bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in Pediatric Palliative Care Allocation Among Critically Ill Children in the United States*
Authors: O’Keefe Siobhán , Maddux Aline B. , Bennett Kimberly S. , Youngwerth Jeanie , Czaja Angela S. 
Published: October 2020

OBJECTIVES:
The objectives are as follows: 1) estimate palliative care consult rates and trends among critically ill children and 2) characterize which children receive palliative care consults, including those meeting previously proposed ICU-specific palliative care screening criteria.

DESIGN:
Retrospective cohort.

SETTING:
Fifty-two United States children’s hospitals participating in the Pediatric Health Information Systems database.

PATIENTS:
Hospitalized children with nonneonatal ICU admissions from 2007 to 2018.

MEASUREMENTS AND MAIN RESULTS:
The primary outcome was palliative care consultation, as identified by the palliative care International Classification of Disease code. Patient characteristics and outcomes were compared between those with and without palliative care. We used a mixed-effects multivariable model to estimate the independent association between the palliative care and patient characteristics accounting for institution and subject clustering. Hospitalizations were categorized into three mutually exclusive groups for comparative analyses: 1) meeting ICU-specific palliative care criteria, 2) presence of a complex chronic condition not in ICU-specific palliative care criteria, or 3) not meeting ICU-specific palliative care or complex chronic condition criteria. Rates and trends of palliative care consultation were estimated including variation among institutions and variation among subcategories of ICU-specific palliative care criteria. The study cohort included 740,890 subjects with 1,024,666 hospitalizations. About 1.36% of hospitalizations had a palliative care consultation. Palliative care consult was independently associated with older age, female sex, government insurance, inhospital mortality, and ICU-specific palliative care or complex chronic condition criteria. Among the hospitalizations, 30% met ICU-specific palliative care criteria, 40% complex chronic condition criteria, and 30% neither. ICU-specific palliative care patients received more mechanical ventilation and cardiopulmonary resuscitation, had longer hospital and ICU lengths of stay, and had higher inhospital mortality (p < 0.001). Palliative care utilization increased over the study period with considerable variation between the institutions especially in the ICU-specific palliative care cohort and its subgroups.

CONCLUSIONS:
Palliative care consultation for critically ill children in the United States is low. Palliative care utilization is increasing but considerable variation exists across institutions, suggesting inequity in palliative care allocation among this vulnerable population. Future studies should evaluate factors influencing allocation of palliative care among critically ill children in the United States and the drivers of differences between the institutional practices.
Evaluation of a Modified Early Warning Score (MEWS) adjusted for COVID-19 patients (CEWS) to identify risk of ICU admission or death
Authors: Smid Linda , Osman Lano , Arend Sandra M. , de Groot Stefanie , de Boer Mark G.J. 
Published: October 2020

AbstractThe commonly used Modified Early Warning score (MEWS) may poorly predict deterioration in COVID-19 patients. Therefore, an adjusted MEWS for COVID-19 patients (CEWS) was constructed. CEWS exceeded MEWS at all time points and impending death or intensive care unit (ICU) admission was strongly correlated with a persistently high CEWS.
Life Expectancy and Voting Patterns in the 2020 U.S. Presidential Election
Authors: Curtis Lesley H. , Hoffman Molly N. , Califf Robert M. , Hammill Bradley G. 
Published: October 2020

AbstractIntroductionIn the 2016 U.S. Presidential election, voters in communities with recent stagnation or decline in life expectancy were more likely to vote for the Republican candidate than in prior Presidential elections. We aimed to assess the association between change in life expectancy and voting patterns in the 2020 Presidential election.MethodsWith data on county-level life expectancy from the Institute for Health Metrics and Evaluation and voting data from GitHub, we used weighted multivariable linear regression to estimate the association between the change in life expectancy from 1980 to 2014 and the proportion of votes for the Republican candidate in the 2020 Presidential election.ResultsAmong 3,110 U.S counties and Washington, D.C., change in life expectancy at the county level was negatively associated with Republican share of the vote in the 2020 Presidential election (parameter estimate −7.2, 95% confidence interval, −7.8 to −6.6). With the inclusion of state, sociodemographic, and economic variables in the model, the association was attenuated (parameter estimate −0.8; 95% CI, −1.5 to −0.2).ConclusionCounties with a less positive trajectory in life expectancy were more likely to vote for Republican candidates in the 2020 U.S. Presidential election, but the association was mediated by demographic, social and economic factors.
The energy balance theory: an unsatisfactory model of body composition fluctuations
Authors: Arencibia-Albite Francisco , Manninen Anssi H. 
Published: October 2020

