bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Outcomes of Children Diagnosed Dengue-Associated Acute Liver Failure with or without N-Acetylcysteine Treatment: A Retrospective Cohort Study
Authors: Sriphongphankul Hansa , Liabsuetrakul Tippawan , Osatakul Seksit 
Published: April 2021

Abstract

Objectives
N-acetylcysteine (NAC) has been shown to prevent hepatic damage and improve microcirculatory blood flow and oxygen delivery to the tissue. Previous studies have proposed the benefit of NAC in dengue-associated acute liver failure (ALF). However, most studies are descriptive and lack comparison between groups. We aimed to compare the ALF resolution rate and mortality rate of those who received and did not receive NAC treatment.

Methods
A retrospective cohort study was conducted among children aged &lt;15 years who were diagnosed with dengue-associated ALF at a tertiary hospital in Thailand, between January 2002 and July 2019. Demographic and clinical information were collected. Main outcomes were ALF resolution and mortality rate.

Results
Thirty-three patients were included of which 16 received NAC treatment (48.5%). Mean ages were 8.5 years (SD 3.7) and mean onset of ALF was 6.3 days (SD 1.6) after onset of fever. The grading of hepatic encephalopathy (HE) and organ failure was not significantly different between the two groups. In the NAC group, 13/16 children were prescribed 100 mg/kg/day of NAC until INR &lt;2 without HE or &lt;1.5 with HE. NAC was initiated 1.1 days (SD 0.3) after the ALF diagnosis. The NAC group showed a higher rate of ALF resolution (75% vs. 53% in the non-NAC group, p = 0.34) with a lower mortality rate (31% vs. 53%, p = 0.36). Side effects of NAC were not found.

Conclusion
NAC may be beneficial in dengue-associated pediatric ALF. Further well-designed randomized control trials should be carried out.
Early Pension Claiming and Expected Longevity: A Register-Based Study on the Take-up of the Partial Old-Age Pension in Finland
Authors: Nivalainen Satu 
Published: April 2021

Abstract
As of February 2017, Finns have been able to claim a partial old-age pension early at age 61 independent of their working hours or earnings. Focusing on the take-up of the partial old-age pension in Finland, this article investigates whether early pension claiming is associated with expected longevity. We assume parental longevity to signal expected longevity. We use total register data on those eligible to claim a partial pension at age 61 in 2018 or 2019 and link this data to the information on their parents’ birth and death dates. To our knowledge, there exists no previous register-based study that uses parental longevity to explain pension claiming behavior. Since the longevity of the same-sex parent in particular influences subjective life expectancy, the variables of interest were the same-sex parent being alive and the age (at death) of the same-sex parent. The baseline results show a negative connection between the same-sex parent being alive and claiming. The connection disappears after controlling for gender, but the negative connection between the age (at death) of the same-sex parent and the claiming remains significant in a fully adjusted model. Known risk factors for shorter longevity, such as being male, having a lower income and wealth, also increase the likelihood of claiming. The results indicate that people take their expected longevity into account when making pension claiming decisions. This may hold critical implications for actuarial neutrality, the key assumption of the pension system design, and can lead to an unexpected increase in public pension expenditure.
Pushing the Needle of Entrepreneurship and Innovation: Where Do Plastic and Reconstructive Surgeons Stand?
Authors: Khetpal Sumun , Reátegui Alvaro , Lopez Joseph , Sacks Justin M. , Prsic Adnan 
Published: April 2021

Background:
Plastic and reconstructive surgery has a well-recognized history of disruption and innovation. It remains unclear, however, how the specialty’s priority on innovation materializes into commercialization or bench to bedside led by plastic surgeons.

Methods:
Our analysis utilized Pitchbook (Seattle, Wash.), a market database of companies and investors, for ventures that have designed innovations related to plastic and reconstructive surgery. Companies were categorized into 5 focus areas: provider (outpatient surgical or hospital entity), aesthetics (cosmetics/injectables), devices (instrumentation, lasers, implants), regenerative medicine (tissue engineering/wound healing), and software (digital solutions). Company websites, LinkedIn (Sunnyvale, Calif.) profiles, and Crunchbase (San Francisco, Calif.) were reviewed to determine the leadership roles of plastic surgeons.

