bluuebunny/crossref_metadata_2025_split huggingface dataset:
A physician-pharmacist collaborative care model to prevent opioid misuse
Authors: Lagisetty Pooja , Smith Alex , Antoku Derek , Winter Suzanne , Smith Michael , Jannausch Mary , Mi Choe Hae , Bohnert Amy S B , Heisler Michele 
Published: April 2020

Abstract

Purpose
Clinical pharmacists in primary care clinics can potentially help manage chronic pain and opioid prescriptions by providing services similar to those provided within their scope of practice to patients with diabetes and hypertension. We evaluated the feasibility and acceptability of a pharmacist-physician collaborative care model for patients with chronic pain.

Methods
The program consisted of an in-person pharmacist consultation and optional follow-up visits over 4 months in 2 primary care practices. Eligible patients had chronic pain and a long-term prescription for opioids or buprenorphine or were referred by their primary care physician (PCP). Pharmacist recommendations were communicated to PCPs via the electronic medical record (EMR) and direct communication. Mixed-methods evaluation included baseline and follow-up surveys with patients, EMR review of opioid-related clinical encounters, and provider interviews.

Results
Between January and October 2018, 47 of the 182 eligible patients enrolled, with 46 completing all follow-up; 43 patients (91%) had received opioids over the past 6 months. The pharmacist recommended adding or switching to a nonopioid pain medication for 30 patients, switching to buprenorphine for pain and complex persistent opioid dependence for 20 patients, and tapering opioids for 3 patients. All physicians found the intervention acceptable but wanted more guidance on prescribing buprenorphine for pain. Most patients found the intervention helpful, but some reported a lack of physician follow-up on recommended changes.

Conclusion
The study demonstrated that comanagement of patients with chronic pain is feasible and acceptable. Policy changes to increase pharmacists’ authority to prescribe may increase physician willingness and confidence to carry out opioid tapers and prescribe buprenorphine for pain.
gutMEGA: a database of the human gut MEtaGenome Atlas
Authors: Zhang Qingfeng , Yu Kai , Li Shihua , Zhang Xiaolong , Zhao Qi , Zhao Xia , Liu Zekun , Cheng Han , Liu Ze-Xian , Li Xiaoxing 
Published: April 2020

Abstract
The gut microbiota plays important roles in human health through regulating both physiological homeostasis and disease emergence. The accumulation of metagenomic sequencing studies enables us to better understand the temporal and spatial variations of the gut microbiota under different physiological and pathological conditions. However, it is inconvenient for scientists to query and retrieve published data; thus, a comprehensive resource for the quantitative gut metagenome is urgently needed. In this study, we developed gut MEtaGenome Atlas (gutMEGA), a well-annotated comprehensive database, to curate and host published quantitative gut microbiota datasets from Homo sapiens. By carefully curating the gut microbiota composition, phenotypes and experimental information, gutMEGA finally integrated 59 132 quantification events for 6457 taxa at seven different levels (kingdom, phylum, class, order, family, genus and species) under 776 conditions. Moreover, with various browsing and search functions, gutMEGA provides a fast and simple way for users to obtain the relative abundances of intestinal microbes among phenotypes. Overall, gutMEGA is a convenient and comprehensive resource for gut metagenome research, which can be freely accessed at http://gutmega.omicsbio.info.
Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes
Authors: He Xiaoyu , Chen Shanyu , Li Ruilin , Han Xinyin , He Zhipeng , Yuan Danyang , Zhang Shuying , Duan Xiaohong , Niu Beifang 
Published: April 2020

