bluuebunny/crossref_metadata_2025_split huggingface dataset:
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing
Authors: Bhoyar Rahul C. , Jain Abhinav , Sehgal Paras , Divakar Mohit Kumar , Sharma Disha , Imran Mohamed , Jolly Bani , Ranjan Gyan , Rophina Mercy , Sharma Sumit , Siwach Sanjay , Pandhare Kavita , Sahoo Swayamprabha , Sahoo Maheswata , Nayak Ananya , Mohanty Jatindra Nath , Das Jayashankar , Bhandari Sudhir , Mathur Sandeep K , Kumar Anshul , Sahlot Rahul , Rojarani Pallavali , Lakshmi Juturu Vijaya , Surekha Araveti , Sekhar Pulala Chandra , Mahajan Shelly , Masih Shet , Singh Pawan , Kumar Vipin , Jose Blessy , Mahajan Vidur , Gupta Vivek , Gupta Rakesh , Arumugam Prabhakar , Singh Anjali , Nandy Ananya , Raghavendran P.V. , Jha Rakesh Mohan , Kumari Anupama , Gandotra Sheetal , Rao Vivek , Faruq Mohammed , Kumar Sanjeev , Betsy Reshma G , Narendra Varma G , Roy Shuvra Shekhar , Sengupta Antara , Chattopadhyay Sabyasachi , Singhal Khushboo , Pradhan Shalini , Jha Diksha , Naushin Salwa , Wadhwa Saruchi , Tyagi Nishu , Poojary Mukta , Scaria Vinod , Sivasubbu Sridhar 
Published: August 2020

AbstractThe rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.
Predictive coding of natural images by V1 activity revealed by self-supervised deep neural networks
Authors: Uran Cem , Peter Alina , Lazar Andreea , Barnes William , Klon-Lipok Johanna , Shapcott Katharine A , Roese Rasmus , Fries Pascal , Singer Wolf , Vinck Martin 
Published: August 2020

AbstractPredictive coding is an important candidate theory of self-supervised learning in the brain. Its central idea is that neural activity results from an integration and comparison of bottom-up inputs with contextual predictions, a process in which firing rates and synchronization may play distinct roles. Here, we quantified stimulus predictability for natural images based on self-supervised, generative neural networks. When the precise pixel structure of a stimulus falling into the V1 receptive field (RF) was predicted by the spatial context, V1 exhibited characteristic γ-synchronization (30-80Hz), despite no detectable modulation of firing rates. In contrast to γ, β-synchronization emerged exclusively for unpredictable stimuli. Natural images with high structural predictability were characterized by high compressibility and low dimensionality. Yet, perceptual similarity was mainly determined by higher-level features of natural stimuli, not by the precise pixel structure. When higher-level features of the stimulus in the receptive field were predicted by the context, neurons showed a strong reduction in firing rates and an increase in surround suppression that was dissociated from synchronization patterns. These findings reveal distinct roles of synchronization and firing rates in the predictive coding of natural images.
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
Authors: Alqassem Israa , Sonthalia Yash , Klitzke-Feser Erika , Shim Heejung , Canzar Stefan 
Published: August 2020

AbstractAlternative splicing removes intronic sequences from transcripts in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts and their alternative forms give specific functionalities to cells in a particular condition or developmental stage. In addition, a large fraction of human disease mutations affect splicing and lead to aberrant mRNA and protein products. Current methods that interrogate the transcriptome based on RNA-seq either suffer from short read length when trying to infer full-length transcripts, or are restricted to predefined units of alternative splicing that they quantify from local read evidence. Instead of attempting to quantify individual outcomes of the splicing process such as local splicing events or full-length transcripts, we propose to quantify alternative splicing using a simplified probabilistic model of the underlying splicing process. Our model is based on the usage of individual splice sites and can generate arbitrarily complex types of splicing patterns. In our method, McSplicer, we estimate the parameters of our model using all read data at once and we demonstrate in our experiments that this yields more accurate estimates compared to competing methods. Our model is able to describe multiple effects of splicing mutations using few, easy to interpret parameters, as we illustrate in an experiment on RNA-seq data from autism spectrum disorder patients. McSplicer is implemented in Python and available as open-source athttps://github.com/canzarlab/McSplicer.
Capturing Neonatal Cardiomyocyte – Endothelial interactions on-a-Chip
Authors: Tavassoli Hossein , Kang Young Chan , Rorimpandey Prunella , Pimanda John E , Chandrakanthan Vashe , Chan Peggy P.Y. 
Published: August 2020

