bluuebunny/crossref_metadata_2025_split huggingface dataset:
COMPADRE: an R and web resource for pathway activity analysis by component decompositions
Authors: Ramos-Rodriguez Roberto-Rafael , Cuevas-Diaz-Duran Raquel , Falciani Francesco , Tamez-Peña Jose-Gerardo , Trevino Victor 
Published: August 2012

Abstract
Summary: The analysis of biological networks has become essential to study functional genomic data. Compadre is a tool to estimate pathway/gene sets activity indexes using sub-matrix decompositions for biological networks analyses. The Compadre pipeline also includes one of the direct uses of activity indexes to detect altered gene sets. For this, the gene expression sub-matrix of a gene set is decomposed into components, which are used to test differences between groups of samples. This procedure is performed with and without differentially expressed genes to decrease false calls. During this process, Compadre also performs an over-representation test. Compadre already implements four decomposition methods [principal component analysis (PCA), Isomaps, independent component analysis (ICA) and non-negative matrix factorization (NMF)], six statistical tests (t- and f-test, SAM, Kruskal–Wallis, Welch and Brown–Forsythe), several gene sets (KEGG, BioCarta, Reactome, GO and MsigDB) and can be easily expanded. Our simulation results shown in Supplementary Information suggest that Compadre detects more pathways than over-representation tools like David, Babelomics and Webgestalt and less false positives than PLAGE. The output is composed of results from decomposition and over-representation analyses providing a more complete biological picture. Examples provided in Supplementary Information show the utility, versatility and simplicity of Compadre for analyses of biological networks.
Availability and implementation: Compadre is freely available at http://bioinformatica.mty.itesm.mx:8080/compadre. The R package is also available at https://sourceforge.net/p/compadre.
Contact: vtrevino@itesm.mx
Supplementary information: Supplementary Data are available at Bioinformatics online
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line
Authors: Hill Steven M. , Lu Yiling , Molina Jennifer , Heiser Laura M. , Spellman Paul T. , Speed Terence P. , Gray Joe W. , Mills Gordon B. , Mukherjee Sach 
Published: August 2012

AbstractMotivation: Protein signaling networks play a key role in cellular function, and their dysregulation is central to many diseases, including cancer. To shed light on signaling network topology in specific contexts, such as cancer, requires interrogation of multiple proteins through time and statistical approaches to make inferences regarding network structure.Results: In this study, we use dynamic Bayesian networks to make inferences regarding network structure and thereby generate testable hypotheses. We incorporate existing biology using informative network priors, weighted objectively by an empirical Bayes approach, and exploit a connection between variable selection and network inference to enable exact calculation of posterior probabilities of interest. The approach is computationally efficient and essentially free of user-set tuning parameters. Results on data where the true, underlying network is known place the approach favorably relative to existing approaches. We apply these methods to reverse-phase protein array time-course data from a breast cancer cell line (MDA-MB-468) to predict signaling links that we independently validate using targeted inhibition. The methods proposed offer a general approach by which to elucidate molecular networks specific to biological context, including, but not limited to, human cancers.Availability: http://mukherjeelab.nki.nl/DBN (code and data).Contact: s.hill@nki.nl; gmills@mdanderson.org; s.mukherjee@nki.nlSupplementary information: Supplementary data are available at Bioinformatics online.
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
Authors: Feng Jianxing , Meyer Clifford A. , Wang Qian , Liu Jun S. , Shirley Liu X. , Zhang Yong 
Published: August 2012

