gebhart/patrepeval huggingface dataset:
<title>Multiresolution texture analysis of bone radiographs using Gaussian Markov random-field models</title> (1994)

Texture analysis of bone radiographs can play an important role in characterizing the progression of bone diseases by computing texture measures on the digitized bone radiographs. Fractal dimension is one such texture measure which has been used with success as radiographs of trabecular bone are shown to exhibit self-similar characteristics. Markov random fields (MRF) have been used successfully to classify texture by modeling it as stochastic processes. But it has been shown that MRF models do not perform well in modeling self-similar textures such as fractional Brownian motion (FBM). This limitation can be overcome by characterizing statistical properties of the incremental process which builds up a fractal object. Since we try to characterize the statistical properties of the incremental process which builds the fractal object rather than its multi scale behavior using Gaussian MRF, this approach is complimentary to using fractal dimension as a feature in characterizing texture.
Ferroptosis-Mediated Cell Death Induced by NCX4040, The Non-Steroidal Nitric Oxide Donor, in Human Colorectal Cancer Cells: Implications in Therapy (2023)

Our recent studies show that the treatment of human ovarian tumor cells with NCX4040 results in significant depletions of cellular glutathione, the formation of reactive oxygen/nitrogen species and cell death. NCX4040 is also cytotoxic to several human colorectal cancer (CRC) cells in vitro and in vivo. Here, we examined the ferroptosis-dependent mechanism(s) of cytotoxicity of NCX4040 in HT-29 and K-RAS mutant HCT 116 colon cell lines. Ferroptosis is characterized by the accumulation of reactive oxygen species (ROS) within the cell, leading to an iron-dependent oxidative stress-mediated cell death. However, its relevance in the mechanism of NCX4040 cytotoxicity in CRCs is not known. We found that NCX4040 generates ROS in CRC cells without any depletion of cellular GSH. Combinations of NCX4040 with erastin (ER) or RSL3 (RAS-selective lethal 3), known inducers of ferroptosis, enhanced CRC death. In contrast, ferrostatin-1, an inhibitor of ferroptosis, significantly inhibited NCX4040-induced cell death. Treatment of CRC cells with NCX4040 resulted in the induction of lipid peroxidation in a dose- and time-dependent manner. NCX4040 treatment induced several genes related to ferroptosis (e.g., CHAC1, GPX4 and NOX4) in both cell lines. Metabolomic studies also indicated significant increases in both lipid and energy metabolism following the drug treatment in HT-29 and HCT 116 cells. These observations strongly suggest that NCX4040 causes the ferroptosis-mediated cell death of CRC cells. Furthermore, combinations of NCX4040 and ER or RSL3 may contribute significantly to the treatment of CRC, including those that are difficult to treat due to the presence of Ras mutations in the clinic. NCX4040-induced ferroptosis may also be a dynamic form of cell death for the treatment of other cancers.
МЕМРИСТОРНЫЕ СТРУКТУРЫ НА ОСНОВЕ ЭЛЕКТРОХИМИЧЕСКОГО ОКСИДА ТИТАНА ДЛЯ RERAM И НЕЙРОМОРФНЫХ ПРИМЕНЕНИЙ (2021)

Представлены результаты экспериментальных исследований влияния толщины наноструктур оксида титана, полученных локальным анодным окислением, на их мемристивные свойства. Показана возможность управляемого формирования мемристивных структур, не требующих формовки, имеющих напряжение переключения менее 3 В.
Investigating the Relationship Between Latent Driving Patterns and Traffic Safety Using Smartphone-Based Mobile Sensor Data (2016)

