gebhart/patrepeval huggingface dataset:
Evidence for indirect involvement of the H-2Kb gene in the regulation of natural killer sensitivity of BL6 melanoma cells. (1994)

We have previously demonstrated that transfection of BL6-8 melanoma cells with the H-2Kb gene increased their sensitivity to natural killer (NK)- and natural cytotoxic (NC) cell-mediated cytotoxicity, and resulted in alterations of various cell characteristics such as the loss of melanoma-associated antigen (MAA), and the appearance of Griffonia simplicifolia 1B4 (GS1B4)- and soybean agglutinin (SBA)-lectin-binding sites. In the present study the BL6-8 melanoma clone was transfected with the H-2Kb gene without cotransfection of the neomycin resistance (neor) gene, and transfected cells were isolated on the basis of their low sialylation and ability to bind to SBA-agarose beads. 38 out of 47 analyzed clones were morphologically distinguishable, expressed the H-2Kb gene, lost the MAA and gained SBA- and GS1B4-lectin-binding sites (H-2Kb+, MAA-, SBA+, GS1B4+), whereas only 5 clones were morphologically and phenotypically unchanged (H-2Kb-, MAA+, SBA-, GS1B4-). The remaining 4 clones were morphologically changed, lost MAA and gained SBA- and GS1B4-binding epitopes, but did not express H-2Kb antigen (H-2Kb-, MAA-, SBA+, GS1B4+). Analysis of the NK sensitivity of H-2Kb-gene-transfected clones revealed that H-2Kb+, MAA-, SBA+, GS1B4+ clones were highly sensitive to NK cell lysis, whereas H-2Kb-, MAA+, SBA-, GS1B4- clones were NK resistant. It is of particular note that the 4 clones that did not express H-2Kb antigen but had other phenotypic changes (H-2Kb-, MAA-, SBA+, GS1B4+) were also highly sensitive to NK cells. The NK sensitivity of H-2Kb-transfected cells was closely associated with their increased ability to compete with YAC-1 cells for effector cells in a cold-target inhibition assay. Thus, the data obtained indicate that H-2Kb molecules in BL6-8 melanoma cells are not required for interaction with the effector cells, and H-2Kb-induced alterations in membrane carbohydrates and/or expression of the retrovirus-associated MAA might be important for the increase NK sensitivity of BL6-8 melanoma cells.
Temporal radiance caching (2008)

We present a novel method for fast, high quality computation of glossy global illumination in complex animated environments. Building on the irradiance caching and radiance caching algorithms, our method leverages temporal coherence by introducing temporal gradients. Using our approach, part of the global illumination solution computed in previous frames is adaptively reused in the current frame. Our simple adaptive reusing scheme allows to obtain fast rendering times while avoiding the presence of flickering artifacts and global illumination ghosts. By reusing data in several frames, our method yields a significant speedup compared to classical computation in which a new cache is computed for every frame. Moreover, temporal gradients do not rely on any new, complicated data structure. This method can be straightforwardly included in any existing renderer based on irradiance and radiance caching. Furthermore, our method can be easily implemented using GPUs for improved performance.
Healthy Older Observers Cannot Use Biological-Motion Point-Light Information Efficiently within 4 m of Themselves (2012)

Healthy aging is associated with a number of perceptual changes, but measures of biological-motion perception have yielded conflicting results. Biological motion provides information about a walker, from gender and identity to speed, direction, and distance. In our natural environment, as someone approaches us (closer distances), the walker spans larger areas of our field of view, the extent of which can be underutilized with age. Yet, the effect of age on biological-motion perception in such real-world scenarios remains unknown. We assessed the effect of age on discriminating walking direction in upright and inverted biological-motion patterns, positioned at various distances in virtual space. Findings indicate that discrimination is worse at closer distances, an effect exacerbated by age. Older adults' performance decreases at distances as far away as 4 m, whereas younger adults maintain their performance as close as 1 m (worse at 0.5 m). This suggests that older observers are limited in their capacity to integrate information over larger areas of the visual field and supports the notion that age-related effects are more apparent when larger neural networks are required to process simultaneous information. This has further implications for social contexts where information from biological motion is critical.
Large Enhancement of Electrical Conductivity in Magnesium Phosphate Glasses by Ion Implantation of Proton (1996)

