bluuebunny/crossref_metadata_2025_split huggingface dataset:
Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny
Authors: Tsang Alan K. L. , Lee Hwei Huih , Yiu Siu-Ming , Lau Susanna K. P. , Woo Patrick C. Y. 
Published: June 2017

AbstractAlthough multilocus sequence typing (MLST) is highly discriminatory and useful for outbreak investigations and epidemiological surveillance, it has always been controversial whether clustering and phylogeny inferred from the MLST gene loci can represent the real phylogeny of bacterial strains. In this study, we compare the phylogenetic trees constructed using three approaches, (1) concatenated blocks of homologous sequence shared between the bacterial genomes, (2) genome single-nucleotide polymorphisms (SNP) profile and (3) concatenated nucleotide sequences of gene loci in the corresponding MLST schemes, for 10 bacterial species with >30 complete genome sequences available. Major differences in strain clustering at more than one position were observed between the phylogeny inferred using genome/SNP data and MLST for all 10 bacterial species. Shimodaira-Hasegawa test revealed significant difference between the topologies of the genome and MLST trees for nine of the 10 bacterial species, and significant difference between the topologies of the SNP and MLST trees were present for all 10 bacterial species. Matching Clusters and R-F Clusters metrics showed that the distances between the genome/SNP and MLST trees were larger than those between the SNP and genome trees. Phylogeny inferred from MLST failed to represent genome phylogeny with the same bacterial species.
Chronic stress and intestinal barrier dysfunction: Glucocorticoid receptor and transcription repressor HES1 regulate tight junction protein Claudin-1 promoter
Authors: Zheng Gen , Victor Fon Gordon , Meixner Walter , Creekmore Amy , Zong Ye , K. Dame Michael , Colacino Justin , Dedhia Priya H. , Hong Shuangsong , Wiley John W. 
Published: June 2017

AbstractChronic stress and elevated glucocorticoid hormone are associated with decreases in the intestinal epithelial tight junction protein claudin-1 (CLDN1). Human/rat CLDN1 promoters contain glucocorticoid response elements (GREs) and adjacent transcription repressor HES1 binding N-boxes. Notch signaling target HES1 expression was high and glucocorticoid receptor (NR3C1) low at the crypt base and the pattern reversed at the crypt apex. Chronic stress reduced overall rat colon HES1 and NR3C1 that was associated with CLDN1 downregulation. Chromatin-immunoprecipitation experiments showed that HES1 and NR3C1 bind to the CLDN1 promoter in rat colon crypts. The binding of NR3C1 but not HES1 to CLDN1 promoter significantly decreased in chronically stressed animals, which was prevented by the NR3C1 antagonist RU486. We employed the 21-day Caco-2/BBe cell model to replicate cell differentiation along the crypt axis. HES1 siRNA treatment early in differentiation increased CLDN1. In contrast, stress levels of cortisol decreased CLDN1 in late differentiation stage but not in the early stage. HES1 was high, whereas NR3C1 and CLDN1 were low in the early stage which reversed in the late stage, e.g. HES1/NR3C1 binding to CLDN1 promoter demonstrates a dynamic and reciprocal pattern. These results suggest that chronic stress impairs colon epithelium homeostasis and barrier function via different mechanisms along the crypt axis.
Sea ice phenology and primary productivity pulses shape breeding success in Arctic seabirds
Authors: Ramírez Francisco , Tarroux Arnaud , Hovinen Johanna , Navarro Joan , Afán Isabel , Forero Manuela G. , Descamps Sébastien 
Published: June 2017

