bluuebunny/crossref_metadata_2025_split huggingface dataset:
Schistosome-induced cholangiocyte proliferation and osteopontin secretion correlate with fibrosis and portal hypertension in human and murine schistosomiasis mansoni
Authors: Pereira Thiago A. , Syn Wing-Kin , Machado Mariana V. , Vidigal Paula V. , Resende Vivian , Voieta Izabela , Xie Guanhua , Otoni Alba , Souza Márcia M. , Santos Elisângela T. , Chan Isaac S. , Trindade Guilherme V.M. , Choi Steve S. , Witek Rafal P. , Pereira Fausto E. , Secor William E. , Andrade Zilton A. , Lambertucci José Roberto , Diehl Anna Mae 
Published: July 2015

Schistosomiasis is a major cause of portal hypertension worldwide. It associates with portal fibrosis that develops during chronic infection. The mechanisms by which the pathogen evokes these host responses remain unclear. We evaluated the hypothesis that schistosome eggs release factors that directly stimulate liver cells to produce osteopontin (OPN), a pro-fibrogenic protein that stimulates hepatic stellate cells to become myofibroblasts. We also investigated the utility of OPN as a biomarker of fibrosis and/or severity of portal hypertension. Cultured cholangiocytes, Kupffer cells and hepatic stellate cells were treated with soluble egg antigen (SEA); OPN production was quantified by quantitative reverse transcriptase polymerase chain reaction (qRTPCR) and ELISA; cell proliferation was assessed by BrdU (5-bromo-2'-deoxyuridine). Mice were infected with Schistosoma mansoni for 6 or 16 weeks to cause early or advanced fibrosis. Liver OPN was evaluated by qRTPCR and immunohistochemistry (IHC) and correlated with liver fibrosis and serum OPN. Livers from patients with schistosomiasis mansoni (early fibrosis n=15; advanced fibrosis n=72) or healthy adults (n=22) were immunostained for OPN and fibrosis markers. Results were correlated with plasma OPN levels and splenic vein pressures. SEA-induced cholangiocyte proliferation and OPN secretion (P&lt;0.001 compared with controls). Cholangiocytes were OPN (+) in Schistosoma-infected mice and humans. Liver and serum OPN levels correlated with fibrosis stage (mice: r=0.861; human r=0.672, P=0.0001) and myofibroblast accumulation (mice: r=0.800; human: r=0.761, P=0.0001). Numbers of OPN (+) bile ductules strongly correlated with splenic vein pressure (r=0.778; P=0.001). S. mansoni egg antigens stimulate cholangiocyte proliferation and OPN secretion. OPN levels in liver and blood correlate with fibrosis stage and portal hypertension severity.
Clinician-Supported Internet-Delivered Psychological Treatment of Tinnitus
Authors: Andersson Gerhard 
Published: July 2015

Purpose
Internet-delivered psychological treatments for tinnitus distress have existed for more than 15 years, and there are a slowly growing number of studies. The aim of this brief report is to review the evidence and to comment on the future potentials of Internet treatments for tinnitus.

Method
Studies were retrieved, and in total 6 controlled studies were included in the review with 9 different comparisons (6 in which the treatment was compared against a control group and 3 in which Internet treatment was compared against group treatment). Moreover, 2 open studies based on clinical samples in regular care were also included in the review. The outcomes for the 2 controlled sets of studies were analyzed using meta-analytic methods.

Results

For the 6 studies comparing Internet treatment against a no-treatment control condition, a moderate effect size was found (Hedges's
g
= 0.58). The 3 studies comparing Internet treatment against face-to-face group treatments showed a small difference of Hedges's
g
= 0.13.

