bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureumSchum.)
Authors: Zhang Shengkui , Xia Zhiqiang , Zhang Wenqing , Li Can , Wang Xiaohan , Lu Xianqin , Zhao Xianyan , Ma Haizhen , Zhou Xincheng , Zhang Weixiong , Zhu Tingting , Liu Pandao , Liu Guodao , Yang Hubiao , Arango Jacobo , Peters Michael , Wang Wenquan , Xia Tao 
Published: March 2020

AbstractElephant grass (Pennisetum purpureumSchum., A’A’BB, 2n=4x=28), which is characterized as robust growth and high biomass, and widely distributed in tropical and subtropical areas globally, is an important forage, biofuels and industrial plant. We sequenced its allopolyploid genome and assembled 2.07 Gb (96.88%) into A’ and B sub-genomes of 14 chromosomes with scaffold N50 of 8.47 Mb. A total of 38,453 and 36,981 genes were annotated in A’ and B sub-genomes, respectively. A phylogenetic analysis with species inPennisetumidentified that the speciation of the allotetraploid occurred approximately 15 MYA after the divergence betweenS.italicaandP. glaucum. Double whole-genome duplication (WGD) and polyploidization events resulted in large scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional differentiation between sub-genomes; A’ sub-genome contributed more to plant growth, development and photosynthesis whereas B sub-genome primarily offered functions of effective transportation and resistance to stimulation. The results uncovered enhanced cellulose and lignin biosynthesis pathways with 645 and 666 genes expanded in A’ and B sub-genomes, respectively. Our findings provided deep insights into the speciation and genetic basis of fast growth and high biomass accumulation in the species. The genetic, genomic, and transcriptomic resources generated in this study will pave the way for further domestication and selection of these economical species and making them more adaptive to industrial utilization.
Precautions are Needed for COVID-19 Patients with Coinfection of Common Respiratory Pathogens
Authors: Xing Quan-sheng , Li Guo-ju , Xing Yu-han , Chen Ting , Li Wen-jie , Ni Wei , Deng Kai , Gao Ru-qin , Chen Chang-zheng , Gao Yang , Li Qiang , Yu Gui-ling , Tong Jian-ning , Li Wei , Hao Gui-liang , Sun Yue , Zhang Ai , Wu Qin , Li Zi-pu , Pan Si-lin 
Published: March 2020

AbstractBackgroundWith the ongoing outbreak of Coronavirus Disease 2019 (COVID-19), infected patients within and beyond the epidemic area, Wuhan, China, showed different epidemiological and clinical characteristics. There is a paucity of data concerning coinfection with other common respiratory pathogens in COVID-19 patients outside of Wuhan.MethodsWe conducted a double-centre study recruiting 68 patients with severe acute respiratory coronavirus 2 (SARS-CoV-2) infection confirmed by nucleic acid testing in Qingdao and Wuhan from January 17 to February 16, 2020. Indirect immunofluorescence was performed to detect the specific IgM antibody against common respiratory pathogens in collected acute phase serum.ResultsOf the 68 patients with SARS-CoV-2 infection, 30 (44.12%) were from Qingdao. The median age of Qingdao and Wuhan patients were 50 (IQR: 37-59) and 31 (IQR: 28-38) years, respectively, and the majority of patients were female in Qingdao (60.00%) and Wuhan (55.26%). Among COVID-19 patients in Qingdao, 24 (80.00%) of them had IgM antibodies against at least one respiratory pathogen, whereas only one (2.63%) of the patients in Wuhan had positive results for serum IgM antibody detection (P<0.0001). The most common respiratory pathogens detected in Qingdao COVID-19 patients were influenza virus A (60.00%) and influenza virus B (53.33%), followed by mycoplasma pneumoniae (23.33%) and legionella pneumophila (20.00%). While the pattern for coinfection in patients with community-acquired pneumonia in Qingdao was quite different, with a positive rate of only 20.90%.InterpretationWe reported a large proportion of COVID-19 patients with coinfection of seasonal respiratory pathogens in Qingdao, northeast China, which differed greatly from the patients in Wuhan, central China. Precautions are needed when dealing with COVID-19 patients beyond the epidemic centre who have coinfection with other respiratory pathogens. We highly recommend adding SARS-CoV-2 to routine diagnostic testing in capable hospitals to prevent misdetection of the virus.
Smartphone addiction and its association with common mental disorders among students attending the university of Dschang, West region, Cameroon
Authors: Sonkoue Martial Pianta , Kadia Benjamin Momo , Esong Miranda Baame , Douanla Cyrielle Djouda , Ateudjieu Jerome 
Published: March 2020

