bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology
Authors: Sun Lina , Gao Tian , Wang Feilong , Qin Zuliang , Yan Longxia , Tao Wenjing , Li Minghui , Jin Canbiao , Ma Li , Kocher Thomas D. , Wang Deshou 
Published: May 2020

AbstractOnychostoma macrolepis is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome‐level assembly of the O.macrolepis genome obtained from the integration of nanopore long‐read sequencing with physical maps produced using Bionano and Hi‐C technology. A total of 87.9 Gb of nanopore sequence provided approximately 100‐fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi‐C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein‐coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non‐coding RNAs, in the genome. Evolutionary analysis revealed that O. macrolepis diverged from common carp approximately 24.25 million years ago. The chromosomes of O. macrolepis showed an unambiguous correspondence to the chromosomes of zebrafish. The high‐quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of O. macrolepis.
Combining genotype, phenotype, and environmental data to delineate site‐adjusted provenance strategies for ecological restoration
Authors: Carvalho Carolina S. , Forester Brenna R. , Mitre Simone K. , Alves Ronnie , Imperatriz‐Fonseca Vera L. , Ramos Silvio J. , Resende‐Moreira Luciana C. , Siqueira José O. , Trevelin Leonardo C. , Caldeira Cecilio F. , Gastauer Markus , Jaffé Rodolfo 
Published: May 2020

AbstractDespite the importance of climate‐adjusted provenancing to mitigate the effects of environmental change, climatic considerations alone are insufficient when restoring highly degraded sites. Here we propose a comprehensive landscape genomic approach to assist the restoration of moderately disturbed and highly degraded sites. To illustrate it we employ genomic data sets comprising thousands of single nucleotide polymorphisms from two plant species suitable for the restoration of iron‐rich Amazonian Savannas. We first use a subset of neutral loci to assess genetic structure and determine the genetic neighbourhood size. We then identify genotype‐phenotype‐environment associations, map adaptive genetic variation, and predict adaptive genotypes for restoration sites. Whereas local provenances were found optimal to restore a moderately disturbed site, a mixture of genotypes seemed the most promising strategy to recover a highly degraded mining site. We discuss how our results can help define site‐adjusted provenancing strategies, and argue that our methods can be more broadly applied to assist other restoration initiatives.
Effect of TNF‐inhibitor therapy on spinal structural progression in ankylosing spondylitis patients: A systematic review and meta‐analysis
Authors: Ajrawat Prabjit , Touma Zahi , Sari Ismail , Taheri Cameron , Diaz Martinez Juan Pablo , Haroon Nigil 
Published: May 2020

AbstractTo review the effect of tumor necrosis factor‐alpha inhibitor (TNFi) therapies on radiographic progression in ankylosing spondylitis (AS) patients as evaluated by the modified Stoke Ankylosing Spondylitis Spine Score (mSASSS). Pubmed, MEDLINE, EMBASE, and the Cochrane Library databases were searched from inception to August 2019. All comparative and non‐comparative studies that evaluated the clinical effectiveness of TNFi on radiographic progression as assessed by mSASSS change at a minimum follow‐up of 1 year were included. The Newcastle–Ottawa Scale and Cochrane Collaboration Risk of Bias Tool were utilized to assess the methodological quality. Pooled analysis was performed for continuous and binomial variables where appropriate. Inter‐rater reliability of mSASSS status and change scores were assessed with intra‐class coefficients (ICC). Twenty‐one studies were identified with a total of 4460 patients (mean age: 40.4 years [range 25.3‐50 years]; 76% male; mean baseline mSASSS: 12.7 units [range 5.5‐19.8 units]). All studies (3 randomized and 18 observational studies) were considered to have moderate‐to‐high methodological quality. The inter‐rater reliability of mSASSS status and change scores from 14 of the 21 studies were excellent (ICC ranges, 0.91‐0.99) and moderate‐to‐excellent (ICC ranges, 0.58‐0.90), respectively. From the 21 studies, 11/21 (50%) demonstrated a delayed effect in mSASSS in AS patient administered TNFi. When stratifying these studies into those with ≤4 years of follow‐up and >4 years follow‐up, 3/11 (27%) and 8/10 (80%) studies respectively indicated a delayed effect of mSASSS with TNFi in AS patients. Pooling for meta‐analysis from 3 studies (1159 patients) with study durations ranging 4‐8 years, indicated that TNFi‐treated patients had reduced odds of structural progression (odds ratio 0.81; 95% CI 0.68‐0.96; P = .01; I2 = 0%). Mean rate of mSASSS change from 16 studies ranged from −0.15 to 7.3 mSASSS units for all AS patients. Meta‐analysis indicated a numerical, but statistically non‐significant, reduction in the rate of mSASSS change with TNFi treatment (7 studies [1438 patients]; mean difference, −0.24; 95% CI, −0.49‐0.01; P = .06; I2 = 0%). This systematic review and meta‐analysis indicated that >4 years of TNFi usage was associated with delayed structural progression by mSASSS. The narrative analysis of the data from 21 studies further confirmed that studies with >4 years of follow‐up had delayed structural progression with TNFi use in AS patients. The systematic review also confirmed that mSASSS has good‐to‐excellent inter‐rater reliability in AS.
A first response to osmostress inAcinetobacter baumannii: transient accumulation of K+and its replacement by compatible solutes
Authors: König Patricia , Averhoff Beate , Müller Volker 
Published: May 2020

