bluuebunny/crossref_metadata_2025 huggingface dataset:
netClass: an R-package for network based, integrative biomarker signature discovery
Authors: Cun Yupeng , Fröhlich Holger
Published: January 2014

In the past years, there has been a growing interest in methods that incorporate network information into classification algorithms for biomarker signature discovery in personalized medicine. The general hope is that this way the typical low reproducibility of signatures, together with the difficulty to link them to biological knowledge, can be addressed. Complementary to these efforts, there is an increasing interest in integrating different data entities (e.g. gene and miRNA expressions) into comprehensive models. To our knowledge, R-package netClass is the first software that addresses both, network and data integration. Besides several published approaches for network integration, it specifically contains our recently published stSVM method, which allows for additional integration of gene and miRNA expression data into one predictive classifier.

Availability:  netClass is available on http://sourceforge.net/p/netclassr and CRAN (http://cran.r-project.org).

Contact:  yupeng.cun@gmail.com
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
Authors: Rosikiewicz Marta , Robinson-Rechavi Marc
Published: January 2014

Motivation: Microarray results accumulated in public repositories are widely reused in meta-analytical studies and secondary databases. The quality of the data obtained with this technology varies from experiment to experiment, and an efficient method for quality assessment is necessary to ensure their reliability.

Results: The lack of a good benchmark has hampered evaluation of existing methods for quality control. In this study, we propose a new independent quality metric that is based on evolutionary conservation of expression profiles. We show, using 11 large organ-specific datasets, that IQRray, a new quality metrics developed by us, exhibits the highest correlation with this reference metric, among 14 metrics tested. IQRray outperforms other methods in identification of poor quality arrays in datasets composed of arrays from many independent experiments. In contrast, the performance of methods designed for detecting outliers in a single experiment like Normalized Unscaled Standard Error and Relative Log Expression was low because of the inability of these methods to detect datasets containing only low-quality arrays and because the scores cannot be directly compared between experiments.

Availability and implementation: The R implementation of IQRray is available at: ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R.

Contact:  Marta.Rosikiewicz@unil.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
Evidence of fjord spawning by southern Norwegian Atlantic halibut (Hippoglossus hippoglossus)
Authors: Seitz Andrew C. , Michalsen Kathrine , Nielsen Jennifer L. , Evans Mark D.
Published: January 2014

Atlantic halibut (Hippoglossus hippoglossus) in a Norwegian fjord were tagged with pop-up archival transmitting (PAT) tags to investigate whether they join offshore spawning events with halibut from other regions. All fish (n = 4) remained in the fjord throughout the spawning season, suggesting that they may be reproductively segregated from other stocks.
Comparative ribosome profiling reveals extensive translational complexity in differentTrypanosoma bruceilife cycle stages
Authors: Vasquez Juan-José , Hon Chung-Chau , Vanselow Jens T. , Schlosser Andreas , Siegel T. Nicolai
Published: January 2014

While gene expression is a fundamental and tightly controlled cellular process that is regulated at multiple steps, the exact contribution of each step remains unknown in any organism. The absence of transcription initiation regulation for RNA polymerase II in the protozoan parasite Trypanosoma brucei greatly simplifies the task of elucidating the contribution of translation to global gene expression. Therefore, we have sequenced ribosome-protected mRNA fragments in T. brucei, permitting the genome-wide analysis of RNA translation and translational efficiency. We find that the latter varies greatly between life cycle stages of the parasite and ∼100-fold between genes, thus contributing to gene expression to a similar extent as RNA stability. The ability to map ribosome positions at sub-codon resolution revealed extensive translation from upstream open reading frames located within 5′ UTRs and enabled the identification of hundreds of previously un-annotated putative coding sequences (CDSs). Evaluation of existing proteomics and genome-wide RNAi data confirmed the translation of previously un-annotated CDSs and suggested an important role for >200 of those CDSs in parasite survival, especially in the form that is infective to mammals. Overall our data show that translational control plays a prevalent and important role in different parasite life cycle stages of T. brucei.
Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation
Authors: Zhou Xuexia , Wu Wenwu , Li Huang , Cheng Yuanming , Wei Ning , Zong Jie , Feng Xiaoyan , Xie Zhiqin , Chen Dai , Manley James L. , Wang Hui , Feng Ying
Published: January 2014

Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Motif analysis revealed that SRSF10 binding to cassette exons was associated with exon inclusion, whereas the binding of SRSF10 within downstream constitutive exons was associated with exon exclusion. This positional effect was further demonstrated by the mutagenesis of potential SRSF10 binding motifs in two minigene constructs. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Consistent with this observation, cells depleted of SRSF10 expression were far more susceptible to endoplasmic reticulum stress-induced apoptosis than control cells. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions.
A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis
Authors: Pimentel Harold , Parra Marilyn , Gee Sherry , Ghanem Dana , An Xiuli , Li Jie , Mohandas Narla , Pachter Lior , Conboy John G.
Published: January 2014

