bluuebunny/crossref_metadata_2025_split huggingface dataset:
Positionspapier zur Detektion von Vorhofflimmern nach ischämischem Schlaganfall
Authors: Häusler Karl , Gröschel Klaus , Köhrmann Martin , Schnabel Renate , Anker Stefan , Brachmann Johannes , Böhm Michael , Diener Hans-Christoph , Doehner Wolfram , Endres Matthias , Gerloff Christian , Huttner Hagen , Kaps Manfred , Kirchhof Paulus , Nabavi Darius , Nolte Christian , Pfeilschifter Waltraud , Pieske Burkert , Poli Sven , Schäbitz Wolf , Thomalla Götz , Veltkamp Roland , Steiner Thorsten , Laufs Ulrich , Röther Joachim , Wachter Rolf 
Published: October 2017

ZusammenfassungDas vorliegende Positionspapier zur Detektion von Vorhofflimmern nach ischämischem Schlaganfall beinhaltet eine Stellungnahme der Arbeitsgemeinschaft „Herz und Hirn“ der Deutschen Gesellschaft für Kardiologie – Herz- und Kreislaufforschung e. V. (DGK) und der Deutschen Schlaganfallgesellschaft e. V. (DSG), die in Zusammenarbeit mit der Stroke Unit-Kommission der DSG und dem Kompetenznetz Vorhofflimmern (AFNET) e. V. erstellt wurde.Vorhofflimmern ist in den Leitlinien der Europäischen Gesellschaft für Kardiologie als eine mindestens 30 Sekunden anhaltende Episode einer Vorhofarrhythmie mit fehlenden P-Wellen definiert. Die 30-Sekundengrenze ist arbiträr gewählt und es ist unbekannt, ob das Schlaganfallrisiko bei Episoden von länger als 30 Sekunden höher ist als bei kürzeren Episoden. Bei Patienten, die einen Schlaganfall erlitten haben, sollte die Detektion von Vorhofflimmern üblicherweise zu einer Umstellung der medikamentösen Sekundärprävention führen, da eine orale Antikoagulation einer Thrombozytenaggregationshemmung überlegen ist. Die Detektion eines bis dato nicht diagnostizierten Vorhofflimmerns sollte daher bei Patienten mit ischämischem Schlaganfall verbessert werden, um die medikamentöse Sekundärprävention des Schlaganfalls zu optimieren. In diesem Positionspapier werden interdisziplinär erarbeitete Standards für eine „strukturierte Rhythmusvisite“ auf der Stroke Unit und ein diagnostisches „Stufenschema“ zur Detektion von Vorhofflimmern vorgeschlagen. Das Positionspapier fasst zudem den gegenwärtigen Kenntnisstand zur Detektion von Vorhofflimmern nach ischämischem Schlaganfall zusammen. Das Positionspapier soll den in der Versorgung von Schlaganfallpatienten tätigen Ärzten eine Handhabe geben, auch wenn bisher nicht abschließend geklärt ist, wie lange und mit welcher EKG-Methode Schlaganfallpatienten ohne bisher bekannte Herzrhythmusstörung bestmöglich monitoriert werden sollten. Dem Charakter eines Positionspapiers angemessen, wurde auf die Kennzeichnung von Evidenzgraden verzichtet, da es sich überwiegend um die Meinung von Experten handelt, die auf berichteten Fallserien und klinischer Erfahrung beruht und somit nicht mit einer Leitlinie gleichzusetzen ist und so auch nicht verstanden werden will.
Vorstellung eines pragmatischen Konzeptes zur bedarfsadaptierten Ernährungstherapie des kritisch kranken Patienten
Authors: Reckefuß Norbert , Kampa Ulrich 
Published: October 2017

