bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of Mangiferin in the Prevention of Experimentally Induced Iron Overload in an Animal Model
Authors: Estuningtyas Ari , Setiabudy Rianto , Wahidiyat Pustika , Freisleben Hans-Joachim 
Published: September 2018

Abstract
Background The leaves, fruit peels, and bark of mango trees (Mangifera indica L) contain mangiferin as an active compound with known anti-oxidative and iron chelating properties. This study aims to evaluate the benefits of mangiferin in the management of iron overload.
Methods Thirty rats were divided into five groups: normal control, rats with iron overload, and rats with iron overload treated with oral mangiferin doses of 50, 100, or 200 mg/kg BW, respectively. The iron overload in this rat model was induced by means of 15 mg intraperitoneal iron dextran, twice a week for 4 weeks. Plasma mangiferin was measured using high performance liquid chromatography, plasma ferritin by using enzyme linked immunosorbent assay, and iron contents of plasma, urine, and tissues by using atomic absorbance spectrophotometry.
Results Plasma mangiferin concentration at doses of 50, 100, or 200 mg/kg BW were 416.10±112.04, 310.55±134.18, and 450.11±165.99 ng/mL, respectively. At 50 mg/kg BW, mangiferin significantly decreased plasma ferritin levels (from 7051.14±1368.24 to 5543.80±1225.53 ng/mL, (p=0.037). Mangiferin also showed tendency to increase urinary iron excretion and to decrease cardiac and hepatic iron accumulation.
Conclusion In our model, oral administration of mangiferin showed non-linear pharmacokinetics and low bioavailability. At a dose of 50 mg/kg BW, mangiferin decreased plasma ferritin levels significantly. Mangiferin did not prevent the increase of plasma iron, although it exerted tendency to increase urinary iron excretion and to decrease iron accumulation in liver and heart.
Ask PCOS: Identifying Need to Inform Evidence-Based App Development for Polycystic Ovary Syndrome
Authors: Xu Rebecca , Gilbert Emily , Kuczynska-Burggraf Millicent , Tan Bryan , Teede Helena , Vincent Amanda , Gibson-Helm Melanie , Boyle Jacqueline 
Published: September 2018

Background People are increasingly seeking health information and managing their health through electronic technologies. We aimed to determine if women with polycystic ovary syndrome (PCOS) identified a need for PCOS-related mobile health apps and to evaluate related apps currently available.
Design A national survey of women and a review of apps available on the iOS and Android platforms.
Setting Community recruitment in Australia in 2016 and review of mobile apps available in 2017.
Sample The survey received 264 responses. Sixteen apps related to PCOS were evaluated.
Main Outcome Measures Survey: Women's likeliness to use mobile health apps, specifically a PCOS-related app and preferred features of apps. App review: Mapping of available apps and evaluation using the Mobile Application Rating Scale (MARS).
Results Of 264 respondents, almost all women had a smartphone (98%), 72% had previously used an app to manage their health, and most (91%) would use a PCOS-specific app if available. The most important feature was the availability of current, evidence-based information. Current apps on PCOS lack provision of quality information.
Conclusion Women with PCOS would use a PCOS-specific app of good quality that responds to their needs and facilitates self-care; however, currently available apps are unlikely to meet their information needs.
Survey of Ventilation Practices in the Neonatal Intensive Care Units of the United States and Canada: Use of Volume-Targeted Ventilation and Barriers to Its Use
Authors: Gupta Ashish , Keszler Martin 
Published: September 2018

