bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiographic Comparison between Cervical Spine Lateral and Whole-Spine Lateral Standing Radiographs
Authors: Park Moon Soo , Moon Seong-Hwan , Kim Tae-Hwan , Oh Jae Keun , Kang Hwa Jun , Riew K. Daniel 
Published: June 2015

Study Design Retrospective radiologic study. Objective The sagittal alignment of the cervical spine can be evaluated using either a lateral cervical radiograph or a whole-spine lateral view on which the cervical spine is included. To our knowledge, however, no report has compared the two. The purpose of this work is to identify the difference in radiographic parameters between the cervical spine lateral view and the whole-spine lateral view. Methods We retrospectively analyzed 59 adult patients suffering from neck pain with cervical spine lateral radiographs and whole-spine lateral radiographs from November 2007 to December 2011. The radiographs were measured using standard techniques to obtain the following parameters from the two different radiographs: occipital–C2 angle, C2–C7 angle, C7–sternal angle, sternal slope, T1 slope, C2 central offset distance, the distance between C2 and C7 plumb lines, C4 anteroposterior (AP) diameter, the ratio of C2 central off distance to C4 AP diameter, the ratio of plumb lines’ distance to C4 AP diameter. Results We found that the occipital–C2 angle, sternal slope, and C4 AP diameter were similar, but the C2–C7 angle, C7–sternal angle, T1 slope, C2 central offset distance, distance between C2 and C7 plumb lines, ratio of C2 central off distance to C4 AP diameter, and ratio of plumb lines’ distance to C4 AP diameter were different. However, the error of measurement was greater than the small angular and linear differences between the two views. Conclusions Most numerical values of the measured radiographic parameters appear to be different between the two views. However, the two views are comparable because the numerical differences were smaller than the errors of measurement.
The Effect of the Fresh Fruit and Vegetable Program on Childhood Obesity
Authors: Qian Yiwei , Nayga Rodolfo M. , Thomsen Michael R. , Rouse Heather L. 
Published: June 2015

AbstractThis paper investigates how the Fresh Fruit and Vegetable Program (FFVP), a nutrition assistance program that provides funding for the distribution of free fresh fruits and vegetables to students in participating schools, affects childhood obesity using a panel data set of Arkansas public schoolchildren with two different approaches. First, we combine matching methodology and difference‐in‐differences (DID) analysis. Second, we use the synthetic control method to compare each FFVP participating school to a similar, albeit synthetic, control school. Both analyses show that FFVP program causes an economically meaningful reduction in the obesity outcome of participating children.
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications
Authors: Laird Matthew R. , Langille Morgan G.I. , Brinkman Fiona S.L. 
Published: June 2015

Abstract
Motivation: A simple static image of genomes and associated metadata is very limiting, as researchers expect rich, interactive tools similar to the web applications found in the post-Web 2.0 world. GenomeD3Plot is a light weight visualization library written in javascript using the D3 library. GenomeD3Plot provides a rich API to allow the rapid visualization of complex genomic data using a convenient standards based JSON configuration file. When integrated into existing web services GenomeD3Plot allows researchers to interact with data, dynamically alter the view, or even resize or reposition the visualization in their browser window. In addition GenomeD3Plot has built in functionality to export any resulting genome visualization in PNG or SVG format for easy inclusion in manuscripts or presentations.
Results: GenomeD3Plot is being utilized in the recently released Islandviewer 3 (www.pathogenomics.sfu.ca/islandviewer/) to visualize predicted genomic islands with other genome annotation data. However, its features enable it to be more widely applicable for dynamic visualization of genomic data in general.
Availability and implementation: GenomeD3Plot is licensed under the GNU-GPL v3 at https://github.com/brinkmanlab/GenomeD3Plot/.
Contact: brinkman@sfu.ca
An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics
Authors: Lan Shiwei , Palacios Julia A. , Karcher Michael , Minin Vladimir N. , Shahbaba Babak 
Published: June 2015

