bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions
Authors: Bundgaard-Nielsen Caspar , Hagstrøm Søren , Sørensen Suzette 
Published: November 2018

AbstractDue to ease of acquisition, fecal samples are often used in studies investigating gut microbiota. Improper handling of these samples can lead to bacterial growth and alter bacterial composition. While freezing samples at −80 °C is considered gold standard, this is not suitable for studies utilizing self-sampling by lay participants or field studies. Thus to effectively prevent bacterial growth, techniques that allow efficient fecal storage outside laboratory facilities are needed. Fecal samples were collected from three donors. From each donor feces, 45 samples were collected and stored either freshly frozen at −80 or −20 °C, or in three separate storage buffers at room temperature or 4 °C for 24 or 72 hours. Bacterial composition was analyzed using Illumina amplicon sequencing of the V4 region of the 16 S rRNA gene. While storage conditions did affect bacterial composition and diversity compared to storage at −80 °C, the variation between donors superseded the variations introduced by storage. Samples stored at −20 °C most closely resembled those stored at −80 °C. When investigating variations in bacterial composition between separate study populations, fecal samples can efficiently be stored in −20 °C freezers or in one of the presented storage buffers, without severe alterations in bacterial composition.
Radar micro-Doppler signatures of drones and birds at K-band and W-band
Authors: Rahman Samiur , Robertson Duncan A. 
Published: November 2018

AbstractDue to the substantial increase in the number of affordable drones in the consumer market and their regrettable misuse, there is a need for efficient technology to detect drones in airspace. This paper presents the characteristic radar micro-Doppler properties of drones and birds. Drones and birds both induce micro-Doppler signatures due to their propeller blade rotation and wingbeats, respectively. These distinctive signatures can then be used to differentiate a drone from a bird, along with studying them separately. Here, experimental measurements of micro-Doppler signatures of different types of drones and birds are presented and discussed. The data have been collected using two radars operating at different frequencies; K-band (24 GHz) and W-band (94 GHz). Three different models of drones and four species of birds of varying sizes have been used for data collection. The results clearly demonstrate that a phase coherent radar system can retrieve highly reliable and distinctive micro-Doppler signatures of these flying targets, both at K-band and W-band. Comparison of the signatures obtained at the two frequencies indicates that the micro-Doppler return from the W-band radar has higher SNR. However, micro-Doppler features in the K-band radar returns also reveal the micro-motion characteristics of drones and birds very effectively.
A reference set of curated biomedical data and metadata from clinical case reports
Authors: Caufield J. Harry , Zhou Yijiang , Garlid Anders O. , Setty Shaun P. , Liem David A. , Cao Quan , Lee Jessica M. , Murali Sanjana , Spendlove Sarah , Wang Wei , Zhang Li , Sun Yizhou , Bui Alex , Hermjakob Henning , Watson Karol E. , Ping Peipei 
Published: November 2018

AbstractClinical case reports (CCRs) provide an important means of sharing clinical experiences about atypical disease phenotypes and new therapies. However, published case reports contain largely unstructured and heterogeneous clinical data, posing a challenge to mining relevant information. Current indexing approaches generally concern document-level features and have not been specifically designed for CCRs. To address this disparity, we developed a standardized metadata template and identified text corresponding to medical concepts within 3,100 curated CCRs spanning 15 disease groups and more than 750 reports of rare diseases. We also prepared a subset of metadata on reports on selected mitochondrial diseases and assigned ICD-10 diagnostic codes to each. The resulting resource, Metadata Acquired from Clinical Case Reports (MACCRs), contains text associated with high-level clinical concepts, including demographics, disease presentation, treatments, and outcomes for each report. Our template and MACCR set render CCRs more findable, accessible, interoperable, and reusable (FAIR) while serving as valuable resources for key user groups, including researchers, physician investigators, clinicians, data scientists, and those shaping government policies for clinical trials.
A data citation roadmap for scientific publishers
Authors: Cousijn Helena , Kenall Amye , Ganley Emma , Harrison Melissa , Kernohan David , Lemberger Thomas , Murphy Fiona , Polischuk Patrick , Taylor Simone , Martone Maryann , Clark Tim 
Published: November 2018

