bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis
Authors: Liu Ke , Yan Zhangming , Li Yuchao , Sun Zhirong 
Published: June 2013

Abstract
Summary: Large numbers of long intergenic non-coding RNA (lincRNA) have been detected through high-throughput sequencing technology. However, currently we still know very little about their functions. Therefore, a lincRNA function annotation database is needed to facilitate the study in this field. In this article, we present Linc2GO, a web resource that aims to provide comprehensive functional annotations for human lincRNA. MicroRNA-mRNA and microRNA-lincRNA interaction data were integrated to generate lincRNA functional annotations based on the ‘competing endogenous RNA hypothesis’. To the best of our knowledge, Linc2GO is the first database that makes use of the ‘competing endogenous RNA hypothesis’ to predict lincRNA functions.
Availability: Freely available at http://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/index.html
Contact: sunzhr@mail.tsinghua.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
The human genome contracts again
Authors: Pavlichin Dmitri S. , Weissman Tsachy , Yona Golan 
Published: June 2013

Abstract
Summary: The number of human genomes that have been sequenced completely for different individuals has increased rapidly in recent years. Storing and transferring complete genomes between computers for the purpose of applying various applications and analysis tools will soon become a major hurdle, hindering the analysis phase. Therefore, there is a growing need to compress these data efficiently. Here, we describe a technique to compress human genomes based on entropy coding, using a reference genome and known Single Nucleotide Polymorphisms (SNPs). Furthermore, we explore several intrinsic features of genomes and information in other genomic databases to further improve the compression attained. Using these methods, we compress James Watson’s genome to 2.5 megabytes (MB), improving on recent work by 37%. Similar compression is obtained for most genomes available from the 1000 Genomes Project. Our biologically inspired techniques promise even greater gains for genomes of lower organisms and for human genomes as more genomic data become available.
Availability: Code is available at sourceforge.net/projects/genomezip/
Contact: golan.yona@stanford.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Differential gene expression analysis using coexpression and RNA-Seq data
Authors: Yang Ei-Wen , Girke Thomas , Jiang Tao 
Published: June 2013

AbstractMotivation: RNA-Seq is increasingly being used for differential gene expression analysis, which was dominated by the microarray technology in the past decade. However, inferring differential gene expression based on the observed difference of RNA-Seq read counts has unique challenges that were not present in microarray-based analysis. The differential expression estimation may be biased against low read count values such that the differential expression of genes with high read counts is more easily detected. The estimation bias may further propagate in downstream analyses at the systems biology level if it is not corrected.Results: To obtain a better inference of differential gene expression, we propose a new efficient algorithm based on a Markov random field (MRF) model, called MRFSeq, that uses additional gene coexpression data to enhance the prediction power. Our main technical contribution is the careful selection of the clique potential functions in the MRF so its maximum a posteriori estimation can be reduced to the well-known maximum flow problem and thus solved in polynomial time. Our extensive experiments on simulated and real RNA-Seq datasets demonstrate that MRFSeq is more accurate and less biased against genes with low read counts than the existing methods based on RNA-Seq data alone. For example, on the well-studied MAQC dataset, MRFSeq improved the sensitivity from 11.6 to 38.8% for genes with low read counts.Availability: MRFSeq is implemented in C and available at http://www.cs.ucr.edu/~yyang027/mrfseq.htmContact: yyang027@ucr.edu or jiang@cs.ucr.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Co-regulation in embryonic stem cells via context-dependent binding of transcription factors
Authors: Lee Yuju , Zhou Qing 
Published: June 2013

