bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mortality of Care Home Residents and Community-Dwelling Controls During the COVID-19 Pandemic in 2020: Matched Cohort Study
Authors: Gulliford Martin C , Prevost A. Toby , Clegg Andrew , Rezel-Potts Emma 
Published: April 2021

ABSTRACTObjectiveTo estimate mortality of care home (CH) residents, and matched community-dwelling controls, during the Covid-19 pandemic from primary care electronic health records.DesignMatched cohort studySettingGeneral practices contributing to the Clinical Practice Research Datalink Aurum Database in England.ParticipantsThere were 83,627 CH residents contributing data in 2020, with 26,923 deaths; 80,730 (97%) were matched on age, gender and general practice with 300,445 community-dwelling adults.Main outcome measuresAll-cause mortality. Adjusted rate ratios (RR) by negative binomial regression were adjusted for age, gender, number of long-term conditions (LTCs), frailty category, region, calendar month or week, and clustering by general practice.ResultsDuring April 2020, the mortality rate of CH residents was 27.2 deaths per 1,000 patients per week, compared with 2.31 per 1,000 for controls, RR 11.1 (95% confidence interval 10.1 to 12.2). Compared with CH residents, LTCs and frailty were differentially associated with greater mortality in community-dwelling controls. During April 2020, mortality rates per 1,000 patients per week for persons with 9+ LTCs were: CH, 37.9; controls 17.7; RR 2.14 (1.18 to 3.89). In severe frailty, mortality rates were: CH, 29.6; controls 5.1; RR 6.17 (5.74 to 6.62).ConclusionsIndividual-patient data from primary care electronic health records may be used to estimate mortality in care home residents. Mortality is substantially higher than for community-dwelling comparators and showed a disproportionate increase in the first wave of the Covid-19 pandemic. Multiple morbidity and frailty were associated with greater absolute risks but lower relative risks because community-dwelling frail or multi-morbid patients also experienced high mortality.
High-sensitivity detection of facial features on MRI brain scans with a convolutional network
Authors: Bansal Shashank , Kori Avinash , Zulfikar Wazeer , Wexler Joseph , Markiewicz Christopher J. , Feingold Franklin F. , Poldrack Russell A. , Esteban Oscar 
Published: April 2021

AbstractPlatforms and institutions that support MRI data sharing need to ensure that identifiable facial features are not present in shared images. Currently, this assessment requires manual effect as no auto-mated tools exist that can efficiently and accurately detect if an image has been “defaced”. The scarcity of publicly available data with pre-served facial features, as well as the meager incentives to create such a cohort privately, have averted the development of face-detection models. Here, we introduce a framework to detect whether an input MRI brain scan has been defaced, with the ultimate goal of streamlining it within the submission protocols of MRI data archiving and sharing platforms. We present a binary (defaced/”nondefaced”) classifier based on a custom convolutional neural network architecture. We train the model on 980 de-faced MRI scans from 36 different studies that are publicly available at OpenNeuro.org. To overcome the unavailability of nondefaced examples, we augment the dataset by inpainting synthetic faces into each training image. We show the adequacy of such a data augmentation in a cross-validation evaluation. We demonstrate the performance estimated with cross-validation matches that of an evaluation on a held-out dataset (N=581) preserving real faces, and obtain accuracy/sensitivity/speci-ficity scores of 0.978/0.983/0.972, respectively. Data augmentations are key to boosting the performance of models bounded by limited sample sizes and insufficient diversity. Our model contributes towards developing classifiers with∼100% sensitivity detecting faces, which is crucial to ensure that no identifiable data are inadvertently made public.
Therapeutic targeting of SLC6A8 creatine transporter inhibits KRAS mutant and wildtype colon cancer and modulates human creatine levels
Authors: Kurth Isabel , Yamaguchi Norihiro , Andreu-Agullo Celia , Tian Helen S. , Sridhar Subhasree , Takeda Shugaku , Gonsalves Foster C. , Loo Jia Min , Barlas Afsar , Manova-Todorova Katia , Busby Robert , Bendell Johanna C. , Strauss James , Fakih Marwan , McRee Autumn J. , Hendifar Andrew E. , Rosen Lee S. , Cercek Andrea , Wasserman Robert , Spector Scott L. , Raza Syed , Tavazoie Masoud F. , Tavazoie Sohail F. 
Published: April 2021