Abstract
Motivation: RNA-seq has been widely used in transcriptome analysis to effectively measure gene expression levels. Although sequencing costs are rapidly decreasing, almost 70% of all the human RNA-seq samples in the gene expression omnibus do not have biological replicates and more unreplicated RNA-seq data were published than replicated RNA-seq data in 2011. Despite the large amount of single replicate studies, there is currently no satisfactory method for detecting differentially expressed genes when only a single biological replicate is available.
Results: We present the GFOLD (generalized fold change) algorithm to produce biologically meaningful rankings of differentially expressed genes from RNA-seq data. GFOLD assigns reliable statistics for expression changes based on the posterior distribution of log fold change. In this way, GFOLD overcomes the shortcomings of P-value and fold change calculated by existing RNA-seq analysis methods and gives more stable and biological meaningful gene rankings when only a single biological replicate is available.
Availability: The open source C/C++ program is available at http://www.tongji.edu.cn/∼zhanglab/GFOLD/index.html
Contact: xsliu@jimmy.harvard.edu or yzhang@tongji.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
The GlycomeAtlas tool for visualizing and querying glycome data
Authors: Konishi Yoshitsugu , Aoki-Kinoshita Kiyoko F. 
Published: August 2012

Abstract
Motivation: The development of glycomics technologies in recent years has produced a sufficient amount of data to begin analyzing the glycan structures present in various organisms and tissues. In particular, glycan profiling using mass spectrometry (MS) and tandem MS has generated a large amount of data that are waiting to be analyzed. The Consortium for Functional Glycomics (CFG) has provided a web resource for obtaining such glycan profiling data easily. Although an interactive spectrum viewer is provided on the website as a Java applet, it is not necessarily easy to search for particular glycans or to find commonalities between different tissues in a single organism, for example. Therefore, to allow users to better take advantage of the valuable glycome data that can be obtained from mass spectra and other leading technologies, we have developed a tool called Glycome Atlas which is pre-loaded with the data from the CFG and is also able to visualize local glycan profiling data for human and mouse.
Results: We have developed a tool to allow users to visualize and perform queries of glycome data. This tool, called GlycomeAtlas, is pre-loaded with glycome data as provided by the CFG. Moreover, users can load their own local glycome data into this tool to visualize and perform queries on their own data.
Availability: This tool is available at the following URL: http://www.rings.t.soka.ac.jp/GlycomeAtlas/GUI.html.
Contact: kkiyoko@soka.ac.jp
Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone
Authors: Kumar Sudhir , Boccia Kelly , McCutchan Michael , Ye Jieping 
Published: August 2012

Abstract
Mobile technologies provide unique opportunities for ubiquitous distribution of scientific information through user-friendly interfaces. Therefore, we have developed a new FlyExpress mobile application that makes available a growing collection (&gt;100 000) of standardized in situ hybridization images containing spatial patterns of gene expression from Drosophila melanogaster (fruit fly) embryogenesis. Using this application, scientists can visualize and compare expression patterns of &gt;4000 developmentally relevant genes. The FlyExpress app displays the expression patterns of the selected gene for different visual projections (e.g. lateral) and displays them according to their developmental stages, which shows a gene’s progression of spatial expression over developmental time. Ultimately, we envision the use of FlyExpress app in the laboratory where scientists may wish to immediately conduct a visual comparison of a known expression pattern with the one observed on the bench top or to display expression patterns of interest during scientific discussions at large.
Availability: Search “FlyExpress” on the Apple iTunes store
Contact: s.kumar@asu.edu
HiTC: exploration of high-throughput ‘C’ experiments
Authors: Servant Nicolas , Lajoie Bryan R. , Nora Elphège P. , Giorgetti Luca , Chen Chong-Jian , Heard Edith , Dekker Job , Barillot Emmanuel 
Published: August 2012

Abstract
Summary: The R/Bioconductor package HiTC facilitates the exploration of high-throughput 3C-based data. It allows users to import and export ‘C’ data, to transform, normalize, annotate and visualize interaction maps. The package operates within the Bioconductor framework and thus offers new opportunities for future development in this field.
Availability and implementation: The R package HiTC is available from the Bioconductor website. A detailed vignette provides additional documentation and help for using the package.
Contact: nicolas.servant@curie.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Comparison of Expandable and Fixed Interbody Cages in a Human Cadaver Corpectomy Model
Authors: Pekmezci Murat , Tang Jessica A. , Cheng Liu , Modak Ashin , McClellan Robert T. , Buckley Jenni M. , Ames Christopher P. 
Published: August 2012

Study Design:
In vitro cadaver biomechanics study.

