gebhart/patrepeval huggingface dataset:
Inhibition of enzyme activity by nanomaterials: Potential mechanisms and implications for nanotoxicity testing (2011)

The objective of this study was to investigate whether nanoparticle-exposure affects enzyme function and to determine the mechanisms responsible. Silicon, Au, and CdSe nanoparticles were synthesized in house and their physicochemical properties were characterized. The activity of purified lactate dehydrogenase (LDH) was inhibited or abolished by all nanoparticles tested. Inhibition was dependent upon particle core and surface-functional group composition. Inhibition of LDH was absent in crude tissue homogenates, in the presence of albumin, and at the isoelectric point of the protein, indicating that nanoparticles bind non-specifically to abundant proteins via a charge interaction. Circular dichroism spectroscopy suggests that the structure of LDH may be altered by nanoparticles in a manner different from that of bulk controls. We present new data on the specific physicochemical properties of nanoparticles that may lead to bioactivity and highlight a number of potentially serious problems with common nanotoxicity testing methods.
Metamaterial-enhanced arrays by innovative QCTO approaches (2014)

Quasi Conformal Transformation Optics (QCTO) is applied in innovative antenna array enhancement applications. The QCTO is implemented numerically. Examples provided include miniaturization of a linear array using isotropic metamaterial lens and transformation of an arbitrary shaped conformal array to a well known (for example circular) array. A full-wave electromagnetic simulation is used to validate the approach.
Site‐specific casein kinase 1ε‐dependent phosphorylation of Dishevelled modulates β‐catenin signaling (2006)

Careful regulation of the Wnt-Beta-catenin signaling pathway is critical to many aspects of development and cancer. Casein kinase Iepsilon is a Wnt-activated positive regulator of this pathway. Members of the Dishevelled family have been identified as key substrates of casein kinase I (CKI). However, the specific sites phosphorylated in vivo by CKI and their relative importance in the physiologic regulation of these proteins in the canonical Wnt-beta-catenin signaling pathway remain unclear. To address this question, recombinant mouse Dishevelled (mDvl-1) was phosphorylated by CKIin vitro and phosphorylation sites were identified by MS. CKI phosphorylation of mDvl-1 at two highly conserved residues, serines 139 and 142, was observed by MS and confirmed by phosphopeptide mapping of in vivo phosphorylated protein. Phosphorylation of these sites is dependent on casein kinase I epsilon activity in vivo. Phenotypic analysis of mutant mDvl-1 indicates that phosphorylation of these sites stimulates the Dvl-activated beta-catenin-dependent Wnt signaling pathway in both cell culture and in Xenopus development. Casein kinase I epsilon is a Wnt-regulated kinase, and regulated phosphorylation of Dvl allows fine tuning of the Wnt-beta-catenin signaling pathway.
Optimization with skewed majorization constraints: Application to MIMO systems (2008)

This paper considers the problem of optimizing a Schur-convex objective under a linearly shifted, or skewed, majorization constraint. Similar to the case with a regular majorization constraint, the solution is found to be the same for the entire class of cost functions. Furthermore, it is shown that the problem is equivalent to identifying the convex hull under a simple polygon defined by the constraint parameters. This leads to an algorithm that produces the exact optimum with linear computational complexity. As an application, we present a novel precoder design for a multi-input multi-output communication system with heterogeneous signal constellations utilizing decision feedback detection at the receiver.
Sonochemical Coatings of ZnO and CuO Nanoparticles Inhibit Streptococcus mutans Biofilm Formation on Teeth Model (2012)

Antibiotic resistance has prompted the search for new agents that can inhibit bacterial growth. We recently reported on the antibiofilm activities of nanosized ZnO and CuO nanoparticles (NPs) synthesized by using sonochemical irradiation. In this study, we examined the antibacterial activity of ZnO and CuO NPs in a powder form and also examined the antibiofilm behavior of teeth surfaces that were coated with ZnO and CuO NPs using sonochemistry. Free ZnO and CuO NPs inhibited biofilm formation of Streptococcus mutans . Furthermore, by using the sonochemical procedure, we were able to coat teeth surfaces that inhibited bacterial colonization.
Field testing of silicone rubber compositions (1999)

