bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long COVID in hospitalized and non-hospitalized patients in a large cohort in Northwest Spain, a prospective cohort study
Authors: Pérez-González Alexandre , Araújo-Ameijeiras Alejandro , Fernández-Villar Alberto , Crespo Manuel , Poveda Eva 
Published: August 2021

AbstractBackgroundSurvivors to COVID-19 have described long-term symptoms after acute disease. These signs constitute a heterogeneous group named long COVID or persistent COVID.ObjectiveThe aim of this study is to describe persisting symptoms six months after COVID-19 diagnosis in a prospective cohort in the Northwest SpainDesignThis is a prospective cohort study performed in the COVID-19 Cohort of Galicia Sur Health Institute (COHVID-GS).ParticipantsThis cohort includes patients in clinical follow-up in a health area of 569,534 inhabitants after SARS-CoV-2/COVID-19 diagnosis. Clinical and epidemiological characteristics were collected during the follow up.Main measures and key resultsA total of 284 patients completed 6 months follow-up, 176 (69.4%) required hospitalization and 29 (10.2%) of them needed critical care. At six months, 119 (48.0%) patients described one or more persisting symptoms. The most prevalent were: extra-thoracic symptoms (39.1%), chest symptoms (27%), dyspnoea (20.6%), and fatigue (16.1%). These symptoms were more common in hospitalized patients (52.3% vs 38.2%) and in women (59.0% vs 40.5%). The multivariate analysis identified Chronic Obstructive Pulmonary Disease (COPD), female gender and tobacco consumption as risk factors for long COVID.ConclusionsPersisting symptoms are common after COVID-19 especially in hospitalized patients compared to outpatients (52.3% vs. 38.2%). Based on these findings, special attention and clinical follow-up after acute SARS-CoV-2 infection should be provided for hospitalized patients with previous lung diseases, tobacco consumption, and females.
The Impact for implementing Balanced Scorecard in Health Care Organizations: A Systematic Review
Authors: Amer Faten , Hammoud Sahar , Khatatbeh Haitham , Lohner Szimonetta , Boncz Imre , Endrei Dóra 
Published: August 2021

AbstractAimsThis systematic review aims to assess the impact of Balanced Scorecard (BSC) implementation at Health Care Organizations (HCOs) on Health Care Workers’ (HCWs’) satisfaction, patient satisfaction, and financial performance. Up to now, no previous systematic reviews have performed a comprehensive and rigorous methodological approach to figure out the impact of BSC implementation in HCOs.MethodsThis systematic review was prepared according to PRISMA guidelines. PubMed, Embase, Cochrane, and Google Scholar databases, as well as Google search engine, were inspected to find all BSC implementations at HCOs until 20 September 2020. Then the resulted articles were screened to find the implementations which measured the impact of BSC on HCWs’ satisfaction, patient satisfaction, and financial performance. Quality assessment was performed using the Standards for Reporting Implementation Studies: (StaRI) checklist.ResultsOut of 4031 records, 20 articles were finally included for measuring one or more of the three impact types. 17 measured the impact of BSC on patient satisfaction, 7 on HCWs’ satisfaction, and 12 on financial performance. Studies with higher quality had a higher positive impact.ConclusionThis paper offers evidence to HCOs and policymakers on the benefits of implementing BSC. BSC implementations showed a positive impact on patient satisfaction and financial performance in HCOs. However, less impact was found on HCWs’ satisfaction, which should be given better consideration in future BSC implementations. High and medium-quality BSC studies were associated with higher positive impacts than low ones. BSC can be utilized as an effective tool to improve HCOs’ performance during the COVID-19 pandemic.
OtoXNet - Automated Identification of Eardrum Diseases from Otoscope Videos: A Deep Learning Study for Video-representing Images
Authors: Binol Hamidullah , Niazi M. Khalid Khan , Elmaraghy Charles , Moberly Aaron C. , Gurcan Metin N. 
Published: August 2021