AbstractDifferential weight and fat losses under isocaloric diets of distinct macronutrient composition are well-documented findings in obesity research.1-6 Such data are considered a result of inadequate methodology as it disagree with the energy balance theory.7 A recent mathematical analysis of this paradigm has found, however, serious analytical contradictions in its foundations.8 As an alternative, a mass balance model was proposed to explain the aforesaid body composition alterations. Here, we expand on this observation by contrasting both models. We show that mass balance explains a wide range of fending experiments including those concurring with the energy balance principle. The latter, however, is less flexible and results in poor forecasts in settings consistent with mass balance. The energy balance theory is thus an unsatisfactory model of body composition changes. Consequently, by shifting to a mass balance paradigm of obesity a much deeper understanding of this disease may follow in the near future.
Physical properties of the cytoplasm modulate the rates of microtubule polymerization and depolymerization
Authors: Molines Arthur T. , Lemière Joël , Gazzola Morgan , Steinmark Emilie I. , Edrington Claire H. , Hsu Chieh-Ting (Jimmy) , Suhling Klaus , Goshima Gohta , Holt Liam J. , Thery Manuel , Brouhard Gary. J. , Chang Fred 
Published: October 2020

AbstractThe cytoplasm is a crowded, visco-elastic environment whose physical properties change according to physiological or developmental states. How the physical properties of the cytoplasm impact cellular functionsin vivoremain poorly understood. Here, we probed the effects of cytoplasmic concentration on microtubules by applying osmotic shifts to fission yeast, moss, and mammalian cells. We show that both the rates of microtubule polymerization and depolymerization scale linearly and inversely with cytoplasmic concentration; an increase in cytoplasmic concentration decreases the rates of microtubule polymerization and depolymerization proportionally, while a decrease in cytoplasmic concentration leads to the opposite. Numerous lines of evidence indicate that these effects are due to changes in cytoplasmic viscosity rather than cellular stress responses or macromolecular crowdingper se. We reconstituted these effects on microtubulesin vitroby tuning viscosity. Our findings indicate that, even in normal conditions, the viscosity of cytoplasm modulates the reactions underlying microtubule dynamic behaviors.
Clonal propagation history shapes the intra-cultivar genetic diversity in ‘Malbec’ grapevines
Authors: Calderón Luciano , Mauri Nuria , Muñoz Claudio , Carbonell-Bejerano Pablo , Bree Laura , Sola Cristobal , Gomez-Talquenca Sebastian , Royo Carolina , Ibáñez Javier , Martinez-Zapater Jose Miguel , Lijavetzky Diego 
Published: October 2020

AbstractGrapevine (Vitis viniferaL.) cultivars are clonally propagated to preserve their varietal attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic diversity, we have focused on ‘Malbec’. This cultivar is appreciated for red wines elaboration, it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, we generated whole-genome resequencing data for four ‘Malbec’ clones with different historical backgrounds. A stringent variant calling procedure was established to identify reliable clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of validated SNVs, a genotyping experiment was custom-designed to survey ‘Malbec’ genetic diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long history of clonal propagation in Argentina, while Group-Fr was driven by clones that have longer remained in Europe. Findings show the ability of such approaches for clonal genotypes identification in grapevines. In particular, we provide evidence on how human actions may have shaped ‘Malbec’ extant genetic diversity pattern.
Availability of Medications Used for Puberty Induction and Maintenance in Adolescents with Hypogonadism in the Arab Region
Authors: Deeb Asma , AlSaffar Hussain , Hamza Rasha Tarif , Habeb Abdelhadi 
Published: October 2020

AbstractPurposeInducing puberty in hypogonadal patients enables achieving normal final adult height, healthy bone mass accrual and improves fertility potential. Reliable availability and access to medicines remain a challenge around the world, particularly in low income countries. We aim to study the availability/access to medications used for inducing and maintaining puberty in centers within the Arab region.Patients and MethodsA cross-sectional survey was conducted using a link to an online questionnaire which was emailed to paediatric endocrinologists in the Arab region. The questionnaire consisted of three questions related to availability of various forms of sex hormones.Results99 physicians from 16 countries participated in the study. The commonest available form of estrogen was conjugated estrogen (29% of centers) followed by ethinylestradiol in 26%. Depot estradiol was available in 11centers while topical estrogen preparations of gel and patches were available in 6 and 10 centers respectively. Medroxy progesterone was available in 26% of the centers followed by noresthisterone (24%). The combined forms of oral and transdermal patches of estrogen/progestorne were available in 35 and 9% of centers. Intramuscular testosterone (Sustanon) was the most commonly available preparation of testosterone followed by the depot injection (Nebido), oral testosterone and testosterone gel and cream.ConclusionsWe report the first availability data of medications used for puberty induction and maintenance in paediatric hypogonadism in the Arab region. Recommended preparations for this purpose are not widely available. Creating essential list of medications used in paediatric endocrinology disorders might improve availability, access and consequently practice.
Seed encrusting with salicylic acid: a novel approach to improve establishment of grass species in ecological restoration
Authors: Pedrini Simone , Stevens Jason C. , Cross Adam , Dixon Kingsley W. 
Published: October 2020

