancer progression. However, our knowledge of the niches of individual TAM subsets and their development and function remain incomplete. Here, we describe a population of lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1)-expressing TAMs, which form coordinated multi-cellular "nest" structures that are heterogeneously distributed proximal to vasculature in tumors of a spontaneous murine model of breast cancer. We demonstrate that LYVE-1+ TAMs develop in response to IL-6, which induces their expression of the immune-suppressive enzyme heme oxygenase-1 and promotes a CCR5-dependent signaling axis, which guides their nest formation. Blocking the development of LYVE-1+ TAMs or their nest structures, using gene-targeted mice, results in an increase in CD8+ T cell recruitment to the tumor and enhanced response to chemotherapy. This study highlights an unappreciated collaboration of a TAM subset to form a coordinated niche linked to immune exclusion and resistance to anti-cancer therapy.
Collapse
Affiliation(s)
- Joanne E Anstee
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Karen T Feehan
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - James W Opzoomer
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Isaac Dean
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Henrike P Muller
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Meriem Bahri
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Tik Shing Cheung
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | | | - Ziyan Liu
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Desmond Choy
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Jonathan Caron
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Dominika Sosnowska
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Richard Beatson
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Tamara Muliaditan
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Zhengwen An
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Cheryl E Gillett
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Guocheng Lan
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 ORE, UK
| | - Xiangang Zou
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 ORE, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Tony Ng
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Joy M Burchell
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK
| | - Shahram Kordasti
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK; Haematology Department, Guy's Hospital, London SE1 9RT, UK
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Toby Lawrence
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology & Microbial Sciences, King's College London, London SE1 1UL, UK; Aix Marseille University, CNRS, INSERM, CIML, Marseille, France; Henan Key Laboratory of Immunology and Targeted Therapy, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - James N Arnold
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1UL, UK.
| |
Collapse
|
29
|
Asmamaw DB, Debebe Negash W, Aragaw FM, Eshetu HB, Asratie MH, Belachew TB. Spatial distribution and associated factors of poor tetanus toxoid immunization among pregnant women in Ethiopia: spatial and multilevel analysis. Front Glob Womens Health 2023; 4:1138579. [PMID: 37732165 PMCID: PMC10507278 DOI: 10.3389/fgwh.2023.1138579] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 08/09/2023] [Indexed: 09/22/2023] Open
Abstract
Background Neonatal mortality from tetanus can be reduced by 94% when pregnant women receive at least two doses of tetanus toxoid. In Ethiopia, immunization programs are suboptimal despite their importance. Therefore, the aim of this study was to examine the geographic distribution and associated factors of poor tetanus toxoid (TT) immunization among pregnant women in Ethiopia. Methods Secondary data analysis was used using the 2016 Ethiopian Demographic and Health Survey (EDHS). ArcGIS version 10.8 statistical software was used to explore the spatial distribution of poor TT immunization and SaTScan version 9.6 software was used to identify significant hotspot areas of poor TT immunization. For associated factors, a multilevel binary logistic regression model was fitted using STATA version 14 software. In the multivariable multilevel analysis, adjusted OR (AOR) with 95% CI was reported to reveal significantly associated factors of poor TT immunization. Result In Ethiopia, the spatial distribution of poor tetanus toxoid immunization was clustered with Global Moran's I = 0.59 at p-value of <0.0001. The highest poor TT immunization clusters were observed in the East and South Tigray, the central part of Amhara, West Afar, East Somali, and West Gambella. Pregnant women with no Antenatal care (ANC) visits [Adjusted Odds Ratio (aOR) = 10.46, 95% CI: (8.82, 12.41))], pregnant women with 1-3 ANC visits [aOR = 1.51, 95% CI: (1.31, 1.73)], media exposure [aOR = 1.45, 95% CI: (1.26, 1.67)], poor wealth index [aOR = 1.22; 95% CI: (1.03, 1.45)], middle wealth index [aOR = 1.23; 95% CI: (1.03, 1.47)], family planning use [aOR = 1.28; 95% CI: (1.11, 1.57)] and community level education [aOR = 1.43, 95% CI: (1.14, 1.80)] were significantly associated with poor tetanus toxoid immunization. Conclusion Poor tetanus toxoid immunization among pregnant women varies in Ethiopia. It was highest in East and South Tigray, the central part of Amhara, West Afar, East Somali, and West Gambella. Therefore, public health programs should design targeted interventions in identified hot spots to improve tetanus toxoid immunization. Health programmers should be promoting optimal ANC visits, women's education, and family planning use.
