bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of compatibilizer and processing method on the mechanical, thermal and barrier properties of polystyrene/organoclay nanocomposites
Authors: Panwar Artee , Choudhary Veena , Sharma DK
Published: February 2013

This study describes the role of compatibilizer i.e. styrene-maleic anhydride copolymer, its content and compounding method on the properties of polystyrene/clay nanocomposites. The nanocomposites were fabricated using three different methods: (i) simultaneous mixing of all the components i.e. polystyrene, required amounts of styrene-maleic anhydride and nanoclay using twin-screw extruder; (ii) stepwise mixing method i.e. in which blending of polystyrene and organoclay was first done using single-screw extruder and the mixed compound was then blended with varying amounts of styrene-maleic anhydride copolymer using twin-screw extruder and (iii) the effective combination of in situ polymerization of styrene-maleic anhydride copolymer in presence of varying amounts of nanoclay by free radical polymerization followed by melt mixing with polystyrene using twin-screw extruder. The effect of processing method on the micrsostructure of nanocomposites was investigated using X-ray diffraction and transmission electron microscopy. The mechanical properties of nanocomposites such as tensile, flexural and Izod impact strength were measured and discussed in relation to their microstructure. All the fabrication methods yielded nanocomposites with different microstructure ranging from intercalated to exfoliated structure of nanoclay. As expected the stepwise mixing method yielded more intercalated and exfoliated structure as compared to the simultaneous mixing method resulting in improvement in the properties of nanocomposites. On the other hand, combination of in situ polymerization with melt mixing method produced better exfoliation as compared to other two methods. Thermal stability and mechanical strength of polystyrene showed a significant improvement upon incorporation of nanoclay.
Rapid Onset of Hippocampal Atrophy in Febrile-Infection Related Epilepsy Syndrome (FIRES)
Authors: Byler Debra L. , Grageda Melissa R. , Halstead E. Scott , Kanekar Sangam
Published: February 2013

Febrile infection-related epilepsy syndrome (FIRES) is a catastrophic and usually refractory epilepsy syndrome that occurs after a febrile illness in previously normal children. The pathogenesis of the syndrome is unknown, and the diagnosis is typically made by exclusion after an exhaustive negative workup for central nervous system infections and autoimmune or metabolic disorders. Magnetic resonance imaging of patients with this condition has previously shown hippocampal abnormalities, typically found several months or longer after initial seizures. We report a previously healthy 5-year-old child who developed hippocampal atrophy by day 37 of his illness. The development of early hippocampal atrophy in this epileptic encephalopathy may provide insight into pathogenesis and highlights the need for aggressive and effective interventions early in the disease process.
The degradation of work and the end of the skilled emotion worker at Aer Lingus: is it all trolley dollies now?
Authors: Curley Caitriona , Royle Tony
Published: February 2013

The article focuses on emotional labour and self-identity at the Irish-owned Aer Lingus airline from 1998 to 2008. It has been suggested that emotional labour is likely to be an increasingly important feature of frontline service jobs. However, in this case management has reduced the level of emotional labour requirement while work organization, recruitment policy and training have changed to focus on sales and lower labour costs, intensifying workloads and reducing cabin crew autonomy. Although some may suggest that a reduction in emotional labour requirement would be a positive outcome for employees, this is not how it has been perceived by some cabin crew. Long-serving cabin crew in particular see these changes as an attack on their professionalism and a challenge to their identity as skilled emotion workers.
CFD analysis of a syngas-fired burner for ceramic industrial roller kiln
Authors: Cavazzuti Marco , Corticelli Mauro A , Nuccio Antonino , Zauli Bruno
Published: February 2013

Kiln burners for industrial tile production are usually fuelled by methane gas. However, the interest towards the use of coal or synthesis gases is rapidly increasing, mainly due to the opening of important markets in developing countries. The widely variable chemical composition of these fuels demands the gas burner to be adapted on case-by-case basis, since the firing parameters are strictly fixed, to guarantee the required temperature distribution within the kiln. In this context, computational fluid dynamics analysis represents a very convenient alternative to the traditional design based on experiments. In this article three-dimensional numerical predictions are presented for a syngas-fired burner. Three different fuels, two burner layouts and two burner nominal power are considered. Temperature, velocity and oxygen mass fraction distributions are discussed, and general design lines for low lower heating value gas burners are extracted.
Fictitious Inhibitory Differences
Authors: Verbruggen Frederick , Chambers Christopher D. , Logan Gordon D.
Published: February 2013

The stop-signal paradigm is a popular method for examining response inhibition and impulse control in psychology, cognitive neuroscience, and clinical domains because it allows the estimation of the covert latency of the stop process: the stop-signal reaction time (SSRT). In three sets of simulations, we examined to what extent SSRTs that were estimated with the popular mean and integration methods were influenced by the skew of the reaction time distribution and the gradual slowing of the response latencies. We found that the mean method consistently overestimated SSRT. The integration method tended to underestimate SSRT when response latencies gradually increased. This underestimation bias was absent when SSRTs were estimated with the integration method for smaller blocks of trials. Thus, skewing and response slowing can lead to spurious inhibitory differences. We recommend that the mean method of estimating SSRT be abandoned in favor of the integration method.
Long-Run Performance of Emerging Market ADRs: Evidence From Issues Listed on the New York Stock Exchange From 1990 Through 2009
Authors: Schaub Mark
Published: February 2013

