bluuebunny/crossref_metadata_2025 huggingface dataset:
Intensification of grassland and forage use: driving forces and constraints
Authors: Oenema Oene , de Klein Cecile , Alfaro Marta
Published: June 2014

The increasing demand for safe and nutritional dairy and beef products in a globalising world, together with the needs to increase resource use efficiency and to protect biodiversity, provide strong incentives for intensification of grassland and forage use. This paper addresses the question: ‘Does intensification of grassland and forage use lead to efficient, profitable and sustainable ecosystems?’ We present some notions about intensification of agricultural production, and then discuss the intensification of grassland-based dairy production in The Netherlands, Chile and New Zealand. Finally, we arrive at some conclusions. External driving forces and the need to economise (the law of the optimum) provide strong incentives for intensification, that is, for increasing the output per unit surface area and labour. The three country cases illustrate that intensification of grassland use is a global phenomenon, with winners and losers. Winners are farmers who are able to achieve a high return on investments. Losers are small farmers who drop out of the business unless they broaden their income base. The relationship between intensification and environmental impact is complex. Within certain ranges, intensification leads to increased emissions of nutrients and greenhouse gases to air and use of water per unit surface area, but to decreased emissions when expressed per unit of product. The sustainability of a grassland-based ecosystem is ultimately defined by the societal appreciation of that system and by biophysical and socioeconomic constraints. In conclusion, intensification may lead to more efficient and profitable and, thereby, more sustainable grassland ecosystems. This holds especially for those systems that are currently not sustainable because they are either underutilised and of low productivity or over-exploited and unregulated, and as long as the adapted systems meet societal and ecological constraints.
Pattern of variation of zooplankton assemblages under the influence of river runoffs: a study case along the Apulian marine coastal waters (southern Italy, Mediterranean Sea)
Authors: Barbone Enrico , Pastorelli Annamaria , Perrino Vito , Blonda Massimo , Ungaro Nicola
Published: June 2014

The distribution and composition of zooplankton assemblages was investigated along the Apulian marine–coastal area (Mediterranean Sea) in the time period between January 2008 and February 2010. Zooplankton samples were collected monthly from 15 monitoring stations located in two sub-basins, namely, the southern Adriatic (11 stations) and the northern Ionian (4 stations). Results indicated a strong influence of river runoffs on zooplankton assemblages in terms of an increase in the abundance of tolerant species and a reduction of overall richness and diversity of species. Compared with the Ionian, in the Adriatic stations, zooplankton standing stocks showed higher abundances. Results also suggest that the zooplankton can be considered a useful biological indicator of water quality for the Apulian coastal waters and could be used in environmental monitoring programs.
Uncertainty analysis for large-scale prediction of the van Genuchten soil-water retention parameters with pedotransfer functions
Authors: Liao K. , Xu S. , Wu J. , Zhu Q.
Published: June 2014

Hydrological, environmental and ecological modellers require van Genuchten soil-water retention parameters that are difficult to measure. Pedotransfer functions (PTFs) are thus routinely applied to predict hydraulic parameters (θs, ln(α) and n) from basic soil properties (e.g. bulk density, soil texture and organic matter content). This study investigated the spatial variations of van Genuchten parameters via geostatistical methods (e.g. kriging and co-kriging with remote-sensing data) and multiple-stepwise-regression-based PTFs with a limited number of samples (58) collected in Pingdu City, Shandong Province, China. The uncertainties in the spatial estimation of van Genuchten parameters were evaluated using bootstrap and Latin hypercube sampling methods. Results show that PTF-estimated parameters are less varied than observed parameters. The uncertainty in the parameter estimation is mainly due to the limited number of samples used for deriving PTFs (intrinsic uncertainty) and spatial interpolations of basic soil properties by (co)kriging (input uncertainty). When considering the intrinsic uncertainty, 36%, 29% and 47% of measurements are within the corresponding error bars (95% confidence intervals of the predictions) for the θs, ln(α) and n, respectively. When considering both intrinsic and input uncertainties, 86%, 66% and 88% of observations are within the corresponding error bars for the θs, ln(α) and n, respectively. Therefore, the input uncertainty is more important in the spatial estimation of van Genuchten parameters than the intrinsic uncertainty. Measurement of basic soil properties at high resolution and properly use of powerful spatial interpolation approach are both critical in the accurate spatial estimation of van Genuchten parameters.
Molecular evidence for mid-Pleistocene divergence of populations of three freshwater amphipod species (Talitroidea : Chiltoniidae) on Kangaroo Island, South Australia, with a new spring-associated genus and species
Authors: King Rachael A. , Leys Remko
Published: June 2014

