Miracle-dz/UniFAR-FTUs huggingface dataset:
Reuse and reengineering of multitasking real-time applications in LACATRE

LACATRE is a graphical environment dedicated to the development of real time applications. Several integrated tools assist the user, not only during the preliminary and detailed design, but also during the maintenance step. Thanks to the reverse engineering techniques, a user can rebuild a diagram of his application using low level objects and actions provided by the LACATRE environment (detailed view). The aim of the paper is to present a methodology which, from this detailed view, helps to restructure real time applications using the LACATRE high level objects in terms of client server relation. These components then become reusable interfaces in a new high level design or can be replaced by more reliable and efficient components from the current high level object database.
Comparison of the temperature‐dependence of rapid axonal transport and microtubules in nerves of the rabbit and bullfrog.

1. The average velocity of transport of dopamine‐beta‐hydroxylase, an enzyme confined to unmyelinated adrenergic nerves, was measured in rabbit and bullfrog sciatic nerves or branches incubated in vitro at various temperatures. In parallel experiments, the number and density of microtubules were measured in cross‐sections of randomly selected unmyelinated axons from another set of nerves incubated under the same conditions. 2. Average transport velocity was exponentially related to temperature over a wide range, but it fell abruptly towards zero at temperatures below 13 degrees C in the case of rabbit nerves and 10 degrees C in the case of frog nerves. 3. The number of microtubules per unmyelinated axon had declined considerably before the transport of dopamine‐beta‐hydroxylase was impaired. At 13 degrees C, axons in rabbit nerves lost 30% of their microtubules. Axons in bullfrog nerves were, if anything, more sensitive to cold, losing 35% of their microtubules at 15 degrees C and 65% of them at 10 degrees C. 4. Since the temperature‐dependence of the axonal transport of dopamine‐beta‐hydroxylase is probably typical of rapid axonal transport in general, it was concluded that transport in unmyelinated axons can continue unaffected when a substantial fraction of the microtubular population has been lost. 5. Although these results could imply that microtubules are not essential for transport, they are equally compatible with the view that these organelles determine the capacity of the transport system and are normally present in excess.
Gender-specific relationships between plasma oxidized low-density lipoprotein cholesterol, total antioxidant capacity, and central adiposity indicators

Background: Oxidative stress has a pivotal role in the onset of obesity-related chronic diseases. This study assessed potential gender differences in the associations of adiposity (total vs. central) with oxidative stress markers in healthy young adults. Methods: This cross-sectional study enrolled 272 subjects (97 males, 175 females; 22 ± 3 years, body mass index 22.0 ± 2.8 kg/m2). Body composition, cardiometabolic and lifestyle features, oxidized low-density lipoprotein cholesterol (ox-LDL) concentrations, plasma total antioxidant capacity (TAC), and glutathione peroxidase (GPx) activity in erythrocytes were determined by validated procedures. Results: Compared to women, men had statistically higher concentrations of ox-LDL (61.7 vs. 53.5 U/l, p = 0.022). In analyses with the whole sample, those individuals included in the highest tertile of central adiposity indicators (waist circumference, WC, or waist-to-hip ratio, WHR) presented higher ox-LDL and lower TAC values (p < 0.01), while no statistical differences were found across tertiles of total body fat. WHR values were more strongly associated with ox-LDL and TAC concentrations, compared to other adiposity indicators, with higher slopes for women. Sex differences in ox-LDL concentrations were abolished (p > 0.05) after individual pairing of men and women for WC (53.8 vs. 61.6 U/l, p = 0.225) or WHR (56.1 vs. 56.3 U/l, p = 0.471). No differences were found in GPx values concerning gender or adiposity indicators. Conclusions: Plasma ox-LDL and TAC values were more strongly influenced by central adiposity indicators (WHR and WC) in women than in men, suggesting that the change of the gynoid to android pattern phenotype among young women could lead to a steeper unfavourable redox status compared to men.
Dramatic increase in negative superhelicity of plasmid DNA in the forespore compartment of sporulating cells of Bacillus subtilis

