bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of genomic functional hotspots with copy number alteration in liver cancer
Authors: Hsiao Tzu-Hung , Chen Hung-I Harry , Roessler Stephanie , Wang Xin Wei , Chen Yidong
Published: October 2013

Copy number alterations (CNAs) can be observed in most of cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumor. However, the systematic survey of CNA-affected functions is still lack. By employing systems biology approaches, instead of examining individual genes, we directly identified the functional hotspots on human genome. A total of 838 hotspots on human genome with 540 enriched Gene Ontology functions were identified. Seventy-six aCGH array data of hepatocellular carcinoma (HCC) tumors were employed in this study. A total of 150 regions which putatively affected by CNAs and the encoded functions were identified. Our results indicate that two immune related hotspots had copy number alterations in most of patients. In addition, our data implied that these immune-related regions might be involved in HCC oncogenesis. Also, we identified 39 hotspots of which copy number status were associated with patient survival. Our data implied that copy number alterations of the regions may contribute in the dysregulation of the encoded functions. These results further demonstrated that our method enables researchers to survey biological functions of CNAs and to construct regulation hypothesis at pathway and functional levels.
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

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

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

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

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

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.
Integration of surface seismic, microseismic, and production logs for shale gas characterization: Methodology and field application
Authors: Alzate John Henry , Devegowda Deepak
Published: October 2013

Technologies such as horizontal drilling and multistage hydraulic fracturing are central to ensuring the viability of shale oil and gas resource development by maximizing contact with the most productive reservoir volumes. However, characterization efforts based on the use of well logs and cores, although very informative, may be associated with substantial uncertainty in interwell volumes. Consequently, this work is centered around the development of a predictive tool based on surface seismic data analysis to rapidly demarcate the most prolific reservoir volumes, to identify zones more amenable to hydraulic fracturing, and to provide a methodology to locate productive infill wells for further development. Specifically, we demonstrate that surface seismic attributes such as [Formula: see text]/[Formula: see text] crossplots can successfully be employed to quantitatively grade reservoir rocks in unconventional plays. We also investigate the role of seismically inverted Poisson’s ratio as a fracability discriminator and Young’s modulus as an indicator of total organic carbon richness and porosity. The proposed predictive tool for sweet spot identification relies on classifying reservoir volumes on the basis of their amenability to fracturing and reservoir quality. The classification scheme is applied to a field case study from the Lower Barnett Shale and we validate these results using production logs recorded in four horizontal wells and microseismic data acquired while fracturing these wells. The integration of seismic data, production logs, and microseismic data underscores the value of shale reservoir characterization with a diverse suite of measurements to determine optimal well locations and to locate hydraulic fracture treatments. A key advantage of the methodology developed here is the ease of regional-scale characterization that can easily be generalized to other shale plays.
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

Background

Hoarding 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.

Aims

To 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.

Method

We 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.

Results

In 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.

Conclusions

With 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.
Ritual as Religious Communication
Authors: Гойхман  , Goykhman Oskar
Published: October 2013

The article addresses rituals and procedures in the communicative space. It analyses how ritual is presented in various literary sources and explains why it is inappropriate to use the phrase «ritual communication». The author gives his own model ritualization in communication and provides examples proving his idea. At the end of the article the author draws motivated conclusions.
Translated texts as an object of forensic linguistic expertise
Authors: Аблин  , Ablin Maxim
Published: October 2013

The article considers the characteristic features of translated texts as objects of forensic linguistic expertise and points out the problems in carrying out expert examination of corresponding texts. The authors estimates the possibility of using psycho- and pragmolinguistics in analysing translated texts.
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.
Ordering Behavior Under Supply Risk:An Experimental Investigation
Authors: Gurnani Haresh , Ramachandran Karthik , Ray Saibal , Xia Yusen
Published: October 2013

