bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design- and Model-Based Approaches to Small-Area Estimation in a Low- and Middle-Income Country Context: Comparisons and Recommendations
Authors: Paige John , Fuglstad Geir-Arne , Riebler Andrea , Wakefield Jon 
Published: April 2020

Abstract
The need for rigorous and timely health and demographic summaries has provided the impetus for an explosion in geographic studies in low- and middle-income countries. Many of these studies present fine-scale pixel-level maps in an attempt to answer the needs of the current era of precision public health. However, even though household surveys with a two-stage cluster design stratified by region and urbanicity are a major source of data, cavalier approaches are taken to acknowledging the survey design. We investigate the extent to which accounting for the sample design affects the predictive performance at the aggregate level of interest for health policy decisions. We consider various commonly used models and introduce a new Bayesian cluster-level model with a discrete spatial smoothing prior. The investigation is performed through a simulation study in which realistic sampling frames are created for Kenya, based on the population and demographic information, with a survey design that mimics a Demographic Health Survey (DHS). We find that including stratification and cluster-level random effects can improve predictive performance. Spatially smoothed direct (weighted) estimates and area-level models accounting for stratification were robust to the underlying population and survey design. Continuous spatial models showed some promise in the presence of fine-scale variation; however, these models require the most “hand holding.” Subsequently, we examine how the models perform on real data, estimating the prevalence of secondary education for women aged 20–29 and neonatal mortality rates, using data from the 2014 Kenya DHS.
Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans
Authors: Woodruff Gavin C , Teterina Anastasia A 
Published: April 2020

AbstractThe abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.
PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures
Authors: Drew Elliot D , Janes Robert W 
Published: April 2020

Abstract
PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user. Using MD enables exploration of systems that cannot be monitored by direct experimentation. Validation of MD-derived data from these types of trajectories can be difficult via conventional structure-determining techniques such as crystallography or nuclear magnetic resonance spectroscopy. CD is an experimental technique that can provide protein structure information from such conditions. The website utilizes a much faster (minimum ∼1000×) and more accurate approach for calculating CD spectra than its predecessor, PDB2CD (1). As well as improving on the speed and accuracy of current methods, new analysis tools are provided to cluster predictions or compare them against experimental CD spectra. By identifying a subset of the closest predicted CD spectra derived from PDBMD2CD to an experimental spectrum, the associated cluster of structures could be representative of those found under the conditions in which the MD studies were undertaken, thereby offering an analytical insight into the results. PDBMD2CD is freely available at: https://pdbmd2cd.cryst.bbk.ac.uk.
Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets
Authors: Erbe Rossin , Kessler Michael D , Favorov Alexander V , Easwaran Hariharan , Gaykalova Daria A , Fertig Elana J 
Published: April 2020

Abstract
While the methods available for single-cell ATAC-seq analysis are well optimized for clustering cell types, the question of how to integrate multiple scATAC-seq data sets and/or sequencing modalities is still open. We present an analysis framework that enables such integration across scATAC-seq data sets by applying the CoGAPS Matrix Factorization algorithm and the projectR transfer learning program to identify common regulatory patterns across scATAC-seq data sets. We additionally integrate our analysis with scRNA-seq data to identify orthogonal evidence for transcriptional regulators predicted by scATAC-seq analysis. Using publicly available scATAC-seq data, we find patterns that accurately characterize cell types both within and across data sets. Furthermore, we demonstrate that these patterns are both consistent with current biological understanding and reflective of novel regulatory biology.
Predictors of the Best Outcomes Following Minimally Invasive Surgery for Grade 1 Degenerative Lumbar Spondylolisthesis
Authors: Chan Andrew K , Bisson Erica F , Bydon Mohamad , Glassman Steven D , Foley Kevin T , Shaffrey Christopher I , Potts Eric A , Shaffrey Mark E , Coric Domagoj , Knightly John J , Park Paul , Wang Michael Y , Fu Kai-Ming , Slotkin Jonathan R , Asher Anthony L , Virk Michael S , Kerezoudis Panagiotis , Alvi Mohammed A , Guan Jian , Haid Regis W , Mummaneni Praveen V 
Published: April 2020

Abstract

BACKGROUND
The factors driving the best outcomes following minimally invasive surgery (MIS) for grade 1 degenerative lumbar spondylolisthesis are not clearly elucidated.

OBJECTIVE
To investigate the factors that drive the best 24-mo patient-reported outcomes (PRO) following MIS surgery for grade 1 degenerative lumbar spondylolisthesis.

