bluuebunny/crossref_metadata_2025 huggingface dataset:
Resonance for the isothermal system of isentropic gas dynamics
Authors: Lu Yun-guang
Published: February 2011

In this paper, we remove the restriction

z

0

(
x
)
≥
0

z_{0}(x) \geq 0

or

w

0

(
x
)
≤
0

w_{0}(x) \leq 0

in the paper “Existence of Solutions to Hyperbolic Conservation Laws with a Source” (Commun. Math. Phys., 187 (1997), 327–340) and obtain the existence of solutions for the resonant, isothermal system of isentropic gas dynamics.
Phage display can select over-hydrophobic sequences that may impair prediction of natural domain–peptide interactions
Authors: Luck Katja , Travé Gilles
Published: February 2011

Motivation: The phage display peptide selection approach is widely used for defining binding specificities of globular domains. PDZ domains recognize partner proteins via C-terminal motifs and are often used as a model for interaction predictions. Here, we investigated to which extent phage display data that were recently published for 54 human PDZ domains can be applied to the prediction of human PDZ–peptide interactions.

Results: Promising predictions were obtained for one-third of the 54 PDZ domains. For the other two-thirds, we detected in the phage display peptides an important bias for hydrophobic amino acids that seemed to impair correct predictions. Therefore, phage display-selected peptides may be over-hydrophobic and of high affinity, while natural interaction motifs are rather hydrophilic and mostly combine low affinity with high specificity. We suggest that potential amino acid composition bias should systematically be investigated when applying phage display data to the prediction of specific natural domain–linear motif interactions.

Contact:  katja.luck@unistra.fr; gilles.trave@unistra.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
HLA*IMP—an integrated framework for imputing classical HLA alleles from SNP genotypes
Authors: Dilthey Alexander T. , Moutsianas Loukas , Leslie Stephen , McVean Gil
Published: February 2011

Motivation: Genetic variation at classical HLA alleles influences many phenotypes, including susceptibility to autoimmune disease, resistance to pathogens and the risk of adverse drug reactions. However, classical HLA typing methods are often prohibitively expensive for large-scale studies. We previously described a method for imputing classical alleles from linked SNP genotype data. Here, we present a modification of the original algorithm implemented in a freely available software suite that combines local data preparation and QC with probabilistic imputation through a remote server.

Results: We introduce two modifications to the original algorithm. First, we present a novel SNP selection function that leads to pronounced increases (up by 40% in some scenarios) in call rate. Second, we develop a parallelized model building algorithm that allows us to process a reference set of over 2500 individuals. In a validation experiment, we show that our framework produces highly accurate HLA type imputations at class I and class II loci for independent datasets: at call rates of 95–99%, imputation accuracy is between 92% and 98% at the four-digit level and over 97% at the two-digit level. We demonstrate utility of the method through analysis of a genome-wide association study for psoriasis where there is a known classical HLA risk allele (HLA-C*06:02). We show that the imputed allele shows stronger association with disease than any single SNP within the region. The imputation framework, HLA*IMP, provides a powerful tool for dissecting the architecture of genetic risk within the HLA.

Availability: HLA*IMP, implemented in C++ and Perl, is available from http://oxfordhla.well.ox.ac.uk and is free for academic use.

Contact:  mcvean@stats.ox.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID
Authors: Winter Andrew G. , Wildenhain Jan , Tyers Mike
Published: February 2011

Summary: The Biological General Repository for Interaction Datasets (BioGRID) representational state transfer (REST) service allows full URL-based access to curated protein and genetic interaction data at the BioGRID database. Appending URL parameters allows filtering of data by various attributes including gene names and identifiers, PubMed ID and evidence type. We also describe two visualization tools that interface with the REST service, the BiogridPlugin2 for Cytoscape and the BioGRID WebGraph.

Availability and implementation: BioGRID data and applications are completely free for commercial and non-commercial use. http://webservice.thebiogrid.org/resources/interactions (REST Service), http://wiki.thebiogrid.org/doku.php/biogridrest(REST Service parameter list and help), http://webservice.thebiogrid.org/resources/application.wadl(REST Service WADL), http://thebiogrid.org/download.php (BiogridPlugin2, v2.1 download), http://wiki.thebiogrid.org/doku.php/biogridplugin2 (BiogridPlugin2 help) and http://tyerslab.bio.ed.ac.uk/tools/BioGRID_webgraph.php(BioGRID WebGraph).

Contact:  andrew.winter@ed.ac.uk, m.tyers@ed.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application
Authors: Dwight Zachary , Palais Robert , Wittwer Carl T.
Published: February 2011

Summary: uMeltSM is a flexible web-based tool for predicting DNA melting curves and denaturation profiles of PCR products. The user defines an amplicon sequence and chooses a set of thermodynamic and experimental parameters that include nearest neighbor stacking energies, loop entropy effects, cation (monovalent and Mg++) concentrations and a temperature range. Using an accelerated partition function algorithm along with chosen parameter values, uMelt interactively calculates and visualizes the mean helicity and the dissociation probability at each sequence position at temperatures within the temperature range. Predicted curves display the mean helicity as a function of temperature or as derivative plots. Predicted profiles display stability as a function of sequence position either as 50% helicity temperatures or as the helicity probability at specific temperatures. The loss of helicity associated with increasing temperature may be viewed dynamically to visualize domain formation within the molecule. Results from fluorescent high-resolution melting experiments match the number of predicted melting domains and their relative temperatures. However, the absolute melting temperatures vary with the selected thermodynamic parameters and current libraries do not account for the rapid melting rates and helix stabilizing dyes used in fluorescent melting experiments. uMelt provides a convenient platform for simulation and design of high-resolution melting assays.