(1) D. C. conductivity of Mg(PO3)2 glasses at room temperature was drastically enhanced from -1015S·cm-1 to -5×10-4S·cm-1 and the activation energy of the conduction was greatly reduced from 1.1eV to 0.18eV upon implantation of 120keV H+ to a fluence of 1×1018cm-2. Almost the same changes in conductivities and the activation energy were obtained for the glasses implanted with 100keV D+ (the calculated depth, -1μm, corresponds to that of 120keV H+) to the same fluence. No high proton conduction (>10-8S·cm-1 at room temperature) was observed for SiO2 glasses implanted with 120keV H+ to a fluence of 1×1018cm-2.(2) The observed conductivity in the H+ (1×1018cm-2)-implanted Mg(PO3)2 glasses was higher by 8 orders of magnitude than the conductivity calculated using an empirical relation which was obtained for various oxides glasses containing residual X-OH groups (H2O-free). The activation energy (-0.2eV) of the conduction was close to that in fast proton conducting crystals of hydrated heteropolyacids containing POH and H2O such as H3Mo12PO4⋅29H2O. These results indicate that coexistence of acidic X-OH such as P-OH and molecular water is a structural requirement for the emergence of fast proton conduction in oxide glasses.
Real-world Studies Link NSAID Use to Improved Overall Lung Cancer Survival (2022)

Inflammation is a cancer hallmark. Nonsteroidal anti-inflammatory drugs (NSAIDs) improve overall survival (OS) in certain cancers. Real-world studies explored here if NSAIDs improve non-small cell lung cancer (NSCLC) OS. Analyses independently interrogated clinical databases from The University of Texas MD Anderson Cancer Center (MDACC cohort, 1987 to 2015; 33,162 NSCLCs and 3,033 NSAID users) and Georgetown-MedStar health system (Georgetown cohort, 2000 to 2019; 4,497 NSCLCs and 1,993 NSAID users). Structured and unstructured clinical data were extracted from electronic health records (EHRs) using natural language processing (NLP). Associations were made between NSAID use and NSCLC prognostic features (tobacco use, gender, race, and body mass index, BMI). NSAIDs were statistically-significantly (P < 0.0001) associated with increased NSCLC survival (5-year OS 29.7% for NSAID users versus 13.1% for non-users) in the MDACC cohort. NSAID users gained 11.6 months over nonusers in 5-year restricted mean survival time. Stratified analysis by stage, histopathology and multicovariable assessment substantiated benefits. NSAID users were pooled independent of NSAID type and by NSAID type. Landmark analysis excluded immortal time bias. Survival improvements (P < 0.0001) were confirmed in the Georgetown cohort. Thus, real-world NSAID usage was independently associated with increased NSCLC survival in the MDACC and Georgetown cohorts. Findings were confirmed by landmark analyses and NSAID type. The OS benefits persisted despite tobacco use and did not depend on gender, race, or BMI (MDACC cohort, P < 0.0001). These real-world findings could guide future NSAID lung cancer randomized trials.
Multilevel trellis-coded modulations for mobile multimedia satellite systems using synchronous CDMA (1998)

In this paper the performance of multilevel trellis-coded modulations (MTCMs) for satellite mobile multimedia systems using synchronous CDMA is investigated. A model for the multiple-access interference arising from the non-orthogonality of the spreading waveforms is developed for different modulation and spreading schemes and transmission over the mobile satellite channel. Using this model, the performance of MTCMs for synchronous CDMA is analysed and compared with the Ungerboeck and Schegel–Costello trellis-coded modulation (TCM) designs. The impact on the transmission of synchronization errors between the different users is presented and the power control requirements are derived. © 1998 John Wiley & Sons, Ltd.
Structure determination of a novel cyclic phosphocompound isolated from Desulfovibrio desulfuricans (1992)

