bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining Medical Student Volunteering During The COVID-19 Pandemic As A Prosocial Behavior During An Emergency
Authors: Byrne Matthew H V , Ashcroft James , Wan Jonathan C M , Alexander Laith , Harvey Anna , Schindler Nicholas , Brown Megan E L , Brassett Cecilia 
Published: July 2021

ABSTRACTIntroductionCOVID-19 has caused major disruptions to healthcare, with voluntary opportunities offered to medical students to provide clinical support. We used the conceptual framework of prosocial behavior during an emergency – behaviors whose primary focus is benefiting others – to examine volunteering during COVID-19.MethodsWe conducted an in-depth, mixed-methods cross-sectional survey, from 2nd May to 15th June 2020, of medical students studying at UK medical schools. Data analysis was informed by Latane and Darley’s theory of prosocial behavior during an emergency and aimed to understand students’ decision-making processes.ResultsA total of 1145 medical students from 36 medical schools completed the survey. While 947 (82.7%) of students were willing to volunteer, only 391 (34.3%) had volunteered. The majority (92.7%) of students understood that they may be asked to volunteer; however, we found that deciding one’s responsibility to volunteer was mitigated by a complex interaction between the interests of others and self-interest. Further, concerns revolving around professional role boundaries influenced students’ decisions over whether they had the required skills and knowledge to volunteer. Deciding to volunteer depended not only on possession of necessary skills, but also seniority and identification with the nature of volunteering roles offered.ConclusionsWe propose two additional domains to Latane and Darley’s theory of prosocial behavior during an emergency that students consider before making their final decision to volunteer. These are ‘logistics’ – whether it is logistically feasible to volunteer – and ‘safety’ – whether it is safe to volunteer. This study highlights a number of modifiable barriers to prosocial behavior that medical students encounter and provides suggestions regarding how Latane and Darley’s theory of prosocial behavior can be operationalized within educational strategies to address these barriers. Optimizing the process of volunteering can aid healthcare provision and may facilitate a safer volunteering process for all.
Life on leaves : uncovering temporal dynamics in Arabidopsis’ leaf microbiota
Authors: Almario Juliana , Mahmudi Maryam , Kroll Samuel , Agler Mathew , Placzek Aleksandra , Mari Alfredo , Kemen Eric 
Published: July 2021

AbstractLeaves are primarily responsible for the plant’s photosynthetic activity. Thus, changes in the phyllosphere microbiota, which includes deleterious and beneficial microbes, can have far reaching effects on plant fitness and productivity. In this context, identifying the processes and microorganisms that drive the changes in the leaf microbiota over a plant’s lifetime is crucial. In this study we analyzed the temporal dynamics in the leaf microbiota ofArabidopsis thaliana, integrating both compositional changes and changes in microbe-microbe interactions via the study of microbial networks. Field-grownArabidopsiswere used to follow leaf bacterial, fungal and oomycete communities, throughout the plant’s growing season (extending from November to March), over three consecutive years. Our results revealed the existence of conserved time patterns, with microbial communities and networks going through a stabilization phase (decreasing diversity and variability) at the beginning of the plant’s growing season. Despite a high turnover in these communities, we identified 19 ‘core’ taxa persisting in Arabidopsis leaves across time and plant generations. With the hypothesis these microbes could be playing key roles in the structuring of leaf microbial communities, we conducted a time-informed microbial network analysis which showed core taxa are not necessarily highly connected network ‘hubs’ and ‘hubs’ alternate with time. Our study shows that leaf microbial communities exhibit reproducible dynamics and patterns, suggesting it could be possible to predict and drive these microbial communities to desired states.
Considerations for furbearer trapping regulations to prevent grizzly bear toe amputation and injury
Authors: Lamb Clayton , Smit Laura , Mclellan Bruce , Vander Vennen Lucas M. , Proctor Michael 
Published: July 2021