Results:
Plastic surgeons primarily serve as advisors, as opposed to founders or chief executive officers (CEOs). Our analysis additionally found that provider and software solutions had a greater degree of plastic surgeon-led leadership, whereas regenerative medicine and device innovation remains less frequented. There was a relatively balanced representation of academic and private plastic surgeons in entrepreneurial pursuits.

Conclusions:
Plastic surgeons typically serve as board advisors, as opposed to founders and CEOs. Reasons for disengagement from leadership roles may include satisfaction with clinical work, time constraint, lack of business knowledge, financial constraint, and opportunity cost associated with starting a venture. To promote participation in innovation, future studies should explore tangible ways to engage in such opportunities. In doing so, plastic surgeons can own the “organ” of innovation, and continue to contribute to the legacy and the advancement of the specialty.
The Impact of the COVID-19 Pandemic on Cleft Care
Authors: Bruce Madeleine K. , Pfaff Miles J. , Anstadt Erin E. , Losee Joseph E. , Goldstein Jesse A. 
Published: April 2021

Background:The COVID-19 pandemic had multiple effects on the provision of health care, including the suspension of elective and nonessential surgeries. The objective of this study was to determine the early effect of the COVID-19 pandemic on the surgical care of patients with cleft lip and/or palate at a high-volume cleft center.Methods:A retrospective comparative cohort study of patients with cleft lip and/or palate undergoing lip adhesion, cleft lip and nose repair, and palatoplasty before and during the pandemic was conducted. There were 50 patients in the prepandemic cohort and 53 in the pandemic cohort.Results:Mean age at lip adhesion was 3.1 ± 1.1 months prepandemic (n = 8) and 3.5 ± 2.5 months in the pandemic cohort (n = 8) (P= 0.75). One lip adhesion was delayed by 1.6 months. Mean age at cleft lip and nose repair was 6.6 ± 1.9 months prepandemic (n = 23) and 8.0 ± 2.1 months in the pandemic cohort (n = 23) (P= 0.03). Six pandemic cleft lip and nose repairs were delayed; the mean delay was 2.6 ± 1.8 months. The mean age at palatoplasty was 13.9 ± 2.2 months prepandemic (n = 26) and 14.1 ± 2.9 months in the pandemic cohort (n = 26) (P= 0.79). Seven pandemic palatoplasties were delayed; the mean delay was 3.3 ± 1.4 months.Conclusions:The COVID-19 pandemic caused delays at each stage of repair for cleft lip and/or palate-related procedures; however, only cleft lip and nose repair were significantly affected. This study emphasizes the importance of remaining vigilant regarding the care of this vulnerable population during this challenging time.
PATTERNS OF OCCUPATIONAL MORBIDITY IN ZAMBIA, 2008-2018: A DESCRIPTIVE DATABASE STUDY
Authors: Zambwe M. , Bwembya P.C. , Mutemwa R. , Gasana J. 
Published: April 2021

