bluuebunny/crossref_metadata_2025_split huggingface dataset:
HST/STIS analysis of the first main sequence pulsar CU Virginis
Authors: Krtička J. , Mikulášek Z. , Henry G. W. , Janík J. , Kochukhov O. , Pigulski A. , Leto P. , Trigilio C. , Krtičková I. , Lüftinger T. , Prvák M. , Tichý A. 
Published: March 2019

Context. CU Vir has been the first main sequence star that showed regular radio pulses that persist for decades, resembling the radio lighthouse of pulsars and interpreted as auroral radio emission similar to that found in planets. The star belongs to a rare group of magnetic chemically peculiar stars with variable rotational period.
Aims. We study the ultraviolet (UV) spectrum of CU Vir obtained using STIS spectrograph onboard the Hubble Space Telescope (HST) to search for the source of radio emission and to test the model of the rotational period evolution.
Methods. We used our own far-UV and visual photometric observations supplemented with the archival data to improve the parameters of the quasisinusoidal long-term variations of the rotational period. We predict the flux variations of CU Vir from surface abundance maps and compare these variations with UV flux distribution. We searched for wind, auroral, and interstellar lines in the spectra.
Results. The UV and visual light curves display the same long-term period variations supporting their common origin. New updated abundance maps provide better agreement with the observed flux distribution. The upper limit of the wind mass-loss rate is about 10−12 M⊙ yr−1. We do not find any auroral lines. We find rotationally modulated variability of interstellar lines, which is most likely of instrumental origin.
Conclusions. Our analysis supports the flux redistribution from far-UV to near-UV and visual domains originating in surface abundance spots as the main cause of the flux variability in chemically peculiar stars. Therefore, UV and optical variations are related and the structures leading to these variations are rigidly confined to the stellar surface. The radio emission of CU Vir is most likely powered by a very weak presumably purely metallic wind, which leaves no imprint in spectra.
Schlafstörungen bei Multipler Sklerose
Authors: Veauthier Christian 
Published: March 2019

ZusammenfassungGegenstand und Ziel: Patienten mit Multipler Sklerose (MS) leiden häufig an einer die Lebensqualität deutlich beeinträchtigenden Schlafstörung. Es soll ein Überblick über den gegenwärtigen Stand der Literatur gegeben werden. Material und Methoden: Übersichtsarbeit. Ergebnisse: Mehrere Studien haben bei der MS im Vergleich zur Allgemeinbevölkerung eine erhöhte Prävalenz für ein Restless-legs-Syndrom (RLS) gezeigt, im Besonderen bei MS-Patienten mit einem erhöhten Grad der Behinderung. Rund ein Viertel der MS-Patienten leidet an einer chronischen Insomnie. Es existieren symptomatische Formen der Narkolepsie und der REM-Schlaf-Verhaltensstörung (RBD), am ehesten durch akute Läsionen hervorgerufen. Ob Läsionen auch schlafbezogene Atmungsstörungen verursachen können, kann noch nicht ausreichend beurteilt werden. Schlussfolgerung und klinische Relevanz: Beim Neuauftreten einer Narkolepsie oder eines RBD sollte zügig eine kraniale Kernspintomografie mit Kontrastmittel erfolgen. Bei der Behandlung schlafmedizinischer Erkrankungen kommen die von den Fachgesellschaften empfohlenen Behandlungsrichtlinien zur Anwendung (die Behandlung unterscheidet sich bei MS-Patienten nicht grundsätzlich von der Behandlung dieser Erkrankungen in der Allgemeinbevölkerung). MS-Fatigue-Patienten sollten niedrigschwellig eine Polygrafie oder Polysomnografie erhalten.
Non-24h-Schlaf-Wach-Rhythmusstörung bei blinden Patienten
Authors: Dirks Christina , Young Peter , Heidbreder Anna 
Published: March 2019

