bluuebunny/crossref_metadata_2025_split huggingface dataset:
Instructor-learner neural synchronization during elaborated feedback predicts learning transfer
Authors: Zhu Yi , Leong Victoria , Hou Yingying , Zhang Dingning , Pan Yafeng , Hu Yi 
Published: March 2021

AbstractThe provision of feedback with complex information beyond the correct answer, i.e., elaborated feedback, can powerfully shape learning outcomes such as transfer, i.e., the ability to extend what has been learned in one context to new contexts. However, an understanding of neurocognitive processes of elaborated feedback during instructor-learner interactions remains elusive. Here, a two-person interactive design is used during simultaneous recording of functional near-infrared spectroscopy (fNIRS) signals from adult instructor-learner dyads. Instructors either provided elaborated feedback (i.e., correct answer and an example) or simple feedback (i.e., correct answer only) to learners during a concept learning task. Our results showed that elaborated feedback produced comparable levels of retention to simple feedback, however, transfer was significantly enhanced by elaboration. We also noted significant instructor-learner neural synchronization in frontoparietal regions during the provision of elaborated feedback, especially when examples were provided. Further, interpersonal neural synchronization in the parietal cortex successfully predicted transfer of knowledge to novel contexts. This prediction was retained for both learner-delayed and learner-preceding neural synchronization. These findings point toward transfer effects of elaborated feedback provided in a social context can be predictable through interpersonal neural synchronization, which may hold important implications for real-world learning and pedagogical efficacy.Educational Impact and Implications StatementFeedback provides learners with crucial information regarding the gap between what has currently been achieved and what remains to be achieved, and thus plays a critical role in any learning process. In real-world settings, feedback is typically provided and received through social interaction, and high-quality “elaborated feedback” contains complex information that goes beyond the correct answer. This study aims to elucidate the neurocognitive processes underpinning elaborated feedback during instructor-learner interactions. We detected significant instructor-learner neural synchronization in mutual frontoparietal brain regions during elaborated feedback, particularly during the provision of specific elaborated information (i.e., concrete examples). Moreover, this synchronization (including learner-delayed and learner-preceded synchronization) in the parietal region predicted whether the learners transferred learning to novel examples of learned psychology concepts. This study advances current understanding on the neural mechanisms for elaborated feedback and the role of social interaction in feedback effects. These results may have important implications for successful real-world learning and communication, and related pedagogical applications in educational settings.
The E3 Ubiquitin Ligase RNF5 Facilitates SARS-CoV-2 Membrane Protein-Mediated Virion Release
Authors: Yuan Zhen , Hu Bing , Wang Yulei , Tan Xuan , Xiao Hurong , Yue Mengzhen , Cai Kun , Tang Ke , Ding Binbin 
Published: March 2021

AbstractAs enveloped virus, SARS-CoV-2 membrane protein (M) mediates viral release from cellular membranes, but the molecular mechanisms of SARS-CoV-2 virions release remain poorly understood. Here, we performed RNAi screening and identified the E3 ligase RNF5 which mediates ubiquitination of SARS-CoV-2 M at residue K15 to enhance the interaction of viral envelope (E) with M. M-E complex ensures the uniform size of viral particles for viral maturation and mediates viral release. Moreover, overexpression of M induces complete autophagy which is dependent on RNF5-mediated ubiquitin modification. M inhibits the activity of lysosome protease, and uses autolysosomes for virion release. Consequently, all these results demonstrate that RNF5 mediates ubiquitin modification of SARS-CoV-2 M to stabilize the M-E complex and induce autophagy for virion release.
Persistence of G10P[11] neonatal rotavirus infections in southern India
Authors: Babji Sudhir , Sindhu Kulandaipalayam Natarajan , Selvarajan Sribal , Ramani Sasirekha , Venugopal Srinivasan , Khakha Shainey Alokit , Hemavathy Priya , Ganesan Santhosh Kumar , Giri Sidhartha , Reju Sudhabharathi , Gopalakrishnan Krithika , Ninan Binu , Iturriza-Gomara Miren , Srikanth Padma , Kang Gagandeep 
Published: March 2021