Recent molecular and morphological analyses have shown that chiltoniid amphipods, once thought to be a relictual group, are a diverse and speciose family of Australian freshwater amphipods. As part of a larger examination of the family, chiltoniids from Kangaroo Island in South Australia were collected and analysed using molecular (COI and 28S) and morphological methods in order to understand species distributional patterns and relationships. Kartachiltonia moodyi gen. nov., sp. nov., a spring-associated species endemic to the island, was discovered and populations of three additional mainland species (Austrochiltonia australis, A. dalhousiensis and A. subtenuis) were examined. The island populations of A. australis, A. dalhousiensis and A. subtenuis were found to form natural groups with differing haplotype coalescence times dating from the Early to Mid-Pleistocene. Numerous cycles of regional climate change throughout the Pleistocene are likely to have driven speciation in chiltoniid amphipods in southern Australia and the presence of multiple chiltoniid species at Kangaroo Island indicates that it exists at a likely convergence of species distribution patterns. Three possible hypotheses to explain the evolution and diversity of chiltoniids in southern Australia are discussed as are evidence for potential introduction and long-distance dispersal events.
Carbohydrate availability and exercise training adaptation: Too much of a good thing?
Authors: Bartlett Jonathan D. , Hawley John A. , Morton James P.
Published: June 2014

Traditional nutritional approaches to endurance training have typically promoted high carbohydrate (CHO) availability before, during and after training sessions to ensure adequate muscle substrate to meet the demands of high daily training intensities and volumes. However, during the past decade, data from our laboratories and others have demonstrated that deliberately training in conditions of reduced CHO availability can promote training‐induced adaptations of human skeletal muscle (i.e. increased maximal mitochondrial enzyme activities and/or mitochondrial content, increased rates of lipid oxidation and, in some instances, improved exercise capacity). Such data have led to the concept of ‘training low, but competing high’ whereby selected training sessions are completed in conditions of reduced CHO availability (so as to promote training adaptation), but CHO reserves are restored immediately prior to an important competition. The augmented training response observed with training‐low strategies is likely regulated by enhanced activation of key cell signalling kinases (e.g. AMPK, p38MAPK), transcription factors (e.g. p53, PPARδ) and transcriptional co‐activators (e.g. PGC‐1α), such that a co‐ordinated up‐regulation of both the nuclear and mitochondrial genomes occurs. Although the optimal practical strategies to train low are not currently known, consuming additional caffeine, protein, and practising CHO mouth‐rinsing before and/or during training may help to rescue the reduced training intensities that typically occur when ‘training low’, in addition to preventing protein breakdown and maintaining optimal immune function. Finally, athletes should practise ‘train‐low’ workouts in conjunction with sessions undertaken with normal or high CHO availability so that their capacity to oxidise CHO is not blunted on race day.
Barriers and opportunities for research in publishing studies
Authors: BAVERSTOCK Alison , STEINITZ Jackie
Published: June 2014

This paper reports findings from an international survey into the research involvement and support of university teaching staff in a relatively new profession‐orientated discipline, publishing studies (PS). It uses these findings to consider barriers and opportunities for academic research both specifically in PS and more broadly in other profession‐orientated disciplines. Greater understanding was felt to be of value as universities internationally are increasingly being pressurized to create close links with the wider economy, produce employable students, and encourage relevant and implementable research. The survey suggests that while there is strong agreement among respondents that it is beneficial for those teaching PS to be research‐active, there was considerable variation in current levels of research activity. Respondents rated their research activity highest in departments with an active research culture and effective research support processes. Lack of time was the main reason cited for reduced or non‐involvement in academic research and while this is a common issue for academics, PS respondents isolated a number of exacerbating factors. Suggestions are offered for addressing identified barriers and pursuing new opportunities for research. The paper argues that as research outputs of academics are increasingly monitored it is important to consider how the full range of disciplines housed within institutions can be accommodated within research support. Overall, the research has a strong relevance for interdisciplinary areas, and other profession‐ and practice‐orientated subjects within universities.
Toward a scalable and sustainable approach to open access publishing and archiving for humanities and social sciences societies: a proposal
Authors: KENNISON Rebecca , NORBERG Lisa
Published: June 2014

The proposal we offer here (and in the more extensive ‘white paper’ proposal on which this article is based) tackles head‐on the open access (OA) business models that have proven particularly problematic for implementation of OA in the humanities and social sciences (HSS). Our proposal suggests all tertiary institutions contribute to systemic support of the research process itself, including its entire scholarly output. A bold rethinking of the economics of OA by way of partnerships among scholarly societies and academic libraries funded by an institutional fee structure based on a student‐and‐faculty per‐capita sliding scale, our plan is nevertheless intentionally incremental. Our proposal focuses first on HSS and primarily in the United States, but just as research and scholarship are increasingly global and collaborative, our plan is not bound by discipline or national borders, but can be adopted by all those looking for a more equitable and sustainable OA model.
Book review
Authors: McIlroy Thad
Published: June 2014

The Book Publishing Industry, 3rd edn Albert N. Greco, Jim Milliot, Robert Wharton London and New York, Routledge, 2013, 490pp. ISBN 978‐0‐415‐88725‐0 (hbk) £85.00/$130.00; 978‐0‐415‐88724‐3 (pbk) £39.99/$59.95; 978‐0‐203‐83456‐5 (ebk) £39.99/$61.95
Cohomology of Coxeter arrangements and Solomon’s descent algebra
Authors: Douglass J. , Pfeiffer Götz , Röhrle Gerhard
Published: June 2014

