bluuebunny/crossref_metadata_2025_split huggingface dataset:
KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping
Authors: Alsamman Alsamman M , Ibrahim Shafik D , Hamwieh Aladdin 
Published: January 2019

Abstract

Motivation
Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool.

Results
To convert classical QTL markers into KASP assay primers, KASPspoon simulates a PCR by running an approximate-match searching analysis on user-entered primer pairs against the provided sequences, and then comparing in vitro and in silico PCR results. KASPspoon reports amplimers close to or adjoining genes/SNPs/simple sequence repeats and those that are shared between in vitro and in silico PCR results to select the most appropriate amplimers for gene discovery. KASPspoon compares physical and genetic maps, and reports the primer set genome coverage for PCR-walking. KASPspoon could be used to design KASP assay primers to convert QTL acquired by classical molecular markers into high-throughput genotyping assays and to provide major SNP resource for the dissection of genotypic and phenotypic variation. In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in vitro results.

Availability and implementation
Code available under GNU GPL at (http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon).

Supplementary information
Supplementary data are available at Bioinformatics online.
Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints
Authors: Ferrari Allan J R , Gozzo Fabio C , Martínez Leandro 
Published: January 2019

Abstract

Motivation
Chemical cross-linking/mass spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms.

Results
A force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. First, the strategy suggests that XL constraints should be set to shorter distances than usually assumed. Second, the complete statistical force-field improves the models obtained and can be easily incorporated into current modeling methods and software. The force-field was implemented and is distributed to be used within the Rosetta ab initio relax protocol.

Availability and implementation
Force-field parameters and usage instructions are freely available online (http://m3g.iqm.unicamp.br/topolink/xlff).

Supplementary information
Supplementary data are available at Bioinformatics online.
Late-career Physicians Prescribe Longer Courses of Antibiotics
Authors: Fernandez-Lazaro Cesar I , Brown Kevin A , Langford Bradley J , Daneman Nick , Garber Gary , Schwartz Kevin L 
Published: January 2019

Abstract

Background
Antibiotic duration is often longer than necessary. Understanding the reasons for variability in antibiotic duration can inform interventions to reduce prolonged antibiotic use. We aim to describe patterns of interphysician variability in prescribed antibiotic treatment durations and determine physician predictors of prolonged antibiotic duration in the community setting.

Methods
We performed a retrospective cohort analysis of family physicians in Ontario, Canada, between 1 March 2016 and 28 February 2017, using the Xponent dataset from IQVIA. The primary outcome was proportion of prolonged antibiotic course prescribed, defined as >8 days of therapy. We used multivariable logistic regression models, with generalized estimating equations to account for physician-level clustering to evaluate predictors of prolonged antibiotic courses.

Results
There were 10 616 family physicians included in the study, prescribing 5.6 million antibiotic courses. There was substantial interphysician variability in the proportion of prolonged antibiotic courses (median, 33.3%; interdecile range, 13.5%–60.3%). In the multivariable regression model, later physician career stage, rural location, and a larger pediatric practice were significantly associated with greater use of prolonged courses. Prolonged courses were more likely to be prescribed by late-career physicians (adjusted odds ratio [aOR], 1.48; 95% confidence interval, 1.38–1.58) and mid-career physicians (aOR, 1.25; 1.16–1.34) when compared to early-career physicians.

Conclusions
We observed substantial variability in prescribed antibiotic duration across family physicians, with durations particularly long among late-career physicians. These findings highlight opportunities for community antimicrobial stewardship interventions to improve antibiotic use by addressing practice differences in later-career physicians.
Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia
Authors: Ingle Danielle J , Easton Marion , Valcanis Mary , Seemann Torsten , Kwong Jason C , Stephens Nicola , Carter Glen P , Gonçalves da Silva Anders , Adamopoulos James , Baines Sarah L , Holt Kathryn E , Chow Eric P F , Fairley Christopher K , Chen Marcus Y , Kirk Martyn D , Howden Benjamin P , Williamson Deborah A 
Published: January 2019

AbstractBackgroundIn urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages.MethodsA population-level study of all cultured Shigella isolates in the state of Victoria, Australia, was undertaken from 1 January 2016 through 31 March 2018. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 545 Shigella isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Risk factor data on travel and sexual exposure were collected through enhanced surveillance forms or by interviews.ResultsRates of antimicrobial resistance were high, with 17.6% (95/541) and 50.6% (274/541) resistance to ciprofloxacin and azithromycin, respectively. There were strong associations between antimicrobial resistance, phylogeny, and epidemiology. Specifically, 2 major MSM-associated lineages were identified: a Shigellasonnei lineage (n = 159) and a Shigella flexneri 2a lineage (n = 105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harbored mutations associated with reduced susceptibility to recommended oral antimicrobials: namely, azithromycin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Long-read sequencing demonstrated global dissemination of multidrug-resistant plasmids across Shigella species and lineages, but predominantly associated with MSM isolates.ConclusionsOur contemporary data highlight the ongoing public health threat posed by resistant Shigella, both in Australia and globally. Urgent multidisciplinary public health measures are required to interrupt transmission and prevent infection.
The Effects of Hepatitis C Treatment Eligibility Criteria on All-cause Mortality Among People With Human Immunodeficiency Virus
Authors: Breskin Alexander , Westreich Daniel , Hurt Christopher B , Cole Stephen R , Hudgens Michael G , Seaberg Eric C , Thio Chloe L , Tien Phyllis C , Adimora Adaora A 
Published: January 2019

