bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geriatrisches Assessment Mini-Mental-Status-Test (MMST)
Authors: Zemke Jens 
Published: April 2018

Zusammenfassung
Standardassessment Bei älteren Patienten sind Alltagskompetenz und Selbsthilfefähigkeit in besonderem Maße durch eine Verminderung kognitiver Fähigkeiten
bedroht. Zur Verhinderung von Abhängigkeit und Pflegebedürftigkeit ist die Abklärung der kognitiven Leistungsfähigkeit von essenzieller Bedeutung. Im Rahmen
einer geriatrischen Komplexbehandlung gehört der MMST (oder Mini Mental State Examination, MMSE) nach Folstein mittlerweile zu den Standardassessments. Der MMST
ist das am häufigsten angewandte Screeningverfahren für kognitive Defizite.
Kulturabhängigkeit der Einstellung gegenüber psychotherapeutischer Behandlung bei Türkeistämmigen und Personen ohne Migrationshintergrund
Authors: Bretz Joachim , Sahin Dilek , Brandl Eva , Schouler-Ocak Meryam 
Published: April 2018

Zusammenfassung
Ziel Die vorliegende Arbeit vergleicht die Einstellung zur Inanspruchnahme psychotherapeutischer Hilfe bei in Deutschland lebenden Personen ohne und mit türkischem Migrationshintergrund. Dabei werden auch geschlechts- und störungsspezifische sowie soziodemographische Unterschiede hinsichtlich der Aufgeschlossenheit gegenüber psychotherapeutischen Behandlungen mitberücksichtigt.
Methoden Im Rahmen dieser Studie wurden türkeistämmige (n=129) Personen und Probanden ohne türkischen Migrationshintergrund (n=129) mit dem Fragebogen zu Einstellungen gegenüber der Inanspruchnahme psychotherapeutischer Hilfe, dem Fragebogen zur sozialen Unterstützung, der Kurzversion der Symptom-Checkliste mit den Teilskalen Angst, Depression und Somatisierung sowie einem soziobiografischen Fragebogen untersucht.
Ergebnisse Die Einstellung gegenüber einer psychotherapeutischen Behandlung ist bei Menschen mit türkischem Migrationshintergrund weniger positiv als bei Menschen ohne Migrationshintergrund. Frauen, Depressive, Menschen mit einer hohen sozialen Unterstützung, einer hohen Schulbildung und mit eigenen Kindern stehen einer psychotherapeutischen Behandlung aufgeschlossener gegenüber.
Diskussion Die Einstellung zur Inanspruchnahme psychotherapeutischer Hilfe wird von soziodemografischen, geschlechts- sowie störungsspezifischen und insbesondere von kulturspezifischen Faktoren beeinflusst.
Schlussfolgerung Diese Befunde verdeutlichen die Notwendigkeit einer breiteren Aufklärung der Gesellschaft über Psychotherapie und des Aufbaus interkultureller Beratungsmöglichkeiten für Migranten.
Ärztliches Gesprächsführungstraining in simulierten Situationen: Wahrnehmungen und Empfindungen von Simulationspatienten bei patientenzentrierter Gesprächsführung
Authors: Butollo Maria , Holzinger Anita , Wagner-Menghin Michaela 
Published: April 2018

