bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response
Authors: Gao Yu , Flori Laurence , Lecardonnel Jérome , Esquerré Diane , Hu Zhi-Liang , Teillaud Angélique , Lemonnier Gaëtan , Lefèvre Francois , Oswald Isabelle P , Rogel-Gaillard Claire 
Published: June 2010

AbstractBackgroundDesigning sustainable animal production systems that better balance productivity and resistance to disease is a major concern. In order to address questions related to immunity and resistance to disease in pig, it is necessary to increase knowledge on its immune system and to produce efficient tools dedicated to this species.ResultsA long-oligonucleotide-based chip referred to as SLA-RI/NRSP8-13K was produced by combining a generic set with a newly designed SLA-RI set that targets all annotated loci of the pig major histocompatibility complex (MHC) region (SLA complex) in both orientations as well as immunity genes outside the SLA complex.The chip was used to study the immune response of pigs following stimulation of porcine peripheral blood mononuclear cells (PBMCs) with lipopolysaccharide (LPS) or a mixture of phorbol myristate acetate (PMA) and ionomycin for 24 hours. Transcriptome analysis revealed that ten times more genes were differentially expressed after PMA/ionomycin stimulation than after LPS stimulation. LPS stimulation induced a general inflammation response with over-expression of SAA1, pro-inflammatory chemokines IL8, CCL2, CXCL5, CXCL3, CXCL2 and CCL8 as well as genes related to oxidative processes (SOD2) and calcium pathways (S100A9 and S100A12). PMA/ionomycin stimulation induced a stronger up-regulation of T cell activation than of B cell activation with dominance toward a Th1 response, including IL2, CD69 and TNFRSF9 (tumor necrosis factor receptor superfamily, member 9) genes. In addition, a very intense repression of THBS1 (thrombospondin 1) was observed. Repression of MHC class I genes was observed after PMA/ionomycin stimulation despite an up-regulation of the gene cascade involved in peptide processing. Repression of MHC class II genes was observed after both stimulations. Our results provide preliminary data suggesting that antisense transcripts mapping to the SLA complex may have a role during immune response.ConclusionThe SLA-RI/NRSP8-13K chip was found to accurately decipher two distinct immune response activations of PBMCs indicating that it constitutes a valuable tool to further study immunity and resistance to disease in pig. The transcriptome analysis revealed specific and common features of the immune responses depending on the stimulation agent that increase knowledge on pig immunity.
Omega-3 fatty acids in high-risk cardiovascular patients: a meta-analysis of randomized controlled trials
Authors: Filion Kristian B , El Khoury Fouad , Bielinski Michael , Schiller Ian , Dendukuri Nandini , Brophy James M 
Published: June 2010

AbstractBackgroundMultiple randomized controlled trials (RCTs) have examined the cardiovascular effects of omega-3 fatty acids and have provided unexplained conflicting results. A meta-analysis of these RCTs to estimate efficacy and safety and potential sources of heterogeneity may be helpful.MethodsThe Cochrane library, MEDLINE, and EMBASE were systematically searched to identify all interventional trials of omega-3 fatty acids compared to placebo or usual diet in high-risk cardiovascular patients. The primary outcome was all-cause mortality and secondary outcomes were coronary restenosis following percutaneous coronary intervention and safety. Meta-analyses were carried out using Bayesian random-effects models, and heterogeneity was examined using meta-regression.ResultsA total of 29 RCTs (n = 35,144) met our inclusion criteria, with 25 reporting mortality and 14 reporting restenosis. Omega-3 fatty acids were not associated with a statistically significant decreased mortality (relative risk [RR] = 0.88, 95% Credible Interval [CrI] = 0.64, 1.03) or with restenosis prevention (RR = 0.89, 95% CrI = 0.72, 1.06), though the probability of some benefit remains high (0.93 and 0.90, respectively). However in meta-regressions, there was a >90% probability that larger studies and those with longer follow-up were associated with smaller benefits. No serious safety issues were identified.ConclusionsAlthough not reaching conventional statistical significance, the evidence to date suggests that omega-3 fatty acids may result in a modest reduction in mortality and restenosis. However, caution must be exercised in interpreting these benefits as results were attenuated in higher quality studies, suggesting that bias may be at least partially responsible. Additional high quality studies are required to clarify the role of omega-3 fatty acid supplementation for the secondary prevention of cardiovascular disease.
Validation of the GenoType®MTBDRplus assay for diagnosis of multidrug resistant tuberculosis in South Vietnam
Authors: Huyen Mai NT , Tiemersma Edine W , Lan Nguyen TN , Cobelens Frank GJ , Dung Nguyen H , Sy Dinh N , Buu Tran N , Kremer Kristin , Hang Pham T , Caws Maxine , O'Brien Richard , van Soolingen Dick 
Published: June 2010

