bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homepeptide Repeats: Implications for Protein Structure, Function and Evolution
Authors: Uthayakumar Muthukumarasamy , Benazir Bowdadu , Patra Sanjeev , Vaishnavi Marthandan Kirti , Gurusaran Manickam , Sureka Kanagarajan , Jeyakanthan Jeyaraman , Sekar Kanagaraj 
Published: August 2012

Abstract
Analysis of protein sequences from Mycobacterium tuberculosis H37Rv (Mtb H37Rv) was performed to identify homopeptide repeat-containing proteins (HRCPs). Functional annotation of the HRCPs showed that they are preferentially involved in cellular metabolism. Furthermore, these homopeptide repeats might play some specific roles in protein–protein interaction. Repeat length differences among Bacteria, Archaea and Eukaryotes were calculated in order to identify the conservation of the repeats in these divergent kingdoms. From the results, it was evident that these repeats have a higher degree of conservation in Bacteria and Archaea than in Eukaryotes. In addition, there seems to be a direct correlation between the repeat length difference and the degree of divergence between the species. Our study supports the hypothesis that the presence of homopeptide repeats influences the rate of evolution of the protein sequences in which they are embedded. Thus, homopeptide repeat may have structural, functional and evolutionary implications on proteins.
Structure of the yeast F
1
F
o
-ATP synthase dimer and its role in shaping the mitochondrial cristae
Authors: Davies Karen M. , Anselmi Claudio , Wittig Ilka , Faraldo-Gómez José D. , Kühlbrandt Werner 
Published: August 2012

We used electron cryotomography of mitochondrial membranes from wild-type and mutant
Saccharomyces cerevisiae
to investigate the structure and organization of ATP synthase dimers in situ. Subtomogram averaging of the dimers to 3.7 nm resolution revealed a V-shaped structure of twofold symmetry, with an angle of 86° between monomers. The central and peripheral stalks are well resolved. The monomers interact within the membrane at the base of the peripheral stalks. In wild-type mitochondria ATP synthase dimers are found in rows along the highly curved cristae ridges, and appear to be crucial for membrane morphology. Strains deficient in the dimer-specific subunits
e
and
g
or the first transmembrane helix of subunit 4 lack both dimers and lamellar cristae. Instead, cristae are either absent or balloon-shaped, with ATP synthase monomers distributed randomly in the membrane. Computer simulations indicate that isolated dimers induce a plastic deformation in the lipid bilayer, which is partially relieved by their side-by-side association. We propose that the assembly of ATP synthase dimer rows is driven by the reduction in the membrane elastic energy, rather than by direct protein contacts, and that the dimer rows enable the formation of highly curved ridges in mitochondrial cristae.
Identifying multi-layer gene regulatory modules from multi-dimensional genomic data
Authors: Li Wenyuan , Zhang Shihua , Liu Chun-Chi , Zhou Xianghong Jasmine 
Published: August 2012

Abstract
Motivation: Eukaryotic gene expression (GE) is subjected to precisely coordinated multi-layer controls, across the levels of epigenetic, transcriptional and post-transcriptional regulations. Recently, the emerging multi-dimensional genomic dataset has provided unprecedented opportunities to study the cross-layer regulatory interplay. In these datasets, the same set of samples is profiled on several layers of genomic activities, e.g. copy number variation (CNV), DNA methylation (DM), GE and microRNA expression (ME). However, suitable analysis methods for such data are currently sparse.
Results: In this article, we introduced a sparse Multi-Block Partial Least Squares (sMBPLS) regression method to identify multi-dimensional regulatory modules from this new type of data. A multi-dimensional regulatory module contains sets of regulatory factors from different layers that are likely to jointly contribute to a local ‘gene expression factory’. We demonstrated the performance of our method on the simulated data as well as on The Cancer Genomic Atlas Ovarian Cancer datasets including the CNV, DM, ME and GE data measured on 230 samples. We showed that majority of identified modules have significant functional and transcriptional enrichment, higher than that observed in modules identified using only a single type of genomic data. Our network analysis of the modules revealed that the CNV, DM and microRNA can have coupled impact on expression of important oncogenes and tumor suppressor genes.
Availability and implementation: The source code implemented by MATLAB is freely available at: http://zhoulab.usc.edu/sMBPLS/.
Contact: xjzhou@usc.edu
Supplementary information: Supplementary material are available at Bioinformatics online.
An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection
Authors: Wang Xingbin , Kang Dongwan D. , Shen Kui , Song Chi , Lu Shuya , Chang Lun-Ching , Liao Serena G. , Huo Zhiguang , Tang Shaowu , Ding Ying , Kaminski Naftali , Sibille Etienne , Lin Yan , Li Jia , Tseng George C. 
Published: August 2012