The structure of a novel diphosphodiester compound recently detected in Desulfovibrio desulfuricans cells [Santos, Fareleira, Pedregal, LeGall & Xavier (1991) Eur. J. Biochem. 201, 283-287] was fully elucidated using a combination of n.m.r. techniques in aqueous and in methanolic solutions. The novel metabolite was identified as 3-methyl-1,2,3,4-tetrahydroxybutane-1,3-cyclic bisphosphate, and the minimum energy conformation is presented. The two chiral centres have the relative configuration RS.
Electrostatic interactions in the GCN4 leucine zipper: Substantial contributions arise from intramolecular interactions enhanced on binding (1999)

The GCN4 leucine zipper is a peptide homodimer that has been the subject of a number of experimental and theoretical investigations into the determinants of affinity and specificity. Here, we utilize this model system to investigate electrostatic effects in protein binding using continuum calculations. A particularly novel feature of the computations made here is that they provide an interaction-by-interaction breakdown of the electrostatic contributions to the free energy of docking that includes changes in the interaction of each functional group with solvent and changes in interactions between all pairs of functional groups on binding. The results show that (1) electrostatic effects disfavor binding by roughly 15 kcal/mol due to desolvation effects that are incompletely compensated in the bound state, (2) while no groups strongly stabilize binding, the groups that are most destabilizing are charged and polar side chains at the interface that have been implicated in determining binding specificity, and (3) attractive intramolecular interactions (e.g., backbone hydrogen bonds) that are enhanced on binding due to reduced solvent screening in the bound state contribute significantly to affinity and are likely to be a general effect in other complexes. A comparison is made between the results obtained in an electrostatic analysis carried out calculationally and simulated results corresponding to idealized data from a scanning mutagenesis experiment. It is shown that scanning experiments provide incomplete information on interactions and, if overinterpreted, tend to overestimate the energetic effect of individual side chains that make attractive interactions. Finally, a comparison is made between the results available from a continuum electrostatic model and from a simpler surface-area dependent solvation model. In this case, although the simpler model neglects certain interactions, on average it performs rather well.
Experimental Generation of Near-Diffraction-Free OAM Pulses Having a Controllable Group Velocity from 1.0069c-0.9933c by Coherently Combining Different Beams of Multiple Correlated Bessel Modes and Frequencies (2021)

We experimentally demonstrate the generation of near-diffraction-free OAM +1 and +3 pulses having a controllable group velocity from 1.0069 c -0.9933 c . The diffraction of such OAM pulses and the effects of transmitter aperture size are also explored.
Prototype Assitive Device for Parkinson’s Disease and Essential Tremor “TREAME” (2022)

Parkinson’s disease is a progressive disease of the nervous system that causes a movement disorder in people, affecting the quality and independence of their lives. This tremor is involuntary and it increases over time as the disease takes over the brain and the medication, Carbidopa-Levodopa ceases to be effective, limiting a person’s motor activity. This problem can be solved in the early stage of the disease, with an MCU and an electromyography sensor, by digitizing the information of the tremor, then treating it and analyzing it, allowing us to identify the fundamental frequency of the tremor and then, try to reduce it, with a muscular electroestimulation device and historic data, recorded in the cloud.
Appropriate subcellular localisation of prodrug-activating enzymes has important consequences for suicide gene therapy (2001)

Escherichia coli B nitroreductase (NR) has been expressed stably in MDA-MB-361 human breast adenocarcinoma cells either as the wild-type protein (wtNR), which is distributed evenly between the cytoplasmic and nuclear compartments, or targeted to the mitochondrion (mtNR). Whereas bacterial NR is active as a dimer, a proportion of wtNR is monomeric. In contrast, mtNR is mostly dimeric, suggesting that it adopts a more stable, native conformation. Despite this, when tested in gene-directed enzyme prodrug therapy cell cytotoxicity studies, cells expressing wtNR or mtNR had similar sensitivity to the prodrug CB1954 and mounted similar bystander killing effects. Furthermore, when short prodrug exposures were given, wtNR was more efficient at killing cells than mtNR. These data demonstrate that the site of enzyme expression and prodrug activation is an important variable that requires consideration in suicide gene therapy approaches.
Dynamics of microbial communities, ethyl carbamate, biogenic amines, and major metabolites during fermentation of soy sauce (2021)