Alternative pre-messenger RNA splicing remodels the human transcriptome in a spatiotemporal manner during normal development and differentiation. Here we explored the landscape of transcript diversity in the erythroid lineage by RNA-seq analysis of five highly purified populations of morphologically distinct human erythroblasts, representing the last four cell divisions before enucleation. In this unique differentiation system, we found evidence of an extensive and dynamic alternative splicing program encompassing genes with many diverse functions. Alternative splicing was particularly enriched in genes controlling cell cycle, organelle organization, chromatin function and RNA processing. Many alternative exons exhibited differentiation-associated switches in splicing efficiency, mostly in late-stage polychromatophilic and orthochromatophilic erythroblasts, in concert with extensive cellular remodeling that precedes enucleation. A subset of alternative splicing switches introduces premature translation termination codons into selected transcripts in a differentiation stage-specific manner, supporting the hypothesis that alternative splicing-coupled nonsense-mediated decay contributes to regulation of erythroid-expressed genes as a novel part of the overall differentiation program. We conclude that a highly dynamic alternative splicing program in terminally differentiating erythroblasts plays a major role in regulating gene expression to ensure synthesis of appropriate proteome at each stage as the cells remodel in preparation for production of mature red cells.
Expanding the zinc-finger recombinase repertoire: directed evolution and mutational analysis of serine recombinase specificity determinants
Authors: Sirk Shannon J. , Gaj Thomas , Jonsson Andreas , Mercer Andrew C. , Barbas Carlos F.
Published: January 2014

The serine recombinases are a diverse family of modular enzymes that promote high-fidelity DNA rearrangements between specific target sites. Replacement of their native DNA-binding domains with custom-designed Cys2–His2 zinc-finger proteins results in the creation of engineered zinc-finger recombinases (ZFRs) capable of achieving targeted genetic modifications. The flexibility afforded by zinc-finger domains enables the design of hybrid recombinases that recognize a wide variety of potential target sites; however, this technology remains constrained by the strict recognition specificities imposed by the ZFR catalytic domains. In particular, the ability to fully reprogram serine recombinase catalytic specificity has been impeded by conserved base requirements within each recombinase target site and an incomplete understanding of the factors governing DNA recognition. Here we describe an approach to complement the targeting capacity of ZFRs. Using directed evolution, we isolated mutants of the β and Sin recombinases that specifically recognize target sites previously outside the scope of ZFRs. Additionally, we developed a genetic screen to determine the specific base requirements for site-specific recombination and showed that specificity profiling enables the discovery of unique genomic ZFR substrates. Finally, we conducted an extensive and family-wide mutational analysis of the serine recombinase DNA-binding arm region and uncovered a diverse network of residues that confer target specificity. These results demonstrate that the ZFR repertoire is extensible and highlights the potential of ZFRs as a class of flexible tools for targeted genome engineering.
Fish species introductions provide novel insights into the patterns and drivers of phylogenetic structure in freshwaters
Authors: Strecker Angela L. , Olden Julian D.
Published: January 2014

Despite long-standing interest of terrestrial ecologists, freshwater ecosystems are a fertile, yet unappreciated, testing ground for applying community phylogenetics to uncover mechanisms of species assembly. We quantify phylogenetic clustering and overdispersion of native and non-native fishes of a large river basin in the American Southwest to test for the mechanisms (environmental filtering versus competitive exclusion) and spatial scales influencing community structure. Contrary to expectations, non-native species were phylogenetically clustered and related to natural environmental conditions, whereas native species were not phylogenetically structured, likely reflecting human-related changes to the basin. The species that are most invasive (in terms of ecological impacts) tended to be the most phylogenetically divergent from natives across watersheds, but not within watersheds, supporting the hypothesis that Darwin's naturalization conundrum is driven by the spatial scale. Phylogenetic distinctiveness may facilitate non-native establishment at regional scales, but environmental filtering restricts local membership to closely related species with physiological tolerances for current environments. By contrast, native species may have been phylogenetically clustered in historical times, but species loss from contemporary populations by anthropogenic activities has likely shaped the phylogenetic signal. Our study implies that fundamental mechanisms of community assembly have changed, with fundamental consequences for the biogeography of both native and non-native species.
Flavobacterium longum sp. nov. and Flavobacterium urocaniciphilum sp. nov., isolated from a wastewater treatment plant, and emended descriptions of Flavobacterium caeni and Flavobacterium terrigena
Authors: Fujii Daichi , Nagai Fumiko , Watanabe Yohei , Shirasawa Yukio
Published: January 2014

Two Gram-staining-negative, strictly aerobic, non-endospore-forming, non-motile, rod-shaped bacteria, designated strains YIT 12745T and YIT 12746T, were isolated from sludge from a wastewater treatment plant. 16S rRNA gene sequence analyses indicated that these strains belonged to the genus

Flavobacterium

. In these analyses, strains YIT 12745T and YIT 12746T were most closely related to the type strains of

