bluuebunny/crossref_metadata_2025_split huggingface dataset:
Terminal Ileum Thickness During Maintenance Therapy Is a Predictive Marker of the Outcome of Infliximab Therapy in Crohn Disease
Authors: Albshesh Ahmad , Ungar Bella , Ben-Horin Shomron , Eliakim Rami , Kopylov Uri , Carter Dan 
Published: August 2020

Abstract

Background
Mucosal healing has been associated with long-term response to therapy for Crohn disease (CD). However, little is known about the significance of terminal ileum (TI) transmural thickness in predicting clinical outcomes.

Methods
In this retrospective observational cohort study, we examined the association of an index ultrasonographic assessment of TI thickness during the maintenance phase and the subsequent clinical outcome of CD in a cohort of patients treated with infliximab (IFX). Treatment failure was defined as treatment discontinuation because of lack of efficacy, a need for dose escalation, or surgery. Clinical response was defined as treatment continuation in the absence of any of the aforementioned failure criteria.

Results
Sixty patients with CD receiving IFX therapy were included in the study. The patients were followed for a median of 16 months (5-24 months) after an index intestinal ultrasound. Thirty-eight patients (63.3%) maintained response to the therapy and 22 patients (36.6%) failed the treatment, with a mean follow up of 10.5 months (6.5-17 months) vs 9.25 months (1-10.25 months), respectively. On univariate analysis, the only variables differing between treatment response and failure were a TI thickness of 2.8 vs 5 mm (P &lt; 0.0001) and an IFX trough level of 6.6 vs 3.9 µg/mL (P = 0.008).
On multivariable analysis, only a small bowel thickness of ≥4 mm was associated with the risk of treatment failure (odds ratio, 2.9; 95% CI, 1.49-5.55; P = 0.002).

Conclusions
Our findings suggest that transmural thickness of ≥4 mm can predict subsequent treatment failure in patients with CD treated using IFX, indicating transmural thickness &lt;4 mm as a potential novel valuable therapeutic target.
Clinical Variables Associated With Statural Growth in Pediatric Crohn’s Disease Differ by Sex (The Growth Study)
Authors: Gupta Neera , Lustig Robert H , Andrews Howard , Gokhale Ranjana , Goyal Alka , Patel Ashish S , Guthery Stephen , Sylvester Francisco , Siebold Leah , Leu Cheng-Shiun 
Published: August 2020

Abstract

Background
Statural growth impairment is more common in male patients with Crohn’s disease (CD). We identified clinical variables associated with height z score differences by sex in children participating in the Growth Study, a prospective multicenter longitudinal study examining sex differences in growth impairment in pediatric CD.

Methods
Patients with CD (female patients with bone age [BA] ≥4 years 2 months and ≤12 years; male patients with BA ≥5 years and ≤14 years at screening) who had completed study visit 1 qualified. The height z score difference was computed as height z score based on chronological age minus height z score based on BA.

Results
One hundred thirteen patients with CD (36% female) qualified. The mean chronological age was 12.0 ± 1.8 (SD) years. The magnitude of the mean height z score difference was significantly greater in female patients (–0.9 ± 0.8) than in male patients (–0.5 ± 0.9; P = 0.021). An initial classification of inflammatory bowel disease as CD (P = 0.038) and perianal disease behavior at diagnosis (P = 0.009) were associated with higher standardized height gain with BA progression, and arthralgia at symptom onset (P = 0.016), azathioprine/6-merpcaptopurine (P = 0.041), and probiotics (P ≤ 0.021) were associated with lower standardized height gain with BA progression in female patients. Patient-reported poor growth at symptom onset (P = 0.001), infliximab (P ≤ 0.025), biologics (P ≤ 0.015), methotrexate (P = 0.042), and vitamin D (P ≤ 0.010) were associated with higher standardized height gain with BA progression, and initial classification as CD (P = 0.025) and anorexia (P = 0.005) or mouth sores (P = 0.004) at symptom onset were associated with lower standardized height gain with BA progression in male patients.