ABSTRACTColorectal cancer (CRC) is a leading cause of cancer mortality. Creatine metabolism was previously shown to critically regulate colon cancer progression. We report that RGX-202, an oral small-molecule SLC6A8 creatine transporter inhibitor, robustly inhibits creatine import in vitro and in vivo, reduces intracellular phosphocreatine and ATP levels and induces tumor cell apoptosis in CRC. RGX-202 suppressed tumor growth across KRAS wild-type and KRAS mutant xenograft, syngeneic and patient-derived xenograft colorectal cancers. Anti-tumor efficacy correlated with tumoral expression of creatine kinase B. Combining RGX-202 with 5- fluorouracil or the DHODH inhibitor leflunomide caused regressions of multiple colorectal xenograft and PDX tumors of distinct mutational backgrounds. RGX-202 also perturbed creatine metabolism in metastatic CRC patients enrolled in a Phase-1 trial, mirroring pharmacodynamic effects on creatine metabolism observed in mice. This is, to our knowledge, the first demonstration of pre-clinical and human pharmacodynamic activity for creatine metabolism targeting in oncology, revealing a critical target for CRC.
Premovement inhibition protects motor actions from interference
Authors: McInnes Aaron N. , Lipp Ottmar V. , Tresilian James R. , Vallence Ann-Maree , Marinovic Welber 
Published: April 2021

AbstractShortly before movement initiation, the corticospinal system undergoes a transient suppression. This phenomenon has been observed across a range of motor tasks, suggesting that it may be a obligatory component of movement preparation. We probed whether this was also the case when the urgency to perform a motor action was high, in a situation where little time was available to engage in preparatory processes. We controlled the urgency of an impending motor action by increasing or decreasing the foreperiod duration in an anticipatory timing task. Transcranial magnetic stimulation (TMS; experiment one) or a loud acoustic stimulus (LAS; experiment two) were used to examine how corticospinal and subcortical excitability were modulated during motor preparation. Preparatory inhibition of the corticospinal tract was absent when movement urgency was high, though motor actions were initiated on time. In contrast, subcortical circuits were progressively inhibited as the time to prepare increased. Interestingly, movement force and vigour were reduced by both TMS and the LAS when movement urgency was high, and enhanced when movement urgency was low. Our findings indicate that preparatory inhibition may not be a obligatory component of motor preparation. The behavioural effects we observed in the absence of preparatory inhibition were induced by both TMS and the LAS, suggesting that accessory sensory stimulation may disrupt motor output when such stimulation is presented in the absence of preparatory inhibition. We conclude that preparatory inhibition may be an adaptive strategy which can serve to protect the prepared motor action from external interference.
Isolation and characterization of barley (Hordeum vulgare) extracellular vesicles and their role in RNAi-based crop protection
Authors: Schlemmer T , Weipert L , Preußer C , Hardt M , Möbus A , Barth P , Busche T , Koch A 
Published: April 2021

AbstractThe demonstration that spray-induced gene silencing (SIGS) can confer strong disease resistance bypassing the laborious and time-consuming transgenic expression of double-stranded (ds)RNA to induce gene silencing of pathogenic targets was groundbreaking. However, future field applications will require fundamental mechanistic knowledge on dsRNA uptake, processing, and its transfer. There is increasing evidence that extracellular vesicles (EVs) mediate the transfer of transgene-derived small interfering (si)RNAs in host-induced gene silencing (HIGS) applications. Here, we examined the role of EVs regarding the translocation of sprayed dsRNA from barley (Hordeum vulgare) to the target fungusFusarium graminearum. We found barley EVs with 156 nm in size containing predominantly 21 and 19 nucleotide (nt) siRNAs starting with a 5’-terminal Adenine. Notably, barley EVs contain less siRNA compared to EVs isolated from transgenic HIGS Arabidopsis plants. Together our results further underpin mechanistic differences between HIGS and SIGS applications and a minor role of EVs in SIGS.
An ALE meta-analytic review of top-down and bottom-up processing of music in the brain
Authors: Pando-Naude Victor , Patyczek Agata , Bonetti Leonardo , Vuust Peter 
Published: April 2021

