Miracle-dz/UniFAR-FTUs huggingface dataset:
Large Eddy Simulation of Solar Photosphere Convection with Realistic Physics

Three-dimensional large eddy simulations of solar surface convection using realistic model physics are conducted. The thermal structure of convective motions into the upper radiative layers of the photosphere, the range of convection cell sizes, and the penetration depths of convection are investigated. A portion of the solar photosphere and the upper layers of the convection zone, a region extending 60 x 60 Mm horizontally from 0 Mm down to 20 Mm below the visible surface, is considered. We start from a realistic initial model of the Sun with an equation of state and opacities of stellar matter. The equations of fully compressible radiation hydrodynamics with dynamical viscosity and gravity are solved. We use: 1) a high order conservative TVD scheme for the hydrodynamics, 2) the diffusion approximation for the radiative transfer, 3) dynamical viscosity from subgrid scale modeling. The simulations are conducted on a uniform horizontal grid of 600 x 600, with 168 nonuniformly spaced vertical grid points, on 144 processors with distributed memory multiprocessors on supercomputer MVS-15000BM in the Computational Centre of the Russian Academy of Sciences.
Relationships between Nursing Converstaions and Activities

In this paper, we determine the relationships between nursing activities and nurseing conversations based on the principle of maximum entropy. For analysis of the features of nursing activities, we built nursing corpora from actual nursing conversation sets collected in hospitals that involve various information about nursing activities. Ex-nurses manually assigned nursing activity information to the nursing conversations in the corpora. Since it is inefficient and too expensive to attach all information manually, we introduced an automatic nursing activity determination method for which we built models of relationships between nursing conversations and activities. In this paper, we adopted a maximum entropy approach for learning. Even though the conversation data set is not large enough for learning, acceptable results were obtained.
A Physically‐Based BSDF for Modeling the Appearance of Paper

We present a novel appearance model for paper. Based on our appearance measurements for matte and glossy paper, we find that paper exhibits a combination of subsurface scattering, specular reflection, retroreflection, and surface sheen. Classic microfacet and simple diffuse reflection models cannot simulate the double‐sided appearance of a thin layer. Our novel BSDF model matches our measurements for paper and accounts for both reflection and transmission properties. At the core of the BSDF model is a method for converting a multi‐layer subsurface scattering model (BSSRDF) into a BSDF, which allows us to retain physically‐based absorption and scattering parameters obtained from the measurements. We also introduce a method for computing the amount of light available for subsurface scattering due to transmission through a rough dielectric surface. Our final model accounts for multiple scattering, single scattering, and surface reflection and is capable of rendering paper with varying levels of roughness and glossiness on both sides.
Transferable tetracycline resistance in Clostridium difficile

The transfer of tetracycline resistance among strains of Clostridium difficile is described. Transfer occurred by a conjugation-like event that was insensitive to deoxyribonuclease, could not be mediated by donor culture filtrates or chloroform-treated donor cultures, and required cell-to-cell contact. Tetracycline-resistant progeny recovered from matings displayed a resistance phenotype identical to that of the donor in level of resistance, constitutive expression, and transmissibility. Although the original tetracycline-resistant donor contained 5 x 10(6)- and 22 x 10(6)-dalton plasmids, standard physical analyses of antibiotic-resistant transconjugants revealed no plasmid deoxyribonucleic acid molecules in common with the donor strain. Furthermore, tetracycline-susceptible derivatives of the original donor always possessed a plasmid complement identical to that of the resistant parental strain as determined by restriction endonuclease digestion analysis. The results indicate that the tetracycline resistance determinant(s) was not encoded by readily detectable plasmid deoxyribonucleic acid and may be chromosomally located.
Immunomodulation of Antigen Presenting Cells Promotes Natural Regulatory T Cells That Prevent Autoimmune Diabetes in NOD Mice

Progression towards type 1 diabetes (T1D) in susceptible patients is linked to a progressive decline in the capacity of regulatory T cells (Treg) to maintain tolerance. As such, therapies aimed at redressing the failing Treg compartment have been the subject of intense investigation. Treg dysfunction in T1D has recently been linked to a reduced capacity of antigen presenting cells (APCs) to maintain Treg function rather than Treg intrinsic defects. This suggests that therapies aimed simply at addressing the failing Treg compartment are unlikely to provide long-term protection. Here, we demonstrate that modulation of the inflammatory status of CD11b+CD11c− APCs favors the upregulation of protective Tregs in a mouse model of T1D. We further demonstrate that reduced expression of the costimulatory molecule CD40 plays a role in this increased immunoregulatory capacity. Strikingly, Treg upregulation resulted exclusively from an increase in natural Tregs rather than the peripheral conversion of conventional T cells. This suggests that modulation of CD11b+ CD11c− APCs inflammatory properties favors the establishment of natural Treg responses that, unlike adaptive Treg responses, are likely to maintain tolerance to a broad range of antigens. As such, modulation of this APC subset represents a potential therapeutic avenue to reestablish peripheral tolerance and protect from autoimmune diseases such as T1D.
New and continuing developments at PROSITE

PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule a collection of rules, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRules.
New modeling and experimental framework to characterize hindered and restricted water diffusion in brain white matter

To characterize anisotropic water diffusion in brain white matter, a theoretical framework is proposed that combines hindered and restricted models of water diffusion (CHARMED) and an experimental methodology that embodies features of diffusion tensor and q‐space MRI. This model contains a hindered extra‐axonal compartment, whose diffusion properties are characterized by an effective diffusion tensor, and an intra‐axonal compartment, whose diffusion properties are characterized by a restricted model of diffusion within cylinders. The hindered model primarily explains the Gaussian signal attenuation observed at low b values; the restricted non‐Gaussian model does so at high b. Both high and low b data obtained along different directions are required to estimate various microstructural parameters of the composite model, such as the nerve fiber orientation(s), the T2‐weighted extra‐ and intra‐axonal volume fractions, and principal diffusivities. The proposed model provides a description of restricted diffusion in 3D given by a 3D probability distribution (average propagator), which is obtained by 3D Fourier transformation of the estimated signal attenuation profile. The new model is tested using synthetic phantoms and validated on excised spinal cord tissue. This framework shows promise in determining the orientations of two or more fiber compartments more precisely and accurately than with diffusion tensor imaging. Magn Reson Med 52:965–978, 2004. Published 2004 Wiley‐Liss, Inc.
The threat of stereotype

To close the achievement gap, we must address negative stereotypes that suppress student achievement. Not long ago, I was asked to explain why Jews were so rich. I had just accepted an offer to be assistant professor at a large university, and my wife and I, hunting for our new home, were in a restaurant having lunch with the realtor. “I mean it,” the realtor said. “Do you people have some genetic thing that makes you good at making money? ” She explained that in her experience, her Jewish clients had the biggest houses and the nicest cars. I bristled. “What do you mean? That's a wornout stereotype. My wife and I are not rich, and we're Jewish . ” I proceeded to give her a brief anti-stereotyping primer to which she responded with interest. I was reassured.
350 Micron Dust Emission from High-Redshift Objects

We report observations of a sample of high-redshift sources (1.8 ≲ z ≲ 4.7), mainly radio-quiet quasars, at 350 μm using the bolometer camera SHARC (Submillimeter High Angular Resolution Camera) at the Caltech Submillimeter Observatory. Nine sources were detected (≳4 σ), and upper limits were obtained for 11 with 350 μm flux density limits (3 σ) in the range 30-125 mJy. Combining published results at other far-infrared and millimeter wavelengths with the present data, we are able to estimate the temperature of the dust, finding relatively low values, averaging 50 K. From the spectral energy distribution, we derive dust masses of a few times 108 h M☉ and luminosities of (4-33) × 1012 h L☉ (uncorrected for any magnification), which imply substantial star formation activity. Thus, both the temperature and dust masses are not very different from those of local ultraluminous infrared galaxies. For this redshift range, the 350 μm observations trace the 60-100 μm rest-frame emission and are thus directly comparable with IRAS studies of low-redshift galaxies.
Seeking Progress in El Niño Prediction

T he primary goal of predicting El Niño is to better anticipate the relative likelihood of regional climate anomalies. Much progress has been made in the last several decades to better understand El Niño and its global consequences (McPhaden et al. 1998, Trenberth et al. 1998). This knowledge has motivated more complex and sophisticated prediction models, but it’s not clear whether these advances have translated into increased prediction skill of El Niño. By the standard verification measures of NINO indices, complex dynamical models do not outperform simpler statistical models. Comparison of skill and event evolution suggests that dynamical and statistical models are approximately equivalent (Barnston et al. 1999, Kirtman et al. 2000). Ultimately what is communicated by these verification measures is whether or not a forecast system can indicate an imminent El Niño or La Niña event. However, the impact of a particular El Niño on the seasonal climate depends on more than the value of a static box average. Knowledge of the event’s evolution, in terms of timing, amplitude and structure are important characteristics of the event. Studies are beginning to show that the atmosphere may be sensitive to the relative placement of warm SST anomalies in the equatorial Pacific (e.g. Barsulgi and Sardeshmukh, 2002); however, the limited observational record and relative infrequency of El Niño events makes such distinctions difficult to verify in nature. Still, an event focused in the central Pacific will carry a different precipitation forecast for certain parts of the world than one focused farther in the eastern Pacific. The ability to predict seasonal climate anomalies increases significantly during El Niño and La Niña events (Shukla 2000; Goddard and Dilley 2005); skill over land (world-wide) increases linearly with the strength of the event. The opportunity of obtaining better climate forecast information during El Niño events is to some degree conditional upon the accuracy of information about the particular El Niño event. Therefore, the more reliably ENSO prediction systems can capture the characteristics of amplitude, timing and structure of El Niño events, the more reliably the associated regional climate anomalies can be forecast.
Database Intrusion Detection using Weighted Sequence Mining

