bluuebunny/crossref_metadata_2025_split huggingface dataset:
̃Evaluating reduction in CoViD-19 cases by isolation and protective measures in São Paulo State, Brazil, and scenarios of release
Authors: Yang Hyun Mo , Junior Luis Pedro Lombardi , Castro Fabio Fernandes Morato , Yang Ariana Campos 
Published: May 2020

AbstractSão Paulo State registered the first case of CoViD-19 on 26 February, the first death due to CoViD-19 on 16 March, and implemented the isolation of the population in non-essential activities on 24 March, which is programmed to end on 1 June. A mathematical model considering young (below 60 years old) and elder (above 60 years) subpopulations was formulated based on the natural history of CoViD-19 to study the transmission of the new coronavirus in São Paulo State, Brazil. This deterministic model used the data collected in São Paulo State to estimate the model parameters and to evaluate the effects of herd protection, that is, isolation and personal and collective protective measures. Based on the estimated parameters, we evaluated the scenarios of three releases divided in equal proportions elapsed by 14 days between releases, but beginning in three different times (the first release occurring on 1 and 23 June, and 6 July). We concluded that these three strategies of release are equivalent (little difference) in reducing the number of severe CoViD-19 if social behaviour does not change. However, if protective measures as using face mask and hygiene (washing hands, for instance) and social distancing could be massively disseminated in the population to decrease the transmission of CoViD-19 by 80%, we concluded that the health care system may not collapse with release.
A simple criterion to design optimal non-pharmaceutical interventions for epidemic outbreaks
Authors: Angulo Marco Tulio , Castaños Fernando , Moreno-Morton Rodrigo , Velasco-Hernández Jorge X. , Moreno Jaime A. 
Published: May 2020

AbstractFor mitigating the COVID-19 pandemic, much emphasis is made on implementing non-pharmaceutical interventions to keep the reproduction number below one. However, using that objective ignores that some of these interventions, like bans of public events or lockdowns, must be transitory and as short as possible because of their significative economic and societal costs. Here we derive a simple and mathematically rigorous criterion for designing optimal transitory non-pharmaceutical interventions for mitigating epidemic outbreaks. We find that reducing the reproduction number below one is sufficient but not necessary. Instead, our criterion prescribes the required reduction in the reproduction number according to the desired maximum of disease prevalence and the maximum decrease of disease transmission that the interventions can achieve. We study the implications of our theoretical results for designing non-pharmaceutical interventions in 16 cities and regions during the COVID-19 pandemic. In particular, we estimate the minimal reduction of each region’s contact rate necessary to control the epidemic optimally. Our results contribute to establishing a rigorous methodology to guide the design of optimal non-pharmaceutical intervention policies.
Maturation of complex synaptic connections of layer 5 cortical axons in the posterior thalamic nucleus requires SNAP25
Authors: Hayashi Shuichi , Hoerder-Suabedissen Anna , Kiyokage Emi , Maclachlan Catherine , Toida Kazunori , Knott Graham , Molnár Zoltán 
Published: May 2020

AbstractSynapses are able to form in the absence of neuronal activity, but how is their subsequent maturation affected in the absence of regulated vesicular release? We explored this question using 3D electron microscopy and immuno electron microscopy analyses in the large, complex synapses formed between cortical sensory efferent axons and dendrites in the posterior thalamic nucleus. Using aSnap25conditional knockout we found that during the first two postnatal weeks the axonal boutons emerge and increase in the size similar to the control animals. However, by P18, when an adult-like architecture should normally be established, axons were significantly smaller with 3D reconstructions showing that eachSnap25-cko bouton only forms a single synapse with the connecting dendritic shaft. No excrescences from the dendrites were formed, and none of the normally large glomerular axon endings were seen. These results show that activity mediated through regulated vesicular release from the presynaptic terminal is not necessary for the formation of synapses, but it is required for the maturation of the specialised synaptic structures between layer 5 corticothalamic projections in Po.
Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy
Authors: Xiang Xi , Qu Kunli , Liang Xue , Pan Xiaoguang , Wang Jun , Han Peng , Dong Zhanying , Liu Lijun , Zhong Jiayan , Ma Tao , Wang Yiqing , Yu Jiaying , Zhao Xiaoying , Li Siyuan , Xu Zhe , Wang Jinbao , Zhang Xiuqing , Jiang Hui , Xu Fengping , Zou Lijin , Teng Huajing , Liu Xin , Xu Xun , Wang Jian , Yang Huanming , Bolund Lars , Church George M. , Lin Lin , Luo Yonglun 
Published: May 2020

