bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling the evolutionary dynamics of ancient and recent polyploidization events in Avena (Poaceae)
Authors: Liu Qing , Lin Lei , Zhou Xiangying , Peterson Paul M. , Wen Jun 
Published: February 2017

AbstractUnderstanding the diversification of polyploid crops in the circum-Mediterranean region is a challenging issue in evolutionary biology. Sequence data of three nuclear genes and three plastid DNA fragments from 109 accessions of Avena L. (Poaceae) and the outgroups were used for maximum likelihood and Bayesian analyses. The evolution of cultivated oat (Avena sativa L.) and its close relatives was inferred to have involved ancient allotetraploidy and subsequent recent allohexaploidy events. The crown ages of two infrageneric lineages (Avena sect. Ventricosa Baum ex Romero-Zarco and Avena sect. Avena) were estimated to be in the early to middle Miocene, and the A. sativa lineages were dated to the late Miocene to Pliocene. These periods coincided with the mild seasonal climatic contrasts and the Mediterranean climate established in the Mediterranean Basin. Our results suggest that polyploidy, lineage divergence, and complex reticulate evolution have occurred in Avena, exemplifying the long-term persistence of tetraploids and the multiple origins of hexaploids related to paleoclimatic oscillations during the Miocene-Pliocene interval in the circum-Mediterranean region. This newly-resolved infrageneric phylogenetic framework represents a major step forward in understanding the origin of the cultivated oat.
Oxytocin: its role in benign prostatic hyperplasia via the ERK pathway
Authors: Xu Huan , Fu Shi , Chen Yanbo , Chen Qi , Gu Meng , Liu Chong , Qiao Zhiguang , Zhou Juan , Wang Zhong 
Published: January 2017

The aim of the present study was to evaluate oxytocin and benign prostatic hyperplasia (BPH), and study the cell signalling mechanism. Investigation was performed in patients about the correlation between oxytocin level and BPH. Mice were injected with oxytocin or oxytocin antagonist for 2 weeks and the prostate morphology was studied after their sacrifice. Furthermore, in vitro experiments were performed to evaluate the oxytocin effect through the MEK/ERK/RSK pathway. Oxytocin was significantly elevated in the serum and prostate tissue of patients with BPH, and a positive correlation with prostate volume indicated. In the animal experiments, prostate enlargement was observed in the oxytocin-treated group, whereas oxytocin antagonist reduced prostate hyperplasia. The in vitro study confirmed this result and also revealed activation of the MEK/ERK/RSK pathway. Oxytocin is highly expressed in the serum and prostate tissue of patients with BPH. In addition, oxytocin aggravates BPH and the oxytocin-induced proliferative effect on prostatic cells is mediated through the MEK/ERK/RSK pathway, at least partly. Thus, the hypothalamic regulation may be involved in development of BPH, which may open a new door to more medications for BPH in the future.
Circular polarised antenna fabricated with low‐cost 3D and inkjet printing equipment
Authors: Jun S. , Sanz‐Izquierdo B. , Heirons J. , Mao C.X. , Gao S. , Bird D. , McClelland A. 
Published: January 2017

The fabrication of a patch antenna using low‐cost 3D printing equipment is presented. The circular polarised patch antenna is manufactured by combining inkjet printing and stereolithography technology. The substrate has been fabricated by curing photosensitive resin while the patch element of the antenna has been inkjet printed using silver ink. The printed antenna satisfies the required reflection coefficient, axial ratio and radiation pattern at 1575 MHz. The aim is to demonstrate an inexpensive technology that could be used for the fabrication of antennas on customised 3D printed substrates. The performance of the antenna is summarised through simulations and experimental results.
Thickness‐dependent photoelectrochemical property of tin disulphide nanosheets
Authors: Fang Jiaxin , Chen Mengna , Fang Zhen 
Published: January 2017