Zusammenfassung
Hintergrund Die korrekte Anpassung der Ernährungstherapie des kritisch kranken Patienten stellt eine Herausforderung für jeden Intensivmediziner dar. Vor allem eine Überernährung muss hierbei in den ersten Tagen der kritischen Erkrankung unbedingt vermieden werden. Bisher publizierte Arbeiten zu dieser Thematik sind oft komplex und teilweise widersprüchlich, was die praktische Umsetzung weiter erschwert. Unser Ziel ist daher die Vorstellung eines einfachen und praktikablen Ernährungskonzepts, welches neben pathophysiologischen Grundlagen auch die Implementierung der neueren wissenschaftlichen Literatur und der aktuellen Leitlinien beinhaltet.
Ergebnisse Unser Ernährungsalgorithmus beruht auf den Veränderungen des Metabolismus kritisch kranker Patienten und bezieht daher die endogene Substratproduktion mit ein. In der Akutphase führen die Ausschöpfung vorhandener Leberglykogenreserven sowie eine gesteigerte Glukoneogenese in Verbindung mit einer peripheren Insulinresistenz in der Regel zu einer ausgeprägten Hyperglykämie. Sofern keine Kontraindikationen vorliegen, wird die Ernährungstherapie frühzeitig mit zunächst nur geringer Zufuhr begonnen (10 – 20 ml/h). In den folgenden Stunden und Tagen wird die (par)enterale Zufuhr abhängig von der aktuellen individuellen metabolischen Toleranz – erkennbar anhand von Blutzuckerwerten sowie notwendiger Insulindosierung – schrittweise erhöht (oder reduziert), bis das angestrebte Ernährungsziel erreicht ist.
Zusammenfassung Unser Konzept erweitert bisher publizierte Ernährungsalgorithmen, indem es eine praktikable Handlungsanweisung unter Beachtung der endogenen Substratproduktion bietet. Durch Einbeziehung von einfachen, günstigen und ubiquitär verfügbaren Parametern ermöglicht es eine frühe, bedarfsadaptierte Ernährung, die das Risiko einer Überernährung minimiert.
Spontane IOL-Dislokation – was können wir tun zur Prävention?
Authors: Kuchenbecker Joern 
Published: October 2017

ZusammenfassungDie IOL-Dislokation stellt neben den Eintrübungen von IOLs (Intraokularlinsen) eine weitere Komplikation der modernen IOL-Implantation dar. Zurzeit ist eine Zunahme der IOL-Dislokationen zu beobachten, die verschiedene Ursachen hat. Durch Kapselsackschrumpfung, insbesondere bei Patienten mit Pseudoexfoliation (PEX) und anderen okulären Ursachen, kommt es zu einer weiteren Belastung der oft bereits geschwächten Zonula. Der Einsatz eines Kapselspannrings allein hat sich bisher als nicht ausreichend effektiv erwiesen. Die Schrumpfung des Kapselsacks und damit weitere Belastung der Zonula kann z. B. durch zusätzliche Vorderkapselinzisionen vermindert werden und die IOL bei Zonulaschwäche auch bei erhaltenem Kapselsack oder geringer intraoperativer Zonulolyse vorzugsweise retroiridal fixiert werden, um eine spätere Dislokation zu verhindern. Die Effektivität dieser Maßnahmen sollte zukünftig in größeren Studien untersucht werden.
Das Humboldt’sche Bildungsideal in der Plastischen Chirurgie – Studentenumfrage zur Lehre und Venia
Legendi
Authors: Alawi Seyed Arash , Busch Lukas , Limbourg Anne , Jokuszies Andreas , Ipaktchi Ramin , Vogt Peter 
Published: October 2017

Zusammenfassung
Hintergrund Universitätskliniken und Kliniken mit universitärer Anbindung haben neben der klinischen Patientenversorgung vor allem den
Auftrag der Lehre und Forschung. In der aktuellen Entwicklung zeigt sich verschärft eine finanzielle Orientierung der ärztlichen Tätigkeit
mit einer Reduktion von Kapazitäten für Lehre und Forschung. Auf Basis einer betriebswirtschaftlichen Orientierung erfolgt eine Verlagerung
von Prioritäten innerhalb chirurgischer Disziplinen.
Methoden Im Rahmen einer Online-Umfrage wurden Medizinstudenten hinsichtlich ihrer subjektiven Einschätzung der akademischen
Qualifikation von Habilitanden und über die Einschätzung der aktuellen Lehrqualität befragt. Hierbei evaluierten die Studenten sowohl die
aktuelle Qualität der Lehre als auch die Perspektive einer akademischen Laufbahn und machten Vorschläge zur Verbesserung.
Ergebnisse An der Studentenumfrage nahmen insgesamt 166 Studenten teil. Von 123 Studenten gaben 78 % an, dass das Ansehen mit der
Habilitation steige. 85 % der Studenten gaben an, dass sich mit der Habilitation aber auch die Erwartungshaltung im Hinblick auf die
fachliche Qualifikation erhöht. 43 % der Studenten gaben an, sich in Zukunft habilitieren zu wollen.
Diskussion Unter den Studenten ist weiterhin die wissenschaftliche Karriere attraktiv, daher muss durch die Anpassung und
Modernisierung bestehender Arbeitszeitmodelle eine Umstrukturierung zugunsten attraktiver Arbeitsplatzbedingungen stattfinden.
Stent-over-sponge (SOS): a novel technique complementing endosponge therapy for foregut leaks and perforations
Authors: Valli Piero , Mertens Joachim , Kröger Arne , Gubler Christoph , Gutschow Christian , Schneider Paul , Bauerfeind Peter 
Published: October 2017