Zusammenfassung
Einleitung Der Einsatz von Simulationspatienten zum Trainieren ärztlicher Gesprächsführung hat sich in medizinischen Curricula als wichtige didaktische Methode etabliert. Gegenstand dieser Studie ist die Frage, ob patientenzentrierte Kommunikation die Grundlage adäquater positiver und negativer Wahrnehmungen und Empfindungen von SP ist.
Material und Methoden 22 von 37 SP, der Medizinischen Universität Wien (12 Frauen, 10 Männer), wurden mittels halbstrukturierten Interviewleitfaden zu deren Befindlichkeit bei einem SP Einsatz befragt. Die transkribierten Interviews wurden in Situationsanalyseeinheiten geteilt und deduktiv inhaltsanalytisch ausgewertet. Wir orientierten uns literaturbasiert an Merkmalen patientenzentrierter Kommunikation sowie am „Nationalen Kompetenzbasierten Lernzielkatalog Medizin“.
Ergebnisse Aus 192 gewonnenen Analyseeinheiten wurden 67 positiv und 125 negativ durch die SP bewertet. Nach 22% der Aussagen der SP bewirkte die Wahrnehmung von „Stabilität und Vertrauen in die Beziehung“ positive Gefühle, ebenso bei der Wahrnehmung von Kongruenz (15%), Akzeptanz (27%) sowie Empathie (36%). Negative Gefühle berichteten SP durch die Wahrnehmung von Instabilität (18%), Inkongruenz (11%), mangelnder Akzeptanz (40%) und fehlender Empathie (30%). Zusätzlich stellte sich bei 50% der SP positive Befindlichkeit beim Beobachten des Lernerfolgs von Studierenden ein.
Diskussion SP berichten positive Befindlichkeit, wenn die Merkmale für patientenzentrierte Kommunikation von Studierenden eingehalten werden und negatives Empfinden, wenn keine Patientenzentrierung vorhanden ist. Empathische Grundhaltung sowie mangelnde Akzeptanz waren die Kommunikationsmerkmale, die den stärksten Einfluss auf die SP hatten. SP reagieren hinreichend authentisch auf Patientenzentrierung, um die Lernziele erreichen zu können. Lernerfolg von Studierenden ist für die Emotionen von SP relevant, spielt im Arzt-Patienten Gespräch jedoch keine Rolle.
Schlussfolgerung Da die Einstellung von Studierenden für das Erleben der SP wichtig ist, sollten Studierende diesbezüglich vorbereitet werden. Gleichzeitig zeigen SP eine hinreichend authentische Reaktion auf patientenzentrierte Gesprächsführung zum Erreichen der Lernziele. Sie sollten jedoch unterrichtet werden ihre Freude über den Lernerfolg der Studierenden während des Rollenspiels nicht offen zu zeigen.
Free Flap Reconstruction after Complications of Total Ankle Arthroplasty: Case Series and Review of the Literature
Authors: Lu Jocelyn , Elmarsafi Tammer , Steinberg John , Kim Paul , Attinger Christopher , Cooper Paul , Evans Karen 
Published: April 2018

Background Postoperative complications of total ankle arthroplasty (TAA) include anterior surgical site dehiscence, hardware failure, infection, and amputation. Early intervention with free flap may provide TAA salvage. We report the largest series of failed TAA require microsurgical free tissue transfer, identify risk factors, and examine the long-term post-free flap outcomes.
Materials and Methods This is a case series of consecutive patients from a single institution dedicated to limb salvage. Inclusion criteria included patients who underwent TAA with complications related to the index surgery and underwent microsurgical free tissue transfer. Nine patients were identified within the inclusion parameters.
Results Patients presented with osteomyelitis 4 (44%), soft tissue infections 4 (44%), and wound dehiscence 1 (11%) following TAA. Three (33%) radial forearm free flaps and six (67%) anterolateral thigh flaps were used, with a 100% microsurgical success rate. Preoperative angiography revealed six (67%) patients with anterior tibial artery occlusion at the level of the ankle or below. Patients required an average of 2.7 ± 1 (range 1–4) operative débridements prior to free flap, with successful flap outcome and return to full weight bearing status in nine (100%) patients. The mean long-term lower extremity functional scale score was 62 out of 80 points.
Conclusion Microsurgical free tissue transfer is an effective and favorable strategy to attain a stable soft tissue envelope for patients presenting with surgical site complications following TAA. We recommend early involvement with plastic surgery and endovascular angiography to evaluate the integrity of the anterior tibial artery.
Die drei großen D: Demenz – Delir – Depression
Authors: Zemke Jens 
Published: April 2018

Zusammenfassung
Abgrenzung Nicht jede kognitive Störung ist ein demenzielles Syndrom. Herauszufinden, ob ein Mensch an einer Demenz, einem Delir oder einer Depression
leidet, stellt für das geriatrische Team eine diagnostische Herausforderung dar.
Beratung zu technischen Assistenzsystemen – die Onlineplattform „Wegweiser Alter und Technik“
Authors: Lautenschläger Sindy 
Published: April 2018