AbstractSpring sea ice phenology regulates the timing of the two consecutive pulses of marine autotrophs that form the base of the Arctic marine food webs. This timing has been suggested to be the single most essential driver of secondary production and the efficiency with which biomass and energy are transferred to higher trophic levels. We investigated the chronological sequence of productivity pulses and its potential cascading impacts on the reproductive performance of the High Arctic seabird community from Svalbard, Norway. We provide evidence that interannual changes in the seasonal patterns of marine productivity may impact the breeding performance of little auks and Brünnich’s guillemots. These results may be of particular interest given that current global warming trends in the Barents Sea region predict one of the highest rates of sea ice loss within the circumpolar Arctic. However, local- to regional-scale heterogeneity in sea ice melting phenology may add uncertainty to predictions of climate-driven environmental impacts on seabirds. Indeed, our fine-scale analysis reveals that the inshore Brünnich’s guillemots are facing a slower advancement in the timing of ice melt compared to the offshore-foraging little auks. We provide a suitable framework for analyzing the effects of climate-driven sea ice disappearance on seabird fitness.
Increased methylation and decreased expression of homeobox genes TLX1, HOXA10 and DLX5 in human placenta are associated with trophoblast differentiation
Authors: Novakovic Boris , Fournier Thierry , Harris Lynda K. , James Joanna , Roberts Claire T. , Yong Hannah E. J. , Kalionis Bill , Evain-Brion Danièle , Ebeling Peter R. , Wallace Euan M. , Saffery Richard , Murthi Padma 
Published: June 2017

AbstractHomeobox genes regulate embryonic and placental development, and are widely expressed in the human placenta, but their regulatory control by DNA methylation is unclear. DNA methylation analysis was performed on human placentae from first, second and third trimesters to determine methylation patterns of homeobox gene promoters across gestation. Most homeobox genes were hypo-methylated throughout gestation, suggesting that DNA methylation is not the primary mechanism involved in regulating HOX genes expression in the placenta. Nevertheless, several genes showed variable methylation patterns across gestation, with a general trend towards an increase in methylation over gestation. Three genes (TLX1, HOXA10 and DLX5) showed inverse gains of methylation with decreasing mRNA expression throughout pregnancy, supporting a role for DNA methylation in their regulation. Proteins encoded by these genes were primarily localised to the syncytiotrophoblast layer, and showed decreased expression later in gestation. siRNA mediated downregulation of DLX5, TLX1 and HOXA10 in primary term villous cytotrophoblast resulted in decreased proliferation and increased expression of differentiation markers, including ERVW-1. Our data suggest that loss of DLX5, TLX1 and HOXA10 expression in late gestation is required for proper placental differentiation and function.
Re-distribution of oxygen at the interface between γ-Al2O3 and TiN
Authors: Filatova E. O. , Konashuk A. S. , Sakhonenkov S. S. , Sokolov A. A. , Afanas’ev V. V. 
Published: June 2017

AbstractInterface of TiN electrode with γ-Al2O3 layers was studied using near edge X-ray absorption fine structure, conventional X-ray photoelectron spectroscopy and photoelectron spectroscopy with high energies. Despite the atomic-layer deposited Al2O3 being converted into thermodynamically-stable polycrystalline cubic γ-phase by high-temperature (1000 or 1100 °C) anneal, our results reveal formation of a thin TiNxOy (≈1-nm thick) interlayer at the interface between γ-Al2O3 film and TiN electrode due to oxygen scavenging from γ-Al2O3 film. Formation of the TiO2 was not observed at this interface. As environmental effect, a strong oxidation resulting in formation of a TiO2(1.4 nm)/TiNxOy(0.9 nm) overlayers on the top of the TiN electrode is traced. Development of O-deficiency of γ-Al2O3 is observed and related to the polarization anisotropy due to the preferential orientation of spin states involved in the X-ray absorption in the plane parallel to the surface. Investigation of the TiN electrode reveals the predominantly “stretched” octahedra in its structure with the preferential orientation relative the interface with γ-Al2O3. This anisotropy can be correlated with ≈200 meV electron barrier height increase at the O-deficient TiN/γ-Al2O3 interface as compared to the TiN/γ-Al2O3 barrier formed under abundant oxidant supply condition as revealed by internal photoemission of electrons from TiN into the oxide.
Investigation of multilevel data storage in silicon-based polycrystalline ferroelectric tunnel junction
Authors: Hou Pengfei , Wang Jinbin , Zhong Xiangli 
Published: June 2017

