bluuebunny/crossref_metadata_2025_split huggingface dataset:
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
Authors: Hovhannisyan Hrant , Hafez Ahmed , Llorens Carlos , Gabaldón Toni 
Published: August 2019

Abstract

Motivation
Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library could significantly reduce experimental costs but requires careful planning and assessment of the impact of cross-mapping. Having these applications in mind we designed Crossmapper, the first to our knowledge tool able to assess cross-mapping prior to sequencing, therefore allowing optimization of experimental design.

Results
Using any combination of reference genomes, Crossmapper performs read simulation and back-mapping of those reads to the pool of references, quantifies and reports the cross-mapping rates for each organism. Crossmapper performs these analyses with numerous user-specified parameters, including, among others, read length, read layout, coverage, mapping parameters, genomic or transcriptomic data. Additionally, it outputs the results in highly interactive and publication-ready reports. This allows the user to perform multiple comparisons at once and choose the experimental setup minimizing cross-mapping rates. Moreover, Crossmapper can be used for resource optimization in sequencing facilities by pooling different samples into one sequencing library.

Availability and implementation
Crossmapper is a command line tool implemented in Python 3.6 and available as a conda package, allowing effortless installation. The source code, detailed information and a step-by-step tutorial is available at our GitHub page https://github.com/Gabaldonlab/crossmapper.

Supplementary information
Supplementary data are available at Bioinformatics online.
Impact of aortic stenosis on layer-specific longitudinal strain: relationship with symptoms and outcome
Authors: Ilardi Federica , Marchetta Stella , Martinez Christophe , Sprynger Muriel , Ancion Arnaud , Manganaro Roberta , Sugimoto Tadafumi , Tsugu Toshimitsu , Postolache Adriana , Piette Caroline , Cicenia Marianna , Esposito Giovanni , Galderisi Maurizo , Oury Cécile , Dulgheru Raluca , Lancellotti Patrizio 
Published: August 2019

Abstract

Aims
The present study sought to assess the impact of aortic stenosis (AS) on myocardial function as assessed by layer-specific longitudinal strain (LS) and its relationship with symptoms and outcome.

Methods and results
We compared 211 patients (56% males, mean age 73 ± 12 years) with severe AS and left ventricular ejection fraction (LVEF) ≥50% (114 symptomatic, 97 asymptomatic) with 50 controls matched for age and sex. LS was assessed from endocardium, mid-myocardium, and epicardium by 2D speckle-tracking echocardiography. Despite similar LVEF, multilayer strain values were significantly lower in symptomatic patients, compared to asymptomatic and controls [global LS: 17.9 ± 3.4 vs. 19.1 ± 3.1 vs. 20.7 ± 2.1%; endocardial LS: 20.1 ± 4.9 vs. 21.7 ± 4.2 vs. 23.4 ± 2.5%; epicardial LS: 15.8 ± 3.1 vs. 16.8 ± 2.8 vs. 18.3 ± 1.8%; P < 0.001 for all]. On multivariable logistic regression analysis, endocardial LS was independently associated to symptoms (P = 0.012), together with indexed left atrial volume (P = 0.006) and LV concentric remodelling (P = 0.044). During a mean follow-up of 22 months, 33 patients died of a cardiovascular event. On multivariable Cox-regression analysis, age (P = 0.029), brain natriuretic peptide values (P = 0.003), LV mass index (P = 0.0065), LV end-systolic volume (P = 0.012), and endocardial LS (P = 0.0057) emerged as independently associated with cardiovascular death. The best endocardial LS values associated with outcome was 20.6% (sensitivity 70%, specificity 52%, area under the curve = 0.626, P = 0.022). Endocardial LS (19.1 ± 3.3 vs. 20.7 ± 3.3, P = 0.02) but not epicardial LS (15.2 ± 2.8 vs. 15.9 ± 2.5, P = 0.104) also predicted the outcome in patients who were initially asymptomatic.