Collapse
Affiliation(s)
- Desale Bihonegn Asmamaw
- Department of Reproductive Health, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Wubshet Debebe Negash
- Department of Health Systems and Policy, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Fantu Mamo Aragaw
- Department of Epidemiology and Biostatistics, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Habitu Birhan Eshetu
- Department of Health Education and Behavioral Sciences, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Melaku Hunie Asratie
- Department of Women’s and Family Health, School of Midwifery, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Tadele Biresaw Belachew
- Department of Health Systems and Policy, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| |
Collapse
|
30
|
Smoothey AF, Niella Y, Brand C, Peddemors VM, Butcher PA. Bull Shark ( Carcharhinus leucas) Occurrence along Beaches of South-Eastern Australia: Understanding Where, When and Why. Biology (Basel) 2023; 12:1189. [PMID: 37759589 PMCID: PMC10526001 DOI: 10.3390/biology12091189] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/14/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Unprovoked shark bites have increased over the last three decades, yet they are still relatively rare. Bull sharks are globally distributed throughout rivers, estuaries, nearshore areas and continental shelf waters, and are capable of making long distance movements between tropical and temperate regions. As this species is implicated in shark bites throughout their range, knowledge of the environmental drivers of bull shark movements are important for better predicting the likelihood of their occurrence at ocean beaches and potentially assist in reducing shark bites. Using the largest dataset of acoustically tagged bull sharks in the world, we examined the spatial ecology of 233 juvenile and large (including sub-adult and adult) bull sharks acoustically tagged and monitored over a 5.5-year period (2017-2023) using an array of real-time acoustic listening stations off 21 beaches along the coast of New South Wales, Australia. Bull sharks were detected more in coastal areas of northern NSW (<32° S) but they travelled southwards during the austral summer and autumn. Juveniles were not detected on shark listening stations until they reached 157 cm and stayed north of 31.98° S (Old Bar). Intra-specific diel patterns of occurrence were observed, with juveniles exhibiting higher nearshore presence between 20:00 and 03:00, whilst the presence of large sharks was greatest from midday through to 04:00. The results of generalised additive models revealed that large sharks were more often found when water temperatures were higher than 20 °C, after >45 mm of rain and when swell heights were between 1.8 and 2.8 m. Understanding the influence that environmental variables have on the occurrence of bull sharks in the coastal areas of NSW will facilitate better education and could drive shark smart behaviour amongst coastal water users.
Collapse
Affiliation(s)
- Amy F. Smoothey
- NSW Department of Primary Industries, Fisheries Research, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia;
| | - Yuri Niella
- Department of Biological Sciences, Macquarie University, North Ryde, Sydney, NSW 2113, Australia;
| | - Craig Brand
- NSW Department of Primary Industries, Fisheries Research, National Marine Science Centre, Coffs Harbour, NSW 2450, Australia; (C.B.); (P.A.B.)
| | - Victor M. Peddemors
- NSW Department of Primary Industries, Fisheries Research, Sydney Institute of Marine Science, Mosman, NSW 2088, Australia;
| | - Paul A. Butcher
- NSW Department of Primary Industries, Fisheries Research, National Marine Science Centre, Coffs Harbour, NSW 2450, Australia; (C.B.); (P.A.B.)
| |
Collapse
|
31
|
Maxwell SP, Brooks C, Kim D, McNeely CL, Cho S, Thomas KC. Improving Surveillance of Human Tick-Borne Disease Risks: Spatial Analysis Using Multimodal Databases. JMIR Public Health Surveill 2023; 9:e43790. [PMID: 37610812 PMCID: PMC10483298 DOI: 10.2196/43790] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 10/24/2022] [Revised: 04/24/2023] [Accepted: 06/27/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND The extent of tick-borne disease (TBD) risk in the United States is generally unknown. Active surveillance using entomological measures, such as presence and density of infected nymphal Ixodes scapularis ticks, have served as indicators for assessing human risk, but results have been inconsistent and passive surveillance via public health systems suggests TBDs are underreported. OBJECTIVE Research using various data sources and collection methods (eg, Google Trends, apps, and tick bite encounters [TBEs] reports) has shown promise for assessing human TBD risk. In that vein, and engaging a One Health perspective, this study used multimodal databases, geographically overlaying patient survey data on TBEs and concomitant reports of TBDs with data drawn from other sources, such as canine serological reports, to glean insights and to determine and assess the use of various indicators as proxies for human TBD risk. METHODS This study used a mixed methods research strategy, relying on triangulation techniques and drawing on multiple data sources to provide insights into various aspects of human disease risk from TBEs and TBDs in the United States. A web-based survey was conducted over a 15-month period beginning in December 2020 to collect data on TBEs. To maximize the value of the covariate data, related analyses included TBE reports that occurred in the United States between January 1, 2000, and March 31, 2021. TBEs among patients diagnosed with Lyme disease were analyzed at the county level and compared to I scapularis and I pacificus tick presence, human cases identified by the Centers for Disease Control and Prevention (CDC), and canine serological data. Spatial analyses employed multilayer thematic mapping and other techniques. RESULTS After cleaning, survey results showed a total of 249 (75.7%) TBEs spread across 148 respondents (61.9% of all respondents, 81.7% of TBE-positive respondents); 144 (4.7%) counties in 30 states (60%) remained eligible for analysis, with an average of 1.68 (SD 1.00) and median of 1 (IQR 1) TBEs per respondent. Analysis revealed significant spatial matching at the county level among patient survey reports of TBEs and disease risk indicators from the CDC and other official sources. Thematic mapping results included one-for-one county-level matching of reported TBEs with at least 1 designated source of human disease risk (ie, positive canine serological tests, CDC-reported Lyme disease, or known tick presence). CONCLUSIONS Use of triangulation methods to integrate patient data on TBE recall with established canine serological reports, tick presence, and official human TBD information offers more granular, county-level information regarding TBD risk to inform clinicians and public health officials. Such data may supplement public health sources to offer improved surveillance and provide bases for developing robust proxies for TBD risk among humans.