ABSTRACTScience and adaptive management form crucial components of the North American model of wildlife management. Under this model, wildlife managers are encouraged to update management approaches when new information arises whose implementation could improve the stewardship and viability of wildlife populations and the well-being of animals. Here we detail a troubling observation of several grizzly bears with amputated toes in southeast British Columbia and assemble evidence to inform management strategies to remedy the issue. During the capture of 59 grizzly bears, we noticed that four individuals (~7%) had amputated toes on one of their front feet. The wounds were all healed and linear in nature. Further opportunistic record collection revealed that similar examples of amputated toes occurred beyond our study area, and that furbearer traps were frequently responsible for toe loss. We found evidence that seasonal overlap between the active season for grizzly bears and the fall trapping seasons for small furbearers with body grip traps and for wolves with foothold traps may explain the issue. Multiple options to reduce or eliminate this issue exist, but have varying degrees of expected efficacy and require differing levels of monitoring. The most certain approach to greatly reduce the issue is to delay the start of the marten trapping season until December 1, when most bears have denned, instead of opening the season on or prior to November 1, when more than 50% of bears are still active. Additionally, innovative solutions, such as narrowing trap entrances to exclude bear feet while still allowing entrance of target furbearers, have the potential to minimize accidental capture of bears, but the effectiveness of these approaches is unknown. Experimental evidence suggested that better anchoring traps was not a viable solution. Solutions that do not involve season changes will require monitoring of efficacy and compliance to ensure success.
Reduction of nucleolar NOC1 accumulates pre-rRNAs and induces Xrp1 affecting growth and resulting in cell competition in Drosophila
Authors: Destefanis Francesca , Manara Valeria , Santarelli Stefania , Zola Sheri , Brambilla Marco , Viola Giacomo , Maragno Paola , Signoria Ilaria , Viero Gabriella , Pasini Maria Enrica , Penzo Marianna , Bellosta Paola 
Published: July 2021

AbstractNOC1 is a nucleolar protein necessary in yeast for both transport and maturation of ribosomal subunits. Here we show that in Drosophila NOC1 is essential for the correct animal development, and that its ubiquitous downregulation results in small larvae with reduced polysome abundance and decreased protein synthesis. NOC1 expression in multiple organs, such as the prothoracic gland and the fat body, is necessary for proper organ functioning. Reduction of NOC1 in clones from the imaginal discs results in small clones with cells that die by apoptosis, an event that is partially rescued using a M/+ background, suggesting that reduction of NOC1 causes the cells to acquire a loser state. This event was supported also by an increase in the transcription of Xrp1 and by activation of the pro-apoptotic eiger-JNK pathway, resulting in the upregulation of DILP8 as an indication of cellular damage. Here, we show that Drosophila NOC1 is important in the control of pre-rRNAs maturation and essential step in the regulation of ribosome biogenesis and its downregulation results in defects in growth and in cell competition, highlighting its novel function in this field.summary statementNOC1 is a nucleolar protein necessary for protein synthesis and ribosomal assembling. Its modulation induces cell competition and affects animal growth.
MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants
Authors: Dueholm Morten Simonsen , Nierychlo Marta , Andersen Kasper Skytte , Rudkjøbing Vibeke , Knutsson Simon ,   the MiDAS Global Consortium, Albertsen Mads , Nielsen Per Halkjær 
Published: July 2021