SummaryThe extraordinary desiccation resistance of the opportunistic human pathogenAcinetobacter baumanniiis a key to its survival and spread in medical care units. The accumulation of compatible solute such as glutamate, mannitol and trehalose contributes to the desiccation resistance. Here, we have used osmolarity as a tool to study the response of cells to low water activities and studied the role of a potential inorganic osmolyte, K+, in osmostress response. Growth ofA. baumanniiwas K+‐dependent and the K+‐dependence increased with the osmolarity of the medium. After an osmotic upshock, cells accumulated K+and K+accumulation increased with the salinity of the medium. K+uptake was reduced in the presence of glycine betaine. The intracellular pools of compatible solutes were dependent on the K+concentration: mannitol and glutamate concentrations increased with increasing K+concentrations whereas trehalose was highest at low K+. After osmotic upshock, cells first accumulated K+followed by synthesis of glutamate; later, mannitol and trehalose synthesis started, accompanied with a decrease of intracellular K+and glutamate. These experiments demonstrate K+uptake as a first response to osmostress inA. baumanniiand demonstrate a hierarchy in the time‐dependent accumulation of K+and different organic solutes.
Switching administration of anti‐PD‐1 and anti‐PD‐L1 antibodies as immune checkpoint inhibitor rechallenge in individuals with advanced non‐small cell lung cancer: Case series and literature review
Authors: Kitagawa Shingo , Hakozaki Taiki , Kitadai Rui , Hosomi Yukio 
Published: May 2020

BackgroundBased on several phase III studies, immune checkpoint inhibitors (ICIs) are essential and promising drugs for the treatment of non‐small cell lung cancer (NSCLC). However, in patients previously treated with ICI, the efficacy and safety of rechallenging the same or another type of ICI inhibitor remain unclear. Moreover, clinical data about the efficacy of switching the administration of anti‐programmed death‐1 (PD‐1) antibodies (e.g. nivolumab, pembrolizumab) and anti‐programmed death‐ligand 1 (PD‐L1) antibodies (e.g. atezolizumab) as ICI rechallenge are limited. Thus, the current study aimed to evaluate the efficacy and safety of such treatment strategy in NSCLC patients.MethodsWe retrospectively reviewed the medical records of 17 patients with advanced or recurrent NSCLC who received both anti‐PD‐1 and anti‐PD‐L1 antibodies during their clinical courses.ResultsAmong the 17 patients, one (5.9%) and nine (52.9%) achieved partial response and stable disease, respectively, after ICI rechallenge. The median progression‐free survival of ICI rechallenge in these patients was 4.0 (range: 0.4–8.0) months, and the median overall survival from the start of the initial ICI was 31.0 (range: 7.6–46.8) months. Of the 10 patients who developed immune‐related adverse events (irAEs) during the first ICI treatment, five presented with these events after the readministration of ICI. Among them, four experienced relapsed irAEs and two patients had pneumonitis, which is a grade 3 or higher irAE. Almost all irAEs during the rechallenge treatment were manageable.ConclusionsSwitching the administration of anti‐PD‐1 and anti‐PD‐L1 antibodies as ICI rechallenge could be a treatment option for some NSCLC patients.Key points• Significant findings of the studyIn this study, switching the administration of anti‐PD‐1 and anti‐PD‐L1 antibodies as ICI rechallenge could be an effective and safe treatment option for some patients with advanced or recurrent NSCLC.• What this study addsSwitching the administration of ICI may increase the efficacy of readministration. However, the mechanism is unknown. Thus, further accumulation of cases is required, and extensive investigations must be conducted to elucidate the mechanism and benefits of such treatment.
A randomized clinical trial of a group cognitive–behavioral therapy to reduce alcohol use among human immunodeficiency virus‐infected outpatients in western Kenya
Authors: Papas Rebecca K. , Gakinya Benson N. , Mwaniki Michael M. , Lee Hana , Keter Alfred K. , Martino Steve , Klein Debra A. , Liu Tao , Loxley Michelle P. , Sidle John E. , Schlaudt Kathryn , Nafula Tobista , Omodi Victor M. , Baliddawa Joyce B. , Kinyanjui Daniel W. , Maisto Stephen A. 
Published: May 2020