ABSTRACTOBJECTIVEThis study aimed to describe characteristics of occupational morbidity in Zambia over an eleven year period: 2008-2018.METHODSA descriptive retrospective observational study based on compensation claims database from the Workers Compensation Fund Control Board (WCFCB) in Zambia over the period 2008 to 2018 was conducted. All the accepted compensation claims at WCFCB during the period 2008 to 2018 were reviewed. The reference population of the study was all workers in Zambia covered by WCFCB at the time. All the accepted compensation claims during the period were taken up into the study. Stata version 14 was used to analyze the data, and make descriptive tables and graphs.RESULTSThe total number of reviewed and analyzed cases was 8,009. The gender most affected by occupational morbidity was males (94%). Married males were more affected (72%) compared to single males. However, single females were more affected than the married females at 4% and 2%, respectively. The major morbidity types were wounds (30%), fractures (29%), and amputations (17%). The biggest contributing industries to the cause of occupational morbidity were manufacturing (27%), and mining (19%). Lusaka and Copperbelt regions were the main epicenters at 49% and 34% respectively.CONCLUSIONWounds, fractures and amputations were the most prominent types of occupational morbidity. Traditional gender-based practices of married males seem to underlie their over-exposure to occupational hazards. Manufacturing sector which is poorly regulated compared to the mining sector, was the highest contributor to the occupational morbidity. The manufacturing sector should be subjected to stronger government regulation and inspectorate, with emphasis on compliance to relevant international occupational health and safety protocols.ARTICLE SUMMARYStrengths and limitations of the studyThe study utilized the WCFCB injury and disease compensation claims data as a proxy to establish the national burden of occupational morbidity in Zambia during the study period, hence contributing to the body of knowledge.WCFCB does not cover government ministries and the informal sector in the country which accounts for about 89.3% of the total labour force, the injuries and diseases being contracted in the foretasted sectors were never reported to the institution; and hence making findings of our study an understatement of the actual national burden.Since submission of compensation claims is generally motivated by receiving monetary benefits for an injury or disease contracted, cases of less magnitude are not reported to WCFCB, hence could not be captured in the study.Out of many diseases WCFCB only recognize pneumoconiosis and pulmonary tuberculosis as occupational diseases, hence our study could only assess those two making the study an understatement of the actual occupational disease burden.
Prediction of RNA-protein interactions using a nucleotide language model
Authors: Yamada Keisuke , Hamada Michiaki 
Published: April 2021

AbstractMotivationThe accumulation of sequencing data has enabled researchers to predict the interactions between RNA sequences and RNA-binding proteins (RBPs) using novel machine learning techniques. However, existing models are often difficult to interpret and require additional information to sequences. Bidirectional encoder representations from Transformer (BERT) is a language-based deep learning model that is highly interpretable. Therefore, a model based on BERT architecture can potentially overcome such limitations.ResultsHere, we propose BERT-RBP as a model to predict RNA-RBP interactions by adapting the BERT architecture pre-trained on a human reference genome. Our model outperformed state-of-the-art prediction models using the eCLIP-seq data of 154 RBPs. The detailed analysis further revealed that BERT-RBP could recognize both the transcript region type and RNA secondary structure only from sequence information. Overall, the results provide insights into the fine-tuning mechanism of BERT in biological contexts and provide evidence of the applicability of the model to other RNA-related problems.AvailabilityPython source codes are freely available athttps://github.com/kkyamada/bert-rbp.Contactmhamada@waseda.jp
DeepRegFinder: Deep Learning-Based Regulatory Elements Finder
Authors: Ramakrishnan Aarthi , Wangensteen George , Kim Sarah , Nestler Eric J. , Shen Li 
Published: April 2021

AbstractMotivationEnhancers and promoters are important classes of DNA regulatory elements that control gene expression. Identifying them at the genomic scale is a critical and challenging task in bioinformatics. The most successful method so far is to train machine learning models on known enhancer and promoter sites and predict them at other genomic regions using ChIP-seq and related data.ResultsWe have developed a highly customizable program called DeepRegFinder which automates data processing, model training and genome-wide prediction of enhancers and promoters using convolutional and recurrent neural networks. Our program further classifies the enhancers and promoters into active and poised states to facilitate downstream analysis. Based on mean average precision scores of different classes across multiple cell types, our method significantly outperforms the existing algorithms.Availabilityhttps://github.com/shenlab-sinai/DeepRegFinder
Helios is a marker, not a driver, of human Treg stability
Authors: Lam Avery J. , Uday Prakruti , Gillies Jana K. , Levings Megan K. 
Published: April 2021