We refine a conjecture by Lehrer and Solomon on the structure of the Orlik-Solomon algebra of a finite Coxeter groupWWand relate it to the descent algebra ofWW. As a result, we claim that both the group algebra ofWWand the Orlik-Solomon algebra ofWWcan be decomposed into a sum of induced one-dimensional representations of element centralizers, one for each conjugacy class of elements ofWW. We give a uniform proof of the claim for symmetric groups. In addition, we prove that a relative version of the conjecture holds for every pair(W,WL)(W, W_L), whereWWis arbitrary andWLW_Lis a parabolic subgroup ofWW, all of whose irreducible factors are of typeAA.
SUMOylation of GPS2 protein regulates its transcription-suppressing function
Authors: Bi Hailian , Li Shujing , Wang Miao , Jia Zhaojun , Chang Alan K. , Pang Pengsha , Wu Huijian
Published: June 2014

G-protein pathway suppressor 2 (GPS2) is a human suppressor of G protein–activated mitogen-activated protein kinase signaling. It is involved in many physiological processes, including DNA repair, cell proliferation, apoptosis, and brain development. In this study, we show that GPS2 can be modified by the small ubiquitin-like modifier (SUMO) SUMO-1 but not SUMO-2 or -3. Two SUMOylation sites (K45 and K71) are identified in the N-terminal coiled-coil domain of GPS2. Substitution of K45 with arginine reduces SUMOylation, whereas substitution of K71 or both K45 and K71 with arginine abolishes SUMOylation, with more of the double mutant GPS2 appearing in the cytosol than in the nucleus compared with wild type and the two-single-mutant GPS2. SUMOylation stabilizes GPS2 protein by promoting its interaction with TBL1 and reducing its ubiquitination. SUMOylation also enhances the ability of GPS2 to suppress transcription and promotes its ability to inhibit estrogen receptor α–mediated transcription by increasing its association with SMRT, as demonstrated in MCF-7 and T47D cells. Moreover, SUMOylation of GPS2 also represses the proliferation of MCF-7 and T47D cells. These findings suggest that posttranslational modification of GPS2 by SUMOylation may serve as a key factor that regulates the function of GPS2 in vivo.
Effects of high glucose on integrin activity and fibronectin matrix assembly by mesangial cells
Authors: Miller Charles G. , Pozzi Ambra , Zent Roy , Schwarzbauer Jean E.
Published: June 2014

The filtration unit of the kidney is the glomerulus, a capillary network supported by mesangial cells and extracellular matrix (ECM). Glomerular function is compromised in diabetic nephropathy (DN) by uncontrolled buildup of ECM, especially type IV collagen, which progressively occludes the capillaries. Increased levels of the ECM protein fibronectin (FN) are also present; however, its role in DN is unknown. Mesangial cells cultured under high glucose conditions provide a model system for studying the effect of elevated glucose on deposition of FN and collagen IV. Imaging of mesangial cell cultures and analysis of detergent-insoluble matrix show that, under high glucose conditions, mesangial cells assembled significantly more FN matrix, independent of FN protein levels. High glucose conditions induced protein kinase C–dependent β1 integrin activation, and FN assembly in normal glucose was increased by stimulation of integrin activity with Mn2+. Collagen IV incorporation into the matrix was also increased under high glucose conditions and colocalized with FN fibrils. An inhibitor of FN matrix assembly prevented collagen IV deposition, demonstrating dependence of collagen IV on FN matrix. We conclude that high glucose induces FN assembly, which contributes to collagen IV accumulation. Enhanced assembly of FN might facilitate dysregulated ECM accumulation in DN.
Articulating Medieval Logic
Authors: Parsons Terence
Published: June 2014

Medieval logic consists of theories and practices clustered around a core of rules and axioms; the logic contains widely known principles which can be derived from the core. These are used by Aristotle to prove conversion principles, and reduce some syllogisms to others: Exposition (“existential instantiation”), Expository Syllogism (“existential generalization”) and Reductio. Medieval logicians expand on Aristotle’s notation, and this brings new logical principles, such as quantifier interchanges. Theorists use the flexible word order to Latin to let surface order of expressions determine semantic scope. They also make assumptions about existential import that need dealing with. More important, medieval logic is formulated within a natural language, Latin, so there is no logical form except for grammatical form. We look at what is most distinctive of late medieval logic, the useful theory of modes of personal supposition. We examine special terms used to accommodate sentences containing three or more main quantified phrases. Logicians theorize about the logical behavior of pronouns with antecedents; without such pronouns the system of logic is weak; with them added it is expressively as rich as contemporary predicate logic. Also touched on are tense and modality, and intentional contexts, and artificial signs used to alter scope.
Aristotle’s Proofs of Conversions and Syllogisms
Authors: Parsons Terence
Published: June 2014