AbstractThis article presents a practical roadmap for scholarly publishers to implement data citation in accordance with the Joint Declaration of Data Citation Principles (JDDCP), a synopsis and harmonization of the recommendations of major science policy bodies. It was developed by the Publishers Early Adopters Expert Group as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH BioCADDIE program. The structure of the roadmap presented here follows the “life of a paper” workflow and includes the categories Pre-submission, Submission, Production, and Publication. The roadmap is intended to be publisher-agnostic so that all publishers can use this as a starting point when implementing JDDCP-compliant data citation. Authors reading this roadmap will also better know what to expect from publishers and how to enable their own data citations to gain maximum impact, as well as complying with what will become increasingly common funder mandates on data transparency.
Complementary proteomics strategies capture an ataxin-1 interactome in Neuro-2a cells
Authors: Zhang Sunyuan , Williamson Nicholas A. , Bogoyevitch Marie A. 
Published: November 2018

AbstractAtaxin-1 mutation, arising from a polyglutamine (polyQ) tract expansion, is the underlying genetic cause of the late-onset neurodegenerative disease Spinocerebellar ataxia type 1 (SCA1). To identify protein partners of polyQ-ataxin-1 in neuronal cells under control or stress conditions, here we report our complementary proteomics strategies of proximity-dependent biotin identification (BioID) and affinity purification (via GFP-Trap pulldown) in Neuro-2a cells expressing epitope-tagged forms of ataxin-1[85Q]. These approaches allowed our enrichment of proximal proteins and interacting partners, respectively, with the subsequent protein identification performed by liquid chromatography-MS/MS. Background proteins, not dependent on the presence of the polyQ-ataxin-1 protein, were additionally defined by their endogenous biotinylation (for the BioID protocol) or by their non-specific interaction with GFP only (in the GFP-Trap protocol). All datasets were generated from biological replicates. Following the removal of the identified background proteins from the acquired protein lists, our experimental design has captured a comprehensive polyQ-ataxin-1 proximal and direct protein partners under normal and stress conditions. Data are available via ProteomeXchange, with identifier PXD010352.
Kinderanästhesie mit Sicherheit: Update Medikamentensicherheit
Authors: Kaufmann Jost , Laschat Michael , Wappler Frank 
Published: November 2018

ZusammenfassungMedikamentenfehler kommen in allen Versorgungsbereichen vor. Bei Kindern steigt die Fehlerwahrscheinlichkeit im Vergleich zu Erwachsenen aufgrund altersgruppenspezifischer Besonderheiten und der erforderlichen Dosisberechnung. Wesentliche Aspekte sind: die Erkenntnis, dass jeder Versorger fehlbar ist, und die Akzeptanz von Sicherheitsstrukturen. Dieser Beitrag beschreibt einen Katalog alltagstauglicher Maßnahmen zur Medikamentensicherheit.
Tetraplegie nach radikaler Zystektomie
Authors: Hachenberg Thomas , Schaffartzik Walter , Wohlers Christine 
Published: November 2018

ZusammenfassungSchlichtungsstellen für Arzthaftpflichtfragen bieten Patienten, Ärzten und Versicherern eine Möglichkeit, Arzthaftungsstreitigkeiten außergerichtlich zu klären. In der Rubrik „Fälle der Schlichtungsstelle“ stellen wir abgeschlossene Fälle aus der Schlichtungsstelle für Arzthaftpflichtfragen der norddeutschen Ärztekammern vor.
Genetische Ursachen und genetische Diagnostik bei hereditären Optikusatrophien
Authors: Wissinger Bernd 
Published: November 2018

