bluuebunny/crossref_metadata_2025_split huggingface dataset:
The variability and seasonality of the environmental reservoir of Mycobacterium bovis shed by wild European badgers
Authors: King Hayley C. , Murphy Andrew , James Phillip , Travis Emma , Porter David , Hung Yu-Jiun , Sawyer Jason , Cork Jennifer , Delahay Richard J. , Gaze William , Courtenay Orin , Wellington Elizabeth M. 
Published: August 2015

AbstractThe incidence of Mycobacterium bovis, the causative agent of bovine tuberculosis, has been increasing in UK cattle herds resulting in substantial economic losses. The European badger (Meles meles) is implicated as a wildlife reservoir of infection. One likely route of transmission to cattle is through exposure to infected badger urine and faeces. The relative importance of the environment in transmission remains unknown, in part due to the lack of information on the distribution and magnitude of environmental reservoirs. Here we identify potential infection hotspots in the badger population and quantify the heterogeneity in bacterial load; with infected badgers shedding between 1 × 103 − 4 × 105M. bovis cells g−1 of faeces, creating a substantial and seasonally variable environmental reservoir. Our findings highlight the potential importance of monitoring environmental reservoirs of M. bovis which may constitute a component of disease spread that is currently overlooked and yet may be responsible for a proportion of transmission amongst badgers and onwards to cattle.
Regional patterns of postglacial changes in the Palearctic mammalian diversity indicate retreat to Siberian steppes rather than extinction
Authors: Řičánková Věra Pavelková , Robovský Jan , Riegert Jan , Zrzavý Jan 
Published: August 2015

AbstractWe examined the presence of possible Recent refugia of Pleistocene mammalian faunas in Eurasia by analysing regional differences in the mammalian species composition, occurrence and extinction rates between Recent and Last Glacial faunas. Our analyses revealed that most of the widespread Last Glacial species have survived in the central Palearctic continental regions, most prominently in Altai–Sayan (followed by Kazakhstan and East European Plain). The Recent Altai–Sayan and Kazakhstan regions show species compositions very similar to their Pleistocene counterparts. The Palearctic regions have lost 12% of their mammalian species during the last 109,000 years. The major patterns of the postglacial changes in Palearctic mammalian diversity were not extinctions but rather radical shifts of species distribution ranges. Most of the Pleistocene mammalian fauna retreated eastwards, to the central Eurasian steppes, instead of northwards to the Arctic regions, considered Holocene refugia of Pleistocene megafauna. The central Eurasian Altai and Sayan mountains could thus be considered a present-day refugium of the Last Glacial biota, including mammals.
Reconstruction of micron resolution mouse brain surface from large-scale imaging dataset using resampling-based variational model
Authors: Li Jing , Quan Tingwei , Li Shiwei , Zhou Hang , Luo Qingming , Gong Hui , Zeng Shaoqun 
Published: August 2015

AbstractBrain surface profile is essential for brain studies, including registration, segmentation of brain structure and drawing neuronal circuits. Recent advances in high-throughput imaging techniques enable imaging whole mouse brain at micron spatial resolution and provide a basis for more fine quantitative studies in neuroscience. However, reconstructing micron resolution brain surface from newly produced neuronal dataset still faces challenges. Most current methods apply global analysis, which are neither applicable to a large imaging dataset nor to a brain surface with an inhomogeneous signal intensity. Here, we proposed a resampling-based variational model for this purpose. In this model, the movement directions of the initial boundary elements are fixed, the final positions of the initial boundary elements that form the brain surface are determined by the local signal intensity. These features assure an effective reconstruction of the brain surface from a new brain dataset. Compared with conventional typical methods, such as level set based method and active contour method, our method significantly increases the recall and precision rates above 97% and is approximately hundreds-fold faster. We demonstrated a fast reconstruction at micron level of the whole brain surface from a large dataset of hundreds of GB in size within 6 hours.
Network analysis reveals a stress-affected common gene module among seven stress-related diseases/systems which provides potential targets for mechanism research
Authors: Guo Liyuan , Du Yang , Wang Jing 
Published: August 2015