Abstract
Motivation: The field of phylodynamics focuses on the problem of reconstructing population size dynamics over time using current genetic samples taken from the population of interest. This technique has been extensively used in many areas of biology but is particularly useful for studying the spread of quickly evolving infectious diseases agents, e.g. influenza virus. Phylodynamic inference uses a coalescent model that defines a probability density for the genealogy of randomly sampled individuals from the population. When we assume that such a genealogy is known, the coalescent model, equipped with a Gaussian process prior on population size trajectory, allows for nonparametric Bayesian estimation of population size dynamics. Although this approach is quite powerful, large datasets collected during infectious disease surveillance challenge the state-of-the-art of Bayesian phylodynamics and demand inferential methods with relatively low computational cost.
Results: To satisfy this demand, we provide a computationally efficient Bayesian inference framework based on Hamiltonian Monte Carlo for coalescent process models. Moreover, we show that by splitting the Hamiltonian function, we can further improve the efficiency of this approach. Using several simulated and real datasets, we show that our method provides accurate estimates of population size dynamics and is substantially faster than alternative methods based on elliptical slice sampler and Metropolis-adjusted Langevin algorithm.
Availability and implementation: The R code for all simulation studies and real data analysis conducted in this article are publicly available at http://www.ics.uci.edu/∼slan/lanzi/CODES.html and in the R package phylodyn available at https://github.com/mdkarcher/phylodyn.
Contact: S.Lan@warwick.ac.uk or babaks@uci.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Chimira: analysis of small RNA sequencing data and microRNA modifications
Authors: Vitsios Dimitrios M. , Enright Anton J. 
Published: June 2015

Abstract
Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications (e.g. uridylation, adenylation), 5′-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface.
Availability and implementation: Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira.
Contact: aje@ebi.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
LFQC: a lossless compression algorithm for FASTQ files
Authors: Nicolae Marius , Pathak Sudipta , Rajasekaran Sanguthevar 
Published: June 2015

Abstract
Motivation: Next Generation Sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large FASTQ files using innovative compression techniques.
Results: We introduce a new lossless non-reference based FASTQ compression algorithm named Lossless FASTQ Compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz (Bonfield and Mahoney, 2013), fqzcomp (Bonfield and Mahoney, 2013), Quip (Jones et al., 2012), DSRC2 (Roguski and Deorowicz, 2014). This comparison reveals that our algorithm achieves better compression ratios on LS454 and SOLiD datasets.
Availability and implementation: The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/rajasek/lfqc-v1.1.zip.
Contact: rajasek@engr.uconn.edu
First Report of Pythium spinosum as a Pathogen of Watermelon and in Association with a Dieback of Watermelon in Southwest Florida
Authors: Hendricks K. E. , Roberts P. D. 
Published: June 2015

The objective of the study was to elucidate the identity of pathogens associated with a dieback of mature watermelon vines in Southwest Florida. This is the first report of Pythium spinosum associated with dieback of watermelon in Southwest Florida. Accepted for publication 23 March 2015. Published 1 May 2015.
Identification of Races of Colletotrichum orbiculare on Muskmelon in South Carolina
Authors: Keinath Anthony P. 
Published: June 2015

Anthracnose caused by the fungus Colletotrichum orbiculare was observed on commercial cantaloupe grown in South Carolina for the first time in decades. Isolates from leaves were inoculated onto standard differential cultivars, and races 1, 2, and 2B were identified. This is the first report of C. orbiculare race 2B from South Carolina. Accepted for publication 27 March 2015. Published 1 May 2015.
First Report of Phytophthora Fruit Rot on Bitter Gourd (Mormodica charantia) and Sponge Gourd (Luffa cylindrica) Caused by Phytophthora capsici
Authors: Kousik Chandrasekar S. , Parada Camilo , Quesada-Ocampo Lina 
Published: June 2015

Luffa sponge (smooth gourd) and bitter gourds (bitter melon) are specialty vegetables grown in the U.S. on a small scale for select markets. Luffa gourds are also grown for sponges. In Sept. 2014, heavy rainfall resulted in rot of >50% of bitter gourd and >25% on sponge gourd in a field in Charleston, SC. The microbe causing the fruit rot was identified using microscopy and molecular tools. Prior to this study it was not known if this microbe could cause fruit rot of bitter gourd. This knowledge will be useful to suggest management strategies. Accepted for publication 17 March 2015. Published 6 May 2015.
Monitoring of a Single Point Mutation in the PvCesA3 Allele Conferring Resistance to Carboxylic Acid Amide Fungicides in Plasmopara viticola Populations In Yamanashi Prefecture, Japan
Authors: Aoki Yoshinao , Kawagoe Yumi , Fujimori Nozomi , Tanaka Sayumi , Suzuki Shunji 
Published: June 2015

