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Military Medical Research Oct 2023In the United States (US), the Surveillance, Epidemiology, and End Results (SEER) program is the only comprehensive source of population-based information that includes... (Review)
Review
In the United States (US), the Surveillance, Epidemiology, and End Results (SEER) program is the only comprehensive source of population-based information that includes stage of cancer at the time of diagnosis and patient survival data. This program aims to provide a database about cancer incidence and survival for studies of surveillance and the development of analytical and methodological tools in the cancer field. Currently, the SEER program covers approximately half of the total cancer patients in the US. A growing number of clinical studies have applied the SEER database in various aspects. However, the intrinsic features of the SEER database, such as the huge data volume and complexity of data types, have hindered its application. In this review, we provided a systematic overview of the commonly used methodologies and study designs for retrospective epidemiological research in order to illustrate the application of the SEER database. Therefore, the goal of this review is to assist researchers in the selection of appropriate methods and study designs for enhancing the robustness and reliability of clinical studies by mining the SEER database.
Topics: Humans; United States; Retrospective Studies; Reproducibility of Results; Research Design; SEER Program; Neoplasms
PubMed: 37899480
DOI: 10.1186/s40779-023-00488-2 -
Mathematical Biosciences and... Aug 2023Social media contains useful information about people and society that could help advance research in many different areas of health (e.g. by applying opinion mining,...
Social media contains useful information about people and society that could help advance research in many different areas of health (e.g. by applying opinion mining, emotion/sentiment analysis and statistical analysis) such as mental health, health surveillance, socio-economic inequality and gender vulnerability. User demographics provide rich information that could help study the subject further. However, user demographics such as gender are considered private and are not freely available. In this study, we propose a model based on transformers to predict the user's gender from their images and tweets. The image-based classification model is trained in two different methods: using the profile image of the user and using various image contents posted by the user on Twitter. For the first method a Twitter gender recognition dataset, publicly available on Kaggle and for the second method the PAN-18 dataset is used. Several transformer models, i.e. vision transformers (ViT), LeViT and Swin Transformer are fine-tuned for both of the image datasets and then compared. Next, different transformer models, namely, bidirectional encoders representations from transformers (BERT), RoBERTa and ELECTRA are fine-tuned to recognize the user's gender by their tweets. This is highly beneficial, because not all users provide an image that indicates their gender. The gender of such users could be detected from their tweets. The significance of the image and text classification models were evaluated using the Mann-Whitney U test. Finally, the combination model improved the accuracy of image and text classification models by 11.73 and 5.26% for the Kaggle dataset and by 8.55 and 9.8% for the PAN-18 dataset, respectively. This shows that the image and text classification models are capable of complementing each other by providing additional information to one another. Our overall multimodal method has an accuracy of 88.11% for the Kaggle and 89.24% for the PAN-18 dataset and outperforms state-of-the-art models. Our work benefits research that critically require user demographic information such as gender to further analyze and study social media content for health-related issues.
Topics: Humans; Social Media; Electric Power Supplies; Research Design
PubMed: 37919997
DOI: 10.3934/mbe.2023711 -
European Urology Focus Sep 2023Clinical trials are essential for establishing the benefits and harms of various treatments. Among the various trial designs, superiority trials aim to establish the... (Review)
Review
Clinical trials are essential for establishing the benefits and harms of various treatments. Among the various trial designs, superiority trials aim to establish the superiority of one treatment over another, while noninferiority trials demonstrate that a new treatment is not inferior to an established one while minimizing harms or patient burdens. In recent years, noninferiority trials have gained prominence. This mini-review explores noninferiority trials, focusing on challenges in their interpretation. Ultimately, we argue that the focus should be on the results from trials rather than their design, as clinicians and other stakeholders primarily seek evidence that helps patients and clinicians in trade-offs of the benefits and harms and burdens of treatment options. PATIENT SUMMARY: Our mini-review shows that looking at the overall treatment benefits and harms in noninferiority trials is better than focusing on the trial design. This approach would help patients and clinicians to better understand trial results and their implications.
Topics: Humans; Research Design; Equivalence Trials as Topic
PubMed: 37880063
DOI: 10.1016/j.euf.2023.10.003 -
Journal of Translational Medicine Aug 2023To gain deeper insights into the microenvironment of breast cancer, we utilized GeoMx Digital Spatial Profiling (DSP) technology to analyze transcripts from 107 regions...
To gain deeper insights into the microenvironment of breast cancer, we utilized GeoMx Digital Spatial Profiling (DSP) technology to analyze transcripts from 107 regions of interest in 65 untreated breast cancer tissue samples. Our study revealed spatial heterogeneity in the expression of marker genes in tumor cell enriched, immune cell enriched, and normal epithelial areas. We evaluated a total of 55 prognostic markers in tumor cell enriched regions and 15 in immune cell enriched regions, identifying that tumor cell enriched regions had higher levels of follicular helper T cells, resting dendritic cells, and plasma cells than immune cell enriched regions, while the levels of resting CD4 memory in T cells and regulatory (Treg) T cells were lower. Additionally, we analyzed the heterogeneity of HLA gene families, immunological checkpoints, and metabolic genes in these areas. Through univariate Cox analysis, we identified 5 prognosis-related metabolic genes. Furthermore, we conducted immunostaining experiments, including EMILIN2, SURF4, and LYPLA1, to verify our findings. Our investigation into the spatial heterogeneity of the breast cancer tumor environment has led to the discovery of specific diagnostic and prognostic markers in breast cancer.
