Miracle-dz/UniFAR-FTUs huggingface dataset:
An unsteady single‐phase level set method for viscous free surface flows

The single‐phase level set method for unsteady viscous free surface flows is presented. In contrast to the standard level set method for incompressible flows, the single‐phase level set method is concerned with the solution of the flow field in the water (or the denser) phase only. Some of the advantages of such an approach are that the interface remains sharp, the computation is performed within a fluid with uniform properties and that only minor computations are needed in the air. The location of the interface is determined using a signed distance function, and appropriate interpolations at the fluid/fluid interface are used to enforce the jump conditions. A reinitialization procedure has been developed for non‐orthogonal grids with large aspect ratios. A convective extension is used to obtain the velocities at previous time steps for the grid points in air, which allows a good estimation of the total derivatives. The method was applied to three unsteady tests: a plane progressive wave, sloshing in a two‐dimensional tank, and the wave diffraction problem for a surface ship, and the results compared against analytical solutions or experimental data. The method can in principle be applied to any problem in which the standard level set method works, as long as the stress on the second phase can be specified (or neglected) and no bubbles appear in the flow during the computation. Copyright © 2006 John Wiley & Sons, Ltd.
Meta-analysis of studies on individual consumption of chlorinated drinking water and bladder cancer

Study objective: To evaluate whether consumption of chlorinated drinking water is associated with bladder cancer. Design: A bibliographic search was conducted and the authors selected studies evaluating individual consumption of chlorinated drinking water and bladder cancer. The authors extracted from each study risk estimates for intermediate and long term (>40 years) consumption of chlorinated water, stratified by sex when possible, and performed meta-analysis for the two exposure levels. A meta-analysis was also performed of the dose-response regression slopes. Setting: Populations in Europe and North America. Participants: Those included in six case-control studies (6084 incident bladder cancer cases, 10 816 controls) and two cohort studies (124 incident bladder cancer cases) fulfilling the inclusion criteria. Main results: Ever consumption of chlorinated drinking water was associated with an increased risk of bladder cancer in men (combined OR=1.4, 95%CI 1.1 to 1.9) and women (combined OR=1.2, 95%CI 0.7 to 1.8). The combined OR for mid-term exposure in both genders was 1.1 (95% CI 1.0 to 1.2) and for long term exposure was 1.4 (95%CI 1.2 to 1.7). The combined estimate of the slope for a linear increase in risk was 1.13 (95% CI 1.08 to 1.20) for 20 years and 1.27 (95% CI 1.15 to 1.43) for 40 years of exposure in both sexes. Conclusions: This meta-analysis of the best available epidemiological evidence indicates that long term consumption of chlorinated drinking water is associated with bladder cancer, particularly in men. The observed relative risk is only moderately high, but the population attributable risk could be important as the vast majority of the population of industrialised countries is potentially exposed to chlorination byproducts for long time periods.
Increased sensitivity to radiochemotherapy in IDH1 mutant glioblastoma as demonstrated by serial quantitative MR volumetry.

BACKGROUND Isocitrate dehydrogenase 1 (IDH1) mutations have been linked to favorable outcomes in patients with glioblastoma multiforme (GBM). Recent in vitro experiments suggest that IDH1 mutation sensitizes tumors to radiation damage. We hypothesized that radiographic treatment response would be significantly different between IDH1 mutant versus wild-type GBMs after radiotherapy (RT) and concurrent temozolomide (TMZ). METHODS A total of 39 newly diagnosed GBM patients with known IDH1 mutational status (10 IDH1 mutants), who followed standard therapy and had regular post-contrast T1W (T1+C) and T2W/ fluid-attenuated inversion recovery (FLAIR) images in the 6-month period after starting RT, were enrolled. The volume of contrast-enhancing and FLAIR hyperintensity were calculated from each scan. Linear and polynomial regression techniques were used to estimate the rate of change and temporal patterns in tumor volumes. RESULTS IDH1 mutant GBMs demonstrated a favorable response to RT/TMZ in the study period, as demonstrated by 10 of 10 mutants showing radiographic response (decreasing V(T1+C)), compared with 13 of 29 wild-types (P < .001). During the study period, V(T1+C) and V(FLAIR) changed at -3.6% per week and +0.6% per week in IDH1 mutant tumors, respectively, as compared with +0.8% per week and +5.2% per week in IDH1 wild-type tumors (P = .0076 and P = .0118, respectively). Amongst the radiographic responders, IDH1 mutant GBMs still demonstrated significant progression-free and overall survival benefit. Aggregated tumor kinetics by group showed significant lower rate in IDH1 mutant GBMs in specific periods: >105 days for V(FLAIR) and 95-120 and >150 days for V(T1+C) from starting RT/TMZ. CONCLUSIONS The current study supports the hypothesis that IDH1 mutant GBMs are more sensitive to radiochemotherapy than IDH1 wild-type GBMs.
Management of extremity arterial pseudoaneurysms associated with osteochondromas

