bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zusammenhang von Obstipation und Dialysatauslaufstörungen bei Peritonealdialysepatienten
Authors: Nipshagen Sabine 
Published: February 2019

ZusammenfassungZur Erstellung einer nephrologischen Pflegeplanung braucht es wissenschaftliche Daten. Dass eine Obstipation Auslaufstörungen bei der Peritonealdialyse verursachen kann, beruht auf Erfahrungswerten. Mit dieser Untersuchung soll erfasst werden, ob eine Obstipation Auswirkungen auf Dialysatauslaufstörungen hat. Für diese prospektive Studie wurde an 23 Patienten aus 3 Dialysezentren in Hessen ein Fragebogen verteilt. Dieser basiert auf der Grundlage der Rom-III-Kriterien zur Erfassung der chronischen Obstipation unter Zuhilfenahme der Bristol-Stuhlformen-Skala. Auslaufstörungen wurden anhand der Dialyseprotokolle erfasst. In die Auswertung wurden 19 Fragebögen einbezogen. Ein Zusammenhang zwischen Obstipation und Auslaufstörungen konnte mit dieser Studie nicht nachgewiesen werden. Die Obstipationsinzidenz in dieser Gruppe liegt bei 31 % und damit deutlich höher als in der Gesamtbevölkerung Deutschlands. 68 % der Teilnehmer weisen Obstipationssymptome auf. Besonders oft gaben die Teilnehmer ein Gefühl der inkompletten Entleerung an. Eine Laxanziengabe bewirkte nur bei einem Teilnehmer eine Symptomfreiheit. Da Peritonealdialysepatienten überdurchschnittlich häufig eine Obstipation und Obstipationssymptome aufweisen, ist eine Berücksichtigung dieser Problematik in der nephrologischen Pflegeplanung zu empfehlen. Wünschenswert sind weitere Erhebungen in einem größeren Rahmen, um den Zusammenhang zwischen Obstipation und Auslaufstörungen darzustellen.
Individuelle Schulung von Hämodialysepatienten
Authors: Dreyer Antje 
Published: February 2019

ZusammenfassungAdhärenz verringert Komplikationen im Krankheitsverlauf und erhöht die Lebensqualität und -erwartung von Patienten. Die vorliegende Arbeit überprüft, ob sich die Adhärenz bei Menschen mit Chronic Kidney Disease (CKD) durch eine 2-teilige Schulung zur Nieren- und Dialysefunktion steigern lässt. Nach den Prinzipien der Salutogenese sowie einem ressourcen-orientierten Verständnis von Adhärenz wurde vermutet, dass die Schulungen die Betroffenen dazu ermutigen, sich selbstbestimmt und eigenverantwortlich an der Therapie zu beteiligen. Dazu wurde in dem Schulungsprogramm auf leichte Verständlichkeit der Sachinformationen, gehirngerechtes Lernen und individuelle Zielsetzung fokussiert. Es zeigte sich, dass die Schulung den Menschen mit CKD dabei half, niedrigere Serum-Phosphat-Werte und verringerte Ultrafiltrationswerte zu erreichen. Die Auswertung einer zusätzlichen Befragung der Patienten ergab, dass der Grund hierfür v. a. ein gesteigertes Wissen über Nieren- und Dialysefunktion war. Es wird diskutiert, unter welchen Bedingungen eine derartige Intervention in der Praxis sinnvoll implementiert werden kann. Die Ergebnisse werden im Kontext der nephrologischen Pflege gesehen.
Current Practical Concepts for Using Rib in Secondary Rhinoplasty
Authors: Penna Waldemar , Robotti Enrico 
Published: February 2019

