bluuebunny/crossref_metadata_2025_split huggingface dataset:
The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene
Authors: Silva-Rocha Rafael , de Jong Hidde , Tamames Javier , de Lorenzo Víctor 
Published: November 2011

Abstract

Background
The genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants. Although nearly every metabolic and transcriptional component of this regulatory system is known to an extraordinary molecular detail, the complexity of its architecture is still perplexing. To gain an insight into the inner layout of this network a logic model of the TOL system was implemented, simulated and experimentally validated. This analysis made sense of the specific regulatory topology out on the basis of an unprecedented network motif around which the entire genetic circuit for m-xylene catabolism gravitates.

Results
The most salient feature of the whole TOL regulatory network is the control exerted by two distinct but still intertwined regulators (XylR and XylS) on expression of two separated catabolic operons (upper and lower) for catabolism of m-xylene. Following model reduction, a minimal modular circuit composed by five basic variables appeared to suffice for fully describing the operation of the entire system. In silico simulation of the effect of various perturbations were compared with experimental data in which specific portions of the network were activated with selected inducers: m-xylene, o-xylene, 3-methylbenzylalcohol and 3-methylbenzoate. The results accredited the ability of the model to faithfully describe network dynamics. This analysis revealed that the entire regulatory structure of the TOL system enables the action an unprecedented metabolic amplifier motif (MAM). This motif synchronizes expression of the upper and lower portions of a very long metabolic system when cells face the head pathway substrate, m-xylene.

Conclusion
Logic modeling of the TOL circuit accounted for the intricate regulatory topology of this otherwise simple metabolic device. The found MAM appears to ensure a simultaneous expression of the upper and lower segments of the m-xylene catabolic route that would be difficult to bring about with a standard substrate-responsive single promoter. Furthermore, it is plausible that the MAM helps to avoid biochemical conflicts between competing plasmid-encoded and chromosomally-encoded pathways in this bacterium.
A new baseline for fascioliasis in Venezuela: lymnaeid vectors ascertained by DNA sequencing and analysis of their relationships with human and animal infection
Authors: Bargues M Dolores , González L Carolina , Artigas Patricio , Mas-Coma Santiago 
Published: November 2011

AbstractBackgroundHuman and animal fascioliasis poses serious public health problems in South America. In Venezuela, livestock infection represents an important veterinary problem whereas there appear to be few human cases reported, most of which are passively detected in health centres. However, results of recent surveys suggest that the situation may be underestimated in particular areas. To obtain a baseline for future fascioliasis assessment, studies were undertaken by means of rDNA ITS-2 and ITS-1 and mtDNAcox1 sequencing to clarify the specific status of Venezuelan lymnaeids, their geographical distribution and fascioliasis transmission capacity, by comparison with other American countries and other continents.ResultsResults obtained completely change the lymnaeid scenario known so far. The relatively rich lymnaeid fauna of Venezuela has been proven to include (i)Lymnaea meridensisandL. neotropicaas the only native members, (ii)L. cubensisandPseudosuccinea columellaintroduced from the Caribbean area, and (iii)Galba truncatulaandL. schirazensisintroduced from the Old World. The absence of representatives of the stagnicoline andRadixgroups is remarkable. Four species are fascioliasis vectors:G. truncatula,L. cubensisandL. neotropica, which have the capacity to give rise to human endemic areas, andP. columella, which is a source of animal infection and is responsible for the spread of disease. Vector capacity in the apparently highland endemicL. meridensisis to be confimed, although may be expected given its phylogenetic relationships. Similarly as elsewhere, the non-transmittingL. schirazensishas been confused withL. cubensis, also withG. truncatulaand possibly withL. neotropica.ConclusionsThe new scenario leads to the re-opening of many disease aspects. In Venezuela, altitude appears to be the main factor influencing fascioliasis distribution. Human infection shows an altitude pattern similar to other Andean countries, although a differing highland/lowland impact on animal infection does not appear evident. The overlap ofG. truncatula,L. cubensisand probably alsoL. neotropicain temperate and cold zones suggests a higher risk for human infection in mid and high altitude areas. A lymnaeid species mapping by means of DNA markers becomes a priority to determine human and animal fascioliasis distribution in Venezuela, owing to the importance of lymnaeid vectors in defining transmission and epidemiological patterns.
Risk of allergic reactions to wine, in milk, egg and fish‐allergic patients
Authors: Vassilopoulou Emilia , Karathanos Athanassios , Siragakis George , Giavi Stavroula , Sinaniotis Athanassios , Douladiris Nikolaos , Fernandez‐Rivas Montserrat , Clausen Michael , Papadopoulos Nikolaos G 
Published: November 2011

