bluuebunny/crossref_metadata_2025_split huggingface dataset:
VAN: an R package for identifying biologically perturbed networks via differential variability analysis
Authors: Jayaswal Vivek , Schramm Sarah-Jane , Mann Graham J , Wilkins Marc R , Yang Yee Hwa 
Published: October 2013

Abstract

Background
Large-scale molecular interaction networks are dynamic in nature and are of special interest in the analysis of complex diseases, which are characterized by network-level perturbations rather than changes in individual genes/proteins. The methods developed for the identification of differentially expressed genes or gene sets are not suitable for network-level analyses. Consequently, bioinformatics approaches that enable a joint analysis of high-throughput transcriptomics datasets and large-scale molecular interaction networks for identifying perturbed networks are gaining popularity. Typically, these approaches require the sequential application of multiple bioinformatics techniques – ID mapping, network analysis, and network visualization. Here, we present the Variability Analysis in Networks (VAN) software package: a collection of R functions to streamline this bioinformatics analysis.

Findings
VAN determines whether there are network-level perturbations across biological states of interest. It first identifies hubs (densely connected proteins/microRNAs) in a network and then uses them to extract network modules (comprising of a hub and all its interaction partners). The function identifySignificantHubs identifies dysregulated modules (i.e. modules with changes in expression correlation between a hub and its interaction partners) using a single expression and network dataset. The function summarizeHubData identifies dysregulated modules based on a meta-analysis of multiple expression and/or network datasets. VAN also converts protein identifiers present in a MITAB-formatted interaction network to gene identifiers (UniProt identifier to Entrez identifier or gene symbol using the function generatePpiMap) and generates microRNA-gene interaction networks using TargetScan and Microcosm databases (generateMicroRnaMap). The function obtainCancerInfo is used to identify hubs (corresponding to significantly perturbed modules) that are already causally associated with cancer(s) in the Cancer Gene Census database. Additionally, VAN supports the visualization of changes to network modules in R and Cytoscape (visualizeNetwork and obtainPairSubset, respectively). We demonstrate the utility of VAN using a gene expression data from metastatic melanoma and a protein-protein interaction network from the Human Protein Reference Database.

Conclusions
Our package provides a comprehensive and user-friendly platform for the integrative analysis of -omics data to identify disease-associated network modules. This bioinformatics approach, which is essentially focused on the question of explaining phenotype with a 'network type’ and in particular, how regulation is changing among different states of interest, is relevant to many questions including those related to network perturbations across developmental timelines.
Temporal changes in mosquito abundance (Culex pipiens), avian malaria prevalence and lineage composition
Authors: Lalubin Fabrice , Delédevant Aline , Glaizot Olivier , Christe Philippe 
Published: October 2013

Abstract

Background
Knowledge on the temporal dynamics of host/vector/parasite interactions is a pre-requisite to further address relevant questions in the fields of epidemiology and evolutionary ecology of infectious diseases. In studies of avian malaria, the natural history of Plasmodium parasites with their natural mosquito vectors, however, is mostly unknown.

Methods
Using artificial water containers placed in the field, we monitored the relative abundance of parous females of Culex pipiens mosquitoes during two years (2010–2011), in a population in western Switzerland. Additionally, we used molecular tools to examine changes in avian malaria prevalence and Plasmodium lineage composition in female C. pipiens caught throughout one field season (April-August) in 2011.

Results

C. pipiens relative abundance varied both between years and months, and was associated with temperature fluctuations. Total Plasmodium prevalence was high and increased from spring to summer months (13.1-20.3%). The Plasmodium community was composed of seven different lineages including P. relictum (SGS1, GRW11 and PADOM02 lineages), P. vaughani (lineage SYAT05) and other Plasmodium spp. (AFTRU5, PADOM1, COLL1). The most prevalent lineages, P. vaughani (lineage SYAT05) and P. relictum (lineage SGS1), were consistently found between years, although they had antagonistic dominance patterns during the season survey.

