bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the effects of seasonality and chemical pollution on the hepatopancreas transcriptome of the Manila clam
Authors: Milan Massimo , Ferraresso Serena , Ciofi Claudio , Chelazzi Guido , Carrer Claudio , Ferrari Giorgio , Pavan Lino , Patarnello Tomaso , Bargelloni Luca 
Published: March 2013

AbstractThe assessment of marine environmental health is a complex but fundamental task both for ecosystem conservation and food safety related to the human consumption of marine products. Manila clams inhabiting the Venice Lagoon constitute an excellent case study for evaluating the effects of complex mixtures of industrial and urban effluents on aquatic organisms. Clams were collected in different seasons at four locations within the Venice Lagoon. The sampling sites were characterized by a range of pollutant concentrations and included Porto Marghera, a highly polluted industrial area where clam harvesting for human consumption is strictly forbidden. Pooled soft tissues were subjected to mass spectroscopy analysis to measure the concentrations of PCDDs/PCDFs/PCBs‐DL, PCBs, PBDEs, HCB and PAHs, and pooled digestive gland samples were used for gene expression profiling. While seasonal variation was found to be responsible for the largest proportion of transcriptional changes, significance analysis of microarrays quantitative correlation analysis identified 162 transcripts that were correlated with at least one class of chemicals measured in the samples from the four different sampling sites. Prediction Analysis of Microarrays (PAM) identified a minimal set of seven genes that correctly assigned samples collected in the restricted polluted area (Porto Marghera), independent of the season in which they were collected. An integrated approach combining transcriptomics and chemical analyses of the Manila clam provided a global picture of how Manila clams respond to complex mixtures of xenobiotics and their interplay with other biotic and abiotic factors. We were also able to identify gene expression signatures for different classes of chemicals and a set of robust biomarkers of exposure to these chemicals.
Fuzzy‐Entropy Neural Network Freeway Incident Duration Modeling with Single and Competing Uncertainties
Authors: Vlahogianni Eleni I. , Karlaftis Matthew G. 
Published: March 2013

AbstractAn approach for predicting incident durations that are susceptible to severe congestion, the occurrence of secondary incidents, and their joint effect is proposed. First, a fuzzy entropy feature selection methodology is applied to determine redundant factors and rank factor importance with respect to their contribution on the predictability of incident duration. Second, neural network models for incident duration prediction with single and competing uncertainties are developed. The results indicate that alignment, collision type, and downstream geometry may be considered as redundant when modeling incident duration. Rainfall intensity is a highly contributing feature, while lane volume, number of blocked lanes, as well as number of vehicles involved in the incident are among the top ranking factors for determining the extent of duration. Finally, the joint consideration of severe congestion and secondary incident occurrence may improve the generalization power of the prediction models.
Case–Control Study of Eczema in Relation to IL4Rα Genetic Polymorphisms in Japanese Women: The Kyushu Okinawa Maternal and Child Health Study
Authors: Miyake Y. , Tanaka K. , Arakawa M. 
Published: March 2013

AbstractEpidemiological research on the relationship between single nucleotide polymorphisms (SNPs) in the IL4Rα gene and eczema is sparse. We investigated the associations between IL4Rα SNPs rs1805011, rs1805015 and rs1801275 and risk of eczema in young adult Japanese women. Included were 188 women who met the criteria of the International Study of Asthma and Allergies in Childhood (ISAAC) for eczema. Controls were 635 women without eczema according to the ISAAC criteria who also had not been diagnosed with asthma, atopic eczema and/or allergic rhinitis by a doctor. Adjustment was made for age, region of residence, number of children, smoking and education. Under the additive model, SNP rs1805011 was significantly related to eczema: the adjusted OR was 0.55 (95% CI: 0.31−0.99). SNP rs1805015 was significantly associated with eczema in the additive and dominant models: the adjusted ORs were 0.55 (95% CI: 0.30−0.98) and 0.55 (95% CI: 0.30−0.997), respectively. There was no significant association between SNP rs1801275 and eczema. None of the haplotypes were significantly related to eczema. Significant associations between SNPs rs1805011 and rs1805015 and eczema were reported in women who had never smoked, but not in those who had ever smoked; the multiplicative interactions, however, were not significant. This is the first study to demonstrate significant associations between IL4Rα SNPs rs1805011 and rs1805015 and eczema. We do not find evidence for interactions affecting eczema between IL4Rα SNPs and smoking.
Anomalous far‐field geodetic signature related to the 2009 L'Aquila (central Italy) earthquake
Authors: Atzori Simone , Chiarabba Claudio , Devoti Roberto , Bonano Manuela , Lanari Riccardo 
Published: March 2013