AbstractThe neonatal heart has been the focus of numerous investigations due to its inherent regenerative potential. However, the interactions between neonatal cardiomyocytes (CMs) and endothelial cells (ECs) have been difficult to model and study due to the lack of an appropriate device. Here, we developed a method to culture primary neonatal CMs and ECs in a microchip and characterise their behavioural properties over a 14-day period. By implementing cell migration analyses coupled with immunostaining and confocal microscopy, we were able to identify and quantify sub-populations of migratory and non-migratory ECs. In CM–EC co-cultures, migrating ECs were found to move in higher numbers and longer distances compared to migrating CMs. In the presence of CMs, non-migrating ECs established connexin gap junctions and formed CM–EC cell aggregates, which were likely a priming event for endothelial organoid formation. This microfluidic device also enabled us to visualise the temporal sequence organoid formation and phenomena such as collective cell migration, CM–EC trans-differentiation and synchronisation of CM beating. This microchip based culture system has potential applications for tissue engineering and drug discovery.
Dissecting the microenvironment around biosynthetic scaffolds in murine skin wound healing
Authors: Hu Chen , Chu Chenyu , Liu Li , Jin Shue , Yang Renli , Rung Shengan , Li Jidong , Qu Yili , Man Yi 
Published: August 2020

AbstractStructural properties of biomaterials play critical roles in guiding cell behaviors and influence the immune response against them. We fabricated electrospun membranes with three types of surface topography (Random, Aligned, and Latticed). The aligned membranes showed immunomodulatory ability, and led to faster wound healing, reduced fibrotic response and enhanced regeneration of cutaneous appendages when used in skin wound repair. Based on that, we performed single-cell RNA sequencing analysis on cells from wounded mouse skin in the presence or absence of the Aligned scaffold. Keratinocytes, fibroblasts, and immune cells including neutrophils, monocytes, macrophages, dendritic cells, and T cells showed diverse cellular heterogeneity. More hair follicle progenitor cells, inner root sheath cells (anagen-related) and fibroblast subsets were found in the Aligned group, which corresponded to the improved regeneration of hair follicles and faster wound closure in the presence of scaffold. Immune responses towards the biomaterial differed from that of control group. In aligned samples, infiltrated macrophages and neutrophils were reduced, whereas more effector T cells were recruited. The time course of immune response was possibly advanced towards an adaptive immunity-dominant stage by the scaffold. The microenvironment around scaffold involved intricate interplay of immune cells and cutaneous cells, and wound healing was the comprehensive results of numerous influencing factors working together.
Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan)
Authors: Marla Soma , Mishra Pallavi , Maurya Ranjeet , Singh Mohar , Wankhede D. P. , Gupta Anil. K. , Rao N. S. , Singh S. K. , Kumar Rajesh 
Published: August 2020

