bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and evaluation of risk factors of anti-retroviral therapy failure among human immunodeficiency virus/acquired immune deficiency syndrome patients in North India
Authors: Basu Ayan , Biswas Ashutosh , Wig Naveet , Sood Rita , Soneja Manish , Nischal Neeraj , Das Bimal Kumar 
Published: January 2021

Abstract

Background
The prevalence of anti-retroviral therapy (ART) failure is not uniform in India. In this study we attempted to determine the prevalence and risk factors of treatment failure among patients who were on ART for &gt;1 y.

Methods
We conducted an ambispective study from 2017 to 2019 in the All India Institute of Medical Sciences, New Delhi, India. Patients and their past medical records were examined to determine clinical, immunological and virological failure.

Results
Among 301 enrolled patients, the majority was male (61.8%), with a mean age of 36.98±10.84 y. The prevalence of ART failure in our study was 10.63% (32/301). Clinical, immunological and virological failure rates were 1.66%, 10.63% and 5.65%, respectively. The maximum chance of failure was the tenofovir–lamivudine–nevirapine (33.3%) regimen followed by the stavudine–lamivudine–nevirapine (30.4%) regimen. Among the nucleoside reverse transcriptase inhibitors, a stavudine-based regimen had a significantly greater chance of failure (25.8%) compared with tenofovir (9.6%) and zidovudine (7.9%) regimens (p&lt;0.005). Low baseline CD4 count and development of tuberculosis after ART initiation were significantly (p&lt;0.05) associated with treatment failure in univariate analysis. Patients with a low peak CD4 count (adjusted odds ratio [AOR 4.26 {95% confidence interval &lt;CI&gt; 1.83 to 9.88}]) and who developed symptoms after ART initiation (AOR 3.77 [95% CI 1.47 to 9.69]) had significantly higher odds of treatment failure in the multivariate analysis (p&lt;0.001).

Conclusions
Early identification of risk factors by regular follow-up and selection of the proper ART regimen can reduce the rate of treatment failure.
Experimental increase of worker diversity benefits brood production in ants
Authors: Psalti Marina N. , Gohlke Dustin , Libbrecht Romain 
Published: January 2021

AbstractThe reproductive division of labor of eusocial insects, whereby one or several queens monopolize reproduction, evolved in a context of high genetic relatedness. However, many extant eusocial species have developed strategies that decrease genetic relatedness in their colonies, suggesting some benefits of the increased diversity. Multiple studies support this hypothesis by showing positive correlations between genetic diversity and colony fitness, as well as finding effects of experimental manipulations of diversity on colony performance. However, alternative explanations could account for most of these reports, and the benefits of diversity on fitness in eusocial insects still await validation. In this study, we experimentally increased worker diversity in the antLasius nigerwhile controlling for typical confounding factors. We found that experimental colonies composed of workers coming from three different source colonies produced more larvae and showed more variation in size compared to groups of workers coming from a single colony. We propose that the benefits of increased diversity stemmed from an improved division of labor. Our study confirms that worker diversity enhances colony performance, thus providing a possible explanation for the evolution of multiply mated queens and multiple-queen colonies in many species of eusocial insects.
Chitinase 3-like-1 is a Therapeutic Target That Mediates the Effects of Aging in COVID-19
Authors: Kamle Suchitra , Ma Bing , He Chuan Hua , Akosman Bedia , Zhou Yang , Lee Chang Min , El-Deiry Wafik S. , Huntington Kelsey , Liang Olin , Machan Jason T. , Kang Min-Jong , Shin Hyeon Jun , Mizoguchi Emiko , Lee Chun Geun , Elias Jack A. 
Published: January 2021

