bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing
Authors: Zhang Jin , Ruhlman Tracey A , Mower Jeffrey P , Jansen Robert K 
Published: December 2013

Abstract

Background
Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum.

Results
Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional.

Conclusions
The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition, results indicated no major improvements in breadth of coverage with data sets larger than six billion nucleotides or when sampling RNA from four tissue types rather than from a single tissue. Finally, this work demonstrates the power of cross-compartmental genomic analyses to deepen our understanding of the correlated evolution of the nuclear, plastid, and mitochondrial genomes in plants.
Addressing the contribution of previously described genetic and epidemiological risk factors associated with increased prostate cancer risk and aggressive disease within men from South Africa
Authors: Tindall Elizabeth A , Bornman MS Riana , van Zyl Smit , Segone Alpheus M , Monare L Richard , Venter Philip A , Hayes Vanessa M 
Published: December 2013

Abstract

Background
Although African ancestry represents a significant risk factor for prostate cancer, few studies have investigated the significance of prostate cancer and relevance of previously defined genetic and epidemiological prostate cancer risk factors within Africa. We recently established the Southern African Prostate Cancer Study (SAPCS), a resource for epidemiological and genetic analysis of prostate cancer risk and outcomes in Black men from South Africa. Biased towards highly aggressive prostate cancer disease, this is the first reported data analysis.

Methods
The SAPCS is an ongoing population-based study of Black men with or without prostate cancer. Pilot analysis was performed for the first 837 participants, 522 cases and 315 controls. We investigate 46 pre-defined prostate cancer risk alleles and up to 24 epidemiological measures including demographic, lifestyle and environmental factors, for power to predict disease status and to drive on-going SAPCS recruitment, sampling procedures and research direction.

Results
Preliminary results suggest that no previously defined risk alleles significantly predict prostate cancer occurrence within the SAPCS. Furthermore, genetic risk profiles did not enhance the predictive power of prostate specific antigen (PSA) testing. Our study supports several lifestyle/environmental factors contributing to prostate cancer risk including a family history of cancer, diabetes, current sexual activity and erectile dysfunction, balding pattern, frequent aspirin usage and high PSA levels.

Conclusions
Despite a clear increased prostate cancer risk associated with an African ancestry, experimental data is lacking within Africa. This pilot study is therefore a significant contribution to the field. While genetic risk factors (largely European-defined) show no evidence for disease prediction in the SAPCS, several epidemiological factors were associated with prostate cancer status. We call for improved study power by building on the SAPCS resource, further validation of associated factors in independent African-based resources, and genome-wide approaches to define African-specific risk alleles.
Xiaochaihu Decoction attenuates the vicious circle between the oxidative stress and the ALP inactivation through LPS-catecholamines interactions in gut, liver and brain during CCI4+ethanol-induced mouse HCC
Authors: Liu Xiao-qiu , Hu Xiao-jian , Xu Hong-Xing , Zeng Xiao-Ying 
Published: December 2013

Abstract

Background
Xiaochaihu Decoction (XCHD) prevents hepatocarcinogenesis in association with inhibition of oxidative stress. However, alkaline phosphatase (ALP) activity, lipopolysaccharides (LPS)-catecholamines (CA) interactions in gut, liver and brain may play an important role in the status of oxidative stress. This study was to assess whether XCHD attenuates the vicious circle between oxidative stress and ALP inactivation through LPS-CA interactions.

Methods
Hepatocellular carcinoma group (HCC) were induced by CCI4 + ethanol; HCC with Liver Depression and Spleen Deficiency (HCC + LDSD) were induced by squeezing tails (30 min/day), solitary breeding and intermittent fasting on the basis of HCC; XCHD was administered after 4 weeks of the HCC + LDSD. The degree of tissue injury were studied using a scoring system, and brain weights were measured. Peroxynitrite (ONOO−), malondialdehyde (MDA), 4-hydroxy-3-methoxymandelic acid (VMA, CA metabolites), lipopolysaccharide-phosphate (LPS-P), ALP activity (ALP-A) and Concanavalin A (ConA)-binding rate of ALP (ALP-C) were determined by colorimetric method and lectin (ConA) affinity precipitation method.

