Some teaching resources using R with illustrative examples exploring COVID‐19 data
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ABSTRACT:
SUBMITTER: Berg A
PROVIDER: S-EPMC8447407 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Obesity is a significant health problem in westernized societies, particularly in the United States where it has reached epidemic proportions in both adults and children. The prevalence of childhood obesity has doubled in the past 30 years. The causation is complex with multiple sources, including an obesity promoting environment with plentiful highly dense food sources and overall decreased physical activity noted for much of the general population, but genetic factors clearly play a role. Advances in genetic technology using candidate gene approaches, genome-wide association studies, structural and expression microarrays, and next generation sequencing have led to the discovery of hundreds of genes recognized as contributing to obesity. Polygenic and monogenic causes of obesity are now recognized including dozens of examples of syndromic obesity with Prader-Willi syndrome, as a classical example and recognized as the most common known cause of life-threatening obesity. Genetic factors playing a role in the causation of obesity will be discussed along with the growing evidence of single genes and the continuum between monogenic and polygenic obesity. The clinical and genetic aspects of four classical but rare obesity-related syndromes (ie, Prader-Willi, Alström, fragile X, and Albright hereditary osteodystrophy) will be described and illustrated in this review of single gene and syndromic causes of obesity.
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Project description:Autocatalytic reactions are in certain contrast with the linear algebra of reaction stoichiometry, on which rate equations respecting the permanence of atoms are constructed. These mathematical models of chemical reactions are called conservative. Using a non-equilibrium thermodynamics-based theory of chemical kinetics, it is shown how to introduce autocatalytic step into such (conservative) rate equation properly. Further, rate equations based on chemical potentials or affinities are derived, and conditions for the consistency of rate equations with the entropic inequality (the second law of thermodynamics) are illustrated. The theory illustrated here can be viewed as a tool for verifying and generalizing traditional mass-action kinetics by means of modern non-equilibrium thermodynamics, which is able to deal also with such rather problematic cases.
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Project description:BackgroundA considerable amount of various types of data have been collected during the COVID-19 pandemic, the analysis and understanding of which have been indispensable for curbing the spread of the disease. As the pandemic moves to an endemic state, the data collected during the pandemic will continue to be rich sources for further studying and understanding the impacts of the pandemic on various aspects of our society. On the other hand, naïve release and sharing of the information can be associated with serious privacy concerns.MethodsWe use three common but distinct data types collected during the pandemic (case surveillance tabular data, case location data, and contact tracing networks) to illustrate the publication and sharing of granular information and individual-level pandemic data in a privacy-preserving manner. We leverage and build upon the concept of differential privacy to generate and release privacy-preserving data for each data type. We investigate the inferential utility of privacy-preserving information through simulation studies at different levels of privacy guarantees and demonstrate the approaches in real-life data. All the approaches employed in the study are straightforward to apply.ResultsThe empirical studies in all three data cases suggest that privacy-preserving results based on the differentially privately sanitized data can be similar to the original results at a reasonably small privacy loss ([Formula: see text]). Statistical inferences based on sanitized data using the multiple synthesis technique also appear valid, with nominal coverage of 95% confidence intervals when there is no noticeable bias in point estimation. When [Formula: see text] and the sample size is not large enough, some privacy-preserving results are subject to bias, partially due to the bounding applied to sanitized data as a post-processing step to satisfy practical data constraints.ConclusionsOur study generates statistical evidence on the practical feasibility of sharing pandemic data with privacy guarantees and on how to balance the statistical utility of released information during this process.
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Project description:The unrestricted use of antibiotics has resulted in rapid acquisition of antibiotic resistance (AR) and spread of multidrug-resistant (MDR) bacterial pathogens. With the advent of next-generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. However, due to the absence of a centralized platform for AR gene resources, availability, consistency, and accuracy of information vary considerably across different databases. In this article, we explore existing AR gene data resources in order to make them more visible to the clinical microbiology community, to identify their limitations, and to propose potential solutions.
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Project description:The COVID-19 pandemic has challenged undergraduate instructors and students in an unprecedented manner. Each has needed to find creative ways to continue the engaged teaching and learning process in an environment defined by physical separation and emotional anxiety and uncertainty. As a potential tool to meet this challenge, we developed a set of curricular materials that combined our respective life science teaching interests with the real-time scientific problem of the COVID-19 pandemic in progress. Discrete modules were designed that are engaging to students, implement active learning-based coursework in a variety of institutional and learning settings, and can be used either in person or remotely. The resulting interdisciplinary curriculum, dubbed "COVID-360," enables instructors to select from a menu of curricular options that best fit their course content, desired activities, and mode of class delivery. Here we describe how we devised the COVID-360 curriculum and how it represents our efforts to creatively and effectively respond to the instructional needs of diverse students in the face of an ongoing instructional crisis.