Arterial pseudoaneurysms associated with osteochondromas are rare and most publications on this topic are case reports. The management of this double entity is not standardized. We wanted to update it. Literature searches on MEDLINE and EMBASE were performed using the keywords “artery pseudoaneurysm” and “osteochondroma”. Patient demographics, clinical presentations, diagnostic and therapeutic modalities were reviewed. In sum, 101 cases were analyzed. Overall, young adults represented the majority of the affected population with a masculine preponderancy (86%). Painful swelling (51%) was the most commonly physical finding. Distal femur was the most common site of the osteochondroma (86%). Multiple hereditary exostosis was seldom reported (36%). Diagnostic confirmation was dominated by arteriography (55%). Popliteal artery (77%) was the most commonly injured vessel. The treatment was open surgery with vascular repair and optimal exostectomy. Arterial repair was performed with saphenous vein grafting (40%) or lateral suture (39%). Postoperative courses were often uneventful (97%). Arterial pseudoaneurysms resulted from osteochondromas were dominated by those involving the popliteal artery. The use of arteriography to confirm the diagnosis may be limited to the benefit of non-invasive radiological methods because endovascular treatment is not relevant in the setting of osteochondroma-induced arterial pseudoaneurysm.
A Process Similar to Autophagy Is Associated with Cytocidal Chloroquine Resistance in Plasmodium falciparum

Resistance to the cytostatic activity of the antimalarial drug chloroquine (CQ) is becoming well understood, however, resistance to cytocidal effects of CQ is largely unexplored. We find that PfCRT mutations that almost fully recapitulate P. falciparum cytostatic CQ resistance (CQRCS) as quantified by CQ IC50 shift, account for only 10–20% of cytocidal CQR (CQRCC) as quantified by CQ LD50 shift. Quantitative trait loci (QTL) analysis of the progeny of a chloroquine sensitive (CQS; strain HB3)×chloroquine resistant (CQR; strain Dd2) genetic cross identifies distinct genetic architectures for CQRCS vs CQRCC phenotypes, including identification of novel interacting chromosomal loci that influence CQ LD50. Candidate genes in these loci are consistent with a role for autophagy in CQRCC, leading us to directly examine the autophagy pathway in intraerythrocytic CQR parasites. Indirect immunofluorescence of RBC infected with synchronized CQS vs CQR trophozoite stage parasites reveals differences in the distribution of the autophagy marker protein PfATG8 coinciding with CQRCC. Taken together, the data show that an unusual autophagy – like process is either activated or inhibited for intraerythrocytic trophozoite parasites at LD50 doses (but not IC50 doses) of CQ, that the pathway is altered in CQR P. falciparum, and that it may contribute along with mutations in PfCRT to confer the CQRCC phenotype.
Tranching and Rating

In this paper we analyse the source and magnitude of marketing gains from selling structured debt securities at yields that reflect only their credit ratings, or specifically at yields on equivalently rated corporate bonds. We distinguish between credit ratings that are based on probabilities of default and ratings that are based on expected default losses. We show that subdividing a bond issued against given collateral into subordinated tranches can yield significant profits under the hypothesised pricing system. Increasing the systematic risk or reducing the total risk of the bond collateral increases the profits further. The marketing gain is generally increasing in the number of tranches and decreasing in the rating of the lowest rated tranche.
O R I G I N a L C L I N I C a L I N V E S T I G a T I O N Open Access

