bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of signatures of fatal neonatal illness in vital signs using highly comparative time-series analysis
Authors: Niestroy Justin C , Moorman J Randall , Levinson Maxwell A , Al Manir Sadnan , Clark Timothy W , Fairchild Karen D , Lake Douglas E 
Published: March 2021

AbstractObjectiveTo seek new signatures of illness in heart rate and oxygen saturation vital signs from Neonatal Intensive Care Unit (NICU), we implemented highly comparative time-series analysis to discover features of all-cause mortality in the next 7 days.DesignWe collected 0.5Hz heart rate and oxygen saturation vital signs of infants in the University of Virginia NICU from 2009 to 2019. We applied 4988 algorithmic operations from 11 mathematical families to random daily ten-minute segments. We clustered the results and selected a representative from each, and examined multivariable logistic regression models.SettingNeonatal ICUPatients5957 NICU infants; 205 died.Measurements and main results3555 operations were usable; 20 cluster medoids held more than 81% of the information. A multivariable model had AUC 0.83. Five algorithms outperformed others: moving threshold, successive increases, surprise, and random walk. We computed provenance of the computations and constructed a software library with links to the data.ConclusionsHighly comparative time-series analysis revealed new vital sign measures to identify NICU patients at the highest risk of death in the next week.
TPST-dependent and -independent regulation of root development and signaling by PSK LRR receptor kinases in Arabidopsis
Authors: Kaufmann Christine , Stührwohldt Nils , Sauter Margret 
Published: March 2021

AbstractTyrosine-sulfated peptides are key regulators of plant growth and development. The disulfated pentapeptide phytosulfokine (PSK) mediates growth via leucine-rich repeat receptor-like kinases, PSKR1 and PSKR2. PSKRs are part of a response module at the plasma membrane that mediates short-term growth responses, but downstream signaling of transcriptional regulation remains unexplored. In Arabidopsis, tyrosine sulfation is catalyzed by a single-copy gene (TPST). We performed a microarray-based transcriptome analysis in thetpst-1mutant background that lacks sulfated peptides to identify PSK-regulated genes and genes that are regulated by other sulfated peptides. Of the 160 PSK-regulated genes, several had functions in root growth and development in agreement with shorter roots and a higher lateral root density intpst-1. Further,tpst-1roots developed higher numbers of root hairs and PSK induced expression ofWEREWOLF (WER), its paralogMYB DOMAIN PROTEIN 23 (MYB23)andAt1g66800that maintain non-hair cell fate. Thetpst-1 pskr1-3 pskr2-1mutant showed even shorter roots, and higher lateral root and root hair density thantpst-1revealing unexpected synergistic effects of ligand and PSK receptor deficiencies. While residual activities may exist, overexpression ofPSKR1in thetpst-1background induced root growth suggesting that PSKR1 may be active in the absence of sulfated ligands.HighlightPhytosulfokine (PSK) receptor signaling promotes root elongation, determines lateral root density and maintains non-hair cell fate partially independent of TPST responsible for the activating sulfation of PSK.
RENANO: a REference-based compressor for NANOpore FASTQ files
Authors: Álvarez Guillermo Dufort y , Seroussi Gadiel , Smircich Pablo , Sotelo-Silveira José , Ochoa Idoia , Martín Álvaro 
Published: March 2021

AbstractNanopore sequencing technologies are rapidly gaining popularity, in part, due to the massive amounts of genomic data they produce in short periods of time (up to 8.5 TB of data in less than 72 hours). In order to reduce the costs of transmission and storage, efficient compression methods for this type of data are needed. Unlike short-read technologies, nanopore sequencing generates long noisy reads of variable length. In this note we introduce RENANO, a reference-based lossless FASTQ data compressor, specifically tailored to compress FASTQ files generated with nanopore sequencing technologies. RENANO builds on the recent compressor ENANO, which is the current state of the art. RENANO focuses on improving the compression of the base call sequence portion of the FASTQ file, leaving the other parts of ENANO intact. Two novel reference-based compression algorithms are introduced, contemplating different scenarios: in the first scenario, a reference genome is available without cost to both the compressor and the decompressor; in the second, the reference genome is availableonlyon the compressor side, and a compacted version of the reference is transmitted to the decompressor as part of the compressed file. To evaluate the proposed algorithms, we compare RENANO against ENANO on several publicly available nanopore datasets. In the first scenario considered, RENANO improves the base call sequences compression of ENANO by 39.8%, on average, over all the datasets. As for total compression (including the other parts of the FASTQ file), the average improvement is 12.7%. In the second scenario considered, the base call compression improvements of RENANO over ENANO range from 15.2% to 49.0%, depending on the coverage of the compressed dataset, while in terms of total size, the improvements range from 5.1% to 16.5%.Implementations of the proposed algorithms are freely available for download athttps://github.com/guilledufort/RENANO.
The phosphate starvation response recruits the TOR pathway to regulate growth in Arabidopsis cell cultures
Authors: Dobrenel Thomas , Kushwah Sunita , Mubeen Umarah , Jansen Wouter , Delhomme Nicolas , Caldana Camila , Hanson Johannes 
Published: March 2021