Conclusions
Internet-delivered psychological treatment holds promise as a treatment alternative to other standard forms of treatment delivery, including group treatment. Larger studies are needed as well as ways to blend information technology with regular services.
The Development of Balance Retraining: An Online Intervention for Dizziness in Adults Aged 50 Years and Older
Authors: Essery Rosie , Kirby Sarah , Geraghty Adam W. A. , Andersson Gerhard , Carlbring Per , Bronstein Adolfo , Little Paul , Yardley Lucy 
Published: July 2015

Purpose
This article outlines the rationale and development process for an online intervention based on vestibular rehabilitation therapy (VRT). The intervention aims to assist adults aged 50 years and older to self-manage and reduce dizziness symptoms.

Method
The intervention was developed according to the person-based approach to digital intervention design focused on accommodating perspectives of target users. A prototype version of the intervention was provided to 18 adults (11 women, 7 men) aged 50 years and older with dizziness. These adults were invited to use the intervention over a 6-week period and, during this time, took part in a think-aloud session. This session sought to understand users' perceptions of how acceptable, engaging, and easy to use they found the online intervention.

Results
Users were extremely positive regarding how easy to navigate, visually appealing, and informative they found the intervention. Think-aloud sessions provided valuable data for informing small amendments to further enhance acceptability of the intervention for target users.

Conclusions
Informed by these development-phase data, a finalized version of the intervention is now being investigated in a primary care–based randomized controlled trial. Results should provide an understanding of whether VRT can be effectively—especially, cost-effectively—delivered via an online intervention to adults aged 50 years and older.
SoundSpace Online: The Development of an Online Resource About Hearing Loss
Authors: Ng Zheng Yen , Archbold Sue , Mayer Connie , Mulla Imran 
Published: July 2015

Purpose
The Internet has been a growing source of health information on hearing loss, but the information provided often varies in quality, readability, and usability. Additionally, the information is provided across a wide range of domains, making access challenging to those who need it. This research forum article describes the development of a new website, SoundSpace Online (Ng, Archbold, Mayer, & Mulla, 2014), which aims to tackle these issues and bring together information and resources for all those concerned with hearing loss.

Method
The SoundSpace Online website's current developmental state was reached through the following methods: (a) discussions with a group of individuals that included experts in e-learning, education, research, and hearing loss; (b) interviews with different target groups (e.g., users, families, and professionals); and (c) collaboration with contributors.

Result
The website is structured to become a go-to resource on various topics related to hearing loss, providing accurate, comprehensive, and functional information and resources at varying levels of complexity for the intended users.

Conclusion
The literature and the range of interest have illustrated the need for an up-to-date website providing information and resources on hearing loss. Challenges include monitoring and keeping the website up to date; in this article, a plan of action is discussed. The website is currently in development, with plans for a launch in the near future.
Computer and Internet Interventions to Optimize Listening and Learning for People With Hearing Loss: Accessibility, Use, and Adherence
Authors: Ferguson Melanie , Henshaw Helen 
Published: July 2015

Purpose
The aim of this research forum article was to examine accessibility, use, and adherence to computerized and online interventions for people with hearing loss.

Method
Four intervention studies of people with hearing loss were examined: 2 auditory training studies, 1 working memory training study, and 1 study of multimedia educational support.

Results
A small proportion (approximately 15%) of participants had never used a computer, which may be a barrier to the accessibility of computer and Internet-based interventions. Computer competence was not a factor in intervention use or adherence. Computer skills and Internet access influenced participant preference for the delivery method of the multimedia educational support program.

Conclusions
It is important to be aware of current barriers to computer and Internet-delivered interventions for people with hearing loss. However, there is a clear need to develop and future-proof hearing-related applications for online delivery.
Electrically small uniplanar antenna with pattern‐agile performance
Authors: Tang Ming‐Chun , Shi Ting , Ziolkowski Richard 
Published: July 2015

A novel electrically small uniplanar antenna with pattern‐agile performance is reported. It consists of a split semi‐loop connected to the ground strips of a coplanar waveguide‐fed semi‐loop antenna. The angle of its maximum directivity can be controlled simply by changing the position of the gap in the ground‐connected semi‐loop. The measured results of this behaviour are in good agreement with the simulated values. A peak realised gain of 1.93 dBi is achieved experimentally. The radiation efficiency is observed to be higher than 95% for every angle selected.
Tissue fusion over nonadhering surfaces
Authors: Nier Vincent , Deforet Maxime , Duclos Guillaume , Yevick Hannah G. , Cochet-Escartin Olivier , Marcq Philippe , Silberzan Pascal 
Published: July 2015

