bluuebunny/crossref_metadata_2025_split huggingface dataset:
EXPANDS: expanding ploidy and allele frequency on nested subpopulations
Authors: Andor Noemi , Harness Julie V. , Müller Sabine , Mewes Hans W. , Petritsch Claudia 
Published: November 2013

Abstract
Motivation: Several cancer types consist of multiple genetically and phenotypically distinct subpopulations. The underlying mechanism for this intra-tumoral heterogeneity can be explained by the clonal evolution model, whereby growth advantageous mutations cause the expansion of cancer cell subclones. The recurrent phenotype of many cancers may be a consequence of these coexisting subpopulations responding unequally to therapies. Methods to computationally infer tumor evolution and subpopulation diversity are emerging and they hold the promise to improve the understanding of genetic and molecular determinants of recurrence.
Results: To address cellular subpopulation dynamics within human tumors, we developed a bioinformatic method, EXPANDS. It estimates the proportion of cells harboring specific mutations in a tumor. By modeling cellular frequencies as probability distributions, EXPANDS predicts mutations that accumulate in a cell before its clonal expansion. We assessed the performance of EXPANDS on one whole genome sequenced breast cancer and performed SP analyses on 118 glioblastoma multiforme samples obtained from TCGA. Our results inform about the extent of subclonal diversity in primary glioblastoma, subpopulation dynamics during recurrence and provide a set of candidate genes mutated in the most well-adapted subpopulations. In summary, EXPANDS predicts tumor purity and subclonal composition from sequencing data.
Availability and implementation: EXPANDS is available for download at http://code.google.com/p/expands (matlab version - used in this manuscript) and http://cran.r-project.org/web/packages/expands (R version).
Contact: claudia.petritsch@ucsf.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data
Authors: Li Jun , Wei Hairong , Liu Tingsong , Zhao Patrick Xuechun 
Published: November 2013

Abstract
The accurate construction and interpretation of gene association networks (GANs) is challenging, but crucial, to the understanding of gene function, interaction and cellular behavior at the genome level. Most current state-of-the-art computational methods for genome-wide GAN reconstruction require high-performance computational resources. However, even high-performance computing cannot fully address the complexity involved with constructing GANs from very large-scale expression profile datasets, especially for the organisms with medium to large size of genomes, such as those of most plant species. Here, we present a new approach, GPLEXUS (http://plantgrn.noble.org/GPLEXUS/), which integrates a series of novel algorithms in a parallel-computing environment to construct and analyze genome-wide GANs. GPLEXUS adopts an ultra-fast estimation for pairwise mutual information computing that is similar in accuracy and sensitivity to the Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNE) method and runs ∼1000 times faster. GPLEXUS integrates Markov Clustering Algorithm to effectively identify functional subnetworks. Furthermore, GPLEXUS includes a novel ‘condition-removing’ method to identify the major experimental conditions in which each subnetwork operates from very large-scale gene expression datasets across several experimental conditions, which allows users to annotate the various subnetworks with experiment-specific conditions. We demonstrate GPLEXUS’s capabilities by construing global GANs and analyzing subnetworks related to defense against biotic and abiotic stress, cell cycle growth and division in Arabidopsis thaliana.
Quantifying the Effect of Pyraclostrobin on Grainfill Period and Kernel Dry Matter Accumulation in Maize
Authors: Byamukama E. , Abendroth L. J. , Elmore R. W. , Robertson A. E. 
Published: November 2013

