bluuebunny/crossref_metadata_2025_split huggingface dataset:
Does coaching in the 3rd year of medical school affect stress, anxiety and depression?
Authors: Ross Elizabeth , Faw Timothy , Covington Kyle 
Published: July 2021

AbstractBackgroundMedical students experience significant stress and anxiety during undergraduate education. Coaching is a possible way of supporting these students throughout this challenging time. To assess the benefits of coaching for medical students, a pilot study providing coaching was performed. This pilot assessed how coaching affected the mental health of medical students and how coaching was received by them.MethodsTwelve third-year medical students were each given eight 30-60 minute coaching sessions. Each participant took the Hospital Anxiety and Depression Scale (HADS) and the Perceived Stress Scale (PSS) pre-, mid-and post-coaching. After coaching, there were three open-ended questions to measure the reactions to coaching and a scale to determine the likelihood of accessing coaching in the future.ResultsThere was a significant effect of coaching on perceived stress(p=.023); a trend toward significant effect of coaching on anxiety(p=.057); and no effect of coaching on depression. Qualitative analysis indicated Affective responses (gaining perspective and self-awareness); Cognitive responses (goal setting and working through solving problems); and Skills responses (developing reflection abilities and critical thinking). Attributes of coaching included perceiving coaching as a positive, individualized and supportive experience that students were highly likely to access again.ConclusionsCoaching holds promise as an intervention offered to medical students to reduce stress and anxiety, and provide positive support for students, preparing them for their professional futures.Key PointsAppreciate the stress and anxiety that medical students manage in medical school.Coaching is an option that holds promise to support medical students.Coaching has possible long-term outcomes that could help future physicians navigate their professional paths more effectively.Students value individualized, positive support during medical school
Genome Alert!: a standardized procedure for genomic variant reinterpretation and automated genotype-phenotype reassessment in clinical routine
Authors: Yauy Kevin , Lecoquierre François , Baert-Desurmont Stéphanie , Trost Detlef , Boughalem Aicha , Luscan Armelle , Costa Jean-Marc , Geromel Vanna , Raymond Laure , Richard Pascale , Coutant Sophie , Broutin Mélanie , Lanos Raphael , Fort Quentin , Cackowski Stenzel , Testard Quentin , Diallo Abdoulaye , Soirat Nicolas , Holder Jean-Marc , Duforet-Frebourg Nicolas , Bouge Anne-Laure , Beaumeunier Sacha , Bertrand Denis , Audoux Jerome , Genevieve David , Mesnard Laurent , Nicolas Gael , Thevenon Julien , Philippe Nicolas 
Published: July 2021

AbstractNumerous countries have set up population genomics plans, allowing an unprecedented growth in the ability of interpreting variants in human diseases. Retrospective interpretation of sequenced data in the light of the current literature is a major concern of the field. Moreover, such reinterpretation is manual and both the human resources and the variable operating procedures are main bottlenecks.This work describes the Genome Alert! standardized procedure. This open-source method automatically reports changes with potential clinical significance in variant classification between releases of the ClinVar database. Using ClinVar submissions across time, this method assigns gene-disease associations validity category. Genome Alert! was assessed on a retrospective 29 months multicentric series of 5,959 consecutive individuals screened by targeted or exome sequencing.Between July 2017 and December 2019, the retrospective analysis of ClinVar submissions revealed a monthly median of 1,247 changes in variant classification with potential clinical significance and 23 new gene-disease associations. Reexamination of 4,929 targeted sequencing files highlighted 45 changes, which 89% classifications were expert validated, leading to four additional diagnoses. Genome Alert! gene-disease association catalog provided 75 high-confidence associations not available in the OMIM morbid list, where 20% became OMIM morbid 8 months later. Over 356 negative exome sequencing data that were reannotated for variants in these 75 genes, this elective approach led to a new diagnosis.Genome Alert! (https://genomealert.univ-grenoble-alpes.fr/) enables the systematic and reproducible reinterpretation of acquired sequencing data in a clinical routine with a limited human resource impact.Graphical abstract
hnRNPA1 regulates early translation to replication switch in SARS-CoV-2 life cycle
Authors: Kumar Ram , Chander Yogesh , Khandelwal Nitin , Nagori Himanshu , Verma Assim , Pal Yash , Gulati Baldev R. , Tripathi Bhupendra N. , Barua Sanjay , Kumar Naveen 
Published: July 2021