Conclusions
Our results suggest that the time window of analysis is critical in evaluating changes in the community of avian malaria lineages infecting mosquitoes. The potential determinants of the observed changes as well as their implications for future prospects on avian malaria are discussed.
Low oxygen tension increased fibronectin fragment induced catabolic activities - response prevented with biomechanical signals
Authors: Parker Eleanor , Vessillier Sandrine , Pingguan-Murphy Belinda , Abas Wan Abu Baker Wan , Bader Dan L , Chowdhury Tina T 
Published: October 2013

Abstract
Introduction
The inherent low oxygen tension in normal cartilage has implications on inflammatory conditions associated with osteoarthritis (OA). Biomechanical signals will additionally contribute to changes in tissue remodelling and influence the inflammatory response. In this study, we investigated the combined effects of oxygen tension and fibronectin fragment (FN-f) on the inflammatory response of chondrocytes subjected to biomechanical signals.

Methods
Chondrocytes were cultured under free-swelling conditions at 1%, 5% and 21% oxygen tension or subjected to dynamic compression in an ex vivo 3D/bioreactor model with 29 kDa FN-f, interleukin-1beta (IL-1β) and/or the nitric oxide synthase (NOS) inhibitor for 6 and 48 hours. Markers for catabolic activity (NO, PGE2), tissue remodelling (GAG, MMPs) and cytokines (IL-1β, IL-6 and TNFα) were quantified by biochemical assay. Aggrecan, collagen type II, iNOS and COX-2 gene expression were examined by real-time quantitative PCR. Two-way ANOVA and a post hoc Bonferroni-corrected t-test were used to analyse data.

Results
Both FN-fs and IL-1β increased NO, PGE2 and MMP production (all P < 0.001). FN-f was more active than IL-1β with greater levels of NO observed at 5% than 1% or 21% oxygen tension (P < 0.001). Whilst FN-f reduced GAG synthesis at all oxygen tension, the effect of IL-1β was significant at 1% oxygen tension. In unstrained constructs, treatment with FN-f or IL-1β increased iNOS and COX-2 expression and reduced aggrecan and collagen type II (all P < 0.001). In unstrained constructs, FN-f was more effective than IL-1β at 5% oxygen tension and increased production of NO, PGE2, MMP, IL-1β, IL-6 and TNFα. At 5% and 21% oxygen tension, co-stimulation with compression and the NOS inhibitor abolished fragment or cytokine-induced catabolic activities and restored anabolic response.

Conclusions
The present findings revealed that FN-fs are more potent than IL-1β in exerting catabolic effects dependent on oxygen tension via iNOS and COX-2 upregulation. Stimulation with biomechanical signals abolished catabolic activities in an oxygen-independent manner and NOS inhibitors supported loading-induced recovery resulting in reparative activities. Future investigations will utilize the ex vivo model as a tool to identify key targets and therapeutics for OA treatments.
Pubertal high fat diet: effects on mammary cancer development
Authors: Zhao Yong , Tan Ying Siow , Aupperlee Mark D , Langohr Ingeborg M , Kirk Erin L , Troester Melissa A , Schwartz Richard C , Haslam Sandra Z 
Published: October 2013

Abstract
Introduction
Epidemiological studies linking dietary fat intake and obesity to breast cancer risk have produced inconsistent results. This may be due to the difficulty of dissociating fat intake from obesity, and/or the lack of defined periods of exposure in these studies. The pubertal mammary gland is highly sensitive to cancer-causing agents. We assessed how high fat diet (HFD) affects inflammation, proliferative, and developmental events in the pubertal gland, since dysregulation of these can promote mammary tumorigenesis. To test the effect of HFD initiated during puberty on tumorigenesis, we utilized BALB/c mice, for which HFD neither induces obesity nor metabolic syndrome, allowing dissociation of HFD effects from other conditions associated with HFD.

Methods
Pubertal BALB/c mice were fed a low fat diet (12% kcal fat) or a HFD (60% kcal fat), and subjected to carcinogen 7,12-dimethylbenz[a]anthracene (DMBA)-induced tumorigenesis.