Availability and implementation: The application was developed in Actionscript and can be found online at http://www.dna.utah.edu/umelt/umelt.html. Adobe Flash is required to run in all browsers.

Contact:  zach.dwight@path.utah.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Found in Translation: High-Throughput Chemical Screening in Arabidopsis thaliana Identifies Small Molecules That Reduce Fusarium Head Blight Disease in Wheat
Authors: Schreiber Karl J. , Nasmith Charles G. , Allard Ghislaine , Singh Jasbir , Subramaniam Rajagopal , Desveaux Darrell
Published: February 2011

Despite the tremendous economic impact of cereal crop pathogens such as the fungus Fusarium graminearum, the development of strategies for enhanced crop protection is hampered by complex host genetics and difficulties in performing high-throughput analyses. To bypass these challenges, we have developed an assay in which the interaction between F. graminearum and the model plant Arabidopsis thaliana is monitored in liquid media in 96-well plates. In this assay, fungal infection is associated with the development of dark lesion-like spots on the cotyledons of Arabidopsis seedlings by 4 days postinoculation. These symptoms can be alleviated by the application of known defense-activating small molecules and in previously described resistant host genetic backgrounds. Based on this infection phenotype, we conducted a small-scale chemical screen to identify small molecules that protect Arabidopsis seedlings from infection by F. graminearum. We identified sulfamethoxazole and the indole alkaloid gramine as compounds with strong protective activity in the liquid assay. Remarkably, these two chemicals also significantly reduced the severity of F. graminearum infection in wheat. As such, the Arabidopsis-based liquid assay represents a biologically relevant surrogate system for high-throughput studies of agriculturally important plant–pathogen interactions.
Virulence and Molecular Genotyping Studies of Sporisorium reilianum Isolates in Sorghum
Authors: Prom Louis K. , Perumal Ramasamy , Erattaimuthu Saradha R. , Erpelding John E. , Montes Noe , Odvody Gary N. , Greenwald Charles , Jin Zheyu , Frederiksen Richard , Magill Clint W.
Published: February 2011

Head smut, caused by the fungal pathogen Sporisorium reilianum, has been reported with increasing frequency in the grain sorghum growing areas of Texas. To facilitate analysis of changes in pathogen virulence, four inoculation techniques were examined: soil and teliospore mixture, seed coating, media placement, and syringe injection. Of the four, syringe injection was determined to be the most effective. Inoculations of sorghum host differentials BTx643, BTx7078, BTx635, SC170-6-17 (TAM2571), SA281 (Early Hegari), and Tx414 showed 23 of 32 Texas isolates were race 4. Two isolates from College Station, TX, were classified as race 1, but no race 2 or 3 isolates were found. New, virulent races 5 and 6 were identified among isolates from south Texas. Using 16 amplified fragment length polymorphism (AFLP) primer combinations, genetic diversity was assessed in DNA samples from 49 S. reilianum isolates, including 44 sorghum isolates from Texas, two from Uganda, and one from Mali; and two maize isolates from Mexico. Single-base extensions with EcoRI and MseI primers in the selective amplification increased the number of informative polymorphic bands. High genetic dissimilarity (50%) was observed between isolates originating from maize and those originating from sorghum. The resultant dendrogram, made using cluster analysis, grouped the Texas S. reilianum isolates into four small clusters with ≥82% similarity. Other than for two race 6 isolates from Weslaco, TX, no evidence for geographical or other restrictions on gene flow was evident.
Tillage, Crop Rotation, and Hybrid Effects on Residue and Corn Anthracnose Occurrence in Wisconsin
Authors: Jirak-Peterson Jennifer C. , Esker Paul D.
Published: February 2011

Corn anthracnose (Colletotrichum graminicola) is an important disease of field corn (Zea mays). Two phases, leaf blight and stalk rot, can reduce yield through either premature leaf senescence or reduced grain harvest due to stalk lodging. Corn residue is an important source of primary inoculum and is increased through cultural practices such as no-tillage and continuous corn cropping, which are common practices in Wisconsin. Field studies conducted at the Arlington Agricultural Research Station (ARS) and the West Madison ARS showed that the incidence and severity of anthracnose leaf blight were higher in continuous-corn crop rotations than in soybean–corn rotations (91% higher incidence, 24 to 78% higher severity). Anthracnose stalk rot was marginally affected by tillage in 2008 (P = 0.09), with higher incidence in chisel-plowed treatments. There was a positive association between spring residue cover and anthracnose leaf blight but no association was found between residue and stalk rot. No association was found between anthracnose leaf blight and stalk rot. There was a negative association between anthracnose leaf blight and yield but not between anthracnose stalk rot and yield. Managing residue levels through crop rotation would help to reduce anthracnose leaf blight but further work is needed to elucidate factors that lead to stalk lodging prior to harvest.
Genetic Differentiation of Puccinia triticina Populations in the Middle East and Genetic Similarity with Populations in Central Asia
Authors: Kolmer J. A. , Ordoñez M. E. , Manisterski J. , Anikster Y.
Published: February 2011