Topics: Animals; Prognosis; Tumor Microenvironment; Mammary Neoplasms, Animal; Plasma Cells; Research Design
PubMed: 37644433
DOI: 10.1186/s12967-023-04395-x -
Cancer Medicine Jul 2023Patient and public involvement (PPI) in research emphasizes the importance of doing research with, rather than for people with lived health/illness experience(s). The... (Review)
Review
INTRODUCTION
Patient and public involvement (PPI) in research emphasizes the importance of doing research with, rather than for people with lived health/illness experience(s). The purpose of this scoping review is to investigate the breadth and depth of scientific literature on PPI in cancer research and to identify how is PPI applied and reported in cancer research.
METHODS
We searched MEDLINE, Embase, CINAHL, and PsycInfo up to March 2022. All titles/abstracts and full-text results were screened by two reviewers. Data were analyzed and are presented in both narrative and tabular format.
RESULTS
We screened 22,009 titles/abstract, reviewed 375 full-text articles, of which 101 studies were included in this review. 66 papers applied PPI; 35 used co-design methodologies. PPI in cancer research in published research has increased steadily since 2015 and often includes those with a past diagnosis of cancer or relatives/informal caregivers. The most common applied methods were workshops or interviews. PPI was generally used at the level of consultation/advisor and occurred mainly in early stages of research. Costs related to PPI were mentioned in 25 papers and four papers described training provided for PPI.
CONCLUSIONS
Results of our review demonstrate the nature and extent of PPI expansion in cancer research. Researchers and research organizations entering the fray of PPI should consider planning and reporting elements such as the stage, level, and role type of PPI, as well as methods and strategies put in place to assure diversity. Furthermore, a thorough evaluation of whether all these elements meet the stated PPI purpose will help to grasp its impact on research outcomes.
PATIENT OR PUBLIC CONTRIBUTION
Two patients participated in the stakeholder consultation as part of the scoping review methodology, contributed to the discussion on refining the results, and critically reviewed the manuscript. Both are co-authors of this manuscript.
Topics: Humans; Patient Participation; Research Design; Neoplasms; Caregivers
PubMed: 37329180
DOI: 10.1002/cam4.6200 -
Annual Review of Genomics and Human... Aug 2023Recent advancements in single-cell technologies have enabled expression quantitative trait locus (eQTL) analysis across many individuals at single-cell resolution.... (Review)
Review
Recent advancements in single-cell technologies have enabled expression quantitative trait locus (eQTL) analysis across many individuals at single-cell resolution. Compared with bulk RNA sequencing, which averages gene expression across cell types and cell states, single-cell assays capture the transcriptional states of individual cells, including fine-grained, transient, and difficult-to-isolate populations at unprecedented scale and resolution. Single-cell eQTL (sc-eQTL) mapping can identify context-dependent eQTLs that vary with cell states, including some that colocalize with disease variants identified in genome-wide association studies. By uncovering the precise contexts in which these eQTLs act, single-cell approaches can unveil previously hidden regulatory effects and pinpoint important cell states underlying molecular mechanisms of disease. Here, we present an overview of recently deployed experimental designs in sc-eQTL studies. In the process, we consider the influence of study design choices such as cohort, cell states, and ex vivo perturbations. We then discuss current methodologies, modeling approaches, and technical challenges as well as future opportunities and applications.
Topics: Humans; Quantitative Trait Loci; Genome-Wide Association Study; Chromosome Mapping; Research Design
PubMed: 37196361
DOI: 10.1146/annurev-genom-101422-100437 -
Brain : a Journal of Neurology Dec 2023The capacity and power of data from cohorts, registries and randomized trials to provide answers to contemporary clinical questions in neurology has increased... (Review)
Review
The capacity and power of data from cohorts, registries and randomized trials to provide answers to contemporary clinical questions in neurology has increased considerably over the past two decades. Novel sophisticated statistical methods are enabling us to harness these data to guide treatment decisions, but their complexity is making appraisal of clinical evidence increasingly demanding. In this review, we discuss several methodological aspects of contemporary research of treatment effectiveness in observational data in neurology, aimed at academic neurologists and analysts specializing in outcomes research. The review discusses specifics of the sources of observational data and their key features. It focuses on the limitations of observational data and study design, as well as statistical approaches aimed to overcome these limitations. Among the examples of leading clinical themes typically studied with analyses of observational data, the review discusses methodological approaches to comparative treatment effectiveness, development of diagnostic criteria and definitions of clinical outcomes. Finally, this review provides a brief summary of key points that will help clinical audience critically evaluate design and analytical aspects of studies of disease outcomes using observational data.