In Prior Analytics Aristotle proves the conversion principles, using three logical techniques: reductio (indirect derivation), exposition (a kind of existential instantiation: given ‘Some S is a P’, introduce a previously unused name m, and write ‘m is an S’ and ‘m is a P’), and expository syllogism (given ‘m is a P’ and ‘m is an S’ infer ‘Some S is a P’). He assumes four basic forms of syllogism, and uses them together with reductio, exposition, and expository syllogisms to prove the remaining forms. The four basic forms can be proved too, though this was unknown to him or to medieval logicians. Monotonicity properties of the determiners ‘every’, ‘no’, and ‘some’ are explained; Aristotle’s four basic argument forms allow easy proofs of their monotonicity properties. By the 13th century a memorizable verse was developed that encodes Aristotle’s validation of all syllogistic forms from the basic four.
Linguish
Authors: Parsons Terence
Published: June 2014

When propositions become complex, one must keep track of the grammatical structures that medieval logicians use. The notation “Linguish” is devised. Syntactical rules generate logical forms based on grammatical roles; the roles are supplied by verbs and participles; denoting phrases are allowed into a structure only by filling a specific role. An algorithm that converts logical forms into the surface sentences of Latin that logicians made use of. The logical forms encode only grammatical structure, since there is no logical form in addition to grammatical form in the medieval tradition. Rules of inference are formulated for Linguish logical forms. Using the medieval notions of signification and supposition a modern semantics is developed that agrees with medieval logicians’ judgments about truth conditions of propositions. A notion of validity is defined, and a completeness theorem is proved for the stated rules of inference.
Modes of Personal Supposition
Authors: Parsons Terence
Published: June 2014

A mode of supposition is a quantificational status a term has, defined in terms of ascents and descents. ‘Cat’ has determinate supposition in ‘Some cat is grey’ because from that proposition one can descend to ‘This cat is grey or that cat is grey or . . . for all cats’, and from any disjunct one can ascend back to the original proposition. Distributive supposition is a kind of universal status; merely confused supposition is more complex. Modes are caused by logical signs; ‘every’ confers distributive supposition on a term. A variant account by Ockham is discussed. Modes figure in general rules; if a term has determinate supposition it may be replaced by a superior term preserving truth. A refined version of the theory is discussed; this permits a more accurate theory of causes of the modes. The refined modes correspond to kinds of global quantificational import.
The Empty Church
Authors: Craigo-Snell Shannon
Published: June 2014

This book offers a novel vision of church through interdisciplinary conversation between performance studies, theater directors, and Christian theologians. Each chapter brings a theater director into dialogue with a theologian, teasing out how the concept of performance enriches hermeneutics, anthropology, and epistemology. The result is a compelling depiction of church as performance of relationship with Jesus Christ, mediated by Scripture, in hope of the Holy Spirit. This description expands church beyond the sanctuary. It also emphasizes the importance of liturgical worship in forming Christians as characters crafted by the texts of the Bible, as these texts are interpreted in community. This formation includes shaping how Christians know in ways that involve the intellect, emotions, body, and will. Through worship, Christians develop a repertoire of whole-personed knowledge, or affections. Christian churches often perform in ways that do serious harm in the world. Yet there are Christian traditions that can actively work against this. Both imaginatively (in liturgical worship) and concretely (in work for justice), Christians step into multiple roles and begin to see the stage from various perspectives. Through liturgical worship, Christians can be formed as people who hope, and therefore as people who live in expectation of the presence and grace of God. This entails a discipline of emptiness that awaits and appreciates the Spirit of God. Church performance should therefore be provisional, ongoing, and open to further inspiration.
Changing Scenes
Authors: Craigo-Snell Shannon
Published: June 2014

Chapter 4 argues for the vitally alienating role of academic theology through the pairing of theologian Delores Williams and director Bertholt Brecht. Finite and flawed, we resist the role switching that can help our performances be liberating. Often church rehearses us in a singular perspective, such that the intellectual and volitional aspects of our knowing are compromised. Then we need a prophetic voice, a productive alienation, to startle us out of well-worn patterns of belief and practice. We need to see the world made strange, as it was on Calvary when God hung lifeless on the Cross. The prophetic voices of theologians and pastors are needed to critique church performances and the employment of Christian affections. Such voices enact a holy alienation and reengage the intellectual and volitional challenges of Christian faith.
A statistical approach for inferring the 3D structure of the genome
Authors: Varoquaux Nelle , Ay Ferhat , Noble William Stafford , Vert Jean-Philippe
Published: June 2014

Motivation: Recent technological advances allow the measurement, in a single Hi-C experiment, of the frequencies of physical contacts among pairs of genomic loci at a genome-wide scale. The next challenge is to infer, from the resulting DNA–DNA contact maps, accurate 3D models of how chromosomes fold and fit into the nucleus. Many existing inference methods rely on multidimensional scaling (MDS), in which the pairwise distances of the inferred model are optimized to resemble pairwise distances derived directly from the contact counts. These approaches, however, often optimize a heuristic objective function and require strong assumptions about the biophysics of DNA to transform interaction frequencies to spatial distance, and thereby may lead to incorrect structure reconstruction.

Methods: We propose a novel approach to infer a consensus 3D structure of a genome from Hi-C data. The method incorporates a statistical model of the contact counts, assuming that the counts between two loci follow a Poisson distribution whose intensity decreases with the physical distances between the loci. The method can automatically adjust the transfer function relating the spatial distance to the Poisson intensity and infer a genome structure that best explains the observed data.

