bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-seq liver transcriptome analysis reveals an activated MHC-I pathway and an inhibited MHC-II pathway at the early stage of vaccine immunization in zebrafish
Authors: Yang Dahai , Liu Qin , Yang Minjun , Wu Haizhen , Wang Qiyao , Xiao Jingfan , Zhang Yuanxing 
Published: July 2012

Abstract

Background
Zebrafish (Danio rerio) is a prominent vertebrate model of human development and pathogenic disease and has recently been utilized to study teleost immune responses to infectious agents threatening the aquaculture industry. In this work, to clarify the host immune mechanisms underlying the protective effects of a putative vaccine and improve its immunogenicity in the future efforts, high-throughput RNA sequencing technology was used to investigate the immunization-related gene expression patterns of zebrafish immunized with Edwardsiella tarda live attenuated vaccine.

Results
Average reads of 18.13 million and 14.27 million were obtained from livers of zebrafish immunized with phosphate buffered saline (mock) and E. tarda vaccine (WED), respectively. The reads were annotated with the Ensembl zebrafish database before differential expressed genes sequencing (DESeq) comparative analysis, which identified 4565 significantly differentially expressed genes (2186 up-regulated and 2379 down-regulated in WED; p<0.05). Among those, functional classifications were found in the Gene Ontology database for 3891 and in the Kyoto Encyclopedia of Genes and Genomes database for 3467. Several pathways involved in acute phase response, complement activation, immune/defense response, and antigen processing and presentation were remarkably affected at the early stage of WED immunization. Further qPCR analysis confirmed that the genes encoding the factors involved in major histocompatibility complex (MHC)-I processing pathway were up-regulated, while those involved in MHC-II pathway were down-regulated.

Conclusion
These data provided insights into the molecular mechanisms underlying zebrafish immune response to WED immunization and might aid future studies to develop a highly immunogenic vaccine against gram-negative bacteria in teleosts.
Chlamydophila Psittaci Eradication With Doxycycline As First-Line Targeted Therapy for Ocular Adnexae Lymphoma: Final Results of an International Phase II Trial
Authors: Ferreri Andrés J.M. , Govi Silvia , Pasini Elisa , Mappa Silvia , Bertoni Francesco , Zaja Francesco , Montalbán Carlos , Stelitano Caterina , Cabrera Maria Elena , Giordano Resti Antonio , Politi Letterio Salvatore , Doglioni Claudio , Cavalli Franco , Zucca Emanuele , Ponzoni Maurilio , Dolcetti Riccardo 
Published: July 2012

Purpose The pathogenic association between Chlamydophila psittaci (Cp) and ocular adnexal marginal zone lymphoma (OAMZL) and the efficacy of doxycycline monotherapy have been investigated in retrospective series with variations in stage, management, and follow-up duration. To our knowledge, this is the first international phase II trial aimed at clarifying Cp prevalence and activity of first-line doxycycline in a homogeneous series of consecutive patients with newly diagnosed stage I OAMZL. Patients and Methods Forty-seven patients were registered. Tumor tissue, conjunctival swabs, and peripheral blood from 44 patients were assessed for seven Chlamydiaceae infections by three polymerase chain reaction protocols. Thirty-four patients with measurable or parametrable disease were treated with doxycycline and assessed for chlamydial eradication and lymphoma response (primary end point). Results Cp DNA was detected in biopsies of 39 patients (89%); no other Chlamydiaceae were detected. Twenty-nine patients had Cp DNA in baseline swabs and/or blood samples and were evaluable for chlamydial eradication, which was achieved in 14 patients (48%). Lymphoma regression was complete in six patients and partial in 16 (overall response rate, 65%; 95% CI, 49% to 81%); 11 had stable disease, and one had progressive disease. At a median follow-up of 37 months (range, 15 to 62 months), 20 patients remained relapse free (5-year progression-free survival [PFS] ± standard deviation, 55% ± 9%). Cp eradication was associated with improved response rate (86% v 47%; P = .02) and 5-year PFS (68% v 47%; P = .11). Conclusion Upfront doxycycline is a rational and active treatment for patients with stage I Cp-positive OAMZL. Lymphoma regression is consequent to Cp eradication, which can easily be monitored on conjunctival and blood samples. Prospective trials aimed at identifying more effective administration schedules for doxycycline are warranted.
MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA
Authors: Lee Ka Cheong , Padget Kay , Curtis Hannah , Cowell Ian G. , Moiani Davide , Sondka Zbyslaw , Morris Nicholas J. , Jackson Graham H. , Cockell Simon J. , Tainer John A. , Austin Caroline A. 
Published: July 2012

