bluuebunny/crossref_metadata_2025 huggingface dataset:
Uncertainty and Sensitivity Analysis for Building Energy Rating
Authors: Corrado Vincenzo , Mechri Houcem Eddine
Published: June 2009

One of the main tasks of the European Energy Performance of Buildings Directive 2002/91/EC (EPBD) pertains to energy building certification. For this purpose, recent European standards have defined a methodology for the assessment of the energy use of buildings through the calculation of energy ratings. The accuracy of the energy rating depends both on the detail level of the model and on the confidence of the input data. In this work, the quasi-steady simplified monthly method, presented in the ISO 13790: 2008 standard, has been applied to a dwelling in Turin, Italy, in order to calculate its energy rating. A widespread list of 129 input data was identified and grouped into three sets: climatic data, envelope data, and building use data. Probability density functions were assigned after a detailed bibliographic research. The Monte Carlo Latin hypercube sampling technique has been used to assess the building energy needs confidence interval and the energy performance class uncertainty. A sensitivity analysis based on the Morris method, has also been performed for the different building heat balance terms, in order to identify the most important parameter set that takes into account for the uncertainty in the model output. The main results demonstrate that the asset energy rating is only slightly affected by data uncertainties; moreover, the analysis highlights the importance of associating an operational energy rating to the asset rating in order to show the influence of user behavior on building energy performance. On the other hand, the results show that less than 10 input data, among the considered 129 ones, have a significant influence on the energy rating uncertainties.
Thermal Benefits of Tiled Roofs with Above-sheathing Ventilation
Authors: De With Govert , Cherry Nigel , Haig John
Published: June 2009

Computer simulations are conducted to demonstrate the thermal benefits of good roofing design in hot climates. The work is aimed to quantify the thermal benefits from batten-space ventilation, commonly referred to as above sheathing ventilation (ASV), and thermal mass. Both roof features are effective in reducing the heat transmission into the habitable space. Nevertheless, the use of roof ventilation is often misunderstood and most procedures for energy assessment of building structures do not recognize the contribution from ASV and thermal mass.

As part of this work, a computer algorithm is developed to predict the heat, air and moisture (HAM) transport in the building envelope. The algorithm predicts the transient temperature and moisture behavior in the building envelope and takes account of the air movement from bouyancy and wind driven airflows.
Separate Spaces
Authors: Singer Jane B.
Published: June 2009

In May 2007, Scots voted into office a party and a political leader publicly committed to holding a referendum on independence from Great Britain within four years. This study analyzes nearly forty-eight hundred comments appended to stories on the scotsman.com Web site, offering one of the first detailed looks at user-generated content on a newspaper-affiliated Web site in the context of a national election. It explores the evolving nature of online political community and the ways in which newspapers are accommodating a networked environment in their political coverage, addressing issues of citizen and journalistic engagement within a communal space.
Fabrication of low-cost Nd–Fe–B sintered magnets reusing ultrafine powders
Authors: Cui X. G. , Yan M. , Ma T. Y. , Luo W. , Tu S. J.
Published: June 2009

To reduce the cost of Nd–Fe–B sintered magnets, the ultrafine powders recycled during the jet-milling process were added into intergranular regions by blending. The effects of ultrafine powder content on the magnetic properties, thermal stability and microstructure were investigated. It was found that the intrinsic coercivity Hcj was significantly improved from 1048 to 1396 kA m−1 on increasing the ultrafine powder content to 10 wt-%. Meanwhile, the reversible temperature coefficient βH of Hcj over the range 20–100°C was decreased in the absolute value, indicating that the thermal stability was improved. Moreover, the maximum energy product ( BH)m increased slightly on adding 5 wt-% ultrafine powder, which can be attributed to the combined effects on the normal coercivity Hcb and on the remanent induction Br.
Industry perspective on ultrafine grained steels
Authors: Howe A. A.
Published: June 2009

Steels with ultrafine grain sizes have been the subject of major international research efforts. The step change sought from the ‘ultrafine’ 1 μm grain projects has now largely been back-tracked to focus on ‘very fine’ 2–3 μm grains. Particularly, this research has concentrated on dual phase and multiphase steels, thus merging with the ongoing developments that continued the advance of established products, though giving such developments a dramatic boost. In single phase material, refinement to 1 μm grains inherently reduces the ductility, but some applications are being designed around such properties. Moreover, poor ductility from a tensile test need not mean inadequate formability for high strength automotive sheet. For various applications, established steels remain more cost-effective, but ‘very fine’ grained steels have now become a standard item already selling in large tonnages. The production technology developed under these ‘ultrafine grain’ projects is also now used to produce plain carbon/carbon–manganese steels with grain sizes that were previously the preserve of microalloyed steels.
A JMAK-like approach for isochronal austenite–ferrite transformation kinetics in Fe–0·055 wt-%N alloy
Authors: Chen H. , Liu Y. C. , Wang D. J. , Yan Z. S. , Fu J. C. , Shi Q. Z.
Published: June 2009