In this study, the dynamics of the microbial communities and metabolites for soy sauce were investigated. The succession of microbiota was divided into three phases in process. Dynamics of physicochemical properties coincided with the succession of dominant genera in the first 3 months, hereafter changed slightly. The contents of L-malic acid, pyroglutamic acid, and lactic acid were increased by 11.79, 11.39, and 3.19 times (p < 0.05), respectively, compared with that in the initial moromi. The contents of volatiles were changed in the later phase significantly, and dominant constituents were positive correlated with the dominant genera. The ethyl carbamate (EC) and seven kinds of biogenic amines (BAs) reached the maximum in the third month, then their contents decreased. The EC forming involved in two phases, the metabolic pathway was partly shared with that of putrescine biosynthesis. These results laid an important foundation in reducing the endogenous hazards by bioturbating.
Optimisation Technique for DC-Excited Vernier Reluctance Synchronous Condensers (2022)

The use of distributed renewable energy led to a renewed interest in synchronous condensers. To solve the disadvantages of conventional wound rotor synchronous condensers, the DC-excited vernier reluctance synchronous condenser was recently proposed. This paper presents a developed optimisation technique to optimise this machine technology as a synchronous condenser. The primary optimisation objective is to maximise the reactive power per losses for a fixed machine volume. An optimum synchronous condenser selection criterion from the optimisation Pareto front is proposed, based on the relationship between the required reactive power and an efficiency indicator of reactive power per losses. The paper presents a case study in which the optimisation technique and selection criterion are applied to an existing machine. The optimisation results prove that the proposed optimisation technique can be used to design the DC-excited vernier reluctance machine as synchronous condenser with a balanced capability of absorbing and supplying reactive power.
Systems biology in personalized medicine in oncology: A case study in non-small cell lung cancer. (2012)

e21096 Background: Systems biology together with translational oncology is a new approach to discover sensitive pathways in specific cancers. In this study, we propose a computational modeling technique to investigate the possible effects various alterations, such as protein overexpression, gene amplification or mutations, may have on signaling, through of the EGFR and IGF1R pathways, in non-small cell lung cancer (NSCLC). Methods: EGFR and IGF1R pathways and the downstream MAPK and PIK3 networks have been reproduced through a mathematical model. One hundred-twenty five tumors from surgical NSCLC patients were evaluated for EGFR and IGF1R protein expression, by immunohistochemistry (IHC) and gene amplification, by fluorescence in situ hybridization (FISH). KRAS mutations (exons 2 and 3) were evaluated by direct sequencing Results: To correlate EGFR and IGF1R expression levels, and KRAS mutations to tumor cell proliferation, we focused on the ERK signaling pathway, which plays a central role in several steps of cancer development including proliferation and cancer cell migration. The mathematical model predicts a relationship between a simultaneous high expression level of both receptors and a modification on ERK time behavior, implying a stronger attitude for cell proliferation. Furthermore KRAS activating mutations predict high level of active ERK and high probability to have cell proliferation. Cell growth can be closely related to disease progression and act, in survival analysis, as DFS estimator. Patients with concomitant IGF1R/EGFR FISH/IHC positivity had a worse DFS ( p=0.005). KRAS mutations have a statistically significant shorter DFS (p&lt;0.001) as well Conclusions: We propose a Systems Biology approach, combined with Translational Oncology methodologies, to understand the interaction between EGFR, IGF1R and KRAS pathways in NSCLC. Computational model predictions confirm clinical evidences of survival analysis. Future work will validate our model with experiments on various NSCLC cell cultures and further investigate the response to drug administration. We thank AIRC and Fondazione Cassa di Risparmio for supporting the study.
Method-Specific Java Access Control via RMI Proxy Objects Using Annotations (Short Paper) (2009)

We propose a novel approach for granting to remote clients partial access on arbitrary objects at the granularity of methods. The applications that we target use Remote Method Invocation (RMI). We automatically build proxy objects, and give them to untrusted clients instead of the originals. Proxy objects expose a subset of methods to prevent potentially dangerous calls from clients. We present the system's semantics, implementation, and its evaluation. Creating a proxy takes an order of magnitude less time than the corresponding RMI lookup.
Analysis of the roles of HIV-derived microRNAs (2010)

