Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between markers of endothelial dysfunction and inflammation and subclinical atherosclerosis in HIV-infected male patients below 55 years of age.

INTRODUCTION Antiretroviral therapy in HIV-infected patients appears to be associated with increased incidence of cardiovascular disease (CVD). The aim of our study was to investigate the differences in markers of inflammation, endothelial dysfunction and prothrombotic state between treated and untreated HIV-infected patients with or without subclinical atherosclerosis. METHODS Eighty-six Slovenian HIV-infected male patients below the age of 55 participated in our study. Levels of high-sensitivity C-reactive protein (hsCRP), vascular cell adhesion molecule 1 (VCAM-1) and plasminogen activator inhibitor 1 (PAI-1) were measured. The presence of subclinical atherosclerosis was determined by measuring carotid intima-media thickness. RESULTS The level of hsCRP was significantly increased in HIV-infected patients; it was higher in treated than untreated patients. VCAM-1 was significantly increased; it was higher in untreated than treated patients. PAI 1 was significantly increased; there were no differences between untreated and treated patients. Patients with subclinical atherosclerosis had elevated hsCRP; levels of VCAM-1 and PAI-1 were not significantly different. CONCLUSION Signs of systemic and vascular inflammation persist in both untreated and treated HIV infected patients. None of the studied markers contributed to improved assessment of subclinical atherosclerosis. The usefulness of such markers in routine clinical evaluation of CVD risk in HIV infected patients remains unclear.
BOLD - Binary online learned descriptor for efficient image matching

In this paper we propose a novel approach to generate a binary descriptor optimized for each image patch independently. The approach is inspired by the linear discriminant embedding that simultaneously increases inter and decreases intra class distances. A set of discriminative and uncorrelated binary tests is established from all possible tests in an offline training process. The patch adapted descriptors are then efficiently built online from a subset of tests which lead to lower intra class distances thus a more robust descriptor. A patch descriptor consists of two binary strings where one represents the results of the tests and the other indicates the subset of the patch-related robust tests that are used for calculating a masked Hamming distance. Our experiments on three different benchmarks demonstrate improvements in matching performance, and illustrate that per-patch optimization outperforms global optimization.
A CMOS implementation of current-mode min-max circuits and a sample fuzzy application

A new design of CMOS min-max circuits in current-mode is presented. These kinds of circuits have a growing number of fuzzy applications in fuzzy logic controllers. As a sample fuzzy application, membership function generator (MFG) based on min circuit, is presented. The proposed circuits have wide input and output dynamic range. A 3.3 V power supply has been applied and simulation results are presented in 0.35 /spl mu/m CMOS process.
Analysis of Quorum-Sensing-Dependent Control of Rhizosphere-Expressed (rhi) Genes in Rhizobium leguminosarum bv. viciae

ABSTRACT The rhi genes of Rhizobium leguminosarumbiovar viciae are expressed in the rhizosphere and play a role in the interaction with legumes, such as the pea. Previously (K. M. Gray, J. P. Pearson, J. A. Downie, B. E. A. Boboye, and E. P. Greenberg, J. Bacteriol. 178:372–376, 1996) therhiABC operon had been shown to be regulated by RhiR and to be induced by addedN-(3-hydroxy-7-cis-tetradecenoyl)-l-homoserine lactone (3OH,C14:1-HSL). Mutagenesis of a cosmid carrying the rhiABC and rhiR gene region identified a gene (rhiI) that affects the level of rhiAexpression. Mutation of rhiI slightly increased the number of nodules formed on the pea. The rhiI gene is (likerhiA) regulated by rhiR in a cell density-dependent manner. RhiI is similar to LuxI and other proteins involved in the synthesis of N-acyl-homoserine lactones (AHLs). Chemical analyses of spent culture supernatants demonstrated that RhiI produces N-(hexanoyl)-l-homoserine lactone (C6-HSL) andN-(octanoyl)-l-homoserine lactone (C8-HSL). Both of these AHLs induced rhiA-lacZand rhiI-lacZ expression on plasmids introduced into anAgrobacterium strain that produces no AHLs, showing thatrhiI is positively regulated by autoinduction. However, in this system no induction of rhiA or rhiI with 3OH,C14:1-HSL was observed. Analysis of the spent culture supernatant of the wild-type R. leguminosarum bv. viciae revealed that at least seven different AHLs are made. Mutation ofrhiI decreased the amounts of C6-HSL and C8-HSL but did not block their formation, and in this background the rhiI mutation did not significantly affect the expression levels of the rhiI gene orrhiABC genes or the accumulation of RhiA protein. These observations suggest that there are additional loci involved in AHL production in R. leguminosarum bv. viciae and that they affect rhiI and rhiABC expression. We postulate that the previously observed induction of rhiA by 3OH,C14:1-HSL may be due to an indirect effect caused by induction of other AHL production loci.
Genomic Structure of the Cyanobacterium Synechocystis sp. PCC 6803 Strain GT-S