Topics: Humans; Treatment Outcome; Outcome Assessment, Health Care; Registries; Research Design; Neurology
PubMed: 37587541
DOI: 10.1093/brain/awad278 -
Nature Communications Oct 2023The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample of 94,812 longitudinal RT-qPCR...
The impact of a prior SARS-CoV-2 infection on the progression of subsequent infections has been unclear. Using a convenience sample of 94,812 longitudinal RT-qPCR measurements from anterior nares and oropharyngeal swabs, we identified 71 individuals with two well-sampled SARS-CoV-2 infections between March 11, 2020, and July 28, 2022. We compared the SARS-CoV-2 viral kinetics of first vs. second infections in this group, adjusting for viral variant, vaccination status, and age. Relative to first infections, second infections usually featured a faster clearance time. Furthermore, a person's relative (rank-order) viral clearance time, compared to others infected with the same variant, was roughly conserved across first and second infections, so that individuals who had a relatively fast clearance time in their first infection also tended to have a relatively fast clearance time in their second infection (Spearman correlation coefficient: 0.30, 95% credible interval (0.12, 0.46)). These findings provide evidence that, like vaccination, immunity from a prior SARS-CoV-2 infection shortens the duration of subsequent acute SARS-CoV-2 infections principally by reducing viral clearance time. Additionally, there appears to be an inherent element of the immune response, or some other host factor, that shapes a person's relative ability to clear SARS-CoV-2 infection that persists across sequential infections.
Topics: Humans; COVID-19; SARS-CoV-2; COVID-19 Testing; Research Design; Kinetics
PubMed: 37798265
DOI: 10.1038/s41467-023-41941-z -
The Journal of Endocrinology Jul 2023In biomedicine and many other fields, there are growing concerns around the reproducibility of research findings, with many researchers being unable to replicate their... (Review)
Review
In biomedicine and many other fields, there are growing concerns around the reproducibility of research findings, with many researchers being unable to replicate their own or others' results. This raises important questions as to the validity and usefulness of much published research. In this review, we aim to engage researchers in the issue of research reproducibility and equip them with the necessary tools to increase the reproducibility of their research. We first highlight the causes and potential impact of non-reproducible research and emphasise the benefits of working reproducibly for the researcher and broader research community. We address specific targets for improvement and steps that individual researchers can take to increase the reproducibility of their work. We next provide recommendations for improving the design and conduct of experiments, focusing on in vivo animal experiments. We describe common sources of poor internal validity of experiments and offer practical guidance for limiting these potential sources of bias at different experimental stages, as well as discussing other important considerations during experimental design. We provide a list of key resources available to researchers to improve experimental design, conduct, and reporting. We then discuss the importance of open research practices such as study preregistration and the use of preprints and describe recommendations around data management and sharing. Our review emphasises the importance of reproducible work and aims to empower every individual researcher to contribute to the reproducibility of research in their field.
Topics: Animals; Animal Experimentation; Reproducibility of Results; Research Design
PubMed: 37074416
DOI: 10.1530/JOE-22-0330 -
The Journal of Antimicrobial... Nov 2023The COVID-19 pandemic, while unfortunately notable for immense strain and death throughout the world, has also shown great promise in the development of medical... (Review)
Review
BACKGROUND
The COVID-19 pandemic, while unfortunately notable for immense strain and death throughout the world, has also shown great promise in the development of medical countermeasures. As the global scientific community shifted almost entirely towards vaccines, diagnostics and therapeutics, new trial designs most significantly adaptive platform trials, began to be used with greater speed and broader reach. These designs allowed for deploying and investigating new therapeutics, repurposing currently existing therapeutics and flexibly removing or adding additional medications as data appeared in real-time. Moreover, public-private sector partnering occurred at a level not seen before, contributing greatly to the rapid development and deployment of vaccines.
OBJECTIVES
To provide a brief overview of the advances in preventative and therapeutic medical countermeasure development for COVID-19.
METHODS
A narrative review of relevant major medical countermeasure trials was conducted using the date range February 2020-December 2022, representing the period of greatest productivity in research to investigate COVID-19.
RESULTS
Among the most influential trial designs are the adaptive platform designs, which have been applied to the development of initial COVID-19 antivirals, monoclonal antibodies, repurposing of existing immunomodulatory therapy and assisted in the disproof of ineffective medical therapies. Some of the most prominent examples include the REMAP-CAP, RECOVERY and TOGETHER trials.
CONCLUSIONS
Adaptive platform trial designs hold great promise for utility in future pandemics and mass casualty events. Additionally, public-private sectoring is essential for rapid medical countermeasure development and should be further enhanced for future biopreparedness.
Topics: Humans; COVID-19; Medical Countermeasures; Pandemics; Vaccines; Research Design
PubMed: 37995353
DOI: 10.1093/jac/dkad312