bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mason Valley Groundwater Model: Linking Surface Water and Groundwater in the Walker River Basin, Nevada1
Authors: Carroll Rosemary W.H. , Pohll Greg , McGraw David , Garner Chris , Knust Anna , Boyle Doug , Minor Tim , Bassett Scott , Pohlmann Karl 
Published: March 2010

Carroll, Rosemary W.H., Greg Pohll, David McGraw, Chris Garner, Anna Knust, Doug Boyle, Tim Minor, Scott Bassett, and Karl Pohlmann, 2010. Mason Valley Groundwater Model: Linking Surface Water and Groundwater in the Walker River Basin, Nevada. Journal of the American Water Resources Association (JAWRA) 46(3):554‐573. DOI: 10.1111/j.1752‐1688.2010.00434.xAbstract:  An integrated surface water and groundwater model of Mason Valley, Nevada is constructed to replicate the movement of water throughout the different components of the demand side of water resources in the Walker River system. The Mason Valley groundwater surface water model (MVGSM) couples the river/drain network with agricultural demand areas and the groundwater system using MODFLOW, MODFLOW’s streamflow routing package, as well as a surface water linking algorithm developed for the project. The MVGSM is capable of simulating complex feedback mechanisms between the groundwater and surface water system that is not dependent on linearity among the related variables. The spatial scale captures important hydrologic components while the monthly stress periods allow for seasonal evaluation. A simulation spanning an 11‐year record shows the methodology is robust under diverse climatic conditions. The basin‐wide modeling approach predicts a river system generally gaining during the summer irrigation period but losing during winter months and extended periods of drought. River losses to the groundwater system approach 25% of the river’s annual budget. Reducing diversions to hydrologic response units will increase river flows exiting the model domain, but also has the potential to increase losses from the river to groundwater storage.
Rural–urban migration brings conservation threats and opportunities to Amazonian watersheds
Authors: Parry Luke , Peres Carlos A. , Day Brett , Amaral Silvana 
Published: March 2010

AbstractThe spatial distribution and growth of human populations have been overlooked by current debates concerning the impact of rural–urban migration for forest conservation in tropical countries. We investigated human settlement and population change in the Brazilian Amazon, combining government census data with field surveys along rivers. Rural populations were clustered and growing within 300 km of urban centers, whereas depopulation and land abandonment dominated farther from towns. The permanently inhabited extent of rivers contracted by 33 ± 8 SE% in recent decades, and households farther upriver were more likely to be considering rural–urban migration. However, harvesting of aquatic and terrestrial wildlife by nonresidents continued into headwater regions, hundreds of kilometers beyond the last household on any given river. Policy makers should consider that expanding cities may drive deforestation and overexploitation near towns while unclear property rights threatens overharvesting and unregulated land speculation in abandoned headwaters.
Differences in stress response after UVC or UVA irradiation in Vibrio parahaemolyticus
Authors: Hamamoto Akiko , Bandou Chiyo , Nakano Masayuki , Mawatari Kazuaki , Lian Xin , Yamato Masayuki , Harada Nagakatsu , Akutagawa Masatake , Kinouchi Yohsuke , Nakaya Yutaka , Takahashi Akira 
Published: March 2010

SummaryThe SOS response is a global regulatory network for repairing DNA damage induced by various environmental stresses such as UV irradiation. The Escherichia coli SOS response has been extensively studied. However, there are no reports on the SOS response in Vibrio parahaemolyticus. In this study, we examined the SOS response in V. parahaemolyticus and compared the differential expression of genes induced by UVC and UVA irradiation. In UVC‐exposed wild‐type cells, expression of several DNA repair genes was increased. However, expression of these genes was not increased in ΔrecA or lexA mutants. Cell filamentation was observed in wild‐type cells, but not in ΔrecA and lexA mutant cells. Sensitivity to UVC was significantly increased in ΔrecA, lexA mutant and Δlon strains compared with wild type. In the case of UVA irradiation, LexA‐controlled DNA repair genes were minimally induced and cell filamentation was not observed. Sensitivity to UVA was the same in the mutant and wild‐type strains. These findings suggest that there is a RecA‐LexA‐mediated SOS response in V. parahaemolyticus, and that this response is important to UVC tolerance but does not contribute to UVA tolerance.
The acylase PvdQ has a conserved function among fluorescent Pseudomonas spp.
Authors: Koch Gudrun , Jimenez Pol Nadal , Muntendam Remco , Chen Yixi , Papaioannou Evelina , Heeb Stephan , Cámara Miguel , Williams Paul , Cool Robbert H. , Quax Wim J. 
Published: March 2010

