bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soret and Dufour features in peristaltic motion of chemically reactive fluid in a tapered asymmetric channel in the presence of Hall current
Authors: Khan Nargis , Riaz Muhammad , Hashmi Muhammad Sadiq , Khan Sami Ullah , Tlili Iskander , Ijaz Khan M , Nazeer Mubbashar 
Published: August 2020

AbstractThe present work examines heat and mass transfer characteristics of peristaltic motion of Johnson-Segalman fluid in a tapered asymmetric channel along with chemical reaction, by taking into account the Soret and Dufour effects. Effects of Hall current have also been discussed in mathematical modeling and analysis. Following the peristaltic wave procedure, the tapered asymmetric channel is based on the non uniform boundaries having diverse phases and amplitudes. The channel walls show excellent agreement with more realistic convective conditions. The modeled flow problem is directed into ordinary differential equations set with proper utilization of similarity quantities. The estimation of high wavelength as well as small Reynolds number are acknowledged to deduce the equations of Johnson-Segalman liquid model. The adopted solution procedure is constructed via homotopic algorithm. The results have been analyzed for various parameters of interest and sketched for better understanding. The velocity profile reveals decreasing behavior for increasing values of Weissenberg number and Hartman number while converse behavior is found for mean flow rate and Hall parameter. The temperature profile falloffs for heat transfer Biot number and Hartman number whereas it increases for Prandtl number, Brinkman number, Dufour number and Hall parameter. The concentration profile tends to decrease for mass transfer Biot number and increase for Schmidt constant.
Epithelioid Sarcoma of the Peripheral Nerve: Clinicopathologic Series of Three Cases and Literature Review
Authors: Diaz-Perez Julio A , Spasic Smiljana , Velez-Torres Jaylou M , McCarthy Edward F , Rosenberg Andrew E 
Published: August 2020

Abstract

Objectives
Epithelioid sarcoma (ES) rarely arises in the nerve. To increase our understanding of this unusual tumor originating in the nerve, we describe the features of three cases and review the literature.

Methods
Clinical data, imaging, pathology, treatment, and follow-up are detailed. A systematic literature review was conducted.

Results
Two patients were male and one female; the median age was 24 years. The patients had neurologic symptoms, and the tumors arose in large nerves and ranged from 2.4 to 5.8 cm. The tumors were avid on positron emission tomography–computed tomography and showed increased signal intensity on T2-weighted magnetic resonance imaging. Centered in the nerve, the tumors grew with an infiltrative pattern and encased the nerve fascicles. All were treated with wide resection, and adjuvant treatment included combinations of chemotherapy and radiation. One recurred, and the limb was amputated. Metastases were documented to lymph nodes, lung, pleura, and skin. One patient died of disease after 54 months. Literature review including our cases showed that tumors stained with pancytokeratin (9/9), EMA (4/4), and CD34 (7/7); there was loss of INI1 in all six cases tested.

Conclusions
ES rarely arises in the peripheral nerve, and its infiltrative nature often requires morbid surgery. The differential includes a variety of benign and malignant epithelioid neoplasms.
Sine-skewed toroidal distributions and their application in protein bioinformatics
Authors: Ameijeiras-Alonso Jose , Ley Christophe 
Published: August 2020

SummaryIn the bioinformatics field, there has been a growing interest in modeling dihedral angles of amino acids by viewing them as data on the torus. This has motivated, over the past years, new proposals of distributions on the torus. The main drawback of most of these models is that the related densities are (pointwise) symmetric, despite the fact that the data usually present asymmetric patterns. This motivates the need to find a new way of constructing asymmetric toroidal distributions starting from a symmetric distribution. We tackle this problem in this article by introducing the sine-skewed toroidal distributions. The general properties of the new models are derived. Based on the initial symmetric model, explicit expressions for the shape and dependence measures are obtained, a simple algorithm for generating random numbers is provided, and asymptotic results for the maximum likelihood estimators are established. An important feature of our construction is that no extra normalizing constant needs to be calculated, leading to more flexible distributions without increasing the complexity of the models. The benefit of employing these new sine-skewed toroidal distributions is shown on the basis of protein data, where, in general, the new models outperform their symmetric antecedents.
Re-empowering into voice: experiments in organic community co-production
Authors: Green Roger , Baker Chris 
Published: August 2020