The kinetics of the isochronal austenite γ to ferrite α transformation of Fe–0·055 wt-%N alloy was investigated for cooling rates in the range of 5–15 K min− by high resolution dilatometry. In accordance with thermodynamic characteristics of γ→ α transformation investigated in this study and previous kinetic theory, a Johnson–Mehl–Avrami–Kologoromov (JMAK)-like approach for the kinetics of isochronal phase transformations was developed that incorporates three overlapping processes: site saturation nucleation, alternate growth modes (transition from interface- to diffusion-controlled growth) as well as impingement for random distribution nuclei. The JMAK-like approach has been employed to fit the experimental results, and the fitting results show that the γ→ α transformation of Fe–0·055 wt-%N alloy does have two stages: a first, short interface-controlled growth stage and a second, long diffusion-controlled growth stage. In addition, soft impingement effect has been recognised to become serious in the later part of the second stage.
Phase transformation and microstructural changes during aging process in Ag–Pd–Cu–Pt–Zn alloy
Authors: Noh D.-J. , Lee D.-H. , Cho M.-H. , Kim H.-I. , Kwon Y.-H. , Seol H.-J.
Published: June 2009

The Ag–Pd–Cu–Pt–Zn alloy was studied in order to elucidate the age hardening behaviour, phase transformation and changes in microstructure and element distribution during the aging process. The grain interior precipitation of the Cu rich phase from the Ag rich α1 matrix caused an apparent increase in hardness, and the formation and expansion of the Cu rich entanglement structures decreased the hardness. The phase transformation of the Cu–Pd rich α2 phase occurred during softening in the later stage of the aging process, which resulted in the retardation of further softening. Pt was concentrated in the Cu–Pd-rich α2 particle-like structures, and Zn was exclusively concentrated in the CuPd β particle-like structures at approximately four times its concentration in the original alloy composition. The Cu–Pd rich α2 and CuPd β phases, which contained large amounts of Cu, constituted the particle-like structures of various sizes without an apparent contribution to the age hardenability.
Investigation of boundary migration during grain growth in fully recrystallised high purity nickel
Authors: Zhang Y. B. , Godfrey A. , Liu W. , Liu Q.
Published: June 2009

The movement of individual boundaries during grain growth after primary recrystallisation in a 96% cold rolled sample of pure nickel has been followed using electron backscatter diffraction maps of the same surface area taken after each of several annealing steps. Particular attention is given to the migration of boundaries with near Σ3 misorientations. During annealing, a small reduction in the length fraction the Σ3 boundaries was observed in the early stages of annealing. Analysis of individual boundaries shows that only those boundary segments with a misorientation angle greater than 4° move during annealing. In addition, the Σ3 boundaries can be divided into two groups: those with misorientations very close to the ideal twin misorientation (‘twin type') and those with a larger deviation to the ideal twin misorientation, but still satisfying the Brandon criterion (‘neighbour type'). Of these, only neighbour type Σ3 boundaries are observed to move during annealing. Some implications of these observations for twin development during grain boundary engineering are discussed.
Forodesine has high antitumor activity in chronic lymphocytic leukemia and activates p53-independent mitochondrial apoptosis by induction of p73 and BIM
Authors: Alonso Roberto , López-Guerra Mónica , Upshaw Ramanda , Bantia Shanta , Smal Caroline , Bontemps Françoise , Manz Chantal , Mehrling Thomas , Villamor Neus , Campo Elias , Montserrat Emili , Colomer Dolors
Published: June 2009

Chronic lymphocytic leukemia (CLL) is an incurable disease derived from the monoclonal expansion of CD5+ B lymphocytes. High expression levels of ZAP-70 or CD38 and deletions of 17p13 (TP53) and 11q22-q23 (ATM) are associated with poorer overall survival and shorter time to disease progression. DNA damage and p53 play a pivotal role in apoptosis induction in response to conventional chemotherapy, because deletions of ATM or p53 identify CLL patients with resistance to treatment. Forodesine is a transition-state inhibitor of the purine nucleoside phosphorylase with antileukemic activity. We show that forodesine is highly cytotoxic as single agent or in combination with bendamustine and rituximab in primary leukemic cells from CLL patients regardless of CD38/ZAP-70 expression and p53 or ATM deletion. Forodesine activates the mitochondrial apoptotic pathway by decreasing the levels of antiapoptotic MCL-1 protein and induction of proapoptotic BIM protein. Forodesine induces transcriptional up-regulation of p73, a p53-related protein able to overcome the resistance to apoptosis of CLL cells lacking functional p53. Remarkably, no differences in these apoptotic markers were observed based on p53 or ATM status. In conclusion, forodesine induces apoptosis of CLL cells bypassing the DNA-damage/ATM/p53 pathway and might represent a novel chemotherapeutic approach that deserves clinical investigation.
Cautious epoprostenol therapy is a safe bridge to lung transplantation in pulmonary veno-occlusive disease
Authors: Montani D. , Jaïs X. , Price L. C. , Achouh L. , Degano B. , Mercier O. , Mussot S. , Fadel E. , Dartevelle P. , Sitbon O. , Simonneau G. , Humbert M.
Published: June 2009

Pulmonary veno-occlusive disease (PVOD) carries a poor prognosis and lung transplantation is the only curative treatment. In PVOD, epoprostenol therapy is controversial, as this condition may be refractory to specific therapy with an increased risk of pulmonary oedema.

We retrospectively reviewed clinical, functional and haemodynamic data of 12 patients with PVOD (10 with histological confirmation) treated with continuous intravenous epoprostenol and priority listed for lung transplantation after January 1, 2003.

