bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach
Authors: Mukhopadhyay Anirban , Ray Sumanta , Maulik Ujjwal 
Published: January 2014

Abstract

Background
Discovering novel interactions between HIV-1 and human proteins would greatly contribute to different areas of HIV research. Identification of such interactions leads to a greater insight into drug target prediction. Some recent studies have been conducted for computational prediction of new interactions based on the experimentally validated information stored in a HIV-1-human protein-protein interaction database. However, these techniques do not predict any regulatory mechanism between HIV-1 and human proteins by considering interaction types and direction of regulation of interactions.

Results
Here we present an association rule mining technique based on biclustering for discovering a set of rules among human and HIV-1 proteins using the publicly available HIV-1-human PPI database. These rules are subsequently utilized to predict some novel interactions among HIV-1 and human proteins. For prediction purpose both the interaction types and direction of regulation of interactions, (i.e., virus-to-host or host-to-virus) are considered here to provide important additional information about the regulation pattern of interactions. We have also studied the biclusters and analyzed the significant GO terms and KEGG pathways in which the human proteins of the biclusters participate. Moreover the predicted rules have also been analyzed to discover regulatory relationship between some human proteins in course of HIV-1 infection. Some experimental evidences of our predicted interactions have been found by searching the recent literatures in PUBMED. We have also highlighted some human proteins that are likely to act against the HIV-1 attack.

Conclusions
We pose the problem of identifying new regulatory interactions between HIV-1 and human proteins based on the existing PPI database as an association rule mining problem based on biclustering algorithm. We discover some novel regulatory interactions between HIV-1 and human proteins. Significant number of predicted interactions has been found to be supported by recent literature.
Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner–toward the identification of candidate genes for marker assisted-selection
Authors: Cardoso Danielle C , Martinati Juliana C , Giachetto Poliana F , Vidal Ramon O , Carazzolle Marcelo F , Padilha Lilian , Guerreiro-Filho Oliveiro , Maluf Mirian P 
Published: January 2014

Abstract

Background
A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense response. To understand the transcriptional basis of this response, we compare gene expression profiles of two coffee genotypes, susceptible and resistant to leaf miner (Leucoptera coffella). A total of 22000 EST sequences from the Coffee Genome Database were selected for a microarray analysis. Fluorescence probes were synthesized using mRNA from the infested and non-infested coffee plants. Array hybridization, scanning and data normalization were performed using Nimble Scan® e ArrayStar® platforms. Genes with foldchange values +/-2 were considered differentially expressed. A validation of 18 differentially expressed genes was performed in infected plants using qRT-PCR approach.

Results
The microarray analysis indicated that resistant plants differ in gene expression profile. We identified relevant transcriptional changes in defense strategies before insect attack. Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated). Up-regulated genes include those responsible for defense mechanisms, hypersensitive response and genes involved with cellular function and maintenance. Also, our analyses indicated that differential expression profiles between resistant and susceptible genotypes are observed in the absence of leaf-miner, indicating that defense is already build up in resistant plants, as a priming mechanism. Validation of selected genes pointed to four selected genes as suitable candidates for markers in assisted-selection of novel cultivars.

Conclusions
Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions. Also analyses suggest a major metabolic reconfiguration that highlights the complexity of this response.
Race/ethnicity and HAART initiation in a military HIV infected cohort
Authors: Johnson Erica N , Roediger Mollie P , Landrum Michael L , Crum-Cianflone Nancy F , Weintrob Amy C , Ganesan Anuradha , Okulicz Jason F , Macalino Grace E , Agan Brian K ,   the Infectious Disease Clinical Research Program HIV Working Group
Published: January 2014

Abstract

Background
Prior studies have suggested that HAART initiation may vary by race/ethnicity. Utilizing the U.S. military healthcare system, which minimizes confounding from healthcare access, we analyzed whether timing of HAART initiation and the appropriate initiation of primary prophylaxis among those at high risk for pneumocystis pneumonia (PCP) varies by race/ethnicity.