Abstract
Summary: With the rapid advances and prevalence of high-throughput genomic technologies, integrating information of multiple relevant genomic studies has brought new challenges. Microarray meta-analysis has become a frequently used tool in biomedical research. Little effort, however, has been made to develop a systematic pipeline and user-friendly software. In this article, we present MetaOmics, a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis. MetaQC provides a quantitative and objective tool to assist study inclusion/exclusion criteria for meta-analysis. MetaDE and MetaPath were developed for candidate marker and pathway detection, which provide choices of marker detection, meta-analysis and pathway analysis methods. The system allows flexible input of experimental data, clinical outcome (case–control, multi-class, continuous or survival) and pathway databases. It allows missing values in experimental data and utilizes multi-core parallel computing for fast implementation. It generates informative summary output and visualization plots, operates on different operation systems and can be expanded to include new algorithms or combine different types of genomic data. This software suite provides a comprehensive tool to conveniently implement and compare various genomic meta-analysis pipelines.
Availability: http://www.biostat.pitt.edu/bioinfo/software.htm
Contact: ctseng@pitt.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
A Land-Plant-Specific Glycerol-3-Phosphate Acyltransferase Family in Arabidopsis: Substrate Specificity, sn-2 Preference, and Evolution
Authors: Yang Weili , Simpson Jeffrey P. , Li-Beisson Yonghua , Beisson Fred , Pollard Mike , Ohlrogge John B. 
Published: August 2012

Abstract
Arabidopsis (Arabidopsis thaliana) has eight glycerol-3-phosphate acyltransferase (GPAT) genes that are members of a plant-specific family with three distinct clades. Several of these GPATs are required for the synthesis of cutin or suberin. Unlike GPATs with sn-1 regiospecificity involved in membrane or storage lipid synthesis, GPAT4 and -6 are unique bifunctional enzymes with both sn-2 acyltransferase and phosphatase activity resulting in 2-monoacylglycerol products. We present enzymology, pathway organization, and evolutionary analysis of this GPAT family. Within the cutin-associated clade, GPAT8 is demonstrated as a bifunctional sn-2 acyltransferase/phosphatase. GPAT4, -6, and -8 strongly prefer C16:0 and C18:1 ω-oxidized acyl-coenzyme As (CoAs) over unmodified or longer acyl chain substrates. In contrast, suberin-associated GPAT5 can accommodate a broad chain length range of ω-oxidized and unsubstituted acyl-CoAs. These substrate specificities (1) strongly support polyester biosynthetic pathways in which acyl transfer to glycerol occurs after oxidation of the acyl group, (2) implicate GPAT specificities as one major determinant of cutin and suberin composition, and (3) argue against a role of sn-2-GPATs (Enzyme Commission 2.3.1.198) in membrane/storage lipid synthesis. Evidence is presented that GPAT7 is induced by wounding, produces suberin-like monomers when overexpressed, and likely functions in suberin biosynthesis. Within the third clade, we demonstrate that GPAT1 possesses sn-2 acyltransferase but not phosphatase activity and can utilize dicarboxylic acyl-CoA substrates. Thus, sn-2 acyltransferase activity extends to all subbranches of the Arabidopsis GPAT family. Phylogenetic analyses of this family indicate that GPAT4/6/8 arose early in land-plant evolution (bryophytes), whereas the phosphatase-minus GPAT1 to -3 and GPAT5/7 clades diverged later with the appearance of tracheophytes.
Lotus japonicus ARPC1 Is Required for Rhizobial Infection
Authors: Hossain Md Shakhawat , Liao Jinqiu , James Euan K. , Sato Shusei , Tabata Satoshi , Jurkiewicz Anna , Madsen Lene H. , Stougaard Jens , Ross Loretta , Szczyglowski Krzysztof 
Published: August 2012

