bluuebunny/crossref_metadata_2025 huggingface dataset:
Neonatal treatment with lipopolysaccharide differentially affects adult anxiety responses in the light–dark test and taste neophobia test in male and female rats
Authors: Tenk Christine M. , Kavaliers Martin , Ossenkopp Klaus‐Peter
Published: December 2012

Neonatal administration of the bacterial cell wall component, lipopolysaccharide (LPS) has been shown to alter a variety of behavioural and physiological processes in the adult rat, including altering adult anxiety‐like behaviour. Research conducted to date, however, has produced conflicting findings with some results demonstrating increases in adult anxiety‐like behaviour while others report decreases or no changes in anxiety‐like behaviour. Thus, the current study conducted additional evaluation of the effects of neonatal LPS exposure on adult anxiety‐like behaviours by comparing the behavioural outcomes in the more traditional light–dark test, together with the less common hyponeophagia to sucrose solution paradigm. Male and female Long–Evans rats were treated systemically with either LPS (50 μg/kg) or saline (0.9%) on postnatal days 3 and 5. Animals were then tested in the light–dark apparatus on postnatal day 90 for 30 min. Next, following 5 days of habituation to distilled water delivery in Lickometer drinking boxes, animal were tested for neophagia to a 10% sucrose solution (0.3 M) for 30 min daily on postnatal days 96 and 97. In the light–dark test, neonatal LPS treatment decreased adult anxiety‐like behaviour in females, but not males. In contrast, neonatal exposure to LPS did not influence adult anxiety‐like behaviour as measured by hyponeophagia, but altered the licking patterns of drinking displayed towards a novel, palatable sucrose solution in adult males and females, in a manner that may reflect a decrease in situational anxiety. The current study supports the idea that neonatal LPS treatment results in highly specific alterations of adult anxiety‐like behaviour, the nature of which seems to depend not only on the measure of anxiety behaviour used, but also possibly, on the degree of anxiety experienced during the behavioural test.
Fewer adults add salt at the table after initiation of a national salt campaign in the UK: a repeated cross-sectional analysis
Authors: Sutherland Jennifer , Edwards Phil , Shankar Bhavani , Dangour Alan D.
Published: January 2013

In 2003, the UK Food Standards Agency and the Department of Health began attempts to reduce national salt intakes via reformulation of processed foods and a consumer awareness campaign on the negative impacts of salt on health. The present study uses large nationally representative samples of households in England to assess whether discretionary salt use was affected by the national salt reduction campaign. Large cross-sectional datasets from the Health Survey for England were used to analyse trends in adults adding salt at the table between 1997 and 2007. Since 1997, there has been a steady decline in salt use at the table. Ordinal logistic regression analysis controlling for age, sex, total household income, region, ethnicity and background trends revealed that the reduction in salt use was significantly greater after the campaign (OR 0·58; 95 % CI 0·54, 0·63). Women (OR 0·71; 95 % CI 0·68, 0·74), non-white ethnic groups (OR 0·69; 95 % CI 0·62, 0·77), high-income households (OR 0·75; 95 % CI 0·69, 0·82), middle-income households (OR 0·79; 95 % CI 0·75, 0·84) and households in central (OR 0·90; 95 % CI 0·84, 0·98) or the south of England (OR 0·82; 95 % CI 0·77, 0·88) were less likely to add salt at the table. The results extend previous evidence of a beneficial response to the salt campaign by demonstrating the effect on salt use at the table. Future programmatic and research efforts may benefit from targeting specific population groups and improving the evidence base for evaluating the impact of the campaign.
Memories, identity and homeliness: the social construction of mealtimes in residential care homes in South Wales
Authors: PHILPIN SUSAN , MERRELL JOY , WARRING JOANNE , HOBBY DEBRA , GREGORY VIC
Published: January 2013

Mealtimes in residential care homes are fundamentally social occasions, providing temporal structure to the day and opportunities for conversation and companionship. Food and drink are imbued with social meanings and used to express and create relationships between people. There is a dearth of research exploring care home residents' mealtime experiences in the United Kingdom. This paper reports on particular findings from a qualitative study which investigated factors influencing nutritional care provided to residents in two different types of residential care settings in South Wales, UK. Data were generated through focus group interviews with relevant staff members (N = 15), individual interviews with managers (N = 4) and residents (N = 16) of the care homes and their informal carers (N = 10), observation of food preparation and mealtimes throughout the day, and analysis of appropriate documents. Data were analysed using thematic analysis. This paper's focus is on the ways in which care home residents' experiences and understandings of mealtimes were influenced by various environmental factors, such as the home's geographical location, physical lay-out and ambience. Moreover, the shared meaning of mealtimes for residents, informal carers and staff was constructed from each group's socio-cultural background, family experiences and memories, and was integral to residents' sense of normality, community and identity.
Time-resolved metabolomics analysis of β-cells implicates the pentose phosphate pathway in the control of insulin release
Authors: Spégel Peter , Sharoyko Vladimir V. , Goehring Isabel , Danielsson Anders P. H. , Malmgren Siri , Nagorny Cecilia L. F. , Andersson Lotta E. , Koeck Thomas , Sharp Geoffrey W. G. , Straub Susanne G. , Wollheim Claes B. , Mulder Hindrik
Published: January 2013

