bluuebunny/crossref_metadata_2025_split huggingface dataset:
Economics of Agricultural Supply Chain Design: A Portfolio Selection Approach
Authors: Du Xiaoxue , Lu Liang , Reardon Thomas , Zilberman David 
Published: September 2016

AbstractAgrifood firms in a globalizing and competitive market, both in developing and developed countries, often undertake innovations in products and technologies. Innovators such as firms and other agents develop supply chains to accommodate the nature of the innovations. In this article we analyze an innovator's supply chain design problem. The design of the supply chain involves three sets of decisions. The first is how much to produce. The second involves how to undertake production, and how many resources to allocate to the production of feedstock (agricultural products that are inputs for processing), processing, and marketing. The third set involves deciding on the amount of feedstock to be obtained through contracts with farmers. We show that the innovator determines its overall level of production by taking advantage of its monopoly power, derived from the innovation in the output market, and behaves as a monopsony in buying feedstock from contractors. These decisions are constrained by the marginal cost of capital and the properties of production and marketing technologies. When the innovator is risk averse, risks in farm production, processing, and marketing will affect both processed output and the share of feedstock bought through contracts.
AKT: ancestry and kinship toolkit
Authors: Arthur Rudy , Schulz-Trieglaff Ole , Cox Anthony J , O’Connell Jared 
Published: September 2016

Abstract

Motivation
Ancestry and Kinship Toolkit (AKT) is a statistical genetics tool for analysing large cohorts of whole-genome sequenced samples. It can rapidly detect related samples, characterize sample ancestry, calculate correlation between variants, check Mendel consistency and perform data clustering. AKT brings together the functionality of many state-of-the-art methods, with a focus on speed and a unified interface. We believe it will be an invaluable tool for the curation of large WGS datasets.

Availability and Implementation
The source code is available at https://illumina.github.io/akt.

Supplementary information
Supplementary data are available at Bioinformatics online.
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Authors: Zhong Yi , Karaletsos Theofanis , Drewe Philipp , Sreedharan Vipin T , Kuo David , Singh Kamini , Wendel Hans-Guido , Rätsch Gunnar 
Published: September 2016

Abstract

Motivation
Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case–control studies are needed.

Results
We present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy.

Availability and Implementation
RiboDiff webpage http://bioweb.me/ribodiff. Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff.

Supplementary information
Supplementary data are available at Bioinformatics online.
Seeksv: an accurate tool for somatic structural variation and virus integration detection
Authors: Liang Ying , Qiu Kunlong , Liao Bo , Zhu Wen , Huang Xuanlin , Li Lin , Chen Xiangtao , Li Keqin 
Published: September 2016

Abstract

Motivation
Many forms of variations exist in the human genome including single nucleotide polymorphism, small insert/deletion (DEL) (indel) and structural variation (SV). Somatically acquired SV may regulate the expression of tumor-related genes and result in cell proliferation and uncontrolled growth, eventually inducing tumor formation. Virus integration with host genome sequence is a type of SV that causes the related gene instability and normal cells to transform into tumor cells. Cancer SVs and viral integration sites must be discovered in a genome-wide scale for clarifying the mechanism of tumor occurrence and development.

Results
In this paper, we propose a new tool called seeksv to detect somatic SVs and viral integration events. Seeksv simultaneously uses split read signal, discordant paired-end read signal, read depth signal and the fragment with two ends unmapped. Seeksv can detect DEL, insertion, inversion and inter-chromosome transfer at single-nucleotide resolution. Different types of sequencing data, such as single-end sequencing data or paired-end sequencing data can accommodate to detect SV. Seeksv develops a rescue model for SV with breakpoints located in sequence homology regions. Results on simulated and real data from the 1000 Genomes Project and esophageal squamous cell carcinoma samples show that seeksv has higher efficiency and precision compared with other similar software in detecting SVs. For the discovery of hepatitis B virus integration sites from probe capture data, the verified experiments show that more than 90% viral integration sequences detected by seeksv are true.

