bluuebunny/crossref_metadata_2025_split huggingface dataset:
PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data
Authors: Larson Nicholas B. , Fridley Brooke L. 
Published: June 2013

Abstract
Summary: We have developed a novel Bayesian method, PurBayes, to estimate tumor purity and detect intratumor heterogeneity based on next-generation sequencing data of paired tumor-normal tissue samples, which uses finite mixture modeling methods. We demonstrate our approach using simulated data and discuss its performance under varying conditions.
Availability: PurBayes is implemented as an R package, and source code is available for download through CRAN at http://cran.r-project.org/package=PurBayes.
Contact: larson.nicholas@mayo.edu
Supplementary information: Supplementary data are available online at Bioinformatics online.
SVGenes: a library for rendering genomic features in scalable vector graphic format
Authors: Etherington Graham J. , MacLean Daniel 
Published: June 2013

Abstract
Motivation: Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data. Scalable Vector Graphics (SVG) format is a modern and flexible open standard that provides advanced features including modular graphic design, advanced web interactivity and animation within a suitable client. SVGs do not suffer from loss of image quality on re-scaling and provide the ability to edit individual elements of a graphic on the whole object level independent of the whole image. These features make SVG a potentially useful format for the preparation of publication quality figures including genomic objects such as genes or sequencing coverage and for web applications that require rich user-interaction with the graphical elements.
Results: SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface. The library implements a simple Page object that spaces and contains horizontal Track objects that in turn style, colour and positions features within them. Tracks are the level at which visual information is supplied providing the full styling capability of the SVG standard. Genomic entities like genes, transcripts and histograms are modelled in Glyph objects that are attached to a track and take advantage of SVG primitives to render the genomic features in a track as any of a selection of defined glyphs. The feature model within SVGenes is simple but flexible and not dependent on particular existing gene feature formats meaning graphics for any existing datasets can easily be created without need for conversion.
Availability: The library is provided as a Ruby Gem from https://rubygems.org/gems/bio-svgenes under the MIT license, and open source code is available at https://github.com/danmaclean/bioruby-svgenes also under the MIT License.
Contact: dan.maclean@tsl.ac.uk
Network2Canvas: network visualization on a canvas with enrichment analysis
Authors: Tan Christopher M. , Chen Edward Y. , Dannenfelser Ruth , Clark Neil R. , Ma’ayan Avi 
Published: June 2013

Abstract
Motivation: Networks are vital to computational systems biology research, but visualizing them is a challenge. For networks larger than ∼100 nodes and ∼200 links, ball-and-stick diagrams fail to convey much information. To address this, we developed Network2Canvas (N2C), a web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas. The network nodes are clustered on the canvas using simulated annealing to maximize local connections where a node’s brightness is made proportional to its local fitness. The interactive canvas is implemented in HyperText Markup Language (HTML)5 with the JavaScript library Data-Driven Documents (D3). We applied N2C to visualize 30 canvases made from human and mouse gene-set libraries and 6 canvases made from the Food and Drug Administration (FDA)-approved drug-set libraries. Given lists of genes or drugs, enriched terms are highlighted on the canvases, and their degree of clustering is computed. Because N2C produces visual patterns of enriched terms on canvases, a trained eye can detect signatures instantly. In summary, N2C provides a new flexible method to visualize large networks and can be used to perform and visualize gene-set and drug-set enrichment analyses.
Availability: N2C is freely available at http://www.maayanlab.net/N2C and is open source.
Contact: avi.maayan@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
NOA: a cytoscape plugin for network ontology analysis
Authors: Zhang Chao , Wang Jiguang , Hanspers Kristina , Xu Dong , Chen Luonan , Pico Alexander R. 
Published: June 2013

