bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut ofOdontotaenius disjunctus
Authors: Ceja-Navarro Javier A , Nguyen Nhu H , Karaoz Ulas , Gross Stephanie R , Herman Donald J , Andersen Gary L , Bruns Thomas D , Pett-Ridge Jennifer , Blackwell Meredith , Brodie Eoin L 
Published: August 2013

AbstractCoarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by 15N2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni–Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N2 that is important for this beetle to subsist on woody biomass.
Host-specific adaptation governs the interaction of the marine diatom, Pseudo-nitzschia and their microbiota
Authors: Sison-Mangus Marilou P , Jiang Sunny , Tran Kevin N , Kudela Raphael M 
Published: August 2013

Abstract
The association of phytoplankton with bacteria is ubiquitous in nature and the bacteria that associate with different phytoplankton species are very diverse. The influence of these bacteria in the physiology and ecology of the host and the evolutionary forces that shape the relationship are still not understood. In this study, we used the Pseudo-nitzschia–microbiota association to determine (1) if algal species with distinct domoic acid (DA) production are selection factors that structures the bacterial community, (2) if host-specificity and co-adaptation govern the association, (3) the functional roles of isolated member of microbiota on diatom–hosts fitness and (4) the influence of microbiota in changing the phenotype of the diatom hosts with regards to toxin production. Analysis of the pyrosequencing-derived 16S rDNA data suggests that the three tested species of Pseudo-nitzschia, which vary in toxin production, have phylogenetically distinct bacterial communities, and toxic Pseudo-nitzschia have lower microbial diversity than non-toxic Pseudo-nitzschia. Transplant experiments showed that isolated members of the microbiota are mutualistic to their native hosts but some are commensal or parasitic to foreign hosts, hinting at co-evolution between partners. Moreover, Pseudo-nitzschia host can gain protection from algalytic bacteria by maintaining association with its microbiota. Pseudo-nitzschia also exhibit different phenotypic expression with regards to DA production, and this depends on the bacterial species with which the host associates. Hence, the influences of the microbiota on diatom host physiology should be considered when studying the biology and ecology of marine diatoms.
The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis
Authors: Tamas Ivica , Smirnova Angela V , He Zhiguo , Dunfield Peter F 
Published: August 2013

Abstract
The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy.
Measurement of crystal growth velocity in a melt-quenched phase-change material
Authors: Salinga Martin , Carria Egidio , Kaldenbach Andreas , Bornhöfft Manuel , Benke Julia , Mayer Joachim , Wuttig Matthias 
Published: August 2013

AbstractPhase-change materials are the basis for next-generation memory devices and reconfigurable electronics, but fundamental understanding of the unconventional kinetics of their phase transitions has been hindered by challenges in the experimental quantification. Here we obtain deeper understanding based on the temperature dependence of the crystal growth velocity of the phase-change material AgInSbTe, as derived from laser-based time-resolved reflectivity measurements. We observe a strict Arrhenius behaviour for the growth velocity over eight orders of magnitude (from ~10 nm s−1to ~1 m s−1). This can be attributed to the formation of a glass at elevated temperatures because of rapid quenching of the melt. Further, the temperature dependence of the viscosity is derived, which reveals that the supercooled liquid phase must have an extremely high fragility (>100). Finally, the new experimental evidence leads to an interpretation, which comprehensively explains existing data from various different experiments reported in literature.
Sobre la particular similitud de los neutros español y noruego
Authors: Martínez López Juan A. , Jørgensen Annette Myre 
Published: August 2013

The Spanish particle lo can appear in three different syntactic structures which are described in this paper. Depending on the structure in which it is inserted, lo can have three different functions: pronoun, intensifier and emphatic particle/element.
At the same time, the Norwegian definite neutrum particle det is analysed, in order to see to what extent the Norwegian det covers the three functions the Spanish lo can have.
La néologie expressive et onomatopéique dans l’étymologie du français
Authors: Quentel Gilles 
Published: August 2013

It is generally well-accepted that, in every language, a significant amount of unknown etymologies can be explained by the means of “echoism”, which states that a historically unexplained word can be of onomatopoeic origins.
This paper objects to the theory in general, taking the particular case of French to illustrate its drifts. It aims at demonstrating that most onomatopeic or “expressive” related etymologies are speculative, unattested and based upon very thin argumentation. It proposes other ways to undertake the search for etymologies of French words.
The Effects of Pulse Pressure from Seismic Water Gun Technology on Northern Pike
Authors: Gross Jackson A. , Irvine Kathryn M. , Wilmoth Siri , Wagner Tristany L. , Shields Patrick A. , Fox Jeffrey R. 
Published: August 2013