ZusammenfassungSchlafstörungen sind bei blinden und sehbehinderten Patienten ein häufig unterschätztes Problem. Hierbei kommt der Non-24h-Schlaf-Wach-Rhythmusstörung (Non-24) in der Gruppe der Patienten ohne Lichtwahrnehmung eine besondere Bedeutung zu. Durch den Wegfall des stärksten externen Taktgebers Tageslicht kommt es zu einer Desynchronisation der endogenen circadianen Rhythmik, welche über die Masterclock im suprachiasmatischen Nucleus generiert wird, mit dem externen 24h-Tag-Nacht-Rhythmus. Die Ausschüttung von Melatonin, als wichtigster Botenstoff in der Regulation des Schlaf-Wach-Rhythmus, wird durch den Wegfall der Information über Helligkeit und Dunkelheit nicht mehr extern gesteuert und folgt allein der endogenen Rhythmik, welche häufig nicht exakt 24 Stunden entspricht, sondern bei den meisten Menschen eine längere Periodik aufweist. Die Symptome einer solchen fortlaufenden Verschiebung des Schlaf-Wach-Rhythmus beinhalten zyklisch wiederkehrende Phasen mit insomnischen Beschwerden und Tagesschläfrigkeit, welche mit symptomfreien Phasen alternieren. Die Diagnostik der Non-24 umfasst neben einer ausführlichen schlafspezifischen Anamnese auch die Durchführung einer Aktimetrie für einen Zeitraum von mindestens 2 Wochen und das Führen von Schlafprotokollen. Zudem kann die Messung von Biomarkern z. B. des Melatonins, im Serum oder Speichel, oder dessen Abbauprodukt zur Sicherung einer Diagnose sinnvoll sein.Als Therapieoptionen stehen nicht medikamentöse und medikamentöse Maßnahmen zur Verfügung, welche als Kombinationstherapie angewandt werden sollten. Aktuell ist der Melatonin-Rezeptoragonist Tasimelteon das einzige zugelassen Medikament zur Behandlung der Non-24 bei blinden Menschen.
Direct Percutaneous Embolization of a Lymphocutaneous Fistula
Authors: Singhal Soumil , Uthappa Mangerira 
Published: March 2019

AbstractLymphocutaneous fistula is a rare clinical condition and presents both a diagnostic and a therapeutic challenge. The authors report a case of secondary lymphocutaneous fistula that was undiagnosed and untreated on several occasions but was successfully treated with direct percutaneous embolization.
Coexistence of Temporo-Occipital Polymicrogyria with Choroidal Fissure Cyst in a Case of Focal Onset Seizures
Authors: Kiran M. , Karthik A. , Lekshmi L. V. , Nagarajan K. 
Published: March 2019

AbstractFocal-onset seizures can be caused by underlying brain lesions including focal lesions such as granulomas, low-grade neoplasms, vascular lesions, or neuronal migration disorders. Polymicrogyria is a congenital abnormality of cortical formation occurring during embryonic life. Choroidal fissure cysts are either arachnoid or neuroepithelial cysts arising at the choroidal fissure, and mostly they are incidental findings having no significant clinical implications. Coexistence of both of these can lead to dilemma in the management decisions. We present a case of focal-onset seizures with an unreported coexistence of polymicrogyria with choroidal fissure cyst.
Female choice for related males in wild red-backed toadlets (Pseudophryne coriacea)
Authors: O’Brien Daniel M , Keogh J Scott , Silla Aimee J , Byrne Phillip G 
Published: March 2019

AbstractMate choice for genetic benefits is assumed to be widespread in nature, yet very few studies have comprehensively examined relationships between female mate choice and male genetic quality in wild populations. Here, we use exhaustive sampling and single nucleotide polymorphisms to provide a partial test of the “good genes as heterozygosity” hypothesis and the “genetic compatibility” hypothesis in an entire population of terrestrial breeding red-backed toadlets, Pseudophryne coriacea. We found that successful males did not display higher heterozygosity, despite a positive relationship between male heterozygosity and offspring heterozygosity. Rather, in the larger of 2 breeding events, we found that successful males were more genetically similar to their mate than expected under random mating, indicating that females can use pre- or post-copulatory mate choice mechanisms to bias paternity toward more related males. These findings provide no support for the good genes as heterozygosity hypothesis but lend support to the genetic compatibility hypothesis. A complete test of this hypothesis will now require evaluating how parental genetic similarity impacts offspring fitness. Terrestrial toadlets show a high degree of site fidelity, high levels of genetic structuring between populations, and frequently hybridize with sister species. As such, female mate choice for related males may be an adaptive strategy to reduce outbreeding depression. Our findings provide the first population-wide evidence for non-random preferential inbreeding in a wild amphibian. We argue that such reproductive patterns may be common in amphibians because extreme genetic differentiation within meta-populations creates an inherently high risk of outbreeding depression.
ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data
Authors: Chen Xun , Li Dawei 
Published: March 2019

Abstract

Motivation
Approximately 8% of the human genome is derived from endogenous retroviruses (ERVs). In recent years, an increasing number of human diseases have been found to be associated with ERVs. However, it remains challenging to accurately detect the full spectrum of polymorphic (unfixed) ERVs using whole-genome sequencing (WGS) data.

