bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop
Authors: Stahlke Amanda , Bell Donavan , Dhendup Tashi , Kern Brooke , Pannoni Samuel , Robinson Zachary , Strait Jeffrey , Smith Seth , Hand Brian K , Hohenlohe Paul A , Luikart Gordon 
Published: January 2020

AbstractThe increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists.
Solar cycle variation of νmax in helioseismic data and its implications for asteroseismology
Authors: Howe Rachel , Chaplin William J , Basu Sarbani , Ball Warrick H , Davies Guy R , Elsworth Yvonne , Hale Steven J , Miglio Andrea , Nielsen Martin Bo , Viani Lucas S 
Published: January 2020

ABSTRACT
The frequency, νmax, at which the envelope of pulsation power peaks for solar-like oscillators is an important quantity in asteroseismology. We measure νmax for the Sun using 25 yr of Sun-as-a-star Doppler velocity observations with the Birmingham Solar-Oscillations Network (BiSON), by fitting a simple model to binned power spectra of the data. We also apply the fit to Sun-as-a-star Doppler velocity data from Global Oscillation Network Group and Global Oscillations at Low Frequency, and photometry data from VIRGO/SPM on the ESA/NASA SOHO spacecraft. We discover a weak but nevertheless significant positive correlation of the solar νmax with solar activity. The uncovered shift between low and high activity, of $\simeq 25\, \rm \mu Hz$, translates to an uncertainty of 0.8 per cent in radius and 2.4 per cent in mass, based on direct use of asteroseismic scaling relations calibrated to the Sun. The mean νmax in the different data sets is also clearly offset in frequency. Our results flag the need for caution when using νmax in asteroseismology.
Uncovering tissue-specific binding features from differential deep learning
Authors: Phuycharoen Mike , Zarrineh Peyman , Bridoux Laure , Amin Shilu , Losa Marta , Chen Ke , Bobola Nicoletta , Rattray Magnus 
Published: January 2020

Abstract
Transcription factors (TFs) can bind DNA in a cooperative manner, enabling a mutual increase in occupancy. Through this type of interaction, alternative binding sites can be preferentially bound in different tissues to regulate tissue-specific expression programmes. Recently, deep learning models have become state-of-the-art in various pattern analysis tasks, including applications in the field of genomics. We therefore investigate the application of convolutional neural network (CNN) models to the discovery of sequence features determining cooperative and differential TF binding across tissues. We analyse ChIP-seq data from MEIS, TFs which are broadly expressed across mouse branchial arches, and HOXA2, which is expressed in the second and more posterior branchial arches. By developing models predictive of MEIS differential binding in all three tissues, we are able to accurately predict HOXA2 co-binding sites. We evaluate transfer-like and multitask approaches to regularizing the high-dimensional classification task with a larger regression dataset, allowing for the creation of deeper and more accurate models. We test the performance of perturbation and gradient-based attribution methods in identifying the HOXA2 sites from differential MEIS data. Our results show that deep regularized models significantly outperform shallow CNNs as well as k-mer methods in the discovery of tissue-specific sites bound in vivo.
Presumed Nonalcoholic Fatty Liver Disease Among Medicare Beneficiaries With HIV, 2006–2016
Authors: Paik James M , Henry Linda , Golabi Pegah , Alqahtani Saleh A , Trimble Gregory , Younossi Zobair M 
Published: January 2020

