bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnostik und ambulante Eradikationstherapie von Trägern mit MRSA in der vertragsärztlichen Versorgung – Eine Analyse der Erstattungssituation im Kontext aktueller Vergütungsveränderungen
Authors: Schwendler M. , Hübner C. , Fleßa S. 
Published: June 2016

ZusammenfassungDer Methicillin-resistente Staphylococcus aureus (MRSA) tritt in Deutschland sektorenübergreifend auf. Der deutsche Gesetzgeber hat die Vergütung für ärztliche Leistungen bei Trägern von MRSA im niedergelassenen Bereich erstmalig zum 01.04.2012 geregelt und nach einem 2-jährigen Erprobungszeitraum in die Regelversorgung aufgenommen. Die vorliegende retrospektive Arbeit soll einerseits einen Überblick über die MRSA-bezogene Leistungs- und Erstattungssituation geben und andererseits die MRSA-Patienten und deren Behandlung im ambulanten Sektor beschreiben. Mit dieser Zielrichtung wurden Sekundärdaten – standardmäßig erfasste Leistungsabrechnungsdaten – der Kassenärztlichen Bundesvereinigung (KBV) und der Kassenärztlichen Vereinigung (KV) Mecklenburg-Vorpommern analysiert und ausgewertet. Die Analyse bezieht sich auf den Zeitraum 01.04.2012 bis 31.03.2014. Die Ergebnisse zeigen, dass bundesweit MRSA-Leistungen in Höhe von 3 235 870,18 € vergütet werden und die Diagnostikkosten die Behandlungskosten übersteigen. In Deutschland rechnen 5 627 Ärzte Leistungen im Zusammenhang mit MRSA ab. Davon sind 51,56% Allgemeinmediziner und 21,25% hausärztlich tätige Internisten. In der KV Mecklenburg-Vorpommern sind die Patienten älter (Altersmittelwert 69,13 Jahre), die Leistungen kosten im Durchschnitt 27,76 € und 76,85% der Patienten werden innerhalb eines Quartals behandelt. Insgesamt ist festzustellen, dass sich die Identifikation von MRSA-Trägern und deren ambulante Sanierung regional unterschiedlich darstellen. Um weitere Grundlagen für eine effizientere Ressourcenverteilung im Gesundheitswesen zu schaffen ist es notwendig, die ambulante MRSA-Eradikation nicht nur medizinisch detaillierter zu analysieren, sondern auch die Nahtstellen des sektorenübergreifenden Patientenstroms und die Ökonomie zu betrachten.
Der Umgang mit MRSA bei Beschäftigten im Gesundheitsdienst aus Sicht der Krankenhaushygiene
Authors: Peters C. , Dulon M. , Lietz J. , Nienhaus A. 
Published: June 2016

Zusammenfassung
Hintergrund: Die Besiedlung mit Methicillin-resistentem Staphylococcus aureus (MRSA) stellt für Mitarbeiter und die medizinischen Einrichtungen eine besondere Herausforderung dar. In diesem Zusammenhang spielen Mitarbeiter der Krankenhaushygiene neben Betriebsärzten eine wesentliche Rolle.
Methoden: 2014 wurden Krankenhaushygiene-Mitarbeiter schriftlich zum Umgang mit MRSA-besiedeltem Personal befragt. Der Erhebungsbogen enthielt Fragen zum MRSA-Management in Krankenhäusern sowie der Zusammenarbeit zwischen Hygienefachpersonal und Betriebsarzt. Als Vergleich wurde eine Untersuchung von Betriebsärzten zu ihren Erfahrungen bei der Betreuung von Mitarbeitern mit MRSA-Besiedlung hinzugezogen.
Ergebnisse: An der Befragung nahmen 124 Krankenhaushygiene-Mitarbeiter teil. Ein allgemeines Personalscreening findet vor allem in Ausbruchssituationen statt. Unterschieden wird zwischen vorübergehender und dauerhafter Besiedlung (47%). Als häufigstes Kriterium für eine MRSA-Dauerbesiedlung gelten 2 erfolglose Dekolonisierungsrunden. Eine Kooperation zwischen Hygienemitarbeiter und Betriebsarzt bei MRSA-Trägerschaft des Personals findet überwiegend statt. Die Verantwortung für Betreuung, Screening sowie Dekolonisierung der Mitarbeiter liegt bei beiden Berufsgruppen mit unterschiedlichen Schwerpunkten. Über den Umgang mit MRSA-positivem Personal wird unterschiedlich berichtet. Die Empfehlungen zur Weiterarbeit trotz Besiedlung reichen von der Einhaltung der Standardhygiene bis zum patientenfernen Einsatz oder einer Freistellung.
Schlussfolgerung: Der Umgang mit MRSA bei Beschäftigten im Gesundheitsdienst ist in Deutschland unterschiedlich. Krankenhaushygiene-Mitarbeiter und Betriebsärzte sind gleichermaßen in die Betreuung involviert. Klare Regelungen würden im Umgang mit multiresistenten Erregern beim Personal helfen.
Biogenesis of sperm acrosome is regulated by pre-mRNA alternative splicing ofAcrbpin the mouse
Authors: Kanemori Yoshinori , Koga Yoshitaka , Sudo Mai , Kang Woojin , Kashiwabara Shin-ichi , Ikawa Masahito , Hasuwa Hidetoshi , Nagashima Kiyoshi , Ishikawa Yu , Ogonuki Narumi , Ogura Atsuo , Baba Tadashi 
Published: June 2016