Results
We designed a new tool, ERVcaller, to detect and genotype transposable element (TE) insertions, including ERVs, in the human genome. We evaluated ERVcaller using both simulated and real benchmark WGS datasets. Compared to existing tools, ERVcaller consistently obtained both the highest sensitivity and precision for detecting simulated ERV and other TE insertions derived from real polymorphic TE sequences. For the WGS data from the 1000 Genomes Project, ERVcaller detected the largest number of TE insertions per sample based on consensus TE loci. By analyzing the experimentally verified TE insertions, ERVcaller had 94.0% TE detection sensitivity and 96.6% genotyping accuracy. Polymerase chain reaction and Sanger sequencing in a small sample set verified 86.7% of examined insertion statuses and 100% of examined genotypes. In conclusion, ERVcaller is capable of detecting and genotyping TE insertions using WGS data with both high sensitivity and precision. This tool can be applied broadly to other species.

Availability and implementation
http://www.uvm.edu/genomics/software/ERVcaller.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
FLAS: fast and high-throughput algorithm for PacBio long-read self-correction
Authors: Bao Ergude , Xie Fei , Song Changjin , Song Dandan 
Published: March 2019

AbstractMotivationThe third generation PacBio long reads have greatly facilitated sequencing projects with very large read lengths, but they contain about 15% sequencing errors and need error correction. For the projects with long reads only, it is challenging to make correction with fast speed, and also challenging to correct a sufficient amount of read bases, i.e. to achieve high-throughput self-correction. MECAT is currently among the fastest self-correction algorithms, but its throughput is relatively small (Xiao et al., 2017).ResultsHere, we introduce FLAS, a wrapper algorithm of MECAT, to achieve high-throughput long-read self-correction while keeping MECAT’s fast speed. FLAS finds additional alignments from MECAT prealigned long reads to improve the correction throughput, and removes misalignments for accuracy. In addition, FLAS also uses the corrected long-read regions to correct the uncorrected ones to further improve the throughput. In our performance tests on Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana and human long reads, FLAS can achieve 22.0–50.6% larger throughput than MECAT. FLAS is 2–13× faster compared to the self-correction algorithms other than MECAT, and its throughput is also 9.8–281.8% larger. The FLAS corrected long reads can be assembled into contigs of 13.1–29.8% larger N50 sizes than MECAT.Availability and implementationThe FLAS software can be downloaded for free from this site: https://github.com/baoe/flas.Supplementary informationSupplementary data are available at Bioinformatics online.
The Contemporary Repertoire of Contentious Identity Politics and Religious Conflicts in France
Authors: D’Appollonia Ariane Chebel 
Published: March 2019

Abstract
This paper analyses the framing and meaning of contentious politics in contemporary France. Building on the work of Charles Tilly and Sidney Tarrow, this study of contention involves two interrelated dimensions. The first one relates to inherited, historical forms of collective action (repertoires). Here, contentious politics varies in connection with political power, institutional regimes, and the dominant culture. In early modern history, such forms of contention were linked to a traditional repertoire of grievances (about bread, belief, or land) and concerns about the purity of the religious community. A new repertoire emerged in the 18th century, as well as new forms of contention. Yet, key components of contentious politics remained, such as concerns about the purity of the nation, and grievances fuelled by the threat posed by “Others.” As a result, there are significant similarities between past conflicts about religion, and the current debate over the alleged threats to French secularism.
Solitary Day, Solitary Activities, and Associations With Well-Being Among Older Adults
Authors: Lam Jack , García-Román Joan 
Published: March 2019

Abstract

Objectives
Drawing on activity theory of aging, we examined whether solitary activities may be associated with negative well-being, as they may reflect social isolation. Using American Time Use Surveys, with information on “with whom” individuals engaged in activities over a 24 hr period, we created measures capturing solitary days and solitary activities to understand their prevalence and associations with well-being.