AbstractNext-generation sequencing (NGS) technology has revolutionised human cancer research, particularly via detection of genomic variants with its ultra-high-throughput sequencing and increasing affordability. However, the inundation of rich cancer genomics data has resulted in significant challenges in its exploration and translation into biological insights. One of the difficulties in cancer genome sequencing is software selection. Currently, multiple tools are widely used to process NGS data in four stages: raw sequence data pre-processing and quality control (QC), sequence alignment, variant calling and annotation and visualisation. However, the differences between these NGS tools, including their installation, merits, drawbacks and application, have not been fully appreciated. Therefore, a systematic review of the functionality and performance of NGS tools is required to provide cancer researchers with guidance on software and strategy selection. Another challenge is the multidimensional QC of sequencing data because QC can not only report varied sequence data characteristics but also reveal deviations in diverse features and is essential for a meaningful and successful study. However, monitoring of QC metrics in specific steps including alignment and variant calling is neglected in certain pipelines such as the ‘Best Practices Workflows’ in GATK. In this review, we investigated the most widely used software for the fundamental analysis and QC of cancer genome sequencing data and provided instructions for selecting the most appropriate software and pipelines to ensure precise and efficient conclusions. We further discussed the prospects and new research directions for cancer genomics.
Prediction scores for risk of allograft loss in patients receiving kidney transplants: nil satis nisi optimum
Authors: Montero Nuria , Codina Sergi , Cruzado Josep M 
Published: April 2020

AbstractLong-term graft survival is the main concern of kidney transplantation. Some strategies have been tested to predict graft survival using estimated glomerular filtration rate or proteinuria at different time points, histologic assessment, non-invasive biomarkers or even machine-learning methods. However, the 'magical formulae' for allograft survival prediction does not exist yet.
A novel bioaugmentation technique effectively increases the skin-associated microbial diversity of captive eastern hellbenders
Authors: Kenison Erin K , Hernández-Gómez Obed , Williams Rod N 
Published: April 2020

Abstract
Captive environments are maintained in hygienic ways that lack free-flowing microbes found in animals’ natural environments. As a result, captive animals often have depauperate host-associated microbial communities compared to conspecifics in the wild and may have increased disease susceptibility and reduced immune function. Eastern hellbenders (Cryptobranchus alleganiensis alleganiensis) have suffered precipitous population declines over the past few decades. To bolster populations, eastern hellbenders are reared in captivity before being translocated to the wild. However, the absence of natural microbial reservoirs within the captive environment diminishes the diversity of skin-associated bacteria on hellbender skin and may negatively influence their ability to defend against pathogenic species once they are released into the wild. To prepare hellbenders for natural bacteria found in riverine environments, we devised a novel bioaugmentation method to increase the diversity of skin microbial communities within a captive setting. We exposed juvenile hellbenders to increasing amounts of river water over 5 weeks before translocating them to the river. We genetically identified and phylogenetically compared bacteria collected from skin swabs and river water for alpha (community richness) and beta (community composition) diversity estimates. We found that hellbenders exposed to undiluted river water in captivity had higher alpha diversity and distinct differentiation in the community composition on their skin, compared to hellbenders only exposed to well water. We also found strong evidence that hellbender skin microbiota is host-specific rather than environmentally driven and is colonized by rare environmental operational taxonomic units in river water. This technique may increase hellbender translocation success as increasing microbial diversity is often correlated with elevated disease resistance. Future work is necessary to refine our methods, investigate the relationship between microbial diversity and hellbender health and understand how this bioaugmentation technique influences hellbenders’ survival following translocation from captivity into the wild.
Enteroids Generated from Patients with Severe Inflammation in Crohn’s Disease Maintain Alterations of Junctional Proteins
Authors: Meir Michael , Salm Jonas , Fey Christina , Schweinlin Matthias , Kollmann Catherine , Kannapin Felix , Germer Christoph-Thomas , Waschke Jens , Beck Christopher , Burkard Natalie , Metzger Marco , Schlegel Nicolas 
Published: April 2020