Abstract
Motivation: With the accumulation of genome-wide binding data for many transcription factors (TFs) in the same cell type or cellular condition, it is of great current interest to systematically infer the complex regulatory logic among multiple TFs. In particular, ChIP-Seq data have been generated for 14 core TFs critical to the maintenance and reprogramming of mouse embryonic stem cells (ESCs). This provides a great opportunity to study the regulatory collaboration and interaction among these TFs and with other unknown co-regulators.
Results: In combination with liquid association among gene expression profiles, we develop a computational method to predict context-dependent (CD) co-egulators of these core TFs in ESCs from pairwise binding datasets. That is, co-occupancy between a core TF and a predicted co-regulator depends on the presence or absence of binding sites of another core TF, which is regarded as a binding context. Unbiased external validation confirms that the predicted CD binding of a co-regulator is reliable. Our results reveal a detailed CD co-regulation network among the 14 core TFs and provide many other potential co-regulators showing strong agreement with the literature.
Availability: See www.stat.ucla.edu/~zhou/CMF for software and source code.
Contact: zhou@stat.ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
cisExpress: motif detection in DNA sequences
Authors: Triska Martin , Grocutt David , Southern James , Murphy Denis J. , Tatarinova Tatiana 
Published: June 2013

Abstract
Motivation: One of the major challenges for contemporary bioinformatics is the analysis and accurate annotation of genomic datasets to enable extraction of useful information about the functional role of DNA sequences. This article describes a novel genome-wide statistical approach to the detection of specific DNA sequence motifs based on similarities between the promoters of similarly expressed genes. This new tool, cisExpress, is especially designed for use with large datasets, such as those generated by publicly accessible whole genome and transcriptome projects. cisExpress uses a task farming algorithm to exploit all available computational cores within a shared memory node. We demonstrate the robust nature and validity of the proposed method. It is applicable for use with a wide range of genomic databases for any species of interest.
Availability: cisExpress is available at www.cisexpress.org.
Contact: tatiana.tatarinova@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Mechanistic insights into mutually exclusive splicing in dynamin 1
Authors: Suyama Mikita 
Published: June 2013

Abstract
Summary: Mutually exclusive splicing is a strictly regulated pattern of alternative splicing. A specific group of mutually exclusive splicing events has been shown to be regulated by the formation of specific RNA secondary structures. This type of regulation has been shown to exist only in arthropods. The present study involved a detailed sequence analysis of human gene structures that undergo mutually exclusive splicing, which showed that this type of regulation may also occur in dynamin 1 in mammals. A phylogenetic analysis revealed that the dynamin 1 orthologs in invertebrates did not share the same sequence features, which suggests that the regulatory mechanism has independently evolved in the mammalian lineage. Therefore, the emergence of this elaborate mechanism for mutually exclusive splicing may be attributable to mechanistic convergence.
Contact: mikita@bioreg.kyushu-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Fungibility and Consumer Choice: Evidence from Commodity Price Shocks*
Authors: Hastings Justine S. , Shapiro Jesse M. 
Published: June 2013

AbstractWe formulate a test of the fungibility of money based on parallel shifts in the prices of different quality grades of a commodity. We embed the test in a discrete-choice model of product quality choice and estimate the model using panel microdata on gasoline purchases. We find that when gasoline prices rise, consumers substitute to lower octane gasoline, to an extent that cannot be explained by income effects. Across a wide range of specifications, we consistently reject the null hypothesis that households treat “gas money” as fungible with other income. We compare the empirical fit of three psychological models of decision making. A simple model of category budgeting fits the data well, with models of loss aversion and salience both capturing important features of the time series.
Modern contraceptive behaviour of Indian women: is spousal violence a constraint?
Authors: Debnath Avijit , Roy Niranjan , Mazumder Nazira 
Published: June 2013