Insulin secretion is coupled with changes in β-cell metabolism. To define this process, 195 putative metabolites, mitochondrial respiration, NADP+, NADPH and insulin secretion were measured within 15 min of stimulation of clonal INS-1 832/13 β-cells with glucose. Rapid responses in the major metabolic pathways of glucose occurred, involving several previously suggested metabolic coupling factors. The complexity of metabolite changes observed disagreed with the concept of one single metabolite controlling insulin secretion. The complex alterations in metabolite levels suggest that a coupling signal should reflect large parts of the β-cell metabolic response. This was fulfilled by the NADPH/NADP+ ratio, which was elevated (8-fold; P<0.01) at 6 min after glucose stimulation. The NADPH/NADP+ ratio paralleled an increase in ribose 5-phosphate (>2.5-fold; P<0.001). Inhibition of the pentose phosphate pathway by trans-dehydroepiandrosterone (DHEA) suppressed ribose 5-phosphate levels and production of reduced glutathione, as well as insulin secretion in INS-1 832/13 β-cells and rat islets without affecting ATP production. Metabolite profiling of rat islets confirmed the glucose-induced rise in ribose 5-phosphate, which was prevented by DHEA. These findings implicate the pentose phosphate pathway, and support a role for NADPH and glutathione, in β-cell stimulus-secretion coupling.
Mechanistic studies of FosB: a divalent-metal-dependent bacillithiol-S-transferase that mediates fosfomycin resistance in Staphylococcus aureus
Authors: Roberts Alexandra A. , Sharma Sunil V. , Strankman Andrew W. , Duran Shayla R. , Rawat Mamta , Hamilton Chris J.
Published: January 2013

FosB is a divalent-metal-dependent thiol-S-transferase implicated in fosfomycin resistance among many pathogenic Gram-positive bacteria. In the present paper, we describe detailed kinetic studies of FosB from Staphylococcus aureus (SaFosB) that confirm that bacillithiol (BSH) is its preferred physiological thiol substrate. SaFosB is the first to be characterized among a new class of enzyme (bacillithiol-S-transferases), which, unlike glutathione transferases, are distributed among many low-G+C Gram-positive bacteria that use BSH instead of glutathione as their major low-molecular-mass thiol. The Km values for BSH and fosfomycin are 4.2 and 17.8 mM respectively. Substrate specificity assays revealed that the thiol and amino groups of BSH are essential for activity, whereas malate is important for SaFosB recognition and catalytic efficiency. Metal activity assays indicated that Mn2+ and Mg2+ are likely to be the relevant cofactors under physiological conditions. The serine analogue of BSH (BOH) is an effective competitive inhibitor of SaFosB with respect to BSH, but uncompetitive with respect to fosfomycin. Coupled with NMR characterization of the reaction product (BS–fosfomycin), this demonstrates that the SaFosB-catalysed reaction pathway involves a compulsory ordered binding mechanism with fosfomycin binding first followed by BSH which then attacks the more sterically hindered C-1 carbon of the fosfomycin epoxide. Disruption of BSH biosynthesis in S. aureus increases sensitivity to fosfomycin. Together, these results indicate that SaFosB is a divalent-metal-dependent bacillithiol-S-transferase that confers fosfomycin resistance on S. aureus.
Ribosomal protein S19 is a novel therapeutic agent in inflammatory kidney disease
Authors: Lv Jun , Huang Xiao Ru , Klug Jörg , Fröhlich Suada , Lacher Philipp , Xu Anping , Meinhardt Andreas , Lan Hui Yao
Published: January 2013

RPS19 (ribosomal protein S19), a component of the 40S small ribosomal subunit, has recently been identified to bind the pro-inflammatory cytokine macrophage MIF (migration inhibitory factor). In vitro experiments identify RPS19 as the first endogenous MIF inhibitor by blocking the binding of MIF to its receptor CD74 and MIF functions on monocyte adherence to endothelial cells. In the present study, we sought to establish whether recombinant RPS19 can exert anti-inflammatory effects in a mouse model of anti-GBM (glomerular basement membrane) GN (glomerulonephritis) in which MIF is known to play an important role. Accelerated anti-GBM GN was induced in C57BL/6J mice by immunization with sheep IgG followed 5 days later by administration of sheep anti-mouse GBM serum. Groups of eight mice were treated once daily by intraperitoneal injection with 6 mg of RPS19/kg of body weight or an irrelevant control protein (human secretoglobin 2A1), or received no treatment, from day 0 until being killed on day 10. Mice that received control or no treatment developed severe crescentic anti-GBM disease on day 10 with increased serum creatinine, declined creatinine clearance and increased proteinuria. These changes were associated with up-regulation of MIF and its receptor CD74 activation of ERK (extracellular-signal-regulated kinase) and NF-κB (nuclear factor κB) signalling, prominent macrophage and T-cell infiltration, as well as up-regulation of Th1 [T-bet and IFNγ (interferon γ)] and Th17 [STAT3 (signal transducer and activator of transcription 3) and IL (interleukin)-17A] as well as IL-1β and TNFα (tumour necrosis factor α). In contrast, RPS19 treatment largely prevented the development of glomerular crescents and glomerular necrosis, and prevented renal dysfunction and proteinuria (all P<0.001). Of note, RPS19 blocked up-regulation of MIF and CD74 and inactivated ERK and NF-κB signalling, thereby inhibiting macrophage and T-cell infiltration, Th1 and Th17 responses and up-regulation of pro-inflammatory cytokines (all P<0.01). These results demonstrate that RPS19 is a potent anti-inflammatory agent, which appears to work primarily by inhibiting MIF signalling.
Absolute hypoxic exercise training enhancesin vitrothrombin generation by increasing procoagulant platelet-derived microparticles under high shear stress in sedentary men
Authors: Chen Yu-Wen , Chen Yi-Ching , Wang Jong-Shyan
Published: January 2013