Strobilurin fungicides are effective against a wide range of foliar fungal diseases on several crops and may offer additional physiological benefits, including plants staying green longer than normal (the “stay-green effect”). It has been hypothesized that the stay-green effect may extend the grain fill period leading to increased grain yield due to a longer period of dry matter accumulation. We investigated the effect of pyraclostrobin fungicide applied at tasseling on foliar disease suppression, stalk rot severity, the stay-green effect of leaves in the upper canopy, dry matter accumulation, time at physiological maturity, grain yield, and moisture at harvest in maize from 2008 through 2010 in Iowa at six location years. Foliar disease severity was <5% in all location years. Pyraclostrobin-treated plots had a significantly higher area under green leaves incidence curve compared to non-treated maize. Although grain yield and grain moisture at harvest were not different (P > 0.1) between pyraclostrobin-treated and non-treated maize in all location years, treated plots tended to have higher yield and grain moisture. Time at physiological maturity did not differ between pyraclostrobin-treated and non-treated plots (P > 0.1). Although we demonstrated an application of pyraclostrobin to maize delayed senescence of the leaves thus contributing to the stay-green effect, our data did not show grain-fill period extension. Accepted for publication 21 August 2013. Published 24 October 2013.
Kidney Protection by Hypothermic Total Liquid Ventilation after Cardiac Arrest in Rabbits
Authors: Tissier Renaud , Giraud Sebastien , Quellard Nathalie , Fernandez Béatrice , Lidouren Fanny , Darbera Lys , Kohlhauer Matthias , Pons Sandrine , Chenoune Mourad , Bruneval Patrick , Goujon Jean-Michel , Ghaleh Bijan , Berdeaux Alain , Hauet Thierry 
Published: November 2013

Abstract

Background:
Total liquid ventilation (TLV) with perfluorocarbons has been shown to induce rapid protective cooling in animal models of myocardial ischemia and cardiac arrest, with improved neurological and cardiovascular outcomes after resuscitation. In this study, the authors hypothesized that hypothermic TLV can also limit kidney injury after cardiac arrest.

Methods:
Anesthetized rabbits were submitted to 15 min of untreated ventricular fibrillation. After resuscitation, three groups of eight rabbits each were studied such as (1) life support plus hypothermia (32°–33°C) induced by cold TLV (TLV group), (2) life support without hypothermia (control group), and (3) Sham group (no cardiac arrest). Life support was continued for 6 h before euthanasia and kidney removal.

Results:
Time to target esophageal temperature was less than 5 min in the TLV group. Hypothermia was accompanied by preserved renal function in the TLV group as compared with control group regarding numerous markers including creatinine blood levels (12 ± 1 vs. 16 ± 2 mg/l, respectively; mean ± SEM), urinary N-acetyl-β-(d)-glucosaminidase (1.70 ± 0.11 vs. 3.07 ± 0.10 U/mol of creatinine), γ-glutamyltransferase (8.36 ± 0.29 vs. 12.96 ± 0.44 U/mol of creatinine), or β2-microglobulin (0.44 ± 0.01 vs. 1.12 ± 0.04 U/mol of creatinine). Kidney lesions evaluated by electron microscopy and conventional histology were also attenuated in TLV versus control groups. The renal-protective effect of TLV was not related to differences in delayed inflammatory or immune renal responses because transcriptions of, for example, interferon-γ, tumor necrosis factor-α, interleukin-1β, monocyte chemoattractant protein-1, toll-like receptor-2, toll-like receptor-4, and vascular endothelial growth factor were similarly altered in TLV and control versus Sham.

Conclusion:
Ultrafast cooling with TLV is renal protective after cardiac arrest and resuscitation, which could increase kidney availability for organ donation.
HFR1 Sequesters PIF1 to Govern the Transcriptional Network Underlying Light-Initiated Seed Germination in Arabidopsis
Authors: Shi Hui , Zhong Shangwei , Mo Xiaorong , Liu Na , Nezames Cynthia D. , Deng Xing Wang 
Published: November 2013