AbstractThe CRISPR RNA-guided endonucleases Cas9, and Cas9-derived adenine/cytosine base editors (ABE/CBE), have been used in both research and therapeutic applications. However, broader use of this gene editing toolbox is hampered by the great variability of efficiency among different target sites. Here we present TRAP-seq, a versatile and scalable approach in which the CRISPR gRNA expression cassette and the corresponding surrogate site are captured byTargetedReporterAnchoredPositionalSequencing in cells. TRAP-seq can faithfully recapitulate the CRISPR gene editing outcomes introduced to the corresponding endogenous genome site and most importantly enables massively parallel quantification of CRISPR gene editing in cells. We demonstrate the utility of this technology for high-throughput quantification of SpCas9 editing efficiency and indel outcomes for 12,000 gRNAs in human embryonic kidney cells. Using this approach, we also showed that TRAP-seq enables high throughput quantification of both ABE and CBE efficiency at 12,000 sites in cells. This rich amount of ABE/CBE outcome data enable us to reveal several novel nucleotide features (e.g. preference of flanking bases, nucleotide motifs, STOP recoding types) affecting base editing efficiency, as well as designing improved machine learning-based prediction tools for designing SpCas9, ABE and CBE gRNAs of high efficiency and accuracy (>70%). We have integrated all the 12,000 CRISPR gene editing outcomes for SpCas9, ABE and CBE into a CRISPR-centered portal: The Human CRISPR Atlas. This study extends our knowledge on CRISPR gene and base editing, and will facilitate the application and development of CRISPR in both research and therapy.
Traction Force Microscopy by Deep Learning
Authors: Wang Y.L. , Lin Y.-C. 
Published: May 2020

AbstractCells interact mechanically with their surrounding by exerting forces and sensing forces or force-induced displacements. Traction force microscopy (TFM), purported to map cell-generated forces or stresses, represents an important tool that has powered the rapid advances in mechanobiology. However, to solve the ill-posted mathematical problem, its implementation has involved regularization and the associated compromises in accuracy and resolution. Here we applied neural network-based deep learning as a novel approach for TFM. We modified a network for processing images to process vector fields of stress and strain. Furthermore, we adapted a mathematical model for cell migration to generate large sets of simulated stresses and strains for training the network. We found that deep learning-based TFM yielded results qualitatively similar to those from conventional methods but at a higher accuracy and resolution. The speed and performance of deep learning TFM make it an appealing alternative to conventional methods for characterizing mechanical interactions between cells and the environment.Statement of SignificanceTraction Force Microscopy has served as a fundamental driving force for mechanobiology. However, its nature as an ill-posed inverse problem has posed serious challenges for conventional mathematical approaches. The present study, facilitated by large sets of simulated stresses and strains, describes a novel approach using deep learning for the calculation of traction stress distribution. By adapting the UNet neural network for handling vector fields, we show that deep learning is able to minimize much of the limitations of conventional approaches to generate results with speed, accuracy, and resolution.
The Effect of Non-Pharmacologic Strategies on Prevention or Management of Intensive Care Unit Delirium: A Systematic Review
Authors: Hashemighouchani Haleh , Cupka Julie , Lipori Jessica , Ruppert Matthew M , Ozrazgat-Baslanti Tezcan , Rashidi Parisa , Bihorac Azra 
Published: May 2020