Summary
Topoisomerase II creates a double-strand break intermediate with topoisomerase covalently coupled to the DNA via a 5′-phosphotyrosyl bond. These intermediate complexes can become cytotoxic protein-DNA adducts and DSB repair at these lesions requires removal of topoisomerase II. To analyse removal of topoisomerase II from genomic DNA we adapted the trapped in agarose DNA immunostaining assay. Recombinant MRE11 from 2 sources removed topoisomerase IIα from genomic DNA in vitro, as did MRE11 immunoprecipitates isolated from A-TLD or K562 cells. Basal topoisomerase II complex levels were very high in A-TLD cells lacking full-length wild type MRE11, suggesting that MRE11 facilitates the processing of topoisomerase complexes that arise as part of normal cellular metabolism. In K562 cells inhibition of MRE11, PARP or replication increased topoisomerase IIα and β complex levels formed in the absence of an anti-topoisomerase II drug.
Cardiovascular findings and management in Turner syndrome: insights from a French cohort
Authors: Donadille Bruno , Rousseau Alexandra , Zenaty Delphine , Cabrol Sylvie , Courtillot Carine , Samara-Boustani Dinane , Salenave Sylvie , Monnier-Cholley Laurence , Meuleman Catherine , Jondeau Guillaume , Iserin Laurence , Duranteau Lise , Cabanes Laure , Bourcigaux Nathalie , Bonnet Damien , Bouchard Philippe , Chanson Philippe , Polak Michel , Touraine Philippe , Lebouc Yves , Carel Jean-Claude , Léger Juliane , Christin-Maitre Sophie 
Published: July 2012

ObjectiveCongenital cardiovascular malformations and aortic dilatation are frequent in patients with Turner syndrome (TS). The objective of this study was to investigate the cardiovascular findings and management in a large cohort of patients, including children and adults.Design/methodsWe recruited 336 patients with TS from a network of tertiary centers. We reviewed their files, checking for cardiovascular events, cardiac valve abnormalities, and aortic diameters indexed to body surface area (BSA) from magnetic resonance imaging (n=110) or echocardiography (n=300).ResultsInformative cardiovascular data were available for only 233 patients. Vascular surgery was reported in 7.4% of the cohort. The first cause of surgery was aortic coarctation, detected in 6.9% at a median age of 9.5 (range: 0–60) years. Bicuspid aortic valve (BAV) was detected in 21% at a median age of 20 years (25th–75th percentiles: 15–30). At least one aortic diameter exceeded 32 mm in 12% of the cohort. This was detected at a median age of 19 (7–30) years. When indexed to BSA, at least one aortic diameter exceeded 20 mm/m2 in 39% of the cohort.ConclusionOur study shows that cardiovascular monitoring for TS patients is currently insufficient in France. BAV is present at birth, but often remains undiagnosed until later in life. Therefore, improved management in cardiovascular monitoring is required and a more systematic approach should be taken.
Real-Time Integrated Petrophysics: Geosteering in Challenging Geology & Fluid Systems
Authors: Kanfar Majed F. 
Published: July 2012

Abstract
Since the advent of horizontal wells, the oil and gas industry has come a long way to ensure optimal drilling and well placement practices. The proper placement of these wells has meant that Measurement and Logging While Drilling, MWD and LWD, have come to play a primary role in geosteering, placement and evaluation of highly deviated or horizontal wells.
This paper presents a case study from a complex carbonate reservoir that has low permeability zone in the middle of the reservoir and rimmed by a tar mat, which complicate the optimal placement of the horizontal producers and injectors. Conventional triple-combo logs lack the critical data to geosteer in this multifactorial environment. A comprehensive logging program was developed to integrate additional petrophysical data such as Formation Pressure While Drilling (FPWD), cuttings analysis, Nuclear Magnetic Resonance While Drilling (NMR-WD), and neural-network processing.
Formation pressure while drilling is used in real-time to detect penetrated low mobililty/low permeability zones. Pressure build-up and drawdown measurements along with fluid mobility are used to modify the well trajectory. NMR while drilling is applied for placement of power-water injection wells to detect zones bearing heavy immobile oil where the ability to inject is unlikely. Algorithms were developed to estimate the in-situ oil viscosity. Moreover, neural-network models that incorporate legacy well log and core data were used to predict litho-facies and rock permeability in real-time.
The workflow developed for this study demonstrates the necessity of additional petrophysical data and vigilance for real-time solutions to geosteer extended reach horizontal wells in heterogeneous geological systems.
To Develop the Optimum Field Development Plan for Condensate Wells using Integrated Production Modeling (IPM)
Authors: Memon Shoaib , Zameer Asif 
Published: July 2012

