Miracle-dz/UniFAR-FTUs huggingface dataset:
Gag-Protease Sequence Evolution Following Protease Inhibitor Monotherapy Treatment Failure in HIV-1 Viruses Circulating in East Africa

Abstract Around 2.5 million HIV-infected individuals failing first-line therapy qualify for boosted protease inhibitor (bPI)-based second-line therapy globally. Major resistance mutations are rarely present at treatment failure in patients receiving bPI and the determinants of failure in these patients remain unknown. There is evidence that Gag can impact PI susceptibility. Here, we have sequenced Gag-Protease before and following failure in 23 patients in the SARA trial infected with subtypes A, C, and D viruses. Before bPI, significant variation in Protease and Gag was observed at positions previously associated with PI exposure and resistance including Gag mutations L449P, S451N, and L453P and Protease K20I and L63P. Following PI failure, previously described mutations in Protease and Gag were observed, including those at the cleavage sites such as R361K and P453L. However, the emergence of clear genetic determinants of therapy failure across patients was not observed. Larger Gag sequence datasets will be required to comprehensively identify mutational correlates of bPI failure across subtypes.
Efficient displacement Mapping by Image Warping

While displacement maps can provide a rich set of visual detail on otherwise simple surfaces, they have always been very expensive to render. Rendering has been done using ray-tracing and by introducing a great number of micro-polygons. We present a new image-based approach by showing that rendering displacement maps is sufficiently similar to image warping for parallel displacements and displacements originating form a single point. Our new warping algorithm is particularly well suited for this class of displacement maps. It allows efficient modeling of complicated shapes with few displacement mapped polygons and renders them at interactive rates.
Combinatorial Testing of Full Text Search in Web Applications

Database driven web applications are some of the most widely developed systems today. In this paper, we demonstrate use of combinatorial testing for testing database supported web applications, especially where full-text search is provided or many combinations of search options are utilized. We develop test-case selection techniques, where test strings are synthesized using characters or string fragments that may lead to system failure. We have applied our approach to the National Vulnerability Database (NVD) application and have discovered a number of "corner-cases" that had not been identified previously. We also present simple heuristics for isolating the fault causing factors that can lead to such system failures. The test method and input model described in this paper have immediate application to other systems that provide complex full text search.
Increased p53 level, Bax/Bcl-x(L) ratio, and TRAIL receptor expression in human emphysema.

RATIONALE Emphysema is mainly known for the complex inflammatory processes associated with its development. In addition to lung inflammation, it is now accepted that increased alveolar cell apoptosis is also part of emphysema pathophysiology. However, little is known about the mechanisms involved in alveolar apoptosis. We postulate that oxidative stress and proinflammatory cytokines could lead to p53 accumulation, Bax/Bcl-x(L) ratio elevation, and higher tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) receptor levels in the emphysematous lung. OBJECTIVES To evaluate the expression of p53, Bax, Bcl-x(L), TRAIL, and TRAIL receptors in lung parenchyma from nonemphysematous nonsmokers and smokers and emphysematous smokers and ex-smokers and to determine whether H2O2 and/or TNF can modulate the expression of these apoptotic proteins. METHODS p53, Bax, Bcl-x(L), and TRAIL receptor protein levels in lung parenchyma were measured by Western blot, and TRAIL mRNA levels were measured by real-time polymerase chain reaction. Changes in TRAIL receptor, Bax, Bcl-x(L), and p53 protein levels after in vitro H2O2 and/or TNF stimulation of A549 cells were also assessed by Western blot. MEASUREMENTS AND MAIN RESULTS The p53 protein levels, the Bax/Bcl-x(L) ratio, and TRAIL receptors 1, 2, and 3 protein levels were significantly higher in subjects with emphysema. Moreover, they were also increased after H2O2 and TNF treatments of A549 cells. CONCLUSIONS These findings suggest that oxidative stress and proinflammatory cytokines may be involved in the elevation of p53 levels, the Bax/Bcl-x(L) ratio, and TRAIL receptor levels, new mechanisms that may be implicated in the increased alveolar cell apoptosis that occurs in emphysema.
Renin Secretion in the Chronically Perfused Pulseless Calf: Evidence for Failure of Stimulation by Decreased Pulse Pressure

