bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toytree: A minimalist tree visualization and manipulation library for Python
Authors: Eaton Deren A. R. 
Published: October 2019

Abstract

Toytree is a lightweight Python library for programmatically visualizing and manipulating tree‐based data structures. It implements a minimalist design aesthetic and modern plotting architecture suited for interactive coding in IPython/Jupyter.

Tree drawings are generated in HTML using the toyplot library backend, and display natively in Jupyter notebooks with interactivity features. Tree drawings can be combined with other plotting functions from the toyplot library (e.g. scatterplots, histograms) to create composite figures on a shared coordinate grid, and can be exported to additional formats including PNG, PDF and SVG.

To parse and store tree data, toytree uses a modified fork of the ete3 TreeNode object, which includes functions for manipulating, annotating and comparing trees. Toytree integrates these functions with a plotting layout to allow node values to be extracted from trees in the correct order to style nodes for plotting. In addition, toytree provides functions for parsing additional tree formats, generating random trees, inferring consensus trees and drawing grids or clouds from multiple trees to visualize discordance.

The goal of toytree is to provide a simple Python equivalent to commonly used tree manipulation and plotting libraries in R, and in doing so, to promote further development of phylogenetic and other tree‐based methods in Python. Toytree is released under the GPLv3 license. Source code is available on GitHub and documentation is available at https://toytree.readthedocs.io.
Understanding decisions to use e‐cigarettes or behavioural support to quit tobacco: a qualitative study of current and ex‐smokers and stop smoking service staff
Authors: Hartwell Greg , Egan Matt , Petticrew Mark 
Published: October 2019

AbstractAimTo examine factors influencing current and ex‐smokers’ decisions to use e‐cigarettes or behavioural support, including potential impacts of any differences in perspectives between smokers and their local stop smoking services (SSSs).DesignSemi‐structured qualitative interviews followed by framework analysis, with the ‘capability’, ‘opportunity’, ‘motivation’ and ‘behaviour’ (COM‐B) model of behaviour change used to frame findings.SettingSSSs and surrounding local areas in England.ParticipantsInterviewees (n = 46) were current or recent smokers (n = 29) and SSS staff or stakeholders (n = 17).MeasurementsInterview topic guides explored influences on smokers' choice of quit method and characteristics of support offered by local SSSs.FindingsCurrent and ex‐smokers showed a range of views on potential risks from long‐term vaping, which appeared to be particularly relevant for the capability dimension of COM‐B. These different attitudes to vaping appeared to be linked to variations in people's perceived capability to assess evidence around e‐cigarettes’ safety. Motivations for using or avoiding e‐cigarettes and SSSs often appeared to overlap: attitudes to both e‐cigarettes and nicotine replacement therapy from SSSs often reflected personal experiences and views on whether switching from smoking to these alternatives represented successful quitting or simply ongoing nicotine addiction. For smokers, opportunities to use e‐cigarettes or SSSs appeared to be largely determined by perceived time requirements. Furthermore, interviews with SSS professionals suggested that opportunities to access SSSs for ex‐smokers who were now regular vapers may be being influenced by different e‐cigarette policies adopted in individual areas.ConclusionsIn England, smokers’ decisions to use e‐cigarettes and local stop smoking services appear to be determined by varied influences across the COM‐B framework. Both smokers and stop smoking service professionals display diverse views about potential risks from e‐cigarettes, which has relevance for the provision of behavioural support as well as the uptake of vaping.
Validation of a comorbidity index for use in obstetric patients: A nationwide cohort study
Authors: Bliddal Mette , Möller Sören , Vinter Christina A. , Rubin Katrine H. , Gagne Joshua J. , Pottegård Anton 
Published: October 2019

