bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Flexible Database for Combinatorial and High‐Throughput Materials Science
Authors: Frantzen Andreas , Sanders Daniel , Scheidtmann Jens , Simon Ulrich , Maier Wilhelm F. 
Published: March 2005

AbstractA new project‐oriented database concept for high‐throughput materials research and development is presented. The relational database is built on the common software MS‐Access. Its advantages are high versatility and compatibility as well as simple data import and export. Due to its modular conception, it is easily adapted and modified to various projects in combinatorial materials research. With the aid of standardized ASCII tables for data exchange, it was not only possible to share results between different research groups but also to use their individual expertise for a collective evaluation based on an identical data stock. The database application for visualization and data mining is demonstrated with examples from a search for new solid state sensor materials.
QSAR Models for the Analysis of Bioresponse Data from Combinatorial Libraries of Biomaterials
Authors: Smith Jack R. , Kholodovych Vladyslav , Knight Doyle , Welsh William J. , Kohn Joachim 
Published: March 2005

AbstractWe present two surrogate (semi‐empirical) models for prediction of both Protein Adsorption (PA) onto, and Cellular Response (CR) to, the surfaces of biodegradable polymers that have been designed for tissue engineering applications. We explore several of the key issues in the modeling process including the selection of adequate input variables, and the influence of the choice of the training set and the number of input variables on the accuracy of the predictions. The models are each built using five input variables selected from over 800 choices that include experimentally measured values, empirical estimates of chain hydrophobicity, and parameters that describe molecular shape. For both the PA and CR surrogate models, increasing the number of input variables from five up to seventeen resulted in no significant increase in model accuracy. Further, we examined the influence of the number of iterations in a Monte Carlo analysis designed to ensure that the amount of experimental error is realistically accounted for in the models. We found two ANN‐based surrogate models that predict PA and CR for 77 and 71% of the validation sets to within experimental uncertainty, respectively.
Property Prediction and Hybrid Modeling for Combinatorial Materials
Authors: Kyrylyuk Andriy V. , Case Fiona H. , Fraaije Johannes G. E. M. (Hans) 
Published: March 2005

AbstractIn combinatorial research, one seeks to mimic a natural evolution process, such that a diverse collection of materials improves over time, in response to an external challenge. Modeling such experiments is important for validation and rational design challenges. We present a new hybrid modeling method, which allows more efficient simulation of mesoscale (10−9–10−6 m) phenomena, and is a prototype for a broader approach, which we intend to encompass molecular interactions, nanoscale, and microfluidics. As an example and proof of principle, we examined partition and self‐assembly of surfactant from aqueous solution onto the surface of an oil droplet, and the phase separation of a block copolymer to an oil/water interface by using a hybrid self‐consistent field/dissipative particle dynamics (SCF‐DPD) model.
Waterbird breeding and environmental flow management in the Macquarie Marshes, arid Australia
Authors: Kingsford Richard T. , Auld Kristin M. 
Published: March 2005

AbstractColonial waterbirds breed in relatively few parts of Australia and the Macquarie Marshes are one of the more important wetlands for these species on the continent in terms of size of breeding colonies and frequency of breeding. Breeding data were collected for ten species of colonial waterbirds in the period 1986–2001: Little Black Cormorant Phalacrocorax sulcirostris, Little Pied Cormorant P. melanoleucos, Great Egret Ardea alba, Intermediate Egret A. intermedia, Little Egret A. garzetta, Cattle Egret A. ibis, Rufous Night Heron Nyctiorax caledonicus, Glossy Ibis Plegadis falcinellus, Straw‐necked Ibis Threskiornis spinicollis and Australian White Ibis T. molucca. Breeding of most colonial waterbirds in the Macquarie Marshes was positively related to flow in the three months before breeding and triggered when flows were usually above 200 000 Ml. Flow was also positively related to wetland area. These relationships allowed modelling of three different options for management of environmental flow, nominally an annual allocation of 125 000 Ml. Even though the Macquarie River is highly regulated, there were predicted to be major differences in breeding frequency, flow variability and wetland flooding for different options delivering environmental flows. Use of all environmental flows each year provided the least variable option while accumulating the flow in the major dam and delivering it at high thresholds provided considerably more variability for the Macquarie Marshes, increased breeding of colonial waterbirds and increased frequency of large floods. The size of a waterbird breeding event and flooding extent were still primarily affected by river flooding and diversions upstream, despite the amount of environmental flow and the predicted ecological differences among the environmental flow options. Copyright © 2005 John Wiley & Sons, Ltd.
Population status of eucalypt trees on the River Murray floodplain, South Australia
Authors: George Amy K. , Walker Keith F. , Lewis Megan M. 
Published: March 2005