AbstractBackgroundThe mechanisms underlying loss of intestinal epithelial barrier [IEB] function in Crohn’s disease [CD] are poorly understood. We tested whether human enteroids generated from isolated intestinal crypts of CD patients serve as an appropriate in vitro model to analyse changes of IEB proteins observed in patients’ specimens.MethodsGut samples from CD patients and healthy individuals who underwent surgery were collected. Enteroids were generated from intestinal crypts and analyses of junctional proteins in comparison to full wall samples were performed.ResultsHistopathology confirmed the presence of CD and the extent of inflammation in intestinal full wall sections. As revealed by immunostaining and Western blot analysis, profound changes in expression patterns of tight junction, adherens junction and desmosomal proteins were observed in full wall specimens when CD was present. Unexpectedly, when enteroids were generated from specimens of CD patients with severe inflammation, alterations of most tight junction proteins and the majority of changes in desmosomal proteins but not E-cadherin were maintained under culture conditions. Importantly, these changes were maintained without any additional stimulation of cytokines. Interestingly, qRT-PCR demonstrated that mRNA levels of junctional proteins were not different when enteroids from CD patients were compared to enteroids from healthy controls.ConclusionsThese data indicate that enteroids generated from patients with severe inflammation in CD maintain some characteristics of intestinal barrier protein changes on a post-transcriptional level. The enteroid in vitro model represents an appropriate tool to gain further cellular and molecular insights into the pathogenesis of barrier dysfunction in CD.
Combined effect of lasioglossin LL-III derivative with azoles against Candida albicans virulence factors: biofilm formation, phospholipases, proteases and hemolytic activity
Authors: Vaňková Eva , Kašparová Petra , Dulíčková Nikola , Čeřovský Václav 
Published: April 2020

ABSTRACT
Candida albicans has several virulence factors at its disposal, including yeast–hyphal transition associated with biofilm formation, phospholipases, proteases and hemolytic activity, all of which contribute to its pathogenesis. We used synthetic derivative LL-III/43 of antimicrobial peptide lasioglossin LL-III to enhance effect of azoles on attenuation of C. albicans virulence factors. LL-III/43 was able to inhibit initial adhesion or biofilm formation of C. albicans strains at 50 µM. Azoles, however, were ineffective at this concentration. Using fluorescently labeled LL-III/43, we observed that peptide covered C. albicans cells, partially penetrated through their membranes and then accumulated inside cells. LL-III/43 (25 µM) in combination with clotrimazole prevented biofilm formation already at 3.1 µM clotrimazole. Neither LL-III/43 nor azoles were able to significantly inhibit phospholipases, proteases, or hemolytic activity of C. albicans. LL-III/43 (25 µM) and clotrimazole (50 µM) in combination decreased production of these virulence factors, and it completely attenuated its hemolytic activity. Scanning electron microscopy showed that LL-III/43 (50 µM) prevented C. albicans biofilm formation on Ti-6Al-4 V alloy used in orthopedic surgeries and combination of LL-III/43 (25 µM) with clotrimazole (3.1 µM) prevented biofilm formation on urinary catheters. Therefore, mixture of LL-III/43 and clotrimazole is suitable candidate for future pharmaceutical research.
Active Bilingualism in Aging: Balanced Bilingualism Usage and Less Frequent Language Switching Relate to Better Conflict Monitoring and Goal Maintenance Ability
Authors: Chan Clara G H , Yow Wei Quin , Oei Adam 
Published: April 2020

Abstract

Objectives
Experience-related neuroplasticity suggests that bilinguals who actively manage their two languages would develop more efficient neural organization at brain regions related to language control, which also overlap with areas involved in executive control. Our aim was to examine how active bilingualism—manifested as the regular balanced use of two languages and language switching—may be related to the different domains of executive control in highly proficient healthy older adult bilinguals, controlling for age, processing speed, and fluid intelligence.

Methods
Participants were 76 community-dwelling older adults who reported being physically and mentally healthy and showed no signs of cognitive impairment. They completed a self-report questionnaire on their language background, two computer measures for previously identified covariates (processing speed as measured by two-choice reaction time (RT) task and fluid intelligence as measured by the Raven’s Progressive Matrices), as well as a battery of computerized executive control tasks (Color-shape Task Switching, Stroop, Flanker, and Spatial 2-back task).

Results
Regression analyses showed that, even after controlling for age, processing speed, and fluid intelligence, more balanced bilingualism usage and less frequent language switching predicted higher goal maintenance (nonswitch trials RT in Color-shape Task Switching) and conflict monitoring abilities (global RT in Color-shape Task Switching and Flanker task).