Zusammenfassung
Anwendung Technische Assistenzsysteme werden oft skeptisch betrachtet und finden daher nur zögerlich Anwendung. Doch gerade technische Alltagshilfen haben ein großes Potenzial, Menschen im Alter zu unterstützen, damit sie so lange wie möglich in der eigenen Häuslichkeit leben können. Ältere Menschen und ihre Angehörigen werden jetzt und vor allem in Zukunft verstärkt Beratungen hinsichtlich technischer Assistenzsysteme benötigen und diese auch einfordern. Damit Pflegekräfte Beratungen zu technischen Assistenzsystemen durchführen können, wird in diesem Artikel an einem Beispiel gezeigt, wie die Onlineplattform „Wegweiser Alter und Technik“ angewendet werden kann.
Egophoricity in Mangghuer
Authors: Fried Robert W. 
Published: April 2018

Abstract
Egophoricity in Mangghuer is a binary distinction expressed in finite verbal morphology and the system of copulas. In declarative contexts, egophoric forms are used with first person subjects (or predicate nominals containing first person possessors) if the subject is perceived to be in control of the action or state; non-egophoric forms are used elsewhere. In interrogative contexts, egophoric forms are used with second person subjects, while non-egophoric forms are used with non-second person subjects. Previous work on Mangghuer has reported on uses of the egophoric distinction that do not conform to this pattern expressing things such as degree of speaker certainty, mirativity, and lack of control. This paper explores further complexities in pragmatic uses of egophoric marking. Of particular interest are situations in which the pragmatically neutral use of speaker perspective is contrary to the basic pattern and situations in which the non-basic use of the speaker perspective has multiple possible meanings. In these situations, the discourse context must be taken into account to correctly interpret the pragmatic function of the egophoric marking. This paper concludes that the common thread underlying the uses of egophoric forms is the degree of “involvement in the event being reported, or in the reporting activity itself” (Slater 2003a: 194–220). While a strictly objective rubric for determining speaker involvement is elusive, this paper examines the use of egophoric marking in a broad range of pragmatic contexts and confirms that egophoric forms consistently indicate a higher degree of speaker involvement while non-egophoric forms indicate a lower degree of speaker involvement.
Self-ascription in conjunct-disjunct systems
Authors: Wechsler Stephen 
Published: April 2018

Abstract
Conjunct markers, in at least some languages, are analyzed here as grammatically specialized for the semantic function of self-ascription: such markers indicate that a participant in the described event ascribed to herself the property described in the sentence. The hypothesis proposed here is that grammatically enabled self-ascription is fundamental to such systems, and that mirativity, as well as various other observed factors such as speaker ignorance, volitionality, and irony, are secondary effects that follow from this self-ascription analysis.
Convolutional neural networks for classification of alignments of non-coding RNA sequences
Authors: Aoki Genta , Sakakibara Yasubumi 
Published: April 2018

Abstract

Motivation
The convolutional neural network (CNN) has been applied to the classification problem of DNA sequences, with the additional purpose of motif discovery. The training of CNNs with distributed representations of four nucleotides has successfully derived position weight matrices on the learned kernels that corresponded to sequence motifs such as protein-binding sites.

Results
We propose a novel application of CNNs to classification of pairwise alignments of sequences for accurate clustering of sequences and show the benefits of the CNN method of inputting pairwise alignments for clustering of non-coding RNA (ncRNA) sequences and for motif discovery. Classification of a pairwise alignment of two sequences into positive and negative classes corresponds to the clustering of the input sequences. After we combined the distributed representation of RNA nucleotides with the secondary-structure information specific to ncRNAs and furthermore with mapping profiles of next-generation sequence reads, the training of CNNs for classification of alignments of RNA sequences yielded accurate clustering in terms of ncRNA families and outperformed the existing clustering methods for ncRNA sequences. Several interesting sequence motifs and secondary-structure motifs known for the snoRNA family and specific to microRNA and tRNA families were identified.

Availability and implementation
The source code of our CNN software in the deep-learning framework Chainer is available at http://www.dna.bio.keio.ac.jp/cnn/, and the dataset used for performance evaluation in this work is available at the same URL.
Driver gene mutations based clustering of tumors: methods and applications
Authors: Zhang Wensheng , Flemington Erik K , Zhang Kun 
Published: April 2018

Abstract

Motivation
Somatic mutations in proto-oncogenes and tumor suppressor genes constitute a major category of causal genetic abnormalities in tumor cells. The mutation spectra of thousands of tumors have been generated by The Cancer Genome Atlas (TCGA) and other whole genome (exome) sequencing projects. A promising approach to utilizing these resources for precision medicine is to identify genetic similarity-based sub-types within a cancer type and relate the pinpointed sub-types to the clinical outcomes and pathologic characteristics of patients.