Results
More injuries and ONOO−, MDA, VMA, LPS-P, ALP-C were increased, ALP-A were decreased in the gut, liver and brain of HCC group, the most in HCC + LDSD group, after treatment with XCHD, all of which were improved. A positive association found between gut-liver-brain injury and ONOO−, MDA, VMA, LPS-P, ALP-C, between ONOO−, MDA, VMA, LPS-P and ALP-C in the gut, liver and brain, and a negative association found between gut-liver-brain injury and ALP-A, between ALP-A and ONOO−, MDA, VMA, LPS-P, ALP-C in the gut, liver and brain.

Conclusions
XCHD can attenuates the vicious circle between the oxidative stress, nitrosative stress, N-glycan deficiency and inactivation of ALP through LPS-CA interactions in gut, liver and brain.
Adsorption of Fluoride Ion onto Zirconyl-Impregnated Activated Carbon Prepared from Lapsi Seed Stone
Authors: Joshi Sahira , Adhikari Mandira , Pradhananga Raja Ram 
Published: December 2013

The potentials of activated carbon derived from Lapsi (Choerospondias axillaries) seed stone after impregnation with zirconium for adsorptive removal of fluoride is presented. Activated carbons from Lapsi seed stone were prepared by three different techniques. Firstly by directly burning in limited supply of air, secondly by treating with a mixture of conc. H2SO4 and HNO3 (in the ratio of 1:1 by weight) and thirdly by activation with zinc chloride (in the ratio of 1:1 by weight) followed by carbonization at 400°C and 500°C under nitrogen atmosphere. Thus prepared carbons were impregnated with zirconyl oxychloride and effects of pH, adsorbent dose, and contact time and adsorbate concentration for the removal of fluoride were evaluated by batch mode. The optimum pH for adsorption of fluoride was observed at pH 3-4, and a minimum contact time for the maximum defluoridation was found to be 180 min. The Langmuir and Freundlich isotherms were used to describe adsorption equilibrium. Zirconium impregnation increased the fluoride adsorption capacity of carbon to considerable extent. Among carbon prepared by three different techniques, the carbon prepared from zinc chloride activation followed by carbonization showed relatively higher fluoride adsorption capacity. From the experiment it is concluded that activated carbon prepared from Lapsi seed is an efficient, low-cost alternative to commercial activated carbon for defluoridation of water.DOI: http://dx.doi.org/10.3126/jncs.v30i0.9330Journal of Nepal Chemical Society Vol. 30, 2012 Page: 13-23 Uploaded date: 12/16/2013
Removal of As(III) from Aqueous Solution Using Fe(III) Loaded Pomegranate Waste
Authors: Thapa Sheela , Pokhrel Megh Raj 
Published: December 2013

A study on As(III) removal using Fe(III) loaded pomegranate waste as an adsorbent is presented. The effects of initial metal ion concentration, contact time, adsorbent dose and pH of the solution on the removal of arsenic were investigated in a batch system. The optimum pH for As(III) adsorption using Fe(III)-loaded charred pomegranate waste [Fe-CPW] was found to be 9. The equilibrium has beenachieved in 2 hours. The maximum adsorption capacity (qmax) for the adsorption of As (III) was found tobe 50 mg/g. The experimental data fitted well with the Langmuir adsorption isotherm model.DOI: http://dx.doi.org/10.3126/jncs.v30i0.9332Journal of Nepal Chemical Society Vol. 30, 2012 Page: 29-36 Uploaded date: 12/16/2013
Synthesis of Geopolymer from Inorganic Construction Waste
Authors: Pathak Arbind , Jha Vinay Kumar 
Published: December 2013

