Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk of Cardiovascular Disease from Antiretroviral Therapy for HIV: A Systematic Review

Background Recent studies suggest certain antiretroviral therapy (ART) drugs are associated with increases in cardiovascular disease. Purpose We performed a systematic review and meta-analysis to summarize the available evidence, with the goal of elucidating whether specific ART drugs are associated with an increased risk of myocardial infarction (MI). Data Sources We searched Medline, Web of Science, the Cochrane Library, and abstract archives from the Conference on Retroviruses and Opportunistic Infections and International AIDS Society up to June 2011 to identify published articles and abstracts. Study Selection Eligible studies were comparative and included MI, strokes, or other cardiovascular events as outcomes. Data Extraction Eligibility screening, data extraction, and quality assessment were performed independently by two investigators. Data Synthesis Random effects methods and Fisher’s combined probability test were used to summarize evidence. Findings Twenty-seven studies met inclusion criteria, with 8 contributing to a formal meta-analysis. Findings based on two observational studies indicated an increase in risk of MI for patients recently exposed (usually defined as within last 6 months) to abacavir (RR 1.92, 95% CI 1.51–2.42) and protease inhibitors (PI) (RR 2.13, 95% CI 1.06–4.28). Our analysis also suggested an increased risk associated with each additional year of exposure to indinavir (RR 1.11, 95% CI 1.05–1.17) and lopinavir (RR 1.22, 95% CI 1.01–1.47). Our findings of increased cardiovascular risk from abacavir and PIs were in contrast to four published meta-analyses based on secondary analyses of randomized controlled trials, which found no increased risk from cardiovascular disease. Conclusion Although observational studies implicated specific drugs, the evidence is mixed. Further, meta-analyses of randomized trials did not find increased risk from abacavir and PIs. Our findings that implicate specific ARTs in the observational setting provide sufficient evidence to warrant further investigation of this relationship in studies designed for that purpose.
Evidence for differential localization of noradrenaline and neuropeptide Y in neuronal storage vesicles isolated from rat vas deferens

Using the technique of homogenization and subsequent density gradient centrifugation combined with ultrastructural analysis, the subcellular localization of noradrenaline and neuropeptide Y (NPY) was studied in vas deferens of castrated male rats. Noradrenaline showed two peaks in the gradient: one major peak at low density and another at high density. Only one NPY peak was seen, which coincided with the high density peak of noradrenaline. Electron microscopic analysis revealed high proportions of small and large vesicles in the light and heavy fractions, respectively. The present results indicate a differential subcellular localization of noradrenaline and NPY in the noradrenergic nerve endings of vas deferens. Thus, small vesicles seem to contain only noradrenaline, whereas the large vesicles may contain both noradrenaline and NPY.
Different levels of hsp70 and hsc70 mRNA expression in Iberian fish exposed to distinct river conditions

Comprehension of the mechanisms by which ectotherms, such as fish, respond to thermal stress is paramount for understanding the threats that environmental changes may pose to wild populations. Heat shock proteins are molecular chaperones with an important role in several stress conditions such as high temperatures. In the Iberian Peninsula, particularly in Portugal, freshwater fish of the genus Squalius are subject to daily and seasonal temperature variations. To examine the extent to which different thermal regimes influence the expression patterns of hsp70 and hsc70 transcripts we exposed two species of Squalius (S. torgalensis and S. carolitertii) to different temperatures (20, 25, 30 and 35 °C). At 35 °C, there was a significant increase in the expression of hsp70 and hsc70 in the southern species, S. torgalensis, while the northern species, S. carolitertii, showed no increase in the expression of these genes; however, some individuals of the latter species died when exposed to 35 °C. These results suggest that S. torgalensis may cope better with harsher temperatures that are characteristic of this species natural environment; S. carolitertii, on the other hand, may be unable to deal with the extreme temperatures faced by the southern species.
T cell receptor ligation induces the formation of dynamically regulated signaling assemblies