In this paper the design of the facility (power supply and leakage current (LC) measuring system) and experience from first 12 months of aging on 4 compositions of high temperature vulcanized (HTV) silicone rubber (SIR) are reported. Samples were selected according to a 2/sup 3/ factorial test plan, where electrical stress, content of ATH-filler and content of silicone oil were the factors. A high filler level significantly increased the leakage current activity on AC energized insulators. Short DC energized insulators show already traces of erosion, the erosion are more pronounced for samples with extra silicone oil.
Temperature adaptation in yeasts: the role of fatty acids (1990)

Studies on the yeasts Candida oleophila, Candida utilis, Lipomyces starkeyi, Rhodosporidium toruloides and Saccharomyces cerevisiae revealed the existence of three different temperature adaptation responses involving changes in fatty acid composition. These conclusions were drawn by determining the growth rates, total cellular fatty acid content, fatty acid composition, degree of unsaturation, and the mean chain length of fatty acids over a range of growth temperatures. Within temperatures permitting growth, there were no changes in the major fatty acids of any of the yeasts, but the absolute amounts and relative compositions of the fatty acids did alter. In S. cerevisiae there were temperature-induced changes in the mean fatty acid chain length, whereas in R. toruloides there were changes in the degree of unsaturation. C. oleophila, C. utilis and L. starkeyi showed both responses, depending on whether the growth temperature was above or below 20-26 degrees C. Below 20-26 degrees C temperature-dependent changes were observed in the mean chain length whereas above 20-26 degrees C there were changes in the degree of unsaturation.
xDNN: Inference for Deep Convolutional Neural Networks (2022)

We present xDNN, an end-to-end system for deep-learning inference based on a family of specialized hardware processors synthesized on Field-Programmable Gate Array (FPGAs) and Convolution Neural Networks (CNN). We present a design optimized for low latency, high throughput, and high compute efficiency with no batching. The design is scalable and a parametric function of the number of multiply-accumulate units, on-chip memory hierarchy, and numerical precision. The design can produce a scale-down processor for embedded devices, replicated to produce more cores for larger devices, or resized to optimize efficiency. On Xilinx Virtex Ultrascale+ VU13P FPGA, we achieve 800 MHz that is close to the Digital Signal Processing maximum frequency and above 80% efficiency of on-chip compute resources. On top of our processor family, we present a runtime system enabling the execution of different networks for different input sizes (i.e., from 224× 224 to 2048× 1024). We present a compiler that reads CNNs from native frameworks (i.e., MXNet, Caffe, Keras, and Tensorflow), optimizes them, generates codes, and provides performance estimates. The compiler combines quantization information from the native environment and optimizations to feed the runtime with code as efficient as any hardware expert could write. We present tools partitioning a CNN into subgraphs for the division of work to CPU cores and FPGAs. Notice that the software will not change when or if the FPGA design becomes an ASIC, making our work vertical and not just a proof-of-concept FPGA project. We show experimental results for accuracy, latency, and power for several networks: In summary, we can achieve up to 4 times higher throughput, 3 times better power efficiency than the GPUs, and up to 20 times higher throughput than the latest CPUs. To our knowledge, we provide solutions faster than any previous FPGA-based solutions and comparable to any other top-of-the-shelves solutions.
Evaluation of an automated system for the collection of packed RBCs, platelets, and plasma (2000)

Blood components collected with the Trima are equivalent to currently available components, and they meet the applicable regulatory standards. This system provides consistent, standardized components with predictable yields. It provides the option of fully automating the collection of all blood components.
Oxygen, pH, and mitochondrial oxidative phosphorylation (2012)