Data mining is widely used to identify interesting, potentially useful and understandable patterns from a large data repository. With many organizations focusing on web-based on-line transactions, the threat of security violations has also increased. Since a database stores valuable information of an application, its security has started getting attention. An intrusion detection system (IDS) is used to detect potential violations in database security. In every database, some of the attributes are considered more sensitive to malicious modifications compared to others. We propose an algorithm for finding dependencies among important data items in a relational database management system. Any transaction that does not follow these dependency rules are identified as malicious. We show that this algorithm can detect modification of sensitive attributes quite accurately. We also suggest an extension to the Entity- Relationship (E-R) model to syntactically capture the sensitivity levels of the attributes.
Predictors of Health-Promoting Behavior Associated With Cardiovascular Diseases Among Korean Blue-Collar Workers

The aim of this study was to investigate the contribution of actual cardiovascular disease (CVD) risks, psychosocial and work-related factors as predictors of health behavior. A sample of 234 Korean blue-collar workers, who worked in small companies, was included in this cross-sectional study. Data collection included a survey; anthropometric and blood pressure measures; and blood sampling. Multiple regression analyses showed that the model explained 30% of the variance in health behavior of blue-collar workers. The significant predictors for health behavior included education level, perceived general health, greater family function, higher social support, decision latitude, and non-shift work. Future research should focus on incorporating these significant predictors into effective behavioral interventions designed to promote cardiovascular health in this population.
Do We Need Incentive Mechanisms for Peer-to-Peer Media Streaming ?

Peer-to-Peer (P2P) streaming can be extremely effective in alleviating the load on popular servers and proxies but only if there is a sufficient level of cooperation among the peers. Hence, the question is: do we need incentive mechanisms for P2P streaming? We quantify the cost of sharing and show that, unlike traditional file sharing systems, a streaming system cannot provide good streaming quality to its users if only a few altruistic users cooperate and everybody else defects. To provide service assurance in P2P media streaming, it is necessary to select streaming sources based on their offered rates, availability, and the network dynamics of the paths from the sources to the receivers. We provide a comparative study among incentive mechanisms for file sharing and media streaming, and show that a percentile-based incentive mechanism provides service differentiation. Using the level of contribution, the mechanism provides a way to compute the percentile of each user among all users to estimate the quality it can receive at any time and how much contribution is necessary to improve the future stream quality. The experimental evaluation shows that the incentive mechanism provides near optimal quality if the network is not heavily congested.
Circulating Human Interleukin-8 as an Indicator of Cancer Progression in a Nude Rat Orthotopic Human Non–Small Cell Lung Carcinoma Model

Clinically relevant animal models of human cancer are necessary for the evaluation of putative therapeutics. We hypothesized that circulating human lung cancer–associated proteins would correlate with physiologic measurements from an orthotopic H460 human non–small cell lung carcinoma model that we developed in immunodeficient rats. Physiologic measurements and serum samples were collected over time. Serum interleukin-8 (IL-8), p53, vascular endothelial growth factor, and matrix metalloproteinase-9 were quantitated for correlation with physiologic measurements. Matrix metalloproteinase-9 and p53 were not significantly detectable. Circulating vascular endothelial growth factor was detected at high levels in some tumor-bearing animals. Human IL-8 was detectable in all tumor-bearing animals and correlated positively with markers of respiratory acidosis (pH, P = 0.012; TCO2, P = 0.024; pCO2, P = 0.007; and HCO3−, P = 0.029) and with surface body temperature (P = 0.001) beginning on day 16 after implantation. IL-8 levels negatively correlated with survival (P < 0.001), indicating an association with tumor burden. Circulating human IL-8 might be a useful, clinically relevant circulating tumor protein marker due to its positive correlation with multiple physiologic variables associated with lung cancer progression. (Cancer Epidemiol Biomarkers Prev 2008;17(8):2180–7)
A Cost-Effectiveness Analysis of Alternative Disease Management Strategies in Patients with Crohn's Disease Treated with Azathioprine or 6-Mercaptopurine