Significance
Tissue fusion is a frequent and important event in embryonic development during which two facing identical tissues meet and bridge collectively over a gap before merging into a continuous structure. Illustrations of tissue fusion include the formation of the palate or epithelial wound healing. In vivo fusion events, particularly in embryonic development, often involve the purse-string contraction of a pluricellular actomyosin cable present at the free edge. By studying the fusion of a monolayer over imprinted nonadherent domains, we provide evidence and characterize the purse-string mechanism in the situation where cells do not develop adhesions with their underlying substrate. A model that also involves active epithelial fluctuations describes well the experimental observations.
Modulation of the cGAS-STING DNA sensing pathway by gammaherpesviruses
Authors: Ma Zhe , Jacobs Sarah R. , West John A. , Stopford Charles , Zhang Zhigang , Davis Zoe , Barber Glen N. , Glaunsinger Britt A. , Dittmer Dirk P. , Damania Blossom 
Published: July 2015

Significance
Kaposi’s sarcoma-associated herpesvirus (KSHV) is a DNA virus that is linked to several human malignancies. The cGMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) pathway is able to detect KSHV during primary infection and regulates the reactivation of KSHV from latency. We screened KSHV proteins for their ability to inhibit this pathway and block IFN-β activation. One KSHV protein, vIRF1, inhibited this pathway by preventing STING from interacting with TBK1 and inhibiting STING’s phosphorylation and concomitant activation. Moreover, depletion of vIRF1 in the context of KSHV infection prevented efficient viral reactivation and replication, and increased the host IFN response to KSHV. Collectively, our results demonstrate that the modulation of this pathway is important for viral transmission and the lifelong persistence of gammaherpesviruses in the human population.
Analysis of Short-Term Cortisol Stress Response in Channel Catfish by Anesthetization with Metomidate Hydrochloride and Tricaine Methanesulfonate
Authors: Smith M. S. , Booth N. J. , Peterson B. C. , Stephens W. S. , Goudie C. A. , Simco B. A. 
Published: July 2015

Abstract
The ability of the anesthetics metomidate hydrochloride and tricaine methanesulfonate (MS-222) to mitigate the cortisol stress response of Channel Catfish Ictalurus punctatus was evaluated during a 10-min confinement stress. The cortisol concentrations of Channel Catfish anesthetized in metomidate hydrochloride remained consistent throughout the 10-min exposure; however, for fish anesthetized with MS-222 and nonanesthetized fish, cortisol concentrations were approximately 7- and 22-fold higher, respectively, than the baseline concentrations. While both anesthetics reduced cortisol concentrations relative to those of nonanesthetized fish, these results suggest that MS-222 is an appropriate anesthetic to use during the initial 5 min of sedation and that metomidate hydrochloride is appropriate for longer periods of sedation.
Received November 18, 2014; accepted April 9, 2015
CEMAsuite: open source degenerate PCR primer design
Authors: Lane Courtney E. , Hulgan Daniel , O’Quinn Kelly , Benton Michael G. 
Published: July 2015

Abstract
Summary: The codon-equivalent multiple alignment suite begins conservational analysis for polymerase chain reaction primer design at the protein level, allowing the user to design consensus primers capable of detecting homologous coding sequences even when low-to-moderate sequence information is available. This package also condenses the wealth of information associated with multiple sequence alignments and presents them in an intuitive manner, allowing the user to quickly and effectively address degenerate primer design considerations.
Availability and implementation: https://sourceforge.net/projects/cemasuite/.
Contact: benton@lsu.edu or cemasuite@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Roary: rapid large-scale prokaryote pan genome analysis
Authors: Page Andrew J. , Cummins Carla A. , Hunt Martin , Wong Vanessa K. , Reuter Sandra , Holden Matthew T.G. , Fookes Maria , Falush Daniel , Keane Jacqueline A. , Parkhill Julian 
Published: July 2015