Collapse
Affiliation(s)
- Sarah P Maxwell
- School of Economic, Political and Policy Sciences, University of Texas at Dallas, Richardson, TX, United States
| | - Chris Brooks
- Laboratory for Human Neurobiology, Boston University School of Medicine, Boston, MA, United States
| | - Dohyeong Kim
- School of Economic, Political and Policy Sciences, University of Texas at Dallas, Richardson, TX, United States
| | - Connie L McNeely
- Schar School of Policy and Government, George Mason University, Fairfax, VA, United States
| | - Seonga Cho
- Department of Geography, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Kevin C Thomas
- Laboratory for Human Neurobiology, Boston University School of Medicine, Boston, MA, United States
| |
Collapse
|
32
|
Khanduri I, Maru DM, Parra ER. Exploratory study of macrophage polarization and spatial distribution in colorectal cancer liver metastasis: a pilot study. Front Immunol 2023; 14:1223864. [PMID: 37637998 PMCID: PMC10449458 DOI: 10.3389/fimmu.2023.1223864] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023] Open
Abstract
Background The liver is the most typical site of metastatic disease for patients with colorectal cancer (CRC), and up to half the patients with CRC will develop colorectal liver metastasis (CLM). Studying the tumor microenvironment, particularly macrophages and their spatial distribution, can give us critical insight into treatment. Methods Ten CLMs (five treatment-naïve and five post-neoadjuvant chemotherapy) were stained with multiplex immunofluorescence panels against cytokeratins, CD68, Arg1, CD206, CD86, CD163, PD-L1, and MRP8-14. Densities of cell phenotypes and their spatial distribution in the tumor center and the normal liver-tumor interface were correlated with clinicopathological variables. Results M2 macrophages were the predominant subtype in both the tumor center and the periphery, with a relatively higher density at the periphery. The larger tumors, more than 3.9 cm, were associated with higher densities of total CD68+ macrophages and CD68+CD163+ CD206neg and CD68+CD206+ CD163neg M2 macrophage subtypes. Total macrophages in the tumor periphery demonstrated significantly greater proximity to malignant cells than did those in the tumor center (p=0.0371). The presence of higher than median CD68+MRP8-14+CD86neg M1 macrophages in the tumor center was associated with poor overall survival (median 2.34 years) compared to cases with lower than median M1 macrophages at the tumor center (median 6.41 years) in univariate analysis. Conclusion The dominant polarization of the M2 macrophage subtype could drive new therapeutic approaches in CLM patients.
Collapse
Affiliation(s)
- Isha Khanduri
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Dipen M. Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Edwin R. Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| |
Collapse
|
33
|
Higham M, Dumelle M, Hammond C, Ver Hoef J, Wells J. An Application of Spatio-temporal Modeling to Finite Population Abundance Prediction. J Agric Biol Environ Stat 2023; 28:1-25. [PMID: 37844016 PMCID: PMC10569113 DOI: 10.1007/s13253-023-00565-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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 10/18/2023]
Abstract
Spatio-temporal models can be used to analyze data collected at various spatial locations throughout multiple time points. However, even with a finite number of spatial locations, there may be a lack of resources to collect data from every spatial location at every time point. We develop a spatio-temporal finite-population block kriging (ST-FPBK) method to predict a quantity of interest, such as a mean or total, across a finite number of spatial locations. This ST-FPBK predictor incorporates an appropriate variance reduction for sampling from a finite population. Through an application to moose surveys in the east-central region of Alaska, we show that the predictor has a substantially smaller standard error compared to a predictor from the purely spatial model that is currently used to analyze moose surveys in the region. We also show how the model can be used to forecast a prediction for abundance in a time point for which spatial locations have not yet been surveyed. A separate simulation study shows that the spatio-temporal predictor is unbiased and that prediction intervals from the ST-FPBK predictor attain appropriate coverage. For ecological monitoring surveys completed with some regularity through time, use of ST-FPBK could improve precision. We also give an R package that ecologists and resource managers could use to incorporate data from past surveys in predicting a quantity from a current survey.
Collapse
Affiliation(s)
- Matt Higham
- Department of Math, Computer Science, and Statistics, St. Lawrence University
| | | | | | | | | |
Collapse
|
34
|
Watson J, Green MA, Giebel C, Darlington-Pollock F, Akpan A. Social and spatial inequalities in healthcare use among people living with dementia in England (2002-2016). Aging Ment Health 2023; 27:1476-1487. [PMID: 35959941 PMCID: PMC9612936 DOI: 10.1080/13607863.2022.2107176] [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] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/01/2022]
Abstract
OBJECTIVES Healthcare services for people living with dementia (PLWD) are stretched, and government promises of increased funding remain undelivered. With the UK dementia population to surpass 1 million by 2024, and dementia care costs predicted to almost treble by 2040, it is essential we understand differences in healthcare use among PLWD. This study aimed to explore social and spatial variations in healthcare use among people diagnosed with dementia (2002-2016). METHODS Data were derived from Electronic Health Records of Clinical Practice Research Datalink GP patients in England (n = 142,302). To standardise healthcare contacts, rates of healthcare contacts per year were calculated for three primary (GP observations and medications) and three secondary healthcare types [Accident & Emergency (A&E) attendances and, emergency and elective hospital admissions]. Fully-adjusted generalised linear regression models were used to identify healthcare use variation by social and spatial groups. Twelve models were generated, one for each healthcare type in early- and late-onset populations separately. RESULTS This study highlights numerous social and spatial variations in healthcare use among PLWD. Among PLWD, several groups tended to have healthcare service use more closely associated with negative outcomes, including a greater likelihood of A&E attendances and emergency and elective hospital admissions. These groups include: men, people from White ethnicity groups and people from more deprived and rural areas. CONCLUSIONS Systemic and social measures are needed to reduce variations in healthcare use inequalities in PWLD. These include greater healthcare continuity, health checks and medicines reviews, culturally appropriate services, better and more accessible treatment and improved infrastructure.