AbstractChronic stress (CS) was reported to associate with many complex diseases and stress-related diseases show strong comorbidity; however, molecular analyses have not been performed to date to evaluate common stress-induced biological processes across these diseases. We utilized networks constructed by genes from seven genetic databases of stress-related diseases or systems to explore the common mechanisms. Genes were connected based on the interaction information of proteins they encode. A common sub-network constructed by 561 overlapping genes and 8863 overlapping edges among seven networks was identified and it provides a common gene module among seven stress-related diseases/systems. This module is significantly overlapped with network that constructed by genes from the CS gene database. 36 genes with high connectivity (hub genes) were identified from seven networks as potential key genes in those diseases/systems, 33 of hub genes were included in the common module. Genes in the common module were enriched in 190 interactive gene ontology (GO) functional clusters which provide potential disease mechanism. In conclusion, by analyzing gene networks we revealed a stress-affected common gene module among seven stress-related diseases/systems which provides insight into the process of stress induction of disease and suggests potential gene and pathway candidates for further research.
Metalloprotease meprin β is activated by transmembrane serine protease matriptase-2 at the cell surface thereby enhancing APP shedding
Authors: Jäckle Felix , Schmidt Frederike , Wichert Rielana , Arnold Philipp , Prox Johannes , Mangold Martin , Ohler Anke , Pietrzik Claus U. , Koudelka Tomas , Tholey Andreas , Gütschow Michael , Stirnberg Marit , Becker-Pauly Christoph 
Published: August 2015

Increased expression of metalloprotease meprin β is associated with fibrotic syndromes and Alzheimer's disease (AD). Hence, regulation of meprin activity might be a suitable strategy for the treatment of these conditions. Meprin β is a type 1 transmembrane protein, but can be released from the cell surface by ectodomain shedding. The protease is expressed as an inactive zymogen and requires proteolytic maturation by tryptic serine proteases. In the present study, we demonstrate, for the first time, the differences in the activation of soluble and membrane bound meprin β and suggest transmembrane serine protease 6 [TMPRSS6 or matriptase-2 (MT2)] as a new potent activator, cleaving off the propeptide of meprin β between Arg61 and Asn62 as determined by MS. We show that MT2, but not TMPRSS4 or pancreatic trypsin, is capable of activating full-length meprin β at the cell surface, analysed by specific fluorogenic peptide cleavage assay, Western blotting and confocal laser scanning microscopy (CLSM). Maturation of full-length meprin β is required for its activity as a cell surface sheddase, releasing the ectodomains of transmembrane proteins, as previously shown for the amyloid precursor protein (APP).
Factors Influencing Hearing Aid Use in the Classroom: A Pilot Study
Authors: Gustafson Samantha J. , Davis Hilary , Hornsby Benjamin W. Y. , Bess Fred H. 
Published: August 2015

Purpose
This pilot study examined factors influencing classroom hearing aid use in school-age children with hearing loss.

Method
The research team visited classrooms of 38 children with mild-to-moderate hearing loss (Grades 1–7) on 2 typical school days, twice per day, to document hearing aid use. In addition, parents reported the number of hours their children used hearing aids at school.

Results
Nearly 24% of children were observed not wearing their hearing aids in the classroom on either observation day. Both grade level and degree of hearing loss appeared to affect hearing aid use. Children in Grades 5–7 and those with milder hearing losses were less likely to wear hearing aids. Overall, parents accurately reported classroom hearing aid use; however, those with children in Grades 5–7 were less accurate than those with children in earlier grades.

Conclusions
These preliminary results suggest that children with milder hearing loss and those in Grades 5–7 are at increased risk for reduced hearing aid use in the classroom. Also, parents of school-age children in these later grades are less accurate reporters of classroom hearing aid use compared to parents of children in earlier grades.
Using Spoken Language Benchmarks to Characterize the Expressive Language Skills of Young Children With Autism Spectrum Disorders
Authors: Ellawadi Allison Bean , Weismer Susan Ellis 
Published: August 2015

PurposeSpoken language benchmarks proposed by Tager-Flusberg et al. (2009) were used to characterize communication profiles of toddlers with autism spectrum disorders and to investigate if there were differences in variables hypothesized to influence language development at different benchmark levels.MethodThe communication abilities of a large sample of toddlers with autism spectrum disorders (N= 105) were characterized in terms of spoken language benchmarks. The toddlers were grouped according to these benchmarks to investigate whether there were differences in selected variables across benchmark groups at a mean age of 2.5 years.ResultsThe majority of children in the sample presented with uneven communication profiles with relative strengths in phonology and significant weaknesses in pragmatics. When children were grouped according to one expressive language domain, across-group differences were observed in response to joint attention and gestures but not cognition or restricted and repetitive behaviors.ConclusionThe spoken language benchmarks are useful for characterizing early communication profiles and investigating features that influence expressive language growth.
A Case Study on Vocal Loudness With a Young Adult With Autism Spectrum Disorder and Developmental Delay
Authors: Pack Amanda , Colozzo Paola , Bernhardt B. May , Radanov Bosko , Rosebush Riley , Marinova-Todd Stefka H. 
Published: August 2015