SignificanceMammalian sperm possess a Golgi-derived exocytotic organelle, the acrosome, located on the apical region of the head. Proper biogenesis of the acrosome is essential for the fertilization process because the aberrant acrosome formation results in the sterility or subfertility of males. Here, we show that the acrosome formation is governed by two forms of proacrosin-binding protein ACRBP, wild-type ACRBP-W and variant ACRBP-V5, which are generated by pre-mRNA alternative splicing ofAcrbp. ACRBP-V5 is involved in the formation and configuration of the acrosomal granule during early spermiogenesis, whereas the inactive status of proacrosin in the acrosome is maintained by ACRBP-W until acrosomal exocytosis.
Cross-class metallo-β-lactamase inhibition by bisthiazolidines reveals multiple binding modes
Authors: Hinchliffe Philip , González Mariano M. , Mojica Maria F. , González Javier M. , Castillo Valerie , Saiz Cecilia , Kosmopoulou Magda , Tooke Catherine L. , Llarrull Leticia I. , Mahler Graciela , Bonomo Robert A. , Vila Alejandro J. , Spencer James 
Published: June 2016

Significance
Bacterial diseases remain a huge burden on healthcare worldwide, with the emergence and re-emergence of strains resistant to currently used antibiotics posing an increasing clinical threat. Metallo-β-lactamases (MBLs) are key determinants of antibiotic resistance because they hydrolyze almost all β-lactam antibiotics and are unaffected by currently available β-lactamase inhibitors (βLIs). The structural diversity between MBLs has proved problematic when designing βLIs effective against all MBL targets. Here we show a series of small compounds, bisthiazolidines, which act as inhibitors of all MBL types, restoring the efficacy of currently used antibiotics against resistant bacterial strains producing different MBLs. High-resolution crystal structures reveal how diverse MBLs are inhibited by the unexpected versatility of bisthiazolidine binding, raising implications for future βLI design.
HIFI-α activation underlies a functional switch in the paradoxical role of Ezh2/PRC2 in breast cancer
Authors: Mahara Sylvia , Lee Puay Leng , Feng Min , Tergaonkar Vinay , Chng Wee Joo , Yu Qiang 
Published: June 2016

Significance
The plasticity of Polycomb repressive complex 2 (PRC2) in the context of tumorigenesis has remained a subject of contention. Here we demonstrate that the equilibrium between the oncogenic and tumor-suppressive activity of PRC2 in promoting breast cancer invasion is tightly regulated by hypoxia-inducible factor 1-α. PRC2 acts as a tumor-suppressor barrier to the hypoxia-driven invasion pathway, and the impaired PRC2 activity upon hypoxia promotes a chromatin switch at proinvasion matrix metalloproteinase gene loci. The study fundamentally changed our understanding of the role of PRC2 in breast cancer and also identified a previously unidentified function of enhancer of zeste 2 to complex with Forkhead box M1 to promote cancer invasion.
Examination of Predation on Early Life Stage Delta Smelt in the San Francisco Estuary Using DNA Diet Analysis
Authors: Schreier Brian M. , Baerwald Melinda R. , Conrad J. Louise , Schumer Gregg , May Bernie 
Published: June 2016