AbstractIntroductionA previously developed Obstetric Comorbidity Index has been validated in highly selected cohorts. Validation of the index in an unselected population as well as in other health registers is, however, of high importance to determine external validity.Material and methodsUsing nationwide registers, we formed a nationwide cohort including completed pregnancies (both live‐ and stillborn) in Denmark from 2000 through 2014. Maternal age and 20 comorbid conditions were assessed and weighted. Outcomes were maternal end‐organ injury or death within 30 days postpartum. The index's predictive and discriminative ability was estimated by Brier score and the area under the receiver operating characteristic curve (AUC), respectively. Logistic regression analysis was used to estimate odds ratios (OR) with 95% confidence interval (CI).ResultsIn 876 496 completed pregnancies by 527 079 women, 1.40% (n = 12 314) experienced an outcome. The majority of women (64.1%) did not have any record of a condition included in the index and only 0.3% (n = 3044) had a score >6. The incidence of an outcome increased with increasing comorbidity score from 0.9% (95% CI 0.8‐0.9) in women scoring 0% to 10.4% (95% CI 7.6‐13.9) in women scoring 9‐10. Compared with women scoring 0, a score of 1‐2 yielded an OR of 2.34 (95% CI 2.25‐2.44), 3‐4 an OR of 5.16 (95% CI 4.81‐5.54), 5‐6 an OR of 4.84 (95% CI 4.31‐5.44), and 8‐9 an OR of 7.97 (95% CI 6.54‐9.72) for experiencing the outcome. The index had a Brier score of 0.01 and an AUC of 0.64.ConclusionsDespite potential weaknesses in the outcome definition, the Obstetric Comorbidity Index showed a moderate ability to discriminate and predict end‐organ injury and death in a nationwide cohort in Denmark, in accordance with previous findings. These results suggest that the index may be a useful tool to control for confounding in health research and clinically to identify women at high risk for adverse maternal outcomes.
Target populations to reduce cesarean rates after induced labor: A national population‐based cohort study
Authors: Blanc‐Petitjean Pauline , Schmitz Thomas , Salomé Marina , Goffinet François , Le Ray Camille ,   for the MEDIP Study Group
Published: October 2019

AbstractIntroductionGreat variations in cesarean rates after induction of labor exist and reasons for these disparities remain unclear. They may be explained by individual characteristics or obstetric practices. Ten‐group classification systems have proved their utility to monitor cesarean rates in general population. We aimed to identify groups of women that account for most cesareans after induction of labor using the Nippita reproducible 10‐group classification, specifically designed for induced population.Material and methodsA prospective population‐based cohort study was performed in 94 French maternity units, including 3042 women undergoing induction of labor. Women were sorted according to 10 mutually exclusive groups based on parity, weeks of gestation, number of fetuses, fetal presentation and previous cesarean delivery. Relative size, cesarean delivery rate and contribution to the overall cesarean rate were described for each group. Cesarean rates were compared according to the Bishop score at the onset of labor induction. Indications for cesarean delivery were also described in the groups that contributed most to the overall cesarean rate. The MEDIP protocol was registered in ClinicalTrial (NCT02477085).ResultsThe overall cesarean rate was 21.0% among this population of induced women. Nulliparous women with a term singleton cephalic fetus (groups 1, 2 and 3; at 37‐38, 39‐40 and ≥41 weeks of gestation, respectively) accounted for two‐thirds of the overall cesarean rate because they were the largest group (relative size of 10.6, 16.6 and 18.1%, respectively) and had higher cesarean rates (27.2, 30.9 and 33.0%, respectively). When the Bishop score was <6 (n = 2270/3042), cesarean delivery rates were higher (24.1 vs 10.7% if Bishop score ≥6, P < 0.01), in particular for group 1 (29.1 vs 12.5%, P = 0.02), and group 2 (33.3 vs 19.3%, P = 0.01). In groups 1, 2 and 3, which contributed most to the overall cesarean rate, a significant part of the cesareans were performed before 6 cm of cervical dilation for dystocia only (40.0, 16.7 and 17.6%, respectively).ConclusionsNulliparous women with a term singleton cephalic fetus and an unfavorable cervix represent the population to target for auditing induction practices. Specific actions could be implemented among this population to weigh the benefits and risks of induction and improve the management of labor induction.
Synthetic hydrosilicate nanotubes induce low pro‐inflammatory and cytotoxic responses compared to natural chrysotile in lung cell cultures
Authors: Skuland Tonje , Maslennikova Tatiana , Låg Marit , Gatina El´mira , Serebryakova Maria K. , Trulioff Andrey S. , Kudryavtsev Igor V. , Klebnikova Natalia , Kruchinina Irina , Schwarze Per E. , Refsnes Magne 
Published: October 2019