Objective:
The goal of this study is to compare the in situ fatigue life of expandable versus fixed interbody cage designs.

Summary of Background Data:
Expandable cages are becoming more popular, in large part, due to their versatility; however, subsidence and catastrophic failure remain a concern. This in vitro analysis investigates the fatigue life of expandable and fixed interbody cages in a single level human cadaver corpectomy model by evaluating modes of subsidence of expandable and fixed cages as well as change in stiffness of the constructs with cyclic loading.

Methods:
Nineteen specimens from 10 human thoracolumbar spines (T10-L2, L3-L5) were biomechanically evaluated after a single level corpectomy that was reconstructed with an expandable or fixed cage and anterior dual rod instrumentation. All specimens underwent 98 K cycles to simulate 3 months of postoperative weight bearing. In addition, a third group with hyperlordotic cages was used to simulate catastrophic failure that is observed in clinical practice.

Results:
Three fixed and 2 expandable cages withstood the cyclic loading despite perfect sagittal and coronal plane fitting of the endcaps. The majority of the constructs settled in after initial subsidence. The catastrophic failures that were observed in clinical practice could not be reproduced with hyperlordotic cages. However, all cages in this group subsided, and 60% resulted in endplate fractures during deployment of the cage.

Conclusions:
Despite greater surface contact area, expandable cages have a trend for higher subsidence rates when compared with fixed cages. When there is edge loading as in the hyperlordotic cage scenario, there is a higher risk of subsidence and intraoperative fracture during deployment of expandable cages.
A camera trap assessment of terrestrial vertebrates in Bwindi Impenetrable National Park, Uganda
Authors: Mugerwa Badru , Sheil Douglas , Ssekiranda Peter , van Heist Miriam , Ezuma Pontious 
Published: August 2012

AbstractWe placed camera traps for a month at sixty locations in Bwindi Impenetrable National Park to determine the species composition and distribution of medium‐to‐large terrestrial vertebrates. A total of 15912 images were recorded from 1800 camera trap days. These provided a total of 625 and 338 camera events when filtered by hour and day, respectively. Twenty mammal species were recorded from 594 and 314 camera events by hour and day, respectively. Four bird species were recorded from 31 and 24 camera events by hour and day, respectively. The African golden cat Profelis aurata Temminck was recorded from 27 and nineteen camera events by hour and day, respectively. The black‐fronted duiker Cephalophus nigrifrons Gray was most frequently photographed with 179 and 65 camera events by hour and day, respectively. Analyses reveal two species possessed a significantly interior‐biased distribution. One species showed an edge‐biased pattern. Five species were detected to have significantly biased altitudinal distributions with higher elevations. Distance to park edge and elevation can significantly influence species distribution. The selective use of the park limits the area that each species utilizes, with implications for maximum population sizes and viability. Our observations provide a baseline for long‐term terrestrial vertebrate monitoring in Bwindi.
Structural diversity and regeneration of the endangered Prunus africana (Rosaceae) in Zimbabwe
Authors: Jimu Luke , Ngoroyemoto Nelson , Mujuru Lizzie 
Published: August 2012

AbstractPrunus africana is endemic to Africa and was included in Appendix II of the Convention on International Trade in Endangered Species (CITES) in 1995. In Zimbabwe, the species was reported to be rare and confined to the Eastern Highlands. The objective of this study was to assess size–class distribution and regeneration levels and to characterize structural diversity of P. africana. Given the clustered nature of the species, adaptive cluster sampling was used based on the assumption that there were more P. africana trees in the neighbourhood of reference trees. Each cluster was terminated when there were no more P. africana trees within a distance of 500 m. Data on diameter and height were collected in each cluster using standard forestry procedures. Regeneration was determined by counting seedlings and saplings within a radial distance of 14 m from the mother tree. Structural indices, that ie, diameter and height differentiation and mingling were determined for a structural group of four trees. Findings from this study indicated poor regeneration, fewer P. africana trees in small and large size classes, dominance of positive height and diameter differentiation and high mingling. These findings have implications on management and conservation of P. africana in Zimbabwe.
The use of morphological descriptors to study variability in wild populations of Capparis spinosa L. (Capparaceae) in Tunisia
Authors: Awatef Rhimi , Hédia Hannachi , Sonia Hjaoujia , Mohamed Boussaid 
Published: August 2012