Abstract
Background and study aims Endoluminal vacuum therapy (EVT) has evolved as a promising option for endoscopic treatment of foregut wall injuries in addition to the classic closure techniques using clips or stents. To improve vacuum force and maintain esophageal passage, we combined endosponge treatment with a partially covered self-expandable metal stent (stent-over-sponge; SOS).
Patients and methods Twelve patients with infected upper gastrointestinal wall defects were treated with the SOS technique.
Results Indications for SOS were anastomotic leakage after surgery (n = 11) and chronic foregut fistula (n = 1). SOS treatment was used as a first-line treatment in seven patients with a success rate of 71.4 % (5/7) and as a second-line treatment after failed previous EVT treatment in five patients (success rate 80 %; 4/5). Overall, SOS treatment was successful in 75 % of patients (9/12). No severe adverse events occurred.
Conclusion SOS is an effective method to treat severely infected foregut wall defects in patients where EVT has failed, and also as a first-line treatment. Comparative prospective studies are needed to confirm our preliminary results.
Identification of Potential Biomarkers from Aconitum carmichaelii, a Traditional Chinese Medicine, Using a Metabolomic Approach
Authors: Zhao Dake , Shi Yana , Zhu Xinyan , Liu Li , Ji Pengzhang , Long Chunlin , Shen Yong , Kennelly Edward 
Published: October 2017

AbstractDespite their well-known toxicity, Aconitum species are important traditional medicines worldwide. Aconitum carmichaelii, known in Chinese as 附子 (fuzi), is an officially recognized traditional Chinese medicine with characteristic analgesic and anti-inflammatory activities, whose principal pharmacological ingredients are considered as aconitine-type diterpene alkaloids. Notwithstanding the long-recorded use of A. carmichaelii in traditional Chinese medicine, no single-entity aconitum alkaloid drug has been developed for clinical use. UPLC-Q-TOF-MS was used to investigate the marker compounds that can be used to differentiate A. carmichaelii from seven other Aconitum species collected in Yunnan Province. Nontargeted principle component analysis scores plots found that all the tested Aconitum species clustered into three distinct groups, and A. carmichaelii was significantly different chemically than the other seven species. Furthermore, the primary and lateral roots of A. carmichaelii also showed significant differences. Using orthogonal partial least squares discriminate analysis analysis, eight marker compounds were identified, including 14-acetylkarakoline, aconitine, carmichaeline, fuziline, hypaconitine, mesaconitine, neoline, and talatisamine. Four of these aconitum alkaloids, fuziline, hypaconitine, mesaconitine, and neoline, showed significant analgesic activity in a dose-dependent manner compared to the negative and positive controls. However, hypaconitine, mesaconitine, and neoline exhibited significant acute toxicity activity, while fuziline showed no acute toxicity in mice, suggesting the relative safety of this alkaloid. This study provides a good example of how to differentiate an authentic medicinal plant from common adulterants using a metabolomics approach, and to identify compounds that may be developed into new drugs.
Assessing fish welfare.
Authors: Braithwaite V. A. 
Published: October 2017