AbstractBiological wastewater treatment and an increased focus on resource recovery is fundamental for environmental protection, human health, and sustainable development. Microbial communities are responsible for these processes, but our knowledge of their diversity and function is still poor, partly due to the lack of good reference databases and comprehensive global studies. Here, we sequenced more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and used the sequences to construct MiDAS 4, a full-length amplicon sequence variant resolved 16S rRNA gene reference database with a comprehensive taxonomy from the domain to species-level for all references. Using a study-independent amplicon dataset from the Global Water Microbiome Consortium project (269 WWTPs), we showed that the MiDAS 4 database provides much better coverage for bacteria in WWTPs worldwide compared to commonly applied universal references databases, and greatly improved the rate of genus and species-level classification. Hence, MiDAS 4 provides a unifying taxonomy for the majority of prokaryotic diversity in WWTPs globally, which can be used for linking microbial identities with their functions across studies. Taking advantage of MiDAS 4, we carried out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting the V1-V3 and V4 region of the 16S rRNA gene. We found that the V1-V3 primers were generally best suited for this ecosystem, and revealed how environmental conditions and biogeography shape the activated sludge microbiota. We also identified process-critical taxa (core and conditionally rare or abundant taxa), encompassing 966 genera and 1530 species. These represented approximately 80% and 50% of the accumulated read abundance, respectively, and represent targets for further investigations. Finally, we showed that for well-studied functional guilds, such as nitrifiers or polyphosphate accumulating organisms, the same genera were prevalent worldwide, with only a few abundant species in each genus.
Automatic decomposition of electrophysiological data into distinct non-sinusoidal oscillatory modes
Authors: Fabus Marco S. , Quinn Andrew J. , Warnaby Catherine E. , Woolrich Mark W. 
Published: July 2021

ABSTRACTNeurophysiological signals are often noisy, non-sinusoidal, and consist of transient bursts. Extraction and analysis of oscillatory features (such as waveform shape and cross-frequency coupling) in such datasets remains difficult. This limits our understanding of brain dynamics and its functional importance. Here, we develop Iterated Masking Empirical Mode Decomposition (itEMD), a method designed to decompose noisy and transient single channel data into relevant oscillatory modes in a flexible, fully data-driven way without the need for manual tuning. Based on Empirical Mode Decomposition (EMD), this technique can extract single-cycle waveform dynamics through phase-aligned instantaneous frequency. We test our method by extensive simulations across different noise, sparsity, and non-sinusoidality conditions. We find itEMD significantly improves the separation of data into distinct non-sinusoidal oscillatory components and robustly reproduces waveform shape across a wide range of relevant parameters. We further validate the technique on multi-modal, multi-species electrophysiological data. Our itEMD extracts known rat hippocampal theta waveform asymmetry and identifies subject-specific human occipital alpha without any prior assumptions about the frequencies contained in the signal. Notably, it does so with significantly less mode mixing compared to existing EMD-based methods. By reducing mode mixing and simplifying interpretation of EMD results, itEMD will enable new analyses into functional roles of neural signals in behaviour and disease.New & NoteworthyWe introduce a novel, data-driven method to identify oscillations in neural recordings. This approach is based on Empirical Mode Decomposition and reduces mixing of components, one of its main problems. The technique is validated and compared with existing methods using simulations and real data. We show our method better extracts oscillations and their properties in highly noisy and non-sinusoidal datasets.Running HeadDecomposition of data into non-sinusoidal oscillatory modes
MONI: A Pangenomics Index for Finding MEMs
Authors: Rossi Massimiliano , Oliva Marco , Langmead Ben , Gagie Travis , Boucher Christina 
Published: July 2021