Crash frequency modelling has been used in the past as an attempt to quantify the expected number of crashes occurring on a certain segment of roadway given a set of variables and factors describing the roadway segment and the traffic along that segment. These models are referred to as the Safety Performance Functions (SPFs) in the Highway Safety Manual (HSM). In past studies, these SPFs have focused primarily on roadway geometric information along with limited traffic exposure data such as traffic volume. Alternate data sources for probe vehicle data are increasingly available and this research sought to exploit this new information in order to obtain an improved model. Specifically, this research aims to make use of the accelerometer sensors in smartphones to extract microscopic traffic measures that can serve as better indicators of driving patterns. The study focused on crash frequency along roadway segments in the Hampton Roads region. To start-off, mobile sensor data was collected by driving along major roadways in the Hampton Roads region during the evening peak period (4 to 6 pm). Next, this data was overlaid on the transportation network to map probe data and the roadway segments. Then, several acceleration and deceleration metrics were calculated for each roadway using the mobile sensor data. Subsequently, these metrics were appended to the VDOT crash data for the past one year. Supplementary data sources were used to assemble information regarding roadway inventory data and traffic exposure information. Next, statistical model estimation was undertaken to identify the factors affecting crash frequency along major interstates in Hampton Roads. The results indicate that when comparing a model based solely on roadway geometrics to a model including both roadway geometrics and probe vehicle data, the combined model was a significant improvement. Several probe vehicle data parameters capturing microscopic traffic conditions were significant in the final model. Lastly, elasticity analysis was undertaken to quantify the relative impact of different factors in the model. With regard to statistical modeling, this research considered both a Poisson and a negative binomial model that served as standard models for crash frequency modeling in the literature. The negative binomial model was found to be a significant improvement over the Poisson model. Previous research has indicated that negative binomial models tend to perform better than Poisson models when there is over-dispersion present in the dataset. This research supports this claim. Overall, this research has determined that the addition of probe vehicle data to roadway inventory data and the usage of a negative binomial model have proved to provide a robust crash frequency model.
Engineering SARS-CoV-2 specific cocktail antibodies into a bispecific format improves neutralizing potency and breadth (2022)

One major limitation of neutralizing antibody-based COVID-19 therapy is the requirement of costly cocktails to reduce emergence of antibody resistance. Here we engineer two bispecific antibodies (bsAbs) using distinct designs and compared them with parental antibodies and their cocktail. Single molecules of both bsAbs block the two epitopes targeted by parental antibodies on the receptor-binding domain (RBD). However, bsAb with the IgG-(scFv)<sub>2</sub> design (14-H-06) but not the CrossMAb design (14-crs-06) shows increased antigen-binding and virus-neutralizing activities against multiple SARS-CoV-2 variants as well as increased breadth of neutralizing activity compared to the cocktail. X-ray crystallography and cryo-EM reveal distinct binding models for individual cocktail antibodies, and computational simulations suggest higher inter-spike crosslinking potentials by 14-H-06 than 14-crs-06. In mouse models of infections by SARS-CoV-2 and multiple variants, 14-H-06 exhibits higher or equivalent therapeutic efficacy than the cocktail. Rationally engineered bsAbs represent a cost-effective alternative to antibody cocktails and a promising strategy to improve potency and breadth.
Fast seismic modeling and reverse time migration on a graphics processing unit cluster (2011)

SUMMARY We designed a fast parallel simulator that solves the acoustic wave equation on a graphics processing unit (GPU) cluster. Solving the acoustic wave equation in an oil exploration industrial context aims at speeding up seismic modeling and reverse time migration (RTM). We considered a finite difference approach on a regular mesh, in both two‐dimensional and three‐dimensional cases. The acoustic wave equation is solved in a constant density or a variable density domain. All the computations were carried out in single precision (both in the CPU reference implementation and in the GPU implementation), because double precision was not required in our context. We used Compute Unified Device Architecture to take advantage of the GPU computational power. We studied different implementations and their impact on the application performance. The described application handles all the steps of seismic modeling and RTM and is used to solve real‐world problems in an industrial production context. We obtained a speedup of 16 for RTM and up to 43 for the modeling application over a sequential code running on general‐purpose CPUs. A CPU rack versus a GPU rack comparison was described and showed a 4.3 speedup. Copyright © 2011 John Wiley &amp; Sons, Ltd.
[(3-Methylphenyl)(triphenylphosphonio)methanide-κC]triphenylphosphorane}(pentafluorophenyl-κC)gold(I) diethyl ether solvate (2009)

The metal atom in the title ylid-gold(I) adduct, [Au(C(6)F(5))(C(26)H(23)P)]·C(4)H(10)O, exists in a linear coordination environment [C-Au-C = 174.1 (2)°]. The mol-ecule has a short intra-molecular contact involving an aromatic H atom (Au⋯H = 2.64 Å); two adjacent mol-ecules are linked by an Au⋯H(ylid) inter-action (Au⋯H = 3.14 Å).
Solute Transport (2014)