Results: We compare two variants of our Poisson method, with or without optimization of the transfer function, to four different MDS-based algorithms—two metric MDS methods using different stress functions, a non-metric version of MDS and ChromSDE, a recently described, advanced MDS method—on a wide range of simulated datasets. We demonstrate that the Poisson models reconstruct better structures than all MDS-based methods, particularly at low coverage and high resolution, and we highlight the importance of optimizing the transfer function. On publicly available Hi-C data from mouse embryonic stem cells, we show that the Poisson methods lead to more reproducible structures than MDS-based methods when we use data generated using different restriction enzymes, and when we reconstruct structures at different resolutions.

Availability and implementation: A Python implementation of the proposed method is available at http://cbio.ensmp.fr/pastis.

Contact:  william-noble@uw.edu or jean-philippe.vert@mines.org
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
Authors: Äijö Tarmo , Butty Vincent , Chen Zhi , Salo Verna , Tripathi Subhash , Burge Christopher B. , Lahesmaa Riitta , Lähdesmäki Harri
Published: June 2014

Motivation: Gene expression profiling using RNA-seq is a powerful technique for screening RNA species’ landscapes and their dynamics in an unbiased way. While several advanced methods exist for differential expression analysis of RNA-seq data, proper tools to anal.yze RNA-seq time-course have not been proposed.

Results: In this study, we use RNA-seq to measure gene expression during the early human T helper 17 (Th17) cell differentiation and T-cell activation (Th0). To quantify Th17-specific gene expression dynamics, we present a novel statistical methodology, DyNB, for analyzing time-course RNA-seq data. We use non-parametric Gaussian processes to model temporal correlation in gene expression and combine that with negative binomial likelihood for the count data. To account for experiment-specific biases in gene expression dynamics, such as differences in cell differentiation efficiencies, we propose a method to rescale the dynamics between replicated measurements. We develop an MCMC sampling method to make inference of differential expression dynamics between conditions. DyNB identifies several known and novel genes involved in Th17 differentiation. Analysis of differentiation efficiencies revealed consistent patterns in gene expression dynamics between different cultures. We use qRT-PCR to validate differential expression and differentiation efficiencies for selected genes. Comparison of the results with those obtained via traditional timepoint-wise analysis shows that time-course analysis together with time rescaling between cultures identifies differentially expressed genes which would not otherwise be detected.

Availability: An implementation of the proposed computational methods will be available at http://research.ics.aalto.fi/csb/software/

Contact:  tarmo.aijo@aalto.fi or harri.lahdesmaki@aalto.fi

Supplementary information:  Supplementary data are available at Bioinformatics online.
Detecting differential protein expression in large-scale population proteomics
Authors: Ryu So Young , Qian Wei-Jun , Camp David G. , Smith Richard D. , Tompkins Ronald G. , Davis Ronald W. , Xiao Wenzhong
Published: June 2014

Motivation: Mass spectrometry (MS)-based high-throughput quantitative proteomics shows great potential in large-scale clinical biomarker studies, identifying and quantifying thousands of proteins in biological samples. However, there are unique challenges in analyzing the quantitative proteomics data. One issue is that the quantification of a given peptide is often missing in a subset of the experiments, especially for less abundant peptides. Another issue is that different MS experiments of the same study have significantly varying numbers of peptides quantified, which can result in more missing peptide abundances in an experiment that has a smaller total number of quantified peptides. To detect as many biomarker proteins as possible, it is necessary to develop bioinformatics methods that appropriately handle these challenges.

Results: We propose a Significance Analysis for Large-scale Proteomics Studies (SALPS) that handles missing peptide intensity values caused by the two mechanisms mentioned above. Our model has a robust performance in both simulated data and proteomics data from a large clinical study. Because varying patients’ sample qualities and deviating instrument performances are not avoidable for clinical studies performed over the course of several years, we believe that our approach will be useful to analyze large-scale clinical proteomics data.

Availability and Implementation: R codes for SALPS are available at http://www.stanford.edu/%7eclairesr/software.html .

Contact:  wenzhong.xiao@mgh.harvard.edu

Supplementary information:  Supplementary materials are available at Bioinformatics online.
NetBioV: an R package for visualizing large network data in biology and medicine
Authors: Tripathi Shailesh , Dehmer Matthias , Emmert-Streib Frank
Published: June 2014

Summary: NetBioV (Network Biology Visualization) is an R package that allows the visualization of large network data in biology and medicine. The purpose of NetBioV is to enable an organized and reproducible visualization of networks by emphasizing or highlighting specific structural properties that are of biological relevance.

Availability and implementation: NetBioV is freely available for academic use. The package has been tested for R 2.14.2 under Linux, Windows and Mac OS X. It is available from Bioconductor.