Abstract
There is a growing need to understand how our current interactions and practices influence fish welfare and wellbeing. Particularly given the increasing use of fish both as model organisms in research, for example zebrafish used in biomedical experiments, and also in terms of food production in aquaculture, where we now rear and harvest several different species of fish on farms. Determining which factors matter from a fish welfare perspective and finding appropriate ways to assay fish welfare have been the focus of several research projects over the last decade. These have led to a much better appreciation of what kinds of situation result in poor fish welfare, and what can be done to promote positive welfare through best practice. Assays of fish welfare depend on the species of concern, the environment in which the fish are housed, how the fish are handled, the routine husbandry practices that they are exposed to, and how they are killed. Approaches that address welfare span from regular, repeated behavioural observations, to the use of multiple traits to create a welfare index, through to the use of molecular tools to act as an early warning system by detecting early changes in stress physiology gene expression. The field of fish welfare is still at a relatively early stage of development, but a growing interest in this topic has promoted innovative new tools and techniques that are delivering better welfare assays for the fish we maintain in captivity.
Rajini’s Finger, Indexicality, and the Metapragmatics of Presence
Authors: Nakassis Constantine V. 
Published: October 2017

AbstractThis article explores the ways in which Tamil film stars, so-called mass heroes such as the “Superstar” Rajinikanth, are presenced in theatrical events of their onscreen revelation and apperception. Drawing on film analysis, ethnographic accounts of theatrical reception, and metadiscourse by filmgoers and industry personnel, I focus on Rajini’s onscreen pointing gestures in highly charged moments of presencing. As I argue, these data provoke reflection on indexicality—defined by Charles Sanders Peirce as a semiotic ground based on “real connection” or “existential relation,” such as copresence, contiguity, or causality—for at issue with Rajini’s fingers is precisely the question of his auratic being and presence. Instead of analyzing performative acts of presencing through appeal to the analytic of indexicality, then, what if we interrogate those ethnographic particularities of existence and presence that constitute the ground for indexical relations and effects as such? Such an inquiry would refuse to leave indexicality as a self-evident, pregiven analytic, but instead pose it as an open ethnographic question. Opening up the question of existence and presence, as I show, allows us to unearth other semiotic “grounds” of indexicality and representation beyond those that we all too often take for granted.
The Tuhao and the Bureaucrat: The Qualia of “Quality” in Rural China
Authors: Ingebretson Britta 
Published: October 2017

AbstractFor the past thirty years, the Chinese state has focused on raising the quality (suzhi) of rural Chinese, who are seen as particularly lacking. This article shows how local bureaucrats undertake this project through distinguishing the stereotyped figure of the tuhao “rural rich,” who represents the façade of modernity without its substance, from the truly modern high-quality citizen. These oppositional figures are defined and identified through a dialectic process of rhematization and dicentization, which ties together and locates the qualities of coarseness, carelessness, and ruralness in the tuhao, and qualities of fineness, meticulousness, and carefulness in the high-quality bureaucrat. These qualia, which organize preexisting cultural logics of difference, are thereby subsumed to the state project of quality-raising. Through this process of identification, local bureaucrats commensurate local forms of valorization with those of the Chinese state and devalue nongovernmental local elites as tuhao.
From the Page to the Floor: Baroque Dance Notation and Kellom Tomlinson’s The Art of Dancing Explained
Authors: Karl-Johnson Gabriella 
Published: October 2017

AbstractThe late seventeenth century gave rise to a powerful innovation in Western European social and theatrical dance, the art of dance notation. The new representational technology of dance notation provided a means to broadcast fashionable dances emerging from the French court as well as new compositions from dancing masters operating in London and elsewhere. In the first three decades of the eighteenth century, dance notation quickly reached faddish heights, with published dance manuals in high demand among upper levels of English society. One publication from the era, Kellom Tomlinson’s The Art of Dancing Explained by Reading and Figures, provides a window onto the descriptive tool of dance notation, its function in society, and its eventual decline. While providing a previously unimagined communicational technology, the completeness and specificity of the dominant form of dance notation ultimately spelled its demise.
Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra
Authors: Deepaisarn S , Tar P D , Thacker N A , Seepujak A , McMahon A W 
Published: October 2017

Abstract

Motivation
Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI) facilitates the analysis of large organic molecules. However, the complexity of biological samples and MALDI data acquisition leads to high levels of variation, making reliable quantification of samples difficult. We present a new analysis approach that we believe is well-suited to the properties of MALDI mass spectra, based upon an Independent Component Analysis derived for Poisson sampled data. Simple analyses have been limited to studying small numbers of mass peaks, via peak ratios, which is known to be inefficient. Conventional PCA and ICA methods have also been applied, which extract correlations between any number of peaks, but we argue makes inappropriate assumptions regarding data noise, i.e. uniform and Gaussian.

