Nevin Manimala

PLoS One. 2021 May 10;16(5):e0244122. doi: 10.1371/journal.pone.0244122. eCollection 2021.

ABSTRACT

During last years “irreproducibility” became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools. We describe the main functionalities and illustrate the organization of an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we show how to use easyreporting in other projects to trace R functions automatically. This latter feature helps developers to implement procedures that automatically keep track of the analysis steps. Easyreporting can be useful in supporting the reproducibility of any data analysis project and shows great advantages for the implementation of R packages and GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.

PMID:33970927 | DOI:10.1371/journal.pone.0244122

PLoS One. 2021 May 10;16(5):e0240706. doi: 10.1371/journal.pone.0240706. eCollection 2021.

ABSTRACT

Hibernating mammals exhibit unique metabolic and physiological phenotypes that have potential applications in medicine or spaceflight, yet our understanding of the genetic basis and molecular mechanisms of hibernation is limited. The meadow jumping mouse, a small North American hibernator, exhibits traits-including a short generation time-that would facilitate genetic approaches to hibernation research. Here we report the collection, captive breeding, and laboratory hibernation of meadow jumping mice. Captive breeders in our colony produced a statistically significant excess of male offspring and a large number of all-male and all-female litters. We confirmed that short photoperiod induced pre-hibernation fattening, and cold ambient temperature facilitated entry into hibernation. During pre-hibernation fattening, food consumption exhibited non-linear dependence on both body mass and temperature, such that food consumption was greatest in the heaviest animals at the coldest temperatures. Meadow jumping mice exhibited a strong circadian rhythm of nightly activity that was disrupted during the hibernation interval. We conclude that it is possible to study hibernation phenotypes using captive-bred meadow jumping mice in a laboratory setting.

PMID:33970917 | DOI:10.1371/journal.pone.0240706

Acta Otorhinolaryngol Ital. 2021 May 6. doi: 10.14639/0392-100X-N1229. Online ahead of print.

ABSTRACT

OBJECTIVE: The changing trends in medical practice, uncertainties and monetary apprehensions due to the COVID-19 pandemic may influence the sense of well-being among otorhinolaryngologists. The present study was conducted to evaluate quality of life (QOL) and perceived financial implications in otorhinolaryngologists during the COVID-19 pandemic across India.

METHODS: A cross-sectional study was carried out among otorhinolaryngology specialists across India using WHOQOL-BREF and Consumer Financial Protection Bureau (CFPB) Financial Well-Being Scale questionnaires on Google Forms, which was kept open for the latter half of July 2020.

RESULTS: A total of 358 responses were obtained; the response rate was 26.64%. Twenty-four percent of respondents worked exclusively in academic settings; 40.22% of specialists had over 10 years of work experience. Average monthly income in 2019 was between 1-3 lakhs Indian Rupees (INR) in 43.85%, while in 2020, 62.57% of the specialists had an average monthly income of below one lakh INR; this difference was statistically significant (p < 0.001). Mean WHOQOL-BREF scores for physical, psychological, social and environmental domains were 68.8 ± 1, 62.3 ± 0.75, 68.9 ± 1.17 and 65.8 ± 1.01, respectively; mean CFPB financial well-being scale score was 55.5 ± 0.66. QOL and financial well-being were better in otolaryngologists older than 60 years, male specialists and private consultants.

CONCLUSIONS: There has been a tremendous impact on quality of life and financial well-being among otorhinolaryngologists in India during the COVID-19 pandemic. The study outcome may help otolaryngologists comprehend and perceive the extent to which it has affected their professional and personal lives, and explore ways to face and overcome the situation.

PMID:33970895 | DOI:10.14639/0392-100X-N1229

J Vet Med Educ. 2021 May 10:e20200105. doi: 10.3138/jvme-2020-0105. Online ahead of print.