To study the influence of arterial pulse pressure on renin release, a chronic pulseless calf preparation was developed using a centrifugal left ventricular bypass blood pump. After pump implantation and recovery, control measurements of renal vein and arterial plasma renin activity, arterial pressure, and renal artery flow were obtained. The centrifugal bypass pump rate then was increased to capture cardiac output completely, and nine conscious calves were perfused in a nonpulsatile manner (pulse pressure <5-10 mm Hg) for 48 hours. Nonpulsatile perfusion was well tolerated and serum sodium, potassium, creatinine, and blood urea nitrogen were unchanged during bypass. Mean arterial pressure remained relatively constant [117 ± 3 (SE) mm Hg] during bypass, and was not significantly changed from control. Although renal blood flow decreased slightly from control (667 ± 84 ml/min) during the nonpulsatile perfusion period (SS5 ± 73 ml/min), renin secretion did not increase significantly from control (482 ± 81 ng angiotensin I/ml per hr per min) during the bypass period (531 ± 99). A diurnal cycle of renin secretion was observed during the pulseless pet-fusions. These data document the lack of any significant stimulatory influence of decreased pulse pressure on renin secretion in a chronic awake calf model. Ore Res 46:100-107, 1979
Experimental analysis and modelling of fatigue behaviour of thick woven laminated composites

The objective of this work was to analyse the fatigue behaviour and the damage development in unidirectional and angle-ply 2/2 twill weave T800 carbon/epoxy woven fabric composite laminates. Fatigue tensile-tensile tests were performed and internal damage has been observed by using camera and optical microscope during testing. The experimental results show that the damage evolution can be characterized by two or three stages according to the 0° ply and angle-ply laminates respectively. An original fatigue criterion for onset delamination during fatigue loading of angle-ply laminates has been proposed. Validation of fatigue model was made with tensile fatigue tests performed on angle-ply textile laminates with drilled circular hole. Further numerical predictions are in good agreement with experimental results. RÉSUMÉ. L’objectif de cette étude est d’analyser l’ensemble des comportements mécaniques et des mécanismes d’endommagement dans un composite tissé (2x2 twill) T800 carbone/époxy. Des essais en traction-traction de fatigue ont été faits en observant les évolutions des endommagements par caméra optique. Les résultats expérimentaux montrent que l’évolution des endommagements se décompose en deux ou trois étapes selon les orientations des plis (pli unidirectionnel ou pli croisé). Un modèle d’initiation du délaminage en fatigue a été également proposé. La validation de ce modèle a été ensuite étudiée sur une plaque composite trouée soumis à des sollicitations de fatigue en traction-traction. Le calcul numérique montre une bonne corrélation avec ces résultats expérimentaux.
Erosion Wear Investigation of HVOF Sprayed WC-10Co4Cr Coating on Slurry Pipeline Materials

In the present work, erosion wear due to slurry mixture flow has been investigated using a slurry erosion pot tester. Erosion tests are conducted on three different slurry pipe materials, namely, mild steel, SS202, and SS304, to establish the influence of rotational speed, concentration, and time period. In order to increase erosion wear resistance, a high-velocity oxy-fuel (HVOF) coating technique is used to deposit a WC-10Co4Cr coating on the surface of all piping materials. Experimental results show that rotational speed is a highly-influencing parameter for the erosion wear rate as compared to solid concentration, time duration, and weighted mean diameter. WC-10Co4Cr HVOF coating improved the erosion resistance of piping materials up to 3.5 times. From experimental data, the exponents of solid concentration, velocity, and the size of particles are calculated for the empirical erosion wear equation. A functional equation of the erosion wear rate is developed. The predicted erosion wear is in agreement with the experimental data and found to be within a deviation of ±12%.
Identification of Staphylococcus argenteus in Eastern China based on a nonribosomal peptide synthetase (NRPS) gene.