Abstract
Now a days integrated production modeling is been regarded as a vital part of the oil industry and its very important to manage our reservoir properly as many important decisions regarding the field development depend on it. It is an approach for modeling an entire asset from reservoir to the final delivery point. It facilitates complete integration, and hence full interaction, of different key components of an asset including reservoir, wellbore and surface facilities. It gives the holistic understanding of the entire asset necessary to know how one end of the delivery chain affects the other like separator pressure effect on reservoir pressure, etc. It defines design and operating criteria for a given field, not just for today, but also for the future. In short, it provides the economic optimization of oil and gas recovery.
In this paper, the concept of IPM has been utilized for a newly developed condensate field to come up with the optimum field development strategy using the real field data necessary to evaluate different economic ways of producing the wells. This work presents a methodology which uses compositional modeling, nodal analysis, material balance, reservoir modeling and pressure transient analysis to determine original fluid in place (OFIP), reservoir deliverability and size, number of wells require for developing the field and the optimum producing strategy for the wells. Petroleum Expert's software "Integrated production modeling (IPM) suite 7.5" has been used to carry out this work.
PVT, well test, well logs and production history Data was fed as input to modeling software; PVTP, Prosper and MBAL. A compositional model was prepared in PVTP and was regretted by using laboratory data to minimize error. The results showed very limited production options due to the lower liquid drop-out (less than 12%) and lower volumes of OGIP in the upper bed of the reservoir. Gas recycling option at assumed rate of 30% increases the life of the well upto 5 years and condensate recovery upto 57.5%. After going through all available options, the only option available having economic priorities was to select an optimum wellhead pressure as suggested by the sensitivity analysis to optimize the production was recommended.
Generation of the vorticity mode by sound in a vibrationally relaxing gas
Authors: Perelomova Anna , Wojda Pawel 
Published: July 2012

Abstract
The procedure of derivation of a new dynamical equation governing the vorticity mode that is generated by sound, is discussed in detail. It includes instantaneous quantities and does not require averaging over sound period. The resulting equation applies to both periodic and aperiodic sound as the origin of the vorticity mode. Under certain conditions, the direction of streamlines of the vorticity mode may be inverted as compared with that in a fluid with standard attenuation. This reflects an anomalous absorption of sound, when transfer of momentum of the vorticity mode into momentum of sound occurs. The theory is illustrated by a representative example of the generation of vorticity in a vibrationally relaxing gas in the field of periodic weakly diffracting acoustic beam.
A Review of Mathematical Models for the Atmospheric Dispersion of Heavy Gases. Part I. A Classification of Models
Authors: Markiewicz Maria 
Published: July 2012

A Review of Mathematical Models for the Atmospheric Dispersion of Heavy Gases. Part I. A Classification of ModelsIn this two part article in its first part models of heavy gas dispersion in the atmosphere are classified and the distinguished groups of models are characterised. In the second part the procedures for the model quality evaluation are described and the main results of model evaluation projects are summarised. Substances released to the atmosphere which have a density greater than the density of the atmospheric air are called heavy gases or dense gases. The dispersion of heavy gases is different from that encountered in the case of neutrally or positively buoyant gases. Specific models have been developed to describe it. The heavy gas dispersion models differ in the complexity and mathematical description. Based on these criteria four main groups of models are distinguished: simple/empirical models, intermediate/integral and shallow layer models, advanced/Lagrangian particle trajectory and Lagrangian puff dispersion models and sophisticated/Computer Fluid Dynamics (CFD) models. This classification is an extension of the classification proposed earlier in the literature.
Study of the Biodegrability of Degradable/Biodegradable Plastic Material in a Controlled Composting Environment
Authors: Vaverková Magdalena , Toman František , Adamcová Dana , Kotovicová Jana 
Published: July 2012