Plasmid pUB110, isolated from vegetative cells of Bacillus subtilis, has an average of 34 negative supertwists (tau av = -34). This value falls to -30 early in sporulation, and the plasmid in the mother cell compartment maintains a tau av of -30. However, the plasmid within the developing forespore becomes much more negatively supercoiled, reaching a tau av of -47 in the dormant spore. This increased negative supercoiling in the forespore plasmid takes place in parallel with the synthesis of small, acid-soluble spore proteins, alpha and beta; and the plasmid from spores lacking small, acid-soluble proteins alpha and beta has a tau av of -40. The large increase in negative supercoiling of spore plasmid was also observed with Bacillus megaterium and in B. subtilis containing a plasmid with an origin different from that of pUB110. During spore germination plasmid pUB110 rapidly relaxed back to the tau av value characteristic of vegetative cells. It is possible that the observed changes in forespore plasmid topology are involved in modulating gene expression, DNA photochemistry, or both of these parameters in this compartment.
In vivo NMR studies of regional cerebral energetics in MPTP model of Parkinson's disease: recovery of cerebral metabolism with acute levodopa treatment

In this study, we have evaluated cerebral atrophy, neurometabolite homeostasis, and neural energetics in 1‐methyl‐4‐phenyl‐1,2,3,6‐tetrahydropyridin (MPTP) model of Parkinson's disease. In addition, the efficacy of acute l‐DOPA treatment for the reversal of altered metabolic functions was also evaluated. Cerebral atrophy and neurochemical profile were monitored in vivo using MRI and 1H MR Spectroscopy. Cerebral energetics was studied by 1H‐[13C]‐NMR spectroscopy in conjunction with infusion of 13C labeled [1,6‐13C2]glucose or [2‐13C]acetate. MPTP treatment led to reduction in paw grip strength and increased level of GABA and myo‐inositol in striatum and olfactory bulb. 13C Labeling of glutamate‐C4 (1.93 ± 0.24 vs. 1.48 ± 0.06 μmol/g), GABA‐C2 (0.24 ± 0.04 vs. 0.18 ± 0.02 μmol/g) and glutamaine‐C4 (0.26 ± 0.04 vs. 0.20 ± 0.04 μmol/g) from [1,6‐13C2]glucose was found to be decreased with MPTP exposure in striatum as well as in other brain regions. However, glutamine‐C4 labeling from [2‐13C]acetate was found to be increased in the striatum of the MPTP‐treated mice. Acute l‐DOPA treatment failed to normalize the increased ventricular size and level of metabolites but recovered the paw grip strength and 13C labeling of amino acids from [1,6‐13C2]glucose and [2‐13C]acetate in MPTP‐treated mice. These data indicate that brain energy metabolism is impaired in Parkinson's disease and acute l‐DOPA therapy could temporarily recover the cerebral metabolism.
pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Background Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. Results The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. Conclusions pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.
Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme

The products of the yeast CDC73 and PAF1 genes were originally identified as RNA polymerase II-associated proteins. Paf1p is a nuclear protein important for cell growth and transcriptional regulation of a subset of yeast genes. In this study we demonstrate that the product of CDC73 is a nuclear protein that interacts directly with purified RNA polymerase II in vitro. Deletion of CDC73 confers a temperature-sensitive phenotype. Combination of the cdc73 mutation with the more severe paf1 mutation does not result in an enhanced phenotype, indicating that the two proteins may function in the same cellular processes. To determine the relationship between Cdc73p and Paf1p and the recently described holoenzyme form of RNA polymerase II, we created yeast strains containing glutathione S-transferase (GST)-tagged forms of CDC73, PAF1, and TFG2 functionally replacing the chromosomal copies of the genes. Isolation of GST-tagged Cdc73p and Paf1p complexes has revealed a unique form of RNA polymerase II that contains both Cdc73p and Paf1p but lacks the Srbps found in the holoenzyme. The Cdc73p-Paf1p-RNA polymerase II-containing complex also includes Gal11p, and the general initiation factors TFIIB and TFIIF, but lacks TBP, TFIIH, and transcription elongation factor TFIIS as well as the Srbps. The Srbp-containing holoenzyme does not include either Paf1p or Cdc73p, demonstrating that these two forms of RNA polymerase II are distinct. In confirmation of the hypothesis that the two forms coexist in yeast cells, we found that a TFIIF-containing complex isolated via the GST-tagged Tfg2p construct contains both (i) the Srbps and (ii) Cdc73p and Paf1p. The Srbps and Cdc73p-Paf1p therefore appear to define two complexes with partially redundant, essential functions in the yeast cell. Using the technique of differential display, we have identified several genes whose transcripts require Cdc73p and/or Paf1p for normal levels of expression. Our analysis suggests that there are multiple RNA polymerase II-containing complexes involved in the expression of different classes of protein-coding genes.
Spectral analysis of the cooling phase of an x-ray superburst in 4 U 1636-53