This chapter discusses solute transport in Archaea. The fluidity and permeability properties of the lipid membranes are mainly determined by their lipid composition. The archaeal lipid chain contains isoprenoid units where every fourth carbon atom is linked to a methyl group. Most of the archaeal phytanyl chains are fully saturated isoprenoids. ATP-binding cassettes (ABC) transporters have a typical modular domain structure which usually comprises two integral membrane proteins that form the permease domain, and two cytoplasm-located ATPases which drive the transport of the substrate by the hydrolysis of ATP. In a report on secondary transporters in archaea, a lactose transporter was identified in Sulfolobus solfataricus by functionally complementing a mutant strain that was unable to grow on lactose. The distinction between the carbohydrate uptake transporters (CUT) and di/oligopeptide classes of ATP-binding cassettes (ABC) transporters is also evident for the protein-domain organization of the binding proteins. Members of the CUT class of binding proteins from S. solfataricus contain type IV pilinlike signal peptides and do not contain secretory signal peptides. A general feature of bacteria and archaea is that they are equipped with defense systems against toxic compounds from the environment. This protection mechanism involves multiple drug transport systems that extrude toxic compounds from the cell. In general, the drug transport systems belong to the class of secondary transporters or ABC transporters.
Effects of GaP Cap Layer Growth on Self-Assembled InAs Islands Grown on GaP (001) by Organometallic Vapor Phase Epitaxy (2000)

We have fabricated GaP/InAs islands/GaP structures using various growth sequences for the GaP cap layer, by low-pressure organometallic vapor phase epitaxy (LP-OMVPE). The effects of the growth sequences on the buried InAs islands and the GaP cap layers have been investigated by cross-sectional transmission electron microscopy (TEM). The two-step growth sequence is effective for the growth of GaP cap layers, whereby the first GaP layer is grown at the same temperature as InAs islands and the second GaP layer is successively grown at the optimized growth temperature of GaP. The growth sequence yields good-quality GaP/InAs islands/GaP structures with small InAs islands (15 nm in width and 5 nm in height) and a high-quality GaP cap layer. Droplet heteroepitaxy of GaP cap layers is feasible for the control of the size of buried InAs islands.
A Hit Map-Based Statistical Method to Predict Best Ligands for Orphan Olfactory Receptors: Natural Key Odorants Versus “Lock Picks” (2013)

Smell is a multidimensional chemical sense. It creates a perception of our odorous environment by integrating the information of a plethora of volatile chemicals with other sensory inputs, emotions and memories. We are almost always exposed to odorant mixtures, not just single chemicals. Olfactory processing of complex odorant mixtures, such as coffee or wine, first is decoded at the site of perception by the hundreds of different olfactory receptor types, each residing in the cilia of their olfactory sensory neurons in the nose. Often, only a few odorants from many are essential to determine complex olfactory perception. But merely using the chemical structure of odorants is insufficient to identify and predict characteristic odor qualities and low odor thresholds. An understanding of odorant coding critically depends on knowledge about the interaction of key odorants of biologically relevant odor bouquets with their best cognate receptors. Here, we describe a hit map-based method of correlating the information content of all bioassay-tested odorants with their cognate odorant-receptor frequency in four phylogenetic subsets of human olfactory/chemosensory receptors.
Effect of mercuric chloride on the activities of some hepatic enzymes of regenerating rabbit liver following partial hepatectomy. (1995)

Mercuric chloride (HgCl2) administered at a dose of 1mg/kg body wt/day for 5 days decreased hepatic lactate dehydrogenase (LDH) activity (63%) and increased isocitrate dehydrogenase (ICDH) activity (127%). After withdrawal of HgCl2 treatment for 10 days, the LDH and glutamate pyruvate transaminase (GPT) activities showed 56% and 40% decrease, respectively, while alkaline phosphatase (AkP) activity increased 4.12 fold. The ICDH activity got normalized. Glutamate oxaloacetate transaminase (GDT) was not affected at all. The hepatic LDH, ICDH and GPT activities decreased 58%, 72% and 82%, respectively, five days after partial hepatectomy (PH), while AkP activity increased 90%. At the end of 15 days after PH, the hepatic ICDH activity increased 4.27 fold, while GPT and GOT activities decreased 67% and 91%, respectively. The hepatic ICDH activity of PH-rabbit increased 53%, after 5 days of HgCl2 treatment post-PH, while GPT and AkP activities decreased 89% and 97%, respectively, during this period. The ICDH activity increased 416%, 10 days after the last dose, while all other enzymes showed normal values. The total body growth rate and relative liver weight decreased under all experimental conditions.
Aerosol processing: a wind of innovation in the field of advanced heterogeneous catalysts (2018)