AbstractWe examined the efficacy of sound pressure pulses generated from a water gun for controlling invasive Northern Pike Esox lucius. Pulse pressures from two sizes of water guns were evaluated for their effects on individual fish placed at a predetermined random distance. Fish mortality from a 5,620.8‐cm3 water gun (peak pressure source level = 252 dB referenced to 1 μP at 1 m) was assessed every 24 h for 168 h, and damage (intact, hematoma, or rupture) to the gas bladder, kidney, and liver was recorded. The experiment was replicated with a 1,966.4‐cm3 water gun (peak pressure source level = 244 dB referenced to 1 μP at 1 m), but fish were euthanized immediately. The peak sound pressure level (SPLpeak), peak‐to‐peak sound pressure level (SPLp‐p), and frequency spectrums were recorded, and the cumulative sound exposure level (SELcum) was subsequently calculated. The SPLpeak, SPLp‐p, and SELcum were correlated, and values varied significantly by treatment group for both guns. Mortality increased and organ damage was greater with decreasing distance to the water gun. Mortality (31%) by 168 h was only observed for Northern Pike exhibiting the highest degree of organ damage. Mortality at 72 h and 168 h postexposure was associated with increasing SELcum above 195 dB. The minimum SELcum calculated for gas bladder rupture was 199 dB recorded at 9 m from the 5,620.8‐cm3 water gun and 194 dB recorded at 6 m from the 1,966.4‐cm3 water gun. Among Northern Pike that were exposed to the large water gun, 100% of fish exposed at 3 and 6 m had ruptured gas bladders, and 86% exposed at 9 m had ruptured gas bladders. Among fish that were exposed to pulse pressures from the smaller water gun, 78% exhibited gas bladder rupture. Results from these initial controlled experiments underscore the potential of water guns as a tool for controlling Northern Pike.
Contemporary Population Structure in Klamath River Basin Chinook Salmon Revealed by Analysis of Microsatellite Genetic Data
Authors: Kinziger Andrew P. , Hellmair Michael , Hankin David G. , Garza John Carlos 
Published: August 2013

AbstractChinook Salmon Oncorhynchus tshawytscha exhibit substantial population genetic structure at multiple scales. Although geography is generally more important than life history, particularly migration and run timing, for describing genetic structure in Chinook Salmon, there are several exceptions to this general pattern, and hatchery supplementation has altered natural genetic structure in some areas. Given that genetic structure of Chinook Salmon is often basin‐specific, we assessed genetic variation of 27 microsatellite loci in geographically and temporally distinct natural populations and hatchery stocks in the Klamath River basin, California. Multiple analyses support recognition of three major genetic lineages from separate geographic regions in the Klamath River basin: the lower basin, the Klamath River, and the Trinity River. The lower basin group was sharply distinct, but populations in the Klamath and Trinity river lineages were connected by processes that can be described by a one‐dimensional, linear, stepping‐stone model where gene exchange occurred primarily, but not exclusively, between adjacent populations. Genetic structure by migration timing was also evident, although divergences among populations that differed by migration timing only were fewer than those observed between geographic regions. Distinct run‐timing ecotypes in the Klamath River basin thus appear to have evolved independently through a process of parallel evolution. Introgressive pressure from the hatchery stocks into natural populations was attenuated by distance from the hatchery, but comparison of historical population genetic structure to contemporary patterns would be needed to fully evaluate the extent to which hatchery stocks may have altered natural genetic structure.
Impact of Change to Molecular Testing for Clostridium difficile Infection on Healthcare Facility–Associated Incidence Rates
Authors: Moehring Rebekah W. , Lofgren Eric T. , Anderson Deverick J. 
Published: August 2013