Abstract
Summary: The Network Ontology Analysis (NOA) plugin for Cytoscape implements the NOA algorithm for network-based enrichment analysis, which extends Gene Ontology annotations to network links, or edges. The plugin facilitates the annotation and analysis of one or more networks in Cytoscape according to user-defined parameters. In addition to tables, the NOA plugin also presents results in the form of heatmaps and overview networks in Cytoscape, which can be exported for publication figures.
Availability: The NOA plugin is an open source, Java program for Cytoscape version 2.8 available via the Cytoscape App Store (http://apps.cytoscape.org/apps/noa) and plugin manager. A detailed user manual is available at http://nrnb.org/tools/noa.
Contact: apico@gladstone.ucsf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Characterization of AtSTOP1 Orthologous Genes in Tobacco and Other Plant Species
Authors: Ohyama Yoshinao , Ito Hiroki , Kobayashi Yuriko , Ikka Takashi , Morita Akio , Kobayashi Masatomo , Imaizumi Ryujiro , Aoki Toshio , Komatsu Kenji , Sakata Yoichi , Iuchi Satoshi , Koyama Hiroyuki 
Published: June 2013

Abstract
Aluminum (Al) and proton (H+) tolerances are essential traits for plants to adapt to acid soil environments. In Arabidopsis (Arabidopsis thaliana), these tolerances are mediated by a zinc-finger transcription factor, SENSITIVE TO PROTON RHIZOTOXICITY1 (AtSTOP1), which regulates the transcription of multiple genes critical for tolerance to both stressors. Here, the functions of orthologous proteins (STOP1-like proteins) in other plant species were characterized by reverse genetics analyses and in planta complementation assays. RNA interference of a gene for NtSTOP1 repressed Al and H+ tolerances of tobacco (Nicotiana tabacum) roots. Tobacco roots released citrate in response to Al, concomitant with the up-regulated transcription of an ortholog of an Al tolerance gene encoding a citrate-transporting multidrug and toxic compound extrusion protein. The RNA interference repression of NtSTOP1 blocked this process and also repressed the transcription of another orthologous gene for Al tolerance, ALUMINUM SENSITIVE3, which encodes a prokaryote-type transporter. These results demonstrated that NtSTOP1 regulates Al tolerance in tobacco through the transcriptional regulation of these genes. The in planta complementation assays revealed that other plant species, including woody plants, a legume, and a moss (Physcomitrella patens), possess functional STOP1-like proteins that can activate several H+ and Al-tolerance genes in Arabidopsis. Knocking out the gene encoding the STOP1-like protein decreased the Al tolerance of P. patens. Together, our results strongly suggest that transcriptional regulation by STOP1-like proteins is evolutionarily conserved among land plants and that it confers the ability to survive in acid soils through the transcriptional regulation of Al- and H+-tolerance genes.
Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales
Authors: Kleessen Sabrina , Klie Sebastian , Nikoloski Zoran 
Published: June 2013

Abstract
Plant behaviors across levels of cellular organization, from biochemical components to tissues and organs, relate and reflect growth habitats. Quantification of the relationship between behaviors captured in various phenotypic characteristics and growth habitats can help reveal molecular mechanisms of plant adaptation. The aim of this article is to introduce the power of using statistics originally developed in the field of geographic variability analysis together with prominent network models in elucidating principles of biological organization. We provide a critical systematic review of the existing statistical and network-based approaches that can be employed to determine patterns of covariation from both uni- and multivariate phenotypic characteristics in plants. We demonstrate that parameter-independent network-based approaches result in robust insights about phenotypic covariation. These insights can be quantified and tested by applying well-established statistics combining the network structure with the phenotypic characteristics. We show that the reviewed network-based approaches are applicable from the level of genes to the study of individuals in a population of Arabidopsis thaliana. Finally, we demonstrate that the patterns of covariation can be generalized to quantifiable biological principles of organization. Therefore, these network-based approaches facilitate not only interpretation of large-scale data sets, but also prediction of biochemical and biological behaviors based on measurable characteristics.
Multiscale measurement of cardiac energetics
Authors: Goo Soyeon , Pham Toan , Han Jun‐Chiew , Nielsen Poul , Taberner Andrew , Hickey Anthony , Loiselle Denis 
Published: June 2013

Summary

Herein we describe our laboratories' experimental methods for interrogating cardiac energetics at the organ (whole heart), tissue (trabecula) and perforated fibre (mitochondrial) levels.