AbstractThis article explores and extrapolates an emerging concept within community practice: namely that of organic community co-production. The concept is influenced by previous uses of the term ‘organic’, specifically as applied by Tönnies in relation to certain types of community, and Gramsci in respect of a concept of leadership. Our development of the term has been generated within the context of reflective practitioner experience, located in a community-led action campaign Voice4Deptford, in South East London. The case study explores the interdisciplinary roots of this form of co-production. It highlights the way that these pre-existing principles and methods have been adapted, reflected upon and improvised in the light of 30 years’ grassroots engagement by Green to evolve a bespoke approach that we are proposing to call ‘organic community coproduction’.The case study outlines several original dimensions or modalities of community organic co-production including; stepping aside; the academic as a non-expert and giving voice. It unpacks the different elements of impact and transformation, that are consequent upon organic community co-production. These include; evidence of change; working together and community reflective time. The article concludes with a discussion of the issues involved in reframing of local power, the campaigns early successes and its continuing challenges.
Postprescription Review With Threat of Infectious Disease Consultation and Sustained Reduction in Meropenem Use Over Four Years
Authors: Mani Nandita S , Lan Kristine F , Jain Rupali , Bryson-Cahn Chloe , Lynch John B , Krantz Elizabeth M , Bryan Andrew , Liu Catherine , Chan Jeannie D , Pottinger Paul S , Kim H Nina 
Published: August 2020

Abstract

Background
Following a meropenem shortage, we implemented a postprescription review with feedback (PPRF) in November 2015 with mandatory infectious disease (ID) consultation for all meropenem and imipenem courses &gt; 72 hours. Providers were made aware of the policy via an electronic alert at the time of ordering.

Methods
A retrospective study was conducted at the University of Washington Medical Center (UWMC) and Harborview Medical Center (HMC) to evaluate the impact of the policy on antimicrobial consumption and clinical outcomes pre- and postintervention during a 6-year period. Antimicrobial use was tracked using days of therapy (DOT) per 1000 patient-days, and data were analyzed by an interrupted time series.

Results
There were 4066 and 2552 patients in the pre- and postintervention periods, respectively. Meropenem and imipenem use remained steady until the intervention, when a marked reduction in DOT/1000 patient-days occurred at both hospitals (UWMC: percentage change −72.1% (95% confidence interval [CI] −76.6, −66.9), P &lt; .001; HMC: percentage change −43.6% (95% CI −59.9, −20.7), P = .001). Notably, although the intervention did not address antibiotic use until 72 hours after initiation, there was a significant decline in meropenem and imipenem initiation (“first starts”) in the postintervention period, with a 64.9% reduction (95% CI 58.7, 70.2; P &lt; .001) at UWMC and 44.7% reduction (95% CI 28.1, 57.4; P &lt; .001) at HMC.

Conclusions
PPRF and mandatory ID consultation for meropenem and imipenem use beyond 72 hours resulted in a significant and sustained reduction in the use of these antibiotics and notably impacted their up-front usage.
Household Transmission of Carbapenemase-producing Enterobacterales in Ontario, Canada
Authors: Jamal Alainna J , Faheem Amna , Farooqi Lubna , Zhong Xi Zoe , Armstrong Irene , Boyd David A , Borgundvaag Emily , Coleman Brenda L , Green Karen , Jayasinghe Kithsiri , Johnstone Jennie , Katz Kevin , Kohler Philipp , Li Angel X , Mataseje Laura , Melano Roberto , Muller Matthew P , Mulvey Michael R , Nayani Sarah , Patel Samir N , Paterson Aimee , Poutanen Susan , Rebbapragada Anu , Richardson David , Sarabia Alicia , Shafinaz Shumona , Simor Andrew E , Willey Barbara M , Wisely Laura , McGeer Allison J 
Published: August 2020

Abstract

Background
Data on household transmission of carbapenemase-producing Enterobacterales (CPE) remain limited. We studied risk of CPE household co-colonization and transmission in Ontario, Canada.

Methods
We enrolled CPE index cases (identified via population-based surveillance from January 2015 to October 2018) and their household contacts. At months 0, 3, 6, 9, and 12, participants provided rectal and groin swabs. Swabs were cultured for CPE until September 2017, when direct polymerase chain reaction (PCR; with culture of specimens if a carbapenemase gene was detected) replaced culture. CPE risk factor data were collected by interview and combined with isolate whole-genome sequencing to determine likelihood of household transmission. Risk factors for household contact colonization were explored using a multivariable logistic regression model with generalized estimating equations.

Results
Ninety-five households with 177 household contacts participated. Sixteen (9%) household contacts in 16 (17%) households were CPE-colonized. Household transmission was confirmed in 3/177 (2%) cases, probable in 2/177 (1%), possible in 9/177 (5%), and unlikely in 2/177 (1%). Household contacts were more likely to be colonized if they were the index case’s spouse (odds ratio [OR], 6.17; 95% confidence interval [CI], 1.05–36.35), if their index case remained CPE-colonized at household enrollment (OR, 7.00; 95% CI, 1.92–25.49), or if they had at least 1 set of specimens processed after direct PCR was introduced (OR, 6.46; 95% CI, 1.52–27.40).