Aerosol processing is long known and implemented industrially to obtain various types of divided materials and nanomaterials. The atomisation of a liquid solution or suspension produces a mist of aerosol droplets which can then be transformed via a diversity of processes including spray-drying, spray pyrolysis, flame spray pyrolysis, thermal decomposition, micronisation, gas atomisation, etc. The attractive technical features of these aerosol processes make them highly interesting for the continuous, large scale, and tailored production of heterogeneous catalysts. Indeed, during aerosol processing, each liquid droplet undergoes well-controlled physical and chemical transformations, allowing for example to dry and aggregate pre-existing solid particles or to synthesise new micro- or nanoparticles from mixtures of molecular or colloidal precursors. In the last two decades, more advanced reactive aerosol processes have emerged as innovative means to synthesise tailored-made nanomaterials with tunable surface properties, textures, compositions, etc. In particular, the "aerosol-assisted sol-gel" process (AASG) has demonstrated tremendous potential for the preparation of high-performance heterogeneous catalysts. The method is mainly based on the low-cost, scalable, and environmentally benign sol-gel chemistry process, often coupled with the evaporation-induced self-assembly (EISA) concept. It allows producing micronic or submicronic, inorganic or hybrid organic-inorganic particles bearing tuneable and calibrated porous structures at different scales. In addition, pre-formed nanoparticles can be easily incorporated or formed in a "one-pot" bottom-up approach within the porous inorganic or hybrid spheres produced by such spray drying method. Thus, multifunctional catalysts with tailored catalytic activities can be prepared in a relatively simple way. This account is an overview of aerosol processed heterogeneous catalysts which demonstrated interesting performance in various relevant chemical reactions like isomerisation, hydrogenation, olefin metathesis, pollutant total oxidation, selective oxidation, CO2 methanation, etc. A short survey of patents and industrial applications is also presented. Our objective is to demonstrate the tremendous possibilities offered by the coupling between bottom up synthesis routes and these aerosol processing technologies which will most probably represent a major route of innovation in the mushrooming field of catalyst preparation research.
Ions inside a parabolic mirror - Surrounding absorbers with reflective geometry allows for efficient free space-coupling (2011)

Our research aims at the free-space interaction of a single ion with a surrounding light field. A particularly important ingredient is the illumination of the ion from almost the full solid angle. Conventional ion traps are not built with wide open optical access as their primary design goal and are thus restricting the solid angle accessible to incoming light. By combining a reflective optical element such as a parabolic mirror with a specially designed wide open ion trap we aim to overcome this limitation.
Enantioselective LC–ESI–MS/MS method for quantitation of (−)‐lumefantrine and (+)‐lumefantrine in mice plasma and application to a pharmacokinetic study (2020)

We developed and validated a simple, sensitive, selective, and reliable LC-MS/MS-ESI method for the direct quantitation of lumefantrine (LFN) enantiomers [(-)-LFN and (+)-LFN] in mice plasma as per regulatory guideline. LFN enantiomers and carbamazepine (internal standard) were extracted from mice plasma using Strata X SPE (solid-phase extraction) cartridges. Good resolution between enantiomers was achieved on a Chiralpak IA-3 column using an isocratic mobile phase (0.1% of diethyl amine in methanol), which was delivered at a flow rate of 0.8 mL/min. Detection and quantitation were performed using multiple reaction monitoring mode following the transitions m/z 530.27 → 512.30 and 237.00 → 194.00 for LFN enantiomers and the internal standard, respectively, in the positive-ionization mode. The proposed method provided accurate and reproducible results over the linearity range of 2.39-895 ng/mL for each enantiomer. The intra- and inter-day precisions were in the range of 1.03-6.14 and 6.36-8.70 and 2.03-4.88 and 5.82-11.5 for (-)-LFN and (+)-LFN, respectively. Both (-)-LFN and (+)-LFN were found to be stable under different stability conditions. The method was successfully used to delineate stereoselective pharmacokinetics of LFN enantiomers in mice after an oral administration of rac-LFN (20 mg/kg). The pharmacokinetic results indicated that the disposition of LFN enantiomers was stereoselective in mice.
Polyelectrolyte Synthesis and in Situ Complex Formation in Ionic Liquids (2009)