AbstractIn eukaryotes, TOR (Target Of Rapamycin) is a conserved regulator of growth that integrates both endogenous and exogenous signals. These signals include the internal nutritional status, and in plants, TOR has been shown to be regulated by carbon, nitrogen and sulfur availability. In this study, we show that in Arabidopsis the TOR pathway also integrates phosphorus availability to actively modulate the cell cycle, which in turn regulates the intracellular content of amino acids and organic acids. We observed a substantial overlap between the phenotypic, metabolic and transcriptomic responses of TOR inactivation and phosphorus starvation in Arabidopsis cell culture. Although phosphorus availability modulates TOR activity, changes in the levels of TOR activity do not alter the expression of marker genes for phosphorus status. These data prompted us to place the sensing of phosphorus availability upstream of the modulation of TOR activity which, in turn, regulates the cell cycle and primary metabolism to adjust plant growth in plants.
Subthalamic-Cortical Network Reorganization during Parkinson’s Tremor
Authors: Lauro Peter M. , Lee Shane , Akbar Umer , Asaad Wael F. 
Published: March 2021

ABSTRACTTremor, a common and often primary symptom of Parkinson’s disease, has been modeled with distinct onset and maintenance dynamics. To identify the neurophysiologic correlates of each state, we acquired intraoperative cortical and subthalamic nucleus recordings from ten patients performing a naturalistic visual-motor task. From this task we isolated short epochs of tremor onset and sustained tremor. Comparing these epochs, we found that the subthalamic nucleus was central to tremor onset, as it drove both motor cortical activity and tremor output. Once tremor became sustained, control of tremor shifted to cortex. At the same time, changes in directed functional connectivity across sensorimotor cortex further distinguished the sustained tremor state.SIGNIFICANCE STATEMENTTremor is a common symptom of Parkinson’s disease (PD). While tremor pathophysiology is thought to involve both basal ganglia and cerebello-thalamic-cortical circuits, it is unknown how these structures functionally interact to produce tremor. In this manuscript, we analyzed intracranial recordings from the subthalamic nucleus and sensorimotor cortex in patients with PD undergoing deep brain stimulation (DBS) surgery. Using an intraoperative task, we examined tremor in two separate dynamic contexts: when tremor first emerged, and when tremor was sustained. We believe that these findings reconcile several models of Parkinson’s tremor, while describing the short-timescale dynamics of subcortical-cortical interactions during tremor for the first time. These findings may describe a framework for developing proactive and responsive neurostimulation models for specifically treating tremor.
Building the Mega Single Cell Transcriptome Ocular Meta-Atlas
Authors: Swamy Vinay S , Fufa Temesgen D , Hufnagel Robert B , McGaughey David M 
Published: March 2021

AbstractThe development of highly scalable single cell transcriptome technology has resulted in the creation of thousands of datasets, over 30 in the retina alone. Analyzing the transcriptomes between different projects is highly desirable as this would allow for better assessment of which biological effects are consistent across independent studies. However it is difficult to compare and contrast data across different projects as there are substantial batch effects from computational processing, single cell technology utilized, and the natural biological variation. While many single cell transcriptome specific batch correction methods purport to remove the technical noise it is difficult to ascertain which method functions works best. We developed a lightweight R package (scPOP) that brings in batch integration methods and uses a simple heuristic to balance batch merging and celltype/cluster purity. We use this package along with a Snakefile based workflow system to demonstrate how to optimally merge 766,615 cells from 33 retina datsets and three species to create a massive ocular single cell transcriptome meta-atlas. This provides a model how to efficiently create meta-atlases for tissues and cells of interest.
Tactile spatial discrimination on the torso using vibrotactile and force stimulation
Authors: Fadaei J. Atena , Franza Matteo , Kannape Oliver Alan , Hara Masayuki , Blanke Olaf 
Published: March 2021