AbstractRhinoplasty is universally considered as the most demanding procedure in facial plastic surgery. Secondary rhinoplasty is its crown jewel, even more complex, and likewise highly fascinating. The evolution of thought and practice in rhinoplasty in the last decades has been quick and steady, progressively acknowledging the importance of maintaining structure in primary rhinoplasty and rebuilding structure in secondary procedures. No longer is the paradigm to achieve a small, thin, and pointy nose, but rather a well-proportioned nose which looks natural, albeit elegant and breathing well. Rib is an essential tool in many secondary procedures, and thus some important concepts have to be well understood and some finesse points mastered. This will provide an elegant reconstruction, identical if possible, or at least not far apart, to what could be achieved by a well-executed primary rhinoplasty, while avoiding the feared luck of a bulky nose stuffed with grafts. These guiding concepts and specific nuances regarding harvesting rib and working with it are the scope and contents of this article.
Extracellular vesicles derived from cancer‐associated fibroblasts induce the migration and invasion of oral squamous cell carcinoma
Authors: Dourado Mauricio Rocha , Korvala Johanna , Åström Pirjo , De Oliveira Carine Ervolino , Cervigne Nilva K. , Mofatto Luciana Souto , Bastos Debora Campanella , Messetti Ana Camila Pereira , Graner Edgard , Leme Adriana Franco Paes , Coletta Ricardo D. , Salo Tuula 
Published: February 2019

ABSTRACTAs one of the most abundant constituents of the tumour microenvironment (TME), cancer‐associated fibroblasts (CAF) display critical roles during tumour progression and metastasis. Multiple classes of molecules including growth factors, cytokines, proteases and extracellular matrix proteins, are produced by CAF to act as mediators of the stroma‐tumour interactions. One of the main channels for this communication is associated with extracellular vesicles (EV), which are secreted particles loaded with protein and genetic information. In this study, we evaluated the effects of EV derived from CAF primary human cell lines (n = 5) on proliferation, survival, migration, and invasion of oral squamous cell carcinoma (OSCC) cells. As controls, EV from human primary‐established normal oral fibroblasts (NOF, n = 5) were used. Our in vitro assays showed that CAF‐EV significantly induces migration and invasion of OSCC cells and promote a disseminated pattern of HSC‐3 cell invasion in the 3D organotypic assay. Furthermore, gene expression analysis of EV‐treated cancer cells revealed changes in the pathways associated with tumour metabolism and up‐regulation of tumour invasion genes. Our findings suggest a significant role of CAF‐EV in promoting the migration and invasion of OSCC cells, which are related to the activation of cancer‐related pathways.
Comparison of six breast cancer classifiers using qPCR
Authors: Berchtold Evi , Vetter Martina , Gündert Melanie , Csaba Gergely , Fathke Christine , Ulbrich Susanne E , Thomssen Christoph , Zimmer Ralf , Kantelhardt Eva J 
Published: February 2019

Abstract

Motivation
Several gene expression-based risk scores and subtype classifiers for breast cancer were developed to distinguish high- and low-risk patients. Evaluating the performance of these classifiers helps to decide which classifiers should be used in clinical practice for personal therapeutic recommendations. So far, studies that compared multiple classifiers in large independent patient cohorts mostly used microarray measurements. qPCR-based classifiers were not included in the comparison or had to be adapted to the different experimental platforms.

Results
We used a prospective study of 726 early breast cancer patients from seven certified German breast cancer centers. Patients were treated according to national guidelines and the expressions of 94 selected genes were measured by the mid-throughput qPCR platform Fluidigm. Clinical and pathological data including outcome over five years is available. Using these data, we could compare the performance of six classifiers (scmgene and research versions of PAM50, ROR-S, recurrence score, EndoPredict and GGI). Similar to other studies, we found a similar or even higher concordance between most of the classifiers and most were also able to differentiate high- and low-risk patients. The classifiers that were originally developed for microarray data still performed similarly using the Fluidigm data. Therefore, Fluidigm can be used to measure the gene expressions needed by several classifiers for a large cohort with little effort. In addition, we provide an interactive report of the results, which enables a transparent, in-depth comparison of classifiers and their prediction of individual patients.

Availability and implementation
https://services.bio.ifi.lmu.de/pia/.

Supplementary information
Supplementary data are available at Bioinformatics online.
rMETL: sensitive mobile element insertion detection with long read realignment
Authors: Jiang Tao , Liu Bo , Li Junyi , Wang Yadong 
Published: February 2019

Abstract

Summary
Mobile element insertion (MEI) is a major category of structure variations (SVs). The rapid development of long read sequencing technologies provides the opportunity to detect MEIs sensitively. However, the signals of MEI implied by noisy long reads are highly complex due to the repetitiveness of mobile elements as well as the high sequencing error rates. Herein, we propose the Realignment-based Mobile Element insertion detection Tool for Long read (rMETL). Benchmarking results of simulated and real datasets demonstrate that rMETL enables to handle the complex signals to discover MEIs sensitively. It is suited to produce high-quality MEI callsets in many genomics studies.