Availability and Implementation
seeksv is implemented in C ++ and can be downloaded from https://github.com/qkl871118/seeksv.

Supplementary information
Supplementary data are available at Bioinformatics online.
Time-lapse joint inversion of geophysical data with automatic joint constraints and dynamic attributes
Authors: Rittgers J.B. , Revil A. , Mooney M.A. , Karaoulis M. , Wodajo L. , Hickey C.J. 
Published: September 2016

Summary
Joint inversion and time-lapse inversion techniques of geophysical data are often implemented in an attempt to improve imaging of complex subsurface structures and dynamic processes by minimizing negative effects of random and uncorrelated spatial and temporal noise in the data. We focus on the structural cross-gradient (SCG) approach (enforcing recovered models to exhibit similar spatial structures) in combination with time-lapse inversion constraints applied to surface-based electrical resistivity and seismic traveltime refraction data. The combination of both techniques is justified by the underlying petrophysical models. We investigate the benefits and trade-offs of SCG and time-lapse constraints. Using a synthetic case study, we show that a combined joint time-lapse inversion approach provides an overall improvement in final recovered models. Additionally, we introduce a new approach to reweighting SCG constraints based on an iteratively updated normalized ratio of model sensitivity distributions at each time-step. We refer to the new technique as the Automatic Joint Constraints (AJC) approach. The relevance of the new joint time-lapse inversion process is demonstrated on the synthetic example. Then, these approaches are applied to real time-lapse monitoring field data collected during a quarter-scale earthen embankment induced-piping failure test. The use of time-lapse joint inversion is justified by the fact that a change of porosity drives concomitant changes in seismic velocities (through its effect on the bulk and shear moduli) and resistivities (through its influence upon the formation factor). Combined with the definition of attributes (i.e. specific characteristics) of the evolving target associated with piping, our approach allows localizing the position of the preferential flow path associated with internal erosion. This is not the case using other approaches.
Identification and validation of seven new loci showing differential DNA
methylation related to serum lipid profile: an epigenome-wide approach. The REGICOR
study
Authors: Sayols-Baixeras S , Subirana I , Lluis-Ganella C , Civeira F , Roquer J , Do AN , Absher D , Cenarro A , Muñoz D , Soriano-Tárraga C , Jiménez-Conde J , Ordovas J M , Senti M , Aslibekyan S , Marrugat J , Arnett D K , Elosua R 
Published: September 2016

Abstract
Lipid traits (total, low-density and high-density lipoprotein cholesterol, and triglycerides) are risk factors for cardiovascular disease. DNA methylation is not only an inherited but also modifiable epigenetic mark that has been related to cardiovascular risk factors. Our aim was to identify loci showing differential DNA methylation related to serum lipid levels. Blood DNA methylation was assessed using the Illumina Human Methylation 450 BeadChip. A two-stage epigenome-wide association study was performed, with a discovery sample in the REGICOR study (n = 645) and validation in the Framingham Offspring Study (n = 2,542). Fourteen CpG sites located in nine genes (SREBF1, SREBF2, PHOSPHO1, SYNGAP1, ABCG1, CPT1A, MYLIP, TXNIP and SLC7A11) and 2 intergenic regions showed differential methylation in association with lipid traits. Six of these genes and 1 intergenic region were new discoveries showing differential methylation related to total cholesterol (SREBF2), HDL-cholesterol (PHOSPHO1, SYNGAP1 and an intergenic region in chromosome 2) and triglycerides (MYLIP, TXNIP and SLC7A11). These CpGs explained 0.7%, 9.5% and 18.9% of the variability of total cholesterol, HDL cholesterol and triglycerides in the Framingham Offspring Study, respectively. The expression of the genes SREBF2 and SREBF1 was inversely associated with methylation of their corresponding CpGs (P-value = 0.0042 and 0.0045, respectively) in participants of the GOLDN study (n = 98). In turn, SREBF1 expression was directly associated with HDL cholesterol (P-value = 0.0429). Genetic variants in SREBF1, PHOSPHO1, ABCG1 and CPT1A were also associated with lipid profile. Further research is warranted to functionally validate these new loci and assess the causality of new and established associations between these differentially methylated loci and lipid metabolism.
Surrogate-assisted feature extraction for high-throughput phenotyping
Authors: Yu Sheng , Chakrabortty Abhishek , Liao Katherine P , Cai Tianrun , Ananthakrishnan Ashwin N , Gainer Vivian S , Churchill Susanne E , Szolovits Peter , Murphy Shawn N , Kohane Isaac S , Cai Tianxi 
Published: September 2016