Methods
Participants in the U.S. Military HIV Natural History Study from 1998-2009 who had not initiated HAART before 1998 and who, based on DHHS guidelines, had a definite indication for HAART (CD4 <200, AIDS event or severe symptoms; Group A), an indication to consider HAART (including CD4 <350; Group B) or electively started HAART (CD4 >350; Group C) were analyzed for factors associated with HAART initiation. In a secondary analysis, participants were also evaluated for factors associated with starting primary PCP prophylaxis within four months of a CD4 count <200 cells/mm3. Multiple logistic regression was used to compare those who started vs. delayed therapy; comparisons were expressed as odds ratios (OR).

Results
1262 participants were evaluated in the analysis of HAART initiation (A = 208, B = 637, C = 479 [62 participants were evaluated in both Groups A and B]; 94% male, 46% African American, 40% Caucasian). Race/ethnicity was not associated with HAART initiation in Groups A or B. In Group C, African American race/ethnicity was associated with lower odds of initiating HAART (OR 0.49, p = 0.04). Race and ethnicity were also not associated with the initiation of primary PCP prophylaxis among the 408 participants who were at risk.

Conclusions
No disparities in the initiation of HAART or primary PCP prophylaxis according to race/ethnicity were seen among those with an indication for therapy. Among those electively initiating HAART at the highest CD4 cell counts, African American race/ethnicity was associated with decreased odds of starting. This suggests that free healthcare can potentially overcome some of the observed disparities in HIV care, but that unmeasured factors may contribute to differences in elective care decisions.
The effect of antiviral therapy on hepatitis C virus-related thrombocytopenia: a case report
Authors: Lebano Rita , Rosato Valerio , Masarone Mario , Romano Marco , Persico Marcello 
Published: January 2014

Abstract

Background
Autoimmune thrombocytopenic purpura is an immunological disorder characterized by increased platelet destruction due to presence of anti-platelet autoantibodies. Hepatitis C virus infection, which is one of the most common chronic viral infections worldwide, may cause secondary chronic immune thrombocytopenic purpura.

Case presentation
We report a case of a 51-year-old Caucasian female with hepatitis C virus infection who developed a severe, reversible, immune thrombocytopenia. Platelet count was as low as 56.000/mm3, hepatitis C virus serology was positive, serum glutamic oxaloacetic transaminase, serum glutamic pyruvic transaminase and gamma-glutamyltransferase serum levels were elevated. Disorders potentially associated with autoimmune thrombocytopenic purpura were ruled out. A corticosteroid treatment was started and led to an increase in platelet count. The patient was then treated with pegylated-interferon alpha 2a and ribavirin. After four weeks of treatment hepatitis C virus - ribonucleic acid became undetectable and steroid treatment was discontinued. Six months of antiviral therapy achieved a sustained biochemical and virological response together with persistence of normal platelet count.

Conclusion
In our case report hepatitis C virus seemed to play a pathogenic role in autoimmune thrombocytopenic purpura. Moreover, the successful response (negative hepatitis C virus - ribonucleic acid) to tapered steroids and antiviral therapy was useful to revert thrombocytopenia.
Purification and characterization of a specific late-larval esterase from two species of the Drosophila repleta group: contributions to understand its evolution
Authors: Lopes Vanessa F , Cabral Hamilton , Machado Luciana PB , Mateus Rogério P 
Published: January 2014

Abstract

Background
After duplication, one copy of an original gene can become redundant and decay toward a pseudogene status or functionally diverge. Here, we performed the purification and biochemical characterization of EST-4 (a late larval β-esterase) from two Drosophila repleta group species, Drosophila mulleri and Drosophila arizonae, in order to establish comparative parameters between these enzymes in these species and to contribute to better understand their evolution.