Recently, the demolition of old houses and the construction of new buildings in Kathmandu valley are in the peak which in turn generates a huge amount of construction waste. There are two major types of construction wastes which are burden for disposal namely cement-sand-waste (CSW) and the coal fly ash (CFA). These construction wastes are rich source of alumino-silicate and thus used as raw material for the synthesis of geopolymer in this study. Geopolymers have been synthesized from CSW and CFA using NaOH-KOH and Na2SiO3 as activators. Some parameters like alkali concentration, amount of Na2SiO3 and curing time have been varied in order to improve the quality of geopolymeric product. The geopolymerization process has been carried out using 3-8M KOH/NaOH solutions, Na2SiO3 to CFA and CSW mass ratio of 0.25-2.00 and curing time variation from 5-28 days. The curing temperature was fixed at 40ºC in all the cases. 6M NaOH and 7M KOH solutions were found appropriate alkali concentrations while the ratio of sodium silicate to CSW and CFA of 0.5 and 1.75 respectively were found suitable mass ratio for the process of geopolymer synthesis. The maximum compressive strength of only 7.3 MPa after 15 days curing time with CSW raw material was achieved while with CFA, the compressive strength was found to be 41.9 MPa with increasing the curing time up to 28 days.DOI: http://dx.doi.org/10.3126/jncs.v30i0.9334Journal of Nepal Chemical Society Vol. 30, 2012 Page: 45-51 Uploaded date: 12/16/2013
Highly concentrated emulsion with a cubic liquid crystal as the external phase: characterization and obtaining of meso/macroporous material
Authors: Santamaría E. , Cortés M. , Maestro A. , Porras M. , Gutiérrez J. M. , González C. 
Published: December 2013

High internal phase ratio emulsions (HIPRE) or highly concentrated emulsions are characterized by their large internal phase volume.The nature and concentration of surfactant affects several features of the final emulsion, such as stability, droplet size and structure of the external phase. Therefore, an ordered external mesophase (structure of liquid crystal) can be obtained. The present work studies the influence of composition and preparation variables on the final properties of HIPRE with an external phase formed by a bicontinuous cubic liquid crystal. The studied outputs variables were droplet size, stability and rheological parameters as yield stress, viscosity at a fixed shear rate and the plateau value of the storage modulus. O/W HIPREs were prepared with a decane/brij 35/water system. Once the emulsions were characterized the meso/macroporous material was obtained. In order to prepare the materials, the emulsions were formed by incorporating the catalyst of the reaction (HCl) in the continuous phase. When the emulsions were formed, tetraethylorthosilicate (TEOS) was added as a silica source In order to optimize the production process a study of reutilization and recovery of some of the raw materials (i.e: the surfactant and the EtOH used) was done.DOI: http://dx.doi.org/10.3126/jncs.v30i0.9374Journal of Nepal Chemical Society Vol. 30, 2012 Page: 87-96 Uploaded date: 12/19/2013
Synthesis of Antimony Sulphoiodide by CVD and its Characterization
Authors: Dubey Harish K. , Deshmukh L. P. , Kshirsagar D. E. , Jadhav Vijay S. , Sharon Madhuri , Sharon Maheshwar 
Published: December 2013

Antimony Sulphoiodide is most widely studied compound in group V-VI-VII family due to its largenumber of properties. Varoius methods of synthesis have been reported. We are the first to reportsynthesis of shiny SbSI crystals by the Chemical Vapor Deposition (CVD) technique using powder ofAntimony, Sulphur and Iodine as the starting material. Needle shaped thin crystals of SbSI were foundgrown vertically on the walls of the quartz tube. Characterizations of the sample were done usingdifferent techniques such as powder X-ray diffraction (XRD), scanning electron microscopy (SEM)and energy dispersive X-ray analysis (EDAX). The charcteristcs peaks in Raman scattering plots (0-500 cm-1) match with the reported results. The compound exibits high resitivity at room temperaturein the order of 10-7 Ω-cm and dielectric constant in the order of 10-3 measured at 1 KHz.DOI: http://dx.doi.org/10.3126/jncs.v30i0.9381Journal of Nepal Chemical Society Vol. 30, 2012 Page: 111-117 Uploaded date: 12/20/2013
Is Political Science Meant for Every Tom, Dick, or Harriet? The Role of First Names and Middle Initials as Predictors of Academic Success
Authors: Wuffle A , Coulter Kristine 
Published: December 2013