Results
We provide evidence that the Gaussian assumption is incorrect, motivating the need for our Poisson approach. The method is demonstrated by making proportion measurements from lipid-rich binary mixtures of lamb brain and liver, and also goat and cow milk. These allow our measurements and error predictions to be compared to ground truth.

Availability and implementation
Software is available via the open source image analysis system TINA Vision, www.tina-vision.net.

Supplementary information
Supplementary data are available at Bioinformatics online.
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota
Authors: Olekhnovich Evgenii I , Vasilyev Artem T , Ulyantsev Vladimir I , Kostryukova Elena S , Tyakht Alexander V 
Published: October 2017

Abstract

Motivation
Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens.

Results
We developed MetaCherchant—an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new ‘shotgun’ metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data.

Availability and implementation
Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent.

Supplementary information
Supplementary data are available at Bioinformatics online.
Machine learning annotation of human branchpoints
Authors: Signal Bethany , Gloss Brian S , Dinger Marcel E , Mercer Tim R 
Published: October 2017

Abstract

Motivation
The branchpoint element is required for the first lariat-forming reaction in splicing. However current catalogues of human branchpoints remain incomplete due to the difficulty in experimentally identifying these splicing elements. To address this limitation, we have developed a machine-learning algorithm—branchpointer—to identify branchpoint elements solely from gene annotations and genomic sequence.

Results
Using branchpointer, we annotate branchpoint elements in 85% of human gene introns with sensitivity (61.8%) and specificity (97.8%). In addition to annotation, branchpointer can evaluate the impact of SNPs on branchpoint architecture to inform functional interpretation of genetic variants. Branchpointer identifies all published deleterious branchpoint mutations annotated in clinical variant databases, and finds thousands of additional clinical and common genetic variants with similar predicted effects. This genome-wide annotation of branchpoints provides a reference for the genetic analysis of splicing, and the interpretation of noncoding variation.

Availability and implementation
Branchpointer is written and implemented in the statistical programming language R and is freely available under a BSD license as a package through Bioconductor.

Supplementary information
Supplementary data are available at Bioinformatics online.
Simulating the dynamics of targeted capture sequencing with CapSim
Authors: Cao Minh Duc , Ganesamoorthy Devika , Zhou Chenxi , Coin Lachlan J M 
Published: October 2017

Abstract

Motivation
Targeted sequencing using capture probes has become increasingly popular in clinical applications due to its scalability and cost-effectiveness. The approach also allows for higher sequencing coverage of the targeted regions resulting in better analysis statistical power. However, because of the dynamics of the hybridization process, it is difficult to evaluate the efficiency of the probe design prior to the experiments which are time consuming and costly.

Results
We developed CapSim, a software package for simulation of targeted sequencing. Given a genome sequence and a set of probes, CapSim simulates the fragmentation, the dynamics of probe hybridization and the sequencing of the captured fragments on Illumina and PacBio sequencing platforms. The simulated data can be used for evaluating the performance of the analysis pipeline, as well as the efficiency of the probe design. Parameters of the various stages in the sequencing process can also be evaluated in order to optimize the experiments.

Availability and implementation
CapSim is publicly available under BSD license at https://github.com/Devika1/capsim.

Supplementary information
Supplementary data are available at Bioinformatics online.
pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration
Authors: Gopi Soundhararajan , Devanshu Devanshu , Krishna Praveen , Naganathan Athi N 
Published: October 2017

Abstract

Summary
We present a web-server for rapid prediction of changes in protein stabilities over a range of temperatures and experimental conditions upon single- or multiple-point substitutions of charged residues. Potential mutants are identified by a charge-shuffling procedure while the stability changes (i.e. an unfolding curve) are predicted employing an ensemble-based statistical-mechanical model. We expect this server to be a simple yet detailed tool for engineering stabilities, identifying electrostatically frustrated residues, generating local stability maps and in constructing fitness landscapes.

Availability and implementation
The web-server is freely available at http://pbl.biotech.iitm.ac.in/pStab and supports recent versions of all major browsers.

Supplementary information
Supplementary data are available at Bioinformatics online.