scholarly journals Feasibility of an Assessment Tool as a Data-Driven Approach to Reducing Racial Bias in Biomedical Publications

2021 ◽  
Vol 46 (1) ◽  
Author(s):  
Siobhan Wescott ◽  
Ronn Johnson ◽  
Sangeeta Lamba ◽  
Devon Olson ◽  
Yolanda Haywood ◽  
...  
Keyword(s):  
Biomedical Research ◽  
Assessment Tool ◽  
Racial Bias ◽  
Phase 1 ◽  
Three Dimensions ◽  
Complete Agreement ◽  
Biomedical Journals ◽  
Wide Range ◽  
Data Driven Approach ◽  
Biomedical Publications

AbstractThe editorial independence of biomedical journals allows flexibility to meet a wide range of research interests. However, it also is a barrier for coordination between journals to solve challenging issues such as racial bias in the scientific literature. A standardized tool to screen for racial bias could prevent the publication of racially biased papers. Biomedical journals would maintain editorial autonomy while still allowing comparable data to be collected and analyzed across journals. A racially diverse research team carried out a three-phase study to generate and test a racial bias assessment tool for biomedical research. Phase 1, an in-depth, structured literature search to identify recommendations, found near complete agreement in the literature on addressing race in biomedical research. Phase 2, construction of a framework from those recommendations, provides the major innovation of this paper. The framework includes three dimensions of race: 1) context, 2) tone and terminology, and 3) analysis, which are the basis for the Race Equity Vetting Instrument for Editorial Workflow (REVIEW) tool. Phase 3, pilot testing the assessment tool, showed that the REVIEW tool was effective at flagging multiple concerns in widely criticized articles. This study demonstrates the feasibility of the proposed REVIEW tool to reduce racial bias in research. Next steps include testing this tool on a broader sample of biomedical research to determine how the tool performs on more subtle examples of racial bias.

Turbulent three-dimensional dielectric electrohydrodynamic convection between two plates

2012 ◽  
Vol 696 ◽  
pp. 228-262 ◽  
Author(s):  
A. Kourmatzis ◽  
J. S. Shrimpton
Keyword(s):  
Spatial Data ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Energy Budgets ◽  
Turbulent Regime ◽  
Scalar Flux ◽  
Wide Range ◽  
Scalar Variance

AbstractThe fundamental mechanisms responsible for the creation of electrohydrodynamically driven roll structures in free electroconvection between two plates are analysed with reference to traditional Rayleigh–Bénard convection (RBC). Previously available knowledge limited to two dimensions is extended to three-dimensions, and a wide range of electric Reynolds numbers is analysed, extending into a fully inherently three-dimensional turbulent regime. Results reveal that structures appearing in three-dimensional electrohydrodynamics (EHD) are similar to those observed for RBC, and while two-dimensional EHD results bear some similarities with the three-dimensional results there are distinct differences. Analysis of two-point correlations and integral length scales show that full three-dimensional electroconvection is more chaotic than in two dimensions and this is also noted by qualitatively observing the roll structures that arise for both low (${\mathit{Re}}_{E} = 1$) and high electric Reynolds numbers (up to ${\mathit{Re}}_{E} = 120$). Furthermore, calculations of mean profiles and second-order moments along with energy budgets and spectra have examined the validity of neglecting the fluctuating electric field ${ E}_{i}^{\ensuremath{\prime} } $ in the Reynolds-averaged EHD equations and provide insight into the generation and transport mechanisms of turbulent EHD. Spectral and spatial data clearly indicate how fluctuating energy is transferred from electrical to hydrodynamic forms, on moving through the domain away from the charging electrode. It is shown that ${ E}_{i}^{\ensuremath{\prime} } $ is not negligible close to the walls and terms acting as sources and sinks in the turbulent kinetic energy, turbulent scalar flux and turbulent scalar variance equations are examined. Profiles of hydrodynamic terms in the budgets resemble those in the literature for RBC; however there are terms specific to EHD that are significant, indicating that the transfer of energy in EHD is also attributed to further electrodynamic terms and a strong coupling exists between the charge flux and variance, due to the ionic drift term.

