Miracle-dz/UniFAR-FTUs huggingface dataset:
Treatment modification in human immunodeficiency virus-infected individuals starting combination antiretroviral therapy between 2005 and 2008.

BACKGROUND Adverse effects of combination antiretroviral therapy (CART) commonly result in treatment modification and poor adherence. METHODS We investigated predictors of toxicity-related treatment modification during the first year of CART in 1318 antiretroviral-naive human immunodeficiency virus (HIV)-infected individuals from the Swiss HIV Cohort Study who began treatment between January 1, 2005, and June 30, 2008. RESULTS The total rate of treatment modification was 41.5 (95% confidence interval [CI], 37.6-45.8) per 100 person-years. Of these, switches or discontinuations because of drug toxicity occurred at a rate of 22.4 (95% CI, 19.5-25.6) per 100 person-years. The most frequent toxic effects were gastrointestinal tract intolerance (28.9%), hypersensitivity (18.3%), central nervous system adverse events (17.3%), and hepatic events (11.5%). In the multivariate analysis, combined zidovudine and lamivudine (hazard ratio [HR], 2.71 [95% CI, 1.95-3.83]; P < .001), nevirapine (1.95 [1.01-3.81]; P = .050), comedication for an opportunistic infection (2.24 [1.19-4.21]; P = .01), advanced age (1.21 [1.03-1.40] per 10-year increase; P = .02), female sex (1.68 [1.14-2.48]; P = .009), nonwhite ethnicity (1.71 [1.18-2.47]; P = .005), higher baseline CD4 cell count (1.19 [1.10-1.28] per 100/microL increase; P < .001), and HIV-RNA of more than 5.0 log(10) copies/mL (1.47 [1.10-1.97]; P = .009) were associated with higher rates of treatment modification. Almost 90% of individuals with treatment-limiting toxic effects were switched to a new regimen, and 85% achieved virologic suppression to less than 50 copies/mL at 12 months compared with 87% of those continuing CART (P = .56). CONCLUSIONS Drug toxicity remains a frequent reason for treatment modification; however, it does not affect treatment success. Close monitoring and management of adverse effects and drug-drug interactions are crucial for the durability of CART.
Matrix-bound thrombospondin promotes angiogenesis in vitro

Thrombospondin (TSP) is a multidomain adhesive protein postulated to play an important role in the biological activity of the extracellular matrix. To test this hypothesis, TSP-containing fibrin and collagen matrices were evaluated for their capacity to support angiogenesis and cell growth from explants of rat aorta. This serum-free model allowed us to study the angiogenic effect of TSP without the interference of attachment and growth factors present in serum. TSP promoted dose- dependent growth of microvessels and fibroblast-like cells. The number of microvessels in TSP-containing collagen and fibrin gels increased by 136 and 94%, respectively. The TSP effect was due in part to cell proliferation since a 97% increase in [3H]thymidine incorporation by the aortic culture was observed. The effect was TSP-specific because TSP preparations adsorbed with anti-TSP antibody showed no activity. TSP did not promote angiogenesis directly since no TSP-dependent growth of isolated endothelial cells could be demonstrated. Rather TSP directly stimulated the growth of aortic culture-derived myofibroblasts which in turn promoted microvessel formation when cocultured with the aortic explants. Angiogenesis was also stimulated by myofibroblast- conditioned medium. Partial characterization of the conditioned medium suggests that the angiogenic activity is due to heparin-binding protein(s) with molecular weight > 30 kD. These results indicate that matrix-bound TSP can indirectly promote microvessel formation through growth-promoting effects on myofibroblasts and that TSP may be an important stimulator of angiogenesis and wound healing in vivo.
The 2dF QSO Redshift Survey – IX. A measurement of the luminosity dependence of QSO clustering