AbstractA remarkable feature of the human brain is its ability to integrate information from the environment with internally generated content. The integration of top-down and bottom-up processes during complex multi-modal human activities, however, is yet to be fully understood. Music provides an excellent model for understanding this since music listening leads to the urge to move, and music making entails both playing and listening at the same time (i.e. audio-motor coupling). Here, we conducted activation likelihood estimation (ALE) meta-analyses of 130 neuroimaging studies of music perception, production and imagery, with 2660 foci, 139 experiments, and 2516 participants. We found that music perception and production rely on auditory cortices and sensorimotor cortices, while music imagery recruits distinct parietal regions. This indicates that the brain requires different structures to process similar information which is made available either by an interaction with the environment (i.e. bottom-up) or by internally generated content (i.e. top-down).
Changes in Cellular Crosstalk between Skeletal Muscle Myoblasts and Bone Osteoblasts with Aging
Authors: Doering Jonathan A. , Britt Carly E. , Sawicki Gregory S. , Cole Jacqueline H. 
Published: April 2021

AbstractMusculoskeletal function declines with aging, resulting in an increased incidence of trips and falls. Both bone and muscle experience age-related losses in tissue mass that alter their mechanical interactions in a well characterized manner, but changes in the biochemical interactions between bone and muscle with aging are not well understood. Of note, insulin-like growth factor 1 (IGF-1), a potent growth factor for bone and muscle, can be negatively altered with aging and may help explain losses in these tissues. We recently developed a co-culture system for simultaneous growth of bone mesenchymal stem cells (MSCs) and muscle satellite cells (SCs) to investigate the biochemical crosstalk between the two cell types. Here, we utilized an aging rat model to study cellular changes between young and old rat MSCs and SCs, in particular whether 1) young MSCs and SCs have increased proliferation and differentiation compared to old MSCs and SCs; 2) young cells have increased IGF-1 and collagen expression as a measure of crosstalk compared to old cells; and 3) young cells can mitigate the aging phenotype of old cells in co-culture. Rat MSCs and SCs were either mono- or co-cultured in Transwell®plates, grown to confluence, and allowed to differentiate for 14 days. Across the 14 days, cell proliferation was measured, with differentiation and crosstalk measurements evaluated at 14 days. The results suggest that in both young and old, proliferation is greater in mono-cultures compared to co-cultures, yet age and cell type did not have a significant effect. Differentiation did not differ between young and old cells, yet MSCs and SCs demonstrated the greatest amount of differentiation in co-culture. Finally, age, cell type, and culture type did not have a significant effect on collagen or IGF-1 expression. These results suggest co-culture may have a controlling effect, with the two cell types acting together to promote differentiation more than in mono-cultures, yet this response was not altered by age. In general, results for old cells had higher variability, suggesting a wider variety in the aging phenotypes demonstrated in these animals. This study was the first to use this rat aging model to investigate changes between bone and skeletal muscle cells, however further investigations are required to determine what signaling changes occur in response to age. Determining these signaling changes could lead to new targets for mitigating the progression of aging.
A pro-metastatic tRNA fragment drives Nucleolin oligomerization and stabilization of bound metabolic mRNAs
Authors: Liu Xuhang , Alwaseem Hanan , Molina Henrik , Tavora Bernardo , Tavazoie Sohail F. 
Published: April 2021

SUMMARYStress-induced cleavage of transfer RNAs (tRNAs) into tRNA-derived fragments (tRFs) occurs across organisms from yeast to human, yet its mechanistic bases and pathological consequences remain poorly defined. By performing genome-wide small RNA profiling, we detected increased abundance of a Cysteine tRNA fragment (5’-tRFCys) during breast cancer metastatic progression. 5’’-tRFCys is required for efficient breast cancer metastatic lung colonization and metastatic cell survival. We identified Nucleolin as the direct binding partner of 5’-tRFCys. 5’-tRFCys binding enhanced the stability of Nucleolin’s associated pro-metastatic transcripts encoding metabolic enzymes Mthfd1l and Pafah1b1. 5’-tRFCys stabilized these transcripts by promoting Nucleolin oligomerization and the assembly of Nucleolin and its bound transcripts into a higher-order ribonucleoprotein complex. Our findings reveal that a tRF can promote oligomerization of an RNA binding protein into a stabilizing ribonucleoprotein complex containing specific target transcripts, thereby driving specific metabolic pathways underlying cancer progression.
Fitness estimation for viral variants in the context of cellular coinfection
Authors: Zhu Huisheng , Allman Brent E , Koelle Katia 
Published: April 2021