Collapse
Affiliation(s)
- James Watson
- School of Environmental Sciences, The University of Liverpool, Liverpool, United Kingdom
| | - Mark A. Green
- School of Environmental Sciences, The University of Liverpool, Liverpool, United Kingdom
| | - Clarissa Giebel
- Department of Primary Care and Mental Health, University of Liverpool, Liverpool, United Kingdom
- NIHR ARC NWC, Liverpool, United Kingdom
| | | | - Asangaedem Akpan
- Department of Medicine for Older People and Stroke, Liverpool University Hospitals NHS FT, Liverpool, United Kingdom
- Healthy Ageing Group, University of Cumbria, Cumbria, United Kingdom
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- NIHR CRN NWC, Liverpool, United Kingdom
| |
Collapse
|
35
|
Bai P, Schipperijn J, Rosenberg M, Christian H. Neighborhood Places for Preschool Children's Physical Activity: A Mixed-Methods Study Using Global Positioning System, Geographic Information Systems, and Accelerometry Data. J Phys Act Health 2023:1-11. [PMID: 37295785 DOI: 10.1123/jpah.2022-0462] [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: 08/25/2022] [Revised: 01/06/2023] [Accepted: 04/17/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND This study adds to the current literature by using a novel device-based method to explore where preschool children are physically active outside of home and childcare settings. This study combined accelerometry with geospatial data to explore the influence of the environment on preschool children's physical activity by objectively identifying the locations where preschool children engage in moderate to vigorous physical activity (MVPA) within and outside of their neighborhood. METHODS Accelerometry, Global Positioning System, and Geographic Information Systems data from 168 preschool children aged 2-5 years were processed in ArcGIS Pro to identify locations (per 25 × 25-m fishnet cell) with high MVPA counts. Locations with high MVPA counts were defined as those with the top 20% of MVPA counts per fishnet cell. The land use for high MVPA count location was determined for 3 domains: <500 m from home, 500 to 1600 m from home, and >1600 m from home. RESULTS Locations with high MVPA counts <500 m from home were playgrounds (66.6%), schools (16.7%), and parks (16.7%). Locations with high MVPA counts 500 to 1600 m from home included playgrounds (33.3%), nonhome residential (29.6%), childcare centers (11.1%), and parks (3.7%). Locations with high MVPA counts >1600 m from home included nonhome residential (54.7%), sports and recreation centers (11.1%), playgrounds (6.8%), and parks (5.3%). CONCLUSIONS Our findings highlight that local parks and playgrounds provide physical activity opportunities for preschool children, yet beyond the local neighborhood, the homes of others are important locations for preschool children to accumulate MVPA. These findings can be used to inform the design of current and future neighborhood places to better accommodate preschool children's MVPA.
Collapse
Affiliation(s)
- Pulan Bai
- School of Population and Global Health, The University of Western Australia, Perth, WA,Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA,Australia
| | - Jasper Schipperijn
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense,Denmark
| | - Michael Rosenberg
- School of Human Sciences (Exercise and Sport Science), The University of Western Australia, Perth, WA,Australia
| | - Hayley Christian
- School of Population and Global Health, The University of Western Australia, Perth, WA,Australia
- Telethon Kids Institute, The University of Western Australia, Perth, WA,Australia
| |
Collapse
|
36
|
Botz J, Lohner V, Schirmer MD. Spatial patterns of white matter hyperintensities: a systematic review. Front Aging Neurosci 2023; 15:1165324. [PMID: 37251801 PMCID: PMC10214839 DOI: 10.3389/fnagi.2023.1165324] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Background White matter hyperintensities are an important marker of cerebral small vessel disease. This disease burden is commonly described as hyperintense areas in the cerebral white matter, as seen on T2-weighted fluid attenuated inversion recovery magnetic resonance imaging data. Studies have demonstrated associations with various cognitive impairments, neurological diseases, and neuropathologies, as well as clinical and risk factors, such as age, sex, and hypertension. Due to their heterogeneous appearance in location and size, studies have started to investigate spatial distributions and patterns, beyond summarizing this cerebrovascular disease burden in a single metric-its volume. Here, we review the evidence of association of white matter hyperintensity spatial patterns with its risk factors and clinical diagnoses. Design/methods We performed a systematic review in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) Statement. We used the standards for reporting vascular changes on neuroimaging criteria to construct a search string for literature search on PubMed. Studies written in English from the earliest records available until January 31st, 2023, were eligible for inclusion if they reported on spatial patterns of white matter hyperintensities of presumed vascular origin. Results A total of 380 studies were identified by the initial literature search, of which 41 studies satisfied the inclusion criteria. These studies included cohorts based on mild cognitive impairment (15/41), Alzheimer's disease (14/41), Dementia (5/41), Parkinson's disease (3/41), and subjective cognitive decline (2/41). Additionally, 6 of 41 studies investigated cognitively normal, older cohorts, two of which were population-based, or other clinical findings such as acute ischemic stroke or reduced cardiac output. Cohorts ranged from 32 to 882 patients/participants [median cohort size 191.5 and 51.6% female (range: 17.9-81.3%)]. The studies included in this review have identified spatial heterogeneity of WMHs with various impairments, diseases, and pathologies as well as with sex and (cerebro)vascular risk factors. Conclusion The results show that studying white matter hyperintensities on a more granular level might give a deeper understanding of the underlying neuropathology and their effects. This motivates further studies examining the spatial patterns of white matter hyperintensities.