AbstractThe broad availability of geodetic measurements for the Mw 6.3 April 6th 2009 L'Aquila earthquake allowed an unprecedented description of the co‐ and post‐seismic ground deformations, leading to the definition of the Paganica fault geometry and kinematics. Through DInSAR, we found, in a wide area of 20 kilometres on the Paganica hangingwall, a further displacement up to 7 cm, which might have occurred in the earthquake proximity. In this study, we explore the possibility of the co‐, post‐ and pre‐seismic alternative scenarios. Although our data are not sufficient to undoubtedly prove that this signal occurred before the main event, this seems to be the most likely hypothesis based on tectonics constraints and image acquisition times. The nature of this deformation remains unclear, but we speculate that deep fluids played a role. These results can drive ad hoc requirements for future space‐based missions and design of the GPS network.
Transitive RNA silencing signals induce cytosine methylation of a transgenic but not an endogenous target
Authors: Vermeersch Leen , De Winne Nancy , Nolf Jonah , Bleys Annick , Kovařík Aleš , Depicker Ann 
Published: March 2013

SummaryPost‐transcriptional gene silencing of a primary target gene in plants can coincide with the production of secondary small interfering RNAs (siRNAs) of coding sequences adjacent to the target region and with de novo RNA‐directed DNA methylation (RdDM) thereof. Here, we analyzed the susceptibility of transgenic and endogenous targets to RdDM induced by primary and secondary silencing signals. In three different configurations, primary silencing signals were able to direct in trans methylation of chimeric transgenes and the CATALASE2 (CAT2) endogene; however, extensive spreading of methylation occurred only in the transgene, resulting in the methylation of the flanking CAT2 sequence, whereas methylation of the CAT2 endogene was restricted to the target region and the enclosed introns. The secondary silencing signals arising from this transgenic primary target simultaneously silenced a secondary transgene target and the CAT2 endogene, but were only capable of directing RdDM to the transgene. Our data indicate that RdDM is correlated with the in situ generation of secondary siRNAs, occurring in P35S‐driven transgenes but not in most endogenes. We conclude that although both endogenes and transgenes are equally sensitive to transitive silencing, differences exist in their susceptibility to undergo secondary RdDM.
Contribution of sympathetic activation to coronary vasodilatation during the cold pressor test in healthy men: effect of ageing
Authors: Monahan Kevin D. , Feehan Robert P. , Sinoway Lawrence I. , Gao Zhaohui 
Published: March 2013

Key points
The sympathetic nervous system is an important regulator of coronary blood flow.
How ageing may effect sympathetic nervous system regulation of coronary blood flow during physiological stress is unknown.
We measured coronary vascular responses to sympathetic activation before and during systemic α‐ and β‐adrenergic receptor blockade in young and older healthy men.
Our results indicate that the normal coronary vascular response to sympathetic activation in young men is pronounced vasodilatation and that this effect is lost with advancing age, as the result of an apparent adrenergic mechanism.
These findings may help explain how acute sympathetic activation may trigger angina and coronary ischaemic events, particularly in older adults.
Abstract  The sympathetic nervous system is an important regulator of coronary blood flow. The cold pressor test (CPT) is a powerful sympathoexcitatory stressor. We tested the hypotheses that: (1) CPT‐induced sympathetic activation elicits coronary vasodilatation in young adults that is impaired with advancing age and (2) combined α‐ and β‐adrenergic blockade diminishes/abolishes these age‐related differences. Vascular responses of the left anterior descending artery to the CPT were determined by transthoracic Doppler echocardiography before (pre‐blockade) and during (post‐blockade) systemic co‐administration of α‐ and β‐adrenergic antagonists in young (n= 9; 26 ± 1 years old, mean ± SEM) and older healthy men (n= 9; 66 ± 2 years old). Coronary vascular resistance (CVR; mean arterial pressure/coronary blood velocity) was used as an index of vascular tone. CPT decreased CVR (i.e. coronary vasodilatation occurred) in young (Δ–33 ± 6%), but not older men (Δ–3 ± 4%; P < 0.05 vs. young) pre‐blockade. Adrenergic blockade abolished CPT‐induced coronary vasodilatation in young men (Δ–33 ± 6%vs. Δ 0 ± 6%, pre‐blockade vs. post‐blockade, respectively; P < 0.05) such that responses post‐blockade mirrored those of older men (Δ–3 ± 4%vs. Δ 8 ± 9%; both P > 0.05 compared to young pre‐blockade). Impaired CPT‐induced coronary vasodilatation could not be explained by a reduced stimulus for vasodilatation as group and condition effects persisted when CVR responses were expressed relative to myocardial oxygen demand (rate–pressure product). These data indicate that the normal coronary vascular response to sympathetic activation in young men is pronounced vasodilatation and this effect is lost with age as the result of an adrenergic mechanism. These findings may help explain how acute sympathoexcitation may precipitate angina and coronary ischaemic events, particularly in older adults.
Hydrogenosome Metabolism Is the Key Target for Antiparasitic Activity of Resveratrol against Trichomonas vaginalis
Authors: Mallo Natalia , Lamas Jesús , Leiro José M. 
Published: March 2013