AbstractBackgroundSmartphones are an integral part of modern communication but addiction to these devices could predispose to common mental disorders.ObjectivesTo determine the prevalence of smartphone addiction and common mental disorders as well as the association between smartphone addiction and these mental disorders in Dschang university students who use smartphones.MethodsA cross-sectional study was conducted. Randomly selected students completed a survey comprising Patient Health Questionnaires seven and nine (PHQ-9 and PHQ-7) to screen for depression and anxiety respectively, and the Smartphone Addiction Scale-Short Version (SAS-SV) to grade smartphone use. The association between smartphone use and common mental disorders was assessed using logistic regression modelling.ResultsWe recruited 634 participants. The prevalence of smartphone addiction was 20.98% [C.I:17.99%-24.32%]. The prevalence of depression and anxiety were 34.86% [95% CI: 31.25-38.65] and 19.27% [95% CI: 16.81-22.99] respectively. The odds of depression in students with addiction was 5 times the odds of depression in students without addiction [OR: 4.96, 95% CI: 3.30-7.45, p<0.001]. The odds of anxiety in students with addiction was 2 times the odds of anxiety in students without addiction [OR: 2.44, 95% CI: 1.58-3.77, p<0.001]. After adjusting for age, sex, faculty, cycle of study, marital status, religion, chronic diseases, sexual abuse and suicidal ideation, there remained a statistically-significant association between smartphone addiction and both depression [OR: 4.46, 95%CI; 2.92-6.84, p<0.001] and anxiety [OR: 2.08, 95% CI; 1.31-3.30, p=0.002].ConclusionIn this setting, it is crucial to foster strategies of prevention and promotion in mental health especially among problematic smartphone users.
An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types
Authors: Yao Zizhen , Liu Hanqing , Xie Fangming , Fischer Stephan , Booeshaghi A. Sina , Adkins Ricky S , Aldridge Andrew I. , Ament Seth A. , Pinto-Duarte Antonio , Bartlett Anna , Behrens M. Margarita , Van den Berge Koen , Bertagnolli Darren , Biancalani Tommaso , Bravo Héctor Corrada , Casper Tamara , Colantuoni Carlo , Creasy Heather , Crichton Kirsten , Crow Megan , Dee Nick , Dougherty Elizabeth L , Doyle Wayne I. , Dudoit Sandrine , Fang Rongxin , Felix Victor , Fong Olivia , Giglio Michelle , Goldy Jeff , Hawrylycz Mike , de Bézieux Hector Roux , Herb Brian R. , Hertzano Ronna , Hou Xiaomeng , Hu Qiwen , Crabtree Jonathan , Kancherla Jayaram , Kroll Matthew , Lathia Kanan , Li Yang Eric , Lucero Jacinta D. , Luo Chongyuan , Mahurkar Anup , McMillen Delissa , Nadaf Naeem , Nery Joseph R. , Niu Sheng-Yong , Orvis Joshua , Osteen Julia K. , Pham Thanh , Poirion Olivier , Preissl Sebastian , Purdom Elizabeth , Rimorin Christine , Risso Davide , Rivkin Angeline C. , Smith Kimberly , Street Kelly , Sulc Josef , Nguyen Thuc Nghi , Tieu Michael , Torkelson Amy , Tung Herman , Vaishnav Eeshit Dhaval , Svensson Valentine , Vanderburg Charles R. , Ntranos Vasilis , van Velthoven Cindy , Wang Xinxin , White Owen R. , Huang Z. Josh , Kharchenko Peter V. , Pachter Lior , Ngai John , Regev Aviv , Tasic Bosiljka , Welch Joshua D. , Gillis Jesse , Macosko Evan Z. , Ren Bing , Ecker Joseph R. , Zeng Hongkui , Mukamel Eran A. 
Published: March 2020

