bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agreement between endoscopic ultrasound-guided fine-needle aspiration and endobiliary brush cytology in suspected pancreaticobiliary malignancies
Authors: Sullivan Matthew , Kincaid Hope , Shah Shashin , Shah Hiral 
Published: December 2017

Abstract
Background and study aims For suspected pancreaticobiliary malignancies, endobiliary brush cytology during endoscopic retrograde cholangiopancreatography (ERCP) remains the diagnostic test of choice despite historically poor and variable sensitivity. This has led to increased use of endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) as an initial test. Recently, our institution began using a cytology brush that was designed specifically to collect a more substantial and higher-quality sample. The aim of this study was to investigate whether this brush design would provide more adequate samples and have high agreement with EUS-FNA in patients who underwent both procedures.
Patients and methods A retrospective chart review was conducted of all patients who underwent both EUS-FNA and endobiliary brush cytology for suspicion of pancreaticobiliary malignancy from January 2013 to May 2015. A total of 41 patients met the inclusion criteria. Initially, sample quality was evaluated. Final cytology results were then assessed for agreement with EUS-FNA using Cohen’s kappa. The effect of considering atypical cytology as negative was also uniquely evaluated by running separate analyses.
Results Brush cytology provided an adequate sample in 95.1 % of cases. Cohen’s Kappa demonstrated moderate agreement between brush cytology and EUS-FNA: κ = 0.42 (P = 0.001). When atypical results were excluded, agreement increased: κ = 0.60 (P = 0.02), but remained moderate. If atypical results were considered “positive,” the two procedures demonstrated equal cancer detection rates of 80.8 %.
Conclusions The studied brush provided more adequate samples compared with historical rates for brush cytology and had moderate agreement with EUS-FNA. If this brush truly increases sample adequacy, it could potentially provide results comparable to EUS-FNA at lower cost.
Seitwärtsbewegung auf einer Unterstützungsfläche
Authors: Muesse André , Vehma Stefanie , Brutscher Petra , Eppler Sonja 
Published: December 2017

Zusammenfassung
Auf vielen Wegen zur Fortbewegung Aufbauend auf den Transfer aus der Rücken- in die Seitenlage erläutern die Autoren hier die Bewegung
seitwärts auf einer Unterstützungsfläche – beispielsweise im Bett – und stellen ihre Anwendbarkeit im pflegerischen Kontext dar. Wie schon
in den vorangegangenen Artikeln dieser Serie wird es auch hierbei die Unterscheidung der Anwendung beim Früh-/Neugeborenen und der beim
älteren Kind geben. Das zugrundeliegende Bewegungsmuster ist in beiden Fällen dasselbe, bedarf jedoch individuell unterschiedlicher
Unterstützung durch die Pflegekraft oder eine andere helfende Person.
Besuche mit Struktur
Authors: Thielmann Susanna 
Published: December 2017

Zusammenfassung
Geschwisterkinder auf der interdisziplinären pädiatrischen Intensivstation Jedes Kind reagiert anders, wenn es zum ersten Mal sein
krankes Geschwister auf einer Intensivstation besucht. Eine Begleitung dieser Kinder sollte daher individuell und dem Alter und der
Situation angemessen sein. Wie Pflegende diese Begleitung professionell gestalten können, zeigt dieser Beitrag.
Demenzielle Syndrome: die Grundlagen
Authors: Zemke Jens 
Published: December 2017

Zusammenfassung
Neurodegeneration In westlichen Industrienationen leiden mehr als 8 % der über 65-Jährigen unter mittelschweren oder schweren
Demenzformen. Der Begriff demenzielles Syndrom steht für eine heterogene Gruppe von Erkrankungen mit der gemeinsamen Endstrecke des
allgemeinen intellektuellen Abbaus. Häufig wird das demenzielle Syndrom gleichbedeutend mit dem Begriff Demenz verwendet.
Konfundierungen und Störfaktoren in rehabilitationswissenschaftlichen Beobachtungs- und Interventionsstudien
Authors: Wirtz Markus 
Published: December 2017