AbstractRegulatory T cell (Treg) therapy holds promise as a potentially curative approach to establish immune tolerance in transplantation and autoimmune disease. An outstanding question is whether therapeutic Tregs have the potential to transdifferentiate into effector T cells and thus exacerbate rather than suppress immune responses. In mice, the transcription factor Helios is thought to promote Tregs lineage stability in a range of inflammatory contexts. In humans, the role of Helios in Tregs is less clear, in part due to the inability to enrich and study subsets of Helios-positive versus Helios-negative Tregs. Using an in vitro expansion system, we found that loss of high Helios expression and emergence of an intermediate Helios (Heliosmid)-expressing population correlated with Treg destabilization. We then used CRISPR/Cas9 to genetically ablate Helios expression in human naive or memory Tregs and found that Helios-knockout and unedited Tregs were equivalent in their suppressive function and stability in inflammation. Thus, high Helios expression is a marker, but not a driver, of human Treg stability in vitro. These data highlight the importance of monitoring Helios expression in therapeutic Treg manufacturing and provide new insight into the biological function of this transcription factor in human T cells.
Transcriptome diversity is a systematic source of bias in RNA-sequencing data
Authors: García-Nieto Pablo E. , Wang Ban , Fraser Hunter B. 
Published: April 2021

ABSTRACTBackgroundRNA sequencing has been widely used as an essential tool to probe gene expression. While standard practices have been established to analyze RNA-seq data, it is still challenging to detect and remove artifactual signals. Several factors such as sex, age, and sequencing technology have been found to bias these estimates. Probabilistic estimation of expression residuals (PEER) has been used to account for some systematic effects, but it has remained challenging to interpret these PEER factors.ResultsHere we show that transcriptome diversity – a simple metric based on Shannon entropy – explains a large portion of variability in gene expression, and is a major factor detected by PEER. We then show that transcriptome diversity has significant associations with multiple technical and biological variables across diverse organisms and datasets. This prevalent confounding factor provides a simple explanation for a major source of systematic biases in gene expression estimates.ConclusionsOur results show that transcriptome diversity is a metric that captures a systematic bias in RNA-seq and is the strongest known factor encoded in PEER covariates.
Visual temporal integration by multi-level regularities fosters the emergence of dynamic conscious experience
Authors: Hu Ruichen , Yuan Peijun , Wang Ying , Jiang Yi 
Published: April 2021

AbstractThe relationship between information integration and visual awareness is central to contemporary theories and research on human consciousness. While there is evidence that humans are adept at integrating spatially structured information to form a coherent conscious percept, to date, little is known about how we integrate visual information over time based on its temporal structure and whether such temporal integration process contributes to our awareness of the dynamic world. Using binocular rivalry, we demonstrated that a diverse set of structured visual streams, constituted either by idiom, shape, or motion stimuli, predominated over their non-structured but otherwise matched counterparts in the competition for conscious access. Despite the apparent resemblance, there was a substantial dissociation of these observed privileges between the semantic- and perceptual-level structures, specifically regarding their resistance to spatiotemporal perturbations and demands for conscious processing over the visual integration process. These findings corroborate the essential role of structure-guided information integration in the generation of conscious content and highlight temporal integration by multi-level regularities as a fundamental mechanism to foster the emergence of continuous conscious experience.
Floral scents of a deceptive plant are hyperdiverse and under population-specific phenotypic selection
Authors: Eva Gfrerer , Danae Laina , Marc Gibernau , Roman Fuchs , Martin Happ , Till Tolasch , Wolfgang Trutschnig , Hörger Anja C. , Peter Comes Hans , Stefan Dötterl 
Published: April 2021

ABSTRACTFloral scent is a key mediator in plant-pollinator interactions; however, little is known to what extent intraspecific scent variation is shaped by phenotypic selection, with no information yet in deceptive plants. We recorded 291 scent compounds in deceptive moth fly-pollinated Arum maculatumfrom various populations north vs. south of the Alps, the highest number so far reported in a single plant species. Scent and fruit set differed between regions, and some, but not all differences in scent could be explained by differential phenotypic selection in northern vs. southern populations. Our study is the first to provide evidence that phenotypic selection is involved in shaping geographic patterns of floral scent in deceptive plants. The hyperdiverse scent ofA. maculatummight result from the plant’s imitation of various brood substrates of its pollinators.
Towards comprehensive plasma proteomics by orthogonal protease digestion
Authors: Fossati Andrea , Richards Alicia L. , Chen Kuei-Ho , Jaganath Devan , Cattamanchi Adithya , Ernst Joel D. , Swaney Danielle L. 
Published: April 2021