METHODS
A total of 259 patients from the Quality Outcomes Database lumbar spondylolisthesis module underwent single-level surgery for degenerative grade 1 lumbar spondylolisthesis with MIS techniques (188 fusions, 72.6%). Twenty-four-month follow-up PROs were collected and included the Oswestry disability index (ODI) change (ie, 24-mo minus baseline value), numeric rating scale (NRS) back pain change, NRS leg pain change, EuroQoL-5D (EQ-5D) questionnaire change, and North American Spine Society (NASS) satisfaction questionnaire. Multivariable models were constructed to identify predictors of PRO change.

RESULTS
The mean age was 64.2 ± 11.5 yr and consisted of 148 (57.1%) women and 111 (42.9%) men. In multivariable analyses, employment was associated with superior postoperative ODI change (β-7.8; 95% CI [−12.9 to −2.6]; P = .003), NRS back pain change (β −1.2; 95% CI [−2.1 to −0.4]; P = .004), EQ-5D change (β 0.1; 95% CI [0.01-0.1]; P = .03), and NASS satisfaction (OR = 3.7; 95% CI [1.7-8.3]; P < .001). Increasing age was associated with superior NRS leg pain change (β −0.1; 95% CI [−0.1 to −0.01]; P = .03) and NASS satisfaction (OR = 1.05; 95% CI [1.01-1.09]; P = .02). Fusion surgeries were associated with superior ODI change (β −6.7; 95% CI [−12.7 to −0.7]; P = .03), NRS back pain change (β −1.1; 95% CI [−2.1 to −0.2]; P = .02), and NASS satisfaction (OR = 3.6; 95% CI [1.6-8.3]; P = .002).

CONCLUSION
Preoperative employment and surgeries, including a fusion, were predictors of superior outcomes across the domains of disease-specific disability, back pain, leg pain, quality of life, and patient satisfaction. Increasing age was predictive of superior outcomes for leg pain improvement and satisfaction.
Antidepressant drug use in glioblastoma patients: an epidemiological view
Authors: Gramatzki Dorothee , Rogers James Louis , Neidert Marian Christoph , Hertler Caroline , Le Rhun Emilie , Roth Patrick , Weller Michael 
Published: April 2020

Abstract

Background
Antidepressant drugs have shown antitumor activity in preclinical glioblastoma studies. Antidepressant drug use, as well as its association with survival, in glioblastoma patients has not been well characterized on a population level.

Methods
Patient characteristics, including the frequency of antidepressant drug use, were assessed in a glioblastoma cohort diagnosed in a 10-year time frame between 2005 and 2014 in the Canton of Zurich, Switzerland. Cox proportional hazards regression models were applied for multivariate analysis. Kaplan-Meier survival curves were used to estimate overall survival (OS) data and the log-rank test was performed for comparisons.

Results
A total of 404 patients with isocitrate dehydrogenase wild-type glioblastoma were included in this study. Sixty-five patients (16.1%) took antidepressant drugs at some point during the disease course. Patients were most commonly prescribed selective serotonin reuptake inhibitors at any time (N = 46, 70.8%). Nineteen patients (29.2%) were on antidepressant drugs at the time of their tumor diagnosis. No differences were observed in OS between those patients who had taken antidepressants at some point in their disease course and those who had not (P = .356). These data were confirmed in a multivariate analysis including age, Karnofsky Performance Scale (KPS), sex, extent of resection, O6-methylguanine DNA methyltransferase (MGMT) promoter methylation status, and first-line treatment as cofounders (P = .315). Also, there was no association of use of drugs modulating voltage-dependent potassium channels (citalopram; escitalopram) with survival (P = .639).

Conclusions
This signal-seeking study does not support the hypothesis that antidepressants have antitumor efficacy in glioblastoma on a population level.
Plasma metabolomic and lipidomic alterations associated with COVID-19
Authors: Wu Di , Shu Ting , Yang Xiaobo , Song Jian-Xin , Zhang Mingliang , Yao Chengye , Liu Wen , Huang Muhan , Yu Yuan , Yang Qingyu , Zhu Tingju , Xu Jiqian , Mu Jingfang , Wang Yaxin , Wang Hong , Tang Tang , Ren Yujie , Wu Yongran , Lin Shu-Hai , Qiu Yang , Zhang Ding-Yu , Shang You , Zhou Xi 
Published: April 2020