AbstractAsbestos (Mg‐hydrosilicate; chrysotile) is known to cause pleural diseases, pulmonary fibrosis and lung cancers, via mechanisms strongly depending on diameter‐length ratio and possibly metal content. A critical question is whether synthetic hydrosilicate nanotubes (NTs) of short length possess little toxic potential compared to chrysotile. Five Mg‐ and two NiNTs of different lengths were assessed for cytotoxicity and pro‐inflammatory responses in THP‐1 macrophages and human bronchial epithelial lung cells (HBEC3‐KT), in comparison with chrysotile. NT lengths/diameters were characterized by TEM, surface areas by BET‐ and BJH analysis, and chemical composition by XRD. The different Mg‐ and NiNTs induced little cytotoxicity in both cell models, in contrast to chrysotile that induced marked cytotoxicity. The two longest synthetic MgNTs, with median lengths of 3 and 5 µm, induced increased levels of pro‐inflammatory cytokines in THP‐1 macrophages, but much less than chrysotile (median length 15 µm) and silica nanoparticles (Si10). The shortest NTs did not induce any increase in cytokines. In HBEC3‐KT cells, all synthetic NTs induced no or only small changes in cytokine responses, in contrast to chrysotile and Si10. The synthetic NTs induced lower TGF‐β responses than chrysotile in both cell models. In conclusion, the pro‐inflammatory responses were associated with the length of synthetic hydrosilicate NTs in THP‐1 macrophages, but not in HBEC3‐KT cells. Notably, the shortest NTs showed no or little pro‐inflammatory activity or cytotoxicity in both cell models. Such a safety by design approach is important for development of new materials being candidates for various new products.
Interaction potential between clarithromycin and individual statins—A systematic review
Authors: Hougaard Christensen Mette Marie , Bruun Haastrup Maija , Øhlenschlæger Thomas , Esbech Peter , Arnspang Pedersen Sidsel , Bach Dunvald Ann‐Cathrine , Bjerregaard Stage Tore , Pilsgaard Henriksen Daniel , Thestrup Pedersen Andreas James 
Published: October 2019

AbstractThe high prevalence of statin and clarithromycin utilization creates potential for overlapping use. The objectives of this MiniReview were to investigate the evidence base for drug‐drug interactions between clarithromycin and currently marketed statins and to present management strategies for these drug combinations. We conducted a systematic literature review following PRISMA guidelines with English language studies retrieved from PubMed and EMBASE (from inception through March 2019). We included 29 articles (16 case reports, 5 observational, 5 clinical pharmacokinetic and 3 in vitro studies). Based on mechanistic/clinical studies involving clarithromycin or the related macrolide erythromycin (both strong inhibitors of CYP3A4 and of hepatic statin uptake transporters OATP1B1 and OATP1B3), clarithromycin is expected to substantially increase systemic exposure to simvastatin and lovastatin (>5‐fold increase in area under the plasma concentration‐time curve (AUC)), moderately increase AUCs of atorvastatin and pitavastatin (2‐ to 4‐fold AUC increase) and slightly increase pravastatin exposure (≈2‐fold AUC increase) while having little effect on fluvastatin or rosuvastatin. The 16 cases of statin‐clarithromycin adverse drug reactions (rhabdomyolysis (n = 14) or less severe clinical myopathy) involved a CYP3A4‐metabolized statin (simvastatin, lovastatin or atorvastatin). In line, a cohort study found concurrent use of clarithromycin and CYP3A4‐metabolized statins to be associated with a doubled risk of hospitalization with rhabdomyolysis or other statin‐related adverse events as compared with azithromycin‐statin co‐administration. If clarithromycin is necessary, we recommend (a) avoiding co‐administration with simvastatin, lovastatin or atorvastatin; (b) withholding or dose‐reducing pitavastatin; (c) continuing pravastatin therapy with caution, limiting pravastatin dose to 40 mg daily; and (d) continuing fluvastatin or rosuvastatin with caution.
Discovery of prolyl hydroxylase 2 inhibitors with new chemical scaffolds as in vivo active erythropoietin inducers through a combined virtual screening strategy
Authors: Yu Zhan , Li Zhihong , Yu Quanwei , Wang Zhi , Song Huilin , Sun Hanyu , Fan Rufeng , Bi Angzhi , Zhang Jun , Zhang Xiaojin 
Published: October 2019