Methods
At the daily level, we examined associations between solitary days and proportion of the day in solitary activities with life satisfaction. At the activity level, we examined associations between engaging in an activity alone versus with others and emotional state during the activity.

Results
Solitary days and higher proportion of the day spent in solitary activities were associated with lower life satisfaction. These associations were attenuated controlling for individual covariates. Engagement in activities alone was associated with lower levels of happiness and higher levels of sadness and pain during the activity, and association with happiness remained even adjusting for covariates.

Discussion
A sizable proportion of older adults reported solitary days, and proportion of the day spent in solitary activities increases by age. Examining lived experiences of older adults and presence of others during activities could contribute to research on social isolation.
Tissue regulatory T cells and neural repair
Authors: Ito Minako , Komai Kyoko , Nakamura Toshihiro , Srirat Tanakorn , Yoshimura Akihiko 
Published: March 2019

Abstract
Inflammation and immune responses after tissue injury play pivotal roles in the pathology, resolution of inflammation, tissue recovery, fibrosis and remodeling. Regulatory T cells (Tregs) are the cells responsible for suppressing immune responses and can be activated in secondary lymphatic tissues, where they subsequently regulate effector T cell and dendritic cell activation. Recently, Tregs that reside in non-lymphoid tissues, called tissue Tregs, have been shown to exhibit tissue-specific functions that contribute to the maintenance of tissue homeostasis and repair. Unlike other tissue Tregs, the role of Tregs in the brain has not been well elucidated because the number of brain Tregs is very small under normal conditions. However, we found that Tregs accumulate in the brain at the chronic phase of ischemic brain injury and control astrogliosis through secretion of a cytokine, amphiregulin (Areg). Brain Tregs resemble other tissue Tregs in many ways but, unlike the other tissue Tregs, brain Tregs express neural-cell-specific genes such as the serotonin receptor (Htr7) and respond to serotonin. Administering serotonin or selective serotonin reuptake inhibitors (SSRIs) in an experimental mouse model of stroke increases the number of brain Tregs and ameliorates neurological symptoms. Knowledge of brain Tregs will contribute to the understanding of various types of neuroinflammation.
‘Warning: allergic to penicillin’: association between penicillin allergy status in 2.3 million NHS general practice electronic health records, antibiotic prescribing and health outcomes
Authors: West R M , Smith C J , Pavitt S H , Butler C C , Howard P , Bates C , Savic S , Wright J M , Hewison J , Sandoe J A T 
Published: March 2019

AbstractBackgroundThe prevalence of reported penicillin allergy (PenA) and the impact these records have on health outcomes in the UK general population are unknown. Without such data, justifying and planning enhanced allergy services is challenging.ObjectivesTo determine: (i) prevalence of PenA records; (ii) patient characteristics associated with PenA records; and (iii) impact of PenA records on antibiotic prescribing/health outcomes in primary care.MethodsWe carried out cross-sectional/retrospective cohort studies using patient-level data from electronic health records. Cohort study: exact matching across confounders identified as affecting PenA records. Setting: English NHS general practices between 1 April 2013 and 31 March 2014. Participants: 2.3 million adult patients. Outcome measures: prevalence of PenA, antibiotic prescribing, mortality, MRSA infection/colonization and Clostridioides difficile infection.ResultsPenA prevalence was 5.9% (IQR = 3.8%–8.2%). PenA records were more common in older people, females and those with a comorbidity, and were affected by GP practice. Antibiotic prescribing varied significantly: penicillins were prescribed less frequently in those with a PenA record [relative risk (RR)  = 0.15], and macrolides (RR = 4.03), tetracyclines (RR = 1.91) nitrofurantoin (RR = 1.09), trimethoprim (RR = 1.04), cephalosporins (RR = 2.05), quinolones (RR = 2.10), clindamycin (RR = 5.47) and total number of prescriptions were increased in patients with a PenA record. Risk of re-prescription of a new antibiotic class within 28 days (RR = 1.32), MRSA infection/colonization (RR = 1.90) and death during the year subsequent to 1 April 2013 (RR = 1.08) increased in those with PenA records.ConclusionsPenA records are common in the general population and associated with increased/altered antibiotic prescribing and worse health outcomes. We estimate that incorrect PenA records affect 2.7 million people in England. Establishing true PenA status (e.g. oral challenge testing) would allow more people to be prescribed first-line antibiotics, potentially improving health outcomes.
An electronic health record–based interoperable eReferral system to enhance smoking Quitline treatment in primary care
Authors: Fiore Michael , Adsit Rob , Zehner Mark , McCarthy Danielle , Lundsten Susan , Hartlaub Paul , Mahr Todd , Gorrilla Allison , Skora Amy , Baker Timothy 
Published: March 2019