AbstractWe examined predation by nonnative Mississippi Silversides Menidia audens, other small fishes, and invertebrates on the early life stages of the endangered Delta Smelt Hypomesus transpacificus, which is endemic to the Sacramento–San Joaquin Delta in California. Mississippi Silversides and other putative predators were collected primarily via boat electrofishing in the northern reaches of the upper San Francisco Estuary, an area targeted for substantial tidal wetland restoration to enhance habitat for Delta Smelt and other endangered fishes. Predators’ digestive tracts were removed and analyzed for the presence of Delta Smelt DNA by using quantitative PCR TaqMan assays. Across all sites, 69 of 550 Mississippi Silversides tested positive for Delta Smelt DNA. The number of sampled Mississippi Silversides that were positive for Delta Smelt DNA was significantly greater in offshore habitats than in nearshore habitats. Delta Smelt DNA detection data indicated that a wide variety of other species were also predators of Delta Smelt. Additionally, we used generalized linear modeling to analyze the relationship between Delta Smelt predation detections in Mississippi Silversides and concurrently collected habitat parameters. Turbidity was identified as a significant predictor of predation, as Delta Smelt DNA was detected more often in Mississippi Silverside samples from clearer water. These results suggest that restoration efforts designed to increase turbidity in the estuary may be beneficial in reducing Mississippi Silversides’ predatory impacts on Delta Smelt.Received August 24, 2015; accepted February 3, 2016 Published online June 15, 2016
Pacific Lamprey in Coastal Drainages of California: Occupancy Patterns and Contraction of the Southern Range
Authors: Reid Stewart B. , Goodman Damon H. 
Published: June 2016

AbstractPacific Lamprey Entosphenus tridentatus have been overlooked historically in fish surveys using standard salmonid methods along the Pacific coast of North America. As a result, little is known of even their broader distribution patterns at the drainage level. Over the last 2 decades, the species has shown a northward range contraction of over 900 km, and at this time the southernmost population is the Big Sur River in California. This study evaluates the hypothesis that Pacific Lampreys do not typically utilize relatively small coastal drainages (<100 km2). We examined historical Pacific Lamprey records throughout California and surveyed 349 current sites in 102 coastal drainages along the California coastline and into Baja California. Within their currently occupied range (north of Big Sur), Pacific Lampreys were found in all drainages >100 km2, but in only 3 of 29 drainages <50 km2, and they were absent in all drainages <25 km2. All historical records are from drainages >50 km2, and primarily from larger drainages in southern California. Our results will support greater exploration of the ecological roles of lampreys in coastal streams, where they act as importers of marine nutrients, substrate engineers and filter feeders, as well as providing a rich prey base for many species. This paper also provides resource managers with an understanding of where Pacific Lampreys are likely to be found and where they were probably not a natural component of the fish fauna, allowing prioritization of conservation actions and more effective use of resources.Received December 3, 2015; accepted February 22, 2016 Published online June 15, 2016
Ploidy Variation and Viability of Aneuploid Ornamental Koi Carp Obtained by Crossing Triploid Females with Diploid Males
Authors: Gomelsky Boris , Delomas Thomas A , Warner Jeffrey L 
Published: June 2016

Abstract
Results of crossing triploid females of ornamental koi, a variant of Common Carp Cyprinus carpio, with diploid koi males in two consecutive spawning seasons (2014 and 2015) are presented. A total of seven progenies from six triploid females (one female was spawned twice) were produced and analyzed. The same as normal diploid females, triploid females were highly fertile and produced hundreds of thousands of eggs (up to 400,000 per female). Processes of embryo incubation and hatching of larvae in progenies obtained from triploid females proceeded normally; however, mass mortality of hatched larvae occurred at the swim-up stage. Nevertheless about 200,000 swim-up larvae were obtained and stocked for further rearing. A total of about 1,000 juveniles (or 0.5% of the number of stocked larvae) was collected from outdoor tanks. As expected, all analyzed larvae and juveniles in control progenies obtained by crosses of diploid females with diploid males were diploid. About 95% of analyzed fish (larvae and juveniles) obtained by crossing triploid females with diploid males were aneuploids with ploidy ranging from 2.14n to 3.0n; mean values of fish ploidy in progenies obtained from different triploid females varied from 2.47n to 2.63n. Since aneuploid fish have in their genomes one haploid set from parental males, the data obtained indicate that triploid koi females produced aneuploid eggs with ploidy range from haploid to diploid level and a modal ploidy level around 1.5n, similar to the production of aneuploid spermatozoa observed earlier for triploid males in fish. About 5% of juveniles obtained from triploid females had ploidy range from 3.21n to 4.0n. Apparently these fish resulted from spontaneous suppression of the second meiotic division in aneuploid eggs.
Effects of Initial Feed Timing on Early Survival and Growth of Triploid Hatchery Rainbow Trout
Authors: Gunter Beau J , Grant Bryan L 
Published: June 2016