Leaf rust of wheat, caused by Puccinia triticina, is a common and widespread disease in the Middle East. The objective of this study was to determine whether genetically differentiated groups of P. triticina are present in the Middle East region and to compare the population from the Middle East with the previously characterized population from Central Asia to determine whether genetically similar groups of isolates are found in the two regions. In total, 118 isolates of P. triticina collected from common wheat and durum wheat in Egypt, Israel, Turkey, Ethiopia, and Kenya were tested for virulence on 20 lines of wheat with single genes for leaf rust resistance and for molecular genotypes with 23 simple-sequence repeat (SSR) markers. After removal of isolates with identical virulence and SSR genotype in each country, 103 isolates were retained for further analysis. Clustering of SSR genotypes based on two-dimensional principal coordinates and virulence to wheat differential lines grouped the isolates into four Middle East (ME) groups. The two largest ME groups had virulence phenotypes typical of isolates collected from common wheat and two smaller ME groups had virulence typical of isolates collected from durum wheat. All pairs of ME groups were significantly differentiated for SSR genotype based on RST and FST statistics, and for virulence phenotype based on ΦPT. All ME groups had observed values of heterozygosity greater than expected and significant fixation indices that indicated the clonal reproduction of urediniospores in the overall population. Linkage disequilibria for SSR genotypes was high across the entire population. The overall values of RST and FST were lower when isolates were grouped by country of origin that indicated the likely migration of isolates within the region. Although the two ME groups with virulence typical of isolates from common wheat were not differentiated for SSR genotype from groups of isolates from Central Asia based on RST, there was no direct evidence for migration between the two regions because all ME isolates differed from the Central Asia isolates for SSR genotypes.
Electron and hole trapping in polycrystalline metal oxide materials
Authors: McKenna Keith P. , Shluger Alexander L.
Published: February 2011

Electron and hole trapping by grain boundaries and dislocations in polycrystalline materials is important for wide ranging technological applications such as solar cells, microelectronics, photo-catalysts and rechargeable batteries. In this article, we first give an overview of the computational and methodological challenges involved in modelling such effects. This is followed by a discussion of two recent studies we have made on electron/hole trapping in wide gap insulators. The results suggest that such effects can be important for many applications which we discuss. These computationally demanding calculations have made extensive use of both the HPCx and HECToR services.
A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes
Authors: Choufani Sanaa , Shapiro Jonathan S. , Susiarjo Martha , Butcher Darci T. , Grafodatskaya Daria , Lou Youliang , Ferreira Jose C. , Pinto Dalila , Scherer Stephen W. , Shaffer Lisa G. , Coullin Philippe , Caniggia Isabella , Beyene Joseph , Slim Rima , Bartolomei Marisa S. , Weksberg Rosanna
Published: February 2011

Imprinted genes are critical for normal human growth and neurodevelopment. They are characterized by differentially methylated regions (DMRs) of DNA that confer parent of origin-specific transcription. We developed a new strategy to identify imprinted gene-associated DMRs. Using genome-wide methylation profiling of sodium bisulfite modified DNA from normal human tissues of biparental origin, candidate DMRs were identified by selecting CpGs with methylation levels consistent with putative allelic differential methylation. In parallel, the methylation profiles of tissues of uniparental origin, i.e., paternally-derived androgenetic complete hydatidiform moles (AnCHMs), and maternally-derived mature cystic ovarian teratoma (MCT), were examined and then used to identify CpGs with parent of origin-specific DNA methylation. With this approach, we found known DMRs associated with imprinted genomic regions as well as new DMRs for known imprinted genes, NAP1L5 and ZNF597, and novel candidate imprinted genes. The paternally methylated DMR for one candidate, AXL, a receptor tyrosine kinase, was also validated in experiments with mouse embryos that demonstrated Axl was expressed preferentially from the maternal allele in a DNA methylation-dependent manner.
Partners in Time: EARLY BIRD Associates with ZEITLUPE and Regulates the Speed of the Arabidopsis Clock
Authors: Johansson Mikael , McWatters Harriet G. , Bakó László , Takata Naoki , Gyula Péter , Hall Anthony , Somers David E. , Millar Andrew J. , Eriksson Maria E.
Published: February 2011

The circadian clock of the model plant Arabidopsis (Arabidopsis thaliana) is made up of a complex series of interacting feedback loops whereby proteins regulate their own expression across day and night. early bird (ebi) is a circadian mutation that causes the clock to speed up: ebi plants have short circadian periods, early phase of clock gene expression, and are early flowering. We show that EBI associates with ZEITLUPE (ZTL), known to act in the plant clock as a posttranslational mediator of protein degradation. However, EBI is not degraded by its interaction with ZTL. Instead, ZTL counteracts the effect of EBI during the day and increases it at night, modulating the expression of key circadian components. The partnership of EBI with ZTL reveals a novel mechanism involved in controlling the complex transcription-translation feedback loops of the clock. This work highlights the importance of cross talk between the ubiquitination pathway and transcriptional control for regulation of the plant clock.
Paediatric parenting stress in inflammatory bowel disease: application of the Pediatric Inventory for Parents
Authors: Guilfoyle S. M. , Denson L. A. , Baldassano R. N. , Hommel K. A.
Published: February 2011

Background  The psychosocial functioning of caregivers of adolescents managing inflammatory bowel disease (IBD) has been understudied; yet, poor caregiver functioning can place youth at risk for compromised disease management. The current study addressed this limitation by examining a sample of caregivers of adolescents with IBD. Study aims included (1) documenting rates of paediatric parenting stress; (2) identifying associated sociodemographic predictors of parenting stress; and (3) comparing previously published rates of parenting stress to those within other paediatric chronic conditions, including cancer, type 1 diabetes, obesity, sickle cell disease, bladder exstrophy.

