bluuebunny/crossref_metadata_2025_split huggingface dataset:
LOH in the HLA Class I Region at 6p21 Is Associated with Shorter Survival in Newly Diagnosed Adult Glioblastoma
Authors: Yeung Jacky T. , Hamilton Ronald L. , Ohnishi Koji , Ikeura Maki , Potter Douglas M. , Nikiforova Marina N. , Ferrone Soldano , Jakacki Regina I. , Pollack Ian F. , Okada Hideho 
Published: February 2013

Abstract
Purpose: Glioblastoma (GBM) shows downregulated expression of human leukocyte antigen (HLA) class I, thereby escaping from cytotoxic T cells and limiting the efficacy of immunotherapy. Loss of heterozygosity (LOH) of HLA class I (6p21) and/or β-2 microglobulin (B2m) (15q21) regions represents irreversible downregulation. In this study, we examined the prevalence of these LOH events and their relations with overall survival in GBM.
Experimental Design: In a cross-sectional analysis on 60 adult patients with GBM, DNA from formalin-fixed, paraffin-embedded specimens were evaluated for 10 microsatellite regions of HLA class I, B2m, HLA class II, HLA class III, and 6q by PCR as well as immunohistochemical evaluation of HLA class I expression and CD8+ T-cell infiltration.
Results: LOH in HLA class I, B2m, HLA class II, HLA class III, and 6q regions was present in 41.4%, 18.2%, 9.4%, 77.8%, and 36.0% of informative cases, respectively. LOH of HLA class I was associated with shorter overall survival (HR = 4.89, P = 0.0078). HLA class I was downregulated in 22% to 43% of cases based on immunohistochemistry. Cases that displayed negative staining were significantly younger. HLA class I expression correlated with intratumoral CD8+ T-cell infiltration.
Conclusion: LOH in the HLA class I region is frequent in adult GBMs. The association of shorter survival with LOH in this region suggests a crucial role for these genes in immunosurveillance. Clin Cancer Res; 19(7); 1816–26. ©2013 AACR.
Macrophage Gene Expression and Foam Cell Formation Are Regulated by Plasminogen
Authors: Das Riku , Ganapathy Swetha , Mahabeleshwar Ganapati H. , Drumm Carla , Febbraio Maria , Jain Mukesh K. , Plow Edward F. 
Published: February 2013

Background—
Deciphering the molecular and cellular processes that govern macrophage foam cell formation is critical to understanding the basic mechanisms underlying atherosclerosis and other vascular pathologies.

Methods and Results—

Here, we identify a pivotal role of plasminogen (Plg) in regulating foam cell formation. Deficiency of Plg inhibited macrophage cholesterol accumulation on exposure to hyperlipidemic conditions in vitro, ex vivo, and in vivo. Gene expression analysis identified CD36 as a regulated target of Plg, and macrophages from Plg
−/−
mice had decreased CD36 expression and diminished foam cell formation. The Plg-dependent CD36 expression and foam cell formation depended on conversion of Plg to plasmin, binding to the macrophage surface, and the consequent intracellular signaling that leads to production of leukotriene B
4
. Leukotriene B
4
rescued the suppression of CD36 expression and foam cell formation arising from Plg deficiency.

Conclusions—
Our findings demonstrate an unanticipated role of Plg in the regulation of gene expression and cholesterol metabolism by macrophages and identify Plg-mediated regulation of leukotriene B4 as an underlying mechanism.
The Political Economy of Social Production Companies in Venezuela
Authors: Purcell Thomas Francis 
Published: February 2013