Conclusion
In patients with severe AS, LS impairment involves all myocardial layers and is more prominent in the advanced phases of the disease, when the symptoms occur. In this setting, the endocardial LS is independently associated with symptoms and patient outcome.
Routine preoperative aortic computed tomography angiography is associated with reduced risk of stroke in coronary artery bypass grafting: a propensity-matched analysis
Authors: Sandner Sigrid E , Nolz Richard , Loewe Christian , Gregorich Mariella , Heinze Georg , Andreas Martin , Kolh Philippe , Zimpfer Daniel , Laufer Guenther 
Published: August 2019

Abstract

OBJECTIVES
The aim of this study was to determine stroke rates in patients who did or did not undergo routine computed tomography angiography (CTA) aortic imaging before isolated coronary artery bypass grafting (CABG).

METHODS
We conducted a retrospective analysis of a prospectively maintained single-centre registry. Between 2009 and 2016, a total of 2320 consecutive patients who underwent isolated CABG at our institution were identified. Propensity score matching was used to create a paired cohort of patients with similar baseline characteristics who did (CTA cohort) or did not (non-CTA cohort) undergo preoperative aortic CTA. The primary end point of the analysis was in-hospital stroke.

RESULTS
In 435 propensity score-matched pairs, stroke occurred in 4 patients (0.92%) in the CTA cohort and in 14 patients (3.22%) in the non-CTA cohort (P = 0.017). Routine preoperative aortic CTA was associated with a significantly reduced risk of in-hospital stroke [relative risk 0.29, 95% confidence interval (CI) 0.09–0.86; P = 0.026; absolute risk reduction 2.3%, 95% CI 0.4–4.2; P = 0.017; number needed to treat = 44, 95% CI 24–242].

CONCLUSIONS
A preoperative screening for atheromatous aortic disease using CTA is associated with reduced risk of stroke after CABG. The routine use of preoperative aortic CTA could be applied so that surgical manipulation of the ascending aorta can be selectively reduced or avoided in patients with atheromatous aortic disease.
Atrial fibrillation diagnosed after stroke and dementia risk: cohort study of first-ever ischaemic stroke patients aged 65 or older
Authors: Krawczyk Michal , Fridman Sebastian , Cheng Yi , Fang Jiming , Saposnik Gustavo , Sposato Luciano A 
Published: August 2019

Abstract

Aims
Atrial fibrillation (AF) is a risk factor for dementia among ischaemic stroke patients in whom the AF was known before the stroke (KAF). Atrial fibrillation detected after stroke (AFDAS) has a different profile compared to KAF, including less frequent cardiovascular comorbidities and lower CHA2-DS2-VASC scores. Currently, it is unknown if AFDAS is also associated with increased dementia risk. We assessed the association between AFDAS and the incident risk of dementia. We also evaluated whether the use of oral anticoagulants (OAC) was associated with lower dementia risk among AFDAS patients.

Methods and results
In this cohort study, we classified 9791 first-ever ischaemic stroke patients from the Ontario Stroke Registry into four groups: (i) No AF, (ii) KAF, (iii) Inpatient AFDAS (diagnosed during admission), and (iv) Outpatient AFDAS (diagnosed after discharge). We used multivariable Cox proportional models to estimate hazard ratios (HR) for the association between AFDAS and incident dementia risk. Dementia was determined through administrative datasets based on previously validated algorithms. In adjusted analyses, the dementia risk was higher for inpatient AFDAS [HR 1.78, 95% confidence interval (CI) 1.51–2.10] and outpatient AFDAS (HR 1.74, 95% CI 1.47–2.05) relative to no AF. Oral anticoagulants use was associated with lower dementia risk among patients with inpatient AFDAS (HR 0.58, 95% CI 0.43–0.79) and outpatient AFDAS (HR 0.60, 95% CI 0.43–0.83).