Availability and implementation
rMETL is available from https://github.com/hitbc/rMETL.

Supplementary information
Supplementary data are available at Bioinformatics online.
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
Authors: Senapathi Tharindu , Bray Simon , Barnett Christopher B , Grüning Björn , Naidoo Kevin J 
Published: February 2019

Abstract

Motivation
The pathway from genomics through proteomics and onto a molecular description of biochemical processes makes the discovery of drugs and biomaterials possible. A research framework common to genomics and proteomics is needed to conduct biomolecular simulations that will connect biological data to the dynamic molecular mechanisms of enzymes and proteins. Novice biomolecular modelers are faced with the daunting task of complex setups and a myriad of possible choices preventing their use of molecular simulations and their ability to conduct reliable and reproducible computations that can be shared with collaborators and verified for procedural accuracy.

Results
We present the foundations of Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) developed on the Galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages, such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor. We illustrate the basic BRIDGE simulation and analytics capabilities on a previously reported CBH1 protein simulation.

Availability and implementation
Publicly available at https://github.com/scientificomputing/BRIDGE and https://usegalaxy.eu

Supplementary information
Supplementary data are available at Bioinformatics online.
Direct-Acting Antiviral Treatment Failure Among Hepatitis C and HIV–Coinfected Patients in Clinical Care
Authors: Rossi Carmine , Young Jim , Martel-Laferrière Valérie , Walmsley Sharon , Cooper Curtis , Wong Alexander , Gill M John , Klein Marina B ,   The Canadian Co-Infection Cohort Investigators, Barrett Lisa , Cohen Jeff , Conway Brian , Cooper Curtis , Côté Pierre , Cox Joseph , Gill John , Haider Shariq , Hull Mark , Klein Marina , Montaner Julio , Moodie Erica , Pick Neora , Rachlis Anita , Rouleau Danielle , Sadr Aida , Sanche Steve , Sandre Roger , Tyndall Mark , Vachon Marie-Louise , Walmsley Sharon , Wong Alex 
Published: February 2019

Abstract

Background
There are limited data on the real-world effectiveness of direct-acting antiviral (DAA) treatment in patients coinfected with hepatitis C virus (HCV) and HIV—a population with complex challenges including ongoing substance use, cirrhosis, and other comorbidities. We assessed how patient characteristics and the appropriateness of HCV regimen selection according to guidelines affect treatment outcomes in coinfected patients.

Methods
We included all patients who initiated DAA treatment between November 2013 and July 2017 in the Canadian Co-Infection Cohort. Sustained virologic response (SVR) was defined as an undetectable HCV RNA measured between 10 and 18 weeks post-treatment. We defined treatment failure as virologic failure, relapse, or death without achieving SVR. Bayesian logistic regression was used to estimate the posterior odds ratios (ORs) associated with patient demographic, clinical, and treatment-related risk factors for treatment failure.

Results
Two hundred ninety-five patients initiated DAAs; 31% were treatment-experienced, 29% cirrhotic, and 80% HCV genotype 1. Overall, 92% achieved SVR (263 of 286, 9 unknown), with the highest rates in females (97%) and lowest in cirrhotics (88%) and high-frequency injection drug users (89%). Many patients (38%) were prescribed regimens that were outside current clinical guidelines. This did not appreciably increase the risk of treatment failure—particularly in patients with genotype 1 (prior odds ratio [OR], 1.5; 95% credible interval [CrI], 0.38–6.0; posterior OR, 1.0; 95% CrI, 0.40–2.5).