AbstractMultilevel data ferroelectric tunnel junction is a breakthrough for further improving the storage density of ferroelectric random access memories. However, the application of these ferroelectric tunnel junctions is limited by high cost of epitaxial perovskite heterostructures, unsatisfactory retention and difficulty of exactly controlling the middle polarization states. In order to overcome the issues, we develop a ferroelectric tunnel junction with smooth ultrathin polycrystalline BiFeO3 (BFO) film. Through controlling the polarization state and oxygen vacancy migration using voltage pulses, we demonstrate that voltage-controlled barrier yields a memristive behavior in the device, in which the resistance variations exceed over two orders of magnitude. And we achieve multi logic states written and read easily using voltage pulses in the device. Especially the device is integrated with the silicon technology in modern microelectronics. Our results suggest new opportunity for ferroelectrics as high storage density nonvolatile memories.
On noise-resolution uncertainty in quantum field theory
Authors: Gureyev Timur E. , Kozlov Alexander , Nesterets Yakov I. , Paganin David M. , Quiney Harry M. 
Published: June 2017

AbstractAn uncertainty inequality is presented that establishes a lower limit for the product of the variance of the time-averaged intensity of a mode of a quantized electromagnetic field and the degree of its spatial localization. The lower limit is determined by the vacuum fluctuations within the volume corresponding to the width of the mode. This result also leads to a generalized form of the Heisenberg uncertainty principle for boson fields in which the lower limit for the product of uncertainties in the spatial and momentum localization of a mode is equal to the product of Planck’s constant and a dimensionless functional which reflects the joint signal-to-noise ratio of the position and momentum of vacuum fluctuations in the region of the phase space occupied by the mode. Experimental X-ray synchrotron measurements provide an initial verification of the proposed theory in the case of Poisson statistics.
Comparison of laboratory testing methods for the diagnosis of tuberculous pleurisy in China
Authors: Zhang Qing , Zhou Caicun 
Published: June 2017

AbstractTo evaluate the diagnostic utilities of different methods forMycobacterium tuberculosis(M. tuberculosis) detection in pleural fluid that represent potentially cost-effective measures for resource-limited settings in China. We compared diagnostic characteristics of the AmpSure simultaneous amplification and testing method, the BACTEC MGIT 960 system, and acid-fast bacilli staining of specimen smears for detection ofM. tuberculosisin pleural fluids of 438 patients with suspected tuberculous pleurisy. Chest radiographs, computed tomography scans and the results of sputum and pleural biopsy testing were used for confirmations of tuberculosis diagnoses. The sensitivity of the AmpSure test (21.2%) was significantly higher than that of smear analysis (3.1%; p < 0.001), but was similar to that of the BACTEC culture method (17.8%; p > 0.05). The specificity of the AmpSure, BACTEC, and smear tests were 100%, 96.4%, and 100%, respectively. The positive and negative predictive values of the AmpSure, BACTEC, and smear tests were 100%/23.1%; 78.6%/19.8%; and 100%/22.4%, respectively. The sensitivity of ADA, IFNγ and histopathological analyses of pleural biopsies were all 100%. The sensitivities of all three methods were suboptimal for the detection ofM. tuberculosisin pleural fluid. Future studies of a composite diagnostic index consisting of a combination of these tests are warranted.
Random lasing from structurally-modulated silk fibroin nanofibers
Authors: Kim Soocheol , Yang SungYeun , Choi Seung Ho , Kim Young L. , Ryu WonHyoung , Joo Chulmin 
Published: June 2017