Conclusion
Atrial fibrillation detected after stroke was independently associated with higher risk of dementia relative to no AF. Among patients with AFDAS, the use of OACs was associated with lower dementia risk.
Barriers and opportunities for prolonging working life across different occupational groups: the SeniorWorkingLife study
Authors: Andersen Lars L , Jensen Per H , Sundstrup Emil 
Published: August 2019

Abstract

Background
Increasing retirement age is a pivotal issue in labour market reforms. This study analyses factors conditioning retirement intentions.

Methods
In SeniorWorkingLife, 11 444 employed workers ≥50 years replied to questions in random order about expected reasons for leaving and potential reasons for staying longer at the labour market. Respondents were stratified based on the Danish version of International Standard Classification of Occupations (ISCO). Representative estimates were produced using the SurveyFreq and SurveyLogistic procedures of SAS combined with model-assisted weights based on national registers.

Results
For ISCO groups 1–4 (seated work) main expected reasons for retiring were freedom to choose and desire for more leisure time, but many would consider staying longer if there were better possibilities for additional senior days, longer vacations and flexible working hours. For ISCO groups 5–9 (physical work), poor physical health and not being capable of doing the job were common expected reasons for retiring, but many would consider staying longer if the work were less physically demanding and there were more senior days. Possibility for pension was a general expected reason for retiring. Expected reasons differed to a less extent between genders than between ISCO groups, e.g. economic factors were more important for men and high work demands more important for women.

Conclusion
Different barriers and opportunities for prolonging working life exist across different occupational groups of the labour market—with most consistent differences between those with seated and physical work. Targeting these specifically seems opportune for policy makers and future interventions.
Utility of catastrophizing, body symptom diagram score and history of opioid use to predict future health care utilization after a primary care visit for musculoskeletal pain
Authors: Rhon Daniel I , Lentz Trevor A , George Steven Z 
Published: August 2019

Abstract

Background
Self-report information about pain and pain beliefs are often collected during initial consultation for musculoskeletal pain. These data may provide utility beyond the initial encounter, helping provide further insight into prognosis and long-term interactions of the patient with the health system.

Objective
The aim of this study was to determine if pain catastrophizing and pain-related body symptoms can predict future health care utilization.

Methods
This was a longitudinal cohort study. Baseline data were collected after receiving initial care for a musculoskeletal disorder in a multidisciplinary clinic within a large military hospital. Subjects completed the Pain Catastrophizing Scale, a region-specific disability measure, numeric pain rating scale and a body symptom diagram. Health care utilization data for 1 year prior and after the visit were extracted from the Military Health System Data Repository. Multivariable regression models appropriate for skewed and count data were developed to predict (i) musculoskeletal-specific medical visits, (ii) 12-month opioid use, (iii) musculoskeletal-specific medical costs and (iv) total medical costs. We investigated whether a pain catastrophizing × body symptom diagram interaction improved prediction, and developed separate models for opioid-naïve individuals and those with a history of opioid use in an exploratory analysis.

Results
Pain catastrophizing but not body symptom diagram was a significant predictor of musculoskeletal visits, musculoskeletal costs and total medical costs. Exploratory analyses suggest these relationships are most robust for patients with a history of opioid use.

Conclusions
Pain catastrophizing can identify risk of high health care utilization and costs, even after controlling for common clinical variables. Addressing pain catastrophizing in the primary care setting may help to mitigate future health care utilization and costs, while improving clinical outcomes. These results provide direction for future validation studies in larger and more traditional primary care settings.
Measurement Invariance and Developmental Trajectories of Multidimensional Self-Perceptions of Aging in Middle-Aged and Older Adults
Authors: Jung Seojung , Cham Heining , Siedlecki Karen L , Jopp Daniela S 
Published: August 2019

Abstract

Objectives
This study examined the measurement invariance and longitudinal trajectories of multidimensional self-perceptions of aging (SPA) and factors that predict between-person variability in the level and change of SPA in middle-aged and older adults.

Method
Data were drawn from the German Ageing Survey spanning four waves, covering a 15-year period. Multidimensional SPA was assessed with the Personal Experience of Aging Scale, consisting of three dimensions, physical decline, social loss, and continuous growth.