AIM To investigate whether the Staphylococcus argenteus is present in Eastern China and to verify the utility of a new screening process. MATERIALS & METHODS Phenotype observation, PCR assay targeting a hypothetical nonribosomal peptide synthetase (NRPS) gene, phylogenetic analysis of rpoB and multilocus sequence typing were used to screen and identify strains of S. argenteus from 839 presumptive S. aureus isolates. RESULTS Eighty-nine (89/839, 10.6%) of the presumptive S. aureus isolates produced white colonies on tryptone soya agar plates. Of the white-colony isolates, six (6/89, 7%) were S. argenteus, 75 (75/89, 84%) were S. aureus and eight (8/89, 9%) were other bacteria. CONCLUSION The PCR-based method targeting the NRPS gene can simultaneously identify and distinguish S. argenteus and S. aureus. All representative sequences of rpoB generated in this study were deposited in GenBank under accession numbers SJTU F20002, KT767581; SJTU F20269, KT767582; SJTU F20419, KT767583; SJTU F20420, KT767584; SJTU F20124, KT767585; SJTU F21164, KT767586; SJTU F21285, KT767587; SJTU F21224, KT767588; SJTU F21155, KT767589; SJTU F21294, KT767590; SJTU F20030, KT767591; SJTU F20044, KT767592; SJTU F20135, KT767593; SJTU F20123, KT767594; SJTU F21319, KT767595, respectively. All the new sequence types (STs) were submitted to a multilocus sequence typing database and the assigned ST numbers are ST3261 (151-469-20-101-145-150-131), ST3262 (12-3-1-1-4-4-410) and ST3267 (2-471-2-2-6-3-2).
The Effects of C-peptide on Type 1 Diabetic Polyneuropathies and Encephalopathy in the BB/Wor-rat

Diabetic polyneuropathy (DPN) occurs more frequently in type 1 diabetes resulting in a more severe DPN. The differences in DPN between the two types of diabetes are due to differences in the availability of insulin and C-peptide. Insulin and C-peptide provide gene regulatory effects on neurotrophic factors with effects on axonal cytoskeletal proteins and nerve fiber integrity. A significant abnormality in type 1 DPN is nodal degeneration. In the type 1 BB/Wor-rat, C-peptide replacement corrects metabolic abnormalities ameliorating the acute nerve conduction defect. It corrects abnormalities of neurotrophic factors and the expression of neuroskeletal proteins with improvements of axonal size and function. C-peptide corrects the expression of nodal adhesive molecules with prevention and repair of the functionally significant nodal degeneration. Cognitive dysfunction is a recognized complication of type 1 diabetes, and is associated with impaired neurotrophic support and apoptotic neuronal loss. C-peptide prevents hippocampal apoptosis and cognitive deficits. It is therefore clear that substitution of C-peptide in type 1 diabetes has a multitude of effects on DPN and cognitive dysfunction. Here the effects of C-peptide replenishment will be extensively described as they pertain to DPN and diabetic encephalopathy, underpinning its beneficial effects on neurological complications in type 1 diabetes.
The tomography dementia rating scale (TDR)—The rating scale of Alzheimer's disease stages