In whole heart and trabecula experiments, we focus on measuring pressure–volume (force–length) work and oxygen consumption (heat production) from which mechanical efficiency is derived. In both preparations (i.e. across scales differing by three orders of magnitude) we find efficiency values of 10%–15%.

Mitochondrial experiments invoke a trio of titration protocols to yield information on oxygen consumption, ATP flux, membrane potential, electron leak and reactive oxygen species production, the latter two of which index energy transfer inefficiencies.
The effect of enriching milk‐based beverages with plant sterols or stanols on the fatty acid composition of the products
Authors: Garcia‐Llatas Guadalupe , Cilla Antonio , Higueras Laura , Pons María , Ripollés Susana , Bañuls Celia , Lagarda María Jesús 
Published: June 2013

Five plant sterol (PS)‐enriched dairy products from the Spanish market were characterised for fatty acids (FA), volatile compounds and lipid stability. The ingredients used for PS enrichment by the food industry may come from different sources, thus influencing the composition and stability of the lipid fraction. In this study, the FA profile proved highly variable among samples, not agreeing with the nutritional labelling of the products. The volatile profile was characterised. A total of 55 volatile compounds were identified in the samples by GC–MS. Concentrations of hexanal (from 1.1 to 7.5 ng/g), nonanal (from 0.9 to 1.2 ng/g) and decane (from n.d. to 11.9 ng/g) indicated a low lipid oxidation extent. Peroxide value, ranking between 0.7 and 3.2 meq of active oxygen per kilogram of fat, except sample with fish oil, where peroxide value was 7.7 meq of active oxygen per kilogram of fat, and thiobarbituric acid reactive species, from 2 to 21 μg malondialdehyde (MDA)/g of fat, were in the lower limits of the ranges found in the literature.
Interferon‐gamma release assays versus tuberculin skin testing in patients with rheumatoid arthritis
Authors: Song Gwan Gyu , Bae Sang‐Cheol , Lee Young Ho 
Published: June 2013

AbstractObjectiveThe aim of this study was to analyze the results of interferon‐gamma release assays (IGRAs) and tuberculin skin tests (TST) performed to detect latent tuberculosis infection (LTBI) in patients with rheumatoid arthritis (RA).MethodsInterferon‐γ release assays and TST test results were summarized and systematically reviewed.ResultsFour hundred and five RA patients and 339 controls that underwent IGRA and/or TST were identified in seven studies. Five studies were case‐control studies and two were cross‐sectional studies. Among RA patients, the IGRA positivity rate was 31.6% (89/282; range 11.4%–44.6%), and the TST positivity rate was 23.0% (78/339; range from 14.60% to 45%). Concordance rates ranged from 40% to 76% and discordance rates from 24% to 29.7%. Agreement between IGRAs and TST in RA was poor (69.6%, k = 0.33, 95% CI 0.188–0.478). The IGRA positivity rate was 31.0% in RA and 40.0% in controls, which was not significant (relative risk [RR] 0.802, 95% CI 0.629–1.023, P = 0.075). The TST positivity rate was 24.7% in RA and 50.5% in controls, and this difference was not significant (RR 0.680, 95% CI 0.331–1.339, P = 0.295).ConclusionsPositivity rates of IGRA and TST were 31.6 and 23.0%, respectively, in RA patients. Agreement between IGRA and TST results in RA was poor. Our data suggest that both IGRA and TST are needed to detect LTBI in RA.
Urbanization and poverty reduction: the role of rural diversification and secondary towns1
Authors: Christiaensen Luc , De Weerdt Joachim , Todo Yasuyuki 
Published: June 2013

AbstractA rather unique panel tracking more than 3,300 individuals from households in rural Kagera, Tanzania, during 1991/1994–2010 shows that about one out of two individuals/households who exited poverty did so by transitioning out of agriculture into the rural nonfarm economy or secondary towns. Only one out of seven exited poverty by migrating to the big cities, even though those moving to the city experienced on average faster consumption growth. Further analysis of a much larger cross‐country panel of 51 developing countries cannot reject that rural diversification and secondary town development lead to more inclusive growth patterns than metropolitization. Indications are that this follows because more of the poor find their way to the rural nonfarm economy and secondary towns, than to distant cities. The development discourse would benefit from shifting beyond the rural–urban dichotomy and focusing more instead on how best to urbanize and develop its rural nonfarm economy and secondary towns.
Nonfarm diversification, poverty, economic mobility, and income inequality: a case study in village India
Authors:   Himanshu, Lanjouw Peter , Murgai Rinku , Stern Nicholas 
Published: June 2013