Abstract

Background
To control multidrug resistant tuberculosis (MDR-TB), the drug susceptibility profile is needed to guide therapy. Classical drug susceptibility testing (DST) may take up to 2 to 4 months. The GenoType® MTBDRplus test is a commercially available line-probe assay that rapidly detects Mycobacterium tuberculosis (MTB) complex, as well as the most common mutations associated with rifampin and isoniazid resistance.
We assessed sensitivity and specificity of the assay by using a geographically representative set of MTB isolates from the South of Vietnam.

Methods
We re-cultured 111 MTB isolates that were MDR, rifampin-resistant or pan-susceptible according to conventional DST and tested these with the GenoType® MTBDRplus test.

Results
By conventional DST, 55 strains were classified as MDR-TB, four strains were rifampicin mono-resistant and 52 strains were susceptible to all first-line drugs. The sensitivity of the GenoType® MTBDRplus was 93.1% for rifampicin, 92.6% for isoniazid and 88.9% for the combination of both; its specificity was 100%. The positive predictive value of the GenoType® MTBDRplus test for MDR-TB was 100% and the negative predictive value 90.3%.

Conclusions
We found a high specificity and positive predictive value of the GenoType® MTBDRplus test for MDR-TB which merits its use in the MDR-TB treatment program in Vietnam.
Evaluation of 6 candidate genes on chromosome 11q23 for coeliac disease susceptibility: a case control study
Authors: Brophy Karen , Ryan Anthony W , Turner Graham , Trimble Valerie , Patel Kunal D , O'Morain Colm , Kennedy Nicholas P , Egan Brian , Close Eimear , Lawlor Garrett , MacMathuna Padraic , Stevens Fiona M , Abuzakouk Mohamed , Feighery Conleth , Kelleher Dermot , McManus Ross 
Published: June 2010

Abstract

Background
Recent whole genome analysis and follow-up studies have identified many new risk variants for coeliac disease (CD, gluten intolerance). The majority of newly associated regions encode candidate genes with a clear functional role in T-cell regulation. Furthermore, the newly discovered risk loci, together with the well established HLA locus, account for less than 50% of the heritability of CD, suggesting that numerous additional loci remain undiscovered. Linkage studies have identified some well-replicated risk regions, most notably chromosome 5q31 and 11q23.

Methods
We have evaluated six candidate genes in one of these regions (11q23), namely CD3E, CD3D, CD3G, IL10RA, THY1 and IL18, as risk factors for CD using a 2-phase candidate gene approach directed at chromosome 11q. 377 CD cases and 349 ethnically matched controls were used in the initial screening, followed by an extended sample of 171 additional coeliac cases and 536 additional controls.

Results
Promotor SNPs (-607, -137) in the IL18 gene, which has shown association with several autoimmune diseases, initially suggested association with CD (P < 0.05). Follow-up analyses of an extended sample supported the same, moderate effect (P < 0.05) for one of these. Haplotype analysis of IL18-137/-607 also supported this effect, primarily due to one relatively rare haplotype IL18-607C/-137C (P < 0.0001), which was independently associated in two case-control comparisons. This same haplotype has been noted in rheumatoid arthritis.

