bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of
bvgR
Expression in
Bordetella pertussis
Authors: Merkel Tod J. , Boucher Philip E. , Stibitz Scott , Grippe Vanessa K. 
Published: November 2003

ABSTRACT

Bordetella pertussis
, the causative agent of whooping cough, produces a wide array of factors that are associated with its ability to cause disease. The expression and regulation of these virulence factors are dependent upon the
bvg
locus, which encodes three proteins: BvgA, a 23-kDa cytoplasmic protein; BvgS, a 135-kDa transmembrane protein; and BvgR, a 32-kDa protein. It is hypothesized that BvgS responds to environmental signals and interacts with BvgA, a transcriptional regulator, which upon modification by BvgS binds to specific promoters and activates transcription. An additional class of genes is repressed by the products of the
bvg
locus. The repression of these genes is dependent upon the third gene,
bvgR
. Expression of
bvgR
is dependent upon the function of BvgA and BvgS. This led to the hypothesis that the binding of phosphorylated BvgA to the
bvgR
promoter activates the expression of
bvgR
. We undertook an analysis of the transcriptional activation of
bvgR
expression. We identified the
bvgR
transcript by Northern blot analysis and identified the start site of transcription by primer extension. We determined that transcriptional activation of the
bvgR
promoter in an in vitro transcription system requires the addition of phosphorylated BvgA. Additionally, we have identified
cis
-acting regions that are required for BvgA activation of the
bvgR
promoter by in vitro footprinting and in vivo deletion and linker scanning analyses. A model of BvgA binding to the
bvgR
promoter is presented.
The
Bacillus thuringiensis
Linear Double-Stranded DNA Phage Bam35, Which Is Highly Similar to the
Bacillus cereus
Linear Plasmid pBClin15, Has a Prophage State
Authors: Strömsten Nelli J. , Benson Stacy D. , Burnett Roger M. , Bamford Dennis H. , Bamford Jaana K. H. 
Published: November 2003

ABSTRACT

Bam35, a 15-kbp double-stranded DNA phage, infects
Bacillus thuringiensis
. Recently, sequencing of the related
Bacillus cereus
revealed a 15.1-kbp linear plasmid, pBClin15. We show that pBClin15 closely resembles Bam35 and demonstrate conversion of Bam35 to a prophage. This state is common, as several
B. thuringiensis
strains release Bam35-related viruses.
FolM, A New Chromosomally Encoded Dihydrofolate Reductase in
Escherichia coli
Authors: Giladi Moshe , Altman-Price Neta , Levin Itay , Levy Liat , Mevarech Moshe 
Published: November 2003

ABSTRACT

Escherichia coli
(
thyA ΔfolA
) mutants are viable and can grow in minimal medium when supplemented with thymidine alone. Here we present evidence from in vivo and in vitro studies that the
ydgB
gene determines an alternative dihydrofolate reductase that is related to the trypanosomatid pteridine reductases. We propose to rename this gene
folM
.
Reappraisal With Meta-Analysis of the Addition of Gram-Positive Prophylaxis to Fluoroquinolone in Neutropenic Patients
Authors: Cruciani Mario , Malena Marina , Bosco Oliviero , Nardi Stefano , Serpelloni Giovanni , Mengoli Carlo 
Published: November 2003