ABSTRACTNeonatal rotavirus infections are predominantly caused by distinct genotypes restricted to this age-group and are mostly asymptomatic. Stool samples from neonates admitted for >48 hours in neonatal intensive care units (NICUs) in Vellore (2014-2015) and Chennai (2015-2016) in southern India, and from neonates born at hospitals in Vellore but not admitted to NICUs (2015-2016) were tested for rotavirus by ELISA and genotyped by hemi-nested RT-PCR. Of the 791 neonates, 150 and 336 were recruited from Vellore and Chennai NICUs, and 305 were born in five hospitals in Vellore. The positivity rates in the three settings were 49.3% (74/150), 29.5% (99/336) and 54% (164/305), respectively. G10P[11] was the commonly identified genotype in 87.8% (65/74), 94.9% (94/99) and 98.2% (161/164) of the neonates in Vellore and Chennai NICUs, and those born at Vellore hospitals, respectively. Neonates delivered by lower segment caesarean section (LSCS) at Vellore hospitals, not admitted to NICUs, had a significantly higher odds of acquiring rotavirus infection compared to those delivered vaginally [p=0.002, OR=2.4 (1.4-4.3)]. This report demonstrates the persistence of G10P[11] strain in Vellore and Chennai, indicating widespread neonatal G10P[11] strain in southern India and their persistence over two decades, leading to interesting questions about strain stability.
Distinct systemic and mucosal immune responses to SARS-CoV-2
Authors: Smith Nikaïa , Goncalves Pedro , Charbit Bruno , Grzelak Ludivine , Beretta Maxime , Planchais Cyril , Bruel Timothée , Rouilly Vincent , Bondet Vincent , Hadjadj Jérôme , Yatim Nader , Pere Helene , Merkling Sarah H , Kernéis Solen , Rieux-Laucat Frederic , Terrier Benjamin , Schwartz Olivier , Mouquet Hugo , Duffy Darragh , Di Santo James P. 
Published: March 2021

SummaryCoordinated local mucosal and systemic immune responses following SARS-CoV-2 infection protect against COVID-19 pathologies or fail leading to severe clinical outcomes. To understand this process, we performed an integrated analysis of SARS-CoV-2 spike-specific antibodies, cytokines, viral load and 16S bacterial communities in paired nasopharyngeal swabs and plasma samples from a cohort of clinically distinct COVID-19 patients during acute infection. Plasma viral load was associated with systemic inflammatory cytokines that were elevated in severe COVID-19, and also with spike-specific neutralizing antibodies. In contrast, nasopharyngeal viral load correlated with SARS-CoV-2 humoral responses but inversely with interferon responses, the latter associating with protective microbial communities. Potential pathogenic microrganisms, often implicated in secondary respiratory infections, were associated with mucosal inflammation and elevated in severe COVID-19. Our results demonstrate distinct tissue compartmentalization of SARS-CoV-2 immune responses and highlight a role for the nasopharyngeal microbiome in regulating local and systemic immunity that determines COVID-19 clinical outcomes.
AB12PHYLO: an integrated pipeline for Maximum Likelihood phylogenetic inference from ABI trace data
Authors: Kaindl Leo , Small Corinn , Stam Remco 
Published: March 2021

AbstractMulti-gene phylogenies constructed from multiplexed and Sanger sequencing data are regularly used in mycology and other disciplines as a cost-effective way of species identification and as a first means to investigate genetic diversity samples.Today, a number of tools exist for each of the steps in this analysis, including quality control and trimming, the generation of a multiple sequence alignment (MSA), extraction of informative sites, and the construction of the final phylogenetic tree. A BLAST search in a reference database is often performed to identify sequences of type specimens to compare the samples with in the phylogeny. Made over the past decades, these tools are all independent from and often not perfectly adapted to one another.We present AB12PHYLO, an integrated pipeline that can perform all necessary steps from reading in raw Sanger sequencing data through visualizing and editing phylogenies. In addition, AB12PHYLO can calculate basic summary statistics for each gene in the phylogeny.AB12PHYLO is designed as a wrapper of several open access and commonly used tools for each of the intermediate stages, and intended to simplify the phylogenetic pipeline while still allowing a high degree of access. It comes as a command-line version for the highest reproducibility and an intuitive graphical user interface (GUI) for easy adoption by IT-agnostic end-users. The use of AB12PHYLO significantly reduces the hands-on working time for these analyses.
Species-wide transposable element repertoires retrace the evolutionary history of theSaccharomyces cerevisiaehost
Authors: Bleykasten-Grosshans Claudine , Fabrizio Romeo , Friedrich Anne , Schacherer Joseph 
Published: March 2021

