bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oleic Acid Attenuates trans‐10,cis‐12 Conjugated Linoleic Acid‐Mediated Inflammatory Gene Expression in Human Adipocytes
Authors: Reardon Meaghan , Gobern Semone , Martinez Kristina , Shen Wan , Reid Tanya , McIntosh Michael 
Published: September 2012

AbstractThe weight loss supplement conjugated linoleic acid (CLA) consists of an equal mixture of trans‐10,cis‐12 (10,12) and cis‐9,trans‐11 (9,11) isomers. However, high levels of mixed CLA isomers, or the 10,12 isomer, causes chronic inflammation, lipodystrophy, or insulin resistance. We previously demonstrated that 10,12 CLA decreases de novo lipid synthesis along with the abundance and activity of stearoyl‐CoA desaturase (SCD)‐1, a δ‐9 desaturase essential for the synthesis of monounsaturated fatty acids (MUFA). Thus, we hypothesized that the 10,12 CLA‐mediated decrease in SCD‐1, with the subsequent decrease in MUFA, was responsible for the observed effects. To test this hypothesis, 10,12 CLA‐treated human adipocytes were supplemented with oleic acid for 12 h to 7 days, and inflammatory gene expression, insulin‐stimulated glucose uptake, and lipid content were measured. Oleic acid reduced inflammatory gene expression in a dose‐dependent manner, and restored the lipid content of 10,12 CLA‐treated adipocytes without improving insulin‐stimulated glucose uptake. In contrast, supplementation with stearic acid, a substrate for SCD‐1, or 9,11 CLA did not prevent inflammatory gene expression by 10,12 CLA. Notably, 10,12 CLA impacted the expression of several G‐protein coupled receptors that was attenuated by oleic acid. Collectively, these data show that oleic acid attenuates 10,12 CLA‐induced inflammatory gene expression and lipid content, possibly by alleviating cell stress caused by the inhibition of MUFA needed for phospholipid and neutral lipid synthesis.
Cenancestor, the Last Universal Common Ancestor
Authors: Delaye Luis , Becerra Arturo 
Published: September 2012

Abstract
Darwin suggested that all life on Earth could be phylogenetically related. Modern biology has confirmed Darwin’s extraordinary insight; the existence of a universal genetic code is just one of many evidences of our common ancestry. Based on the three domain phylogeny proposed by Woese and Fox in the early 1970s that all living beings can be classified on one of three main cellular lineages (Archaea, Bacteria, and Eukarya), it is possible to reconstruct some of the characteristics of the Last Universal Common Ancestor or cenancestor. Comparative genomics of organisms from the three domains has shown that the cenancestor was not a direct descendant of the prebiotic soup nor a primitive cellular entity where the genotype and the phenotype had an imprecise relationship (i.e., a progenote), rather it was an organism similar in complexity to extant cells. Due to the process of horizontal gene transfer and secondary gene losses, several questions regarding the nature of the cenancestor remain unsolved. However, attempts to infer its nature have led to the identification of a set of universally conserved genes. The research on the nature of the last universal common ancestor promises to shed light on fundamental aspects of living beings.
Evaluation of a novel training package among frontline maternal, newborn, and child health workers in South Sudan
Authors: Nelson Brett D. , Ahn Roy , Fehling Maya , Eckardt Melody J. , Conn Kathryn L. , El‐Bashir Alaa , Tiernan Margaret , Purcell Genevieve , Burke Thomas F. 
Published: September 2012