ABSTRACTMetronidazole (MDZ) and related 5-nitroimidazoles are the recommended drugs for treatment of trichomoniasis, a sexually transmitted disease caused by the protozoan parasiteTrichomonas vaginalis. However, novel treatment options are needed, as recent reports have claimed resistance to these drugs inT. vaginalisisolates. In this study, we analyzed for the first time thein vitroeffects of the natural polyphenol resveratrol (RESV) onT. vaginalis. At concentrations of between 25 and 100 μM, RESV inhibited thein vitrogrowth ofT. vaginalistrophozoites; doses of 25 μM exerted a cytostatic effect, and higher doses exerted a cytotoxic effect. At these concentrations, RESV caused inhibition of the specific activity of a 120-kDa [Fe]-hydrogenase (Tvhyd). RESV did not affect Tvhyd gene expression and upregulated pyruvate-ferredoxin oxidoreductase (a hydrogenosomal enzyme) gene expression only at a high dose (100 μM). At doses of 50 to 100 μM, RESV also caused overexpression of heat shock protein 70 (Hsp70), a protective protein found in the hydrogenosome ofT. vaginalis. The results demonstrate the potential of RESV as an antiparasitic treatment for trichomoniasis and suggest that the mechanism of action involves induction of hydrogenosomal dysfunction. In view of the results, we propose hydrogenosomal metabolism as a key target in the design of novel antiparasitic drugs.
Effectiveness of Disinfectants Used in Hemodialysis against both Candida orthopsilosis and C. parapsilosis Sensu Stricto Biofilms
Authors: Pires Regina Helena , da Silva Julhiany de Fátima , Gomes Martins Carlos Henrique , Fusco Almeida Ana Marisa , Pienna Soares Christiane , Soares Mendes-Giannini Maria José 
Published: March 2013

ABSTRACT

Biofilms have been observed in the fluid pathways of hemodialysis machines. The impacts of four biocides used for the disinfection of hemodialysis systems were tested against
Candida parapsilosis
sensu stricto and
Candida orthopsilosis
biofilms generated by isolates obtained from a hydraulic circuit that were collected in a hemodialysis unit. Acetic acid was shown to be the most effective agent against
Candida
biofilms. Strategies for effective disinfection procedures used for hemodialysis systems should also seek to kill and inhibit biofilms.
Differential Distribution of Plasmid-Mediated Quinolone Resistance Genes in Clinical Enterobacteria with Unusual Phenotypes of Quinolone Susceptibility from Argentina
Authors: Andres Patricia , Lucero Celeste , Soler-Bistué Alfonso , Guerriero Leonor , Albornoz Ezequiel , Tran Tung , Zorreguieta Angeles , Galas Marcelo , Corso Alejandra , Tolmasky Marcelo E. , Petroni Alejandro 
Published: March 2013