Contact:  v@bio-complexity.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
BioBlend.objects: metacomputing with Galaxy
Authors: Leo Simone , Pireddu Luca , Cuccuru Gianmauro , Lianas Luca , Soranzo Nicola , Afgan Enis , Zanetti Gianluigi
Published: June 2014

Summary: BioBlend.objects is a new component of the BioBlend package, adding an object-oriented interface for the Galaxy REST-based application programming interface. It improves support for metacomputing on Galaxy entities by providing higher-level functionality and allowing users to more easily create programs to explore, query and create Galaxy datasets and workflows.

Availability and implementation: BioBlend.objects is available online at https://github.com/afgane/bioblend . The new object-oriented API is implemented by the galaxy/objects subpackage.

Contact:  simone.leo@crs4.it
Incidence of Herpes Simplex Virus Type 2 Infections in Africa: A Systematic Review
Authors: Rajagopal Sharanya , Magaret Amalia , Mugo Nelly , Wald Anna
Published: June 2014

The burden of HSV type 2 varies substantially by region, with the highest incidence and prevalence in sub-Saharan Africa. We undertook a systematic review to identify studies reporting prospective data on incidence rates in men and women in Africa. Of 18 eligible studies, 7 were conducted in high-risk populations. Among women, incidence rates appeared to be higher in those with high-risk sexual behavior, with rates ranging from 3 to 23 per 100 person-years. In contrast, incidence rates in men appeared to be lower, ranging from 1 to 12 per 100 person-years. Risk factors for HSV-2 in women included prevalent human immunodeficiency virus (HIV) infection, younger age at sexual initiation, and sexual activity. Among men, condom use and circumcision had a protective effect, whereas prevalent HIV increased the risk of HSV-2 acquisition. This review draws attention to the high HSV-2 acquisition rates reported in Africa, thereby identifying an efficient setting for preventative HSV-2 vaccine trials.
Invasive Haemophilus influenzae Disease in Adults ≥65 Years, United States, 2011
Authors: Blain Amy , MacNeil Jessica , Wang Xin , Bennett Nancy , Farley Monica M. , Harrison Lee H. , Lexau Catherine , Miller Lisa , Nichols Megin , Petit Susan , Reingold Arthur , Schaffner William , Thomas Ann , Clark Thomas , Cohn Amanda , Briere Elizabeth
Published: June 2014

Background.  Since the introduction of the Haemophilus influenzae serotype b vaccine, H influenzae epidemiology has shifted. In the United States, the largest burden of disease is now in adults aged ≥65 years. However, few data exist on risk factors for disease severity and outcome in this age group.

Methods.  A retrospective case-series review of invasive H influenzae infections in patients aged ≥65 years was conducted for hospitalized cases reported to Active Bacterial Core surveillance in 2011.

Results.  There were 299 hospitalized cases included in the analysis. The majority of cases were caused by nontypeable H influenzae, and the overall case fatality ratio (CFR) was 19.5%. Three or more underlying conditions were present in 63% of cases; 94% of cases had at least 1. Patients with chronic heart conditions (congestive heart failure, coronary artery disease, and/or atrial fibrillation) (odds ratio [OR], 3.27; 95% confidence interval [CI], 1.65–6.46), patients from private residences (OR, 8.75; 95% CI, 2.13–35.95), and patients who were not resuscitate status (OR, 2.72; 95% CI, 1.31–5.66) were more likely to be admitted to the intensive care unit (ICU). Intensive care unit admission (OR, 3.75; 95% CI, 1.71–8.22) and do not resuscitate status (OR, 12.94; 95% CI, 4.84–34.55) were significantly associated with death.

Conclusions.  Within this age group, burden of disease and CFR both increased significantly as age increased. Using ICU admission as a proxy for disease severity, our findings suggest several conditions increased risk of disease severity and patients with severe disease were more likely to die. Further research is needed to determine the most effective approach to prevent H influenzae disease and mortality in older adults.
The Photosystem II Oxygen-Evolving Complex Protein PsbP Interacts With the Coat Protein of Alfalfa mosaic virus and Inhibits Virus Replication
Authors: Balasubramaniam Muthukumar , Kim Bong-Suk , Hutchens-Williams Heather M. , Loesch-Fries L. Sue
Published: June 2014

Alfalfa mosaic virus (AMV) coat protein (CP) is essential for many steps in virus replication from early infection to encapsidation. However, the identity and functional relevance of cellular factors that interact with CP remain unknown. In an unbiased yeast two-hybrid screen for CP-interacting Arabidopsis proteins, we identified several novel protein interactions that could potentially modulate AMV replication. In this report, we focus on one of the novel CP-binding partners, the Arabidopsis PsbP protein, which is a nuclear-encoded component of the oxygen-evolving complex of photosystem II. We validated the protein interaction in vitro with pull-down assays, in planta with bimolecular fluorescence complementation assays, and during virus infection by co-immunoprecipitations. CP interacted with the chloroplast-targeted PsbP in the cytosol and mutations that prevented the dimerization of CP abolished this interaction. Importantly, PsbP overexpression markedly reduced virus accumulation in infected leaves. Taken together, our findings demonstrate that AMV CP dimers interact with the chloroplast protein PsbP, suggesting a potential sequestration strategy that may preempt the generation of any PsbP-mediated antiviral state.
An Automatic Method to Detect and Measure Leaf Disease Symptoms Using Digital Image Processing
Authors: Barbedo Jayme Garcia Arnal
Published: June 2014