All PVOD patients had severe clinical, functional and haemodynamic impairment at presentation. Epoprostenol was used at low dose ranges with slow dose increases and high dose diuretics. Only one patient developed mild reversible pulmonary oedema. After 3–4 months, improvements were seen in the New York Heart Association functional class (class IV to III in seven patients), cardiac index (1.99±0.68 to 2.94±0.89 L·min−1·m−2) and indexed pulmonary vascular resistance (28.4±8.4 to 17±5.2 Wood units·m−2; all p<0.01). A nonsignificant improvement in the 6-min walk distance was also observed (+41 m, p = 0.11). Two patients died, one patient was alive on the transplantation waiting list on December 1, 2008 and nine patients were transplanted.

Cautious use of continuous intravenous epoprostenol improved clinical and haemodynamic parameters in PVOD patients at 3–4 months without commonly causing pulmonary oedema, and may be a useful bridge to urgent lung transplantation.
Clinical characteristics and prognostic factors of pulmonary MALT lymphoma
Authors: Borie R. , Wislez M. , Thabut G. , Antoine M. , Rabbat A. , Couderc L-J. , Monnet I. , Nunes H. , Blanc F-X. , Mal H. , Bergeron A. , Dusser D. , Israël-Biet D. , Crestani B. , Cadranel J.
Published: June 2009

Mucosa-associated lymphoid tissue-derived (MALT) lymphoma, a low grade B-cell extranodal lymphoma, is the most frequent subset of primary pulmonary lymphoma. Our objective was to evaluate the initial extent of disease and to analyse the characteristics and long-term outcome of these patients.

All chest and pathological departments of teaching hospitals in Paris were contacted in order to identify patients with a histological diagnosis of primary pulmonary lymphoma of the MALT subtype.

63 cases were identified. The median age was 60 yrs. 36% of cases had no symptoms at diagnosis. 46% of patients had at least one extrapulmonary location of lymphoma. The estimated 5- and 10-yr overall survival rates were 90% and 72%, respectively. Only two of the nine observed deaths were related to lymphoma. Age and performance status were the only two adverse prognostic factors for survival. Extrapulmonary location of lymphoma was not a prognostic factor for overall survival or for progression-free survival. Treatment with cyclophosphamide or anthracyclin was associated with shorter progression-free survival, when compared with chlorambucil.

The survival data confirm the indolent nature of pulmonary MALT lymphoma. Better progression-free survival was observed with chlorambucil when compared with cyclophosphamide or anthracyclin.
Measuring airway dimensions during bronchoscopy using anatomical optical coherence tomography
Authors: Williamson J. P. , Armstrong J. J. , McLaughlin R. A. , Noble P. B. , West A. R. , Becker S. , Curatolo A. , Noffsinger W. J. , Mitchell H. W. , Phillips M. J. , Sampson D. D. , Hillman D. R. , Eastwood P. R.
Published: June 2009

Airway dimensions are difficult to quantify bronchoscopically because of optical distortion and a limited ability to gauge depth. Anatomical optical coherence tomography (aOCT), a novel imaging technique, may overcome these limitations. This study evaluated the accuracy ofaOCT against existing techniques in phantom, excised pig andin vivohuman airways.

Three comparative studies were performed: 1) micrometer-derived area measurements in 10 plastic tubes were compared withaOCT-derived area; 2)aOCT-derived airway compliance curves from excised pig airways were compared with curves derived using an endoscopic technique; and 3) airway dimensions from the trachea to subsegmental bronchi were measured usingaOCT in four anaesthetised patients during bronchoscopy and compared with computed tomography (CT) measurements.

Measurements in plastic tubes revealedaOCT to be accurate and reliable. In pig airways,aOCT-derived compliance measurements compared closely with endoscopic data. In human airways, dimensions measured withaOCT and CT correlated closely. Bland–Altman plots showed thataOCT diameter and area measurements were higher than CT measurements by 7.6% and 15.1%, respectively.

Airway measurements usingaOCT are accurate, reliable and compare favourably with existing imaging techniques. UsingaOCT with conventional bronchoscopy allows real-time measurement of airway dimensions and could be useful clinically in settings where knowledge of airway calibre is required.
A randomised crossover trial of chest physiotherapy in non-cystic fibrosis bronchiectasis
Authors: Murray M. P. , Pentland J. L. , Hill A. T.
Published: June 2009

Regular chest physiotherapy is advocated in non-cystic fibrosis bronchiectasis despite little evidence supporting its routine use. This study aimed to establish the efficacy of regular chest physiotherapy in non-cystic fibrosis bronchiectasis compared with no regular chest physiotherapy.

20 patients not practising regular chest physiotherapy were enrolled in a randomised crossover trial of 3 months of twice daily chest physiotherapy using an oscillatory positive expiratory pressure device compared with 3 months of no chest physiotherapy. The primary end-point was the Leicester Cough Questionnaire (LCQ). Additional outcomes included 24-h sputum volume, forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), forced expiratory flow at 25–75% of FVC (FEF25–75%), maximum inspiratory pressure (MIP), maximum expiratory pressure (MEP), exercise capacity, sputum microbiology and St George's Respiratory Questionnaire (SGRQ). The treatment effect was estimated using the differences of the pairs of observations from each patient.