This article examines the three-year monthly aftermarket returns of emerging market firm equities traded on the New York Stock Exchange as American Depository Receipts (ADRs). Excess return results are broken down by the type of issue (IPO versus SEO) and the date of issue (those issued in the 1990s versus the 2000s). The total emerging market sample of 193 ADRs significantly outperformed the S&P 500 index by 8.5 percent for the three-year holding period; however, those issued before 2000 underperformed the index by nearly 18 percent while those listed after January 1, 2000 outperformed the index by nearly 41 percent. SEOs outperformed the market index by 32 percent while IPOs underperformed by 2 percent. Both portfolios (IPOs and SEOs) significantly outperformed the market for issues that were listed in the 2000s.
New Evidence Points to Robust but Uneven Productivity Growth in Global Agriculture
Authors: Fuglie Keith O. , Wang Sun Ling
Published: February 2013

This article is drawn from Productivity Growth in Agriculture: An International Perspective, edited by Fuglie, Wang, and Ball. It is a review of agricultural productivity around the world, with an analysis of prices, population, and productivity over the past 50 years. In developing and transition countries, agricultural productivity growth has been found to be strong over the past 10 years. Developed countries have also experienced robust agricultural total factor productivity growth, though it is now slowing in many countries.
ASEAN Dynamism: Agricultural Transformation and Food Security
Authors: Golan Amnon , Kohli Harinder
Published: February 2013

This article assesses performance of the agricultural sector in Vietnam, Indonesia, and the Philippines (VIP countries) during the period 1980–2011, future prospects up to 2040 and food security in these countries and in the ASEAN region. Analysis of the past performance and likely future scenarios was carried out with the aid of the Centennial Group’s Global Growth Model after introducing several modifications to address the needs of the agricultural sector. Our modeling efforts were divided into two parts. The first part comprised a macro-economic analysis of future scenarios at the global level and for VIP countries. The second part included analysis at the country level of future total factor productivity (TFP), agricultural production and changes in national food consumption habits. As a countercheck use was also made of IFPRI’s updated IMPACT Model, and in the case of the Philippines, the AMPLE model.
Differentiating Behavioral Ratings of Inattention, Impulsivity, and Hyperactivity in Children
Authors: Pham Andy V.
Published: February 2013

Objective: The purpose of the study is to differentiate between behaviors of ADHD: inattention, hyperactivity, and impulsivity and how each domain contributes to reading achievement in elementary school-aged children. Method: Data from 131 children were collected, which include performance from reading fluency and comprehension measures as well as parent and teacher ratings of ADHD behaviors based on the Diagnostic and Statistical Manual of Mental Disorders (4th ed.; DSM-IV) criteria. Results: Correlation and regression analyses revealed that inattentive behaviors were strongly linked to reading fluency and comprehension. Hyperactivity and impulsive behaviors did not predict reading achievement. A significant two-way interaction was found only for gender and inattention with reading comprehension as the outcome. Conclusion: Many of the behaviors related to inattention strongly predicted reading fluency, reading comprehension, and overall reading ability. Boys who exhibited inattentive behaviors performed more poorly on reading comprehension measures than girls with inattentive behaviors.
Occurrence of bacteriuria in 18 catheterised cats with obstructive lower urinary tract disease: a pilot study
Authors: Hugonnard Marine , Chalvet-Monfray Karine , Dernis Jérémy , Pouzot-Nevoret Céline , Barthélémy Anthony , Vialard Jacquemine , Goy-Thollot Isabelle
Published: February 2013

The incidence of catheter-associated urinary tract infections in cats catheterised for an obstructive lower urinary tract disease (LUTD) has not previously been evaluated. The objective of this study was to evaluate the frequency of significant bacteriuria in cats with obstructive LUTD managed for 48 h with a closed urine collection system. Eighteen male cats admitted for a non-infectious obstructive LUTD were evaluated. This was a prospective study. A standard protocol was used for aseptic catheter placement and maintenance. Three urine samples were collected from each animal through the catheter immediately after placement, 24 h after placement and just before removal. All samples underwent complete urinalysis, including bacterial culture. Catheter tips were tested by bacterial culture. Six cats (33.3%) developed significant bacteriuria during catheterisation. The causative bacteria were common feline uropathogens ( Escherichia coli, Staphylococcus species) in five cases, and Streptococcus bovis in one. One cat developed a fungal infection. The presence of bacteria in urinary sediment was correlated strongly with positive urine culture results. The catheter tips from 10/18 cats (55.5%) were positive for culture. The positive predictive value of a positive culture from the urinary catheter tip was 87.5%. The specificity was 53.8%. The same infectious agents were cultured from both urine and catheter tip in six cases. In summary, one-third of cats developed significant bacteriuria during catheterisation. Silent bacteriuria could not be clearly differentiated from true urinary tract infection. The presence of bacteria in the urinary sediment was strongly indicative of bacteriuria. The specificity of urinary catheter tip culture was low.
Management learning: A scholarship of practice centred on attention?
Authors: Ramsey Caroline
Published: February 2013