AbstractRecently, Gagie et al. proposed a version of the FM-index, called the r-index, that can store thousands of human genomes on a commodity computer. Then Kuhnle et al. showed how to build the r-index efficiently via a technique called prefix-free parsing (PFP) and demonstrated its effectiveness for exact pattern matching. Exact pattern matching can be leveraged to support approximate pattern matching but the r-index itself cannot support efficiently popular and important queries such as finding maximal exact matches (MEMs). To address this shortcoming, Bannai et al. introduced the concept of thresholds, and showed that storing them together with the r-index enables efficient MEM finding — but they did not say how to find those thresholds. We present a novel algorithm that applies PFP to build the r-index and find the thresholds simultaneously and in linear time and space with respect to the size of the prefix-free parse. Our implementation called MONI can rapidly find MEMs between reads and large sequence collections of highly repetitive sequences. Compared to other read aligners – PuffAligner, Bowtie2, BWA-MEM, and CHIC – MONI used 2–11 times less memory and was 2–32 times faster for index construction. Moreover, MONI was less than one thousandth the size of competing indexes for large collections of human chromosomes. Thus, MONI represents a major advance in our ability to perform MEM finding against very large collections of related references.AvailabilityMONI is publicly available at https://github.com/maxrossi91/moni.
Genome Profiling of SARS-CoV-2 in Indonesia, ASEAN, and the Neighbouring East Asian Countries: Features, Challenges, and Achievements
Authors: Cahyani Inswasti , Putro Eko W. , Ridwanuloh Asep M. , Wibowo Satrio H.B. , Hariyatun Hariyatun , Syahputra Gita , Akbariani Gilang , Utomo Ahmad R. , Ilyas Mohammad , Loose Matthew W. , Kusharyoto Wien ,   Indonesian SARS-CoV-2 Genomics Surveillance Network, Susanti Susanti 
Published: July 2021

AbstractA year after the World Health Organisation (WHO) declared COVID-19 as a pandemic, much has been learned regarding SARS-CoV-2 epidemiology, vaccine production, and disease treatment. Whole-genome sequencing (WGS) has played a significant role in contributing to our understanding of the epidemiology and biology of this virus. In this paper, we investigate the use of SARS-CoV-2 WGS in Southeast and East Asia and the impact of technological development, access to resources, and demography of individual countries on its uptake. Using Oxford Nanopore Technology (ONT), Nottingham-Indonesia Collaboration for Clinical Research and Training (NICCRAT) initiative has facilitated collaboration between the University of Nottingham and a team in Research Centre for Biotechnology, Indonesian Institute of Sciences (Lembaga Ilmu Pengetahuan Indonesia/LIPI) to carry out a small number of SARS-CoV-2 WGS in Indonesia. The ONT offers sequencing advantages that fit within the Indonesian context. Analyses of SARS-CoV-2 genomes deposited on GISAID from Southeast and East Asian countries reveal the importance of collecting clinical and demographic metadata and the importance of open access and data sharing. Lineage and phylogenetic analyses per 1 June 2021 found that: 1) B.1.466.2 variants were the most predominant in Indonesia, with mutations in the spike protein including D614G at 100%, N439K at 99.1%, and P681R at 69.7% frequency, 2) The variants of concern (VoCs) B.1.1.7 (Alpha), B.1.351 (Beta), and B.1.617.2 (Delta) were first detected in Indonesia in January 2021, 3) B.1.470 was first detected in Indonesia and spread to the neighbouring regions, and 4) The highest rate of virus transmissions between Indonesia and the rest of the world appears to be through interactions with Singapore and Japan, two neighbouring countries with a high degree of access and travels to and from Indonesia.
Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate
Authors: Marques Ines J. , Ernst Alexander , Arora Prateek , Vianin Andrej , Hetke Tanja , Sanz-Morejón Andrés , Naumann Uta , Odriozola Adolfo , Langa Xavier , Andrés-Delgado Laura , Haberthür David , Zuber Benoît , Torroja Carlos , Hlushchuk Ruslan , Osterwalder Marco , Simões Filipa , Englert Christoph , Mercader Nadia 
Published: July 2021