Purpose: Past reports and meta-analyses indicate that fluoroquinolones are highly effective in preventing Gram-negative infections in neutropenic cancer patients, but offer inadequate coverage for Gram-positive infections. We evaluated by meta-analysis the efficacy of the addition of antimicrobial agents with enhanced Gram-positive activity to prophylaxis with quinolones. Materials and Methods: Randomized trials comparing fluoroquinolones alone (ciprofloxacin, ofloxacin, pefloxacin, or norfloxacin) with fluoroquinolone in combination with Gram-positive prophylaxis (rifampin, vancomycin, amoxicillin, roxithromycin, or penicillin) were retrieved. We pooled relative risks (RRs) using a fixed-effects model. Results: Nine trials (1,202 patients) published between 1993 and 2000 meet inclusion criteria. Compared with fluoroquinolone alone, Gram-positive prophylaxis reduced total bacteremic episodes (RR, 1.54; 95% CI, 1.26 to 1.88), streptococcal infections (RR, 2.20; 95% CI, 1.44 to 3.37), coagulase-negative staphylococcal infections (RR, 1.46; 95% CI, 1.04 to 2.04), and rate of febrile patients (RR 1.08; 95% CI, 1.00 to 1.16). Occurrence of clinically documented infections, unexplained fever, and infectious mortality was similar in the two groups. The addition of Gram-positive prophylaxis, however, significantly increased side effects (RR, 0.46; 95% CI, 0.28 to 0.76). Rifampin use resulted in a higher incidence of undesirable effects. Conclusion: Considering the lack of cut-clear benefit on some parameters of morbidity and mortality, routine use of Gram-positive prophylaxis is not advisable. This strategy, however, should be particularly valuable in subgroups of patients at high risk of streptococcal infection (eg, those with severe and prolonged neutropenia or mucositis, and those receiving cytarabine). Problems of tolerability and the potential for the emergence of resistant microorganisms should be considered when prescribing prophylaxis with enhanced Gram-positive activity to neutropenic patients.
Fallopian Tube and Primary Peritoneal Carcinomas Associated With BRCA Mutations
Authors: Levine Douglas A. , Argenta Peter A. , Yee Cindy J. , Marshall David S. , Olvera Narciso , Bogomolniy Faina , Rahaman Jamal A. , Robson Mark E. , Offit Kenneth , Barakat Richard R. , Soslow Robert A. , Boyd Jeff 
Published: November 2003

Purpose: The aims of this study were to determine the incidence of BRCA mutations among Ashkenazi Jewish patients with fallopian tube carcinoma (FTC) or primary peritoneal carcinoma (PPC), to study the clinicopathologic features of these cancers, and to estimate the risks of these cancers in association with a BRCA mutation. Patients and Methods: A retrospective review at two institutions identified 29 Jewish patients with FTC and 22 Jewish patients with PPC. These patients were genotyped for the three Ashkenazi Jewish BRCA founder mutations (185delAG and 5382insC in BRCA1 and 6174delT in BRCA2). Surgical and pathologic information, family history, and survival data were obtained from hospital records. All statistical tests were two sided. Results: Germline BRCA mutations were identified in five of 29 patients with FTC (17%) and nine of 22 patients with PPC (41%). Mutation carriers had a younger mean age at diagnosis than patients without a mutation (60 v 70 years; P = .002). The overall median survival was 148 months for mutation carriers and 41 months for patients without a mutation (P = .04). For BRCA mutation carriers, the lifetime risks of FTC and PPC were 0.6% and 1.3%, respectively. Conclusion: Substantial proportions of Ashkenazi Jewish patients with FTC or PPC are BRCA mutation carriers. Patients with BRCA-associated FTC or PPC are younger at diagnosis and have improved survival compared with patients without a BRCA mutation. Although the lifetime risks of FTC or PPC for patients with BRCA heterozygotes are greater than those for the general population, the absolute risks seem relatively low.
Breast Cancer in Younger Women: Reproductive and Late Health Effects of Treatment
Authors: Ganz Patricia A. , Greendale Gail A. , Petersen Laura , Kahn Barbara , Bower Julienne E. 
Published: November 2003

Purpose: In 1997, we initiated a cohort study to evaluate quality of life (QOL) and reproductive health outcomes in younger female breast cancer survivors. Materials and Methods: Using listings from two tumor registries, we recruited women with stage 0, I, or II breast cancer who were 50 years or younger at diagnosis and were also disease-free survivors for 2 to 10 years. A mailed survey questionnaire assessed medical and demographic factors, health-related QOL, mood, outlook on life, and reproductive health outcomes. Results: We recruited 577 women, who ranged in age from 30 to 61.6 years (mean, 49.5 years) and were surveyed approximately 6 years after diagnosis. Almost three fourths had received some form of adjuvant therapy. Amenorrhea occurred frequently as a result of treatment in women ≥ 40 years at diagnosis, and treatment-associated menopause was associated with poorer health perceptions. Across the cohort, physical functioning was quite good, but the youngest women experienced poorer mental health (P = .0002) and less vitality (energy; P = .03). Multiple regression analyses predicting QOL demonstrated better outcomes in African-American women, married or partnered women, and women with better emotional and physical functioning, whereas women who reported greater vulnerability had poorer QOL. Conclusion: Overall QOL in younger women who survive breast cancer is good, but there is evidence of increased emotional disruption, especially among the youngest women. Factors that may contribute to poorer health perceptions and QOL include experiencing a menopausal transition as part of therapy, and feeling more vulnerable after cancer.
Intensive Methotrexate and Cytarabine Followed by High-Dose Chemotherapy With Autologous Stem-Cell Rescue in Patients With Newly Diagnosed Primary CNS Lymphoma: An Intent-to-Treat Analysis
Authors: Abrey Lauren E. , Moskowitz Craig H. , Mason Warren P. , Crump Michael , Stewart Douglas , Forsyth Peter , Paleologos Nina , Correa Denise D. , Anderson Nicole D. , Caron Dawn , Zelenetz Andrew , Nimer Stephen D. , DeAngelis Lisa M. 
Published: November 2003