AbstractBackground and aimsCulturally relevant and feasible interventions are needed to address limited professional resources in sub‐Saharan Africa for behaviorally treating the dual epidemics of HIV and alcohol use disorder. This study tested the efficacy of a cognitive–behavioral therapy (CBT) intervention to reduce alcohol use among HIV‐infected outpatients in Eldoret, Kenya.DesignRandomized clinical trial.SettingA large HIV outpatient clinic in Eldoret, Kenya, affiliated with the Academic Model Providing Access to Healthcare collaboration.ParticipantsA total of 614 HIV‐infected outpatients [312 CBT; 302 healthy life‐styles (HL); 48.5% male; mean age: 38.9 years; mean education 7.7 years] who reported a minimum of hazardous or binge drinking.Intervention and comparatorA culturally adapted six‐session gender‐stratified group CBT intervention compared with HL education, each delivered by paraprofessionals over six weekly 90‐minute sessions with a 9‐month follow‐up.MeasurementsPrimary outcome measures were percentage of drinking days (PDD) and mean drinks per drinking day (DDD) computed from retrospective daily number of drinks data obtained by use of the time‐line follow‐back from baseline to 9 months post‐intervention. Exploratory analyses examined unprotected sex and number of partners.FindingsMedian attendance was six sessions across condition. Retention at 9 months post‐intervention was high and similar by condition: CBT 86% and HL 83%. PDD and DDD marginal means were significantly lower in CBT than HL at all three study phases. Maintenance period, PDD – CBT = 3.64 (0.696), HL = 5.72 (0.71), mean difference 2.08, 95% confidence interval (CI) = 0.13 – 4.04; DDD – CBT = 0.66 (0.96), HL = 0.98 (0.098), mean difference = 0.31, 95% CI = 0.05 – 0.58. Risky sex decreased over time in both conditions, with a temporary effect for CBT at the 1‐month follow‐up.ConclusionsA cognitive–behavioral therapy intervention was more efficacious than healthy lifestyles education in reducing alcohol use among HIV‐infected Kenyan outpatient drinkers.
Morphometric analysis of the mandible of Bardhoka autochthonous sheep in Kosovo
Authors: Özkan Ermiş , Jashari Tefik , Gündemir Ozan , Gezer İnce Nazan 
Published: May 2020

AbstractKosovo, one of the countries in the Balkan Peninsula, has a long tradition in sheep farming, and sheep breeds share triple purpose breed characteristics: milk, meat and wool. Bardhoka sheep, also with triple productive profile, is an important sheep breed because of its economic value with its milk production. In this study, 24 mandibles of adult Bardhoka sheep (12 male and 12 female) aged between 2 and 5 were used. The sheep were acquired from slaughterhouse around Kosovo, and the mandibles were selected without any deformities from healthy sheep. After cleaning the mandibles, a total of 12 morphometric measurements were taken from each sample using digital calliper. The difference between female and male was statistically significant (p < .05) for measurement 11 (height of mandible level of alveolar edge of 3rd molar tooth). The mean value of measurement 11 in male individuals was 42.26 ± 3.96, and it had a higher value than in female individuals (39.37 ± 2.57). In the literature, knowledge related to mandible morphometry of Bardhoka sheep was insufficient. The aim of this study was to determine mean values from osteometric measurements of Bardhoka sheep mandible and obtain references with the values acquired.
Enhancing the intentional self‐regulation skills of Chinese adolescents living in orphanages: A school‐based intervention
Authors: Liu Fangqing , Bowers Edmond P. , Gai Xiaosong , Ren Wei 
Published: May 2020