AbstractTransposable elements (TE) are an important source of genetic variation with a dynamic and content that greatly differ in a wide range of species. The origin of the intraspecific content variation is not always clear and little is known about the precise nature of it. Here, we surveyed the species-wide content of the Ty LTR-retrotransposons in a broad collection of 1,011Saccharomyces cerevisiaenatural isolates to understand what can stand behind the variation of the repertoire,i.e.the type and number of Ty elements. We have compiled an exhaustive catalog of all TE variants present in theS. cerevisiaespecies by identifying a large set of new variants. The characterization of the TE content in each isolate clearly highlighted that each subpopulation exhibits a unique and specific repertoire, retracing the evolutionary history of the species. Most interestingly, we have shown that ancient interspecific hybridization events had a major impact in the birth of new variants and therefore in the shaping of the TE repertoires. We also investigated the transpositional activity of these elements in a large set of natural isolates, and we found a broad variability related to the level of ploidy as well as the genetic background. Overall, our results pointed out that the evolution of the Ty content is deeply impacted by clade-specific events such as introgressions and therefore follows the population structure. In addition, our study lays the foundation for future investigations to better understand the transpositional regulation and more broadly the TE-host interactions.Authors summaryMobile DNA elements are widely distributed in the genomes of many eukaryotes, but their contents greatly vary between species, populations and even individuals. In fact, little is known about the origin of this variation of transposable element (TE) content across individuals of the same species. Here, we surveyed the Ty LTR-retrotransposon content in a broad collection of 1,011Saccharomyces cerevisiaeyeast natural isolates. We have defined an exhaustive and precise catalog of the TE variants present in theS. cerevisiaespecies. We found that the TE content follows the evolutionary history of the species because each subpopulation has a unique and specific content. Interestingly, our results highlighted that ancient interspecific hybridization events led to the appearance of new TE variants and therefore had a strong impact on the variation of the TE repertoires in this species. We also investigated the transpositional activity of these elements and found a wide variability related to the genetic background diversity. Altogether, our results have led to a better understanding of the variability of TE content at a species level.
Social behaviour and vocalizations of the tent-roosting Honduran White Bat
Authors: Fernandez Ahana Aurora , Schmidt Christian , Schmidt Stefanie , Rodríguez-Herrera Bernal , Knörnschild Mirjam 
Published: March 2021

AbstractBats are highly gregarious animals, displaying a large spectrum of social systems with different organizational structures. One important factor shaping sociality is group stability. To maintain group cohesion and stability, bats often rely on social vocal communication. The Honduran white bat,Ectophylla albaexhibits an unusual social structure compared to other tent-roosting species. This small white-furred bat lives in perennial stable mixed-sex groups. Tent construction requires several individuals and, as the only tent roosting species so far, involves both sexes. The bats’ social system and ecology render this species an interesting candidate to study social behaviour and social vocal communication. In our study, we investigated the social behaviour and vocalizations ofE. albain the tent by observing two stable groups, including pups, in the wild. We documented 16 different behaviours, among others, play and fur chewing, a behaviour presumably used for scent-marking. Moreover, we found 10 distinct social call types in addition to echolocation calls, and, for seven call types, we were able to identify the corresponding behavioural context. Most of the social call types were affiliative, including two types of contact calls, maternal directives, pup isolation calls and a call type related to the fur-chewing behaviour. In sum, this study entails an ethogram and describes the first vocal repertoire of a tent-roosting phyllostomid bat, providing the basis for further in-depth studies about the sociality and vocal communication inE. alba.
ASSOCIATION STUDY OF SIX CANDIDATE GENES WITH MAJOR DEPRESSIVE DISORDER IN THE NORTH-WESTERN POPULATION OF PAKISTAN
Authors: Alam Naqash , Ali Sadiq , Akbar Nazia , Ilyas Muhammad , Ahmed Habib , Mustafa Arooj , Khurram Shehzada , Sajid Zeeshan , Ullah Najeeb , Qayyum Shumaila , Rahim Tariq , Usman Mian Syed , Ali Nawad , Khan Imad , Pervez Khola , Sumaira BiBi , Ali Nasir , Sultana Nighat , Tanoli Adeel Yunus , Islam Madiha 
Published: March 2021