ABSTRACT

Neuropathology is a challenging subject for most medical students. Delivering a gamified learning tool on this topic may motivate students and increase knowledge in the discipline. We report the development of such a tool in iBook format for the systemic pathology course delivered at Ross University School of Veterinary Medicine. Composed of 10 chapters (cases), this Neuropathology iBook (NP-iB) reviews basic clinical manifestations, neuropathology, and pathogenesis of common non-neoplastic conditions that cause brain disease in domestic animals. The goal of each chapter is to reach a diagnosis by interactively answering specific questions after reviewing relevant medical history, clinical pathology, and autopsy findings. Our hypothesis: the NP-iB improves students’ ability to recognize these diseases, reflected in higher test scores. Using a post-test only control group design, data were gathered from all students enrolled in the course in two different semesters, fall 2017 and spring 2018 (n = 300). NP-iB users (n = 51, 17%) and usage time were identified by answers to multiple-choice questions embedded in the course assessments. Ninety percent of users had a positive perception although no statistically significant differences were found in median test scores between users and non-users. Statistically significant test score differences were found across how much time students used the NP-iB (p = .005); the lowest test score median values were found for neuropathology questions not related to the NP-iB, in students who used it for more than 3 hours. Unexpectedly, a low number of students preferred this digital learning tool, and its use did not improve their learning outcomes.

PMID:33970836 | DOI:10.3138/jvme-2020-0105

Med Ref Serv Q. 2021 Apr-Jun;40(2):151-167. doi: 10.1080/02763869.2021.1912567.

ABSTRACT

Between 2018 and 2019, the librarians at the Strauss Health Sciences Library improved the efficiency and reach of their reference service by implementing four small-scale changes. These changes included revising the method of collecting statistics, creating FAQs, utilizing an appointment scheduler, and launching proactive chat. This case study will provide the background and research to support these changes, details on how the changes were implemented using Springshare tools, as well as the results and implications. Finally, the librarians will share their lessons learned along with recommendations for institutions interested in adopting similar changes.

PMID:33970824 | DOI:10.1080/02763869.2021.1912567

Arch Environ Occup Health. 2021 May 10:1-7. doi: 10.1080/19338244.2021.1919857. Online ahead of print.

ABSTRACT

Silicosis is one of the major occupational lung diseases among miners worldwide. The objective of this study was to characterize respirable dust and crystalline silica from limestone, iron, and bauxite mines in India. In total, 86 personal dust samples were collected from limestone (n = 30), iron (n = 30), and bauxite (n = 26) mines using dust sampler. The concentration of crystalline silica was analyzed using FTIR spectroscopy. Geometric mean respirable dust concentrations observed were 0.92, 1.08, and 1.07 mg/m³ for limestone, iron, and bauxite mines respectively, similarly for crystalline silica concentration observations were 0.015, 0.012 and 0.008 mg/m³ respectively. Among the three studied ores, mean crystalline silica concentration was statistically significant (p < 0.05) using an analysis of variance test. Although the detected levels of exposure are within the Indian exposure limits, attention should be paid to lower crystalline silica levels to minimize the risk of silicosis.

PMID:33970811 | DOI:10.1080/19338244.2021.1919857

J Biomol Struct Dyn. 2021 May 10:1-21. doi: 10.1080/07391102.2021.1924271. Online ahead of print.

ABSTRACT

The main-protease (M^pro) catalyzes a crucial step for the SARS-CoV-2 life cycle. The recent SARS-CoV-2 presents the main protease (M^CoV2_pro) with 12 mutations compared to SARS-CoV (M^CoV1_pro). Recent studies point out that these subtle differences lead to mobility variances at the active site loops with functional implications. We use metadynamics simulations and a sort of computational analysis to probe the dynamic, pharmacophoric and catalytic environment differences between the monomers of both enzymes. So, we verify how much intrinsic distinctions are preserved in the functional dimer of M^CoV2_pro, as well as its implications for ligand accessibility and optimized drug screening. We find a significantly higher accessibility to open binding conformers in the M^CoV2_pro monomer compared to M^CoV1_pro. A higher hydration propensity for the M^CoV2_pro S2 loop with the A46S substitution seems to exercise a key role. Quantum calculations suggest that the wider conformations for M^CoV2_pro are less catalytically active in the monomer. However, the statistics for contacts involving the N-finger suggest higher maintenance of this activity at the dimer. Docking analyses suggest that the ability to vary the active site width can be important to improve the access of the ligand to the active site in different ways. So, we carry out a multiconformational virtual screening with different ligand bases. The results point to the importance of taking into account the protein conformational multiplicity for new promissors anti M^CoV2_pro ligands. We hope these results will be useful in prospecting, repurposing and/or designing new anti SARS-CoV-2 drugs.Communicated by Ramaswamy H. Sarma.