AbstractBackgroundEuropean legislators and wine producers still debate on the requirement for labeling of wines fined with potentially allergenic food proteins (casein, egg white or fish‐derived isinglass). We investigated whether wines fined with known concentrations of these proteins have the potential to provoke clinical allergic reactions in relevant patients.MethodsIn‐house wines were produced for the study, fined with different concentrations of casein (n = 7), egg albumin (n = 1) and isinglass (n = 3). ELISA and PCR kits specific for the respective proteins were used to identify the fining agents. Skin prick tests and basophil activation tests were performed in patients with confirmed IgE‐mediated relevant food allergies (n = 24). A wine consumption questionnaire and detailed history on possible reactions to wine was obtained in a multinational cohort of milk, egg or fish allergic patients (n = 53) and patients allergic to irrelevant foods as controls (n = 13).ResultsFining agents were not detectable in wines with the available laboratory methods. Nevertheless, positive skin prick test reactions and basophil activation to the relevant wines were observed in the majority of patients with allergy to milk, egg or fish, correlating with the concentration of the fining agent. Among patients consuming wine, reported reactions were few and mild and similar with the ones reported from the control group.ConclusionCasein, isinglass or egg, remaining in traces in wine after fining, present a very low risk for the respective food allergic consumers. Physician and patient awareness campaigns may be more suitable than generalized labeling to address this issue, as the latter may have negative impact on both non‐allergic and allergic consumers.
Postextubation dysphagia is persistent and associated with poor outcomes in survivors of critical illness
Authors: Macht Madison , Wimbish Tim , Clark Brendan J , Benson Alexander B , Burnham Ellen L , Williams André , Moss Marc 
Published: November 2011

Abstract
Introduction
Dysphagia is common among survivors of critical illness who required mechanical ventilation during treatment. The risk factors associated with the development of postextubation dysphagia, and the effects of dysphagia on patient outcomes, have been relatively unexplored.

Methods
We conducted a retrospective, observational cohort study from 2008 to 2010 of all patients over 17 years of age admitted to a university hospital ICU who required mechanical ventilation and subsequently received a bedside swallow evaluation (BSE) by a speech pathologist.

Results
A BSE was performed after mechanical ventilation in 25% (630 of 2,484) of all patients. After we excluded patients with stroke and/or neuromuscular disease, our study sample size was 446 patients. We found that dysphagia was present in 84% of patients (n = 374) and classified dysphagia as absent, mild, moderate or severe in 16% (n = 72), 44% (n = 195), 23% (n = 103) and 17% (n = 76), respectively. In univariate analyses, we found that statistically significant risk factors for severe dysphagia included long duration of mechanical ventilation and reintubation. In multivariate analysis, after adjusting for age, gender and severity of illness, we found that mechanical ventilation for more than seven days remained independently associated with moderate or severe dysphagia (adjusted odds ratio (AOR) = 2.84 [interquartile range (IQR) = 1.78 to 4.56]; P < 0.01). The presence of severe postextubation dysphagia was significantly associated with poor patient outcomes, including pneumonia, reintubation, in-hospital mortality, hospital length of stay, discharge status and surgical placement of feeding tubes. In multivariate analysis, we found that the presence of moderate or severe dysphagia was independently associated with the composite outcome of pneumonia, reintubation and death (AOR = 3.31 [IQR = 1.89 to 5.90]; P < 0.01).