HS (high shear) stress associated with artery stenosis facilitates TG (thrombin generation) by increasing the release of procoagulant PDMPs (platelet-derived microparticles). Physical exercise and hypoxia may paradoxically modulate vascular thrombotic risks. The aim of the present study was to investigate how exercise training with/without hypoxia affected TG mediated by PDMPs under physio-pathological shear flows. A total of 75 sedentary males were randomly divided into five groups (n=15 in each group): 21% O2 [NC (normoxic control)] or 15% O2 [HC (hypoxic control)] at rest or were trained at 50% of peak work rate under 21% O2 [NT (normoxic training)] or 15% O2 [HAT (hypoxic-absolute training)], or 50% of HR (heart rate) reserve under 15% O2 [HRT (hypoxic-relative training)] for 30 min/day, 5 days/week for 4 weeks. The PDMP characteristics and dynamic TG were measured by flow cytometry and thrombinography respectively. Before the intervention, strenuous exercise markedly increased the PDMP count (14.8%) and TG rate (19.5%) in PDMP-rich plasma at 100 dynes/cm2 of shear stress (P<0.05). After the interventions, both NT and HRT significantly attenuated the enhancement of HS-induced PDMPs (4.7 and 4.9%) and TG rate (3.8 and 3.0%) (P<0.05) by severe exercise. Conversely, HAT notably promoted the PDMP count (37.3%) and TG rate (38.9%) induced by HS (P<0.05), concurrent with increasing plasma TF (tissue factor) and coagulation factor V levels at rest or following exercise. We conclude that both HRT and NT depress similarly HS-mediated TG during exercise, but HAT accelerates the prothrombotic response to vigorous exercise. These findings provide new insights into how exercise training under a hypoxic condition influences the risk of thrombosis associated with stenotic arteries.
The nonlinear Rashba effect in Hg0.77Cd0.23Te inversion layers probed by weak antilocalization analysis
Authors: Liu X. Z. , Yu G. , Wei L. M. , Lin T. , Xu Y. G. , Yang J. R. , Wei Y. F. , Guo S. L. , Chu J. H. , Rowell N. L. , Lockwood D. J.
Published: January 2013

The Rashba spin-orbit interaction of the two-dimensional electron gas with high mobility in the inversion layer of p-type Hg0.77Cd0.23Te is investigated by magnetotransport measurements. Both the Rashba spin splitting and Rashba coefficient are extracted by analysis of the weak anti-localization effect using the Golub model. It is found that both the splitting and coefficient increase with increasing electron density (∼3.0–6.0 × 1015 m−2), i.e., with the gate voltage. A self-consistent Schrodinger-Poisson calculation is performed and suggests that the nonlinear Rashba effect caused by the weakening of interband coupling, especially at high electron density, dominates this system.
Chirped-pulse millimeter-wave spectroscopy: Spectrum, dynamics, and manipulation of Rydberg–Rydberg transitions
Authors: Colombo Anthony P. , Zhou Yan , Prozument Kirill , Coy Stephen L. , Field Robert W.
Published: January 2013

We apply the chirped-pulse millimeter-wave (CPmmW) technique to transitions between Rydberg states in calcium atoms. The unique feature of Rydberg–Rydberg transitions is that they have enormous electric dipole transition moments (∼5 kiloDebye at n* ∼ 40, where n* is the effective principal quantum number), so they interact strongly with the mm-wave radiation. After polarization by a mm-wave pulse in the 70–84 GHz frequency region, the excited transitions re-radiate free induction decay (FID) at their resonant frequencies, and the FID is heterodyne-detected by the CPmmW spectrometer. Data collection and averaging are performed in the time domain. The spectral resolution is ∼100 kHz. Because of the large transition dipole moments, the available mm-wave power is sufficient to polarize the entire bandwidth of the spectrometer (12 GHz) in each pulse, and high-resolution survey spectra may be collected. Both absorptive and emissive transitions are observed, and they are distinguished by the phase of their FID relative to that of the excitation pulse. With the combination of the large transition dipole moments and direct monitoring of transitions, we observe dynamics, such as transient nutations from the interference of the excitation pulse with the polarization that it induces in the sample. Since the waveform produced by the mm-wave source may be precisely controlled, we can populate states with high angular momentum by a sequence of pulses while recording the results of these manipulations in the time domain. We also probe the superradiant decay of the Rydberg sample using photon echoes. The application of the CPmmW technique to transitions between Rydberg states of molecules is discussed.
Control over the interface properties of carbon nanotube-based optoelectronic memory devices
Authors: Brunel D. , Levesque P. L. , Ardiaca F. , Martel R. , Derycke V.
Published: January 2013