PurposeThe main goal of the paper is to study the effect of intimate partner violence on wives' participation in adopting modern contraceptive as a method of family planning in India.Design/methodology/approachThe authors' analysis uses data from the NFHS‐III (2005‐2006) based on a nationally representative sample of 109,041 households, and 124,385 women (15‐49 years). The sample covers 99 percent of India's population living in all 29 states. Both bivariate and multivariate techniques have been used to analyze data. The bivariate analysis in the form of scatter diagram has been used to examine the association between “use of modern contraceptive” and “spousal violence”, while multivariate analysis in the form of logistic regression has been carried out to assess this association after controlling other variables.FindingsThe study reveals that spousal violence negatively affects wives' participation in adoption of modern contraceptive, but that their knowledge of contraceptive, religion, and level of women empowerment should be taken into account as well. Women with higher knowledge about contraceptive have been found to use more modern contraceptive. Muslim women have relatively lower modern contraceptive prevalence rate and they have an inclination for traditional methods. Similarly, modern contraceptive prevalence is lower among women who enjoy relatively higher empowerment. In fact, it has been found from the study that women empowerment has a high positive correlation with traditional contraceptive prevalence rate.Originality/valueThis paper is the first attempt at examining the association between spousal violence and contraceptive behaviour in India on a national basis covering every corner of the country. The findings of the study clearly stress the importance of spousal violence prevention measures as supplemental to family planning measures. However, it will be erroneous to assume that mere passing of bills in the parliament and making laws will solve the problem which is deeply rooted in the society.
Basic equality as a post‐revolutionary requisite
Authors: Doomen Jasper 
Published: June 2013

PurposeThe Arab Spring poses challenges to governments of the countries involved; the author aims to present a way to respond to them. To this end, the notion of “basic equality” is proffered as a decisive element to be realized in a democratic form of government, democracy itself being necessary if one seeks to evade a return to the former forms of government.Design/methodology/approachNo single answer suffices to realize stable while generally acceptable forms of government; basic equality is shown to be a necessary starting point in each case, to be supplemented by specific policies. The practical implications of the article's analysis are evidenced in the limitations governments must recognize and warrant: through legislation, basic equality is to be realized.FindingsPeople's (formal) equality must be acknowledged. It may be difficult to reconcile this demand with, for example, religious convictions, but it is not necessary to compromise what one believes. One need only act in accordance with the dictates of formal equality, which is the corollary of basic equality. For example, an employer only has to treat his employees equally, and may, accordingly, not distinguish between race, gender or religion, but he is not required to believe that people are, in some fundamental sense, equal.Originality/valueEqual treatment has often been proposed as a “moral” directive. The author presents a realistic alternative to this approach while realizing a state of affairs in which people are treated equally. Since this alternative is based on their self‐interest, this will lead to both a convincing theory and a viable practice.
Fungal endophyte infection and host genetic background jointly modulate host response to an aphid‐transmitted viral pathogen
Authors: Rúa Megan A. , McCulley Rebecca L. , Mitchell Charles E. 
Published: June 2013

Summary

Despite their ubiquitous nature, interactions between multiple micro‐organisms and their effects on host growth and each other's success have received limited scientific attention. In particular, grasses can be commonly infected by both endophytic fungi and viruses, which are typically transmitted by aphids. In this study, we investigated how an aphid‐transmitted viral pathogen and a symbiotic endophytic fungus altered host growth and allocation. We hypothesized that, by reducing aphid feeding, endophyte infection would lower viral titre and consequently decrease the negative effects of virus infection on host biomass production.

In a greenhouse experiment, we manipulated fungal endophyte status and virus infection (Barley Yellow Dwarf Virus – PAV) of two tall fescue cultivars with different genetic backgrounds [KY 31 and pasture demonstration farm (PDF)]. In one cultivar (PDF), we also manipulated endophyte strain, using two strains that had been selected for differences in alkaloid production. We assessed host, virus and vector responses.

As hypothesized, endophyte infection decreased reproduction and abundance of aphid vectors; however, in contrast to our hypothesis, this response by aphids did not impact viral titre. For both tall fescue cultivars, endophyte infection alleviated the negative effect of virus infection on the proportion of total plant biomass allocated to roots. On the other hand, for the KY 31 cultivar only, virus infection decreased tillering in endophyte‐infected individuals, but not endophyte‐free individuals. Within the PDF cultivar, both endophyte strains produced similar effects on host, virus and vector responses.

