bluuebunny/crossref_metadata_2025_split huggingface dataset:
The End of Farm Labor Abundance
Authors: Taylor J. Edward , Charlton Diane , Yúnez‐Naude Antonio 
Published: November 2012

AbstractAn analysis of nationally representative panel data from rural Mexico, with observations in years 2002, 2007, and 2010, suggests that the same shift out of farm work that characterized U.S. labor history is well underway in Mexico. Meanwhile, the demand for agricultural labor in Mexico is rising. In the future, U.S. agriculture will compete with Mexican farms for a dwindling supply of farm labor. Since U.S. domestic workers are unwilling to do farm work and the United States can feasibly import farm workers from only a few countries in close geographic proximity, the agricultural industry will eventually need to adjust production to use less labor. The decline in foreign labor supply to farms in the United States ultimately will need to be accompanied by farm labor conservation, switching to less labor intensive crops and technologies, and labor management practices that match fewer workers with more farm jobs.
Front‐of‐Package Nutritional Labels and Consumer Beverage Perceptions
Authors: Kim Hyeyoung , House Lisa A. , Rampersaud Gail , Gao Zhifeng 
Published: November 2012

AbstractThe pressure to find solutions for high rates of obesity and overweight in the U.S. population has led industry groups to introduce voluntary front‐of‐package (FOP) nutritional labeling for beverages. This research examines the impact of these labels on consumers' perceptions of the healthiness of beverages. Though consumers reacted differently depending on the information in the label, in general, the perception of milks and 100% juices decreased, while perception of soft drinks and less than 100% juice drinks increased. If the purpose of FOP labels is to encourage healthier choices, the changes observed appear to be at odds with the goal.
Largenet2: an object-oriented programming library for simulating large adaptive networks
Authors: Zschaler Gerd , Gross Thilo 
Published: November 2012

Abstract
Summary: The largenet2 C++ library provides an infrastructure for the simulation of large dynamic and adaptive networks with discrete node and link states.
Availability: The library is released as free software. It is available at http://biond.github.com/largenet2. Largenet2 is licensed under the Creative Commons Attribution-NonCommercial 3.0 Unported License.
Contact: gerd@biond.org.
VAGUE: a graphical user interface for the Velvet assembler
Authors: Powell David R. , Seemann Torsten 
Published: November 2012

Abstract
Summary: Velvet is a popular open-source de novo genome assembly software tool, which is run from the Unix command line. Most of the problems experienced by new users of Velvet revolve around constructing syntactically and semantically correct command lines, getting input files into acceptable formats and assessing the output. Here, we present Velvet Assembler Graphical User Environment (VAGUE), a multi-platform graphical front-end for Velvet. VAGUE aims to make sequence assembly accessible to a wider audience and to facilitate better usage amongst existing users of Velvet.
Availability and implementation: VAGUE is implemented in JRuby and targets the Java Virtual Machine. It is available under an open-source GPLv2 licence from http://www.vicbioinformatics.com/.
Contact: torsten.seemann@monash.edu
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
Authors: Chen Yunxin , Yao Hui , Thompson Erika J. , Tannir Nizar M. , Weinstein John N. , Su Xiaoping 
Published: November 2012

Abstract
Summary: We developed a new algorithmic method, VirusSeq, for detecting known viruses and their integration sites in the human genome using next-generation sequencing data. We evaluated VirusSeq on whole-transcriptome sequencing (RNA-Seq) data of 256 human cancer samples from The Cancer Genome Atlas. Using these data, we showed that VirusSeq accurately detects the known viruses and their integration sites with high sensitivity and specificity. VirusSeq can also perform this function using whole-genome sequencing data of human tissue.
Availability: VirusSeq has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/∼xsu1/VirusSeq.html.
Contact: xsu1@mdanderson.org
Supplementary information: Supplementary data are available at Bioinformatics online.
NetCAD: a network analysis tool for coronary artery disease-associated PPI network
Authors: Ren Guomin , Liu Zhihua 
Published: November 2012