AbstractAnimal models are frequently used to characterize the within-host dynamics of emerging zoonotic viruses. More recent studies have also deep-sequenced longitudinal viral samples originating from experimental challenges to gain a better understanding of how these viruses may evolvein vivoand between transmission events. These studies have often identified nucleotide variants that can replicate more efficiently within hosts and also transmit more effectively between hosts. Quantifying the degree to which a mutation impacts viral fitness within a host can improve identification of variants that are of particular epidemiological concern and our ability to anticipate viral adaptation at the population level. While methods have been developed to quantify the fitness effects of mutations using observed changes in allele frequencies over the course of a host’s infection, none of the existing methods account for the possibility of cellular coinfection. Here, we develop mathematical models to project variant allele frequency changes in the context of cellular coinfection and, further, integrate these models with statistical inference approaches to demonstrate how variant fitness can be estimated alongside cellular multiplicity of infection. We apply our approaches to empirical longitudinally-sampled H5N1 sequence data from ferrets. Our results indicate that previous studies may have significantly underestimated the within-host fitness advantage of viral variants. These findings underscore the importance of considering the process of cellular coinfection when studying within-host viral evolutionary dynamics.
New phylogenetic Markov models for inapplicable morphological characters
Authors: Tarasov Sergei 
Published: April 2021

AbstractThis paper proposes new Markov models for phylogenetic inference with anatomically dependent (inapplicable) morphological characters. The proposed models can explicitly model an anatomical dependency in which one or several characters are allowed to evolve only within a specific state of the hierarchically upstream character. The new models come up in two main types depending on the type of character hierarchy. The functions for constructing custom character hierarchies are provided in the R packagerphenoscate. The performance of the new models is assessed using theory and simulations. This paper provides practical recommendations for using the new models in Bayesian phylogenetic inference withRevBayes.
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
Authors: Rebboah Elisabeth , Reese Fairlie , Williams Katherine , Balderrama-Gutierrez Gabriela , McGill Cassandra , Trout Diane , Rodriguez Isaryhia , Liang Heidi , Wold Barbara J. , Mortazavi Ali 
Published: April 2021

AbstractAlternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard short-read RNA-seq because of the uncertainties it leaves about the full-length structure and precise termini of transcripts. The rise in throughput and quality of long-read sequencing now makes it possible, in principle, to unambiguously identify most transcript isoforms from beginning to end. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here, we develop and characterize long-read Split-seq (LR-Split-seq), which uses a combinatorial barcoding-based method for sequencing single cells and nuclei with long reads. We show that LR-Split-seq can associate isoforms with cell types with relative economy and design flexibility. We characterize LR-Split-seq for whole cells and nuclei by using the well-studied mouse C2C12 system in which mononucleated myoblast cells differentiate and fuse into multinucleated myotubes. We show that the overall results are reproducible when comparing long- and short-read data from the same cell or nucleus. We find substantial evidence of differential isoform expression during differentiation including alternative transcription start site (TSS) usage. We integrate the resulting isoform expression dynamics with snATAC-seq chromatin accessibility to validate TSS-driven isoform choices. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells that can be further quantified with companion deep short-read scRNA-seq from the same cell populations.
Force-dependent interactions between talin and full-length vinculin
Authors: Wang Yinan , Yao Mingxi , Baker Karen B. , Gough Rosemarie E. , Le Shimin , Goult Benjamin T. , Yan Jie 
Published: April 2021