Objective To provide current data on ventilation practices and use of volume-targeted ventilation (VTV) in neonatal intensive care units of the United States and Canada, to identify the perceived barriers to the implementation of VTV, and to assess the knowledge base of appropriate initial tidal volume (VT
) settings for different hypothetical clinical scenarios.
Study Design This was a cross-sectional online survey of individual neonatologists practicing in the United States and Canada.
Results We received 387 responses (estimated response rate: ∼20%). Use of VTV was much higher in Canada (81%) compared with 39% in the United States. In the United States, VTV use is highest in the Northwest at 77% and lowest in the Northeast at 32.5%. The chief barrier to use of VTV was lack of knowledge about VTV and lack of appropriate equipment. The five clinical scenarios revealed that the majority of responders failed to select appropriate evidence-based VT
for the specific scenario.
Conclusion Pressure-controlled ventilation remains the predominant approach to neonatal ventilation in the United States, while VTV is the preferred mode in Canada. Despite available data and important pathophysiological differences between patients, there is insufficient understanding of how to choose an appropriate VT
in a variety of common clinical scenarios among users of VTV.
Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways
Authors: Xu Fangda , Bandara Asanga , Akiyama Hisashi , Eshaghi Behnaz , Stelter David , Keyes Tom , Straub John E. , Gummuluru Suryaram , Reinhard Björn M. 
Published: September 2018

Significance
Membrane-wrapped noble metal nanoparticles provide a synthetic platform to investigate lipid-mediated, glycoprotein-independent virus–cell interactions. Different from membrane-wrapped virus-like particles (VLPs), these artificial virus nanoparticles (AVNs) are not derived from cellular systems and can contain organic or inorganic cores optimized for imaging or delivery purposes. A particular advantage is the rational control over the AVN membrane composition, which can be complex or undefined in VLP. This work shows that monosialodihexosylganglioside-presenting AVNs accumulate in virus-containing compartments (VCCs) that represent assembly sites for HIV-1. VCCs provide evasion for HIV-1 from the immune system as well as antiviral therapeutics. The ability to target VCCs with AVNs provides opportunities for eradicating a putative reservoir of HIV-1 persistence.
Dante: genotyping of known complex and expanded short tandem repeats
Authors: Budiš Jaroslav , Kucharík Marcel , Ďuriš František , Gazdarica Juraj , Zrubcová Michaela , Ficek Andrej , Szemes Tomáš , Brejová Broňa , Radvanszky Jan 
Published: September 2018

AbstractMotivationShort tandem repeats (STRs) are stretches of repetitive DNA in which short sequences, typically made of 2–6 nucleotides, are repeated several times. Since STRs have many important biological roles and also belong to the most polymorphic parts of the human genome, they became utilized in several molecular-genetic applications. Precise genotyping of STR alleles, therefore, was of high relevance during the last decades. Despite this, massively parallel sequencing (MPS) still lacks the analysis methods to fully utilize the information value of STRs in genome scale assays.ResultsWe propose an alignment-free algorithm, called Dante, for genotyping and characterization of STR alleles at user-specified known loci based on sequence reads originating from STR loci of interest. The method accounts for natural deviations from the expected sequence, such as variation in the repeat count, sequencing errors, ambiguous bases and complex loci containing several different motifs. In addition, we implemented a correction for copy number defects caused by the polymerase induced stutter effect as well as a prediction of STR expansions that, according to the conventional view, cannot be fully captured by inherently short MPS reads. We tested Dante on simulated datasets and on datasets obtained by targeted sequencing of protein coding parts of thousands of selected clinically relevant genes. In both these datasets, Dante outperformed HipSTR and GATK genotyping tools. Furthermore, Dante was able to predict allele expansions in all tested clinical cases.Availability and implementationDante is open source software, freely available for download at https://github.com/jbudis/dante.Supplementary informationSupplementary data are available at Bioinformatics online.
CATANA: a tool for generating comprehensive annotations of alternative transcript events
Authors: Shiau Cheng-Kai , Huang Jia-Hsin , Tsai Huai-Kuang 
Published: September 2018

Abstract

Summary
In higher eukaryotes, the generation of transcript isoforms from a single gene through alternative splicing (AS) and alternative transcription (AT) mechanisms increases functional and regulatory diversities. Annotating these alternative transcript events is essential for genomic studies. However, there are no existing tools that generate comprehensive annotations of all these alternative transcript events including both AS and AT events. In the present study, we develop CATANA, with the encoded exon usage patterns based on the flattened gene model, to identify ten types of AS and AT events. We demonstrate the power and versatility of CATANA by showing greater depth of annotations of alternative transcript events according to either genome annotation or RNA-seq data.