Study of the Biodegrability of Degradable/Biodegradable Plastic Material in a Controlled Composting EnvironmentThe objective of this study was to determine the degrability/biodegradability of disposable plastic bags available on the market that are labeled as degradable/biodegradable and those certified as compost. The investigated materials were obtained from chain stores in the Czech Republic and Poland. Seven kinds of bags (commercially available) were used in this study. One of them was a disposable bag made of HDPE and mixed with totally degradable plastic additive (TDPA additive). Another was a disposable made of polyethylene with the addition of pro-oxidant additive (d2w additive). One was labeled as 100% degradable within various periods of time, from three months up to three years, and four were certified as compostable. The test was carried out in a controlled composting environment. The biodisintegration degree of the obtained pieces was evaluated following a modified version of ČSN EN 14806 Norm "Packaging - Preliminary evaluation of the disintegration of the packaging materials under simulated composting conditions in a laboratory scale test" and a modified version of ČSN EN ISO 20200 "Plastics - Determination of the degree of disintegration of plastic materials under simulated composting conditions in laboratory-scale test" (ISO 20200:2004). The emphasis was put on determination whether the bags are degradable/biodegradable or not.
Pollution of the Natural Environment in Intensive Cultures Under Greenhouses
Authors: Kleiber Tomasz 
Published: July 2012

Pollution of the Natural Environment in Intensive Cultures Under GreenhousesThe last two decades have brought a significant modernization in methods of cultivation in greenhouses. Soilless cultures, isolated from soils, have become a common practice, similarly as fertigation (fertilization + irrigation) installations, although most of them are applied in the open system (with no recirculation), where excess nutrient solution is removed straight to soil. This situation was the reason why it was decided to conduct studies, extended over a period of many years, on the estimation of environmental pollution caused by discharged drainage waters containing mineral fertilizers in economically important cultures in Poland (anthurium, tomato, cucumber). On the basis of the chemical composition of drainage waters and amounts of nutrient solution spillway from culture beds data were estimated concerning pollution of the soil medium by the nutrient solution. The level of pollution was dependent on nutrient requirements of crops and the length of the vegetation period. The highest environmental pollution is caused by intensive tomato growing (in kg·month·ha-1): N-NO3(up to 245), K (up to 402), Ca (up to 145) and S-SO4(up to 102). A lesser threat is posed by metal microelements: Fe (up to 2.69), Mn (up to 0.19), Zn (up to 0.52) and Cu (up to 0.09). Lower contamination of the natural environment is generated in cultures with lower nutrient requirements (anthurium) and in the case of culture on organic substrates. With an increase in ecological awareness of producers recirculation systems should be implemented in the production practice, in which drainage waters do not migrate directly to soil, but are repeatedly used to feed crops.
Horizontal Distribution of Psammonic Ciliates in Two Lakes of Different Trophic Status: Relationship to Physical and Chemical Parameters
Authors: Mieczan Tomasz , Nawrot Dorota 
Published: July 2012

Horizontal Distribution of Psammonic Ciliates in Two Lakes of Different Trophic Status: Relationship to Physical and Chemical ParametersThe aims of this study were to identify the taxonomic diversity and abundance of psammonic ciliate communities in mesotrophic and eutrophic lakes (Łęczna-Włodawa Lakeland, eastern Poland). The effect of selected physical and chemical water parameters on ciliates community was also analysed. Psammon samples were collected during three seasons: spring, summer and autumn of 2010. In each lake, in the psammolittoral, samples were collected in the euarenal, higroarenal, and hydroarenal zones. A total of 53 ciliate taxa were recorded. The highest value of the Shannon-Weaver index was recorded in summer in eutrophic lake (2.79). At the same time in mesotrophic lake, a lower value of the index was determined (0.79). The mean numbers of ciliates ranged from 516 ind.cm-3in the eutrophic lake to 191 ind. cm-3in the mesotrophic lake. In eutrophic lake, the highest number of ciliates was recorded in the euarenal (649 ind. cm-3), and the lowest in the higroarenal (425 ind. cm-3). In the mesotrophic lake, the highest average numbers were determined in the higroarenal (235 ind. cm-3), and the lowest in the hydroarenal (155 ind. cm-3). Irrespective of the lake trophy, Hymenostomata (Paramecium sp., Glaucoma sp., Uronema nigricans) occurred in the highest numbers (from 13 to 95%). The results demonstrated that N-NH4, P-PO4and TOC can strongly regulate the abundance and taxonomic composition of ciliates. The strongest correlations between numbers of ciliates and physical and chemical water parameters were observed in the higro- and hydroarenal zones of the eutrophic lake.
Factor Associated with Neutral Sphingomyelinase Activity Mediates Navigational Capacity of Leukocytes Responding to Wounds and Infection: Live Imaging Studies in Zebrafish Larvae
Authors: Boecke Alexandra , Sieger Dirk , Neacsu Cristian Dan , Kashkar Hamid , Krönke Martin 
Published: July 2012