Flavobacterium caeni

and

Flavobacterium terrigena

, with 16S rRNA gene sequence similarity values of 94.9 % and 96.2 %, respectively. For both novel strains, menaquinone (MK-6) was the only respiratory quinone. The major fatty acids of strain YIT 12745T were iso-C15 : 1 G (14.4 %), iso-C16 : 0 (13.2 %), C15 : 0 (12.9 %), iso-C15 : 0 (12.9 %) and iso-C17 : 0 3-OH (11.5 %). Those of strain YIT 12746T were iso-C15 : 0 (21.5 %), iso-C16 : 0 (13.3 %), C15 : 0 (12.0 %) and iso-C15 : 1 G (11.9 %). The genomic DNA G+C contents of strains YIT 12745T and YIT 12746T were 48.7 and 30.9 mol%, respectively. From their differential phenotypic and phylogenetic characteristics, these strains are considered to represent two novel species of the genus

Flavobacterium

, for which the names Flavobacterium longum sp. nov. (type strain YIT 12745T = JCM 19141T = DSM 27077T) and Flavobacterium urocaniciphilum sp. nov. (type strain YIT 12746T = JCM 19142T = DSM 27078T) are proposed. Emended descriptions of

Flavobacterium caeni

and

Flavobacterium terrigena

are also proposed.
Illumina TruSeq synthetic long-reads empowerde novoassembly and resolve complex, highly repetitive transposable elements
Authors: McCoy Rajiv C. , Taylor Ryan W. , Blauwkamp Timothy A. , Kelley Joanna L. , Kertesz Michael , Pushkarev Dmitry , Petrov Dmitri A. , Fiston-Lavier Anna-Sophie
Published: January 2014

High-throughput DNA sequencing technologies have revolutionized genomic analysis, including thede novoassembly of whole genomes. Nevertheless, assembly of complex genomes remains challenging, in part due to the presence of dispersed repeats which introduce ambiguity during genome reconstruction. Transposable elements (TEs) can be particularly problematic, especially for TE families exhibiting high sequence identity, high copy number, or present in complex genomic arrangements. While TEs strongly affect genome function and evolution, most currentde novoassembly approaches cannot resolve long, identical, and abundant families of TEs. Here, we applied a novel Illumina technology called TruSeq synthetic long-reads, which are generated through highly parallel library preparation and local assembly of short read data and achieve lengths of 1.5-18.5 Kbp with an extremely low error rate (∼0.03% per base). To test the utility of this technology, we sequenced and assembled the genome of the model organismDrosophila melanogaster(reference genome strainy;cn,bw,sp) achieving an N50 contig size of 69.7 Kbp and covering 96.9% of the euchromatic chromosome arms of the current reference genome. TruSeq synthetic long-read technology enables placement of individual TE copies in their proper genomic locations as well as accurate reconstruction of TE sequences. We entirely recovered and accurately placed 4,229 (77.8%) of the 5,434 of annotated transposable elements with perfect identity to the current reference genome. As TEs are ubiquitous features of genomes of many species, TruSeq synthetic long-reads, and likely other methods that generate long reads, offer a powerful approach to improvede novoassemblies of whole genomes.
Novel Roles for the Polyphenol Oxidase Enzyme in Secondary Metabolism and the Regulation of Cell Death in Walnut
Authors: Araji Soha , Grammer Theresa A. , Gertzen Ross , Anderson Stephen D. , Mikulic-Petkovsek Maja , Veberic Robert , Phu My L. , Solar Anita , Leslie Charles A. , Dandekar Abhaya M. , Escobar Matthew A.
Published: January 2014

The enzyme polyphenol oxidase (PPO) catalyzes the oxidation of phenolic compounds into highly reactive quinones. Polymerization of PPO-derived quinones causes the postharvest browning of cut or bruised fruit, but the native physiological functions of PPOs in undamaged, intact plant cells are not well understood. Walnut (Juglans regia) produces a rich array of phenolic compounds and possesses a single PPO enzyme, rendering it an ideal model to study PPO. We generated a series of PPO-silenced transgenic walnut lines that display less than 5% of wild-type PPO activity. Strikingly, the PPO-silenced plants developed spontaneous necrotic lesions on their leaves in the absence of pathogen challenge (i.e. a lesion mimic phenotype). To gain a clearer perspective on the potential functions of PPO and its possible connection to cell death, we compared the leaf transcriptomes and metabolomes of wild-type and PPO-silenced plants. Silencing of PPO caused major alterations in the metabolism of phenolic compounds and their derivatives (e.g. coumaric acid and catechin) and in the expression of phenylpropanoid pathway genes. Several observed metabolic changes point to a direct role for PPO in the metabolism of tyrosine and in the biosynthesis of the hydroxycoumarin esculetin in vivo. In addition, PPO-silenced plants displayed massive (9-fold) increases in the tyrosine-derived metabolite tyramine, whose exogenous application elicits cell death in walnut and several other plant species. Overall, these results suggest that PPO plays a novel and fundamental role in secondary metabolism and acts as an indirect regulator of cell death in walnut.
Thylakoid FtsH Protease Contributes to Photosystem II and Cytochromeb 6 fRemodeling inChlamydomonas reinhardtiiunder Stress Conditions
Authors: Malnoë Alizée , Wang Fei , Girard-Bascou Jacqueline , Wollman Francis-André , de Vitry Catherine
Published: January 2014

