bluuebunny/crossref_metadata_2025_split huggingface dataset:
The poor growth of Rhodospirillum rubrum mutants lacking PII proteins is due to an excess of glutamine synthetase activity
Authors: Zhang Yaoping , Pohlmann Edward L. , Conrad Mary C. , Roberts Gary P. 
Published: June 2006

SummaryThe PII family of proteins is found in all three domains of life and serves as a central regulator of the function of proteins involved in nitrogen metabolism, reflecting the nitrogen and carbon balance in the cell. The genetic elimination of the genes encoding these proteins typically leads to severe growth problems, but the basis of this effect has been unknown except with Escherichia coli. We have analysed a number of the suppressor mutations that correct such growth problems in Rhodospirillum rubrum mutants lacking PII proteins. These suppressors map to nifR3, ntrB, ntrC, amtB1 and the glnA region and all have the common property of decreasing total activity of glutamine synthetase (GS). We also show that GS activity is very high in the poorly growing parental strains lacking PII proteins. Consistent with this, overexpression of GS in glnE mutants (lacking adenylyltransferase activity) also causes poor growth. All of these results strongly imply that elevated GS activity is the causative basis for the poor growth seen in R. rubrum mutants lacking PII and presumably in mutants of some other organisms with similar genotypes. The result underscores the importance of proper regulation of GS activity for cell growth.
Application of the competing risks analysis to fracture toughness of silicon‐killed C‐Mn plate steels
Authors: MOSKOVIC R. 
Published: June 2006

ABSTRACTThe available Mode I fracture toughness data measured in the brittle‐to‐ductile transition temperature region on C‐Mn silicon‐killed plate steels used in the construction of Magnox reactor pressure vessels have been examined with the view to obtain statistically based estimates of fracture toughness parameters for use in structural integrity assessments. Although fracture toughness data have been measured for several pressure vessel materials, in all cases, except one, the number of test results per station is small.A statistical analysis based on the maximum likelihood method has been performed on fracture toughness data for all plate steels to investigate the effect of test temperature and specimen thickness on pre‐cleavage ductile crack growth and the effect of all three on cleavage fracture toughness. For the purpose of the analyses, Weibull distributions have been assumed for pre‐cleavage ductile crack growth and cleavage fracture toughness with a threshold of zero. The equations derived for pre‐cleavage ductile crack growth and cleavage fracture toughness have been used to estimate their joint distribution.The methodology accommodates the unfailed (censored) data by use of survival statistics. The probabilities of cleavage fracture are evaluated by use of the method of competing risks. Equations for cleavage fracture toughness given for the plate steels are of the same form as already available for C‐Mn submerged arc weld metal.
Histological changes in prostate biopsies after salvage cryotherapy: effect of chronology and the method of biopsy
Authors: IZAWA JONATHAN I. , BUSBY J. ERIK , MORGANSTERN NORA , VAKAR‐LOPEZ FUNDA , SCOTT SHELLIE M. , PISTERS LOUIS L. 
Published: June 2006

OBJECTIVESTo examine changes in prostate biopsies at different intervals after salvage cryotherapy and the effect of biopsy type (transrectal ultrasonography‐guided vs transurethral resection, TUR), as the sequence and extent of histological changes occurring in the prostate after salvage cryotherapy for local failure of prostate cancer treatment are unknown.PATIENTS AND METHODSIn all, 158 prostate biopsies from 150 patients were examined histologically after salvage cryotherapy for prostate cancer after radiotherapy had failed. Specimens were grouped by time from cryotherapy and biopsy technique.RESULTSBiopsies showed hyalinization, necrosis, inflammation and residual cancer. Hyalinization became predominant over time, most notably in biopsies with no residual cancer. Core biopsies showed more hyalinization and regenerating glands, while TUR biopsies showed more necrosis and inflammation.CONCLUSIONSTissue cryo‐injury and reactive changes last for >1 year; more extensive cryo‐injury suggests more effective cancer ablation. A long‐term follow‐up is necessary, as prostate cancer might remain indolent for >1 year.
Glucose tolerance of offspring of mother with gestational diabetes mellitus in a low‐risk population
Authors: Malcolm J. C. , Lawson M. L. , Gaboury I. , Lough G. , Keely E. 
Published: June 2006