The use of the carboxylic acid amide (CAA) fungicide mandipropamid to manage grapevine downy mildew in vineyards in Japan has been increasing since 2010, because of widespread quinone outside inhibitor fungicide resistance in the Plasmopara viticola population. However, CAA fungicide resistance in P. viticola is becoming a serious problem worldwide. In 2013, we monitored for the presence of a single point mutation at codon 1105 of the cellulose synthase gene PvCesA3, which confers resistance to mandipropamid in P. viticola samples collected from four vineyards in Yamanashi prefecture in Japan. Five out of 157 samples were found to be heterozygotes, carrying both the mutated and nonmutated PvCesA3 alleles. Although CAA fungicide-resistant P. viticola isolates have not been reported yet in Japan, the emergence of heterozygous P. viticola populations indicates the potential risk of emergence of resistant homozygotes. Accepted for publication 14 March 2015. Published 1 May 2015
Decision Models for Fungicide Applications for Soybean Rust
Authors: Kelly Heather M. , Wright David L. , Dufault Nicholas S. , Marois James J. 
Published: June 2015

Soybean rust (SBR), caused by Phakopsora pachyrhizi, can be a devastating disease to southeastern U.S. soybean (Glycine max) production. Fungicides can be applied to avoid yield loss, but growers need to know when an application will be most beneficial. To better understand and manage SBR epidemics in the southeastern U.S., fungicide application decision models were developed and validated. Application decision models were developed based on SBR presence and hours of leaf wetness or amount of cumulative rain and compared to non-treated controls and applications based on crop growth stage. The models were evaluated in 2009, 2010, and 2011. High disease pressure and conducive weather conditions in 2009 resulted in significantly greater disease severity and lower yields in non-treated plots compared to treated plots. In 2010 and 2011, low disease pressure and drought conditions resulted in no significant differences in disease severity or yields among most treatments. Results indicate two fungicide applications during early reproductive stage can reduce yield loss due to SBR, but subsequent applications need to be determined based on disease pressure, weather conditions, and crop growth stage. Accepted for publication 1 March 2015. Published 1 May 2015.
U-shaped Osteotomy Around the Descending Palatine Artery to Prevent Posterior Osseous Interference for Superior/Posterior Repositioning of the Maxilla in Le Fort I Osteotomy
Authors: Omura Susumu , Iwai Toshinori , Honda Koji , Shibutani Naoki , Fujita Koichi , Yamashita Yosuke , Takasu Hikaru , Murata Shogo , Tohnai Iwai 
Published: June 2015

Abstract
In maxillary orthognathic surgery, superior repositioning of the maxilla is sometimes difficult, and removal of bony interference, especially around the descending palatine artery (DPA), is very time-consuming in cases of severe maxillary impaction. Posterior repositioning of the maxilla for removal of bony interference between the posterior maxilla and the pterygoid process is also technically difficult. Because the most common site of hemorrhage in Le Fort I osteotomy is the posterior maxilla, this bone removal is a source of frustration for surgeons in DPA injury. When the DPA is injured during bone removal and ligation is performed, aseptic necrosis of the maxilla may occur. Therefore, a simple and safe method for maxillary superior/posterior repositioning is required to remove osseous interference around the DPA. The authors describe here U-shaped osteotomy around the DPA to prevent posterior osseous interference for superior/posterior repositioning of the maxilla in Le Fort I osteotomy.
Mutation-Profile-Based Methods for Understanding Selection Forces in Cancer Somatic Mutations: A Comparative Analysis
Authors: Zhou Zhan , Zou Yangyun , Liu Gangbiao , Zhou Jingqi , Wu Jingcheng , Zhao Shimin , Su Zhixi , Gu Xun 
Published: June 2015

ABSTRACTHuman genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN/CS) and normal populations (pN/pS). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels. Both the relaxation of purifying selection on passenger mutations and the positive selection of driver mutations may contribute to the increasedCN/CSvalues of human genes in cancer genomes compared with thepN/pSvalues in human populations. TheCN/CSvalues also contribute to the improved classification of cancer genes and a better understanding of the onco-functionalization of cancer genes during oncogenesis. The use of our computational pipeline to identify cancer-specific positively and negatively selected genes may provide useful information for understanding the evolution of cancers and identifying possible targets for therapeutic intervention.
Epidemiology of deep cutaneous fungal infections in Korea (2006–2010)
Authors: Kim Myoung Shin , Kim Jae Kyung , Lee Mi Woo , Moon Kee‐Chan , Kim Beom Joon , Son Sang Wook , Ahn Hyo Hyun , Oh Sang Ho , Yu Hee Joon , Lee Dong Youn , Cho Kwang Hyun , Cho Baik Kee , Kim Moon Bum , Suh Kee Suck , Kim You Chan , Ro Byung In , Park Joon Soo , Choi Jong Soo , Lee Jee Bum 
Published: June 2015