Optoelectronic nonvolatile memory elements based on polymer-coated carbon nanotube devices can serve as building blocks in programmable circuits. Although essential for improving the circuit performances, the details of the charge trapping mechanism in these mixed organic/inorganic optoelectronic devices are not fully elucidated. The detailed mechanism was investigated by intercalating layers of a hydrophobic organic dielectric (parylene) at different interfaces in the device structure. A thin parylene layer separating the SiO2/nanotube interface from the photosensitive polymer coating is presented as an optimized solution in terms of charging, stability, and robustness.
Marr: An Appreciation
Authors: Frisby John P , Stone James V
Published: January 2013

The following is based largely on sections of our two recent books: Frisby and Stone (2010, Seeing MIT Press), and Stone (2012, Vision and Brain MIT Press). Those books are aimed at student/novice audiences, and so we have eliminated material of a wholly introductory nature for this special issue of Perception. However, various debates we have had at vision conferences recently suggest to us that going over basic material on Marr could be useful to many current vision researchers who have had little contact with his work, so we have left in some content of that kind.
Loss of the repressor REST in uterine fibroids promotes aberrant G protein-coupled receptor 10 expression and activates mammalian target of rapamycin pathway
Authors: Varghese Binny V. , Koohestani Faezeh , McWilliams Michelle , Colvin Arlene , Gunewardena Sumedha , Kinsey William H. , Nowak Romana A. , Nothnick Warren B. , Chennathukuzhi Vargheese M.
Published: January 2013

Uterine fibroids (leiomyomas) are the most common tumors of the female reproductive tract, occurring in up to 77% of reproductive-aged women, yet molecular pathogenesis remains poorly understood. A role for atypically activated mammalian target of rapamycin (mTOR) pathway in the pathogenesis of uterine fibroids has been suggested in several studies. We identified that G protein-coupled receptor 10 [GPR10, a putative signaling protein upstream of the phosphoinositide 3-kinase–protein kinase B/AKT–mammalian target of rapamycin (PI3K/AKT–mTOR) pathway] is aberrantly expressed in uterine fibroids. The activation of GPR10 by its cognate ligand, prolactin releasing peptide, promotes PI3K–AKT–mTOR pathways and cell proliferation specifically in cultured primary leiomyoma cells. Additionally, we report that RE1 suppressing transcription factor/neuron-restrictive silencing factor (REST/NRSF), a known tumor suppressor, transcriptionally represses GPR10 in the normal myometrium, and that the loss of REST in fibroids permits GPR10 expression. Importantly, mice overexpressing human GPR10 in the myometrium develop myometrial hyperplasia with excessive extracellular matrix deposition, a hallmark of uterine fibroids. We demonstrate previously unrecognized roles for GPR10 and its upstream regulator REST in the pathogenesis of uterine fibroids. Importantly, we report a unique genetically modified mouse model for a gene that is misexpressed in uterine fibroids.
RAC1
P29S
is a spontaneously activating cancer-associated GTPase
Authors: Davis Matthew J. , Ha Byung Hak , Holman Edna C. , Halaban Ruth , Schlessinger Joseph , Boggon Titus J.
Published: January 2013

RAC1 is a small, Ras-related GTPase that was recently reported to harbor a recurrent UV-induced signature mutation in melanoma, resulting in substitution of P29 to serine (RAC1
P29S
), ranking this the third most frequently occurring gain-of-function mutation in melanoma. Although the Ras family GTPases are mutated in about 30% of all cancers, mutations in the Rho family GTPases have rarely been observed. In this study, we demonstrate that unlike oncogenic Ras proteins, which are primarily activated by mutations that eliminate GTPase activity, the activated melanoma RAC1
P29S
protein maintains intrinsic GTP hydrolysis and is spontaneously activated by substantially increased inherent GDP/GTP nucleotide exchange. Determination and comparison of crystal structures for activated RAC1 GTPases suggest that RAC1
F28L
—a known spontaneously activated RAC1 mutant—and RAC1
P29S
are self-activated in distinct fashions. Moreover, the mechanism of RAC1
P29S
and RAC1
F28L
activation differs from the common oncogenic mutations found in Ras-like GTPases that abrogate GTP hydrolysis. The melanoma RAC1
P29S
gain-of-function point mutation therefore represents a previously undescribed class of cancer-related GTPase activity.
Developmental changes in the cochlear hair cell mechanotransducer channel and their regulation by transmembrane channel–like proteins
Authors: Kim Kyunghee X. , Fettiplace Robert
Published: December 2012