Conclusions
Nine percent of household contacts were CPE-colonized; 3% were a result of household transmission. Hospitals may consider admission screening for patients known to have CPE-colonized household contacts.
Fatty Liver Disease in a Prospective North American Cohort of Adults With Human Immunodeficiency Virus and Hepatitis B Virus Coinfection
Authors: Khalili Mandana , King Wendy C , Kleiner David E , Jain Mamta K , Chung Raymond T , Sulkowski Mark , Lisker-Melman Mauricio , Wong David K , Ghany Marc , Sanyal Arun , Sterling Richard K 
Published: August 2020

Abstract

Background
Hepatitis B virus (HBV) and fatty liver disease (FLD) are common in human immunodeficiency virus (HIV). Correlates of FLD and its relationship with alanine aminotransferase (ALT) were examined longitudinally in HIV-HBV coinfection.

Methods
From 28/4/2014–7/11/2018, 114 HIV-HBV adults had liver biopsy and were followed for a median of 3 years (ancillary study of Hepatitis B Research Network). Steatohepatitis was based on presence of steatosis, ballooning, and perisinusoidal fibrosis. FLD was defined as ≥5% steatosis and/or steatohepatitis.

Results
Median age was 49 years, 93% were male, 51% black, 93% had HIV RNA &lt;400 copies/mL and 83% HBV DNA &lt;1000 IU/mL. Thirty percent had FLD (20% steatosis, 10% steatohepatitis). Those with FLD had higher median triglyceride (171 vs 100 mg/dL, P &lt; .01) and small, dense LDL (44 vs 29 mg/dL, P &lt; .01) and lower HDL-2-C (9 vs 12 mg/dL, P = .001). After adjusting for age, sex, and alcohol use, white and other versus black race (ORs, 8.49 and 16.54, respectively), ALT (OR, 3.13/doubling), hypertension (OR, 10.93), hyperlipidemia (OR, 4.36), and diabetes family history (OR, 5.38) were associated with having FLD (all P &lt; .05). Steatohepatitis or steatosis alone (vs none) was associated with higher ALT over time (1.93 and 1.34 times higher, respectively; P &lt; .001), with adjustment for age, sex, and HBV DNA.

Conclusions
About 30% with HIV-HBV coinfection had FLD including 10% with steatohepatitis. FLD was associated with non-black race, metabolic risks, an atherogenic lipid profile, and elevated ALT over time. Thus, identification of FLD and management of adverse metabolic profiles are critically important in HIV-HBV coinfection.
Clinical Trial Registration. NCT 01924455.
ANMCO POSITION PAPER: Considerations on in-hospital cardiological consultations and cardiology outpatient clinics during the COVID-19 pandemic
Authors: Valente Serafina , Colivicchi Furio , Caldarola Pasquale , Murrone Adriano , Di Lenarda Andrea , Roncon Loris , Amodeo Enzo , Aspromonte Nadia , Cipriani Manlio Gianni , Domenicucci Stefano , Francese Giuseppina Maura , Imazio Massimo , Scotto di Uccio Fortunato , Urbinati Stefano , Gulizia Michele Massimo , Gabrielli Domenico 
Published: August 2020

Abstract
Infections by SARS CoV2 - COVID-19 have become in a short time a worldwide health emergency. Due to cardiovascular implications of COVID-19 and to very frequent previous cardiovascular disorders of COVID-19 patients, it is presently crucial that Cardiologists are fully aware of COVID-19 related epidemiological, pathophysiological and therapeutic problems, in order to manage at best the present emergency by appropriate protocols developed on the basis of the competences acquired and shared on the field. The aim of this document is to propose algorithms for the management of cardiovascular diseases during COVID-19 emergency with the objective of providing patients with optimal care, minimizing contagion risk and appropriately managing personal protective equipment.
ANMCO POSITION PAPER: The cardiological clinical activities in the transition phase of the COVID-19 pandemic
Authors: Valente Serafina , Colivicchi Furio , Francese Maura Giuseppina , Di Lenarda Andrea , Roncon Loris , Murrone Adriano , Caldarola Pasquale , Bilato Claudio , Amodeo Enzo , Aspromonte Nadia , Cipriani Manlio , Domenicucci Stefano , Imazio Massimo , Scotto di Uccio Fortunato , Urbinati Stefano , Gulizia Michele Massimo , Gabrielli Domenico 
Published: August 2020