Background.Change from nonmolecular to molecular testing techniques is thought to contribute to the increasing trend in incidence of Clostridium difficile infection (CDI); however the degree of effect attributed to this versus other time-related epidemiologic factors is unclear.Methods.We compared the relative change in incidence rate (IRR) of healthcare facility–associated (HCFA) CDI among hospitals in the Duke Infection Control Outreach Network before and after the date of switch from nonmolecular tests to polymerase chain reaction (PCR) using prospectively collected surveillance data from July 2009 to December 2011. Data from 10 hospitals that switched and 22 control hospitals were included. Individual hospital estimates were determined using Poisson regression. We used an interrupted time series approach to develop a Poisson mixed-effects model. Additional regression adjustments were made for clustering and proportion of intensive care unit patient-days. The variable for PCR was treated as a fixed effect; other modeled variables were random effects.Results.For those hospitals that switched to PCR, mean incidence rate of HCFA CDI before the switch was 6.0 CDIs per 10,000 patient-days compared with 9.6 CDIs per 10,000 patient-days after the switch. Estimates of hospital-specific IRR that compared after the switch with before the switch ranged from 0.89 (95% confidence interval [CI], 0.32–2.44) to 6.91 (95% CI, 1.12–42.54). After adjustment in the mixed-effects model, the overall IRR comparing CDI incidence after the switch to before the switch was 1.56 (95% CI, 1.28–1.90). Time-trend variables did not reach statistical significance.Conclusion.Hospitals that switched from nonmolecular to molecular tests experienced an approximate 56% increase in the rate of HCFA CDI after testing change.
Healthcare Epidemiology Practicum Rotation for Postgraduate Physician Trainees in Medicine–Infectious Diseases
Authors: Sreeramoju Pranavi , Fernandez-Rojas Maria Eva 
Published: August 2013

Practicum education in healthcare epidemiology and infection control (HEIC) for postgraduate physician trainees in infectious diseases is necessary to prepare them to be future participants and leaders in patient safety. Voss et al suggested that training in HEIC should be offered as a “common trunk” for physicians being trained in clinical microbiology or infectious diseases. A 1-month rotation has been recommended previously. A survey by Joiner et al indicated that only 50% of infectious diseases fellows found the infection control training adequate. The objective of this article is to report our 2-year experience with a 1-month practicum rotation we designed and implemented at our institution.The setting is the Adult Infectious Diseases fellowship program at the University of Texas Southwestern Medical Center (UTSW), Dallas, Texas. The fellows have clinical rotations at the Parkland Health and Hospital System, UTSW University hospitals, North Texas Veterans Affairs Health Care System, and Children's Medical Center Dallas. The 2-year program recruits 7 fellows every 2 years. The 1-month core rotation was established in July 2011 and is ongoing. Fellows who completed the rotation during the period July 2011 to April 2013 are included in this study.
Stick and Tell A Survey of Emergency Medicine Residents and Needlestick Exposures
Authors: Zuraw Jessica , Sanford Gretchen , Winston Lori , Chan Shu 
Published: August 2013

An estimated 400,000–800,000 sharps-related injuries occur among healthcare workers (HCWs) annually in the United States. The risk of needlestick exposure may be particularly high among emergency medicine (EM) residents, who are learning new procedures in a relatively uncontrolled environment. Despite the potentially serious consequences of percutaneous injuries (PCIs), practitioners in training often down-play the occurrence of PCIs and do not report exposures.Current literature implies that underreporting of needlestick injuries is multifactorial. By not seeking care after needlesticks occur and thereby delaying treatment, residents incur more risk from exposures. We sought to elucidate the underlying issues that might contribute to this lack of reporting needlestick injuries. Using an anonymous survey, we collected information regarding factors that contributed to sustaining a PCI as well as perceived barriers that prevented residents from reporting these exposures. This information is desirable for both residency programs and employee health departments to reduce the occurrence of unreported exposures.The survey contained 19 questions, and all subjects were EM residents from the 8 Accreditation Council for Graduate Medical Education–accredited programs in the state of Illinois during the period January–February 2011. The voluntary survey was distributed via e-mail and through a paper version distributed at a regional EM residency conference.
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
Authors: Mariani Valerio , Biasini Marco , Barbato Alessandro , Schwede Torsten 
Published: August 2013