FtsH is the major thylakoid membrane protease found in organisms performing oxygenic photosynthesis. Here, we show that FtsH from Chlamydomonas reinhardtii forms heterooligomers comprising two subunits, FtsH1 and FtsH2. We characterized this protease using FtsH mutants that we identified through a genetic suppressor approach that restored phototrophic growth of mutants originally defective for cytochrome b  6  f accumulation. We thus extended the spectrum of FtsH substrates in the thylakoid membranes beyond photosystem II, showing the susceptibility of cytochrome b  6  f complexes (and proteins involved in the c  i heme binding pathway to cytochrome b  6) to FtsH. We then show how FtsH is involved in the response of C. reinhardtii to macronutrient stress. Upon phosphorus starvation, photosynthesis inactivation results from an FtsH-sensitive photoinhibition process. In contrast, we identified an FtsH-dependent loss of photosystem II and cytochrome b  6  f complexes in darkness upon sulfur deprivation. The D1 fragmentation pattern observed in the latter condition was similar to that observed in photoinhibitory conditions, which points to a similar degradation pathway in these two widely different environmental conditions. Our experiments thus provide extensive evidence that FtsH plays a major role in the quality control of thylakoid membrane proteins and in the response of C. reinhardtii to light and macronutrient stress.
(Z)-N-[(Z)-3-(2,5-Dimethylphenylimino)butan-2-ylidene]-2,5-dimethylaniline
Authors: Lv Wen-Xian , Li Jian , Hu Yu-Lai , Su Ying-Peng , Huang Dan-Feng
Published: January 2014

The asymmetric unit of the title compound, C20H24N2, contains one half-molecule, with the single C—C bond of the 1,4-diazabutadiene fragment situated on a centre of symmetry. The benzene rings are inclined to the 1,4-diazabutadiene mean plane by 59.5 (1)°.
[1H-1,2,4-Triazole-5(4H)-thione-κS]bis(triphenylphosphane-κP)(nitrato-κO)silver(I) methanol monosolvate
Authors: Wattanakanjana Yupa , Palamae Sureeporn , Ratthiwan Jenejira , Nimthong Ruthairat
Published: January 2014

In the title complex, [Ag(NO3)(C2H3N3S)(C18H15P)2]·CH3OH, the AgIion exhibits a distorted tetrahedral coordination geometry formed by two P atoms from two triphenylphosphine ligands, one S atom from a 1H-1,2,4-triazole-5(4H)-thione ligand and one O atom from a nitrate ion. In the crystal, complex and solvent molecules are linked by O—H...O and N—H...O hydrogen bonds forming a chain along theb-axis direction. The chains are linked by weak C—H...O hydrogen bonds forming a two-dimensional supramolecular architecture parallel to (001). In addition, an intramolecular N—H...O hydrogen bond is observed.
Bis(n-dodecylammonium) bis(chloranilato)diethanolcuprate(II)
Authors: Himegi Akiko , Kawata Satoshi
Published: January 2014

In the title compound, (C12H25NH3)2[Cu(C6Cl2O4)2(C2H5OH)2], the CuIIatom lies on a crystallographic inversion center and is coordinated in a distorted octahedral geometry by four O atoms of two chloranilate ligands and two O atoms of two ethanol molecules which aretransto each other in the axial positions. In the crystal, the CuIImononuclear dianions are linked by O—H...O hydrogen bonds into a tape along thea-axis direction. The tapes are linked through N—H...O hydrogen bonds between the dianion and then-dodecylammonium cation, forming a two-dimensional network parallel to theabplane.
1-(2,4-Dinitrophenyl)-2-[(E)-(3,4,5-trimethoxybenzylidene)]hydrazine
Authors: Chantrapromma Suchada , Ruanwas Pumsak , Boonnak Nawong , Chidan Kumar C. S. , Fun Hoong-Kun
Published: January 2014

Molecules of the title compound, C16H16N4O7, are not planar with a dihedral angle of 5.50 (11)° between the substituted benzene rings. The twometa-methoxy groups of the 3,4,5-trimethoxybenzene moiety lie in the plane of the attached ring [Cmethyl–O–C–C torsion angles −0.1 (4)° and −3.7 (3)°] while thepara-methoxy substituent lies out of the plane [Cmethyl—O—C—C, −86.0 (3)°]. An intramolecular N—H...O hydrogen bond involving the 2-nitro substituent generates anS(6) ring motif. In the crystal structure, molecules are linked by weak C—H...O interactions into screw chains, that are arranged into a sheet parallel to thebcplane. These sheets are connected by π–π stacking interactions between the nitro and methoxy substituted aromatic rings with a centroid–centroid separation of 3.9420 (13) Å. C—H...π contacts further stabilize the two-dimensional network.
2,2′-Bi(9,9-diethylfluorene)
Authors: Park Ki-Min , Oh Hankook , Kang Youngjin
Published: January 2014