Conclusions
Different clinical variables were associated with statural growth in male patients vs female patients, suggesting that sex-specific molecular pathways lead to statural growth impairment in CD.
The Diverse Roles of the IL-36 Family in Gastrointestinal Inflammation and Resolution
Authors: Leon Gemma , Hussey Seamus , Walsh Patrick T 
Published: August 2020

AbstractThe interleukin (IL)-36 family is a member of the IL-1 superfamily of cytokines and, in common with other IL-1 family members, has been shown to exhibit pleiotropic effects in homeostasis and inflammation. Although the important role these cytokines play in the skin has been widely reported, recent evidence suggests that IL-36 family members are expressed and can also exert significant influence at the intestinal mucosa. In this review, we summarize current knowledge surrounding the role of the IL-36 in the intestines. In particular, we examine its likely dichotomous role as a mediator of both inflammation and resolution, highlighting its overlapping roles in innate and adaptive inflammation at the mucosa and its contribution to pathophysiology of inflammatory bowel disease. We also summarize the complexities of targeting this cytokine family in a clinical setting.
Genetic and nongenetic factors influencing ewe prolificacy and lamb body weight in a closed Romanov flock
Authors: Murphy Thomas W , Keele John W , Freking Brad A 
Published: August 2020

Abstract
The U.S. Meat Animal Research Center was the first entity in the United States to import the Romanov breed and it has been maintained as a closed flock for over 30 yr. Incorporating this super-prolific breed into crossbred and composite populations has resulted in large improvements in ewe productivity. However, few have quantified factors contributing to genetic and nongenetic variation in ewe reproduction and lamb growth within purebred Romanov populations, which were the objectives of this study. The pedigree contained a total of 8,683 lambs born to 218 and 1,600 unique sires and dams, respectively. Number of lambs born on a per ewe exposed (NLBE) and lambing (NLBL) basis were analyzed in univariate repeatability animal models. As expected, the proportion of phenotypic variance (σP2) in litter size attributable to additive genetic (0.06 to 0.08) and permanent environmental (0.05 to 0.07) effects of the ewe was low. The service sire permanent environmental effect contributed to a small but significant amount of σP2 in NLBE (0.03) but not NLBL. However, the service sire additive genetic effect did not influence σP2 in NLBE or NLBL. Lamb body weight was recorded at birth (BWB) and upon weaning from either milk replacer (~30 d; BWW-N) or their dam (~60 d; BWW-D) and were analyzed in a three-trait model with random additive direct and maternal effects. Estimated direct heritabilities were low for all body weight (BW) traits (0.07 to 0.10). Maternal heritability was moderate for BWB (0.34) but low for weaning BW (0.11 to 0.18). This was the first to report direct and maternal genetic correlations between BW of nursery- and dam-reared lambs, and both were estimated to be moderate (0.43 to 0.47). Additionally, the direct and maternal effects of BWB were more strongly correlated with BWW-N (0.74 to 0.82) than BWW-D (0.17 to 0.33). Despite inbreeding coefficients having increased at a rate of 0.33% per birth year (1986 to 2019) in this flock, they were not consistently associated with reductions in ewe or lamb performance. Parameter estimates generally agreed with those from less-prolific breeds, and results indicate that selection can be an effective means of improving subcomponents of ewe productivity.
Effect of supplementation of unprotected or protected arginine to prolific ewes on maternal amino acids profile, lamb survival at birth, and pre- and post-weaning lamb growth
Authors: Gootwine Elisha , Rosov Alexander , Alon Tamir , Stenhouse Claire , Halloran Katherine M , Wu Guoyao , Bazer Fuller W 
Published: August 2020

Abstract
This research determined the effects of dietary supplementation with rumen-protected arginine (Pro-Arg) on metabolites and amino acids in maternal plasma and lamb survival rate at birth (LSRAB) in prolific Afec–Assaf ewes. The hypothesis was that Pro-Arg, the precursor for nitric oxide and polyamines, would increase placental development and vascularity, uteroplacental blood flow, and nutrient transport and reduce oxidative stress to increase LSRAB. Ewes were fed either their basal diet, basal diet with Pro-Arg, or basal diet with unprotected arginine (Unp-Arg; 18 g/head/d). The supplemental arginine was about 1% of the dry matter intake from day 40 or 60 of gestation until parturition. Ninety-two of 98 ewes produced live lambs. Ewes fed Pro-Arg had greater (P = 0.002) concentrations of arginine and other amino acids in plasma, whereas Unp-Arg did not affect concentrations of arginine, but decreased (P &lt; 0.05) concentrations of some amino acids. There was no effect of treatments on gestation length (144 ± 2 d), prolificacy (2.65 lambs born per ewe), LSRAB (0.80), body weight (88.8 ± 10.8 kg), and body condition score (2.8 ± 0.6) of ewes, or birth weight and crown-rump length of lambs. The GI (BW/CRL1.5) was affected by sex of lamb (P = 0.008), parity of ewe (P = 0.002), litter size (P = 0.0001), and lamb status (P = 0.003). Of 229 lambs born, 32 were dead and 16 died before 5 mo of age, leaving 181 lambs with records on weights at birth and 5 mo of age. Interestingly, lambs born to ewes fed the Unp-Arg and Pro-Arg weighed 3.6 kg less at postnatal day 150 than lambs from control ewes.
Media Freedom in the Shadow of a Coup
Authors: Boleslavsky Raphael , Shadmehr Mehdi , Sonin Konstantin 
Published: August 2020