Tcell antigen receptor (TCR) ligation initiates tyrosine kinase activation, signaling complex assembly, and immune synapse formation. Here, we studied the kinetics and mechanics of signaling complex formation in live Jurkat leukemic T cells using signaling proteins fluorescently tagged with variants of enhanced GFP (EGFP). Within seconds of contacting coverslips coated with stimulatory antibodies, T cells developed small, dynamically regulated clusters which were enriched in the TCR, phosphotyrosine, ZAP-70, LAT, Grb2, Gads, and SLP-76, excluded the lipid raft marker enhanced yellow fluorescent protein–GPI, and were competent to induce calcium elevations. LAT, Grb2, and Gads were transiently associated with the TCR. Although ZAP-70–containing clusters persisted for more than 20 min, photobleaching studies revealed that ZAP-70 continuously dissociated from and returned to these complexes. Strikingly, SLP-76 translocated to a perinuclear structure after clustering with the TCR. Our results emphasize the dynamically changing composition of signaling complexes and indicate that these complexes can form within seconds of TCR engagement, in the absence of either lipid raft aggregation or the formation of a central TCR-rich cluster.
Bayesian tangent shape model: estimating shape and pose parameters via Bayesian inference

In this paper we study the problem of shape analysis and its application in locating facial feature points on frontal faces. We propose a Bayesian inference solution based on tangent shape approximation called Bayesian tangent shape model (BTSM). Similarity transform coefficients and the shape parameters in BTSM are determined through MAP estimation. Tangent shape vector is treated as the hidden state of the model, and accordingly, an EM based searching algorithm is proposed to implement the MAP procedure. The major results of our algorithm are: 1) tangent shape is updated by a weighted average of two shape vectors, the projection of the observed shape onto tangent space, and the reconstruction of shape parameters. 2) Shape parameters are regularized by multiplying a ratio of the noise variations, which is a continuous function instead of a truncated function. We discussed the advantages conveyed by these results, and demonstrate the accuracy and the stability of the algorithm by extensive experiments.
Molecular Mechanisms of Drug Abuse, Dependency and Craving

Drug abuse and dependence are major medical, social, and economic problems for the world. Whereas the means to reduce abuse are well known, drug dependency is a complex medical disease and current treatments attempt to reduce or prevent drug craving in dependent people as part of therapy. With the increased understanding of the neural mechanisms of drug dependence and the availability of several drugs that can treat craving in certain drug dependent populations it is important to summarize development of anti-craving therapeutics world-wide. The present paper briefly outlines the problems of drug abuse and dependence, key aspects of the drug dependence process, the nature and mechanisms of drug craving in dependent people, current drug dependence theories, and finally mechanisms of action of anti-craving agents. We conclude with suggestions about potentially useful leads for anti-craving therapy. *Corresponding author: Richard E. Wilcox, Ph.D, Professor of Neuropharmacology, University of Texas, College of Pharmacy 2409, University Avenue STOP A1900 Austin, TX 78712-1113; Tel: +(512) 471-5199; E-mail: wilcoxrich@austin.utexas. edu Received Date: November 4, 2015 Accepted Date: December 30, 2015 Published Date: January 5, 2016
Interactive visual editing of grammars for procedural architecture

We introduce a real-time interactive visual editing paradigm for shape grammars, allowing the creation of rulebases from scratch without text file editing. In previous work, shape-grammar based procedural techniques were successfully applied to the creation of architectural models. However, those methods are text based, and may therefore be difficult to use for artists with little computer science background. Therefore the goal was to enable a visual work-flow combining the power of shape grammars with traditional modeling techniques. We extend previous shape grammar approaches by providing direct and persistent local control over the generated instances, avoiding the combinatorial explosion of grammar rules for modifications that should not affect all instances. The resulting visual editor is flexible: All elements of a complex state-of-the-art grammar can be created and modified visually.
Data Normalization Strategies for MicroRNA Quantification.