Abstract
Summary: The systematic and unbiased charting of protein–protein interaction (PPI) networks relevant to health or diseases has become an important and burgeoning challenge in systems biology. Further, current reports have supported that good correlation exists between the topological properties and biological function of protein nodes in networks. Coronary artery disease (CAD, also called coronary heart disease) is the most common type of heart disease worldwide. Traditional approaches of studying individual gene or protein have shown their weakness in such complex disease. Here, we provide NetCAD, a web-based tool for systematic investigation of CAD-specific proteins in human PPI network. The features of NetCAD includes the following: proposing a novel method combining biological principles and graph theory, quantified topological analysis tools, build-in PPI information database consolidated from major public databases, creating CAD-associated subnetwork and visualizing network graph with good visual effects. NetCAD may provide important biological information for uncovering the molecular mechanisms and potential targets for therapies of CAD, which could not be found merely through molecular biology methods.
Availability and implementation: NetCAD is freely available at: http://www.herbbol.org/netcad/.
Contact: zhliu@implad.ac.cn or zhliu.liulab@foxmail.com
Drug–target interaction prediction by learning from local information and neighbors
Authors: Mei Jian-Ping , Kwoh Chee-Keong , Yang Peng , Li Xiao-Li , Zheng Jie 
Published: November 2012

Abstract
Motivation: In silico methods provide efficient ways to predict possible interactions between drugs and targets. Supervised learning approach, bipartite local model (BLM), has recently been shown to be effective in prediction of drug–target interactions. However, for drug-candidate compounds or target-candidate proteins that currently have no known interactions available, its pure ‘local’ model is not able to be learned and hence BLM may fail to make correct prediction when involving such kind of new candidates.
Results: We present a simple procedure called neighbor-based interaction-profile inferring (NII) and integrate it into the existing BLM method to handle the new candidate problem. Specifically, the inferred interaction profile is treated as label information and is used for model learning of new candidates. This functionality is particularly important in practice to find targets for new drug-candidate compounds and identify targeting drugs for new target-candidate proteins. Consistent good performance of the new BLM–NII approach has been observed in the experiment for the prediction of interactions between drugs and four categories of target proteins. Especially for nuclear receptors, BLM–NII achieves the most significant improvement as this dataset contains many drugs/targets with no interactions in the cross-validation. This demonstrates the effectiveness of the NII strategy and also shows the great potential of BLM–NII for prediction of compound–protein interactions.
Contact: jpmei@ntu.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
DoseSim: a tool for pharmacokinetic/pharmacodynamic analysis and dose reconstruction
Authors: Reisfeld Brad , Ivy Jaime H. , Lyons Michael A. , Wright Jesse M. , Rogers Justin L. , Mayeno Arthur N. 
Published: November 2012

Abstract
Summary: Assessing and improving the safety of chemicals and the efficacy of drugs depends on an understanding of the biodistribution, clearance and biological effects of the chemical(s) of interest. A promising methodology for the prediction of these phenomena is physiologically based pharmacokinetic/pharmacodynamic modeling, which centers on the prediction of chemical absorption, distribution, metabolism and excretion (pharmacokinetics) and the biological effects (pharmacodynamics) of the chemical on the organism. Strengths of this methodology include modeling across multiple scales of biological organization and facilitate the extrapolation of results across routes of exposure, dosing levels and species. It is also useful as the foundation for tools to (i) predict biomarker levels (concentrations of chemical species found in the body that indicate exposure to a foreign chemical), given a chemical dose or exposure; (ii) reconstruct a dose, given the levels of relevant biomarkers; and (iii) estimate population variability. Despite the importance and promise of physiologically based pharmacokinetic /pharmacodynamics-based approaches to forward and reverse dosimetry, there is currently a lack of user-friendly, freely available implementations that are accessible and useful to a broad range of users. DoseSim was developed to begin to fill this gap.
Availability: The application is available under the GNU General Public License from http://scb.colostate.edu/dosesim.html.
Contact: brad.reisfeld@colostate.edu
mzMatch–ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data
Authors: Chokkathukalam Achuthanunni , Jankevics Andris , Creek Darren J. , Achcar Fiona , Barrett Michael P. , Breitling Rainer 
Published: November 2012