ABSTRACT

We studied a collection of 105 clinical enterobacteria with unusual phenotypes of quinolone susceptibility to analyze the occurrence of plasmid-mediated quinolone resistance (PMQR) and
oqx
genes and their implications for quinolone susceptibility. The
oqxA
and
oqxB
genes were found in 31/34 (91%)
Klebsiella pneumoniae
and 1/3
Klebsiella oxytoca
isolates. However, the
oqxA
- and
oqxB
-harboring isolates lacking other known quinolone resistance determinants showed wide ranges of susceptibility to nalidixic acid and ciprofloxacin. Sixty of the 105 isolates (57%) harbored at least one PMQR gene [
qnrB19
,
qnrB10
,
qnrB2
,
qnrB1
,
qnrS1
, or
aac
(
6
′)
-Ib-cr
)], belong to 8 enterobacterial species, and were disseminated throughout the country, and most of them were categorized as susceptible by the current clinical quinolone susceptibility breakpoints. We developed a disk diffusion-based method to improve the phenotypic detection of
aac
(
6
′)
-Ib-cr
. The most common PMQR genes in our collection [
qnrB19
,
qnrB10
, and
aac
(
6
′)
-Ib-cr
] were differentially distributed among enterobacterial species, and two different epidemiological settings were evident. First, the species associated with community-acquired infections (
Salmonella
spp. and
Escherichia coli
) mainly harbored
qnrB19
(a unique PMQR gene) located in small ColE1-type plasmids that might constitute its natural reservoirs.
qnrB19
was not associated with an extended-spectrum β-lactamase phenotype. Second, the species associated with hospital-acquired infections (
Enterobacter
spp.,
Klebsiella
spp., and
Serratia marcescens
) mainly harbored
qnrB10
in IS
CR1
-containing class 1 integrons that may also have
aac
(
6
′)
-Ib-cr
as a cassette within the variable region. These two PMQR genes were strongly associated with an extended-spectrum β-lactamase phenotype. Therefore, this differential distribution of PMQR genes is strongly influenced by their linkage or lack of linkage to integrons.
Meta-Analysis of Antibiotics and the Risk of Community-Associated Clostridium difficile Infection
Authors: Brown Kevin A. , Khanafer Nagham , Daneman Nick , Fisman David N. 
Published: March 2013

ABSTRACT

The rising incidence of
Clostridium difficile
infection (CDI) could be reduced by lowering exposure to high-risk antibiotics. The objective of this study was to determine the association between antibiotic class and the risk of CDI in the community setting. The EMBASE and PubMed databases were queried without restriction to time period or language. Comparative observational studies and randomized controlled trials (RCTs) considering the impact of exposure to antibiotics on CDI risk among nonhospitalized populations were considered. We estimated pooled odds ratios (OR) for antibiotic classes using random-effect meta-analysis. Our search criteria identified 465 articles, of which 7 met inclusion criteria; all were observational studies. Five studies considered antibiotic risk relative to no antibiotic exposure: clindamycin (OR = 16.80; 95% confidence interval [95% CI], 7.48 to 37.76), fluoroquinolones (OR = 5.50; 95% CI, 4.26 to 7.11), and cephalosporins, monobactams, and carbapenems (CMCs) (OR = 5.68; 95% CI, 2.12 to 15.23) had the largest effects, while macrolides (OR = 2.65; 95% CI, 1.92 to 3.64), sulfonamides and trimethoprim (OR = 1.81; 95% CI, 1.34 to 2.43), and penicillins (OR = 2.71; 95% CI, 1.75 to 4.21) had lower associations with CDI. We noted no effect of tetracyclines on CDI risk (OR = 0.92; 95% CI, 0.61 to 1.40). In the community setting, there is substantial variation in the risk of CDI associated with different antimicrobial classes. Avoidance of high-risk antibiotics (such as clindamycin, CMCs, and fluoroquinolones) in favor of lower-risk antibiotics (such as penicillins, macrolides, and tetracyclines) may help reduce the incidence of CDI.
Treatment of Refractory Mycobacterium avium Complex Lung Disease with a Moxifloxacin-Containing Regimen
Authors: Koh Won-Jung , Hong Goohyeon , Kim Su-Young , Jeong Byeong-Ho , Park Hye Yun , Jeon Kyeongman , Kwon O Jung , Lee Seung-Heon , Kim Chang Ki , Shin Sung Jae 
Published: March 2013

ABSTRACT

Moxifloxacin (MXF) has
in vitro
and
in vivo
activity against
Mycobacterium avium
complex (MAC) in experimental models. However, no data are available concerning its treatment effect in patients with MAC lung disease. The aim of this study was to evaluate the clinical efficacy of an MXF-containing regimen for the treatment of refractory MAC lung disease. Patients with MAC lung disease who were diagnosed between January 2002 and December 2011 were identified from our hospital database. We identified 41 patients who received MXF for ≥4 weeks for the treatment of refractory MAC lung disease. A total of 41 patients were treated with an MXF-containing regimen because of a persistent positive culture after at least 6 months of clarithromycin-based standardized antibiotic therapy. The median duration of antibiotic therapy before MXF administration was 410 days (interquartile range [IQR], 324 to 683 days). All patients had culture-positive sputum when MXF treatment was initiated. The median duration of MXF administration was 332 days (IQR, 146 to 547 days). The overall treatment success rate was 29% (12/41), and the median time to sputum conversion was 91 days (IQR, 45 to 190 days). A positive sputum acid-fast-bacillus smear at the start of treatment with MXF-containing regimens was an independent predictor of an unfavorable microbiological response. Our results indicate that MXF may improve treatment outcomes in about one-third of patients with persistently culture-positive MAC lung disease who fail to respond to clarithromycin-based standardized antibiotic treatment. Prospective studies are required to assess the clinical efficacy of MXF treatment for refractory MAC lung disease.
Granule Exocytosis of Granulysin and Granzyme B as a Potential Key Mechanism in Vaccine-Induced Immunity in Cattle against the Nematode Ostertagia ostertagi
Authors: Van Meulder Frederik , Van Coppernolle Stefanie , Borloo Jimmy , Rinaldi Manuela , Li Robert W. , Chiers Koen , Van den Broeck Wim , Vercruysse Jozef , Claerebout Edwin , Geldhof Peter 
Published: March 2013