There was a significant improvement in all domains and total LCQ score with regular chest physiotherapy (median (interquartile range) total score improvement 1.3 (-0.17–3.25) units; p = 0.002). 24-h sputum volume increased significantly with regular chest physiotherapy (2 (0–6) mL; p = 0.02), as did exercise capacity (40 (15–80) m; p = 0.001) and SGRQ total score (7.77 (-0.99–14.5) unit improvement; p = 0.004). No significant differences were seen in sputum bacteriology, FEV1, FVC, FEF25–75%, MIP or MEP.

Regular chest physiotherapy in non-cystic fibrosis bronchiectasis has small, but significant benefits.
Prognostic factors for lung function in systemic sclerosis: prospective study of 105 cases
Authors: Gilson M. , Zerkak D. , Wipff J. , Dusser D. , Dinh-Xuan A. T. , Abitbol V. , Chaussade S. , Legmann P. , Kahan A. , Allanore Y.
Published: June 2009

The aims of the present study were to identify prognostic factors for systemic sclerosis (SSc)-related interstitial lung disease and to clarify the possible causative role of manometric oesophageal involvement.

Consecutive SSc patients underwent pulmonary function tests and oesophageal manometry. They were included in the study if pulmonary function tests were repeated >12 months after baseline. The primary end-point was a decrease of ≥10% of the predicted value in forced vital capacity (FVC). The secondary end-points were a decrease of ≥15% pred in lung carbon monoxide diffusing capacity (DL,CO) and a decrease of ≥20% pred in FVC.

Of the 105 patients (45 diffuse SSc; median disease duration 2.0 yrs), 23 (23%) had a FVC of <80% pred, 60 (59%) had aDL,COof <80% pred and 57 (54%) showed severe oesophageal hypomotility at baseline. Over 72±46 months, 29 (28%) patients displayed a decrease of ≥10% pred in FVC, 39 (40%) of 98 patients displayedDL,COdecline and 19 (18%) patients displayed a decrease of ≥20% pred in FVC. On multivariate analysis, diffuse SSc was a significant predictor for a decrease of ≥10% pred in FVC (p = 0.01). No other predictor of a decrease in pulmonary function was identified.

Only diffuse SSc was predictive of a decrease in pulmonary function in this early-SSc cohort. This does not support preliminary data suggestive of a causative role of oesophageal involvement.
Does educational level influence lung function decline (Doetinchem Cohort Study)?
Authors: Tabak C. , Spijkerman A. M. W. , Verschuren W. M. M. , Smit H. A.
Published: June 2009

Low socioeconomic status is associated with reduced lung function in adults. In addition, there are indications that lung function decline with age is accelerated in low socioeconomic groups, but, to date, findings have been inconclusive.

In order to investigate the relation between educational level, forced expiratory volume in 1 s (FEV1) and decline in FEV1over time, linear mixed-effects models were fitted to baseline and 10-yr-follow-up data from the Doetinchem Cohort Study. The study population (26–66 yrs at baseline) consisted of 2,679 males and 3,026 females with an FEV1measurement in at least one of the three rounds of follow-up and information on relevant covariables. High educational level was used as the reference class.

Low educational level was associated with a higher prevalence of smoking and with a lower smoking-adjusted FEV1at baseline (-148 mL in males and -47 mL in females). In females, low educational level was associated with a faster FEV1decline (3.4 mL·yr−1, age- and height-adjusted), which was not explained by smoking. In males, no differences in rates of decline between educational levels were observed.

FEV1decline was faster in less-educated females, independent of smoking. In males, FEV1decline did not differ between educational levels.
Hyperpolarised3He MRIversusHRCT in COPD and normal volunteers: PHIL trial
Authors: van Beek E. J. R. , Dahmen A. M. , Stavngaard T. , Gast K. K. , Heussel C. P. , Krummenauer F. , Schmiedeskamp J. , Wild J. M. , Søgaard L. V. , Morbach A. E. , Schreiber L. M. , Kauczor H-U.
Published: June 2009

The aim of the present study was to apply hyperpolarised (HP)3He magnetic resonance imaging (MRI) to identify patients with chronic obstructive pulmonary disease (COPD) and α1-antitrypsin deficiency (α1-ATD) from healthy volunteers and compare HP3He MRI findings with high-resolution computed tomography (HRCT) in a multicentre study. Quantitative measurements of HP3He MRI (apparent diffusion coefficient (ADC)) and HRCT (mean lung density (MLD)) were correlated with pulmonary function tests.

A prospective three centre study enrolled 122 subjects with COPD (either acquired or genetic) and age-matched never-smokers. All diagnostic studies were completed in 94 subjects (52 with COPD; 13 with α1-ATD; 29 healthy subjects; 63 males; and 31 females; median age 62 yrs). The consensus assessment of radiologists, blinded for other test results, estimated nonventilated lung volume (HP3He MRI) and percentage diseased lung (HRCT). Quantitative evaluation of all data for each centre consisted of ADC (HP3He MRI) and MLD measurements (HRCT), and correlation with forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) indicating airway obstruction, and the diffusing capacity of the lung for carbon monoxide (DL,CO) indicating alveolar destruction.

