bluuebunny/crossref_metadata_2025_split huggingface dataset:
The presentation of Legg−Calvé−Perthes disease in females
Authors: Georgiadis Andrew G. , Seeley Mark A. , Yellin Joseph L. , Sankar Wudbhav N. 
Published: July 2015

Purpose Legg−Calvé−Perthes disease (LCPD) is uncommon in girls. The presentation of LCPD in female patients has been reported as later in onset and associated with certain high-impact activities. Our aim is to characterize the presentation of female LCPD at a large center, with particular attention to the clinical and radiographic features of late-onset disease (>ten years of age). We perceived an increasing burden of late-onset disease with adult-like radiographic features. Methods All patients presenting to a single large urban children's hospital from 1990−2014 with a diagnosis of LCPD were reviewed. Demographic, clinical, and radiographic data for all female patients were examined and compared to historical norms. Results Four-hundred and fifty-one patients presented with LCPD in the study period, of which 82 (18.2 %) were female. The average age at presentation was 6.58 years in girls, which is similar to the classically reported mean age. Fourteen patients participated in high-impact repetitive activities or those with deep flexion and abduction, although few were late presenters. There were four female patients who presented for initial diagnosis >ten years of age. Conclusions There was a paucity of late-onset LCPD in girls in the study population, and the females with LCPD had a very similar age and character to their presentation as did males. Although their presentation is infrequent, three of four older females with LCPD were engaged in high-level physical activity, and their disease may be attributed to high-impact, repetitive athletics. Level of evidence Case series, Level IV.
The stability of alcohol consumption between age 16 and 26: Evidence from a National Birth Cohort Study
Authors: Percy Andrew , McKay Michael 
Published: July 2015

AbstractThis study examined the association between moderate drinking at age 16 (adolescence) and alcohol consumption at age 26 (young adulthood), whilst controlling for possible confounding effects at the individual and family level (assessed at birth and age 10). Using the British Cohort Study (BCS70), 6515 respondents provided data on their adolescent alcohol consumption and other behaviours. Of these, 4392 also completed the survey at age 26. Consumption patterns established in adolescence persisted, to a large degree, into early adulthood. Those adolescents who drank moderately in adolescence drank significantly less in adulthood than those adolescents who drank to heavy or hazardous levels. Implications for health promotion strategies and guidance are discussed.
Oxidized Low Density Lipoprotein Among the Elderly in Qinghai-Tibet Plateau
Authors: Sakamoto Ryota , Okumiya Kiyohito , Wang Hongxin , Dai Qingxiang , Fujisawa Michiko , Wada Taizo , Imai Hissei , Kimura Yumi , Ishimoto Yasuko , Fukutomi Eriko , Chen Wingling , Sasiwongsaroj Kwanchit , Kato Emiko , Ge Ri-Li , Matsubayashi Kozo 
Published: July 2015

Objective Several environmental factors including hypoxia have been reported to contribute to oxidative stress in individuals living in the highlands. However, little is known about the role of oxidized low-density lipoprotein (ox-LDL) among community-dwelling elderly in the Qinghai-Tibet plateau. Methods The study population comprised 168 community-dwelling elderly subjects aged 60 years or older (male to female ratio, 70:98; mean age, 65.8 years) living in Haiyan County, located 3000 to 3200 m above sea level, 30 km northwest of Xining, Qinghai. The subjects were volunteers who joined a Comprehensive Geriatric Assessment. Plasma ox-LDL was measured in 168 community-dwelling elderly subjects aged 60 years or older (23 Tibetans and 145 Hans) with a monoclonal antibody-based enzyme-linked immunosorbent assay. Results Mean ox-LDL level was higher among Tibetan elderly than Han elderly (Tibetan, 79.0 ± 29.6 U/L; Han, 62.8 ± 23.5 U/L; P = .003). Tibetan ethnicity was significantly associated with ox-LDL levels after adjusting for LDL cholesterol levels. In addition, high ox-LDL levels (≥70 U/L) were significantly associated with a homeostasis model assessment insulin resistance index of at least 1.6 (odds ratio [OR], 2.82; 95% confidence interval [95% CI], 1.11 to 7.15; P = .029) and ankle brachial pressure index of less than 1.0 (OR, 4.85; 95% CI, 1.14 to 10.00; P = .028), after adjusting for age, sex, and ethnicity. Conclusions Our findings support the hypothesis that ox-LDL levels are higher among Tibetan elderly highlanders compared with those among Han elderly. As ox-LDL levels can affect insulin resistance and arteriosclerosis, further research is needed to determine how oxidative stress influences the health situation among elderly individuals at high altitudes.
Local axonal protection by WldS as revealed by conditional regulation of protein stability
Authors: Wang Jack T. , Medress Zachary A. , Vargas Mauricio E. , Barres Ben A. 
Published: July 2015