AbstractAims  To describe the prevalence of impaired glucose tolerance and obesity in offspring of mothers whose pregnancies were complicated by gestational diabetes mellitus (GDM) in a low‐risk population and to investigate the effect on these outcomes of minimal intervention compared with tight control for management of GDM.Methods  Eighty‐nine children (mean age 9.1 years, 93% Caucasian) were recruited through a follow‐up study of women previously involved in a randomized controlled trial of minimal intervention (control group) vs. tight glycaemic control (treatment group) for GDM. Fasting blood glucose (FBG) and 2‐h glucose tolerance tests (2hGTT) were performed on offspring and body mass index (BMI) calculated. Glucose tolerance and BMI of treatment groups were compared using non‐inferiority tests (non‐inferiority margin −15%).Results  Of those offspring, 6.9% (5/72) had abnormal glucose metabolism [four children had impaired glucose tolerance (IGT) and one had Type 2 diabetes mellitus (DM) (all Caucasian)]. Of the four children with IGT, three were male, three had normal BMI, and three had a family history of Type 2 diabetes. Of the 71 offspring who underwent 2hGTT, 25/25 (100%) of the control offspring and 46/46 (100%) of the treatment offspring had normal FBG (FBG < 5.7 mmol/l). Twenty‐five of 25 (100%) of control and 42/46 (91.3%) of the treatment offspring had normal glucose tolerance (2hGTT < 7.8 mmol/l) (% difference 8.7, 95% CI −5.6, 20.3). BMI < 85th percentile was found in 25/33 (75.8%) of the treatment group and 44/52 (84.6%) of the control group (difference in percentage −8.9, 95% CI −27.2, 7.8).Conclusions  School‐age children of mothers with GDM are at risk of IGT and overweight, even if from a low‐risk ethnic population. FBG was not adequate for screening this population. Minimal intervention for glycaemic control in GDM pregnancies appears to be as effective as tight control for preventing IGT in childhood but not for preventing obesity.
Pocket protein function in melanocyte homeostasis and neoplasia
Authors: Tonks Ian D. , Hayward Nicholas K. , Kay Graham F. 
Published: June 2006

SummaryMelanoma is the most lethal of human skin cancers and its incidence is increasing worldwide [L.K. Dennis (1999). Arch. Dermatol. 135, 275; C. Garbe et al. (2000). Cancer 89, 1269]. Melanomas often metastasize early during the course of the disease and are then highly intractable to current therapeutic regimens [M.F. Demierre and G. Merlino (2004). Curr. Oncol. Rep. 6, 406]. Consequently, understanding the factors that maintain melanocyte homeostasis and prevent their neoplastic transformation into melanoma is of utmost interest from the perspective of therapeutic interdiction. This review will focus on the role of the pocket proteins (PPs), Rb1 (retinoblastoma protein), retinoblastoma‐like 1 (Rbl1 also known as p107) and retinoblastoma‐like 2 (Rbl2 also known as p130), in melanocyte homeostasis, with particular emphasis on their functions in the cell cycle and the DNA damage repair response. The potential mechanisms of PP deregulation in melanoma and the possibility of PP‐independent pathways to melanoma development will also be considered. Finally, the role of the PP family in ultraviolet radiation (UVR)‐induced melanoma and the precise contribution that each PP family member makes to melanocyte homeostasis will be discussed in the context of a number of genetically engineered mouse models.1
Cloning of a Resistance Gene Analog from Wheat and Development of a Codominant PCR Marker for Pm21
Authors: Chen Ya‐Ping , Wang Hua‐Zhong , Cao Ai‐Zhong , Wang Chun‐Mei , Chen Pei‐Du 
Published: June 2006