ABSTRACTOur study suggests that methylation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is essential for its optimal replication in the target cells. Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1, an RNA-binding protein) was shown to mediate deposition of N6-methyladenosine (m6A) in internal SARS-CoV-2 RNA. The levels of hNRNPA1 expression and extent of methylation varied, depending on the course of SARS-CoV-2 life cycle. The recruitment of eIF4E (translational initiation factor) facilitated viral RNA translation at 1 hour post infection (1 hpi). However, at 2 hpi, methylation of internal SARS-CoV-2 RNA recruited hNRNPA1 which facilitated viral RNA transcription but resulted in translational repression, a phenomenon contributing in understanding the early translation to replication switch in the viral life cycle. Besides, the abrogation of methylation also produced a defective 5’ cap of viral RNA which failed to interact with eIF4E, thereby resulting in a decreased synthesis of viral proteins. To conclude, methylation of the internal and 5’ cap of SARS-CoV-2 RNA was shown to regulate transcription and translation of SARS-CoV-2 in a time dependent manner.IMPORTANCERNA modifications are found in all life forms and have been linked to development, health and diseases. Our study reveals that internal SARS-CoV-2 RNA methylation (m6A) is essential for interaction with hNRNPA1 to effectively synthesize viral genome. Besides, m6A-marked RNA and hRNPA1 interaction was also shown to regulate early translation to replication switch in SARS-CoV-2 life cycle. Blocking SARS-CoV-2 RNA methylation resulted in reduced virus yield, suggesting epitranscriptomic machinery (methylation) facilitates SARS-CoV-2 replication and might represent potential target for new antiviral drugs against COVID-19.
Antibody persistence and neutralising activity in primary school students and staff: prospective active surveillance, June to December 2020, England
Authors: Ireland Georgina , Jeffery-Smith Anna , Zambon Maria , Hoschler Katja , Harris Ross , Poh John , Baawuah Frances , Beckmann Joanne , Okike Ifeanyichukwu O , Ahmad Shazaad , Garstang Joanna , Brent Andrew J , Brent Bernadette , Aiano Felicity , Amin-Chowdhury Zahin , Letley Louise , Jones Samuel E I , Kall Meaghan , Patel Monika , Gopal Robin , Borrow Ray , Linley Ezra , Amirthalingam Gayatri , Brown Kevin E , Ramsay Mary E , Ladhani Shamez N 
Published: July 2021

AbstractIntroductionSARS-CoV-2 serological studies have so far focused mainly on adults. Public Health England initiated prospective, longitudinal SARS-CoV-2 sero-surveillance in schools across England after the first national lockdown, which allowed comparison of child and adult responses to SARS-CoV-2 infection over time.MethodsStaff and students had venepuncture for SARS-CoV-2 antibodies in school during June, July and December 2020. Blood samples were tested for nucleocapsid (Abbott) and receptor binding domain (RBD) antibodies (in-house assay), and student samples were additionally assessed for live virus neutralising activity.ResultsIn June 2020, 1,344 staff and 835 students were tested. Overall, 11.5% (95% CI: 9.4-13.9) and 11.3% (95% CI: 9.2-13.6; p=0.88) of students had nucleoprotein and RBD antibodies, compared to 15.6% (95% CI: 13.7-17.6) and 15.3% (95% CI: 13.4-17.3; p=0.83) of staff. Live virus neutralising activity was detected in 79.8% (n=71/89) of nucleocapsid and 85.5% (71/83) of RBD antibody positive children. RBD antibodies correlated more strongly with neutralising antibodies (rs=0.7527; p<0.0001) than nucleocapsid antibodies (rs=0.3698; p<0.0001). A median of 24.4 weeks later, 58.2% (107/184) participants had nucleocapsid antibody seroreversion, compared to 20.9% (33/158) for RBD (p<0.001). Similar seroreversion rates were observed between staff and students for nucleocapsid (p=0.26) and RBD-antibodies (p=0.43). Nucleocapsid and RBD antibody quantitative results were significantly lower in staff compared to students (p=0.028 and <0.0001 respectively) at baseline, but not at 24 weeks (p=0.16 and p=0.37, respectively).ConclusionRBD antibodies correlated more strongly with live virus neutralising activity. Most seropositive students and staff retained RBD antibodies for >6 months after SARS-CoV-2 infection.
Supra-physiological levels of Gibberellins/DELLAs alter the patterning, morphology and abundance of root hairs in root tips of A. thaliana seedlings
Authors: McCarthy-Suárez Iva 
Published: July 2021