scholarly journals Mini-Review Regarding the Applicability of Genome Editing Techniques Developed for Studying Infertility

Diagnostics ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 246
Author(s):  
Bogdan Doroftei ◽  
Ovidiu-Dumitru Ilie ◽  
Maria Puiu ◽  
Alin Ciobica ◽  
Ciprian Ilea
Keyword(s):  
Motor Activity ◽  
Experimental Model ◽  
Zinc Finger ◽  
Biomedical Research ◽  
Zinc Finger Nucleases ◽  
Loss Of Function ◽  
Transcription Activator ◽  
Phenotypic Changes ◽  
Wide Range ◽  
Short Palindromic Repeat

Infertility is a highly debated topic today. It has been long hypothesized that infertility has an idiopathic cause, but recent studies demonstrated the existence of a genetic substrate. Fortunately, the methods of editing the human genome proven to be revolutionary. Following research conducted, we identified a total of 21 relevant studies; 14 were performed on mice, 5 on zebrafish and 2 on rats. We concluded that over forty-four genes in total are dispensable for fertility in both sexes without affecting host homeostasis. However, there are genes whose loss-of-function induces moderate to severe phenotypic changes in both sexes. There were situations in which the authors reported infertility, exhibited by the experimental model, or other pathologies such as cryptorchidism, cataracts, or reduced motor activity. Overall, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 are techniques that offer a wide range of possibilities for studying infertility, even to create mutant variants. It can be concluded that ZFNs, TALENs, and CRISPR/Cas9 are crucial tools in biomedical research.

scholarly journals INSPECTOR: free software for magnetic resonance spectroscopy data inspection, processing, simulation and analysis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Martin Gajdošík ◽  
Karl Landheer ◽  
Kelley M. Swanberg ◽  
Christoph Juchem
Keyword(s):  
Magnetic Resonance ◽  
Quality Management ◽  
Magnetic Resonance Spectroscopy ◽  
Data Processing ◽  
Biomedical Research ◽  
Clinical Diagnostics ◽  
Resonance Spectroscopy ◽  
User Friendliness ◽  
Wide Range

AbstractIn vivo magnetic resonance spectroscopy (MRS) is a powerful tool for biomedical research and clinical diagnostics, allowing for non-invasive measurement and analysis of small molecules from living tissues. However, currently available MRS processing and analytical software tools are limited in their potential for in-depth quality management, access to details of the processing stream, and user friendliness. Moreover, available MRS software focuses on selected aspects of MRS such as simulation, signal processing or analysis, necessitating the use of multiple packages and interfacing among them for biomedical applications. The freeware INSPECTOR comprises enhanced MRS data processing, simulation and analytical capabilities in a one-stop-shop solution for a wide range of biomedical research and diagnostic applications. Extensive data handling, quality management and visualization options are built in, enabling the assessment of every step of the processing chain with maximum transparency. The parameters of the processing can be flexibly chosen and tailored for the specific research problem, and extended confidence information is provided with the analysis. The INSPECTOR software stands out in its user-friendly workflow and potential for automation. In addition to convenience, the functionalities of INSPECTOR ensure rigorous and consistent data processing throughout multi-experiment and multi-center studies.

scholarly journals Methods Used and Application of the Mouse Grimace Scale in Biomedical Research 10 Years On: A Scoping Review

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 673
Author(s):  
Alexandra L. Whittaker ◽  
Yifan Liu ◽  
Timothy H. Barker
Keyword(s):  
Animal Models ◽  
Mouse Models ◽  
Biomedical Research ◽  
Scoping Review ◽  
Facial Features ◽  
Inclusion Criteria ◽  
Academic Literature ◽  
Research Fields ◽  
Neuroscience Research ◽  
Wide Range