Synechocystis sp. PCC 6803 is the most popular cyanobacterial strain, serving as a standard in the research fields of photosynthesis, stress response, metabolism and so on. A glucose-tolerant (GT) derivative of this strain was used for genome sequencing at Kazusa DNA Research Institute in 1996, which established a hallmark in the study of cyanobacteria. However, apparent differences in sequences deviating from the database have been noticed among different strain stocks. For this reason, we analysed the genomic sequence of another GT strain (GT-S) by 454 and partial Sanger sequencing. We found 22 putative single nucleotide polymorphisms (SNPs) in comparison to the published sequence of the Kazusa strain. However, Sanger sequencing of 36 direct PCR products of the Kazusa strains stored in small aliquots resulted in their identity with the GT-S sequence at 21 of the 22 sites, excluding the possibility of their being SNPs. In addition, we were able to combine five split open reading frames present in the database sequence, and to remove the C-terminus of an ORF. Aside from these, two of the Insertion Sequence elements were not present in the GT-S strain. We have thus become able to provide an accurate genomic sequence of Synechocystis sp. PCC 6803 for future studies on this important cyanobacterial strain.
Prognostic Value of the Index of Microcirculatory Resistance Measured After Primary Percutaneous Coronary Intervention

Background— Most methods for assessing microvascular function are not readily available in the cardiac catheterization laboratory. The aim of this study is to determine whether the Index of Microcirculatory Resistance (IMR), measured at the time of primary percutaneous coronary intervention, is predictive of death and rehospitalization for heart failure. Methods and Results— IMR was measured immediately after primary percutaneous coronary intervention in 253 patients from 3 institutions with the use of a pressure–temperature sensor wire. The primary end point was the rate of death or rehospitalization for heart failure. The prognostic value of IMR was compared with coronary flow reserve, TIMI myocardial perfusion grade, and clinical variables. The mean IMR was 40.3±32.5. Patients with an IMR >40 had a higher rate of the primary end point at 1 year than patients with an IMR ⩽40 (17.1% versus 6.6%; P=0.027). During a median follow-up period of 2.8 years, 13.8% experienced the primary end point and 4.3% died. An IMR >40 was associated with an increased risk of death or rehospitalization for heart failure (hazard ratio [HR], 2.1; P=0.034) and of death alone (HR, 3.95; P=0.028). On multivariable analysis, independent predictors of death or rehospitalization for heart failure included IMR >40 (HR, 2.2; P=0.026), fractional flow reserve ⩽0.8 (HR, 3.24; P=0.008), and diabetes mellitus (HR, 4.4; P<0.001). An IMR >40 was the only independent predictor of death alone (HR, 4.3; P=0.02). Conclusions— An elevated IMR at the time of primary percutaneous coronary intervention predicts poor long-term outcomes.
Comparison of the fatty acid composition of maternal blood and cord blood of mothers who delivered healthy full-term babies, preterm babies, and full-term small for gestational age infants