This article explores the scholarly processes involved in management learning and education. Drawing on a practice turn in social sciences, the article develops current thinking on epistemologies of practice, Aristotle’s intellectual virtue of phronesis and Shotter’s social poetics to suggest a scholarship of practice. Building upon Shotter’s interpretation of Wittgenstein’s later work and the literatures on mindfulness, it is argued that such a scholarship of practice is centred on deliberative attention rather than knowledge. An account of a 30-month action research project is then used to illustrate a scholarship of practice, in which three domains of attention are identified: an engagement with ideas, a practice of inquiry and a navigation of relations.
Coming out in the field: A queer reflexive account of shifting researcher identity
Authors: McDonald James
Published: February 2013

This article contributes to the literature on reflexivity by articulating a queer reflexivity lens, which entails engaging in a reflexive questioning of the categories we use to identify people and recognizing the shifting nature of researcher and participant identities over the course of the research process. Queer reflexivity enables us to think differently about an important debate in qualitative methods concerning who can study whom. For instance, are white researchers in a position to study people of color? Are men able to study women and women’s issues? Can “straight”-identified researchers study the Lesbian, Gay, Bisexual, Transgender and Queer community? I argue that the question of whether or not to “match” for categories of difference in research studies is complicated by the fluid, shifting nature of identities that queer theory highlights. In order to demonstrate how qualitative organizational researchers can learn about the craft of research through the concept of queer reflexivity, I recount an auto-ethnographic “coming-out” tale in which I discuss the implications of my shifting sexual identity over the course of a research project.
Relating health-related Quality of Life to disability progression in multiple sclerosis, using the 5-level EQ-5D
Authors: Fogarty Emer , Walsh Cathal , Adams Roisin , McGuigan Christopher , Barry Michael , Tubridy Niall
Published: February 2013

Background:

Increasing use of the Quality-Adjusted Life-Year to inform resource allocation decision-making has highlighted the importance of relating clinical and health-related quality of life (HRQoL) outcomes in multiple sclerosis (MS) patients.

Objective and Methods:

To investigate the relationship between the Expanded Disability Status Scale (EDSS) and HRQoL utility, using the 5-level EQ-5D (EQ-5D-5L). The discriminatory power of the EQ-5D-5L was assessed using Shannon’s indices.

Results:

A linear decline in utility was observed with changes in EDSS score from 0 to 6, after which point the relationship exhibited greater variability. Mean utility values ranged from −0.22 at EDSS 9 to 0.88 at EDSS 0. We found that the discriminative capacity of the EQ-5D-5L was considerably lower for the domains self-care and anxiety/depression, compared with other health-related domains.

Conclusion:

In its first reported use in an MS population, the EQ-5D-5L displayed good discriminatory capacity, although performance differed between the various domains of health, with evidence of a ceiling effect present in the domains of self-care and anxiety/depression. The EQ-5D-5L demonstrated a high correlation with EDSS in our MS cohort up to EDSS 6, after which point the utility valuation of severe health states exhibited much greater variability. Utility estimates from this study may be used in economic evaluations of disease-modifying therapies in MS, to inform resource-allocation decisions.
Altered expression of the plasminogen activation pathway in peripheral blood mononuclear cells in multiple sclerosis: possible pathomechanism of matrix metalloproteinase activation
Authors: Cox Mathew B , Bowden Nikola A , Scott Rodney J , Lechner-Scott Jeannette
Published: February 2013

Background:

Multiple sclerosis (MS) is an autoimmune disorder where a breakdown in the integrity of the blood-brain barrier is thought to allow lymphocytes to enter the central nervous system.

Objectives:

The purpose of this study was to examine gene expression profiles between MS patients and healthy controls to identify genes intimately involved in the pathobiology of MS.

Methods:

Whole-genome gene expression analysis was performed using peripheral blood mononuclear cells from 39 healthy controls and 37 MS patients, 24 MS patients receiving no disease modifying therapy and 13 MS patients receiving interferon-beta (IFN-beta). Pathway analysis was performed to identify pathways dysregulated in MS.

Results:

Gene expression profiling of MS identified a signature of predominately immune associated genes. The plasminogen activation pathway contained an over-representation of significantly differentially expressed genes, including matrix metallopeptidase 9 (MMP9). Treatment with IFN-beta ameliorated the over-expression of MMP9, however the expression of two genes, plasminogen activator urokinase (PLAU) and serpin peptidase inhibitor, clade B (ovalbumin), member 2 (SERPINB2), forming part of the plasminogen activation pathway were not affected by IFN-beta therapy.