AbstractCOVID-19 is caused by the SARS-CoV-2 (SC2) virus and is more prevalent and severe in the elderly and patients with comorbid diseases (CM). Because chitinase 3-like-1 (CHI3L1) is induced during aging and CM, the relationships between CHI3L1 and SC2 were investigated. Here we demonstrate that CHI3L1 is a potent stimulator of the SC2 receptor ACE2 and viral spike protein priming proteases (SPP), that ACE2 and SPP are induced during aging and that anti-CHI3L1, kasugamycin and inhibitors of phosphorylation, abrogate these ACE2- and SPP-inductive events. Human studies also demonstrated that the levels of circulating CHI3L1 are increased in the elderly and patients with CM where they correlate with COVID-19 severity. These studies demonstrate that CHI3L1 is a potent stimulator of ACE2 and SPP; that this induction is a major mechanism contributing to the effects of aging during SC2 infection and that CHI3L1 coopts the CHI3L1 axis to augment SC2 infection. CHI3L1 plays a critical role in the pathogenesis of and is an attractive therapeutic target in COVID-19.
A multi-dimensional integrative scoring framework for predicting functional variants in the human genome
Authors: Li Xihao , Yung Godwin , Zhou Hufeng , Sun Ryan , Li Zilin , Liu Yaowu , Ionita-Laza Iuliana , Lin Xihong 
Published: January 2021

AbstractAttempts to identify and prioritize functional DNA elements in coding and noncoding regions, particularly through use of in silico functional annotation data,continue to increase in popularity. However, specific functional roles may vary widely from one variant to another, making it challenging to summarize different aspects of variant function. Here we propose Multi-dimensional Annotation Class Integrative Estimation (MACIE), an unsupervised multivariate mixed model framework capable of integrating annotations of diverse origin to assess multi-dimensional functional roles for both coding and noncoding variants. Unlike existing one-dimensional scoring methods, MACIE views variant functionality as a composite attribute encompassing multiple characteristics, and estimates the joint posterior functional probability vector of each genomic position, a quantity that offers richer and more interpretable information in the presence of multiple aspects of functionality. Applied to a variety of independent coding and non-coding datasets, MACIE demonstrates powerful and robust performance in discriminating between functional and non-functional variants. We also show an application of MACIE to fine-mapping using lipids GWAS summary statistics data from the European Network for Genetic and Genomic Epidemiology Consortium.
A guide to between-community functional dissimilarity measures
Authors: Lengyel Attila , Botta-Dukát Zoltán 
Published: January 2021

AbstractOne of the effective tools to study the variation between communities is the use of pairwise dissimilarity indices. Besides species as variables, the involvement of trait information provides valuable insight into the functioning of ecosystems. In recent years, a variety of indices have been proposed to quantify functional dissimilarity between communities. These indices follow different approaches to account for between-species similarities in calculating community dissimilarity, yet they all have been proposed as straightforward tools.In this paper, we review the trait-based dissimilarity indices available in the literature and identify the most important conceptual and technical properties that differentiate among them and that must be considered before their application.We identify two primary aspects that need to be considered before choosing a functional dissimilarity index. The first one is the way communities are represented in the trait space. The three main types of representations are the typical values, the combination of species×sites and species×trait matrices, and the hypervolumes. The second decision is the concept of dissimilarity to follow, including two options: distances and (lack of) overlaps. We use the above scheme to discuss the available functional dissimilarity indices and evaluate their relations to each other, their capabilities, and accessibility.
Decoding the single-cell landscape and intercellular crosstalk in the transplanted liver: a 4-dimension mouse model
Authors: Huang Haitao , Zhang Xueyou , Chen Hui , Feng Shi , Zhang Cheng , Chen Ruihan , Lin Yimou , Ji Qinghua , Ling Qi 
Published: January 2021