Objective: The aim of this study was to determine and compare the fatty acid (FA) profile of maternal blood and cord blood of children born at term (group A); those born prematurely (group B); and children born with hypotrophic features (group C). Methods: The study consisted of 109 women. FA composition was determined by gas chromatography–mass spectrometry. Results: Twenty-two FAs were identified in the maternal blood and 33 FAs were identified in the cord blood. Significant differences in the levels of C18:3n–6 and C20:5n–3 were noted when comparing the FA composition of maternal blood samples from the three different groups (A, B, and C). Seven statistical differences were detected in the cord blood. They concerned C12:0, C18:0, C18:1c, C18:3n–6, C20:0, C20:3n–6, and C20:4n–6. Conclusion: Our research has shown that the FA profile of both the maternal blood and the cord blood undergoes changes in response to pregnancy duration and the presence of reduced fetal growth. Statistical differences between groups B and C compared with group A, show that the placental-fetal transport of FA in group B and C infants may differ from that of group A children.
C-terminal truncations of the yeast nucleoporin Nup145p produce a rapid temperature-conditional mRNA export defect and alterations to nuclear structure

A screen for temperature-sensitive mutants of Saccharomyces cerevisiae defective in nucleocytoplasmic trafficking of poly(A)+ RNA has identified an allele of the NUP145 gene, which encodes an essential nucleoporin. NUP145 was previously identified by using a genetic synthetic lethal screen (E. Fabre, W. C. Boelens, C. Wimmer, I. W. Mattaj, and E. C. Hurt, Cell 78:275-289, 1994) and by using a monoclonal antibody which recognizes the GLFG family of vertebrate and yeast nucleoporins (S. R. Wente and G. Blobel, J. Cell Biol. 125:955-969, 1994). Cells carrying the new allele, nup145-10, grew at 23 and 30 degrees C but were unable to grow at 37 degrees C. Many cells displayed a modest accumulation of poly(A)+ RNA under permissive growth conditions, and all cells showed dramatic and rapid nuclear accumulation of poly(A)+ RNA following a shift to 37 degrees C. The mutant allele contains a nonsense codon which truncates the 1,317-amino-acid protein to 698 amino acids. This prompted us to examine the role of the carboxyl half of Nup145p. Several additional alleles that encode C-terminally truncated proteins or proteins containing internal deletions of portions of the carboxyl half of Nup145p were constructed. Analysis of these mutants indicates that some sequences between amino acids 698 and 1095 are essential for RNA export and for growth at 37 degrees C. In these strains, nuclear accumulation of poly(A)+ RNA and fragmentation of the nucleolus occurred rapidly following a shift to 37 degrees C. Constitutive defects in nuclear pore complex distribution and nuclear structure were also seen in these strains. Although cells lacking Nup145p grew extremely slowly at 23 degrees C and did not grow at 30 degrees C, efficient growth at 23 or 30 degrees C occurred as long as cells produced either the amino 58% or the carboxyl 53% of Nup145p. Strains carrying alleles of NUP145 lacking up to 200 amino acids from the carboxy terminus were viable at 37 degrees C but displayed nucleolar fragmentation and some nuclear accumulation of poly(A)+ RNA following a shift to 37 degrees C. Surprisingly, these strains grew efficiently at 37 degrees C in spite of a reduction in the level of synthesis of rRNAs to approximately 25% of the wild-type level.
Locations of Z-DNA in polytene chromosomes

In polytene chromosomes of Drosophila hydei and D. melanogaster, Z-DNA was identified in varying distribution after different conditions for fixation were used. When salivary glands were fixed and squashed in 50% acetic acid alone, Z-DNA was found in the less dense DNA regions, such as interbands, some puffs, and a few of the less dense bands. Prefixation that combined ethanol and acetic acid exposure led to prominent immunofluorescent staining of the bands, generally but not strictly correlating with the total DNA content. Separate exposure to ethanol and acetic acid did not cause this band to stain, but if residual ethanol was present after ethanol fixation, subsequent exposure to acid did cause it. Under the more selective acid fixation conditions, Z-DNA reactivity was seen in portions of certain ecdysone- inducible puffs in the induced but not in the resting state; in other inducible regions, the Z-DNA immunoreactivity was not changed on induction. Z-DNA was also identified in polytene chromosomes within isolated nuclei that had been frozen and fixed in ethanol without exposure to acid; this Z-DNA was present in regions of low DNA density.
SIRC, a multiple isolation level protocol for middleware-based data replication