Purpose
This clinical focus article describes an exploratory case study addressing reduction of vocal loudness in a young adult with a history of autism spectrum disorder and developmental delay. The need for a short-term pullout individual intervention arose from his participation in the Advancing Language and Literacy group, a program that provides support for enhancement of speech, language, and literacy skills for young adults with developmental disabilities.

Method
The participant attended individual treatment sessions weekly for 9 sessions, all of which were digitally audio-recorded. Client awareness of different loudness levels was first established using nonspeech sounds and speech samples. Loudness in spontaneous speech was monitored with support of verbal and visual feedback in the individual sessions and tracked in individual sessions as well as sessions of the Advancing Language and Literacy group, which served as a generalization context.

Results
In the individual sessions, the participant's spontaneous production of acceptable volume improved from 42% to 92% of utterances. Observation of group participation indicated generalization, with the majority of utterances produced posttreatment at an acceptable volume.

Conclusions
This clinical focus article emphasizes suprasegmental aspects as a dimension of communicative competence and highlights the need for continued intervention research and services for young adults with developmental disabilities.
Effects of Alphabet-Supplemented Speech on Brain Activity of Listeners: An fMRI Study
Authors: Fercho Kelene , Baugh Lee A. , Hanson Elizabeth K. 
Published: August 2015

Purpose
The purpose of this article was to examine the neural mechanisms associated with increases in speech intelligibility brought about through alphabet supplementation.

Method
Neurotypical participants listened to dysarthric speech while watching an accompanying video of a hand pointing to the 1st letter spoken of each word on an alphabet display (treatment condition) or a scrambled display (control condition). Their hemodynamic response was measured with functional magnetic resonance imaging, using a sparse sampling event-related paradigm. Speech intelligibility was assessed via a forced-choice auditory identification task throughout the scanning session.

Results
Alphabet supplementation was associated with significant increases in speech intelligibility. Further, alphabet supplementation increased activation in brain regions known to be involved in both auditory speech and visual letter perception above that seen with the scrambled display. Significant increases in functional activity were observed within the posterior to mid superior temporal sulcus/superior temporal gyrus during alphabet supplementation, regions known to be involved in speech processing and audiovisual integration.

Conclusion
Alphabet supplementation is an effective tool for increasing the intelligibility of degraded speech and is associated with changes in activity within audiovisual integration sites. Changes in activity within the superior temporal sulcus/superior temporal gyrus may be related to the behavioral increases in intelligibility brought about by this augmented communication method.

Supplemental Material

https://doi.org/10.23641/asha.14963610
Shape control and compartmentalization in active colloidal cells
Authors: Spellings Matthew , Engel Michael , Klotsa Daphne , Sabrina Syeda , Drews Aaron M. , Nguyen Nguyen H. P. , Bishop Kyle J. M. , Glotzer Sharon C. 
Published: August 2015

Significance
Advances in simulation and synthesis of nanoparticles and colloids are leading to a new class of active colloidal systems where self-propelled and self-rotated particles convert energy to motion. Such systems hold promise for the possibility of colloidal machines––integrated systems of colloids able to carry out functions. An important step in this direction is appropriately confining colloids within cells whose shape can be controlled and within which activity can be compartmentalized. This paper uses theory and computer simulation to propose active colloidal cells and investigates their behavior. Our findings provide motivation and design rules for the fabrication of primitive colloidal machines.
A common glycan structure on immunoglobulin G for enhancement of effector functions
Authors: Lin Chin-Wei , Tsai Ming-Hung , Li Shiou-Ting , Tsai Tsung-I , Chu Kuo-Ching , Liu Ying-Chih , Lai Meng-Yu , Wu Chia-Yu , Tseng Yung-Chieh , Shivatare Sachin S. , Wang Chia-Hung , Chao Ping , Wang Shi-Yun , Shih Hao-Wei , Zeng Yi-Fang , You Tsai-Hong , Liao Jung-Yu , Tu Yu-Chen , Lin Yih-Shyan , Chuang Hong-Yang , Chen Chia-Lin , Tsai Charng-Sheng , Huang Chiu-Chen , Lin Nan-Horng , Ma Che , Wu Chung-Yi , Wong Chi-Huey 
Published: August 2015