AbstractObjectiveTo develop, implement, and evaluate an evidence‐based Maternal, Newborn, and Child Survival (MNCS) package for frontline health workers (FHWs) in South Sudan.MethodsA multimodal needs assessment was conducted to develop a best‐evidence package comprised of targeted training, pictorial checklists, and reusable equipment and commodities. Implementation utilized a training‐of‐trainers model. Program effectiveness was assessed through knowledge assessments, objective structured clinical examinations (OSCEs), focus groups, and questionnaires.ResultsA total of 72 trainers and 708 FHWs were trained in 7 South Sudan states. Trainer knowledge assessments improved significantly: from 62.7% to 92.0% (P < 0.001). Mean FHW scores on maternal OSCEs were 21.1% pre‐training, 83.4% post‐training, and 61.5% 2–3 months after training (P < 0.001). Corresponding mean newborn OSCE scores were 41.6%, 89.8%, and 45.7% (P < 0.001). Questionnaires revealed high levels of use, satisfaction, and confidence. FHWs reported an average of 3.0 referrals (range, 0–20) to healthcare facilities during the 2–3 months following training, and 78.3% of FHWs were more likely to refer patients. Seven focus groups showed high satisfaction with trainings, commodities, and checklists, with few barriers.ConclusionThe MNCS package has led to improved FHW knowledge, skills, and referral. A novel package of training, checklists, and equipment can be successfully implemented in resource‐limited settings and enhance links between community‐based providers and healthcare facilities.
Physicochemical prerequisites for the formation of primary orebody zoning at copper-nickel sulfide deposits (by the example of the systemsFe–Ni–SandCu–Fe–S)
Authors: Kosyakov V.I. , Sinyakova E.F. 
Published: September 2012

AbstractThe zoning of massive orebodies at Cu–Ni sulfide deposits such as Noril’sk and Sudbury is commonly explained by fractional crystallization of magmatic sulfide melt. On the theoretical description of fractionation of its components, the results of mineralogical studies of orebodies are usually interpreted using the Rayleigh equation or its modification. But this equation is not applicable to describe crystallization of multicomponent melt and cocrystallization of several phases. In this work we present strict equations describing the distribution of components in a directly crystallized sample. We analyzed the influence of phase reactions on the successive formation of phases during crystallization and on the formation of primary zoning in the sample. This approach permits one to compute the component distribution curves and the crystallization paths by the quantitative phase diagram model. An experimental study of fractionation in the systems Fe–Ni–S and Cu–Fe–S was carried out. They can be regarded as systems modeling the formation of Ni- or Cu-rich sulfide ores. Such studies also yield qualitative and quantitative information about the phase diagrams of geochemical systems. We demonstrated that directed crystallization can be applied to determine the equations of phase reactions and the dependence of partition coefficients on the melt composition and to construct the paths of crystallization and evolution of the tie-line position during one-phase and cotectic crystallization. By the example of the system Fe–Ni–S, all possible types of sample zoning after fractional crystallization are shown. The main regularities of fractionation have been formulated, which are also applicable to multicomponent systems, e.g., Cu–Fe–Ni–S, which is widely used on the modeling of formation of zonal Cu–Ni sulfide ores.
Geodynamic nature of the Baikal Rift Zone and its sedimentary filling in the Cretaceous–Cenozoic: the effect of the far-range impact of the Mongolo-Okhotsk and Indo-Eurasian collisions
Authors: Buslov M.M. 
Published: September 2012