ABSTRACTIn spite of the known role of gibberellins (GAs), and of their antagonistic proteins, the DELLAs, in leaf hair production, no investigations, however, have assessed their hypothetical function in the production of root hairs. To this aim, the effects of supra-physiological levels of GAs/DELLAs on the spatial patterning of gene expression of the root hair (CPC) and root non-hair (GL2, EGL3 and WER) epidermal cell fate markers, as well as on the distribution, morphology and abundance of root hairs, were studied in root tips of 5-day-old A. thaliana seedlings. Results showed that excessive levels of GAs/DELLAs impaired the spatial patterning of gene expression of the root hair/non-hair epidermal cell fate markers, as well as the arrangement, shape and frequency of root hairs, giving rise to ectopic hairs and ectopic non-hairs, two-haired cells, two-tipped hairs, branched hairs, longer and denser hairs near the root tip under excessive DELLAs, and shorter and scarcer hairs near the root tip under excessive GAs. However, when the gai-1 (GA-insensitive-1) DELLA mutant protein was specifically over-expressed at the root epidermis, no changes in the patterning or abundance of root hairs occurred. Thus, these results suggest that, in seedlings of A. thaliana, the GAs/DELLAs might have a role in regulating the patterning, morphology and abundance of root hairs by acting from the sub-epidermal tissues of the root.
A completely parameter-free method for graph-based single cell RNA-seq clustering
Authors: Zand Maryam , Ruan Jianhua 
Published: July 2021

AbstractSingle-cell RNA sequencing (scRNAseq) offers an unprecedented potential for scrutinizing complex biological systems at single cell resolution. One of the most important applications of scRNAseq is to cluster cells into groups of similar expression profiles, which allows unsupervised identification of novel cell subtypes. While many clustering algorithms have been tested towards this goal, graph-based algorithms appear to be the most effective, due to their ability to accommodate the sparsity of the data, as well as the complex topology of the cell population. An integral part of almost all such clustering methods is the construction of a k-nearest-neighbor (KNN) network, and the choice of k, implicitly or explicitly, can have a profound impact on the density distribution of the graph and the structure of the resulting clusters, as well as the resolution of clusters that one can successfully identify from the data. In this work, we propose a fairly simple but robust approach to estimate the best k for constructing the KNN graph while simultaneously identifying the optimal clustering structure from the graph. Our method, named scQcut, employs a topology-based criterion to guide the construction of KNN graph, and then applies an efficient modularity-based community discovery algorithm to predict robust cell clusters. The results obtained from applying scQcut on a large number of real and synthetic datasets demonstrated that scQcut —which does not require any user-tuned parameters—outperformed several popular state-of-the-art clustering methods in terms of clustering accuracy and the ability to correctly identify rare cell types. The promising results indicate that an accurate approximation of the parameter k, which determines the topology of the network, is a crucial element of a successful graph-based clustering method to recover the final community structure of the cell population.AvailabilityScQcut is written in both Matlab and Python and maybe be accessed through the links below.Matlab version: cs.utsa.edu/ jruan/scQcutPython version: https://github.com/mary77/scQcutContactJianhua.ruan@utsa.edu
Dynamic variations of resting-state BOLD signal spectra in white matter
Authors: Li Muwei , Gao Yurui , Anderson Adam W. , Ding Zhaohua , Gore John C. 
Published: July 2021