Conclusion
Haplotypes of the IL18 promotor region may contribute to CD risk, consistent with this cytokine's role in maintaining inflammation in active CD.
Low level exposure to cadmium increases the risk of chronic kidney disease: analysis of the NHANES 1999-2006
Authors: Ferraro Pietro Manuel , Costanzi Stefano , Naticchia Alessandro , Sturniolo Antonio , Gambaro Giovanni 
Published: June 2010

Abstract

Background
Environmental factors have been associated with the outbreak of chronic kidney disease (CKD). We evaluated the association of Cadmium (Cd) exposure with the risk of CKD in U.S. adults who participated in the 1999-2006 National Health and Nutrition Examination Surveys (NHANES).

Methods
5426 subjects ≥ 20 years were stratified for values of urinary and blood Cd and a multivariate logistic regression was performed to test the association between blood and urinary Cd, CKD and albuminuria (ALB) after adjustment for age, gender, race/ethnicity, body mass index and smoking habits.

Results
Subjects with urinary Cd > 1 mcg/g and subjects with blood Cd > 1 mcg/L showed a higher association with ALB (OR 1.63, 95% CI 1.23, 2.16; P = 0.001). Subjects with blood Cd > 1 mcg/L showed a higher association with both CKD (OR 1.48, 95% CI 1.01, 2.17; P = 0.046) and ALB (OR 1.41, 95% CI 1.10, 1.82; P = 0.007). An interaction effect on ALB was found for high levels of urinary and blood Cd (P = 0.014).

Conclusions
Moderately high levels of urinary and blood Cd are associated with a higher proportion of CKD and ALB in the United States population.
Stable expression and phenotypic impact of attacin Etransgene in orchard grown apple trees over a 12 year period
Authors: Borejsza-Wysocka Ewa , Norelli John L , Aldwinckle Herb S , Malnoy Mickael 
Published: June 2010

Abstract

Background
Transgenic trees currently are being produced by Agrobacterium-mediated transformation and biolistics. The future use of transformed trees on a commercial basis depends upon thorough evaluation of the potential environmental and public health risk of the modified plants, transgene stability over a prolonged period of time and the effect of the gene on tree and fruit characteristics. We studied the stability of expression and the effect on resistance to the fire blight disease of the lytic protein gene, attacin E, in the apple cultivar 'Galaxy' grown in the field for 12 years.

Results
Using Southern and western blot analysis, we compared transgene copy number and observed stability of expression of this gene in the leaves and fruit in several transformed lines during a 12 year period. No silenced transgenic plant was detected. Also the expression of this gene resulted in an increase in resistance to fire blight throughout 12 years of orchard trial and did not affect fruit shape, size, acidity, firmness, weight or sugar level, tree morphology, leaf shape or flower morphology or color compared to the control.

Conclusion
Overall, these results suggest that transgene expression in perennial species, such as fruit trees, remains stable in time and space, over extended periods and in different organs. This report shows that it is possible to improve a desirable trait in apple, such as the resistance to a pathogen, through genetic engineering, without adverse alteration of fruit characteristics and tree shape.
An experimental and numerical study of the flow and mass transfer in a model of the wearable artificial kidney dialyzer
Authors: Rambod Edmond , Beizai Masoud , Rosenfeld Moshe 
Published: June 2010

Abstract

Background
Published studies of the past decades have established that mass transfer across the dialyzer membrane is governed by diffusion, convection and osmosis. While the former is independent of the pressure in the liquids, the latter two are pressure dependent and are enhanced when the pressure difference across the membrane is increased. The goal of the present study is to examine the impact of pulsatile flow on the transport phenomena across the membrane of a high-flux dialyzer in a wearable artificial kidney (WAK) with a novel single small battery-operated pulsatile pump that drives both the blood and dialysate in a counter-phased manner, maximizing the trans-membrane pressure.

Methods
Both in-vitro experimental and numerical tools are employed to compare the performance of the pulsatile WAK dialyzer with a traditional design of a single-channel roller blood pump together with a centrifugal pump that drives the dialysate flow. The numerical methods utilize the axisymmetric Navier-Stokes and mass transfer equations to model the flow in the fibers of the dialyzer.

Results
While diffusion is still the dominating transport regime, the WAK pump enhances substantially the trans-membrane pressure and thus increases mass convection that might be as high as 30% of the overall transfer. This increase is obtained due to the design of the pulsatile WAK pump that increases ultrafiltration by increasing the trans-membrane pressure.