AbstractObjectiveThe aim of this systematic review is to examine and report on recently available literature evaluating the relationship between non-pharmacologic management strategies and the reduction of delirium in the intensive care unit.MethodsSix major research databases were systematically searched for articles analyzing the efficacy of non-pharmacologic delirium interventions in the past five years. Search results were restricted to adult human patients aged 18 years or older in the intensive care unit setting, excluding terminally ill subjects and withdrawal-related delirium. Following title, abstract, and full text review, 27 articles fulfilled the inclusion criteria and are included in this report.ResultsThe 27 reviewed articles consist of 12 interventions with a single-component investigational approach, and 15 with multi-component bundled protocols. Delirium incidence was the most assessed outcome followed by duration. Family visitation was the most effective individual intervention and mobility interventions were the least effective. Two of the three family studies significantly reduced delirium incidence, while one in five mobility studies did the same. Multi-component bundle approaches were the most effective of all; of the reviewed studies, eight of 11 bundles significantly improved delirium incidence and seven of eight bundles decreased the duration of delirium.ConclusionsMulti-component, bundled interventions were more effective at managing intensive care unit delirium than those utilizing an approach with a single interventional element. Although better management of this condition suggests a decrease in resource burden and improvement in patient outcomes, comparative research should be performed to identify the importance of specific bundle elements.
Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation
Authors: Sheffer Monica M. , Hoppe Anica , Krehenwinkel Henrik , Uhl Gabriele , Kuss Andreas W. , Jensen Lars , Jensen Corinna , Gillespie Rosemary G. , Hoff Katharina J. , Prost Stefan 
Published: May 2020

AbstractBackgroundArgiope bruennichi, the European wasp spider, has been studied intensively as to sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies.FindingsWe generated,de novo, a 1.67Gb genome assembly ofA. bruennichiusing 21.5X PacBio sequencing, polished with 30X Illumina paired-end sequencing data, and proximity ligation (Hi-C) based scaffolding. This resulted in an N50 scaffold size of 124Mb and an N50 contig size of 288kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high quality of the assembly.ConclusionsWe present the first chromosome-level genome assembly in the class Arachnida. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation inA. bruennichi, as well as on several interesting topics in Arachnids, such as the genomic architecture of traits, whole genome duplication and the genomic mechanisms behind silk and venom evolution.
BTP-7, a novel peptide for therapeutic targeting of malignant brain tumors
Authors: von Spreckelsen Niklas , Ghotmi Yarah , Fadzen Colin M. , Wolfe Justin M. , Hartrampf Nina , Farquhar Charlotte , Bergmann Sonja , Zdioruk Mykola , Wasserburg J. Roscoe , Murrell Emily , Bononi Fernanda C. , Luyt Leonard G. , Lamfers Martine L. M. , Ligon Keith L. , Chiocca E. Antonio , Viapiano Mariano S. , Pentelute Bradley L. , Lawler Sean E. , Cho Choi-Fong 
Published: May 2020