Quality of vitamin K antagonist control and outcomes in atrial fibrillation patients: a meta-analysis and meta-regression Abstract Background: Atrial fibrillation (AF) patients frequently require anticoagulation with vitamin K antagonists (VKAs) to prevent thromboembolic events, but their use increases the risk of hemorrhage. We evaluated time spent in therapeutic range (TTR), proportion of international normalized ratio (INR) measurements in range (PINRR), adverse events in relation to INR, and predictors of INR control in AF patients using VKAs.
Radiation transmission, leakage and beam penumbra measurements of a micro‐multileaf collimator using GafChromic EBT film

Micro‐multileaf collimator systems coupled to linear accelerators for radioneurosurgery treatments require a rigorous dosimetric characterization in order to be used in 3D conformal and intensity modulated stereotactic radiosurgery and radiotherapy applications. This characterization involves high precision measurements of leaf transmission, leakage and beam penumbra through the collimation system and requires the use of detectors with high spatial resolution, high sensitivity and practically no energy dependence. In this work the use of GafChromic EBT radiochromic film to measure the basic dosimetric properties of the m3‐mMLC (BrainLAB, Germany) micro‐multileaf collimator system integrated to a 6 MV linear accelerator, is reported. Results show that average values of transmission and leakage radiation are 0.93±0.05% and 1.08±0.08%, respectively. The 80–20% beam penumbra were found to be 2.26±0.11 mm along the leaf side (perpendicular to leaf motion) and 2.31±0.11 mm along the leaf end (parallel to leaf motion) using square field sizes ranging from 9.1 to 1.8 cm. These measurements are in agreement with values reported in the literature for the same type of mMLC using different radiation detectors. PACS number: 87.56. N‐
Improved body weight and performance status and reduced serum PGE2 levels after nutritional intervention with a specific medical food in newly diagnosed patients with esophageal cancer or adenocarcinoma of the gastro-esophageal junction

The majority of cancer patients loses weight and becomes malnourished during the course of their disease. Metabolic alterations and reduced immune competence lead to wasting and an increased risk of infectious complications. In the present study, the effect of a nutritionally complete medical food, which is high in protein and leucine and enriched with fish oil and specific oligosaccharides, was investigated on immune function, nutritional status, and inflammation in patients with esophageal cancer and compared with routine care.
Cross-reactive CD8+ T-cell immunity between the pandemic H1N1-2009 and H1N1-1918 influenza A viruses

Preexisting T-cell immunity directed at conserved viral regions promotes enhanced recovery from influenza virus infections, with there being some evidence of cross-protection directed at variable peptides. Strikingly, many of the immunogenic peptides derived from the current pandemic A(H1N1)-2009 influenza virus are representative of the catastrophic 1918 “Spanish flu” rather than more recent “seasonal” strains. We present immunological and structural analyses of cross-reactive CD8+ T-cell–mediated immunity directed at a variable (although highly cross-reactive) immunodominant NP418–426 peptide that binds to a large B7 family (HLA-B*3501/03/0702) found throughout human populations. Memory CD8+ T-cell specificity was probed for 12 different NP418 mutants that emerged over the 9 decades between the 1918 and 2009 pandemics. Although there is evidence of substantial cross-reactivity among seasonal NP418 mutants, current memory T-cell profiles show no preexisting immunity to the 2009-NP418 variant or the 1918-NP418 variant. Natural infection with the A(H1N1)-2009 virus, however, elicits CD8+ T cells specific for the 2009-NP418 and 1918-NP418 epitopes. This analysis points to the potential importance of cross-reactive T-cell populations that cover the possible spectrum of T-cell variants and suggests that the identification of key residues/motifs that elicit cross-reactive T-cell sets could facilitate the evolution of immunization protocols that provide a measure of protection against unpredicted pandemic influenza viruses. Thus, it is worth exploring the potential of vaccines that incorporate peptide variants with a proven potential for broader immunogenicity, especially to those that are not recognized by the current memory T-cell pool generated by exposure to influenza variants that cause successive seasonal epidemics.
Comprehensive Description of RESPONSE