Results
The measurement invariance models across age groups (middle-aged versus older adults) and across time showed a good fit after allowing one item to vary at metric and/or scalar levels. Growth curve models showed only minor declining trajectories in two of the three dimensions of SPA, social loss and continuous growth dimensions, toward more negative views. Participants with poor resources in general were more likely to have negative SPA across all three dimensions. The protective effect of having a spouse was observed on only the social dimension of SPA, supporting a domain-specific effect of having a spouse.

Discussion
The study demonstrates the usefulness of a multidimensional understanding of SPA and recognizes the need for identifying different factors that may promote positive perceptions on aging in different dimensions of life.
Life Histories and National Narratives: Remembering Occupied Manchuria in Postwar China
Authors: Dryburgh Marjorie 
Published: August 2019

Abstract
Recent studies of memory work in China have explored productively the uses of national narratives of war and victimhood, at times supported by personal testimony, in service of a ‘public transcript’ of Party-state legitimacy. However, oral histories of education in Japanese-occupied north-east China, collected by Chinese researchers and published in 2005, hint at more complex relations between story, storyteller and imagined audience. Without challenging established judgements on the occupation itself, these personal histories articulate more nuanced and ambivalent social histories of wartime schooling, suggesting that former students were neither passive victims of occupation nor passive consumers of state-sponsored historical narrative.
Western Gunrunners, (Middle-)Eastern Casualties: Unlawfully Trading Arms with States Engulfed in Yemeni Civil War?
Authors: Ferro Luca 
Published: August 2019

Abstract
According to the United Nations Secretary-General, Yemen today constitutes the worst man-made humanitarian crisis in the world. It is fuelled by extensive third-state involvement, with none of the warring parties championing respect for international human rights and humanitarian law (to put it mildly). Conversely, primary rules of international law already prohibit arms transfers from the moment there is a significant risk that they could be used to commit or facilitate grave breaches, with the recipient’s past and present record of respect for international law qualifying as the crucial factor to predict future transgressions. From that perspective, it appears deeply disingenuous for western states to continue transferring military equipment to members of the multilateral coalition in Yemen while maintaining adherence to the international legal framework. This article thus aims to examine whether the legal framework lives up to its noble goals or rather serves to defend state decisions that primarily serve their economic interests. It is structured as follows: Section 1 starts with an overview of the facts, and the focus and aim of this article. Section 2 then sets out the international legal framework as it applies to the trade in conventional arms with states that are involved in a non-international armed conflict. Section 3 analyses key domestic judgments (in the UK, Canada, Belgium and France) to test the available facts against the legal framework as elaborated. Finally, Section 4 concludes.
Pittsburgh’s Freedom House Ambulance Service: The Origins of Emergency Medical Services and the Politics of Race and Health
Authors: Edwards Matthew L 
Published: August 2019

Abstract
This manuscript explores the history of the Freedom House Enterprises Ambulance Service, a social and medical experiment that trained “unemployable” black citizens during the late 1960s and early 1970s to provide then state of the art prehospital care. Through archives, newspapers, personal correspondence, university memoranda, and the medical literature, this paper explores the comparable, yet different roles of the program’s two leaders, Drs. Peter Safar and Nancy Caroline. Despite its success in demonstrating national standards for paramedic training and equipment, the program ended abruptly in 1975. And though Pittsburgh’s city administration cited economic constraints for its fledgling support of Freedom House, black and majority newspapers and citizens alike understood the city’s diminishing support of the program in racial terms. The paper discusses Safar and Caroline’s well-intentioned efforts in developing this novel program, while confronting the racial, social, and structural constraints on the program and the limits of racial liberalism.
Phylogeography and taxonomic revision of Nelson’s pocket mouse (Chaetodipus nelsoni)
Authors: Neiswenter Sean A , Hafner David J , Light Jessica E , Cepeda Gabriella D , Kinzer Kathleen C , Alexander Lois F , Riddle Brett R 
Published: August 2019