For the first time, polyelectrolyte complex (PEC) capsules were prepared from a water insoluble polyanion, namely cellulose sulfates (CSs) with a degree of substitution (DS) below 0.2 in ionic liquids (IL). Capsules prepared via interaction with the polycation poly(dimethyldiallyammonium chloride) were free of residual IL and possessed an outer shell and a hollow inner core that made them ideal containers for enzyme mediated reactions. Due to the reestablished hydrogen bond system of the low substituted CS, the capsules showed increased stability, compared to the products obtained by application of the common aqueous preparation. Encapsulation of glucose oxidase demonstrated that the steps of CS preparation, PEC capsule formation, and encapsulation could be combined in a single pot, with the elimination of time and cost consuming isolation and purification steps.
Optimizing Parametric Factors in CIELAB and CIEDE2000 Color-Difference Formulas for 3D-Printed Spherical Objects (2022)

The current color-difference formulas were developed based on 2D samples and there is no standard guidance for the color-difference evaluation of 3D objects. The aim of this study was to test and optimize the CIELAB and CIEDE2000 color-difference formulas by using 42 pairs of 3D-printed spherical samples in Experiment I and 40 sample pairs in Experiment II. Fifteen human observers with normal color vision were invited to attend the visual experiments under simulated D65 illumination and assess the color differences of the 82 pairs of 3D spherical samples using the gray-scale method. The performances of the CIELAB and CIEDE2000 formulas were quantified by the STRESS index and F-test with respect to the collected visual results and three different optimization methods were performed on the original color-difference formulas by using the data from the 42 sample pairs in Experiment I. It was found that the optimum parametric factors for CIELAB were kL = 1.4 and kC = 1.9, whereas for CIEDE2000, kL = 1.5. The visual data of the 40 sample pairs in Experiment II were used to test the performance of the optimized formulas and the STRESS values obtained for CIELAB/CIEDE2000 were 32.8/32.9 for the original formulas and 25.3/25.4 for the optimized formulas. The F-test results indicated that a significant improvement was achieved using the proposed optimization of the parametric factors applied to both color-difference formulas for 3D-printed spherical samples.
Effects of a buried p-layer on alpha-particle immunity of MESFET's fabricated on semi-insulating GaAs substrates (1986)

Measurements of alpha-particle-induced charge are carried out for the first time on both conventional MESFET's fabricated directly on semi-insulating GaAs substrates and MESFET's with a buried p-layer. The maximum collected charge is found to be 65 fC in the MESFET's with a buried p-layer, one order smaller than in conventional MESFET's.
Supplementary Figure 5 from Enhanced Cancer Radiotherapy through Immunosuppressive Stromal Cell Destruction in Tumors (2023)

&lt;p&gt;PDF file - 809K, Evaluation of antitumor effect after radiation combined with intratumoral E7 peptide treatment in TLR9-/- and WT C57BL/6 mice.&lt;/p&gt;
The intriguing role of soluble urokinase receptor in inflammatory diseases (2017)

Inflammation is a key player in the development of an increasing amount of diseases. The soluble urokinase plasminogen activator receptor (suPAR) is a highly flexible molecule with intrinsic chemotactic properties. This glycoprotein has been evaluated as a biomarker of inflammation, immune activation, organ damage and clinical outcome in several pathologies, including cardiovascular disease, hepatitis, renal disorders and rheumatic pathologies. The use of this early warning inflammatory biomarker could potentially improve the prediction of the severity of these diseases and mortality. In the present paper, we describe the general characteristics of suPAR and its intriguing role as a biomarker in different inflammatory diseases.
Supplementary Figure 3 from Androgen Receptor Splice Variants Determine Taxane Sensitivity in Prostate Cancer (2023)

&lt;p&gt;PDF file - 182KB, R1881 treatment in M12 cells transfected with ARv567 and ARv7 does not increase AR-variant nuclear accumulation.&lt;/p&gt;