AbstractTo achieve global ambitions in large scale ecological restoration, there is a need for approaches that improve the efficiency of seed-based restoration, particularly in overcoming the bottleneck in the transition from germination to seedling establishment. In this study we tested a novel seed-based application of the plant stress modulator compound, salicylic acid, as a means to reduce seedling losses in seed-to-seedling phase. First-time seed coating technology (encrusting) was developed as a precursor for optimising field sowing for three grass species commonly used in restoration programs,Austrostipa scabra, Microlaena stipoides, andRytidosperma geniculata. Salicylic acid (SA, 0.1mM) was delivered to seeds via imbibition and seed encrusting with the effects tested on seed germination under controlled conditions (to test for resilience to drought), and in field conditions on seedling emergence, plant survival, and seedling growth. SA did not significantly impact germination under water stress in controlled laboratory condition and did not affect seedling emergence in the field. However, seedling survival and growth was improved in plants from SA treated seeds (imbibed and encrusted) under field conditions. When SA delivery mechanisms of imbibing and coating were compared, there was no significant difference in survival and growth, showing that seed coating has potential to deliver SA. Effect of intraspecific competition as a result of seedling density was also considered. Seedling survival over the dry summer season more than doubled when seed was sown at low density (40 plants/m2) compared to high density seeding (380 plants/m2). Overall, adjustment of seeding rate according to expected emergence combined with the use of salicylic acid is a cost-effective means for improving seed use efficiency in seed-based restoration.
Light intensity affects the coloration and structure of chimeric leaves ofAnanas comosus var. bracteatus
Authors: Yang Wei , Lin Yuke , Xue Yanbin , Mao Meiqin , Zhou Xuzixing , Hu Hao , Liu Jiawen , Feng Lijun , Zhang Huiling , Luo Jiaheng , Ma Jun 
Published: October 2020

AbstractAnanas comosus var. bracteatusis an important tropical ornamental plant because of its green/white chimeric leaves. The accumulation of anthocyanin makes the leaf red especially the white margin. However, the leaves lost red color in summer and winter. Light intensity is one of the most important factors affecting leaf color along the season. In order to understand the effects of light intensity on the growth and coloration of the chimeric leaves,Ananas comosus var. bracteatuswas grown under full sunlight, 50% shade and 75% shade for 75 days to evaluate the content of pigments, the color parameters (value L*, a*, b*) and structural histocytology characteristics of chimeric leaves. The results showed that high irradiance was beneficial to keep the chimeric leaves red. However, prolonged exposure to high irradiance caused light damage, some of the leaves wrinkled and even burned. Shading decreased the content of anthocyanin and increased the content of chlorophyll especially in the white margin of the leaves. Numerous chloroplasts were found in the mesophyll cells of the white margin part of chimeric leaves under shading for 75 days. The increase of chlorophyll content resulted in better growth of plants. In order to balance the growth and ornamental value of the leaves, approximately 50% shade is suggested to be the optimum light irradiance condition forAnanas comosus var. bracteatusin summer.
NETMAGE: a humaN-disEase phenoType MAp GEnerator for the Visualization of PheWAS
Authors: Sriram Vivek , Shivakumar Manu , Jung Sang-Hyuk , Bang Lisa , Verma Anurag , Lee Seunggeun , Choe Eun Kyung , Kim Dokyoon 
Published: October 2020

AbstractSummaryGiven genetic associations from a PheWAS, a disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes. To improve the accessibility of the visualization of shared genetic components across phenotypes, we developed the humaN-disEase phenoType MAp GEnerator (NETMAGE), a web-based tool that produces interactive phenotype network visualizations from summarized PheWAS results. Users can search the map by a variety of attributes, and they can select nodes to view information such as related phenotypes, associated SNPs, and other network statistics. As a test case, we constructed a network using UK BioBank PheWAS summary data. By examining the associations between phenotypes in our map, we can potentially identify novel instances of pleiotropy, where loci influence multiple phenotypic traits. Thus, our tool provides researchers with a means to identify prospective genetic targets for drug design, contributing to the exploration of personalized medicine.Availability and implementationOur service runs athttps://hdpm.biomedinfolab.com. Source code can be downloaded athttps://github.com/dokyoonkimlab/netmage.Contactdokyoon.kim@pennmedicine.upenn.eduSupplementary informationSupplementary data and user guide are available atBioinformaticsonline.
Retinoic Acid Inducible Gene-I like Receptors Activate Snail and Slug to Limit RNA Viral Infections
Authors: Vedagiri Dhiviya , Gupta Divya , Mishra Anurag , Krishna Gayathri , Bhaskar Meenakshi , Basu Anirban , Nayak Debasis , Kalia Manjula , Veettil Mohanan Valiya , Harshan Krishnan Harinivas 
Published: October 2020