As supply chains become increasingly complex and global in their scale, supplier selection and management in the face of disruption risk has become one of the most challenging tasks for modern managers. Several novel model-based approaches to managing such risks have been developed in the academic literature, but how behavioral tendencies may affect procurement decisions under such conditions has received relatively less attention. In this paper, we present results from a study where paid subjects were asked to place orders from two suppliers who differ in their costs and risks to satisfy a fixed amount of end-customer demand. We show that under such a scenario, it is theoretically optimal to sole source either from the more reliable (and more costly) supplier or from the more risky but cheaper supplier, depending on cost and risk parameters. Subjects in our experiment, however, show a systematic tendency to diversify their orders between the two sources. We document this diversification tendency in procurement decisions and its possible impact on profits under various cost and risk settings as well as comment on various ordering behavior observed during the experiments. We also establish that bounded rationality of subjects can provide a possible rationale for the above phenomenon.
Getting back to work? Claim trajectories and destinations of Employment and Support Allowance claimants
Authors: Sissons Paul , Barnes Helen
Published: October 2013

Individuals claiming Employment and Support Allowance (ESA), the replacement benefit for Incapacity Benefits, are increasingly being expected to prepare for a return to work. Drawing on a survey with claimants, this paper highlights the critical role which pre-claim experiences have on these outcomes. Those coming onto the benefit from a work background are likely to move off from ESA and into employment more quickly. The evidence presented, however, also demonstrates that health and health trajectories remain central determinants of future employment experiences. Overall, the analysis suggests that ESA is least effective at helping the most disadvantaged groups.
Agricultural Case Studies of Classification Accuracy, Spectral Resolution, and Model Over-Fitting
Authors: Nansen Christian , Geremias Leandro Delalibera , Xue Yingen , Huang Fangneng , Parra Jose Roberto
Published: October 2013

This paper describes the relationship between spectral resolution and classification accuracy in analyses of hyperspectral imaging data acquired from crop leaves. The main scope is to discuss and reduce the risk of model over-fitting. Over-fitting of a classification model occurs when too many and/or irrelevant model terms are included (i.e., a large number of spectral bands), and it may lead to low robustness/repeatability when the classification model is applied to independent validation data. We outline a simple way to quantify the level of model over-fitting by comparing the observed classification accuracies with those obtained from explanatory random data. Hyperspectral imaging data were acquired from two crop–insect pest systems: (1) potato psyllid ( Bactericera cockerelli) infestations of individual bell pepper plants ( Capsicum annuum) with the acquisition of hyperspectral imaging data under controlled-light conditions (data set 1), and (2) sugarcane borer ( Diatraea saccharalis) infestations of individual maize plants ( Zea mays) with the acquisition of hyperspectral imaging data from the same plants under two markedly different image-acquisition conditions (data sets 2a and b). For each data set, reflectance data were analyzed based on seven spectral resolutions by dividing 160 spectral bands from 405 to 907 nm into 4, 16, 32, 40, 53, 80, or 160 bands. In the two data sets, similar classification results were obtained with spectral resolutions ranging from 3.1 to 12.6 nm. Thus, the size of the initial input data could be reduced fourfold with only a negligible loss of classification accuracy. In the analysis of data set 1, several validation approaches all demonstrated consistently that insect-induced stress could be accurately detected and that therefore there was little indication of model over-fitting. In the analyses of data set 2, inconsistent validation results were obtained and the observed classification accuracy (81.06%) was only a few percentage points above that obtained using random data (66.7–77.4%). Thus, our analysis highlights a potential risk of model over-fitting and emphasizes the importance of testing for this important aspect as part of developing reliable and robust classification models.
A Novel Classification Method for Multispectral Imaging Combined with Portable Raman Spectroscopy for the Analysis of a Painting by Vincent Van Gogh
Authors: Cesaratto Anna , Nevin Austin , Valentini Gianluca , Brambilla Luigi , Castiglioni Chiara , Toniolo Lucia , Fratelli Maria , Comelli Daniela
Published: October 2013

In this work, a novel combination of portable micro-Raman spectroscopy and semi-automatic methods of data treatment are proposed for the classification and mapping of visible multispectral imaging data for the analysis of a painting on paper by Vincent Van Gogh. Analysis of multispectral imaging data with the sequential maximum-angle convex cone (SMACC) and spectral angle mapper (SAM) algorithms differentiated the surface into areas on the basis of the presence of pigment mixtures. Complementary analytical information was obtained through portable Raman spectroscopy was performed on a few selected points of the painting, allowing for the determination of Van Gogh's palette and the mapping of pigment mixtures on the painting's surface; the number of mixtures employed is varied and at least two different blues are present. The results obtained were integrated with the information from prior ultraviolet (UV)-induced luminescence analysis performed on the same painting to better understand the materials used by the artist. The mathematical treatment of multispectral data using the proposed methods could be extended to the analysis of other painted surfaces.
Atmospheric Compensation in Fourier Transform Infrared (FT-IR) Spectra of Clinical Samples
Authors: Perez-Guaita David , Kuligowski Julia , Quintás Guillermo , Garrigues Salvador , de la Guardia Miguel
Published: October 2013