AbstractFor populations to persist, recruitment must keep pace with mortality. In variable environments, opportunities for reproduction occur patchily in time and space, and favourable conditions must occur sufficiently often to allow growth to maturity (hence ‘recruitment’). The risks of local extinctions may be increased by anthropogenic factors. This scenario is illustrated by two tree species, river red gum (Eucalyptus camaldulensis) and black box (E. largiflorens), on the floodplain of the River Murray, South Australia. Fixed area plots were established at Banrock Station, where large, mature trees are common, although red gum outnumber black box by about four to one. Trunk diameter was measured as a surrogate for tree age. The smallest diameter (0–10 cm) black box are nearly as common as seedlings of that species, whereas the smallest diameter red gum (0–10 cm) are 10 times more abundant than seedlings. Small trees of both species occur in localized clumps, and the respective size‐class distributions exhibit series of peaks and falls, suggesting episodic recruitment and opportunistic survival. Population viability calculations suggest that more than 100% of existing saplings need to survive to maintain the local black box population (i.e. there are too few saplings). The red gum population apparently requires a smaller proportion of survivors, but the calculations may be biased by the clumped distribution of the saplings. Based on population structure and viability estimates, black box at this site appear to lack sufficient regeneration to compensate for adult mortality while red gum appear to have a much better balance. The methods established here may be useful for assessment of stands of these species in other areas. Copyright © 2005 John Wiley & Sons, Ltd.
Seed inputs in riparian zones: implications for plant invasion
Authors: Tabacchi Eric , Planty‐Tabacchi Anne‐Marie , Roques Lydie , Nadal Etienne 
Published: March 2005

AbstractSeed inputs were studied from January 2001 to August 2002 along a tranverse successional gradient of a riparian zone within the mid‐reaches of the Garonne River (SW France). Seeds were trapped monthly at ten sites distributed along the gradient. In total, 117 000 seeds belonging to 296 species were collected, among which 145 were exotic species. Seed inputs were overall dissimilar to the extant vegetation; however, similarity among seed input samples was higher than similarity among the extant vegetation samples. Exotic seed inputs resulted from distinct modes of dispersal in comparison to the native ones. Exotic guilds also comprised more short‐lived species. A significant positive linear relationship was observed between exotic and native species richness for both seed inputs and extant vegetation. Flood events were responsible for species richness peaks in seed inputs. They also contributed towards peaks in exotic species and individuals. However, most exotic seeds were recruited during low water period, with a significant lag in time compared to native inputs. Species composition, densities of species and individuals as well as the percentages of exotic species distinguished the infrequently agricultural zone from the frequently disturbed riparian zone. The latter zone was the most invaded both in terms of seed input and extant vegetation. Copyright © 2005 John Wiley & Sons, Ltd.
A new approach to pile‐up modelling in PIXE
Authors: Maxwell J. A. , Campbell J. L. 
Published: March 2005

AbstractIn the conventional approach to pile‐up modelling when fitting x‐ray spectra, a pile‐up ‘element’ is introduced, whose peak energies are defined as the sums of energies of primary peaks in the spectrum. We introduce a new approach that includes peak + peak, peak + continuum and continuum + continuum pile‐up. Tests show that, in addition to replicating the results of the conventional approach for peak pile‐up, it accounts accurately for broad continuum pile‐up features in the spectrum. The new approach also allows the user to include pile‐up peaks that arise from summing of peaks within the region of fit with peaks that lie below the lower energy limit of the region of fit. Copyright © 2005 John Wiley & Sons, Ltd.
Increased Preference for Ethanol in the Infant Rat after Prenatal Ethanol Exposure, Expressed on Intake and Taste Reactivity Tests
Authors: Arias Carlos , Chotro M Gabriela 
Published: March 2005