Abstract
Motivation: Stable isotope-labelling experiments have recently gained increasing popularity in metabolomics studies, providing unique insights into the dynamics of metabolic fluxes, beyond the steady-state information gathered by routine mass spectrometry. However, most liquid chromatography–mass spectrometry data analysis software lacks features that enable automated annotation and relative quantification of labelled metabolite peaks. Here, we describe mzMatch–ISO, a new extension to the metabolomics analysis pipeline mzMatch.R.
Results: Targeted and untargeted isotope profiling using mzMatch–ISO provides a convenient visual summary of the quality and quantity of labelling for every metabolite through four types of diagnostic plots that show (i) the chromatograms of the isotope peaks of each compound in each sample group; (ii) the ratio of mono-isotopic and labelled peaks indicating the fraction of labelling; (iii) the average peak area of mono-isotopic and labelled peaks in each sample group; and (iv) the trend in the relative amount of labelling in a predetermined isotopomer. To aid further statistical analyses, the values used for generating these plots are also provided as a tab-delimited file. We demonstrate the power and versatility of mzMatch–ISO by analysing a 13C-labelled metabolome dataset from trypanosomal parasites.
Availability: mzMatch.R and mzMatch–ISO are available free of charge from http://mzmatch.sourceforge.net and can be used on Linux and Windows platforms running the latest version of R.
Contact: rainer.breitling@manchester.ac.uk .
Supplementary information: Supplementary data are available at Bioinformatics online
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads
Authors: Campagna Davide , Telatin Andrea , Forcato Claudio , Vitulo Nicola , Valle Giorgio 
Published: November 2012

Abstract
Summary: The sequencing of bisulfite-treated DNA (Bi-Seq) is becoming a gold standard for methylation studies. The mapping of Bi-Seq reads is complex and requires special alignment algorithms. This problem is particularly relevant for SOLiD color space, where the bisulfite conversion C/T changes two adjacent colors into 16 possible combinations. Here, we present an algorithm that efficiently aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands.
Availability and implementation: The algorithm has been implemented as an option of the program PASS, freely available at http://pass.cribi.unipd.it.
Contact: pass@cribi.unipd.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Age determination of Atlantic halibut (Hippoglossus hippoglossus L.) along the coast of Norway: status and improvements
Authors: Karlson Stine , Michalsen Kathrine , Folkvord Arild 
Published: November 2012

Abstract
Karlson, S., Michalsen, K., and Folkvord, A. 2013. Age determination of Atlantic halibut (Hippoglossus hippoglossus L.) along the coast of Norway: status and improvements. – ICES Journal of Marine Science, 70:50–55. This study re-evaluates the current ageing methodology for the Atlantic halibut, Hippoglossus hippoglossus. The traditional method is through surface readings of otoliths, but, based on new experiments with different preparation treatments and techniques, a more accurate and cost-efficient procedure for the age determination of Atlantic halibut is proposed.
Prognostic Significance of Blood Lactate and Lactate Clearance in Trauma Patients
Authors: Régnier Marie-Alix , Raux Mathieu , Le Manach Yannick , Asencio Yves , Gaillard Johann , Devilliers Catherine , Langeron Olivier , Riou Bruno 
Published: November 2012

Background
Lactate has been shown to be a prognostic biomarker in trauma. Although lactate clearance has already been proposed as an intermediate endpoint in randomized trials, its precise role in trauma patients remains to be determined.

Methods
Blood lactate levels and lactate clearance (LC) were calculated at admission and 2 and 4 h later in trauma patients. The association of initial blood lactate level and lactate clearance with mortality was tested using receiver-operating characteristics curve, logistic regression using triage scores, Trauma Related Injury Severity Score as a reference standard, and reclassification method.