Conclusions:

High expression levels of MMP9 have been associated with MS and the breakdown of the blood-brain barrier, while IFN-beta therapy decreases MMP9 expression. We confirm altered MMP9 expression in MS, and identify dysregulation within the plasminogen activation cascade, a pathway involved in the activation of MMP9.
From intuition to database: Translating justice
Authors: Hutton Neil
Published: February 2013

The article tells the story of the development of a Sentencing Information System for the High Court in Scotland from its genesis as an exploratory research project to its final implementation in the court. The article uses Actor Network Theory to understand how the database was assembled through the social practices of academic researchers, government officials, judges and court officers. It offers a corrective to theories which exaggerate the de-humanizing effect of information technology and argues that an Actor Network Theory approach is not incompatible with an understanding of how institutionally located power operates through social practices.
Sexual orientation and self-rated health: the role of social capital, offence, threat of violence, and violence
Authors: Axelsson Jakob , Modén Birgit , Rosvall Maria , Lindström Martin
Published: February 2013

Objective: To study the association between sexual orientation and self-rated health, including trust, offence, threat of violence, and violence. Design/setting/participants/measurement: The 2008 Public Health Survey in Skåne is a cross-sectional postal questionnaire study. A total of 28,198 persons aged 18–80 years responded (55%). Logistic regressions analysed the association between sexual orientation and self-rated health. Results: 27.4% of all men and 30.0% of all women rated their health as poor. Poor self-rated health was significantly more prevalent in higher age, among immigrants, people with lower education, low social support, low trust, experience of being offended, experience of threat of violence and violence, and bisexual and other orientation. Homosexual and bisexual men and women had higher age-adjusted odds ratios of having felt offended compared to heterosexual respondents. The odds ratios of low trust, threat of violence (men), and experience of violence (women) were significant for respondents with bisexual orientation but not for respondents with homosexual orientation. In the age-adjusted model, no significant association was observed between homosexual orientation and poor self-rated health among women. All other associations between sexual orientation and health were significant in the age-adjusted model but non-significant in the multiple models. Conclusions: Associations between sexual orientation and health disappear after multiple adjustments including trust and experience of offence, threat of violence, and violence. The study suggests that the group with bisexual orientation seems to be more exposed to low social capital (trust), threat of violence, and violence than the group with homosexual orientation.
Financial news and market panics in the age of high-frequency sentiment trading algorithms
Authors: Kleinnijenhuis Jan , Schultz Friederike , Oegema Dirk , van Atteveldt Wouter
Published: February 2013

Whether financial news may contribute to market panics is not an innocent question. A positive answer is easily used as a legitimation to limit the freedom of financial journalists. Long-term effects of news are moreover inconsistent with the Efficient Market Hypothesis (EMH), which maintains that new information gives immediately rise to a new equilibrium. The EMH is under discussion, however, as a result of the transformation of financial markets and of financial journalism due to new economic thoughts, new communication theories, high-frequency trading and high-frequency sentiment analysis. As a case study of a market panic we show the impact of US news, UK news and Dutch news on three Dutch banks during the financial crisis of 2007–9. To avoid market panics, financial journalists may strive for greater transparency, not only on asset prices and corporate philosophies, but also on network dependencies in the worldwide financial markets.
Bayesian P-spline estimation in hierarchical models specified by systems of affine differential equations
Authors: Jaeger Jonathan , Lambert Philippe
Published: February 2013

Ordinary differential equations (ODEs) are widely used to model physical, chemical and biological processes. Current methods for parameter estimation can be computationally intensive and/or not suitable for inference and prediction. Frequentist approaches based on ODE-penalized smoothing techniques have recently solved part of these drawbacks. A full Bayesian approach based on ODE-penalized B-splines is proposed to jointly estimate ODE parameters and state functions from affine systems of differential equations. Simulations inspired by pharmacokinetic studies show that the proposed method provides comparable results to methods based on explicit solution of the ODEs and outperforms the frequentist ODE-penalized smoothing approach. The basic model is extended to a hierarchical one in order to study cases where several subjects are involved. This Bayesian hierarchical approach is illustrated on real data for the study of perfusion ratio after a femoral artery occlusion. Model selection is feasible through the analysis of the posterior distributions of the ODE adhesion parameters and is illustrated on a real pharmacokinetic dataset.
Clustering in linear mixed models with approximate Dirichlet process mixtures using EM algorithm
Authors: Heinzl Felix , Tutz Gerhard
Published: February 2013

In linear mixed models, the assumption of normally distributed random effects is often inappropriate and unnecessarily restrictive. The proposed approximate Dirichlet process mixture assumes a hierarchical Gaussian mixture that is based on the truncated version of the stick breaking presentation of the Dirichlet process. In addition to the weakening of distributional assumptions, the specification allows to identify clusters of observations with a similar random effects structure. An Expectation-Maximization algorithm is given that solves the estimation problem and that, in certain respects, may exhibit advantages over Markov chain Monte Carlo approaches when modelling with Dirichlet processes. The method is evaluated in a simulation study and applied to the dynamics of unemployment in Germany as well as lung function growth data.
Smoothing constrained generalized linear models with an application to the Lee-Carter model
Authors: Currie Iain D
Published: February 2013

We consider a generalized linear model (GLM) with canonical link function in which parameters can be subject to (i) a set of linear constraints and (ii) smoothing. We apply Lagrange methods to give a general Newton-Raphson algorithm for such a GLM in which parameters are estimated, constraints are applied and smoothing is performed simultaneously. We express the Lee-Carter model, an important model for the forecasting of human mortality, in terms of GLMs, and use our method to estimate the parameters in the model. The smoothing option allows us to improve the forecasting properties of the model. We compare the performance of (i) the Poisson model with log link for the force of mortality and (ii) the binomial model with logit link for the probability of death in a calendar year. Examples using UK Office for National Statistics data are provided.
Speciesism
Authors: Jean Moore Lisa
Published: February 2013