Discussion
Results suggest that active bilingualism may provide benefits to maintaining specific executive control abilities in older adult bilinguals against the natural age-related declines.
SRPRISM (Single Read Paired Read Indel Substitution Minimizer): an efficient aligner for assemblies with explicit guarantees
Authors: Morgulis Aleksandr , Agarwala Richa 
Published: April 2020

Abstract

Background
Alignment of sequence reads generated by next-generation sequencing is an integral part of most pipelines analyzing next-generation sequencing data. A number of tools designed to quickly align a large volume of sequences are already available. However, most existing tools lack explicit guarantees about their output. They also do not support searching genome assemblies, such as the human genome assembly GRCh38, that include primary and alternate sequences and placement information for alternate sequences to primary sequences in the assembly.

Findings
This paper describes SRPRISM (Single Read Paired Read Indel Substitution Minimizer), an alignment tool for aligning reads without splices. SRPRISM has features not available in most tools, such as (i) support for searching genome assemblies with alternate sequences, (ii) partial alignment of reads with a specified region of reads to be included in the alignment, (iii) choice of ranking schemes for alignments, and (iv) explicit criteria for search sensitivity. We compare the performance of SRPRISM to GEM, Kart, STAR, BWA-MEM, Bowtie2, Hobbes, and Yara using benchmark sets for paired and single reads of lengths 100 and 250 bp generated using DWGSIM. SRPRISM found the best results for most benchmark sets with error rate of up to ~2.5% and GEM performed best for higher error rates. SRPRISM was also more sensitive than other tools even when sensitivity was reduced to improve run time performance.

Conclusions
We present SRPRISM as a flexible read mapping tool that provides explicit guarantees on results.
Chromosome-level reference genome of the jellyfish Rhopilema esculentum
Authors: Li Yunfeng , Gao Lei , Pan Yongjia , Tian Meilin , Li Yulong , He Chongbo , Dong Ying , Sun Yamin , Zhou Zunchun 
Published: April 2020

Abstract

Background
Jellyfish belong to the phylum Cnidaria, which occupies an important phylogenetic location in the early-branching Metazoa lineages. The jellyfish Rhopilema esculentum is an important fishery resource in China. However, the genome resource of R. esculentum has not been reported to date.

Findings
In this study, we constructed a chromosome-level genome assembly of R. esculentum using Pacific Biosciences, Illumina, and Hi-C sequencing technologies. The final genome assembly was ~275.42 Mb, with a contig N50 length of 1.13 Mb. Using Hi-C technology to identify the contacts among contigs, 260.17 Mb (94.46%) of the assembled genome were anchored onto 21 pseudochromosomes with a scaffold N50 of 12.97 Mb. We identified 17,219 protein-coding genes, with an average CDS length of 1,575 bp. The genome-wide phylogenetic analysis indicated that R. esculentum might have evolved more slowly than the other scyphozoan species used in this study. In addition, 127 toxin-like genes were identified, and 1 toxin-related “hub” was found by a genomic survey.

Conclusions
We have generated a chromosome-level genome assembly of R. esculentum that could provide a valuable genomic background for studying the biology and pharmacology of jellyfish, as well as the evolutionary history of Cnidaria.
Regtech as an antitrust enforcement tool
Authors: Nicholls Rob 
Published: April 2020

Abstract
Financial technology (Fintech) has been applied to business models in the financial services sector. Associated with this has been the rise of regulatory technology (Regtech) in that sector. However, the major application of Regtech in financial services is as a tool for regulatory compliance, rather than for regulatory enforcement. This article explores an approach to applying Regtech techniques to antitrust enforcement. It does this by applying those techniques to the detection of resale price maintenance (vertical price fixing). The exploration is limited to pricing on e-commerce platforms such as AliExpress, eBay, and Amazon Marketplace. The Regtech application is effected by presenting the literature and cases on resale price maintenance and the application of the law in Australia, the US, and the EU. The article examines the application of machine learning in the Regtech environment and the ways in which application programming interfaces could be used. The article proposes approaches to machine learning solutions for the detection of potentially infringing resale price maintenance conduct. It also presents the basis of an algorithm for detecting that conduct.
Influence of Warfarin Therapy on Prothrombin Production and Its Posttranslational Modifications
Authors: Kondo Akira , Kondo Hirokazu , Nakagawa Yoshihisa , Ito Hiroyuki , Shimomura Daiki , Hatanaka Noriko , Yamamoto Yoshikazu , Nakatani Misato , Iwai-Kanai Eri , Matsuo Shuji 
Published: April 2020