SummaryPyoverdine biosynthesis in fluorescent Pseudomonas spp. and especially in the opportunistic human pathogen Pseudomonas aeruginosa has been extensively studied. The acylase PvdQ is required for a maturation step in pyoverdine biosynthesis but also has been proven to be effective in degrading long‐chain N‐acyl homoserine lactones (AHLs). These molecules are used as quorum‐sensing molecules by Gram‐negative bacteria such as Pseudomonads themselves. Interestingly, the pvdQ gene is part of a pyoverdine cluster in P. aeruginosa and P. syringae but not in other fluorescent Pseudomonas spp. In this study we have compared the activities of PvdQ orthologues from various species and provide evidence for conserved functions in Pseudomonas fluorescens PfO‐1, P. putida KT2440 and P. aeruginosa PA14. Despite large differences in genomic organization, expression of each of these pvdQ orthologues is regulated by iron availability. Moreover, PvdQ and its orthologues have conserved substrate specificity for AHLs and play a role in pyoverdine production in all tested Pseudomonas species. These data strongly suggest that the role of PvdQ in pyoverdine biosynthesis is conserved among Pseudomonas spp., while the control that PvdQ exerts in P. aeruginosa over its own quorum‐sensing signals seems to be unique to this bacterium.
Comparative microarray analysis reveals that the core biofilm‐associated transcriptome ofPseudomonas aeruginosacomprises relatively few genes
Authors: Patell Sanaya , Gu Muxin , Davenport Peter , Givskov Michael , Waite Richard D. , Welch Martin 
Published: March 2010

SummaryPseudomonas aeruginosais a model organism for the study of intercellular communication and biofilm formation. As such,P. aeruginosahas been the subject of several microarray analyses comparing gene expression in biofilms and planktonic cultures. In the current work, we carried out a meta‐analysis of these data sets to try and identify genes that are generically associated with biofilm formation in all of the conditions examined. Although the total number of transcripts modulated in the biofilms was large within the individual studies, the overlap between the data sets was small. Indeed, only five transcripts were upregulated and six transcripts were downregulated by more than twofold in the three data sets analysed. However, when the threshold modulation was relaxed to less than twofold, the overlap between the data sets increased, revealing a set of transcripts common to all of the studies. Transcriptional fusions and quantitative real‐time PCR were used to independently confirm a selection of the observed modulations. Notably, we found that the expression profile of genes encoding the catabolic pathways for branched chain and aromatic amino acids was altered in biofilms, and that these alterations correlated with the onset of anaerobic growth. These findings were confirmed by quantitative amino acid analysis of culture supernatants. A mutant in one of the genes that we identified showed diminished biofilm formation in an attachment assay. The relatively small number of common biofilm‐specific endpoint transcripts throws doubt on the suggestion that biofim formation proceeds through a pre‐determined developmental pathway.
Featuring 10 phenological estimators using simulated data
Authors: Moussus Jean‐Pierre , Julliard Romain , Jiguet Frédéric 
Published: March 2010

Summary 1. Studies reporting phenological changes in response to climate change are numerous and concern all groups of living organisms. Phenological changes could cause mismatching in food chains, thus inducing important perturbations in ecosystem functioning. Nevertheless, the relevancy of the conclusions drawn from phenological studies strongly depends on the estimation accuracy of such phenological changes. Many different estimators exist and some have already raised major criticism, although they continue to be used. Therefore, there is a crucial need for an extensive study documenting the behaviour of phenological estimators. 2. Here, we compare the estimation efficiency of 10 phenological estimators: different first appearance dates, mean dates, different percentile dates and a smoothing method based on spline functions using simulated phenological data. Root mean‐squared errors and bias of the phenological estimations are calculated in relation to different parameters of the simulated phenological data. 3. Results show that first appearance dates behave as a very inaccurate and biased estimator regarding any phenological data set. Mean dates and estimates calculated using the smoothing method provided in general the most accurate estimates of phenological shifts. They were also the most robust to variation in sample sizes and to imperfect detectability. 4. Our results allow us to warn against the use of first appearance dates in future phenological studies and to recommend using mean dates or smoothing techniques to estimate phenological change of entire distributions. We also provide advice concerning phenological monitoring effort. These recommendations should most importantly apply to studies aiming at comparing phenological variation among sites or among species.
Numerical Investigations on Leakage Performance of the Rotating Labyrinth Honeycomb Seal
Authors: Li Jun , Kong Shengru , Yan Xin , Obi Shinnosuke , Feng Zhengping 
Published: March 2010