AbstractBackgroundThe lack of an objective method to evaluate the eardrum is a critical barrier to an accurate diagnosis. Eardrum images are classified into normal or abnormal categories with machine learning techniques. If the input is an otoscopy video, a traditional approach requires great effort and expertise to manually determine the representative frame(s).MethodsIn this paper, we propose a novel deep learning-based method, called OtoXNet, which automatically learns features for eardrum classification from otoscope video clips. We utilized multiple composite image generation methods to construct a highly representative version of otoscopy videos to diagnose three major eardrum diseases, i.e., otitis media with effusion, eardrum perforation, and tympanosclerosis versus normal (healthy). We compared the performance of OtoXNet against methods with that either use a single composite image or a keyframe selected by an experienced human. Our dataset consists of 394 otoscopy videos from 312 patients and 765 composite images before augmentation.ResultsOtoXNet with multiple composite images achieved 84.8% class-weighted accuracy with 3.8% standard deviation, whereas with the human-selected keyframes and single composite images, the accuracies were respectively, 81.8% ± 5.0% and 80.1% ± 4.8% on multi-class eardrum video classification task using an 8-fold cross-validation scheme. A paired t-test shows that there is a statistically significant difference (p-value of 1.3 × 10−2) between the performance values of OtoXNet (multiple composite images) and the human-selected keyframes. Contrarily, the difference in means of keyframe and single composites was not significant (p = 5.49 × 10−1). OtoXNet surpasses the baseline approaches in qualitative results.ConclusionThe use of multiple composite images in analyzing eardrum abnormalities is advantageous compared to using single composite images or manual keyframe selection.
Determinants of the COVID-19 Vaccine Hesitancy Spectrum
Authors: Piltch-Loeb Rachael , Silver Diana , Kim Yeerae , Norris Hope , McNeill Elizabeth , Abramson David 
Published: August 2021

AbstractPolls report nearly one-third of the United States population is skeptical or opposed to getting the COVID-19 vaccine. Most of these polls, as well as the scientific research that has been conducted on vaccine hesitancy, was done prior to vaccine eligibility opening to all adults. Now that COVID-19 vaccines are widely available, further research is needed to understand the factors contributing to vaccine intentions across the vaccine hesitancy spectrum. This study conducted an online survey using the Social Science Research Solution (SSRS) Opinion Panel web panelists, representative of U.S. adults age 18 and older who use the internet, with an oversample of rural-dwelling and minority populations between April 8 and April 22, 2021- as vaccine eligibility opened to the country. We examined the relationship between COVID-19 exposure and socio-demographics with vaccine intentions [eager-to-take, wait-and-see, undecided, refuse] among the unvaccinated using multinomial logistic regressions [ref: fully/partially vaccinated]. Results showed vaccine intentions varied by demographic characteristics and risk exposures during the period that eligibility for the vaccine was extended to all adults.Funding statementFunding for this research was provided by a grant from the National Science Foundation (Grant #2049886). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Phenotyping of acute and persistent COVID-19 features in the outpatient setting: exploratory analysis of an international cross-sectional online survey
Authors: Sahanic Sabina , Tymoszuk Piotr , Ausserhofer Dietmar , Rass Verena , Pizzini Alex , Nordmeyer Goetz , Hüfner Katharina , Kurz Katharina , Weber Paulina Maria , Sonnweber Thomas , Boehm Anna , Aichner Magdalena , Cima Katharina , Boeckle Barbara , Holzner Bernhard , Rumpold Gerhard , Puelacher Christoph , Kiechl Stefan , Huber Andreas , Wiedermann Christian J. , Sperner-Unterweger Barbara , Tancevski Ivan , Bellmann-Weiler Rosa , Bachler Herbert , Piccoliori Giuliano , Helbok Raimund , Weiss Guenter , Loeffler-Ragg Judith 
Published: August 2021