We analyzed the cooling phase of an x-ray superburst of the low-mass X-ray binary 4U 1636-53 using different models in XSPEC software. Our goal was to find the behavior of certain properties of the neutron star, e.g. radius and temperature, and to find the chemical composition of the neutron star atmosphere. We tried 6 different models for the cooling phase of the superburst and found that the best fit came from a model consisting of a blackbody, a power law, a gaussian emission line and an absorption edge. We found that the bolometric flux versus blackbody temperature relation, F ∝ T 4 bb, does not hold, telling us that the blackbody radius changes over time. We also conclude from the color-correction factor that the superburst is a product of metal burning, fueled most likely by carbon.
Revisiting: "Comparison of intravascular ultrasound versus angiography-guided drug-eluting stent implantation: a meta-analysis of one randomised trial and ten observational studies involving 19,619 patients".

Recently, we have published the manuscript entitled “Comparison of intravascular ultrasound versus angiography-guided drug-eluting stent (DES) implantation: a meta-analysis of one randomised trial and ten observational studies involving 19,619 patients”. Two additional important studies (namely, the ADAPT-DES and the RESET), comparing IVUSand angiography-guided DES implantation have recently been reported1,2. In addition, the two-year clinical follow-up of the randomised AVIO trial was published recently3. Therefore, our meta-analysis needs to be updated. The ADAPT-DES (Assessment of Dual AntiPlatelet Therapy with Drug-Eluting Stents) trial was a prospective multicentre registry study that enrolled approximately 11,000 patients1. The outcomes, after IVUS-guided percutaneous coronary intervention (PCI), were compared to the non-IVUS-guided PCI group in 8,575 patients. A significant reduction in the primary endpoint of definite/probable stent thrombosis was evident in patients who underwent PCI under IVUS guidance (vs. angiography guidance) at one-year follow-up (0.52% vs. 1.04%, p=0.011). In the pre-specified long lesion subset of the RESET (Real Safety and Efficacy of a 3-month Dual Antiplatelet Therapy Following Zotarolimus-eluting Stents Implantation) trial2, 543 patients were enrolled and randomised to either the IVUSor angiographyguided PCI group. IVUS-guided PCI was related to a significantly lower risk of major adverse cardiac events (MACE) at one-year follow-up compared to angiographic guidance (4.0% vs. 8.1%, p=0.048). In the AVIO trial, no statistical differences were observed in MACE (16.9% vs. 23.2%) or target lesion revascularisation (TLR, 9.2% vs. 11.9%) between the IVUSand angiography-guided groups3. Based on the available data, the currently updated meta-analysis includes 14 studies involving 29,029 patients (Figure 1)1-4. The revisited meta-analysis not only confirms our previous findings that IVUS guidance was associated with reductions in death (hazard ratio [HR]: 0.66, 95% confidence interval [CI]: 0.55-0.78, p<0.001), stent thrombosis (HR: 0.57, 95% CI: 0.44-0.73, p<0.001), myocardial infarction (MI) (HR: 0.74, 95% CI: 0.62-0.90, p=0.002) and MACE (HR: 0.86, 95% CI: 0.77-0.95, p=0.003), but also shows the beneficial effect of IVUS guidance in reducing TLR (HR: 0.82, 95% CI: 0.68-0.97, p=0.02). Since the present meta-analysis included mostly observational studies, no significant publication bias was identified using Egger’s linear regression test (p=0.50 for death; p=0.85 for ST; p=0.69 for MI, p=0.33 for MACE, p=0.67 for TLR). Although the present meta-analysis supports and strengthens the previously reported results, appropriately powered randomised trials are necessary to provide robust evidence and verify the practical value of IVUS-guided DES implantation.
Topical treatment of psoriasis