Objective: Phenotyping algorithms are capable of accurately identifying patients with specific phenotypes from within electronic medical records systems. However, developing phenotyping algorithms in a scalable way remains a challenge due to the extensive human resources required. This paper introduces a high-throughput unsupervised feature selection method, which improves the robustness and scalability of electronic medical record phenotyping without compromising its accuracy.
Methods: The proposed Surrogate-Assisted Feature Extraction (SAFE) method selects candidate features from a pool of comprehensive medical concepts found in publicly available knowledge sources. The target phenotype’s International Classification of Diseases, Ninth Revision and natural language processing counts, acting as noisy surrogates to the gold-standard labels, are used to create silver-standard labels. Candidate features highly predictive of the silver-standard labels are selected as the final features.
Results: Algorithms were trained to identify patients with coronary artery disease, rheumatoid arthritis, Crohn’s disease, and ulcerative colitis using various numbers of labels to compare the performance of features selected by SAFE, a previously published automated feature extraction for phenotyping procedure, and domain experts. The out-of-sample area under the receiver operating characteristic curve and F-score from SAFE algorithms were remarkably higher than those from the other two, especially at small label sizes.
Conclusion: SAFE advances high-throughput phenotyping methods by automatically selecting a succinct set of informative features for algorithm training, which in turn reduces overfitting and the needed number of gold-standard labels. SAFE also potentially identifies important features missed by automated feature extraction for phenotyping or experts.
ALMA observations of the supergiant B[e] star Wd1-9
Authors: Fenech D. M. , Clark J. S. , Prinja R. K. , Morford J. C. , Dougherty S. , Blomme R. 
Published: September 2016

Abstract
Mass-loss in massive stars plays a critical role in their evolution, although the precise mechanism(s) responsible – radiatively driven winds, impulsive ejection and/or binary interaction – remain uncertain. In this Letter, we present Atacama Large Millimetre/Submillimeter Array line and continuum observations of the supergiant B[e] star Wd1-9, a massive post-main-sequence object located within the starburst cluster Westerlund 1 (Wd1). We find it to be one of the brightest stellar point sources in the sky at millimetre wavelengths, with (serendipitously identified) emission in the H41α radio recombination line. We attribute these properties to a low velocity (∼100 km s−1 ) ionized wind, with an extreme mass-loss rate ≳6.4 × 10−5(d/5 kpc)1.5 M⊙yr− 1. External to this is an extended aspherical ejection nebula indicative of a prior phase of significant mass-loss. Taken together, the millimetre properties of Wd1-9 show a remarkable similarity to those of the highly luminous stellar source MWC349A. We conclude that these objects are interacting binaries evolving away from the main sequence and undergoing rapid case-A mass transfer. As such they – and by extension the wider class of supergiant B[e] stars – may provide a unique window into the physics of a process that shapes the life-cycle of ∼70 per cent of massive stars found in binary systems.
The origin of the eccentricity of the hot Jupiter in CI Tau
Authors: Rosotti G. P. , Booth R. A. , Clarke C. J. , Teyssandier J. , Facchini S. , Mustill A. J. 
Published: September 2016