Abstract
The pandemic of the coronavirus disease 2019 (COVID-19) has become a global public health crisis. The symptoms of COVID-19 range from mild to severe, but the physiological changes associated with COVID-19 are barely understood. In this study, we performed targeted metabolomic and lipidomic analyses of plasma from a cohort of patients with COVID-19 who had experienced different symptoms. We found that metabolite and lipid alterations exhibit apparent correlation with the course of disease in these patients, indicating that the development of COVID-19 affected their whole-body metabolism. In particular, malic acid of the TCA cycle and carbamoyl phosphate of the urea cycle result in altered energy metabolism and hepatic dysfunction, respectively. It should be noted that carbamoyl phosphate is profoundly down-regulated in patients who died compared with patients with mild symptoms. And, more importantly, guanosine monophosphate (GMP), which is mediated not only by GMP synthase but also by CD39 and CD73, is significantly changed between healthy subjects and patients with COVID-19, as well as between the mild and fatal cases. In addition, dyslipidemia was observed in patients with COVID-19. Overall, the disturbed metabolic patterns have been found to align with the progress and severity of COVID-19. This work provides valuable knowledge about plasma biomarkers associated with COVID-19 and potential therapeutic targets, as well as an important resource for further studies of the pathogenesis of COVID-19.
Candida Infective Endocarditis During the Infectious Diseases and Substance Use Disorder Syndemic: A Six-Year Case Series
Authors: Sankar N P , Thakarar K , Rokas Kristina E 
Published: April 2020

Abstract
Treatment for Candida infective endocarditis (IE) has not been extensively studied in the setting of rising injection drug use. There were 12 cases of Candida IE at the Maine Medical Center between 2013 and 2018. The patient characteristics, treatment regimens, and outcomes were retrospectively analyzed.
Medical Cannabis for the Management of Pain and Quality of Life in Chronic Pain Patients: A Prospective Observational Study
Authors: Safakish Ramin , Ko Gordon , Salimpour Vahid , Hendin Bryan , Sohanpal Imrat , Loheswaran Gena , Yoon Sun Young Rosalia 
Published: April 2020

AbstractObjectiveTo evaluate the short-term and long-term effects of plant-based medical cannabis in a chronic pain population over the course of one year.DesignA longitudinal, prospective, 12-month observational study.SettingPatients were recruited and treated at a clinic specializing in medical cannabis care from October 2015 to March 2019.SubjectsA total of 751 chronic pain patients initiating medical cannabis treatment.MethodsStudy participants completed the Brief Pain Inventory and the 12-item Short Form Survey (SF-12), as well as surveys on opioid medication use and adverse events, at baseline and once a month for 12 months.ResultsMedical cannabis treatment was associated with improvements in pain severity and interference (P &lt; 0.001) observed at one month and maintained over the 12-month observation period. Significant improvements were also observed in the SF-12 physical and mental health domains (P &lt; 0.002) starting at three months. Significant decreases in headaches, fatigue, anxiety, and nausea were observed after initiation of treatment (P ≤ 0.002). In patients who reported opioid medication use at baseline, there were significant reductions in oral morphine equivalent doses (P &lt; 0.0001), while correlates of pain were significantly improved by the end of the study observation period.ConclusionsTaken together, the findings of this study add to the cumulative evidence in support of plant-based medical cannabis as a safe and effective treatment option and potential opioid medication substitute or augmentation therapy for the management of symptoms and quality of life in chronic pain patients.
High-Intensity Exercise Improves Fatigue, Sleep, and Mood in Patients With Axial Spondyloarthritis: Secondary Analysis of a Randomized Controlled Trial
Authors: Sveaas Silje Halvorsen , Dagfinrud Hanne , Berg Inger Jorid , Provan Sella Arrestad , Johansen Melissa Woll , Pedersen Elisabeth , Bilberg Annelie 
Published: April 2020

Abstract

Objective
Although exercise is recommended in the treatment of axial spondyloarthritis (axSpa), the focus has been on flexibility, and the effect of high-intensity exercises is unknown. The purpose of this study was to investigate the effect of high-intensity exercises on fatigue, sleep, and mood in patients with axSpA.

Methods
In this secondary analysis of a randomized controlled trial, participants were recruited from outpatient clinics at 4 hospitals in Scandinavia. A total of 100 patients with axSpA were randomized to either an exercise group (n = 50) or a control group (n = 50). High-intensity exercise was provided 3 times per week for 3 months and supervised by a physical therapist. The controls received no intervention. Measurements were self-reported at baseline, 3 months, and 12 months: fatigue, using the Fatigue Severity Scale (range = 0–7, 7 = worst, ≥5 = severe); vitality, using the RAND 36-item short-form health survey (SF-36, range = 0–100, 100 = best); sleep, using the Pittsburgh Sleep Quality Index (range = 0–21, 21 = worst, &gt;5 = poor quality); mood, using the General Health Questionnaire 12 (range = 0–36, 36 = worst); and general health, using the EUROQoL (range = 0–100, 100 = best).

Results
A total of 38 participants (76%) in the exercise group followed ≥80% of the exercise protocol. At 3 months, there was a significant beneficial effect on fatigue (mean group differences = −0.4, 95% CI = −0.7 to −0.1), vitality (5.0, 95% CI = 1.1 to 10.5), mood (−2, 95% CI = −3.7 to −0.04), and general health (9.0, 95% CI = 3.3 to 14.7) but no effect on sleep (−1.1, 95% CI = −2.1 to 0.2). Compared with the control group, the exercise group had a reduced rate of severe fatigue and poor sleep. No differences were seen between the groups at 12 months.