AbstractCapparis spinosa L. is a perennial shrub and drought‐resistant plant and is well adapted to Mediterranean Ecosystem. Seventeen populations of caper, belonging to different bioclimatic zones, were assessed by morphological descriptors including nine parameters of seed (seed colour, major, medium and minor axial dimension, thousand seed mass, arithmetic mean diameter, geometric mean diameter, surface area and sphericity). The data underwent an analysis of variance, principal coordinate's analysis (PCO) and hierarchical classification analysis (HCA). Results showed that the dimensions of the major, medium and minor axes varied from 2.79 to 3.94 mm, 2.30 to 3.17 mm and 1.66 to 2.36 mm, respectively. The arithmetic and geometric mean diameters ranged, respectively, from 2.66 to 3.16 mm and from 2.19 to 3.05 mm. The sphericity and surface area ranged from 0.38 to 0.40 and from 1.20 to 1.24 mm2, respectively. The thousand seed mass varied from 4.71 to 12.05 g. The analysis of variance of studied descriptors showed significant differences according to the population. Both PCO and HCA generated from Gower general similarity coefficient among all populations showed two distinct clusters each corresponding to one subspecies. Grouping of populations did not reflect bioclimatic patterns, indicating specific adaptation of population to local environments. The divergence between the two caper subspecies (C. spinosa subsp. spinosa and C. spinosa subsp. rupestris), based on morphological traits, corroborates their taxonomic status.
Increased risk of arterial thromboembolism after a prior episode of venous thromboembolism: results from the Prevention of REnal and Vascular ENd stage Disease (PREVEND) Study
Authors: van Schouwenburg Inge M. , Gansevoort Ron T. , Mahmoodi Bakhtawar K. , Visser Margaretha M. , Kluin‐Nelemans Hanneke C. , Lijfering Willem M. , Veeger Nic J. G. M. 
Published: August 2012

SummaryLarge population‐based studies are needed to establish the magnitude and duration of the recently suggested association between arterial and venous thromboembolism. In 1997–98, all inhabitants of Groningen, the Netherlands, aged 28–75 years (n = 85 421), were invited to participate in a study that followed and monitored responding subjects (n = 40 856) for venous and arterial thromboembolism until 2009. Thromboembolism was verified with national registries of hospital discharge diagnoses and death certificates, anticoagulation clinic and medical records. During a median follow‐up of 10·7 years, 549 participants developed venous thromboembolism and 3283 developed arterial thromboembolism. Annual incidence of arterial thromboembolism after venous thromboembolism was 2·03% [95% confidence interval (CI), 1·48–2·71], compared to 0·87% (95% CI, 0·84–0·90) in subjects without venous thromboembolism. The hazard ratio (HR) of arterial thromboembolism after venous thromboembolism was 1·40 (95% CI, 1·04–1·88) after adjustment for age, sex and cardiovascular risk factors. This risk was highest during the first year after venous thromboembolism [annual incidence, 3·00% (95% CI, 1·64–5·04); adjusted HR, 2·01 (95% CI, 1·19–3·40)] and after an unprovoked event [annual incidence, 2·53% (95% CI, 1·68–3·66); adjusted HR, 1·62 (95% CI, 1·11–2·34)]. This study showed that subjects with venous thromboembolism are at increased risk for arterial thromboembolism, particularly in the first year after venous thromboembolism and after an unprovoked event.
Risk of coronary artery disease is not linked to head and neck cancers: a population‐based retrospective cohort study
Authors: Sun L.‐M. , Liang J.‐A. , Chang S.‐N. , Sung F.‐C. , Muo C.‐H. , Kao C.‐H. 
Published: August 2012