AbstractBackgroundNewer treatments for HIV and hepatitis C virus (HCV) have decreased mortality in HIV/HCV patients. Nonalcoholic fatty liver disease (NAFLD) has increased globally; therefore, the prevalence and mortality of NAFLD among HIV (+) patients was assessed.MethodsUsing Medicare denominator, inpatient, and outpatient files (random 5% sample per year), serial cross-sectional analysis (2006 to 2016) was performed. Joinpoint trend analysis evaluated prevalence and mortality with average annual percent change (AAPC). HIV (+) patients and liver diseases (LDs) were identified using International Classification of Diseases 9/10 codes. NAFLD was presumed using diagnosis codes or codes for metabolic dysfunction and obesity in absence of other LDs. Liver-related HIV (+) indicated HIV (+) patients with LDs.ResultsAmong 28 675 887 Medicare beneficiaries, 47 062 were HIV (+) (mean [SD] age, 51.4 [11.3] years); 11 920 had liver diseases (6923 HCV, 2019 hepatitis B virus [HBV], 2472 presumed NAFLD, 278 alcoholic liver disease [ALD], and 1653 other LDs); 2882 HIV (+) patients died; 1260 had LDs. The prevalence and mortality for non-liver-related HIV (+) decreased (AAPC, –1.1% and –9.1%). Liver-related HIV (+) increased (AAPC, 1.7%; P = .007); mortality leveled off. Prevalence and mortality worsened for presumed NAFLD (AAPC, 9.7% and 10.0%) and improved for HBV and HCV (HBV: AAPC, –3.5% and –8.8%; HCV: AAPC, –0.7% and –4.9%). After adjustments, HCV (odds ratio [OR], 2.00; 95% confidence interval [CI], 1.24–172), HBV (OR, 2.40; 95% CI, 2.09–2.77), ALD (OR, 5.70; 95% CI, 4.34–7.48), and presumed NAFLD (OR, 1.46; 95% CI, 1.24–1.72) increased 1-year mortality.ConclusionsAmong HIV (+) subjects, viral hepatitis remains the leading LD for increased 1-year mortality, but the prevalence and mortality with presumed NAFLD are increasing.
‘Everybody in Nigeria is a doctor…’: a qualitative study of stakeholder perspectives on lay diagnosis of malaria and pneumonia in Nigeria
Authors: Elimian Kelly O , Myles Puja R , Phalkey Revati , Sadoh Ayebo , Pritchard Catherine 
Published: January 2020

AbstractBackgroundLay diagnosis is a widely used diagnostic approach for home management of common illnesses in Nigeria. This study aimed to explore the perspectives of caregivers and healthcare professionals on lay diagnosis of childhood malaria and pneumonia. Aligned to this, the study sought to explore the feasibility of training caregivers in the Integrated Management of Childhood Illness (IMCI) guidelines for improved recognition and treatment of these diseases.MethodsA qualitative study using individual face-to-face semi-structured interviews was conducted in Benin City, Nigeria. Participants included 13 caregivers with children under 5 years and 17 healthcare professionals (HPs). An inductive approach to thematic analysis was used to generate themes and analyses.ResultsCaregivers relied on lay diagnosis but recognised its limitations. The perceived severity of malaria and pneumonia significantly influenced caregivers’ preference for reliance on lay diagnosis practices, health-seeking behaviour and willingness to undertake training in IMCI guidelines for home management of diseases. Safety and potential unintended misuse of medications were recognised by caregivers and HPs as the main challenges.ConclusionsThe high level of acceptance among caregivers to receive IMCI training could help improve effective management of childhood malaria and pneumonia at the community level through early recognition and prompt treatment.
Engaging Religion in a Contested Age: Contestations, Postmodernity, and Social Change
Authors: Nesbitt Paula D 
Published: January 2020

AbstractBoth secular and religious contestations have threatened the character of contemporary civic discourse, signifying underlying issues needing to be addressed. Postmodern and globalization influences have contributed to their scope and intensity, adding underlying complexities to the presenting issues. Drawing upon case examples of a secular plant closure in a racially and ethnically diverse company town and strife threatening organizational viability in the cross-cultural Anglican Communion, I argue first that religion either directly influences or indirectly serves as a latent resource within secularized morality, and second that cross-cultural contestations involving religion typically contain underlying societal concerns; both need to be addressed in analyzing meaning and hope for change. Sociologists of religion have opportunity to explore how religion is deployed as a moral basis of contestation, and how it might interact with postcolonial and other cultural dynamics, with implications for solutions in building social cohesion across worldviews and cultures.
Beta-Blocker Dose Stratifies Mortality Risk in a Racially Diverse Heart Failure Population
Authors: Lteif Christelle , Arwood Meghan J. , Kansal Mayank , Cavallari Larisa H. , Desai Ankit A. , Duarte Julio D. 
Published: January 2020