Results
In D. mulleri, EST-4 had an optimal activity in temperatures ranging from 40° to 45°C and at pH 7.5, maintaining stability in alkaline pH (8.0 to 10.0). It was classified as serine esterase as its activity was inhibited by PMSF. No ion negatively modulated EST-4 activity, and iron had the most positive modulating effect. In D. arizonae, it showed similar optimum temperature (40°C), pH (8.0), and was also classified as a serine esterase, but the enzymatic stability was maintained in an acidic pH (5.5 to 6.5). Fe+2 had the opposite effect found in D. mulleri, that is, negative modulation. Al+3 almost totally inhibited the EST-4 activity, and Na+ and Cu+2 had a positive modulation effect. Kinetic studies, using ρ-nitrophenyl acetate as substrate, showed that EST-4 from D. mulleri had higher affinity, while in D. arizonae, it showed higher V
max and catalytic efficiency in optimal reaction conditions.

Conclusions
EST-4 from D. mulleri and D. arizonae are very closely related and still maintain several similar features; however, they show some degree of differentiation. Considering that EST-4 from D. mulleri has more conspicuous gel mobility difference among all EST-4 studied so far and a lower catalytic efficiency was observed here, we proposed that after duplication, this new copy of the original gene became redundant and started to decay toward a pseudogene status in this species, which probably is not occurring in D. arizonae.
Comparative study of the adsorption of acetaminophen on activated carbons in simulated gastric fluid
Authors: Rey-Mafull Carlos A , Tacoronte Juan E , Garcia Raquel , Tobella Jorge , Llópiz Julio C , Iglesias Alberto , Hotza Dachamir 
Published: January 2014

Abstract
Samples of commercial activated carbons (AC) obtained from different sources: Norit E Supra USP, Norit B Test EUR, and ML (Baracoa, Cuba) were investigated. The adsorption of acetaminophen, Co = 2500 mg/L, occured in simulated gastric fluid (SGF) at pH 1.2 in contact with activated carbon for 4 h at 310 K in water bath with stirring. Residual acetaminophen was monitored by UV visible. The results were converted to scale adsorption isotherms using alternative models: Langmuir TI and TII, Freundlich, Dubinin-Radushkevich (DR) and Temkin. Linearized forms of the characteristic parameters were obtained in each case. The models that best fit the experimental data were Langmuir TI and Temkin with R2 ≥0.98. The regression best fits followed the sequence: Langmuir TI = Temkin > DR > LangmuirTII > Freundlich. The microporosity determined by adsorption of CO2 at 273 K with a single term DR regression presented R2 > 0.98. The adsorption of acetaminophen may occur in specific sites and also in the basal region. It was determined that the adsorption process of acetaminophen on AC in SGF is spontaneous (ΔG <0) and exothermic (−ΔHads.). Moreover, the area occupied by the acetaminophen molecule was calculated with a relative error from 7.8 to 50%.
Pharmaceutical company perspectives on current safety risk communications in Japan
Authors: Urushihara Hisashi , Kobashi Gen , Masuda Hideaki , Taneichi Setsuko , Yamamoto Michiko , Nakayama Takeo , Kawakami Koji , Matsuda Tsutomu , Ohta Kaori , Sugimori Hiroki 
Published: January 2014

Abstract
In 1987, a group infection of hepatitis in patients receiving a contaminated fibrinogen product was first reported to the Japanese regulatory agency. Eventually, this serious drug incident involved more than 10,000 cases of infection. In response, the Government of Japan established a responding inspection committee in 2008 to make recommendations for the restructuring of drug regulatory administration. The final report was issued in 2010. One agenda item of this restructuring was the improvement of drug-related safety risk communications. Our research group on drug safety risk communications, which is funded by the Government of Japan, surveyed pharmaceutical companies regarding their perspective on current risk communications. The survey was conducted using an anonymous questionnaire developed for this study which included the three operational domains of targets, contents, and measures of drug risk communication. Fifty-two of the 74 member companies of the Post-marketing Surveillance Subcommittee of the Japan Pharmaceutical Manufacturer’s Association participated, and this response rate of more than 70% was considered sufficient to ensure the external validity of the survey results. Results showed that the most highly prioritized aspect of risk messaging was the strength of evidence, and that outcome evaluation of risk communication gained recognition. Further, while physicians and pharmacists were the most prioritized communication targets, pharmacovigilance departments devoted the most resources to regulators, at more than 30%. The Internet was recognized as a useful public source of risk information, whereas Drug Guides for Patients delivered on the web were considered under-recognized. Further discussion of these results with the aim of enhancing the restructuring of the Japanese drug regulatory administration system are warranted.
Mechanisms of endothelial dysfunction in rheumatoid arthritis: lessons from animal studies
Authors: Totoson Perle , Maguin-Gaté Katy , Prati Clément , Wendling Daniel , Demougeot Céline 
Published: January 2014