Using lung function tests as a reference, regional analysis of HP3He MRI and HRCT correctly categorised normal volunteers in 100% and 97%, COPD in 42% and 69% and α1-ATD in 69% and 85% of cases, respectively. Direct comparison of HP3He MRI and CT revealed 23% of subjects with moderate/severe structural abnormalities had only mild ventilation defects. In comparison with lung function tests, ADC was more effective in separating COPD patients from healthy subjects than MLD (p<0.001versus0.038). ADC measurements showed better correlation withDL,COthan MLD (r = 0.59versus0.29).

Hyperpolarised3He MRI correctly categorised patients with COPD and normal volunteers. It offers additional functional information, without the use of ionising radiation whereas HRCT gives better morphological information. We showed the feasibility of a multicentre study using different magnetic resonance systems.
Hydrophobic profiles of the tail anchors in SLMAP dictate subcellular targeting
Authors: Byers Joseph T , Guzzo Rosa M , Salih Maysoon , Tuana Balwant S
Published: June 2009

Background

Tail anchored (TA) membrane proteins target subcellular structures via a C-terminal transmembrane domain and serve prominent roles in membrane fusion and vesicle transport. Sarcolemmal Membrane Associated Protein (SLMAP) possesses two alternatively spliced tail anchors (TA1 or TA2) but their specificity of subcellular targeting remains unknown.

Results

TA1 or TA2 can direct SLMAP to reticular structures including the endoplasmic reticulum (ER), whilst TA2 directs SLMAP additionally to the mitochondria. Despite the general structural similarity of SLMAP to other vesicle trafficking proteins, we found no evidence for its localization with the vesicle transport machinery or a role in vesicle transport. The predicted transmembrane region of TA2 is flanked on either side by a positively charged amino acid and is itself less hydrophobic than the transmembrane helix present in TA1. Substitution of the positively charged amino acids, in the regions flanking the transmembrane helix of TA2, with leucine did not alter its subcellular targeting. The targeting of SLMAP to the mitochondria was dependent on the hydrophobic nature of TA2 since targeting of SLMAP-TA2 was prevented by the substitution of leucine (L) for moderately hydrophobic amino acid residues within the transmembrane region. The SLMAP-TA2-4L mutant had a hydrophobic profile that was comparable to that of SLMAP-TA1 and had identical targeting properties to SLMAP-TA1.

Conclusion

Thus the overall hydrophobicity of the two alternatively spliced TAs in SLMAP determines its subcellular targeting and TA2 predominantly directs SLMAP to the mitochondira where it may serve roles in the function of this organelle.
7TMRmine: a Web server for hierarchical mining of 7TMR proteins
Authors: Lu Guoqing , Wang Zhifang , Jones Alan M , Moriyama Etsuko N
Published: June 2009

Background

Seven-transmembrane region-containing receptors (7TMRs) play central roles in eukaryotic signal transduction. Due to their biomedical importance, thorough mining of 7TMRs from diverse genomes has been an active target of bioinformatics and pharmacogenomics research. The need for new and accurate 7TMR/GPCR prediction tools is paramount with the accelerated rate of acquisition of diverse sequence information. Currently available and often used protein classification methods (e.g., profile hidden Markov Models) are highly accurate for identifying their membership information among already known 7TMR subfamilies. However, these alignment-based methods are less effective for identifying remote similarities, e.g., identifying proteins from highly divergent or possibly new 7TMR families. In this regard, more sensitive (e.g., alignment-free) methods are needed to complement the existing protein classification methods. A better strategy would be to combine different classifiers, from more specific to more sensitive methods, to identify a broader spectrum of 7TMR protein candidates.

Description

We developed a Web server, 7TMRmine, by integrating alignment-free and alignment-based classifiers specifically trained to identify candidate 7TMR proteins as well as transmembrane (TM) prediction methods. This new tool enables researchers to easily assess the distribution of GPCR functionality in diverse genomes or individual newly-discovered proteins. 7TMRmine is easily customized and facilitates exploratory analysis of diverse genomes. Users can integrate various alignment-based, alignment-free, and TM-prediction methods in any combination and in any hierarchical order. Sixteen classifiers (including two TM-prediction methods) are available on the 7TMRmine Web server. Not only can the 7TMRmine tool be used for 7TMR mining, but also for general TM-protein analysis. Users can submit protein sequences for analysis, or explore pre-analyzed results for multiple genomes. The server currently includes prediction results and the summary statistics for 68 genomes.

Conclusion

7TMRmine facilitates the discovery of 7TMR proteins. By combining prediction results from different classifiers in a multi-level filtering process, prioritized sets of 7TMR candidates can be obtained for further investigation. 7TMRmine can be also used as a general TM-protein classifier. Comparisons of TM and 7TMR protein distributions among 68 genomes revealed interesting differences in evolution of these protein families among major eukaryotic phyla.
Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population
Authors: Tay Chin Yen , Mitchell Hazel , Dong Quanjiang , Goh Khean-Lee , Dawes Ian W , Lan Ruiting
Published: June 2009

Background

Helicobacter pyloriis a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the globalH. pyloripopulation has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recentH. pylorimigration and admixture.

Results

Seventy eightH. pyloriisolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST) of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identifiedH. pyloriancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide theH. pyloripopulations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates.