AbstractGenome assembly of short reads from large plant genomes remains a challenge in computational biology despite major developments in Next Generation sequencing. Of late multiple draft assemblies of plant genomes are reported in many organisms. The draft assemblies ofCajanus cajanare with different levels of genome completeness; contain large number of repeats, gaps and segmental duplications. Draft assemblies with portions of genome missing, are shorter than the referenced original genome. These assemblies come with low map accuracy affecting further functional annotation and prediction of gene component as desired by crop researchers. Genome coveragei.e.number of sequenced raw reads mapped on to certain locations of the genome is an important quality indicator of completeness and assembly quality in draft assemblies. Present work was aimed at improvement of coverage in reportedde novosequenced draft genomes (GCA_000340665.1 and GCA_000230855.2) of Pigeonpea, a legume widely cultivated in India. The two assemblies comprised 72% and 75% of estimated coverage of genome respectively. We employed assembly reconciliation approach to compare draft assemblies and merged them to generate a high quality near complete assembly with enhanced contiguity. Finished assembly has reduced number of gaps than reported in draft assemblies and improved genome coverage of 82.4%. Quality of the finished assembly was evaluated using various quality metrics and for presence of specific trait related functional genes. Employed pair-end and mate-pair local library data sets enabled to resolve gaps, repeats and other sequence errors yielding lengthier scaffolds compared to two draft assemblies. We report prediction of putative host resistance genes from improved sequence againstFusariumwilt disease and evaluated them in both wet laboratory and field phenotypic conditions.
The influence of heart rate variability biofeedback on cardiac regulation and functional brain connectivity
Authors: Schumann Andy , Cruz Feliberto de la , Köhler Stefanie , Brotte Lisa , Bär Karl-Jürgen 
Published: August 2020

AbstractBackgroundHeart rate variability (HRV) biofeedback has a beneficial impact on perceived stress and emotion regulation. However, its impact on brain function is still unclear. In this study, we aimed to investigate the effect of an 8-week HRV-biofeedback intervention on functional brain connectivity in healthy subjects.MethodsHRV biofeedback was carried out in five sessions per week, including four at home and one in our lab. A control group playedjump‘n’run gamesinstead of the training. Functional magnetic resonance imaging was conducted before and after the intervention in both groups. To compute resting state functional connectivity (RSFC), we defined regions of interest in the ventral medial prefrontal cortex (VMPFC) and a total of 260 independent anatomical regions for network-based analysis. Changes of RSFC of the VMPFC to other brain regions were compared between groups. Temporal changes of HRV during the resting state recording were correlated to dynamic functional connectivity of the VMPFC.ResultsFirst, we corroborated the role of the VMPFC in cardiac autonomic regulation. We found that temporal changes of HRV were correlated to dynamic changes of prefrontal connectivity, especially to the middle cingulate cortex, left anterior insula, right amygdala, supplementary motor area, dorsal and ventral lateral prefrontal regions. The biofeedback group showed a drop in heart rate by 5.5 beats/min and an increased RMSSD as a measure of HRV by 10.1ms (33%) after the intervention. Functional connectivity of the VMPFC increased mainly to the right anterior insula, the dorsal anterior cingulate cortex and the dorsolateral prefrontal cortex after biofeedback intervention when compared to changes in the control group. Network-based statistic showed that biofeedback had an influence on a broad functional network of brain regions.ConclusionOur results show that increased vagal modulation induced by HRV-biofeedback is accompanied by changes in functional brain connectivity during resting state.
High-Resolution Satellite Imagery to AssessSargassumInundation Impacts to Coastal Areas
Authors: Hernandez William J. , Morell Julio M. , Armstrong Roy A. 
Published: August 2020