Results
The authors evaluated 586 trauma patients (mean age 38±16 yr, 84% blunt and 16% penetrating, mortality 13%). Blood lactate levels at admission were elevated in 327 (56%) patients. The lactate clearance should be calculated within the first 2 h after admission as LC0-2 h was correlated with LC0-4 h (R=0.55, P<0.001) but not with LC2-4 h (R=0.04, not significant). The lactate clearance provides additional predictive information to initial blood lactate levels and triage scores and the reference score. This additional information may be summarized using a categorical approach (i.e., less than or equal to -20 %/h) in contrast to initial blood lactate. The results were comparable in patients with high (5 mM/l or more) initial blood lactate.

Conclusions
Early (0-2 h) lactate clearance is an important and independent prognostic variable that should probably be incorporated in future decision schemes for the resuscitation of trauma patients.
Asymmetric Facet Joint Osteoarthritis and Its Relationships to Facet Orientation, Facet Tropism, and Ligamentum Flavum Thickening
Authors: Liu Hai-xiao , Shen Yue , Shang Ping , Ma Yan-xu , Cheng Xiao-jie , Xu Hua-zi 
Published: November 2012

Study Design:
The degrees of osteoarthritis of the left and right facet joints were evaluated by using computerized tomography among elderly patients with low back or leg pain.

Objective:
To reveal the phenomenon of asymmetry regarding facet joint osteoarthritis (FJOA) in old patients and establish its relationships to spinal level, facet orientation, facet tropism and ligamentum flavum (LF) thickening.

Summary of Background Data:
There were few reports regarding left-right asymmetry among severity of FJOA and its relationships to spinal level, facet orientation, facet tropism, and LF thickening remained unclear.

Methods:
The grade of bilateral FJOA was evaluated using 4-grade scale on computerized tomography images at the L3–4, L4–5, and L5–S1 levels of patients with age ranging from 60 to 80 years. All subjects were divided into 2 groups: symmetric FJOA group (FJOA I–II on both sides or FJOA III–IV on both sides) and asymmetric FJOA group (FJOA I–II on one side and FJOA III–IV on the other side). The relationships of FJOA to spinal level, facet orientation, facet tropism, and LF hypertrophy were evaluated.

Results:
No association between asymmetric FJOA and spinal level was noted (P>0.05). In asymmetric FJOA group, significant difference in facet orientation between 2 sides was observed at the L4–5 (P=0.018) and L5–S1 levels (P=0.033). Compared with symmetric FJOA, asymmetric FJOA showed significant difference in prevalence of facet tropism at the L5–S1 level (P<0.001). The LF showed significantly thicker on the side of FJOA III–IV than the side of FJOA I–II at each level in asymmetric FJOA group (P<0.05). However, no difference was found in thickness between 2 sides in symmetric FJOA group (P>0.05).

Conclusions:
Asymmetric FJOA is associated with facet orientation and tropism, but not with spinal level. There is a close relationship between severity of FJOA and LF thickness.
Hybrid Decompression and Fixation Technique Versus Plated 3-Vertebra Corpectomy for 4-Segment Cervical Myelopathy
Authors: Odate Seiichi , Shikata Jitsuhiko , Kimura Hiroaki , Soeda Tsunemitsu 
Published: November 2012

Study Design:
A retrospective comparative study.

Objective:
The purpose of this study was to compare the stability and outcomes of a hybrid technique with those of a 3-vertebra corpectomy in the management of 4-segment cervical myelopathy.

Summary of Background Data:
Patients with primarily ventral disease and loss of cervical lordosis are considered good candidates for anterior surgery. Cervical corpectomy is commonly performed in patients with multilevel cervical myelopathy. Corpectomies including >3 vertebraes entail an extremely high risk of reconstruction failure. To avoid the need to perform a 3-vertebra corpectomy, we use a hybrid decompression and fixation technique. This hybrid technique is a technique to obtain optimum decompression and fixation in patients with multilevel cervical myelopathy.

Methods:
A total of 81 patients with multilevel cervical myelopathy who underwent 4-segment cervical fixation with a minimum 2-year follow-up were included.