Synthesis These results indicate that some of the beneficial effects provided by endophyte infection, particularly alleviating the negative effect of virus infection on the proportion of total plant biomass allocated to roots, do not arise strictly from altering host interactions with herbivores (aphids), but also occur by changing host responses to viral infection. Furthermore, these results emphasize the importance of exploring multispecies microbial interactions and genetic controls on these interactions in order to more fully understand their role in community‐ and ecosystem‐level dynamics.
Effects of native pollinator specialization, self‐compatibility and flowering duration ofEuropean plant species on their invasiveness elsewhere
Authors: Chrobock Thomas , Weiner Christiane N. , Werner Michael , Blüthgen Nico , Fischer Markus , van Kleunen Mark 
Published: June 2013

SummaryWhen entomophilous plants are introduced to a new region, they may leave behind their usual pollinators. In particular, plant species with specialized pollination may then be less likely to establish and spread (i.e. become invasive). Moreover, other reproductive characteristics such as self‐compatibility and flowering duration may also affect invasion success.Here, we specifically asked whether plant species' specialization towards pollinator species and families, respectively, as measured in the native range, self‐compatibility, flowering duration and their interactions are related to the degree of invasion (i.e. a measure of regional abundance) in non‐native regions.We used plant–pollinator interaction data from 119 German grassland sites to calculate unbiased indices of plant specialization towards pollinator species and families for 118European plant species. We related these specialization indices, flowering duration, self‐compatibility and their interactions to the degree of invasion of each species in seven large countries on four non‐Eurasian continents.In all models, plant species with long flowering durations had the highest degree of invasion. The best model included the specialization index based on pollinator species instead of the one based on pollinator families. Specialization towards pollinator species had a marginally significant positive effect on the degree of invasion in non‐native regions for self‐compatible, but not for self‐incompatible species.Synthesis. We showed that long flowering duration is related to the degree of invasion in other parts of the world, and a trend that pollinator generalization in the native range may interact with self‐compatibility in determining the degree of invasion. Therefore, we conclude that such reproductive characteristics should be considered in risk assessment and management of introduced plant species.
Patient characteristics and outcomes in metastatic upper tract urothelial carcinoma after radical nephroureterectomy: the experience of Japanese multi‐institutions
Authors: Tanaka Nobuyuki , Kikuchi Eiji , Kanao Kent , Matsumoto Kazuhiro , Kobayashi Hiroaki , Miyazaki Yasumasa , Ide Hiroki , Obata Jun , Hoshino Katsura , Shirotake Suguru , Hayakawa Nozomi , Kosaka Takeo , Miyajima Akira , Momma Tetsuo , Nakagawa Ken , Hasegawa Shintaro , Nakajima Yosuke , Oya Mototsugu 
Published: June 2013

Objectives
To investigate oncological outcomes and prognostic factors in patients with upper tract urothelial carcinoma (UTUC) who experienced disease recurrence after radical nephroureterectomy (RNU).
Few studies have focused on the clinical courses of patients who experienced disease recurrence after RNU.
Patients and Methods
A total of 204 UTUC patients who experienced disease recurrence from a retrospective multi‐institutional cohort were included in the present study.
Associated patient outcomes were analyzed using multivariate analysis.
Results
The mean time from RNU to first disease recurrence was 15.0 months and ≈90% of patients experienced disease recurrence within the first 3 years after RNU.
During a median follow‐up of 8.1 month after disease recurrence, 165 patients died from UTUC and five patients died from other causes. In the 204 cohorts, 1‐ and 3‐year cancer‐specific survival rates were 40.2% and 9.7%, respectively, and 1‐ and 3‐year overall survival rates were 39.5% and 9.4%, respectively.
After disease recurrence, 132 patients underwent systemic chemotherapy, and a subgroup analysis of patients who underwent systemic chemotherapy multivariate analysis showed that performance status, the presence of liver metastasis and the number of recurrence sites were independently prognostic of cancer‐specific and overall survival after relapsing.
According to three significant variables, 1‐ and 3‐year cancer‐specific survival rates were 72.7% and 20.8% in patients with no risk factors, 46.5% and 7.5% in patients with one risk factor, and 26.4% and 4.4% in patients with two or three risk factors, respectively (P < 0.001).
Conclusions
Most patients died from UTUC within 3 years, even though systemic chemotherapies were administered after relapsing.
Multivariate analysis showed that performance status, the presence of liver metastasis and the number of recurrence sites were independently related to poor survival after systemic chemotherapy.
Effect of statin use on outcomes of non‐muscle‐invasive bladder cancer
Authors: Crivelli Joseph J. , Xylinas Evanguelos , Kluth Luis A. , da Silva Rodrigo Donalisio , Chrystal James , Novara Giacomo , Karakiewicz Pierre I. , David Scott G. , Scherr Douglas S. , Lotan Yair , Shariat Shahrokh F. 
Published: June 2013