Abstract
Following the recent discovery of the first radial velocity planet in a star still possessing a protoplanetary disc (CI Tau), we examine the origin of the planet's eccentricity (e ∼0.3). We show through long time-scale (105 orbits) simulations that the planetary eccentricity can be pumped by the disc, even when its local surface density is well below the threshold previously derived from short time-scale integrations. We show that the disc may be able to excite the planet's orbital eccentricity in &lt;1 Myr for the system parameters of CI Tau. We also perform two-planet scattering experiments and show that alternatively the observed planet may plausibly have acquired its eccentricity through dynamical scattering of a migrating lower mass planet, which has either been ejected from the system or swallowed by the central star. In the latter case the present location and eccentricity of the observed planet can be recovered if it was previously stalled within the disc's magnetospheric cavity.
On the selection of damped Lyman α systems using Mg ii absorption at 2 &lt; zabs &lt; 4
Authors: Berg T. A. M. , Ellison S. L. , Prochaska J. X. , Sánchez-Ramírez R. , Lopez S. , D'Odorico V. , Becker G. , Christensen L. , Cupani G. , Denney K. , Worseck G. 
Published: September 2016

Abstract
The XQ-100 survey provides optical and near-infrared coverage of 36 blindly selected, intervening damped Lyman α systems (DLAs) at 2 &lt; zabs &lt; 4, simultaneously covering the Mg ii doublet at λλ2796, 2803Å, and the Ly α transition. Using the XQ-100 DLA sample, we investigate the completeness of selecting DLA absorbers based on their Mg ii rest-frame equivalent width ($W_{0}^{2796}$) at these redshifts. Of the 29 DLAs with clean Mg ii profiles, we find that six (20 per cent of DLAs) have $W_{0}^{2796}$ &lt; 0.6 Å. The DLA incidence rate of $W_{0}^{2796}$ &lt; 0.6 Å absorbers is a factor of ∼5 higher than what is seen in z ∼ 1 samples, indicating a potential evolution in the Mg ii properties of DLAs with redshift. All of the $W_{0}^{2796}$ &lt; 0.6 Å DLAs have low metallicities (−2.5 &lt; [M/H] &lt; −1.7), small velocity widths (v90 &lt; 50 km s−1), and tend to have relatively low N(H i). We demonstrate that the exclusion of these low $W_{0}^{2796}$ DLAs results in a higher mean N(H i) which in turn leads to an ∼7 per cent increase in the cosmological gas density of H i of DLAs at 2 &lt; zabs &lt; 4; and that this exclusion has a minimal effect on the H i-weighted mean metallicity.
A photoevaporative gap in the closest planet-forming disc
Authors: Ercolano Barbara , Rosotti Giovanni P. , Picogna Giovanni , Testi Leonardo 
Published: September 2016

Abstract
The dispersal of the circum-stellar discs of dust and gas surrounding young low-mass stars has important implications for the formation of planetary systems. Photoevaporation from energetic radiation from the central object is thought to drive the dispersal in the majority of discs, by creating a gap which disconnects the outer from the inner regions of the disc and then disperses the outer disc from the inside-out, while the inner disc keeps draining viscously on to the star. In this Letter, we show that the disc around TW Hya, the closest protoplanetary disc to Earth, may be the first object where a photoevaporative gap has been imaged around the time at which it is being created. Indeed, the detected gap in the Atacama large millimeter/submillimeter array images is consistent with the expectations of X-ray photoevaporation models, thus not requiring the presence of a planet. The photoevaporation model is also consistent with a broad range of properties of the TW Hya system, e.g. accretion rate and the location of the gap at the onset of dispersal. We show that the central, unresolved 870 μm continuum source might be produced by free–free emission from the gas and/or residual dust inside the gap.
Pediatric Injuries at an Annual Motocross Competition: Rates and Severity
Authors: Williams Brendan A. , McFadden James P. , Teurlings Tyler L. , Blakemore Laurel C. 
Published: September 2016

Purpose:
Pediatric motocross injuries occur frequently and with significant associated morbidity; however, data are limited regarding injury occurring during competition. North Central Florida hosts an annual motocross competition with numerous pediatric competitors. We sought to evaluate the rate and severity of injuries sustained at this event over a multiyear period. Our primary hypothesis was that motocross injury rates and severity in competition exceed that of other competitive sports in this age group.