Background:Previous studies have shown that prenatal exposure during gestational days 17 to 20 to low or moderate doses of ethanol (1 or 2 g/kg) increases alcohol intake in infant rats. Taking into account that higher consumption does not necessarily suggest a preference for alcohol, in the present study, the hedonic nature of the prenatal experience was analyzed further with the use of a taste reactivity test.Method:General activity, wall climbing, passive drips, paw licking, and mouthing in response to intraoral infusions of alcohol, water, and a sucrose‐quinine solution (which resembles alcohol taste in rats) were tested in 161 preweanling 14‐day‐old rat pups that were prenatally exposed to 0, 1, or 2 g/kg of alcohol during gestational days 17 to 20. Consumption of those substances was measured during the taste reactivity test and on postnatal day 15.Results:Pups that were prenatally exposed to both doses of ethanol displayed lower levels of general activity and wall climbing than controls in response to ethanol. Infant rats that were treated prenatally with both doses of ethanol showed higher intake of the drug and also more mouthing and paw licking in response to ethanol taste. Only pups that were exposed to the higher ethanol dose in utero generalized those responses to the sucrose‐quinine compound.Conclusions:These results seem to indicate that for the infant rat, the palatability of ethanol is enhanced after exposure to the drug during the last days of gestation.
Short‐Term Neuropsychological Recovery in Clients with Substance Use Disorders
Authors: Bates Marsha E. , Voelbel Gerald T. , Buckman Jennifer F. , Labouvie Erich W. , Barry Danielle 
Published: March 2005

Background:Cognitive impairments are frequently observed in clients who enter treatment programs for substance abuse. The potential for early recovery of cognitive abilities is suggested by previous research; however, the extent of improvement and risk factors that may help predict individual differences in rates of recovery remain unclear. This study is a 6‐week follow‐up and retest of an original sample of 197 men and women who had received a broad neuropsychological assessment at addiction treatment entry. The aim was to examine the potential clinical significance of changes in cognitive functioning and the extent to which differential recovery was predictable from client background information.Methods:Fifteen neuropsychological tests were readministered to 169 of 197 clients 6 weeks after treatment entry. Structural equation modeling was used to estimate separately the practice effects and recovery in four cognitive domains: executive function, memory, information processing speed, and verbal ability. Client background information included age, sex, education, substance use and consequences, psychopathology, medical problems, familial alcoholism history, and childhood behavior problems.Results:A four‐factor model of latent neuropsychological ability that was previously identified at treatment entry was replicated at follow‐up. Statistically significant increases in the means of the four latent abilities were found. Memory showed a medium effect size improvement. Executive function, verbal ability, and information processing speed, however, showed only small effect size improvements, suggesting limited clinical significance. Substance use between treatment entry and follow‐up, antisocial personality disorder, negative use consequences, less education, and medical problems were modestly predictive of less recovery.Conclusion:Cognitive recovery in the first 6 weeks of treatment is possible, but, with the possible exception of memory, improvement may be minor in terms of clinical relevance.
BvgA functions as both an activator and a repressor to control Bvgi phase expression of bipA in Bordetella pertussis
Authors: Williams Corinne L. , Boucher Philip E. , Stibitz Scott , Cotter Peggy A. 
Published: March 2005