Abstract
Remodeling of the plant cell cytoskeleton precedes symbiotic entry of nitrogen-fixing bacteria within the host plant roots. Here we identify a Lotus japonicus gene encoding a predicted ACTIN-RELATED PROTEIN COMPONENT1 (ARPC1) as essential for rhizobial infection but not for arbuscular mycorrhiza symbiosis. In other organisms ARPC1 constitutes a subunit of the ARP2/3 complex, the major nucleator of Y-branched actin filaments. The L. japonicus arpc1 mutant showed a distorted trichome phenotype and was defective in epidermal infection thread formation, producing mostly empty nodules. A few partially colonized nodules that did form in arpc1 contained abnormal infections. Together with previously described L. japonicus Nck-associated protein1 and 121F-specific p53 inducible RNA mutants, which are also impaired in the accommodation of rhizobia, our data indicate that ARPC1 and, by inference a suppressor of cAMP receptor/WASP-family verpolin homologous protein-ARP2/3 pathway, must have been coopted during evolution of nitrogen-fixing symbiosis to specifically mediate bacterial entry.
New Insights into Roles of Cell Wall Invertase in Early Seed Development Revealed by Comprehensive Spatial and Temporal Expression Patterns of GhCWIN1 in Cotton
Authors: Wang Lu , Ruan Yong-Ling 
Published: August 2012

Abstract
Despite substantial evidence on the essential roles of cell wall invertase (CWIN) in seed filling, it remains largely unknown how CWIN exerts its regulation early in seed development, a critical stage that sets yield potential. To fill this knowledge gap, we systematically examined the spatial and temporal expression patterns of a major CWIN gene, GhCWIN1, in cotton (Gossypium hirsutum) seeds from prefertilization to prestorage phase. GhCWIN1 messenger RNA was abundant at the innermost seed coat cell layer at 5 d after anthesis but became undetectable at 10 d after anthesis, at the onset of its differentiation into transfer cells characterized by wall ingrowths, suggesting that CWIN may negatively regulate transfer cell differentiation. Within the filial tissues, GhCWIN1 transcript was detected in endosperm cells undergoing nuclear division but not in those cells at the cellularization stage, with similar results observed in Arabidopsis (Arabidopsis thaliana) endosperm for CWIN, AtCWIN4. These findings indicate a function of CWIN in nuclear division but not cell wall biosynthesis in endosperm, contrasting to the role proposed for sucrose synthase (Sus). Further analyses revealed a preferential expression pattern of GhCWIN1 and AtCWIN4 in the provascular region of the torpedo embryos in cotton and Arabidopsis seed, respectively, indicating a role of CWIN in vascular initiation. Together, these novel findings provide insights into the roles of CWIN in regulating early seed development spatially and temporally. By comparing with previous studies on Sus expression and in conjunction with the expression of other related genes, we propose models of CWIN- and Sus-mediated regulation of early seed development.
Investigations into the improvement of the metal grinding process: application of a sub‐zero temperature cutting fluid
Authors: Daisley Richard P. , Chowdary Boppana V. 
Published: August 2012

PurposeThe purpose of this paper is to investigate the effects of liquid carbon dioxide (LCO2) on grinding of stainless steel.Design/methodology/approachA factorial experimental approach was used to compare the LCO2's performance against grinding under dry air and emulsion coolants.FindingsThe experimental results have a great use to practitioners. It was found that under special conditions, LCO2 proves to be an alternative coolant for grinding of temperature sensitive materials. Furthermore, grinding under LCO2 conditions produced the lowest tangential force, while the normal forces were close to the values found under emulsion fluid environment. When compared to grinding under dry conditions, LCO2 coolant was successful in reducing the work piece temperatures. LCO2 and emulsion conditions inhibit work hardening by reducing material deformation at the grinding zone.Originality/valueThe paper shows that sub‐zero temperature coolants have the ability to bring about lower grinding temperatures than what is typically achieved under conventional fluids.
The artiﬁcial neural network based prediction of friction properties of Al2O3‐TiO2 coatings
Authors: Cetinel Hakan 
Published: August 2012