One of the weaknesses of database replication protocols, compared to centralized DBMSs, is that they are unable to manage concurrent execution of transactions at different isolation levels. In the last years, some theoretical works related to this research line have appeared but none of them has proposed and implemented a real replication protocol with support to multiple isolation levels. This paper takes advantage of our MADIS middleware and one of its implemented Snapshot Isolation protocols to design and implement SIRC, a protocol that is able to execute concurrently both generalized snapshot isolation (GSI) and generalized loose read committed (GLRC) transactions. We have also made a performance analysis to show how this kind of protocols can improve the system performance and decrease the transaction abortion rate in applications that do not require the strictest isolation level in every transaction.
Mycophenolate mofetil combination therapy improves long‐term outcomes after liver transplantation in patients with and without hepatitis C

To evaluate the impact of mycophenolate mofetil (MMF) on long‐term outcomes of tacrolimus and corticosteroids, we analyzed data reported to the Scientific Registry of Transplant Recipients for 11,670 adult patients (3463 with hepatitis C [HCV]) who underwent primary, single‐organ, liver transplantation between 1995 and 2001. Patients who were discharged from the hospital on tacrolimus‐based immunosuppression with (n = 4466; n = 1323 HCV) or without MMF (n = 7204; n = 2140 HCV) were included in the analysis. Recipients treated at discharge with MMF, tacrolimus, and corticosteroids had significantly increased patient survival (81.0% vs. 77.0% at 4 years, P < 0.0001) and graft survival (76.4% vs. 72.9%, P < 0.0001), and lower rates of acute rejection (29.0% vs. 33.4%, P < 0.001) as compared to recipients treated at discharge with tacrolimus and corticosteroids alone. A trend toward lower rates of death from infection was observed (6.1% at 4 years for MMF vs. 7.1% at 4 years for tacrolimus and corticosteroids, P = 0.0508), but this result did not reach statistical significance. In multiple regression analyses, MMF triple therapy at discharge was associated with a reduced risk of death (hazard ratio [HR] = 0.77, P < 0.001), graft loss (HR = 0.81, P < 0.001), acute rejection (HR = 0.89, P = 0.002), and death from infectious complications (HR = 0.80, P = 0.007). Outcomes were similar for the cohort with HCV.
Differences in the association of sea surface temperature—precipitating systems over the Bay of Bengal and the Arabian Sea during southwest monsoon season

The intriguing, but complex, association among sea surface temperature (SST) and different types of precipitating systems (deep and shallow) over the Bay of Bengal and the Arabian Sea has been elucidated utilizing 16 years of tropical rainfall measuring mission (TRMM) data. The characteristics and their convective forcing of these two seas are fundamentally different due to differences in SST. At a given SST, the occurrence of deeper (shallow) systems is higher (lower) over the Bay of Bengal than in the Arabian Sea. The occurrence of deeper systems increases with SST over both the seas till 30°C and decreases from 30 to 31°C. On the other hand, the occurrence of shallow systems is independent of SST over the Bay of Bengal while it decreases with rise in SST over the Arabian Sea. The prevalence of weaker convective available potential energy and drier mid‐troposphere over the Arabian Sea than over the Bay of Bengal is detrimental for cloud growth and is responsible for lower occurrence of deep systems and higher occurrence of shallow systems. The differences in mid‐tropospheric dynamics and moisture between the Arabian Sea and the Bay of the Bengal play a major role in the occurrence of deep and shallow systems.
Accepted for Publication in Ieee Transactions on Vlsi Systems Configuration Relocation and Defragmentation for Run-time Reconfigurable Computing

Due to its potential to greatly accelerate a wide variety of applications, reconfigurable computing has become a subject of a great deal of research. By mapping the compute-intensive sections of an application to reconfigurable hardware, custom computing systems exhibit significant speedups over traditional microprocessors. However, this potential acceleration is limited by the requirement that the speedups provided must outweigh the considerable cost of reconfiguration. The ability to relocate and defragment configurations on an FPGA can dramatically decrease the overall reconfiguration overhead incurred by the use of the reconfigurable hardware. We therefore present hardware solutions to provide relocation and defragmentation support with a negligible area increase over a generic partially reconfigurable FPGA, as well as software algorithms for controlling this hardware. This results in factors of 8 to 12 improvement in the configuration overheads displayed by traditional serially programmed FPGAs.
Idiopathic thrombocytopenic purpura in childhood: a 10-year audit