AbstractThree-dimensional Reynolds-averaged Navier–Stokes (RANS) solutions from CFX were utilized to investigate the leakage flow characteristics in the labyrinth honeycomb seal of steam turbines. At first, the accuracy and reliability of the utilized RANS approach was demonstrated using the published experimental data of the honeycomb seal. It showed that the utilized numerical method has sufficient precision to predict the leakage performance in seals. Then a range of sealing clearances, cell diameters, cell depths, rotation speeds, and pressure ratios were investigated to determine how these factors affect the leakage flow rate of the labyrinth honeycomb seal. The computed leakage flow rate increased with increasing sealing clearance and pressure ratios. Furthermore, the results show that the studied labyrinth honeycomb seal has the optimum sealing performance in the case of honeycomb cell diameter equals labyrinth step width, and the ratio of the honeycomb cell depth to honeycomb cell diameter is 0.93 under the designed condition. The flow pattern of each case is also illustrated to describe the leakage flow characteristics in labyrinth honeycomb seals.
In VitroAntiviral Activity of Favipiravir (T-705) against Drug-Resistant Influenza and 2009 A(H1N1) Viruses
Authors: Sleeman Katrina , Mishin Vasiliy P. , Deyde Varough M. , Furuta Yousuke , Klimov Alexander I. , Gubareva Larisa V. 
Published: March 2010

ABSTRACTFavipiravir (T-705) has previously been shown to have a potent antiviral effect against influenza virus and some other RNA viruses in both cell culture and in animal models. Currently, favipiravir is undergoing clinical evaluation for the treatment of influenza A and B virus infections. In this study, favipiravir was evaluatedin vitrofor its ability to inhibit the replication of a representative panel of seasonal influenza viruses, the 2009 A(H1N1) strains, and animal viruses with pandemic (pdm) potential (swine triple reassortants, H2N2, H4N2, avian H7N2, and avian H5N1), including viruses which are resistant to the currently licensed anti-influenza drugs. All viruses were tested in a plaque reduction assay with MDCK cells, and a subset was also tested in both yield reduction and focus inhibition (FI) assays. For the majority of viruses tested, favipiravir significantly inhibited plaque formation at 3.2 μM (0.5 μg/ml) (50% effective concentrations [EC50s] of 0.19 to 22.48 μM and 0.03 to 3.53 μg/ml), and for all viruses, with the exception of a single dually resistant 2009 A(H1N1) virus, complete inhibition of plaque formation was seen at 3.2 μM (0.5 μg/ml). Due to the 2009 pandemic and increased drug resistance in circulating seasonal influenza viruses, there is an urgent need for new drugs which target influenza. This study demonstrates that favipiravir inhibitsin vitroreplication of a wide range of influenza viruses, including those resistant to currently available drugs.
Role of CD4+and CD8+T Cells in Clearance of Primary Pulmonary Infection withCoxiella burnetii
Authors: Read Amanda J. , Erickson Sara , Harmsen Allen G. 
Published: March 2010

ABSTRACTThe mechanisms of the primary adaptive immune response toCoxiella burnetiiare not well known. Following inoculation of the lungs withC. burnetiiNine Mile phase I (NMI), SCID mice developed pneumonia and splenomegaly and succumbed to infection, whereas wild-type mice cleared the infection by 24 days. SCID mice reconstituted with either CD4+T cells or CD8+T cells alone were able to control the infection, indicating that the presence of either type of T cells was sufficient to control infection, and B cells were not necessary for primary immunity. Similarly, wild-type mice depleted of either CD4+T cells or CD8+T cells controlled infections in their lungs, but these mice were highly susceptible if they were depleted of both types of T cells. However, compared to CD4+T-cell-dependent protection, CD8+T-cell-dependent protection resulted in less inflammation in the lungs and less growth of bacteria in the spleens.
Identification and Characterization of TwoBordetella aviumGene Products Required for Hemagglutination
Authors: Temple Louise M. , Miyamoto David M. , Mehta Manju , Capitini Christian M. , Von Stetina Stephen , Barnes H. John , Christensen Vern L. , Horton John R. , Spears Patricia A. , Orndorff Paul E. 
Published: March 2010

