bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modelling construction material logistics system with stochastic Petri nets
Authors: Ng S. Thomas , Fang Yuan , Ugwu Onuegbu O. 
Published: January 2008

PurposeThe purpose of this paper is to examine the potential of applying Petri nets to improve construction material logistics analysis and modelling.Design/methodology/approachThe characteristics of construction logistics are unveiled by analysing the existing practices of logistics management. In views of the dynamic nature of construction logistics problem, a stochastic Petri nets (SPNs) approach is proposed to tackle the time‐evolution property. Using a simulation package called PetriTool™ a simulation model is developed. Finally, a case example is applied to illustrate the way in which SPNs is used for analysing and modelling construction material logistics problems.FindingsThe results indicate that the impacts triggered by variations in delivery lead‐time and changes in delivery quantities can be approximated thereby facilitating decision makers to devise a more reliable and optimal materials management plan for construction projects.Research limitations/implicationsThe complex routing patterns in demand analysis and materials procurement methods that results in the enlarged supply chains have not been considered in this paper.Practical implicationsThe lack of a simple but powerful formalism to analyse and model the decision process under a dynamic environment hinders the implementation of efficient logistics systems in the construction industry. The SPNs model presented in this paper can support planners and managers in making construction logistics management decisions under dynamic environment.Originality/valueThis paper demonstrates that the time‐based SPNs can offer more enriched solutions especially when modelling the time‐evolution behaviours of construction logistics.
Evaluating the Flow-Cytometric Nucleic Acid Double-Staining Protocol in Realistic Situations of Planktonic Bacterial Death
Authors: Falcioni Tania , Papa Stefano , Gasol Josep M. 
Published: January 2008

ABSTRACT

Since heterotrophic prokaryotes play an important biogeochemical role in aquatic ecosystems and have a high capacity to survive in extreme environments, easy-to-perform protocols that probe their physiological states and the effects of environmental variables on those states are highly desired. Some methodologies combine a general nucleic acid stain with a membrane integrity probe. We calibrated one of these, the nucleic acid double-staining (NADS) protocol (G. Grégori, S. Citterio, A. Ghiani, M. Labra, S. Sgorbati, S. Brown, and M. Denis, Appl. Environ. Microbiol. 67:4662-4670, 2001), determining the optimal stain concentrations in seawater and the response to conditions that generate prokaryote death (such as heat) and to conditions that are known to produce death in plankton, such as nutrient limitation or flagellate grazing. The protocol was validated by comparison to two methods used to detect viability: active respiration by 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) and incorporation of tritiated leucine. We show that concentrations in the range of 5 to 20 μg ml
−1
of propidium iodide, simultaneous to a 10× concentration of Sybr green I, are best for detecting two separated populations of “live” (green cells) and “dead” (red cells) organisms. During exposure to heat and UVC, we observed that the number of live cells declined concurrently with that of actively respiring cells (CTC positive) and with total leucine incorporation. In seawater mesocosms, the NADS protocol allowed detection of bacterioplankton starvation-related death and flagellate predation. The protocol was also tested in deep profiles in the northwest Atlantic, demonstrating its potential for routine characterization of this fraction of the physiological diversity of marine heterotrophic prokaryotic plankton.
Direct Visualization of Spatial and Temporal Patterns of Antimicrobial Action within Model Oral Biofilms
Authors: Takenaka Shoji , Trivedi Harsh M. , Corbin Audrey , Pitts Betsey , Stewart Philip S. 
Published: January 2008