ABSTRACTGraft remodeling after transplantation maintains graft functionality and determines graft survival. However, a comprehensive understanding of cellular diversity and interplay during graft remodeling remains to be fully characterized. In this study, we established a well tolerant C57BL/6 to C57BL/6 orthotopic liver transplantation (LT) mice model and observed two stages of graft recovery including an acute phase and a steady phase. We next performed single-cell RNA sequencing (scRNA-seq) and cytometry by time-of-flight (CyTOF) and recorded the cellular hierarchy in the transplanted liver during the two stages. Besides the dynamic change of cell proportion, it was notable that recipient-derived cells took over the transplanted liver in most cell types (e.g., B cells, T cells, dendritic cells, granulocytes and monocytes) except CD206+MerTK+macrophages and CD161+CD49a+CD49b−natural killer cells. We then focused on macrophages and captured 5 distinct transcriptional signatures to define novel subclusters. Using a ligand-receptor interaction strategy, we identified specific macrophage-hepatocyte interactions during the acute and stable phases, causing metabolic remodeling in the transplanted liver. Our results delineated a 4-dimension cell atlas (type-proportion-source-time) of the transplanted liver, which sheds light on the physiological process of liver graft maintenance and graft-recipient crosstalk.
The role of water mobility in protein misfolding
Authors: Stephens Amberley D. , Kölbel Johanna , Moons Rani , Ruggerio Michael T. , Mahmoudi Najet , Shmool Talia A. , McCoy Thomas M. , Nietlispach Daniel , Routh Alexander F. , Sobott Frank , Zeitler J. Axel , Schierle Gabriele S. Kaminski 
Published: January 2021

AbstractThe propensity for intrinsically disordered proteins to aggregate is heavily influenced by their surrounding environment. Here, we show that the mobility of the surrounding water molecules directly influences the aggregation rate of α-synuclein (aSyn), a protein associated with Parkinson’s disease. We observe that the addition of NaCl reduces the mobility of water, while addition of CsI increases the mobility of water. In turn, this reduces and increases the mobility of aSyn, respectively, given the change in strength and lifetime of the intermolecular forces. The reduction of aSyn mobility in the presence of NaCl ions leads to increased aggregation rates, which may be due to aggregation-competent conformations being stable for longer, thereby increasing the likelihood of establishing interactions between two adjacent monomers. In contrast, aSyn is more mobile when CsI is dissolved in the aqueous phase which leads to a reduction of successful monomeric interactions. We thus highlight the importance of the surrounding environment and describe how ion content can influence water mobility and the misfolding rate of amyloidogenic proteins, such as aSyn. By modulating the cellular environment to increase water mobility or finding small molecules to increase protein dynamics, new therapeutic targets may be found.
Modulated termination of non-coding transcription partakes in the regulation of gene expression
Authors: Haidara Nouhou , Porrua Odil 
Published: January 2021

ABSTRACTPervasive transcription is a universal phenomenon leading to the production of a plethora of non-coding RNAs. If left uncontrolled, pervasive transcription can be harmful for genome expression and stability. However, non-coding transcription can also play important regulatory roles, for instance by promoting the repression of specific genes by a mechanism of transcriptional interference. The efficiency of transcription termination can strongly influence the regulatory capacity of non-coding transcription events, yet very little is known about the mechanisms modulating the termination of non-coding transcription in response to environmental cues.Here, we address this question by investigating the mechanisms that regulate the activity of the main actor in termination of non-coding transcription in budding yeast, the helicase Sen1. We identify a phosphorylation at a conserved threonine of the catalytic domain of Sen1 and we provide evidence that phosphorylation at this site reduces the efficiency of Sen1-mediated termination. Interestingly, we find that this phosphorylation impairs termination at an unannotated non-coding gene, thus repressing the expression of a downstream gene encoding the master regulator of Zn homeostasis, Zap1. Consequently, many additional genes exhibit an expression pattern mimicking conditions of Zn excess, whereZAP1is naturally repressed.Our findings provide a novel paradigm of gene regulatory mechanism relying on the direct modulation of non-coding transcription termination.
In vivo deciduous dental eruption in LuiKotale bonobos and Gombe chimpanzees
Authors: Lee Sean M. , Sutherland L. J. , Fruth Barbara , Murray Carson M. , Lonsdorf Elizabeth V. , Arbenz-Smith Keely , Augusto Rafael , Brogan Sean , Canington Stephanie L. , Lee Kevin C. , McGrath Kate , McFarlin Shannon C. , Hohmann Gottfried 
Published: January 2021