The Mouse Grimace Scale (MGS) was developed 10 years ago as a method for assessing pain through the characterisation of changes in five facial features or action units. The strength of the technique is that it is proposed to be a measure of spontaneous or non-evoked pain. The time is opportune to map all of the research into the MGS, with a particular focus on the methods used and the technique’s utility across a range of mouse models. A comprehensive scoping review of the academic literature was performed. A total of 48 articles met our inclusion criteria and were included in this review. The MGS has been employed mainly in the evaluation of acute pain, particularly in the pain and neuroscience research fields. There has, however, been use of the technique in a wide range of fields, and based on limited study it does appear to have utility for pain assessment across a spectrum of animal models. Use of the method allows the detection of pain of a longer duration, up to a month post initial insult. There has been less use of the technique using real-time methods and this is an area in need of further research.

scholarly journals Foslevodopa/Foscarbidopa Is Well Tolerated and Maintains Stable Levodopa and Carbidopa Exposure Following Subcutaneous Infusion

2021 ◽  
pp. 1-8
Author(s):  
Matthew Rosebraugh ◽  
Wei Liu ◽  
Melina Neenan ◽  
Maurizio F. Facheris
Keyword(s):  
Steady State ◽  
Phase 1 ◽  
The United States ◽  
Therapeutic Window ◽  
Fixed Dose ◽  
Advanced Parkinson’S Disease ◽  
Subcutaneous Infusion ◽  
Study Results ◽  
Wide Range ◽  
Favorable Safety

Background: Foslevodopa/foscarbidopa, formerly known as ABBV-951, is a formulation of levodopa/carbidopa prodrugs with solubility that allows for subcutaneous (SC) infusion and is in development for the treatment of motor complications for patients with advanced Parkinson’s disease (aPD). Objective: The current work characterizes the levodopa (LD) and carbidopa (CD) pharmacokinetics (PK) following SC infusions of foslevodopa/foscarbidopa delivered at four different infusion rates in PD patients. Methods: This was a Phase 1, single ascending dose, single-blind study conducted in 28 adult male and female subjects at seven sites in the United States. Foslevodopa/foscarbidopa was administered via abdominal SC infusion in PD patients over 72 hours. Patients were stratified in 4 groups and received a fixed dose of foslevodopa/foscarbidopa based on their oral daily LD intake. Serial plasma PK samples were collected to assay for LD and CD concentrations. Safety and tolerability were assessed throughout the study. Results: LD exposure quickly reached steady state and remained stable with minimal fluctuations. Foslevodopa/foscarbidopa infusion provides stable LD and CD exposures compared to oral LD/CD dosing with the average steady-state exposure ranging from 747-4660 ng/mL for the different groups. Conclusion: Foslevodopa/foscarbidopa was able to provide stable LD and CD exposures in PD patients over 72 hours via SC route of delivery with very low fluctuation in LD concentration level across a wide range of clinically relevant exposures. Foslevodopa/foscarbidopa had a favorable safety profile. The low PK fluctuation following foslevodopa/foscarbidopa infusion is expected to maintain LD exposure to treat aPD patients within a narrow therapeutic window.

Quantifying The Impact That Coxswain Behaviour Has on Whole Body Vibration - Simulator Trial

2021 ◽  
Vol 163 (A3) ◽  
Author(s):  
T J Newman
Keyword(s):  
Phase 1 ◽  
Whole Body Vibration ◽  
Whole Body ◽  
Motion Platform ◽  
Body Vibration ◽  
Sea Trial ◽  
Data Driven Approach ◽  
Exposure Levels ◽  
Transit Speed ◽  
The Impact

A common risk to personnel is from Whole Body Vibration (WBV) and shock when transiting at speed in heavy seas, and much research has been done by maritime organisations to reduce this risk and the associated health impacts. It is well known that coxswain ‘driving style’ can radically affect exposure levels for a given sea state and sustained transit speed. A data-driven approach to define what makes a good coxswain from a WBV perspective is currently being developed by the Naval Design Partnering team (NDP). In phase 1, a systematic coxswain behaviour tracking methodology has been developed and demonstrated using a motion platform-based fast craft simulator at MARIN. The performance of several experienced volunteer coxswains from MOD, RNLI and KNRM has been evaluated based on a set pattern of tests. The advantages of using the simulator, over a sea trial, have been demonstrated: it is more repeatable, more controllable, accurate and more accessible. The potential disadvantages of the approach are also discussed with reference to feedback gathered from coxswains. Analysis has shown effective throttle control is much more important than steering to reduce WBV. Several interesting trends in WBV reduction potential have been shown which it is thought, with further validation, could aid mission planning, mission execution and provide data for training autonomous feedback/control algorithms. Further work is required before the findings of this study can be fully exploited. These subsequent phases, which include sea trials, aim to provide validation and further evidence to support the initial findings.