A new method is proposed for the elimination of the spectral contribution of two atmospheric gases (CO2 and H2O) in Fourier transform infrared (FT-IR) spectra of clinical samples. The algorithm is based on the measurement of reference spectra of H2O followed by an automatic calculation of the spectral contribution of the above-mentioned gases to the sample spectra. Then this contribution is compensated by spectral subtraction. Attenuated total reflectance FT-IR spectra of serum and urine samples in the presence of atmospheric gases were corrected and compared with spectra obtained with an N2 purge. Visual inspection of the spectra as well as calculated noise levels confirmed that the method compensated for the contribution of CO2 and H2O to serum and urine spectra to a great extent. As compared with the correction performed by a commercial software package, the proposed method clearly improved the correction of CO2 and provided similar results for H2O compensation. Correlation values between corrected spectra and those obtained under N2-purged conditions in the fingerprint region were higher than 0.995, and noise values in regions where samples did not absorb confirmed the suitability of the correction. The proposed method is fast, easy, and extensible to other gaseous interferences, devices, and acquisition conditions.
A Novel Approach for a Functional Group to Predict Protein in Undigested Residue and Protein Digestibility by Mid-Infrared Spectroscopy
Authors: Wang Li Fang , Swift Mary Lou , Zijlstra Ruurd T.
Published: October 2013

To evaluate nutrient digestibility, we propose the novel approach of functional group digestibility (FGD). The FGD was based on the absorbance of specific Fourier transform infrared (FT-IR) peaks and the ratio of an inorganic indigestible marker in diet and digesta, without calibration. For application, samples of diet and digesta of wheat with predetermined crude protein (CP) digestibility were scanned on an FT-IR spectrometer equipped with a single-reflection attenuated total reflection (ATR) attachment. The FGD in the amide I region (1689–1631 cm−1) of digesta spectra was strongly related ( R 2 = 0.99) with CP digestibility. The measured diet CP digestibility ranged from 60.4 to 87.8% with a standard error of prediction of 1.09%. In conclusion, instead of predictions based on calibrations, FGD can be calculated directly from spectra, provided the ratio of marker in diet and undigested residue is known, and then accurately predicts nutrient digestibility.
The social semiotics of hijab: Negotiating the body politics of veiled women
Authors: Al-Mahadin Salam
Published: October 2013

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

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

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

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

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

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

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.
Impact of Rapid Thermal Annealing on Thermoelectric Properties of Bulk Nanostructured Zinc Oxide
Authors: Engenhorst Markus , Gautam Devendraprakash , Schilling Carolin , Winterer Markus , Schierning Gabi , Schmechel Roland
Published: October 2013

In search for non-toxic thermoelectric materials that are stable in air at elevated temperatures, zinc oxide has been shown to be one of only few efficient n-type oxidic materials. Our bottom-up approach starts with very small (<10 nm) Al-doped ZnO nanoparticles prepared from organometallic precursors by chemical vapor synthesis using nominal doping concentrations of 2 at% and 8 at%. In order to obtain bulk nanostructured solids, the powders were compacted in a current-activated pressure-assisted densification process. Rapid thermal annealing was studied systematically as a means of further dopant activation. The thermoelectric properties are evaluated with regard to charge carrier concentration and mobility. A Jonker-type analysis reveals the potential of our approach to achieve high power factors. In the present study, power factors larger than 4×10-4 Wm-1K-2 were measured at temperatures higher than 600 °C.
Giant Thermoelectric Effect in Graded Micro-Nanoporous Materials
Authors: Niarchos Dimitrios G. , Tarkhanyan Roland H. , Ioannidou Alexandra
Published: October 2013