BACKGROUND Different technologies, such as quantitative real-time PCR or microarrays, have been developed to measure microRNA (miRNA) expression levels. Quantification of miRNA transcripts implicates data normalization using endogenous and exogenous reference genes for data correction. However, there is no consensus about an optimal normalization strategy. The choice of a reference gene remains problematic and can have a serious impact on the actual available transcript levels and, consequently, on the biological interpretation of data. CONTENT In this review article we discuss the reliability of the use of small RNAs, commonly reported in the literature as miRNA expression normalizers, and compare different strategies used for data normalization. SUMMARY A workflow strategy is proposed for normalization of miRNA expression data in an attempt to provide a basis for the establishment of a global standard procedure that will allow comparison across studies.
Application of Differential Evolution to determine the HEPWM angles of a three phase voltage source inverter

This paper presents an efficient Differential Evolution (DE) based solution for harmonic elimination pulse-width modulation (HEPWM). The aim is to solve for the set of transcendental equations that determine the switching angles of the HEPWM waveform. The objective function of the DE is designed to minimize (to near zero) the selected harmonics and at the same time allows for the fundamental component of the output voltage to be controlled independently. To verify the method, simulation is carried out using MATLAB simulink. The computed switching angles are applied to a three phase voltage source inverter. Typical results are shown and discussed.
Cancer protection of soy resembles cancer protection during pregnancy

Abstract It has been established that carrying a pregnancy to full-term at an early age can protect against contracting cancer by up to 50% in later life. The trophoblast theory of cancer states that trophoblast and cancer tissue are very similar. New findings suggest that the loss of fetal cells during pregnancy resemble those cells responsible for causing metastasis in cancer. Fetal cells and spreading cancer cells are highly proliferative. They are similar to stem cells, exhibiting no or low hormone receptor expression, and require a hormone receptor independent mechanism for control. Control of membrane stability during pregnancy is of vital importance for a successful pregnancy and is mediated by androstenediol and 2-methoxyestradiol. 2-Methoxyestradiol has no hormone receptor affinity and elicits strong anticancer effects particularly against cancer stem cells and fetal cells, for which currently no treatment has yet been established. There is a discussion whether pregnancy reduces cancer stem cells in the breast. Soy isoflavones are structurally similar to both hormones, and elicit strong anticancer effects and antiangiogenesis via inhibition of NF-κB, even in hormone receptor independent breast cancers seen in epidemiologic studies. The trophoblast theory of cancer could help to explain why soy baby nutrition formulas have no effect on baby physiology, other than the nutritional aspect, although soy elicits many effects on the adult immune system. To survive the immune system of the mother, the immune system of the fetus has to be separated; otherwise, the reduction of the immune system in the mother, a necessary feature for the blastocyst to grow, would immediately reduce the immunity for the fetus and endanger its survival. Similar to a fetus, newly born babies show immune insensitive to Th1 and Th2 cytokines, which are necessary and crucial for regulating the immune system of the mother, thus raising the risk of the baby of developing allergies and neurodermatitis. Gene expression studies in vitro as well as in circulating tumor cells from patients consuming a fermented soy product support the antiangiogenic as well as antiproliferative effects of soy.
PREDICTION OF ANCHORAGE FAILURE FOR REINFORCED CONCRETE BEAMS STRENGTHENED WITH FIBER-REINFORCED POLYMER PLATES

This paper examines the anchorage failure mode of fiber-reinforced polymer (FRP)-strengthened reinforced concrete beams. An improved analytical procedure for calculating shear and normal stresses at the plate curtailment is presented. The analytical expressions are developed from linear elastic theory and statistical analyses of experimental results. The procedure is validated by comparisons with experimental results reported in the literature. Simplified, closed-form expressions to estimate the anchorage failure load for FRP-strengthened beams subjected to either concentrated or uniform loads are provided.
Abnormal Localization and Accumulation of FLT3-ITD, a Mutant Receptor Tyrosine Kinase Involved in Leukemogenesis