PMID:33970798 | DOI:10.1080/07391102.2021.1924271

Int J Radiat Biol. 2021 May 10:1-33. doi: 10.1080/09553002.2021.1917786. Online ahead of print.

ABSTRACT

PURPOSE: Risks of occupational radiation exposures of workers involved in uranium refining and processing (“uranium processing workers“) may be different from risks of other workers from the nuclear fuel cycle. Pooling of individual-level data from published studies and analysis using similar dosimetry and statistical methods might provide valuable insights into risks from occupational uranium and external ionizing radiation exposures.

METHODS: We pooled the data for workers from four uranium processing facilities (Fernald Feed Materials Production Center, Ohio; Mallinckrodt Chemical Works Uranium Division, Missouri; Middlesex Sampling Plant, New Jersey; and the Port Hope Radium and Uranium Refining and Processing Plant, Canada). Employment began as early as the 1930s in Canada and follow-up for vital status was as late as 2017. These facilities used similar methods to process Belgian Congo pitchblende ore which contained high concentrations of uranium, radium, and their decay products. In addition, workers were exposed to elevated levels of gamma radiation, fission product contaminants in recycled uranium and ambient radon decay products. Non-radiation exposures of industrial hygiene concern were silica dust inhalation, heavy metal toxicity from uranium, solvents, acid mists and chemicals associated with uranium processing. Exposure and outcome data were harmonized using similar definitions and dose reconstruction methods. Standardized mortality ratios (SMR) were estimated by comparing mortality in the pooled cohort with age-, sex- and calendar time-specific general population mortality rates for the U.S. and Canada.

RESULTS: Over 12,400 workers will be evaluated for cancer and non-cancer mortality in relation to exposures to uranium byproducts and gamma radiation (including ∼1,300 females). In total, death from 560 lung cancers, 503 nonmalignant respiratory diseases, 67 renal diseases, 1,596 ischemic heart diseases, and 101 dementia and Alzheimer’s diseases (AD) were detected among male workers during follow-up. Mean cumulative doses were 45 millisievert for whole-body external exposures and 172 milligray for lung dose from radon decay products. Of the 16 pooled SMRs, seven were above 1.00, none were significantly low, and only one was significantly high, i.e., dementia and AD among males (SMR =1.29; 95% confidence interval: 1.04,1.54).

CONCLUSIONS: This is the largest study to date to examine health risks in uranium processing workers (excluding uranium enrichment workers). The pooling of uranium processing worker data will address issues of importance today, specifically the concerns for cleanup workers and environmental contamination from the operation of past and present nuclear reactor and radiation facilities, reactor accidents, and possible terrorist events.

PMID:33970767 | DOI:10.1080/09553002.2021.1917786

Stat Methods Med Res. 2021 May 10:9622802211009265. doi: 10.1177/09622802211009265. Online ahead of print.

ABSTRACT

This functional joint model paper is motivated by a chronic kidney disease study post kidney transplantation. The available kidney organ is a scarce resource because millions of end-stage renal patients are on the waiting list for kidney transplantation. The life of the transplanted kidney can be extended if the progression of the chronic kidney disease stage can be slowed, and so a major research question is how to extend the transplanted kidney life to maximize the usage of the scarce organ resource. The glomerular filtration rate is the best test to monitor the progression of the kidney function, and it is a continuous longitudinal outcome with repeated measures. The patient’s survival status is characterized by time-to-event outcomes including kidney transplant failure, death with kidney function, and death without kidney function. Few studies have been carried out to simultaneously investigate these multiple clinical outcomes in chronic kidney disease stage patients based on a joint model. Therefore, this paper proposes a new functional joint model from this clinical chronic kidney disease study. The proposed joint models include a longitudinal sub-model with a flexible basis function for subject-level trajectories and a competing-risks sub-model for multiple time-to event outcomes. The different association structures can be accomplished through a time-dependent function of shared random effects from the longitudinal process or the whole longitudinal history in the competing-risks sub-model. The proposed joint model that utilizes basis function and competing-risks sub-model is an extension of the standard linear joint models. The application results from the proposed joint model can supply some useful clinical references for chronic kidney disease study post kidney transplantation.

PMID:33970050 | DOI:10.1177/09622802211009265