Abstract:
Heart failure (HF) is highly prevalent and a major cause of death in the United States. The effect of HF medications on survival has been predicted by validated models studied in populations predominantly of European descent. This study aimed to identify medications associated with survival in a racially diverse HF population. Patients with HF were recruited and followed from 2001 to 2015. Data were collected from electronic health records and the Social Security Death Index. The primary analysis tested the association between medication dose and all-cause mortality, with a secondary analysis assessing the composite outcome of death or cardiac-related hospitalization. Circulating concentration of the fibrotic marker procollagen type III N-terminal peptide (PIIINP) was also compared with medication doses in patients with concentrations available. The study population consisted of 337 patients, of which 25.2% died and 46% were hospitalized. Increased beta-blocker (BB) dose was significantly associated with survival in the base model [hazard ratio (HR) = 0.71, P = 0.017] and marginally associated in the comprehensive model (HR = 0.75, P = 0.068). BB dose was also associated with decreased risk of the composite end point in the base model (HR = 0.80, P = 0.029) and to a lesser extent in the comprehensive model (HR = 0.83, P = 0.085). Furthermore, increased BB dose was inversely associated with circulating PIIINP concentration (P = 0.041). In conclusion, our study highlights the importance of BB dose escalation for survival and decreased hospitalization in patients with HF, regardless of race or HF type. It also suggests that benefits observed with high-dose BBs could be mediated, at least in part, by decreased cardiac fibrosis.
A Report of Intracranial Meningioma Recurring as Ectopic Orbital Meningioma Associated With Basal Encephalocele
Authors: Satija Celine E. , Mehta Viraj J. , Maltry Amanda C. , Nussbaum Eric , Nussbaum Leslie , Harrison Andrew R. 
Published: January 2020

The authors describe a rare case of recurrent ectopic meningioma associated with sphenoid encephalocele in the medial anterior orbit of a 52-year-old man with a history of a resected intracranial meningioma. Typical features of ectopic meningioma are reviewed as well as potential etiologies of this very rare recurrence of intracranial meningioma in the orbit. Treatment is typically surgical excision.
The authors report a rare case of recurrent orbital ectopic meningioma in the right medial canthus of a 52-year-old man.
The serum interleukin-26 level is a potential biomarker for chronical hepatitis B
Authors: Luo Liwen , Jiang Li , Tian Zhiqiang , Zhang Xinqi 
Published: January 2020

Abstract
Proinflammatory interleukin-26 (IL-26) is involved in chronic inflammation; however, the role of IL-26 in chronic hepatitis B (CHB) remains unknown.
In this study, serum IL-26 was quantified in a cohort of CHB patients at baseline and during telbivudine (LdT) treatment.
Our results showed that the serum IL-26 level was significantly elevated in CHB patients compared with that in healthy controls and was time-dependently decreased during LdT treatment, accompanying hepatitis B e antigen (HBeAg) seroconversion and reduced serum levels of hepatitis B virus (HBV) DNA, aspartate transaminase, and alanine transaminase across baseline and treatment. In addition, the serum level of IL-26 exhibited a similar declining trend to that of T helper 17 (Th17) cell-secreted IL-17 during LdT treatment in CHB patients. The percentage of IL-26-expressing CD4+ cells was significantly higher than that of IL-26-expressing CD4- cells isolated from the peripheral blood mononuclear cells of CHB patients, suggesting that serum IL-26 might be mainly released from CD4+ T cells. Furthermore, the baseline mRNA levels of IL-26 and orphan nuclear receptor RORγt—an important transcription factor expressed by Th17 cells—were positively correlated and displayed the same declining trend across the baseline and LdT treatment in CHB patients, suggesting that Th17 cells could be a possible cellular source of the increased serum IL-26 in CHB patients.
Taken together, our results suggest that serum IL-26, possibly produced by Th17 CD4+ cells, is a novel and potential biomarker for CHB prognosis and treatment.
Clinical nutrition for the gastroenterologist: bedside strategies for feeding the hospitalized patient
Authors: McClave Stephen A. , Omer Endashaw 
Published: January 2020