AbstractSingle cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningful cell types. We used a battery of single-cell transcriptome and epigenome measurements generated by the BRAIN Initiative Cell Census Network (BICCN) to comprehensively assess the molecular signatures of cell types in the mouse primary motor cortex (MOp). We further developed computational and statistical methods to integrate these multimodal data and quantitatively validate the reproducibility of the cell types. The reference atlas, based on more than 600,000 high quality single-cell or -nucleus samples assayed by six molecular modalities, is a comprehensive molecular account of the diverse neuronal and non-neuronal cell types in MOp. Collectively, our study indicates that the mouse primary motor cortex contains over 55 neuronal cell types that are highly replicable across analysis methods, sequencing technologies, and modalities. We find many concordant multimodal markers for each cell type, as well as thousands of genes and gene regulatory elements with discrepant transcriptomic and epigenomic signatures. These data highlight the complex molecular regulation of brain cell types and will directly enable design of reagents to target specific MOp cell types for functional analysis.
The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 Receptor Binding Domain undergoes conformational change upon heparin binding
Authors: Mycroft-West Courtney , Su Dunhao , Elli Stefano , Li Yong , Guimond Scott , Miller Gavin , Turnbull Jeremy , Yates Edwin , Guerrini Marco , Fernig David , Lima Marcelo , Skidmore Mark 
Published: March 2020

AbstractMany pathogens take advantage of the dependence of the host on the interaction of hundreds of extracellular proteins with the glycosaminoglycans heparan sulphate to regulate homeostasis and use heparan sulphate as a means to adhere and gain access to cells. Moreover, mucosal epithelia such as that of the respiratory tract are protected by a layer of mucin polysaccharides, which are usually sulphated. Consequently, the polydisperse, natural products of heparan sulphate and the allied polysaccharide, heparin have been found to be involved and prevent infection by a range of viruses including S-associated coronavirus strain HSR1. Here we use surface plasmon resonance and circular dichroism to measure the interaction between the SARS-CoV-2 Spike S1 protein receptor binding domain (SARS-CoV-2 S1 RBD) and heparin. The data demonstrate an interaction between the recombinant surface receptor binding domain and the polysaccharide. This has implications for the rapid development of a first-line therapeutic by repurposing heparin and for next-generation, tailor-made, GAG-based antivirals.
An ultrasensitive, rapid, and portable coronavirus SARS-CoV-2 sequence detection method based on CRISPR-Cas12
Authors: Lucia Curti , Federico Pereyra-Bonnet , Alejandra Gimenez Carla 
Published: March 2020

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has received global attention due to the recent outbreak in China. In this work, we report a CRISPR-Cas12 based diagnostic tool to detect synthetic SARS-CoV-2 RNA sequences in a proof-of-principle evaluation. The test proved to be sensitive, rapid, and potentially portable. These key traits of the CRISPR method are critical for virus detection in regions that lack resources to use the currently available methods.
Structural basis of transcription-translation coupling and collision in bacteria
Authors: Webster Michael William , Takacs Maria , Zhu Chengjin , Vidmar Vita , Eduljee Ayesha , Abdelkareem Mo’men , Weixlbaumer Albert 
Published: March 2020

AbstractProkaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The pioneering ribosome potentially contacts RNA polymerase (RNAP), forming a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here we present a series of structures representing uncoupled, coupled and collided expressome states determined by electron cryomicroscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, stabilizing an otherwise variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance-channel to the RNAP exit-channel. In this collided complex, NusG-linkage is no longer possible.These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.One Sentence SummaryStructures of the molecular assembly executing gene expression shed light on transcription translation coupling.
Induced Polarization in MD Simulations of the 5HT3Receptor Channel
Authors: Klesse Gianni , Rao Shanlin , Tucker Stephen J. , Sansom Mark S.P. 
Published: March 2020

AbstractIon channel proteins form water-filled nanoscale pores within lipid bilayers and their properties are dependent on the complex behavior of water in a nano-confined environment. Using the pore of the 5HT3 receptor (5HT3R) we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular Dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model, to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl− ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl− whilst it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.ToC Graphic
Expression of the endocannabinoid system in the human airway epithelial cells – Impact of sex and chronic respiratory disease status
Authors: Fantauzzi Matthew F. , Aguiar Jennifer A. , Tremblay Benjamin J-M. , Yanagihara Toyoshi , Chandiramohan Abiram , Revill Spencer , Ryu Min Hyung , Carlsten Chris , Ask Kjetil , Stämpfli Martin , Doxey Andrew C. , Hirota Jeremy A. 
Published: March 2020

ABSTRACTRecreational and medicinal cannabis consumption in the past 12 months has been reported in 1/5th of Canadians, with greater use in males relative to females. Cannabis smoking is the dominant route of delivery in consumers, with the airway epithelium functioning as the site of first contact for inhaled phytocannabinoids. The endocannabinoid system is responsible for mediating the physiological effects of inhaled phytocannabinoids. Acute cannabis smoke inhalation can result in bronchodilation, which may have applications in chronic respiratory disease management. In contrast, chronic cannabis smoke inhalation is associated with reduced lung function and bronchitis, which challenges potential applications in the lung. The contribution of the endocannabinoid system in the airway epithelium to either beneficial or harmful physiological responses remains to be clearly defined in males and females and those with underlying chronic respiratory disease.To begin to address this knowledge gap, a curated dataset of 1090 unique human bronchial brushing gene expression profiles was created from Gene Expression Omnibus deposited microarray datasets. The dataset included 616 healthy subjects, 136 subjects with asthma, and 338 subjects with COPD. A 27-gene endocannabinoid signature was analyzed across all samples with sex and disease specific-analyses performed. Immunohistochemistry and immunoblots were performed to confirm in situ and in vitro protein expression of select genes in human airway epithelial cells.We confirm three receptors for cannabinoids, CB1, CB2, and TRPV1, are expressed at the protein level in human airway epithelial cells in situ and in vitro, justifying examining the downstream endocannabinoid pathway more extensively at the gene expression level. Sex status was associated with differential expression of 6/27 genes. In contrast, disease status was associated with differential expression of 18/27 genes in asthmatics and 22/27 genes in COPD subjects. We confirm at the protein level that TRPV1, the most differentially expressed candidate in our analyses, was up-regulated in airway epithelial cells from asthmatics relative to healthy subjects.Our data demonstrate that endocannabinoid system is expressed in human airway epithelial cells with expression impacted by disease status and minimally by sex. The data suggest that cannabis consumers may have differential physiological responses in the respiratory mucosa, which could impact both acute and chronic effects of cannabis smoke inhalation.
Forecasting the Cumulative Number of COVID-19 Deaths in China: a Boltzmann Function-based Modeling Study
Authors: Gao Yuanyuan , Li Zhongyan , Ying Qi , Long Cheng , Fu Xinmiao 
Published: March 2020

AbstractThe COVID-19 outbreak is on-going in China. Here we estimated the potential total numbers of COVID-19 deaths in China, outside Hubei (in China), Hubei Province, Wuhan City and outside Wuhan (in Hubei) by Boltzmann function-based analyses, which are 3342 (95% CI, 3214, 3527), 111 (109, 114), 3245 (3100, 3423), 2613 (2498, 2767) and 627 (603, 654), respectively. The results may help to evaluate the severity of COVID-19 outbreaks and facilitate timely mental service for the families of passed patients.
Diversification of molecularly defined myenteric neuron classes revealed by single cell RNA-sequencing
Authors: Morarach Khomgrit , Mikhailova Anastassia , Knoflach Viktoria , Memic Fatima , Kumar Rakesh , Li Wei , Ernfors Patrik , Marklund Ulrika 
Published: March 2020