IV–VI group compounds are excellent candidates for optoelectronics. Here, a solvothermal controlled synthesis of SnS2 nanosheets with different thickness is reported. The bandgap of nanosheets with thickness of 15 nm was estimated as 2.0 eV which is quite suitable for visible light harvesting. The nanosheets show about 180 times photoinduced current compare with the 35 nm nanosheets and fast response time of 4.9 ms, indicating that the SnS2 nanosheets are potential materials for high‐performance photodetectors.
Thermodynamics of manganese oxides: Sodium, potassium, and calcium birnessite and cryptomelane
Authors: Birkner Nancy , Navrotsky Alexandra 
Published: January 2017

Significance
Manganese oxides with layer and tunnel structures occur widely in the natural environment and inspire technological applications. In addition to having variable compositions, these structures often are found as small particles (nanophases). This study explores, using experimental thermochemistry, the role of composition, oxidation state, structure, and surface energy in the thermodynamic stability of synthetic birnessites and cryptomelane. These quantitative thermodynamic findings help explain and support qualitative observations of phase-transformation patterns gathered over the past five decades.
GDISC: a web portal for integrative analysis of gene–drug interaction for survival in cancer
Authors: Spainhour John Christian Givhan , Lim Juho , Qiu Peng 
Published: January 2017

Abstract

Summary
Survival analysis has been applied to The Cancer Genome Atlas (TCGA) data. Although drug exposure records are available in TCGA, existing survival analyses typically did not consider drug exposure, partly due to naming inconsistencies in the data. We have spent extensive effort to standardize the drug exposure data, which enabled us to perform survival analysis on drug-stratified subpopulations of cancer patients. Using this strategy, we integrated gene copy number data, drug exposure data and patient survival data to infer gene–drug interactions that impact survival. The collection of all analyzed gene–drug interactions in 32 cancer types are organized and presented in a searchable web-portal called gene–drug Interaction for survival in cancer (GDISC). GDISC allows biologists and clinicians to interactively explore the gene-drug interactions identified in the context of TCGA, and discover interactions associated to their favorite cancer, drug and/or gene of interest. In addition, GDISC provides the standardized drug exposure data, which is a valuable resource for developing new methods for drug-specific analysis.

Availability and Implementation
GDISC is available at https://gdisc.bme.gatech.edu/.
A comprehensive quality control workflow for paired tumor-normal NGS experiments
Authors: Schroeder Christopher M , Hilke Franz J , Löffler Markus W , Bitzer Michael , Lenz Florian , Sturm Marc 
Published: January 2017

Abstract

Summary
Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additional metrics specific for tumor-normal pairs can be calculated. The segmentation into different tools offers a high flexibility and allows reuse for other purposes. All tools produce qcML, a generic XML format for QC of -omics experiments. qcML uses quality metrics defined in an ontology, which was adapted for NGS.

Availability and Implementation
All QC tools are implemented in C ++ and run both under Linux and Windows. Plotting requires python 2.7 and matplotlib. The software is available under the ‘GNU General Public License version 2’ as part of the ngs-bits project: https://github.com/imgag/ngs-bits

Supplementary information
Supplementary data are available at Bioinformatics online.
Hierarchical sets: analyzing pangenome structure through scalable set visualizations
Authors: Pedersen Thomas Lin 
Published: January 2017

Abstract

Motivation
The increase in available microbial genome sequences has resulted in an increase in the size of the pangenomes being analyzed. Current pangenome visualizations are not intended for the pangenome sizes possible today and new approaches are necessary in order to convert the increase in available information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis.

Results
We present a new hierarchical clustering algorithm based on set arithmetics that optimizes the intersection sizes along the branches. The intersection and union sizes along the hierarchy are visualized using a composite dendrogram and icicle plot, which, in pangenome context, shows the evolution of pangenome and core size along the evolutionary hierarchy. Outlying elements, i.e. elements whose presence pattern do not correspond with the hierarchy, can be visualized using hierarchical edge bundles. When applied to pangenome data this plot shows putative horizontal gene transfers between the genomes and can highlight relationships between genomes that is not represented by the hierarchy. We illustrate the utility of hierarchical sets by applying it to a pangenome based on 113 Escherichia and Shigella genomes and find it provides a powerful addition to pangenome analysis.