Aberrant subcellular localization of mutant transmembrane receptors is increasingly acknowledged as a possible mechanism for an altered signaling quality leading to transformation. There is evidence that mutated receptor tyrosine kinases of subclass III, for example the platelet-derived growth factor receptor (PDGFR) and KIT-protein, are aberrantly localized in human cancers. In order to further analyze this phenomenon, we investigated the localization of FLT3, a subclass III receptor tyrosine kinase frequently mutated in leukemia. By immunofluorescence staining and confocal laser scanning microscopy we found that in retrovirally transduced COS7 cells, wild type FLT3 receptor protein is localized primarily at the cell surface. In contrast, a mutant FLT3 receptor protein with an internal tandem duplication (ITD) accumulates in a perinuclear region and is not detectable at the plasma membrane. Surprisingly, and in contrast to previously published data, intracellular FLT3-ITD accumulation could neither be detected in the endoplasmic reticulum (ER) nor in the Golgi apparatus. Furthermore, transient overexpression per se leads to accumulation of wild type FLT3 receptor protein in the ER in addition to surface localization, probably due to inefficient intracellular transport by the overloaded sorting machinery of the secretory pathway. Based on our data and the immature glycosylation pattern of FLT3-ITD, we speculate that the mutant protein resides most probably in an unidentified compartment of the secretory pathway between the ER and the Golgi apparatus.
Development of silk fibroin tissue engineering scaffolds via indirect additive manufacturing for cartilage regeneration.

xvii Chapter 1 Introduction . 1 1.1 Background . 1 1.2 Motivation . 5 1.3 Objectives . 7 1.4 Scope . 8 1.5 Organization of Report . 9 Chapter 2 Literature Review . 11 2.1 Cartilage . 11 2.2 Tissue Engineering . 16 2.3 Clinical Applications of Tissue Engineering Scaffolds . 17 2.4 Requirements of Tissue Engineering Scaffolds . 20 2.5 Biomaterials . 23 2.5. 1 Natural Polymers . 23 2.5. 2 Synthetic Polymers . 26 2.5. 3 Composites . 27 2.6 Silk Fibroin . 29 2.7 Applications of Silk Fibroin in Tissue Engineering . 30 2.7. 1 SF Thin Films . 31 2.7. 2 SF Fibres . 31 2.7. 3 SF Foams . 32 2.8 Challenges of Silk Fibroin in Tissue Engineering . 33 ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library
CD4 count and tuberculosis risk in HIV-positive adults not on ART: a systematic review and meta-analysis

Background CD4 cell count in adults with human immunodeficiency virus (HIV) infection (PLHIV) not receiving antiretroviral therapy (ART) influences tuberculosis (TB) risk. Despite widespread use in models informing resource allocation, this relationship has not been systematically reviewed. Methods We systematically searched MEDLINE, Aidsinfo, Cochrane review database and Google Scholar for reports in English describing TB incidence stratified by updated CD4 cell count in cohorts of HIV-positive adults (age ≥15 years) not on ART (PROSPERO protocol no: CRD42016048888). Among inclusion criteria were: reporting precision for TB incidence, repeated CD4 measurements, and TB incidence reported for those not on ART or monotherapy. Study quality was assessed via the Newcastle-Ottawa tool for cohort studies. A Bayesian hierarchical model was fitted to estimate the pooled factor increase in TB incidence with respect to CD4 cell count decrement. Results A total of 1,555 distinct records were identified from which 164 full text articles were obtained. Common reasons for exclusion of full texts were: no valid TB incidence, no repeat CD4 measurements, and not reporting TB incidence by ART status. The seven studies included reported on 1,206 TB cases among 41,271 individuals, with a typical median follow-up of four years. Studies were generally rated as moderate or high quality. Our meta-analysis estimated a 1.43 (95% credible interval: 1.16–1.88)-fold increase in TB incidence per 100 cells per mm3 decrease in CD4 cell count. Discussion Our analysis confirms previous estimates of exponential increase in TB incidence with declining CD4 cell count in adults, emphasizing the importance of early ART initiation to reduce TB risk in PLHIV.
Modelling of Damage Evolution in Laminated Viscoelastic Composites