AbstractWe take advantage of the data set compiled by Masuoka et al. (2007,PS: Political Science and Politics40 (1): 361–66) on lifetime citation counts of political science faculty at PhD granting institutions in the United States to look for “lucky names,” that is, names parents can give babies that predispose them toward scholarly success in political science. Seeking to test an hypothesis offered by Wuffle (1972,PS: Political Science and Politics(Summer): 290), we also briefly look at the importance of middle initials for citation success in political science.
Restructuring the Social Sciences: Reflections from Harvard's Institute for Quantitative Social Science
Authors: King Gary 
Published: December 2013

AbstractThe social sciences are undergoing a dramatic transformation from studying problems to solving them; from making do with a small number of sparse data sets to analyzing increasing quantities of diverse, highly informative data; from isolated scholars toiling away on their own to larger scale, collaborative, interdisciplinary, lab-style research teams; and from a purely academic pursuit focused inward to having a major impact on public policy, commerce and industry, other academic fields, and some of the major problems that affect individuals and societies. In the midst of all this productive chaos, we have been building the Institute for Quantitative Social Science at Harvard, a new type of center intended to help foster and respond to these broader developments. We offer here some suggestions from our experiences for the increasing number of other universities that have begun to build similar institutions and for how we might work together to advance social science more generally.
Perceptions of Rivalry
Authors: Dreyer David R. 
Published: December 2013

AbstractRivalry is pervasive in politics and beyond. Drawing on unique survey data, this article examines how instructors can draw on students' perceptions of rivalry to explore different aspects of the rivalry concept. The data show that different ways in which students tend to think about rivalry tend to reflect differences in scholarly conceptualizations of interstate rivalry. The data also suggest that referencing sports rivalries may be useful to introduce the concept of rivalry, drawing on parallels between sports rivalries and interstate rivalries and students' greater interest in and familiarity with sports than international affairs. This article provides an understanding of how students tend to think about rival relations to help instructors effectively lead classroom discussions on interstate rivalry.
HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data
Authors: Fourches Denis , Sassano Maria F. , Roth Bryan L. , Tropsha Alexander 
Published: December 2013

Abstract
Summary: We report on the development of the high-throughput screening (HTS) Navigator software to analyze and visualize the results of HTS of chemical libraries. The HTS Navigator processes output files from different plate readers' formats, computes the overall HTS matrix, automatically detects hits and has different types of baseline navigation and correction features. The software incorporates advanced cheminformatics capabilities such as chemical structure storage and visualization, fast similarity search and chemical neighborhood analysis for retrieved hits. The software is freely available for academic laboratories.
Availability and implementation: http://fourches.web.unc.edu/
Contact: fourches@email.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
‘ENVIRONMENTAL AKALISM’ AND THE WAR ON FILTH: THE PERSONIFICATION OF SANITATION IN URBAN NIGERIA
Authors: Manton John 
Published: December 2013

ABSTRACTIn Nigerian cities, as across much of Africa, sanitation practices at zone, ward and street levels inscribe – in patterns of circulation and interaction around waste – not only the hopes and fears of urban residents and managers, but also the aspirations and failures encoded in colonial and post-colonial national and regional histories. Adjusting to numerous challenges – the interplay of racist colonial zoning strategies, rapid post-colonial urban expansion, the withdrawal of public services amid the liberalization programmes of the 1980s, the increasingly abject character of the social contract, and the ongoing tenuousness of economic life and activity – urban environmental sanitation in Nigeria has long struggled to keep pace with the historical dynamics of the country's emergent metropolises. Following the activities of a cohort of inspectors and volunteers at the Ministry of Environment and Water Resources, Oyo State, this article examines the politics of performance and coercion surrounding the monthly observance of Environmental Sanitation Day in Ibadan amid the heightened political tensions of the electoral season in 2011.
PHARMACY, MONEY AND PUBLIC HEALTH IN DAKAR
Authors: Tousignant Noémi 
Published: December 2013