AbstractTalin and vinculin are part of a multi-component system involved in mechanosensing in cell-matrix adhesions. Both exist in auto-inhibited forms, and activation of vinculin requires binding to mechanically activated talin, yet how forces affect talin’s interaction with vinculin has not been investigated. Here by quantifying the force-dependent talin-vinculin interactions and kinetics using single-molecule analysis, we show that mechanical exposure of a single vinculin binding site (VBS) in talin is sufficient to relieve the autoinhibition of vinculin resulting in high-affinity binding. We provide evidence that the vinculin undergoes dynamic fluctuations between an auto-inhibited closed conformation and an open conformation that is stabilized upon binding to the VBS. Furthermore, we discover an additional level of regulation in which the mechanically exposed VBS binds vinculin significantly more tightly than the isolated VBS alone. Molecular dynamics simulations reveal the basis of this new regulatory mechanism, identifying a sensitive force-dependent change in the conformation of an exposed VBS that modulates binding. Together, these results provide a comprehensive understanding of how the interplay between force and autoinhibition provides exquisite complexity within this major mechanosensing axis.
Predicting daily COVID-19 case rates from SARS-CoV-2 RNA concentrations across a diversity of wastewater catchments
Authors: Zulli Alessandro , Pan Annabelle , Bart Stephen M. , Crawford Forrest W. , Kaplan Edward H. , Cartter Matthew , Ko Albert I. , Cozens Duncan , Sanchez Marcela , Brackney Doug E. , Peccia Jordan 
Published: April 2021

AbstractWe assessed the relationship between municipality COVID-19 case rates and SARS-CoV-2 concentrations in the primary sludge of corresponding wastewater treatment facilities. Over 1,000 daily primary sludge samples were collected from six wastewater treatment facilities with catchments serving 18 cities and towns in the State of Connecticut, USA. Samples were analyzed for SARS-CoV-2 RNA concentrations during a six-month time period that overlapped with fall 2020 and winter 2021 COVID-19 outbreaks in each municipality. We fit a single regression model to estimate reported case rates in the six municipalities from SARS-CoV-2 RNA concentrations collected daily from corresponding wastewater treatment facilities. Results demonstrate the ability of SARS-CoV-2 RNA concentrations in primary sludge to estimate COVID-19 reported case rates across treatment facilities and wastewater catchments, with coverage probabilities ranging from 0.94 to 0.96. Leave-one-out cross validation suggests that the model can be broadly applied to wastewater catchments that range in more than one order of magnitude in population served. Estimation of case rates from wastewater data can be useful in locations with limited testing availability or testing disparities, or delays in individual COVID-19 testing programs.
Long-lasting humoral immunity in Covid-19 infected patients at a University Hospital Clinic in Östergötland County Council during 2020-2021
Authors: Azharuddin M , Aili D , Selegård R , Naeimipour Sajjad , Sunnerhagen M , Patra HK , Sjöberg K S , Niward K , Hanberger H , Östholm-Balkhed Å , Hinkula J 
Published: April 2021

AbstractLongitudinal serum samples and nasopharyngeal/nasal swab samples were collected from forty-eight individuals (median age 66yrs) with Covid-19 PCR-positive test results at Linköping University Hospital. Samples were collected from initial visit and for 6 months follow up. Presence of serum IgG and IgA against SARS-CoV-2 antigens (S1-spike, nucleocapsid and NSP3) were analyzed. Nasal swabs were tested for presence of IgA against the outer envelope S1 spike protein. Ninety-two percent of participants were seropositive against SARS-CoV-2 recombinant proteins at day 28 from study entry and all (100%) were seropositive from samples collected at 2 months or later. The most common antibody responses (both serum IgG, mainly IgG1 and IgA) were detected against the S1-spike protein and the nucleoprotein. In samples collected from nasal tissues considerably lower frequencies of IgA-positive reactivities were detected. Sixteen to 18 percent of study participants showed detectable IgA levels in nasal samples, except at day 60 when 36% of tested individuals showed presence of IgA against the S1-spike protein. The study suggests that the absolute majority of studied naturally infected Covid-19 patient in the Linkoping, Ostergotland health region develop over 6 months lasting detectable levels of serum IgG and IgA responses towards the SARS-CoV-2 S1-spike protein as well as against the nucleoprotein, but not against the non-structural protein 3.