Abstract
The problem of the Late Meso-Cenozoic tectonics and geodynamics of the southern framing of the Siberian Platform is discussed. This area abounds in Late Meso-Cenozoic structures composed of sedimentary deposits. Analysis of voluminous geologo-stratigraphic, geophysical, and geochronological (track dating) data showed that these structures, including the Baikal Rift Zone, resulted from the far-range impact of two collisions related to the prolonged convergence of the North China and Indian continents with Eurasia, which took place in the Late Jurassic–Paleocene and Cenozoic, respectively. The synchronous occurrence of two great tectonic events led to the formation of a complex structure and a sedimentary basin, which are of different geodynamic nature and cannot be united into the same sequence of Late Cretaceous–Cenozoic formation of the Baikal Rift Zone. The Baikal system of shears and conjugate rifts formed in the Pliocene–Quaternary as a result of the far-range impact of the Indo-Eurasian collision. The latter led to the accumulation of the upper layered undeformed seismostratigraphic complex in all three Baikal basins. The sediments in Central Baikal are up to 3 km thick, and in the Selenga River valley they reach 5–6 km in thickness. The active intracontinental rift structures are characterized by zonal sedimentation. The middle layered deformed seismostratigraphic complex 1–1.5 km thick is recognized in all three Baikal basins and is similar to the Upper Oligocene–Lower Pliocene sediments of lacustrine-littoral, deltaic, and lacustrine facies widespread throughout the Baikal and Altai–Sayan regions and in Mongolia, where they formed in the environments of large lake systems. As a result of the deformations caused by the Indo-Eurasian collision, the Upper Oligocene–Lower Pliocene sediments were involved in the Pliocene–Quaternary ramp and unilateral-ramp structures in intermontane basins of the Altai–Sayan region and in Mongolia. The lower seismically transparent seismostratigraphic complex occurs only in South Baikal and Central Baikal. It is 1 km thick in the east and up to 45 km thick in the west. The complex is a fragment of the Late Cretaceous–Paleogene lacustrine-river sediments of the large fore-Baikal piedmont basin, which formed at the final stage of evolution of the vast Mongolo-Okhotsk orogen.
A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
Authors: Plagnol Vincent , Curtis James , Epstein Michael , Mok Kin Y. , Stebbings Emma , Grigoriadou Sofia , Wood Nicholas W. , Hambleton Sophie , Burns Siobhan O. , Thrasher Adrian J. , Kumararatne Dinakantha , Doffinger Rainer , Nejentsev Sergey 
Published: September 2012

Abstract
Motivation: Exome sequencing has proven to be an effective tool to discover the genetic basis of Mendelian disorders. It is well established that copy number variants (CNVs) contribute to the etiology of these disorders. However, calling CNVs from exome sequence data is challenging. A typical read depth strategy consists of using another sample (or a combination of samples) as a reference to control for the variability at the capture and sequencing steps. However, technical variability between samples complicates the analysis and can create spurious CNV calls.
Results: Here, we introduce ExomeDepth, a new CNV calling algorithm designed to control for this technical variability. ExomeDepth uses a robust model for the read count data and uses this model to build an optimized reference set in order to maximize the power to detect CNVs. As a result, ExomeDepth is effective across a wider range of exome datasets than the previously existing tools, even for small (e.g. one to two exons) and heterozygous deletions. We used this new approach to analyse exome data from 24 patients with primary immunodeficiencies. Depending on data quality and the exact target region, we find between 170 and 250 exonic CNV calls per sample. Our analysis identified two novel causative deletions in the genes GATA2 and DOCK8.
Availability: The code used in this analysis has been implemented into an R package called ExomeDepth and is available at the Comprehensive R Archive Network (CRAN).
Contact: v.plagnol@ucl.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
Antisense transcription is coupled to nucleosome occupancy in sense promoters
Authors: Dai Zhiming , Dai Xianhua 
Published: September 2012

Abstract
Motivation: Genome-wide pervasive transcription is widespread in eukaryotes, revealing an extensive array of antisense transcription that involves hundreds of previously unknown non-coding RNAs. Individual cases have shown that antisense transcription influences sense transcription, however, genome-wide mechanisms of how antisense transcription regulates sense transcription remain to be elucidated.
Results: Here, we performed a systematic analysis of sense–antisense transcription and nucleosome occupancy in yeast. We found that antisense transcription is associated with nucleosome occupancy in sense promoters. Using RNA polymerase II inactivation data as a reasonable approximation to antisense transcription inactivation data, we further showed that antisense transcripts increase nucleosome occupancy in sense promoter regions they overlap, and reduce nucleosome occupancy in sense promoter regions around their transcription termination sites. These results reveal the previously unappreciated roles of antisense transcription in directing nucleosome occupancy in sense promoters. Our findings will have implications in understanding regulatory functions of antisense transcription.
Contact: zhimdai@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Statistical challenges associated with detecting copy number variations with next-generation sequencing
Authors: Teo Shu Mei , Pawitan Yudi , Ku Chee Seng , Chia Kee Seng , Salim Agus 
Published: September 2012