The title compound, C34H34, systematic name 9,9,9′,9′-tetraethyl-2,2′-bi(9H-fluorene), crystallized with two crystallographically independent molecules (AandB) in the asymmetric unit. These differ mainly in the orientation of the lateral ethyl chains: in moleculeA, they are both on the same side of the molecule whereas in moleculeB, one diethylfluorene moiety has undergone a 180° rotation such that the two pairs of ethyl residues appear on opposite sides of the molecule. The fluorene ring systems subtend dihedral angles of 31.37 (4) and 43.18 (3)° in moleculesAandB, respectively. Hence the two fluorene moieties are tilted slightly toward one another. This may be due to the presence of intermolecular C—H...π interactions between neighboring molecules. The lateral ethyl chains (excluding H atoms) are also almost planar, with each pair almost perpendicular to the plane of the fluorene system to which they are attached with dihedral angles between the ethyl and fluorene planes in the range 86.04 (8)–89.5 (1)°.
Fruits and vegetables intake are associated with ethnicity and socio‐demographic factors in Mauritius
Authors: Badurally Adam B.T. , Mahomoodally M.F. , Subratty A.H. , Ramasawmy D.
Published: January 2014

Purpose

Fruits and vegetables intake (FVI) in the human diet is strongly related to health status and incidence of diseases. The purpose of this paper is to hypothesize that demographic factors and food insecurity could be associated with the frequency of FVI in a multicultural community such as Mauritius.

Design/methodology/approach

Information pertaining to socio‐demographic factors, anthropometric measurements, medical history, lifestyle factors, reason(s) for dietary choice and food insecurity factors were amassed randomly from 374 adults.

Findings

The mean FVI was found to be significantly lower (p<0.05) for the food insecure respondents (n=39). Also, significant (p<0.05) associations between FVI and the level of education (p=0.031 and p=0.012, respectively), ethnic groups (p=0.028 and p=0.013, respectively), income ranges (p<0.001 and p<0.001, respectively), and food insecurity (p<0.001 and p<0.001, respectively) were noted. A high income was also significantly related to a higher FVI. With respect to disease occurrence, a significant (p=0.035) relationship was found with respect to FVI and respiratory diseases.

Originality/value

The paper shows that there is a pressing need to re‐evaluate efficiency of existing nutrition policies and programs. Also that it is important to establish more sensitization campaigns geared towards the above‐mentioned target groups with respect to FVI. Authorities concerned should also endeavour to achieve affordable, accessible and safe fruits and vegetables as a mean to promote a healthy eating culture in Mauritius.
Resource sharing challenges and prospects in Nigerian university libraries
Authors: Anasi Stella , Ali Hussaini
Published: January 2014

Purpose

The purpose of this paper is to examine the barriers to effective resource sharing among academic libraries in Nigeria.

Design/methodology/approach

Professional librarians from six randomly selected federal university libraries representing the six geopolitical zones in Nigeria were surveyed using a descriptive survey research design. Questionnaires were sent to 124 librarians; 85 were returned and found to be usable, for a response rate of 68.5 per cent.

Findings

The study revealed that the prospect for resource sharing among university libraries in Nigeria is high. However, factors that hinder effective resource sharing include inadequate funding, a dearth of skilled librarians, power outages, an absence of web‐accessible OPACs, uneven development of libraries, and slow progress of library automation. It is recommended that each university library have a specific annual budget allocation for ICT development and maintenance and for training of librarians to pilot resource sharing projects.

Originality/value

This paper presents resource‐sharing challenges facing academic libraries in Nigeria. It encourages information professionals to embark on capacity building for effective resource sharing. This paper was prepared for the 12th Interlending and Document Supply Conference, held in September 2011.
Retail Insights ‐ Winter 1997
Authors: Pollitt David
Published: January 2014

Prioritizing should be a company’s No. 1 virtue. In the absence of priority, companies flounder, and employees become distracted. This inevitably leads to missed deadlines,
over‐extended budgets, and a resulting output different from what was originally intended. This is excruciatingly evident when implementing an information technology (IT) strategy. Few industries can compete with the heap of wasteful, incomplete, and underutilized projects IT has amassed over the past two decades. The core of the problem is not the technology, but a failure clearly to define priorities at all levels in a company.
Interventionist grid development projects: a research framework based on three frames
Authors: Venters Will , Kyriakidou‐Zacharoudiou Avgousta
Published: January 2014

Purpose

This paper seeks to consider the collaborative efforts of developing a grid computing infrastructure within problem‐focused, distributed and multi‐disciplinary projects – which the authors term interventionist grid development projects – involving commercial, academic and public collaborators. Such projects present distinctive challenges which have been neglected by existing escience research and information systems (IS) literature. The paper aims to define a research framework for understanding and evaluating the social, political and collaborative challenges of such projects.

Design/methodology/approach

The paper develops a research framework which extends Orlikowski and Gash's concept of technological frames to consider two additional frames specific to such grid projects; bureaucratic frames and collaborator frames. These are used to analyse a case study of a grid development project within Healthcare which aimed to deploy a European data‐grid of medical images to facilitate collaboration and communication between clinicians across the European Union.

Findings

That grids are shaped to a significant degree by the collaborative practices involved in their construction, and that for projects involving commercial and public partners such collaboration is inhibited by the differing interpretive frames adopted by the different relevant groups.

Research limitations/implications

The paper is limited by the nature of the grid development project studied, and the subsequent availability of research subjects.