Collapse
Affiliation(s)
- Jonas Botz
- Computational Neuroradiology, Department of Neuroradiology, University Hospital Bonn, Bonn, Germany
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany
| | - Valerie Lohner
- Cardiovascular Epidemiology of Aging, Department of Cardiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Markus D. Schirmer
- Computational Neuroradiology, Department of Neuroradiology, University Hospital Bonn, Bonn, Germany
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
37
|
Johnston RJ, Moeltner K, Peery S, Ndebele T, Yao Z, Crema S, Wollheim WM, Besedin E. Spatial dimensions of water quality value in New England river networks. Proc Natl Acad Sci U S A 2023; 120:e2120255119. [PMID: 37094143 PMCID: PMC10160974 DOI: 10.1073/pnas.2120255119] [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] [Indexed: 04/26/2023] Open
Abstract
Households' willingness to pay (WTP) for water quality improvements-representing their economic value-depends on where improvements occur. Households often hold higher values for improvements close to their homes or iconic areas. Are there other areas where improvements might hold high value to individual households, do effects on WTP vary by type of improvement, and can these areas be identified even if they are not anticipated by researchers? To answer these questions, we integrated a water quality model and map-based, interactive choice experiment to estimate households' WTP for water quality improvements throughout a river network covering six New England states. The choice experiment was implemented using a push-to-web survey over a sample of New England households. Voting scenarios used to elicit WTP included interactive geographic information system (GIS) maps that illustrated three water quality measures at various zoom levels across the study domain. We captured data on how respondents maneuvered through these maps prior to answering the value-eliciting questions. Results show that WTP was influenced by regionwide quality improvements and improvements surrounding each respondent's home, as anticipated, but also by improvements in individualized locations identifiable via each respondent's map interactions. These spatial WTP variations only appear for low-quality rivers and are focused around particular areas of New England. The study shows that dynamic map interactions can convey salient information for WTP estimation and that predicting spatial WTP heterogeneity based primarily on home or iconic locations, as typically done, may overlook areas where water quality has high value.
Collapse
Affiliation(s)
- Robert J Johnston
- George Perkins Marsh Institute, Clark University, Worcester, MA 01610
| | - Klaus Moeltner
- Department of Agricultural and Applied Economics, Virginia Tech, Blacksburg, VA 24061
| | - Seth Peery
- Enterprise GIS, Virginia Tech, Blacksburg, VA 24061
| | - Tom Ndebele
- George Perkins Marsh Institute, Clark University, Worcester, MA 01610
| | - Zhenyu Yao
- Department of Agricultural and Applied Economics, Virginia Tech, Blacksburg, VA 24061
| | | | - Wilfred M Wollheim
- Department of Natural Resources & the Environment, University of New Hampshire, Durham, NH 03824
| | | |
Collapse
|
38
|
Ye D, Wu L, Li X, Atoba TO, Wu W, Weng H. A Synthetic Review of Various Dimensions of Non-Destructive Plant Stress Phenotyping. Plants (Basel) 2023; 12:1698. [PMID: 37111921 PMCID: PMC10146287 DOI: 10.3390/plants12081698] [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] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/08/2023] [Accepted: 04/16/2023] [Indexed: 06/19/2023]
Abstract
Non-destructive plant stress phenotyping begins with traditional one-dimensional (1D) spectroscopy, followed by two-dimensional (2D) imaging, three-dimensional (3D) or even temporal-three-dimensional (T-3D), spectral-three-dimensional (S-3D), and temporal-spectral-three-dimensional (TS-3D) phenotyping, all of which are aimed at observing subtle changes in plants under stress. However, a comprehensive review that covers all these dimensional types of phenotyping, ordered in a spatial arrangement from 1D to 3D, as well as temporal and spectral dimensions, is lacking. In this review, we look back to the development of data-acquiring techniques for various dimensions of plant stress phenotyping (1D spectroscopy, 2D imaging, 3D phenotyping), as well as their corresponding data-analyzing pipelines (mathematical analysis, machine learning, or deep learning), and look forward to the trends and challenges of high-performance multi-dimension (integrated spatial, temporal, and spectral) phenotyping demands. We hope this article can serve as a reference for implementing various dimensions of non-destructive plant stress phenotyping.
Collapse
Affiliation(s)
- Dapeng Ye
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Agricultural Information Sensing Technology, College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Libin Wu
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Agricultural Information Sensing Technology, College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaobin Li
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Agricultural Information Sensing Technology, College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tolulope Opeyemi Atoba
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Agricultural Information Sensing Technology, College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhao Wu
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Agricultural Information Sensing Technology, College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haiyong Weng
- College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Key Laboratory of Agricultural Information Sensing Technology, College of Mechanical and Electrical Engineering, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
39
|
Nabi SU, Mir JI, Yasmin S, Din A, Raja WH, Madhu GS, Parveen S, Mansoor S, Chung YS, Sharma OC, Sheikh MA, Al-Misned FA, El-Serehy HA. Tissue and Time Optimization for Real-Time Detection of Apple Mosaic Virus and Apple Necrotic Mosaic Virus Associated with Mosaic Disease of Apple ( Malus domestica). Viruses 2023; 15:v15030795. [PMID: 36992503 PMCID: PMC10059951 DOI: 10.3390/v15030795] [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: 01/05/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
Besides apple mosaic virus (ApMV), apple necrotic mosaic virus (ApNMV) has also been found to be associated with apple mosaic disease. Both viruses are unevenly distributed throughout the plant and their titer decreases variably with high temperatures, hence requiring proper tissue and time for early and real-time detection within plants. The present study was carried out to understand the distribution and titer of ApMV and ApNMV in apple trees from different plant parts (spatial) during different seasons (temporal) for the optimization of tissue and time for their timely detection. The Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) was carried out to detect and quantify both viruses in the various plant parts of apple trees during different seasons. Depending on the availability of tissue, both ApMV and ApNMV were detected in all the plant parts during the spring season using RT-PCR. During the summer, both viruses were detected only in seeds and fruits, whereas they were detected in leaves and pedicel during the autumn season. The RT-qPCR results showed that during the spring, the ApMV and ApNMV expression was higher in leaves, whereas in the summer and autumn, the titer was mostly detected in seeds and leaves, respectively. The leaves in the spring and autumn seasons and the seeds in the summer season can be used as detection tissues through RT-PCR for early and rapid detection of ApMV and ApNMV. This study was validated on 7 cultivars of apples infected with both viruses. This will help to accurately sample and index the planting material well ahead of time, which will aid in the production of virus-free, quality planting material.