AbstractPopular protests and palace coups are the two domestic threats to dictators. We show that free media, which informs citizens about their rulers, is a double-edged sword that alleviates one threat, but exacerbates the other. Informed citizens may protest against a ruler, but they may also protest to restore her after a palace coup. We develop a model in which citizens engage in a regime-change global game, and media freedom is a ruler’s instrument for Bayesian persuasion, used to manage the competing risks of coups and protests. A coup switches the status quo from being in the ruler’s favor to being against her. This introduces convexities in the ruler’s Bayesian persuasion problem, causing her to benefit from an informed citizenry. Rulers tolerate freer press when citizens are pessimistic about them, or coups signal information about them to citizens.
Dietary Supplementation With Vitamins and Minerals Improves Larvae and Adult Rearing Conditions of Anopheles darlingi (Diptera: Culicidae)
Authors: Nascimento Débora Aline Souza , Trindade Frances Tatiane Tavares , Silva Alexandre de Almeida e 
Published: August 2020

AbstractSeveral experiments with Anopheles darlingi Root, an important malaria vector in the Amazon region, were carried out in the laboratory, depending on the large-scale production of viable larvae and adults. Certainly, improvements in rearing conditions, including dietary requirements, can strongly affect mosquito production. In order to increase the production of this species in the laboratory, we first supplemented the regular larval diet (TetraMin Tropical Flakes) with different concentrations of vitamins and minerals and recorded several biological variables: survival and larval development time, emergence ratio, and adult longevity under a small-scale rearing condition. Second, we established an experimental design under regular lab-rearing conditions based on the concentration of vitamins and minerals that best contributed to the development of these anophelines, and evaluated the biological parameters already mentioned. Moreover, under regular rearing conditions, we recorded sex ratio, adult size, and longevity of adults fed with supplemented sucrose. The lowest concentration of vitamins (V5) and the average concentration of minerals (M3) increased larval survival and decreased larval development time compared with the control. Under regular rearing conditions, minerals provided higher larval survival and increased the longevity of adults fed with supplemented sucrose. Supplementing the regular larval diet and sucrose solutions with vitamins and minerals increased the production of immatures and the longevity of An. darlingi adults.
Population Growth Rates of Aedes atropalpus (Diptera: Culicidae) Are Depressed at Lower Temperatures Where Aedes japonicus japonicus (Diptera: Culicidae) Are Naturally Abundant in Rock Pools
Authors: Day Corey A , Armstrong Eleanor G , Byrd Brian D 
Published: August 2020

Abstract
Recent studies report extensive reductions in the abundance of the North American rock pool mosquito, Aedes atropalpus (Diptera: Culicidae), following the invasion of Ae. japonicus japonicus in the United States. Although developmental temperature is recognized as an important component of the invasion biology of Ae. j. japonicus, its impacts on the population growth and fitness of Ae. atropalpus remain largely undefined. In this study we reared Ae. atropalpus larvae at three temperature ranges reflecting ecologically important temperatures in natural rock pools: a low temperature range (mean: 19°C) where Ae. j. japonicus is common and Ae. atropalpus is often rare, a middle temperature range (mean: 25°C) where both species are naturally found in similar relative abundances, and a higher temperature range (mean: 31°C) where Ae. atropalpus is the dominant species. We measured survival, development time, wing length, and fecundity to calculate a finite population growth rate at each temperature. Our results indicate that Ae. atropalpus population growth suffers in colder rock pools, which informs the perceived displacement of the species in temperate habitats. The population growth rate was highest in the middle temperature range, but not significantly higher than in the highest temperature range used in this study. The developmental success of Ae. atropalpus at the intermediate temperature range suggests that competition with Ae. j. japonicus in rock pools within that range may significantly impact natural Ae. atropalpus populations.
Dimensionality reduction for single cell RNA sequencing data using constrained robust non-negative matrix factorization
Authors: Zhang Shuqin , Yang Liu , Yang Jinwen , Lin Zhixiang , Ng Michael K 
Published: August 2020