Conclusions
In a large cohort of critically ill patients, long duration of mechanical ventilation was independently associated with postextubation dysphagia, and the development of postextubation dysphagia was independently associated with poor patient outcomes.
Strain-dependent induction of neutrophil histamine production and cell death byPseudomonas aeruginosa
Authors: Xu Xiang , Zhang Hong , Song Yuanlin , Lynch Susan V , Lowell Clifford A , Wiener-Kronish Jeanine P , Caughey George H 
Published: November 2011

ABSTRACTAirway diseases often feature persistent neutrophilic inflammation and infection. In cystic fibrosis bronchitis, for example, Pseudomonas aeruginosa is isolated frequently. Previously, this laboratory revealed that neutrophils become major sources of histamine in mice with tracheobronchitis caused by the wall-less bacterium Mycoplasma pulmonis. To test the hypothesis that more-broadly pathogenic P. aeruginosa (which expresses cell wall-associated LPS and novel toxins) has similar effects, we incubated naïve mouse neutrophils with two strains of P. aeruginosa. Strain PAO1 greatly increased neutrophil histamine content and secretion, whereas strain PA103 depressed histamine production by killing neutrophils. The histamine-stimulating capacity of PAO1, but not PA103-mediated toxicity, persisted in heat-killed organisms. In PAO1-infected mice, lung and neutrophil histamine content increased. However, PAO1 did not alter production by mast cells (classical histamine reservoirs), which also resisted PA103 toxicity. To explore mechanisms of neutrophil-selective induction, we measured changes in mRNA encoding histidine decarboxylase (rate-limiting for histamine synthesis), probed involvement of endotoxin-TLR pathways in Myd88-deficient neutrophils, and examined contributions of pyocyanin and exotoxins. Results revealed that PAO1 increased histamine production by up-regulating histidine decarboxylase mRNA via pathways largely independent of TLR, pyocyanin, and type III secretion system exotoxins. PAO1 also increased histidine decarboxylase mRNA in neutrophils purified from infected lung. Stimulation required direct contact with neutrophils and was blocked by phagocytosis inhibitor cytochalasin D. In summary, Pseudomonas-augmented histamine production by neutrophils is strain-dependent in vitro and likely mediated by up-regulation of histidine decarboxylase. These findings raise the possibility that Pseudomonas-stimulated neutrophils can enhance airway inflammation by producing histamine.
Evolutionary History and Functional Characterization of the Amphibian Xenosensor CAR
Authors: Mathäs Marianne , Burk Oliver , Qiu Huan , Nußhag Christian , Gödtel-Armbrust Ute , Baranyai Dorothea , Deng Shiwei , Römer Kristin , Nem Dieudonné , Windshügel Björn , Wojnowski Leszek 
Published: November 2011

AbstractThe xenosensing constitutive androstane receptor (CAR) is widely considered to have arisen in early mammals via duplication of the pregnane X receptor (PXR). We report that CAR emerged together with PXR and the vitamin D receptor from an ancestral NR1I gene already in early vertebrates, as a result of whole-genome duplications. CAR genes were subsequently lost from the fish lineage, but they are conserved in all taxa of land vertebrates. This contrasts with PXR, which is found in most fish species, whereas it is lost from Sauropsida (reptiles and birds) and plays a role unrelated to xenosensing in Xenopus. This role is fulfilled in Xenopus by CAR, which exhibits low basal activity and pronounced responsiveness to activators such as drugs and steroids, altogether resembling mammalian PXR. The constitutive activity typical for mammalian CAR emerged first in Sauropsida, and it is thus common to all fully terrestrial land vertebrates (Amniota). The constitutive activity can be achieved by humanizing just two amino acids of the Xenopus CAR. Taken together, our results provide a comprehensive reconstruction of the evolutionary history of the NR1I subfamily of nuclear receptors. They identify CAR as the more conserved and remarkably plastic NR1I xenosensor in land vertebrates. Nonmammalian CAR should help to dissect the specific functions of PXR and CAR in the metabolism of xeno- and endobiotics in humans. Xenopus CAR is a first reported amphibian xenosensor, which opens the way to toxicogenomic and bioaugmentation studies in this critically endangered taxon of land vertebrates.
Neuronal correlates of a preference for leading signals in the synchronizing bushcricketMecopoda elongata(Orthoptera, Tettigoniidae)
Authors: Siegert M. E. , Römer H. , Hashim R. , Hartbauer M. 
Published: November 2011