Abstract
The timing of initial feeding for trout fry varies greatly among hatchery professionals and may affect early survival and growth. The purpose of this study was to determine if there is a number of days posthatch to begin feeding triploid hatchery Rainbow Trout Oncorhynchus mykiss where they will experience the least mortality and most favorable growth rates. Treatment groups of triploid Rainbow Trout fry were fed for 30 d with initial feeding times of 13, 15, 17, 19, 21, and 25 d posthatch on 12.2°C water. Variations in survival, condition factor, size, and feed conversions between initial feed times were evaluated. The number of days posthatch prior to initial feeding did not have a significant impact on survival. The growth parameters measured showed significant variation depending on days posthatch prior to initial feeding, with the most favorable growth parameters found at 21 and 25 d posthatch.
Structural Complexity Improves the Rearing Performance of Rainbow Trout in Circular Tanks
Authors: Kientz Jeremy L , Barnes Michael E 
Published: June 2016

Abstract
While structural complexity has been used extensively during hatchery rearing in an attempt to improve poststocking survival, the potential impact of this complexity on hatchery rearing performance has largely been ignored. This study examined the growth and condition of juvenile Rainbow Trout Oncorhynchus mykiss reared in nearly fully covered circular tanks containing nine vertically oriented round aluminum rods (structurally complex) compared with that of trout reared in almost fully covered tanks with no rods (control) at two water velocities (2.0 body length (BL)/s and 2.75 BL/s). After 51 days, total tank weight gain was significantly higher in the structurally complex tanks than in the control tanks, regardless of water velocity. The feed conversion ratio was also significantly better in the structurally complex tanks [mean (SD) 1.25 (0.10)] than in the control tanks [1.66 (0.41)]. There were no significant differences in hepatosomatic index, splenosomatic index, and viscerosomatic index between the fish from the structurally complex and the control tanks. Total tank weight gain was significantly higher and the feed conversion ratio significantly lower in the lower water velocity tanks than in the higher water velocity tanks. These results indicate that vertically oriented aluminum rods can be used to increase structural complexity and improve Rainbow Trout rearing performance in circular rearing tanks, with minimal effects on regular tank cleaning.
Evaluation of Dietary Lipid Sources for the Juvenile Lost River Sucker
Authors: Twibell Ronald G , Barron James M , Gannam Ann L 
Published: June 2016

Abstract
The establishment of a propagation program is among the recommended actions of the U.S. Fish and Wildlife Service recovery plan for the endangered Lost River Sucker Deltistes luxatus. As an initial step in diet development, a feeding trial was conducted to identify appropriate dietary lipid sources to feed juvenile Lost River Suckers at a rate of 0.47 g/fish. Six dietary treatments were produced by adding the following to a basal diet: (1) marine fish oil (Fish) as a control, (2) flaxseed oil (Flax), (3) soybean oil (Soy), or a 1:1 mixture of (4) fish and flax oil (Fish/Flax), (5) fish and soy oil (Fish/Soy), or (6) flax and soy oil (Flax/Soy). At the conclusion of the feeding trial weight gain of fish fed the control diet (Fish) was not significantly different than that of fish fed the other dietary treatments. However, weight gain of fish fed Soy was significantly higher than that of fish fed Fish/Flax. Whole-body lipid was significantly higher in fish fed Soy than in fish fed Fish, Flax, Fish/Flax, or Fish/Soy, but not significantly different than that in fish fed Flax/Soy. Generally, whole body fatty acid profiles reflected the fatty acid profiles of their respective dietary treatments. These results suggest soybean oil is an appropriate dietary lipid source for the Lost River Sucker, but more research on quantitative dietary requirements is needed for successful propagation of this species.
How to assess the efficiency of synchronization experiments in tokamaks
Authors: Murari A. , Craciunescu T. , Peluso E. , Gelfusa M. , Lungaroni M. , Garzotti L. , Frigione D. , Gaudio P. 
Published: June 2016