In this paper we present a clustering analysis of quasi-stellar objects (QSOs) as a function of luminosity over the redshift range z = 0.3-2.9. We use a sample of 10 566 QSOs taken from the preliminary data release catalogue of the 2dF QSO Redshift Survey (2QZ). We analyse QSO clustering as a function of apparent magnitude. The strong luminosity evolution of QSOs means that this is approximately equivalent to analysing the data as a function of absolute magnitude relative to M* over the redshift range that the 2QZ probes. Over the relatively narrow range in apparent magnitude of the 2QZ we find no significant (>2σ) variation in the strength of clustering, however, there is marginal evidence for QSOs with brighter apparent magnitudes having a stronger clustering amplitude. QSOs with 18.25 < b J ≤ (19.80 show a correlation scalelength s 0 = 5.50 ′ 0.79h - 1 Mpc in an Einstein-de Sitter (EdS) universe and s 0 = 8.37 ′ 1.17h - 1 Mpc in a universe with Ω 0 = 0.3 and λ 0 = 0.7 (A), while the best-fitting values for the full magnitude interval (18.25 < b J ≤ 20.85) over the same spatial scales are so = 4.29 + 0 . 3 0 - 0 . 2 9 h - 1 Mpc (EdS) and so = 6.35 + 0 . 4 5 - 0 . 4 4 h - 1 Mpc (A). We can therefore determine that the bias of the brightest subsample is a factor 1.22 ′ 0.15 (EdS) or 1.24 ′ 0.15 (A) larger than that of the full data set. An increase in clustering with luminosity, if confirmed, would be in qualitative agreement with models in which the luminosity of a QSO is correlated to the mass of the dark halo in which it resides, implying that the mass of the host plays at least some part in determining the formation of a QSO and evolution. These models predict that the clustering in brighter QSO data sets, such as the Sloan Digital Sky Survey QSO sample or the bright extension of the 2QZ, should show a higher clustering amplitude than the 2QZ.
Contribution of Aerobic Photoheterotrophic Bacteria to the Carbon Cycle in the Ocean

The vertical distribution of bacteriochlorophylla, the numbers of infrared fluorescent cells, and the variable fluorescence signal at 880 nanometers wavelength, all indicate that photosynthetically competent anoxygenic phototrophic bacteria are abundant in the upper open ocean and comprise at least 11% of the total microbial community. These organisms are facultative photoheterotrophs, metabolizing organic carbon when available, but are capable of photosynthetic light utilization when organic carbon is scarce. They are globally distributed in the euphotic zone and represent a hitherto unrecognized component of the marine microbial community that appears to be critical to the cycling of both organic and inorganic carbon in the ocean.
Characterization of Human Metapneumoviruses Isolated from Patients in North America

Abstract Human metapneumovirus (HMPV) was recently identified in The Netherlands and was linked to acute respiratory tract illness. In this study, 11 isolates from 10 patients with respiratory disease from Quebec, Canada, were tested by a reverse-transcriptase polymerase chain reaction based on the fusion protein gene. Identified sequences were consistent with HMPV. The patients were 2 months to 87 years of age (median age, 58 years) and presented with acute respiratory tract illness during the winter season. Sequence studies of the nucleocapsid, fusion, and polymerase genes identified 2 main lineages of HMPV and cocirculation of both lineages during the same year. These findings support a previous finding that HMPV is a human respiratory pathogen that merits further study.
An FPGA-Based Quantum Computing Emulation Framework Based on Serial-Parallel Architecture

Hardware emulation of quantum systems can mimic more efficiently the parallel behaviour of quantum computations, thus allowing higher processing speed-up than software simulations. In this paper, an efficient hardware emulation method that employs a serial-parallel hardware architecture targeted for field programmable gate array FPGA is proposed. Quantum Fourier transform and Grover’s search are chosen as case studies in this work since they are the core of many useful quantum algorithms. Experimental work shows that, with the proposed emulation architecture, a linear reduction in resource utilization is attained against the pipeline implementations proposed in prior works. The proposed work contributes to the formulation of a proof-of-concept baseline FPGA emulation framework with optimization on datapath designs that can be extended to emulate practical large-scale quantum circuits.
Increased prevalence of significant coronary artery calcification in patients with diabetes.