AbstractStructural arrangement and dimension play vital roles in wave transport and amplification as they can restrict the volume explored by the waves. However, it is challenging to systematically investigate the interplay among structural, optical, and mechanical properties, in part because of limited experimental platforms that modulate the structural arrangement in a continuous manner. We present light amplification action in Rhodamine B doped silk fibroin (SF) nanofibrous scaffolds and its modulation via the control of the alignment or directionality of SF nanofibers through an electrospinning procedure. Random lasing features of such scaffolds are examined as a function of structural arrangement of the SF nanofibers, and optical-structural-mechanical relationships of the SF-based structures are examined. As SF nanofibers are aligned parallel undergoing a transition from three to quasi-two dimension, light amplification features (e.g., lasing threshold and output power) enhanced, which also strongly correlated with mechanical characteristics (i.e., Young’s moduli) of the scaffolds. We confirm such optical characteristics using quasi-mode analyses based on the finite element method. We further demonstrate non-contact, in situ measurement of alternations in lasing features of the scaffolds while the specimens are under tensile loads. These results may highlight potential utility of the scaffolds as a flexible and biocompatible sensor.
Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization
Authors: Siegwald Léa , Audebert Christophe , Even Gaël , Viscogliosi Eric , Caboche Ségolène , Chabé Magali 
Published: June 2017

AbstractIn the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity. We report here on the Ion Torrent targeted metagenomic sequencing and analysis of these 96 human faecal samples, and the complete datasets from raw to analysed data. We also provide the key steps of the bioinformatic analyses, from library preparation to data filtering and OTUs tables generation. This data represents a valuable resource for the scientific community, enabling re-processing of these targeted metagenomic datasets through various pipelines and a comparative evaluation of microbiota analysis methods.
Speech Versus Speaking: The Experiences of People With Parkinson's Disease and Implications for Intervention
Authors: Yorkston Kathryn , Baylor Carolyn , Britton Deanna 
Published: June 2017

Purpose
In this project, we explore the experiences of people who report speech changes associated with Parkinson's disease as they describe taking part in everyday communication situations and report impressions related to speech treatment.

Method
Twenty-four community-dwelling adults with Parkinson's disease took part in face-to-face, semistructured interviews. Qualitative research methods were used to code and develop themes related to the interviews.

Results
Two major themes emerged. The first, called “speaking,” included several subthemes: thinking about speaking, weighing value versus effort, feelings associated with speaking, the environmental context of speaking, and the impact of Parkinson's disease on speaking. The second theme involved “treatment experiences” and included subthemes: choosing not to have treatment, the clinician, drills and exercise, and suggestions for change.

Conclusions
From the perspective of participants with Parkinson's disease, speaking is an activity requiring both physical and cognitive effort that takes place in a social context. Although many report positive experiences with speech treatment, some reported dissatisfaction with speech drills and exercises and a lack of focus on the social aspects of communication. Suggestions for improvement include increased focus on the cognitive demands of speaking and on the psychosocial aspects of communication.
Fricative Contrast and Coarticulation in Children With and Without Speech Sound Disorders
Authors: Maas Edwin , Mailend Marja-Liisa 
Published: June 2017

Purpose
The purpose of this study was, first, to expand our understanding of typical speech development regarding segmental contrast and anticipatory coarticulation, and second, to explore the potential diagnostic utility of acoustic measures of fricative contrast and anticipatory coarticulation in children with speech sound disorders (SSD).

Method
In a cross-sectional design, 10 adults, 17 typically developing children, and 11 children with SSD repeated carrier phrases with novel words with fricatives (/s/, /ʃ/). Dependent measures were 2 ratios derived from spectral mean, obtained from perceptually accurate tokens. Group analyses compared adults and typically developing children; individual children with SSD were compared to their respective typically developing peers.

Results
Typically developing children demonstrated smaller fricative acoustic contrast than adults but similar coarticulatory patterns. Three children with SSD showed smaller fricative acoustic contrast than their typically developing peers, and 2 children showed abnormal coarticulation. The 2 children with abnormal coarticulation both had a clinical diagnosis of childhood apraxia of speech; no clear pattern was evident regarding SSD subtype for smaller fricative contrast.

Conclusions
Children have not reached adult-like speech motor control for fricative production by age 10 even when fricatives are perceptually accurate. Present findings also suggest that abnormal coarticulation but not reduced fricative contrast is SSD-subtype–specific.

Supplemental Materials

S1:
https://doi.org/10.23641/asha.5103070
. S2 and S3:
https://doi.org/10.23641/asha.5106508
Factors Associated With Communicative Participation in Amyotrophic Lateral Sclerosis
Authors: Yorkston Kathryn , Baylor Carolyn , Mach Helen 
Published: June 2017

Purpose
People with amyotrophic lateral sclerosis frequently experience bulbar impairment and dysarthria that may restrict their ability to take part in everyday communication situations. The aim of this study is to examine selected variables that may contribute to restrictions in communicative participation.