SUMMARYAcoustically interacting males of the tropical katydid Mecopoda elongata synchronize their chirps imperfectly, so that one male calls consistently earlier in time than the other. In choice situations, females prefer the leader signal, and it has been suggested that a neuronal mechanism based on directional hearing may be responsible for the asymmetric, stronger representation of the leader signal in receivers. Here, we investigated the potential mechanism in a pair of interneurons (TN1 neuron) of the afferent auditory pathway, known for its contralateral inhibitory input in directional hearing. In this interneuron, conspecific signals are reliably encoded under natural conditions, despite high background noise levels. Unilateral presentations of a conspecific chirp elicited a TN1 response where each suprathreshold syllable in the chirp was reliably copied in a phase-locked fashion. Two identical chirps broadcast with a 180 deg spatial separation resulted in a strong suppression of the response to the follower signal, when the time delay was 20 ms or more. Muting the ear on the leader side fully restored the response to the follower signal compared with unilateral controls. Time–intensity trading experiments, in which the disadvantage of the follower signal was traded against higher sound pressure levels, demonstrated the dominating influence of signal timing on the TN1 response, and this was especially pronounced at higher sound levels of the leader. These results support the hypothesis that the female preference for leader signals in M. elongata is the outcome of a sensory mechanism that originally evolved for directional hearing.
Associative learning between odorants and mechanosensory punishment in larval Drosophila
Authors: Eschbach Claire , Cano Carmen , Haberkern Hannah , Schraut Karla , Guan Chonglin , Triphan Tilman , Gerber Bertram 
Published: November 2011

SUMMARY
We tested whether Drosophila larvae can associate odours with a mechanosensory disturbance as a punishment, using substrate vibration conveyed by a loudspeaker (buzz: ). One odour (A) was presented with the buzz, while another odour (B) was presented without the buzz (A/B training). Then, animals were offered the choice between A and B. After reciprocal training (A/B), a second experimental group was tested in the same way. We found that larvae show conditioned escape from the previously punished odour. We further report an increase of associative performance scores with the number of punishments, and an increase according to the number of training cycles. Within the range tested (between 50 and 200 Hz), however, the pitch of the buzz does not apparently impact associative success. Last, but not least, we characterized odour–buzz memories with regard to the conditions under which they are behaviourally expressed – or not. In accordance with what has previously been found for associative learning between odours and bad taste (such as high concentration salt or quinine), we report that conditioned escape after odour–buzz learning is disabled if escape is not warranted, i.e. if no punishment to escape from is present during testing. Together with the already established paradigms for the association of odour and bad taste, the present assay offers the prospect of analysing how a relatively simple brain orchestrates memory and behaviour with regard to different kinds of ‘bad’ events.
IRS and TOR nutrient-signaling pathways act via juvenile hormone to influence honey bee caste fate
Authors: Mutti Navdeep S. , Dolezal Adam G. , Wolschin Florian , Mutti Jasdeep S. , Gill Kulvinder S. , Amdam Gro V. 
Published: November 2011

SUMMARY
Regardless of genetic makeup, a female honey bee becomes a queen or worker depending on the food she receives as a larva. For decades, it has been known that nutrition and juvenile hormone (JH) signaling determine the caste fate of the individual bee. However, it is still largely unclear how these factors are connected. To address this question, we suppressed nutrient sensing by RNA interference (RNAi)-mediated gene knockdown of IRS (insulin receptor substrate) and TOR (target of rapamycin) in larvae reared on queen diet. The treatments affected several layers of organismal organization that could play a role in the response to differential nutrition between castes. These include transcript profiles, proteomic patterns, lipid levels, DNA methylation response and morphological features. Most importantly, gene knockdown abolished a JH peak that signals queen development and resulted in a worker phenotype. Application of JH rescued the queen phenotype in either knockdown, which demonstrates that the larval response to JH remains intact and can drive normal developmental plasticity even when IRS or TOR transcript levels are reduced. We discuss our results in the context of other recent findings on honey bee caste and development and propose that IRS is an alternative substrate for the Egfr (epidermal growth factor receptor) in honey bees. Overall, our study describes how the interplay of nutritional and hormonal signals affects many levels of organismal organization to build different phenotypes from identical genotypes.
Development of a radioscandium immunoconjugate for radioimmunotherapy
Authors: Moghaddam-Banaem L. , Jalilian A. R. , Pourjavid M. , Radfar E. , Bahrami-Samani A. , Yavari K. , Mazidi M. , Ghannadi-Maragheh M. 
Published: November 2011