The purpose of this research is to develop a morphologically determined scale—the Tomography Dementia Rating scale (TDR) to diagnose AD stages, based on the measurement of the severity of voluminal atrophic changes of the temporal lobes of the brain detected among patients during CT and MRI at various stages of the disease. The research included 140 patients aged 28 - 79. Test Group comprised 81 patients aged 34 - 79 suffering from various AD stages. Control Group consisted of 59 patients aged 28 - 78 who had various types of brain lesions with manifestations of dementia and cognitive impairment but who did not suffer from AD. CT and MRI data obtained has made it possible to create a scale that allows determining the severity of atrophic changes in the temporal lobes at each stage of AD development: 1) Pre-clinical AD stage—TDR-0: temporal lobes atrophy with a 4% - 8% decrease in tissue mass (corresponds to 26 - 28 MMSE points); 2) Early AD Stage—mild dementia—TDR-1: temporal lobes atrophy with a 9% - 18% decrease in tissue mass (corresponds to CDR-1 and to 20 - 25 MMSE points); 3) Middle AD stage—moderate dementia—TDR-2: temporal lobes atrophy with a 19% - 32% decrease in tissue mass (corresponds to CDR-2 and to 12 - 19 MMSE points); 4) Late AD stage—heavy dementia—TDR-3: temporal lobes atrophy with a 33% - 62% decrease in tissue mass (corresponds to CDR-3 and to 7 - 11 MMSE points). Thereby, the developed Tomography Dementia Rating scale (TDR) complements the Clinical Dementia Rating scale (CDR) and allows a correct and objective determination of AD stages as well as an easy differentiation of existing lesions with neurodegenerative changes characteristic for other diseases accompanied by dementia and cognitive impairment.
Biofilm formation by Escherichia coli O157:H7

Title of Document: BIOFILM FORMATION BY ESCHERICHIA COLI O157:H7 Karen Suzanne Silagyi, M.S., 2007 Directed By: Associate Professor, Dr. Y. Martin Lo, Nutrition and Food Science Escherichia coli O157:H7 from cattle was evaluated for its ability to produce biofilm on food contact surfaces and quorum sensing signals in various raw meat, raw poultry, and produce broths. Generally, the strain was able to attach and form the most biofilm on stainless steel. Transfer of cells attached to stainless steel was observed onto various raw meat, raw poultry, ready-to-eat deli meats, and produce products as high as 10 CFU/cm. E. coli O157:H7 isolated from 14 animal, food, and human sources were characterized on antimicrobial susceptibility, ability to form biofilm, and production of curli fimbriae and cellulose. Strains isolated from cattle, retail chicken, and retail beef were able to form strong biofilms in addition to curli and cellulose production. Additionally, E. coli O157:H7 from retail chicken showed considerable antimicrobial resistance. This study suggests E. coli O157:H7 biofilms pose significant risk to continuous contamination of a variety of food products. BIOFILM FORMATION BY ESCHERICHIA COLI O157:H7
Rare germline mutations identified by targeted next-generation sequencing of susceptibility genes in pheochromocytoma and paraganglioma.

CONTEXT Pheochromocytomas and paragangliomas have a highly diverse genetic background, with a third of the cases carrying a germline mutation in 1 of 14 identified genes. OBJECTIVE This study aimed to evaluate next-generation sequencing for more efficient genetic testing of pheochromocytoma and paraganglioma and to establish germline and somatic mutation frequencies for all known susceptibility genes. DESIGN A targeted next-generation sequencing approach on an Illumina MiSeq instrument was used for a mutation analysis in 86 unselected pheochromocytoma and paraganglioma tumor samples. The study included the genes EGLN1, EPAS1, KIF1Bβ, MAX, MEN1, NF1, RET, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, and VHL. RESULTS were verified in tumor and constitutional DNA with Sanger sequencing. RESULTS In all cases with clinical syndromes or known germline mutations, a mutation was detected in the expected gene. Among 68 nonfamilial tumors, 32 mutations were identified in 28 of the samples (41%), including germline mutations in EGLN1, KIF1Bβ, SDHA, SDHB, and TMEM127 and somatic mutations in EPAS1, KIF1Bβ, MAX, NF1, RET, and VHL, including one double monoallelic EPAS1 mutation. CONCLUSIONS Targeted next-generation sequencing proved to be fast and cost effective for the genetic analysis of pheochromocytoma and paraganglioma. More than half of the tumors harbored mutations in the investigated genes. Notably, 7% of the apparently sporadic cases carried germline mutations, highlighting the importance of comprehensive genetic testing. KIF1Bβ, which previously has not been investigated in a large cohort, appears to be an equally important tumor suppressor as MAX and TMEM127 and could be considered for genetic testing of these patients.
Towards an eLearning 2 . 0 provisioning strategy for universities

The institutional Personal Learning Environment (iPLE) constitutes our vision of how Web 2.0 tools and services, and people arrangement and data sharing could be applied for delivering open, flexible, distributed and learner-centred learning environments to university members. Based on the iPLE, this paper explores a strategy that universities could follow in order to take advantage of the benefits and opportunities that offering eLearning 2.0 tools and services to learners could bring.
Surgical resection versus non-surgical treatment for hepatic node positive patients with colorectal liver metastases.