Significance
We investigated the molecular basis of Wallerian degeneration slow (WldS) axon protection by defining a spatial and temporal requirement of WldS activity to promote axonal survival. The findings carry clinical significance in showing that the cellular mechanisms governing degeneration of mammalian axons exhibit a latency period before the axon is irreversibly committed to degradation. Moreover, our findings indicate that the progression of Wallerian axon degeneration can be attenuated or halted altogether even long after an injury has occurred. We believe these findings narrow the molecular mechanisms responsible for orchestrating axonal degeneration to events within the axonal compartment and help identify therapeutic targets to halt or reverse the course of axon degeneration in neurological injuries and diseases.
Evaluation of Probabilistic Sampling Designs for Estimating Abundance of Multiple Species of Migratory Fish Using Video Recordings at Fishways
Authors: McCormick Joshua L. , Jackson Laura S. , Carr Fabian M. , Meyer Daniel H. 
Published: July 2015

Abstract
Fifteen years of video census data from a fishway at Winchester Dam on the North Umpqua River, Oregon, were used to evaluate sampling designs to estimate abundance of spring- and fall-run Chinook Salmon Oncorhynchus tshawytscha, summer- and winter-run steelhead O. mykiss, Coho Salmon O. kisutch, and Pacific Lamprey Entosphenus tridentatus. Five probabilistic sampling designs were evaluated via simulation, with variation in the number of days and the number of hours within a day that were sampled over a 1-year period. For most species, stratified one-stage and two-stage cluster designs were more accurate at estimating abundance than simple random sampling designs. There was very little gain in accuracy beyond sampling 8 h per day for all species. The stratified two-stage cluster nonuniform probability design was more accurate than the stratified two-stage cluster uniform probability design at estimating the abundance of steelhead, spring Chinook Salmon, and Coho Salmon, whereas using uniform probabilities resulted in more accurate estimates of abundance for Pacific Lamprey and fall Chinook Salmon. Additionally, the stratified and nonuniform probability designs can be adjusted for high-priority species through allocation of the sample and assigning selection probabilities of secondary sampling units that optimize efficiency for those species. The consistency in patterns observed among species suggests that the results of this study can be applied to other systems where the abundance of multiple species is of interest.
Received December 5, 2014; accepted March 28, 2015
Pr-SNTX, a short-chain three-finger toxin from Papuan pigmy mulga snake, is an antagonist of muscle-type nicotinic acetylcholine receptor (α2βδε)
Authors: Yamauchi Yoko , Kimoto Hikari , Yang Xianyu , Filkin Sergey , Utkin Yuri , Kubo Tai , Inagaki Hidetoshi 
Published: July 2015

Abstract
Three-finger toxins (3FTxs) are one of the major components in snake venoms. In this study, we isolated a cDNA encoding a short-chain 3FTx, Pr-SNTX, from Pseudechis rossignolii. The amino acid sequence of Pr-SNTX is nearly identical to that of its ortholog in Pseudechis australis. Pr-SNTX protein inhibited muscle-type (α2βδε), but not neuronal α7 nicotinic acetylcholine receptor (nAChR) activity.
Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results
Authors: Rahman Mumtahena , Jackson Laurie K. , Johnson W. Evan , Li Dean Y. , Bild Andrea H. , Piccolo Stephen R. 
Published: July 2015