ZusammenfassungUm Effekte von Rehabilitationsmaßnahmen prüfen zu können, muss das Studiendesign so gewählt werden, dass Veränderungen der Zielvariablen (z. B. Gesundheitszustand) möglichst eindeutig auf die Interventionsmaßnahme zurückgeführt werden können. Bei Beobachtungsstudien muss davon ausgegangen werden, dass konfundierende Merkmale den Einfluss der Maßnahme auf die Zielvariable systematisch überlagern und Effektschätzungen verzerren. Die Präferenz für eine Behandlungsalternative, die Behandlungsmotivation sowie das Ausmaß der initialen Beeinträchtigung der Rehabilitanden sind typische Konfundierungen, die insbesondere bei freiwilliger Behandlungsauswahl oder bei Teilnahme nach Behandlungsempfehlung berücksichtigt werden müssen (programmexterne Störfaktoren). Bei gut kontrollierten Interventionsstudien (insb. randomisiert kontrollierte Studien, RCT), bei denen die Inanspruchnahme der Behandlung systematisch kontrolliert erfolgt, können diese Fehlerquellen vermieden werden. Aber auch bei gut kontrollierten Interventionsstudien kann die Studiendurchführung (z. B. aufgrund der Stichprobenauswahl, des Einsatzes von Messinstrumenten, des Austauschs zwischen Vergleichsgruppen; Designeffekte, Treatmentkontaminationen) die eindeutige Interpretierbarkeit der Studienbefunde beeinträchtigen. In diesem Beitrag wird gezeigt, welche Konfundierungen und Störeinflüsse typischerweise die Validität der Schlussfolgerungen aus empirischen Zusammenhängen verringern können. Es wird verdeutlicht, wie potenziell verzerrende Konfundierungen und Effekte von Störfaktoren durch die Gestaltung der Untersuchung vermieden oder bestmöglich kontrolliert werden können.
Visual assessment of colorectal flat and depressed lesions by using narrow band imaging
Authors: Nakamura Hiroshi , Ikematsu Hiroaki , Osera Shozo , Ito Renma , Sato Daiki , Minamide Tatsunori , Okamoto Naoki , Yamamoto Yoichi , Hombu Takuya , Takashima Kenji , Nakajo Keiichiro , Kadota Tomohiro , Yoda Yusuke , Hori Keisuke , Oono Yasuhiro , Yano Tomonori 
Published: December 2017

Abstract
Background and study aims Visual assessment of laterally spreading tumors non-granular type (LST-NG) and depressed lesions by narrow band imaging (NBI) without magnification has not been studied. We investigated the role of non-magnifying NBI in detecting LST-NG and type IIc lesions on colonoscopy.
Patients and methods This retrospective study examined consecutive patients diagnosed as having LST-NG and/or type IIc lesions in our hospital between August 2011 and July 2013. These lesions were classified as “Brownish area (BA),” “Brown only in the margins (O-ring sign),” “Same color as the normal mucosa (SC),” and “Whitish area (WA)” based on their appearance on non-magnifying NBI, and their appearance were compared with their histopathological findings.
Results A total of 18 type IIc and 180 LST-NG lesions were analyzed. Among the type IIc lesions, 5 (28 %), 12 (67 %), and 1 (5 %) were classified as BA, O-ring sign, and SC, respectively. Among the LST-NG lesions, 126 (70 %), 26 (14 %), and 28 lesions (16 %) were classified as BA, O-ring sign, and SC, respectively. The IIc lesions were found to have 1 lesion (20 %) with high-grade dysplasia (HGD) in the BA, and 2 lesions (17 %) with invasive cancer (IC) in the O-ring sign group. Among the LST-NG lesions, 27 (21 %) were found to have IC and 49 (39 %), HGD in the BA group; 8 lesions (31 %) had IC and 4 (15 %) had HGD in the O-ring sign group; and 1 lesion (4 %) had IC and 4 (14 %) had HGD in the SC group.
Conclusions Most flat and depressed colorectal lesions were seen on non-magnifying NBI as brown lesions with the exception of some flat lesions that were indistinguishable in color from the adjacent normal mucosa. Some of these flat lesions were also found to have HGD or IC.
Systematischer Review zur Krankheitslast durch Campylobacter spp.
Authors: Lackner Julia , Schlichting Daniela , Müller-Graf Christine , Greiner Matthias 
Published: December 2017