Collapse
Affiliation(s)
- Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - Javid Iqbal Mir
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - Salwee Yasmin
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - Ambreena Din
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - Wasim H Raja
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - G S Madhu
- ICAR-Indian Institute of Horticultural Research, RS-Chettalli, Bangaluru 571248, Karnataka, India
| | - Shugufta Parveen
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju-si 63243, Republic of Korea
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju-si 63243, Republic of Korea
| | - Om Chand Sharma
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - Muneer Ahmad Sheikh
- ICAR-Central Institute of Temperate Horticulture, Srinagar 191132, Jammu & Kashmir, India
| | - Fahad A Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hamed A El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
40
|
Filipp FV. Spatial cancer systems biology resolves heterotypic interactions and identifies disruption of spatial hierarchy as a pathological driver event. bioRxiv 2023:2023.03.01.530706. [PMID: 36993709 PMCID: PMC10054974 DOI: 10.1101/2023.03.01.530706] [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] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Spatially annotated single-cell datasets provide unprecedented opportunities to dissect cell-cell communication in development and disease. Heterotypic signaling includes interactions between different cell types and is well established in tissue development and spatial organization. Epithelial organization requires several different programs that are tightly regulated. Planar cell polarity (PCP) is the organization of epithelial cells along the planar axis, orthogonal to the apical-basal axis. Here, we investigate PCP factors and explore the implications of developmental regulators as malignant drivers. Utilizing cancer systems biology analysis, we derive a gene expression network for WNT-ligands (WNT) and their cognate frizzled (FZD) receptors in skin cutaneous melanoma. The profiles supported by unsupervised clustering of multiple-sequence alignments identify ligand-independent signaling and implications for metastatic progression based on the underpinning developmental spatial program. Omics studies and spatial biology connect developmental programs with oncological events and explain key spatial features of metastatic aggressiveness. Dysregulation of prominent PCP factors such as specific representatives of the WNT and FZD families in malignant melanoma recapitulates the development program of normal melanocytes but in an uncontrolled and disorganized fashion.
Collapse
Affiliation(s)
- Fabian V. Filipp
- Cancer Systems Biology, Institute of Diabetes and Cancer, Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764 München, Germany
- School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
- Institute for Advanced Study, Technical University München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
- Metaflux, San Diego, CA, 92105, United States of America
| |
Collapse
|
41
|
Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [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] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
Collapse
Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
| |
Collapse
|
42
|
Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat complexity affects microbial growth in fractal maze. Curr Biol 2023; 33:1448-1458.e4. [PMID: 36933553 DOI: 10.1016/j.cub.2023.02.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 07/29/2022] [Revised: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/19/2023]
Abstract
The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.
Collapse
Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Sölvegatan 16, 223 63 Lund, Sweden
| | - Edith C Hammer
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden; Centre for Environmental and Climate Science, CEC, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| |
Collapse
|
43
|
Verweij W, Griswold CK. Spatial structure and benefits to hosts allow plasmids with and without post-segregational killing systems to coexist. Biol Lett 2023; 19:20220376. [PMID: 36855853 PMCID: PMC9975649 DOI: 10.1098/rsbl.2022.0376] [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: 08/17/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
To persist, a plasmid relies on being passed on to a daughter cell, but this does not always occur. Plasmids with post-segregational killing (PSK) systems kill a daughter cell if the plasmid has not been passed on. By killing the host, it also kills competing plasmids in the same host, something competing plasmids without a similar system cannot do. Accordingly, plasmids with PSK systems can displace other plasmids. In nature, plasmids with and without PSK systems coexist and prior theory has suggested this is expected to be very rare or unstable, such that one or the other type of plasmid eventually takes over. Here, we show that if there is spatial structure and plasmids confer benefits to hosts, coexistence of plasmids occurs broadly. Often plasmids confer benefits (even ones with a PSK system) and bacteria are often spatially structured. So, our results may be generally applicable.
Collapse
Affiliation(s)
- Wilco Verweij
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Cortland K. Griswold
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| |
Collapse
|
44
|
Bitew FH, Sparks CS, Nyarko SH, Apgar L. Spatiotemporal Variations and Determinants of Under-Five Stunting in Ethiopia. Food Nutr Bull 2023; 44:27-38. [PMID: 36824032 DOI: 10.1177/03795721231158503] [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] [Indexed: 02/25/2023]
Abstract
BACKGROUND Stunting has been a major concern in sub-Saharan Africa. However, little evidence exists on the spatiotemporal variations in under-five stunting within a national context. OBJECTIVE This paper examines the spatiotemporal variations in under-five stunting and determinants using data from the Ethiopia Demographic and Health Surveys (2000-2016). METHODS Spatial autocorrelation and multilevel logistic regression models were used to conduct the analyses. RESULTS The stunting prevalence has decreased from 51% to 37%, while the prevalence of severe stunting has decreased by more than half (from 28% to 12%). Wide regional variations in stunting have been consistently observed over the years, which exhibited a higher level of stunting in Tigray (48%), Afar (42%), and Amhara (42%). The results show considerable local and regional variations in under-five stunting levels with diverse patterns of improvements in regional stunting levels over time. Stunting levels were associated with child-level factors such as the sex of a child, birth size, age of a child, birth order, preceding birth interval, and place of birth. Maternal educational attainment, nutritional status, household wealth, toilet facility type, and place of residence were linked to under-five stunting. The regional-level infant mortality rate was associated with under-five stunting. CONCLUSIONS Specially tailored policies and interventions should be devised to address persistent spatial inequalities in stunting by focusing on higher risk populations.