Conclusions
DAAs were more effective than anticipated in a diverse, real-world coinfected cohort, despite the use of off-label, less efficacious regimens. High-frequency injection drug use and cirrhosis were associated with an increased risk of failure.
Successful Implementation of an Antibiotic Stewardship Program in an Academic Dental Practice
Authors: Gross Alan E , Hanna Danny , Rowan Susan A , Bleasdale Susan C , Suda Katie J 
Published: February 2019

AbstractBackgroundMost antibiotic use in the United States occurs in the outpatient setting, and 10% of these prescriptions are generated by dentists. The development of comprehensive antibiotic stewardship programs (ASPs) in the dental setting is nascent, and therefore we describe the implementation of a dental ASP.MethodsA collaborative team of dentist, pharmacist, and physician leaders conducted a baseline needs assessment and literature evaluation to identify opportunities to improve antibiotic prescribing by dentists within Illinois’ largest oral health care provider for Medicaid recipients. A multimodal intervention was implemented that included patient and provider education, clinical guideline development, and an assessment of the antibiotic prescribing rate per urgent care visit before and after the educational interventions.ResultsWe identified multiple needs, including standardization of antibiotic prescribing practices for patients with acute oral infections in the urgent care clinics. A 72.9% decrease in antibiotic prescribing was observed in urgent care visits after implementation of our multimodal intervention (preintervention urgent care prescribing rate, 8.5% [24/283]; postintervention, 2.3% [8/352]; P &lt; .001).ConclusionsWe report the successful implementation of a dental ASP that is concordant with the Centers for Disease Control and Prevention Core Elements of Antibiotic Stewardship in the Outpatient Setting. Our approach may be adapted to other dental practices to improve antibiotic prescribing.
Effect of harvest method and ammoniation of baled corn residue on intake and digestibility in lambs
Authors: Conway Ashley C , King Tasha M , Jolly-Breithaupt Melissa L , MacDonald Jim C , Klopfenstein Terry J , Drewnoski Mary E 
Published: February 2019

Abstract
To determine the effect of harvest method and ammoniation on both in vivo and in vitro digestibility of corn residue, six corn residue treatments consisting of three different harvest methods either with or without anhydrous ammonia chemical treatment (5.5% of dry matter [DM]) were evaluated. The harvest methods included conventional rake-and-bale (CONV) and New Holland Cornrower with eight rows (8ROW) or two rows (2ROW) of corn stalks chopped into the windrow containing the tailings (leaf, husk, and upper stem) from eight rows of harvested corn (ammoniated bales of each harvest method resulted in treatments COVAM, 8RAM, and 2RAM). Nine crossbred wether lambs (49.2 ± 0.5 kg BW) were fed 64.2% corn residue, 29.8% wet corn gluten feed, 3.3% smooth-bromegrass hay, and 2.8% mineral mix (DM basis) in a 9 × 6 Latin rectangle metabolism study with a 3 × 2 factorial treatment to measure total tract disappearance. Six 21-d periods consisted of 14-d adaptation and 7-d total fecal collection, and lambs were fed ad libitum (110% of the previous day’s DM intake [DMI]) during days 1 to 12 and reduced to 95% of ad libitum intake for days 13 to 21. There was a harvest method by ammoniation interaction (P &lt; 0.01) for ad libitum DMI (days 7 to 11). Ammoniation increased (P &lt; 0.01) intake across all harvest methods, where 2RAM DMI was 4.1%, COVAM was 3.6%, and 8RAM was 3.1%, which were all different (P &lt; 0.01) from each other, but all untreated residues were consumed at 2.6% of BW (P ≥ 0.92) regardless of harvest method. There were no interactions (P &gt; 0.34) between harvest method and ammoniation for any total tract or in vitro digestibility estimate. Harvest method affected (P &lt; 0.04) DM, neutral detergent fiber (NDF), and acid detergent fiber (ADF) digestibility, where 2ROW was greater than both CONV and 8ROW, which did not differ. The organic matter (OM) digestibility (P = 0.12) and digestible energy (DE; P = 0.30) followed the same numerical trend. Both in vitro DM digestibility (IVDMD) and in vitro OM digestibility (IVOMD) of the residue were affected (P &lt; 0.01) by harvest method, with 2ROW being greater (P &lt; 0.01) than both CONV and 8ROW. For IVDMD, 8ROW was not (P = 0.77) different from CONV, but 8ROW IVOMD was lower (P = 0.03) than CONV. Ammoniation improved (P &lt; 0.01) DM, OM, NDF, and ADF digestibility of all harvest methods, resulting in a 26% increase (P &lt; 0.01) in DE due to ammoniation. Similar digestibility improvements were observed in vitro with ammoniation improving IVDMD and IVOMD by 23% and 20%, respectively. Both selective harvest methods and ammoniation can improve the feeding value of baled corn residue.
Priming Is a Suitable Strategy to Enhance Resistance Towards Leaf Rust in Barley
Authors: Wehner Gwendolin , Kopahnke Doris , Richter Klaus , Kecke Steffen , Schikora Adam , Ordon Frank 
Published: February 2019