Speciesism, coined in the 1970s, means the implicit superiority of one species, usually humans, over all others. Sociologist Lisa Jean Moore discusses this term and how sociologists are primed to use the concept in teaching and research.
The Hearts of Boys
Authors: Way Niobe
Published: February 2013

Five experts, Niobe Way, C.J. Pascoe, Mark McCormack, Amy Schalet, and Freeden Ouer shed light on the everyday lives of teenage boys and their relationships.
Mourning Becomes Democratic
Authors: Xu Bin
Published: February 2013

Public mourning is not a spontaneous expression of grief but a symbolic and political practice. Sociologist Bin Xu examines a new trend in recent decades, the “democratization of public mourning,” that celebrates our symbolic equality and individuality instead of affirming status hierarchies.
Beyond The One-Size-Fits-All College Degree
Authors: Rosenbaum James , Cepa Kennan , Rosenbaum Janet
Published: February 2013

James Rosenbaum, Kennan Cepa, and Janet Rosenbaum examine how commonplace assumptions about higher education limit opportunity.
Missing Romance
Authors: Kim Minjeong
Published: February 2013

Sociologist Minjeong Kim analyzes portrayals of Asian American intimacy in television and film.
Beyond “Post 9/11”
Authors: Love Erik
Published: February 2013

Sociologist Erik Love reviews the books Islamophobia and the Politics of Empire and Terrifying Muslims. Each move beyond “post 9/11” explanations for anti-Muslim sentiment, showing how Islamophobia is best understood not as a temporary backlash, but rather as stemming from longstanding and durable forms of racial bigotry and colonialism.
Body Lessons
Authors: Enke Janet
Published: February 2013

Sociologist Janet Enke explores the challenges of teaching a course on the body. She discusses how to synthesize the subjective experience of the body with academic theory, and convey knowledge about the politics of the body.
Community work and limited online activism among India youth
Authors: Ilavarasan P Vigneswara
Published: February 2013

This article explores how youth in India understand, get involved in and actively use information and communication technologies (ICTs) in civic engagement. Despite a variety of opportunities for civic engagement, young people in India today show little interest in politics. Many cite a perceived inability to effect changes in India’s corrupt political system as the reason for their apathy. Indian youth do, however, engage in other forms of civic engagement. Helping the needy outside of work and college is a common form of community work for young Indians. Others engage with their communities through paid work at non-governmental organizations (NGOs). ICTs are used in the everyday lives of Indian youth for personal purposes like entertainment and social networking, but relatively little for activism. Of all ICTs in India, mobile phones are arguably the most important, with laptops a key ICT at NGOs.
Adolescent Girls With Low Dietary Diversity Score Are Predisposed to Iron Deficiency in Southwestern Nigeria
Authors: Olumakaiye Motunrayo Funke
Published: February 2013

Iron-deficiency anemia is a pervasive public health problem among adolescent girls in sub-Saharan Africa. The aim of this study was to assess the dietary iron intakes of adolescent females using dietary diversity as a proxy in relation to iron status. Purposive sampling procedure was used to select 120 foods and nutrition female students from 6 rural government schools in Ondo West Local Government of Southwestern Nigeria, which was predominantly of Yoruba ethnic group. The students were screened for serum ferritin concentration of less than 12.0 µg/L with normal hemoglobin concentration to determine iron deficiency status. A standardized Food and Agriculture Organization 24-hour diet recall questionnaire was adapted, tested, and used to calculate dietary diversity score. Analyses were done using SPSS version 16. The result indicated that the mean age was 14 ± 1.45 years, 57 (47.5%) adolescent females were iron deficient, and 63 (52.5%) non–iron deficient. Girls in the 16 to 19 years range were significantly more likely to be iron deficient than other groups (odds ratio = 2.81, 95% confidence interval = 1.12-6.54). Mean Dietary Diversity Score (DDS) was 2.6 ± 1.058, which showed a significant difference between the 2 groups ( P = .037). Heme iron source ( P = .032) was consumed lesser than the non-heme iron ( P = .002) by iron-deficient girls. Girls with low DDS were at significantly higher risk (odds ratio = 1.79, 95% confidence interval = 0.50-2.17, P = .006) compared with the high and moderate DDS groups. In conclusion, there was a low intake of dietary iron among adolescent girls. Nutrition education should be intensified among female adolescents to improve their nutritional knowledge.
Immune activation of human brain microvascular endothelial cells inhibits HIV replication in macrophages
Authors: Li Jieliang , Wang Yizhong , Wang Xu , Ye Li , Zhou Yu , Persidsky Yuri , Ho Wenzhe
Published: February 2013

Key Points

Brain ECs possess a functional TLR3/RIG-I system that is able to mount an effective IFN induction upon immune activation. Brain ECs may be a key regulatory bystander, playing a crucial role in the BBB innate immunity against HIV infection.
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis
Authors: LaMarche Brian L , Crowell Kevin L , Jaitly Navdeep , Petyuk Vladislav A , Shah Anuj R , Polpitiya Ashoka D , Sandoval John D , Kiebel Gary R , Monroe Matthew E , Callister Stephen J , Metz Thomas O , Anderson Gordon A , Smith Richard D
Published: February 2013

Background

MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and chromatographic elution features across datasets. Applicable to both label-free proteomics and metabolomics comparative analyses, the software can be operated in several modes. For example, clustered features can be matched to a reference database to identify analytes, used to generate abundance profiles, linked to tandem mass spectra based on parent precursor masses, and culled for targeted liquid chromatography-tandem mass spectrometric analysis. MultiAlign is also capable of tandem mass spectral clustering to describe proteome structure and find similarity in subsequent sample runs.