ZusammenfassungCampylobacter spp. sind Bakterien, die weltweit als einer der häufigsten Auslöser für eine Gastroenteritis gelten und zu schwerwiegenden Folgeerkrankungen führen können. Die Krankheitslast durch Campylobacterbakterien wurde bereits in mehreren Studien mithilfe der quantitativen Maßzahl disability-adjusted life years (DALY) für ausgewählte Länder berechnet. Ziel der Übersichtsarbeit ist es zu evaluieren, ob die berechneten DALYs in den betrachten Ländern und Zeiträume vergleichbar sind und wenn nicht, welche Faktoren die Schätzungen beeinflussen. Da als wichtigster Übertragungsweg für Campylobacter spp. Lebensmittel gelten, wurden auch Publikationen in die Suche einbezogen, die nur die lebensmittelbedingte Krankheitslast abbildeten. Mithilfe einer systematischen Literatursuche, wurden 21 länderspezifische Publikationen und eine Studie der Weltgesundheitsorganisation im Suchzeitraum 1/1996–6/2016 gefunden. Durch unterschiedliche Methoden bei der Berechnung der Krankheitslast sowie die Qualitätsunterschiede der Daten schwanken die Ergebnisse der Schätzungen der Gesamtkrankheitslast in den länderspezifischen Publikationen von 0,4 DALYs in Frankreich bis 109 DALY pro 100000 Einwohner in Polen. Da die Berechnung des attributablen Risikos auf Grundlage der mit Unsicherheiten behafteten Schätzungen der Inzidenzen der campylobacterbedingten Erkrankungen erfolgt, zeigen sich auch bei der lebensmittelbedingten Krankheitslast große Spannweiten von 0,5 DALYs pro 100000 Einwohner in Griechenland bis 21,2 DALY pro 100000 Einwohner in Neuseeland, welche nicht ausschließlich auf die länderspezifischen Variabilität in der Produktion, dem Verzehrsverhalten und dem Vorkommen von Campylobacter spp. zurückzuführen sind.
Accurate mapping of tRNA reads
Authors: Hoffmann Anne , Fallmann Jörg , Vilardo Elisa , Mörl Mario , Stadler Peter F , Amman Fabian 
Published: December 2017

Abstract

Motivation
Many repetitive DNA elements are transcribed at appreciable expression levels. Mapping the corresponding RNA sequencing reads back to a reference genome is notoriously difficult and error-prone task, however. This is in particular true if chemical modifications introduce systematic mismatches, while at the same time the genomic loci are only approximately identical, as in the case of tRNAs.

Results
We therefore developed a dedicated mapping strategy to handle RNA-seq reads that map to tRNAs relying on a modified target genome in which known tRNA loci are masked and instead intronless tRNA precursor sequences are appended as artificial ‘chromosomes’. In a first pass, reads that overlap the boundaries of mature tRNAs are extracted. In the second pass, the remaining reads are mapped to a tRNA-masked target that is augmented by representative mature tRNA sequences. Using both simulated and real life data we show that our best-practice workflow removes most of the mapping artefacts introduced by simpler mapping schemes and makes it possible to reliably identify many of chemical tRNA modifications in generic small RNA-seq data. Using simulated data the FDR is only 2%. We find compelling evidence for tissue specific differences of tRNA modification patterns.

Availability and implementation
The workflow is available both as a bash script and as a Galaxy workflow from https://github.com/AnneHoffmann/tRNA-read-mapping.

Supplementary information
Supplementary data are available at Bioinformatics online.
LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models
Authors: Soto Axel J , Zerva Chrysoula , Batista-Navarro Riza , Ananiadou Sophia 
Published: December 2017

AbstractMotivationPathway models are valuable resources that help us understand the various mechanisms underpinning complex biological processes. Their curation is typically carried out through manual inspection of published scientific literature to find information relevant to a model, which is a laborious and knowledge-intensive task. Furthermore, models curated manually cannot be easily updated and maintained with new evidence extracted from the literature without automated support.ResultsWe have developed LitPathExplorer, a visual text analytics tool that integrates advanced text mining, semi-supervised learning and interactive visualization, to facilitate the exploration and analysis of pathway models using statements (i.e. events) extracted automatically from the literature and organized according to levels of confidence. LitPathExplorer supports pathway modellers and curators alike by: (i) extracting events from the literature that corroborate existing models with evidence; (ii) discovering new events which can update models; and (iii) providing a confidence value for each event that is automatically computed based on linguistic features and article metadata. Our evaluation of event extraction showed a precision of 89% and a recall of 71%. Evaluation of our confidence measure, when used for ranking sampled events, showed an average precision ranging between 61 and 73%, which can be improved to 95% when the user is involved in the semi-supervised learning process. Qualitative evaluation using pair analytics based on the feedback of three domain experts confirmed the utility of our tool within the context of pathway model exploration.Availability and implementationLitPathExplorer is available at http://nactem.ac.uk/LitPathExplorer_BI/.Supplementary informationSupplementary data are available at Bioinformatics online.
DeepSF: deep convolutional neural network for mapping protein sequences to folds
Authors: Hou Jie , Adhikari Badri , Cheng Jianlin 
Published: December 2017