A method is presented to detect and quantify leaf symptoms using conventional color digital images. The method was designed to be completely automatic, eliminating the possibility of human error and reducing time taken to measure disease severity. The program is capable of dealing with images containing multiple leaves, further reducing the time taken. Accurate results are possible when the symptoms and leaf veins have similar color and shade characteristics. The algorithm is subject to one constraint: the background must be as close to white or black as possible. Tests showed that the method provided accurate estimates over a wide variety of conditions, being robust to variation in size, shape, and color of leaves; symptoms; and leaf veins. Low rates of false positives and false negatives occurred due to extrinsic factors such as issues with image capture and the use of extreme file compression ratios.
Mycelial Compatibility and Pathogenic Diversity Among Sclerotium rolfsii Isolates in the Southern United States
Authors: Xie Chenzhao , Huang Cheng-Hua , Vallad Gary E.
Published: June 2014

Sclerotium rolfsii is a soilborne fungus that causes southern blight on a wide range of plants in tropical and subtropical regions of the world. Eighty-four isolates collected from Florida, Georgia, Louisiana, South Carolina, Texas, and Virginia were paired and assigned to 23 mycelial compatibility groups (MCGs), of which 11 MCGs consisted of a single isolate. Isolates within an MCG typically originated from different hosts and different geographical areas, with the exception of MCG 11. In all, 13 of the 15 isolates in MCG 11 originated from peanut in Georgia and Florida, while the other 2 isolates originated from potato in Virginia and from the ornamental Barlaeria cristata in Florida. Significant differences in the size and number of sclerotia produced in vitro existed between isolates from peanut and other hosts. Nineteen isolates representative of the most common MCGs (1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 16, 17, and 18) were tested for pathogenicity on tomato, pepper, and peanut. All isolates were pathogenic on all hosts but virulence differed significantly among isolates. Isolates collected from peanut were the most virulent on all three hosts compared with isolates collected from tomato and pepper. ‘Georgia Green’ peanut was more susceptible to peanut isolates from Georgia than to the other tested isolates. Of the two tomato entries, the commercial tomato ‘Tygress’ was less susceptible than the previously reported resistant breeding line 5635M to many of the S. rolfsii isolates tested, with the exception of the peanut isolates collected from Georgia. These initial findings suggest that considerable variation exists among S. rolfsii isolates throughout the southern United States, with some indications of specialization for the isolates collected from peanut.
Down-regulation of MicroRNA-21 Is Involved in the Propofol-induced Neurotoxicity Observed in Human Stem Cell–derived Neurons
Authors: Twaroski Danielle M. , Yan Yasheng , Olson Jessica M. , Bosnjak Zeljko J. , Bai Xiaowen
Published: June 2014

Background:

Recent studies in various animal models have suggested that anesthetics such as propofol, when administered early in life, can lead to neurotoxicity. These studies have raised significant safety concerns regarding the use of anesthetics in the pediatric population and highlight the need for a better model to study anesthetic-induced neurotoxicity in humans. Human embryonic stem cells are capable of differentiating into any cell type and represent a promising model to study mechanisms governing anesthetic-induced neurotoxicity.

Methods:

Cell death in human embryonic stem cell–derived neurons was assessed using terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate in situ nick end labeling staining, and microRNA expression was assessed using quantitative reverse transcription polymerase chain reaction. miR-21 was overexpressed and knocked down using an miR-21 mimic and antagomir, respectively. Sprouty 2 was knocked down using a small interfering RNA, and the expression of the miR-21 targets of interest was assessed by Western blot.

Results:

Propofol dose and exposure time dependently induced significant cell death (n = 3) in the neurons and down-regulated several microRNAs, including miR-21. Overexpression of miR-21 and knockdown of Sprouty 2 attenuated the increase in terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate in situ nick end labeling–positive cells following propofol exposure. In addition, miR-21 knockdown increased the number of terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate in situ nick end labeling–positive cells by 30% (n = 5). Finally, activated signal transducer and activator of transcription 3 and protein kinase B (Akt) were down-regulated, and Sprouty 2 was up-regulated following propofol exposure (n = 3).

Conclusions:

These data suggest that (1) human embryonic stem cell–derived neurons represent a promising in vitro human model for studying anesthetic-induced neurotoxicity, (2) propofol induces cell death in human embryonic stem cell–derived neurons, and (3) the propofol-induced cell death may occur via a signal transducer and activator of transcription 3/miR-21/Sprouty 2–dependent mechanism.
Analysis of new product development research: 1998-2009
Authors: Kalluri Vinayak , Kodali Rambabu
Published: June 2014

Purpose

– The purpose of this paper is to present a systematic review and analysis of existing research articles on new product development (NPD) published in the 12-year period starting from 1998 to 2009.