Abstract
Seed germination is the first step for seed plants to initiate a new life cycle. Light plays a predominant role in promoting seed germination, where the initial phase is mediated by photoreceptor phytochrome B (phyB). Previous studies showed that PHYTOCHROME-INTERACTING FACTOR1 (PIF1) represses seed germination downstream of phyB. Here, we identify a positive regulator of phyB-dependent seed germination, LONG HYPOCOTYL IN FAR-RED1 (HFR1). HFR1 blocks PIF1 transcriptional activity by forming a heterodimer with PIF1 that prevents PIF1 from binding to DNA. Our whole-genomic analysis shows that HFR1 and PIF1 oppositely mediate the light-regulated transcriptome in imbibed seeds. Through the HFR1–PIF1 module, light regulates expression of numerous genes involved in cell wall loosening, cell division, and hormone pathways to initiate seed germination. The functionally antagonistic HFR1–PIF1 pair constructs a fail-safe mechanism for fine-tuning seed germination during low-level illumination, ensuring a rapid response to favorable environmental changes. This study identifies the HFR1–PIF1 pair as a central module directing the whole genomic transcriptional network to rapidly initiate light-induced seed germination.
Complexity of the Alternative Splicing Landscape in Plants
Authors: Reddy Anireddy S.N. , Marquez Yamile , Kalyna Maria , Barta Andrea 
Published: November 2013

Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
Effect of biochar application in combination with domestic wastewater on biomass yield of bioenergy plantations
Authors: Ramola Sudipta , Kumar Srivastava Rajeev , Vasudevan Padma 
Published: October 2013

Purpose
– The energy demand of growing population is on rise despite the fact that conventional energy reserves are limited and exhaustive in nature. To quench the ever-needing demand of energy, there is an urgent need to find out new energy options. In this regard, role of bioenergy plantation has gained enormous attention of scientist community all over the world. Biochar, a black pyrolysed carbonaceous product, is used as soil amendment and is reported to provide several benefits such as retention of nutrients in soil, better cation exchange capacity, soil carbon sequestration with better biomass yield. The paper aims to discuss these issues.

Design/methodology/approach
– The present study investigated the effect of domestic waste water (grey water) as well as biochar in combination for above-ground biomass of Eucalyptus hybrid (clone 413) and Anthocephalus cadamba plantations under flooded irrigation.

Findings
– Height, girth and above-ground biomass of both plantations increased significantly from control. Above-ground biomass of A. cadamba was observed to be better than Eucalyptus hybrid during initial period of establishment. After application of biochar, treatment WW+BBm was found to produce maximum above-ground biomass followed by treatment WW and WW+ BBg in both plantations system.

Originality/value
– The present study encompassed a real sustainable approach for environmental management by integrating the use of waste water (source of nutrients) as well as biochar (a solid waste pyrolysed material that act as soil fertilizer, an efficient adsorbent as well as a sink for carbon sequestration) for the better biomass yield of bioenergy plantations.
When P-J fit and P-O fit meet guanxi in a Chinese selection context
Authors: Chen Wan-Yu , Wang Mei-Ling , Hsu Bi-Fen 
Published: November 2013

Purpose– Human resource management may have great distinctions in different cultural contexts; past researches have increasingly discovered the differences between Eastern and Western perspectives. For employee selection, Chinese bosses usually employ acquaintances and relative bases on accumulated favors and relationship intensity in Chinese society. This study aims to investigate the relative importance of P-J fit, P-O fit and guanxi when Chinese recruiters judge the qualifications of job applicants.Design/methodology/approach– To test the hypotheses in this paper, the authors use a policy capturing methodology that is widely used for analyses of human judgment and decision making. This design enables the authors to infer the way managers integrate different indices of selection in making decisions. During the period of time, the study was running, 95 participants with hiring experience in Chinese regions completed the task, and they were from several industries for the generalization of this study.Findings– The results indicate that P-J fit, P-O fit and guanxi all have a unique impact on manager's hiring decisions in Chinese society, and P-J fit is weighted more heavily than P-O fit and guanxi.Originality/value– This is the first study that integrates the Eastern and the Western perspectives, supplements the gap between selection and fit theory in the West and proves that P-J fit, P-O fit and Chinese guanxi all have individual influence on hiring decisions. “Guanxi” is the key factor that has great impact on the process of hiring decisions in Chinese societies compared with Western organizations.
“Ask me what I read”: readers' advisory and immigrant adaptation
Authors: Dali Keren 
Published: November 2013

Purpose
– The purpose of this paper is to investigate the potential of readers' advisory (RA) in libraries to help immigrants with psychological and socio-cultural adaptation in a new country.