Conclusion

The majority of the Malay and IndianH. pyloriisolates share the same origin while the Malaysian ChineseH. pyloriis distinctive. The Malay population, known to have a low infection rate ofH. pylori, was likely to be initiallyH. pylorifree and gained the pathogen only recently from cross infection from other populations.
Characteristics and determinants of sexual behavior among adolescents of migrant workers in Shangai (China)
Authors: Li Shenghui , Huang Hong , Cai Yong , Xu Gang , Huang Fengrong , Shen Xiaoming
Published: June 2009

Background

China is facing a critical challenge of rapid and widespread human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) increase. Rural-to-urban migration plays a crucial role in shifting the HIV/sexual transmitted infection (STI) epidemic. The purpose of this study was to assess the prevalence of sexual behaviors and the correlates among the early adolescents of migrant workers in China.

Methods

A cross-sectional study was conducted in 10 junior high schools from April to June of 2008. A total of 2821 adolescents aged 14.06 ± 0.93 years (8.9% of migrant workers vs. 91.1% of general residents) participated in the survey. A self-administrated questionnaire was used to collect information on knowledge, attitude, and behaviors associated with increased risk for HIV/STI.

Results

The percentage of adolescents who ever had sexual intercourse or had sexual intercourse in last three months was 7.2% and 4.3% in adolescents of migrant workers, respectively; in contrast, 4.5% and 1.8% in their peers of general residents, respectively. 47.3% adolescents of migrant workers and 34.3% of those adolescents of general residents reported no condom use in sexual intercourse during last three months. Multivariate logistic regression analyses found that migration was a independent risk factor for sexual intercourse in last three months in our sampled adolescents (odds ratio [OR] = 1.23, 95% confidence interval [CI]: 1.01–1.72). In adolescents of migrant workers, factors such as lower family income (OR: 2.22, CI: 1.09–3.05 for low level; OR:1.25, CI: 1.04–1.59 for medium level), younger age at first sexual intercourse (OR: 1.24, CI: 1.09–1.57), lower knowledge on HIV/AIDS (OR: 0.93, CI: 0.90–0.97), and fewer communication on HIV/AIDS related issues (OR: 0.79, CI: 0.90–0.97) were related to sexual intercourse in last three months.

Conclusion

Based on these results, we advocated that heightened concerns targeting the adolescents of migrant workers be particularly necessary, given their higher level of sexual experience, lower socioeconomic status, restricted reproductive health information, and vulnerability to HIV/STI.
Another optimization trick for the multiple-attenuation method: Multishooting processing of single-shot data
Authors: Ikelle Luc T.
Published: June 2009

We consider marine seismic data collected in a standard shot-gather form, i.e., seismic waves generated from one single-source location at a time. We propose to group these data as if they were acquired with a multishooting technique (to simulate seismic waves generated from several shot locations simultaneously) and then to demultiple them as multishot data. By doing so, we reduce the size of our data and processing time several fold.
Target-oriented curved-wave prestack depth migration by controlled illumination
Authors: Chen Xiumei , Ma Zaitian , Nie Guohua , Wang Huazhong
Published: June 2009

Conventional prestack depth migration (PSDM) based on full prestack data involves many computations for wavefield extrapolation. Areal shot-record technology offers an attractive alternative for efficient PSDM because its synthesis process greatly decreases the amount of prestack data required for migration. Constructing its synthesis operator is key to the image quality of the migrated areal shot record. Curved-wave PSDM technology expands areal shot-record migration. It constructs synthesis operators by defining a complex function as a base kernel of curved wavefields multiplied by a factor of its illumination perturbation related to ray parameter and then synthesizes curved wavefields for migrations. Based on curved-wave-migration theory, we propose an efficient and accurate curved-wave, controlled-illumination method to migrate in a target-oriented way. We construct tar-get-oriented synthesis operators by wave theory, combined with rotation or perturbation of the illuminating direction of a base-kernel synthesis operator. The base-kernel operator is obtained by inverse extrapolation of a predefined source wavefield at the given target level. Different model-constrained synthesis operators are constructed by rotating or perturbing illumination of the kernel operator. Then they are applied to shot records to synthesize curved-wave records. The resulting curved wavefields are entered for depth extrapolation and imaging, combining image results from different curved wavefields to produce the total image. The method controls the illumination of synthesized source wavefields in a target-oriented way directly at the surface and can achieve high-quality images of the target zone with great efficiency. Numerical demonstrations on the standard Marmousi model provide good imaging results of the complicated structure.
Supernatural Realism
Authors: Smajić Srdjan
Published: June 2009

This essay argues that the relationship between realism and supernaturalism in realist novels is more complicated—and more symbiotic—than critics generally acknowledge. Taking Walter Scott's Waverley, George Eliot's Silas Marner, and Charlotte Brönte's Jane Eyre as representative nineteenth-century realist novels, I show that the supernatural is not subversive but in fact constitutive of their respective realist projects. Scott's use of the Bodach Glas ghost to signal the novel's commitment to both historical facts and imaginative interventions in the plot of history, Eliot's foregrounding of the referential/nonreferential duality of realism and the semantic slipperiness of language via a debate on the existence of ghosts, and Brönte's deployment of extrasensory perception to advance an open-ended conception of reality and blur the distinction between “normal” and “paranormal” suggest that the supernatural is integral to realism's formal properties, thematic concerns, and critical self-reflections. Indeed, novel criticism frequently addresses readers in the idiom of the supernatural and paranormal, a language that seems particularly conducive to understanding how realist novels do what they do.
Some Versions of Vitriol (the Novel Circa 1890)
Authors: Matz Aaron
Published: June 2009