Objectives
To assess the impact of statin use on outcomes of patients with non‐muscle‐invasive bladder cancer (NMIBC).
To measure the effect of statin use on the efficacy of intravesical bacillus Calmette‐Guérin (BCG) therapy.
Patients and Methods
A retrospective analysis was performed on 1117 patients treated with transurethral resection of the bladder (TURB) for NMIBC at three institutions between 1996 and 2007.
Statin use at the time of diagnosis was recorded for each patient.
Univariable Cox regression models addressed the association of statin use with disease recurrence, disease progression, cancer‐specific mortality and overall mortality in all patients, patients with primary NMIBC, patients not treated with BCG, and patients treated with BCG.
Results
Overall, 341 patients (30.5%) used statins and 776 (69.5%) did not.
Within a median (interquartile range) follow‐up of 62.7 (25.0–110.7) months, 469 patients (42.0%) experienced disease recurrence, 103 (9.2%) progression, 50 (4.5%) cancer‐specific mortality, and 299 (26.8%) any‐cause mortality.
In univariable Cox regression analyses, statin use was not associated with any of these four endpoints (P > 0.05 for all). In subgroup analyses, statin use was also not associated with prognosis in patients with primary NMIBC or patients not receiving BCG (P > 0.05 for all four endpoints).
Statin use was not associated with response to BCG (P > 0.05 for all four endpoints).
Conclusion
Statin users did not experience different outcomes compared with non‐users and statin use did not affect the efficacy of BCG immunotherapy; these data do not support modification or discontinuation of statin therapy for patients with NMIBC.
Low‐pressure pneumoperitoneum during laparoscopic donor nephrectomy to optimize live donors’ comfort
Authors: Warlé M.C. , Berkers A.W. , Langenhuijsen J.F , van der Jagt M.F. , Dooper Ph.M. , Kloke H.J. , Pilzecker D. , Renes S.H. , Wever K.E. , Hoitsma A.J. , van der Vliet J.A. , D'Ancona F.C.H. 
Published: June 2013

AbstractNowadays, laparoscopic donor nephrectomy (LDN) has become the gold standard to procure live donor kidneys. As the relationship between donor and recipient loosens, it becomes of even greater importance to optimize safety and comfort of the surgical procedure. Low‐pressure pneumoperitoneum has been shown to reduce pain scores after laparoscopic cholecystectomy. Live kidney donors may also benefit from the use of low pressure during LDN. To evaluate feasibility and efficacy to reduce post‐operative pain, we performed a randomized blinded study. Twenty donors were randomly assigned to standard (14 mmHg) or low (7 mmHg) pressure during LDN. One conversion from low to standard pressure was indicated by protocol due to lack of progression. Intention‐to‐treat analysis showed that low pressure resulted in a significantly longer skin‐to‐skin time (149 ± 86 vs. 111 ± 19 min), higher urine output during pneumoperitoneum (23 ± 35 vs. 11 ± 20 mL/h), lower cumulative overall pain score after 72 h (9.4 ± 3.2 vs. 13.5 ± 4.5), lower deep intra‐abdominal pain score (11 ± 3.3 vs. 7.5 ± 3.1), and a lower cumulative overall referred pain score (1.8 ± 1.9 vs. 4.2 ± 3). Donor serum creatinine levels, complications, and quality of life dimensions were not significantly different. Our data show that low‐pressure pneumoperitoneum during LDN is feasible and may contribute to increase live donors’ comfort during the early post‐operative phase.