AbstractA change detection analysis utilizing Very High-resolution (VHR) satellite imagery was performed to evaluate the changes in benthic composition and coastal vegetation in La Parguera, southwestern Puerto Rico, attributable to the increased influx of pelagicSargassum sppand its accumulations in cays, bays, inlets and near-shore environments. Satellite imagery was co-registered, corrected for atmospheric effects, and masked for water and land. A Normalized Difference Vegetation Index (NDVI) and an unsupervised classification scheme were applied to the imagery to evaluate the changes in coastal vegetation and benthic composition. These products were used to calculate the differences from 2010 baseline imagery, to potential hurricane impacts (2018 image), and potentialSargassumimpacts (2020 image). Results show a negative trend in Normalized Difference Vegetation Index (NDVI) from 2010 to 2020 for the total pixel area of 24%, or 546,446 m2. These changes were also observed in true color images from 2010 to 2020. Changes in the NDVI negative values from 2018 to 2020 were higher, especially for the Isla Cueva site (97%) and were consistent with the field observations and drone surveys conducted since 2018 in the area. The major changes from 2018 and 2020 occurred mainly in unconsolidated sediments (e.g.sand, mud) and submerged aquatic vegetation (e.g.seagrass, algae), which can have similar spectra limiting the differentiation from multi-spectral imagery. Areas prone toSargassumaccumulation were identified using a combination of 2018 and 2020 true color VHR imagery and drone observations. This approach provides a quantifiable method to evaluateSargassumimpacts to the coastal vegetation and benthic composition using change detection of VHR images, and to separate these effects from other extreme events.
Development of photosynthetic carbon fixation model using multi-excitation wavelength fast repetition rate fluorometry in Lake Biwa
Authors: Kazama Takehiro , Hayakawa Kazuhide , Kuwahara Victor S. , Shimotori Koichi , Imai Akio , Komatsu Kazuhiro 
Published: August 2020

AbstractDirect measurements of gross primary productivity (GPP) in the water column are essential, but can be spatially and temporally restrictive. Fast repetition rate fluorometry (FRRf) is a bio-optical technique based on chlorophylla(Chl-a) fluorescence that can estimate the electron transport rate (ETRPSII) at photosystem II (PSII) of phytoplankton in real time. However, derivation of phytoplankton GPP in carbon units from ETRPSIIremains challenging because the electron requirement for carbon fixation (Фe,C) can vary depending on multiple factors. Also, the FRRf is still relatively novel, especially in freshwater ecosystems where phosphorus limitation and cyanobacterial blooms are common. The goal of the present study is to construct a robust Фe,Cmodel for freshwater ecosystems using simultaneous measurements of ETRPSIIby FRRf with multi-excitation wavelengths coupled with traditional carbon fixation rate by the13C method. The study was conducted in oligotrophic and mesotrophic areas in Lake Biwa from July 2018 to May 2019. The combination of excitation light at 444, 512 and 633 nm correctly estimated ETRPSIIof cyanobacteria. The range of Фe,Cin the phytoplankton community varied from 1.1 to 31.0 mol e−mol C−1during the study period. Generalized liner model showed the best model including 12 physicochemical and biological factors explained 67% of the variance in Фe,C. Among all factors, water temperature was the most significant, while PAR intensity was not. The GPP values estimated by FRRf (GPPf) with the best Фe,Cmodel relative to13C (GPP13C) varied 0.5–1.5. Further,GPPfestimated with more parsimonious Фe,Cmodels were also comparable toGPP13C. This study quantifies the applicability of thein situFRRf methodology, and supports continuous monitoring of GPP by FRRf in lakes with large spatio-temporal variability of environmental conditions and phytoplankton assemblages.
Aerobic glycolysis supports hepatitis B virus biosynthesis through interaction between viral surface antigen and pyruvate kinase isoform M2
Authors: Wu Yi-Hsuan , Yang Yi , Chen Ching-Hung , Hsiao Chia-Jen , Li Tian-Neng , Liao Kuan-Ju , Chen Bor-Sen , Wang Lily Hui-Ching 
Published: August 2020