ABSTRACTRLRs sense cytosolic non-self RNAs including viral RNAs before mounting a response leading to the activation of Type-I IFNs. Here, we identify a previously unknown regulation of Snail, a transcription regulator known in EMT, during RNA viral infections and describe its possible implication. RNA viral infections, poly (I:C) transfection and ectopic expression of RLR components activated Snail and Slug in epithelial cells. Detailed examination revealed that MAVS and phosphorylated IRF3 are essential in this regulation. We identified two ISREs inSNAI1promoter region and their alterations rendered the promoter non-responsive to phospho-IRF3 in luciferase assay. Ectopic expression of Snail and Slug activated RLR pathway and dramatically limited RNA viral infections in epithelial cells pointing to their antiviral functions. Thus, Snail and Slug are transcriptionally regulated by RLRs in a similar manner as IFN-β and they in turn promote RLR pathway possibly strengthening the antiviral state in the cell.
Shannon Entropy as a metric for conditional gene expression inNeurospora crassa
Authors: Ameri Abigail J. , Lewis Zachary A. 
Published: October 2020

AbstractNeurospora crassahas been an important model organism for molecular biology and genetics for over 60 years.N. crassahas a complex life cycle, with over 28 distinct cell types and is capable of transcriptional responses to many environmental conditions including nutrient availability, temperature, and light. To quantify variation inN. crassagene expression, we analyzed public expression data from 97 conditions and calculated the Shannon Entropy value forNeurospora’sapproximately 11,000 genes. Entropy values can be used to estimate the variability in expression for a single gene over a range of conditions and be used to classify individual genes as constitutive or condition-specific. Shannon entropy has previously been used measure the degree of tissue specificity of multicellular plant or animal genes. We use this metric here to measure variable gene expression in a microbe and provide this information as a resource for theN. crassaresearch community. Finally, we demonstrate the utility of this approach by using entropy values to identify genes with constitutive expression across a wide range of conditions and to identify genes that are activated exclusively during sexual development.
SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility
Authors: Zhou Bin , Thao Tran Thi Nhu , Hoffmann Donata , Taddeo Adriano , Ebert Nadine , Labroussaa Fabien , Pohlmann Anne , King Jacqueline , Portmann Jasmine , Halwe Nico Joel , Ulrich Lorenz , Trüeb Bettina Salome , Kelly Jenna N. , Fan Xiaoyu , Hoffmann Bernd , Steiner Silvio , Wang Li , Thomann Lisa , Lin Xudong , Stalder Hanspeter , Pozzi Berta , de Brot Simone , Jiang Nannan , Cui Dan , Hossain Jaber , Wilson Malania , Keller Matthew , Stark Thomas J. , Barnes John R. , Dijkman Ronald , Jores Joerg , Benarafa Charaf , Wentworth David E. , Thiel Volker , Beer Martin 
Published: October 2020

AbstractDuring the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic1. However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human ACE2, (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro, it provides a real competitive advantage in vivo, particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.
HiCRep.py: Fast comparison of Hi-C contact matrices in Python
Authors: Lin Dejun , Sanders Justin , Noble William Stafford 
Published: October 2020

AbstractHi-C is the most widely used assay for investigating genome-wide 3D organization of chromatin. When working with Hi-C data, it is often useful to calculate the similarity between contact matrices in order to asses experimental reproducibility or to quantify relationships among Hi-C data from related samples. The HiCRep algorithm has been widely adopted for this task, but the existing R implementation suffers from run time limitations on high resolution Hi-C data or on large single-cell Hi-C datasets. We introduce a Python implementation of HiCRep and demonstrate that it is much faster than the existing R implementation. Furthermore, we give examples of HiCRep’s ability to accurately distinguish replicates from non-replicates and to reveal cell type structure among collections of Hi-C data. HiCRep.py and its documentation are available with a GPL license athttps://github.com/Noble-Lab/hicrep. The software may be installed automatically using the pip package installer.