A Comprehensive Assessment Tool for Patient Registry Software Systems: The CIPROS Checklist

2015 ◽  
Vol 54 (05) ◽  
pp. 447-454 ◽  
Author(s):  
U. Mansmann ◽  
D. Lindoerfer
Keyword(s):  
Systematic Review ◽  
Critical Appraisal ◽  
Assessment Tool ◽  
Wide Spectrum ◽  
Patient Registry ◽  
Software Systems ◽  
Software System ◽  
Review Of The Literature ◽  
Patient Registries ◽  
Wide Range

SummaryBackground: Patient registries are an important instrument in medical research. Often their structure is complex and their implementation uses composite software systems to meet the wide spectrum of challenges.Objectives: For the implementation of a registry, there is a wide range of commercial, open source, and self-developed systems available and a minimal standard for the critical appraisal of their architecture is needed.Methods: We performed a systematic review of the literature to define a catalogue of relevant criteria to construct a minimal appraisal standard.Results: The CIPROS list is developed based on 64 papers which were found by our systematic review. The list covers twelve sections and contains 72 items.Conclusions: The CIPROS list supports developers to assess requirements on existing systems and strengthens the reporting of patient registry software system descriptions. It can be a first step to create standards for patient registry software system assessments.

scholarly journals Physicians’ requirements and expectations of future Artificial Intelligence applications for healthcare – a web-based survey in German university hospitals (Preprint)

2020 ◽  
Author(s):  
Oliver Maassen ◽  
Sebastian Fritsch ◽  
Julia Gantner ◽  
Saskia Deffge ◽  
Julian Kunze ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Clinical Practice ◽  
Patient Care ◽  
Biomedical Research ◽  
Positive Attitude ◽  
Patient Data ◽  
University Hospitals ◽  
Web Based ◽  
Wide Range ◽  
Medical Disciplines

BACKGROUND The increasing development of artificial intelligence (AI) systems in medicine driven by researchers and entrepreneurs goes along with enormous expectations for medical care advancement. AI might change the clinical practice of physicians from almost all medical disciplines and in most areas of healthcare. While expectations for AI in medicine are high, practical implementations of AI for clinical practice are still scarce in Germany. Moreover, physicians’ requirements and expectations of AI in medicine and their opinion on the usage of anonymized patient data for clinical and biomedical research has not been investigated widely in German university hospitals. OBJECTIVE Evaluate physicians’ requirements and expectations of AI in medicine and their opinion on the secondary usage of patient data for (bio)medical research e.g. for the development of machine learning (ML) algorithms in university hospitals in Germany. METHODS A web-based survey was conducted addressing physicians of all medical disciplines in 8 German university hospitals. Answers were given on Likert scales and general demographic responses. Physicians were asked to participate locally via email in the respective hospitals. RESULTS 121 (39.9%) female and 173 (57.1%) male physicians (N=303) from a wide range of medical disciplines and work experience levels completed the online survey. The majority of respondents either had a positive (130/303, 42.9%) or a very positive attitude (82/303, 27.1%) towards AI in medicine. A vast majority of physicians expected the future of medicine to be a mix of human and artificial intelligence (273/303, 90.1%) but also requested a scientific evaluation before the routine implementation of AI-based systems (276/303, 91.1%). Physicians were most optimistic that AI applications would identify drug interactions (280/303, 92.4%) to improve patient care substantially but were quite reserved regarding AI-supported diagnosis of psychiatric diseases (62/303, 20.5%). 82.5% of respondents (250/303) agreed that there should be open access to anonymized patient databases for medical and biomedical research. CONCLUSIONS Physicians in stationary patient care in German university hospitals show a generally positive attitude towards using most AI applications in medicine. Along with this optimism, there come several expectations and hopes that AI will assist physicians in clinical decision making. Especially in fields of medicine where huge amounts of data are processed (e.g., imaging procedures in radiology and pathology) or data is collected continuously (e.g. cardiology and intensive care medicine), physicians’ expectations to substantially improve future patient care are high. However, for the practical usage of AI in healthcare regulatory and organizational challenges still have to be mastered.