Abstract
Motivation: The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides ‘Level 3’ data, which have been processed using a pipeline specific to that resource. However, we have found using experimentally derived data that this pipeline produces gene-expression values that vary considerably across biological replicates. In addition, some RNA-Sequencing analysis tools require integer-based read counts, which are not provided with the Level 3 data. As an alternative, we have reprocessed the data for 9264 tumor and 741 normal samples across 24 cancer types using the Rsubread package. We have also collated corresponding clinical data for these samples. We provide these data as a community resource.
Results: We compared TCGA samples processed using either pipeline and found that the Rsubread pipeline produced fewer zero-expression genes and more consistent expression levels across replicate samples than the TCGA pipeline. Additionally, we used a genomic-signature approach to estimate HER2 (ERBB2) activation status for 662 breast-tumor samples and found that the Rsubread data resulted in stronger predictions of HER2 pathway activity. Finally, we used data from both pipelines to classify 575 lung cancer samples based on histological type. This analysis identified various non-coding RNA that may influence lung-cancer histology.
Availability and implementation: The RNA-Sequencing and clinical data can be downloaded from Gene Expression Omnibus (accession number GSE62944). Scripts and code that were used to process and analyze the data are available from https://github.com/srp33/TCGA_RNASeq_Clinical.
Contact: stephen_piccolo@byu.edu or andreab@genetics.utah.edu
Supplementary information: Supplementary material is available at Bioinformatics online.
A mutation profile for top-k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization
Authors: Kim Sungchul , Sael Lee , Yu Hwanjo 
Published: July 2015

Abstract
Motivation: As the quantity of genomic mutation data increases, the likelihood of finding patients with similar genomic profiles, for various disease inferences, increases. However, so does the difficulty in identifying them. Similarity search based on patient mutation profiles can solve various translational bioinformatics tasks, including prognostics and treatment efficacy predictions for better clinical decision making through large volume of data. However, this is a challenging problem due to heterogeneous and sparse characteristics of the mutation data as well as their high dimensionality.
Results: To solve this problem we introduce a compact representation and search strategy based on Gene-Ontology and orthogonal non-negative matrix factorization. Statistical significance between the identified cancer subtypes and their clinical features are computed for validation; results show that our method can identify and characterize clinically meaningful tumor subtypes comparable or better in most datasets than the recently introduced Network-Based Stratification method while enabling real-time search. To the best of our knowledge, this is the first attempt to simultaneously characterize and represent somatic mutational data for efficient search purposes.
Availability: The implementations are available at: https://sites.google.com/site/postechdm/research/implementation/orgos.
Contact: sael@cs.stonybrook.edu or hwanjoyu@postech.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
GeneVetter: a web tool for quantitative monogenic assessment of rare diseases
Authors: Gillies Christopher E. , Robertson Catherine C. , Sampson Matthew G. , Kang Hyun Min 
Published: July 2015

Abstract
Summary: When performing DNA sequencing to diagnose affected individuals with monogenic forms of rare diseases, accurate attribution of causality to detected variants is imperative but imperfect. Even if a gene has variants already known to cause a disease, rare disruptive variants predicted to be causal are not always so, mainly due to imperfect ability to predict the pathogenicity of variants. Existing population-scale sequence resources such as 1000 Genomes are useful to quantify the ‘background prevalence’ of an unaffected individual being falsely predicted to carry causal variants. We developed GeneVetter to allow users to quantify the ‘background prevalence’ of subjects with predicted causal variants within specific genes under user-specified filtering parameters. GeneVetter helps quantify uncertainty in monogenic diagnosis and design genetic studies with support for power and sample size calculations for specific genes with specific filtering criteria. GeneVetter also allows users to analyze their own sequence data without sending genotype information over the Internet. Overall, GeneVetter is an interactive web tool that facilitates quantifying and accounting for the background prevalence of predicted pathogenic variants in a population.
Availability and Implementation: GeneVetter is available at http://genevetter.org/
Contact: mgsamps@med.umich.edu or hmkang@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Separate Brain Circuits Support Integrative and Semantic Priming in the Human Language System
Authors: Feng Gangyi , Chen Qi , Zhu Zude , Wang Suiping 
Published: July 2015