Abstract

Background
The cost of direct-acting antivirals (DAAs) for hepatitis C virus (HCV) prompted many payers to restrict treatment to patients who met non–evidence-based criteria. These restrictions have implications for survival of people with HCV, especially for people with human immunodeficiency virus (HIV)/HCV coinfection who are at high risk for liver disease progression. The goal of this work was to estimate the effects of DAA access policies on 10-year all-cause mortality among people with HIV.

Methods
The study population included 3056 adults with HIV in the Women’s Interagency HIV Study and Multicenter AIDS Cohort Study from 1 October 1994 through 30 September 2015. We used the parametric g-formula to estimate 10-year all-cause mortality under DAA access policies that included treating (i) all people with HCV; (ii) only people with suppressed HIV; (iii) only people with severe fibrosis; and (iv) only people with HIV suppression and severe fibrosis.

Results
The 10-year risk difference of treating all coinfected persons with DAAs compared with no treatment was –3.7% (95% confidence interval [CI], –9.1% to .6%). Treating only those with suppressed HIV and severe fibrosis yielded a risk difference of –1.1% (95% CI, –2.8% to .6%), with 51% (95% CI, 38%–59%) of coinfected persons receiving DAAs. Treating a random selection of 51% of coinfected persons at baseline decreased the risk by 1.9% (95% CI, –4.7% to .3%).

Conclusions
Restrictive DAA access policies may decrease survival compared to treating similar proportions of people with HIV/HCV coinfection with DAAs at random. These findings suggest that lives could be saved by thoughtfully revising access policies.
A comparison of pump-controlled retrograde trial off to arterio-venous bridging for weaning from venoarterial extracorporeal membrane oxygenation†
Authors: Pandya Nischal R , Daley Michael , Mattke Adrian , Shikata Fumiaki , Betts Kim , Haisz Emma , Black Anthony , Anderson Benjamin , Alphonso Nelson , Venugopal Prem 
Published: January 2019

Abstract

OBJECTIVES
The aim of the study is to compare a technique of pump-controlled retrograde trial off (PCRTO) to insertion of an arterio-venous (AV) bridge to conduct a trial from venoarterial extracorporeal membrane oxygenation (VA ECMO).

METHODS
We studied all patients who were weaned from VA ECMO using either PCRTO or AV bridging from November 2014 to April 2018. Demographic data, indications for ECMO, duration of ECMO, duration of trial period off ECMO and survival were compared between the 2 groups.

RESULTS
Seventy-nine patients were placed on VA ECMO from November 2014 to April 2018, of whom, 51 (65%) patients met the study inclusion criteria: 31 (61%) patients who had a trial period from VA ECMO using PCRTO and 20 (39%) patients who were weaned using an AV bridge. The indications for ECMO included cardiac (n = 16 and 11, respectively) and non-cardiac aetiologies (n = 15 and 9, respectively). There was 1 death in each group. The duration of the trial off VA ECMO was significantly shorter in the PCRTO group (median = 88.0 vs 196.6 min, P < 0.001). There were 2 conversions from PCRTO to AV bridging during the trial period off ECMO (2.9-kg neonate following a Norwood procedure and 2.2-kg patient following repair of ectopia cordis).

CONCLUSIONS
PCRTO is a safe, simple and reproducible approach for enabling a trial period while preserving the circuit during weaning from VA ECMO. In our study, the duration of the trial period off VA ECMO was significantly shorter in the PCRTO group. PCRTO avoids manipulation of the ECMO circuit, provides a ‘stress test’ to evaluate cardiorespiratory reserve during the trial period off ECMO, is applicable for a wide variety of cardiac and non-cardiac indications and facilitates multiple attempts at weaning from ECMO.
Risk of death without appropriate defibrillator shock in patients with advanced renal dysfunction
Authors: Goldenberg Ido , Mor Tal , Nof Eyal , Younis Arwa , Berkovitch Anat , Rosso Raphael , Barsheshet Alon , Suleiman Mahmoud , Beinart Roy 
Published: January 2019

Abstract

Aims
Heart failure patients with advanced chronic kidney disease (CKD) may experience an increased rate of non-arrhythmic mortality due to associated comorbidities. We aimed to evaluate the risk of mortality without appropriate implantable cardioverter-defibrillator (ICD) shocks in this high-risk population.