Two late Victorian novels—George Gissing's The Nether World (1889) and Robert Louis Stevenson's The Ebb-Tide (1894)—share something peculiar: both prominently feature scenes of vitriol thrown at or exploding in a character's face. I argue that vitriol proved alluring to these novelists because they understood fictional representation itself as an assault, a means of revenge, a vitriolic mode of writing. For both writers this had everything to do with their conception of realism—and with their own participation in the quintessential late Victorian debate about realism in fiction. The Nether World, more than any other Gissing novel, emerged from a spirit of enmity and revenge. The novel was born out of the experience of Gissing's first wife's death amid poverty and degradation; he saw the novel as a means of avenging injustice, a way to channel resentment into art. The antagonistic vapors swirling around Gissing in life he transmogrified into fiction, such that the vitriol attack on Clara Hewett in The Nether World comes to stand for his own brand of realism: fiery, punishing, and unsentimental. Stevenson's The Ebb-Tide, written by a novelist not known for adhering to the realist movement, nevertheless exemplifies a similar tendency in violent representation. As he worked further on the novel and especially its vitriol-soaked finale, Stevenson felt himself pulled helplessly into a kind of fiction he called realism: “I have got too realistic,” he confessed. This essay contends that vitriol was the perfect metonym for late Victorian realism, a mode of fiction characterized not by its claim to the documentary but by its commitment to the explosive.
The Rise of the State as a Sympathetic Liberal Subject in Hardy'sThe Woodlanders
Authors: Aslami Zarena
Published: June 2009

This essay argues that Thomas Hardy's The Woodlanders registers a historic shift in the political imaginary of late nineteenth-century Britain: the emergence of a fantasy of the state as a heroic actor endowed with the capacity to step in and ameliorate one's pain. While The Woodlanders seems to foster sympathy for rural folk who get caught up and reconfigured in state fantasy, it ultimately indicts sympathy and, by extension, its appropriation by the modern liberal state. With its radical doubt about the stability of the subject and its incisive critique of the politics of compassion for rural folk, The Woodlanders undermines the project of sympathy on either an individual or national scale.
Constitutional Laziness and the Novel: Idleness, Irish Modernism, and Flann O'brien's At Swim-Two-Birds
Authors: Dobbins Gregory
Published: June 2009

This article focuses on what the author calls “Irish time” in Flann O'Brien's 1939 novel At Swim-Two-Birds. The author equates the form of this novel with a tension between a progressive form of modernization advocated by the postcolonial state and a deeper cultural and social recalcitrance to a dominant conception of modernity. He compares this conflict within the novel to the ideology of the nation-state by reading At Swim-Two-Birds in relation to the Irish constitution of 1937. Doing so uncovers a deep relationship between the novel and the political document that exceeds the coincidence that they were written at the same time. While the constitution attempts to fix a version of Irish identity preferred by the state, At Swim-Two-Birds_draws on constitutional rhetoric to stress performativity and the flexibility of identity, a utopian dimension that proves unsustainable in the novel's own terms. Nevertheless, the author concludes, the novel opens the possibility of a temporality—a distinct imaginative formulation of “Irish time”—premised on the pleasures of idleness rather than the alienation of labor.
The Color of His Hair: Nineteenth-Century Literary Portraits of the Historical Jesus
Authors: Gatrall Jefferson J. A.
Published: June 2009

Throughout the nineteenth century, dozens of authors across Europe and the United States—including Honoré de Balzac, Victor Hugo, Gustave Flaubert, Charles Dickens, Fyodor Dostoevsky, Ivan Turgenev, and Rainer Maria Rilke—gave fictional form to the figure of Jesus. This article focuses on literary portraiture in the Jesus novel, a genre of historical fiction that emerged independently in different national literatures from the 1830s onward alongside several parallel developments, including the secularization of biblical scholarship, the rediscovery of early Christian iconography, and western archeological advances into Palestine. The principal authors under consideration—Franz Delitzsch, Lew Wallace, and Ferdinando Petruccelli—each exploited a potent combination of ancient Christ images and modern race theory to construct detailed literary portraits of the historical Jesus. Indeed, among the foremost contributions of nineteenth-century novelists to the larger quest of the historical Jesus was the development and popularization of racialized Christ types, including the Greco-Jewish Jesus, a figure that Wallace introduced to an international readership through his sensational bestseller Ben-Hur_(1880). At the same time, authors of Jesus novels somehow had to negotiate the sacral quality of the imago Christi within the formal constraints of the literary portrait. At their most daring, literary portraits of the historical Jesus, whether they subvert or reify Christ's divinity, offer a limit case for reassessing the ambitions of the realist novel in the realm of the sacred.
LATERAL ORGAN FUSION1andLATERAL ORGAN FUSION2function in lateral organ separation and axillary meristem formation inArabidopsis
Authors: Lee Dong-Keun , Geisler Matt , Springer Patricia S.
Published: June 2009