SummaryThe Bordetella bipA gene is expressed maximally when the BvgAS phosphorelay is semi‐active, i.e. in the Bvg‐intermediate (Bvgi) phase. We used a BvgA‐FeBABE cleavage approach together with site‐directed mutagenesis and bipA–lacZ fusion analyses to determine precisely where BvgA‐phosphate (BvgA∼P) binds at the bipA promoter and how that binding contributes to the complex transcription pattern displayed by bipA. BvgA∼P bound with high affinity and cooperatively with RNAP to sequences at the bipA promoter immediately 5′ to and overlapping those bound by RNAP to activate transcription under Bvgi phase conditions. bipA therefore, like fhaB, appears to be similar to classical class‐II promoters with regard to the mechanism by which its transcription is activated. BvgA∼P bound with relatively low affinity to sequences immediately 3′ of those bound by RNAP at the bipA promoter and this binding mediated repression of bipA transcription under Bvg+ phase conditions. BvgA∼P binding to these sequences occurred simultaneously, if not cooperatively, with RNAP, indicating that BvgA∼P represses bipA expression by inhibiting transcription initiation and/or elongation, rather than by competing with RNAP for binding. As bipA is the first Bvgi phase gene to be characterized, and the first gene shown to be repressed by BvgA∼P directly, our results will provide a basis for comparison as additional Bvg‐regulated genes are identified and characterized.
The cell density‐dependent expression of stewartan exopolysaccharide in Pantoea stewartii ssp. stewartii is a function of EsaR‐mediated repression of the rcsA gene
Authors: Minogue Timothy D. , Carlier Aurelien L. , Koutsoudis Maria D. , Von Bodman Susanne B. 
Published: March 2005

SummaryThe LuxR‐type quorum‐sensing transcription factor EsaR functions as a repressor of exopolysaccharide (EPS) synthesis in the phytopathogenic bacterium Pantoea stewartii ssp. stewartii. The cell density‐dependent expression of EPS is critical for Stewart's wilt disease development. Strains deficient in the synthesis of a diffusible acyl‐homoserine lactone inducer remain repressed for EPS synthesis and are consequently avirulent. In contrast, disruption of the esaR gene leads to hypermucoidy and attenuated disease development. Ligand‐free EsaR functions as a negative autoregulator of the esaR gene and responds to exogenous acyl‐homoserine lactone for derepression. The focus of this study was to define the mechanism by which EsaR governs the expression of the cps locus, which encodes functions required for stewartan EPS synthesis and membrane translocation. Genetic and biochemical studies show that EsaR directly represses the transcription of the rcsA gene. RcsA encodes an essential coactivator for RcsA/RcsB‐mediated transcriptional activation of cps genes. In vitro assays identify an EsaR DNA binding site within the rcsA promoter that is reasonably well conserved with the previously described esaR box. We also describe that RcsA positively controls its own expression. Interestingly, promoter proximal genes within the cps cluster are significantly more acyl‐homoserine lactone responsive than genes located towards the middle or 3′ end of the gene cluster. We will discuss a possible role of EsaR‐mediated quorum sensing in the differential expression of the cps operon.
Evidence that Bacillus catabolite control protein CcpA interacts with RNA polymerase to inhibit transcription
Authors: Kim Jeong‐Ho , Yang Young‐Ki , Chambliss Glenn H. 
Published: March 2005

Summary Bacillus
catabolite control protein (CcpA) mediates carbon catabolite repression (CCR) by controlling expression of catabolite responsive (CR) genes or operons through interaction with catabolite responsive elements (cres) located within or outside of CR promoters. Here, we investigated how CcpA inhibits the transcription of CR promoters in vitro. CcpA has different affinities for different cres, but this does not correlate with its ability to inhibit transcription. In the amyE promoter, which overlaps a CcpA binding site (amyE cre centred at +4.5), CcpA does not prevent RNA polymerase (RNAP) binding to the promoter; it may even interact with RNAP. Inserting non‐integral turns of helix (1.5 and 2.5) between the amyE promoter (−10 hexamer) and the amyE cre relieved CCR of amyE expression. In the xyl operon, despite the downstream location of its cre (a major cre centred at +130.5), CcpA blocked transcription initiation, not  elongation  (roadblock) at the site of the cre. Taken together, our results strongly suggest that CcpA requires interactions with RNAP to inhibit transcription.
The Campylobacter jejuni stringent response controls specific stress survival and virulence‐associated phenotypes
Authors: Gaynor Erin C. , Wells Derek H. , MacKichan Joanna K. , Falkow Stanley 
Published: March 2005