AbstractMotivationProtein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice.ResultsWe develop a deep 1D-convolution neural network (DeepSF) to directly classify any protein sequence into one of 1195 known folds, which is useful for both fold recognition and the study of sequence–structure relationship. Different from traditional sequence alignment (comparison) based methods, our method automatically extracts fold-related features from a protein sequence of any length and maps it to the fold space. We train and test our method on the datasets curated from SCOP1.75, yielding an average classification accuracy of 75.3%. On the independent testing dataset curated from SCOP2.06, the classification accuracy is 73.0%. We compare our method with a top profile–profile alignment method—HHSearch on hard template-based and template-free modeling targets of CASP9-12 in terms of fold recognition accuracy. The accuracy of our method is 12.63–26.32% higher than HHSearch on template-free modeling targets and 3.39–17.09% higher on hard template-based modeling targets for top 1, 5 and 10 predicted folds. The hidden features extracted from sequence by our method is robust against sequence mutation, insertion, deletion and truncation, and can be used for other protein pattern recognition problems such as protein clustering, comparison and ranking.Availability and implementationThe DeepSF server is publicly available at: http://iris.rnet.missouri.edu/DeepSF/.Supplementary informationSupplementary data are available at Bioinformatics online.
Species-specific residence times in the aft part of a pelagic survey trawl: implications for inference of pre-capture spatial distribution using the Deep Vision system
Authors: Underwood Melanie J , Rosen Shale , Engås Arill , Jørgensen Terje , Fernö Anders 
Published: December 2017

Abstract
In-trawl camera systems promise to improve the resolution of trawl sampling used to ground-truth the interpretation of acoustic survey data. In this study, the residence time of fish in front of the Deep Vision camera system, used to identify, measure and count fish inside the trawl, was analysed to determine the reliability of spatial distribution recorded by the system. Although Atlantic herring (Clupea harengus), haddock (Melanogrammus aeglefinus), and most Atlantic cod (Gadus morhua) moved quickly back through the aft part of the pelagic trawl, saithe (Pollachius virens) spent up to 4 min in front of the system. The residence time increased for saithe and cod when other individuals were present, and cod swimming in the low water flow close to the trawl netting spent longer there than cod at the centre of the trawl. Surprisingly, residence time was not related to the size of the fish, which may be explained by the collective behaviour of shoaling fish. Our findings suggest that while in-trawl images can be used to identify, measure and count most species, when sampling fast-swimming species such as saithe the position inferred from when they were imaged may not reflect the actual spatial distribution prior to capture.
Connectedness of Brill–Noether Loci via Degenerations
Authors: Osserman Brian 
Published: December 2017

Abstract
We show that limit linear series spaces for chains of curves are reduced. Using recent advances in the foundations of limit linear series, we then use degenerations to study the question of connectedness for spaces of linear series with imposed ramification at up to two points. We find that in general, these spaces may not be connected even when they have positive dimension, but we prove a criterion for connectedness which generalizes the theorem previously proved by Fulton and Lazarsfeld in the case without imposed ramification.
In Vivo Circuit Analysis
Authors: Bowman Ryan , Schwennesen Hannah , Dzirasa Kafui , Hultman Rainbo 
Published: December 2017

Abstract
Breakthroughs in understanding neural circuit activity hold much promise for developing next generation therapeutics for psychiatric disorders. Determination of how dynamic activity is coordinated across brain regions to effect specific behavioral function (or dysfunction) enables the development of therapeutics with increased specificity and fewer side effects. This chapter discusses methodologies for measuring neural circuit activity in humans and in animal models, and describes a bidirectional research pipeline whereby studies in humans are followed by tightly controlled studies in animal models that can then be applied back to humans. Targeted neural circuit manipulations from these studies are already being applied to a wide range of therapeutic strategies.
Neuromodulation and Psychiatric Disorders
Authors: Goodman Wayne K. , George Mark S. 
Published: December 2017