Design/methodology/approach

– To explore the articles related to NPD, four key words namely new product, product design, product development and product innovation were used in combination of title or abstract or keyword of the articles through several knowledge databases. The abstracts of journal papers were read and a decision as to whether article belongs to any NPD research issue or not was made. In total, 1,127 research articles were categorized systematically and then analyzed on various principal NPD information groups.

Findings

– Analysis of selected articles led to a certain level of dispersion in the publication of NPD research in different journals. It is found that more attention needs to be on knowledge and creativity management, communication and information transfer in any NPD process.

Originality/value

– By observing extended literature from authors reviewing articles from various journals, growth in research, and variety of topics covered in NPD, a broad systematic multi journal review of NPD literature is clearly overdue. The authors have developed a comprehensive listing of publications on NPD where they have classified the surveyed papers according to various principal NPD information groups like: published year, NPD research stream, type of organization studied (industrial/consumer/service), level of innovation (high/moderate/low), NPD focus on frameworks, performance perspective (success, failure or both), NPD research design (conceptual/empirical and qualitative/quantitative) and NPD relevant best practice element. Based on the classification scheme, the issues were analyzed from the system's perspective and their implications to NPD research.
Relative leader-member exchange and employee voice
Authors: Zhao Hongdan
Published: June 2014

Purpose

– This study aims to examine the effect of relative leader-member exchange (RLMX) on employee voice by developing a moderated mediation model. The model focuses on the mediating role of affective commitment underpinning the relationship between RLMX and employee voice, and the moderating role of Chinese traditionality in influencing the mediation.

Design/methodology/approach

– We tested the model with data from 358 supervisor-subordinate dyads in a large Chinese company. Employees and their immediate supervisors provided data on separate questionnaires and on different occasions. And then, we used an identification number to match each employee questionnaire with the response of his/her immediate supervisor.

Findings

– Results indicated that affective commitment fully mediated the positive relationship between RLMX and employee voice, even after controlling for personal leader-member exchange (LMX) quality. We also found that Chinese traditionality moderated the mediated relationship between RLMX and employee voice via affective commitment, such that the mediation was stronger for people lower, rather than higher, in Chinese traditionality.

Research limitations/implications

– Testing the moderated mediation model helps to advance our theoretical understanding of the psychological mechanisms that underlie the effect of RLMX on employees’ behaviour.

Originality/value

– This empirical study provides preliminary evidence of the mediating role of affective commitment in the positive relationship between RLMX and employee voice. Our moderated mediation model also extends the existing finding by adding substantive moderators (Chinese traditionality) to explain how the effect of RLMX on employees’ behaviours unfolds.
Psychological ownership, organization-based self-esteem and positive organizational behaviors
Authors: Pan Xiao-Fu , Qin Qiwen , Gao Fei
Published: June 2014

Purpose

– The purpose of this paper is to explore the effect of organizational psychological ownership (OPO) and organization-based self-esteem (OBSE) on positive organizational behaviors (POBs).

Design/methodology/approach

– Based on empirical survey, 2,566 employees from 45 production enterprises in China were surveyed by a self-designed questionnaire on OPO, OBSE and POB. Then, the methods of correlation analysis, multiple regressions, impact effect and path analysis were used to verify the research hypothesis.

Findings

– The results showed that POB is positively related to OPO and OBSE, and that OPO and OBSE are positive predictors of POBs. The results also demonstrated that OBSE has partial mediating effects on OPO and POB. In particular, psychological ownership has a significant impact on each sub-factor of POB, while OBSE has a remarkable effect on the behavior of devotion and interpersonal harmony.

Research limitations/implications

– This is a non-experimental field study and as such inferences about causality are limited, and there is a possibility that the results may be influenced by common method variance.

Practical implications

– The findings of the present study reveal that to strengthen employees’ POBs, manager should enhance employees’ OPO and OBSE, and therefore the organizational performance and the individual efficacy will be improved.

Originality/value

– This is the first research which studies the relationship among OPO, POB and OBSE under the background of China.
Exploring the direct and indirect effects of CSR on organizational commitment
Authors: Anthony Wong IpKin , Hong Gao Jennifer
Published: June 2014

Purpose

– The purpose of this study is to investigate the effect of perceived corporate social responsibility (CSR) on employees’ affective commitment through the mediating role of perceived corporate culture.

Design/methodology/approach

– Data were collected by means of self-administered survey. A total of 379 complete responses were obtained from tourism and hospitality organizations in China. The proposed relationships were tested using structural equation modeling in four nested models.

Findings

– Results show that CSR to employees and CSR to customers are fully mediated by employee development, harmony and customer orientation of the corporate culture, while CSR to stakeholders is partially mediated.

Practical implications

– The findings also suggest that the literature should reconsider how CSR initiatives could pinpoint a specific dimension in developing loyal employees. This study also shows that employees are social actors who seek a corporate culture that best suits their self-interest; hence, they are more committed to an organization particularly in respect to employee development and social harmony.

Originality/value

– This study adds to the literature by showing that not all CSR efforts would directly lead to employee commitment. It shows that the CSR-to-employee and CSR-to-customer dimensions play the most salient roles in nurturing a corporate culture that is perceived to focus on employee development, harmony, customers and innovation.