Abstract
Control of instabilities such as ELMs and sawteeth is considered an important ingredient in the development of reactor-relevant scenarios. Various forms of ELM pacing have been tried in the past to influence their behavior using external perturbations. One of the main problems with these synchronization experiments resides in the fact that ELMs are periodic or quasi-periodic in nature. Therefore, after any pulsed perturbation, if one waits long enough, an ELM is always bound to occur. To evaluate the effectiveness of ELM pacing techniques, it is crucial to determine an appropriate interval over which they can have a real influence and an effective triggering capability. In this paper, three independent statistical methods are described to address this issue: Granger causality, transfer entropy and recurrence plots. The obtained results for JET with the ITER-like wall (ILW) indicate that the proposed techniques agree very well and provide much better estimates than the traditional heuristic criteria reported in the literature. Moreover, their combined use allows for the improvement of the time resolution of the assessment and determination of the efficiency of the pellet triggering in different phases of the same discharge. Therefore, the developed methods can be used to provide a quantitative and statistically robust estimate of the triggering efficiency of ELM pacing under realistic experimental conditions.
Classifying and segmenting microscopy images with deep multiple instance learning
Authors: Kraus Oren Z. , Ba Jimmy Lei , Frey Brendan J. 
Published: June 2016

Abstract
Motivation : High-content screening (HCS) technologies have enabled large scale imaging experiments for studying cell biology and for drug screening. These systems produce hundreds of thousands of microscopy images per day and their utility depends on automated image analysis. Recently, deep learning approaches that learn feature representations directly from pixel intensity values have dominated object recognition challenges. These tasks typically have a single centered object per image and existing models are not directly applicable to microscopy datasets. Here we develop an approach that combines deep convolutional neural networks (CNNs) with multiple instance learning (MIL) in order to classify and segment microscopy images using only whole image level annotations.
Results : We introduce a new neural network architecture that uses MIL to simultaneously classify and segment microscopy images with populations of cells. We base our approach on the similarity between the aggregation function used in MIL and pooling layers used in CNNs. To facilitate aggregating across large numbers of instances in CNN feature maps we present the Noisy-AND pooling function, a new MIL operator that is robust to outliers. Combining CNNs with MIL enables training CNNs using whole microscopy images with image level labels. We show that training end-to-end MIL CNNs outperforms several previous methods on both mammalian and yeast datasets without requiring any segmentation steps.
Availability and implementation : Torch7 implementation available upon request.
Contact : oren.kraus@mail.utoronto.ca
Reconstructing the temporal progression of HIV-1 immune response pathways
Authors: Jain Siddhartha , Arrais Joel , Venkatachari Narasimhan J. , Ayyavoo Velpandi , Bar-Joseph Ziv 
Published: June 2016

Abstract
Motivation: Most methods for reconstructing response networks from high throughput data generate static models which cannot distinguish between early and late response stages.
Results: We present TimePath, a new method that integrates time series and static datasets to reconstruct dynamic models of host response to stimulus. TimePath uses an Integer Programming formulation to select a subset of pathways that, together, explain the observed dynamic responses. Applying TimePath to study human response to HIV-1 led to accurate reconstruction of several known regulatory and signaling pathways and to novel mechanistic insights. We experimentally validated several of TimePaths’ predictions highlighting the usefulness of temporal models.
Availability and Implementation: Data, Supplementary text and the TimePath software are available from http://sb.cs.cmu.edu/timepath
Contact: zivbj@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats
Authors: Schaeffer Carly E. , Figueroa Nathaniel D. , Liu Xiaolin , Karro John E. 
Published: June 2016

Abstract
Motivation : Transposable elements (TEs) and repetitive DNA make up a sizable fraction of Eukaryotic genomes, and their annotation is crucial to the study of the structure, organization, and evolution of any newly sequenced genome. Although RepeatMasker and nHMMER are useful for identifying these repeats, they require a pre-compiled repeat library—which is not always available. De novo identification tools such as Recon, RepeatScout or RepeatGluer serve to identify TEs purely from sequence content, but are either limited by runtimes that prohibit whole-genome use or degrade in quality in the presence of substitutions that disrupt the sequence patterns.
Results : phRAIDER is a de novo TE identification tool that address the issues of excessive runtime without sacrificing sensitivity as compared to competing tools. The underlying model is a new definition of elementary repeats that incorporates the PatternHunter spaced seed model, allowing for greater sensitivity in the presence of genomic substitutions. As compared with the premier tool in the literature, RepeatScout, phRAIDER shows an average 10× speedup on any single human chromosome and has the ability to process the whole human genome in just over three hours. Here we discuss the tool, the theoretical model underlying the tool, and the results demonstrating its effectiveness.
Availability and implementation : phRAIDER is an open source tool available from https://github.com/karroje/phRAIDER .
Contact : karroje@miamiOH.edu or
Supplementary information: Supplementary data are available at Bioinformatics online.