PurposeThe purpose of this paper is to predict friction/wear properties of Al2O3‐TiO2 coatings using artificial neural networks (ANN).Design/methodology/approachWear experiments were conducted in dry and acidic conditions. Wear loss values were determined and an ANN model was fixed in order to predict wear loss and friction coefficient values.FindingsExperimental and theoretical study results were well matched for wear loss and friction coefficient values.Research limitations/implicationsThe paper covers comparison of experimental and theoretical friction/wear results.Practical implicationsA practical implication is that wear loss values can be predicted without further wear experiments.Originality/valueIn this paper, the wear behavior of Al2O3‐TiO2 coatings has been investigated, both experimentally and theoretically, for the first time.
Inverse approach for the pressure, temperature, and pressure‐viscosity index determination in TEHL of line contacts
Authors: Chu Li‐Ming , Hsu Hsiang‐Chen , Lin Jaw‐Ren , Chang Yuh‐Ping 
Published: August 2012

PurposeThe purpose of this paper is to describe an inverse approach to estimate the pressure distribution, temperature distribution, and pressure‐viscosity index (z) in a thermal elastohydrodynamic lubrication (TEHL) line contact.Design/methodology/approachOnce the film thickness is given, the pressure distribution can be calculated using the inverse approach. Subsequently, thermal expansivity and temperature‐viscosity coefficient of lubricant are given, and then the z is guessed initially. The Gauss‐Seidel iteration is employed to calculate the temperature distribution from the rheology, energy, and surface temperature equations. In order to increase the algorithm stability, the least‐squares method must be employed to calculate the optimum value of the z in the computational domain. Furthermore, the pressure‐viscosity index must be updated by the iteration method to calculate accurate temperature distribution and apparent viscosity until convergence.FindingsThis approach presents a smooth curve of the pressure and temperature distributions with the measurement error from the resolution in the film thickness measurement and z value. Furthermore, this approach still provides a superior solution in apparent viscosity, whereas the direct method provides a much larger error in apparent viscosity.Originality/valueThe paper describes an inverse approach to estimate the pressure distribution, temperature distribution, and pressure‐viscosity index in a TEHL line contact. This approach overcomes the problems of pressure and temperature rise fluctuations and generates accurate results of pressure and temperature distribution from a small number of measured points of film thickness, which also saves computing time. Furthermore, this approach still provides a superior solution in apparent viscosity.
The effects of welding parameters on wear performance of clad layer with TiC ceramic
Authors: Peng De‐Xing 
Published: August 2012

PurposeThe purpose of this paper is to test whether TiC clad layer deposited on carbon steel by gas tungsten arc welding (GTAW) improves carbon steel substrate wear resistance.Design/methodology/approachCladding microstructure and cladded surface hardness were tested in samples prepared under varying welding parameters. The chemical composition, microstructure and surface morphology of the cladded layer were analyzed by optical microscope, scanning electron microscopy and energy dispersive X‐ray spectroscopy. The wear behavior of the cladded layer was studied with a block‐on‐ring tribometer. Wear mechanisms in the specimens are discussed based on microscopic study of wear surface characteristics.FindingsThe experimental results revealed an excellent metallurgical bond between the composite coating and substrate. Hardness was increased from HRb 6.6 in the substrate to HRb 65 in the modified layer due to the presence of the hard TiC phase. Experimental comparison of varying welding parameters revealed that welding speed and current had the largest effect on the hardness and wear resistance of the cladded layer.Originality/valueThe paper shows that by using cladding techniques to improve surface properties such as resistances to wear, corrosion, and oxidation, service life can be increased, and machinery costs can be reduced.
The interplay of structure and agency dynamics in strike activity
Authors: Darlington Ralph 
Published: August 2012