Abstract
Developing monoclonal antibodies labeled with beta-emitters has led to the introduction of important agents in radioimmunotherapy. In this work, Sc-46 chloride was obtained by thermal neutron activation flux of natural metallic scandium sample followed by dissolution in acidic media (radionuclidic purity via beta and gamma ray spectroscopy, 99.9% ; radiochemical purity via ITLC, >99%) and used in radiolabeling of rituximab after conjugation with DOTA-NHS-ester. The specific activity was however not high. The conjugates were purified by molecular filtration and used in the radiolabeling. The radiochemical purity (ITLC), stability studies (ITLC and size exclusion chromatography), determination of average number of DOTA conjugated per mAb (chelate: antibody ratio, 5.8:1) and gel electrophoresis of [ 46Sc]Sc-DOTA-anti-CD20 were determined followed by biodistribution studies for 46Sc and [ 46Sc]Sc-DOTA-anti-CD20 i n wild type rats up to 72 h. The binding of the radiolabeled antibody was showed to be 60% on Raji cells. The final compound was stable in presence of PBS at 37 ºC and room temperature. The accumulation of the radiolabeled antibody in liver, spleen, kidney, heart and other tissues demonstrates a pattern similar to the other radiolabeled anti-CD20 immunoconjugates. The present study shows the possibility of antibody labeling for future use in radioimmunotherapy by 47Sc.
High-order connected moments expansion for the Rabi Hamiltonian
Authors: Amore Paolo , Fernandez Francisco , Rodriguez Martin 
Published: November 2011

Abstract
We analyze the convergence properties of the connected moments expansion (CMX) for the Rabi Hamiltonian. To this end we calculate the moments and connected moments of the Hamiltonian operator to a sufficiently large order. Our large-order results suggest that the CMX is not reliable for most practical purposes because the expansion exhibits considerable oscillations.
An Esr Study of Free Radicals Scavenging by Red Tea
Authors: Wosiński Stanisław , Jurga Jan , Kruczyński Zdzisław , Górski Romuald , Sobieralski Krzysztof , Siwulski Marek 
Published: November 2011

An Esr Study of Free Radicals Scavenging by Red Tea
Herbal tea is known to exhibit the scavenging of free radicals responsible for cellular damage. We studied the effect of water treated with reverse osmotic filter equipped with a special dielectric ceramic composite on the antioxidant activity of red tea. Methanol solution of DPPH was added to the tea extract and the RT decay of DPPH free radicals was studied by ESR spectroscopy. Red tea brewed from tap water treated with the composite filter was found to exhibit higher radical scavenging efficiency in comparison with that of the tea brewed from tap water, mineral water and reverse osmosis water.
Quality Evaluation of Biogas and Selected Methods of its Analysis
Authors: Zamorska-Wojdyła Dorota , Gaj Kazimierz , Hołtra Anna , Sitarska Magdalena 
Published: November 2011

Quality Evaluation of Biogas and Selected Methods of its Analysis
There were presented technological and ecological aspects of biogas quality evaluation and introduced an overview of the limits of its selected parameters. There were characterized analytical methods for determining the basic composition of biogas, hydrogen sulfide, ammonia, condensation, dust, oils, siloxanes, and aggregated content of sulfur, chlorine and fluorine. The result of comparative analysis and literature studies are proposes of the most adequate to the studies of biogas - analytical methodologies.