In 2005, shortly after the Venezuelan government declared “twenty-first-century socialism” as its development goal, Chávez launched “social production companies” to change the way communities produced and exchanged goods. Investigation of the relationship between these companies, agrarian cooperatives, and the oil economy calls into question assessments by both the right and the left, the former portraying Venezuelan development initiatives as populist profligacy and the latter seeing them as a socialist alternative to neoliberal hegemony. An analytical focus upon ground rent and the way it is distributed through the social production companies that draws upon insights from the Marxian critique of political economy provides an original window onto the contradictions and limits of the Chávez government’s development policies. Three case studies suggest that social production companies and their links with small agrarian cooperatives are reproducing a limited and ground-rent-dependent form of capital accumulation that, coupled with the ideology of popular power, is being presented as a step toward twenty-first-century socialism. En 2005, poco después de que el gobierno venezolano declarara el “socialismo del siglo veintiuno” como su objetivo de desarrollo, Chávez lanzó las “empresas de producción social” para cambiar la forma en que las comunidades producían e intercambiaban bienes. Una investigación de la relación entre estas empresas, las cooperativas agrarias, y la economía petrolera pone en tela de juicio las evaluaciones tanto de la derecha como la izquierda, la primera representando las iniciativas del desarrollo venezolano como derroche populista y la segunda viéndolas como la alternativa socialista a la hegemonía neoliberal. Un enfoque analítico sobre la renta de la tierra y su distribución por medio de las empresas de producción social que se fundamenta en la critica marxiana de la economía política ofrece una ventana original hacia las contradicciones y límites de la política de desarrollo chavista. Tres estudios de caso sugieren que las empresas de producción social y sus vínculos con pequeñas cooperativas agrícolas están reproduciendo una forma de acumulación de capital limitada y dependiente de la renta de la tierra, la cual, junta con la ideología de poder popular, se está presentando como un paso hacia el socialismo del siglo veintiuno.
Mechanical, thermal and flame-retardant properties of epoxy–nylon fabric–clay hybrid laminates
Authors: Prabhu T. Niranjana , Demappa T. , Harish V. , Prashantha K. 
Published: February 2013

Epoxy–nylon fabric laminate composites containing 0.1–0.7 phr clay reinforcements were prepared using a hand layup technique. The fabricated laminates were tested for thermal stability, impact resistance, mechanical properties and flame retardancy. The results indicated an increase in impact resistance, tensile strength, flexural strength and Young’s modulus to an extent and then a decrease as the clay content is increased. Overall results show that a 0.2-phr clay reinforcement into the epoxy–nylon fabric laminate has shown better impact resistance (33.9% more than the neat epoxy–nylon fabric laminate), tensile strength (nearly two times the neat sample), flexural strength (nearly five times the neat sample) and Young’s modulus (39.4% more than the neat sample). Thermal stability is found to decrease slightly upon addition of clay. UL-94 tests conducted on the composite laminate samples have shown a reduction in the burning rate. Also, the tests performed in the present study indicate that the materials under investigation have promising applications in construction, agriculture and decorative purposes.
Gastrocnemius Recession for Chronic Noninsertional Achilles Tendinopathy
Authors: Kiewiet Nathan J. , Holthusen Scott M. , Bohay Donald R. , Anderson John G. 
Published: February 2013

Background: In patients with chronic Achilles tendinopathy, several operative techniques have been described for treatment. A case report has shown that gastrocnemius recession as treatment can normalize MRI findings and relieve clinical symptoms consistent with chronic Achilles tendinopathy. The purpose of this study was to present the results of the treatment of chronic Achilles tendinopathy with gastrocnemius recession. Methods: Of 12 patients, 8 (7 females, 1 male) who underwent gastrocnemius recession for refractory Achilles tendinopathy between July 2004 and January 2009 were available for follow-up. All patients filled out a SF-36 health survey, a foot function index, an AOFAS ankle and hindfoot scale, and a simple survey formulated by our group of investigators. Of the 8 patients, 7 were available to return for clinical assessment. Patients had an average age of 49.9 years (SD = 11.6) at the time of surgery and average time of follow-up was 34.6 months (SD = 18.1). Results: The mean pain score (VAS 0-10 scale) significantly decreased from 7.3 (SD = 1.7) preoperatively to 1 (SD = 1.8) postoperatively at the time of follow-up ( P < .001). The mean AOFAS ankle and hindfoot score was 94.4 (SD = 9.8), which was significantly improved when compared with previously published scores for patients who underwent Achilles debridement with FHL transfer ( P = .007). All 8 categories on the SF-36 health survey showed no significant difference with published data for US population values and previously published data for patients who underwent FHL transfer. Conclusion: Gastrocnemius recession for the treatment of refractory Achilles tendinopathy was a viable treatment option following the failure of nonoperative management. All 8 of our patients had excellent pain relief, good clinical outcome, and were satisfied at the time of follow-up. Level of Evidence: Level IV, case series.
Chaste
Authors: Bernabeu Miguel O , Southern James , Wilson Nicholas , Strazdins Peter , Cooper Jonathan , Pitt-Francis Joe 
Published: February 2013