Availability and Implementation
The described clustering algorithm and visualizations are implemented in the hierarchicalSets R package available from CRAN (https://cran.r-project.org/web/packages/hierarchicalSets)

Supplementary information
Supplementary data are available at Bioinformatics online.
Extracting morphologies from third harmonic generation images of structurally normal human brain tissue
Authors: Zhang Zhiqing , Kuzmin Nikolay V , Groot Marie Louise , de Munck Jan C 
Published: January 2017

Abstract

Motivation
The morphologies contained in 3D third harmonic generation (THG) images of human brain tissue can report on the pathological state of the tissue. However, the complexity of THG brain images makes the usage of modern image processing tools, especially those of image filtering, segmentation and validation, to extract this information challenging.

Results
We developed a salient edge-enhancing model of anisotropic diffusion for image filtering, based on higher order statistics. We split the intrinsic 3-phase segmentation problem into two 2-phase segmentation problems, each of which we solved with a dedicated model, active contour weighted by prior extreme. We applied the novel proposed algorithms to THG images of structurally normal ex-vivo human brain tissue, revealing key tissue components—brain cells, microvessels and neuropil, enabling statistical characterization of these components. Comprehensive comparison to manually delineated ground truth validated the proposed algorithms. Quantitative comparison to second harmonic generation/auto-fluorescence images, acquired simultaneously from the same tissue area, confirmed the correctness of the main THG features detected.

Availability and Implementation
The software and test datasets are available from the authors.

Supplementary information
Supplementary data are available at Bioinformatics online.
ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing
Authors: Wong Ted , Deveson Ira W , Hardwick Simon A , Mercer Tim R 
Published: January 2017

Abstract

Summary
Spike-in controls are synthetic nucleic-acid sequences that are added to a user’s sample and constitute internal standards for subsequent steps in the next generation sequencing workflow.
The Anaquin software toolkit can be used to analyze the performance of spike-in controls at multiple steps during RNA sequencing or genome sequencing analysis, providing useful diagnostic statistics, data visualization and sample normalization.

Availability and Implementation
The software is implemented in C ++/R and is freely available under BSD license. The source code is available from github.com/student-t/Anaquin, binaries and user manual from www.sequin.xyz/software and R package from bioconductor.org/packages/Anaquin

Supplementary information
Supplementary data are available at Bioinformatics online.
Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing
Authors: Zhang Shuai , Qin Chunxia , Cao Guoqiong , Guo Limin , Feng Chengqiang , Zhang Wensheng 
Published: January 2017

Abstract

Motivation
The pathogenesis of AD is complex and contributed by both genetic and environmental factors. Recent work revealed a potential link between DNA methylation and AD. However, a genome-wide study to identify potential DNA methylation sites involved in AD is still at an early stage. WGBS, an up-to-date technology, was used in this study. We investigated mouse brain genome-wide DNA methylation profiles between seven-month-old SAMP8 and SAMR1 models through deep WGBS.

Results
According to the results, the global ML slightly decreased in the SAMP8 mice than in the SAMR1 mice (4.12% versus 4.19%). A total of 1 307 172 280 clean reads were obtained. Subsequently, we identified 63 DMRs from all cases in SAMP8 mice relative to SAMR1 mice. In addition, 26 DMR-related genes were detected. GO analyses revealed that these DMR-related genes were involved in regulating the development of AD from different aspects. Finally, three differentially expressed DMR-related genes (Dlgap1, TMEM51 and Eif2ak2) that were most likely involved in AD were summarized and listed in detail. Our study provided a systematic exploration of DNA methylation profiles in SAMP8 mouse brain for the first time. These novel methylation sites may be considered strong future candidates to combat this life-threatening disease.

Availability and Implementation
The WGBS sequencing clean data and RNA-seq clean data have been deposited in the NCBI Sequence Read Archive (SRA).The accession number of WGBS is SRP097054. The accession number of RNA-seq is SRP096779.

