bluuebunny/crossref_metadata_2025_split huggingface dataset:
The architecture of SARS-CoV-2 transcriptome
Authors: Kim Dongwan , Lee Joo-Yeon , Yang Jeong-Sun , Kim Jun Won , Kim V. Narry , Chang Hyeshik 
Published: March 2020

SummarySARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we here present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical. In addition to the genomic RNA and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces a large number of transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif being AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the internal modification and the 3′ tail. Functional investigation of the unknown ORFs and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2.HighlightsWe provide a high-resolution map of SARS-CoV-2 transcriptome and epitranscriptome using nanopore direct RNA sequencing and DNA nanoball sequencing.The transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical.In addition to the genomic and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces transcripts encoding unknown ORFs.We discover at least 41 potential RNA modification sites with an AAGAA motif.
Nucleotide Analogues as Inhibitors of SARS-CoV Polymerase
Authors: Ju Jingyue , Li Xiaoxu , Kumar Shiv , Jockusch Steffen , Chien Minchen , Tao Chuanjuan , Morozova Irina , Kalachikov Sergey , Kirchdoerfer Robert N. , Russo James J. 
Published: March 2020

SummarySARS-CoV-2, a member of the coronavirus family, has caused a global public health emergency.1 Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously reasoned that the FDA-approved heptatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) should inhibit coronaviruses, including SARS-CoV-2.2 Here, using model polymerase extension experiments, we demonstrate that the activated triphosphate form of Sofosbuvir is incorporated by low-fidelity polymerases and SARS-CoV RNA-dependent RNA polymerase (RdRp), and blocks further incorporation by these polymerases; the activated triphosphate form of Sofosbuvir is not incorporated by a host-like high-fidelity DNA polymerase. Using the same molecular insight, we selected two other anti-viral agents, Alovudine and AZT (an FDA approved HIV/AIDS drug) for evaluation as inhibitors of SARS-CoV RdRp. We demonstrate the ability of two HIV reverse transcriptase inhibitors, 3’-fluoro-3’-deoxythymidine triphosphate and 3’-azido-3’-deoxythymidine triphosphate (the active triphosphate forms of Alovudine and AZT), to be incorporated by SARS-CoV RdRp where they also terminate further polymerase extension. Given the 98% amino acid similarity of the SARS-CoV and SARS-CoV-2 RdRps, we expect these nucleotide analogues would also inhibit the SARS-CoV-2 polymerase. These results offer guidance to further modify these nucleotide analogues to generate more potent broad-spectrum anti-coronavirus agents.
Denoising large-scale biological data using network filters
Authors: Kavran Andrew J. , Clauset Aaron 
Published: March 2020

Large-scale biological data sets, e.g., transcriptomic, proteomic, or ecological, are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell cycle and life history variation, and from exogenous technical factors like sample preparation and instrument variation. Here we describe a general method for automatically reducing noise in large-scale biological data sets. This method uses an interaction network to identify groups of correlated or anti-correlated measurements that can be combined or “filtered” to better recover an underlying biological signal. Similar to the process of denoising an image, a single network filter may be applied to an entire system, or the system may be first decomposed into distinct modules and a different filter applied to each. Applied to synthetic data with known network structure and signal, network filters accurately reduce noise across a wide range of noise levels and structures. Applied to a machine learning task of predicting changes in human protein expression in healthy and cancerous tissues, network filtering prior to training increases accuracy up to 58% compared to using unfiltered data. These results indicate the broad potential utility of network-based filters to applications in systems biology.Author SummarySystem-wide measurements of many biological signals, whether derived from molecules, cells, or entire organisms, are often noisy. Removing or mitigating this noise prior to analysis can improve our understanding and predictions of biological phenomena. We describe a general way to denoise biological data that can account for both correlation and anti-correlation between different measurements. These “network filters” take as input a set of biological measurements, e.g., metabolite concentration, animal traits, neuron activity, or gene expression, and a network of how those measurements are biologically related, e.g., a metabolic network, food web, brain connectome, or protein-protein interaction network. Measurements are then “filtered” for correlated or anti-correlated noise using a set of other measurements that are identified using the network. We investigate the accuracy of these filters in synthetic and real-world data sets, and find that they can substantially reduce noise of different levels and structure. By denoising large-scale biological data sets, network filters have the potential to improve the analysis of many types of biological data.
Limited correspondence in visual representation between the human brain and convolutional neural networks
Authors: Xu Yaoda , Vaziri-Pashkam Maryam 
Published: March 2020