Adolescents living in orphanages are at risk for problematic developmental outcomes. However, adolescents with higher levels of intentional self‐regulation (ISR) often exhibit higher levels of positive youth development and are more likely to avoid risk in such an environment. The present study sought to revise a suite of materials designed to promote ISR skills in U.S. youth, GPS to Success (Goal Selection, Pursuit of Strategies, and Shifting Gears), and examined the effect of these revised materials (GPS‐r) on the ISR skills of orphan adolescents in China. Sixty‐eight adolescents from 14 to 18 years old living in the same orphanage participated in the GPS‐r project. Participants were divided into an experimental group and a control group. The experimental group received training on the GPS‐r materials, which lasted for 11 weeks and took 45 min per week, whereas the control group did not receive training. The results revealed that ISR skills, particularly the dimensions of goal selection and pursuit of strategies, were significantly enhanced after the GPS‐r project for the experimental group, but not the control group. The findings highlight several implications for positive youth development interventions for youth in orphanages.
Prophylactic Foley catheter insertion into defunctioning ileostomy to reduce obstruction after colorectal surgery: pilot randomized controlled trial*
Authors: Kulasegaran Suheelan , Li Ray , Nisbet Sherry , Vasey Carolyn , Otutaha Bacil , Walsh Michael , Jarvis John , Moir Mike H. 
Published: May 2020

AbstractBackgroundDefunctioning ileostomies provide faecal diversion in major colorectal surgery. This reduces the consequences of an anastomotic leak. However, the formation of an ileostomy carries risks including obstruction at the level of the fascia. Post‐operative oedema at the level of the fascia may contribute to obstruction. We hypothesize that the prophylactic insertion of a Foley catheter into the afferent limb of a defunctioning loop ileostomy may help decompress and improve time to low‐residue diet (LRD). The objective of the study was to assess the feasibility of a Foley catheter, prophylactically inserted into the afferent limb of a defunctioning loop ileostomy, after major colorectal surgery.MethodsThe study was a prospective pilot‐randomized controlled trial. Ethical approval was obtained from Northern B Health and Disability Ethics Committee 15/NTB/91 ANZCTR Trial ID: ACTRN12615000691549.ResultsForty‐nine patients undergoing major elective colorectal surgery with a defunctioning ileostomy, between the years of 2015 and 2018 at North Shore Hospital, Auckland, New Zealand were included in this study. Patients were randomly allocated to either the Foley catheter (n = 26) or non‐Foley catheter (n = 23) group. The median time taken to tolerate LRD the primary outcome, was 2 days in the Foley group versus 2 days in the non‐Foley group (P = 0.05). There were no differences in the secondary outcome measures such as time to stoma output, length of stay or complications.ConclusionThis trial failed to show a statistical difference in time taken to tolerate a LRD residue in the Foley catheter group. There was no difference in length of stay, time to flatus or stoma output.
Comparison of objective and subjective visual quality early after implantable collamer lens V4c (ICL V4c) and small incision lenticule extraction (SMILE) for high myopia correction
Authors: Wei Ruoyan , Li Meiyan , Zhang Huihui , Aruma Aruma , Miao Huamao , Wang Xiaoying , Zhou Jin , Zhou Xingtao 
Published: May 2020

AbstractPurposeTo investigate differences in the objective and subjective visual quality of patients with high myopia following implantable collamer lens V4c (ICL V4c) versus small incision lenticule extraction (SMILE) early postoperatively.MethodsThis prospective analysis included 94 eyes of 57 patients (8 males) in the ICL V4c group (mean spherical equivalent (SE), −8.07 ± 1.03 dioptres (D)) and 103 eyes of 57 patients (13 males) in the SMILE group (mean SE, −7.85 ± 0.78 D). Refractive parameters and wavefront aberrations were recorded preoperatively and 6 months postoperatively. Subjective visual quality was scored with the Quality of Vision questionnaire, and operation satisfaction was evaluated 6 months postoperatively.ResultsAt 6 months postoperatively, the efficacy index was 1.17 ± 0.16 in the ICL and 1.09 ± 0.20 in the SMILE group; the safety index was 1.21 ± 0.18 in the ICL and 1.12 ± 0.16 in the SMILE group. A significant increase in total higher‐order aberrations (HOAs) in both the ICL and SMILE groups was observed, but to a lesser degree in ICL (p < 0.05). In the ICL group, trefoil significantly increased (p < 0.05), whereas in the SMILE group, coma, trefoil and spherical aberration significantly increased (p < 0.05). Glare, haloes and blurred vision had the highest incidences after both types of surgery, and postoperative haloes were significantly more common following ICL; 96.1% of ICL‐treated and 94.9% of SMILE‐treated patients were satisfied with their visual outcomes.ConclusionICL V4c caused lower HOAs induction than SMILE. Despite the postoperative visual disturbances, both ICL and SMILE provided good efficacy, safety, predictability and high satisfaction in correcting high myopia.
No evidence from a systematic review for the use of probiotics to prevent otitis media
Authors: Chen Tzu Yu , Hendrickx Anneleen , Stevenson Duncan Scott , Bird Philip , Walls Tony 
Published: May 2020