Supplementary information
Supplementary data are available at Bioinformatics online.
Classification of RNA structure change by ‘gazing’ at experimental data
Authors: Woods Chanin Tolson , Laederach Alain 
Published: January 2017

Abstract

Motivation
Mutations (or Single Nucleotide Variants) in folded RiboNucleic Acid structures that cause local or global conformational change are riboSNitches. Predicting riboSNitches is challenging, as it requires making two, albeit related, structure predictions. The data most often used to experimentally validate riboSNitch predictions is Selective 2′ Hydroxyl Acylation by Primer Extension, or SHAPE. Experimentally establishing a riboSNitch requires the quantitative comparison of two SHAPE traces: wild-type (WT) and mutant. Historically, SHAPE data was collected on electropherograms and change in structure was evaluated by ‘gel gazing.’ SHAPE data is now routinely collected with next generation sequencing and/or capillary sequencers. We aim to establish a classifier capable of simulating human ‘gazing’ by identifying features of the SHAPE profile that human experts agree ‘looks’ like a riboSNitch.

Results
We find strong quantitative agreement between experts when RNA scientists ‘gaze’ at SHAPE data and identify riboSNitches. We identify dynamic time warping and seven other features predictive of the human consensus. The classSNitch classifier reported here accurately reproduces human consensus for 167 mutant/WT comparisons with an Area Under the Curve (AUC) above 0.8. When we analyze 2019 mutant traces for 17 different RNAs, we find that features of the WT SHAPE reactivity allow us to improve thermodynamic structure predictions of riboSNitches. This is significant, as accurate RNA structural analysis and prediction is likely to become an important aspect of precision medicine.

Availability and Implementation
The classSNitch R package is freely available at http://classsnitch.r-forge.r-project.org.

Supplementary information
Supplementary data are available at Bioinformatics online.
Detection of the pedogenic magnetic fraction in volcanic soils developed on basalts using frequency-dependent magnetic susceptibility: comparison of two instruments
Authors: Grison Hana , Petrovsky Eduard , Kapicka Ales , Hanzlikova Hana 
Published: January 2017

Abstract
In studies of the magnetic properties of soils, the frequency-dependent magnetic susceptibility percentage (χFD%) is often used for the identification of ultrafine magnetically superparamagnetic/stable single-domain (SP/SSD) particles. This parameter is commonly used as an indicator for increased pedogenesis. In strongly magnetic soils, the SP/SSD magnetic signal (mostly bio-pedogenic) may be masked by lithological signals; making pedogenesis hard to detect. In this study, we compare results for the detection of ultrafine SP/SSD magnetic particles in andic soils using two instruments: a Bartington MS2B dual-frequency meter and an AGICO Kappabridge MFK1-FA. In particular, the study focuses on the effect of pedogenesis by investigating the relationship between specific soil magnetic and chemical properties (soil organic carbon and pHH2O). The values of χFD% obtained with the MS2B varied from 2.4 to 5.9 per cent, and mass-specific magnetic susceptibility (χLF) from 283 to 1688 × 10−8 m3 kg−1, while values of χFD% and χLF obtained with the MFK1-FA varied from 2.7 to 8.2 per cent and from 299 to 1859 × 10−8 m3 kg−1, respectively. Our results suggest that the detection of the SP/SSD magnetic fraction can be accomplished by comparing relative trends of χFD% along the soil profile. Moreover, the discrimination between bio-pedogenic and lithogenic magnetic contributions in the SP/SSD fraction is possible by comparing the χFD% and χLF data determined in the fine earth (&lt;2 mm) and the coarse fraction (4–10 mm) samples down the soil profile.
PHARYNGEAL ISOLATIONS OF ADENOVIRUS 31 FROM A FAMILY POPULATION
Authors: WANG STEPHEN S. , FELDMAN HARRY A. 
Published: February 2017

Abstract
During a 14-month period in 1965 and 1966, adenovirus type 31 was isolated from 26 pharyngeal swabs obtained on a routine schedule from children and adults during a study of respiratory viruses among members of a family population. Eighteen isolations were made in a four-day period, seven within the preceding five months, and the last, eight months earlier. A significant association between the isolation of adenovirus 31 and respiratory or gastrointestinal illnesses was not demonstrable. Limited tests demonstrated neutralizing antibody increases in a few paired sera of infected adults. The virus is antigenically related to adenoviruses 12 and 18 and is capable of inducing soft tissue tumors in mice.
NOSOCOMIAL INFECTION WITH HIGHLY RESISTANT
Authors: KASLOW RICHARD A. , LINDSEY JAMES O. , BISNO ALAN L. , PRICE ANN 
Published: February 2017