Methods  Caregivers of adolescents with an IBD diagnosis (Mage= 15.4 ± 1.4, 44.4% female, 88.7% Caucasian) and receiving tertiary care within a gastroenterology clinic (n= 62) completed the Pediatric Inventory for Parents (PIP) as a measure of paediatric parenting stress with frequency and difficulty as PIP subscales. Paediatric gastroenterologists provided disease severity assessments.

Results  Adolescents with IBD were experiencing relatively mild disease activity. Bivariate correlations revealed that PIP‐difficulty was positively associated with Crohn's disease severity (r= 0.38, P < 0.01). Caregiver age was negatively associated with the frequency of parenting stress total (r=−0.25, P= 0.05) and communication scores (r=−0.25, P < 0.05). The frequency and difficulty of parenting stressors within the IBD sample were similar to rates within type 1 diabetes, but were significantly lower than rates identified in other paediatric chronic conditions.

Conclusions  Caregivers of adolescents with IBD seem to experience low rates of parenting stress when their adolescents are receiving outpatient care and during phases of IBD relative inactivity. The sociodemographic characteristics of IBD families (i.e. primarily Caucasian, well‐educated and higher socio‐economic status) likely encourage greater access to financial and psychosocial resources, which may aid in promoting more optimal stress management.
Acute hepatitis C infection lowers serum lipid levels
Authors: Corey K. E. , Mendez‐Navarro J. , Barlow L. L. , Patwardhan V. , Zheng H. , Kim A. Y. , Lauer G. M. , Chung R. T.
Published: February 2011

Summary.  Chronic hepatitis C infection is associated with hypolipidaemia that resolves with viral clearance. Lipid levels in a subgroup of patients rebound to levels that may increase the risk of coronary heart disease. The impact of acute hepatitis C infection and its clearance on lipid levels is unknown. We undertook a retrospective evaluation of subjects with acute hepatitis C infection evaluating lipid levels before, during and following acute infection. Thirty‐eight subjects with acute hepatitis C infection had lipid levels available. Twelve patients had pre‐infection and intra‐infection lipid levels available. Cholesterol (197.8–152.4 mg/dL, P = 0.025), low‐density lipoprotein (LDL) (116.1–76.3 mg/dL, P = 0.001) and non‐high‐density lipoprotein (non‐HDL) cholesterol (164.0–122.7 mg/dL, P = 0.007) decreased dramatically during acute hepatitis C virus infection. Nineteen patients who achieved viral clearance had lipid levels available during infection and following resolution of infection. In these patients, cholesterol (145.0–176.0 mg/dL, P = 0.01), LDL (87.0–110.1 P = 0.0046) and non‐HDL cholesterol (108.6–133.6 mg/dL, P = 0.008) increased significantly. No change was seen in patients who developed chronic infection. Four patients had lipid levels before, during and following resolution of infections and had increased postinfection LDL, cholesterol and non‐HDL cholesterol from pre‐infection levels, indicating acute infection may be associated with an increase in postinfection lipid levels and may confer an increased risk of coronary heart disease. Acute hepatitis C infection results in hypolipidaemia with decreased LDL, cholesterol and non‐HDL cholesterol levels that increase following infection resolution. Levels may increase above pre‐infection baseline lipid levels and should be monitored.
Pregnancy outcomes associated with viral hepatitis
Authors: Reddick K. L. B. , Jhaveri R. , Gandhi M. , James A. H. , Swamy G. K.
Published: February 2011

Summary.  The aim of this study was to examine the contribution of hepatitis B virus (HBV) and hepatitis C virus (HCV) to pregnancy‐related complications including gestational diabetes mellitus (GDM), preterm birth (PTB), intrauterine growth restriction (IUGR), pre‐eclampsia, antepartum haemorrhage and cholestasis. The Nationwide Inpatient Sample was queried for all pregnancy‐related discharges, pregnancy complications and viral hepatitis from 1995 to 2005. Logistic regression was used to examine the association between HBV, HCV, HBV + HCV and pregnancy‐related complications including GDM, PTB, IUGR, pre‐eclampsia, antepartum haemorrhage, cholestasis and caesarean delivery. Model covariates included maternal age, race, insurance status, substance use and medical complications including liver complication, hypertension, HIV, anaemia, thrombocytopenia and sexually transmitted infections. Of 297 664 pregnant women data available for analysis, 1446 had a coded diagnosis of HBV, HCV or both. High‐risk behaviours, such as smoking, alcohol and substance use were higher in women with either HBV or HCV. Women with HBV had an increased risk for PTB (aOR 1.65, CI [1.3, 2.0]) but a decreased risk for caesarean delivery (aOR 0.686, CI [0.53, 0.88]). Individuals with HCV had an increased risk for GDM (aOR 1.6, CI [1.0, 2.6]). Individuals with both HBV and HCV co‐infection had an increased risk for antepartum haemorrhage (aOR 2.82, CI [1.1, 7.2]). There was no association of viral hepatitis with IUGR or pre‐eclampsia. Women with hepatitis have an increased risk for complications during pregnancy. Research to determine the efficacy and cost‐effectiveness of counselling patients about potential risks for adverse outcomes is warranted.
Pharmacokinetics and pharmacodynamics of mycophenolate sodium (EC‐MPS) co‐administered with cyclosporine in the early‐phase post‐kidney transplantation
Authors: Stracke Sylvia , Shipkova Maria , Mayer Jens , Keller Frieder , Zarghom Amir , Yang Liying , Henne‐Bruns Doris , Wieland Eberhard
Published: February 2011

Stracke S, Shipkova M, Mayer J, Keller F, Zarghom A, Yang L, Henne‐Bruns D, Wieland E. Pharmacokinetics and pharmacodynamics of mycophenolate sodium (EC‐MPS) co‐administered with cyclosporine in the early‐phase post‐kidney transplantation.  Clin Transplant 2012: 26: 57–66.  © 2011 John Wiley & Sons A/S.