OBJECTIVE — Coronary artery disease is the major cause of morbidity and mortality in patients with diabetes. Detection of coronary artery disease before the first myocardial infarction and before anginal symptoms will allow for strategies designed to reduce the cardiovascular event rate in this group of patients. Electron beam—computed tomography (EBCT) is a noninvasive technology for evaluating the extent of coronary artery atherosclerosis that relies on the detection of coronary artery calcium (CAC). We used EBCT to detect significant coronary artery atherosclerosis in diabetic patients without symptoms of heart disease. RESEARCH DESIGN AND METHODS — We used EBCT to evaluate calcium in the coronary arteries of 139 consecutive diabetic patients scanned over a 20-month period. The CAC scores in this group were compared with a randomly selected nondiabetic control group and a control group that was selected to match a number of established cardiovascular risk factors. RESULTS — Patients with diabetes had a significant increase in the prevalence of CAC scores ≥400 (25.9%) compared with the randomly selected (7.2%) and matched (14.4%) nondiabetic control groups. Scores in this range have been reported to be highly predictive for abnormal stress myocardial perfusion tomography and subsequent coronary events. CONCLUSIONS — Our results, therefore, indicate a substantial prevalence of significant coronary artery disease in an asymptomatic diabetic patient population compared with non-diabetic control subjects. They also suggest that EBCT may be a useful approach for selecting a group of diabetic subjects who would benefit most from additional evaluation for subclinical coronary artery disease.
Mitotic Abnormalities Produced by Juglone in Ehrlich Ascites Tumor Cells.∗

Summary The cytological effects of 16 quinone compounds were tested on Ehrlich ascites tumor cells in vivo. Of these only juglone (5-hydroxy-1.4-naphthoquinone) produced mitotic abnormalities. An accumulation of abnormal metaphase figures occurred and the cells in metaphase were prevented from entering ana-telophase. Chromosomes in prophase cells appeared diffuse and sticky. Juglone administration, either intraperitoneal or oral, caused decreases in the amount of ascitic fluid at a time that marked increases were taking place in control animals.
Cost consequences of implementing an electronic decision support system for ordering laboratory tests in primary care: evidence from a controlled prospective study in the Netherlands.

BACKGROUND The economic consequences of interventions to promote rational, evidence-based use of laboratory tests by physicians are not yet fully understood. We evaluated the cost consequences of a computer-based, guideline-driven decision-support system (CDSS) for ordering blood tests in primary care. METHODS We installed the CDSS in 118 practices [159 general practitioners (GPs)] throughout The Netherlands and calculated the costs of the intervention in this group. During a period of 6 months before and 6 months after installation of the CDSS, the test-ordering behavior of 87 (109 GPs) of these 118 study practices was studied and the results were compared with those of a nonhistorical control group that did not receive the CDSS. In addition the costs of laboratory requests were calculated for both groups. RESULTS Total intervention costs, comprising development costs and installation costs, amounted to 79,000 euro (670 euro per practice). Whereas the introduction of the CDSS did not affect the number of order forms submitted to the laboratories, it did reduce the number of blood tests per order form. As a result, the CDSS yielded mean savings on the costs of laboratory requests of 847 euro per practice per 6 months. CONCLUSIONS This study demonstrates that providing electronic decision support for ordering blood tests in primary care represents an economically promising concept. Savings on laboratory costs are achievable and not offset by disproportionally high intervention costs.
Slipped capital femoral epiphysis : Prediction of contralateral involvement

We performed a retrospective review of the medical records and radiographs of fifty children who had had unilateral slipped capital femoral epiphysis. Our purpose was to determine if there were any epidemiological parameters that were associated with the later development of a contralateral slip. The mean duration of follow-up was thirty-four months (range, twenty-four to sixty-eight months). Physiological maturity, determined with a modified form of the Oxford method for assessment of bone age, strongly correlated with the risk of development of a contralateral slip in patients who were initially seen with a unilateral slip (r = 0.59, p < 0.0005). The scores were determined by four raters; the variation in the predictive value of the scores among the raters was not significant (p = 0.5). The relationship between the score as determined with the modified Oxford method and the risk of contralateral involvement had a linear distribution. The four raters performed a total of 442 observations to determine the modified Oxford scores for the fifty hips. The prevalence of a subsequent slip for the hips that had been assigned a score of 16 points was 85 ± 15 per cent (95 per cent confidence limit) (seventeen of twenty observations). The risk of contralateral involvement when the score was 21 points was 11 ± 9 per cent (six of fifty-four observations). A slip did not develop in any hip with a score of 22 points or more (sixty-nine observations). For boys, the age at the time of the initial slip was predictive of a contralateral slip. A contralateral slip developed in all four boys who had been eleven years and seven months old or less at the time of the initial presentation; however, a contralateral slip developed in only nine of the twenty-two boys who had been eleven years and eight months to fourteen years and eleven months old. A contralateral slip did not develop in the three boys who had been fifteen years old or more. There was no association between age and the risk of a contralateral slip in girls.
In Situ Biochemical Demonstration That P-Glycoprotein Is a Drug Efflux Pump with Broad Specificity