AbstractRecent studies have demonstrated that the mathematical model used for analyzing and interpreting fMRI data in gray matter (GM) is inappropriate for detecting or describing blood-oxygenation-level-dependent (BOLD) signals in white matter (WM). In particular the hemodynamic response function (HRF) which serves as the regressor in general linear models is different in WM compared to GM. We recently reported measurements of the frequency contents of resting-state time courses in WM that showed distinct power spectra which depended on local structural-vascular-functional associations. In addition, multiple studies of GM have revealed how functional connectivity between regions, as measured by the correlation between BOLD time series, varies dynamically over time. We therefore investigated whether and how BOLD signals from WM in a resting state varied over time. We measured voxel-wise spectrograms, which reflect the time-varying spectral patterns of WM time courses. The results suggest that the spectral patterns are non-stationary but could be categorized into five modes that recurred over time. These modes showed distinct spatial distributions of their occurrences and durations, and the distributions were highly consistent across individuals. In addition, one of the modes exhibited a strong coupling of its occurrence between GM and WM across individuals, and two communities of WM voxels were identified according to the hierarchical structures of transitions among modes. Moreover, the total number of transitions in each community predicts specific human behaviors. Last, these modes are coupled to the shape of instantaneous HRFs. Our findings extend previous studies and reveal the non-stationary nature of spectral patterns of BOLD signals over time, providing a spatial-temporal-frequency characterization of resting-state signals in WM.
Effect of Criminalization of Drink-Driving on Road Traffic Mortality in China
Authors: Sha Feng , Li Bingyu , Tang Jinling 
Published: July 2021

AbstractTo evaluate the national effect of CDD on reducing road traffic mortality, we analyzed crude road traffic mortality rates data collected between 2006 and 2016 through China’s National Disease Surveillance System. Linear regression models were fit with the pre-CDD data (2006-2011) and used to predict mortality rates in the post-CDD years (2012-2016). It is estimated that the new law was associated with 317,197 (95% CI: 280,425∼353,968) lives saved in the entire country in the first 5-years of the new law. Similar reduction in mortality rates was observed in both urban and rural areas. The decline in non-occupants was more prominent and occurred earlier than that in occupants, among whom the road traffic mortality rate did not show a statistically significant reduction in the first 4 years of the new law. Our study shows that CDD is particularly effective in protecting non-occupants and is equally effective in both rural and urban areas in China.
Fecal microbiota transplantation increases colonic IL-25 and dampens tissue inflammation in patients with recurrentClostridioides difficile
Authors: Jan Ning-Jiun , Oakland Noah , Kumar Pankaj , Ramakrishnan Girija , Behm Brian W. , Petri William A. , Marie Chelsea 
Published: July 2021

ABSTRACTBackgroundClostridioides difficileinfection (CDI) is the most common hospital-acquired infection in the United States. Antibiotic-induced dysbiosis is the primary cause of susceptibility and fecal microbiota transplantation (FMT) has emerged as an effective therapy for recurrence. We previously demonstrated in the mouse model of CDI that antibiotic-induced dysbiosis reduced colonic expression of IL-25, and that FMT protected in part by restoring gut commensal bacteria-mediated IL-25 signaling. Here we conducted a prospective clinical trial to test the impact of FMT on immunity, specifically testing in humans if FMT induced IL-25 expression in the colon.MethodsSubjects received colonic biopsies and blood sampling at the time of FMT and 60-days later. Colon biopsies were assayed for IL-25 by immunoassay, for mRNA by RNAseq, and for bacterial content by 16 S rDNA sequencing. High dimensional flow cytometry was also conducted on peripheral blood mononuclear cells pre- and post-FMT.ResultsAll 10 subjects who received FMT had no CDI recurrences over a 2 year follow-up post FMT. FMT increased alpha diversity of the colonic microbiota and was associated with several immunologic changes. The cytokine IL-25 was increased in colonic tissue. In addition, increased expression of homeostatic genes and repression of inflammatory genes was observed in colonic mRNA transcripts. Finally, circulating Th17 cells were decreased post-FMT.ConclusionThe increase in the cytokine IL-25 accompanied by decreased inflammation is consistent with FMT acting in part to protect from recurrent CDI via restoration of commensal activation of type 2 immunity.
Sustainable use of plant protection products in heroic viticulture areas. Reducing risks to the environment and winemaking
Authors: Cortiñas J. Antonio , Fernández-Conde M. Eva 
Published: July 2021