Design/methodology/approach
– The data were empirically collected from a sample of Russian-speaking immigrant readers residing in the Greater Toronto Area, Ontario, Canada, by means of background surveys and in-depth interviews.

Findings
– The RA interaction is not merely a conversation about leisure books; it is a powerful intercultural encounter that has the potential to raise the levels of intimacy and attraction between host and immigrant populations, break negative stereotypes, help to build shared networks and create favorable contacts, change intergroup attitudes, and improve readers' mastery of the second language and knowledge of a new country.

Originality/value
– This article makes a contribution to three areas related to RA. It provides insight into the views and perceptions of RA by a selected group of readers; it gives voice to immigrant readers whose experiences with RA are particularly under-represented in the Library and Information Science literature; and it conceptualizes the RA interaction as an intercultural encounter, using the uncertainty reduction based theory of intercultural adaptation to frame the discussion.
Library partnerships: a key to growth
Authors: Massis Bruce 
Published: November 2013

Purpose
– The purpose of this column is to review several recent library partnerships and highlight the benefit of such endeavors for the libraries and their partner institutions.

Design/methodology/approach
– This is a literature review and commentary on this topic that has been addressed by professionals, researchers and practitioners.

Findings
– Visibility and access to the library in some unexpected locations, thanks to a number of creative partnerships, can serve as greater a function to the library as to its partner and the community. The vitality of the library can be at least partially sustained by its partnerships and can serve as a model for other public/private and public/public associations where both sides of the partnership benefit in the estimation of the public.

Originality/value
– The value in addressing this issue is to examine the creative public/private and public/public partnerships of which libraries can avail themselves in an effort to best serve their patrons.
Hybrid direct manufacturing method of metallic parts using deposition and micro continuous rolling
Authors: Zhang Haiou , Wang Xiangping , Wang Guilan , Zhang Yang 
Published: October 2013

Purpose
– The purpose of this paper is to report a new direct metal manufacturing method which integrates freeform deposition process and micro rolling process, introduce the manufacturing principle and show the advantages of this method.

Design/methodology/approach
– This paper introduces the hybrid manufacturing principle and devices first. Then, the key parameters of hybrid manufacturing process are studied by contrast experiments. The results of comparisons of manufacturing accuracy, microstructure and tensile test between freeform fabricated parts and hybrid manufactured parts show the advantages of this new direct manufacturing method.

Findings
– The experiments results show that the accuracy of hybrid manufacturing method is improved obviously comparing with arc-based freeform deposition manufacturing method; the microstructure of the hybrid manufacturing part turns into cellular crystal instead of dendrite; the tensile strength of the part increases by 33 percent and the tensile deformation improved more than two times.

Originality/value
– The paper presents a new hybrid direct metal manufacturing method for the first time. The hybrid manufacturing devices are developed. The experiments results show that the hybrid manufacturing method can be used on directly fabricating large metal components with outstanding quality, efficiency and low cost. The application prospect is great.
Influence of the Thermal Stabilization Process on the Volatile Profile of Canned Tomato‐Based Food
Authors: Cosmai Lucrezia , Summo Carmine , Caponio Francesco , Paradiso Vito M. , Gomes Tommaso 
Published: October 2013