In this work we report on opportunities for a colossal reduction in lattice thermal conductivity (LTC) of graded micro-nanoporous structures with inhomogeneous porosity which leads to the considerable improvement in thermoelectric figure of merit ZT. We employ the effective medium theory to calculate the LTC of a porous media with hole pores of variable radius and show that porous materials with inhomogeneous porosity are expected to have stronger reduction (about 30 times!) in thermal conductivity than those with pores of equal sizes. Such a reduction is caused by enhanced scattering of thermal phonons with the pore boundaries. We have studied the variations of the LTC as a function of porosity, pore sizes, geometry and the number of pore groups with different sizes. Our theoretical results show excellent agreement with experimental data.
Fabrication and Characterization of Nanostructured Bulk Skutterudites
Authors: Tafti Mohsen Y. , Saleemi Mohsin , Jacquot Alexandre , Jägle Martin , Muhammed Mamoun , Toprak Muhammet S.
Published: October 2013

Latest nanotechnology concepts applied in thermoelectric (TE) research have opened many new avenues to improve the ZT value. Low dimensional structures can improve the ZT value as compared to bulk materials by substantial reduction in the lattice thermal conductivity, κL. However, the materials were not feasible for the industrial scale production of macroscopic devices because of complicated and costly manufacturing processes involved. Bulk nanostructured (NS) TEs are normally fabricated using a bulk process rather than a nano-fabrication process, which has the important advantage of producing in large quantities and in a form that is compatible with commercially available TE devices.

We developed fabrication strategies for bulk nanostructured skutterudite materials based on FexCo1-xSb3. The process is based on precipitation of a precursor material with the desired metal atom composition, which is then exposed to thermochemical processing of calcination followed by reduction. The resultant material thus formed maintains nanostructured particles which are then compacted using Spark Plasma Sintering (SPS) by utilizing previously optimized process parameters. Microstructure, crystallinity, phase composition, thermal stability and temperature dependent transport property evaluation has been performed for compacted NS FexCo1-xSb3. Evaluation results are presented in detail, suggesting the feasibility of devised strategy for bulk quantities of doped TE nanopowder fabrication.
Modeling the sensitivity of CERES-Rice model: An experience of Nepal
Authors: Lamsal A , Amgai LP , Giri A
Published: October 2013

The experiment was conducted with four levels of nitrogen (40, 80,120 and 160 kg/ha) and 3 different cultivars (Prithivi hybrid), Masuli (HYV) and Sunaulo Sugandha (Aromatic).RMSE value (747.35 kg/ha, 1.106 days, 2.58 days and 0.004 kg/ha) and D-stat value (0.793, 0.99, 0.99 and 0.633) for grain yield, anthesis days, maturity days, and individual grain weight respectively. The objective of this study was to identify whether CSM-CERES-Rice model can be used in Nepalese condition and to evaluate the sensitivity of model with impact of climate change on rice production. Eight different climate scenarios were built by perturbing maximum and minimum temperature (± 4°C), CO2 (± 20ppm), solar radiation (±1MJ/m2/day) using interactive sensitivity analysis mode in DSSAT. Among the scenario evaluated, temperature (± 40°C), CO2 concentration (+20 ppm) with change in solar radiation (±1MJ m-2 day-1) resulted maximum increase in yield (by 62, 41 and 42%) under decreasing climatic scenarios and sharp decline in yield (by 80, 46 and 40%) was observed under increasing climate change scenarios, in Prithivi, Masuli and Sunaulo Sugandha cultivars respectively.Not surprisingly, increasing yield by (48, 25 and 27 %) and decrease in yield by(77, 41 and 34) by perturbing only maximum and minimum temperature by (± 4) shows that the temperature is most sensitive for yield potentiality of cultivars than other. CERES-Riceversion 4.0 was well calibrated in Chitwan Nepal condition. The model applications show that model could be a tool for precision decision-making. There was variation in yield in response to the change in climatic scenario in the study. RMSE value (747.4 kg/ha, 1.11days, and 2.58 days), and d-stat (0.79, 0.99 and 0.99) for grain yield, anthesis, and maturity days confirm the possibility of CERESRiceuse in Nepalese agriculture. The finding showed that there was sharp decrease in rice yield due to change in temperature, CO2 and solar radiation. Climatic scenario developed by CERES-Rice model in sensitivity analysis resulted yield reduction up to 80%. Among the cultivar, hybrid rice shows more vulnerability with climate change. Decrease in yield were mainly associated with lowering growth duration along with increasing temperature, where as there is very less counter effect of increasing carbon dioxide concentration and solar radiation. Agronomy Journal of Nepal (Agron JN) Vol. 3. 2013, Page 11-22 DOI: http://dx.doi.org/10.3126/ajn.v3i0.8982
Short communication: System of wheat intensification in farmers’ field of Sindhuli, Nepal
Authors: Adhikari D
Published: October 2013