AbstractHypoxia‐inducible factor (HIF) is identified to be a promising target to mediate the response to hypoxia. Its stability and activation are negatively controlled by prolyl hydroxylase 2 (PHD2). Thus, PHD2 inhibition has been perceived as a promising anti‐anemia therapy. In this study, we carried out a structure‐based virtual screening followed by in vitro and in vivo biological validation, with the goal to identify novel PHD2 inhibitors. As a result, a set of hits with new chemical scaffolds were revealed to be active in vitro for PHD2 inhibition. Compounds 2 and 3 were revealed to be capable of stabilizing HIF‐α and stimulating erythropoietin (EPO) expression in cell‐based assays. Notably, further in vivo assays revealed that 2 was capable of elevating the EPO plasma levels in C57BL/6 mice model. These findings provide new chemical scaffolds for further development of PHD2 inhibitors.
Clinical diagnostic exome sequencing in dystonia: Genetic testing challenges for complex conditions
Authors: Powis Zöe , Towne Meghan C. , Hagman Kelly D.F. , Blanco Kirsten , Palmaer Erika , Castro Andrew , Sajan Samin A. , Radtke Kelly , Feyma Timothy J. , Juliette Kali , Tang Sha , Sidiropoulos Christos 
Published: October 2019

AbstractPatients with dystonia are particularly appropriate for diagnostic exome sequencing (DES), due to the complex, diverse features and genetic heterogeneity. Personal and family history data were collected from test requisition forms and medical records from 189 patients with reported dystonia and available family members received for clinical DES. Of them, 20.2% patients had a positive genetic finding associated with dystonia. Detection rates for cases with isolated and combined dystonia were 22.4% and 25.0%, respectively. 71.4% of the cohort had co‐occurring non‐movement‐related findings and a detection rate of 24.4%. Patients with childhood‐onset dystonia trended toward higher detection rates (31.8%) compared to infancy (23.6%), adolescence (12.5%), and early‐adulthood onset (16%). Uncharacterized gene findings were found in 6.7% (8/119) of cases that underwent analysis for genes without an established disease relationship. Patients with intellectual disability/developmental delay, seizures/epilepsy and/or multifocal dystonia were more likely to have positive findings (P = .0093, .0397, .0006). Four (2.1%) patients had findings in two genes, and seven (3.7%) had reclassification after the original report due to new literature, new clinical information or reanalysis request. Pediatric patients were more likely to have positive findings (P = .0180). Our observations show utility of family‐based DES in patients with dystonia and illustrate the complexity of testing.
Non‐enzymatic reaction of carnosine and glyceraldehyde‐3‐phosphate accompanies metabolic changes of the pentose phosphate pathway
Authors: Oppermann Henry , Birkemeyer Claudia , Meixensberger Jürgen , Gaunitz Frank 
Published: October 2019

AbstractObjectivesCarnosine (β‐alanyl‐l‐histidine) is a naturally occurring dipeptide that selectively inhibits cancer cell growth, possibly by influencing glucose metabolism. As its precise mode of action and its primary targets are unknown, we analysed carnosine's effect on metabolites and pathways in glioblastoma cells.Materials and methodsGlioblastoma cells, U87, T98G and LN229, were treated with carnosine, and metabolites were analysed by gas chromatography coupled with mass spectrometry. Furthermore, mitochondrial ATP production was determined by extracellular flux analysis and reaction products of carnosine were investigated using mass spectrometry.ResultsCarnosine decreased the intracellular abundance of several metabolites indicating a reduced activity of the pentose phosphate pathway, the malate‐aspartate shuttle and the glycerol phosphate shuttle. Mitochondrial respiration was reduced in U87 and T98G but not in LN229 cells, independent of whether glucose or pyruvate was used as substrate. Finally, we demonstrate non‐enzymatic reaction of carnosine with dihydroxyacetone phosphate and glyceraldehyde‐3‐phosphate. However, glycolytic flux from glucose to l‐lactate appeared not to be affected by the reaction of carnosine with the metabolites.ConclusionsCarnosine reacts non‐enzymatically with glycolytic intermediates reducing the activity of the pentose phosphate pathway which is required for cell proliferation. Although the activity of the malate‐aspartate and the glycerol phosphate shuttle appear to be affected, reduced mitochondrial ATP production under the influence of the dipeptide is cell‐specific and appears to be independent of the effect on the shuttles.
S3‐Leitlinie: Durchführung des Epikutantests mit Kontaktallergenen und Arzneimitteln – Kurzfassung Teil 1
Authors: Mahler Vera , Nast Alexander , Bauer Andrea , Becker Detlef , Brasch Jochen , Breuer Kristine , Dickel Heinrich , Drexler Hans , Elsner Peter , Geier Johannes , John Swen Malte , Kreft Burkhard , Köllner Arno , Merk Hans , Ott Hagen , Pleschka Silvia , Portisch Maria , Spornraft‐Ragaller Petra , Weisshaar Elke , Werfel Thomas , Worm Margitta , Schnuch Axel , Uter Wolfgang 
Published: October 2019