While P-glycoprotein (Pgp) is the most studied protein involved in resistance to anti-cancer drugs, its mechanism of action is still under debate. Studies of Pgp have used cell lines selected with chemotherapeutics which may have developed many mechanisms of resistance. To eliminate the confounding effects of drug selection on understanding the action of Pgp, we studied cells transiently transfected with a Pgp-green fluorescent protein (GFP) fusion protein. This method generated a mixed population of unselected cells with a wide range of Pgp-GFP expression levels and allowed simultaneous measurements of Pgp level and drug accumulation in living cells. The results showed that Pgp-GFP expression was inversely related to the accumulation of chemotherapeutic drugs. The reduction in drug concentration was reversed by agents that block multiple drug resistance (MDR) and by the UIC2 anti-Pgp antibody. Quantitative analysis revealed an inverse linear relationship between the fluorescence of Pgp-GFP and MDR dyes. This suggests that Pgp levels alone limit drug accumulation by active efflux; cooperativity between enzyme, substrate, or inhibitor molecules is not required. Additionally, Pgp-GFP expression did not change cellular pH. Our study demonstrates the value of using GFP fusion proteins for quantitative biochemistry in living cells.
A Retrospective on: A “Flight Data Recorder” for Enabling Full-system Multiprocessor Deterministic Replay

During 2001-02, junior graduate student Min Xu was searching for a problem to work on for his PhD. With his advisors, Prof. Hill (computer architecture) and Prof. Bodik (compilers), we wanted a problem that people would care about if we solved it and we had some talent toward solving it. We focused on changes that might expose new opportunities, as Hill later articulated [1]. In the early 2000s, we saw that three changes were underway:
COLORFUL-Circuit: A Platform for Rapid Multigene Assembly, Delivery, and Expression in Plants

Advancing basic and applied plant research requires the continuous innovative development of the available technology toolbox. Essential components of this toolbox are methods that simplify the assembly, delivery, and expression of multiple transgenes of interest. To allow simultaneous and directional multigene assembly on the same plant transformation vector, several strategies based on overlapping sequences or restriction enzymes have recently been developed. However, the assembly of homologous and repetitive DNA sequences can be inefficient and the frequent occurrence of target sequences recognized by commonly used restriction enzymes can be a limiting factor. Here, we noted that recognition sites for the restriction enzyme SfiI are rarely occurring in plant genomes. This fact was exploited to establish a multigene assembly system called “COLORFUL-Circuit. ” To this end, we developed a set of binary vectors which provide a flexible and cost efficient cloning platform. The gene expression cassettes in our system are flanked with unique SfiI sites, which allow simultaneous multi-gene cassette assembly in a hosting binary vector. We used COLORFUL-Circuit to transiently and stably express up to four fluorescent organelle markers in addition to a selectable marker and analyzed the impact of assembly design on coexpression efficiency. Finally, we demonstrate the utility of our optimized “COLORFUL-Circuit” system in an exemplary case study, in which we monitored simultaneously the subcellular behavior of multiple organelles in a biotrophic plant–microbe interaction by Confocal Laser Scanning Microscopy.
Predictive Deconvolution and Hybrid Feature Selection for Computer-Aided Detection of Prostate Cancer