Availability and implementation
CATANA is available on https://github.com/shiauck/CATANA.

Supplementary information
Supplementary data are available at Bioinformatics online.
The metagenome of the female upper reproductive tract
Authors: Li Fei , Chen Chen , Wei Weixia , Wang Zirong , Dai Juanjuan , Hao Lilan , Song Liju , Zhang Xiaowei , Zeng Liping , Du Hui , Tang Huiru , Liu Na , Yang Huanming , Wang Jian , Madsen Lise , Brix Susanne , Kristiansen Karsten , Xu Xun , Li Junhua , Wu Ruifang , Jia Huijue 
Published: September 2018

Abstract

Background
The human uterus is traditionally believed to be sterile, while the vaginal microbiota plays an important role in fending off pathogens. Emerging evidence demonstrates the presence of bacteria beyond the vagina. However, a microbiome-wide metagenomic analysis characterizing the diverse microbial communities has been lacking.

Results
We performed shotgun-sequencing of 52 samples from the cervical canal and the peritoneal fluid of Chinese women of reproductive age using the Illumina platform. Direct annotation of sequencing reads identified the taxonomy of bacteria, archaea, fungi and viruses, confirming and extending the results from our previous study. We replicated our previous findings in another 24 samples from the vagina, the cervical canal, the uterus and the peritoneal fluid using the BGISEQ-500 platform revealing that microorganisms in the samples from the same individuals were largely shared in the entire reproductive tract. Human sequences made up more than 99% of the 20GB raw data. After filtering, vaginal microorganisms were well covered in the generated reproductive tract gene catalogue, while the more diverse upper reproductive tract microbiota would require greater depth of sequencing and more samples to meet the full coverage scale.

Conclusions
We provide novel detailed data on the microbial composition of a largely unchartered body site, the female reproductive tract. Our results indicated the presence of an intra-individual continuum of microorganisms that gradually changed from the vagina to the peritoneal fluid. This study also provides a framework for understanding the implications of the composition and functional potential of the distinct microbial ecosystems of the female reproductive tract in relation to health and disease.
Metabolomics investigation of dietary effects on flesh quality in grass carp (Ctenopharyngodon idellus)
Authors: Zhao Honghao , Chong Jasmine , Tang Rong , Li Li , Xia Jianguo , Li Dapeng 
Published: September 2018

Abstract

Background
The ultrahigh density intensive farming model of grass carp (Ctenopharyngodon idellus) may elicit growth inhibition, decrease flesh quality, and increase disease susceptibility of fish. The degradation in quality and excessive fat accumulation in cultured C. idellus have long been attributed to possible alterations in the lipid metabolism of fish muscle tissues as a result of overnutrition from artificial diets. To investigate the effects of different diets on fish muscle quality, a large-scale metabolomics study was performed on 250 tails of C. idellus.

Findings
The experimental fish were divided into four groups based on sex and diet—female artificial feed (FAF), female grass feed, male artificial feed (MAF), and male grass feed (MGF). After a 113-day rearing period, the artificial feed (AF) group showed a significantly higher total mass of muscle fat (P &lt; 0.01), with the FAF group being the highest. Metabolomics profiling based on liquid chromatography-mass spectrometry revealed distinctive patterns of clustering according to the four groups. Overall, artificial feeding was associated with higher concentrations of docosapentaenoic acid, dihomo-gamma-linolenic acid, and arachidonic acid, whereas grass feeding was associated with elevated n-3 unsaturated fatty acids (UFAs) such as eicosapentaenoic acid, alpha-linolenic acid, and gamma-linolenic acid. Artificial feeding also resulted in significant increased docosahexaenoic acid in MAF muscle than in MGF fish, whereas there was no significance in the comparison of female samples. Metabolic pathway analyses using both targeted and untargeted approaches consistently revealed that arachidonic acid metabolism and steroid hormone biosynthesis pathways were significantly different between AF and grass fed groups.