HIV-derived miRNAs are of significance not only to understand host-virus interactions, but also for the design of effective therapeutics.
Urine therapy briefing for scientists (2012)

Urine is a gift of God for the health of human being in proverbs of the Old Testament in Hindu. Urine therapy (UT) is not a mysterious folk remedy, it is doctor's examined prescription based on modern science and UT is recommended strongly with absolute confidence. It is effective and amazing to a number of incurables such as chronic fatigue, lingering, a cold, nose allergy, diabetes, high blood pressure, and gout. Also, UT is applied not only for human beings but also for animals, the latter including amazing effects for pigs and cows. The purpose of this manuscript is to help change the misunderstandings of urine and UT and to help reader realize it is one of the helpful alternative remedies.
The challenges of using detailed chemistry model for simulating direct injection spark ignition engine combustion during cold-start (2021)

Computational Fluid Dynamics (CFD) modeling of gasoline spark-ignited engine combustion has been extensively discussed using both detailed chemistry mechanisms (e.g., SAGE) and flamelet models (e.g., the G-equation). The models have been extensively validated under normal operating conditions; however, few studies have discussed the capability of these models in capturing DISI combustion under cold-start conditions. A cold-start differs from normal operating conditions in various respects, such as (1) having highly retarded spark timing to help generate a high heat flux in the exhaust for a rapid catalyst light-off; (2) having split-injection strategies to ensure a favorable stratification at the vicinity of the spark plug and reduced film formation; and (3) having optimized valve timings for reduced NOx emissions via increased internal residuals and reduced hydrocarbon (HC) emissions via prolonged oxidation of the combustion products. The retarded spark timing introduces the adverse effect of a decaying turbulence field, which results in a reduced turbulent flame speed. The analysis of all these factors happening inside the cylinder appears complicated at first glance; however, it could be made possible by efficient use of the existing CFD models. The current study explored the capability of the SAGE detailed chemistry model in capturing cold-start flame travel in a DISI engine. The results were then compared against the G-equation-based GLR model, which has been validated for excellent predictions of the DISI cold-start combustion as shown by Ravindran et al. The flame travel was captured on a Borghi-Peters diagram to find that the flame travels through corrugated, wrinkled, and laminar regimes. In order to fully evaluate the capability of the detailed chemistry model in predicting such changing turbulence-chemistry interactions, it will need to be studied individually in each regime; however, the scope of the current paper is limited to the study of the model behavior in the laminar regime, which will be shown to be important for DISI engine cold-start. The SAGE detailed chemistry model, with a toluene reference fuel (TRF) mechanism validated for gasoline laminar flame speeds, was found to significantly under-predict the flame propagation speeds because of the effects of numerical viscosity and discrepancies in capturing molecular diffusion. The causes and effects of this under-prediction and the ways in which this can be improved are presented in the paper.
Validation Study of Large-Eddy Simulations of Wake Stabilized Reacting Flows using Artificial Flame Thickening Approaches (2013)

Wake flows are the preferred mode of flame stabilization in lean premixed combustion in gas turbine engines, low NOx burners, afterburners etc. These flows exhibit inherent unsteadiness and for their numerical modeling and simulations, large eddy simulation (LES) techniques with an appropriate combustion model and reaction mechanism afford a balance between computational complexity and predictive accuracy. Before using them in practical systems, these techniques must be validated against experimental measurements in a number of canonical cases. In this work, results from LES of non-reacting and reacting flows are compared to data from a number of experiments, corresponding to the following configurations: a triangular bluff body in a rectangular duct, a backward facing step, and a cylindrical sudden expansion with swirl. The artificial flame thickening approach is applied for modeling turbulence-combustion interactions at small scales. Algebraic and equationbased efficiency function models are implemented, along with an appropriate reduced chemistry mechanism. A novel dynamic formulation for the efficiency function based on the flame-wrinkling equation that explicitly incorporates the influence of strain and time-history effects is proposed, and a detailed combustion chemistry mechanism is also used. Results show that the approaches are effective in simulating turbulent premixed combustion.