Results
We propose two novel methods, ccpwModel and xGeneModel, for mutation-based clustering of tumors. In the former, binary variables indicating the status of cancer driver genes in tumors and the genes’ involvement in the core cancer pathways are treated as the features in the clustering process. In the latter, the functional similarities of putative cancer driver genes and their confidence scores as the ‘true’ driver genes are integrated with the mutation spectra to calculate the genetic distances between tumors. We apply both methods to the TCGA data of 16 cancer types. Promising results are obtained when these methods are compared to state-of-the-art approaches as to the associations between the determined tumor clusters and patient race (or survival time). We further extend the analysis to detect mutation-characterized transcriptomic prognostic signatures, which are directly relevant to the etiology of carcinogenesis.

Availability and implementation
R codes and example data for ccpwModel and xGeneModel can be obtained from http://webusers.xula.edu/kzhang/ISMB2018/ccpw_xGene_software.zip.

Supplementary information
Supplementary data are available at Bioinformatics online.
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data
Authors: Nouri Nima , Kleinstein Steven H 
Published: April 2018

Abstract

Motivation
B cells derive their antigen-specificity through the expression of Immunoglobulin (Ig) receptors on their surface. These receptors are initially generated stochastically by somatic re-arrangement of the DNA and further diversified following antigen-activation by a process of somatic hypermutation, which introduces mainly point substitutions into the receptor DNA at a high rate. Recent advances in next-generation sequencing have enabled large-scale profiling of the B cell Ig repertoire from blood and tissue samples. A key computational challenge in the analysis of these data is partitioning the sequences to identify descendants of a common B cell (i.e. a clone). Current methods group sequences using a fixed distance threshold, or a likelihood calculation that is computationally-intensive. Here, we propose a new method based on spectral clustering with an adaptive threshold to determine the local sequence neighborhood. Validation using simulated and experimental datasets demonstrates that this method has high sensitivity and specificity compared to a fixed threshold that is optimized for these measures. In addition, this method works on datasets where choosing an optimal fixed threshold is difficult and is more computationally efficient in all cases. The ability to quickly and accurately identify members of a clone from repertoire sequencing data will greatly improve downstream analyses. Clonally-related sequences cannot be treated independently in statistical models, and clonal partitions are used as the basis for the calculation of diversity metrics, lineage reconstruction and selection analysis. Thus, the spectral clustering-based method here represents an important contribution to repertoire analysis.

Availability and implementation
Source code for this method is freely available in the SCOPe (Spectral Clustering for clOne Partitioning) R package in the Immcantation framework: www.immcantation.org under the CC BY-SA 4.0 license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Deconvolution and phylogeny inference of structural variations in tumor genomic samples
Authors: Eaton Jesse , Wang Jingyi , Schwartz Russell 
Published: April 2018

Abstract

Motivation
Phylogenetic reconstruction of tumor evolution has emerged as a crucial tool for making sense of the complexity of emerging cancer genomic datasets. Despite the growing use of phylogenetics in cancer studies, though, the field has only slowly adapted to many ways that tumor evolution differs from classic species evolution. One crucial question in that regard is how to handle inference of structural variations (SVs), which are a major mechanism of evolution in cancers but have been largely neglected in tumor phylogenetics to date, in part due to the challenges of reliably detecting and typing SVs and interpreting them phylogenetically.

Results
We present a novel method for reconstructing evolutionary trajectories of SVs from bulk whole-genome sequence data via joint deconvolution and phylogenetics, to infer clonal sub-populations and reconstruct their ancestry. We establish a novel likelihood model for joint deconvolution and phylogenetic inference on bulk SV data and formulate an associated optimization algorithm. We demonstrate the approach to be efficient and accurate for realistic scenarios of SV mutation on simulated data. Application to breast cancer genomic data from The Cancer Genome Atlas shows it to be practical and effective at reconstructing features of SV-driven evolution in single tumors.