AbstractBACKGROUNDLong COVID, defined as presence of COVID-19 related symptoms 28 days or more after the onset of acute SARS-CoV-2 infection, is an emerging challenge to healthcare systems. The objective of this study was to phenotype recovery trajectories of non-hospitalized COVID-19 individuals.METHODSWe performed an international, multi-center, exploratory online survey study on demographics, comorbidities, COVID-19 symptoms and recovery status of non-hospitalized SARS-CoV-2 infected adults (Austria: n=1157), and Italy: n= 893).RESULTSWorking age subjects (Austria median: 43 yrs (IQR: 31 – 53), Italy: 45 yrs (IQR: 35 – 55)) and females (65.1% and 68.3%) predominated the study cohorts. Course of acute COVID-19 was characterized by a high symptom burden (median 13 (IQR: 9 – 18) and 13 (7 – 18) out of 44 features queried), a 47.6 – 49.3% rate of symptom persistence beyond 28 days and 20.9 – 31.9% relapse rate. By cluster analysis, two acute symptom phenotypes could be discerned: the non-specific infection phenotype and the multi-organ phenotype (MOP), the latter encompassing multiple neurological, cardiopulmonary, gastrointestinal and dermatological features. Clustering of long COVID subjects yielded three distinct subgroups, with a subset of 48.7 – 55 % long COVID individuals particularly affected by post-acute MOP symptoms. The number and presence of specific acute MOP symptoms and pre-existing multi-morbidity was linked to elevated risk of long COVID.CONCLUSIONThe consistent findings of two independent cohorts further delineate patterns of acute and post-acute COVID-19 and emphasize the importance of symptom phenotyping of home-isolated COVID-19 patients to predict protracted convalescence and to allocate medical resources.Key PointsQuestionWhich acute symptom patterns of acute COVID-19 are associated with prolonged symptom persistence, symptom relapse or physical performance impairment?FindingsIn this multicenter international comparative survey study on non-hospitalized SARS- CoV-2 infected adults (Austria: n = 1157, Italy: n = 893) we identified distinct and reproducible phenotypes of acute and persistent features. Acute multi-organ symptoms including neurological and cardiopulmonary manifestations are linked to elevated risk of long COVID.MeaningThese findings suggest to employ symptom phenotyping of home-isolated COVID-19 patients to predict protracted convalescence and to allocate medical resources.
An introgression breakthrough left by an anthropogenic contact between two ascidians
Authors: Moan Alan Le , Roby Charlotte , Fraisse Christelle , Daguin-Thiébaut Claire , Bierne Nicolas , Viard Frédérique 
Published: August 2021

AbstractHuman-driven translocations of species have diverse evolutionary consequences such as promoting hybridization between previously geographically isolated taxa. This is well-illustrated by the solitary tunicate, Ciona robusta, native to the North East Pacific and introduced in the North East Atlantic. It is now co-occurring with its congener C. intestinalis in the English Channel, and C. roulei in the Mediterranean Sea. Despite their long allopatric divergence, first and second generation crosses showed a high hybridization success between the introduced and native taxa in the laboratory. However, previous genetic studies failed to provide evidence of recent hybridization between C. robusta and C. intestinalis in the wild. Using SNPs obtained from ddRAD-sequencing of 397 individuals from 26 populations, we further explored the genome-wide population structure of the native Ciona taxa. We first confirmed results documented in previous studies, notably i) a chaotic genetic structure at regional scale, and ii) a high genetic similarity between C. roulei and C. intestinalis, which is calling for further taxonomic investigation. More importantly, and unexpectedly, we also observed a genomic hotspot of long introgressed C. robusta tracts into C. intestinalis genomes at several locations of their contact zone. Both the genomic architecture of introgression, restricted to a 1.5 Mb region of chromosome 5, and its absence in allopatric populations suggest introgression is recent and occurred after the introduction of the non-indigenous species. Overall, our study shows that anthropogenic hybridization can be effective in promoting introgression breakthroughs between species at a late stage of the speciation continuum.
MorphData: Automating the data extraction process of morphological features of microglial cells in ImageJ
Authors: Campos Ana Bela , Duarte-Silva Sara , Ambrósio António Francisco , Maciel Patrícia , Fernandes Bruno 
Published: August 2021