Results

MultiAlign was applied to two large proteomics datasets obtained from liquid chromatography-mass spectrometry analyses of environmental samples. Peptides in the datasets for a microbial community that had a known metagenome were identified by matching mass and elution time features to those in an established reference peptide database. Results compared favorably with those obtained using existing tools such as VIPER, but with the added benefit of being able to trace clusters of peptides across conditions to existing tandem mass spectra. MultiAlign was further applied to detect clusters across experimental samples derived from a reactor biomass community for which no metagenome was available. Several clusters were culled for further analysis to explore changes in the community structure. Lastly, MultiAlign was applied to liquid chromatography-mass spectrometry-based datasets obtained from a previously published study of wild type and mitochondrial fatty acid oxidation enzyme knockdown mutants of human hepatocarcinoma to demonstrate its utility for analyzing metabolomics datasets.

Conclusion

MultiAlign is an efficient software package for finding similar analytes across multiple liquid chromatography-mass spectrometry feature maps, as demonstrated here for both proteomics and metabolomics experiments. The software is particularly useful for proteomic studies where little or no genomic context is known, such as with environmental proteomics.
Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria
Authors: Ravcheev Dmitry A , Best Aaron A , Sernova Natalia V , Kazanov Marat D , Novichkov Pavel S , Rodionov Dmitry A
Published: February 2013

Background

Genome scale annotation of regulatory interactions and reconstruction of regulatory networks are the crucial problems in bacterial genomics. The Lactobacillales order of bacteria collates various microorganisms having a large economic impact, including both human and animal pathogens and strains used in the food industry. Nonetheless, no systematic genome-wide analysis of transcriptional regulation has been previously made for this taxonomic group.

Results

A comparative genomics approach was used for reconstruction of transcriptional regulatory networks in 30 selected genomes of lactic acid bacteria. The inferred networks comprise regulons for 102 orthologous transcription factors (TFs), including 47 novel regulons for previously uncharacterized TFs. Numerous differences between regulatory networks of the Streptococcaceae and Lactobacillaceae groups were described on several levels. The two groups are characterized by substantially different sets of TFs encoded in their genomes. Content of the inferred regulons and structure of their cognate TF binding motifs differ for many orthologous TFs between the two groups. Multiple cases of non-orthologous displacements of TFs that control specific metabolic pathways were reported.

Conclusions

The reconstructed regulatory networks substantially expand the existing knowledge of transcriptional regulation in lactic acid bacteria. In each of 30 studied genomes the obtained regulatory network contains on average 36 TFs and 250 target genes that are mostly involved in carbohydrate metabolism, stress response, metal homeostasis and amino acids biosynthesis. The inferred networks can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. All reconstructed regulons are captured within the Streptococcaceae and Lactobacillaceae collections in the RegPrecise database (http://regprecise.lbl.gov).
Transcriptomic analysis of differentially expressed genes during anther development in genetic male sterile and wild type cotton by digital gene-expression profiling
Authors: Wei Mingming , Song Meizhen , Fan Shuli , Yu Shuxun
Published: February 2013

Background

Cotton (Gossypium hirsutum) anther development involves a diverse range of gene interactions between sporophytic and gametophytic tissues. However, only a small number of genes are known to be specifically involved in this developmental process and the molecular mechanism of the genetic male sterility (GMS) is still poorly understand. To fully explore the global gene expression during cotton anther development and identify genes related to male sterility, a digital gene expression (DGE) analysis was adopted.

Results

Six DGE libraries were constructed from the cotton anthers of the wild type (WT) and GMS mutant (in the WT background) in three stages of anther development, resulting in 21,503 to 37,352 genes detected in WT and GMS mutant anthers. Compared with the fertile isogenic WT, 9,595 (30% of the expressed genes), 10,407 (25%), and 3,139 (10%) genes were differentially expressed at the meiosis, tetrad, and uninucleate microspore stages of GMS mutant anthers, respectively. Using both DGE experiments and real-time quantitative RT-PCR, the expression of many key genes required for anther development were suppressed in the meiosis stage and the uninucleate microspore stage in anthers of the mutant, but these genes were activated in the tetrad stage of anthers in the mutant. These genes were associated predominantly with hormone synthesis, sucrose and starch metabolism, the pentose phosphate pathway, glycolysis, flavonoid metabolism, and histone protein synthesis. In addition, several genes that participate in DNA methylation, cell wall loosening, programmed cell death, and reactive oxygen species generation/scavenging were activated during the three anther developmental stages in the mutant.

