bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposition of Tn
5367
in
Mycobacterium marinum
, Using a Conditionally Recombinant Mycobacteriophage
Authors: Rybniker Jan , Wolke Martina , Haefs Christiane , Plum Georg 
Published: February 2003

ABSTRACT

Mycobacterium marinum
is a close relative of the obligate human pathogen
Mycobacterium tuberculosis
. As with
M. tuberculosis
,
M. marinum
causes intracellular infection of poikilothermic vertebrates and skin infection in humans. It is considered a valid model organism for the study of intracellular pathogenesis of mycobacteria. Low transformation efficiencies for this species have precluded approaches using mutant libraries in pathogenesis studies. We have adapted the conditionally replicating mycobacteriophage phAE94, originally developed as a transposon mutagenesis tool for
M. tuberculosis
, to meet the specific requirements of
M. marinum
. Conditions permissive for phage replication in
M. tuberculosis
facilitated highly efficient transposon delivery in
M. marinum
. Using this technique we succeeded in generating a representative mutant library of this species, and we conclude that TM4-derived mycobacteriophages are temperature-independent suicide vectors for
M. marinum
.
Molecular Cloning of Endo-β-
d
-1,4-Glucanase Genes,
rce1
,
rce2
, and
rce3
, from
Rhizopus oryzae
Authors: Moriya Tatsuki , Murashima Koichiro , Nakane Akitaka , Yanai Koji , Sumida Naomi , Koga Jinichiro , Murakami Takeshi , Kono Toshiaki 
Published: February 2003

ABSTRACT

Three endoglucanase genes, designated the
rce1
,
rce2
, and
rce3
genes, were isolated from
Rhizopus oryzae
as the first cellulase genes from the subdivision
Zygomycota
. All the amino acid sequences deduced from the
rce1
,
rce2
, and
rce3
genes consisted of three distinct domains: cellulose binding domains, linker domains, and catalytic domains belonging to glycosyl hydrolase family 45. The
rce3
gene had two tandem repeated sequences of cellulose binding domains, while
rce1
and
rce2
had only one.
rce1
,
rce2
, and
rce3
had various lengths of linker sequences.
The uninsured and Medicaid Oregon tobacco user experience in a real world, phone based cessation programme
Authors: El-Bastawissi Ay , McAfee T , Zbikowski S M , Hollis J , Stark M , Wassum K , Clark N , Barwinski R , Broughton E 
Published: February 2003

Objective:To describe the experience of uninsured and Medicaid Oregon tobacco users who registered in Free & Clear (F&C), a telephone based cessation programme including five scheduled outbound calls.Design and setting:Using a retrospective cohort design, 1334 (423 uninsured, 806 Medicaid, and 105 commercially insured) Oregon tobacco users who registered in F&C between 18 November 1998 and 28 February 2000 were identified and followed for 12 months post-registration; 648 (48.6%) were successfully contacted at 12 months. Information was collected from the F&C database. Unconditional logistic regression, adjusted for race and education, was used.Results:The seven day quit rate at 12 months, assuming non-respondents were smokers, was 14.8% (95% confidence interval (CI) 13.0 to 16.9). This rate was significantly higher among commercially insured participants (vMedicaid but not uninsured) and among participants who completed ⩾ 5 calls (v< 5 calls). The quit rate for those contacted at 12 months was 30.6% (95% CI 27.0% to 34.3%) and varied, however not significantly, by insurance and number of calls. After adjustment, respondents who completed ⩾ 5 calls were 60% more likely to quit tobacco (odds ratio (OR) 1.6, 95% CI 0.9 to 3.1), and uninsured respondents who completed ⩾ 5 calls were 70% more likely to quit tobacco (OR 1.7, 95% CI 0.9 to 3.5), relative to those who completed < 5 calls, but the difference was not significant.Conclusions:The quit rates are similar to those reported in efficacy trials. The observed variation in quitting tobacco for respondents by number of calls completed and by insurance merits further investigation concentrating on increasing compliance with the call schedule, particularly for the uninsured.
Can parents who smoke socialise their children against smoking? Results from the Smoke-free Kids intervention trial
Authors: Jackson C , Dickinson D 
Published: February 2003