Abstract
Motivation: Analysing next-generation sequencing (NGS) data for copy number variations (CNVs) detection is a relatively new and challenging field, with no accepted standard protocols or quality control measures so far. There are by now several algorithms developed for each of the four broad methods for CNV detection using NGS, namely the depth of coverage (DOC), read-pair, split-read and assembly-based methods. However, because of the complexity of the genome and the short read lengths from NGS technology, there are still many challenges associated with the analysis of NGS data for CNVs, no matter which method or algorithm is used.
Results: In this review, we describe and discuss areas of potential biases in CNV detection for each of the four methods. In particular, we focus on issues pertaining to (i) mappability, (ii) GC-content bias, (iii) quality control measures of reads and (iv) difficulty in identifying duplications. To gain insights to some of the issues discussed, we also download real data from the 1000 Genomes Project and analyse its DOC data. We show examples of how reads in repeated regions can affect CNV detection, demonstrate current GC-correction algorithms, investigate sensitivity of DOC algorithm before and after quality control of reads and discuss reasons for which duplications are harder to detect than deletions.
Contact: g0801862@nus.edu.sg or agus_salim@nuhs.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
Mechanical stretch via transforming growth factor‐β1 activates microRNA208a to regulate endoglin expression in cultured rat cardiac myoblasts
Authors: Shyu Kou‐Gi , Wang Bao‐Wei , Wu Gong‐Jhe , Lin Chiu‐Mei , Chang Hang 
Published: September 2012

AimsMicroRNAs (miRNAs) play a role in cardiac remodelling. MiR208a is essential for the expression of the genes involved in cardiac hypertrophy and fibrosis. The mechanism of regulation of miR208a involved in cardiac hypertrophy by mechanical stress is still unclear. We sought to investigate the mechanism of regulation of miR208a and the target gene of miR208a in cardiac cells by mechanical stretch.Methods and resultsRat H9c2 cells (cardiac myoblasts) grown on a flexible membrane base were stretched via vacuum to 20% of maximum elongation at 60 cycles/min. Mechanical stretch significantly enhanced miR208a expression after 4 h of stretch. Exogenous addition of transforming growth factor‐β1 (TGF‐β1) increased miR208a expression, and pre‐treatment with TGF‐β1 antibody attenuated the miR208a expression induced by stretch. Mechanical stretch significantly increased endoglin and collagen I expression for 6–24 h. Exogenous addition of TGF‐β1 and overexpression of miR208a up‐regulated endoglin and collagen I expression, while antagomir208a and Smad3/4 inhibitor attenuated endoglin and collagen I expression induced by stretch. Mechanical stretch and TGF‐β1 increased Smad3/4–DNA binding activity and miR208a promoter activity, and TGF‐β1 antibody and Smad3/4 inhibitor decreased the Smad3/4–DNA binding activity and miR208a promoter activity induced by stretch.ConclusionCyclic mechanical stretch enhances miR208a expression in cultured rat cardiac myoblasts. The stretch‐induced miR208a is mediated by TGF‐β1. Mir208a activates endoglin expression and may result in cardiac fibrosis.
Accounting for cultural well‐being: an exploratory study of New Zealand regions
Authors: Marriott Lisa , Miller Allan 
Published: September 2012