AbstractThere is a steadily growing number of mobile communication systems that provide spatially encoded tactile information to the humans’ torso. However, the increased use of such hands-off displays is currently not matched with or supported by systematic perceptual characterization of tactile spatial discrimination on the torso. Furthermore, there are currently no data testing spatial discrimination for dynamic force stimuli applied to the torso. In the present study, we measured tactile point localization (PL) and tactile direction discrimination (DD) on the thoracic spine using two unisex torso-worn tactile vests realized with arrays of 3×3 vibrotactile or force feedback actuators. We aimed to, firstly, evaluate and compare the spatial discrimination of vibrotactile and force stimulations on the thoracic spine and, secondly, to investigate the relationship between the PL and DD results across stimulations. Thirty-four healthy participants performed both tasks with both vests. Tactile accuracies for vibrotactile and force stimulations were 60.7% and 54.6% for the PL task; 71.0% and 67.7% for the DD task, respectively. Performance correlated positively with both stimulations, although accuracies were higher for the vibrotactile than for the force stimulation across tasks, arguably due to specific properties of vibrotactile stimulations. We observed comparable directional anisotropies in the PL results for both stimulations; however, anisotropies in the DD task were only observed with vibrotactile stimulations. We discuss our findings with respect to tactile perception research as well as their implications for the design of high-resolution torso-mounted tactile displays for spatial cueing.
Optimized hip-knee-ankle exoskeleton assistance at a range of walking speeds
Authors: Bryan Gwendolyn M. , Franks Patrick W. , Song Seungmoon , Voloshina Alexandra S. , Reyes Ricardo , O’Donovan Meghan P. , Gregorczyk Karen N. , Collins Steven H. 
Published: March 2021

AbstractBackgroundEffective autonomous exoskeletons will need to be useful at a variety of walking speeds, but we do not know how optimal exoskeleton assistance should change with speed. Optimal exoskeleton assistance may increase with speed similar to biological torque changes or a well-tuned assistance profile may be effective at a variety of speeds.MethodsWe optimized hip-knee-ankle exoskeleton assistance to reduce metabolic cost for three participants walking at 1.0 m/s, 1.25 m/s and 1.5 m/s. We measured metabolic cost, muscle activity, exoskeleton assistance and kinematics. We performed two tailed paired t-tests to determine significance.ResultsExoskeleton assistance reduced the metabolic cost of walking compared to wearing the exoskeleton with no torque applied by 26%, 47% and 50% at 1.0, 1.25 and 1.5 m/s, respectively. For all three participants, optimized exoskeleton ankle torque was the smallest for slow walking, while hip and knee torque changed slightly with speed in ways that varied across participants. Total applied positive power increased with speed for all three participants, largely due to increased joint velocities, which consistently increased with speed.ConclusionsExoskeleton assistance is effective at a range of speeds and is most effective at medium and fast walking speeds. Exoskeleton assistance was less effective for slow walking, which may explain the limited success in reducing metabolic cost for patient populations through exoskeleton assistance. Exoskeleton designers may have more success when targeting activities and groups with faster walking speeds. Speed-related changes in optimized exoskeleton assistance varied by participant, indicating either the benefit of participant-specific tuning or that a wide variety of torque profiles are similarly effective.
Every cog and wheel: Identifying biocomplexity at the genomic and phenotypic level in a population complex of Chinook salmon
Authors: O’Leary Shannon J. , Thompson Tasha Q. , Meek Mariah H. 
Published: March 2021