Abstract

Objective
The study sought to determine whether interoperable, electronic health record–based referral (eReferral) produces higher rates of referral and connection to a state tobacco quitline than does fax-based referral, thus addressing low rates of smoking treatment delivery in health care.

Materials and Methods
Twenty-three primary care clinics from 2 healthcare systems (A and B) in Wisconsin were randomized, unblinded, over 2016-2017, to 2 smoking treatment referral methods: paper-based fax-to-quit (system A =6, system B = 6) or electronic (eReferral; system A = 5, system B = 6). Both methods referred adult patients who smoked to the Wisconsin Tobacco Quitline. A total of 14 636 smokers were seen in the 2 systems (system A: 54.5% women, mean age 48.2 years; system B: 53.8% women, mean age 50.2 years).

Results
Clinics with eReferral, vs fax-to-quit, referred a higher percentage of adult smokers to the quitline: system A clinic referral rate = 17.9% (95% confidence interval [CI], 17.2%-18.5%) vs 3.8% (95% CI, 3.5%-4.2%) (P &lt; .001); system B clinic referral rate = 18.9% (95% CI, 18.3%-19.6%) vs 5.2% (95% CI, 4.9%-5.6%) (P &lt; .001). Average rates of quitline connection were higher in eReferral than F2Q clinics: system A = 5.4% (95% CI, 5.0%-5.8%) vs 1.3% (95% CI, 1.1%-1.5%) (P &lt; .001); system B = 5.3% (95% CI, 5.0%-5.7%) vs 2.0% (95% CI, 1.8%-2.2%) (P &lt; .001).

Discussion
Electronic health record–based eReferral provided an effective, closed-loop, interoperable means of referring patients who smoke to telephone quitline services, producing referral rates 3-4 times higher than the current standard of care (fax referral), including especially high rates of referral of underserved individuals.

Conclusions
eReferral may help address the challenge of providing smokers with treatment for tobacco use during busy primary care visits.
ClinicalTrials.gov; No. NCT02735382.
Early experiences with patient generated health data: health system and patient perspectives
Authors: Adler-Milstein Julia , Nong Paige 
Published: March 2019

Abstract

Objective
Although patient generated health data (PGHD) has stimulated excitement about its potential to increase patient engagement and to offer clinicians new insights into patient health status, we know little about these efforts at scale and whether they align with patient preferences. This study sought to characterize provider-led PGHD approaches, assess whether they aligned with patient preferences, and identify challenges to scale and impact.

Materials and Methods
We interviewed leaders from a geographically diverse set of health systems (n = 6), leaders from large electronic health record vendors (n = 3), and leaders from vendors providing PGHD solutions to health systems (n = 3). Next, we interviewed patients with 1 or more chronic conditions (n = 10), half of whom had PGHD experience. We conducted content analysis to characterize health system PGHD approaches, assess alignment with patient preferences, and identify challenges.

Results
In this study, 3 primary approaches were identified, and each was designed to support collection of a different type of PGHD: 1) health history, 2) validated questionnaires and surveys, and 3) biometric and health activity. Whereas patient preferences aligned with health system approaches, patients raised concerns about data security and the value of reporting. Health systems cited challenges related to lack of reimbursement, data quality, and clinical usefulness of PGHD.

Discussion
Despite a federal policy focus on PGHD, it is not yet being pursued at scale. Whereas many barriers contribute to this narrow pursuit, uncertainty around the value of PGHD, from both patients and providers, is a primary inhibitor.

Conclusion
Our results reveal a fairly narrow set of approaches to PGHD currently pursued by health systems at scale.