AbstractThis article assembles data at the all‐India level and for the village of Palanpur, Uttar Pradesh, to document the growing importance, and influence, of the nonfarm sector in the rural economy between the early 1980s and late 2000s. The suggestion from the combined National Sample Survey and Palanpur data is of a slow process of nonfarm diversification, whose distributional incidence, on the margin, is increasingly pro‐poor. The village‐level analysis documents that the nonfarm sector is not only increasing incomes and reducing poverty, but appears as well to be breaking down long‐standing barriers to mobility among the poorest segments of rural society. Efforts by the government of India to accelerate the process of diversification could thus yield significant returns in terms of declining poverty and increased income mobility. The evidence from Palanpur also shows, however, that at the village‐level a significant increase in income inequality has accompanied diversification away from the farm. A growing literature argues that such a rise in inequality could affect the fabric of village society, the way in which village institutions function and evolve, and the scope for collective action at the village level. Failure to keep such inequalities in check could thus undermine the pro‐poor impacts from the process of structural transformation currently underway in rural India.
Consumer preferences for new technology: apples enriched with antioxidant coatings in Uzbekistan
Authors: Zaikin Andrey A. , McCluskey Jill J. 
Published: June 2013

AbstractFood markets in developing countries are experiencing an expansion of new functional products. Even though their market share is small, these food products are usually imported and post a higher price compared to local products. In this article, we investigate the consumer response toward new functional food products in Uzbekistan by focusing on the incorporation of apples enriched with antioxidant coating in the food market. We conduct consumer surveys with two different information treatments. We utilize a dichotomous‐choice contingent valuation methodology to estimate willingness to pay for this product and analyze factors that affect consumer choice. The results suggest that the average Uzbek respondent is willing to purchase functional apples with a 6% discount. The effect of information regarding the potential health benefits of antioxidants is positive and statistically significant. We compare the findings with a previous U.S. study of the same product and discuss how the delivery method provides an additional hurdle in the Uzbek market.
Sparkling wine choice from supermarket shelves: the impact of certification of origin and production practices
Authors: Thiene Mara , Scarpa Riccardo , Galletto Luigi , Boatto Vasco 
Published: June 2013

AbstractWe report the results of a study based on revealed and stated preference data on choice of Prosecco wines in retail stores close to the origin of production in Northern Italy. Emphasis is placed on ability to reconcile the utility structure of stated preference data with that underlying revealed preference data. We extend the analysis to cover nonattendance of key attributes, such as price and certification of origin, while controlling for the large range of brand effects.
The relationship between bone mass and body composition in children with hypothalamic and simple obesity
Authors: Shaikh M. Guftar , Crabtree Nicola , Kirk Jeremy M. W. , Shaw Nicholas J. 
Published: June 2013