AbstractGenomic diversity is the fundamental building block of biodiversity and the necessary ingredient for adaptation. Our rapidly increasing ability to quantify functional, compositional, and structural genomic diversity of populations forces the question of how to balance conservation goals – should the focus be on important functional diversity and key life history traits or on maximizing genomic diversity as a whole? Specifically, the intra-specific diversity (biocomplexity) comprised of phenotypic and genetic variation can determine the ability of a population to respond to changing environmental conditions. Here, we explore the biocomplexity of California’s Central Valley Chinook salmon (Oncorhynchus tshawytscha) population complex at the genomic level. Notably, despite apparent gene flow among individuals with the same migration (life history) phenotypes inhabiting different tributaries, each group is characterized by a surprising component of unique genomic diversity. Our results emphasize the importance of formulating conservation goals focused on maintaining biocomplexity at both the phenotypic and genotypic level. Doing so will maintain the species’ adaptive potential and increase the probability of persistence of the population complex despite changing environmental pressures.
Swimming kinematics and performance of spinal transected lampreys with different levels of axon regeneration
Authors: Fies Jacob. , Gemmell Brad J. , Fogerson Stephanie M. , Costello John H. , Morgan Jennifer R. , Tytell Eric D. , Colin S. P. 
Published: March 2021

AbstractNeural and functional recovery in lampreys from spinal cord transection has been well documented. However, the extent of axon regeneration is highly variable and it is not known whether it is related to the level of behavioral recovery. To address this, we examined how swimming kinematics were related to axon regeneration by quantifying the relationship between swimming performance and percent axon regeneration of transected lampreys after 11 weeks of recovery. We found that swimming speed was not related to percent axon regeneration but it was closely related to body wave frequency and speed. However, wave frequency and speed varied greatly within individuals which resulted in swimming speed also varying within individuals. In fact, most recovered individuals, regardless of percent axon regeneration, could swim at fast and slow speeds. However, none of the transected individuals were able to generate body waves as large as the control lampreys. In order to swim faster, transected lampreys increased their wave frequencies and, as a result, transected lampreys had much higher frequencies than control lamprey at comparable swimming velocities. These data suggest that the control lampreys swam more efficiently than transected lampreys. In conclusion, there appears to be a minimal recovery threshold in terms of percent axon regeneration required for lampreys to be capable of swimming, however, there also seems to be a limit to how much they can behaviorally recover.
Identifying key federal, state and private lands strategies for achieving 30x30 in the US
Authors: Dreiss Lindsay M. , Malcom Jacob W. 
Published: March 2021

AbstractAchieving ambitious conservation goals to conserve at least 30% of US lands and waters by 2030 (“30x30”) will require a multi-scale baseline understanding of current protections, key decision makers, and policy tools for moving forward. To help conservationists and decision makers support the science-based call to address the biodiversity and climate crises, we analyze the current spatial patterns of imperiled species biodiversity and carbon stores in the U.S. relative to protected areas. Analyses demonstrate that 30x30 is numerically achievable nationally, but high spatial heterogeneity highlights the need for tailored approaches from a mix of authorities at federal, regional, and state scales. Critically, current land protections rarely overlap with areas essential for conserving imperiled species biodiversity and mitigating climate change. Nearly one-fifth of unprotected biodiversity hotspots and carbon-rich areas are also at risk of either land conversion or climate exposure by 2050. We discuss this baseline relative to key policy considerations for making practical, substantive progress toward the goal.
Interfacing Seurat with the R tidy universe
Authors: Mangiola Stefano , Doyle Maria A , Papenfuss Anthony T 
Published: March 2021

AbstractMotivationSeurat is one of the most popular software suites for the analysis of single-cell RNA sequencing data. Considering the popularity of the tidyverse ecosystem, which offers a large set of data display, query, manipulation, integration and visualisation utilities, a great opportunity exists to interface the Seurat object with the tidyverse. This gives the large data science community of tidyverse users the possibility to operate with a familiar grammar.ResultsIn order to provide Seurat with a tidyverse-oriented interface without compromising on efficiency, we developed tidyseurat, a light-weight adapter to the tidyverse. Cell information is automatically displayed as a tibble abstraction, which interfaces Seurat with dplyr, tidyr, ggplot2 and plotly packages powering efficient data manipulation, integration and visualisation. Iterative analyses on data subsets is enabled by interfacing with the popular nest-map framework.Availability and implementationThe software is freely available atcran.r-project.org/web/packages/tidyseurat/andgithub.com/stemangiola/tidyseuratContactStefano Mangiola (mangiola.s@wehi.edu.au) and Anthony T Papenfuss (papenfuss@wehi.edu.au).
Exploring biomedical records through text mining-driven complex data visualisation
Authors: Costa Joao Pita , Stopar Luka , Rei Luis , Massri Besher , Grobelnik Marko 
Published: March 2021