Results:
The hybrid technique involved combining a plated 2-vertebra corpectomy and single-level discectomy with stand-alone cage fixation. This technique was performed in 39 patients, and the plated 3-vertebra corpectomy was performed in 42 patients. Nine patients (21%) who underwent the plated 3-vertebra corpectomy were treated with halo immobilization, but no patient in the hybrid group required this treatment (P=0.002). There were fewer instances of reconstruction failure in the hybrid group than in the 3-vertebra corpectomy group (0% vs. 10%, respectively; P=0.048) and fewer instances of C5 palsy (3% vs. 17%, respectively; P <0.0001). The incidence of postoperative C5 palsy was 25% for C3–C5 corpectomy, 19% for C4–C6 corpectomy, and 11% for C4–C5 corpectomy+C6–C7 discectomy.

Conclusions:
The hybrid technique has the following advantages over 3-vertebra corpectomy for 4-segment cervical fixation: a shorter graft bone and plate are required; the fixed segment has greater initial stability; postoperative external immobilization is simplified; and the risk of reconstruction failure and postoperative C5 palsy is reduced markedly.
Two-Year Evaluation of the X-STOP Interspinous Spacer in Different Primary Patient Populations With Neurogenic Intermittent Claudication Because of Lumbar Spinal Stenosis
Authors: Hartjen Charles A. , Resnick Daniel K. , Hsu Ken Y. , Zucherman James F. , Hsu Emily H. , Skidmore Grant A. 
Published: November 2012

Study Design:
Multicenter, prospective single-arm study in patients diagnosed with neurogenic intermittent claudication because of lumbar spinal stenosis.

Objective:
To collect data from 2 different primary patient populations, new participants meeting entry criteria [Continued Access Program (CAP)], or subjects who had been randomly assigned to nonsurgical management in the pivotal Investigational Device Exemption study and failed to respond upon study completion [Crossover Study (COS)].

Summary of Background Data:
The X-STOP interspinous spacer is a minimally invasive treatment option for neurogenic intermittent claudication shown to improve pain, physical functioning, and/or overall quality of life.

Methods:
Fifty-five subjects were enrolled, 42 in CAP and 13 in COS. Zurich Claudication Questionnaire (ZCQ) success rates were obtained based on the number of subjects achieving a threshold level of success. Mean SF-36 domain scores were compared with baseline using repeated measures analysis of variance.

Results:
Eighty percent of subjects completed the study. At 2 years, 26/43 subjects (60.5%) achieved clinically significant improvement in the Symptom Severity domain, 25/43 (58.1%) achieved clinically significant improvement in the Physical Function domain, and 31/44 (70.5%) achieved clinically significant improvement in the Patient Satisfaction domain of the ZCQ. Statistically significant improvement in mean scores was obtained in all physical domains of the SF-36 (with the exception of General Health) at 24 months. Mean improvement in ZCQ and SF-36 scores was not as pronounced in the COS cohort compared with the CAP cohort. The most frequently reported device-related or treatment-related adverse event was stenosis pain reported by 3 subjects.

Conclusions:
Overall data are consistent with the randomized pivotal Investigational Device Exemption trial. On the basis of the COS cohort which was subject to several additional years of failed conservative treatment, overall success rates do not improve as greatly in patients with long-standing lumbar spinal stenosis symptoms.
Camptocormia Due to Inclusion Body Myositis
Authors: Goodman Brent P. , Liewluck Teerin , Crum Brian A. , Spinner Robert J. 
Published: November 2012

Abstract
Inclusion body myositis is the most common idiopathic inflammatory myopathy in elderly individuals. It typically causes proximal and distal limb weakness with forearm flexors and quadriceps being the most severely affected muscles. Axial musculature is infrequently involved. Here, we report an 80-year-old man who presented with an 18-month history of progressive truncal weakness causing stooped posture while standing and walking. Neurologic examination revealed no limb weakness. magnetic resonance imaging studies showed atrophy and findings, suggesting fatty replacement of paraspinal muscles. Needle electromyography confirmed the presence of an axial myopathy. Thoracic paraspinal muscle biopsy showed canonical features of inclusion body myositis. The current patient broadens the clinical presentation of inclusion body myositis.