AbstractTo investigate the mechanism of resistance to wheat (Triticum aestivum L.) powdery mildew, suppression subtractive hybridization was conducted between an isogenic resistant line carrying Pm21 and its recurrent parent Yangmai 5 to isolate the resistance relative genes. A cDNA fragment specifically expressed in the resistant line was obtained and its full length was cloned by in silico cloning and RT‐PCR. This gene encoded a deduced protein of 219 amino acids with a leucine‐rich repeat (LRR) motif, often found in plant resistance genes, and was designated as Ta‐LRR2. Ta‐LRR2 had an increased expression level in the resistant line after inoculation with Erysiphe graminis DC. f. sp. tritici Marchal. PCR analysis with different cytogenetic stocks suggested that Ta‐LRR2 was specifically associated with chromosome arms 6VS and 6AS. Linkage analysis further showed that Ta‐LRR2 could be used as a resistance gene analog polymorphism marker of Pm21 for marker‐assisted selection in germplasm enhancement and breeding practice. Moreover, how to isolate Pm21 based on the information obtained for Ta‐LRR2 is discussed.(Managing editor: Li‐Hui Zhao)
Characterization of the Immune Status of CD8+T Cells in Oral Lesions of Human Immunodeficiency Virus-Infected Persons with Oropharyngeal Candidiasis
Authors: Leigh Janet E. , McNulty Kelly M. , Fidel Paul L. 
Published: June 2006

ABSTRACTOropharyngeal candidiasis (OPC) remains the most common oral infection in human immunodeficiency virus (HIV) disease. In a high percentage of HIV+persons with reduced CD4+T cells, oral lesions withCandidapresent at the outer epithelium have an accumulation of CD8+T cells at the epithelium-lamina propria interface associated with reduced expression of the mucosal cell-trafficking adhesion molecule E-cadherin. The purpose of the present study was to characterize the immune status of these CD8+T cells. Immunohistochemical staining for phenotypic and activation and costimulation markers was performed on frozen biopsy tissue sections from HIV+OPC+persons with accumulated CD8+T cells. CD8+T cells consisted primarily of central memory cells by virtue of positive CD45RO (memory) and CD27 (central memory) expression. However, concomitant negative expression of CD62L and CCR7 (effector memory) was suggestive of a transitioning memory phenotype within the tissue. Despite this, the cells are considered to be activated on the basis of positive expression of CD69. The CD8+T cells are not considered to be NK T cells or anti-HIV CD8+T cells because of negative or low expression of CD161 and vascular cell adhesion molecule, respectively. These results suggest that the accumulated mucosal migratory-challenged CD8+T cells are otherwise normal memory T cells in an activated state.
Comparison of the Digene HC2 Assay and the Roche AMPLICOR Human Papillomavirus (HPV) Test for Detection of High-Risk HPV Genotypes in Cervical Samples
Authors: Sandri Maria T. , Lentati Paola , Benini Elvira , Dell'Orto Patrizia , Zorzino Laura , Carozzi Francesca M. , Maisonneuve Patrick , Passerini Rita , Salvatici Michela , Casadio Chiara , Boveri Sara , Sideri Mario 
Published: June 2006

ABSTRACT
Many different methods with different sensitivity and specificity have been proposed to detect the presence of high-risk human papillomavirus (HR HPV) in cervical samples. The HC2 is one of the most widely used. Recently, a new standardized PCR-based method, the AMPLICOR HPV test, has been introduced. Both assays recognize the same 13 HR HPV genotypes. The performances of these two commercially available assays were compared in 167 consecutive women (for a total of 168 samples) who presented at the Colposcopy Clinic either for a follow-up or for a diagnostic visit. Concordant results were found in 140/168 cervical samples (overall agreement, 83%; Cohen's kappa = 0.63). Twenty-eight samples gave discordant results: 20 were positive with the AMPLICOR HPV test and negative with the HC2 assay, and 8 were negative with the AMPLICOR HPV test and positive with the HC2 assay. The genotyping showed that no HR HPV was detected in the 8 HC2 assay-positive AMPLICOR HPV test-negative samples, while in 8/20 AMPLICOR HPV test-positive HC2 assay-negative samples, an HR HPV genotype was found. The AMPLICOR HPV test scored positive in a significantly higher percentage of subjects with normal Pap smears. All 7 cervical intraepithelial neoplasia grade 3 patients scored positive with the AMPLICOR HPV test, while 2 of them scored negative with HC2. Both tests had positive results in the only patient with squamous cell carcinoma. In conclusion, this study shows that the HC2 assay and the AMPLICOR HPV test give comparable results, with both being suitable for routine use. The differences noted in some cases may suggest a different optimal clinical use.
Evaluation of a Real-Time Nucleic Acid Sequence-Based Amplification Assay Using Molecular Beacons for Detection of Human Immunodeficiency Virus Type 1
Authors: McClernon D. R. , Vavro C. , St. Clair M. 
Published: June 2006