AbstractBackgroundTargeted therapies for malignant brain cancer that are currently available have little clinical activity, highlighting an urgent need for the development of novel precision medicines. Brevican (Bcan), a central nervous system (CNS)-specific extracellular matrix protein is upregulated in glioma cells. A brevican isoform lacking glycosylation, dg-Bcan, is a unique glioma marker and thus represents a valuable target for anti-cancer therapy. In this study, we aimed to find a versatile dg-Bcan specific ligand to facilitate glioma targeting.MethodsWe screened a D-peptide library to identify dg-Bcan-TargetingPeptide (BTP) candidates, which were characterized extensively through binding kinetic analyses, cell uptake tests and animal studies.ResultsThe top candidate, BTP-7 binds dg-Bcan with high affinity and specificity, is preferentially internalized by Bcan-expressing glioma cells and can cross the blood-brain barrierin vitroand in mice. Functionalization of camptothecin with BTP-7 led to increased drug delivery to intracranial glioblastoma and cytotoxicity in tumor tissues, as well as prolonged survival in tumor-bearing mice.Conclusiondg-Bcan is an attractive therapeutic target for high-grade gliomas, and BTP-7 represents a promising lead candidate for further development into novel targeted therapeutics.Key pointsBTP-7 is a high affinity peptide ligand for the dg-Bcan protein and Bcan-expressing cells.BTP-7 targets human intracranial GBM xenografts in mice.Functionalization of a toxic anti-cancer drug with BTP-7 enables targeted delivery of the therapeutic to intracranial GBM in miceImportance of the StudyTargeted therapies for malignant brain cancer that are currently available have little clinical activity, highlighting an urgent need for the development of novel precision medicines that can selectively recognize and kill high-grade glioma tissues. A protein called dg-Bcan is an ideal target because it is present only in the extracellular matrix of high-grade glioma cells and is absent from normal brain tissues. Here, we describe the discovery of a novel dg-Bcan-TargetingPeptide, called BTP-7 that can bind specifically to high-grade glioma cells/tissues, and thus serve as a promising drug delivery vehicle.
Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs
Authors: Floc’hlay Swann , Wong Emily , Zhao Bingqing , Viales Rebecca R. , Thomas-Chollier Morgane , Thieffry Denis , Garfield David A. , Furlong Eileen EM 
Published: May 2020

AbstractPrecise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequence, and chromatin. How DNA mutations affecting any one of these regulatory ‘layers’ is buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eightDrosophilacrosses, at three embryonic stages, yielding a comprehensive dataset of 240 samples spanning multiple regulatory layers. Genetic variation incis-regulatory elements is common, highly heritable, and surprisingly consistent in its effects across embryonic stages. Much of this variation does not propagate to gene expression. When it does, it acts through H3K4me3 or alternatively through chromatin accessibility and H3K27ac. The magnitude and evolutionary impact of mutations is influenced by a genes’ regulatory complexity (i.e. enhancer number), with transcription factors being most robust tocis-acting, and most influenced bytrans-acting, variation. Overall, the impact of genetic variation on regulatory phenotypes appears context-dependent even within the constraints of embryogenesis.
A new dual prokaryotic (E. coli) and mammalian expression system (pgMAXs)
Authors: Murakami Manabu , Murakami Agnieszka M. , Hirota Kazuyoshi , Itagaki Shirou 
Published: May 2020

AbstractWe introduce an efficient subcloning and expression plasmid system with two different modes (prokaryotic for expression inEscherichia coliwith lac promoter and mammalian modes with cytomegalovirus promoter). The efficient subcloning (DNA insertion) is based upon a DNA topoisomerase II toxin-originated gene for effective selection with isopropyl-β-D-thiogalactoside (IPTG) induction. The new pgMAXs system is manageable size (4452 bp) and has also various types of protein tags (flag, myc, poly-histidine, Human influenza hemagglutinin, strep, and v5) for expression analysis. With pgMAXs system, various types of fluorescent proteins were subcloned and prtein expressions were confirmed. We also tried to identify epitope amino acid sequences for anti-calcium channel β2 antibody, by constructing epitope-library with DNaseI-partial digestion and subcloning into EcoRV site in pgMAXs. The new pgMAXs plasmid system enables highly efficient subcloning, simple expression inE. coliand that it has a simple deletion step of rare 8-nucleotide rare-cutter blunt-end enzymes for mammalian expression plasmid construction. Taken together, the pgMAXs system simplifies prokaryotic and mammalian gene expression analyses.
Structural Features and Oligomeric Nature of Human Podocin Domain
Authors: Mulukala Sandeep KN , Irukuvajjula Shivkumar S , Kumar Krishan , Garai Kanchan , Venkatesu Pannuru , Vadrevu Ramakrishna , Pasupulati Anil K 
Published: May 2020