ABSTRACTBordetella aviumcauses bordetellosis in birds, a disease similar to whooping cough caused byBordetella pertussisin children.B. aviumagglutinates guinea pig erythrocytes via an unknown mechanism. Loss of hemagglutination ability results in attenuation. We report the use of transposon mutagenesis to identify two genes required for hemagglutination. The genes (hagAandhagB) were adjacent and divergently oriented and had no orthologs in the genomes of otherBordetellaspecies. Construction of in-frame, unmarked mutations in each gene allowed examination of the role of each in conferring erythrocyte agglutination, explanted tracheal cell adherence, and turkey poult tracheal colonization. In all of thein vitroandin vivoassays, the requirement for thetrans-acting products ofhagAandhagB(HagA and HagB) was readily shown. Western blotting, using antibodies to purified HagA and HagB, revealed proteins of the predicted sizes of HagA and HagB in an outer membrane-enriched fraction. Antiserum to HagB, but not HagA, blockedB. aviumerythrocyte agglutination and explanted turkey tracheal ring binding. Bioinformatic analysis indicated the similarity of HagA and HagB to several two-component secretory apparatuses in which one product facilitates the exposition of the other. HagB has the potential to serve as a useful immunogen to protect turkeys against colonization and subsequent disease.
The
Legionella pneumophila
LetA/LetS Two-Component System Exhibits Rheostat-Like Behavior
Authors: Edwards Rachel L. , Jules Matthieu , Sahr Tobias , Buchrieser Carmen , Swanson Michele S. 
Published: March 2010

ABSTRACT

When confronted with metabolic stress, replicative
Legionella pneumophila
bacteria convert to resilient, infectious cells equipped for transmission. Differentiation is promoted by the LetA/LetS two-component system, which belongs to a family of signal-transducing proteins that employ a four-step phosphorelay to regulate gene expression. Histidine 307 of LetS was essential to switch on the transmission profile, but a threonine substitution at position 311 (T311M) suggested a rheostat-like function. The
letS
(
T311M
) bacteria resembled the wild type (WT) for some traits and
letS
null mutants for others, whereas they displayed intermediate levels of infectivity, cytotoxicity, and lysosome evasion. Although only 30 to 50% of
letS
(
T311M
) mutants became motile, flow cytometry determined that every cell eventually activated the flagellin promoter to WT levels, but expression was delayed. Likewise,
letS
(
T311M
) mutants exhibited delayed induction of RsmY and RsmZ, regulatory RNAs that relieve CsrA repression of transmission traits. Transcriptional profile analysis revealed that
letS
(
T311M
) mutants expressed the flagellar regulon and multiple other transmissive-phase loci at a higher cell density than the WT. Accordingly, we postulate that the
letS
(
T311M
) mutant may relay phosphate less efficiently than the WT LetS sensor protein, leading to sluggish gene expression and a variety of phenotypic profiles. Thus, as first described for BvgA/BvgS, rather than acting as on/off switches, this family of two-component systems exhibit rheostat activity that likely confers versatility as microbes adapt to fluctuating environments.
Tetratricopeptide Repeat Protein-Associated Proteins Contribute to the Virulence ofPorphyromonas gingivalis
Authors: Kondo Yoshio , Ohara Naoya , Sato Keiko , Yoshimura Mamiko , Yukitake Hideharu , Naito Mariko , Fujiwara Taku , Nakayama Koji 
Published: March 2010