Purpose: To assess the safety and efficacy of intensive methotrexate-based chemotherapy followed by high-dose chemotherapy (HDT) with autologous stem-cell rescue in patients with newly diagnosed primary CNS lymphoma (PCNSL). Patients and Methods: Twenty-eight patients received induction chemotherapy using high-dose systemic methotrexate (3.5 g/m2) and cytarabine (3 g/m2 daily for 2 days). Fourteen patients with chemosensitive disease evident on neuroimaging then received high-dose therapy using carmustine, etoposide, cytarabine, and melphalan with autologous stem-cell rescue. Results: The objective response rate to the induction-phase chemotherapy was 57%, and median overall survival is not yet assessable, with a median follow-up time of 28 months. The overall median event-free survival time is 5.6 months for all patients and 9.3 months for 14 patients who underwent transplantation. Six of these 14 patients (43%) remained disease-free at last follow-up. Treatment was well tolerated; there was one transplantation-related death. Prospective neuropsychologic evaluations have revealed no evidence of treatment-related neurotoxicity. Conclusion: This treatment approach is feasible in patients with newly diagnosed PCNSL without evidence of significant related neurotoxicity. Although the transplantation results are similar to those achieved in patients with aggressive or poor-prognosis systemic lymphoma, the low response rate to induction chemotherapy and the significant number of patients who experienced relapse soon after HDT suggest that more aggressive induction chemotherapy may be warranted.
Localized Mucosa-Associated Lymphoid Tissue Lymphoma Treated With Radiation Therapy Has Excellent Clinical Outcome
Authors: Tsang Richard W. , Gospodarowicz Mary K. , Pintilie Melania , Wells Woodrow , Hodgson David C. , Sun Alexander , Crump Michael , Patterson Bruce J. 
Published: November 2003

Purpose: Extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) is a distinct lymphoma with unique clinicopathologic features. We report the clinical outcome of stage I and II MALT lymphoma treated with involved field radiation therapy (RT). Patients and Methods: From 1989 to 2000, 103 patients with stage IE and IIE disease were referred. Their median age was 60 years, with a 2:1 female predominance. Presenting sites were stomach (17 patients), orbital adnexa (31 patients), salivary glands (24 patients), thyroid gland (13 patients), and other sites (18 patients). Ninety-three patients received RT—85 received RT alone, and eight received chemotherapy and RT—with a median dose of 30 Gy. The median follow-up time was 5.1 years. Results: A complete response (CR) to RT alone was achieved in 84 of 85 patients. Among CR patients, 14 experienced relapse. Relapse sites were mostly contralateral paired-organ or distant MALT locations and, infrequently, lymph nodes. The crude local control rate with RT was 95.3% (81 of 85 patients). No relapses were observed in patients with stomach or thyroid lymphoma, whereas 14 of 63 patients (22%) experienced relapse in the other sites. The overall 5-year survival rate was 98%, and the disease-free survival rate was 77%. Transformed lymphoma was observed in 14% of patients (two of 14) experiencing relapse. Conclusion: Moderate-dose RT achieved excellent local control in localized MALT lymphomas and had curative potential for three fourths of the patients. Gastric and thyroid MALT lymphomas had better outcome, whereas distant failures were common for other sites. Despite relapse, the disease often maintained an indolent course.
Electrochemical Detection of Protons Produced in an Electrode Reaction Using Interdigitated Microarray Electrodes
Authors: Ojima Hiroyuki , Umeda Minoru , Mohamedi Mohamed , Uchida Isamu 
Published: November 2003

AbstractThis work describes the use of interdigitated array electrodes (IDAE) for proton detection. Methanol electrooxidation in sulfuric acid solution was exemplified. Reduction currents originating in the reaction product generated by methanol electrooxidation on a Pt generator electrode were observed at the Pt collector electrode, the potential of which was fixed in the hydrogen evolution region. In order to reduce the background current of hydrogen evolution, an Hg‐plated Pt collector electrode was fabricated. Compared to the Pt collector electrode, the reduction current observed at the Hg collector electrode was extremely small. The product detected was found to be a proton from the current responses observed at Pt and Hg collector electrodes.
Electrocapillary Activity and Adsorptive Accumulation of U(VI)‐Cupferron and U(VI)‐Chloranilic Acid Complexes on Mercury Electrode
Authors: Novotný L. , Navrátil T. , Sander S. , Bašová P. 
Published: November 2003