AbstractPeople around the world are currently affected by Major Depressive Disorder (MDD). Despite its many aspects, symptoms, manifestations and impacts, efforts have been made to identify the root causes of the disorder. In particular, genetic studies have concentrated on identifying candidate genes for MDD and exploring associations between these genes and some specific group of individuals. The aim of this research was to find out the association between single nucleotide polymorphisms in 6 candidate genes linked to the neurobiology of major depressive disorder in the North-Western population of Pakistan. We performed a case-control analysis, with 400 MDD and 232 controls. A trained psychiatrist or clinical psychologists evaluated the patients. Six polymorphisms were genotyped and tested for allele and genotype association with MDD. There were no statistical variations between MDD patients and healthy controls for genotypic and allelic distribution of all the polymorphisms observed. Thus, our analysis does not support the major role of these polymorphisms in contributing to MDD susceptibility, although it does not preclude minor impact. The statistically significant correlation between six polymorphisms and major depressive disorder in the studied population was not observed. There are inconsistencies in investigations around the world. Future research, including GWAS and association analysis on larger scale should be addressed for further validation and replication of the present findings.
The time to peak blood bicarbonate (HCO3−), pH, and strong ion difference (SID) following sodium bicarbonate (NaHCO3) ingestion in highly trained adolescent swimmers
Authors: Newbury Josh W. , Cole Matthew , Kelly Adam L. , Chessor Richard J. , Sparks S. Andy , McNaughton Lars R. , Gough Lewis A. 
Published: March 2021

AbstractBackgroundContemporary research suggests that the optimal timing of sodium bicarbonate (NaHCO3) should be based upon an individual time in which bicarbonate (HCO3−) or pH peaks within the blood. However, the mechanisms surrounding acidosis on exercise performance are contested, therefore it is plausible that the ergogenic effects of NaHCO3are instead a result of an increased strong ion difference (SID) following ingestion. Since the post-ingestion time course of the SID is currently unknown, the purpose of this study was to investigate the pharmacokinetics of the SID in direct comparison to HCO3−and pH.MethodsTwelve highly trained, adolescent swimmers (age: 15.9 ± 1.0 yrs, body mass: 65.3 ± 9.6 kg) consumed their typical pre-competition nutrition before ingesting 0.3 g·kg BM-1NaHCO3in gelatine capsules. Capillary blood samples were then taken during quiet, seated rest on nine occasions (0, 60, 75, 90, 105, 120, 135, 150, and 165 min post-ingestion) for the assessment of time course changes in HCO3−, pH, and the SID.ResultsOn a group mean level, no differences were found in the time in which each variable peaked within the blood (HCO3−= 130 ± 35 min, pH = 120 ± 38 min, SID = 96 ± 35 min; p = 0.06). A large effect size was calculated between the timing of peak HCO3−and the SID (g= 0.91), however, suggesting that a difference may occur between these two measures in practice.ConclusionsA time difference between peak HCO3−and the SID presents an interesting avenue for further research since an approach based upon individual increases in extracellular SID has yet to be investigated. Future studies should therefore compare these dosing strategies directly to elucidate whether either one is more ergogenic for exercise performance.
Copy number variant heterogeneity among cancer types reflects inconsistent concordance with diagnostic classifications
Authors: Carrio-Cordo Paula , Baudis Michael 
Published: March 2021