ABSTRACTAutonomous functions of the gastrointestinal tract require the combined activity of functionally distinct neurons of the enteric nervous system (ENS). However, the range of enteric neuron diversity and how it emerges during development remain largely unknown. We here make a novel molecular definition of 12 enteric neuron classes (ENCs) within the myenteric plexus of the mouse small intestine. We identify communication features and provide histochemical markers for discrete motor, sensory, and interneurons together with genetic tools for class-specific targeting. Transcriptome analysis of embryonic ENS reveals a largely post-mitotic principle of diversification, where only ENC1 or ENC8 phenotypic traits arise through a binary neurogenic trajectory, and other identities form through subsequent differentiation. We propose generic and class-specific transcriptional regulators and functionally connect the transcription factorPbx3to one post-mitotic identity conversion. Our results offers a conceptual and molecular resource for dissecting ENS circuits, and predicting key regulators for the directed differentiation of distinct enteric neuron classes.
Interaction of RSC chromatin remodelling complex with nucleosomes is modulated by H3 K14 acetylation and H2B SUMOylationin vivo
Authors: Jain Neha , Tamborrini Davide , Evans Brian , Chaudhry Shereen , Wilkins Bryan J. , Neumann Heinz 
Published: March 2020

AbstractChromatin remodelling complexes are multi-subunit nucleosome translocases that reorganize chromatin in the context of DNA replication, repair and transcription. A key question is how these complexes find their target sites on chromatin. Here, we use genetically encoded photo-crosslinker amino acids to map the footprint of Sth1, the catalytic subunit of the RSC (remodels the structure of chromatin) complex, on the nucleosome in living yeast. We find that the interaction of the Sth1 bromodomain with the H3 tail depends on K14 acetylation by Gcn5. This modification does not recruit RSC to chromatin but mediates its interaction with neighbouring nucleosomes. We observe a preference of RSC for H2B SUMOylated nucleosomesin vivoand show that this modification moderately enhances RSC binding to nucleosomesin vitro. Furthermore, RSC is not ejected from chromatin in mitosis, but its mode of nucleosome binding differs between interphase and mitosis. In sum, ourin vivoanalyses show that RSC recruitment to specific chromatin targets involves multiple histone modifications most likely in combination with other components such as histone variants and transcription factors.Key PointsIn vivophoto-crosslinking reveals the footprint of the ATPase subunit of RSC on the nucleosome.RSC binds to H3 K14ac nucleosomes via the C-terminal bromodomain of its ATPase-subunit Sth1.RSC preferentially localizes to H2B-SUMOylated nucleosomes.
Ultrastructural comparison of dendritic spine morphology preserved with cryo and chemical fixation
Authors: Tamada Hiromi , Blanc Jerome , Korogod Natalya , Petersen Carl CH , Knott Graham W 
Published: March 2020

ABSTRACTPreviously we showed that cryo fixation of brain tissue gave a truer representation of brain ultrastructure in comparison with a standard chemical fixation method (Korogod et al 2005). Extracellular space matched physiological measurements, there were larger numbers of docked vesicles and less glial coverage of synapses and blood capillaries. Here, using the same preservation approaches we compared the morphology of dendritic spines. We show that the length of the spine and the volume of its head is unchanged, however, the spine neck width is thinner by more than 30 % after cryo fixation. In addition, the weak correlation between spine neck width and head volume seen after chemical fixation was not present in cryo-fixed spines. Our data suggest that spine neck geometry is independent of the spine head volume, with cryo fixation showing enhanced spine head compartmentalization and a higher predicted electrical resistance between spine head and parent dendrite.