AbstractInterfacial activity of uranium(VI)‐cupferron and uranium(VI)‐chloranilic acid (CAA) complexes (in 0.1 M acetate buffer pH 4.6 or 0.1 M NaClO4 respectively) on polarized mercury electrode at 110 mV, 10 mV or −240 mV respectively vs. saturated calomel electrode (SCE), and under conditions of the application of adsorptive stripping voltammetric techniques was studied. It revealed a competitive effect of interfacial activity of the mentioned complexes consisting in a nonmonotonous effect of the bulk concentration of U(VI) on the adsorption of the mentioned complexing reagents at their constant concentrations. At concentrations lower than 5×10−5 mol L−1 the complexes U(VI)‐cupferron or U(VI)‐CAA exhibited a relatively strong electrosorption providing the adsorption coefficients β of the order 104 L mol−1, the maximum surface excess Γm ≈ 5 to 10 μmol m−2 and average Frumkin interaction coefficients reaching their absolute values 2 to 2.6.
Hierarchical analysis of large‐scale two‐dimensional gel electrophoresis experiments
Authors: Rubinfeld Amit , Keren‐Lehrer Tsipi , Hadas Gil , Smilansky Zeev 
Published: November 2003

AbstractLarge‐scale two‐dimensional gel experiments have the potential to identify proteins that play an important role in elucidating cell mechanisms and in various stages of drug discovery. Such experiments, typically including hundreds or even thousands of related gels, are notoriously difficult to perform, and analysis of the gel images has until recently been virtually impossible. In this paper we describe a scalable computational model that permits the organization and analysis of a large gel collection. The model is implemented in Compugen's Z4000™ system. Gels are organized in a hierarchical, multidimensional data structure that allow the user to view a large‐scale experiment as a tree of numerous simpler experiments, and carry out the analysis one step at a time. Analyzed sets of gels form processing units that can be combined into higher level units in an iterative framework. The different conditions at the core of the experiment design, termed the dimensions of the experiment, are transformed from a multidimensional structure to a single hierarchy. The higher level comparison is performed with the aid of a synthetic “adaptor” gel image, called a Raw Master Gel (RMG). The RMG allows the inclusion of data from an entire set of gels to be presented as a gel image, thereby enabling the iterative process. Our model includes a flexible experimental design approach that allows the researcher to choose the condition to be analyzed a posteriori. It also enables data reuse, the performing of several different analysis designs on the same experimental data. The stability and reproducibility of a protein can be analyzed by tracking it up or down the hierarchical dimensions of the experiment.
Further advances in the development of a data interchange standard for proteomics data
Authors: Orchard Sandra , Zhu Weimin , Julian Randall K. , Hermjakob Henning , Apweiler Rolf 
Published: November 2003

AbstractAmerican Society for Mass Spectrometry 51st Annual Conference on Mass Spectrometry and Allied Topics, 8–12 June, 2003The Protein Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Significant progress was made in advancing the design and implementation of a draft standard for exchanging experimental data from proteomics experiments involving mass spectrometry at the 51st Annual Conference of the American Society for Mass Spectrometry. In collaboration with the American Society for Tests and Measurements, the PSI propose to publish this first draft at the forthcoming HUPO 2nd World Congress in Montreal, 8–11 October 2003.
RNA interference: on the road to an alternate therapeutic strategy!
Authors: Dave Rajnish S. , Pomerantz Roger J. 
Published: November 2003

AbstractRNA interference (RNAi) is a newly described natural biological phenomenon mediated by small interfering RNA (siRNA) molecules which target viral mRNA for degradation by cellular enzymes. RNAi has become a method of choice for studying gene function, especially in mammalian systems. With proof‐of‐concept studies already presented against a wide variety of human pathogens and several innovative methods of delivering the siRNA to a wide variety of primary cells available, the role for siRNA as a potential therapeutic strategy is becoming increasingly clear. This review presents recent advances in this direction. Copyright © 2003 John Wiley & Sons, Ltd.
Stochastic optimization methods in optimal engineering design under stochastic uncertainty
Authors: Marti K. 
Published: November 2003