Practical implications

The paper provides those involved in such projects, or in policy around such grid developments, with a practical framework by which to evaluate collaborations and their impact on the emergent grid. Further, the paper presents lessons for future such Interventionist grid projects.

Originality/value

This is a new area for research but one which is becoming increasingly important as data‐intensive computing begins to emerge as foundational to many collaborative sciences and enterprises. The work builds on significant literature in escience and IS drawing into this new domain. The research framework developed here, drawn from the IS literature, begins a new stream of systems development research with a distinct focus on bureaucracy, collaboration and technology within such interventionist grid development projects.
From meticulous professionals to superheroes of the business world
Authors: Picard Claire-France , Durocher Sylvain , Gendron Yves
Published: January 2014

Purpose

– The purpose of this paper is to examine the relative cultural shift from professionalism to commercialism in the accounting profession, based on an analysis of the promotional brochures used by theOrdre des comptables agréés du Québec(Institute of Chartered Accountants of Québec), over the last 40 years, to attract new members.

Design/methodology/approach

– The study's specific objectives are: to examine accountancy's cultural representations depicted in promotional brochures; to evaluate the extent to which these representations are indicative of the commercialist shift as documented in the literature; and to establish whether the representations under study provide further insight into the nature of the cultural shift. Drawing on the semiotic approach developed by Roland Barthes, the authors' analysis is predicated on the idea that promotional brochures and advertisements, though often simple in appearance, constitute complex representations that convey meaningful information about influential values and cultural change.

Findings

– The authors found that commercial values are increasingly apparent through the celebration of multidisciplinary services and the emphasis on generous compensation and high dynamism.

Originality/value

– Barthes' framework was especially useful to analyze the interplay between images and text to gain insight into the historical emergence of what has become the accountant's representation of today. As such, this study points to promotional representations participating to the inculcation of a cosmopolitan culture, where the internationalization of business is supposedly natural, inevitable, and beneficial to everyone. The authors' research also highlights the increasingly significant role played by marketing experts in designing professional institutes' brochures, consistent with the broader view of marketization as a key trend within the accounting industry.
JURA: a collaborative solution to Hong Kong academic libraries storage challenge
Authors: Sidorko Peter , Lee Linda
Published: January 2014

Purpose

– The purpose of this paper is to discuss issues and concerns raised in a collaborative and cooperative central storage facility for Hong Kong academic libraries.

Design/methodology/approach

– The approach is to propose and to implement a joint storage business plan and a possibility of acting for others to consider similar storage facilities.

Findings

– Useful experiences have been gained while planning a central storage facility.

Research limitations/implications

– The proposed JURA project is for Hong Kong academic libraries.

Practical implications

– The sharing of JURA proposal to create a central storage will inform the libraries around the region of the benefits of having a useful facility in the long term.

Originality/value

– The paper will inform others wishing to set up collaborative storages on governance, storage systems, business plan, problems and issues in what is still a relatively unexplored approach to storage problems.
Defoliation effects on seed dispersal and seedling recruitment in a tropical rain forest understorey palm
Authors: van Lent Jeffrey , Hernández‐Barrios Juan C. , Anten Niels P. R. , Martínez‐Ramos Miguel
Published: January 2014

Assessing the demographic effects of leaf area losses in perennial plants is important to determine population resilience to natural and anthropogenic disturbances. Yet, while impacts of defoliation on vital rates of adult plants have been well documented, consequences for seed dispersal and seedling recruitment have been barely explored.

Here, we assessed the effects of defoliation on fruit production, fruit/seed size, seed dispersal and seedling recruitment in populations of Chamaedorea ernesti‐augustii, a tropical rain forest, understorey palm from Mesoamerica, whose leaves are exploited as a highly valuable non‐timber forest product (NTFP).

Fruit size and seed production were quantified in mature palms that were subjected to 0% (control), 25%, 50%, 75% and 100% experimental removal of standing leaves, applied every 6 months over 2 years. Seed dispersal by birds and gravity, and seed predation by small vertebrates on the ground were also quantified. Rates of seedling recruitment were recorded in non‐defoliated and ‘sterile’ populations (75% sustained defoliation and periodical removal of all produced fruits). Finally, a stochastic model was used to quantify the overall effect of defoliation on seedlings recruited from locally (i.e. dispersed by gravity) and immigrant produced seeds (i.e. dispersed by birds).

Increasing defoliation strongly reduced seed production. The probability of bird dispersal was positively correlated with fruit/seed size. Isolated (i.e. bird‐dispersed) seeds endured lower predation rates than grouped (i.e. gravity‐dispersed) ones. Modelling showed that seedling recruitment rate is severely reduced in highly defoliated populations due to a strong decline in the number of seedlings coming from local seed sources. Surrounding non‐defoliated populations could partly compensate for this effect via seedlings coming from immigrant seeds.