Conclusions

Compared to the same anther developmental stage of the WT, many key genes involved in various aspects of anther development show a reverse gene expression pattern in the GMS mutant, which indicates that diverse gene regulation pathways are involved in the GMS mutant anther development. These findings provide the first insights into the mechanism that leads to genetic male sterility in cotton and contributes to a better understanding of the regulatory network involved in anther development in cotton.
Using hospital discharge data to identify incident pregnancy-associated cancers: a validation study
Authors: Lee Yuen Yi Cathy , Roberts Christine L , Young Jane , Dobbins Timothy
Published: February 2013

Background

Pregnancy-associated cancer is associated with maternal morbidities and adverse pregnancy outcomes, and is reported to be increasing. Hospital discharge data have the potential to provide timely information on cancer incidence, which is central to evaluation and improvement of clinical care for women. This study aimed to assess the validity of hospital data for identifying incident pregnancy-associated cancers compared with incident cancers from an Australian population-based statutory cancer registry.

Methods

Birth data from 2001–2008, comprised 470,277 women with 679,736 maternities, were linked to cancer registry and hospitalisation records to identify newly diagnosed cancers during pregnancy or within 12 months of delivery. Two hospital-identified cancer groups were examined; “index cancer hospitalisation” – first cancer admission per woman per pregnancy and “all cancer hospitalisations” –the total number of hospitalisations with a cancer diagnosis and women could have multiple hospitalisations during pregnancy. The latter replicates a scenario where identification of individuals is not possible and hospitalisations are used as the unit of analysis.

Results

The incidence of pregnancy-associated cancer (according to cancer registry) was 145.4/100,000 maternities. Incidence of cancer was substantially over-estimated when using hospitalisations as the unit of analysis (incidence rate ratio, IRR 1.7) and under-estimated when using the individual (IRR 0.8). Overall, the sensitivity of “index cancer hospitalisation” was 60.4%, positive predictive value (PPV) 77.7%, specificity and negative predictive value both 100%. Melanoma ascertainment was only 36.1% and breast cancer 62.9%. For other common cancers sensitivities ranged from 72.1% to 78.6% and PPVs 56.4% to 87.3%.

Conclusion

Although hospital data provide another timely source of cancer identification, the validity is insufficient to obtain cancer incidence estimates for the obstetric population.
Retroperitoneal teratoma with somatic malignant transformation: A papillary renal cell carcinoma in a testicular germ cell tumour metastasis following platinum-based chemotherapy
Authors: Zeh Nina , Wild Peter J , Bode Peter K , Kristiansen Glen , Moch Holger , Sulser Tullio , Hermanns Thomas
Published: February 2013

Background

Malignant transformation describes the phenomenon in which a somatic component of a germ cell teratoma undergoes malignant differentiation. A variety of different types of sarcoma and carcinoma, all non-germ cell, have been described as a result of malignant transformation.

Case presentation

A 33-year-old man presented with a left testicular mass and elevated tumour markers. Staging investigations revealed retroperitoneal lymphadenopathy with obstruction of the left ureter and distant metastases. Histopathology from the left radical orchiectomy showed a mixed germ cell tumour (Stage III, poor prognosis). The ureter was stented and four cycles of cisplatin, etoposide and bleomycin chemotherapy administered. After initial remission, the patient recurred four years later with a large retroperitoneal mass involving the renal vessels and the left ureter. Left retroperitoneal lymph node dissection with en-bloc resection of the left kidney was performed.

Histopathology revealed a germ cell tumour metastasis consisting mainly of mature teratoma. Additionally, within the teratoma a papillary renal cell carcinoma was found. The diagnosis was supported by immunohistochemistry showing positivity for AMACR, CD10 and focal expression of RCC and CK7. There was no radiological or histo-pathological evidence of a primary renal cell cancer.

Conclusions

To the best of our knowledge, malignant transformation into a papillary renal cell carcinoma has not been reported in a testicular germ cell tumour metastasis following platinum-based chemotherapy. This histological diagnosis might have implications for potential future therapies. In the case of disease recurrence, renal cell cancer as origin of the recurrent tumour has to be excluded because renal cell carcinoma metastases would not respond well to the classical germ cell tumour chemotherapy regimens.
Si nanopatterning by reactive ion etching through an on-chip self-assembled porous anodic alumina mask
Authors: Gianneta Violetta , Olziersky Antonis , Nassiopoulou Androula G
Published: February 2013

We report on Si nanopatterning through an on-chip self-assembled porous anodic alumina (PAA) masking layer using reactive ion etching based on fluorine chemistry. Three different gases/gas mixtures were investigated: pure SF6, SF6/O2, and SF6/CHF3. For the first time, a systematic investigation of the etch rate and process anisotropy was performed. It was found that in all cases, the etch rate through the PAA mask was 2 to 3 times lower than that on non-masked areas. With SF6, the etching process is, as expected, isotropic. By the addition of O2, the etch rate does not significantly change, while anisotropy is slightly improved. The lowest etch rate and the best anisotropy were obtained with the SF6/CHF3 gas mixture. The pattern of the hexagonally arranged pores of the alumina film is, in this case, perfectly transferred to the Si surface. This is possible both on large areas and on restricted pre-defined areas on the Si wafer.