ABSTRACT
We evaluated the performance characteristics of a new, real-time nucleic acid sequence-based amplification (NASBA) assay that incorporates molecular beacon technology for detection of human immunodeficiency virus type 1 (HIV-1). The quantitative results were comparable to those obtained with three leading commercially available assays. The analytical sensitivity was 37 IU/ml. The NASBA assay detected clinically relevant recombinant viruses and all group M HIV-1 subtypes.
Detection of rtN236T and rtA181V/T Mutations Associated with Resistance to Adefovir Dipivoxil in Samples from Patients with Chronic Hepatitis B Virus Infection by the INNO-LiPA HBV DR Line Probe Assay (Version 2)
Authors: Osiowy Carla , Villeneuve Jean-Pierre , Heathcote E. Jenny , Giles Elizabeth , Borlang Jamie 
Published: June 2006

ABSTRACTThe nucleotide analog adefovir dipivoxil (ADV) is an effective antiviral treatment for chronic hepatitis B virus (HBV) infection, with resistance to ADV estimated to occur less frequently than resistance to lamivudine treatment. The detection of ADV resistance mutations is necessary during therapy to monitor and anticipate possible treatment failure. The INNO-LiPA HBV DR v2 (LiPA; Innogenetics, Ghent, Belgium) is a DNA hybridization line probe assay for the detection of HBV polymerase mutations associated with resistance to lamivudine and ADV. Evaluation of this assay to detect ADV resistance mutations was performed by analyzing 38 patients treated with ADV. Serial samples taken at 6-month intervals during treatment were available for most patients. A total of 124 samples were analyzed by both LiPA and sequencing. By LiPA analysis, 12 patients (31.5%) were found to have mutations associated with resistance to ADV (rtA181V/T and/or rtN236T). This contrasted with sequence analysis, which found nine patients (24%) with either or both mutations. Twice as many samples were rtN236T positive by LiPA (18 of 124) compared to sequence analysis (9 of 124). LiPA detected the rtN236T mutation at least 6 months earlier than its detection by sequencing in patients for whom consecutive serum samples were available. Although less sensitive, sequencing has the advantage of providing information on other polymerase mutations not represented on LiPA strips. The INNO-LiPA HBV DR v2 assay is a very sensitive and specific assay for the detection of the rtN236T mutation associated with resistance to ADV.
The superoxide scavenger TEMPOL induces urokinase receptor (uPAR) expression in human prostate cancer cells
Authors: Lejeune Danielle , Hasanuzzaman Mohammad , Pitcock Amanda , Francis Joseph , Sehgal Inder 
Published: June 2006