Abstract
Factor associated with neutral sphingomyelinase activity (FAN) is an adaptor protein that specifically binds to the p55 receptor for TNF (TNF-RI). Our previous investigations demonstrated that FAN plays a role in TNF-induced actin reorganization by connecting the plasma membrane with actin cytoskeleton, suggesting that FAN may impact on cellular motility in response to TNF and in the context of immune inflammatory conditions. In this study, we used the translucent zebrafish larvae for in vivo analysis of leukocyte migration after morpholino knockdown of FAN. FAN-deficient zebrafish leukocytes were impaired in their migration toward tail fin wounds, leading to a reduced number of cells reaching the wound. Furthermore, FAN-deficient leukocytes show an impaired response to bacterial infections, suggesting that FAN is generally required for the directed chemotactic response of immune cells independent of the nature of the stimulus. Cell-tracking analysis up to 3 h after injury revealed that the reduced number of leukocytes is not due to a reduction in random motility or speed of movement. Leukocytes from FAN-deficient embryos protrude pseudopodia in all directions instead of having one clear leading edge. Our results suggest that FAN-deficient leukocytes exhibit an impaired navigational capacity, leading to a disrupted chemotactic response.
Giant Endometrioma associated with Serous Cystadenoma: A Case Report
Authors: Arroyo Carlos , Espinosa-Villaseñor Natalia , Muñoz-Pérez María José , Soto-Vega Elena 
Published: July 2012

Background Giant endometriomas are a rare condition and the association with cystadenomas has not been reported previously. Case A 37-year-old woman without any previous medical history of disease presented to the emergency department because of dyspnea. During physical examination the patient presented a considerably sized abdominal growth when a tomography was performed; this revealed a large mass which was presumably dependent on the pelvic cavity. Surgery was performed to remove the tumor, during which another cyst was found in the contra-lateral ovary. Conculsions The histopathologic report showed that the tumor found on the left ovary corresponded to a giant endometriosic cyst and on the right ovary, a papillary serous cystadenoma.
Quelques réflexions sur un modèle social européen
Authors: Servais Jean-Michel 
Published: July 2012

L’auteur livre quelques réflexions personnelles sur la spécificité de la réponse européenne à la question sociale telle qu’elle se pose aujourd’hui. Davantage qu’une émanation de la politique de l’Union européenne, il voit dans le modèle social européen un patrimoine commun aux peuples de l’Europe en matière d’emploi et de travail. Ce concept traduit une triple réalité : une régulation sociale fondée sur la concertation ; un régime élaboré de protection sociale et l’existence de services publics à finalité sociale, ainsi qu’un interventionnisme actif de l’État en matières industrielle, économique et sociale. Si ce modèle doit faire face à des critiques et à des difficultés, l’évolution semble davantage aller dans le sens de son adaptation que dans celui de sa disparition.
Négociation collective et régulation du marché du travail en Europe
Authors: Leonard Evelyne 
Published: July 2012

Quel est le rôle de la négociation collective dans la régulation du marché du travail et comment ce rôle évolue-t-il dans le cadre de l’intégration européenne ? Cet article défend l’hypothèse selon laquelle ont récemment émergé dans les pays de l’Union européenne des formes originales de régulation conjointe du marché du travail. Il propose tout d’abord un cadre d’analyse des évolutions récentes en matière de négociations portant sur l’emploi en Europe, avant d’examiner les évolutions nationales. Il met ainsi en évidence la coexistence de divers modes de régulation conjointe du marché du travail dans le contexte européen, pour examiner en finale la nature de cette régulation et ses enjeux pour les relations professionnelles.