Abstract:  Mycophenolate drug levels are decreased by co‐administration of cyclosporine. However, mycophenolate levels may be associated with insufficient immunosuppression.

We investigated the pharmacokinetics of 720 mg mycophenolate sodium (EC‐MPS) and inosine monophosphate dehydrogenase (IMPDH) activity under co‐medication with cyclosporine and steroids within the first 30 d after kidney transplantation (n = 24). Blood samples were drawn at 0, 0.5, 1, 1.5, 2, 3, 4, 6, 8, and 12 h after the morning dose. Plasma concentrations of mycophenolic acid, its glucuronide metabolites (MPAG; AcMPAG), and free MPA were determined using validated HPLC‐DAD. IMPDH activity in leukocytes was analyzed chromatographically.

Only six of 24 patients had an MPA‐AUC12h within the putative therapeutic range of 40–60 mg/L·h. MPA clearance was high with 29 L/h. fMPA‐AUC12h (r = −0.429, p = 0.04) and MPAG‐AUC12h correlated significantly with the glomerular filtration rate, while total MPA did not. The MPAG‐AUC12h was about 52‐fold higher than the corresponding values for MPA, whereas the AcMPAG‐AUC12h reached about 20.4% of the respective MPA‐AUC12h. We found significant correlations between IMPDH inhibition and MPA concentration (r = −0.665; p < 0.0001), fMPA (r = −0.446; p = 0.003), and AcMPAG (r = −0.459; p = 0.002) but not with MPAG.

Only 25% of the patients attained the therapeutic range for MPA‐AUC under standard EC‐MPS dose during the early‐phase post‐transplantation. We recommend that EC‐MPS should be given in higher doses (3 × 720 mg) in the early post‐transplant period when co‐administered with cyclosporine.
Up‐regulation of HLA‐G expression in cervical premalignant and malignant lesions
Authors: Zheng N. , Wang C.‐X. , Zhang X. , Du L.‐T. , Zhang J. , Kan S.‐F. , Zhu C.‐B. , Dong Z.‐G. , Wang L.‐L. , Wang S. , Li W.
Published: February 2011

The human leukocyte antigen G (HLA‐G) molecule, a non‐classical major histocompatibility complex class I antigen, exhibits highly limited tissue distribution and gene variation. Recent studies indicate strong immunoinhibitory properties in tumor cells that may favor their escape from anti‐tumor immune responses. However, the role of HLA‐G in cervical premalignant and malignant lesions has not been defined clearly. In our study, HLA‐G expression was studied in cervical tissue from 119 patients with lesions and 22 normal cervical tissue specimens by immunohistochemistry. HLA‐G was expressed in 45% (54/119) of cervical lesion‐containing tissues while it was rarely detectable (0/22) in the control specimens (P = 0.000). ROC curve analysis showed that HLA‐G has an area under the curve (AUC) of 0.694. Furthermore, we investigated soluble HLA‐G expression in the plasma of 172 patients with cervical lesions and 20 healthy controls. Significant increases were also observed in soluble HLA‐G levels (median, 191.4 vs 45.18 U/ml, P < 0.001). The relative operating characteristic (ROC) curves for soluble HLA‐G (sHLA‐G), squamous cell carcinoma (SCC), and carbohydrate antigen 125 (CA125) show an AUC of 0.710, 0.634, and 0.588, respectively. At the cut‐off values of 108.20 U/ml for sHLA‐G, 1.5 ng/ml for SCC, and 35 U/ml for CA125, the sensitivity was 73.30%, 47.83%, and 44.83%, respectively. The detection of soluble HLA‐G in plasma may have significance in the early detection of cervical malignant lesions.
Challenging the golden standard in defining donor‐specific antibodies: does the solid phase assay meet the expectations?
Authors: Zoet Y. M. , Brand‐Schaaf S. H. , Roelen D. L. , Mulder A. , Claas F. H. J. , Doxiadis I. I. N.
Published: February 2011

The purpose of the study was to compare three different methods defining donor‐specific antibodies (DSA): complement‐dependent cytotoxicity (CDC), the flow cytometry method (FCM), and a special for that purpose commercially available Luminex‐based solid phase assay (SPA). A panel of human monoclonal antibodies (HuMabs) with well‐defined human leukocyte antigen (HLA) specificities was used as antibody source and single HLA antigen expressing cell lines (SAL) were used as targets. Two methods yielded identical results (CDC and FCM). However, the SPA, the method by which solubilized HLA molecules from the SAL are captured by microspheres, showed two additional reactions which could not be explained, neither by the epitope recognized by the HuMab nor by the widely accepted sensitivity of the SPA methodology. These unexplained results suggest that by capturing solubilized HLA molecules on microspheres, conformational changes might occur. Positive results obtained by similar Luminex‐based microsphere methods should be therefore taken with caution and the ‘recognized’ HLA antigens should not automatically be considered as unacceptable for transplantation.
HLA‐C*03:93, a novel HLA‐C*03 allele identified by sequence‐based typing
Authors: Cha C.‐H. , Ko S.‐Y. , Oh H.‐B. , Heo Y.‐S. , Kwon O.‐J.
Published: February 2011