Plant organs are generated from meristems throughout development. Patterning and elaboration of organ primordia occur as a result of organized cell division and expansion, processes that are likely to be controlled, in part, by meristem-derived signals. Communication between the meristem and lateral organs is crucial for meristem maintenance and organ patterning, and organ boundaries are thought to be important for mediating this communication. Arabidopsis thaliana LATERAL ORGAN FUSION1 (LOF1) encodes a MYB-domain transcription factor that is expressed in organ boundaries. lof1 mutants display defects in organ separation as a result of abnormal cell division and expansion during early boundary formation. lof1 mutants also fail to form accessory shoot meristems. Mutations in the closely related LATERAL ORGAN FUSION2 (LOF2) gene enhance the lof1 phenotype, such that lof1 lof2 double mutants display additional fusion defects. Genetic interactions with the CUP-SHAPED COTYLEDON genes CUC2 and CUC3 revealed a role for LOF1 in both organ separation and axillary meristem formation. Expression of the meristem determinant STM was reduced in lof1 mutant paraclade junctions and lof1 enhanced the weak stm-10 mutant, such that double mutants had severe defects in meristem maintenance and organ separation. Our data implicate LOF1and LOF2 in boundary specification, meristem initiation and maintenance, and organ patterning.
FGF signaling is strictly required to maintain early telencephalic precursor cell survival
Authors: Paek Hunki , Gutin Grigoriy , Hébert Jean M.
Published: June 2009

The FGF family of extracellular signaling factors has been proposed to play multiple roles in patterning the telencephalon, the precursor to the cerebrum. In this study, unlike previous ones, we effectively abolish FGF signaling in the anterior neural plate via deletion of three FGF receptor (FGFR) genes. Triple FGFR mutant mice exhibit a complete loss of the telencephalon, except the dorsal midline. Disruption of FGF signaling prior to and coincident with telencephalic induction reveals that FGFs promote telencephalic character and are strictly required to keep telencephalic cells alive. Moreover,progressively more severe truncations of the telencephalon are observed in FGFR single, double and triple mutants. Together with previous gain-of-function studies showing induction of Foxg1 expression and mirror-image duplications of the cortex by exogenous FGF8, our loss-of-function results suggest that, rather than independently patterning different areas, FGF ligands and receptors act in concert to mediate organizer activity for the whole telencephalon.
Insm1 (IA-1) is an essential component of the regulatory network that specifies monoaminergic neuronal phenotypes in the vertebrate hindbrain
Authors: Jacob John , Storm Robert , Castro Diogo S. , Milton Christopher , Pla Patrick , Guillemot François , Birchmeier Carmen , Briscoe James
Published: June 2009

Monoaminergic neurons include the physiologically important central serotonergic and noradrenergic subtypes. Here, we identify the zinc-finger transcription factor, Insm1, as a crucial mediator of the differentiation of both subtypes, and in particular the acquisition of their neurotransmitter phenotype. Insm1 is expressed in hindbrain progenitors of monoaminergic neurons as they exit the cell cycle, in a pattern that partially overlaps with the expression of the proneural factor Ascl1. Consistent with this, a conserved cis-regulatory sequence associated with Insm1 is bound by Ascl1 in the hindbrain, and Ascl1 is essential for the expression of Insm1 in the ventral hindbrain. In Insm1-null mutant mice, the expression of the serotonergic fate determinants Pet1, Lmx1b and Gata2 is markedly downregulated. Nevertheless, serotonergic precursors begin to differentiate in Insm1 mutants, but fail to produce serotonin because of a failure to activate expression of tryptophan hydroxylase 2 (Tph2), the key enzyme of serotonin biosynthesis. We find that both Insm1 and Ascl1 coordinately specify Tph2 expression. In brainstem noradrenergic centres of Insm1 mutants, expression of tyrosine hydroxylase is delayed in the locus coeruleus and is markedly deficient in the medullary noradrenergic nuclei. However, Insm1 is dispensable for the expression of a second key noradrenergic biosynthetic enzyme, dopamine β-hydroxylase, which is instead regulated by Ascl1. Thus, Insm1 regulates the synthesis of distinct monoaminergic neurotransmitters by acting combinatorially with, or independently of, Ascl1 in specific monoaminergic populations.
Computer-assisted engineering determination of the formability limit for thin sheet metals by a modified Marciniak method
Authors: Pepelnjak T , Barisic B
Published: June 2009

Development of a new sheet-metal-forming technology in a digital environment demands accurate and reliable mechanical properties and forming limits of the selected material. It is essential to determine the forming limits for thin sheets and foils. Implementation of the Marciniak procedure with strip-shaped specimens defining the left-hand side of the forming limit diagram (FLD) results in tearing outside the observed area of the specimen. Therefore, new shapes of test pieces were designed with a strip-shaped central area and enlarged outer areas, which were in contact with the die during the forming process. The radius of the specimen enlargement enabled a co-axial contact of its edge and direction of the material flow over the die radius during the forming process. The shape of the redesigned geometry of the specimen was analysed using the finite element (FE) program ABAQUS to minimize undesired stress concentrations at the die radius. Finally, strain paths variations due to shape change were analysed. The new specimen concept was verified on TS-275 tinplate steel with a thickness of 0.24 mm. By implementing the necessary redesigned specimen shapes and by analysis of the tearing limit of the TS-275 material, the forming limit curve for the tinplate material under investigation was constructed.