PurposeThe purpose of this research is to explore the economic and social arguments used in support of government assistance for cultural well‐being, and the accounting measures used to capture cultural well‐being at a regional level in New Zealand.Design/methodology/approachAccounting information reported in city council annual reports is used to examine expenditure on cultural well‐being. The research investigates possible relationships between regional economic growth and regional expenditure on arts, culture and heritage. It also investigates justifications for expenditure on activities classified under the category of arts, culture and heritage in the annual reports produced by New Zealand city councils.FindingsIn most regions, funding for cultural activities has increased over the past ten years. The findings of this research indicate there is no significant relationship between funding on cultural activities and regional economic growth. Instead, the research highlights the emphasis placed on social benefit arising from funding cultural activities.Research limitations/implicationsThe research is limited by access to comparable data. Accordingly, not all New Zealand regions are included in the analysis, resulting in a small number of observations. Moreover, robust city‐based measures of economic growth are unavailable, resulting in the use of labour force participation as a proxy for economic growth, together with the elimination of some regions in part of the analysis.Originality/valueExtant literature indicates that government expenditure on artistic and cultural activities is undertaken for reasons that include: possible economic benefit or generation of externalities, mitigation of market failure, educational purposes or improved national identity. In New Zealand, the “merit good” argument prevails with the objective of spending on artistic and cultural activity by local government expected to generate social rather than economic benefit.
Reporting incentives for accounting conservatism, evidence from asset and equity tunnelling
Authors: Xie Yuying , Zheng Liu , Amy Lau H.L. 
Published: September 2012

PurposeThe purpose of this study is to investigate reporting incentives for accounting conservatism in the context of asset and equity tunnelling and to provide empirical evidence that accounting conservatism can be reported for opportunistic reasons rather than efficiency reasons.Design/methodology/approachA cross‐sectional analysis of data from the period 2002 to 2004 is conducted.FindingsThis study provides empirical evidence that firms undertaking asset or equity tunnelling transactions report higher conservatism than firms undertaking other kinds of connected transactions. Further tests document a positive association between accounting conservatism and the private benefits gained by controlling shareholders from asset and equity tunnelling.Originality/valueContrary to the prevalent view that accounting conservatism signifies better quality accounting and benefits financial statement users, this study shows that accounting conservatism is influenced by institutional factors and the incentives of financial statement preparers. Researchers should exercise caution in interpreting higher accounting conservatism as an indication of better accounting information quality, especially in cross‐country research involving different institutions.
New Zealand shareholder attitudes towards corporate environmental disclosure
Authors: de Villiers Charl , van Staden Chris 
Published: September 2012

PurposeThe natural environment has become an increasingly important business issue over the last ten years while shareholder views on the importance of corporate environmental disclosure have not been extensively investigated. The purpose of this paper is to report the requirements of individual shareholders for the disclosure and regulation of environmental information and their intended use of the information.Design/methodology/approachRespondents were questioned using an online survey whether they want specific types of environmental information from companies and if so, where they want it disclosed, why they want it disclosed and if they feel strongly enough about it to want it made compulsory and be subject to an audit. The authors regard New Zealand as an ideal experimental setting for the investigation of shareholder views and focus on the members of an active shareholders' association in New Zealand and obtain a very high response rate.FindingsThe paper finds that most shareholders are very positive about the disclosure of a range of environmental information items and furthermore they want environmental information to be made compulsory, to be audited, and to be published in the annual report and also on the company website. The most important reason given by shareholders for requiring environmental information is that they want companies to be accountable for their environmental impacts. The results are potentially significant for company governance and management decision making and will also have policy implications for regulators.Practical implicationsThe findings have important implications for the government, the accounting profession and other standard setters. The paper suggests that the time has come for legislators, regulatory bodies and standard setters to take note of the policy implications if such a large proportion (59 percent – 72 percent) of shareholders want environmental disclosure to be compulsory and prescribed and not left to the discretion of companies.Social implicationsThe information needs of individual shareholders who make their own investment decisions should be of great interest to regulators, because such investors rely on publicly available information, whereas institutional investors also collect private information. Regulators need to remove information asymmetry by regulating and/or mandating disclosures and shareholder requirements for information should be an important consideration.Originality/valueThis paper is of high value. The paper addresses why the information is requested and what it would be used for, something that the studies prior to the year 2000 did not cover. In addition this study is the first to survey New Zealand investors 1996, i.e. prior to the resurgence of late in societal interest in environmental issues.