AbstractRheumatoid arthritis (RA) is a chronic systemic inflammatory disease characterized by articular and extra-articular manifestations involving cardiovascular diseases (CVDs), which account for 30% to 50% of all deaths. In patients with RA, atherosclerosis lesions occur earlier and have a more rapid evolution than in the general population. Beyond mortality, the impact of CVD on quality of life, combined with the associated increase in health-care costs, renders CVD in RA a major public health problem. Recent studies showed that patients with RA are characterized by the presence of endothelial dysfunction (ED), which is recognized as a key event in the development of atherosclerosis. By definition, ED is a functional and reversible alteration of endothelial cells, leading to a shift of the actions of the endothelium toward reduced vasodilation, proinflammatory state and proliferative and prothrombotic properties. Although the improvement of endothelial function is becoming an important element of the global management of patients with RA, the mechanistic determinants of ED in RA are still poorly understood. Animal models of RA provide the unique opportunity to unravel the pathophysiological features of ED in RA. The present review summarizes the available data on mechanisms underlying ED in animal models of RA and proposes attractive prospects in order to discover novel therapeutic strategies of RA-associated ED.
Pharmacokinetics, hemodynamic and metabolic effects of epinephrine to prevent post-operative low cardiac output syndrome in children
Authors: Oualha Mehdi , Urien Saïk , Spreux-Varoquaux Odile , Bordessoule Alice , D’Agostino Irène , Pouard Philippe , Tréluyer Jean-Marc 
Published: January 2014

Abstract
Introduction
The response to exogenous epinephrine (Ep) is difficult to predict given the multitude of factors involved such as broad pharmacokinetic and pharmacodynamic between-subject variabilities, which may be more pronounced in children. We investigated the pharmacokinetics and pharmacodynamics of Ep, co-administered with milrinone, in children who underwent open heart surgical repair for congenital defects following cardiopulmonary bypass, including associated variability factors.

Methods
Thirty-nine children with a high risk of low cardiac output syndrome were prospectively enrolled. Ep pharmacokinetics, hemodynamic and metabolic effects were analyzed using the non-linear mixed effects modeling software MONOLIX. According to the final model, an Ep dosing simulation was suggested.

Results
Ep dosing infusions ranged from 0.01 to 0.23 μg.kg-1.min-1 in children whose weight ranged from 2.5 to 58 kg. A one-compartment open model with linear elimination adequately described the Ep concentration-time courses. Bodyweight (BW) was the main covariate influencing clearance (CL) and endogenous Ep production rate (q0) via an allometric relationship: CL(BWi) = θCL x (BWi)3/4 and q0(BWi) = θq0 x (BWi )3/4. The increase in heart rate (HR) and mean arterial pressure (MAP) as a function of Ep concentration were well described using an Emax model. The effect of age was significant on HR and MAP basal level parameters. Assuming that Ep stimulated the production rate of plasma glucose, the increases in plasma glucose and lactate levels were well described by turnover models without any significant effect of age, BW or exogenous glucose supply.