Abstract Objectives: To evaluate clinical course, treatment modalities, complications and referral pattern in paediatric patients treated over a 10-year period. Design: A retrospective, descriptive, hospital based study. Setting and subjects: 123 patients were diagnosed with ITP at Tygerberg Hospital from January 1996 to December 2006. Thirteen were excluded. The information of 106 patients was examined in detail. Outcome measures: Comparison of presenting platelet counts, special investigations, response and complications. Results: The mean age at presentation was 4·9 years (range 2 months – 13 years 3 months). A history of a preceding infection was obtained in 51% of patients. The mean presenting platelet count at diagnosis was 11·5 × 109/L (range 1 × 109 to 104 × 109/L). In 25 patients observation alone was the treatment choice. Specific treatment for ITP was given to 81 patients; steroids were used in 46 patients and intravenous immunoglobulin (IVIG) in seven patients. A combination of steroids and IVIG was used in 28 patients. There was no statistical difference in response to any therapy. Three patients developed an intracranial haemorrhage, two died. Twenty-one patients progressed to chronic ITP (19%). ITP had a benign clinical course with 87% of patients experiencing no major complication and 90% of patients making a complete recovery with or without treatment. Conclusion: ITP in South African children presents similarly to that in other settings, however the rate of intracranial haemorrhage was higher in this series than in literature. There were no statistically significant differences in the effects of various treatments, and observation alone was a successful treatment modality.
Diversification and refinement in collaborative filtering recommender

This paper considers a popular class of recommender systems that are based on Collaborative Filtering (CF) and proposes a novel technique for diversifying the recommendations that they give to users. Items are clustered based on a unique notion of priority-medoids that provides a natural balance between the need to present highly ranked items vs. highly diverse ones. Our solution estimates items diversity by comparing the rankings that different users gave to the items, thereby enabling diversification even in common scenarios where no semantic information on the items is available. It also provides a natural zoom-in mechanism to focus on items (clusters) of interest and recommending diversified similar items. We present DiRec a plug-in that implements the above concepts and allows CF Recommender systems to diversify their recommendations. We illustrate the operation of DiRec in the context of a movie recommendation system and present a thorough experimental study that demonstrates the effectiveness of our recommendation diversification technique and its superiority over previous solutions.
Correlation between photoreceptor layer integrity and visual function in patients with Stargardt disease: implications for gene therapy.

PURPOSE To perform a clinical characterization of Stargardt patients with ABCA4 gene mutation, and to investigate the correlation between the inner and outer segment (IS/OS) junction morphology and visual acuity, fundus lesions, electroretinogram abnormalities, and macular sensitivity. METHODS Sixty-one patients with Stargardt disease (STGD) were given a comprehensive ophthalmic examination. Inner-outer photoreceptor junction morphology evaluated by spectral-domain optical coherence tomography was correlated with visual acuity, fundus lesions, fundus autofluorescence, full-field and multifocal electroretinography responses, and microperimetric macular sensitivities. We classified STGD patients into three groups: (1) IS/OS junction disorganization in the fovea, (2) IS/OS junction loss in the fovea, and (3) extensive loss of IS/OS junction. Mutation analysis of the ABCA4 gene was carried out by sequencing the complete coding region. RESULTS A significant difference in visual acuity was observed between IS/OS groups 1 and 2 and between IS/OS groups 2 and 3 (P < 0.0001). A significant difference in microperimetry sensitivity was observed between IS/OS groups 2 and 3, and between IS/OS groups 1 and 3 (P < 0.0001). There was also a statistically significant correlation between IS/OS abnormalities and the extent of fundus lesions (Spearman P ≤ 0.01), as well as with the type of ERG and multifocal ERG results (Spearman P ≤ 0.01). Finally, the degree of IS/OS junction preservation showed a statistically significant correlation with the extension of foveal abnormalities assessed by fundus autofluorescence imaging (Spearman P ≤ 0.01). The G1961E mutation was more frequent in the patients without extensive loss of IS/OS junction (P = 0.01) confirming its association with a milder STGD phenotype. CONCLUSIONS The results of this study suggest that a comprehensive approach in the examination of Stargardt patients has the potential to improve the understanding of vision loss and may provide a sensitive measure to evaluate the efficacy of future experimental therapies in patients with STGD.