ZusammenfassungHereditäre Optikusatrophien stellen eine heterogene Gruppe seltener degenerativer Erkrankungen der retinalen Ganglienzellen und ihrer Axone, welche den Sehnerv bilden, dar. Mit einer geschätzten Prävalenz von 1 : 10 000 bis 1 : 20 000 betreffen die hereditären Optikusatrophien in ihrer Gesamtheit etwa 4000 – 8000 Menschen in Deutschland. Am verbreitetsten sind die Leberʼsche Optikusatrophie (LHON) und die autosomal-dominante Optikusatrophie (ADOA). Neben den isolierten Optikusatrophien, deren Symptomatik sich auf das visuelle System beschränkt, gibt es zahlreiche Krankheitsbilder, bei welchen die Optikusatrophie Teil einer syndromalen Erkrankung mit vornehmlich neurosensorischer, neurologischer und/oder neuromuskulärer Symptomatik ist. Der Vererbungsmodus ist heterogen mit einer rein maternalen Vererbung bei der LHON und autosomal-dominanter Vererbung bei der ADOA. Deutlich seltener sind Fälle mit autosomal-rezessiver oder X-chromosomal-rezessiver Vererbung. Die Penetranz ist jedoch unvollständig. Bei der LHON erkranken zudem weitaus häufiger Männer als Frauen. Die genetischen Ursachen der hereditären Optikusatrophien sind heterogen, aber größtenteils bekannt. Die molekulargenetische Diagnostik liefert daher in der Mehrzahl der untersuchten Fälle ein aussagekräftiges Ergebnis, mit welchem die klinische Diagnose abgesichert, das Wiederholungsrisiko in der Familie konkret kalkuliert oder im Falle der Bestätigung einer LHON eine therapeutische Behandlung initiiert werden kann. Dieser Artikel gibt eine Übersicht über die genetischen Ursachen der hereditären Optikusatrophien und die Optionen und Modalitäten einer molekulargenetischen Diagnostik einschließlich Hinweisen zu deren Implementierung in der Praxis.
TGF-β–SMAD–miR-520e axis regulates NSCLC metastasis through a TGFBR2-mediated negative-feedback loop
Authors: Kucuksayan Hakan , Akgun Sakir , Ozes Osman Nidai , Alikanoglu Arsenal Sezgin , Yildiz Mustafa , Dal Egemen , Akca Hakan 
Published: November 2018

AbstractTransforming growth factor-β (TGF-β) pathway plays crucial roles during the carcinogenesis and metastasis. TGF-β receptor 2 (TGFBR2) is a key molecule for the regulation of TGF-β pathway and frequently downregulated or lost in several cancer types including non-small cell lung cancer (NSCLC), and TGF-β pathway is often regulated by negative-feedback mechanisms, but little is known about the mechanism of TGFBR2 downregulation in NSCLC. Here, we found that the expression of miR-520e is upregulated in metastatic tumor tissues compared with non-metastatic ones, and its expression is inversely correlated with that of TGFBR2 in clinical samples. We also discovered that TGF-β dramatically increased the expression of miR-520e, which targeted and downregulated TGFBR2, and the suppression of miR-520e significantly impaired TGF-β-induced TGFBR2 downregulation. Chromatin immunoprecipitation–PCR experiments further showed that miR-520e is transcriptionally induced by SMAD2/3 in response to TGF-β. Our findings reveal a novel negative-feedback mechanism in TGF-β signaling and the expression level of miR-520e could be a predictive biomarker for NSCLC metastasis.
The Epidemiology of Herpes Zoster in the United States During the Era of Varicella and Herpes Zoster Vaccines: Changing Patterns Among Older Adults
Authors: Harpaz Rafael , Leung Jessica W 
Published: November 2018

Abstract
Historic herpes zoster incidence trends in US adults have been hard to interpret. Using administrative databases, we extended previous descriptions of these trends through 2016. We observed an age-specific transition, with ongoing increases among younger adults but deceleration in older adults. The patterns are not readily explained.
Dynamic transcriptomic analysis reveals suppression of PGC1α/ERRα drives perturbed myogenesis in facioscapulohumeral muscular dystrophy
Authors: Banerji Christopher R S , Panamarova Maryna , Pruller Johanna , Figeac Nicolas , Hebaishi Husam , Fidanis Efthymios , Saxena Alka , Contet Julian , Sacconi Sabrina , Severini Simone , Zammit Peter S 
Published: November 2018

Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a prevalent, incurable myopathy, linked to epigenetic derepression of D4Z4 repeats on chromosome 4q, leading to ectopic DUX4 expression. FSHD patient myoblasts have defective myogenic differentiation, forming smaller myotubes with reduced myosin content. However, molecular mechanisms driving such disrupted myogenesis in FSHD are poorly understood. We performed high-throughput morphological analysis describing FSHD and control myogenesis, revealing altered myogenic differentiation results in hypotrophic myotubes. Employing polynomial models and an empirical Bayes approach, we established eight critical time points during which human healthy and FSHD myogenesis differ. RNA-sequencing at these eight nodal time points in triplicate, provided temporal depth for a multivariate regression analysis, allowing assessment of interaction between progression of differentiation and FSHD disease status. Importantly, the unique size and structure of our data permitted identification of many novel FSHD pathomechanisms undetectable by previous approaches. For further analysis here, we selected pathways that control mitochondria: of interest considering known alterations in mitochondrial structure and function in FSHD muscle, and sensitivity of FSHD cells to oxidative stress. Notably, we identified suppression of mitochondrial biogenesis, in particular via peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC1α), the cofactor and activator of oestrogen-related receptor α (ERRα). PGC1α knock-down caused hypotrophic myotubes to form from control myoblasts. Known ERRα agonists and safe food supplements biochanin A, daidzein or genistein, each rescued the hypotrophic FSHD myotube phenotype. Together our work describes transcriptomic changes in high resolution that occur during myogenesis in FSHD ex vivo, identifying suppression of the PGC1α-ERRα axis leading to perturbed myogenic differentiation, which can effectively be rescued by readily available food supplements.
Pattern Recognition Receptor Polymorphisms as Predictors of Oxaliplatin Benefit in Colorectal Cancer
Authors: Gray Victoria , Briggs Sarah , Palles Claire , Jaeger Emma , Iveson Timothy , Kerr Rachel , Saunders Mark P , Paul James , Harkin Andrea , McQueen John , Summers Matthew G , Johnstone Elaine , Wang Haitao , Gatcombe Laura , Maughan Timothy S , Kaplan Richard , Escott-Price Valentina , Al-Tassan Nada A , Meyer Brian F , Wakil Salma M , Houlston Richard S , Cheadle Jeremy P , Tomlinson Ian , Church David N 
Published: November 2018

Abstract

Background
Constitutional loss of function (LOF) single nucleotide polymorphisms (SNPs) in pattern recognition receptors FPR1, TLR3, and TLR4 have previously been reported to predict oxaliplatin benefit in colorectal cancer. Confirmation of this association could substantially improve patient stratification.

Methods
We performed a retrospective biomarker analysis of the Short Course in Oncology Therapy (SCOT) and COIN/COIN-B trials. Participant status for LOF variants in FPR1 (rs867228), TLR3 (rs3775291), and TLR4 (rs4986790/rs4986791) was determined by genotyping array or genotype imputation. Associations between LOF variants and disease-free survival (DFS) and overall survival (OS) were analyzed by Cox regression, adjusted for confounders, using additive, dominant, and recessive genetic models. All statistical tests were two-sided.

Results
Our validation study populations included 2929 and 1948 patients in the SCOT and COIN/COIN-B cohorts, respectively, of whom 2728 and 1672 patients had functional status of all three SNPs determined. We found no evidence of an association between any SNP and DFS in the SCOT cohort, or with OS in either cohort, irrespective of the type of model used. This included models for which an association was previously reported for rs867228 (recessive model, multivariable-adjusted hazard ratio [HR] for DFS in SCOT = 1.19, 95% confidence interval [CI] = 0.99 to 1.45, P = .07; HR for OS in COIN/COIN-B = 0.92, 95% CI = 0.63 to 1.34, P = .66), and rs4986790 (dominant model, multivariable-adjusted HR for DFS in SCOT = 0.86, 95% CI = 0.65 to 1.13, P = .27; HR for OS in COIN/COIN-B = 1.08, 95% CI = 0.90 to 1.31, P = .40).

Conclusion
In this prespecified analysis of two large clinical trials, we found no evidence that constitutional LOF SNPs in FPR1, TLR3, or TLR4 are associated with differential benefit from oxaliplatin. Our results suggest these SNPs are unlikely to be clinically useful biomarkers.
Effects of the Refugee Crisis on Perceptions of Asylum Seekers in Recipient Populations
Authors: Bjånesøy Lise Lund 
Published: November 2018