Abstract
Over 22-1/2 months an epidemic of at least 127 cases of nosocomial infection developed from a strain of Proteus rettgeri resistant to all antibiotics commonly tested in hospital laboratories. Although there were at least four cases of septicemia and one related death, the majority of cases consisted of asymptomatic bacteriuria or clinically mild urinary tract infection. Indwelling urinary tract devices and antibiotic therapy were important predisposing factors. Data supported an association between increasing use of gentamicin and increasing rates of resistant infection. No common source was found, and contact spread appeared more likely. Control measures included efforts to reduce unnecessary exposure to the incriminated risk factors and to improve asepsis in the management of catheterized patients. An additional 36 cases and one related death were identified in the 7-1/2 months following the investigation and institution of control measures. Nosocomial infection with extremely resistant organisms may pose a serious hazard wherever indwelling urinary tract devices and antibiotics are used together intensively.
Spontaneous development of cerebrovascular pathology and microinfarcts in a mouse model of sickle cell disease
Authors: Hyacinth Hyacinth I. , Sugihara Cortney L. , Spencer Thomas L. , Archer David R. , Shih Andy Y. 
Published: January 2017

ABSTRACTStroke is a dramatic complication of sickle cell disease (SCD) and is associated with aneurysms, moya moya, intravascular thrombi, cerebral hyperemia and increased vessel tortuosity. We show that aged SCD mice spontaneously develop the characteristics features of cerebral vasculopathy seen in human SCD. Thirteen month old Townes SCD mice and age-matched controls had a cranial windows implanted over the somatosensory cortex. Cortical capillaries were imaged usingin vivotwo-photon microscopy after the blood plasma was labeled with a fluorescent dye. Results showed that SCD mice compared to controls, had significantly higher red blood cell (RBC) velocity and capillary vessel diameter. SCD mice also had a significantly higher number of occlusive events in the capillary bed, resulting in more stalling of RBC flow. Microvascular topology was also altered, as SCD mice had significantly higher vessel tortuosity and shorter capillary branch lengths. Finally,post-mortemanalyses revealed a greater number of cortical microinfarcts, likely caused by vascular occlusion since local tissue hypoxia and blood-brain barrier leakage was prominent. We concluded that aged Townes sickle cell mice spontaneously develop SCD-associated cerebral vasculopathy, and thatin vivotwo-photon imaging is a powerful approach to investigate the mechanisms of vascular complications in SCD.
Health Information Needs and Health Seeking Behavior during the 2014-2016 Ebola Outbreak: A Twitter Content Analysis
Authors: Odlum Michelle L. , Yoon Sunmoo 
Published: January 2017

AbstractIntroductionFor effective public communication during major disease outbreaks like the 2014-2016 Ebola epidemic, health information needs of the population must be adequately assessed. Through content analysis of social media data, like tweets, public health information needs can be effectively assessed and in turn provide appropriate health information to effectively address such needs. The aim of the current study was to assess health information needs about Ebola, at distinct epidemic time points, through longitudinal tracking.MethodsNatural language processing was applied to explore public response to Ebola over time from the beginning of the outbreak (July 2014) to six month post outbreak (March 2015). A total 155,647 tweets (unique 68,736, retweet 86,911) mentioning Ebola were analyzed and visualized with infographics.ResultsPublic fear, frustration, and health information seeking regarding Ebola-related global priorities were observed across time. Our longitudinal content analysis revealed that due to ongoing health information deficiencies, resulting in fear and frustration, social media was at times an impediment and not a vehicle to support health information needs.DiscussionContent analysis of tweets effectively assessed Ebola information needs. Our study also demonstrates the use of Twitter as a method for capturing real-time data to assess ongoing information needs, fear, and frustration over time.All authors have seen and approved the manuscript.