ABSTRACTPharmacy students at the Cheikh Anta Diop University in Dakar must research and write a thesis to graduate.Thésardswho took topics in analytical chemistry and toxicology describe their thesis work as a temporary opportunity to perform ‘street-level’ public health research that they regard as ‘relevant’ to the quality of people's lives. Expecting futures in the private commercial sector,thésardsregretfully leave the thesis behind. This article explores the parenthetical nature of this moment – its brief openings and more durable closures – as part of the history of ways of being a pharmacist in post-colonial Senegal. The thesis as an interlude in students’ biographies, curtailed by narrowed horizons of expectation, evokes other contractions: in the range of professional roles open to Senegalese pharmacists, and in the circuits of public health with which they might engage. Forthésards,fieldwork, government work and commercial work entail spatial practices and imaginations; different ways of moving around the city and of tracing urban space that define pharmacists’ roles in terms of the modes through which they engage with broader collectivities. Mappingthésards’parenthesis in Dakar is a means of capturing both their urban experience of work and the intertwining spatial, temporal and affective dimensions associated with this work. The past, probable and possible trajectories of pharmacy work are imprinted and imagined in the space of the city as field, market and polis. Pharmacists’ prospects and aspirations are caught up in broader shifts in how education, (un)employment and entrepreneurship animate relations of association and exchange in Senegal.
Correlation of dynamic contrast‐enhanced MRI perfusion parameters with angiogenesis and biologic aggressiveness of rectal cancer: Preliminary results
Authors: Yeo Dong‐Myung , Oh Soon Nam , Jung Chan‐Kwon , Lee Myung Ah , Oh Seong Taek , Rha Sung Eun , Jung Seung Eun , Byun Jae Young , Gall Peter , Son Yohan 
Published: December 2013

PurposeTo investigate whether quantitative parameters derived from dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI) are correlated with angiogenesis and biologic aggressiveness of rectal cancer.Materials and MethodsA total of 46 patients with rectal cancer underwent DCE‐MRI. Using a two‐compartmental model, quantitative parameters (Ktrans, kep, ve, and iAUC) were calculated from the whole‐transverse region of interest (ROI) and high Ktrans area ROI of entire tumors. Histological specimens were analyzed for tumor size; T/N stage; lymphatic, vascular, perineural invasion; expression of epidermal growth factor receptor (EGFR); and KRAS gene mutations. Tumor angiogenesis was evaluated based on the microvessel density (MVD) and the expression level of the vascular endothelial growth factor. Correlations of the DCE‐MRI parameters with histological markers and angiogenesis were determined using Student's t‐test and analysis of variance (ANOVA).ResultsThe mean kep from high Ktrans area ROIs showed a significantly positive correlation with MVD (P  =  0.030, r  =  0.514, R2  =  0.264). The mean kep from the whole‐transverse ROIs showed a significant inverse correlation with T stage (T1 vs. T2–4, P  =  0.021). EGFR‐positive cancer displayed higher mean Ktrans (P  =  0.045) and kep (P  =  0.038) than EGFR‐negative cancer in whole‐transverse ROIs.ConclusionThese preliminary results suggest that the determination of kep of high Ktrans area permits the noninvasive estimation of tumor angiogenesis in rectal cancer and that DCE‐MRI parameters can be used as imaging biomarkers to predict the biologic aggressiveness of the tumor and patient prognosis. J. Magn. Reson. Imaging 2015;41:474–480.© 2013 Wiley Periodicals, Inc.