Summary Campylobacter jejuni is a highly prevalent food‐borne pathogen that causes diarrhoeal disease in humans. A natural zoonotic, it must overcome significant stresses both in vivo and during transmission despite the absence of several traditional stress response genes. Although relatively little is understood about its mechanisms of pathogenesis, its ability to interact with and invade human intestinal epithelial cells closely correlates with virulence. A C. jejuni microarray‐based screen revealed that several known virulence genes and several uncharacterized genes, including spoT, were rapidly upregulated during infection of human epithelial cells. spoT and its homologue relA have been shown in other bacteria to regulate the stringent response, an important stress response that to date had not been demonstrated for C. jejuni or any other epsilon‐proteobacteria. We have found that C. jejuni mounts a stringent response that is regulated by spoT. Detailed analyses of a C. jejuniΔspoT mutant revealed that the stringent response is required for several specific stress, transmission and antibiotic resistance‐related phenotypes. These include stationary phase survival, growth and survival under low CO2/high O2 conditions, and rifampicin resistance. A secondary suppressor strain that specifically rescues the low CO2 growth defect of the ΔspoT mutant was also isolated. The stringent response additionally proved to be required for the virulence‐related phenotypes of adherence, invasion, and intracellular survival in two human epithelial cell culture models of infection; spoT is the first C. jejuni gene shown to participate in longer term survival in epithelial cells. Microarray analyses comparing wild‐type to the ΔspoT mutant also revealed a strong correlation between gene expression profiles and phenotype differences observed. Together, these data demonstrate a critical role for the C. jejuni stringent response in multiple aspects of C. jejuni biology and pathogenesis and, further, may lend novel insight into unexplored features of the stringent response in other prokaryotic organisms.
The apicoplast of Plasmodium falciparum is translationally active
Authors: Chaubey Sushma , Kumar Ambrish , Singh Divya , Habib Saman 
Published: March 2005

SummaryApicoplast, the plastid‐like organelle of apicomplexan parasites, has generated interest as a putative drug target. Although transcripts for genes encoded by the 35 kb circular plastid DNA have been detected, the actual presence of their protein products has only been postulated. We provide evidence for translation of the tufA gene encoded by the Plasmodium falciparum apicoplast genome. Translation elongation factor Tu (EF‐Tu), the product of tufA, was localized within the organelle. TufA was found to express maximally in the trophozoite stage of the intraerythrocytic cycle. Additionally, the drug thiostrepton that has a binding site in apicoplast LSU rRNA, reduced P. falciparum apicoplast EF‐Tu levels thus strengthening the view that translation in the apicoplast is the site of action of this drug.
IcmS‐dependent translocation of SdeA into macrophages by the Legionella pneumophila type IV secretion system
Authors: Bardill J. Patrick , Miller Jennifer L. , Vogel Joseph P. 
Published: March 2005

Summary Legionella pneumophila replicates inside alveolar macrophages and causes an acute, potentially fatal pneumonia called Legionnaires’ disease. The ability of this bacterium to grow inside of macrophages is dependent on the presence of a functional dot/icm type IV secretion system (T4SS). Proteins secreted by the Dot/Icm T4SS are presumed to alter the host endocytic pathway, allowing L. pneumophila to establish a replicative niche within the host cell. Here we show that a member of the SidE family of proteins interacts with IcmS and is required for full virulence in the protozoan host Acanthamoeba castellanii. Using immunofluorescence microscopy and adenylate cyclase fusions, we show that SdeA is secreted into host cells by L. pneumophila in an IcmS‐dependent manner. The SidE‐like proteins are secreted very early during macrophage infection, suggesting that they are important in the initial formation of the replicative phagosome. Secreted SidE family members show a similar localization to other Dot/Icm substrates, specifically, to the poles of the replicative phagosome. This common localization of secreted substrates of the Dot/Icm system may indicate the formation of a multiprotein complex on the cytoplasmic face of the replicative phagosome.