This paper offers a comprehensive description of the integrated assessment model (IAM) RESPONSE developed at CIRED. RESPONSE aims at providing a consistent framework to appraise alternative modelling choices made by the main existing IAMs. It is designed as a flexible tool able to take different modelling structures in order to compare results from the modelling frameworks that have driven the so-called ''when flexibility'' controversy since the early 1990s dealing with the optimal timing of mitigation efforts and the optimal time profile of the social cost of carbon. RESPONSE is both sufficiently compact to be easily tractable and detailed enough to be as comprehensive as possible in order to capture a wide array of emblematic modelling choices, namely the forms of the damage function (quadratic vs. sigmoid) and the abatement cost (with or without inertia), the treatment of uncertainty, and the decision framework (one-shot vs. sequential).
Cardiovascular , Pulmonary and Renal Pathology Genetic Ablation of NADPH Oxidase Enhances Susceptibility to Cigarette Smoke-Induced Lung Inflammation and Emphysema in Mice

Cigarette smoke (CS) induces recruitment of inflammatory cells in the lungs leading to the generation of reactive oxygen species (ROS), which are involved in lung inflammation and injury. Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase is a multimeric system that is responsible for ROS production in mammalian cells. We hypothesized that NADPH oxidase-derived ROS play an important role in lung inflammation and injury and that targeted ablation of components of NADPH oxidase (p47 and gp91) would protect lungs against the detrimental effects of CS. To test this hypothesis, we exposed p47 / and gp91 / mice to CS and examined inflammatory response and injury in the lung. Surprisingly, although CS-induced ROS production was decreased in the lungs of p47 / and gp91 / mice compared with wild-type mice, the inflammatory response was significantly increased and was accompanied by development of distal airspace enlargement and alveolar destruction. This pathological abnormality was associated with enhanced activation of the TLR4-nuclear factorB pathway in response to CS exposure in p47 / and gp91 / mice. This phenomenon was confirmed by in vitro studies in which treatment of peritoneal macrophages with a nuclear factorB inhibitor reversed the CS-induced release of proinflammatory mediators. Thus, these data suggest that genetic ablation of components of NADPH oxidase enhances susceptibility to the proinflammatory effects of CS leading to airspace enlargement and alveolar damage. (Am J Pathol 2008, 172:1222–1237; DOI: 10.2353/ajpath.2008.070765)
Observations of the Nocturnal Boundary Layer Associated with the West African Monsoon

A set of night time tethered balloon and kite measurements from the central Sahel (15.2N, 1.3W) in August 2005 were acquired and analyzed. A composite of all nights' data was produced using boundary layer height to normalize measured altitudes. The observations showed some typical characteristics of nocturnal boundary layer development, notably a strong inversion after sunset and the formation of a low-level nocturnal jet later in the night. On most nights, the sampled jet did not change direction signifiantly during the night. The boundary layer thermodynamic structure displayed some variations from one night to the next. This was investigated using two contrasting case studies from the period. In one of these case studies (18 August 2005), the low level wind direction changed signficantly during the night. This change was captured well by two large scale models, suggesting that the large scale dynamics had a significant impact on boundary layer winds on this night. For both case studies, the models tended to underestimate near-surface wind speeds during the night; a feature which may lead to an underestimation of moisture flux northwards by models.
Analysis of the Level Crossing Rates for Ordered Random Processes

Given n independent but not necessarily identical random processes, this paper investigates the general problem of determining how frequently, on average, any given process becomes at least the p-th (p = 1, 2, . . . , n - 1) largest among all processes. This problem requires determining the level crossing rate (LCR) of a carefully defined ordered process, which we solve by developing a general mathematical framework based on the theory of permanents. Our results are very general and may be applicable for a wide range of engineering applications which involve ordered random processes. To demonstrate the applicability to wireless communications, we present closed-form formulas for the LCR for the case where the processes correspond to time-varying Rayleigh fading channels, and use these to characterize the required switching rate for a particular branch of a generalized selection combining diversity receiver.
Mixed-integer formulation of unit commitment problem for power systems: Focus on start-up cost

In this work, the Mixed-Integer (MIP) formulation for unit commitment problem (UC) for power systems is discussed. A new formulation for the start-up cost is suggested as well. This new formulation of the start-up cost exploits the transformation of the conditional statements into inequalities that comprise linear combination of binary variables. Solutions of the suggested optimization problem were obtained. A comparison between these solutions and those of a strategy common in literature is held to show that the new strategy gives same results with less number of constraints and tighter capture of the start-up cost.
Mechanical and electronic properties of diamond nanowires under tensile strain from first principles