Objective:To evaluateSmoke-free Kids, a new home based programme to assist parents who smoke in socialising their children against smoking.Design:Two year randomised controlled trial.Participants:At baseline, 887 adult smokers who had an abstinent child in the third grade (ages 7–8 years); 671 adults and children were retained through the 24 month follow up.Intervention:Programme modules, newsletters, incentives, support calls.Outcomes:Anti-smoking socialisation; susceptibility to smoking.Results:Of 327 parents randomised to treatment, 210 obtained adequate treatment by using at least three of five core modules. Programme efficacy analyses, which compared these parents with controls (n = 344), showed that exposure to adequate treatment predicted significantly higher levels in nearly all categories of anti-smoking socialisation three months post-intervention. Two years post-baseline, children of parents who reported adequate treatment scored significantly higher than controls on attributes that reduce susceptibility to smoking, and they scored significantly lower than controls on attributes that raise susceptibility to smoking. Programme effectiveness analyses compared all parents randomised to treatment (n = 327) with controls (n = 344). Treatment effects were evident for several socialisation outcomes; however, these effects were smaller and less consistent than those from the efficacy analyses. Similarly, although treated children scored higher than controls on attributes that reduce susceptibility and lower than controls on attributes that raise susceptibility, several of these between-group differences were not significant.Conclusions:Given adequate exposure to theSmoke-free Kidsprogramme, significant beneficial effects were observed on anti-smoking socialisation in households where parents smoke cigarettes, and significant beneficial effects were observed on children’s susceptibility to smoking after two years. Improving programme acceptance and utilisation is necessary before programme effectiveness can be demonstrated.
Smoking mothers and snuffing fathers: behavioural influences on youth tobacco use in a Swedish cohort
Authors: Rosendahl K I , Galanti M R , Gilljam H , Ahlbom A 
Published: February 2003

Objective:To analyse the influences of parental use of cigarettes and snus (the Swedish variety of smokeless tobacco) on offspring’s behaviour.Design:Prospective cohort study.Setting:The Stockholm County of Sweden.Subjects:2232 adolescents recruited in the fifth grade (mean age 11.6 years) with follow up in the eighth grade.Main outcome measures:Self reported tobacco use (ever and current use of cigarettes and/or snus) in the eighth grade.Results:Parents’ tobacco use was associated with adolescents’ current use of cigarettes and snus (odds ratio (OR) 2.7, 95% confidence interval (CI) 1.8 to 3.9 if both parents used tobaccovneither parent). Mother’s cigarette smoking was associated with adolescents’ current exclusive smoking (OR 2.4, 95% CI 1.6 to 3.6). Father’s use of snus was associated with current exclusive use of snus among boys (OR 3.0, 95% CI 1.4 to 6.4), but not with current cigarette use. The overall prevalence of current smoking was lower among children whose fathers used snus than among those whose fathers smoked.Conclusions:Parental smoking, especially maternal smoking, enhances the risk of tobacco experimentation in youths, as does paternal use of smokeless tobacco. However, the transition to regular cigarette smoking is not likely to be affected by paternal use of smokeless tobacco. Contextual factors, in particular declining smoking trends and negative social acceptance of smoking, can explain most of these findings.
DEFECT DETECTION FOR EXECUTABLE SPECIFICATIONS — AN EXPERIMENT
Authors: HOUDEK FRANK , SCHWINN THILO , ERNST DIETMAR 
Published: February 2003

The deployment of executable specifications has increased significantly in the last few years. Just as with any other specification documents, these specifications must be examined to ensure the necessary degree of quality. A common and successful technique used for examining traditional specifications is inspection. Now the question has arisen whether inspections on executable specification are the best choice, or if other techniques which use the execution capabilities of the models perform better. In this paper, we empirically compare several defect detection techniques for executable specifications. In particular, we examine inspections, testing, and ad-hoc simulation. Here, we use the specification languages Statemate and Matlab/Simulink. Also, we take a closer look at the inspection process itself and try to quantify the benefits of an inspection meeting for executable specifications.
THE PHYSICAL BASIS FOR PARRONDO'S GAMES
Authors: ALLISON ANDREW , ABBOTT DEREK 
Published: February 2003