ZusammenfassungDer diagnostische Standard zum Nachweis einer bestehenden allergischen Kontaktdermatitis ist der Epikutantest. Die vorliegende Leitlinie richtet sich an Assistenz‐ und Fachärzte der Dermatologie, Allergologie und Ärzte weiterer Fachgruppen in Klinik und Praxis, die an der Indikationsstellung oder Durchführung von Epikutantests bei Patienten mit Kontaktekzemen und weiteren Spättypallergien beteiligt sind, sowie Kooperationspartner der Ärzteschaft (Fachberufe im Gesundheitswesen, Kostenträger).Die Leitlinie zur Durchführung des Epikutantests mit Kontaktallergenen wurde auf der Basis einer systematischen Literatursuche zu definierten Schlüsselfragen evidenzbasiert und im formellen Konsensusverfahren (S3) von Dermatologen unter Einbindung von Pädiatern, Arbeitsmedizinern, Assistenzpersonal und Patientenvertretern erstellt. Bezüglich der methodischen und inhaltlichen Arbeit, auf denen die Empfehlungen basieren, wird auf Methodenbericht und Evidenztabellen verwiesen.Die Leitlinie stellt allgemeine Aspekte der Epikutantestung sowie medizinrechtlicher Aspekte dar. Es werden Empfehlungen gegeben zur Indikationsstellung, Patientenaufklärung, Auswahl von Testsubstanzen und Kammersystemen, Expositionsort, ‐dauer und Ablesezeitpunkten, Interpretation von Testreaktionen, endogenen und exogenen Einflussfaktoren, Testung besonderer Personengruppen (Kinder, Schwangere, Immunsupprimierte) sowie Risiken und unerwünschten Nebenwirkungen bei der Durchführung des Epikutantests mit Kontaktallergenen.
Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland
Authors: McFarlane S. Eryn , Hunter Darren C. , Senn Helen V. , Smith Stephanie L. , Holland Rebecca , Huisman Jisca , Pemberton Josephine M. 
Published: October 2019

AbstractHybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.
Capital and Value in Late Adulthood
Authors: Griffore Robert J. 
Published: October 2019

In the present neoliberal context, life is structured within management of capital. Late adulthood is a period of final decision making about human capital and financial capital. In past generations, older adults were supported by social capital systems of family and voluntary care, largely detached from large systems powered by financial capital. Now, late adulthood is about efficient movement of older adults from the workplace to retirement, from families to residential care, and on to death. Late adulthood is structured by efficient management of financial capital for and by systems that produce, manage, and/or deliver medical care, pharmaceuticals, residential care, insurance, investments, banking, death, and other services. In the present analysis, the focus is on financial capital, human capital, and social capital in late adulthood. The paper organizes some concepts and aspects of capital, value, aging, and late adulthood that are common knowledge and experience, for examination and analysis within systemic contexts.
The exigencies of student participation in university governance: Lip services and bottlenecks
Authors: Tamrat Wondwosen 
Published: October 2019

AbstractThis study was conducted to explore the level, type and quality of student participation in the governance milieu of twenty public universities in Ethiopia based on secondary data availed at a national level. The findings reveal that despite their demands and aspirations, students' participation in university governance is still at its lowest ebb across most of Ethiopian public universities both in terms of their representation at the available hierarchical structures and the quality of participation in matters of substantial importance to the student body. Given the multitude of advantages the institutions and students can garner from meaningful student participation, it is argued that changes need to be made in terms of improved representation, type and quality of student participation.