AbstractAimThis systematic review evaluates the current evidence for the use of probiotics in the prevention of acute otitis media (AOM) in children.MethodsThis study is registered with PROSPERO prior to commencement. PubMed, MEDLINE, EMBASE and Cochrane database were searched using relating keywords. All literature was screened to determine relatability to the topic. Review articles were also screened for additional literature.ResultsThirteen studies were found on probiotics and their role in preventing AOM in children. They ranged in quality from poor to moderate. Half (2/4) of the studies that used nasal probiotic formulations showed a significant difference in reducing otitis media, while only a third (3/9) of the studies using oral formulations suggest benefit in reducing AOM. None of the studies demonstrated significant adverse effects from probiotics.ConclusionThe evidence for any effect of probiotics on the prevention of AOM is limited, and the overall low quality of studies makes it difficult to draw definitive conclusions. No serious adverse events were noted, and there is some evidence to suggest possible benefit with nasal probiotic administration.
Targeting desmosomal adhesion and signalling for intestinal barrier stabilization in inflammatory bowel diseases—Lessons from experimental models and patients
Authors: Schlegel Nicolas , Boerner Kevin , Waschke Jens 
Published: May 2020

AbstractInflammatory bowel diseases (IBD) such as Crohn’s disease (CD) and Ulcerative colitis (UC) have a complex and multifactorial pathogenesis which is incompletely understood. A typical feature closely associated with clinical symptoms is impaired intestinal epithelial barrier function. Mounting evidence suggests that desmosomes, which together with tight junctions (TJ) and adherens junctions (AJ) form the intestinal epithelial barrier, play a distinct role in IBD pathogenesis. This is based on the finding that desmoglein (Dsg) 2, a cadherin‐type adhesion molecule of desmosomes, is required for maintenance of intestinal barrier properties both in vitro and in vivo, presumably via Dsg2‐mediated regulation of TJ. Mice deficient for intestinal Dsg2 show increased basal permeability and are highly susceptible to experimental colitis. In several cohorts of IBD patients, intestinal protein levels of Dsg2 are reduced and desmosome ultrastructure is altered suggesting that Dsg2 is involved in IBD pathogenesis. In addition to its adhesive function, Dsg2 contributes to enterocyte cohesion and intestinal barrier function. Dsg2 is also involved in enterocyte proliferation, barrier differentiation and induction of apoptosis, in part by regulation of p38MAPK and EGFR signalling. In IBD, the function of Dsg2 appears to be compromised via p38MAPK activation, which is a critical pathway for regulation of desmosomes and is associated with keratin phosphorylation in IBD patients. In this review, the current findings on the role of Dsg2 as a novel promising target to prevent loss of intestinal barrier function in IBD patients are discussed.
Will They Stay or Will They Go? Examining the Brain Drain in Canada's Provincial North
Authors: Hillier Cathlene , Sano Yujiro , Zarifa David , Haan Michael 
Published: May 2020

AbstractBrain drain is an increasingly important concern for local governments in northern communities in Canada in maintaining and enhancing human capital levels to sustain vibrant economies and communities. Researchers, however, have yet to examine the magnitude of north‐south out‐migration nor do we know the characteristics of youth who are likely to relocate. Our study contributes to this knowledge gap by employing multiple waves from Statistics Canada's Youth in Transition Survey (Cohort A) linked to each youth's reading scores from the Programme for International Student Assessment (measured at age 15), and longitudinally to their tax filer information until age 30 (T1 Family Files).