The oxygen dependence of mitochondrial oxidative phosphorylation was measured in suspensions of isolated rat liver mitochondria using recently developed methods for measuring oxygen and cytochrome c reduction. Cytochrome-c oxidase (energy conservation site 3) activity of the mitochondrial respiratory chain was measured using an artificial electron donor (N,N,N',N'-tetramethyl-p-phenylenediamine) and ascorbate to directly reduce the cytochrome c, bypassing sites 1 and 2. For mitochondrial suspensions with added ATP, metabolic conditions approximating those in intact cells and decreasing oxygen pressure both increased reduction of cytochrome c and decreased respiratory rate. The kinetic parameters [K(M) and maximal rate (V(M))] for oxygen were determined from the respiratory rates calculated for 100% reduction of cytochrome c. At 22°C, the K(M) for oxygen is near 3 Torr (5 μM), 12 Torr (22 μM), and 18 Torr (32 μM) at pH 6.9, 7.4, and 7.9, respectively, and V(M) corresponds to a turnover number for cytochrome c at 100% reduction of near 80/s and is independent of pH. Uncoupling oxidative phosphorylation increased the respiratory rate at saturating oxygen pressures by twofold and decreased the K(M) for oxygen to <2 Torr at all tested pH values. Mitochondrial oxidative phosphorylation is an important oxygen sensor for regulation of metabolism, nutrient delivery to tissues, and cardiopulmonary function. The decrease in K(M) for oxygen with acidification of the cellular environment impacts many tissue functions and may give transformed cells a significant survival advantage over normal cells at low-pH, oxygen-limited environment in growing tumors.
Can Hydrophobic Oils Spread on Water as Condensed Langmuir Monolayers? (2002)

In contrast to the long-held belief that only amphiphilic molecules can form stable Langmuir monolayers, we show here that even nonvolatile hydrophobic oils can be reversibly spread into liquid-condensed Langmuir films, if the material is in or close to liquid-crystal phase in the bulk. The stability origin of the hydrophobic Langmuir monolayers is entropic, rather than energetic as in the stabilization of common amphiphilic monolayers, primarily driven by the interaction between the polar head and water. This extraordinary spreading mechanism may have impact on the nature of colloidal and biomembrane stabilities.
The role of circulating microRNA in hepatocellular carcinoma (2015)

Hepatocellular carcinoma (HCC) is a rapidly progressing disease that exerts a huge burden on patients and health care systems. Rapid progression and difficulty in detecting early disease are major obstacles in offering potentially curative treatments. Besides the lack of effective chemo- or immunotherapy for advanced disease, there are currently no reliable tumor markers or imaging technologies that can accurately diagnose early HCC or predict disease progression. Since the discovery of microRNA (miRNA) and its involvement in hepatocarcinogenesis, the literature describes their usefulness as potential new biomarkers and treatment targets. Some of these miRNAs can also be found in the systemic circulation. With advances in detection and sequencing technologies, an increasing amount of data demonstrate the possibility of using circulating miRNAs as biomarkers to improve our current management of HCC in a less-invasive manner. This paper will review circulating miRNAs with a known function in HCC, describing their role and function in tumorigenesis. This review discusses their potential use as biomarkers in conjunction with emerging treatments in the diagnosis and targeting of this disease.
Asymmetric Synthesis of Homoallylic Amines Bearing Adjacent Stereogenic Centers by Addition of Substituted Allylic Zinc Reagents to N-tert-Butanesulfinylimines (2008)

A highly diastereoselective addition of substituted racemic allylic zinc reagents to chiral N- tert-butanesulfinylimines resulting in the formation of homoallylic amines is reported. This method is quite general and also efficient for the preparation of enantiomerically pure homoallylic amines bearing quaternary centers and also adjacent quaternary centers.
Application Of Cluster Analysis And Unsupervised Learning To Multivariate Tissue Characterization (1987)