Vibration of the stereociliary bundles activates calcium-permeable mechanotransducer (MT) channels to initiate sound detection in cochlear hair cells. Different regions of the cochlea respond preferentially to different acoustic frequencies, with variation in the unitary conductance of the MT channels contributing to this tonotopic organization. Although the molecular identity of the MT channel remains uncertain, two members of the transmembrane channel–like family, Tmc1 and Tmc2, are crucial to hair cell mechanotransduction. We measured MT channel current amplitude and Ca2+ permeability along the cochlea’s longitudinal (tonotopic) axis during postnatal development of wild-type mice and mice lacking Tmc1 (Tmc1−/−) or Tmc2 (Tmc2−/−). In wild-type mice older than postnatal day (P) 4, MT current amplitude increased ∼1.5-fold from cochlear apex to base in outer hair cells (OHCs) but showed little change in inner hair cells (IHCs), a pattern apparent in mutant mice during the first postnatal week. After P7, the OHC MT current in Tmc1−/− (dn) mice declined to zero, consistent with their deafness phenotype. In wild-type mice before P6, the relative Ca2+ permeability, PCa, of the OHC MT channel decreased from cochlear apex to base. This gradient in PCa was not apparent in IHCs and disappeared after P7 in OHCs. In Tmc1−/− mice, PCa in basal OHCs was larger than that in wild-type mice (to equal that of apical OHCs), whereas in Tmc2−/−, PCa in apical and basal OHCs and IHCs was decreased compared with that in wild-type mice. We postulate that differences in Ca2+ permeability reflect different subunit compositions of the MT channel determined by expression of Tmc1 and Tmc2, with the latter conferring higher PCa in IHCs and immature apical OHCs. Changes in PCa with maturation are consistent with a developmental decrease in abundance of Tmc2 in OHCs but not in IHCs.
We need integrated publishing
Authors: FUND Sven
Published: December 2012

Scholarly publishing has seen a decade of rapid proliferation of business models and emerging technologies. Together with globalization of the publishing market and new challenges, this evolution has also led to rapid advancements in management tasks even within small publishing houses. The outcome of this change for the stakeholders, including researchers, authors, and shareholders, is unclear, and a return to a more cohesive, integrated approach is desirable. One major obstacle must be overcome: organizational inertia.
Book reviews
Authors: WATES Edward
Published: December 2012

Book Production Adrian Bullock (with a Foreword by John Peacock) London, Routledge, 2012, xviii + 198pp. ISBN 978‐0‐415‐59380‐9, pbk (£21.99); 978‐0‐415‐59379‐3, hbk (£70)
Book Reviews
Authors: CONRAD Lettie
Published: December 2012

Preserving Digital Materials, 2nd edition Ross Harvey De Gruyter, 2011, 252pp. 978‐3‐11‐025369‐6, €69,95/$98.00 hbk
Białynicki-Birula decomposition of Deligne-Mumford stacks
Authors: Skowera Jonathan
Published: December 2012

This short note considers the Białynicki-Birula decomposition of Deligne-Mumford stacks under one-dimensional torus actions and extends a result of Oprea.
rBiopaxParser—an R package to parse, modify and visualize BioPAX data
Authors: Kramer Frank , Bayerlová Michaela , Klemm Florian , Bleckmann Annalen , Beißbarth Tim
Published: December 2012

Motivation: Biological pathway data, stored in structured databases, is a useful source of knowledge for a wide range of bioinformatics algorithms and tools. The Biological Pathway Exchange (BioPAX) language has been established as a standard to store and annotate pathway information. However, use of these data within statistical analyses can be tedious. On the other hand, the statistical computing environment R has become the standard for bioinformatics analysis of large-scale genomics data. With this package, we hope to enable R users to work with BioPAX data and make use of the always increasing amount of biological pathway knowledge within data analysis methods.

Results: rBiopaxParser is a software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model. Furthermore, it allows to generate and layout regulatory graphs of controlling interactions and to visualize BioPAX pathways.

Availability: rBiopaxParser is an open-source R package and has been submitted to Bioconductor.

Contact:  frank.kramer@med.uni-goettingen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
SCARPA: scaffolding reads with practical algorithms
Authors: Donmez Nilgun , Brudno Michael
Published: December 2012

Motivation: Scaffolding is the process of ordering and orienting contigs produced during genome assembly. Accurate scaffolding is essential for finishing draft assemblies, as it facilitates the costly and laborious procedures needed to fill in the gaps between contigs. Conventional formulations of the scaffolding problem are intractable, and most scaffolding programs rely on heuristic or approximate solutions, with potentially exponential running time.

Results: We present SCARPA, a novel scaffolder, which combines fixed-parameter tractable and bounded algorithms with Linear Programming to produce near-optimal scaffolds. We test SCARPA on real datasets in addition to a simulated diploid genome and compare its performance with several state-of-the-art scaffolders. We show that SCARPA produces longer or similar length scaffolds that are highly accurate compared with other scaffolders. SCARPA is also capable of detecting misassembled contigs and reports them during scaffolding.

Availability: SCARPA is open source and available from http://compbio.cs.toronto.edu/scarpa.