Significance
Antibodies are important therapeutic agents and have been used for the treatment of many diseases, including infectious and inflammatory diseases, and cancer. The therapeutic efficacy of an antibody is usually determined not only by the selectivity and affinity toward the target but also by the Fc-glycan structure interacting with the Fc receptors on immune cells. This study describes the preparation of various antibodies with different Fc-glycan structures as homogeneous glycoforms for the investigation of their effector activities. During this study, it was discovered that the biantennary N-glycan structure with two terminal alpha-2,6-linked sialic acids is a common and optimal structure that is able to enhance the activities of antibodies against cancer, influenza, and inflammatory diseases.
Enantioselective recognition of menthol by mouse odorant receptors
Authors: Takai Yoshiki , Touhara Kazushige 
Published: August 2015

Abstract
The olfactory system has a remarkable ability to detect and discriminate a vast variety of odorant molecules. In mammals, hundreds to thousands of odorant receptors (ORs) expressed in olfactory sensory neurons play an essential role in this discrimination. Odorants are recognized by ORs in a combinatorial fashion in which a single odorant activates a particular combination of receptors, leading to its perception as a particular aroma. It is well known that enantiomers emit different aromas in spite of exhibiting otherwise identical chemical properties. To elucidate the molecular basis for the difference, we recorded responses to l- and d-menthol in the mouse olfactory bulb and found that enantiomers elicited similar but overlapping and distinct receptor activation patterns. We then identified l-menthol-specific and d-menthol-biased receptors and performed detailed structure–activity relationship studies, revealing high stereoselectivity of the enantiospecific menthol receptor. The binding site on ORs appears to have evolved to distinguish subtle differences in very similar odorant structures.
Improving protein fold recognition with hybrid profiles combining sequence and structure evolution
Authors: Ghouzam Yassine , Postic Guillaume , de Brevern Alexandre G. , Gelly Jean-Christophe 
Published: August 2015

Abstract
Motivation: Template-based modeling, the most successful approach for predicting protein 3D structure, often requires detecting distant evolutionary relationships between the target sequence and proteins of known structure. Developed for this purpose, fold recognition methods use elaborate strategies to exploit evolutionary information, mainly by encoding amino acid sequence into profiles. Since protein structure is more conserved than sequence, the inclusion of structural information can improve the detection of remote homology.
Results: Here, we present ORION, a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure. Our method uses the 16-state structural alphabet Protein Blocks, which provides an accurate 1D description of protein structure local conformations. ORION systematically outperforms PSI-BLAST and HHsearch on several benchmarks, including target sequences from the modeling competitions CASP8, 9 and 10, and detects ∼10% more templates at fold and superfamily SCOP levels.
Availability: Software freely available for download at http://www.dsimb.inserm.fr/orion/.
Contact: jean-christophe.gelly@univ-paris-diderot.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
TIPR: transcription initiation pattern recognition on a genome scale
Authors: Morton Taj , Wong Weng-Keen , Megraw Molly 
Published: August 2015

Abstract
Motivation: The computational identification of gene transcription start sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are arranged in different spatial patterns along the chromosome.
Results: In this work, we present the Transcription Initiation Pattern Recognizer (TIPR), a sequence-based machine learning model that identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns that have previously been difficult to characterize. TIPR predicts not only the locations of TSSs but also the expected spatial initiation pattern each TSS will form along the chromosome—a novel capability for TSS prediction algorithms. As spatial initiation patterns are associated with spatiotemporal expression patterns and gene function, this capability has the potential to improve gene annotations and our understanding of the regulation of transcription initiation. The high nucleotide resolution of this model locates TSSs within 10 nucleotides or less on average.
Availability and implementation: Model source code is made available online at http://megraw.cgrb.oregonstate.edu/software/TIPR/.
Contact: megrawm@science.oregonstate.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements
Authors: De Witte Dieter , Van de Velde Jan , Decap Dries , Van Bel Michiel , Audenaert Pieter , Demeester Piet , Dhoedt Bart , Vandepoele Klaas , Fostier Jan 
Published: August 2015

Abstract
Motivation: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected.
Results: We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays.
Availability and implementation: BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller
Contact: Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be
Supplementary information: Supplementary data are available at Bioinformatics online.