The simulation of cardiac electrophysiology is a mature field in computational physiology. Recent advances in medical imaging, high-performance computing and numerical methods mean that computational models of electrical propagation in human heart tissue are ripe for use in patient-specific simulation for diagnosis, for prognosis and for selection of treatment methods. However, in order to move in this direction, it is necessary to make efficient use of modern petascale computing resources. This paper focuses on an existing open source simulation framework (Chaste) and documents work done to improve the parallel scaling on a small range of electrophysiology benchmark problems. These benchmarks involve the numerical solution of the monodomain or bidomain equations via the finite-element method. At the beginning of this study the electrophysiology libraries within Chaste were already enabled to run in parallel and were able to solve for electrical propagation using the monodomain or bidomain equations, but parallel efficiency dropped rapidly when run on more than about 64 processors. Throughout the course of the study, improvements were made to problem definition input; geometric mesh partitioning; finite-element assembly of large, sparse linear systems; problem-specific matrix preconditioning; numerical solution of the linear system; and output of the approximate solution. The consequence of these improvements is that, at the end of the study, Chaste is able to solve a monodomain benchmark problem in close to real time. While some of the improvements made to the parallel Chaste code are specific to cardiac electrophysiology, many of the techniques documented in this paper are generic to the parallel finite-element method in other scientific application areas.
The BLADE-ON-PETIOLE genes of Arabidopsis are essential for resistance induced by methyl jasmonate
Authors: Canet Juan Vicente , Dobón Albor , Fajmonová Jana , Tornero Pablo 
Published: February 2013

Abstract

Background

NPR1 is a gene of Arabidopsis thaliana required for the perception of salicylic acid. This perception triggers a defense response and negatively regulates the perception of jasmonates. Surprisingly, the application of methyl jasmonate also induces resistance, and NPR1 is also suspected to be relevant. Since an allelic series of npr1 was recently described, the behavior of these alleles was tested in response to methyl jasmonate.

Results
The response to methyl jasmonate of different npr1s alleles and NPR1 paralogs null mutants was measured by the growth of a pathogen. We have also tested the subcellular localization of some npr1s, along with the protein-protein interactions that can be measured in yeast. The localization of the protein in npr1 alleles does not affect the response to methyl jasmonate. In fact, NPR1 is not required. The genes that are required in a redundant fashion are the BOPs. The BOPs are paralogs of NPR1, and they physically interact with the TGA family of transcription factors.

Conclusions
Some npr1 alleles have a phenotype in this response likely because they are affecting the interaction between BOPs and TGAs, and these two families of proteins are responsible for the resistance induced by methyl jasmonate in wild type plants.
Associations between dietary patterns and gene expression profiles of healthy men and women: a cross-sectional study
Authors: Bouchard-Mercier Annie , Paradis Ann-Marie , Rudkowska Iwona , Lemieux Simone , Couture Patrick , Vohl Marie-Claude 
Published: February 2013

AbstractBackgroundDiet regulates gene expression profiles by several mechanisms. The objective of this study was to examine gene expression in relation with dietary patterns.MethodsTwo hundred and fifty four participants from the greater Quebec City metropolitan area were recruited. Two hundred and ten participants completed the study protocol. Dietary patterns were derived from a food frequency questionnaire (FFQ) by factor analysis. For 30 participants (in fasting state), RNA was extracted from peripheral blood mononuclear cells (PBMCs) and expression levels of 47,231 mRNA transcripts were assessed using the Illumina Human-6 v3 Expression BeadChips®. Microarray data was pre-processed with Flexarray software and analysed with Ingenuity Pathway Analysis (IPA).ResultsTwo dietary patterns were identified. The Prudent dietary pattern was characterised by high intakes of vegetables, fruits, whole grain products and low intakes of refined grain products and the Western dietary pattern, by high intakes of refined grain products, desserts, sweets and processed meats. When individuals with high scores for the Prudent dietary pattern where compared to individuals with low scores, 2,083 transcripts were differentially expressed in men, 1,136 transcripts in women and 59 transcripts were overlapping in men and women. For the Western dietary pattern, 1,021 transcripts were differentially expressed in men with high versus low scores, 1,163 transcripts in women and 23 transcripts were overlapping in men and women. IPA reveals that genes differentially expressed for both patterns were present in networks related to the immune and/or inflammatory response, cancer and cardiovascular diseases.ConclusionGene expression profiles were different according to dietary patterns, which probably modulate the risk of chronic diseases.Trial RegistrationNCT:NCT01343342
Silica induces NLRP3 inflammasome activation in human lung epithelial cells
Authors: Peeters Paul M , Perkins Timothy N , Wouters Emiel FM , Mossman Brooke T , Reynaert Niki L 
Published: February 2013