ABSTRACTThe recent events in health call for the prioritization of insightful and meaningful information retrieval from the fastly growing pool of biomedical knowledge. This information has its own challenges both in the data itself and in its appropriate representation, enhancing its usability by health professionals. In this paper we present a framework leveraging the MEDLINE dataset and its controlled vocabulary, the MeSH Headings, to annotate and explore health-related documents. The MEDijs system ingests and automatically annotates text documents, extending their legacy metadata with MeSH Headings. It then uses text mining algorithms that enable interactive data visualisations. These allow the user to the exploration of the enriched data made available by the MEDijs system.CCS CONCEPTS• Information systems; • Computing methodologies → Machine learning approaches;ACM Reference FormatJoao Pita Costa, Luka Stopar, Luis Rei, Besher Massri, and Marko Grobelnik. 2018. Exploring biomedical records through text mining-driven complex data visualisation. In Proceedings of SEBILAN ’21: ACM International Workshop on Semantics-enabled Biomedical Literature Analytics (SEBILAN ’21). ACM, New York, NY, USA, 6 pages. https://doi.org/0
Risk factors for developing COVID-19: a population-based longitudinal study (COVIDENCE UK)
Authors: Holt Hayley , Talaei Mohammad , Greenig Matthew , Zenner Dominik , Symons Jane , Relton Clare , Young Katherine S , Davies Molly R , Thompson Katherine N , Ashman Jed , Rajpoot Sultan Saeed , Kayyale Ahmed Ali , Rifai Sarah El , Lloyd Philippa J. , Jolliffe David A. , Finer Sarah , Ilidriomiti Stamatina , Miners Alec , Hopkinson Nicholas S. , Alam Bodrul , Pfeffer Paul E , McCoy David , Davies Gwyneth A , Lyons Ronan A , Griffiths Christopher J , Kee Frank , Sheikh Aziz , Breen Gerome , Shaheen Seif O , Martineau Adrian R 
Published: March 2021

SummaryBackgroundRisk factors for severe COVID-19 include older age, male sex, obesity, Black or Asian ethnicity and underlying medical conditions. Whether these factors also influence susceptibility to developing COVID-19 is uncertain.MethodsWe undertook a prospective, population-based cohort study (COVIDENCE UK) from 1stMay 2020 to 5thFebruary 2021. Baseline information on potential risk factors was captured by an online questionnaire. Monthly follow-up questionnaires captured incident COVID-19. We used logistic regression models to estimate multivariable-adjusted odds ratios (aORs) for associations between potential risk factors and risk of COVID-19.FindingsWe recorded 446 incident cases of COVID-19 in 15,227 participants (2.9%). Increased risk of developing COVID-19 was independently associated with Asian/Asian Britishvs. White ethnicity (aOR 2.31, 95% CI 1.35-3.95), household overcrowding (aOR per additional 0.5 people/bedroom 1.26, 1.11-1.43), anyvs. no visits to/from other households in previous week (aOR 1.33, 1.07-1.64), number of visits to indoor public places (aOR per extra visit per week 1.05, 1.01-1.09), frontline occupation excluding health/social carevs. no frontline occupation (aOR 1.49, 1.12-1.98), and raised body mass index (BMI) (aOR 1.51 [1.20-1.90] for BMI 25.0-30.0 kg/m2and 1.38 [1.05-1.82] for BMI >30.0 kg/m2vs. BMI <25.0 kg/m2). Atopic disease was independently associated with decreased risk (aOR 0.76, 0.59-0.98). No independent associations were seen for age, sex, other medical conditions, diet, or micronutrient supplement use.InterpretationAfter rigorous adjustment for factors influencing exposure to SARS-CoV-2, Asian/Asian British ethnicity and raised BMI were associated with increased risk of developing COVID-19, while atopic disease was associated with decreased risk.FundingBarts Charity, Health Data Research UK