Food requirement is increasing day by day whereas production of food is not sufficient or decreasing due to various factors. In Nepal, wheat is third major cereal crop after rice and maize both in area and production, and can be grown all over the country successfully during winter season. A study was conducted during 2011/12 to determine the performance of System of Wheat Intensification (SWI) at farmers’ field of Bhimasthan, Sindhuli, Nepal. Germinated seed of wheat variety Bhirkuti was shown on 6th Dec 2011 in the spacing 20x20 cm. Average tiller number and number of effective tillers were 25 and 21 respectively. Average plant height was 61.5 cm. at 65 Days after Sowing. The results of this study showed that plant height, numbers of tillers/ hill, number of productive tillers, panicle length, and production were found higher in SWI method. Yield of wheat variety (Bhirkuti) was found 2.6, 2.4 and 2.3 kg/4 m2 in SWI, Line sown and broadcast practices, respectively. Agronomy Journal of Nepal (Agron JN) Vol. 3. 2013, Page 168-171 DOI: http://dx.doi.org/10.3126/ajn.v3i0.9019
The German Economy and East-Central Europe: The Development of Intra-Industry Trade from Ostpolitik to the Present
Authors: Gross Stephen
Published: October 2013

Over the past decade Germany has had one of the most successful

economies in the developed world. Despite the ongoing Euro crisis unemployment

has fallen below 7 percent, reaching its lowest levels since German

reunification in 1990. Germany’s youth unemployment is among the

lowest in Europe, far beneath the European average.1 One of the most

important engines of the German economy today, and in fact throughout

the twentieth and twenty-first centuries, has been its export sector. As Ludwig

Erhard, West Germany’s Economics Minister during the Wirtschaftswunder

of the 1950s remarked: “foreign trade is quite simply the core and

premise of our economic and social order.”2 According to various estimates,

today exports and imports of goods and services account for nearly a half of

German GDP—up from only a quarter in 1990. Germany is one of only three

economies that do over a trillion dollars worth of exports a year, the other

two being the United States and China.
Smooth-muscle progenitor cells isolated from patients with moyamoya disease: novel experimental cell model
Authors: Kang Hyun-Seung , Moon Youn-Joo , Kim Young-Yim , Park Woong-Yang , Park Ae Kyung , Wang Kyu-Chang , Kim Jeong Eun , Phi Ji Hoon , Lee Ji Yeoun , Kim Seung-Ki
Published: October 2013

Object

Moyamoya disease (MMD) is a cerebrovascular occlusive disease affecting bilateral internal carotid termini. Smooth-muscle cells are one of the major cell types involved in this disease process. The characteristics of circulating smooth-muscle progenitor cells (SPCs) in MMD are poorly understood. The authors purified SPCs from the peripheral blood of patients with MMD and sought to identify differentially expressed genes (DEGs) in SPCs from these patients.

Methods

The authors cultured and isolated SPCs from the peripheral blood of patients with MMD (n = 25) and healthy control volunteers (n = 22). After confirmation of the cellular phenotype, RNA was extracted from the cells and DEGs were identified using a commercially available gene chip. Real-time quantitative reverse transcription polymerase chain reaction was performed to confirm the putative pathogenetic DEGs.

Results

The SPC-type outgrowth cells in patients with MMD invariably showed a hill-and-valley appearance under microscopic examination, and demonstrated high α–smooth muscle actin, myosin heavy chain, and calponin expression (96.5% ± 2.1%, 42.8% ± 18.6%, and 87.1% ± 8.2%, respectively), and minimal CD31 expression (less than 1%) on fluorescence-activated cell sorter analysis. The SPCs in the MMD group tended to make more irregularly arranged and thickened tubules on the tube formation assay. In the SPCs from patients with MMD, 286 genes (124 upregulated and 162 downregulated) were differentially expressed; they were related to cell adhesion, cell migration, immune response, and vascular development.

Conclusions

With adequate culture conditions, SPCs could be established from the peripheral blood of patients with MMD. These cells showed specific DEGs compared with healthy control volunteers. This study provides a novel experimental cell model for further research of MMD.