AbstractBackgroundProtein induced by vitamin K absence-II (PIVKA-II) is produced by the liver during hepatoma and upon warfarin administration. Those patients have disturbed protein synthesis and glycosylation in the liver. This decreases the number of γ-carboxyglutamyl (Gla) residues on prothrombin, converting prothrombin into PIVKA-II. The mechanism of this conversion, however, is not clearly understood.MethodsProthrombin was isolated from healthy and warfarin-treated individuals whose liver function of protein production was quantitatively normal. Glycan structures in the purified prothrombin containing PIVKA-II were qualitatively analyzed by high performance liquid chromatography after labeling the glycan with fluorophore 2-aminobenzamide.ResultsThe concentration of PIVKA-II was significantly higher in the warfarin-treated individuals than in the healthy individuals (P&lt; 0.001). Although protein production in the liver was normal in both groups, the concentration of prothrombin was lower in the warfarin-treated individuals than in the healthy individuals (P &lt; 0.001). The main glycan was A2 in the healthy and warfarin-treated individuals (86.6 ± 4.4% and 85.6 ± 3.4%, respectively). Eight types of glycan were characterized in both groups, although generation of PIVKA-II in the warfarin-treated individuals did not lead to variation in glycosylation of prothrombin.ConclusionsWarfarin therapy leads to lower amounts of prothrombin and Gla residues within prothrombin without exerting qualitative and quantitative change in glycan profile and protein synthetic function in the liver.
Evaluation of the sensitivity of pulmonary arterial pressure to elevation using a reaction norm model in Angus Cattle
Authors: Speidel Scott E , Thomas Milton G , Holt Timothy N , Enns R Mark 
Published: April 2020

Abstract
Pulmonary arterial pressure (PAP) is a diagnostic measure used to determine an individual’s susceptibility to developing high-altitude disease. The importance of PAP measures collected at elevations lower than the intended breeding elevation of the bulls (i.e., ≥1,520 m) is unknown. Therefore, the objective of this study was to determine the genetic relationship between PAP measures collected in a range of elevations using reaction norm models. A total of 9,177 PAP and elevation observations on purebred Angus cattle, which averaged 43.49 ± 11.32 mmHg and 1,878.6 ± 296.8 m, respectively, were used in the evaluation. The average age of the individuals in the evaluation was 434.04 ± 115.9 d. A random regression model containing the effects of sex, a linear covariate of age, a quadratic fixed covariate of elevation, and random effects consisting of a contemporary group and a linear regression of PAP on elevation was used for the evaluation of PAP. Two forms of PAP were evaluated with this model. First, to address the non-normality of the data, PAP was raised to the power of −2.6 (ptPAP) based on the results of a Box–Cox analysis. Second, raw PAP (rPAP) phenotypes were evaluated to compare the results to those obtained from the transformed data. For ptPAP, heritability ranged from 0.25 to 0.37 corresponding to elevations of 1,900 and 1,215 m, respectively. For rPAP, heritability ranged from 0.22 to 0.41 corresponding to elevations of 1,700 and 2,495 m, respectively. Generally, lower elevations corresponded to decreased heritabilities while higher elevations corresponded to increased heritability estimates. For ptPAP, genetic correlations ranged from 0.18 (elevation: 1,215 and 2,495 m) to 1.00. For rPAP, genetic correlations ranged from 0.08 (elevation: 1,215 and 2,495 m) to 1.00. In general, the closer the elevations in which PAP was measured, the greater the genetic relationship. The greater the difference in elevation between PAP measures resulted in lower genetic correlations. The rank correlation between expected progeny differences (EPD) for 1,215 and 2,495 m was 0.65 and 0.49 for the ptPAP and rPAP, respectively. These results suggested that PAP measures collected in lower elevations may be used as an indicator of high-altitude adaptability. In the estimation of EPD to rank sires for their suitability for use in high-elevation production systems, it is important to account for the relationships among varied altitudes.