PurposeThe purpose of this paper is to build on the insights of mobilisation theory to examine the interplay of structure and agency dynamics in strike activity. It proposes to do so by investigating the 2007 36‐hour strike undertaken by 2,300 engineering and infrastructure workers employed by the private consortium Metronet on the London Underground, focusing attention on the relationship between workers’ militancy, trade union leadership and left‐wing politics within a highly distinctive and union favourable “opportunity structure” context.Design/methodology/approachSemi‐structured in‐depth interviews were conducted with 24 RMT union informants within Metronet and the London Underground (including union members, reps, branch and regional officers); analysis was made of documentary industrial relations and trade union material; and personal fieldwork observation.FindingsAlthough favourable specific contextual and contingent factors served as both provocations and resources for strike action, notably in enhancing workers’ bargaining position and lending feasibility to a strike mobilisation approach, the role of trade union leadership and left‐wing politics at every level of the union in collectivising workers’ experiences and aspirations in forms which directly encouraged combativity was also crucial.Research limitations/implicationsThe specificity of the case study limits the degree of generalisation that can be made to other industries. Researchers are encouraged to test the proposed analytical approach further.Originality/valueThe paper provides case‐study empirical evidence into an important arena of employment in the UK, contributes to our understanding of the multi‐dimensional causes of strike activity; and adds an important political dimension to the analysis of collective mobilisation often neglected in both industrial relations and social movement literature.
Role typology for health and safety representatives
Authors: Harris Leigh‐Ann , Bendix Olsen Kirsten , Walker Robyn Jane 
Published: August 2012

PurposeThe purpose of this paper is to focus on the development of a health and safety (HS) representative role typology that demonstrates how representatives enact their roles and improve occupational health and safety (OHS) under New Zealand law. It aims to consider the factors that influence the roles that HS representatives’ assume.Design/methodology/approachThis qualitative, cross‐perceptual study centres on the role enactments of eight HS representatives at two metal manufacturers. Semi‐structured interviews were conducted with HS representatives, managers, workers, senior managers, OHS managers and a union convenor. “Types” were differentiated by the HS representatives’ purpose, activities and OHS impacts.FindingsIn total, four HS representative role “types” were identified: administrators, workshop inspectors, problem solvers and craft experts. Administrators implemented and operated OHS management systems and improved OHS management. Workshop inspectors undertook compliance and monitoring roles and improved workers’ attitudes towards OHS. Problem solvers found solutions to control hazards and improved production from an OHS perspective. Craft experts applied technical knowledge to influence strategic OHS decisions. Role enactment appeared to be influenced by representatives’ expert power, job roles and the organisational role definition. Representatives operating under both managerial and worker defined HS representative systems, increased worker “voice” by providing an avenue to redress OHS concerns.Practical implicationsImplications arise for OHS policy, HS representative training courses and organisational/managerial support.Originality/valueThe paper presents a HS representative role typology distinctively based on cross‐perceptual data that also provides a more holistic perspective of the HS representative role by considering representatives’ purpose, role enactment and OHS impact.
Engineering compliance and worker resistance in UK further education
Authors: Mather Kim , Worrall Les , Mather Graeme 
Published: August 2012

PurposeThe purpose of this paper is to explore control and resistance in the UK further education (FE) sector by examining senior college managers’ attempts to engineer culture change and analysing lecturers’ resistance to such measures.Design/methodology/approachData were derived from interviews with managers and lecturers in two English FE colleges and the analysis of college documents. Interview data were analysed thematically using NVIVO software.FindingsIt was found that college managers sought to build consent to change among lecturers based on values derived from “business‐like” views. Culture change initiatives were framed within the language of empowerment but lecturers’ experiences of change led them to feel disempowered and cynical as managers imposed their view of what lecturers should be doing and how they should behave. This attempt to gain control of the lecturers’ labour process invoked the “Stepford” lecturer metaphor used in the paper. Paradoxically, as managers sought to create lecturers who were less resistant to change, individualised resistance intensified as managers’ attempts to win hearts and minds conspicuously failed.Research limitations/implicationsThe paper draws on data from two case study colleges and this limits the generalisability of its findings.Practical implicationsThe paper provides a critical perspective on the received wisdom of investing in stylised change programmes that promise to win staff over to change but which may alienate those they purport to empower and ultimately lead to degenerative workplace relations.Originality/valueThe paper offers new insights into culture change from the juxtaposed, polarised views of senior managers and lecturers, while highlighting the negative consequences of imposing change initiatives from above.