ABSTRACTObjectiveThe aim and objective of this article is to focus on the importance of the rational use of plant protection products to combat vine fungi and at the same time reduce their risks to human health and the environment. The integrated management of fungal diseases aims to achieve the development of healthy crops with the minimum alteration of agro-ecosystems and the promotion of natural mechanisms.Material and methodsThe study was carried out in one vineyard in Ribeira Sacra (North-West Spain) during 2018. Souto vineyard is located at 438 m above mean sea level (42° 24’ 27.67” N 7° 28’ 20.06” W; northwest-southeast orientation) in the lower terraces of the river Sil’s banks, following the contour lines and with gradients of up to 80%. The variety studied was Godello, for sampling the reproductive structures in the air (spores of Botrytis and Erysiphe and sporangia of Plasmopara), a Lanzoni VPPS-2000® spore trap (Lanzoni s.r.l., Bologna, Italy) was used.ResultsThe Botrytis Seasonal Spore Integral (SSIn) was markedly higher than for the other pathogens under consideration. Taking into account the maximum daily values, a clear dominance of Botrytis spores was also found, with a maximum of 397 spores/m3 at the beginning of June, while Erysiphe and Plasmopara were recorded at around 26 and 227 spores/m3, respectively, at the beginning of august and mid-July. The statistical analysis of the spore concentrations and the main meteorological variables showed for Erysiphe that the highest Spearman’s r correlation coefficient corresponded to the rainfall, as for Plasmopara airbone sporangia, but with a negative sign, while for Botrytis spores, no significant correspondence was found for any meteorological parameter.ConclusionThe use of plant protection products can be much more effective if fungicides are applied at the right time, at the precise doses and combined with agricultural techniques of management of the vineyards. There are sustainable and profitable alternatives that can improve vine yields while protecting the environment in areas of heroic viticulture where the vineyard, is a fundamental element of the wine-growing landscape, combining as it does historical, cultural and landscape characteristics.
Accounting, management and accountability in times of crisis: lessons from the COVID-19 pandemic
Authors: Leoni Giulia , Lai Alessandro , Stacchezzini Riccardo , Steccolini Ileana , Brammer Stephen , Linnenluecke Martina , Demirag Istemi 
Published: July 2021

PurposeThe purpose of this paper is to discuss the themes emerging from the first studies exploring accounting, accountability and management practices during the COVID-19 pandemic and coming from a diversity of experiences, across countries, organizations and individuals. In so doing, the paper gives an overview of the most recent findings about the role of accounting and accountability in times of crisis that are hosted in this special issue of Accounting, Auditing and Accountability Journal (AAAJ).Design/methodology/approachThe paper draws together and identifies emerging themes related to the current COVID-19 pandemic and its impacts on accounting, accountability and management practices and considers how the studies in this issue extend one’s knowledge of accounting and contribute to accounting research.FindingsThree emerging themes are drawn and their contribution to accounting scholarship is discussed. The first theme deals with the role of accounting and numbers in supporting governmental responses to COVID-19. The second theme considers accounting practices used to make exceptional decisions at the organizational level in times of crisis. The third theme addresses a relevant frontier of research into accounting and inequalities.Practical implicationsIn considering the diverse contributions of this special issue, the paper points out how uncertainty and change can impact the design, use and understanding of accounting, management and accountability practices and can be accepted by scholars and practitioners as part of such practices.Originality/valueThis paper provides a timely and comprehensive picture of the first reflections and research findings on the impacts of the COVID-19 pandemic on one’s interpretation of accounting, accountability and management practices.