AbstractMicroglial cells are the first line of defense within the central nervous system, with morphological characterization being widely used to define their activation status. Most methods to evaluate microglia status are manual, and, therefore, often biased, inaccurate, and time consuming. In fact, the process to collect morphological data starts with the acquisition of photomicrographs from where images of single cells are extracted. Then, the researcher collects the morphological features that characterize each cell. However, a manual data collection process from single cells can take weeks to complete. This work describes an open-source ImageJ plugin, MorphData, which automatizes the data extraction process of morphological features of single microglial cells. The plugin collects, processes, and organizes features associated with cell complexity and ramification. In a computer with limited computing power, MorphData was able to handle 699 single cells in less than 14 minutes. The same process, if performed manually, would take almost 19 working days. Overall, MorphData significantly reduces the time taken to collect morphological data from microglial cells, which can then be used to study, understand, and characterize microglia behavior in the brain of human patients or of animal models of neurological and psychiatric diseases.
Establishment of a prognosis prediction model based on pyroptosis-related signatures associated with the immune microenvironment and molecular heterogeneity in clear cell renal carcinoma
Authors: Jiang Aimin , Meng Jialin , Bao Yewei , Wang Anbang , Gong Wenliang , Gan Xinxin , Wang Jie , Bao Yi , Wu Zhenjie , Lu Juan , Liu Bing , Wang Linhui 
Published: August 2021

AbstractBackgroundPytoptosis is essential for tumorigenesis and progression of clear cell renal cell carcinoma (ccRCC). However, the heterogeneity of pyroposis and its relationship with the tumor microenvironment (TME) remain unclear. The aim of the present study was to identify proptosis-related subtypes and construct a prognosis prediction model based on pyroptosis signatures.MethodsFirst, heterogenous pyroptosis subgroups were explored based on 33 pyroptosis-related genes and ccRCC samples from TCGA, and the model establsihed by LASSO regression was verified by ICGC database. Then, the clinical significance, functional status, immune infiltration, cell-cell communication, genomic alteration and drug sensitivity of different subgroups were further analyzed. Finally, the LASSO-Cox algorithm was applied to narrow down the candidate genes to develop a robust and concise prognostic model.ResultsTwo heterogenous pyroptosis subgroups were identified: pyroptosis-low immunity-low C1 subtype, and pyroptosis-high immunity-high C2 subtype. Compared with C1, C2 was associated with a higher clinical stage or grade and a worse prognosis. More immune cell infiltration was observed in C2 than that in C1, while the response rate in C2 subgroup was lower than that in C1 subgroup. Pyroptosis related genes were mainly expressed in myeloid cells, and T cells and epithelial cells might influence other cell clusters via Pyroptosis related pathway. In addition, C1 was characterized by MTOR and ATM mutation, while C2 was characterized by more significant alterations in SPEN and ROS1 mutation. Finally, we constructed and validated a robust and promising signature based on the pyroptosis-related risk score for assessing the prognosis in ccRCC.ConclusionWe identified two heterogeneous pyroptosis subtypes and 5 reliable risk signatures to establish a prognosis prediction model. Our findings may help better understand the role of pyroptosis in ccRCC progression and provide a new perspective in the management of ccRCC patients.
Pupil correlates of decision variables in mice playing a competitive mixed-strategy game
Authors: Wang Hongli , Ortega Heather K. , Atilgan Huriye , Murphy Cayla E. , Kwan Alex C. 
Published: August 2021

AbstractIn a competitive game involving an animal and an opponent, the outcome is contingent on the choices of both players. To succeed, the animal must continually adapt to competitive pressure, or else risk being exploited and lose out on rewards. In this study, we demonstrate that head-fixed mice can be trained to play the iterative competitive game ‘matching pennies’ against a virtual computer opponent. We find that the animals’ performance is well described by a hybrid computational model that includes Q-learning and choice kernels. Comparing between matching pennies and a non-competitive two-armed bandit task, we show that the tasks encourage animals to operate at different regimes of reinforcement learning. To understand the involvement of neuromodulatory mechanisms, we measure fluctuations in pupil size and use multiple linear regression to relate the trial-by-trial transient pupil responses to decision-related variables. The analysis reveals that pupil responses are modulated by observable variables, including choice and outcome, as well as latent variables for value updating, but not action selection. Collectively, these results establish a paradigm for studying competitive decision-making in head-fixed mice and provide insights into the role of arousal-linked neuromodulation in the decision process.
Division of Labor between SOS and PafBC in mycobacterial DNA Repair and Mutagenesis
Authors: Adefisayo Oyindamola O. , Dupuy Pierre , Bean James M. , Glickman Michael S. 
Published: August 2021