BACKGROUND:Azathioprine (AZA) is effective for the maintenance of a steroid free remission in Crohn's disease (CD). Thiopurine methyltransferase (TPMT) is important for the metabolism of AZA and influences the production of active AZA metabolites. AZA dose selection based on pharmacogenetic testing of TPMT and metabolite monitoring (MM) may offer a safety and efficacy advantage over traditional dosing strategies. We performed a decision analysis to estimate the potential costs and effectiveness of TPMT screening and MM as disease management strategies for CD.METHODS:Strategies applying TPMT and/or MM to influence treatment decisions were compared to community care (CC). The impact on toxicity minimization and improved time to initial and sustained response was evaluated. A 1-yr model was developed from the third-party payer perspective for mild to moderately chronically active, steroid-treated CD patients. Effectiveness and toxicity defined by time to response CD activity index (CDAI <150, ± steroids) or time to sustained response (CDAI <150, off steroids × 8 wk) and reduction in leukopenic events, respectively. One- and two-way sensitivity analyses were conducted to determine the effect of varying individual estimates from those used in the base-case analysis.RESULTS:MM, TPMT, and TPMT + MM strategies as compared to CC achieved an earlier time to initial response (18.66, 18.96, and 19.10 vs. 22.41 wk, respectively) and sustained response (39.83, 42.91, and 39.8 vs. 45.36 wk, respectively). The least costly strategy at 1 yr was TPMT ($3,861) and the most costly strategy was CC ($7,142). Each alternative strategy was shown to dominate CC (i.e., less costs and faster time to response or sustained response). The cost-effectiveness rankings were robust to sensitivity analyses on key variables.CONCLUSION:The addition of alternative strategies to CC may improve AZA outcomes and reduce the total cost of care for steroid treated chronically active CD patients, with TPMT being more beneficial for initial response to treatment and MM being more beneficial for sustained response to treatment.
LMI-based neurocontroller for guaranteed cost control of uncertain time-delay systems

This paper considers the application of neural networks for the guaranteed cost control problem of discrete-time uncertain systems that have both state and input delays. In order to guarantee the stability of the closed-loop delay systems with the neurocontroller, the linear matrix inequality (LMI) condition is established, while the neurocontroller is used to reduce the cost of the uncertain time-delay systems caused by the LMI design parameter. The novel contribution is that the neurocontroller is substituted for the additive gain perturbations. It is newly shown that although the neurocontroller is included in the uncertain discrete-time delay systems, the robust stability for the closed-loop systems and the reduction of the cost are attained. Finally, a numerical example is given to verify the efficiency.
Transduction and Plasmid Deoxyribonucleic Acid Analysis in a Multiply Antibiotic-Resistant Strain of Staphylococcus epidermidis

A genetic analysis of a multiply antibiotic-resistant strain of Staphylococcus epidermidis was performed. Experiments designed to show reversion of organisms to antibiotic susceptibility, as well as studies of the influence of ultraviolet irradiation of phage on the transduction frequencies of the resistance markers, indicated that determinants of chloramphenicol (cml), tetracycline (tet), and neomycin (neo) resistance are present on separate plasmids, but the streptomycin marker is chromosomal. In 2 to 6% of tetracycline-resistant transductants, co-transduction of cml was also observed. By using CsCl-dye density gradients followed by neutral sucrose gradients, the plasmids carrying cml, tet, and neo could be isolated and their molecular weights could be determined. The tetracycline plasmid is shown to be incompatible with one of the cryptic plasmids of a recipient strain.
Effects of glucosamine hydrochloride and chondroitin sulphate, alone and in combination, on normal and interleukin-1 conditioned equine articular cartilage explant metabolism.

REASONS FOR PERFORMING STUDY Clinical trials in human and veterinary literature have documented the benefits of oral nutraceutical joint supplements containing glucosamine (GU) and chondroitin sulphate (CS) to treat mild to moderate osteoarthritis, but the effects of these components have not yet been conclusively determined. OBJECTIVES To assess varying dosages of GU and CS on normal and interleukin-1alpha (IL-1) conditioned equine cartilage explants and rationalise the use of these products. HYPOTHESIS Treatment would not be detrimental to cartilage metabolism and higher dosages and the combination of GU and CS would be more beneficial than lower dosages and. GU or CS alone. METHODS Articular cartilage explants collected from the femoral trochlea and condyles were cultured in normal and IL-1 conditioned media. Treatment groups included 0, 12.5, 25,125 and 250 microg/ml concentrations of GU alone, CS alone, or GU+CS in combination. Glycosaminoglycan (GAG) synthesis and total GAG content in the explants and media were analysed. RESULTS There were no detrimental effects of GU, CS or GU+CS on cartilage metabolism. High dosages of GU+CS reduced total GAG release into the media (degradation). CONCLUSIONS Our results suggests that GU+CS may prevent cartilage GAG degradation. POTENTIAL RELEVANCE The combination of GU and CS may be more effective in preventing or treating osteoarthritis in horses than either product alone.