The atomic and electronic structures, heat of formation, Young’s modulus, and ideal strength of hydrogenated diamond nanowires (DNWs) with different cross-sections (from 0.06 to 2.80 nm2) and crystallographic orientations (⟨100⟩, ⟨110⟩, ⟨111⟩, and ⟨112⟩) have been investigated by means of first-principles simulations. For thinner DNWs (cross-sectional area less than 0.6 nm2), preferential growth orientation along ⟨111⟩ is observed. The Young’s modulus and ideal strength of these DNWs decrease with decreasing cross-section and show anisotropic effects. Moreover, the band gap of DNWs is sensitive to the size, crystallographic orientation and tensile strain, implying the possibility of a tunable gap. The effective mass at the edges of the conduction band and valence band are also obtained. These theoretical results are helpful for designing novel optoelectronic devices and electromechanical sensors using diamond nanowires.
A concise review of magnetic resonance molecular imaging of tumor angiogenesis by targeting integrin αvβ3 with magnetic probes

Angiogenesis is an essential step for the growth and spread of malignant tumors. Accurate detection and quantification of tumor angiogenesis is important for early diagnosis of cancers as well as post therapy assessment of antiangiogenic drugs. The cell adhesion molecule integrin αvβ3 is a specific marker of angiogenesis, which is highly expressed on activated and proliferating endothelial cells, but generally not on quiescent endothelial cells. Therefore, in recent years, many different approaches have been developed for imaging αvβ3 expression, for the detection and characterization of tumor angiogenesis. The present review provides an overview of the current status of magnetic resonance molecular imaging of integrin αvβ3, including the new development of high sensitive contrast agents and strategies for improving the specificity of targeting probes and the biological effects of imaging probes on αvβ3 positive cells.
Duration and pauses as cues to discourse boundaries in speech

Duration is a primary factor both to achieve more naturalsounding synthesis and as an indicator of phrasal organization in speech recognition. In this study, we investigate pauses and durational patterns in spontaneous conversation, as well as how reliably such elements can serve as boundary-marking predictors across different types of speech corpora. Our results show that pause duration is significantly correlated with specific boundary status and that syllable duration is inversely correlated with distance to phrase end, suggesting that syllable duration is very significant in predicting phrase boundary status. Our findings show that duration features are highly informative in discourse and that it is crucial to integrate such knowledge to enhance performance in spoken language systems.
Sorghum Biomass Production for Energy Purpose Using Treated Urban Wastewater and Different Fertilization in a Mediterranean Environment

With the aim at enhancing the sustainability of biomass production in the Mediterranean area, this paper analyzes, for the first time, the production of sorghum (Sorghum bicolor (L.) Moench) biomass for bioenergy production using urban treated wastewaters and bio-fertilization. For this purpose, the effects on biomass production of three different fertilizations (no-nitrogen control, biofertilizer, and mineral ammonium nitrate), four levels of constructed wetland (CW) wastewater restitutions (0%, 33%, 66% and 100%) of crop evapotranspiration (ETc) and three harvesting dates (at full plant maturity, at the initial senescence stage, and at the post-senescence stage) were evaluated in a two year trial. For bio-fertilization, a commercial product based on arbuscular mycorrhizal fungi was used. Mineral nitrogen (N) fertilization significantly increased dry biomass (+22.8% in the first year and +16.8% in the second year) compared to the control (95.9 and 188.2 g·plant−1, respectively). The lowest and highest biomass production, in 2008 and 2009, was found at 0% (67.1 and 118.2 g·plant−1) and 100% (139.2 and 297.4 g·plant−1) ETc restitutions. In both years, the first harvest gave the highest biomass yield (124.3 g·plant−1 in the first year and 321.3 g·plant−1 in the second), followed by the second and the third one. The results showed that in Mediterranean areas, constructed wetlands treated wastewaters, when complying with the European restrictions for their use in agriculture, may represent an important tool to enhance and stabilize the biomass of energy crops by recycling scarce quality water and nutrients otherwise lost in the environment.