Abstract

Background
In myeloid cells the inflammasome plays a crucial role in innate immune defenses against pathogen- and danger-associated patterns such as crystalline silica. Respirable mineral particles impinge upon the lung epithelium causing irreversible damage, sustained inflammation and silicosis. In this study we investigated lung epithelial cells as a target for silica-induced inflammasome activation.

Methods
A human bronchial epithelial cell line (BEAS-2B) and primary normal human bronchial epithelial cells (NHBE) were exposed to toxic but nonlethal doses of crystalline silica over time to perform functional characterization of NLRP3, caspase-1, IL-1β, bFGF and HMGB1. Quantitative RT-PCR, caspase-1 enzyme activity assay, Western blot techniques, cytokine-specific ELISA and fibroblast (MRC-5 cells) proliferation assays were performed.

Results
We were able to show transcriptional and translational upregulation of the components of the NLRP3 intracellular platform, as well as activation of caspase-1. NLRP3 activation led to maturation of pro-IL-1β to secreted IL-1β, and a significant increase in the unconventional release of the alarmins bFGF and HMGB1. Moreover, release of bFGF and HMGB1 was shown to be dependent on particle uptake. Small interfering RNA experiments using siNLRP3 revealed the pivotal role of the inflammasome in diminished release of pro-inflammatory cytokines, danger molecules and growth factors, and fibroblast proliferation.

Conclusion
Our novel data indicate the presence and functional activation of the NLRP3 inflammasome by crystalline silica in human lung epithelial cells, which prolongs an inflammatory signal and affects fibroblast proliferation, mediating a cadre of lung diseases.
Effects of the breed, sex and age on cellular content and growth factor release from equine pure-platelet rich plasma and pure-platelet rich gel
Authors: Giraldo Carlos E , López Catalina , Álvarez María E , Samudio Ismael J , Prades Marta , Carmona Jorge U 
Published: February 2013

AbstractBackgroundThere is no information on the effects of the breed, gender and age on the cellular content and growth factor (GF) release from equine pure-platelet rich plasma (P-PRP) and pure-platelet rich gel (P-PRG). The objectives of this study were: 1) to compare the cellular composition of P-PRP with whole blood and platelet poor plasma (PPP); 2) to compare the concentration of transforming GF beta 1 (TGF-β1) and platelet derived GF isoform BB (PDGF-BB) between P-PRP treated with non-ionic detergent (P-PRP+NID), P-PRG (activated with calcium gluconate -CG-), PPP+NID, PPP gel (PPG), and plasma and; 3) to evaluate and to correlate the effect of the breed, gender and age on the cellular and GF concentration for each blood component. Forty adult horses, 20 Argentinean Creole Horses (ACH) and, 20 Colombian Creole Horses (CCH) were included. Data were analyzed by parametric (i.e.: t-test, one way ANOVA) and non parametric (Kruskal-Wallis test, Wilcoxon test) tests. Correlation analysis was also performed by using the Spearman and Pearson tests. A p ≤ 0.05 was set as significant for all tests. All the blood components were compared for platelet (PLT), leukocyte (WBC), TGF-β1and PDGF-BB concentrations. The effect of the breed, gender and age on these variables was analyzed. A P ≤ 0.05 was accepted as significant for all the tests.ResultsPLT counts were 1.8 and 0.6 times higher in P-PRP than in whole blood and PPP, respectively; WBC counts were 0.5 and 0.1 times lower in P-PRP, in comparison with whole blood and PPP, respectively. TGF-β1and PDGF-BB concentrations were 2.3 and 262 times higher, respectively, in P-PRG than in plasma, and 0.59 and 0.48 times higher, respectively, in P-PRG than in PPG. P-PRG derived from CCH females or young horses presented significantly (P < 0.001) higher PDGF-BB concentrations than P-PRG derived from ACH males or older horses.ConclusionsOur results indicated that P-PRP obtained by a manual method was affected by intrinsic factors such as the breed, gender and age. Equine practitioners should be aware that cellular and GF release from P-PRP/P-PRG could change according with the intrinsic variables associated with a patient in particular.
Synthesis, antifungal and antibacterial activity for novel amide derivatives containing a triazole moiety
Authors: Tang Ruping , Jin Linhong , Mou Chengli , Yin Juan , Bai Song , Hu Deyu , Wu Jian , Yang Song , Song Baoan 
Published: February 2013