AbstractExisting data on bonobo and chimpanzee dental eruption timing are derived predominantly from captive individuals or deceased wild individuals. However, recent advances in noninvasive photographic monitoring of living, wild apes have greatly expanded our knowledge of chimpanzee dental eruption in relatively healthy individuals under naturalistic conditions. We employ similar methods to expand on this knowledge by reporting deciduous dental eruption ages in living, wild bonobos and chimpanzees from LuiKotale, Democratic Republic of the Congo and Gombe National Park, Tanzania, respectively. Deciduous dental eruption ages in our sample generally fall within the range of variation previously documented for captive chimpanzees. We also found substantial variation in deciduous canine eruption timing, particularly among bonobos. One bonobo had a deciduous canine present by 227 days old while another did not have a deciduous canine present at 477 days old. As more data accumulate from these populations, future studies should consider sources of variation in deciduous canine eruption timing and relationships with other aspects of life history.
Occupancy-collection models: Towards bias-corrected modeling of species’ distributions using unstructured occurrence data from museums and herbaria
Authors: Erickson Kelley D. , Smith Adam B. 
Published: January 2021

AbstractThe digitization of museum collections as well as an explosion in citizen science initiatives has resulted in a wealth of data that can be useful for understanding the global distribution of biodiversity, provided that the well-documented biases inherent in unstructured opportunistic data are accounted for. While traditionally used to model imperfect detection using structured data from systematic surveys of wildlife, occupancy-detection models provide a framework for modelling the imperfect collection process that results in digital specimen data. In this study, we explore methods for adapting occupancy-detection models for use with biased opportunistic occurrence data from museum specimens and citizen science platforms using 7 species of Anacardiaceae in Florida as a case study. We explored two methods of incorporating information about collection effort to inform our uncertainty around species presence: (1) filtering the data to exclude collectors unlikely to collect the focal species and (2) incorporating collection covariates (collection type and history of previous detections) into a model of collection probability. We found that the best models incorporated both the background data filtration step as well as the incorporation of collector covariates associated with the probability of collection. We found that month, method of collection and whether a collector had previously collected the focal species were important predictors of collection probability. Efforts to standardize meta-data associated with data collection will improve efforts for modeling the spatial distribution of a variety of species.
Combined Ventilation Of Two Subjects With A Single Mechanical Ventilator Using A New Medical Device: AnIn VitroStudy
Authors: Lugones Ignacio , Ramos Matías , Biancolini Fernanda , Giambastiani Roberto Orofino 
Published: January 2021

ABSTRACTINTRODUCTIONThe SARS-CoV2 pandemic has created a sudden lack of ventilators. DuplicAR®is a novel device that allows simultaneous and independent ventilation of two subjects with a single ventilator. The aims of this study are: a) to determine the efficacy of DuplicAR®to independently regulate the peak and positive-end expiratory pressures in each subject, both under pressure-controlled ventilation and volume-controlled ventilation, and b) to determine the ventilation mode in which DuplicAR®presents the best performance and safety.MATERIALS AND METHODSTwo test lungs are connected to a single ventilator using DuplicAR®. Three experimental stages are established: 1) two identical subjects, 2) two subjects with the same weight but different lung compliance, and 3) two subjects with different weight and lung compliance. In each stage, the test lungs are ventilated in two ventilation modes. The positive-end expiratory pressure requirements are increased successively in one of the subjects. The goal is to achieve a tidal volume of 7 ml/kg for each subject in all different stages through manipulation of the ventilator and the DuplicAR®controllers.RESULTSDuplicAR®allows adequate ventilation of two subjects with different weight and/or lung compliance and/or PEEP requirements. This is achieved by adjusting the total tidal volume for both subjects (in volume-controlled ventilation) or the highest peak pressure needed (in pressure-controlled ventilation) along with the basal positive-end expiratory pressure on the ventilator, and simultaneously manipulating the DuplicAR®controllers to decrease the tidal volume or the peak pressure in the subject that needs less and/or to increase the positive-end expiratory pressure in the subject that needs more. While ventilatory goals can be achieved in any of the ventilation modes, DuplicAR®performs better in pressure-controlled ventilation, as changes experienced in the variables of one subject do not modify the other one.CONCLUSIONSDuplicAR®is an effective tool to manage the peak inspiratory pressure and the positive-end expiratory pressure independently in two subjects connected to a single ventilator. The driving pressure can be adjusted to meet the requirements of subjects with different weight and lung compliance. Pressure-controlled ventilation has advantages over volume-controlled ventilation and is therefore the recommended ventilation mode.
Generalized Prediction of Hemodynamic Shock in Intensive Care Units
Authors: Nagori Aditya , Singh Pradeep , Firdos Sameena , Vats Vanshika , Gupta Arushi , Bandhey Harsh , Kalia Anushtha , Sharma Arjun , Ailavadi Prakriti , Awasthi Raghav , Bhadra Wrik , Kaul Ayushmaan , Lodha Rakesh , Sethi Tavpritesh 
Published: January 2021