AbstractAs an intracellular pathogen, the reproduction of hepatitis B virus (HBV) depends on the occupancy of host metabolism machinery. Here we test a hypothesis if HBV may govern intracellular biosynthesis to achieve a productive reproduction. To test this hypothesis, we set up an affinity purification screen for host factors that interact with viral large surface antigen (LHBS). This identified pyruvate kinase isoform M2 (PKM2), a key regulator of glucose metabolism, as a binding partner of LHBS. We showed that the expression of LHBS affected oligomerization of PKM2 in hepatocytes, and thereby increased glucose consumption and lactate production, a phenomenon known as aerobic glycolysis. Interestingly, recovering PKM2 activity in hepatocytes by chemical activators, TEPP-46 or DASA-58, reduced biosynthesis of viral surface and core antigens. In addition, reduction of glycolysis by culturing in low-glucose condition or treatment with 2-deoxyglucose also decreased biosynthesis of viral surface antigen, without affecting general host proteins. Finally, TEPP-46 largely suppressed proliferation of LHBS-positive cells on 3-dimensional agarose plates, but showed no effect on the traditional 2-dimensional cell culture. Taken together, these results indicate that virus-induced metabolic switch may supportde novobiosynthesis of HBV in hepatocytes. In addition, aerobic glycolysis is likely essential for LHBS-mediated oncogenesis. Accordingly, restriction of glucose metabolism may be considered as a novel strategy to restrain viral mediated biosynthesis and oncogenesis during chronic HBV infection.Author summaryChronic HBV infection is a life-long threat of patients, with a 25~40% increased risk of developing liver cirrhosis and cancer. Persistent expression of oncogenic viral products in the liver, especially LHBS, is an oncogenic caveat and resistant to current antiviral agents. Here we show that viral LHBS binds to host PKM2 and diminishes its kinase activity. This virus-host interaction induces metabolic switch from oxidative phosphorylation to aerobic glycolysis, with increased glucose consumption and lactate production. We show that such metabolic switch not only favors biosynthesis of HBV but also provokes hepatocarcinogenesis. Notably, restoration of PKM2 activity by chemical activators decreases expressions of viral products and largely suppresses virus-mediated hepatocarcinogenesis. This study highlights the importance of host metabolism in supporting viral biosynthesis and indicates a novel therapeutic approach to control chronic HBV infection via modulating host metabolic switch.
Social predation in electric eels
Authors: Bastos Douglas A. , Zuanon Jansen , Py-Daniel Lúcia Rapp , de Santana Carlos David 
Published: August 2020

AbstractSocial predation, when groups of predators coordinate actions to find and capture prey, is a common tactic among mammals but comparatively rare in fishes. We report the unexpected social predation by electric eels, an otherwise solitary predator in the Amazon rainforest. Observations made in different years and recorded on video show electric eels herding, encircling shoals of small nektonic fishes, and launching joint predatory high-voltage strikes on the prey ball. These findings challenge the hypothesis that electric eels may have a single foraging strategy, and extend our knowledge on social predation to an organism that employs high-voltage discharge for hunting, thereby offering a novel perspective for studies on the evolutionary interplay between predatory and escape tactics.
SDC3 acts as a timekeeper of myogenic differentiation by regulating the insulin/AKT/mTOR axis in muscle stem cell progeny
Authors: Jones Fiona K. , Phillips Alexander , Jones Andrew R. , Pisconti Addolorata 
Published: August 2020

AbstractMuscle stem cells (MuSCs) are indispensable for muscle regeneration. A multitude of extracellular stimuli direct MuSC fate decisions from quiescent progenitors to differentiated myocytes. The activity of these signals is modulated by coreceptors such as syndecan-3 (SDC3). We investigated the global landscape of SDC3-mediated regulation of myogenesis using a phosphoproteomics approach which revealed, with the precision level of individual phosphosites, the large-scale extent of SDC3-mediated regulation of signal transduction in MuSCs. We then focused on INSR/AKT/mTOR as a key pathway regulated by SDC3 during myogenesis and mechanistically dissected SDC3-mediated inhibition of insulin signaling in MuSCs. SDC3 interacts with INSR limiting insulin signal transduction via AKT/mTOR. Both knockdown of INSR and inhibition of AKT rescueSdc3-/-MuSC differentiation to wild type levels. Since SDC3 is rapidly downregulated at the onset of differentiation, our study suggests that SDC3 acts a timekeeper to restrain proliferating MuSC response to insulin and prevent premature differentiation.