AbstractRapid and consistent protein identification across large clinical cohorts is an important goal for clinical proteomics. With the development of data-independent technologies (DIA/SWATH-MS), it is now possible to analyze hundreds of samples with great reproducibility and quantitative accuracy. However, this technology benefits from empirically derived spectral libraries that define the detectable set of peptides and proteins. Here we apply a simple and accessible tip-based workflow for the generation of spectral libraries to provide a comprehensive overview on the plasma proteome in individuals with and without active tuberculosis (TB). To boost protein coverage, we utilized non-conventional proteases such as GluC and AspN together with the gold standard trypsin, identifying more than 30,000 peptides mapping to 3,309 proteins. Application of this library to quantify plasma proteome differences in TB infection recovered more than 400 proteins in 50 minutes of MS-acquisition, including diagnosticMycobacterium tuberculosis(Mtb) proteins that have previously been detectable primarily by antibody-based assays and intracellular proteins not previously described to be in plasma.
Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis inDrosophila melanogaster
Authors: Tarikere Shreeharsha , Ylla Guillem , Extavour Cassandra G. 
Published: April 2021

AbstractThe survival and evolution of a species is a function of the number of offspring it can produce. In insects the number of eggs that an ovary can produce is a major determinant of reproductive capacity. Insect ovaries are made up of tubular egg-producing subunits called ovarioles, whose number largely determines the number of eggs that can be potentially laid. Ovariole number is directly determined by the number of cellular structures called terminal filaments, which are stacks of cells that assemble in the larval ovary. Elucidating the developmental and regulatory mechanisms of terminal filament formation is thus key to understanding the regulation of insect reproduction through ovariole number regulation. We systematically measured mRNA expression of all cells in the larval ovary at the beginning, middle and end of terminal filament formation. We also separated somatic and germ line cells during these stages and assessed their tissue-specific gene expression during larval ovary development. We found that the number of differentially expressed somatic genes is highest during late stages of terminal filament formation and includes many signaling pathways that govern ovary development. We also show that germ line tissue, in contrast, shows greater differential expression during early stages of terminal filament formation, and highly expressed germ line genes at these stages largely control cell division and DNA repair. We provide a tissue-specific and temporal transcriptomic dataset of gene expression in the developing larval ovary as a resource to study insect reproduction.
OTX2 homeoprotein functions in adult choroid plexus
Authors: Planques Anabelle , Moreira Vanessa Oliveira , Benacom David , Bernard Clémence , Jourdren Laurent , Blugeon Corinne , Dingli Florent , Masson Vanessa , Loew Damarys , Prochiantz Alain , Di Nardo Ariel A. 
Published: April 2021

AbstractChoroid plexus secretes cerebrospinal fluid important for brain development and homeostasis. The OTX2 homeoprotein is critical for choroid plexus development and remains highly expressed in adult choroid plexus. Through RNA sequencing analyses of constitutive and conditional knockdown adult mouse models, we reveal putative roles for OTX2 in choroid plexus function, including cell signaling and adhesion, and show that it regulates the expression of factors secreted into cerebrospinal fluid, notably transthyretin. We show thatOtx2expression impacts choroid plexus immune and stress responses, and also affects splicing which leads to changes in mRNA isoforms of proteins implicated in oxidative stress response and DNA repair. Through mass spectrometry analysis of OTX2 protein partners in the choroid plexus, and in known non-cell autonomous target regions such as visual cortex and ventricular-subventricular zone, we identified putative targets involved in cell adhesion, chromatin structure and RNA processing. Thus, OTX2 retains important roles in choroid plexus function and brain homeostasis throughout life.