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Project description:A growing body of literature suggests that students from underserved backgrounds are more vulnerable to the adverse economic, emotional, and academic effects of the current COVID-19 pandemic. While this vulnerability was attributed to multiple structural and socio-cultural barriers, little attention has been paid to the role of psychological resources in preserving wellbeing in times of crisis and change. Guided by the Self-Determination Theory (SDT), the current study examined the role of the authentic inner compass (AIC) and need-satisfaction in predicting the wellbeing of Bedouin students attending teachers' higher education institutes in the south of Israel during the COVID-19. Participants were 84 Bedouin teaching students (84.1% female) who completed online questionnaires addressing the sense of AIC, need-based experiences, psychological distress, and positive affect. Consistent with the propositions of the SDT, we found that a strong and clear sense of AIC, as well as high need satisfaction and low need frustration, were associated with lower distress and higher positive effect in Bedouin teaching students. We have also found that need satisfaction moderated the effect of the AIC on students' wellbeing so that AIC better predicted lower distress and higher positive effect when students' levels of need satisfaction were higher. Our findings lend further support to the importance of the AIC and need satisfaction to optimal functioning even in collectivist cultural contexts that do not prioritize values of autonomy. The current study provides insight into the interplay between AIC and need-based experience by describing the conditions under which AIC may be beneficial for wellbeing in times of crisis.
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Project description:BackgroundThe Japanese age-standardised death rate of suicide (SDR) had decreased during 2009-2019, but increased in 2020-2021, during the COVID-19 pandemic.MethodsThis study aimed to explain the trend change in the SDR during the pandemic, disaggregated by prefecture, gender, suicide method and household, as compared to predicted SDR derived from pre-pandemic data, using linear mixed-effect and hierarchical linear regression models with robust standard error analyses.FindingsThe SDR was lower during March-June 2020 (during the first wave of the pandemic), but higher during July-December 2020 than the predicted SDR. In 2021, males' SDR was nearly equal to the predicted SDR, whereas females' SDR in the metropolitan-region (17.5%: 95% confidence interval: 13.9-21.2%) and non-metropolitan-region (24.7%: 95% confidence interval: 22.8-26.7%) continued to be higher than the predicted SDR. These gender- and region-dependent temporal fluctuations of SDR were synchronised with those of SDRs caused by hanging, at home and single-person-households. Additionally, the rising number of infected patients with the SARS-CoV-2 and polymerase chain reaction (PCR) diagnostic examinations were positively (β = 0.024) and negatively (β =-0.002) related to the SDR during the pandemic, respectively.InterpretationJapanese suicide statistics have previously established that the predominant method and place of suicide were by hanging and at the individual's home, respectively. The present findings suggest that transformed lifestyles during the pandemic, increasing time spent at home, enhanced the suicide risk of Japanese people by hanging and at home.FundingRegional Suicide Countermeasures Emergency Enhancement Fund of Mie Prefecture (2021-40).
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Project description:The COVID-19 crisis impacts populations globally. This impact seems to differ for groups with low- and high-socioeconomic status (SES). We conducted a qualitative study in the Netherlands using a salutogenic perspective to examine experiences with stressors and coping resources during the pandemic among both SES groups to gain insight on how to promote the health and well-being of these groups. We conducted 10 focus group discussions and 20 interviews to explore the experiences, including resources and stressors, of respondents from low- (N = 37) and high-SES (N = 38) groups (25-55 years, Dutch speaking). We analyzed the findings at individual, community, and national levels. The results show that coping depends on government-imposed measures and the way individuals handle these measures; restriction to the home context with positive and negative consequences for work and leisure; psychological negative consequences and resourcefulness; and social effects related to unity (e.g. social cohesion or support) and division (including polarization). Respondents with lower SES expressed more problems with COVID-19 measures and experienced more social impact in their neighborhood than those with higher SES. Where low-SES groups especially mentioned the effects of staying at home on family life, high-SES groups mentioned effects on work life. At last, psychological consequences seem to differ somewhat across SES groups. Recommendations include consistent government-imposed measures and government communication, support for home schooling children, and strengthening the social fabric of neighborhoods.
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Project description:The appropriate focus in managing the COVID-19 pandemic in the United States has been addressing access and delivery of care to the population affected by the outbreak. All sectors of the U.S. economy have been significantly affected, including physicians. Physician groups of all specialties and sizes have experienced the financial effects of the pandemic. Hospitals have received billions of dollars to support and enable them to manage emergencies and cover the costs of the disruption. However, many vascular surgeons are under great financial pressure because of the postponement of all nonemergency procedures. The federal government has announced a myriad of programs in the form of grants and loans to reimburse physicians for some of their expenses and loss of revenue. It is more than likely that unless the public health emergency subsides significantly, many practices will experience dire consequences without additional financial assistance. We have attempted to provide a concise listing of such programs and resources available to assist vascular surgeons who are small businesses in accessing these opportunities.
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