Importance of the field: The majority of patients with psoriasis can be safely and effectively treated with topical therapy alone, either under the supervision of a family physician or dermatologist. For those requiring systemic agents, topical therapies can provide additional benefit. Optimal use of topical therapy requires an awareness of the range and efficacy of all products. Areas covered in this review: The review covers the efficacy and role of topical therapies including emollients, corticosteroids, vitamin D analogs, calcineurin inhibitors, dithranol, coal tar, retinoids, keratolyics and combination therapy. The report was prepared following a PubMed and Embase literature search up to April 2010. What the reader will gain: The paper provides a broad review of the relevant topical therapeutic options available in routine clinical practice for the management of psoriasis and a recommendation for selection of treatment. Take home message: Topical therapies used appropriately provide a safe and effective option for the management of psoriasis. An awareness of the available products and their efficacy is key to treatment selection and patient satisfaction.
4D cone beam CT-based dose assessment for SBRT lung cancer treatment

The purpose of this research is to develop a 4DCBCT-based dose assessment method for calculating actual delivered dose for patients with significant respiratory motion or anatomical changes during the course of SBRT. To address the limitation of 4DCT-based dose assessment, we propose to calculate the delivered dose using time-varying (‘fluoroscopic’) 3D patient images generated from a 4DCBCT-based motion model. The method includes four steps: (1) before each treatment, 4DCBCT data is acquired with the patient in treatment position, based on which a patient-specific motion model is created using a principal components analysis algorithm. (2) During treatment, 2D time-varying kV projection images are continuously acquired, from which time-varying ‘fluoroscopic’ 3D images of the patient are reconstructed using the motion model. (3) Lateral truncation artifacts are corrected using planning 4DCT images. (4) The 3D dose distribution is computed for each timepoint in the set of 3D fluoroscopic images, from which the total effective 3D delivered dose is calculated by accumulating deformed dose distributions. This approach is validated using six modified XCAT phantoms with lung tumors and different respiratory motions derived from patient data. The estimated doses are compared to that calculated using ground-truth XCAT phantoms. For each XCAT phantom, the calculated delivered tumor dose values generally follow the same trend as that of the ground truth and at most timepoints the difference is less than 5%. For the overall delivered dose, the normalized error of calculated 3D dose distribution is generally less than 3% and the tumor D95 error is less than 1.5%. XCAT phantom studies indicate the potential of the proposed method to accurately estimate 3D tumor dose distributions for SBRT lung treatment based on 4DCBCT imaging and motion modeling. Further research is necessary to investigate its performance for clinical patient data.
Identification of genes controlling collagen-induced arthritis in mice: striking homology with susceptibility loci previously identified in the rat.

The susceptibility to collagen-induced arthritis in the highly susceptible DBA/1 mouse has earlier been shown to be partly controlled by the MHC class II gene Aq. To identify susceptibility loci outside of MHC, we have made crosses between DBA/1 and the less susceptible B10.Q strain, both expressing the MHC class II gene Aq. Analysis of 224 F2 intercross mice with 170 microsatellite markers in a genome-wide scan suggested 4 quantitative trait loci controlling arthritis susceptibility located on chromosomes 6, 7, 8, and 10. The locus on chromosome 6 (Cia6), which was associated with arthritis onset, yielded a logarithm of odds score of 4.7 in the F2 intercross experiment and was reproduced in serial backcross experiments. Surprisingly, the DBA/1 allele had a recessive effect leading to a delay in arthritis onset. The suggestive loci on chromosomes 7 and 10 were associated with arthritis severity rather than onset, and another suggestive locus on chromosome 8 was most closely associated with arthritis incidence. The loci on chromosomes 7, 8, and 10 all appeared to contain disease-promoting alleles derived from the DBA/1 strain. Interestingly, most of the identified loci were situated in chromosomal regions that are homologous to regions in the rat genome containing susceptibility genes for arthritis; the mouse Cia6 locus is homologous with the rat Cia3, Pia5, Pia2, and Aia3; the locus on chromosome 7 (Cia7) is homologous with the rat Cia2; and the locus on chromosome 10 (Cia8) is homologous with the rat Cia4.
Evaluation of Effect of Curcuma longa Supplementation on Production Parameters and Organ Weights in Induced Aflatoxicosis in Broiler Birds