The new allele C*03:93 showed one nucleotide difference with C*03:04:01 at codon 140 (GCT/ACT).
The HLA‐DP2 protein binds the immunodominant epitope from myelin basic protein, MBP85‐99, with high affinity
Authors: Hansen B. E. , Nielsen C. H. , Madsen H. O. , Ryder L. P. , Jakobsen B. K. , Svejgaard A.
Published: February 2011

Myelin basic protein (MBP) is a candidate autoantigen in multiple sclerosis (MS). The immunodominant epitope for T‐cell responses is assigned to the amino acid sequence MBP84‐102, which binds to human leukocyte antigen (HLA)‐DR2a (DRB5*0101) and HLA‐DR2b (DRB1*1501) of the HLA‐DR2 haplotype carrying the strongest genetic association with MS. In contrast with HLA‐DR and ‐DQ molecules, HLA‐DP molecules are poorly characterized with respect to the binding of self‐peptides. We show here that HLA‐DP2 binds MBP85‐99 with high affinity, and that the amino acid residues in position MBP91, MBP92 and MBP93 are influencing the binding, as shown by alanine scans. We further used a series of truncated peptides to identify the core of the binding. Moving the frame along the peptide from residues 87–97 to 89–99 progressively decreased the binding affinity for HLA‐DP2, while moving further towards the C‐terminal completely abrogated the binding of peptides to HLA‐DP2. The data suggest that the docking of the MBP85‐99 peptide into the HLA‐DP2 groove is dependent on MBP88V and MBP89V and may use either of them as primary anchor for the p1 position. HLA‐DP2 might thus present the MBP85‐99 peptide in the same register as the HLA‐DRB1*1501, where the MBP89V is preferred as the p1 anchor. Notably, full‐length MBP was able to compete for peptide binding with an affinity similar to that seen for the high‐affinity binding peptides, DRα170‐83 and IIP53‐65. In summary, the HLA‐DP2 molecule binds the immunodominant epitope in MS, MBP85‐99, possibly in more than one register.
Resolution of HLA class I sequence‐based typing ambiguities by group‐specific sequencing primers
Authors: Lebedeva T. V. , Mastromarino S. A. , Lee E. , Ohashi M. , Alosco S. M. , Yu N.
Published: February 2011

The increasing demand for allele‐level human leukocyte antigen (HLA) typing has led the sequence‐based typing (SBT) to become the preferred method. In turn, the steady increase in the number of HLA alleles driven by the adoption of SBT as the ultimate typing method leads to the ever increasing number of cis/trans ambiguities. Over the last few years, additional sequencing with the commercially available group‐specific sequencing primers (GSSPs) has replaced sequence‐specific primer‐polymerase chain reaction and group‐specific amplification as the means of resolving cis/trans ambiguities in many laboratories. Here we summarize our 3‐year experience in designing and utilizing GSSPs for resolution of HLA class I ambiguities. The panel of GSSPs used in our laboratory includes 14 primers for HLA‐A, 18 for HLA‐B, and 13 primers for HLA‐C. The panel resolves 99.9% of all ambiguities.
A gene‐specific primer extension and liquid bead array system for killer‐cell immunoglobulin‐like receptor genotyping
Authors: Park H. J. , Oh Y. , Kang H. J. , Han E. J. , Shin H. Y. , Ahn H. S. , Ahn K. S. , Yoon B. H. , Han B. D.
Published: February 2011

A simple and accurate method for killer‐cell immunoglobulin‐like receptor (KIR) genotyping is developed using KIR gene‐specific primer extension (GSPE) followed by bead array hybridization (GSPE method). After amplification of exons 4, 5, and 9, KIR GSPE and bead array hybridization were performed to verify the presence or absence of 16 KIR subfamilies. GSPE method was validated with natural killer/KIR reference panel I consisting of 48 cell types provided by 13th International Histocompatibility Working Group (IHWG) and genomic DNA from 17 peripheral blood cells, 8 cell lines, and 8 buccal cells. The results of reference panel from GSPE method were 100% concordant with the IHWG reference typing information. All genomic DNAs except reference panel were typed for KIR genes with sequence‐specific primer methods and showed 100% identical typing results using this novel system. In addition, GSPE method can obtain results in 8 h from DNA with 10 ng genomic DNA in a 96‐well‐based assay format.
Identification of a novel HLA‐B allele, B*56:31, by sequence‐based typing in a Lithuanian individual
Authors: Jakubauskas A. , Vilkeviciene R. , Juskevicius D. , Griskevicius L.
Published: February 2011

A novel allele HLA‐B*56:31 differs from HLA‐B*56:18 by three nucleotide substitutions resulting in a missense mutation Tyr171His (TAC to CAC) encoded in exon 3 and two silent substitutions at codon 188His (CAC to CAT) and codon 228Thr (ACT to ACC) encoded in exon 4.
Autoimmune pancreatitis: Current diagnostic criteria are suboptimal
Authors: Giday Samuel A , Khashab Mouen A , Buscaglia Jonathan M , Krishnamurty Devi Mukkai , Chen Terina , Kalloo Anthony N , Canto Marcia I , Okolo Patrick I , Hruban Ralph H , Jagannath Sanjay B
Published: February 2011

Background and Aims:  The preoperative diagnosis of autoimmune pancreatitis (AIP) is difficult, given its similar clinical presentation to pancreatic cancer. The aims of the study are to describe our center's experience with AIP and apply the Japanese AIP diagnostic criteria to a cohort of patients with histologically‐proven AIP in order to assess their performance characteristics.