AbstractThe literature contains several papers dealing with the volatile constituents contributing to the aroma of fresh and processed tomatoes. Along with the traditional tomato‐based products, tomato‐based pâtés, characterized by complex ingredient formulations, are commonly consumed as a seasoning for pasta, and as a dressing for meats, salads, and sandwiches. To the best of our knowledge, no investigations have been published on the influence of thermal stabilization treatments on the composition of volatile compounds in tomato‐based pâtés. To this aim, thermally stabilized and not stabilized tomato‐based pâtés were subjected to the analysis of volatile compounds. The results obtained highlighted the influence of the thermal stabilization process on the evolution of volatile composition tomato‐based pâtés. In particular, the terpenic compounds showed significant decreases after the thermal stabilization process treatment, due to their degradation and oxidation favored by high temperatures. The thermal stabilization caused, moreover, an increase in volatile compounds deriving from lipid oxidation and Maillard reaction, characterized by low‐sensory thresholds, and from the thermal degradation of carotenoids and fresh tomato‐derived compounds.
HLA‐DR typing in polyarticular juvenile idiopathic arthritis: a study from a tertiary care hospital in northern India
Authors: Dibya Ranjan Behera , Nand Kumar Singh , Usha Singh , Pramod Kumar Verma 
Published: November 2013

AbstractIntroductionMany studies of human leukocyte antigen (HLA) association with juvenile idiopathic arthritis (JIA) have reported conflicting results, which were probably related to ethnic differences. Moreover, in India, studies on HLA‐DR typing on JIA, particularly polyarticular JIA, is lacking.ObjectiveThe aim of our study was to reveal the frequency of HLA DR types in a cohort of polyarticular JIA in northern India.MethodsFifty‐two polyarticular JIA patients were included as per the recent International League of Associations for Rheumatology classification, 2001. HLA‐DR typing was performed in 21 patients (18 rheumatoid factor [RF]+ and three RF−) by a DNA‐based polymerase chain reaction method for the determination of HLA alleles using sequence specific primers (SSP). The results were compared with that of 23 healthy controls of the same age and sex.ResultsHLA‐DR4 was present in five cases (23%) in the diseased group while only in one case (4.3%) in the control group with a relative risk of 5.47, but when compared with only RF+ polyarticular JIA, HLA‐DR4 was found to be significantly high (27.7% vs. 4.43%; P < 0.05) with a relative risk of 6.3. Further, DR4, DR1, DR2, DR9, DR10 were also non‐significantly high in these patients with relative risk of 3.2 for DR9 and 1.8 for DR10. In contrast, HLA‐DR6 was seen only in 5.5% of polyarticular JIA cases, whereas it was present in 39% of controls (P < 0.05), a showing negative association.ConclusionHLA‐DR4 codes for susceptibility to RF+ polyarticular JIA with a six‐fold risk, whereas HLA‐DR6 offers protection.
Wild‐caught rodents retain a majority of their natural gut microbiota upon entrance into captivity
Authors: Kohl Kevin D. , Dearing M. Denise 
Published: October 2013

SummaryExperiments conducted on captive animals allow scientists to control many variables; however, these settings are highly unnatural. Previous research has documented a large difference in microbial communities between wild animals and captive‐bred individuals. However, wild‐caught animals brought into captivity might retain their natural microbiota and thus provide a better study system in which to investigate the ecology of the gut microbiome. We collected individuals of the desert woodrat (Neotoma lepida) from nature and investigated changes in the microbial community over 6 months in captivity. Additionally, we inventoried potential environmental sources of microbes (food, bedding) from the wild and captivity. We found that environmental sources do not make large contributions to the woodrat gut microbial community. We documented a slight decrease in several biodiversity metrics over 6 months in captivity, yet the magnitude of change was small compared with other studies. Wild and captive animals shared 64% of their microbial species, almost twice that observed in other studies of wild and captive‐bred individuals (≤ 37% shared). We conclude that wild‐caught animals brought into captivity retain a substantial proportion of their natural microbiota and represent an acceptable system in which to study the gut microbiome.