ABSTRACTPorphyromonas gingivalisis one of the most etiologically important microorganisms in periodontal disease. We found in a previous study that PG1385 (TprA) protein, a tetratricopeptide repeat (TPR) protein, was upregulated inP. gingivaliswild-type cells placed in a mouse subcutaneous chamber and that atprAmutant was clearly less virulent in the mouse subcutaneous abscess model (M. Yoshimura et al., Oral Microbiol. Immunol. 23:413-418, 2008). In the present study, we investigated the gene expression profile oftprAmutant cells placed in a mouse subcutaneous chamber and found that 9 genes, including PG2102 (tapA), PG2101 (tapB), and PG2100 (tapC) genes, were downregulated in thetprAmutant compared with those in the wild type. Expression of a cluster oftapA,tapB, andtapCgenes of the mutant was also downregulated in anin vitroculture with enriched brain heart infusion medium. The TprA protein has three TPR motifs known as a protein-protein interaction module. Yeast two-hybrid system analysis andin vitroprotein binding assays with immunoprecipitation and surface plasmon resonance detection revealed that the TprA protein could bind to TapA and TapB proteins. TprA and TapB proteins were located in the periplasmic space, whereas TapA, which appeared to be one of the C-terminal domain family proteins, was located at the outer membrane. We constructedtapA,tapB, andtapCsingle mutants and atapA-tapB-tapCdeletion mutant. In the mouse subcutaneous infection experiment, all of the mutants were less virulent than the wild type. These results suggest that TprA, TapA, TapB, and TapC are cooperatively involved inP. gingivalisvirulence.
Establishment of a Novel Quantitative Hepatitis D Virus (HDV) RNA Assay Using the Cobas TaqMan Platform To Study HDV RNA Kinetics
Authors: Mederacke Ingmar , Bremer Birgit , Heidrich Benjamin , Kirschner Janina , Deterding Katja , Bock Thomas , Wursthorn Karsten , Manns Michael P. , Wedemeyer Heiner 
Published: March 2010

ABSTRACT

Determination of hepatitis D virus (HDV) viremia represents the “gold standard” for the diagnosis of HDV infection. Hepatitis B virus (HBV)-HDV coinfection frequently leads to end-stage liver disease and hepatocellular carcinoma. No commercial assay for HDV RNA quantification that includes automated nucleic acid extraction is available, and in-house PCR tests are not well standardized. However, knowledge of HDV RNA levels may give important information for patient management and could be a useful tool for monitoring the response to antiviral therapies. One platform that is widely used for HBV DNA or HCV RNA quantification is the Cobas Ampliprep/TaqMan system. Using the utility channel of this platform, we established a novel protocol for TaqMan-based HDV RNA quantification after automatic extraction of RNA by the Ampliprep system. The assay was specific and showed linearity over a wide range from 3 × 10
2
to 10
7
copies/ml. Reproducibility was demonstrated by determination of the interrun and intrarun variabilities, which were similar to those achieved with the commercially available Cobas TaqMan assays for HCV RNA and HBV DNA. HDV RNA levels were stable in whole blood (
n
= 4), plasma (
n
= 3), and serum (
n
= 3) samples at room temperature for up to 6 days. Importantly, HDV RNA viremia showed only minor fluctuations, with the log
10
coefficient of variation being between 1.3 and 11.2% for hepatitis delta patients studied every 2 weeks for up to 3 months (
n
= 6), while a rapid viral decline was observed early during treatment with pegylated alfa-2a interferon (
n
= 6). In conclusion, this novel automated HDV RNA assay is a useful tool for monitoring HDV-infected patients both before and during antiviral therapy.
Influence of Media and Testing Methodology on Susceptibility to Tigecycline of
Enterobacteriaceae
with Reported High Tigecycline MIC
Authors: Torrico M. , González N. , Giménez M. J. , Alou L. , Sevillano D. , Navarro D. , Díaz-Antolín M. P. , Larrosa N. , Aguilar L. , Garcia-Escribano N. 
Published: March 2010

ABSTRACT

The tigecycline susceptibility of six different
Enterobacteriaceae
strains with reported high tigecycline MICs was determined in quintuplicate by four methodologies using Mueller-Hinton agar and broth from six manufacturers. The MICs determined by Etest were a ≥1-fold dilution lower than those determined by broth microdilution and agar dilution, with the highest modal values given by agar dilution. The highest modal MICs were obtained using Oxoid medium, and the lowest inhibition zone values (disc diffusion) were obtained using Oxoid and bioMérieux media. The lowest MICs were obtained by Etest using Difco or Merck media.