Conclusions
A 3-month exercise program had a beneficial effect on fatigue, sleep, mood, and general health in patients with axSpA at the end of the intervention; however, no long-term effects were seen.

Impact
High-intensity cardiorespiratory and strength exercises should be considered as important in exercise programs for patients with axSpA.
Cell-derived extracellular matrix-coated silk fibroin scaffold for cardiogenesis of brown adipose stem cells through modulation of TGF-β pathway
Authors: Liu Wei , Sun Yanfeng , Dong Xiaohui , Yin Qi , Zhu Huimin , Li Siwei , Zhou Jin , Wang Changyong 
Published: April 2020

AbstractThe cell-derived extracellular matrix (ECM)-modified scaffolds have advantages of mimic tissue specificity and been thought to better mimic the native cellular microenvironment in vitro. ECM derived from cardiac fibroblasts (CFs) are considered as key elements that provide a natural cell growth microenvironment and change the fate of cardiomyocytes (CMs). Here, a new hybrid scaffold is designed based on silk fibroin (SF) scaffold and CFs-derived ECM. CFs were seeded on the SF scaffold for 10 days culturing and decellularized to produce CFs-derived ECM-coated SF scaffold. The results showed that the cell-derived ECM-modified silk fibroin scaffold material contained collagen, laminin, fibronectin and other ECM components with myocardial-like properties. Further to explore its effects on brown adipose stem cells (BASCs) differentiation into CMs. We found that the CF-derived ECM-coated scaffold also increased the expression of CM-specific proteins (e.g. cardiac troponin T and α-actinin) of BASCs. Notably, the β1-integrin-dependent transforming growth factor-β1 signaling pathway was also involved in the regulation of CF-derived ECM by promoting the differentiation of BASCs into CMs. Overall, these findings provide insights into the bionic manufacturing of engineered cardiac tissues (ECTs) and establish a theoretical basis for the construction of ECTs.
Weak Governance by Informed Active Shareholders
Authors: Goldman Eitan , Wang Wenyu 
Published: April 2020

Abstract
Do informed shareholders who can influence corporate decisions improve governance? We demonstrate this may not be generally true in a model of takeovers. The model suggests that a shareholder’s ability to collect information and trade ex post may cause him, ex ante, to support pursuing value-destroying takeovers or oppose value-enhancing takeovers. Surprisingly, we find conditions under which giving the active shareholder greater influence weakens governance and reduces firm value, even if such influence power can be used to reject bad takeovers ex post. Our model sheds light on the limitations of relying on informed, active shareholders to improve governance.
Sleep inconsistency between weekends and weekdays is associated with changes in brain function during task and rest
Authors: Zhang Rui , Tomasi Dardo , Shokri-Kojori Ehsan , Wiers Corinde E , Wang Gene-Jack , Volkow Nora D 
Published: April 2020

AbstractStudy ObjectivesSleep deprivation and circadian disruptions impair brain function and cognitive performance, but few studies have examined the effect of sleep inconsistency. Here, we investigated how inconsistent sleep duration and sleep timing between weekends (WE) and weekdays (WD) correlated with changes in behavior and brain function during task and at rest in 56 (30 female) healthy human participants.MethodsWE–WD differences in sleep duration and sleep midpoint were calculated using 1-week actigraphy data. All participants underwent 3 Tesla blood-oxygen-level-dependent functional Magnetic Resonance Imaging (fMRI) to measure brain activity during a visual attention task (VAT) and in resting-state condition.ResultsWe found that WE–WD inconsistency of sleep duration and sleep midpoint were uncorrelated with each other (r = .08, p = .58) and influenced behavior and brain function differently. Our healthy participants showed relatively small WE–WD differences (WE–WD: 0.59 hours). Longer WE sleep duration (relative to WD sleep duration) was associated with better attentional performance (3-ball: β = .30, t = 2.35, p = .023; 4-ball: β = .30, t = 2.21, p = .032) and greater deactivation of the default mode network (DMN) during VAT (p &lt; .05, cluster-corrected) and greater resting-state functional connectivity (RSFC) between anterior DMN and occipital cortex (p &lt; .01, cluster-corrected). In contrast, later WE sleep timing (relative to WD sleep timing) (WE–WD: 1.11 hours) was associated with worse performance (4-ball: β = −.33, t = −2.42, p = .020) and with lower occipital activation during VAT and with lower RSFC within the DMN.ConclusionsOur results document the importance of consistent sleep timing for brain function in particular of the DMN and provide evidence of the benefits of WE catch-up sleep in healthy adults.