It has been reported that the original inspiration for Parrondo's games was a physical system called a "flashing Brownian ratchet." The relationship seems to be intuitively plausible but has not previously established with rigor. This is the problem that we address in this paper. The dynamics of a Brownian particle in a flashing Brownian ratchet are the result of diffusion and of externally applied forces. The probability density, of finding the particle at a certain place and time, can be mathematically modelled using a Partial Differential Equation (PDE) namely the Fokker-Planck Equation. In this paper, we apply standard finite-difference methods of numerical analysis to the Fokker-Planck Equation. We derive a set of finite difference equations and show that they have the same form as Parrondo's games which justifies the claim that Parrondo's games are a discrete-time, discrete-space version of a flashing Brownian ratchet. We claim that Parrondo's games are effectively a particular way of sampling a Fokker-Planck Equation. Our difference equations are a natural and physically motivated generalization of Parrondo's games. We refer to some well established theorems of numerical analysis to suggest conditions under which the solutions to the difference equations and partial differential equations would converge to the same solution. The diffusion operator, implicitly assumed in Parrondo's original games, reduces to a pre-existing numerical method called "The Schmidt formula." There is actually an infinite continuum of possible diffusion operators and the Schmidt formula is at one extreme of the feasible range. We point out that an operator in the middle of the feasible range, with half-period binomial weightings, would be a better representation of the underlying physics. We present a modified form of Parrondo's games based on the central diffusion operator. We suggest that the finite difference method presented here will be useful in the simulation and design of real physical flashing Brownian ratchets.
Platelet factor 4 promotes adhesion of hematopoietic progenitor cells and binds IL-8: novel mechanisms for modulation of hematopoiesis
Authors: Dudek Arkadiusz Z. , Nesmelova Irina , Mayo Kevin , Verfaillie Catherine M. , Pitchford Simon , Slungaard Arne 
Published: February 2003

AbstractPlatelet factor 4 (PF4) is an abundant platelet α-granule C-X-C chemokine that has weak chemotactic potency but strongly inhibits hematopoiesis through an unknown mechanism. We find that PF4 binds to human CD34+ hematopoietic progenitor cells (HPCs) with a median effective concentration of 1 μg/mL but not after exposure to chondroitinase ABC. PF4 enhances adhesion of HPCs to intact stroma. Committed progenitors also adhere avidly to immobilized PF4. This adhesion is time-dependent, requires metabolic activity, causes cytoskeletal rearrangement, and induces cell-cycle inhibition. Using extracellular acidification rate to indicate transmembrane signaling, we find that interleukin-8 (IL-8), but not PF4, activates CD34+ progenitors, and PF4 blocks IL-8–mediated activation. Surface plasmon resonance analysis shows that PF4 binds IL-8 with high (dissociation constant [Kd] = 42 nM) affinity. Nuclear magnetic resonance analysis of IL-8 and PF4 in solution confirms this interaction. We conclude that PF4 has the capacity to influence hematopoiesis through mechanisms not mediated by a classical high-affinity, 7-transmembrane domain chemokine receptor. Instead, PF4 may modulate the hematopoietic milieu both directly, by promoting progenitor adhesion and quiescence through interaction with an HPC chondroitin sulfate–containing moiety, and indirectly, by binding to or interfering with signaling caused by other, hematopoietically active chemokines, such as IL-8.
Oxidized low-density lipoprotein (oxLDL) triggers hypoxia-inducible factor-1α (HIF-1α) accumulation via redox-dependent mechanisms
Authors: Shatrov Vladimir A. , Sumbayev Vadim V. , Zhou Jie , Brüne Bernhard 
Published: February 2003

AbstractOxidized low-density lipoprotein (oxLDL) and macrophages play a central role in atherosclerosis. Here, we obtained evidence that oxLDL induced hypoxia-inducible factor-1α (HIF-1α) protein accumulation in human macrophages (Mono-Mac-6) under normoxia. HIF-1α accumulation was attenuated by pretreatment with the antioxidant N-acetyl-L-cysteine (NAC), the nitric oxide (NO) donor S-nitrosoglutathione (GSNO), and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase inhibitors such as diphenyleniodonium (DPI) or 4-(2-aminoethyl)-benzenesulfonyl fluoride (AEBSF), thus implicating the contribution of oxLDL-generated reactive oxygen species (ROS). Whereas oxLDL did not modulate HIF-1α mRNA levels, experiments with cycloheximide pointed to a translational mechanism in oxLDL action. HIF-1–dependent luciferase reporter gene analysis underscored HIF-1 transactivation. Our results indicate that oxLDL induced HIF-1α accumulation and HIF-1–dependent reporter gene activation in human macrophages via a redox-mediated pathway. This finding may suggest a role of HIF-1 in atherosclerosis and oxLDL-induced pathogenesis.
Synergy between all-trans retinoic acid and tumor necrosis factor pathways in acute leukemia cells
Authors: Witcher Michael , Ross Douglas T. , Rousseau Caroline , Deluca Leslie , Miller Wilson H. 
Published: February 2003