ABSTRACT

A microscopic method for noninvasively visualizing the action of an antimicrobial agent inside a biofilm was developed and applied to describe spatial and temporal patterns of mouthrinse activity on model oral biofilms. Three species biofilms of
Streptococcus oralis
,
Streptococcus gordonii
, and
Actinomyces naeslundii
were grown in glass capillary flow cells. Bacterial cells were stained with the fluorogenic esterase substrate Calcien AM (CAM). Loss of green fluorescence upon exposure to an antimicrobial formulation was subsequently imaged by time-lapse confocal laser scanning microscopy. When an antimicrobial mouthrinse containing chlorhexidine digluconate was administered, a gradual loss of green fluorescence was observed that began at the periphery of cell clusters where they adjoined the flowing bulk fluid and progressed inward over a time period of several minutes. Image analysis was performed to quantify a penetration velocity of 4 μm/min. An enzyme-based antimicrobial formulation led to a gradual, continually slowing loss of fluorescence in a pattern that was qualitatively different from the behavior observed with chlorhexidine. Ethanol at 11.6% had little effect on the biofilm. None of these treatments resulted in the removal of biomass from the biofilm. Most methods to measure or visualize antimicrobial action in biofilms are destructive. Spatial information is important because biofilms are known for their structural and physiological heterogeneity. The CAM staining technique has the potential to provide information about the rate of antimicrobial penetration, the presence of tolerant subpopulations, and the extent of biomass removal effected by a treatment.
The Iron Stimulon of
Xylella fastidiosa
Includes Genes for Type IV Pilus and Colicin V-Like Bacteriocins
Authors: Zaini Paulo A. , Fogaça Andréa C. , Lupo Fernanda G. N. , Nakaya Helder I. , Vêncio Ricardo Z. N. , da Silva Aline M. 
Published: January 2008

ABSTRACT

Xylella fastidiosa
is the etiologic agent of a wide range of plant diseases, including citrus variegated chlorosis (CVC), a major threat to citrus industry. The genomes of several strains of this phytopathogen were completely sequenced, enabling large-scale functional studies. DNA microarrays representing 2,608 (91.6%) coding sequences (CDS) of
X. fastidiosa
CVC strain 9a5c were used to investigate transcript levels during growth with different iron availabilities. When treated with the iron chelator 2,2′-dipyridyl, 193 CDS were considered up-regulated and 216 were considered down-regulated. Upon incubation with 100 μM ferric pyrophosphate, 218 and 256 CDS were considered up- and down-regulated, respectively. Differential expression for a subset of 44 CDS was further evaluated by reverse transcription-quantitative PCR. Several CDS involved with regulatory functions, pathogenicity, and cell structure were modulated under both conditions assayed, suggesting that major changes in cell architecture and metabolism occur when
X. fastidiosa
cells are exposed to extreme variations in iron concentration. Interestingly, the modulated CDS include those related to colicin V-like bacteriocin synthesis and secretion and to functions of pili/fimbriae. We also investigated the contribution of the ferric uptake regulator Fur to the iron stimulon of
X. fastidiosa
. The promoter regions of the strain 9a5c genome were screened for putative Fur boxes, and candidates were analyzed by electrophoretic mobility shift assays. Taken together, our data support the hypothesis that Fur is not solely responsible for the modulation of the iron stimulon of
X. fastidiosa
, and they present novel evidence for iron regulation of pathogenicity determinants.
Residues near the Amino Terminus of Rns Are Essential for Positive Autoregulation and DNA Binding
Authors: Basturea Georgeta N. , Bodero Maria D. , Moreno Mario E. , Munson George P. 
Published: January 2008

ABSTRACTMost members of the AraC/XylS family contain a conserved carboxy-terminal DNA binding domain and a less conserved amino-terminal domain involved in binding small-molecule effectors and dimerization. However, there is no evidence that Rns, a regulator of enterotoxigenicEscherichia colivirulence genes, responds to an effector ligand, and in this study we found that the amino-terminal domain of Rns does not form homodimers in vivo. Exposure of Rns to the chemical cross-linker glutaraldehyde revealed that the full-length protein is also a monomer in vitro. Nevertheless, deletion analysis of Rns demonstrated that the first 60 amino acids of the protein are essential for the activation and repression of Rns-regulated promoters in vivo. Amino-terminal truncation of Rns abolished DNA binding in vitro, and two randomly generated mutations, I14T and N16D, that independently abolished Rns autoregulation were isolated. Further analysis of these mutations revealed that they have disparate effects at other Rns-regulated promoters and suggest that they may be involved in an interaction with the carboxy-terminal domain of Rns. Thus, evolution may have preserved the amino terminus of Rns because it is essential for the regulator's activity even though it apparently lacks the two functions, dimerization and ligand binding, usually associated with the amino-terminal domains of AraC/XylS family members.
Novel Monofunctional Histidinol-Phosphate Phosphatase of the DDDD Superfamily of Phosphohydrolases
Authors: Lee Hyun Sook , Cho Yona , Lee Jung-Hyun , Kang Sung Gyun 
Published: January 2008