Results
HFD elevated mammary gland expression of inflammatory and growth factor genes at 3 and 4 weeks of diet. Receptor activator of nuclear factor kappa-B ligand (RANKL), robustly induced at 4 weeks, has direct mitogenic activity in mammary epithelial cells and, as a potent inducer of NF-κB activity, may induce inflammatory genes. Three weeks of HFD induced a transient influx of eosinophils into the mammary gland, consistent with elevated inflammatory factors. At 10 weeks, prior to the appearance of palpable tumors, there were increased numbers of abnormal mammary epithelial lesions, enhanced cellular proliferation, increased growth factors, chemokines associated with immune-suppressive regulatory T cells, increased vascularization, and elevated M2 macrophages. HFD dramatically reduced tumor latency. Early developing tumors were more proliferative and were associated with increased levels of tumor-related growth factors, including increased plasma levels of HGF in tumor-bearing animals. Early HFD tumors also had increased vascularization, and more intra-tumor and stromal M2 macrophages.

Conclusions
Taken together in this non-obesogenic context, HFD promotion of inflammatory processes, as well as local and systemically increased growth factor expression, are likely responsible for the enhanced tumorigenesis. It is noteworthy that although DMBA mutagenesis is virtually random in its targeting of genes in tumorigenesis, the short latency tumors arising in animals on HFD showed a unique gene expression profile, highlighting the potent overarching influence of HFD.
A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation
Authors: Iurlaro Mario , Ficz Gabriella , Oxley David , Raiber Eun-Ang , Bachman Martin , Booth Michael J , Andrews Simon , Balasubramanian Shankar , Reik Wolf 
Published: October 2013

Abstract
Background
DNA methylation (5mC) plays important roles in epigenetic regulation of genome function. Recently, TET hydroxylases have been found to oxidise 5mC to hydroxymethylcytosine (5hmC), formylcytosine (5fC) and carboxylcytosine (5caC) in DNA. These derivatives have a role in demethylation of DNA but in addition may have epigenetic signaling functions in their own right. A recent study identified proteins which showed preferential binding to 5-methylcytosine (5mC) and its oxidised forms, where readers for 5mC and 5hmC showed little overlap, and proteins bound to further oxidation forms were enriched for repair proteins and transcription regulators. We extend this study by using promoter sequences as baits and compare protein binding patterns to unmodified or modified cytosine using DNA from mouse embryonic stem cell extracts.

Results
We compared protein enrichments from two DNA probes with different CpG composition and show that, whereas some of the enriched proteins show specificity to cytosine modifications, others are selective for both modification and target sequences. Only a few proteins were identified with a preference for 5hmC (such as RPL26, PRP8 and the DNA mismatch repair protein MHS6), but proteins with a strong preference for 5fC were more numerous, including transcriptional regulators (FOXK1, FOXK2, FOXP1, FOXP4 and FOXI3), DNA repair factors (TDG and MPG) and chromatin regulators (EHMT1, L3MBTL2 and all components of the NuRD complex).

Conclusions
0ur screen has identified novel proteins that bind to 5fC in genomic sequences with different CpG composition and suggests they regulate transcription and chromatin, hence opening up functional investigations of 5fC readers.
Epidemiology of hoarding disorder
Authors: Nordsletten Ashley E. , Reichenberg Abraham , Hatch Stephani L. , de la Cruz Lorena Fernández , Pertusa Alberto , Hotopf Matthew , Mataix-Cols David 
Published: October 2013

BackgroundHoarding disorder is typified by persistent difficulties discarding possessions, resulting in significant clutter that obstructs the individual's living environment and produces considerable functional impairment. The prevalence of hoarding disorder, as defined in DSM-5, is currently unknown.AimsTo provide a prevalence estimate specific to DSM-5 hoarding disorder and to delineate the demographic, behavioural and health features that characterise individuals with the disorder.MethodWe conducted a two-wave epidemiological study of 1698 adult individuals, originally recruited via the South East London Community Health (SELCoH) study. Participants screening positively for hoarding difficulties in wave 1, and who agreed to be re-contacted for wave 2 (n = 99), underwent in-home psychiatric interviews and completed a battery of self-report questionnaires. Current DSM-5 diagnoses were made via consensus diagnostic procedure.ResultsIn total, 19 individuals met DSM-5 criteria for hoarding disorder at the time of interview, corresponding to a weighted prevalence of 1.5% (95% CI 0.7–2.2). Those with hoarding disorder were older and more often unmarried (67%). Members of this group were also more likely to be impaired by a current physical health condition (52.6%) or comorbid mental disorder (58%), and to claim benefits as a result of these issues (47.4%). Individuals with hoarding disorder were also more likely to report lifetime use of mental health services, although access in the past year was less frequent.ConclusionsWith a lower-bound prevalence of approximately 1.5%, hoarding disorder presents as a condition that affects people of both genders and is associated with substantial adversity.
Social and communicative role of a gender
Authors: Кошлякова  , Koshlyakova Mariya 
Published: October 2013