Conclusions
The experimental and numerical results revealed that when pumping at similar flow rates, a small battery-operated pulsatile pump provides clearances of urea and creatinine similar as or better than a large heavy AC-powered roller pump.
A generalized physiologically-based toxicokinetic modeling system for chemical mixtures containing metals
Authors: Sasso Alan F , Isukapalli Sastry S , Georgopoulos Panos G 
Published: June 2010

Abstract

Background
Humans are routinely and concurrently exposed to multiple toxic chemicals, including various metals and organics, often at levels that can cause adverse and potentially synergistic effects. However, toxicokinetic modeling studies of exposures to these chemicals are typically performed on a single chemical basis. Furthermore, the attributes of available models for individual chemicals are commonly estimated specifically for the compound studied. As a result, the available models usually have parameters and even structures that are not consistent or compatible across the range of chemicals of concern. This fact precludes the systematic consideration of synergistic effects, and may also lead to inconsistencies in calculations of co-occurring exposures and corresponding risks. There is a need, therefore, for a consistent modeling framework that would allow the systematic study of cumulative risks from complex mixtures of contaminants.

Methods
A Generalized Toxicokinetic Modeling system for Mixtures (GTMM) was developed and evaluated with case studies. The GTMM is physiologically-based and uses a consistent, chemical-independent physiological description for integrating widely varying toxicokinetic models. It is modular and can be directly "mapped" to individual toxicokinetic models, while maintaining physiological consistency across different chemicals. Interaction effects of complex mixtures can be directly incorporated into the GTMM.

Conclusions
The application of GTMM to different individual metals and metal compounds showed that it explains available observational data as well as replicates the results from models that have been optimized for individual chemicals. The GTMM also made it feasible to model toxicokinetics of complex, interacting mixtures of multiple metals and nonmetals in humans, based on available literature information. The GTMM provides a central component in the development of a "source-to-dose-to-effect" framework for modeling population health risks from environmental contaminants. As new data become available on interactions of multiple chemicals, the GTMM can be iteratively parameterized to improve mechanistic understanding of human health risks from exposures to complex mixtures of chemicals.
Use of monoclonal antibodies against Hendra and Nipah viruses in an antigen capture ELISA
Authors: Chiang Cheng-Feng , Lo Michael K , Rota Paul A , Spiropoulou Christina F , Rollin Pierre E 
Published: June 2010

AbstractBackgroundOutbreaks of Hendra (HeV) and Nipah (NiV) viruses have been reported starting in 1994 and 1998, respectively. Both viruses are capable of causing fatal disease in humans and effecting great economical loss in the livestock industry.ResultsThrough screening of hybridomas derived from mice immunized with γ-irradiated Nipah virus, we identified two secreted antibodies; one reactive with the nucleocapsid (N) protein and the other, the phosphoprotein (P) of henipaviruses. Epitope mapping and protein sequence alignments between NiV and HeV suggest the last 14 amino acids of the carboxyl terminus of the N protein is the target of the anti-N antibody. The anti-P antibody recognizes an epitope in the amino-terminal half of P protein. These monoclonal antibodies were used to develop two antigen capture ELISAs, one for virus detection and the other for differentiation between NiV and HeV. The lower limit of detection of the capture assay with both monoclonal antibodies was 400 pfu. The anti-N antibody was used to successfully detect NiV in a lung tissue suspension from an infected pig.ConclusionThe antigen capture ELISA developed is potentially affordable tool to provide rapid detection and differentiation between the henipaviruses.
A Novel Alternatively Spliced Isoform of the Mu-Opioid Receptor: Functional Antagonism
Authors: Gris Pavel , Gauthier Josee , Cheng Philip , Gibson Dustin G , Gris Denis , Laur Oskar , Pierson John , Wentworth Sean , Nackley Andrea G , Maixner William , Diatchenko Luda 
Published: June 2010