Contact: nild@cs.toronto.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Risk Communication as a Tool for Training Apprentice Welders: A Study about Risk Perception and Occupational Accidents
Authors: Cezar-Vaz Marta Regina , Bonow Clarice Alves , Rocha Laurelize Pereira , Almeida Marlise Capa Verde de , Severo Luana de Oliveira , Borges Anelise Miritz , Vaz Joana Cezar , Turik Claudia
Published: December 2012

The present study has aimed to identify the perceptions of apprentice welders about physical, chemical, biological, and physiological risk factors to which they are exposed; identify types of occupational accidents involving apprentice welders; and report the development of a socioenvironmental education intervention as a tool for risk communication for apprentice welders. A quantitative study was performed with 161 apprentice welders in Southern Brazil in 2011. Data collection was performed via structured interviews with the apprentice welders about risk perception, occupational accidents, and time experienced in welding. The data were analyzed using SPSS 19.0. The participants identified the following risk types: physical (96.9%), chemical (95%), physiological (86.3%), and biological (51.5%). In this sample, 39.7% of apprentice welders reported occupational accidents and 27.3% reported burning. The inferential analysis showed that the frequency of risk perception factors increases with the length of experience, and apprentice welders who have experienced accidents during welding activity perceive a higher amount of risk factors than those who have never experienced them. It is concluded that apprentice welders perceive risks and that they tend to relate risks with the occurrence of occupational accidents as an indicator of the dangerous nature of their activity.
Hierarchical Modular Structure Identification with Its Applications in Gene Coexpression Networks
Authors: Zhang Shuqin
Published: December 2012

Network module (community) structure has been a hot research topic in recent years. Many methods have been proposed for module detection and identification. Hierarchical structure of modules is shown to exist in many networks such as biological networks and social networks. Compared to the partitional module identification methods, less research is done on the inference of hierarchical modular structure. In this paper, we propose a method for constructing the hierarchical modular structure based on the stochastic block model. Statistical tests are applied to test the hierarchical relations between different modules. We give both artificial networks and real data examples to illustrate the performance of our approach. Application of the proposed method to yeast gene coexpression network shows that it does have a hierarchical modular structure with the modules on different levels corresponding to different gene functions.
Actinobaculum suisDetection Using Polymerase Chain Reaction
Authors: Amigo Cristina Román , Gobbi Debora Dirani Sena de , Gomes Vasco Túlio de Moura , Perina Danilo do Prado , Nogueira de Lima Filsner Pedro Henrique , Costa Barbara Letícia Pereira , Spindola Maria Garcia , Ferreira Thais Sebastiana Porfida , Brandão Paulo Eduardo , Moreno Andrea Micke
Published: December 2012

Actinobaculum suisis an important agent related to urinary infection in swine females. Due to its fastidious growth characteristics, the isolation of this anaerobic bacterium is difficult, thus impairing the estimation of its prevalence. The purpose of this study was to develop and test a polymerase chain reaction (PCR) for the detection and identification ofA. suisand then compare these results with traditional isolation methods. Bacterial isolation and PCR were performed on one hundred and ninety-two urine samples from sows and forty-five preputial swabs from boars. The results indicate that this PCR was specific forA. suis, presenting a detection limit between1.0×101 CFU/mL and1.0×102 CFU/mL.A. suisfrequencies, as measured by PCR, were 8.9% (17/192) in sow urine samples and 82.2% (37/45) in preputial swabs. Assessed using conventional culturing techniques, none of the urine samples were positive forA. suis; however,A. suiswas detected in 31.1% (14/45) of the swabs. This PCR technique was shown to be an efficient method for the detection ofA. suisin urine and preputial swabs.
Material Flow Analysis of Fossil Fuels in China during 2000–2010
Authors: Wang Sheng , Dai Jing , Su Meirong
Published: December 2012

Since the relationship between the supply and demand of fossil fuels is on edge in the long run, the contradiction between the economic growth and limited resources will hinder the sustainable development of the Chinese society. This paper aims to analyze the input of fossil fuels in China during 2000–2010 via the material flow analysis (MFA) that takes hidden flows into account. With coal, oil, and natural gas quantified by MFA, three indexes, consumption and supply ratio (C/S ratio), resource consumption intensity (RCI), and fossil fuels productivity (FFP), are proposed to reflect the interactions between population, GDP, and fossil fuels. The results indicated that in the past 11 years, China’s requirement for fossil fuels has been increasing continuously because of the growing mine productivity in domestic areas, which also leads to a single energy consumption structure as well as excessive dependence on the domestic exploitation. It is advisable to control the fossil fuels consumption by energy recycling and new energy facilities’ popularization in order to lead a sustainable access to nonrenewable resources and decrease the soaring carbon emissions.
“Recovery Came First”: Desistance versus Recovery in the Criminal Careers of Drug-Using Offenders
Authors: Colman Charlotte , Vander Laenen Freya
Published: December 2012

The aim of our paper is to gain insight in the desistance process of drug-using offenders. We explore the components of change in the desistance process of drug-using offenders by using the cognitive transformation theory of Giordano et al. as a theoretical framework. The desistance process of drug-using offenders entails a two-fold process: desistance of criminal offending and recovery. The results however indicate that desistance is subordinate to recovery because of the fact that drug-using offenders especially see themselves as drug users and not as “criminals.” Their first goal was to start recovery from drug use. They were convinced that recovery from drug use would lead them to a stop in their offending. In the discussion, we explore the implications of this result for further research.
VATS Lobectomy: Surgical Evolution from Conventional VATS to Uniportal Approach
Authors: Gonzalez-Rivas Diego
Published: December 2012