Collapse
Affiliation(s)
- Fikrewold H Bitew
- Department of Demography, College for Health, Community & Policy, The University of Texas at San Antonio, San Antonio, TX, USA.,Institutional Research, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, USA
| | - Corey S Sparks
- Department of Demography, College for Health, Community & Policy, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Samuel H Nyarko
- Department of Demography, College for Health, Community & Policy, The University of Texas at San Antonio, San Antonio, TX, USA.,Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Lauren Apgar
- Institutional Research, The University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, USA
| |
Collapse
|
45
|
Mirzaee S, Mirzakhani Nafchi A. Monitoring Spatiotemporal Vegetation Response to Drought Using Remote Sensing Data. Sensors (Basel) 2023; 23:2134. [PMID: 36850731 PMCID: PMC9961431 DOI: 10.3390/s23042134] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Environmental factors such as drought significantly influence vegetation growth, coverage, and ecosystem functions. Hence, monitoring the spatiotemporal vegetation responses to drought in a high temporal and adequate spatial resolution is essential, mainly at the local scale. This study was conducted to investigate the aspatial and spatial relationships between vegetation growth status and drought in the southeastern South Dakota, USA. For this purpose, Landsat 8 OLI images from the months of April through September for the years 2016-2021, with cloud cover of less than 10%, were acquired. After that, radiometric calibration and atmospheric correction were performed on all of the images. Some spectral indices were calculated using the Band Math toolbox in ENVI 5.3 (Environment for Visualizing Images v. 5.3). In the present study, the extracted spectral indices from Landsat 8 OLI images were the Normalized Difference Vegetation Index (NDVI) and the Normalized Multiband Drought Index (NMDI). The results showed that the NDVI values for the month of July in different years were at maximum value at mostly pixels. Based on the statistical criteria, the best regression models for explaining the relationship between NDVI and NMDISoil were polynomial order 2 for 2016 to 2019 and linear for 2021. The developed regression models accounted for 96.7, 95.7, 96.2, 88.4, and 32.2% of vegetation changes for 2016, 2017, 2018, 2019, and 2021, respectively. However, there was no defined trend between NDVI and NMDISoil observed in 2020. In addition, pixel-by-pixel analyses showed that drought significantly impacted vegetation coverage, and 69.6% of the pixels were negatively correlated with the NDVI. It was concluded that the Landsat satellite images have potential information for studying the relationships between vegetation growth status and drought, which is the primary step in site-specific management.
Collapse
Affiliation(s)
- Salman Mirzaee
- Department of Agronomy, Horticulture and Plant Science, College of Agriculture, Food and Environmental Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Ali Mirzakhani Nafchi
- Extension Precision Agriculture Specialist, College of Agriculture, Food and Environmental Sciences, South Dakota State University, Brookings, SD 57007, USA
| |
Collapse
|
46
|
Digre A, Lindskog C. The human protein atlas-Integrated omics for single cell mapping of the human proteome. Protein Sci 2023; 32:e4562. [PMID: 36604173 PMCID: PMC9850435 DOI: 10.1002/pro.4562] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/30/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Studying the spatial distribution of proteins provides the basis for understanding the biology, molecular repertoire, and architecture of every human cell. The Human Protein Atlas (HPA) has grown into one of the world's largest biological databases, and in the most recent version, a major update of the structure of the database was performed. The data has now been organized into 10 different comprehensive sections, each summarizing different aspects of the human proteome and the protein-coding genes. In particular, large datasets with information on the single cell type level have been integrated, refining the tissue and cell type specificity and detailing the expression in cell states with an increased resolution. The multi-modal data constitute an important resource for both basic and translational science, and hold promise for integration with novel emerging technologies at the protein and RNA level.
Collapse
Affiliation(s)
- Andreas Digre
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| |
Collapse
|
47
|
Danan CH, Katada K, Parham LR, Hamilton KE. Spatial transcriptomics add a new dimension to our understanding of the gut. Am J Physiol Gastrointest Liver Physiol 2023; 324:G91-G98. [PMID: 36472345 PMCID: PMC9870576 DOI: 10.1152/ajpgi.00191.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023]
Abstract
The profound complexity of the intestinal mucosa demands a spatial approach to the study of gut transcriptomics. Although single-cell RNA sequencing has revolutionized our ability to survey the diverse cell types of the intestine, knowledge of cell type alone cannot fully describe the cells that make up the intestinal mucosa. During homeostasis and disease, dramatic gradients of oxygen, nutrients, extracellular matrix proteins, morphogens, and microbiota collectively dictate intestinal cell state, and only spatial techniques can articulate differences in cellular transcriptomes at this level. Spatial transcriptomic techniques assign transcriptomic data to precise regions in a tissue of interest. In recent years, these protocols have become increasingly accessible, and their application in the intestinal mucosa has exploded in popularity. In the gut, spatial transcriptomics typically involve the application of tissue sections to spatially barcoded RNA sequencing or laser capture microdissection followed by RNA sequencing. In combination with single-cell RNA sequencing, these spatial sequencing approaches allow for the construction of spatial transcriptional maps at pseudosingle-cell resolution. In this review, we describe the spatial transcriptomic technologies recently applied in the gut and the previously unattainable discoveries that they have produced.