ABSTRACT

The TON_0887 gene was identified as the missing histidinol-phosphate phosphatase (HolPase) in the hyperthermophilic archaeon “
Thermococcus onnurineus
” NA1. The protein contained conserved motifs of the DDDD superfamily of phosphohydrolase, and the recombinantly expressed protein exhibited strong HolPase activity. In this study, we functionally assessed for the first time the monofunctional DDDD-type HolPase, which is organized in the gene cluster.
CD38 induces differentiation of immature transitional 2 B lymphocytes in the spleen
Authors: Rodríguez-Alba Juan C. , Moreno-García Miguel E. , Sandoval-Montes Claudia , Rosales-Garcia Víctor H. , Santos-Argumedo Leopoldo 
Published: January 2008

AbstractCD38 is a surface receptor able to induce activation, proliferation, and survival of human and mouse lymphocytes; this molecule is expressed on the surface of both mature and immature B cells. In this work, the function of CD38 in the maturation of murine B lymphocytes in the spleen was analyzed. The results showed that CD38 is highly expressed on Transitional 2 (T2) B lymphocytes with an intermediate expression on Transitional 1 (T1) and mature follicular B cells (M). Correlating with a high expression of CD38, T2 cells are also larger and more granular than T1 or M B cells. T2 cells also showed high levels of other molecules, which indicate an activated phenotype. CD38 crosslinking induced proliferation and maturation of T2 B lymphocytes; in contrast, T1 subset died by apoptosis. Finally, CD38 stimulation of T2 B lymphocytes obtained from Btk-, Lyn-, or Fyn-deficient mice showed a defective differentiation; similarly, drugs interfering with PI3K or ERK decreased the proliferation or differentiation of this subset. This suggests that these molecules participate in the CD38 signaling pathway. As a whole, the results indicate that CD38 plays an important role in the regulation of B-cell maturation in the spleen.
FoxP3 maintains Treg unresponsiveness by selectively inhibiting the promoter DNA-binding activity of AP-1
Authors: Lee Sang-Myeong , Gao Beixue , Fang Deyu 
Published: January 2008

AbstractRegulatory T cells (Tregs) have been shown to play a crucial role in maintaining self-tolerance and suppressing autoimmunity. The forkhead transcription factor, FoxP3, is a key molecule necessary and sufficient for Tregs development and function. However, the molecular mechanisms by which FoxP3 regulates the phenotypic (anergic) and the functional (suppressive) characteristics of Tregs are not well defined. Here we found that the promoter DNA-binding activity of AP-1 transcription factors is selectively inhibited in the naturally occurring CD4+ CD25+ Tregs from mice. The impaired AP-1 DNA binding is not the result of the decreased nuclear translocation of AP-1 family transcription factors, including c-Jun, JunB, and c-Fos. FoxP3 significantly suppresses both the transcriptional activity and promoter DNA-binding of AP-1 by interacting with c-Jun. The N-terminus of FoxP3, but not its C-terminus forkhead domain, specifically interacts with phosphorylated c-Jun and alters c-Jun subnuclear distribution. This N-terminus of FoxP3 with nuclear localization signals (FoxP3N/NLS) is able to suppress AP-1 transcriptional activity. Ectopic expression of FoxP3N/NLS sufficiently induces the unresponsiveness of mouse primary CD4+ CD25− T cells, whereas the full-length FoxP3 is required for the suppressive functions of Tregs. These findings uncover one of the mechanisms underlying how FoxP3 maintains the unresponsiveness of Tregs.
Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis
Authors: Fernandez Paula , Di Rienzo Julio , Fernandez Luis , Hopp H Esteban , Paniego Norma , Heinz Ruth A 
Published: January 2008