Abstract
Infections by SARS CoV2 - COVID-19 became in a short time a worldwide health emergency. The present SARS-CoV-2 pandemic induced in a short time, an unprecedented impact on public health and on the pre-existing care pathways. In order to appropriately address this epidemiological emergency, urgent solutions were needed, such as remodelling or stopping hospitalization and deferrable clinical activities to avoid spreading the SARS-CoV-2 infection. After the first emergency lockdown phase, care pathways must guarantee healthcare to patients and preserve the safety of the healthcare personnel and of all the other subjects that refer to the cardiological surgeries. Rigorous prescriptive appropriateness of the requested exams with consequent reduction of unnecessary examinations is an essential requirement to preserve prioritized diagnostic and care pathways to patients in need, minimizing the risks connected to the SARS-CoV-2 contagion in hospitals. Telemedicine services represent a valid answer to cardiovascular disease patients’ need for care and assistance, including those in quarantine and voluntary isolation. These services successfully contribute to fight the spread of the virus guaranteeing at the same time therapy and support through remote services that must therefore be considered a resource to be implemented and enhanced. This document has to be used by the healthcare personnel working in hospitals and in district offices, if applicable, and aims at managing patients, in complete safety and considered not suspect/not probable (‘not at risk’) of SARS-CoV-2 infection, eligible for diagnostic activity and subsequent therapy in outpatient surgeries. In particular, this document provides indications for patient evaluation to prevent COVID-19 exposure, gives general indications on managing appointments and waiting rooms, on how to strictly adhere to environmental safety measures, on the proper use of Individual Protective Equipment (IPE). It also provides specific indications for outpatient service procedures, like electrocardiogram, cardiologic examination, cardiologic checkup, Dynamic Holter Electrocardiogram, Transthoracic Echocardiography, Echo Stress, Transoesophageal Echocardiography, Bike Ergometer stress test, Ergospirometry, Outpatient Checkup of implantable electronic cardiac devices.
Family medicine physicians’ report strong support, barriers and preferences for Registered Dietitian Nutritionist care in the primary care setting
Authors: Sastre Lauren R , Van Horn Leslie T 
Published: August 2020

Abstract

Background
Previous studies have examined barriers (e.g. time) for Family Medicine Providers (FMPs) to provide nutrition and lifestyle counseling, however, to date no studies have examined access or interest to Registered Dietitian Nutritionist (RDN) care for patients.

Objective
The objective of this study was to explore FMP access, referral practices, barriers and preferences for RDN care.

Methods
A cross-sectional online survey, with content and face validation was conducted with Family Medicine Departments within large academic health care systems in the Southeastern United States. The main variables of interest included: FMP access, interest, current referrals and referral preferences for RDN care, barriers to referrals and overall perceptions regarding RDN care. Descriptive analysis of close-ended responses was performed with SPSS 26.0. Open-ended responses were analysed using inductive content analysis.

Results
Over half of the respondents (n = 151) did not have an RDN on-site (64%) yet were highly interested in integrating an RDN (94.9%), with reported preferences for full-time on-site, part-time on-site or off-site RDN care (49.1%, 39.5% and 11.4% respectively). The greatest reported barriers to RDN referrals were perceived cost for the patient (64.47%) and uncertainty how to find a local RDN (48.6%). The most consistent theme reported in the open-ended responses were concerns regarding reimbursement, e.g. ‘Insurance does not cover all of the ways I would like to use an RDN’.

Conclusions
FMPs report interest and value in RDN services despite multiple perceived barriers accessing RDNs care. Opportunities exist for interprofessional collaboration between dietetic and FMP professional groups to address barriers.
ScanITD: Detecting internal tandem duplication with robust variant allele frequency estimation
Authors: Wang Ting-You , Yang Rendong 
Published: August 2020

Abstract

Background
Internal tandem duplications (ITDs) are tandem duplications within coding exons and are important prognostic markers and drug targets for acute myeloid leukemia (AML). Next-generation sequencing has enabled the discovery of ITD at single-nucleotide resolution. ITD allele frequency is used in the risk stratification of patients with AML; higher ITD allele frequency is associated with poorer clinical outcomes. However, the ITD allele frequency data are often unavailable to treating physicians and the detection of ITDs with accurate variant allele frequency (VAF) estimation remains challenging for short-read sequencing.

Results
Here we present the ScanITD approach, which performs a stepwise seed-and-realignment procedure for ITD detection with accurate VAF prediction. The evaluations on simulated and real data demonstrate that ScanITD outperforms 3 state-of-the-art ITD detectors, especially for VAF estimation. Importantly, ScanITD yields better accuracy than general-purpose structural variation callers for predicting ITD size range duplications.

Conclusions
ScanITD enables the accurate identification of ITDs with robust VAF estimation. ScanITD is written in Python and is open-source software that is freely accessible at https://github.com/ylab-hi/ScanITD.
Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)
Authors: Shao Feng , Ludwig Arne , Mao Yang , Liu Ni , Peng Zuogang 
Published: August 2020

Abstract

Background
The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it.

Results
The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated.

Conclusions
The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.