ABSTRACTConvolutional neural networks (CNNs) have achieved very high object categorization performance recently. It has increasingly become a common practice in human fMRI research to regard CNNs as working model of the human visual system. Here we reevaluate this approach by comparing fMRI responses from the human brain in three experiments with those from 14 different CNNs. Our visual stimuli included original and filtered versions of real-world object images and images of artificial objects. Replicating previous findings, we found a brain-CNN correspondence in a number of CNNs with lower and higher levels of visual representations in the human brain better resembling those of lower and higher CNN layers, respectively. Moreover, the lower layers of some CNNs could fully capture the representational structure of human early visual areas for both the original and filtered real-world object images. Despite these successes, no CNN examined could fully capture the representational structure of higher human visual processing areas. They also failed to capture that of artificial object images in all levels of visual processing. The latter is particularly troublesome, as decades of vision research has demonstrated that the same algorithms used in the processing of natural images would support the processing of artificial visual stimuli in the primate brain. Similar results were obtained when a CNN was trained with stylized object images that emphasized shape representation. CNNs likely represent visual information in fundamentally different ways from the human brain. Current CNNs thus may not serve as sound working models of the human visual system.Significance StatementRecent CNNs have achieved very high object categorization performance, with some even exceeding human performance. It has become common practice in recent neuroscience research to regard CNNs as working models of the human visual system. Here we evaluate this approach by comparing fMRI responses from the human brain with those from 14 different CNNs. Despite CNNs’ ability to successfully perform visual object categorization like the human visual system, they appear to represent visual information in fundamentally different ways from the human brain. Current CNNs thus may not serve as sound working models of the human visual system. Given the current dominating trend of incorporating CNN modeling in visual neuroscience research, our results question the validity of such an approach.
Systematically optimized BCMA/CS1 bispecific CAR-T cells robustly control heterogeneous multiple myeloma
Authors: Zah Eugenia , Nam Eunwoo , Bhuvan Vinya , Tran Uyen , Ji Brenda Y. , Gosliner Stanley B. , Wang Xiuli , Brown Christine E. , Chen Yvonne Y. 
Published: March 2020

ABSTRACTChimeric antigen receptor (CAR)-T cell therapy has shown remarkable clinical efficacy against B-cell malignancies but also demonstrated marked vulnerability to antigen escape and tumor relapse. Here, we report the rational design and systematic optimization of bispecific CAR-T cells with robust activity against multiple myeloma (MM), including heterogeneous MM that is resistant to conventional CAR-T cell therapy targeting B-cell maturation antigen (BCMA). We demonstrate that BCMA/CS1 bispecific CAR-T cells exhibit significantly higher CAR expression levels and greater antigen-stimulated proliferation compared to T cells that co-express individual BCMA and CS1 CARs. Compared to single-input BCMA- or CS1-targeting CAR-T cells, BCMA/CS1 bispecific CAR-T cells significantly prolong the survival of animals bearing heterogeneous MM tumors. Combination therapy with anti–PD-1 antibody further accelerates the rate of initial tumor clearancein vivo, but CAR-T cell treatment alone was able to achieve durable tumor-free survival even upon tumor re-challenge. Taken together, the BCMA/CS1 bispecific CAR presents a promising treatment approach to prevent antigen escape in CAR-T cell therapy against MM, and the vertically integrated optimization process can be used to develop robust cell-based therapy against novel disease targets.
TNPO3-mediated nuclear entry of the Rous sarcoma virus Gag protein is independent of the cargo-binding domain
Authors: Rice Breanna L. , Stake Matthew S. , Parent Leslie J. 
Published: March 2020

AbstractRetroviral Gag polyproteins orchestrate the assembly and release of nascent virus particles from the plasma membranes of infected cells. Although it was traditionally thought that Gag proteins trafficked directly from the cytosol to the plasma membrane, we discovered that the oncogenic avian alpharetrovirus Rous sarcoma virus (RSV) Gag protein undergoes transient nucleocytoplasmic transport as an intrinsic step in virus assembly. Using a genetic approach in yeast, we identified three karyopherins that engage the two independent nuclear localization signals (NLS) in Gag. The primary NLS is in the nucleocapsid (NC) domain of Gag and binds directly to importin-α, which recruits importin-β to mediate nuclear entry. The second NLS, which resides in the matrix (MA) domain, is dependent on importin-11 and transportin-3 (TNPO3), known as MTR10p and Kap120p in yeast, although it is not clear whether these import factors are independent or additive. The functionality of importin α/β and importin-11 has been verified in avian cells, whereas the role of TNPO3 has not been studied. In this report, we demonstrate that TNPO3 mediates nuclear entry of Gag and directly binds to Gag. To our surprise, this interaction did not require the cargo-binding domain of TNPO3, which typically mediates nuclear entry for other binding partners of TNPO3 including SR-domain containing splicing factors and tRNAs that re-enter the nucleus. These results suggest that RSV hijacks the host nuclear import pathway using a unique mechanism, potentially allowing other cargo to bind TNPO3 simultaneously.ImportanceRSV Gag nuclear entry is facilitated using three distinct host import factors that interact with nuclear localization signals in the Gag MA and NC domains. Here we show that the MA region is required for nuclear import of Gag through the TNPO3 pathway. Gag nuclear entry does not require the cargo binding domain of TNPO3. Understanding the molecular basis for TNPO3-mediated nuclear trafficking of the RSV Gag protein may lead to a deeper appreciation for whether different import factors play distinct roles in retrovirus replication.
Angioplasty-induced epigenomic remodeling entails BRD4 and EZH2 hierarchical regulations
Authors: Zhang Mengxue , Wang Bowen , Urabe Go , Ozer Hatice Gulcin , Han Renzhi , Kent K. Craig , Guo Lian-Wang 
Published: March 2020