Methods:  A prospective pathology database was queried for AIP patients who were evaluated and/or treated at Johns Hopkins Hospital from 2002 to 2009. AIP histology was defined by the presence of lymphoplasmacytic infiltration, periductal inflammation, fibrosis, and periphlebitis. Imaging, clinical, and biochemical data were analyzed.

Results:  Thirty patients had pancreatic resection with pathological confirmation of AIP. Imaging revealed pancreatic mass (45%), focal prominence without mass lesion (24%), diffuse enlargement (17%), and normal pancreas (14%). Twenty‐four patients underwent an endoscopic retrograde cholangiopancreatography and/or magnetic resonance cholangiopancreatography, and 4/24 (17%) had pancreatic ductal narrowing or irregularity. Extrapancreaticobiliary organ involvement was found in 6% (n = 2) of patients. Biliary strictures were present in 87% of patients. Of 16 patients who underwent preoperative tissue biopsy, 10 had non‐diagnostic pathology, five had cellular atypia, and one had AIP. Serum immunoglobulin G4 (IgG4) levels were elevated in 12 of 29 (41%) patients. Three (10%) patients had evidence of extrapancreatic manifestations of AIP. When applying the Japanese criteria to the 27 patients who had serum IgG4 measurement, preoperative biopsy, and cross‐sectional abdominal imaging, only 44% of the patients would have been diagnosed accurately.

Conclusions:  When applied to a highly‐selected single‐center referral population in the USA, current Japanese guidelines for the diagnosis of AIP are found to have suboptimal sensitivity.
Fungal infections in severe acute pancreatitis
Authors: Kochhar Rakesh , Noor Mohd Talha , Wig Jaidev
Published: February 2011

Severe acute pancreatitis (SAP) is associated with significant morbidity and mortality. The majority of deaths related to SAP are the result of infectious complications. Although bacterial infections are most commonly encountered, fungal infections are increasingly being recognized. Candida is the most common fungal infection. The occurrence of fungal infection in patients with acute pancreatitis adversely affects the clinical course, leading to a higher incidence of systemic complications, and possibly mortality as well. Important risk factors for fungal infection in patients with acute pancreatitis include broad‐spectrum antibiotics, prolonged hospitalization and surgical/endoscopic interventions, use of total parenteral nutrition, and mechanical ventilation. Patients with higher severity of pancreatitis are at a greater risk. The pathogenesis of fungal infection in patients with acute pancreatitis is multifactorial. Translocation of microorganisms across the gut epithelium, lymphocyte dysfunction, and the virulence of the invading microorganisms play important roles. Histological demonstration of fungi remains the gold standard of diagnosis, but a positive biopsy is rarely obtained. The role of biomarkers in the diagnosis is being investigated. As early diagnosis and treatment can lead to improved outcome, a high index of suspicion is required for prompt diagnosis. Limiting the use of broad‐spectrum antibiotics, early introduction of enteral nutrition, and timely change of vascular catheters are important preventive strategies. The role of antifungal prophylaxis remains controversial. Surgical necrosectomy with antifungal therapy is the most widely used treatment approach. Clinical trials on antifungal prophylaxis are needed, and indications for surgical intervention need to be clearly defined.
LMP2/LMP7 gene variant: A risk factor for intestinal Mycobacterium tuberculosis infection in the Chinese population
Authors: Lv Yuan , Yan Bo , Yang Hongli , Liu Jian , Zhong Wei , Li Kun , Chen Ziping , Xu Changqing
Published: February 2011

Background and Aims:  Low molecular mass protein‐2 (LMP2) and low molecular mass protein‐7 (LMP7) genes play a critical role in foreign antigen processing on the major histocompatibility complex‐I CD8+ cytotoxic T‐lymphocyte pathway. This study was designed to investigate whether the sequence variants in the LMP2/LMP7 coding region were associated with intestinal Mycobacterium tuberculosis (M. tuberculosis) infection or with the co‐infection of pulmonary tuberculosis.

Methods:  A total of 168 patients with intestinal tuberculosis and 235 normal controls were recruited for this study. Two polymorphisms of LMP2 (Arg60–His) and LMP7 (Gln145–Lys) were identified by polymerase chain reaction–restriction fragment length polymorphism method. The associations of the LMP2/LMP7 genotype and haplotype with intestinal M. tuberculosis infection were assessed by using logistic regression analysis.

Results:  The results revealed that LMP7 position codon 145 Lys/Lys and Gln/Lys alleles in the coding region were associated with the infection of intestinal M. tuberculosis (P = 0.003, odds ratio [OR] = 3.86 and P < 0.001, OR = 2.28, respectively). Meanwhile, the Arg–Lys and Cys–Lys haplotypes exhibited significant relation to the intestinal M. tuberculosis infection (P = 0.006, OR = 1.87; P = 0.021, OR = 1.83, respectively). No significant associations were observed for any of the single‐nucleotide polymorphism genotypes or haplotypes with the co‐infection of pulmonary tuberculosis (P > 0.05).