Conclusions
Our results suggest that grass is a better source of dietary fatty acid and protein when compared to artificial feed. Grass feeding could effectively lower triglycerides in serum, reduce fat accumulation, and alter lipid compositions in fish muscle by increasing the concentrations of n-3 UFAs, leading to better nutrition and health.
Temporal partitioning and the effects of climate change on two ecologically similar desert bats
Authors: Lambert Connor T , Hall Lucas K , Larsen Randy T , Knight Robert N , McMillan Brock R 
Published: September 2018

Abstract
Climate change is predicted to create increasingly arid deserts with fewer and smaller water sources. Because free water is already limiting for arid-adapted animals, reductions in water likely will impact desert species and how they compete for this limited resource. Our objective was to examine how the size of water sources influenced competition between 2 ecologically similar bats, Parastrellus hesperus and Myotis californicus, in the American Southwest. Bats are a highly successful taxon in deserts, although many rely upon access to free water. We examined bat activity observationally over 35 different-sized water sources throughout the Mojave Desert in southwestern Utah, United States, and experimentally reduced the surface area of 2 water sources. Parastrellus hesperus and M. californicus typically occurred at the same water sources, but both species temporally partitioned their use of shared water sources regardless of the surface area of the water. Experimentally reducing surface area of water sources negatively affected drinking behaviors of both species and resulted in higher overall activity, but temporal partitioning still occurred. While loss of water may influence some competitive interactions, mechanisms such as temporal partitioning can potentially allow continued co-use of limited resources by competing species.
Regional Molecular Signature of the Symptomatic Atherosclerotic Carotid Plaque
Authors: Caparosa Ellen M , Sedgewick Andrew J , Zenonos Georgios , Zhao Yin , Carlisle Diane L , Stefaneanu Lucia , Jankowitz Brian T , Gardner Paul , Chang Yue-Fang , Lariviere William R , LaFramboise William A , Benos Panayiotis V , Friedlander Robert M 
Published: September 2018

Abstract

BACKGROUND
Many studies have explored molecular markers of carotid plaque development and vulnerability to rupture, usually having examined whole carotid plaques. However, there are regional differences in plaque morphology and known shear-related mechanisms in areas surrounding the lipid core.

OBJECTIVE
To determine whether there are regional differences in protein expression along the long axis of the carotid plaque and how that might produce gaps in our understanding of the carotid plaque molecular signature.

METHODS
Levels of 7 inflammatory cytokines (IL-1β, IL-6, IL-8, IL-10, IL-12 p70, IFN-γ, and TNF-α) and caspase-3 were analyzed in prebifurcation, bifurcation, and postbifurcation segments of internal carotid plaques surgically removed from symptomatic and asymptomatic patients. Expression profiles of miRNAs and mRNAs were determined with microarrays for the rupture-prone postbifurcation segment for comparison with published whole plaque results.

RESULTS
Expression levels of all proteins examined, except IL-10, were lowest in the prebifurcation segment and significantly higher in the postbifurcation segment. Patient group differences in protein expression were observed for the prebifurcation segment; however, no significant differences were observed in the postbifurcation segment between symptomatic and asymptomatic patients. Expression profiles from postbifurcation carotid plaques identified 4 novel high priority miRNAs differentially expressed between patient groups (miR-214, miR-484, miR-942, and miR-1287) and 3 high-confidence miRNA:mRNA targets, including miR-214:APOD, miR-484:DACH1, and miR-942:GPR56.