SummaryIntroductionObesity has been associated with a positive influence on bone mass. This is thought to be due to a mechanical load exerted on the skeleton, together with various hormones and adipocytokines that control appetite and weight, such as leptin, some of which directly affect bone mass. However, there are conflicting reports of the association between fat mass and bone mass in children. Animal studies demonstrate increased bone mass where there is impaired central leptin signalling. Hypothalamic damage can cause abnormal central leptin action, which contributes to the development of obesity.ObjectiveThe objective of this study was to investigate the relationship between body composition and bone mass in hypothalamic and simple childhood obesity, in conjunction with the effect of the adipocytokines, leptin and adiponectin.DesignThis was a cross‐sectional study of three groups of children, those with hypothalamic obesity (HO), those with congenital hypopituitarism (CH) and those with simple obesity (SO).ResultsA total of 65 children (HO = 26 [11 males], CH = 17 [eight males] and SO = 22 [15 males]) had body composition assessed using dual‐energy X‐ray absorptiometry together with measurement of serum leptin and adiponectin. No significant differences were seen in bone mass once bone density (BMD) was adjusted for differences in body size between groups. Significantly elevated levels of leptin and adiponectin were seen in the HO group compared with the SO group (P < 0·01, P < 0·05, respectively).ConclusionAdiposity is associated with increased bone mass; however, this relationship is complex. Despite the presence of hyperleptinaemia, increased bone mass in the HO group was not seen. This may be due to the effects of other factors such as adiponectin, abnormal hypothalamic signalling, pituitary hormone deficiencies and disruption of normal homoeostatic mechanisms within the hypothalamus.
A ten‐year clinical update of a large RET p.Gly533Cys kindred with medullary thyroid carcinoma emphasizes the need for an individualized assessment of affected relatives
Authors: Signorini Priscila S. , França Maria Inez C. , Camacho Cleber P. , Lindsey Susan C. , Valente Flávia O. F. , Kasamatsu Teresa S. , Machado Alberto L. , Salim Camila P. , Delcelo Rosana , Hoff Ana O. , Cerutti Janete M. , Dias‐da‐Silva Magnus R. , Maciel Rui M. B. 
Published: June 2013

SummaryObjectiveReviewing the clinical outcomes of a large kindred with a RET p.Gly533Cys mutation, 10 years after the first description of this kindred, has provided an important set of clinical data for healthcare decision‐making.Design and PatientsWe identified 728 RET533 Brazilian relatives, spread out over 7 generations. We performed clinical examination, biochemical and imaging analyses in the proband and in 103 carriers.Measurement and ResultsThe proband has been followed without evidence of structural disease in the last 10 years but with elevated calcitonin. The clinical and surgical features of 60 thyroidectomized RET533 relatives were also described. Forty‐six patients had MTC (21–72 years), and 11 patients had C‐cell hyperplasia (CCH) (5–42 years). Twelve MTC patients with lymph node metastases had a tumour size of 0·7–2·8 cm. Calcitonin level and CEA were correlated with disease stage, and none of the patients presented with an altered PTH or metanephrine. A 63‐year‐old woman developed pheochromocytoma and breast cancer. Two other RET533 relatives developed lung squamous cell carcinoma and melanoma.ConclusionsA vast clinical variability in RET533 presentation was observed, ranging from only an elevated calcitonin level (3%) to local metastatic disease (25%). Many individuals were cured (42%) and the majority had controlled chronic disease (56%), reinforcing the need for individualized ongoing risk stratification assessment. The importance of this update relies on the fact that it allows us to delineate the natural history of RET 533 MEN2A 10 years after its first description.
Neural responses to witnessing peer rejection after being socially excluded: fMRI as a window into adolescents' emotional processing
Authors: Masten Carrie L. , Eisenberger Naomi I. , Pfeifer Jennifer H. , Dapretto Mirella 
Published: June 2013

AbstractDuring adolescence, concerns about peer rejection and acceptance become increasingly common. Adolescents regularly experience peer rejection firsthand and witness these behaviors among their peers. In the current study, neuroimaging techniques were employed to conduct a preliminary investigation of the affective and cognitive processes involved in witnessing peer acceptance and rejection – specifically when these witnessed events occur in the immediate aftermath of a firsthand experience with rejection. During an fMRI scan, 23 adolescents underwent a simulated experience of firsthand peer rejection. Then, immediately following this experience they watched as another adolescent was ostensibly first accepted and then rejected. Findings indicated that in the immediate aftermath of being rejected by peers, adolescents displayed neural activity consistent with distress when they saw another peer being accepted, and neural activity consistent with emotion regulation and mentalizing (e.g. perspective‐taking) processes when they saw another peer being rejected. Furthermore, individuals displaying a heightened sensitivity to firsthand rejection were more likely to show neural activity consistent with distress when observing a peer being accepted. Findings are discussed in terms of how witnessing others being accepted or rejected relates to adolescents' interpretations of both firsthand and observed experiences with peers. In addition, the potential impact that witnessed events might have on the broader perpetuation of bullying at this age is also considered.