Availability and implementation
Python source code and associated documentation are available at https://github.com/jaebird123/tusv.
A novel methodology on distributed representations of proteins using their interacting ligands
Authors: Öztürk Hakime , Ozkirimli Elif , Özgür Arzucan 
Published: April 2018

Abstract

Motivation
The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand-based approach can be utilized in protein representation. In this study, we propose SMILESVec, a Simplified molecular input line entry system (SMILES)-based method to represent ligands and a novel method to compute similarity of proteins by describing them based on their ligands. The proteins are defined utilizing the word-embeddings of the SMILES strings of their ligands. The performance of the proposed protein description method is evaluated in protein clustering task using TransClust and MCL algorithms. Two other protein representation methods that utilize protein sequence, Basic local alignment tool and ProtVec, and two compound fingerprint-based protein representation methods are compared.

Results
We showed that ligand-based protein representation, which uses only SMILES strings of the ligands that proteins bind to, performs as well as protein sequence-based representation methods in protein clustering. The results suggest that ligand-based protein description can be an alternative to the traditional sequence or structure-based representation of proteins and this novel approach can be applied to different bioinformatics problems such as prediction of new protein–ligand interactions and protein function annotation.

Availability and implementation
https://github.com/hkmztrk/SMILESVecProteinRepresentation

Supplementary information
Supplementary data are available at Bioinformatics online.
AnnotSV: an integrated tool for structural variations annotation
Authors: Geoffroy Véronique , Herenger Yvan , Kress Arnaud , Stoetzel Corinne , Piton Amélie , Dollfus Hélène , Muller Jean 
Published: April 2018

Abstract

Summary
Structural Variations (SV) are a major source of variability in the human genome that shaped its actual structure during evolution. Moreover, many human diseases are caused by SV, highlighting the need to accurately detect those genomic events but also to annotate them and assist their biological interpretation. Therefore, we developed AnnotSV that compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to (i) interpret SV potential pathogenicity and (ii) filter out SV potential false positive. In particular, AnnotSV reports heterozygous and homozygous counts of single nucleotide variations (SNVs) and small insertions/deletions called within each SV for the analyzed patients, this genomic information being extremely useful to support or question the existence of an SV. We also report the computed allelic frequency relative to overlapping variants from DGV (MacDonald et al., 2014), that is especially powerful to filter out common SV. To delineate the strength of AnnotSV, we annotated the 4751 SV from one sample of the 1000 Genomes Project, integrating the sample information of four million of SNV/indel, in less than 60 s.

Availability and implementation
AnnotSV is implemented in Tcl and runs in command line on all platforms. The source code is available under the GNU GPL license. Source code, README and Supplementary data are available at http://lbgi.fr/AnnotSV/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sustainability of community-based women’s groups: reflections from a participatory intervention for newborn and maternal health in Nepal
Authors: Sondaal Annemijn E C , Tumbahangphe Kirti M , Neupane Rishi , Manandhar Dharma S , Costello Anthony , Morrison Joanna 
Published: April 2018

AbstractParticipatory community-based women’s group interventions have been successful in improving maternal and newborn survival. In rural Makwanpur, Nepal, exposure to these Participatory Learning and Action groups resulted in a thirty-percent reduction in neonatal mortality rate and significantly fewer maternal deaths. It is often theorised that participatory approaches are more likely to be sustained than top-down approaches, but this is rarely evaluated after the withdrawal of external support. We sought to understand how participatory learning and action (PLA) groups in Makwanpur fared after the supporting non-governmental organisation withdrew their support as well as factors affecting their sustainability. We used mixed methods, conducting a cross-sectional survey of 239 groups, thirty focus group discussions with group members and thirty key informant interviews within twelve–seventeen months after support was withdrawn. Eighty percent of groups were still active which suggests that PLA groups have a high chance of being sustained over time. Groups were more likely to be sustained if the group had local importance and members continued to acquire new knowledge. However, the participatory nature of the group and local embeddedness were not enough to sustain all groups. They also needed leadership capacity, a unifying activity such as a fund, and a strong belief in the value of their meeting to sustain. These key factors should be considered when seeking to enable sustainability of participatory interventions.