Methods and results
The study population comprised 3542 patients who received an ICD, were enrolled, and prospectively followed-up in the Israeli ICD registry. Study patients were categorized into two groups: those with advanced CKD [defined by a glomerular filtration rate of <30 mL/min/1.73 m2 or being on dialysis at time of implantation (n = 197)], and those without advanced CKD (n = 3344). The primary endpoint was the risk of death without receiving appropriate ICD shock. Kaplan–Meier survival analysis showed that at 5 years of follow-up the rates of death without prior ICD shock were significantly higher in the advanced kidney disease group (46%) compared with the non-advanced CKD group (19%; log-rank P-value <0.001). Consistently, multivariate analysis showed that the risk of death without receiving appropriate ICD shock therapy at 5 years was 2.5-fold (P < 0.001) higher among advanced CKD patients. In contrast, the rate of appropriate ICD shock therapy at 5 years among advanced CKD patients was only 9%, with a very high mortality rate (63%) within 3.5 years subsequent to shock therapy.

Conclusion
Nearly one-half of ICD with advanced CKD die within 5 years without receiving an appropriate ICD shock. These findings stress the importance of appropriate patient selection for primary ICD implantation in this high-risk population.
Extensive Serological Survey of Multiple African Nonhuman Primate Species Reveals Low Prevalence of Immunoglobulin G Antibodies to 4 Ebola Virus Species
Authors: Ayouba Ahidjo , Ahuka-Mundeke Steve , Butel Christelle , Mbala Kingebeni Placide , Loul Severin , Tagg Nikki , Villabona-Arenas Christian-Julian , Lacroix Audrey , Ndimbo-Kumugo Simon-Pierre , Keita Alpha K , Toure Abdoulaye , Couacy-Hymann Emmanuel , Calvignac-Spencer Sebastien , Leendertz Fabian H , Formenty Pierre , Delaporte Eric , Muyembe-Tamfum Jean-Jacques , Mpoudi Ngole Eitel , Peeters Martine 
Published: January 2019

Abstract
Bats are considered a reservoir species for Ebola viruses, but nonhuman primates (NHPs) have represented a source of infection in several outbreaks in humans. Here we report serological screening of blood or fecal samples from monkeys (n = 2322) and apes (n = 2327). Thirty-six NHP species from Cameroon, Democratic Republic of the Congo, and Ivory Coast were tested with a sensitive and specific Luminex-based assay for immunoglobulin G antibodies to 4 Ebola virus species. Using the simultaneous presence of antibodies to nucleoproteins and glycoproteins to define positivity, we showed that specific Ebola virus antibodies are not widespread among NHPs. Only 1 mustached monkey (Cercopithecus cephus) from Cameroon was positive for Sudan ebolavirus. These observations support that NHPs are most likely intermediate hosts for Ebola viruses. With the increasing frequency of Ebola outbreaks, it is crucial to identify the animal reservoir and understand the ecology of Ebola viruses to inform disease control.
WALLABY Early Science – II. The NGC 7232 galaxy group
Authors: Lee-Waddell K , Koribalski B S , Westmeier T , Elagali A , For B-Q , Kleiner D , Madrid J P , Popping A , Reynolds T N , Rhee J , Serra P , Shao L , Staveley-Smith L , Wang J , Whiting M T , Wong O I , Allison J R , Bhandari S , Collier J D , Heald G , Marvil J , Ord S M 
Published: January 2019

Abstract
We report on neutral hydrogen (H i) observations of the NGC 7232 group with the Australian Square Kilometre Array Pathfinder (ASKAP). These observations were conducted as part of the Wide-field ASKAP L-Band Legacy All-sky Blind surveY (WALLABY) Early Science program with an array of 12 ASKAP antennas equipped with Phased Array Feeds, which were used to form 36 beams to map a field of view of 30 deg2. Analysing a subregion of the central beams, we detect 17 H i sources. Eleven of these detections are identified as galaxies and have stellar counterparts, of which five are newly resolved H i galaxy sources. The other six detections appear to be tidal debris in the form of H i clouds that are associated with the central triplet, NGC 7232/3, comprising the spiral galaxies NGC 7232, NGC 7232B, and NGC 7233. One of these H i clouds has a mass of MH i ∼ 3 × 108 M⊙ and could be the progenitor of a long-lived tidal dwarf galaxy. The remaining H i clouds are likely transient tidal knots that are possibly part of a diffuse tidal bridge between NGC 7232/3 and another group member, the lenticular galaxy IC 5181.
The morpho-kinematics of the circumstellar envelope around the AGB star EP Aqr
Authors: Hoai D T , Nhung P T , Tuan-Anh P , Darriulat P , Diep P N , Le Bertre T , Phuong N T , Thai T T , Winters J M 
Published: January 2019