AbstractPodocytes are crucial cells of the glomerular filtration unit and playing a vital role at the interface of the blood-urine barrier. Podocyte slit-diaphragm is a modified tight junction that facilitates size and shape-dependent permselectivity. Several proteins including podocin, nephrin, CD2AP, and TRPC6 form a macromolecular assembly and constitute the slit-diaphragm. Podocin is an integral membrane protein attached to the inner membrane of the podocyte via a short transmembrane region (101-125). The cytosolic N- and C-terminus help podocin to attain a hook-like structure. Podocin shares 44% homology with stomatin family proteins and similar to the stomatin proteins, podocin was shown to associate into higher-order oligomers at the site of slit-diaphragm. However, the stoichiometry of the homo-oligomers and how it partakes in the macromolecular assemblies with other slit-diaphragm proteins remains elusive. Here we investigated the oligomeric propensity of a truncated podocin construct (residues:126-350). We show that the podocin domain majorly homo-oligomerize into a 16mer. Circular dichroism and fluorescence spectroscopy suggest that the 16mer oligomer has considerable secondary structure and moderate tertiary packing.
The global proteome and phosphoproteome landscape of sepsis-induced kidney injury
Authors: Lin Yi-Han , Platt Maryann P. , Gonzalez-Juarbe Norberto , Zhou Dong , Yu Yanbao 
Published: May 2020

AbstractSepsis-induced acute kidney injury (S-AKI) is the most common complication in hospitalized and critically ill patients, highlighted by a rapid decline of kidney function occurring a few hours or days after sepsis onset. Systemic inflammation elicited by microbial infections is believed to lead to kidney damage under immunocompromised conditions. However, while AKI has been recognized as a disease with long-term sequelae, partly due to the associated higher risk of chronic kidney disease (CKD), the understanding of kidney pathophysiology at the molecular level and the global view of dynamic regulationsin situafter S-AKI, including transition to CKD, remains limited. Existing studies of S-AKI mainly focus on deriving sepsis biomarkers from body fluids. In the present study, we constructed a mid-severity septic murine model using cecal ligation and puncture (CLP), and examined the temporal changes to the kidney proteome and phosphoproteome at day 2 and day 7 after CLP surgery, corresponding to S-AKI and the transition to CKD, respectively by employing an ultrafast and economical filter-based sample processing method combined with the label-free quantitation approach. Collectively, we identified 2,119 proteins and 2,950 phosphosites through multi-proteomics analyses. Here we denote the pathways that are specifically responsive to S-AKI and its transition to CKD, which include regulation of cell metabolism regulation, oxidative stress, and energy consumption in the diseased kidneys. Our data can serve as an enriched resource for the identification of mechanisms and biomarkers for sepsis-induced kidney diseases.
CD45 pre-exclusion from the tips of microvilli establishes a phosphatase-free zone for early TCR triggering
Authors: Jung Yunmin , Wen Lai , Altman Amnon , Ley Klaus 
Published: May 2020

SummaryThe tyrosine phosphatase CD45 is a major gatekeeper for restraining T cell activation. Its exclusion from the immunological synapse (IS) is crucial for TCR signal transduction. Here, we used expansion super-resolution microscopy to reveal that CD45 is pre-excluded from the tips of microvilli on primary T cells prior to antigen encounter. This pre-exclusion was diminished by depleting cholesterol or by engineering the transmembrane domain of CD45 to increase its membrane integration length, but was independent of the CD45 extracellular domain. We further show that brief microvilli-mediated contacts can induce Ca2+influx in mouse antigen-specific T cells engaged by antigen-pulsed APCs. We propose that the absence of CD45 phosphatase activity at the tips of microvilli enables or facilitates TCR triggering from brief T cell-APC contacts before formation of a stable IS, and that these microvilli-mediated contacts represent the earliest step in the initiation of a T cell adaptive immune response.Graphical abstract