AbstractMotivation: The assessment of protein structure prediction techniques requires objective criteria to measure the similarity between a computational model and the experimentally determined reference structure. Conventional similarity measures based on a global superposition of carbon α atoms are strongly influenced by domain motions and do not assess the accuracy of local atomic details in the model.Results: The Local Distance Difference Test (lDDT) is a superposition-free score that evaluates local distance differences of all atoms in a model, including validation of stereochemical plausibility. The reference can be a single structure, or an ensemble of equivalent structures. We demonstrate that lDDT is well suited to assess local model quality, even in the presence of domain movements, while maintaining good correlation with global measures. These properties make lDDT a robust tool for the automated assessment of structure prediction servers without manual intervention.Availability and implementation: Source code, binaries for Linux and MacOSX, and an interactive web server are available at http://swissmodel.expasy.org/lddtContact: torsten.schwede@unibas.chSupplementary information: Supplementary data are available at Bioinformatics online.
A general species delimitation method with applications to phylogenetic placements
Authors: Zhang Jiajie , Kapli Paschalia , Pavlidis Pavlos , Stamatakis Alexandros 
Published: August 2013

Abstract
Motivation: Sequence-based methods to delimit species are central to DNA taxonomy, microbial community surveys and DNA metabarcoding studies. Current approaches either rely on simple sequence similarity thresholds (OTU-picking) or on complex and compute-intensive evolutionary models. The OTU-picking methods scale well on large datasets, but the results are highly sensitive to the similarity threshold. Coalescent-based species delimitation approaches often rely on Bayesian statistics and Markov Chain Monte Carlo sampling, and can therefore only be applied to small datasets.
Results: We introduce the Poisson tree processes (PTP) model to infer putative species boundaries on a given phylogenetic input tree. We also integrate PTP with our evolutionary placement algorithm (EPA-PTP) to count the number of species in phylogenetic placements. We compare our approaches with popular OTU-picking methods and the General Mixed Yule Coalescent (GMYC) model. For de novo species delimitation, the stand-alone PTP model generally outperforms GYMC as well as OTU-picking methods when evolutionary distances between species are small. PTP neither requires an ultrametric input tree nor a sequence similarity threshold as input. In the open reference species delimitation approach, EPA-PTP yields more accurate results than de novo species delimitation methods. Finally, EPA-PTP scales on large datasets because it relies on the parallel implementations of the EPA and RAxML, thereby allowing to delimit species in high-throughput sequencing data.
Availability and implementation: The code is freely available at www.exelixis-lab.org/software.html.
Contact: Alexandros.Stamatakis@h-its.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Determination of fretting parameters of hoisting rope in coalmine and fretting-fatigue behavior of steel wires
Authors: Wang Dagang , Zhang Dekun , Ge Shirong 
Published: August 2013

Purpose
– The objective of this paper is to determine fretting parameters of hoisting rope according to the hoisting parameters in coalmine and to explore the effect of contact load on fretting-fatigue behavior of steel wires.

Design/methodology/approach
– Based on the mechanical model of hoisting rope in coalmine, the dynamic tension simulation of hoisting rope was performed. Static equations of hoisting rope under tension and torsion and theories of contact mechanics were applied to obtain fretting parameters. Fretting-fatigue tests of steel wires at different contact loads were conducted using a fretting-fatigue test rig. The fretting regime, normalized tangential force and fretting-fatigue life were studied. The morphologies of fretting contact scars and fracture surfaces were observed by scanning electron microscopy and optical microscopy to examine wear and failure mechanisms.

Findings
– Dynamic tension changes from 0 to 30,900 N. In outer strand layer, contact loads between steel wires in certain wire layers are 60.5 and 38.3 N compared with 378 and 102.7 N between wire layers; relative displacements between wires are 62.5 and 113.2 μm, respectively. Mixed fretting regimes develop in all cases. Increasing contact load decreases the stabilized relative slip and normalized tangential force, reduces the fretting fatigue life, induces accelerated adhesive wear and fatigue wear and results in rougher fracture surface topographies. In all cases, fretting zone induces crack initiation; crack propagation and rupture zones present brittle cleavage and longitudinal splitting, respectively.

Practical implications
– This paper presents the systemic study on determination of fretting parameters of hoisting rope according to the hoisting parameters in coalmine and the fretting-fatigue behavior of its internal steel wires. The results of fretting-fatigue tests show that the increase of contact load decreases the stabilized relative slip in mixed fretting regime and normalized tangential force, reduces the fretting fatigue life, induces accelerated adhesive wear and fatigue wear and results in rougher fracture surface topographies.

Originality/value
– The authors warrant that the paper is original submission and is not being submitted to any other journal. And the research does not involve confidentiality, copyright infringement, leaks and other issues, all the responsibilities that the authors will take.