Conclusions
According to this population analysis, the developmental effects of BW and age explained a part of the pharmacokinetic and pharmacodynamics between-subject variabilities of Ep administration in critically ill children. This approach ultimately leads to a valuable Ep dosing simulation which should help clinicians to determine an appropriate a priori dosing regimen.
Role of Multicultural Education in Development of Students’ Motivational and Cognitive Sphere
Authors: Бикбулатова  , Bikbulatova Valentina , Рабаданова  , Rabadanova Raziyat , Юлина  , Yulina Galina 
Published: January 2014

The article presents the psychological aspects of education and conditions
of realization of the creative potential of the student&#180;s personality in the educational
activity.
Isothermal Recombinase Polymerase Amplification Assay Applied to the Detection of Group B Streptococci in Vaginal/Anal Samples
Authors: Daher Rana K , Stewart Gale , Boissinot Maurice , Bergeron Michel G 
Published: January 2014

Abstract

BACKGROUND
Group B streptococcal infections are the leading cause of sepsis and meningitis in newborns. A rapid and reliable method for the detection of this pathogen at the time of delivery is needed for the early treatment of neonates. Isothermal amplification techniques such as recombinase polymerase amplification have advantages relative to PCR in terms of the speed of reaction and simplicity.

METHODS
We studied the clinical performance of recombinase polymerase amplification for the screening of group B streptococci in vaginal/anal samples from 50 pregnant women. We also compared the limit of detection and the analytical specificity of this isothermal assay to real-time PCR (RT-PCR).

RESULTS
Compared to RT-PCR, the recombinase polymerase amplification assay showed a clinical sensitivity of 96% and a clinical specificity of 100%. The limit of detection was 98 genome copies and the analytical specificity was 100% for a panel of 15 bacterial and/or fungal strains naturally found in the vaginal/anal flora. Time-to-result for the recombinase polymerase amplification assay was &lt;20 min compared to 45 min for the RT-PCR assay; a positive sample could be detected as early as 8 min.

CONCLUSIONS
We demonstrate the potential of isothermal recombinase polymerase amplification assay as a clinically useful molecular diagnostic tool that is simple and faster than PCR/RT-PCR. Recombinase polymerase amplification offers great potential for nucleic acid–based diagnostics at the point of care.
Women and posters as heterotopias in Ousmane Sembene’s Xala
Authors: Dima Vlad 
Published: January 2014

Abstract
This article analyses the connections between the female characters of Ousmane Sembene’s Xala and the diegetic posters seen on the walls during the film, which yields a new conversation on Michel Foucault’s heterotopias as utopias or non-spaces. As a result, women, posters and heterotopias define the spatial evolution of the main characters (including the male) as well as that of the film itself.
How text reflects context: Representation of African film audiences in Aristotle’s Plot
Authors: Groof Matthias De 
Published: January 2014

Abstract
This article analyses how Aristotle’s Plot reflects on the context of film-making and film reception in Africa. Aristotle’s Plot represents the relation between an African film-maker and African film audiences consuming foreign movies and disapproving African cinema. The problem of how the production and consumption of African cinema is affected by the importation of films crafted elsewhere cannot be reduced to the question how to make African films available for their audiences. Neither can the problem solely be posed in terms of the alienation of African audiences and film-makers. In Aristotle’s Plot, Bekolo caricatures both the African film-maker (E.T.) and African audiences (Cinema) and thereby translates two views on spectatorship. However, the film itself suggests a perspective on spectatorship and film-making beyond the opposition of appropriation on the one hand and alienation on the other.
Film cities and competitive advantage: Development factors in South African film
Authors: Tomaselli Keyan G. 
Published: January 2014

Abstract
The post-apartheid film industry is a contested space. This study examines the nature of competitiveness, the idea of film precincts and film and media cities, through the prism of Michael Porter’s Diamond Model for competitive advantage. Issues of globalization, cultural policy and sector development are discussed with regard to linking micro with macro developments in production, distribution and audience development in South Africa. The study examines micro-macro relations within holistic value chain circuits that connect production (small and large scale) with exhibition (in the form of an employment-generating, national roll out of modular-based mini-cinema complexes). Overall, this article delineates the broad parameters of an on-going research project.