BACKGROUND Involvement of hepatic lymph node in patients with colorectal liver metastases is associated with poor prognosis. OBJECTIVES To determine the benefits and harms of curative liver resection with lymphadenectomy versus other treatments for colorectal liver metastases with hepatic node involvement. SEARCH STRATEGY We searched The Cochrane Hepato-Biliary Group Controlled Trials Register, the Cochrane Central Register of Controlled Trials (CENTRAL) in The Cochrane Library, MEDLINE, EMBASE, Science Citation Index Expanded, and LILACS until September 2009 for identifying the randomised trials. SELECTION CRITERIA We considered only randomised clinical trials (irrespective of language, blinding, or publication status) comparing liver resection (alone or in combination with radiofrequency ablation or cryoablation) versus other treatments (neo-adjuvant chemotherapy, chemotherapy, or radiofrequency ablation) in patients with colorectal liver metastases with hepatic node involvement. DATA COLLECTION AND ANALYSIS Two authors independently identified trials for inclusion. MAIN RESULTS We were unable to identify any randomised clinical trial fulfilling the inclusion criteria of this review. We were also unable to identify any quasi-randomised or cohort studies, which could meaningfully answer this important issue. AUTHORS' CONCLUSIONS There is no evidence in the literature to assess the role of surgery versus other treatments for patients with colorectal liver metastases with hepatic node involvement. High quality randomised clinical trials are feasible and are necessary to determine the optimal management of patients with colorectal liver metastases with hepatic node involvement.
Modelling the Duration of Patent Examination at the European Patent Office

We analyze the duration of the patent examination process at the European Patent Office (EPO). Our data contain information related to the patent’s economic and technical relevance, EPO capacity and workload as well as novel citation measures which are derived from the EPO’s search reports. In our multivariate analysis we estimate competing risk specifications in order to characterize differences in the processes leading to a withdrawal of the application by the applicant, a refusal of the patent grant by the examiner or an actual patent grant. Highly cited applications are approved faster by the EPO than less important ones, but they are also withdrawn less quickly by the applicant. The process duration increases for all outcomes with the application’s complexity, originality, number of references (backward citations) in the search report and with the EPO’s workload at the filing date. Endogenous applicant behavior becomes apparent in other results: more controversial claims lead to slower grants, but faster withdrawals, while relatively well-documented applications (identified by a high share of applicant references appearing in the search report) are approved faster and take longer to be withdrawn.
Parameter-free outlier removal of 3D point clouds with large-scale noises

3D point clouds derived from either multi-view-based techniques or direct laser scanners are inevitably contaminated with severe outliers. This paper presents LSNOR, a parameter-free density-based Outlier Removal approach for point clouds corrupted by Large-Scale Noises. The main contributions are three-fold. (i) A local consistency factor (LCF) is proposed to indicate the local density similarity of points. Based on LCF, parameter estimation and cluster screening are performed via consistency checking. In particular, unlike most of the density-based methods requiring user interactions for parameter determination, the proposed approach realizes automated parameter estimation. Besides, the outliers eliminated by screening can reduce the complexity afterwards. (ii) A new distance measure incorporating color factors is proposed to facilitate separating inliers and outliers apart. Taking into consider the color property of most 3D point clouds, the final correctness of outlier removal can be enhanced. (iii) The density-based clustering method is made to be suited to 3D point clouds, being independent of the prior knowledge of the distribution of points. Experimental results on synthetic and real point clouds demonstrate that our approach outperforms the state-of-the-art in both accuracy and computation time.