AbstractThe nuclear receptor ligand all-trans retinoic acid (ATRA) causes dramatic terminal differentiation of acute promyelocytic leukemia (APL) cells in vitro and in patients, but it is less active in other malignancies. However, downstream mediators of the effects of ATRA are not well understood. We used a cDNA microarray to search for ATRA-regulated genes in the APL cell line NB4 and found that ATRA regulated several members of the tumor necrosis factor (TNF) pathway. Here we show that TNF can synergize with ATRA to induce differentiation, showing monocytic characteristics more typical of differentiation mediated by TNF than by ATRA. ATRA and TNF can also induce differentiation of the non-APL cell line U937. Underlying this response was an increase in TNF-induced nuclear factor-κB (NF-κB) DNA binding within 2 hours in the presence of ATRA and activation of NF-κB DNA binding and transcriptional activity in response to ATRA alone within 48 hours of ATRA treatment. Furthermore, we found a synergistic induction of the NF-κB target genes BCL-3, Dif-2, and TNF receptor 2 (TNFR2) in response to the combination of TNF and ATRA. These genes have been previously shown to play a role in TNF signaling, and amplification of such genes may represent a mechanism whereby TNF and ATRA can act synergistically. We propose that ATRA can prime cancer cells for differentiation triggered by TNF and suggest that targeting the TNF pathway in combination with ATRA may represent a novel route to treat leukemias. (Blood. 2003;102:237-245)
Sphingosine 1-phosphate is a novel inhibitor of T-cell proliferation
Authors: Jin Yixin , Knudsen Eirunn , Wang Ling , Bryceson Yenan , Damaj Bassam , Gessani Sandra , Maghazachi Azzam A. 
Published: February 2003

AbstractSphingosine 1-phosphate (S1P) is a pleiotropic lysosphingophospholipid stored and secreted by platelets. Using reverse transcription–polymerase chain reaction and flow cytometric analyses, we determined the expression of S1P receptors (S1P1, S1P3, S1P4, and S1P5) in peripheral blood T cells. T cells were induced to proliferate in the presence of phorbol 12-myristate 13-acetate (PMA) plus ionomycin, anti-CD3 plus anti-CD28, and allogeneic immature or mature dendritic cells. This activity was inhibited by the addition of S1P. Enhanced T-cell proliferation was observed when these cells were stimulated with the same stimuli, but were incubated in serum-free media (SFM). Addition of S1P to SFM inhibited the stimulation of T cells induced by T-cell stimuli, suggesting that S1P is an important inhibitory molecule present in the serum. T-cell proliferation was also inhibited by the addition of dihydrosphingosine 1-phosphate (DHS1P), sphingosine, and ceramide; however, the latter 2 sphingolipids required higher concentrations than S1P. Pretreatment of T cells with pertussis toxin (PTX) blocked the inhibitory effect of S1P on activation with PMA plus ionomycin, but not on activation with anti-CD3 plus anti-CD28. This is corroborated with the down-regulation of S1P1 in T cells stimulated with anti-CD3 plus anti-CD28. Similarly, PTX did not affect the inhibitory effect of S1P on T-cell proliferation when dendritic cells were used as stimuli. Further, S1P or DHS1P but not ceramide or sphingosine enhanced rather than decreased secretion of interleukin 2 and interferon γ by T cells stimulated with anti-CD3 plus anti-CD28. These results show differential effects of S1P on polyclonal T-cell proliferation and cytokine secretion.
Performance- and safety-enhanced lentiviral vectors containing the human interferon-β scaffold attachment region and the chicken β-globin insulator
Authors: Ramezani Ali , Hawley Teresa S. , Hawley Robert G. 
Published: February 2003