Abstract
An increasing number of approaches permit psychiatrists to directly stimulate the brain. Such therapies are sometimes referred to as neuromodulation, as psychiatrists can either excite or inhibit neuronal firing in the brain. This chapter reviews two such technologies—transcranial magnetic stimulation (TMS) and deep brain stimulation (DBS). Both techniques have FDA approval and are moving into mainstream therapeutic use. Daily prefrontal TMS for 4–6 weeks is FDA approved for treating depression, with minimal side effects. It is now accepted in most treatment algorithms as an approach for patients who have not responded to medications or talking therapy. DBS has virtually replaced ablative neurosurgery for use in medication-refractory movement disorders such as Parkinson’s Disease (PD), where it has the advantages of being reversible (explantable) and adjustable. DBS is now being studied in severe psychiatric conditions, such as intractable obsessive-compulsive disorder (OCD) and treatment resistant depression (TRD).
The Neurobiology of Sleep
Authors: Tononi Giulio , Cirelli Chiara 
Published: December 2017

Abstract
Sleep is required for health and well-being, and consumes roughly one-third of a human’s lifetime, yet its functions remain incompletely understood. This chapter provides an overview of so-called sleep architecture—the stages and cycles that characterize sleep, including rapid eye movement (REM) and non-REM periods. Also discussed are the numerous regions of brain and neurotransmitters that control the induction of sleep, the transitions between REM and non-REM sleep cycles, and wakefulness. Key brain systems include GABAergic neurons in the pre-optic area, the neuropeptide orexin in lateral hypothalamic neurons, histaminergic neurons in the hypothalamus, monoaminergic (norepinephrine and serotonin) and acetylcholinergic nuclei in the brainstem, and the brain’s adenosine system, all of which work in integrated circuits to control sleep and wakefulness. Overlaid on sleep-wake cycles are circadian rhythms, and the crucial role played by the suprachiasmatic nucleus in entraining such rhythms to environmental light.
Genetics of Schizophrenia and Bipolar Disorder
Authors: Charney Alexander , Sklar Pamela 
Published: December 2017

Abstract
Schizophrenia and bipolar disorder are the classic psychotic disorders. Both diseases are strongly familial, but have proven recalcitrant to genetic methodologies for identifying the etiology until recently. There is now convincing genetic evidence that indicates a contribution of many DNA changes to the risk of becoming ill. For schizophrenia, there are large contributions of rare copy number variants and common single nucleotide variants, with an overall highly polygenic genetic architecture. For bipolar disorder, the role of copy number variation appears to be much less pronounced. Specific common single nucleotide polymorphisms are associated, and there is evidence for polygenicity. Several surprises have emerged from the genetic data that indicate there is significantly more molecular overlap in copy number variants between autism and schizophrenia, and in common variants between schizophrenia and bipolar disorder.
Neuroimaging of Psychotic Disorders
Authors: Heckers Stephan , Woodward Neil , Öngür Dost 
Published: December 2017

Abstract
Neuroimaging of psychotic disorders began in the 1970s with studies of brain structure, followed by studies of blood flow, glucose metabolism, and receptor chemistry. More recently, studies of functional activation, connectivity, and neurotransmission have been added. The widespread availability of MRI has liberated researchers from the constraints of postmortem research and the limitations of inferring brain abnormalities through neurochemical effects in plasma or urine. Neuroimaging researchers aim to establish diagnostic markers, explain abnormal mental states, test anatomical and neurochemical models, and study the association of risk genes with brain abnormalities. Most studies have been cross-sectional and limited in size. But the ability to assess patients longitudinally and with large-scale study designs will ensure a prominent position for this research domain in the study of psychotic disorders.
Animal and Cellular Models of Psychotic Disorders
Authors: Pletnikov Mikhail V. , Ming Guo-Li , Ross Christopher A. 
Published: December 2017

Abstract
Animal and cell models are experimental systems developed to study particular aspects of a disease, as no model can accurately reflect all features of the disease. In this critical review we mention some of the nongenetic models but focus on genetic mouse models, evaluate their advantages and limitations, and comment on potential new prospects for the field. The ability to reprogram somatic cells from patients and unaffected donors to induced pluripotent stem cells (iPSCs) has the potential to substantially enhance our knowledge of normal cellular development and disease pathogenesis. The use of cell and animal models will help elucidate basic cellular and molecular mechanisms of pathogenesis, which will enable the development of targeted therapeutic approaches.