Computer-aided detection (CAD) schemes are decision making support tools, useful to overcome limitations of problematic clinical procedures. Trans-rectal ultrasound image based CAD would be extremely important to support prostate cancer diagnosis. An effective approach to realize a CAD scheme for this purpose is described in this work, employing a multi-feature kernel classification model based on generalized discriminant analysis. The mutual information of feature value and tissue pathological state is used to select features essential for tissue characterization. System-dependent effects are reduced through predictive deconvolution of the acquired radio-frequency signals. A clinical study, performed on ground truth images from biopsy findings, provides a comparison of the classification model applied before and after deconvolution, showing in the latter case a significant gain in accuracy and area under the receiver operating characteristic curve.
Contrast-induced nephropathy in patients undergoing computed tomography (CONNECT) – a clinical problem in daily practice? a multicenter observational study

Background: Although several studies have examined contrast-induced nephropathy (CIN) following computed tomography (CT) procedures under closely controlled clinical trial conditions, less is known about the incidence of CIN (or its key predictive factors) in a “real world” clinical setting. Purpose: A multicenter, observational registry study was undertaken in Italian hospital radiology departments to retrospectively assess the incidence of CIN in at-risk patients undergoing iodixanol-enhanced CT procedures. Material and Methods: Each department used center-specific (nonstandardized) CT protocols. Data were available from 493 at-risk patients; most (76.4%) had 1 risk factor for CIN, 19.8% had 2, and 3.4% had 3. In all, 169 patients (34.3%) had reduced renal function (estimated glomerular filtration rate [eGFR] <60 ml/min/1.73m2). Prophylactic volume expansion was not used in 70.6% of the study population. Results: The overall incidence of CIN (defined as a ≥44.2 μmol/l [0.5 mg/dl] increase in serum creatinine from baseline 72 h postprocedure) was 2.6%; in the subpopulation of patients with renal impairment (with or without other risk factors), CIN incidence was 4.7%. Multivariate analysis identified renal insufficiency as the only risk factor predictive of CIN (relative risk, 3.850; 95% confidence interval, 1.200–12.348; P=0.023). Conclusion: In the clinical setting of hospital CT radiology practice, where guideline-recommended strategies for CIN prevention may not be consistently followed, use of the iso-osmolar agent iodixanol appears to be associated with a low incidence of CIN in at-risk patients.
Corrosion rate determination of vessel walls agitated by double impeller and gas sparging

Abstract Recently, multiple impeller gas sparged vessels have found wide application in many industries, such as food, pharmaceuticals, and biofuels. In this study, the rate of diffusion-controlled corrosion of the wall of nitrogen gas sparged-double impeller agitated vessel was studied by the dissolution of copper wall in acidified dichromate solution technique. The variables studied were the impeller rotation speed, the superficial gas velocity, and the clearance between the two impellers. The results were reported in terms of dimensionless number depicting the process conditions, Re, Sc, and the impeller clearance. For the agitated vessel, the corrosion rate correlation was CR=1.6 × 10 − 16 ReAg.0.668(C2H)0.183Sc0.33. ${\rm{CR}} = 1.6\; \times \;{10^{\; - \;16}}{\rm{R}}{{\rm{e}}_{{\rm{Ag}}{\rm{. }}}}^{0.668}{\left( {{{{C_2}} \over H}} \right)^{0.183}}{\rm{S}}{{\rm{c}}^{0.33}}. $ For the condition: 2800<ReAg. <19,600, 0.19<C2/H<0.58 and Sc=960, with an average deviation of ±2.9%. For the agitated sparged vessel, the data were correlated by CR=2.5 × 10 − 15 ReAg.0.134 ReSp. 0.381 Sc0.33. ${\rm{CR}} = 2.5\; \times \;{10^{\; - \;15}}{\rm{R}}{{\rm{e}}_{{\rm{Ag}}{\rm{. }}}}^{0.134}{\rm{Re}}_{{\rm{Sp}}{\rm{. }}}^{{\rm{0}}{\rm{. 381}}}{\rm{S}}{{\rm{c}}^{0.33}}. $ For the condition: 2800<ReAg. <19,600, 370<ReSp. <1855 and Sc=960, with an average deviation of ±6.7%. These results show that, under these conditions, the rate of corrosion of agitated vessels is controlled by the rate of agitation and the clearance between the impellers. However, when gas sparging is introduced, the rate of corrosion is much more influenced by the gas flow rate, whereas the effect of the clearance between the impellers nearly disappears.