AbstractSingle cell RNA-sequencing (scRNA-seq) technology, a powerful tool for analyzing the entire transcriptome at single cell level, is receiving increasing research attention. The presence of dropouts is an important characteristic of scRNA-seq data that may affect the performance of downstream analyses, such as dimensionality reduction and clustering. Cells sequenced to lower depths tend to have more dropouts than those sequenced to greater depths. In this study, we aimed to develop a dimensionality reduction method to address both dropouts and the non-negativity constraints in scRNA-seq data. The developed method simultaneously performs dimensionality reduction and dropout imputation under the non-negative matrix factorization (NMF) framework. The dropouts were modeled as a non-negative sparse matrix. Summation of the observed data matrix and dropout matrix was approximated by NMF. To ensure the sparsity pattern was maintained, a weighted ℓ1 penalty that took into account the dependency of dropouts on the sequencing depth in each cell was imposed. An efficient algorithm was developed to solve the proposed optimization problem. Experiments using both synthetic data and real data showed that dimensionality reduction via the proposed method afforded more robust clustering results compared with those obtained from the existing methods, and that dropout imputation improved the differential expression analysis.
The cIMPACT-NOW updates and their significance to current neuro-oncology practice
Authors: Gonzalez Castro L Nicolas , Wesseling Pieter 
Published: August 2020

AbstractOver the past 4 years, advances in molecular pathology have enhanced our understanding of CNS tumors, providing new elements to refine their classification and improve the 2016 World Health Organization (WHO) Classification of CNS tumors. The Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy—Not Official WHO (cIMPACT-NOW) was formed in late 2016 by a group of neuropathology and neuro-oncology experts to provide practical recommendations (published as cIMPACT-NOW updates) to improve the diagnosis and classification of CNS tumors, in advance of the publication of a new WHO Classification of CNS tumors. Here we review the content of all the available cIMPACT-NOW updates and discuss the implications of each update for the diagnosis and management of patients with CNS tumors.
Income Inequality Is Associated With Low Cumulative Antiretroviral Adherence in Persons With Human Immunodeficiency Virus
Authors: Vernon Frances , Morrow Mary , MaWhinney Samantha , Coyle Ryan , Coleman Stacey , Ellison Lucas , Zheng Jia-Hua , Bushman Lane , Kiser Jennifer J , Galárraga Omar , Anderson Peter L , Castillo-Mancilla Jose 
Published: August 2020

Abstract

Background
The adherence biomarker tenofovir diphosphate (TFV-DP) in dried blood spots (DBS) is associated with viral suppression and predicts future viremia. However, its association with social determinants of health (SDoH) in people with human immunodeficiency virus (PWH) remains unknown.

Methods
Dried blood spots for TFV-DP were longitudinally collected from a clinical cohort of PWH receiving tenofovir disoproxil fumarate-based therapy (up to 3 visits over 48 weeks) residing in 5 Colorado counties. To assign SDoH, zip codes at enrollment were matched with SDoH data from AIDSVu (https://aidsvu.org/). The SDoH included household income, percentage living in poverty, education level, and income inequality (quantified using Gini coefficient, where 0 and 1 represent perfect income equality and inequality, respectively). Log-transformed TFV-DP concentrations were analyzed using a mixed-effects model to estimate percentage change (95% confidence interval) in TFV-DP for every significant change in the SDoH and adjusted for relevant covariates including age, gender, race, estimated glomerular filtration rate, body mass index, hematocrit, CD4+ T-cell count, antiretroviral drug class, and 3-month self-reported adherence.

Results
Data from 430 PWH totaling 950 person-visits were analyzed. In an adjusted analysis, income inequality was inversely associated with TFV-DP in DBS. For every 0.1 increase in the Gini coefficient, TFV-DP concentrations decreased by 9.2% (−0.5 to −17.1; P = .039). This remained significant after adjusting for human immunodeficiency virus viral suppression, where a 0.1 increase in Gini was associated with a decrease of 8.7% (−0.3 to −17.9; P = .042) in TFV-DP.