Synthesis. Chronic and intense defoliation negatively affects seed production and dispersal, which reduces the probability of seedling recruitment. Such effects may have a profound impact on the dynamics and genetic variability of populations, which should be taken into account when considering the effects of natural defoliation and sustainability of leaf‐harvesting regimes.
How perceived interpersonal justice relates to job burnout and intention to leave: The role of leader–member exchange and cognition‐based trust in leaders
Authors: Son SuJin , Kim Do‐Yeong , Kim Mina
Published: January 2014

Intense competition among companies makes it particularly important for organizations to retain talented and skilled employees to maintain their competitive advantage. This study examines the linkage between employees' perceptions of the interpersonal justice demonstrated by their leaders and consequent job burnout resulting in turnover intention by focusing on the mediating role of leader–member exchange (LMX) as well as the moderating role of employees' cognition‐based trust in their leaders. Data were obtained from 158 MBA students attending a large university in South Korea. Using structural equation modelling, we examined an integrative model that combines interpersonal justice, LMX, job burnout, and turnover intention. The results reveal that (a) LMX partially mediates the relationships between interpersonal justice and job burnout and (b) employees' cognition‐based trust in their leaders moderates the relationship between LMX and job burnout. By examining the mediating role of LMX as well as the moderating role of cognition‐based trust in the relationship between perceived interpersonal justice and employee job burnout, this study (1) provides a comprehensive explanation of employee job burnout and (2) outlines the implications for job burnout research and practice.
The distribution of intraocular pressure and associated systemic factors in a Korean population: The Korea National Health and Nutrition Examination Survey
Authors: Kim Mi Jeung , Park Ki Ho , Kim Chan Yun , Jeoung Jin Wook , Kim Seok Hwan
Published: January 2014

Purpose

To investigate the distribution of intraocular pressure (IOP) and its associated factors in a large Korean population based on the data from the nationwide cross‐sectional survey.

Methods

We obtained 2009–2010 data from the Korea National Health and Nutrition Examination Survey (KNHANES) (n = 17 901). After excluding individuals under 19 years of age, a total of 13 431 subjects were enrolled. All participants completed a comprehensive questionnaire and underwent an ocular examination including measurement of IOP by Goldmann applanation tonometry, as well as a systemic evaluation including blood pressure measurements, anthropometry and blood tests.

Results

The mean IOP in the right eye was 13.99 ± 2.75 mmHg, and in the left eye, 13.99 ± 2.75 mmHg, representing no significant bilateral difference. There was, however, a significant difference between males (14.19 ± 2.78 mmHg) and females (13.79 ± 2.70 mmHg) (p < 0.001). Multiple regression analysis revealed that higher IOP was significantly correlated with male sex, higher myopic refractive error, higher body mass index, higher systolic blood pressure, higher fasting plasma glucose and higher total cholesterol (all p < 0.05). On the other hand, age, histories of smoking or migraine or cold hands/feet were not significantly correlated with IOP (all p > 0.05).

Conclusions

In the general Korean population, IOP increases with male sex and increasing myopia. Further, IOP is significantly correlated with systemic factors relating to cardiovascular disease and metabolic syndrome.
EQ‐5D‐Y as a health‐related quality of life measure in children and adolescents with functional disability in Sweden: testing feasibility and validity
Authors: Burström K , Bartonek Å , Broström EW , Sun S , Egmar A‐C
Published: January 2014

Aim

The EQ‐5D‐Y is a newly developed generic instrument measuring health‐related quality of life in children and adolescents.

The aim of the study was to test the feasibility and validity of the EQ‐5D‐Y in a Swedish patient sample of children and adolescents with functional motor, orthopaedic and medical disabilities and to compare the results with a general population sample.

Methods

Two samples of children and adolescents answered the EQ‐5D‐Y and a core set of internationally standardised instruments, variables and socio‐demographic questions. Patients with functional disability (n = 71, aged seven to 17 years) and individuals from the general population (n = 407, aged eight to 16 years) were included in this study.

Results

There was a low number of missing answers. Significantly more problems were reported in all dimensions in the patient sample, and the mean visual analogue scale (VAS) score was significantly lower. Any problems were reported by 83% of the patients and by 37% of the general population. In the patient sample, 21% reported problems at the most severe level, compared with 1.5% in the general population sample. By subgroup analyses by diagnoses, the frequency of reported problems in the different dimensions varied.

Conclusion

Even though feasibility and discriminative validity of the EQ‐5D‐Y were supported in our study, further studies are needed including more patients and patient groups.
Natural orifice specimen extraction using prolapsing technique in single‐incision laparoscopic colorectal resections for colorectal cancers
Authors: Katsuno Goutaro , Fukunaga Masaki , Nagakari Kunihiko , Yoshikawa Seiichiro , Ouchi Masakazu , Hirasaki Yoshinori , Azuma Daisuke
Published: January 2014

Introduction

It is often technically difficult to cut the lower rectum with an endoscopic linear stapler in single‐incision laparoscopic colorectal resections (SILC) because some surgical devices are inserted through the same access platform. If the rectum is cut incorrectly, it may cause anastomotic leakage. We recently applied natural orifice specimen extraction (NOSE) using the prolapsing technique to overcome this technical difficulty in SILC procedures in selected patients.