Abstract
There is little understanding of the effect that reactive oxygen metabolites have on cellular behavior during the processes of invasion and metastasis. These oxygen metabolites could interact with a number of targets modulating their function such as enzymes involved in basement membrane dissolution, adhesion molecules involved in motility or receptors involved in proliferation. We investigated the effect of increased scavenging of superoxide anions on the expression of the urokinase receptor (uPAR) in PC-3M human prostate cancer cells. Urokinase receptor is a GPI-linked cell surface molecule which mediates multiple functions including adhesion, proliferation and pericellular proteolysis. Addition of the superoxide scavenger 4-hydroxy-2,2,6,6-tetramethylpiperidinyloxy (TEMPOL) to PC-3M cultures stimulated expression of uPAR protein peaking between 48 and 72 hours. Cell surface expression of the uPAR was also increased. Surprisingly, uPAR transcript levels increased only slightly and this mild increase did not coincide with the striking degree of protein increase. This disparity indicates that the TEMPOL effect on uPAR occurs through a post-transcriptional mechanism. TEMPOL presence in PC-3M cultures reduced intracellular superoxide-type species by 75% as assayed by NBT dye conversion; however this reduction significantly diminished within hours following TEMPOL removal. The time gap between TEMPOL treatment and peak uPAR protein expression suggests that reduction of reactive oxygen metabolites in prostate cancer cells initiates a multistep pathway which requires several hours to culminate in uPAR induction. These findings reveal a novel pathway for uPAR regulation involving reactive oxygens such as superoxide anion.
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Authors: Reguly Teresa , Breitkreutz Ashton , Boucher Lorrie , Breitkreutz Bobby-Joe , Hon Gary C , Myers Chad L , Parsons Ainslie , Friesen Helena , Oughtred Rose , Tong Amy , Stark Chris , Ho Yuen , Botstein David , Andrews Brenda , Boone Charles , Troyanskya Olga G , Ideker Trey , Dolinski Kara , Batada Nizar N , Tyers Mike 
Published: June 2006

Abstract
Background
The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference.

Results
We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID (http://www.thebiogrid.org) and SGD (http://www.yeastgenome.org/) databases.

Conclusion
Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks.
Fabrication of mixed matrix hollow fibers with intimate polymer–zeolite interface for gas separation
Authors: Jiang Lan Ying , Chung Tai Shung , Kulprathipanja Santi 
Published: June 2006

AbstractIt has been demonstrated that a novel p‐xylenediamine/methanol soaking method could efficiently remove the polymer–zeolite interface defects of the mixed‐matrix structure. In this work, the mixed‐matrix structure is in the form of an ultrathin (1.5–3 μm) polysulfone/zeolite beta mixed‐matrix layer that is supported by a neat Matrimid® layer in dual‐layer composite hollow fibers. The particle's loading in this thin layer has reached 30 wt %. The ideal selectivities of the mixed‐matrix hollow fibers (30 wt % of zeolite) for O2/N2 and CO2/CH4 separation were roughly 30 and 50% superior to that of the neat PSF/Matrimid® hollow fibers, respectively. Investigation of the morphology of the mixed‐matrix selective layer and its relation with gas separation performance indicated that without p‐xylenediamine/methanol solution treatment, the outer layer showed various polymer–zeolite interface structures in different fibers with the same heat treatment procedures; this situation might lead to the different selectivities after coating. However, by applying p‐xylenediamine/methanol processing on the fibers before thermal treatment, the fibers obtained a more uniform structure and improved attachment between polymer matrix and zeolite surface. Hydrogen bonding was proposed as the possible mechanism for the tighter attachment between the two phases. The improvement of separation efficiency was presumably related to the polymer chain rigidification, partial pore blockage, and/or favorable interaction between the gas penetrants and zeolite framework. © 2006 American Institute of Chemical Engineers AIChE J, 2006
Biomolecular Modeling: Goals, Problems, Perspectives
Authors: van Gunsteren Wilfred F. , Bakowies Dirk , Baron Riccardo , Chandrasekhar Indira , Christen Markus , Daura Xavier , Gee Peter , Geerke Daan P. , Glättli Alice , Hünenberger Philippe H. , Kastenholz Mika A. , Oostenbrink Chris , Schenk Merijn , Trzesniak Daniel , van der Vegt Nico F. A. , Yu Haibo B. 
Published: June 2006

AbstractComputation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force‐field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.
War and the dis‐eases of othering
Authors: Moglen Helene , Namir Sheila 
Published: June 2006

AbstractThis essay is concerned with ways in which primal psychic relations, socio‐economic structures, and political imperatives have collaborated in the production of othering relations that have supported Bush's war on terror. Drawing on the psychoanalytic conception of the “third,” the authors identify alternative relational structures that can open up dehumanizing and hierarchical dyadic pairings. Finally, they consider how the events of Hurricane Katrina enabled journalists to occupy the space of the third and, therefore, to help in relational reconfigurations that grow out of the raising of consciousness and the acquisition of knowledge. Copyright © 2006 John Wiley & Sons, Ltd.