Background:Opioids are the most widely used analgesics for the treatment of clinical pain. They produce their therapeutic effects by binding to μ-opioid receptors (MORs), which are 7 transmembrane domain (7TM) G-protein-coupled receptors (GPCRs), and inhibiting cellular activity. However, the analgesic efficacy of opioids is compromised by side-effects such as analgesic tolerance, dependence and opioid-induced hyperalgesia (OIH). In contrast to opioid analgesia these side effects are associated with cellular excitation. Several hypotheses have been advanced to explain these phenomena, yet the molecular mechanisms underlying tolerance and OIH remain poorly understood.Results:We recently discovered a new human alternatively spliced isoform of MOR (MOR1K) that is missing the N-terminal extracellular and first transmembrane domains, resulting in a 6TM GPCR variant. To characterize the pattern of cellular transduction pathways activated by this human MOR1K isoform, we conducted a series of pharmacological and molecular experiments. Results show that stimulation of MOR1K with morphine leads to excitatory cellular effects. In contrast to stimulation of MOR1, stimulation of MOR1K leads to increased Ca2+levels as well as increased nitric oxide (NO) release. Immunoprecipitation experiments further reveal that unlike MOR1, which couples to the inhibitory Gαi/ocomplex, MOR1 K couples to the stimulatory Gαscomplex.Conclusion:The major MOR1 and the alternative MOR1K isoforms mediate opposite cellular effects in response to morphine, with MOR1K driving excitatory processes. These findings warrant further investigations that examine animal and human MORK1 expression and function following chronic exposure to opioids, which may identify MOR1K as a novel target for the development of new clinically effective classes of opioids that have high analgesic efficacy with diminished ability to produce tolerance, OIH, and other unwanted side-effects.
In search of traditional bio-ecological knowledge useful for fisheries co-management: the case of jaraquis Semaprochilodus spp. (Characiformes, Prochilodontidae) in Central Amazon, Brazil
Authors: Batista Vandick S , Lima Liane G 
Published: June 2010

AbstractThe jaraquis (Semaprochilodus spp.) are the most abundant group in the fishing landing in Manaus. However, just command and control management strategies have been used by the fishery governmental agency in the region without the power to enforce centralized decisions. The fishermen and their culture represent a source of information on dynamics of the resources and aquatic environments, fundamental in making possible the co-management of the fishing resources. The present study aims to contribute to management through identification of common information available in scientific and traditional knowledge about the jaraquis' bio-ecology. There were 57 semi-structured interviews recorded with fishermen of Manaus and rural areas of Manacapuru in 2002 concerning biological and ecological aspects. Similarity was observed between scientific and traditional knowledge in the following items: size of first sexual maturation, spawning type, parental care, trophic relationships and migratory behavior, as well as in some aspects of the mortality and growth of the species. However, there was less ethnoicthyological information on fecundity and the determination of the age and growth of adult fish. Common information would be used preferably by agencies to start an effective and technical dialogue with commercial and riverine fishermen to design management plans in a decentralized strategy.
Ordered structure of the transcription network inherited from the yeast whole-genome duplication
Authors: Fusco Diana , Grassi Luigi , Bassetti Bruno , Caselle Michele , Cosentino Lagomarsino Marco 
Published: June 2010

Abstract

Background
Gene duplication, a major evolutionary path to genomic innovation, can occur at the scale of an entire genome. One such "whole-genome duplication" (WGD) event among the Ascomycota fungi gave rise to genes with distinct biological properties compared to small-scale duplications.

Results
We studied the evolution of transcriptional interactions of whole-genome duplicates, to understand how they are wired into the yeast regulatory system. Our work combines network analysis and modeling of the large-scale structure of the interactions stemming from the WGD.

Conclusions
The results uncover the WGD as a major source for the evolution of a complex interconnected block of transcriptional pathways. The inheritance of interactions among WGD duplicates follows elementary "duplication subgraphs", relating ancestral interactions with newly formed ones. Duplication subgraphs are correlated with their neighbours and give rise to higher order circuits with two elementary properties: newly formed transcriptional pathways remain connected (paths are not broken), and are preferentially cross-connected with ancestral ones. The result is a coherent and connected "WGD-network", where duplication subgraphs are arranged in an astonishingly ordered configuration.