Abstract
Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors.
Availability and implementation: Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary
Contact: roary@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
SMART on FHIR Genomics: facilitating standardized clinico-genomic apps
Authors: Alterovitz Gil , Warner Jeremy , Zhang Peijin , Chen Yishen , Ullman-Cullere Mollie , Kreda David , Kohane Isaac S. 
Published: July 2015

Abstract
Background Supporting clinical decision support for personalized medicine will require linking genome and phenome variants to a patient’s electronic health record (EHR), at times on a vast scale. Clinico-genomic data standards will be needed to unify how genomic variant data are accessed from different sequencing systems.
Methods A specification for the basis of a clinic-genomic standard, building upon the current Health Level Seven International Fast Healthcare Interoperability Resources (FHIR®) standard, was developed. An FHIR application protocol interface (API) layer was attached to proprietary sequencing platforms and EHRs in order to expose gene variant data for presentation to the end-user. Three representative apps based on the SMART platform were built to test end-to-end feasibility, including integration of genomic and clinical data.
Results Successful design, deployment, and use of the API was demonstrated and adopted by HL7 Clinical Genomics Workgroup. Feasibility was shown through development of three apps by various types of users with background levels and locations.
Conclusion This prototyping work suggests that an entirely data (and web) standards-based approach could prove both effective and efficient for advancing personalized medicine.
Preparation of Mealybugs (Hemiptera: Pseudococcidae) for Genetic Characterization and Morphological Examination
Authors: Bahder B. W. , Bollinger M. L. , Sudarshana M. R. , Zalom F. G. 
Published: July 2015

Abstract
Mealybugs (Hemiptera: Pseudococcidae) are economically significant agricultural pests on many different crops. Because of their small size and lack of easily visible characters for identification, determination of their taxonomic status is difficult and requires technical competency to prepare a slide-mounted specimen. The standard mounting technique does not allow for analysis of the genome of the specimen. Conversely, preparatory techniques for genetic analysis of mealybugs cause either loss of the entire individual or physical damage that can make morphology-based identification difficult. This study describes a simple protocol that does not impact physical integrity of the specimen for fixation and microscopic examination yet enables simultaneous DNA extraction for DNA-based identification of four mealybug species. All species prepared yielded high quality slide mounts, identified as Planococcus citri Risso, Pseudococcus viburni Signoret, Rhizoecus kondonis Kuwana, or Rhizoecus californicus Ferris. DNA extracted in this manner had higher purity and yield in the final eluate than in samples extracted using standard methods. DNA extracted was successfully amplified by polymerase chain reaction using primers for the cytochrome oxidase I gene and subsequently sequenced for all specimens. This protocol is likely to be applicable to other Hemiptera taxa that are preserved by slide mounting, allowing for both the preparation of a high-quality voucher specimen for morphological identification and simultaneous analysis of DNA for the same specimen. The methods used are technically less challenging than current standard procedures.
Automatic Synthesis of Anthropomorphic Pulmonary CT Phantoms
Authors: Jimenez-Carretero Daniel , Jose Estepar Raul San , Cacio Mario Diaz , Ledesma-Carbayo Maria J 
Published: July 2015

AbstractThe great density and structural complexity of pulmonary vessels and airways impose limitations on the generation of accurate reference standards, which are critical in training and in the validation of image processing methods for features such as pulmonary vessel segmentation or artery–vein (AV) separations. The design of synthetic computed tomography (CT) images of the lung could overcome these difficulties by providing a database of pseudorealistic cases in a constrained and controlled scenario where each part of the image is differentiated unequivocally. This work demonstrates a complete framework to generate computational anthropomorphic CT phantoms of the human lung automatically. Starting from biological and image-based knowledge about the topology and relationships between structures, the system is able to generate synthetic pulmonary arteries, veins, and airways using iterative growth methods that can be merged into a final simulated lung with realistic features. Visual examination and quantitative measurements of intensity distributions, dispersion of structures and relationships between pulmonary air and blood flow systems show good correspondence between real and synthetic lungs.
Purging of deleterious variants due to drift and founder effect in Italian populations with extended autozygosity
Authors: Cocca Massimiliano , Pybus Marc , Palamara Pier Francesco , Garrison Erik , Traglia Michela , Sala Cinzia F , Uiivi Sheila , Memari Yasin , Kolb-Kokocinski Anja , McCarthy Shane , Durbin Richard , Gasparini Paolo , Toniolo Daniela , Soranzo Nicole , Colonna Vincenza 
Published: July 2015