This paper describes a procedure for classifying tissue types from unlabeled acoustic measurements (data type unknown) using unsupervised cluster analysis. These techniques are being applied to unsupervised ultrasonic image segmentation and tissue characteriza-tion. The performance of a new clustering technique is measured and compared with supervised methods, such as a linear Bayes classifier. In these comparisons two objectives are sought: a) How well does the clustering method group the data? b) Do the clusters correspond to known tissue classes? The first question is investigated by a measure of cluster similarity and dispersion. The second question involves a comparison with a supervised technique using labeled data.
Supplementary Figure 1 from Cancer Cell Dependence on Unsaturated Fatty Acids Implicates Stearoyl-CoA Desaturase as a Target for Cancer Therapy (2023)

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k Nearest Neighbor Classification Coprocessor with Weighted Clock-Mapping-Based Searching (2016)

Nearest-neighbor-search classifiers are attractive but they have high intrinsic computational demands which limit their practical application. In this paper, we propose a coprocessor for k (k with k≥1) nearest neighbor (kNN) classification in which squared Euclidean distances (SEDs) are mapped into the clock domain for realizing high search speed and energy efficiency. The minimal SED searching is carried out by weighted frequency dividers that drastically reduce the normally exponential increase of the worst-case search-clock number with the bit width of vector components to only a linear increase. This also results in low power dissipation and high area-efficiency in comparison to the traditional method using large numbers of adders and comparators. The kNN classifier determines the class of an unknown input sample with a majority decision among the k nearest reference samples. The required majority-decision circuit is integrated with the clock-mapping-based minimal-SED searching architecture and proceeds with the classification immediately after identification of each of the k nearest references. A test chip in 180 nm CMOS technology, which can process 8 dimensions of 32 reference vectors in parallel, achieves low power dissipation of 40.32 mW (at 51.21 MHz clock frequency and 1.8 V supply voltage). Significantly, the distance search circuit consumes only 5.99 mW. Feature vectors with different dimensionality up to 2048 dimensions can be handled by the designed coprocessor due to a dimension extension circuit, enabling large flexibility for usage in different application.
Novel Mass Tags for Single Nucleotide Polymorphism Detection (2007)

A new method suitable for single nucleotide polymorphism detection and other applications based on oligonucleotide probe extension has been developed. The method is based on mass spectrometry and utilizes a single surface for affinity purification of extended probes and matrix-independent desorption/ionization of the cleavable labels. A new family of sulfur-linked laser-cleavable trityl labels with vastly improved flying abilities is implemented in this study. Corresponding reagents compatible with automated oligonucleotide synthesis are presented. Utility of this method for SNP genotyping is demonstrated.
Thickness-dependent slow light gap solitons in three-dimensional coupled photonic crystal waveguides (2022)

The thickness-dependent multimodal nature of three-dimensional (3D) coupled photonic crystal waveguides is investigated with the aim of realizing a medium for controlled optical gap soliton formation in the slow light regime. In the linear case, spectral properties of the modes (dispersion diagrams), location of the gap regions versus the thickness of the 3D photonic crystal, and the near-field distributions at frequencies in the slow light region are analyzed using a full-wave electromagnetic solver. In the nonlinear regime (Kerr-type nonlinearity), we infer an existence of crystal-thickness-dependent temporal solitons with stable pulse envelope and use the solitonic pulses for driving quantum transitions in localized quantum systems within the photonic crystal waveguide. The results may be useful for applications in optical communications, multiplexing systems, nonlinear physics, and ultrafast spectroscopy.
Synthesis and Structural Characterization of a γ‐Keggin‐Type Dimeric Silicotungstate with a Bis(μ‐hydroxo) Dizirconium Core [(γ‐SiW10O36)2Zr2 (μ‐OH)2]10‐. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Chemical Mechanical Polishing Mechanisms of Low Dielectric Constant Polymers in Copper Slurries (1999)