AbstractBackgroundConsidering that sunflower production is expanding to arid regions, tolerance to abiotic stresses as drought, low temperatures and salinity arises as one of the main constrains nowadays. Differential organ-specific sunflower ESTs (expressed sequence tags) were previously generated by a subtractive hybridization method that included a considerable number of putative abiotic stress associated sequences. The objective of this work is to analyze concerted gene expression profiles of organ-specific ESTs by fluorescence microarray assay, in response to high sodium chloride concentration and chilling treatments with the aim to identify and follow up candidate genes for early responses to abiotic stress in sunflower.ResultsAbiotic-related expressed genes were the target of this characterization through a gene expression analysis using an organ-specific cDNA fluorescence microarray approach in response to high salinity and low temperatures. The experiment included three independent replicates from leaf samples. We analyzed 317 unigenes previously isolated from differential organ-specific cDNA libraries from leaf, stem and flower at R1 and R4 developmental stage. A statistical analysis based on mean comparison by ANOVA and ordination by Principal Component Analysis allowed the detection of 80 candidate genes for either salinity and/or chilling stresses. Out of them, 50 genes were up or down regulated under both stresses, supporting common regulatory mechanisms and general responses to chilling and salinity. Interestingly 15 and 12 sequences were up regulated or down regulated specifically in one stress but not in the other, respectively. These genes are potentially involved in different regulatory mechanisms including transcription/translation/protein degradation/protein folding/ROS production or ROS-scavenging. Differential gene expression patterns were confirmed by qRT-PCR for 12.5% of the microarray candidate sequences.ConclusionEighty genes isolated from organ-specific cDNA libraries were identified as candidate genes for sunflower early response to low temperatures and salinity. Microarray profiling of chilling and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses. This study not only allowed the identification of common transcriptional changes to both stress conditions but also lead to the detection of stress-specific genes not previously reported in sunflower. This is the first organ-specific cDNA fluorescence microarray study addressing a simultaneous evaluation of concerted transcriptional changes in response to chilling and salinity stress in cultivated sunflower.
Stimulated T cells generate microparticles, which mimic cellular contact activation of human monocytes: differential regulation of pro- and anti-inflammatory cytokine production by high-density lipoproteins
Authors: Scanu Anna , Molnarfi Nicolas , Brandt Karim J , Gruaz Lyssia , Dayer Jean-Michel , Burger Danielle 
Published: January 2008

AbstractImbalance in cytokine homeostasis plays an important part in the pathogenesis of chronic inflammatory diseases such as multiple sclerosis and rheumatoid arthritis. We demonstrated that T cells might exert a pathological effect through direct cellular contact with human monocytes/macrophages, inducing a massive up-regulation of the prototypical proinflammatory cytokines IL-1β and TNF. This mechanism that might be implicated in chronic inflammation is specifically inhibited by high-density lipoproteins (HDL). Like many other stimuli, besides proinflammatory cytokines, the contact-mediated activation of monocytes induces the production of cytokine inhibitors such as the secreted form of the IL-1 receptor antagonist (sIL-1Ra). The present study demonstrates that stimulated T cells generate microparticles (MP) that induce the production of TNF, IL-1β, and sIL-1Ra in human monocytes; the production of TNF and IL-1β but not that of sIL-1Ra is inhibited in the presence of HDL. The results were similar when monocytes were stimulated by whole membranes of T cells or soluble extracts of the latter. This suggests that MP carry similar monocyte-activating factors to cells from which they originate. Thus, by releasing MP, T cells might convey surface molecules similar to those involved in the activation of monocytes by cellular contact. By extension, MP might affect the activity of cells, which are usually not in direct contact with T cells at the inflammatory site. Furthermore, this study demonstrates that HDL exert an anti-inflammatory effect in nonseptic activation of human monocytes, not only by inhibiting the production of IL-1β and TNF but also, by leaving sIL-1Ra production unchanged.
Statement from the Editor Regarding “Properties of the Social Discount Rate in a Benthamite Framework with Heterogeneous Degrees of Impatience”
Authors: Hopp Wallace J. 
Published: January 2008