There is no standardized technique for the VATS lobectomy, though most centres use 2 ports and add a utility incision. However, the procedure can be performed by eliminating the two small ports and using only the utility incision with similar outcomes. Since 2010, when the uniportal approach was introduced for major pulmonary resection, the technique has been spreading worldwide. The single-port technique provides a direct view to the target tissue. The conventional triple port triangulation creates a new optical plane with genesis of dihedral or torsional angle that is not favorable with standard two-dimension monitors. The parallel instrumentation achieved during single-port approach mimics inside the maneuvers performed during open surgery. Furthermore, it represents the less invasive approach possible, and avoiding the use of trocar, we minimize the compression of the intercostal nerve. Further development of new technologies like sealing devices for all vessels and fissure, robotic arms that open inside the thorax, and wireless cameras will facilitate the uniportal approach to become the standard surgical procedure for pulmonary resection in most thoracic departments.
Fate and Transport of Polycyclic Aromatic Hydrocarbons in Upland Irish Headwater Lake Catchments
Authors: Scott Heidi E. M. , Aherne Julian , Metcalfe Chris D.
Published: December 2012

Polycyclic aromatic hydrocarbons (PAHs) are a concern due to their carcinogenicity and propensity for transboundary atmospheric transport. Ireland is located on the western periphery of Europe and assumed to receive clean Atlantic air. As such, it has been used as an atmospheric reference for comparison to other regions. Nonetheless, few studies have evaluated concentrations of PAHs within the Irish environment. In the current study, PAHs were measured at five upland (500–800 masl) headwater lake catchments in coastal regions around Ireland, remote from industrial point source emissions. Semipermeable membrane devices were deployed in lakes for a 6-month period in July 2009, and topsoils were sampled from each catchment during October 2010. The concentrations of PAHs were low at most study sites with respect to other temperate regions. Homologue groups partitioned between lake and soil compartments based on their molecular weight were: “lighter” substances, such as Phenanthrene and Fluorene, were found in higher proportions in lakes, whereas “heavier” compounds, such as Chrysene and Benz[a]anthracene, were more prominent in soils. Concentrations of PAHs were highest at the east coast sites, potentially due to contributions from historical transboundary and regional combustion sources.
Sequencing of isolated sperm cells for direct haplotyping of a human genome
Authors: Kirkness Ewen F. , Grindberg Rashel V. , Yee-Greenbaum Joyclyn , Marshall Christian R. , Scherer Stephen W. , Lasken Roger S. , Venter J. Craig
Published: January 2013

There is increasing evidence that the phenotypic effects of genomic sequence variants are best understood in terms of variant haplotypes rather than as isolated polymorphisms. Haplotype analysis is also critically important for uncovering population histories and for the study of evolutionary genetics. Although the sequencing of individual human genomes to reveal personal collections of sequence variants is now well established, there has been slower progress in the phasing of these variants into pairs of haplotypes along each pair of chromosomes. Here, we have developed a distinct approach to haplotyping that can yield chromosome-length haplotypes, including the vast majority of heterozygous single-nucleotide polymorphisms (SNPs) in an individual human genome. This approach exploits the haploid nature of sperm cells and employs a combination of genotyping and low-coverage sequencing on a short-read platform. In addition to generating chromosome-length haplotypes, the approach can directly identify recombination events (averaging 1.1 per chromosome) with a median resolution of <100 kb.
Research on the film‐forming characteristics of octadecylamine at high temperatures
Authors: Cao Shun'an , Hu Jiayuan , Xie Jianli , Liang Qinqin , Yin Li
Published: January 2013

Purpose

The purpose of this paper is to set out a study of the film‐forming characteristics of octadecylamine (ODA), estimate the feasibility of shutdown protection using ODA at high temperatures, and determine the optimum process condition of shutdown protection for units under full load if ODA has a good film‐forming effect at high temperatures.

Design/methodology/approach

An autoclave was used to simulate the water‐vapor environments at 350‐560°C in the water‐steam system of power plants. The decomposition test of ODA was investigated and the ODA film‐forming characteristics were studied for furnace tube materials used in gas‐fired power plants.

Findings

Results showed that ODA had a decomposition equilibrium and the decomposition products did not contain harmful organic substances such as low molecular organic acids. ODA would form a satisfactory protective film in the range of 350‐560°C with the best film at 480°C. The protection effect of the film formed by ODA at 560°C was much stronger than was that of its oxide film, which showed the feasibility of shutdown protection using ODA for gas‐fired power plants operating under full load. The optimal conditions of shutdown protection under full load were as follows: the temperature was 560°C, the concentration of ODA was 80 mg/L, the pH was 9.5 and the exposure time was 2 h. From the experimental results of X‐ray photoelectron spectroscopy, it was known that the surface film on the specimens was composed of a compound of ferroferric oxide and ODA, and the film‐forming mechanism was chemical adsorption between N in the ODA and Fe.

Originality/value

It was found that ODA has a good film‐forming effect at high temperatures and it is practicable to implement shutdown protection for base‐load units. The research results can provide theoretical guidelines for shutdown protection of gas‐fired power plants.
Risk assessment in a multinational company (MNC) operating in Vietnam: a case study approach
Authors: Muthuveloo Rajendran , Pulenthiran Ruben , Ping Teoh Ai
Published: January 2013

Purpose

The purpose of this paper is to study on the risk and preparedness for emergency of a multinational company (MNC) based in Vietnam. This research can assist other MNCs to understand the risk they may face and formulate the necessary emergency preparation to do business in Vietnam.