AbstractProblems from optimal plastic design are based on the convex, linear or linearized yield/strength condition and the linear equilibrium equation for the generic stress (state) vector. Having to take into account, in practice, stochastic variations of the model parameters (e.g. yield stresses, plastic capacities) and external loadings, the basic stochastic optimal plastic design problem must be replaced by an appropriate deterministic substitute problem. After considering stochastic optimization methods based on failure/survival probabilities and presenting differentiation techniques and differentiation formulas for probability of failure/survival functions, a direct approach is presented using the construction and failure costs (e.g. costs for damage, repair, compensation for weakness within the structure, etc.). Based on the basic mechanical survival conditions, the failure costs may be represented by the minimum value of a convex and often linear program. Several mathematical properties of this program are shown. Minimizing then the total expected costs subject to the remaining (simple) deterministic constraints, a stochastic optimization problem is obtained which may be represented by a “Stochastic Convex Program (SCP) with recourse”. Working with linearized yield/strength conditions, a “Stochastic Linear Program (SLP) with complete fixed recourse” results. In case of a discretely distributed probability distribution or after the discretization of a more general probability distribution of the random structural parameters and loadings as well as certain random cost factors one has a linear program (LP) with a so‐called “dual decomposition data” structure. For stochastic programs of this type many theoretical results and efficient numerical solution procedures (LP‐solver) are available. The mathematical properties of theses substitute problems are considered, and numerical solution procedures are described.
Does mass rearing of field collected Trichogramma brassicae wasps influence acceptance of European corn borer eggs?
Authors: Kölliker‐Ott Ursula M. , Bigler Franz , Hoffmann Ary A. 
Published: November 2003

AbstractThe purpose of our study was to identify a trait that changes quickly during Trichogramma mass rearing, and that could therefore be used to monitor stock deterioration. Quality deterioration in mass reared Trichogramma wasps was evaluated by examining host acceptance behaviour of Trichogramma brassicae Bezdenko (Hymenoptera: Trichogrammatidae) on the target host Ostrinia nubilalis Hübner (Lepidoptera: Crambidae). We compared three replicate lines (designated ‘E’) reared in the laboratory on the factitious host Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) for 27 generations, a line ‘O’ reared in the laboratory on O. nubilalis for 24 generations, and a line ‘F’ reared in the laboratory on O. nubilalis for only two generations. All lines were initiated from field collections of O. nubilalis egg masses. We also evaluated natal host effects by rearing each line on E. kuehniella as well as on O. nubilalis for the last generation prior to testing. The percentage of wasps accepting the O. nubilalis egg mass was significantly higher for the E lines (69.6%) than for the F line (46.5%), while wasps of the O line showed intermediate (57.4%) acceptance. Thus, wasps laboratory reared on E. kuehniella performed better than wasps which had recently been collected in the field. Wasps of the O line showed extended probing behaviour compared to the other lines. Lines did not differ in the duration from the first host contact to the beginning of the drilling, probing or trembling behaviour. Natal host (E. kuehniella or O. nubilalis) did not affect acceptance of the target host O. nubilalis. Even though there is some evidence of adaptation to laboratory rearing conditions, we found no indication for quality deterioration in terms of acceptance behaviour of the target host O. nubilalis when T. brassicae was mass reared on the factitious host E. kuehniella.
Florida Scrub‐Jays (Aphelocoma coerulescens) are Sentinels More When Well‐Fed (Even with no Kin Nearby)
Authors: Bednekoff Peter A. , Woolfenden Glen E. 
Published: November 2003

AbstractSentinels occupy high, exposed positions while other group members forage nearby. If sentinel behavior involves a foraging–predation risk trade‐off, animals should be sentinels more when fed supplemental food. When individual Florida scrub‐jays (Aphelocoma coerulescens) were fed fragments of peanuts, during the following 30 min they shifted 30% of their time from foraging to sentinel behavior. In a follow‐up experiment, we fed either one or two members in each group. As before, the jays reduced their foraging and spent much more time as sentinels when given supplemental food. In each treatment, pairs were sentinels simultaneously considerably less often than expected by chance. The dramatic shift from foraging to sentinel behavior suggests that for Florida scrub‐jays sentinel behavior brings substantial benefits for no greater cost than that of lost opportunities to forage. Because the results held for simple mated pairs of scrub‐jays, we argue that kin selection and social prestige are not necessary to explain sentinel behavior.