Abstract
Semantic priming is a crucial phenomenon to study the organization of semantic memory. A novel type of priming effect, integrative priming, has been identified behaviorally, whereby a prime word facilitates recognition of a target word when the 2 concepts can be combined to form a unitary representation. We used both functional and anatomical imaging approaches to investigate the neural substrates supporting such integrative priming, and compare them with those in semantic priming. Similar behavioral priming effects for both semantic (Bread–Cake) and integrative conditions (Cherry–Cake) were observed when compared with an unrelated condition. However, a clearly dissociated brain response was observed between these 2 types of priming. The semantic-priming effect was localized to the posterior superior temporal and middle temporal gyrus. In contrast, the integrative-priming effect localized to the left anterior inferior frontal gyrus and left anterior temporal cortices. Furthermore, fiber tractography showed that the integrative-priming regions were connected via uncinate fasciculus fiber bundle forming an integrative circuit, whereas the semantic-priming regions connected to the posterior frontal cortex via separated pathways. The results point to dissociable neural pathways underlying the 2 distinct types of priming, illuminating the neural circuitry organization of semantic representation and integration.
Seismic attenuation due to heterogeneities of rock fabric and fluid distribution
Authors: Ba Jing , Carcione José M. , Sun Weitao 
Published: July 2015

AbstractThe study of the influence of rock fabric and porefluid distribution on the seismic wavefield is important for the prediction and detection of reservoir properties such as lithology and fluid saturation. Wave-induced local fluid flow (WILFF), which is affected by local heterogeneities of the pore structure and fluid saturation, is believed to be the main mechanism to explain the measured attenuation levels at different frequency bands. These two types of heterogeneity affect seismic waves as a combined WILFF process. In this work, we consider a double-porosity system, each part with a different compressibility and patchy saturation, and derive the wave equations from Hamilton's principle. A plane-wave analysis yields the properties of the classical P-wave and those of the four slow waves. The examples show that patchy fluid saturation dominates the peak frequency of the relaxation mechanism. The relation between seismic anelasticity (velocity dispersion and attenuation) and saturation depends on frequency and on the geometrical features of the two heterogeneities. The proposed theory constitutes the comprehensive description for wave propagation process through reservoirs rocks of shallow Earth and porous media in general, to estimate fluid content and distribution.
Use of data mining at the Food and Drug Administration
Authors: Duggirala Hesha J , Tonning Joseph M , Smith Ella , Bright Roselie A , Baker John D , Ball Robert , Bell Carlos , Bright-Ponte Susan J , Botsis Taxiarchis , Bouri Khaled , Boyer Marc , Burkhart Keith , Steven Condrey G , Chen James J , Chirtel Stuart , Filice Ross W , Francis Henry , Jiang Hongying , Levine Jonathan , Martin David , Oladipo Taiye , O’Neill Rene , Palmer Lee Anne M. , Paredes Antonio , Rochester George , Sholtes Deborah , Szarfman Ana , Wong Hui-Lee , Xu Zhiheng , Kass-Hout Taha 
Published: July 2015

Abstract
Objectives This article summarizes past and current data mining activities at the United States Food and Drug Administration (FDA).
Target audience We address data miners in all sectors, anyone interested in the safety of products regulated by the FDA (predominantly medical products, food, veterinary products and nutrition, and tobacco products), and those interested in FDA activities.
Scope Topics include routine and developmental data mining activities, short descriptions of mined FDA data, advantages and challenges of data mining at the FDA, and future directions of data mining at the FDA.
Inhaled Nitric Oxide as an Adjunctive Treatment for Cerebral Malaria in Children: A Phase II Randomized Open-Label Clinical Trial
Authors: Mwanga-Amumpaire Juliet , Carroll Ryan W. , Baudin Elisabeth , Kemigisha Elisabeth , Nampijja Dorah , Mworozi Kenneth , Santorino Data , Nyehangane Dan , Nathan Daniel I. , De Beaudrap Pierre , Etard Jean-François , Feelisch Martin , Fernandez Bernadette O. , Berssenbrugge Annie , Bangsberg David , Bloch Kenneth D. , Boum Yap , Zapol Warren M. 
Published: July 2015