CONCLUSION
The results demonstrate regional differences in protein expression for the first time and show that focus on the rupture-prone postbifurcation region leads to prioritization for further study of novel miRNA gene regulation mechanisms.
A STUDY OF A DOSE CONSTRAINT FOR OCCUPATIONALLY EXPOSED WORKERS IN THE US NUCLEAR POWER PLANTS
Authors: Kong Tae Young , Akabani Gamal , Poston John W 
Published: September 2018

Abstract
One of the most important issues in the nuclear power industry is the implementation of the 2007 Recommendations of the International Commission on Radiological Protection (ICRP) published in ICRP Publication 103. These recommendations include the implementation of the concept of dose constraints for occupationally exposed workers at nuclear power plants (NPPs). When considering these changes from a cost–benefit standpoint, the implementation of dose constraints is still highly controversial. This study analysed annual occupational dose distributions to determine whether a dose constraint is needed for occupationally exposed workers at the US NPPs. Results of the analysis showed that the use of dose constraints had no positive impact on radiation safety of workers at NPPs in the USA. In fact, it appears that the implementation of dose constraints will impose an unnecessary regulatory burden on licensees. Based on these results, implementation of dose constraints is not recommended.
Turning fibroblasts into cardiomyocytes: technological review of cardiac transdifferentiation strategies
Authors: Klose Kristin , Gossen Manfred , Stamm Christof 
Published: September 2018

ABSTRACTTo date, no viable therapeutic options exist for the effective and sustained reversal of cardiac failure, other than heart transplantation and mechanical circulatory assist devices. Therefore, divergent strategies aiming at the de novo formation of contractile tissue, as a prerequisite for the restoration of cardiac pump function, are currently being pursued. Clinical trials involving the transplantation of somatic progenitor cells failed. The search for alternative cell‐based strategies to combat the consequences of ischemic injury has sparked widespread interest in the genetic and pharmacologic reprogramming of fibroblasts into cardiomyocytes, harnessing the abundant in vivo pool of cardiac fibroblasts. Here, we provide a comprehensive overview of in vitro and in vivo cardiac reprogramming studies identified in an extensive literature search. We systematically review and evaluate feasibility, efficiency, and reproducibility of the different technologies currently being explored. Finally, we discuss potential safety issues deduced from preclinical studies and identify obstacles that must be overcome before clinical translation.—Klose, K., Gossen, M., Stamm, C. Turning fibroblasts into cardiomyocytes: technological review of cardiac transdifferentiation strategies. FASEB J. 33, 49–70 (2019). www.fasebj.org
Hearing and Auditory Processing Abilities in Primary School Children with Learning Difficulties
Authors: Choi Seong Min Robyn , Kei Joseph , Wilson Wayne J. 
Published: September 2018

Objectives:This study aimed to investigate hearing and auditory processing ability in primary school children with learning difficulties (LD).Design:A nonrandomized, cross-sectional single measure research design was used. A total of 486 children, aged 7.7 to 10.8 years and attending years 3 and 4 in six primary schools, were classified as having an LD (n = 67) or being typically developing (TD, n = 419). This classification was based on a Learning Score generated from their school report results and National Assessment Program – Literacy and Numeracy scores. All children attempted a conventional hearing assessment (CHA) involving pure-tone audiometry, tympanometry, acoustic reflexes (AR), and otoacoustic emissions (OAEs). Children returning pure-tone audiometry results within normal limits also attempted an auditory processing assessment (APA) including dichotic digits (DD) and low-pass filtered speech (LPFS) tests.Results:In children with LD, 21/67 (31.4%) failed the CHA, 20/58 (34.5%) failed the APA, and 32/58 (55.2%) failed the overall hearing assessment (OHA) if they failed either or both CHA and APA. In comparison, in TD children, 55/413 (13.3%) failed the CHA, 52/314 (16.6%) failed the APA, and 86/313 (27.5%) failed the OHA. Proportionally, children with LD were 2.4 times more likely than TD children to fail the CHA, 2.1 times more likely to fail the APA, and 2.0 times more likely to fail the OHA. In children who had completed the OHA, multiple linear regressions showed average AR thresholds, DD scores, and LPFS scores explained 13 to 18% of the variance in the Learning Score.Conclusion:The potential for hearing impairment should be investigated in children with LD. These investigations should begin with CHA, and for children returning normal-hearing thresholds, should continue with measures of AR, DD, and LPFS, to ensure these children receive the appropriate auditory support needed to enhance their learning.