AbstractThis article examines the effects of the refugee crisis on perceptions of asylum seekers. Previous research has demonstrated that asylum seekers are perceived in terms of deservingness—either as deserving refugees in need of help or as undeserving and unwelcome exploiters. The article uses unique panel data from a representative sample drawn directly from the Norwegian population registry. Through Structural Topic Modelling (STM) of open-ended survey responses fielded before and after the refugee crisis, this article analyses, first, how ordinary citizens perceive asylum seekers and, second, the article documents that these perceptions of asylum seekers changed. They did, however, not change from perceiving asylum seekers as deserving to perceiving them as undeserving. The change was more subtle. Responses that characterize asylum seekers as deserving prior to the crisis tended to reflect a sense of responsibility to help—of involvement. Responses after the crisis were more distanced, even as they characterized the asylum seekers as deserving. All in all, these findings improve our knowledge about how the refugee crisis affected public opinion in recipient populations.
Mapping museum ‘Soft Power’: Adding geo-visualization to the methodological framework
Authors: Grincheva Natalia 
Published: November 2018

AbstractThe article proposes, justifies, and tests a new methodological framework to measure museum ‘soft power’ by employing geo-visualization as a new method empowered by the rapid development of digital humanities. This research not only demystifies the buzz term of ‘soft power’ that is frequently applied in relation to contemporary museums and their international cultural engagements but also develops an evaluation framework to assess museum capacities to exert global impacts. Specifically, the article draws on the academic scholarship outlining a plethora of approaches for ‘soft power’ evaluation, including Resources, Outputs, Perceptions, and Networks evaluation models. It argues for a new integrative approach that can comprehensively combine different methods to construct a more advanced tool to measure museum ‘soft power’. The article draws on preliminary results of developing a digital mapping system to assess museum soft power. It shares findings from the pilot project, Australian Center of the Moving Image (ACMI) on the Global Map, designed in collaboration with the ACMI in Melbourne.
Generalized Update Semantics
Authors: Goldstein Simon 
Published: November 2018

AbstractThis paper explores the relationship between dynamic and truth conditional semantics for epistemic modals. It provides a generalization of a standard dynamic update semantics for modals. This new semantics derives a Kripke semantics for modals and a standard dynamic semantics for modals as special cases. The semantics allows for new characterizations of a variety of principles in modal logic, including the inconsistency of ‘p and might not p’. Finally, the semantics provides a construction procedure for transforming any truth conditional semantics for modals into a dynamic semantics for modals with similar properties.
Baseline graft status is a critical predictor of kidney graft failure after diarrhoea
Authors: Devresse Arnaud , Morin Lise , Aulagnon Florence , Taupin Jean-Luc , Scemla Anne , Lanternier Fanny , Aubert Olivier , Aidoud Adel A , Lebreton Xavier , Sberro-Soussan Rebecca , Snanoudj Renaud , Amrouche Lucile , Tinel Claire , Martinez Frank , Bererhi Lynda , Anglicheau Dany , Lortholary Olivier , Legendre Christophe , Avettand-Fenoel Véronique , Zuber Julien 
Published: November 2018

AbstractBackgroundDiarrhoea is one of the most frequent complications after kidney transplantation (KT). Non-infectious diarrhoea has been associated with reduced graft survival in kidney transplant recipients. However, the risk factors for renal allograft loss following diarrhoea remain largely unknown.MethodsBetween January 2010 and August 2011, 195 consecutive KT recipients who underwent standardized microbiological workups for diarrhoea at a single centre were enrolled in this retrospective study.ResultsAn enteric pathogen was readily identified in 91 patients (47%), while extensive microbiological investigations failed to find any pathogen in the other 104. Norovirus was the leading cause of diarrhoea in these patients, accounting for 30% of the total diarrhoea episodes. The baseline characteristics were remarkably similar between non-infectious and infectious diarrhoea patients, with the exception that the non-infectious group had significantly lower graft function before diarrhoea (P = 0.039). Infectious diarrhoea was associated with a longer duration of symptoms (P = 0.001) and higher rates of acute kidney injury (P = 0.029) and hospitalization (P &lt; 0.001) than non-infectious diarrhoea. However, the non-infectious group had lower death-censored graft survival than the infectious group (Gehan–Wilcoxon test, P = 0.038). Multivariate analysis retained three independent predictors of graft failure after diarrhoea: diarrhoea occurring ≥5 years after KT [hazard ratio (HR) 4.82; P &lt; 0.001], re-transplantation (HR 2.38; P = 0.001) and baseline estimated glomerular filtration rate &lt;30 mL/min/1.73 m2 (HR 11.02; P &lt; 0.001).ConclusionOur study shows that pre-existing conditions (re-transplantation, chronic graft dysfunction and late occurrence) determine the primary functional long-term consequences of post-transplant diarrhoea.