Materials and Surgical Technique

The access platform is placed in the small umbilical incision area. SILC is performed using a surgical technique similar to the conventional laparoscopic medial‐to‐lateral approach. The proximal part of the tumor site is transected with laparoscopic staplers. Then, the tumor lesion and bowel are pulled out of the body through the anus by means of inversion. Next, the distal side of the bowel is cut with a stapler and the rectal stump is reinforced with sutures under direct vision. The distal side of the bowel is then pushed back into the body. NOSE with prolapsing technique is then complete. After that, the anvil is attached to the proximal part of the bowel at the umbilical incision site, and intracorporeal anastomosis is performed.

Discussion

NOSE with prolapsing technique was applied in 14 SILC procedures for colorectal cancer patients. All procedures were successful, and there were no anastomotic leakages in the series. This technique enabled us to perform pure SILC safely without affecting cosmesis, even in cases where we needed to cut the lower rectum.
Successful thoracoscopic removal of a giant teratoma following extraction of cystic conponents: A case report
Authors: Miyauchi Yoshihiro , Matsubara Hirochika , Uchida Tsuyoshi , Matsuoka Hiroyasu , Ichihara Tomofumi , Matsumoto Masahiko
Published: January 2014

Video‐assisted thoracoscopic surgery is a type of minimal‐access surgery. The nature of the surgery means that there are limitations on the size of a tumor that can be removed through an access incision. Herein, we report our experience removing a giant teratoma (16 × 14 × 13 cm in size) from the anterior mediastinum of a young girl. We employed video‐assisted thoracoscopic surgery to remove the teratoma through a mini‐thoracotomy following the extraction of the cystic components.
Pancreatoduodenal artery aneurysm resulting from median arcuate ligament compression successfully treated with laparoscopic ligament section
Authors: Hiramatsu Yoshihiro , Sakaguchi Takanori , Kawabata Toshiki , Shibasaki Yasushi , Kikuchi Hirotoshi , Takehara Yasuo , Uyama Ichiro , Konno Hiroyuki
Published: January 2014

True aneurysms of the pancreatoduodenal arteries are frequently associated with stenosis or occlusion of the celiac trunk caused by median arcuate ligament compression. Celiac stenosis cannot be cured, even by transarterial embolization, which has recently become a good alternative to open surgical repair. To prevent recurrence, management of median arcuate ligament compression to correct hemodynamics in vascular networks should also be performed. Herein we report a case of pancreatoduodenal arterial aneurysm with median arcuate ligament compression that was successfully treated with minimally invasive laparoscopic median arcuate ligament section. The patient was discharged 4 days after surgery with no complications. Enhanced CT 1 month after surgery revealed no residual celiac trunk stenosis or aneurysm. Normalization of blood flow by laparoscopic median arcuate ligament section is a good option for some patients with a pancreatoduodenal arterial aneurysm.
Ultrahigh dimensional time course feature selection
Authors: Xu Peirong , Zhu Lixing , Li Yi
Published: January 2014

Statistical challenges arise from modern biomedical studies that produce time course genomic data with ultrahigh dimensions. In a renal cancer study that motivated this paper, the pharmacokinetic measures of a tumor suppressor (CCI‐779) and expression levels of 12,625 genes were measured for each of 33 patients at 8 and 16 weeks after the start of treatments, with the goal of identifying predictive gene transcripts and the interactions with time in peripheral blood mononuclear cells for pharmacokinetics over the time course. The resulting data set defies analysis even with regularized regression. Although some remedies have been proposed for both linear and generalized linear models, there are virtually no solutions in the time course setting. As such, a novel GEE‐based screening procedure is proposed, which only pertains to the specifications of the first two marginal moments and a working correlation structure. Different from existing methods that either fit separate marginal models or compute pairwise correlation measures, the new procedure merely involves making a single evaluation of estimating functions and thus is extremely computationally efficient. The new method is robust against the mis‐specification of correlation structures and enjoys theoretical readiness, which is further verified via Monte Carlo simulations. The procedure is applied to analyze the aforementioned renal cancer study and identify gene transcripts and possible time‐interactions that are relevant to CCI‐779 metabolism in peripheral blood.
Semiparametric analysis of incomplete current status outcome data under transformation models
Authors: Wen Chi‐Chung , Chen Yi‐Hau
Published: January 2014

This work, motivated by an osteoporosis survey study, considers regression analysis with incompletely observed current status data. Here the current status data, including an examination time and an indicator for whether or not the event of interest has occurred by the examination time, is not observed for all subjects. Instead, a surrogate outcome subject to misclassification of the current status is available for all subjects. We focus on semiparametric regression under transformation models, including the proportional hazards and proportional odds models as special cases. Under the missing at random mechanism where the missingness of the current status outcome can depend only on the observed surrogate outcome and covariates, we propose an approach of validation likelihood based on the likelihood from the validation subsample where the data are fully observed, with adjustments of the probability of observing the current status outcome, as well as the distribution of the surrogate outcome in the validation subsample. We propose an efficient computation algorithm for implementation, and derive consistency and asymptotic normality for inference with the proposed estimator. The application to the osteoporosis survey data and simulations reveal that the validation likelihood performs well; it removes the bias from the “complete case” analysis discarding subjects with missing data, and achieves higher efficiency than the inverse probability weighting analysis.