1 Department of Veterinary Pharmacology and Toxicology, College of Veterinary Science and A.H. , CGKV, Durg, Chhattisgarh, India 2 Department of Teaching Veterinary Clinical Complex, Faculty of Veterinary and Animal Sciences, West Bengal University of Animal and Fishery Sciences, Kolkata, India 3 Department of Veterinary Surgery and Radiology, College of Veterinary Science, Khanapara, Assam Agricultural University, Assam, India *Corresponding author
CD16 and CR3 receptors distinguish between the two mechanisms of tumour cytotoxicity in neutrophils

Summary Previous studies have suggested that phorbol ester‐activated neutrophils kill both antibody non‐coated and antibody‐coated K562 target cells. In this report the contribution of the receptors FcγIII (CD16) and CR3 (CD11b/CD18) in the lytic process was investigated. In neutrophils CD16 and CR3 are up‐regulated by the phorbol ester up to 4 and 10 times, respectively. As expected, lysis of non‐immunized K562 targets is not affected by the treatment of neutrophils with anti CD16, AB8.28, whereas lysis of immunized targets is decreased by 50%. In addition, the interaction of CD16 and AB8.28 induces calcium mobilization and increases granule secretion. Surprisingly, the simultaneous binding of AB8.28 and anti‐CR3 0KM1 to neutrophils completely abolishes the lysis of antibody‐coated targets. Unlike CD16, CR3 does not possess a functional role and binding of 0KM1 to CR3 does not affect cytotoxicity of immunized K562 targets, but it blocks lysis of non‐coated target almost completely, indicating a function as adhesion protein for CR3.
Appendectomy: A Contemporary Appraisal

ObjectiveThe authors present an accurate and comprehensive snapshot of appendicitis and the practice of appendectomy in the 1990s.MethodsAppendectomies were performed on 4950 patients in 147 Department of Defense hospitals worldwide over a 12-month period ending January 31, 1993.ResultsThe media
Glaucoma—2: Treatment

The main aim of treatment in glaucoma is to reduce intraocular pressure. Good evidence from multiple large randomised trials shows that reducing intraocular pressure is effective in preventing disease progression in ocular hypertension, primary open angle glaucoma, and even in so called normal tension glaucoma. Target pressures in the low teens are associated with the lowest progression rates. ### βblockers blockers—for example, timolol, carteolol, betaxolol levobunolol, and metipranolol—reduce the secretion of aqueous and are the most commonly prescribed topical treatment. Contraindications to their use include a history of lung or heart disease, as the drops may cause systemic β blockade. Topical β blockers can unmask latent and previously undiagnosed chronic obstructive pulmonary disease in elderly people. Systemic effects from eye drops can be reduced by occlusion of the punctum (finger pressed on the caruncle, which is felt as a lump at the inner canthus of the eye) or shutting the eyes for several minutes after putting in the drops. This reduces the lacrimal pumping mechanism and stops the drops running down the lacrimal passages and being absorbed systemically through the nasal mucosa or by inhalation directly into the lungs. It may also enhance ocular absorption of the drugs. Drops are usually given twice a day, but long acting forms can be given once a day, either alone or in combination with other drops. [][1] Eye closure to reduce systemic side effects after instilling drops ### Prostaglandin analogues Prostaglandin analogues (such as, latanoprost, travoprost, and bimatoprost) reduce the intraocular pressure by increasing aqueous outflow from the eye through the uveoscleral pathway. These drugs can reduce intraocular pressure by 30-35%. Systemic side effects are minimal, but a few patients with light irides experience a gradual, permanent darkening of the iris. Eyelashes may also increase in length and darken. For optimum effect, these drops are used once daily (at … [1]: /embed/graphic-1.gif