AbstractChaetodipus nelsoni occurs on rocky substrates across the Mexican Altiplano. We investigated phylogeographic diversity within the species using morphologic, karyotypic, and molecular data. Data from nuclear (AFLP) and mitochondrial DNA support three distinct genetic groups with minimal substructuring coincident with biogeographic barriers previously identified in the Chihuahuan Desert and drainage basins of the Altiplano. We examined the morphological and karyotypic data in light of the molecular data. The results support recognition of three species within the currently accepted widespread C. nelsoni: 1) C. nelsoni restricted to a distribution centered on the El Salado River Basin; 2) elevation of C. n. collis to species, with two subspecies: one centered on Trans-Pecos Texas, the other on the Mapimí Basin (new subspecies); and 3) recognition of a new species, C. durangae, centered on the Nazas Basin and upper Río Mezquital drainage.
A method for determining sex and chromosome copy number: sex-by-sequencing reveals the first two species of marine mammals with XXY chromosome condition
Authors: Einfeldt Anthony L , Orbach Dara N , Feyrer Laura J 
Published: August 2019

AbstractMolecular assays of sex determination typically rely on qualitative evaluation of sex-linked markers, which can lead to uncertainty when results contradict morphological identifiers of sex. To investigate whether disagreement between phenotypic and genotypic assays of sex could be underpinned by variation in sex chromosome copy number, we developed a quantitative genetic method to determine sex that is broadly applicable to mammals with XY sex determination. We sequenced a region of the zinc-finger gene ZF, which has fixed genetic differences between the X and Y chromosomes, and screened 173 cetacean specimens for ZFX–ZFY haplotype identity and read depth. Using a subset of 90 male specimens, we demonstrate that haplotype read depth is an accurate estimator of chromosome copy number. We identified three specimens representing two different cetacean species that had external female morphological traits, Y chromosome haplotypes, and ratios of ZFX:ZFY haplotypes that were above the 1:1 value expected for genetic males. These results provide the first evidence of XXY aneuploidy in cetaceans. Investigation of the reproductive tract of one specimen, a True’s beaked whale (Mesoplodon mirus), revealed an intersex phenotype; despite having external characteristics typically diagnostic for the female sex, a penis and testes were present. Our results suggest that intersex phenotypes may be associated with XXY aneuploidy, and that this phenomenon may be underestimated due to it not being detectable by qualitative assays for determining sex.
Landscape use by two opossums is shaped by habitat preferences rather than by competitive interactions
Authors: Cruz Paula , Iezzi María Eugenia , De Angelo Carlos , Varela Diego , Di Bitetti Mario S 
Published: August 2019

AbstractGiven the phylogenetic proximity and similar morphology of opossums (Didelphis spp.), they are good models to study factors that facilitate or impede coexistence of syntopic species and to better understand how landscape changes affect species distributions and habitat use. For this purpose, we used single-species and two-species occupancy models using records of D. albiventris, considered the dominant species, and D. aurita from a camera-trap survey conducted in an agricultural and conservation landscape in the Atlantic Forest of Argentina. We evaluated which factors determined the probability of species occurrence: habitat preferences or interspecific relationships. We also estimated the overlap in daily activity patterns between species, and evaluated changes in D. aurita activity in response to the occupancy probability of D. albiventris. Didelphis aurita had higher occupancy probabilities in the continuous native forest, whereas D. albiventris had higher occupancy probabilities in fragmented forests with less complex and more open vegetation structure, and greater proximity to buildings. Both opossums were almost absent in pine plantations. Results of the co-occurrence models and the overlap in diel activity suggest that D. aurita is not avoiding D. albiventris. Occurrences of these two opossums most probably reflect different adaptations by each species to different habitats, and competitive interactions seem to play a minor role in shaping their current distributions. Didelphis albiventris may be replacing D. aurita mainly as a result of changing environmental conditions, which become unfavorable to the latter but promote the creation of new habitat for the former.