The notion of the gender will concentrate the attention on socially built differences of men and women, reflects some cultural stereotypes and ideals of masculinity and femininity, sexual division of labor in social institutions and organizations. The comprehension of various gender styles of behavior should be considered in professional activity of a college teacher. The profession of a college teacher is marked with masculine gender markers first of all. A survey among students has been conducted to reveal the gender
speech models of college teachers in the Russian State University of Tourism and Service.
The communicative aspect of the process of argumentation in the German critical text
Authors: Кремер  , Kremer Inessa 
Published: October 2013

The paper dwells upon the communicative aspect of the process of argumentation
in critical texts, written in German. It reveals argumentative strategies
in the interpretation of the scientific critical text from the point of view
of communicative-cognitive paradigm. The object of the analysis is scientific
(research) critical reviews from German journals, communicative intentions
of which are information, assessing, its explanation and influence upon the
reader. In the framework of the informational potential the author investigates
the process of juxtaposition of the informative fund of the critic and the
primary author where the difference between the notions of «knowledge/
opinion» is very important. In the evaluative aspect of the critical text the
axiological axis (center) is centered between the poles «good» — «bad»,
including the evaluative notion of «independence’. The dominant speech
form of the linguistic critical review appears through discourse, containing
either description or debate. The process of assessment goes through logical
steps of argumentation. Argumentation is divided into emotional and rational
and it is juxtaposed to assessment. More than that, argumentation is
a complex phenomenon, linked directly with the composition of the text and
it has explicit communicative character.
The social semiotics of hijab: Negotiating the body politics of veiled women
Authors: Al-Mahadin Salam 
Published: October 2013

Abstract
Hijab and other forms of Islamic head cover have become indelibly associated with notions of inequality and repression in the minds of many non-Muslims. This article queries the meanings and functions of hijab within both Muslim and non-Muslim contexts. It begins by exploring hijab as a transcendental signifier and the epistemological challenges it poses to the gaze. The discussion shifts to focus on the social semiotics of hijab in Arab/Muslim contexts and the myriad fashions and signifieds associated with hijab before situating the hjiab within the western context of the society of enjoyment. The article concludes that the repressive hypothesis associated with hijab is too reductionist to explain the complex and multiple meanings attached to it.
Arab investigative journalism practice
Authors: Hamdy Naila 
Published: October 2013

Abstract
Given investigative journalism’s purpose of providing accountability and exposing wrongdoing of governments and business, this study examines whether changes in political circumstances due to the Arab revolutions have given rise to the production of more investigative reporting, whether Arab journalists have the same understanding of the meaning of investigative journalism as their western counterparts, and if individual or organizational characteristics encourage or hinder journalists’ performance. Findings indicated that changes in the political environment did not generally help them conduct such reporting. Results also indicated that individual, organization or ownership types did not dictate their capacity to perform such investigations. Rather the ability depended on how much the individual journalist believed and understood this to be a unique type of journalism genre as well as whether they were advanced enough in their career to perform such in-depth work. The results also indicated that Arab journalists believe in their ability to make change and are motivated by a sense of self-fulfillment to provide the public with watchdog journalism.
Book Reviews
Authors: Madhavan Arya , Nair Sreenath 
Published: October 2013