Collapse
Affiliation(s)
- Charles H Danan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kay Katada
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Louis R Parham
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
48
|
Harfouche MN, Shields T, Curriero FC. Geo spatial analysis of firearm injuries in an urban setting: Individual rather than community characteristics affect firearm injury risk. Am J Surg 2023; 225:1062-1068. [PMID: 36702734 DOI: 10.1016/j.amjsurg.2023.01.014] [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: 11/02/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND The relationship between individual/socioeconomic characteristics and firearm injury risk in an urban center was evaluated. METHODS A hospital registry was used to identify individuals in Baltimore City who experienced interpersonal firearm injury in 2019 (FA). Injuries that did not satisfy this criterion were used as a comparison group (NF). Socioeconomic characteristics were linked to home address at the block group level. Regression analysis was used to determine predictors of firearm injury. Clusters of high and low firearm relative to non-firearm injuries were identified. RESULTS A total of 1293 individuals were included (FA = 277, NF = 1016). The FA group lived in communities with lower income (p = 0.005), higher poverty (p = 0.007), and more Black residents (p < 0.001). Individual level factors were stronger predictors of firearm injury than community factors on multivariate regression with Black race associated with 5x higher odds of firearm injury (p < 0.001). Firearm injury clustered in areas of low socioeconomic status. CONCLUSIONS Individual versus community factors have a greater influence on firearm injury risk. Prevention efforts should target young, Black men in urban centers.
Collapse
Affiliation(s)
- Melike N Harfouche
- University of Maryland School of Medicine, 22 S Greene St, Baltimore, MD, 21201, USA; Johns Hopkins University School of Public Health, 615 N Wolf St, Baltimore, MD, 21205, USA.
| | - Timothy Shields
- Johns Hopkins University School of Public Health, 615 N Wolf St, Baltimore, MD, 21205, USA.
| | - Frank C Curriero
- Johns Hopkins University School of Public Health, 615 N Wolf St, Baltimore, MD, 21205, USA.
| |
Collapse
|
49
|
Roman ZJ, Brandt H. A Latent Auto-Regressive Approach for Bayesian Structural Equation Modeling of Spatially or Socially Dependent Data. Multivariate Behav Res 2023; 58:90-114. [PMID: 34379011 DOI: 10.1080/00273171.2021.1957663] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Spatial analytic approaches are classic models in econometric literature, but relatively new in social sciences. Spatial analysis models are synonymous with social network auto-regressive models which are also gaining popularity in the behavioral sciences. These models have two major benefits. First, dependent data, either socially or spatially, must be accounted for to acquire unbiased results. Second, analysis of the dependence provides rich additional information such as spillover effects. Structural Equation Models (SEM) are widely used in psychological research for measuring and testing multi-faceted constructs. So far, SEM that allow for spatial or social dependency are limited with regard to their flexibility, for example, when estimating nonlinear effects. Here, we provide a cohesive framework which can simultaneously estimate latent interaction/polynomial effects and account for spatial effects with both exogenous and endogenous latent variables, the Bayesian Spatial Auto-Regressive Structural Equation Model (BARDSEM). First, we briefly outline classic auto-regressive models. Next, we present the BARDSEM and introduce simulation results to exemplify its performance. Finally, we provide an empirical example using the spatially dependent extended US southern homicide data to show the rich interpretations that are possible using the BARDSEM. Finally, we discuss implications, limitations, and future research.
Collapse
|
50
|
Ayele MA, Fenta HM, Zike DT, Tesfaw LM. Spatial distribution and trends of anemia among pregnant women in Ethiopia: EDHS 2005-2016. Front Public Health 2023; 11:1089383. [PMID: 36875390 PMCID: PMC9981153 DOI: 10.3389/fpubh.2023.1089383] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Background Anemia is a public health problem affecting both developed and developing nations worldwide with a significant consequence on health and economic growth. The problem is more severe in pregnant women. Hence, the main purpose of this study was to determine the factors of anemia levels among pregnant women in zones in Ethiopia. Methods We utilized data from 2005, 2011, and 2016 Ethiopian demographic and health survey (EDHSs), a population-based cross-sectional study. The study includes 8,421 pregnant women. An ordinal logistic regression model with spatial analysis was used to explore factors of anemia levels among pregnant women. Result About 224 (2.7%), 1,442 (17.2%), and 1,327 (15.8%) pregnant women were mild, moderate, and severely anemic, respectively. The spatial autocorrelation of anemia among the administrative zones of Ethiopia for the three consecutive was not significant. The middle wealth index of 15.9% (OR = 0.841, CI: 0.72-0.983) and richest wealth index of 51% (OR = 0.49, CI: 0.409-0.586) were less likely anemic compared to the poorest wealth index, age group of mother 30-39 was 42.9% (OR = 0.571, CI: 0.359-0.908) times less likely to be moderate and above anemic compared to <20 years, several household members 4-6 were 51% (OR = 1.51, CI: 1.175-1.94 more likely moderate and above anemic compared to 1-3. Conclusion Over one-third of the pregnant women (34.5%) were anemic in Ethiopia. Wealth index, age group, religion, region, number of household members, source of drinking water, and EDHS were significant factors in anemia levels. The prevalence of anemia among pregnant women varied among Ethiopian administrative zones. North West Tigray, Waghimra, Oromia special woreda, West shewa, and East shewa were a high prevalence of anemia.
Collapse
Affiliation(s)
- Molla Abate Ayele
- Department of Statistics, Mekidela Amba University, Mekane Selam, Ethiopia
| | | | | | - Lijalem Melie Tesfaw
- Department of Statistics, Bahir Dar University, Bahir Dar, Ethiopia.,Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|