Abstract
Background.  Children with cerebral malaria (CM) have high rates of mortality and neurologic sequelae. Nitric oxide (NO) metabolite levels in plasma and urine are reduced in CM.
Methods.  This randomized trial assessed the efficacy of inhaled NO versus nitrogen (N2) as an adjunctive treatment for CM patients receiving intravenous artesunate. We hypothesized that patients treated with NO would have a greater increase of the malaria biomarker, plasma angiopoietin-1 (Ang-1) after 48 hours of treatment.
Results.  Ninety-two children with CM were randomized to receive either inhaled 80 part per million NO or N2 for 48 or more hours. Plasma Ang-1 levels increased in both treatment groups, but there was no difference between the groups at 48 hours (P = not significant [NS]). Plasma Ang-2 and cytokine levels (tumor necrosis factor-α, interferon-γ, interleukin [IL]-1β, IL-6, IL-10, and monocyte chemoattractant protein-1) decreased between inclusion and 48 hours in both treatment groups, but there was no difference between the groups (P = NS). Nitric oxide metabolite levels—blood methemoglobin and plasma nitrate—increased in patients treated with NO (both P &lt; .05). Seven patients in the N2 group and 4 patients in the NO group died. Five patients in the N2 group and 6 in the NO group had neurological sequelae at hospital discharge.
Conclusions.  Breathing NO as an adjunctive treatment for CM for a minimum of 48 hours was safe, increased blood methemoglobin and plasma nitrate levels, but did not result in a greater increase of plasma Ang-1 levels at 48 hours.
High-resolution ALMA observations of SDP.81. II. Molecular clump properties of a lensed submillimeter galaxy at z = 3.042
Authors: Hatsukade Bunyo , Tamura Yoichi , Iono Daisuke , Matsuda Yuichi , Hayashi Masao , Oguri Masamune 
Published: July 2015

Abstract
We present spatially resolved properties of molecular gas and dust in a gravitationally lensed submillimeter galaxy H-ATLAS J090311.6+003906 (SDP.81) at z = 3.042 revealed by the Atacama Large Millimeter/submillimeter Array (ALMA). We identified 14 molecular clumps in the CO(5–4) line data. The surface density of molecular gas ($\Sigma _{\rm H_2}$) and star-formation rate (ΣSFR) of the clumps are more than three orders of magnitude higher than those found in local spiral galaxies. The clumps are placed in the “burst” sequence in the $\Sigma _{\rm H_2}$–ΣSFR plane, suggesting that z ∼ 3 molecular clumps follow the star-formation law derived for local starburst galaxies. With our gravitational lens model, the positions in the source plane are derived for the molecular clumps, dust clumps, and stellar components identified in the Hubble Space Telescope image. The molecular and dust clumps are confined within a ∼ 2 kpc region, while the spatial extent of the stellar components is as large as ∼ 6 kpc and offset toward the west. The molecular clumps have a systematic velocity gradient in the north–south direction, which may indicate a rotating gas disk. One possible scenario is that the components of molecular gas, dust, and stars are distributed in a several-kpc-scale rotating disk, and the stellar emission is heavily obscured by dust in the central star-forming region. Alternatively, SDP.81 can be explained by a merging system, where dusty starbursts occur in the region where the two galaxies collide, surrounded by tidal features traced in the stellar components.
Rapid dissipation of protoplanetary disks in Ophiuchus
Authors: Takagi Yuhei , Itoh Yoichi , Arai Akira , Sai Shoko , Oasa Yumiko 
Published: July 2015

Abstract
We present the results of an age determination study for pre-main sequence stars in the Ophiuchus molecular cloud. The ages of eight pre-main sequence stars were estimated from surface gravities derived from high-resolution spectroscopy. The average age of the target stars was 0.7 Myr. By comparing the individual age and the near-infrared color excess, we found that color excess decreases gradually with a constant rate and the lifetime of the inner disk was determined to be 1.2 Myr. The estimated lifetime is nearly a half of the time compared to that of the pre-main sequence stars in the Taurus molecular cloud estimated with the same method. This result indicates that the disk evolution timescale depends on the environment of the star-forming region.