Purpose of reviewThe timing, advancement, and use of appropriate monitors determine whether the hospitalized patient experiences the full benefit of nutritional therapy. This article reviews management strategies in delivering the optimal nutrition regimen capable of improving outcomes in the hospitalized patient.Recent findingsEnteral nutrition should be initiated in the first 24–36 h after admission. Determination of nutritional risk helps guide the urgency with which nutritional therapy is provided and predicts the likelihood for difficulties in delivering the prescribed regimen. Feeds should be advanced slowly over 3–4 days to meet 70–80% of goal for calories (20 kcal/kg/day) and 100% for protein (2.0 gm/kg/day). Reaching protein goals early on may be more important than achieving energy goals. Patients should be monitored for hemodynamic stability, evidence of refeeding syndrome, and tolerance in the setting of gastrointestinal dysfunction. Parenteral nutrition should be utilized in select high-risk patients where the feasibility of full enteral nutrition is questioned.SummaryTiming with early initiation of enteral nutrition, avoidance of overfeeding, and step-wise advancement of feeds are required to safely realize the benefits of such therapy.
Mini Osteoplastic Flap Through Supra-Eyebrow Incision for Primary Frontal Sinus Squamous Cell Carcinoma
Authors: Lee Yu-Mi , Park Hye-Jin , Kim Sung-Dong , Cho Kyu-Sup 
Published: January 2020

Abstract
Primary carcinoma of the frontal sinus is very rare, with an incidence of 0.3% to 1.0% of all paranasal sinus carcinomas. Although complete resection with a clear margin is definitely essential to achieve tumor control, radical surgery with osteoplastic flap using bicoronal incision has significant postoperative morbidities including scalp numbness, hair loss, and frontalis palsy. This article reports a rare case of primary frontal sinus squamous cell carcinoma extending to the orbit, which was treated successfully by mini osteoplastic flap through supra-eyebrow incision combined transnasal endoscopic approach.
Interactive web application for plotting personalized prognosis prediction curves in allogeneic hematopoietic cell transplantation using machine learning
Authors: Okamura Hiroshi , Nakamae Mika , Koh Shiro , Nanno Satoru , Nakashima Yasuhiro , Koh Hideo , Nakane Takahiko , Hirose Asao , Hino Masayuki , Nakamae Hirohisa 
Published: January 2020

ABSTRACTBackgroundAllogeneic hematopoietic cell transplantation (allo-HCT) is a curative treatment option for malignant hematological disorders. Transplant clinicians estimate patient-specific prognosis empirically in clinical practice based on previous studies on similar patients. However, this approach does not provide objective data. The present study primarily aimed to develop a tool capable of providing accurate personalized prognosis prediction after allo-HCT in an objective manner.MethodsWe developed an interactive web application tool with a graphical user interface capable of plotting the personalized survival and cumulative incidence prediction curves after allo-HCT adjusted by eight patient-specific factors, which are known as prognostic predictors, and assessed their predictive performances. A random survival forest model using the data of patients who underwent allo-HCT at our institution was applied to develop this application.ResultsWe succeeded in showing the personalized prognosis prediction curves of 1-year overall survival (OS), progression-free survival (PFS), relapse/progression, and non-relapse mortality (NRM) interactively using our web application (https://predicted-os-after-transplantation.shinyapps.io/RSF_model/). To assess its predictive performance, the entire cohort (363 cases) was split into a training cohort (70%) to develop the predictive model and test cohort (30%) to confirm its performance time-sequentially. The areas under the receiver-operating characteristic curves for 1-year OS, PFS, relapse/progression, and NRM in test cohort were 0.70, 0.72, 0.73, and 0.77, respectively.ConclusionsThe new web application could allow transplant clinicians to inform a new allo-HCT candidate of the objective personalized prognosis prediction and facilitate decision-making.
Glacier ice archives fifteen-thousand-year-old viruses
Authors: Zhong Zhi-Ping , Solonenko Natalie E. , Li Yueh-Fen , Gazitúa Maria C. , Roux Simon , Davis Mary E. , Van Etten James L. , Mosley-Thompson Ellen , Rich Virginia I. , Sullivan Matthew B. , Thompson Lonnie G. 
Published: January 2020