Abstract
My Tears, My Dreams (trans. Sindhu V. Nair), V. T. Bhattathirippad (2013) New Delhi: Oxford University Press, xxxvi+112 pp., h/bk, Rs. 295.00, ISBN: 0198089627
Critical Essays on British South Asian Theatre, Graham Ley and Sarah Dadswell (eds) (2012) Exeter: Exeter University Press, x+276 pp., p/bk, ISBN: 9780859898355. £25.00
Rhythm embodied: Training Rasa in Hindustani tabla?
Authors: Nuttall Denise 
Published: October 2013

Abstract
As Hindustani music (North Indian classical) and the performance of tabla moves outside of its South Asian origins the underlying aesthetic, rasa, and the structure of the musical system travels across and between musical and cultural borders informing and shaping the performative context. To what extent does the rasa concept, referred to as a ‘tasting’ experience, dominant in the arts of India, affect the global art of tabla? Often overlooked by scholars, and confused with the process of bhava (emotion) by performers, the concept and application of rasa continues to be the dominant aesthetic principle in what we have come to know globally as tabla soloing. I argue that it is in the phenomenological experience of music training and music making that we find a possible connection between the practice of rasa and the embodiment of bhava (performer emotion).
Market-Induced Rationalization and Welfare-Enhancing Cartels
Authors: Tuinstra Jan , in ’t Veld Daan L. 
Published: October 2013

Abstract
We show that incomplete cartels in quantity-setting oligopolies may increase welfare, without any efficiencies or synergies being internalized by cartel formation. The main intuition is that the cartel has an incentive to contract output and that the firms outside the cartel react to this by expanding output. If the outsiders are more efficient than the cartel firms, average production costs go down. We model collusion in a market structure with imperfect substitute goods. Even for relatively moderate differences in efficiency, total welfare may increase due to this market-induced rationalization, whereas the cartel remains profitable. We discuss why the effect can be relevant for sectors where new, superior products are developed. Because anti-cartel enforcement is costly, it is important for competition authorities to realize that not all cartels lead to a welfare loss.
Influence of wood durability on the suppressive effect of increased temperature on wood decay by the brown-rot fungus Postia placenta
Authors: Hietala Ari M. , Stefańczyk Emil , Nagy Nina Elisabeth , Fossdal Carl Gunnar , Alfredsen Gry 
Published: October 2013

Abstract
Local climate conditions have a major influence on the biological decomposition of wood. To examine the influence of different temperature regimes on wood decay caused by the brown rot fungus Postia placenta in wood with differing natural durability, sapwood (sW) and heartwood (hW) of Scots pine, inoculated mini-blocks were incubated for up to 10 weeks at temperatures conducive or above optimal to wood decay. We profiled mass loss (ML) and wood composition, and accompanying changes in wood colonization and transcript level regulation of fungal candidate genes. The suppressive effect of suboptimal temperature on wood decay caused by P. placenta appeared more pronounced in Scots pine hW with increased durability than in sW with low decay resistance. The differences between sW and hW were particularly pronounced for cultures incubated at 30°C: unlike sW, hW showed no ML, poor substrate colonization and marker gene transcript level profiles indicating a starvation situation. As brown rot fungi show considerable species-specific variation in temperature optima and ability to mineralize components that contribute to wood durability, interactions between these factors will continue to shape the fungal communities associated to wood in service.
Mathematical modeling of drying of Masson pine lumber and its asymmetrical moisture content profile
Authors: Zhang Jie , Miao Ping , Zhong Di , Liu Lin 
Published: October 2013

Abstract
A mathematical model is discussed in terms of moisture transfer during the drying process of Masson pine (Pinus massoniana) lumber in industrial practice. The model was validated by comparing the simulated result of moisture distribution with experimental data. In the model, the wood drying process was divided into two phases. The first one dealt with processes above fiber saturation point (FSP), that was driven by capillary flux of free water and conductive flux of vapor, and the second one dealt with those of below FSP, which was driven by diffusive flux of bound water and vapor. Moisture content distribution (MCD) inside wood is simulated by solving a parabolic partial differential equation under Dirichlet boundary conditions. The moisture content profile (MCP) was asymmetrical in experiments, and the simulation result agreed well with the experiments. An easy empirical formulation was also proposed to calculate real wood permeability, as it showed general characteristics of liquid and vapor permeability. This permeability model is verified as the cause of asymmetrical MCP in this paper.