ABSTRACTDuring cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. Proepicardial cells are subsequently transferred to the myocardial surface and give rise to the epicardium, the outer layer covering the myocardium in the adult heart. wt1a/b expression is downregulated during the transition from pericardium to myocardium, but remains high in proepicardial cells. Here we show that sustained wt1 expression impaired cardiomyocyte maturation including sarcomere assembly, ultimately affecting heart morphology and cardiac function. ATAC-seq data analysis of cardiomyocytes overexpressing wt1 revealed that chromatin regions associated with myocardial differentiation genes remain closed upon wt1b overexpression in cardiomyocytes, suggesting that wt1 represses a myocardial differentiation program. Indeed, a subset of wt1a/b-expressing cardiomyocytes changed their cell adhesion properties, delaminated from the myocardial epithelium, and upregulated the expression of epicardial genes, as confirmed by in vivo imaging. Thus, we conclude that wt1 acts as a break for cardiomyocyte differentiation by repressing chromatin opening at specific genomic loci and that sustained ectopic expression of wt1 in cardiomyocytes can lead to their transformation into epicardial cells.
TAF8 regions important for TFIID lobe B assembly, or for TAF2 interactions, are required for embryonic stem cell survival
Authors: Scheer Elisabeth , Luo Jie , Ruffenach Frank , Garnier Jean-Marie , Kolb-Cheynel Isabelle , Gupta Kapil , Berger Imre , Ranish Jeff , Tora László 
Published: July 2021

AbstractThe human general transcription factor TFIID is composed of the TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). In eukaryotic cells, TFIID is thought to nucleate RNA polymerase II (Pol II) preinitiation complex formation on all protein coding gene promoters and thus, be crucial for Pol II transcription. TFIID is composed of three lobes, named A, B and C. Structural studies showed that TAF8 forms a histone fold pair with TAF10 in lobe B and participates in connecting lobe B to lobe C. In the present study, we have investigated the requirement of the different regions of TAF8 for in vitro TFIID assembly, and the importance of certain TAF8 regions for mouse embryonic stem cell (ESC) viability. We have identified a TAF8 region, different from the histone fold domain of TAF8, important for assembling with the 5TAF core complex in lobe B, and four regions of TAF8 each individually required for interacting with TAF2 in lobe C. Moreover, we show that the 5TAF coreinteracting TAF8 domain, and the proline rich domain of TAF8 that interacts with TAF2, are both required for mouse embryonic stem cell survival. Thus, our study demonstrates that distinct TAF8 regions involved in connecting lobe B to lobe C are crucial for TFIID function and consequent ESC survival.
Constitutive gene expression differs in three brain regions important for cognition in neophobic and non-neophobic house sparrows (Passer domesticus)
Authors: Lattin Christine R. , Kelly Tosha R. , Kelly Morgan W. , Johnson Kevin M. 
Published: July 2021

AbstractNeophobia (aversion to new objects, food, and environments) is a personality trait that affects the ability of wildlife to adapt to new challenges and opportunities. Despite the ubiquity and importance of this trait, the molecular mechanisms underlying repeatable individual differences in neophobia in wild animals are poorly understood. We evaluated wild-caught house sparrows (Passer domesticus) for neophobia in the lab using novel object tests. We then selected the most and least neophobic individuals (n=3 of each) and extracted RNA from four brain regions involved in learning, memory, threat perception, and executive function: striatum, dorsomedial hippocampus, medial ventral arcopallium, and caudolateral nidopallium (NCL). Our analysis of differentially expressed genes (DEGs) used 11,889 gene regions annotated in the house sparrow reference genome for which we had an average of 25.7 million mapped reads/sample. PERMANOVA identified significant effects of brain region, phenotype (neophobic vs. non-neophobic), and a brain region by phenotype interaction. Comparing neophobic and non-neophobic birds revealed constitutive differences in DEGs in three of the four brain regions examined: hippocampus (12% of the transcriptome significantly differentially expressed), striatum (4%) and NCL (3%). DEGs included important known neuroendocrine mediators of learning, memory, executive function, and anxiety behavior, including serotonin receptor 5A, dopamine receptors 1, 2 and 5 (downregulated in neophobic birds), and estrogen receptor beta (upregulated in neophobic birds). These results suggest that some of the behavioral differences between phenotypes may be due to underlying gene expression differences in the brain. The large number of DEGs in neophobic and non-neophobic birds also implies that there are major differences in neural function between the two phenotypes that could affect a wide variety of behavioral traits beyond neophobia.