Abstract

Background
Plant fungi (e.g., Pellicularia sasakii, Gibberella zeae, Fusarium oxysporum, and Cytospora mandshurica and Phytophthora infestans) and bacteria (e.g., Ralstonia solanacearum) are extremely difficult to manage in agricultural production. The high incidence of plant mortality and the lack of effective control methods make P. sasakii and R. solanacearum two of the world’s most destructive plant pathogens. Pathogenic fungi and bacteria are responsible for billions of dollars in economic losses worldwide each year. Thus, we designed an active amide structure and synthesized a series of novel amide derivatives containing a triazole moiety to discover new bioactive molecules and pesticides that can act against fungi and bacteria.

Results
A series of amide derivatives containing a triazole moiety were synthesized. All the obtained compounds were characterized through proton and carbon nuclear magnetic resonance spectroscopy, infrared spectroscopy, and elemental analysis. Preliminary antifungal activity test showed that some of the synthesized compounds exhibited moderate antifungal activity against P. sasakii, G. azeae, F. oxysporum, C. mandshurica, and P. infestans at 50 mg/L. Compound 4u displayed more potent antifungal activity against P. sasakii and G. azeae than hymexazol. Preliminary antibacterial activity results showed that some of the synthesized compounds exhibited high anti-bacterial activity against R. solanacearum at 200 mg/L. Compounds 4m and 4q displayed high antibacterial activity against R. solanacearum, with 71% and 65% inhibitory rates, respectively.

Conclusions
A series of novel amide derivatives containing 1,2,4-triazole moiety were synthesized through the reaction of intermediate 3 with different acyl chlorides and anhydrous potassium carbonates in anhydrous tetrahydrofuran at 50°C, using 2,4-dichloroacetophenoneas as a starting material. The title compounds exhibited high inhibitory effects against P. sasakii, R. solanacearum, and G. azeae.
Semiempirical investigations on the stabilization energies and ionic hydrogen-bonded structures of F−(H2O)
n
and Cl−(H2O)
n
(n = 1–4) clusters
Authors: Wang Qi , Suzuki Kimichi , Nagashima Umpei , Tachikawa Masanori , Yan Shiwei 
Published: February 2013

Abstract
Several semiempirical methods were utilized to analyze the structures and stabilities of X
−(H2O)
n
(X = F, Cl; n = 1–4) clusters with respect to the number of water molecules through their comparison with ab initio molecular orbital calculations. Our results show that the recently developed PM6-DH+ semiempirical method can provide reasonable binding energies of hydrated fluoride and chloride ion clusters, which are consistent with the corresponding experimental results. For the optimized geometries of X = F, however, the semiempirical methods show that the global minima are close to HF(OH)−(H2O)
n−1 structures, which are different from the ab initio calculations. Meanwhile, the topological characteristics for the global minima of X = Cl obtained by semiempirical methods have the same symmetries with ab initio calculations. All calculation levels agree on the trend of decreasing ion-water interaction with the increasing number of water molecules. We also found a new structure of Cl−(H2O)4 with a second hydration shell as a complement of previous studies. Those are very important data for our near-future study of on-the-fly semiempirical molecular dynamics (MD) or path integral MD simulation.

PACS

36.40.Mr, 31.15.bu, 31.15.A-