Conclusions
Higher income inequality was associated with lower cumulative antiretroviral adherence. These findings support the need for further research on how SDoH impact adherence and clinical care.
Powassan Virus Neuropathology and Genomic Diversity in Patients With Fatal Encephalitis
Authors: Normandin Erica , Solomon Isaac H , Zamirpour Siavash , Lemieux Jacob , Freije Catherine A , Mukerji Shibani S , Tomkins-Tinch Christopher , Park Daniel , Sabeti Pardis C , Piantadosi Anne 
Published: August 2020

AbstractBackgroundPowassan virus (POWV) is an emerging cause of severe encephalitis; very little is known about human pathogenicity due to challenges in diagnosis and viral RNA recovery. We present 3 patients with fatal encephalitis due to POWV lineage II (deer tick virus).MethodsWe obtained 27 unique samples, including from brain biopsy and autopsy, and used metagenomic sequencing, quantitative reverse transcriptase polymerase chain reaction, and a newly developed CRISPR-based diagnostic assay to perform the first detailed characterization of POWV compartmentalization and genomics between and within human subjects.ResultsIn all 3 patients, imaging and histopathology findings were notable for profound cerebellar involvement. All patients were initially diagnosed with POWV by metagenomic sequencing, and 2 of the 3 had negative clinical testing by serology. We detected POWV RNA in 13 clinical samples; levels were highest in the cerebellum, and there was very little involvement of peripheral tissue. We assembled complete POWV genomes from 8 samples, providing unique information about the strains of POWV lineage II (deer tick virus) that infect humans.ConclusionsWe demonstrate the utility of molecular assays for detecting POWV infection, including in seronegative patients, and nominate viral genomic features that may relate to human infection and neuropathogenicity. The cerebellum was identified as a key target POWV in fatal infection, by radiological and histopathological findings as well as molecular testing.
Successful Antiviral Therapy Reduces Risk of Schizophrenia Among Chronic Hepatitis C Patients: A Nationwide Real-World Taiwanese Cohort (T-COACH)
Authors: Tsai Pei-Chien , Chen Chi-Yi , Kuo Hsing-Tao , Hung Chao-Hung , Tseng Kuo-Chih , Lai Hsueh-Chou , Peng Cheng-Yuan , Wang Jing-Houng , Chen Jyh-Jou , Lee Pei-Lun , Chien Rong-Nan , Yang Chi-Chieh , Lo Gin-Ho , Kao Jia-Horng , Liu Chun-Jen , Liu Chen-Hua , Yan Sheng-Lei , Bair Ming-Jong , Lin Chun-Yen , Su Wei-Wen , Chu Cheng-Hsin , Chen Chih-Jen , Tung Shui-Yi , Tai Chi-Ming , Lin Chih-Wen , Lo Ching-Chu , Cheng Pin-Nan , Chiu Yen-Cheng , Wang Chia-Chi , Cheng Jin-Shiung , Tsai Wei-Lun , Lin Han-Chieh , Huang Yi-Hsiang , Yeh Ming-Lun , Huang Chung-Feng , Hsieh Meng-Hsuan , Huang Jee-Fu , Dai Chia-Yen , Chung Wan-Long , Ke Chiao-Li Khale , Yu Ming-Lung 
Published: August 2020

Abstract

Background
Chronic hepatitis C (CHC) has been associated with major psychoses, and interferon (IFN)-based therapy may cause psychiatric sequelae. We aimed to evaluate the effects of sustained virological response (SVR) on the incidence of major psychoses in a nationwide Taiwanese CHC cohort.

Methods
Fifteen thousand eight hundred thirty-six CHC Taiwanese who received IFN-based therapy were enrolled between 2003 and 2015. Of those, 12 723 patients were linked to the National Health Insurance Research Databases for the incidence of major psychoses. Death before major psychoses was considered a competing risk.

Results
Twenty-four patients developed new-onset major psychoses during 67 554 person-years (3.6 per 10 000 person-years), including 16 affective psychoses, 7 schizophrenia, and 1 organic psychotic condition. The incidence of major psychoses and affective psychoses did not differ between the SVR and non-SVR groups. The 10-year cumulative incidence of schizophrenia were significantly higher in the non-SVR than in SVR patients (0.14% vs 0.04%, P = .036). Cox subdistribution hazards showed that SVR and older age were associated with a significantly lower risk of schizophrenia (hazard ratio = 0.18 and 0.17). Sustained virological response was associated with decreased incidence of schizophrenia and majorly observed among patients with age &lt;45 (P = .02).

Conclusions
Successful IFN-based therapy might reduce the incidence of schizophrenia among CHC patients, especially among younger patients.