Chemical mechanical polishing (CMP) of bis‐benzocyclobutene™ (BCB) and "silicon‐application ‐" (SiLK™) polymers in slurries commonly used for copper removal is studied. Material removal rates were determined for a variety of conditions, with surface roughness measured after polishing by atomic force microscopy. BCB exhibited removal rates of 10–50 nm/min and roughness of 0.5–1.4 nm, while SiLK exhibited removal rates of 20–300 nm/min and roughness of 0.8 to 2.0 nm. X‐ray photoelectron spectroscopy measurements on BCB showed an increase in surface oxygen to 14% after CMP, compared to a bulk concentration of 3.5%. Similarly, SiLK surface oxygen increased to 12% after CMP, compared to near zero in the bulk. A physically based model for polymer CMP is proposed. The model describes chemical and surfactant diffusion, surfactant adsorption, surface reactions, and surface abrasion during polishing. Two cases for the chemical action of the slurries are described by two different removal mechanisms. Case I describes slurry that does not react with polymer structural bonds. Instead, slurry oxidizes the polymer surface layer, deterring physical damage and CMP removal. Case II describes slurry that reacts with polymer structural bonds, forming a weakened layer that is removed rapidly during CMP. © 1999 The Electrochemical Society. All rights reserved.
Case-case comparison of smoking and alcohol risk associations with Epstein-Barr virus-positive gastric cancer: Behavioral Risk Factor in EBV-Positive Gastric Cancer (2021)

Helicobacter pylori is the primary cause of gastric cancer. However, monoclonal Epstein-Barr virus (EBV) nucleic acid is also present in up to 10% of these tumors worldwide. EBV prevalence is increased with male sex, non-antral localization and surgically disrupted anatomy. To further examine associations between EBV and gastric cancer, we organized an international consortium of 11 studies with tumor EBV status assessed by in situ hybridization. We pooled individual-level data on 2,648 gastric cancer patients, including 184 (7%) with EBV-positive cancers; all studies had information on cigarette use (64% smokers) and 9 had data on alcohol (57% drinkers). We compared patients with EBV-positive and EBV-negative tumors to evaluate smoking and alcohol interactions with EBV status. To account for within-population clustering, multi-level logistic regression models were used to estimate interaction odds ratios (OR) adjusted for distributions of sex (72% male), age (mean 59 years), tumor histology (56% Lauren intestinal-type), anatomic subsite (61% noncardia) and year of diagnosis (1983–2012). In unadjusted analyses, the OR of EBV positivity with smoking was 2.2 (95% confidence interval [CI], 1.6–3.2). The OR was attenuated to 1.5 (95% CI, 1.01–2.3) by adjustment for the possible confounders. There was no significant interaction of EBV status with alcohol drinking (crude OR, 1.4; adjusted OR, 1.0). Our data indicate the smoking association with gastric cancer is stronger for EBV-positive than EBV-negative tumors. Conversely, the null association with alcohol does not vary by EBV status. Distinct epidemiologic characteristics of EBV-positive cancer further implicate the virus as a co-factor in gastric carcinogenesis.
High Resolution Proton Radiography Using Sophisticated Image Processing Methods and a Commercial Plug and Play Detector (2017)

International audience
A 60GHz Class F-E Power VCO with Vector-Modulator Feedback in 65nm CMOS Technology (2012)

International audience
Crystallization and solid‐state polymerization of poly(aryl ester)s (2004)

Abstract The crystallization and solid‐state polymerization (SSP) of poly(aryl ester)s was investigated. Oligomers with different end‐groups were prepared by degradation of commercially available poly(aryl ester)s. The SSP of these oligomers was carried out after crystallization and under reduced pressure, in the presence of various catalysts. Polymers were characterized by means of their inherent viscosities and thermal properties. It has been found that Ti(O i Pr) 4 was a better catalyst for SSP. The structures and morphologies of semicrystalline poly(aryl ester)s were investigated by X‐ray diffraction and differential scanning calorimetry (DSC). Copyright © 2004 Society of Chemical Industry