AbstractDNA repair systems allow microbes to survive in diverse environments that compromise chromosomal integrity. Pathogens such as M. tuberculosis must contend with the genotoxic host environment, which generates the mutations that underlie antibiotic resistance. Mycobacteria encode the widely distributed SOS pathway, governed by the LexA repressor, but also encode PafBC, a positive regulator of the transcriptional DNA damage response (DDR). Although the transcriptional outputs of these systems have been characterized, their full functional division of labor in survival and mutagenesis is unknown. Here we specifically ablate the PafBC or SOS pathways, alone and in combination, and test their relative contributions to repair. We find that SOS and PafBC have both distinct and overlapping roles that depend on the type of DNA damage. Most notably, we find that quinolone antibiotics and replication fork perturbation are inducers of the PafBC pathway, and that chromosomal mutagenesis is codependent on PafBC and SOS, through shared regulation of the DnaE2/ImuA/B mutasome. These studies define the complex transcriptional regulatory network of the DDR in mycobacteria and provide new insight into the regulatory mechanisms controlling the genesis of antibiotic resistance in M. tuberculosis.
Functionalized Biomimetic Hydrogels Enhance Salivary Stem/Progenitor Cell Organization
Authors: Martinez Mariane , Witt Robert L. , Farach-Carson Mary C. , Harrington Daniel A. 
Published: August 2021

AbstractComplex branched salivary structures remain challenging to replicate within implant ready hydrogels. We showed previously that hyaluronic acid (HA)-based hydrogels enable growth and organization of primary salivary-derived human stem/progenitor cells (hS/PCs) into multicellular spheroids. Here, we systematically functionalized three components of migration-permissive hydrogels to foster salivary tissue morphogenesis. We separately analyzed contributions of an enzymatically degradable crosslinker, a pendant integrin-binding site, and hydrogel porosity to best support high viability, integrin-dependent cell adhesion and migration. Structure size, frequency, and morphology were all affected by hydrogel crosslink density and integration of biofunctional peptides. Viability and proliferation data suggested that integration of integrin binding sites had the greatest effect on hS/PCs behavior. A larger internal matrix space, created by increasing both crosslinker length and PEG content, was needed to form large multicellular hS/PC structures. Peptide-modified hydrogels with more internal space shifted hS/PC organization from spheroidal, surrounded by thick basement membrane, to an asymmetric arrangement with punctate matrix proteins defining a “wrinkled” perimeter. Integrin-binding peptides activated integrin β1, with highest activation observed in hydrogels having both cleavable peptide and integrin ligand. The design parameters we prescribe allowed us to encapsulate hS/PCs in a humanized biomimetic hydrogel matrix able to support morphogenesis needed for salivary restoration.
Neural manifolds for odor-driven innate and acquired appetitive preferences
Authors: Chandak Rishabh , Raman Barani 
Published: August 2021

AbstractSensory stimuli evoke spiking neural responses that innately or after learning drive suitable behavioral outputs. How are these spiking activities intrinsically patterned to encode for innate preferences, and could the neural response organization impose constraints on learning? We examined this issue in the locust olfactory system. Using a diverse odor panel, we found that ensemble activities both during (‘ON response’) and after stimulus presentations (‘OFF response’) could be linearly mapped onto overall appetitive preference indices. Although diverse, ON and OFF response patterns generated by innately appetitive odorants were still limited to a low-dimensional subspace (a ‘neural manifold’). Similarly, innately non-appetitive odorants evoked responses that were separable yet confined to another neural manifold. Notably, only odorants that evoked neural response excursions in the appetitive manifold were conducive for learning. In sum, these results provide insights on how encoding for innate preferences can also set limits on associative learning.