PACS

78.67.Rb, 81.07.-b, 61.46.-w
Efficiency enhancements in Ag nanoparticles-SiO2-TiO2 sandwiched structure via plasmonic effect-enhanced light capturing
Authors: Xu Jinxia , Xiao Xiangheng , Stepanov Andrey L , Ren Fen , Wu Wei , Cai Guangxu , Zhang Shaofeng , Dai Zhigao , Mei Fei , Jiang Changzhong
Published: February 2013

TiO2-SiO2-Ag composites are fabricated by depositing TiO2 films on silica substrates embedded with Ag nanoparticles. Enhancement of light absorption of the nanostructural composites is observed. The light absorption enhancement of the synthesized structure in comparison to TiO2 originated from the near-field enhancement caused by the plasmonic effect of Ag nanoparticles, which can be demonstrated by the optical absorption spectra, Raman scattering investigation, and the increase of the photocatalytic activity. The embedded Ag nanoparticles are formed by ion implantation, which effectively prevents Ag to be oxidized through direct contact with TiO2. The suggested incorporation of plasmonic nanostructures shows a great potential application in a highly efficient photocatalyst and ultra-thin solar cell.
The expression of interleukin-32 is activated by human cytomegalovirus infection and down regulated by hcmv-miR-UL112-1
Authors: Huang Yujing , Qi Ying , Ma Yanping , He Rong , Ji Yaohua , Sun Zhengrong , Ruan Qiang
Published: February 2013

Background

Interleukin-32 (IL-32) is an important factor in innate and adaptive immune responses, which activates the p38MAPK, NF-kappa B and AP-1 signaling pathways. Recent reports have highlighted that IL-32 is regulated during viral infection in humans.

Methods

Enzyme-linked immunosorbent assays (ELISA) were carried out to detect IL-32 levels in serum samples. Detailed kinetics of the transcription of IL-32 mRNA and expression of IL-32 protein during human cytomegalovirus (HCMV) infection were determined by semi-quantitative RT-PCR and western blot, respectively. The expression levels of hcmv-miR-UL112-1 were detected using TaqMan® miRNA assays during a time course of 96 hours. The effects of hcmv-miR-UL112-1 on IL-32 expression were demonstrated by luciferase assay and western blot, respectively.

Results

Serum levels of IL-32 in HCMV-IgM positive patients (indicating an active HCMV infection) were significantly higher than those in HCMV-IgM negative controls. HCMV infection activated cellular IL-32 transcription mainly in the immediately early (IE) phase and elevated IL-32 protein levels between 6 and 72 hours post infection (hpi) in the human embryonic lung fibroblast cell line, MRC-5. The expression of hcmv-miR-UL112-1 was detected at 24 hpi and increased gradually as the HCMV-infection process was prolonged. In addition, it was demonstrated that hcmv-miR-UL112-1 targets a sequence in the IL-32 3′-UTR. The protein level of IL-32 in HEK293 cells could be functionally down-regulated by transfected hcmv-miR-UL112-1.

Conclusions

IL-32 expression was induced by active HCMV infection and could be functionally down-regulated by ectopically expressed hcmv-miR-UL112-1. Our data may indicate a new strategy of immune evasion by HCMV through post-transcriptional regulation.
An attenuated Lassa vaccine in SIV-infected rhesus macaques does not persist or cause arenavirus disease but does elicit Lassa virus-specific immunity
Authors: Zapata Juan C , Poonia Bhawna , Bryant Joseph , Davis Harry , Ateh Eugene , George Lanea , Crasta Oswald , Zhang Yan , Slezak Tom , Jaing Crystal , Pauza C David , Goicochea Marco , Moshkoff Dmitry , Lukashevich Igor S , Salvato Maria S
Published: February 2013

Background

Lassa hemorrhagic fever (LHF) is a rodent-borne viral disease that can be fatal for human beings. In this study, an attenuated Lassa vaccine candidate, ML29, was tested in SIV-infected rhesus macaques for its ability to elicit immune responses without instigating signs pathognomonic for arenavirus disease. ML29 is a reassortant between Lassa and Mopeia viruses that causes a transient infection in non-human primates and confers sterilizing protection from lethal Lassa viral challenge. However, since the LHF endemic area of West Africa also has high HIV seroprevalence, it is important to determine whether vaccination could be safe in the context of HIV infection.

Results

SIV-infected and uninfected rhesus macaques were vaccinated with the ML29 virus and monitored for specific humoral and cellular immune responses, as well as for classical and non-classical signs of arenavirus disease. Classical disease signs included viremia, rash, respiratory distress, malaise, high liver enzyme levels, and virus invasion of the central nervous system. Non-classical signs, derived from profiling the blood transcriptome of virulent and non-virulent arenavirus infections, included increased expression of interferon-stimulated genes (ISG) and decreased expression of COX2, IL-1β, coagulation intermediates and nuclear receptors needed for stress signaling. All vaccinated monkeys showed ML29-specific antibody responses and ML29-specific cell-mediated immunity.

Conclusion

SIV-infected and uninfected rhesus macaques responded similarly to ML29 vaccination, and none developed chronic arenavirus infection. Importantly, none of the macaques developed signs, classical or non-classical, of arenavirus disease.