scholarly journals Comparison and evaluation of statistical error models for scRNA-seq

2021 ◽  
Author(s):  
Saket Choudhary ◽  
Rahul Satija
Keyword(s):  
Linear Models ◽  
Negative Binomial ◽  
Statistical Error ◽  
Rna Seq ◽  
Multiple Sources ◽  
Error Models ◽  
Wide Range ◽  
Data Driven Approach ◽  
Downstream Analysis ◽  
Experimental Processing

Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple sources, including biological variation in cellular state as well as technical variation introduced during experimental processing. Deconvolving these effects is a key challenge for preprocessing workflows. Recent work has demonstrated the importance and utility of count models for scRNA-seq analysis, but there is a lack of consensus on which statistical distributions and parameter settings are appropriate. Here, we analyze 58 scRNA-seq datasets that span a wide range of technologies, systems, and sequencing depths in order to evaluate the performance of different error models. We find that while a Poisson error model appears appropriate for sparse datasets, we observe clear evidence of overdispersion for genes with sufficient sequencing depth in all biological systems, necessitating the use of a negative binomial model. Moreover, we find that the degree of overdispersion varies widely across datasets, systems, and gene abundances, and argues for a data-driven approach for parameter estimation. Based on these analyses, we provide a set of recommendations for modeling variation in scRNA-seq data, particularly when using generalized linear models or likelihood-based approaches for preprocessing and downstream analysis.

scholarly journals One score to rule them all: severity assessment in laboratory mice

2020 ◽  
Author(s):  
Steven R. Talbot ◽  
Birgitta Struve ◽  
Laura Wassermann ◽  
Miriam Heider ◽  
Nora Weegh ◽  
...  
Keyword(s):  
Heart Rate ◽  
Animal Welfare ◽  
Biomedical Research ◽  
Restraint Stress ◽  
Assessment Tool ◽  
Postoperative Recovery ◽  
Assessment System ◽  
Severity Assessment ◽  
Severity Levels ◽  
Individual Variables

AbstractAnimal welfare and the refinement of experimental procedures are fundamental aspects of biomedical research. They provide the basis for robust experimental designs and reproducibility of results. In many countries, the determination of welfare is a mandatory legal requirement and implies the assessment of the degree of the severity that an animal experiences during an experiment. However, for an effective severity assessment, an objective and exact approach/system/strategy is needed. In light of these demands, we have developed the Relative Severity Assessment (RELSA) score.This comprehensive composite score was established on the basis of physiological and behavioral data from a surgical mouse study. Body weight, the Mouse Grimace Scale score, burrowing behavior, and the telemetry-derived parameters heart rate, heart rate variability, temperature, and general activity were used to investigate the quality of indicating severity during postoperative recovery. The RELSA scores not only revealed individual severity levels but also allowed a comparison of severity in distinct mouse models addressing colitis, sepsis, and restraint stress using a k-means clustering approach with the maximum achieved RELSA scores.We discriminated and classified data from sepsis nonsurvivors into the highest relative severity level. Data from mice after intraperitoneal transmitter implantation and sepsis survivor al were located in the next lower cluster, while data from mice subjected to colitis and restraint stress were placed in the lowest severity cluster. Analysis of individual variables and their combinations revealed model- and time-dependent contributions to severity levels.In conclusion, we propose the RELSA score as a validated tool for objective real-time applicability in severity assessment and as a first step towards a unified and accessible risk assessment tool in biomedical research. As an effective severity assessment system, it will fundamentally improve animal welfare, as well as data quality and reproducibility.

Sign in / Sign up

Export Citation Format

Share Document