AbstractEarly prediction of hemodynamic shock in the ICU can save lives. Several studies have leveraged a combination of vitals, lab investigations, and clinical data to construct early warning systems for shock. However, these have a limited potential of generalization to diverse settings due to reliance on non-real-time data. Monitoring data from vitals can provide an early real-time prediction of Hemodynamic shock which can precede the clinical diagnosis to guide early therapy decisions. Generalization across age and geographical context is an unaddressed challenge. In this retrospective observational study, we built real-time shock prediction models generalized across age groups (adult and pediatric), ICU-types, and geographies. We trained, validated, and tested a shock prediction model on the publicly available eICU dataset on 208 ICUs across the United States. Data from 156 hospitals passed the eligibility criteria for cohort building. These were split hospital-wise in a five-fold training-validation-test set. External validation of the model was done on a pediatric ICU in New Delhi and MIMIC-III database with more than 0.23 million and one million patient-hours vitals data, respectively. Our models identified 92% of all the shock events more than 8 hours in advance with AUROC of 86 %(SD= 1.4) and AUPRC of 93% (SD =1.2) on the eICU testing set. An AUROC of 87 % (SD =1.8), AUPRC 92 % (SD=1.6) were obtained in external validation on the MIMIC-III cohort. The New Delhi Pediatric SafeICU data achieved an AUROC of 87 % (SD =4) AUPRC 91% (SD=3), despite being completely different geography and age group. In this first, we demonstrate a generalizable model for predicting shock, and algorithms are publicly available as a pre-configured Docker environment at https://github.com/tavlab-iiitd/ShoQPred.
A Novel Abnormality Annotation Database for COVID-19 Affected Frontal Lung X-rays
Authors: Mittal Surbhi , Venugopal Vasantha Kumar , Agarwal Vikash Kumar , Malhotra Manu , Chatha Jagneet Singh , Kapur Savinay , Gupta Ankur , Batra Vikas , Majumdar Puspita , Malhotra Aakarsh , Thakral Kartik , Chhabra Saheb , Vatsa Mayank , Singh Richa , Chaudhury Santanu 
Published: January 2021

AbstractPurposeTo advance the usage of CXRs as a viable solution for efficient COVID-19 diagnostics by providing large-scale annotations of the abnormalities in frontal CXRs in BIMCV-COVID19+ database, and to provide a robust evaluation mechanism to facilitate its usage.Materials and MethodsWe provide the abnormality annotations in frontal CXRs by creating bounding boxes. The frontal CXRs are a part of the existing BIMCV-COVID19+ database. We also define four different protocols for robust evaluation of semantic segmentation and classification algorithms. Finally, we benchmark the defined protocols and report the results using popular deep learning models as a part of this study.ResultsFor semantic segmentation, Mask-RCNN performs the best among all the models with a DICE score of 0.43 ± 0.01. For classification, we observe that MobileNetv2 yields the best results for 2-class and 3-class classification. We also observe that deep models report a lower performance for classifying other classes apart from the COVID class.ConclusionBy making the annotated data and protocols available to the scientific community, we aim to advance the usage of CXRs as a viable solution for efficient COVID-19 diagnostics. This large-scale data will be useful for ML algorithms and can be used for learning radiological patterns observed in COVID-19 patients. Further, the protocols will facilitate ML practitioners for unified large-scale evaluation of their algorithms.Data Availability StatementThe data associated with this work is available here : Radiologists’ Annotations on COVID-19+ X-rays https://osf.io/b35xu/ via @OSFramework andhttp://covbase4all.igib.res.in/.