AbstractWhile glacier ice cores provide climate information over tens to hundreds of thousands of years, study of microbes is challenged by ultra-low-biomass conditions, and virtually nothing is known about co-occurring viruses. Here we establish ultra-clean microbial and viral sampling procedures and apply them to two ice cores from the Guliya ice cap (northwestern Tibetan Plateau, China) to study these archived communities. This method reduced intentionally contaminating bacterial, viral, and free DNA to background levels in artificial-ice-core control experiments, and was then applied to two authentic ice cores to profile their microbes and viruses. The microbes differed significantly across the two ice cores, presumably representing the very different climate conditions at the time of deposition that is similar to findings in other cores. Separately, viral particle enrichment and ultra-low-input quantitative viral metagenomic sequencing from ∼520 and ∼15,000 years old ice revealed 33 viral populations (i.e., species-level designations) that represented four known genera and likely 28 novel viral genera (assessed by gene-sharing networks).In silicohost predictions linked 18 of the 33 viral populations to co-occurring abundant bacteria, includingMethylobacterium,Sphingomonas, andJanthinobacterium, indicating that viruses infected several abundant microbial groups. Depth-specific viral communities were observed, presumably reflecting differences in the environmental conditions among the ice samples at the time of deposition. Together, these experiments establish a clean procedure for studying microbial and viral communities in low-biomass glacier ice and provide baseline information for glacier viruses, some of which appear to be associated with the dominant microbes in these ecosystems.ImportanceThis study establishes ultra-clean microbial and viral sampling procedures for glacier ice, which complements priorin silicodecontamination methods and expands, for the first time, the clean procedures to viruses. Application of these methods to glacier ice confirmed prior common microbiological findings for a new ice core climate record, and provides a first window into viral genomes and their ecology from glacier ice across two time horizons, and emphasizes their likely impact on abundant microbial groups. Together these efforts provide clean sampling approaches and foundational datasets that should enable simultaneous access to an archived virosphere in glacier ice.
Mapping Trends in Insecticide Resistance Phenotypes in African Malaria Vectors
Authors: Hancock PA , Hendriks CJM , Tangena J-A , Gibson H , Hemingway J , Coleman M , Gething PW , Cameron E , Bhatt S , Moyes CL 
Published: January 2020

ABSTRACTMitigating the threat of insecticide resistance in African malaria vector populations requires comprehensive information about where resistance occurs, to what degree, and how this has changed over time. Estimating these trends is complicated by the sparse, heterogeneous distribution of observations of resistance phenotypes in field populations. We use 6423 observations of the prevalence of resistance to the most important vector control insecticides to inform a Bayesian geostatistical ensemble modelling approach, generating fine-scale predictive maps of resistance phenotypes in mosquitoes from theAnopheles gambiaecomplex across Africa. Our models are informed by a suite of 111 predictor variables describing potential drivers of selection for resistance. Our maps show alarming increases in the prevalence of resistance to pyrethroids and DDT across Sub-Saharan Africa from 2005-2017 as well as substantial spatial variation in resistance trends.