Methods:
A retrospective review was performed to identify pediatric patients (17 and younger) presenting to a single Level 1 Trauma Center as a result of injury sustained at an annual motocross competition from 2009 to 2012. Demographic, diagnostic, and treatment data were collected including injuries, procedural interventions, and length of hospital stay. Rate, type, and severity of injury were evaluated and compared with established norms of other competitive sports in a similar age group.

Results:
Over a 4-year period, 51 pediatric motocross competitors sustained 75 injuries. Injured riders were 14.2±2.51 years (range, 8 to 17 y) old and 92% (47/51) male. Forty (78%) patients sustained at least 1 orthopaedic injury and 17 (33%) patients suffered polytrauma. The majority of injuries occurred in the upper extremity (36%). Twenty-four (47%) patients required procedural intervention, 15 of which were operative. Thirty-nine (76%) patients necessitated surgical specialty care. Average injury severity score was 6.5 (1 to 75) and 1 death occurred. The injury rate for pediatric motocross riders in this study was 19.9 injuries per 1000 competitors.

Conclusions:
High rates of injury occur among pediatric patients in competitive motocross, exceeding those seen in other competitive sports in a comparable age group. Significant morbidity and at least 1 fatality were demonstrated in the group studied. The majority of patients suffer at least 1 orthopaedic injury and nearly all patients require pediatric surgical specialist care. Polytrauma is common. Motocross participants and parents should be aware of these risks of competition and event organizers should arrange events near facilities with appropriate pediatric surgical specialty services.

Level of Evidence:
Level IV—case series.
Walking Out of the Curve: Thoracolumbar Kyphosis in Achondroplasia
Authors: Margalit Adam , McKean Greg , Lawing Cheryl , Galey Scott , Ain Michael C. 
Published: September 2016

Background:
Thoracolumbar kyphosis (TLK) is common in infants with achondroplasia. Our goals were to examine the natural history of TLK and identify factors associated with persistent TLK.

Methods:
We reviewed records of patients with achondroplasia seen by a board-certified orthopaedic surgeon at a tertiary care medical center between 1997 and 2013. Inclusion criteria were minimum 2-year follow-up and radiographs taken at time of presentation, within 6 months of walking age, and within 6 months of the first anniversary of walking age. We defined TLK as kyphosis of ≥20 degrees centered at T12 and L1. We assessed patient demographic characteristics, radiographic parameters (Cobb angle, apical vertebral translation, and apical vertebral wedging for vertebral height and width), and clinical parameters (developmental motor delay, hydrocephalus, presence of a ventriculoperitoneal shunt, and foramen magnum decompression). Developmental motor delay was defined as the inability to sit or ambulate independently by age 14 or 30 months, respectively. Associations between these factors and persistent TLK (ie, unresolved at final follow-up) were evaluated using logistic regression and χ2, Fisher exact, and independent t tests. Significance was set at P<0.05.

Results:
A total of 60 patients were included. Mean values were as follows: age at presentation, 10.9±7.0 months; length of follow-up, 5.7±3.6 years; initial curve, 43.8±11.0 degrees; independent sitting age, 12.6±5.5 months; and independent walking age, 21.1±7.8 months. At walking age and 1 year after walking age, 15% and 58% of patients, respectively, had spontaneous TLK resolution. In total, 30% of patients had persistent TLK at final follow-up. Apical vertebral translation (P=0.001), percentage of apical vertebral wedging for vertebral height (P=0.031), and developmental motor delay (P=0.043) were associated with unresolved TLK.

Conclusions:
In patients with achondroplasia, TLK resolved at walking age in 15% of patients and after a year of walking in 58% of patients. Earlier bracing may slow TLK progression in patients with achondroplasia and developmental motor delay. Patients with kyphotic curves between 20 and 40 degrees should be examined intermittently for progressive deformity or worsening symptoms of spinal cord compression.

Level of Evidence:
Level II.