ABSTRACTOstertagia ostertagiis considered one of the most economically important bovine parasites. As an alternative to anthelmintic treatment, an experimental host-protective vaccine was previously developed on the basis of ASP proteins derived from adult worms. Intramuscular injection of this vaccine, combined with QuilA as an adjuvant, significantly reduced fecal egg counts by 59%. However, the immunological mechanisms triggered by the vaccine are still unclear. Therefore, in this study, the differences in immune responses at the site of infection, i.e., the abomasal mucosa, between ASP-QuilA-vaccinated animals and QuilA-vaccinated control animals were investigated on a transcriptomic level by using a whole-genome bovine microarray combined with histological analysis. Sixty-nine genes were significantly impacted in animals protected by the vaccine, 48 of which were upregulated. A correlation study between the parasitological parameters and gene transcription levels showed that the transcription levels of two of the upregulated genes, those for granulysin (GNLY) and granzyme B (GZMB), were negatively correlated with cumulative fecal egg counts and total worm counts, respectively. Both genes were also positively correlated with each other and with another upregulated gene, that for the IgE receptor subunit (FCER1A). Surprisingly, these three genes were also correlated significantly withCMA1, which encodes a mast cell marker, and with counts of mast cells and cells previously described as globule leukocytes. Furthermore, immunohistochemical data showed thatGNLYwas present in the granules of globule leukocytes and that it was secreted in mucus. Overall, the results suggest a potential role for granule exocytosis by globule leukocytes, potentially IgE mediated, in vaccine-induced protection againstO. ostertagi.
Neutrophils Mediate Immunopathology and Negatively Regulate Protective Immune Responses during Fatal Bacterial Infection-Induced Toxic Shock
Authors: Yang Qin , Ghose Purnima , Ismail Nahed 
Published: March 2013

ABSTRACTEhrlichia chaffeensisis an obligate intracellular bacterium that infects primarily monocytes and macrophages and causes potentially fatal human monocytic ehrlichiosis (HME) that mimics toxic-shock-like syndrome in immunocompetent hosts. Early recruitment of neutrophils to the sites of infection is critical for the control of bacterial infection and inflammatory responses. We recently observed rapid and sustained neutrophil recruitment at a primary site of infection (peritoneum) following lethal murine ehrlichial infection compared to innocuous ehrlichial infection. We examined here the contribution of neutrophils to protective immunity or immunopathology during infection with monocyticEhrlichia. Unexpectedly, depletion of neutrophils from lethally infected mice enhanced bacterial elimination, decreased immune-mediated pathology, and prolonged survival. Furthermore, compared to lethally infected sham controls, neutrophil depletion in infected mice resulted in amelioration of pathogenic responses, as evidenced by a decreased number of tumor necrosis factor alpha (TNF-α)-producing CD8+T cells, which is known to mediate immunopathology and toxic shock in a murine model of fatal ehrlichiosis. Although neutrophil depletion did not influence the number of CD4+Th1 cells and NKT cells producing gamma interferon (IFN-γ), it increased the ratio of IFN-γ- to IL-10-producing NKT cells as well as the ratio of IFN-γ to interleukin 10 (IL-10) transcripts in the liver. This may ameliorate the net suppressive effect of IL-10 on IFN-γ-mediated activation of infected macrophages and thus may account for the enhanced bacterial elimination. Finally, transcriptional analysis of gene expression in the liver indicated that neutrophils contribute to overproduction of cytokines and chemokines during fatal ehrlichiosis. In conclusion, these results revealed an unexpected role of neutrophils in supporting bacterial replication indirectly and promoting immunopathology during severe infection with an intracellular bacterium.