AbstractPurging through inbreeding occurs when consanguineous marriages increases the rate at which deleterious alleles are present in a homozygous state. In this study we carried out low-read depth (4-10x) whole-genome sequencing in 568 individuals from three Italian founder populations, and compared it to data from other Italian and European populations from the 1000 Genomes Project. We show extended consanguinity and depletion of homozygous genotypes at potentially detrimental sites in the founder populations compared to outbred populations. However these patterns are not compatible with the hypothesis of consanguinity driving the purging of highly deleterious mutations according to simulations. Therefore we conclude that genetic drift and the founder effect should be responsible for the observed purging of deleterious variants.
Calcineurin B-Like Protein-Interacting Protein Kinase CIPK21 Regulates Osmotic and Salt Stress Responses in Arabidopsis
Authors: Pandey Girdhar K. , Kanwar Poonam , Singh Amarjeet , Steinhorst Leonie , Pandey Amita , Yadav Akhlilesh K. , Tokas Indu , Sanyal Sibaji K. , Kim Beom-Gi , Lee Sung-Chul , Cheong Yong-Hwa , Kudla Jörg , Luan Sheng 
Published: July 2015

Abstract
The role of calcium-mediated signaling has been extensively studied in plant responses to abiotic stress signals. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) constitute a complex signaling network acting in diverse plant stress responses. Osmotic stress imposed by soil salinity and drought is a major abiotic stress that impedes plant growth and development and involves calcium-signaling processes. In this study, we report the functional analysis of CIPK21, an Arabidopsis (Arabidopsis thaliana) CBL-interacting protein kinase, ubiquitously expressed in plant tissues and up-regulated under multiple abiotic stress conditions. The growth of a loss-of-function mutant of CIPK21, cipk21, was hypersensitive to high salt and osmotic stress conditions. The calcium sensors CBL2 and CBL3 were found to physically interact with CIPK21 and target this kinase to the tonoplast. Moreover, preferential localization of CIPK21 to the tonoplast was detected under salt stress condition when coexpressed with CBL2 or CBL3. These findings suggest that CIPK21 mediates responses to salt stress condition in Arabidopsis, at least in part, by regulating ion and water homeostasis across the vacuolar membranes.
A subassembly identification method for truss structures manufacturing based on community detection
Authors: Cao Hao , Mo Rong , Wan Neng , Shang Fang , Li Chunlei , Zhang Dongliang 
Published: July 2015

Purpose
– The purpose of this paper is to present an automated method for complicated truss structure subassembly identification.

Design/methodology/approach
– A community-detecting algorithm is introduced and adapted to reach the target. The ratio between oriented bounding boxes of parts is used as the weight to reflect the compact degree of assembly relationships. The authors also propose a method to merge nodes together at cut-vertex in model, by which the solving process could be accelerated.

Findings
– This method could identify the subassemblies of complex truss structures according to the specific requirements.

Research limitations/implications
– This research area is limited to truss structures. This research offers a new method in assembly sequences planning area. It could identify subassemblies in complex truss structures, with which the existing method is not adequate to deal.

Practical implications
– This method could facilitate the complex truss structures assembly planning, lower the human errors and reduce the planning time.

Social implications
– The method could inspire general assembly analysis planning.

Originality/value
– All authors of this paper confirm that this manuscript is original and has not been submitted or published elsewhere.