Design/methodology/approach

This study uses the risk management model as a guideline and risk matrix table as a tool of analysis. This research is an exploratory study base and relevant primary data are gathered through structured interviews and secondary data through the MNC web site and published financial reports.

Findings

The findings of this research indicate that there were many risk areas that were not covered by the company. It categorizes risk areas accordingly from high‐risk, medium‐risk to low risk using risk matrix. The results of the finding were based on pure estimation.

Research limitations/implications

This study is based on a single company and there could be many other risk areas that were not covered.

Originality/value

The data for this research were collected through direct structured interviews among relevant personnel in a MNC based in Vietnam, thus the findings provide the true value of current risk scenario in Vietnam.
Long non‐coding RNA HOTAIR is an independent prognostic marker for nasopharyngeal carcinoma progression and survival
Authors: Nie Yan , Liu Xiang , Qu Shaohua , Song Erwei , Zou Hua , Gong Chang
Published: January 2013

Identification of new nasopharyngeal carcinoma (NPC) biomarkers is of great clinical value for the diagnosis and treatment of NPC. HOTAIR, a cancer‐related long non‐coding RNA, was tested and its prognostic value for NPC was evaluated. As determined using in situ hybridization (ISH), 91 of 160 (56.87%) paraffin‐embedded NPC biopsies showed high expression levels of HOTAIR (staining index score ≥ 6). HOTAIR was upregulated in tumors with a large size (P = 0.021), more advanced clinical stage (P = 0.012) and increased lymph node tumor burden (P = 0.005). Quantified using real‐time PCR, HOTAIR expression levels in fresh tissue and paraffin‐embedded samples were 5.2 ~ 48.4‐fold higher compared with non‐cancer tissue samples. Moreover, HOTAIR expression levels increased with clinical stage progression, which was consistent with ISH findings in the paraffin‐embedded tissue. Most importantly, NPC patients with higher HOTAIR levels had a poor prognosis for overall survival using univariate and multivariate analysis. In addition, HOTAIR mediated the migration, invasion and proliferation of NPC cells in vitro. HOTAIR is a potential biomarker for the prognosis of NPC, and dysregulation of HOTAIR might play an important role in NPC progression.
Hosting strangers: hospitality and family practices in fostering unaccompanied refugee young people
Authors: Sirriyeh Ala
Published: January 2013

Refugee young people entering foster care face transitions as they settle into life in a new country and household. Drawing on findings from a study on foster care for refugee young people in England, this paper examines encounters and negotiations with the public worlds of the asylum system and foster care delivery within the intimate setting of the household and everyday domestic practices in foster care. The paper considers Derrida's neologism ‘hostipitality’ to explore challenges in hospitality in this context. The framework of ‘family practices’ is then applied to explore how foster carers and young people ‘did’ family in foster care. It was found that family practices were inhibited by tensions and challenges in the notion of ‘hospitality’, but family practices also offered opportunities to respond and promote young people's sense of belonging in the family in this environment. It concludes that hospitality at the threshold is necessary, but that the most successful foster care relationships were able to move through and beyond hospitality to relationships of family‐like intimacy.
Wound healing of extraction sockets
Authors: Farina Roberto , Trombelli Leonardo
Published: January 2013

The extraction of a tooth initiates a series of reparative processes involving both hard tissue (i.e. alveolar bone) and soft tissues (periodontal ligament, gingiva). The biological events occurring during the healing of an extraction socket and their chronological sequence have been evaluated in different animal and human studies. In the present review, the healing process of a tooth extraction wound was described. Factors affecting the histological aspects of the healing phase as well as the post extraction alterations of the ridge dimensions were also considered. Additionally, the healing of an extraction socket where a dental implant has been placed immediately after tooth removal was described in details. Finally, the histological and clinical outcomes of the application of different reconstructive technologies to the post‐extraction socket was evaluated.
Assessment of management options for Chilean needle grass in sheep‐grazing systems
Authors: Grech C. J. , McLaren D. A. , Lowien J. , McWhirter L. , Butler K. L. , Sindel B. M.
Published: December 2012

Chilean needle grass [Nassella neesiana (Trin. & Rupr.) Barkworth; CNG] is a perennial spear grass that has invaded pastures in south‐eastern Australia and can lead to a substantial reduction of stockcarrying capacity during the summer months. This study examined a range of grazing, herbicide and pasture resowing options, alone or in combination, on CNG and introduced pasture grass basal cover, for several CNG‐infested sites in south‐eastern Australia. At each site, options were chosen on the basis that they were most likely to control the CNG infestation while maintaining a productive sheep‐grazing enterprise on grass pastures. After 2 years of management, the reduction in CNG basal cover in set stock plots that were sprayed with flupropanate, versus those not sprayed, ranged from non‐detectable to a reduction of 80%, depending on site location. After 5 years of management, the reduction ranged from zero to 50%. Grazing management or sowing of competitive pastures did not generally reduce CNG basal cover to low levels. None of the management options maintained reasonable levels of desirable perennial species by the end of 4–5 years. We conclude that, because of the persistence of CNG, the need for regular spraying of herbicide, and the relative ineffectiveness of other control methods, management systems may need to be developed that utilize CNG while minimizing its input to the soil seedbank.