AbstractAtherosclerosis is commonly treated with angioplasty which, however, evokes neointimal hyperplasia (IH) and recurrent stenotic diseases. Epigenomic investigation was lacking on post-angioplasty IH. The histone acetylation reader BRD4 and H3K27me3 writer EZH2 are potent epigenetic factors; their relationship is little understood. Through genome-wide survey in the rat angioplasty model, we studied BRD4 and EZH2 functional regulations involved in IH.We performed chromatin immunoprecipitation sequencing (ChIPseq) using rat carotid arteries. While H3K27me3 ChIPseq signal prevalently intensified in balloon-injured (vsuninjured) arteries, BRD4 and H3K27ac became more enriched atEzh2. Indeed, BRD4-siRNA or CRISPR-deletion of BRD4-associated enhancer abated the smooth muscle cell (SMC) expression of EZH2, and SMC-specific BRD4 knockout inBRD4fl/fl;Myh11CreERT2mice reduced both H3K27me3 and IH in wire-injured femoral arteries. In accordance, post-angioplasty IH was exacerbated and mitigated, respectively, by lentiviral expression and pharmacological inhibition of EZH2/1; EZH2 (or EZH1) loss- and gain-of-function respectively attenuated and aggravated pro-IH SMC proliferative behaviors. Furthermore, while H3K27me3 ChIPseq signal magnified atP57and ebbed atCcnd1andUhrf1after injury, silencing either EZH2 or EZH1 in SMCs up-regulatedP57and down-regulatedCcnd1andUhrf1.In summary, our results reveal an upsurge of EZH2/H3K27me3 after angioplasty, BRD4’s control over EZH2 expression, and non-redundant EZH2/1 functions. As such, this study unravels angioplasty-induced loci-specific H3K27me3/ac redistribution in the epigenomic landscape rationalizing BRD4/EZH2-governed pro-IH regulations.
Systematics of the oil bee genusLanthanomelissaand its implications to the biogeography of southern grasslands
Authors: Ribeiro Taís M. A. , Martins Aline C. , Silva Daniel P. , Aguiar Antonio J. C. 
Published: March 2020

AbstractLanthanomelissais a controversial taxonomic group of bees that was treated as subgenus ofChalepogenusor an independent genus. All of its species are endemic to the south-eastern grasslands of South America, an endangered and still poorly known environment. We aimed to understand the origin of this group of bees in time and space as well as the influence of Quaternary climatic fluctuations on its current distribution and possible link to the history of the Southern Grasslands. We inferred phylogenetic relationships ofLanthanomelissaspecies using 37 terminals and 3430 nucleotides of three mitochondrial and two nuclear markers and estimated divergence times and ancestral geographic range. We performed an ensemble with the algorithms SVM, Maxent, and Random Forest in a dataset of 192 georeferenced occurrence points using 19 WorldClim bioclimatic variables to analyse species distribution during the current and two past climatic scenarios (LIG, ∼120 kya and LGM, ∼21 kya). The results support the monophyly of the genus and taxonomic changes including the speciesLanthanomelissa parvan. comb. onLanthanomelissa, and the treatment of thegoeldianusgroup ofChalepogenusas the genusLanthanella.The genus originated at the Oligocene-Miocene border in the Chacoan-Pampean region, and the glacial-interglacial models indicated expansion in Last Glacial Maximum and retraction in Last Interglacial. Expansion and retraction ofLanthanomelissadistribution in the last glacial-interglacial indicated grasslands distributional shifts during periods of climate cooling and warming. The diversification ofLanthanomelissasupported the estimated expansion of southern grasslands in South America concurrently with the origin of Cerrado during the late Miocene. Their origin was approximately synchronized with their exclusive floral host,Sisyrinchium(Iridaceae).
Sensitive spatial genome wide expression profiling at cellular resolution
Authors: Stickels Robert R. , Murray Evan , Kumar Pawan , Li Jilong , Marshall Jamie L. , Di Bella Daniela , Arlotta Paola , Macosko Evan Z. , Chen Fei 
Published: March 2020