Method

Community-dwelling participants with amyotrophic lateral sclerosis (
N
= 70) who reported communication changes but continued to use natural speech completed a survey, including the Communicative Participation Item Bank, demographics (age, sex, living situation, employment status, education, and time since diagnosis), and self- reported symptom-related variables (physical activity, emotional problems, fatigue, pain, speech severity, speech usage, and cognitive and communication skills). To identify predictors of restrictions in communicative participation, these variables were entered into a backward stepwise multiple linear regression analysis.

Results
Three variables (speech severity, swallowing severity, and speech usage) were included in the final model and accounted for 55% of the variability.

Conclusions
Better speech and swallowing skills and higher speech usage are associated with better communicative participation in this sample. Thus, when making clinical decisions regarding intervention, clinicians should continue their efforts to target speech and swallow abilities, while recognizing other variables that have the potential of restricting communicative participation.
Enhancing Intervention for Residual Rhotic Errors Via App-Delivered Biofeedback: A Case Study
Authors: Byun Tara McAllister , Campbell Heather , Carey Helen , Liang Wendy , Park Tae Hong , Svirsky Mario 
Published: June 2017

Purpose
Recent research suggests that visual-acoustic biofeedback can be an effective treatment for residual speech errors, but adoption remains limited due to barriers including high cost and lack of familiarity with the technology. This case study reports results from the first participant to complete a course of visual-acoustic biofeedback using a not-for-profit iOS app, Speech Therapist's App for /r/ Treatment.

Method
App-based biofeedback treatment for rhotic misarticulation was provided in weekly 30-min sessions for 20 weeks. Within-treatment progress was documented using clinician perceptual ratings and acoustic measures. Generalization gains were assessed using acoustic measures of word probes elicited during baseline, treatment, and maintenance sessions.

Results
Both clinician ratings and acoustic measures indicated that the participant significantly improved her rhotic production accuracy in trials elicited during treatment sessions. However, these gains did not transfer to generalization probes.

Conclusions
This study provides a proof-of-concept demonstration that app-based biofeedback is a viable alternative to costlier dedicated systems. Generalization of gains to contexts without biofeedback remains a challenge that requires further study. App-delivered biofeedback could enable clinician–research partnerships that would strengthen the evidence base while providing enhanced treatment for children with residual rhotic errors.

Supplemental Material

https://doi.org/10.23641/asha.5116318
Volar Distal Radius Anatomy Applied to the Treatment of Distal Radius Fracture
Authors: Akita Keiichi , Imatani Junya 
Published: June 2017

AbstractVolar locking plate (VLP) fixation has become the standard surgical treatment for distal radius fractures. However, flexor tendon rupture is one of the major complications following volar plating. This detailed review on the anatomy and morphology of the volar distal radius might facilitate appropriate placement of the volar plate and thereby avoid flexor tendon rupture. We introduce safe and secure VLP fixation along standard surgical procedures to avoid complications based on anatomy of the volar surface of the distal radius.
Insect outbreak shifts the direction of selection from fast to slow growth rates in the long-lived conifer
Pinus ponderosa
Authors: de la Mata Raul , Hood Sharon , Sala Anna 
Published: June 2017

Significance
Understanding selection dynamics over time is fundamental for predicting evolutionary potential. This is critical in long-lived organisms, particularly trees, which are at increased risk of mortality because of climate change-related drought and associated stresses. For ponderosa pine, we show rare direct empirical evidence of strong context-dependent fluctuating selection on growth rates over time: fast growth was selected for before a mountain pine beetle outbreak but against after the outbreak, when a growth–survival trade-off emerged. Our results provide insight into the mechanisms contributing to the maintenance of genetic diversity in a long-lived organism, and show that strong and fluctuating selection can contribute to the evolutionary potential of trees under climate change.