Priming allows plants to respond faster and stronger to abiotic or biotic stresses. Leaf rust (Puccinia hordei) is an important pathogen of barley (Hordeum vulgare), for which resistance genes are known, but mostly overcome. Therefore, the aims of this study were (i) to establish a priming system in barley, based on bacterial N-acyl homoserine lactone (AHL), and (ii) to get information on the effect of priming on the reaction to leaf rust. Plants were inoculated with bacteria, i.e., Ensifer meliloti with repaired expR copy, producing the oxo-C14-homoserine lactone (AHL) and an E. meliloti strain carrying the attM lactonase gene from Agrobacterium tumefaciens, which cleaves the AHL and acts here as negative control. After three bacterial inoculations, plants were challenged with P. hordei strain I-80 at the three leaves stage. Twelve days after infection, scoring of the leaf area diseased and the infection type was conducted followed by the calculation of the relative susceptibility. First results indicate a significantly (P < 0.001) higher resistance level to P. hordei after inoculation with E. meliloti. Furthermore, significant (P < 0.001) differences were detected between the accessions tested for priming efficiency, which can be the basis to screen a larger set of barley accessions to detect quantitative trait loci or candidate genes involved in priming. [Formula: see text] Copyright © 2019 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Optogenetic vision restoration with high resolution
Authors: Ferrari U. , Deny S. , Sengupta A. , Caplette R. , Sahel J.A. , Dalkara D. , Picaud S. , Duebel J. , Marre O. 
Published: February 2019

AbstractThe majority of inherited retinal degenerations are due to photoreceptor cell death. In many cases ganglion cells are spared making it possible to stimulate them to restore visual function. Several studies (Bi et al., 2006; Lin et al., 2008; Sengupta et al., 2016; Caporale et al., 2011; Berry et al., 2017) have shown that it is possible to express an optogenetic protein in ganglion cells and make them light sensitive. This is a promising strategy to restore vision since optical targeting may be more precise than electrical stimulation with a retinal prothesis. However the spatial resolution of optogenetically-reactivated retinas has not been measured with fine-grained stimulation patterns. Since the optogenetic protein is also expressed in axons, it is unclear if these neurons will only be sensitive to the stimulation of a small region covering their somas and dendrites, or if they will also respond to any stimulation overlapping with their axon, dramatically impairing spatial resolution. Here we recorded responses of mouse and macaque retinas to random checkerboard patterns following an in vivo optogenetic therapy. We show that optoge-netically activated ganglion cells are each sensitive to a small region of visual space. A simple model based on this small receptive field predicted accurately their responses to complex stimuli. From this model, we simulated how the entire population of light sensitive ganglion cells would respond to letters of different sizes. We then estimated the maximal acuity expected by a patient, assuming it could make an optimal use of the information delivered by this reactivated retina. The obtained acuity is above the limit of legal blindness. This high spatial resolution is a promising result for future clinical studies.
Neural and linguistic differences explain priming and interference during naming
Authors: Wei Tao , Schnur Tatiana T. 
Published: February 2019

AbstractWhen naming an object, humans are faster to produce the name (“cat”) if immediately having named a related object (“dog”) but paradoxically slower to name the same object (“cat”) if there are intervening speech acts (Wei and Schnur 2019). This dependence of behavior on prior experience is ubiquitous in other domains, often termed “priming” (if behavior is speeded) or “interference” (if behavior is slower). However, it is unknown the changes in the language system (conceptual, lexical, and/or connections between representations) and corresponding brain mechanisms which create these paradoxical effects on the same speech act. Using fMRI during simple picture naming, we observed distinct brain regions and different connections associated with priming and interference. Greater priming was associated with increased activation in the ventral occipitotemporal cortex, while greater interference was associated with decreased functional connectivity between the left posterior temporal and angular gyri. To provide neural evidence of where in the language system priming and interference in naming occur, we assayed the response of different brain areas to conceptual or lexical aspects of speech. The brain and language systems adapt to prior naming experience by modulating conceptual representations during priming, but modulating conceptual, lexical and the mapping between representations during interference.