AbstractThe precise spatial localization of molecular signals within tissues richly informs the mechanisms of tissue formation and function. Previously, we developed Slide-seq, a technology which enables transcriptome-wide measurements with 10-micron spatial resolution. Here, we report new modifications to Slide-seq library generation, bead synthesis, and array indexing that markedly improve the mRNA capture sensitivity of the technology, approaching the efficiency of droplet-based single-cell RNAseq techniques. We demonstrate how this modified protocol, which we have termed Slide-seqV2, can be used effectively in biological contexts where high detection sensitivity is important. First, we deploy Slide-seqV2 to identify new dendritically localized mRNAs in the mouse hippocampus. Second, we integrate the spatial information of Slide-seq data with single-cell trajectory analysis tools to characterize the spatiotemporal development of the mouse neocortex. The combination of near-cellular resolution and high transcript detection will enable broad utility of Slide-seq across many experimental contexts.
Cholinergic basal forebrain degeneration due to obstructive sleep apnoea increases Alzheimer’s pathology in mice
Authors: Qian Lei , Kasas Leda , Milne Michael R , Rawashdeh Oliver , Marks Nicola , Sharma Aanchal , Bellingham Mark C , Coulson Elizabeth J 
Published: March 2020

AbstractEpidemiological studies indicate that obstructive sleep apnoea is a strong risk factor for the development of Alzheimer’s disease but the mechanisms of the risk remain unclear. We developed a method of modelling obstructive sleep apnoea in mice that replicates key features of human obstructive sleep apnoea: altered breathing during sleep, sleep disruption, moderate intermittent hypoxemia and cognitive impairment. When we induced obstructive sleep apnoea in a familial Alzheimer’s disease model, the mice displayed exacerbation of cognitive impairment and pathological features of Alzheimer’s disease, including increased levels of amyloid-beta and inflammatory markers, as well as selective degeneration of cholinergic basal forebrain neurons. These pathological features were not induced by chronic hypoxia or sleep disruption alone. Our results also revealed that the neurodegeneration was mediated by the oxygen-sensitive p75 neurotrophin receptor and hypoxia inducible factor 1 alpha activity. Furthermore, restoring blood oxygen levels during sleep to prevent intermittent hypoxia prevented the pathological changes induced by the OSA. These findings provide a signalling mechanism by which obstructive sleep apnoea induces cholinergic basal forebrain degeneration and could thereby increase the risk of developing Alzheimer’s disease, as well as providing a rationale for testing a range of possible prophylactic treatment options for people with obstructive sleep apnoea and hypoxia including increased compliance of continuous positive airway pressure therapy.
Nanopore long-read transcriptome data of fungal pathogen of chalkbrood disease,Ascosphaera apis
Authors: Du Yu , Chen Huazhi , Wang Jie , Zhu Zhiwei , Xiong Cuiling , Zheng Yanzhen , Chen Dafu , Guo Rui 
Published: March 2020

ABSTRACTAscosphaera apisis a fungal pathogen that exclusively infects honeybee larvae, leading to chalkbrood disease, which damages the number of adult honeybees and colony productivity. In this article,A. apismecylia and spores were respectively purified followed by Oxford Nanopore sequencing via PromethION platform. In total, 6,321,704 and 6,259,727 raw reads were generated from Aam and Aas, with a length distribution among 1 kb~10 kb. The quality (Q) scores of majority of raw reads were Q9 (Aam) and Q11 (Aas). Additionally, 5,669,436 and 6,233,159 clean reads were gained, among them 79.32% and 79.62% were identified as being full-length. The lengths of redundant reads-removed full-length transcripts were among 1 kb~8 kb and 1 kb~9 kb, and most abundant length for both was 1 kb. Furthermore, the length of redundant transcripts-removed clean reads was ranged from 1 kb~7 kb, with the largest group of 1 kb. The data reported here provides a beneficial genetic resource for improving genome and transcriptome annotations ofA. apisand for exploring alternative splicing and polyadenylation ofA. apismRNAs.Value of the resultCurrent dataset enables better understanding of the complexity ofA. apistranscriptome.The long-read transcriptome data can be used to identify of genes and transcripts associated withA. apisinfection mechanism.The accessible data provides full-length transcripts for improving gene structure and functional annotation ofA. apistranscriptome.This dataset could be utilized for investigation of alternative splicing and polyadenylation ofA. apismRNAs.
Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants
Authors: Kastner David B. , Kharazia Viktor , Nevers Rhino , Astudillo-Maya Daniela A. , Williams Greer M. , Yang Zhounan , Smyth Clay , Santina Luca Della , Parkinson Dilworth Y. , Frank Loren M. 
Published: March 2020

AbstractAnatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesions studies require removal of the skull and hazardous chemicals, dehydration or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of brain lesions.