A computational finite element model is developed herein for the purpose of predicting the evolution of delaminations in a laminated continuous fiber polymer matrix composite subjected to monotonically increasing loading. Because the temperature of interest is near the glass transition temperature of the matrix, the lamina are modelled as orthotropic linear viscoelastic materials. Crack growth is accommodated in the prediction via the incorporation of a cohesive zone model. Although the resulting algorithm is nonlinear and computationally intensive, it is demonstrated herein to be tenable for predicting delamination evolution. To illustrate this point, results are obtained for a quasi-isotropic [00,450,90°, -45°12 laminate subjected to in-plane loading, as well as a crossply [9006/003], laminate subjected to out-of-plane loading. While results obtained herein are encouraging, they also indicate that further research is warranted to study potential anomalies.
Atypical bacteria in adenoids and tonsils of children requiring adenotonsillectomy

Abstract Conclusions: The results of this study suggest that atypical bacteria may be involved not only in acute upper airway diseases but also in recurrent infections requiring adenoidectomy and/or tonsillectomy. Therefore, their identification, followed by an appropriate treatment, should be considered. Objective: Although viruses and group A beta-haemolytic streptococci (GABHS) represent the most frequent bacterial aetiological agents of paediatric upper respiratory tract infections (URTIs), chlamydia and Mycoplasma pneumoniae have also been found in acute tonsillopharyngitis. Nevertheless their relevance in chronic or recurrent URTI has never been evaluated. This study aimed to further address the role of atypical bacteria in recurrent URTIs requiring adenoidectomy and tonsillectomy. Methods: Samples from 55 consecutive children who underwent adenoidectomy and/or tonsillectomy for recurrent or chronic URTI were cut transversely into smaller sections of 5 mm. Each section was pooled and assayed by specific PCR for viruses and bacteria. Results: Adenovirus was detected in 10 patients (18.2%), influenza A virus in one patient and influenza B virus in another. None of the other tested viruses was found. GABHS was found in 37 patients (67.3%). Moraxella catarrhalis and Haemophilus influenzae were detected in 30 patients (54.5%). M. pneumoniae was detected in 6 patients (10.9%) and C. pneumoniae was found in 10 patients (18.2%).
The Kaposin B Protein of KSHV Activates the p38/MK2 Pathway and Stabilizes Cytokine mRNAs

Cytokine production plays a critical role in diseases caused by Kaposi's sarcoma–associated herpesvirus (KSHV). Here we show that a latent KSHV gene product, kaposin B, increases the expression of cytokines by blocking the degradation of their messenger RNAs (mRNAs). Cytokine transcripts are normally unstable because they contain AU-rich elements (AREs) in their 3′ noncoding regions that target them for degradation. Kaposin B reverses this instability by binding to and activating the kinase MK2, a target of the p38 mitogen-activated protein kinase signaling pathway and a known inhibitor of ARE-mRNA decay. These findings define an important mechanism linking latent KSHV infection to cytokine production, and also illustrate a distinctive mode by which viruses can selectively modulate mRNA turnover.
Precursor decay in several aluminas

Plate impact experiments were performed on three ceramics with alumina content varying from 88 to 99.9% using a 50 mm single stage gas gun. Tiles of ceramic with thicknesses varying from 2 to 12 mm were impacted above their Hugoniot Elastic Limits (HELs) and the rate dependent strength was investigated by monitoring the variation in amplitude of the elastic precursor with propagation distance. Stress levels in the target were recorded using manganin stress transducers and a 1 GS s−1 storage oscilloscope. All grades of alumina were found to exhibit some elastic precursor decay indicating strain rate sensitivity.Plate impact experiments were performed on three ceramics with alumina content varying from 88 to 99.9% using a 50 mm single stage gas gun. Tiles of ceramic with thicknesses varying from 2 to 12 mm were impacted above their Hugoniot Elastic Limits (HELs) and the rate dependent strength was investigated by monitoring the variation in amplitude of the elastic precursor with propagation distance. Stress levels in the target were recorded using manganin stress transducers and a 1 GS s−1 storage oscilloscope. All grades of alumina were found to exhibit some elastic precursor decay indicating strain rate sensitivity.