AbstractDeep cutaneous fungal infections (DCFI) occur worldwide and their prevalence is influenced by personal factors of the affected patients and the geographic and cultural features. Surveillance studies of DCFI with respect to the various clinical backgrounds of affected patients can ultimately help to improve their outcome. Expanding on our previous study, we performed a retrospective analysis of patients with DCFI who were treated in a group of university teaching hospitals in Korea to determine the trends within a 5‐year period. A retrospective medical record review of patients with DCFI treated between 2006 and 2010 at 16 university teaching hospitals located throughout Korea was performed. Among the 51 cases of DCFI (median patient age, 47.0 years), opportunistic infections in immunocompromised hosts accounted for half. Patients in this group included 11 who were transplant recipients and 12 with malignancies. Overall, Candida (13/51) was the most common causative organism, followed by Sporothrix (12) and Aspergillus (6). Papuloplaques and nodular lesions were the typical presentation, with maculopatches and ulcers also occurring in considerable numbers. Ten patients had systemic involvement. Eight immunocompromised patients did not recover from the disease despite systemic antifungal treatment. Our results highlight the equal involvement of opportunistic and primary pathogens in DCFI, as determined in cases from a 5‐year period. Especially in immunocompromised hosts with non‐specific skin findings, clinical suspicion is important because failure to diagnose a DCFI causes significant morbidity and possibly even death.
The Demand for Public Health Care and the Progressivity of Health Care Services in Ghana
Authors: Gaddah Mawuli , Munro Alistair , Quartey Peter 
Published: June 2015

AbstractThis paper examines the choice of health care and progressivity of health care services in Ghana. Using a combination of benefit incidence analysis and a discrete choice model and data from the Ghana Living Standards Survey, our results give clear evidence of progressivity with consistent ordering: postnatal and prenatal services are the most progressive, followed by clinic visits, and then hospital visits. Child health care services are more progressive than adult. Own price and income elasticities are higher for public health care than private health care and for adults than children. Poorer households are substantially more price responsive than wealthy ones, implying that fee increases for public health care will impact negatively on equity in health care. Simulations show the importance of opportunity costs in health care decisions and suggest that reforms that focus only on out‐of‐pocket expenses will have a limited ability to extend public health care to all potential users.
A Spatial, Non‐parametric Analysis of the Determinants of Food Insecurity in Sub‐Saharan Africa
Authors: Sassi Maria 
Published: June 2015

AbstractThis paper investigates the determinants of food insecurity at the macro‐level in cross‐sectional data for a sample of 40 countries in sub‐Saharan Africa and considers the most basic causes of undernourishment, including food availability, access to food and its utilization. The empirical analysis is based on a spatial, non‐parametric technique that allows global and local explanatory variables to be distinguished from one another. The results provide useful information for reconsidering food security policies and programmes that extend beyond the prevailing perspective of food availability and suggest possible directions for regional and sub‐regional approaches to the food crisis in sub‐Saharan Africa.
Price Transmission Asymmetry in Spatial Grain Markets in Ethiopia
Authors: Wondemu Kifle 
Published: June 2015

AbstractAcknowledging the link between competitive and efficient spatial agricultural markets and farm productivity, the government of Ethiopia has implemented various market enhancing policy and institutional measures. The effectiveness of these measures to achieve their policy goals, among others, depends on the degree of symmetry prices transmit across spatial markets as well as on the efficiency of spatial arbitrage. We tested the presence of asymmetric price adjustment in the spatial grain markets in Ethiopia. The result provided clear evidence of asymmetric price adjustment for teff crops, but not for maize. For teff crops, prices adjust quickly to shocks that increase price than shocks that reduce prices. The analysis on the efficiency of the grain markets also showed that the spatial markets are characterized by a significant level of inefficiency. Although further research is necessary to establish the real causes for the observed asymmetric price transmission and market inefficiency, the finding suggests that departure from perfectly competitive settings are partly to be blamed for the recent food crops price hikes. In addition to their undesirable redistributional consequences, price transmissions asymmetry and inefficiency are expected to entail efficiency loss. Future empirical work in this area should strive to explain the underlying reasons for the observed asymmetric price transmission and market inefficiency.