Conclusions:  The results indicated that the genetic variant within the LMP2/LMP7 gene would increase the risk of intestinal M. tuberculosis infection.
Preventing venous thrombosis in critically ill children: what is the right approach?
Authors: Braga Alice J. , Young Amber E.R.
Published: February 2011

Background:  The incidence of venous thromboembolic (VTE) events in children has increased in recent years (J Neurosurg, 101, 2004, 32; J Thromb Haemost, 1, 2003, 1443) yet there is currently no consensus as to what VTE prophylaxis, if any, should be applied to the pediatric population.

Objectives/Aims:  Our aim was to audit current practice in pediatric VTE prophylaxis across England and Wales and to advocate simple measures for prevention. We illustrate the importance of the condition with a series of cases from the South West Paediatric Burns and Neurosurgical Services based in Bristol.

Methods:  Every pediatric intensive care unit (PICU) and burns center admitting children in England and Wales was invited to participate in a structured telephone questionnaire designed to find out how VTE in children were being prevented. We performed a literature review of specific risk factors and management of these factors.

Results:  Only one of the 24 units surveyed had written guidelines specific for children. Four other units used modified adult guidelines in older children. In the remaining 19 units that had no written guidelines, decisions regarding prophylaxis were based on individual cases and consultant‐led.

Conclusion:  There is no consensus in England and Wales as to which VTE prophylactic measures should be applied in patients <18 years of age. The National Institute for Health and Clinical Excellence (NICE) guidelines apply to adults only. Given the rarity of VTE events in children, it is unlikely that randomized controlled trials will provide the answer. We therefore propose that simple empirical measures be formally implemented in critically ill children to reduce the risk of developing this important but under‐recognized condition.
HOW GROUPS REACH AGREEMENT IN RISKY CHOICES: AN EXPERIMENT
Authors: ZHANG JINGJING , CASARI MARCO
Published: February 2011

This paper studies how groups resolve disagreement in lottery choices. In an experiment, subjects submit individual proposals, exchange chat messages, and must reach unanimity. Overall, group choices are more coherent and closer to risk neutrality than individuals'. The proposal of the minority prevails in about one instance out of five. About one third of the groups do not reach immediate agreement after communication. In these groups, extrovert subjects are more likely to lead the group outcome than confused or conscientious subjects. The amount, equality, and timing of chat messages help us to predict which choice prevails in the group. (JEL C92, D81)
MORE INFORMATION IS NOT ALWAYS BETTER: THE CASE OF VOLUNTARY PROVISION OF ENVIRONMENTAL QUALITY
Authors: OWEN ANN L. , VIDERAS JULIO , WU STEPHEN
Published: February 2011

We use a new U.S. survey on pro‐environmental behaviors, attitudes, and knowledge and find that individuals engage in activities that they believe are more effective in reducing carbon emissions, regardless of whether or not these beliefs are accurate. We find that low provision of the public good is greater among people who believe they cannot do much for the environment and do not consider themselves environmentalists. A policy implication of our results is that the effect of more accurate information on the provision of the public good is ambiguous. (JEL Q50, Q54, C10)
GOD AND THE EXTERNAL WORLD
Authors: Smith Martin
Published: February 2011

There are a number of apparent parallels between belief in God and belief in the existence of an external world beyond our experiences. Both beliefs would seem to condition one's overall view of reality and one's place within it – and yet it is difficult to see how either can be defended. Neither belief is likely to receive a purely a priori defence and any empirical evidence that one cites either in favour of the existence of God or the existence of the external world would seem to blatantly beg the question against a doubter. I will explore just how far this parallel can be pushed by examining some strategies for resisting external world scepticism1.
Women and Religion: The Transformation of Leadership Roles
Authors: WALLACE RUTH A.
Published: February 2011

This paper explores women's leadership roles in the sociology of religion. I focus on the women presidents of three social science research organizations that specialize in the study of religious phenomena: the Society for the Scientific Study of Religion, the Association for the Sociology of Religion, and the Religious Research Association, and make some comparisons with women presidents of the American Sociological Association. This paper draws on the work of Marie Augusta Neal for a sociological perspective on women and religion. It suggests policy implications for women and other marginalized groups, and concludes with personal reflections on the transformation process.
American Psychology of Religion and the Journal for the Scientific Study of Religion
Authors: HOOD RALPH W.
Published: February 2011

It is doubtful whether there ever has been a rise‐fall‐rebirth of the psychology of religion. While the claim has marginal merit for American academic psychology, it has little application in other cultures or even within American psychology of religion outside mainstream psychology. The psychology of religion has always been and remains tied to key individuals who sustain the field. This historical fact is important in understanding the role of the JSSR in the field. Early psychologists of religion such as Hall and James set the pattern for two distinctively different approaches to the psychology of religion. Hall's approach was methodologically restrictive, inherently reductive, and came to dominate the academic psychology of religion. James ‘approach was methodological plural, receptive to the evidential force of religious experience, and quickly marginalized within American psychology. These opposing orientation continue to influence the psychology of religion in societies such as the SSR and its journal. A review of the psychologist editors of JSSR illustrates that the psychology of religion remains a marginal interest of mainstream psychology. It survives because of the interdisciplinary nature of the SSSR and its journal.
Suggested Guidelines for Performing Procedures in Patients with Chronic Kidney Disease in Outpatient Centers
Authors: Petrusky Lisa , Friedman Alexander , Miller Gregg , Falk Abigail , Hoggard Jeffrey
Published: February 2011

Maintenance of hemodialysis vascular access is increasingly performed on an outpatient basis by physicians trained in interventional techniques. The adoption of guidelines by national reputable organizations will help identify patients eligible for such outpatient treatments and help optimize the safety and efficacy of their procedures in the outpatient setting.