Clin. Otolaryngol. 2012, 37, 369–375Objectives:  To explore the possible association between the risk of coronary artery disease and head or neck cancer based on some possible shared risk factors and/or treatment‐related complications.Design and setting:  A population‐based retrospective cohort study.Participants:  All new 729 patients with head and neck cancer diagnosed between 2000 and 2003 were followed up till 2009, and the risk of subsequent coronary artery disease was calculated. For each patient, the risk was calculated in 4 age‐and sex‐matched population controls. Matching was not possible for factors including socio‐economic group and smoking.Main outcome measures:  Cox’s proportional hazard regression analysis was conducted to estimate the relationship between head or neck cancer and risk of coronary artery disease.Results:  For patients with head or neck cancer, the overall risk for developing coronary artery disease was almost the same as that of the control group [adjusted hazard ratio (but without control for some lifestyle factors): 0.95; 95% confidence interval: 0.65–1.35]. Overall, we found no increased risk of coronary artery disease for patients with head or neck cancer when the data were categorised either by treatment methods or by cancer subsites.Conclusions:  This population‐based study indicated that patients with head or neck cancer were at no higher risk of developing coronary artery disease than was the general population over a 6‐ to 9‐year period; however, we cannot exclude the risk over a longer period of time.
Edge artefacts and lost performance in national versus continental conservation priority areas
Authors: Moilanen Atte , Anderson Barbara J. , Arponen Anni , Pouzols Federico M. , Thomas Chris D. 
Published: August 2012

AbstractAimGlobal conservation policies, such as the Convention on Biological Diversity (CBD) decision to aim for the protection of 17% of the area of terrestrial ecosystems by 2020, are typically realized at national levels. We investigate the difference between continentally coordinated conservation versus nationally devolved conservation, in a manner relevant for the Nagoya resolution.LocationThe terrestrial areas of the Western Hemisphere.MethodsWe used IUCN distribution data for 8463 species of mammals, birds and amphibians in the Western Hemisphere. We investigated the consequences of prioritizing land at a continental scale, versus analysing priorities within each country separately. Spatial prioritization was performed using the Zonation software, which produces a complementarity‐based hierarchical priority ranking across the area of interest.ResultsWe found that coordinated continent‐wide priorities achieved > 50% higher mean protection levels than national analyses for the top 17% of land. National prioritizations also result in spatial priority patterns that can be considered as artefacts at the continental scale: in bands of high‐priority land concentrated at terrestrial political boundaries, such as at low‐latitude edges of temperate zone countries. We find that this edge artefact also correlates with the present distribution of conservation areas, with the density of conservation areas within 50 km of a national border being > 50% higher than the density of conservation areas away from national borders.Main conclusionsThe means by which national priorities are integrated with continental or global conservation prioritization will have considerable influence on how much is achieved by the CBD resolution. Focus on national species distributions and priorities will result in lost performance because of emphasis on nationally rare species that are comparatively common elsewhere. National borders intersect species distributions (and possibly diversity gradients), leading to clustering of nationally rare species and priority areas close to the border.
Isotopic trophic guild structure of a diverse subtropical South American fish community
Authors: Burress Edward D. , Duarte Alejandro , Gangloff Michael M. , Siefferman Lynn 
Published: August 2012

AbstractCharacterization of food web structure may provide key insights into ecological function, community or population dynamics and evolutionary forces in aquatic ecosystems. We measured stable isotope ratios of 23 fish species from the Rio Cuareim, a fifth‐order tributary of the Rio Uruguay basin, a major drainage of subtropical South America. Our goals were to (i) describe the food web structure, (ii) compare trophic segregation at trophic guild and taxonomic scales and (iii) estimate the relative importance of basal resources supporting fish biomass. Although community‐level isotopic overlap was high, trophic guilds and taxonomic groups can be clearly differentiated using stable isotope ratios. Omnivore and herbivore guilds display a broader δ13C range than insectivore or piscivore guilds. The food chain consists of approximately three trophic levels, and most fishes are supported by algal carbon. Understanding food web structure may be important for future conservation programs in subtropical river systems by identifying top predators, taxa that may occupy unique trophic roles and taxa that directly engage basal resources.