In the original version of the paper “Properties of the Social Discount Rate in a Benthamite Framework with Heterogeneous Degrees of Impatience” by Diego Nocetti (Management Science, Articles in Advance, January 25, 2008), Proposition 2 stated that “First and second order stochastically dominated shifts in the distribution of the individual discount rates reduce the SDR.” However, Elyès Jouini and Clotilde Napp pointed out that this is not always the case, noting that “although first and second order stochastically dominated shifts in the distribution of discount rates increase the present value of the project, they are neither necessary nor sufficient to decrease the SDR for all horizons.” Consequently, the original paper was replaced by a new version by Nocetti, Jouini, and Napp, which corrects this result by introducing stronger notions of stochastic dominance (maximum likelihood ratio dominance and portfolio dominance) to determine conditions under which the SDR unambiguously increases or decreases given a shift in the distribution of individual discount rates. The online appendix, which includes all formal proofs, was also revised accordingly. The new version of “Properties of the Social Discount Rate in a Benthamite Framework with Heterogeneous Degrees of Impatience” by Diego Nocetti, Elyès Jouini, and Clotilde Napp appears on pp. 1822–1826 in this issue of Management Science.
Transgenerational effects of the endocrine disruptor vinclozolin on the prostate transcriptome and adult onset disease
Authors: Anway Matthew D. , Skinner Michael K. 
Published: January 2008

AbstractPURPOSEThe ability of an endocrine disruptor exposure during gonadal sex determination to promote a transgenerational prostate disease phenotype was investigated in the current study.METHODSExposure of an F0 gestating female rat to the endocrine disruptor vinclozolin during F1 embryo gonadal sex determination promoted a transgenerational adult onset prostate disease phenotype. The prostate disease phenotype and physiological parameters were determined for males from F1 to F4 generations and the prostate transcriptome was assessed in the F3 generation.RESULTSAlthough the prostate in prepubertal animals develops normally, abnormalities involving epithelial cell atrophy, glandular dysgenesis, prostatitis, and hyperplasia of the ventral prostate develop in older animals. The ventral prostate phenotype was transmitted for four generations (F1–F4). Analysis of the ventral prostate transcriptome demonstrated 954 genes had significantly altered expression between control and vinclozolin F3 generation animals. Analysis of isolated ventral prostate epithelial cells identified 259 genes with significantly altered expression between control and vinclozolin F3 generation animals. Characterization of regulated genes demonstrated several cellular pathways were influenced, including calcium and WNT. A number of genes identified have been shown to be associated with prostate disease and cancer, including beta‐microseminoprotein (Msp) and tumor necrosis factor receptor superfamily 6 (Fadd).CONCLUSIONSThe ability of an endocrine disruptor to promote transgenerational prostate abnormalities appears to involve an epigenetic transgenerational alteration in the prostate transcriptome and male germ‐line. Potential epigenetic transgenerational alteration of prostate gene expression by environmental compounds may be important to consider in the etiology of adult onset prostate disease. Prostate 68: 517–529, 2008. © 2008 Wiley‐Liss, Inc.
Standardization of Surgical Technique in Antireflux Surgery: The LOTUS Trial Experience
Authors: Attwood Stephen E. A. , Lundell Lars , Ell Christian , Galmiche Jean‐Paul , Hatlebakk Jan , Fiocca Roberto , Lind Tore , Eklund Stefan , Junghard Ola ,   The LOTUS Trial Group
Published: January 2008

AbstractBackgroundTo date, it has been difficult to compare medical therapy for gastroesophageal reflux disease with that of surgical management from a scientific viewpoint, mainly because of the lack of standardization of the operative technique. This study was designed to identify a methodology for standardization of surgical technique and to measure the effectiveness of this standardization.MethodsSurgeons contributing to a major international multicenter trial comparing optimum medical therapy with surgical therapy for treatment of gastroesophageal reflux attempted to optimize their surgical techniques so that a realistic comparison could be made that may aid clinical decision‐making. The surgeons met, shared their techniques using video, and produced a standardized set of criteria for the surgical centers and a common operative technique. Data collection methods ensured accuracy of the records of the procedure applied and the data were analyzed for consistency with set surgical standards.ResultsThere was a high degree of conformity (>95%) between the recommended method of performing a Nissen fundoplication as defined in the trial protocol, and variations were restricted to isolated individuals. The operations were completed without mortality, few conversions, and with very low postoperative morbidity.ConclusionsThis study has shown that, contrary to commonly held belief, surgeons are able to standardize their work for the purposes of measuring the outcome of an operative procedure within the context of a randomized, controlled trial.