AbstractRetroviral vectors are the most efficient means of stable gene delivery to hematopoietic stem cells (HSCs). However, transgene expression from retroviral vectors is frequently subject to the negative influence of chromosomal sequences flanking the site of integration. Toward the development of autonomous transgene expression cassettes, we inserted the human interferon-β scaffold attachment region (IFN-SAR) and the chicken β-globin 5′ DNase I hypersensitive site 4 (5′HS4) insulator both separately and together into a series of self-inactivating (SIN) lentiviral vector backbones. Transduced cells of the human CD34+ hematopoietic progenitor line KG1a—pooled populations as well as individual clones harboring single integrants—were analyzed for reporter expression during culture periods of up to 4 months. Vectors carrying both the 5′HS4 insulator and the IFN-SAR consistently outperformed control vectors without inserts as well as vectors carrying either element alone. The performance of a set of vectors containing the murine stem cell virus long terminal repeat as an internal promoter was subsequently assessed during in vitro monocytic differentiation of transduced primary human CD34+ cord blood cells. Similar to what was observed in the KG1a hematopoietic progenitor cell model, optimal reporter expression in primary monocytes was obtained with the vector bearing both regulatory elements. These findings indicate that the 5′HS4/IFN-SAR combination is particularly effective at maintaining open chromatin domains permissive for high-level transgene expression at early and late stages of hematopoietic development, and thus could be of utility in HSC-directed retroviral vector–mediated gene transfer applications.
Chronic lymphocytic leukemias utilizing the VH3-21 gene display highly restricted Vλ2-14 gene use and homologous CDR3s: implicating recognition of a common antigen epitope
Authors: Tobin Gerard , Thunberg Ulf , Johnson Anna , Eriksson Inger , Söderberg Ola , Karlsson Karin , Merup Mats , Juliusson Gunnar , Vilpo Juhani , Enblad Gunilla , Sundström Christer , Roos Göran , Rosenquist Richard 
Published: February 2003

AbstractThe immunoglobulin variable heavy chain (IgVH) gene mutation status is an important prognostic factor in chronic lymphocytic leukemia (CLL), since cases with mutated VH genes show significantly longer survival than unmutated cases. Recently, we reported a preferential use of the VH3-21 gene in mutated CLL and showed that mutated VH3-21 cases had an inferior overall survival compared with other mutated CLL. In order to further characterize this subset, we performed VH gene analysis in 265 CLL cases and identified 31 VH3-21 cases (11.7%); 21 cases had mutated and 10 cases unmutated VH genes. Regardless of VH gene mutation status, a poor overall survival was found in the VH3-21 cases with a median survival of 83 months. These survival data confirm that VH3-21 cases do not fit into the general prognostic grouping of mutated and unmutated CLL. A large fraction of VH3-21 cases also demonstrated unique features with shorter lengths of the third complementarity determining region (CDR3) and CDR3s with highly homologous amino acid sequences. Furthermore, the VH3-21 cases showed a striking dominance of λ light chain expression, and analysis of the Igλ gene rearrangements revealed highly restricted use of the Vλ2-14/Jλ3 genes in the majority of cases. Taken together, our new findings strengthen the suggestion that VH3-21–using cases comprise a new CLL entity, irrespective of VH gene mutation status, and implicate that a common antigen epitope, perhaps of pathogenic significance, is recognized by the highly homologous VH3-21/Vλ2-14 Ig molecules expressed in individual tumors.
Mechanisms and implications of platelet discoid shape
Authors: Italiano Joseph E. , Bergmeier Wolfgang , Tiwari Sanjay , Falet Hervé , Hartwig John H. , Hoffmeister Karin M. , André Patrick , Wagner Denisa D. , Shivdasani Ramesh A. 
Published: February 2003

AbstractThe platelet marginal band consists of a single peripheral microtubule (MT) that is wound in 8 to 12 coils and maintains discoid cell shape. About 90% of β-tubulin in the marginal band is of the divergent, megakaryocyte (MK)/platelet-restricted β1 isoform. β1-tubulin–null mice show reduced proplatelet formation, thrombocytopenia, and platelet spherocytosis. Here, we show that structural abnormalities in resting β1-tubulin—/— platelets include frequent kinks and breaks in the marginal band. Platelets derived from mice lacking the transcription factor GATA1 show similar defects, probably as a direct consequence of absent β1-tubulin. β1-tubulin+/— platelets have normal ratios of β-tubulin isotypes but the marginal band is half the normal thickness, which is sufficient to maintain elliptical cell shape. Thus, a threshold 50% or less of the normal amount of β1-tubulin is required to preserve marginal band integrity and cell shape. β1-tubulin—/— platelets have normal size and contents and show no defects in serotonin release or aggregation. Accordingly, the apparently isolated spherocytosis allows investigation of the role of discoid platelet shape in hemostasis. On agonist stimulation, the disorganized MTs in β1-tubulin—/— platelets fail to condense into central rings and instead are dispersed in short bundles and linear arrays. Nevertheless, intravital microscopy and flow chamber studies demonstrate full functionality of these spherocytic platelets under physiologic shear conditions. Together, these findings highlight the essential requirements of the MK/platelet-restricted β1-tubulin isoform in platelet structure and suggest that spherocytosis does not impair many aspects of platelet function.