ABSTRACT
ALMA observations of CO(1–0) and CO(2–1) emissions of the circumstellar envelope of EP Aqr, an oxygen-rich asymptotic giant branch star, are reported. A thorough analysis of their properties is presented using an original method based on the separation of the data cube into a low-velocity component associated with an equatorial outflow and a faster component associated with a bipolar outflow. A number of important and new results are obtained concerning the distribution in space of the effective emissivity, the temperature, the density, and the flux of matter. A mass-loss rate of (1.6 ± 0.4)×10−7 solar masses per year is measured. The main parameters defining the morphology and kinematics of the envelope are evaluated and uncertainties inherent to de-projection are critically discussed. Detailed properties of the equatorial region of the envelope are presented including a measurement of the line width and a precise description of the observed inhomogeneity of both morphology and kinematics. In particular, in addition to the presence of a previously observed spiral enhancement of the morphology at very small Doppler velocities, a similarly significant but uncorrelated circular enhancement of the expansion velocity is revealed, both close to the limit of sensitivity. The results of the analysis place significant constraints on the parameters of models proposing descriptions of the mass-loss mechanism, but cannot choose among them with confidence.
Exchange Arrangements Entering the Twenty-First Century: Which Anchor will Hold?*
Authors: Ilzetzki Ethan , Reinhart Carmen M , Rogoff Kenneth S 
Published: January 2019

Abstract
This article provides a comprehensive history of anchor or reference currencies, exchange rate arrangements, and a new measure of foreign exchange restrictions for 194 countries and territories over 1946–2016. We find that the often cited post–Bretton Woods transition from fixed to flexible arrangements is overstated; regimes with limited flexibility remain in the majority. Even if central bankers’ communications jargon has evolved considerably in recent decades, it is apparent that many still place a large implicit weight on the exchange rate. The U.S. dollar scores as the world's dominant anchor currency by a very large margin. By some metrics, its use is far wider today than 70 years ago. In contrast, the global role of the euro appears to have stalled. We argue that in addition to the usual safe assets story, the record accumulation of reserves since 2002 may also have to do with many countries’ desire to stabilize exchange rates in an environment of markedly reduced exchange rate restrictions or, more broadly, capital controls: an important amendment to the conventional portrayal of the macroeconomic trilemma.
Use of population data for assessing trends in work-related asthma mortality
Authors: Mazurek Jacek M. , Henneberger Paul K. 
Published: January 2019

Purpose of review
Work-related asthma has been associated with poorer asthma control and frequent unscheduled healthcare visits, and can be fatal. Case reports of work-related asthma deaths are rare, but can initiate efforts to prevent additional cases. We reviewed relevant literature and data sources to evaluate whether analyzing mortality data at the population level can help identify potential sources of exposures that contribute to work-related asthma.

Recent findings
A limited number of population-based studies have addressed work-related asthma mortality. Data on asthma mortality are derived from death certificates using the International Classification of Diseases (ICD) as a standard for coding cause. However, no discrete code for work-related asthma is available. Analysis of asthma mortality relative to industries and occupations appears to identify high-risk jobs that were not identified by analyzing asthma morbidity data.

Summary
Beyond recognized work-related asthma deaths, it is possible that occupational exposures have contributed to other asthma deaths that have gone unnoticed and could potentially be identified by the analysis of mortality data at the population level. Such analyses in the United States appear to assist in recognizing high-risk occupations and industries. Additional analyses would be possible if a work-related asthma ICD code were available.
The impact of exercise on asthma
Authors: Lang Jason E. 
Published: January 2019

Purpose of review
Asthma is one of the most common chronic diseases in children and adults in developed countries around the world. Despite international treatment guidelines, poor asthma control remains a frequent problem leading to missed school and work, and emergency room visits and hospitalizations. Many patients with asthma report exercise as a trigger for their asthma, which likely leads to exercise avoidance as a means to control symptoms. Evolving research has suggested that routine exercise may actually help improve some aspects of asthma control. This review discusses the recent research addressing how routine exercise affects important asthma-related outcomes including symptoms, lung function and quality of life.

Recent findings
Several systematic reviews and meta-analyses have been conducted in recent years, which strongly support the safety of routine exercise in children and adults with asthma. Exercise appears to favor improvements in aerobic fitness, asthma symptoms and quality of life, but results so far are less consistent in demonstrating improvements to lung function and airway hyperresponsiveness.

Summary
In addition to routine management guidelines, clinicians should recommend for their patients with asthma routine exercise for its general health benefits and likely improvement in asthma symptoms and quality of life.