AbstractDue to frequent genome instability and accumulation of mutations during the neoplastic process, malignant tumors present with patterns of somatic genome variants on diverse levels of heterogeneity. The delineation of pathophysiological consequences of these patterns remains one of the main challenges in cancer prognosis and treatment.Although continuous efforts aim for better characterization of cancer entities through inclusion of molecular characteristics, current ontology systems still heavily rely on clinico-pathological features. Traditionally, malignant diseases have been classified using domain-specific or generalized classification systems, based on histopathological features and clinical gestalt. Aside from the general purpose “International Classification for Diseases in Oncology” (ICD-O; WHO), hierarchical terminologies such as NCIt promote data interoperability and ontology-driven computational analysis.To evaluate two prominent, general cancer classification systems (NCIt and ICD-O) towards their concordance with genomic mutation patterns we have performed a data-driven meta-analysis of 83’505 curated cancer samples with genome-wide CNA (copy number aberration) profiles from our Progenetix database. The analysis provides a basis to assess the correspondence level of existing classification systems with respect to homogeneous molecular groups, and how individual codes represent an adequately detailed classification.
The aging DNA methylome reveals environment-by-aging interactions in a model teleost
Authors: Bertucci Emily M. , Mason Marilyn W. , Rhodes Olin E. , Parrott Benjamin B. 
Published: March 2021

AbstractThe rate at which individuals age underlies variation in life history and attendant health and disease trajectories. Age specific patterning of the DNA methylome (“epigenetic aging”) is strongly correlated with chronological age in humans and can be modeled to produce epigenetic age predictors. However, epigenetic age estimates vary among individuals of the same age, and this mismatch is correlated to the onset of age-related disease and all-cause mortality. Yet, the origins of epigenetic-to-chronological age discordance are not resolved. In an effort to develop a tractable model in which environmental drivers of epigenetic aging can be assessed, we investigate the relationship between aging and DNA methylation in a small teleost, medaka (Oryzias latipes). We find that age-associated DNA methylation patterning occurs broadly across the genome, with the majority of age-related changes occurring during early life. By modeling the stereotypical nature of age-associated DNA methylation dynamics, we built an epigenetic clock, which predicts chronological age with a mean error of 29.1 days (~4% of average lifespan). Characterization of clock loci suggests that aspects of epigenetic aging are functionally similar across vertebrates. To understand how environmental factors interact with epigenetic aging, we exposed medaka to four doses of ionizing radiation for seven weeks, hypothesizing that exposure to such an environmental stressor would accelerate epigenetic aging. While the epigenetic clock was not significantly affected, radiation exposure accelerated and decelerated patterns of normal epigenetic aging, with radiation-induced epigenetic alterations enriched at loci that become hypermethylated with age. Together, our findings advance ongoing research attempting to elucidate the functional role of DNA methylation in integrating environmental factors into the rate of biological aging.
MoBiFC: development of a modular bimolecular fluorescence complementation toolkit for the analysis of chloroplast protein-protein interactions
Authors: Velay Florent , Soula Melanie , Mehrez Marwa , D’Alessandro Stefano , Laloi Christophe , Crete Patrice , Field Ben 
Published: March 2021

SummaryThe bimolecular fluorescence complementation (BiFC) assay has emerged as one of the most popular methods for analysing protein-protein interactions (PPIs) in plant biology. This includes its increasing use as a tool for dissecting the molecular mechanisms of chloroplast function. However, the construction of chloroplast fusion proteins for BiFC can be difficult, and the availability and selection of appropriate controls is not trivial. Furthermore, the challenges of performing BiFC in restricted cellular compartments has not been specifically addressed. Here we describe the development of a flexible modular cloning-based toolkit (MoBiFC) for chloroplast BiFC and proximity labelling using synthetic biology principles. The approach facilitates the cloning process for chloroplast-targeted proteins, allows robust ratiometric quantification, and the toolkit comes with model positive and negative controls. Our study also highlights many potential pitfalls including the choice of fluorescent protein (FP) split, negative controls, cell type, and reference FP. Finally, we provide an example of how users can enrich the toolset by providing functional proximity labelling modules, and we discuss how MoBiFC could be further improved and extended to other compartments of the plant cell.