gebhart/patrepeval huggingface dataset:
Amyloid formation of native folded protein induced by peptide‐based graft copolymer (2002)

We report here that a native folded holo-myoglobin, when incubated with a synthetic amyloidogenic peptide in aqueous solutions, forms fibrils. These fibrils took a cross-beta form (inter-strand spacing: 4.65 A and inter-sheet spacing: 10.65 A) and bound the amyloidophilic dye Congo red as did the authentic amyloid fibrils. In contrast such fibril formation of myoglobin did not occur in the absence of the peptide. These results suggest the possibility that inter-molecular interaction of native protein with the amyloidogenic peptide trigger the amyloid formation even for the non-pathogenic native protein like myoglobin, which itself exists as a globular form, under certain conditions.
Direction of the easy axis in amorphous Tb-Fe (abstract) (1987)

Detailed examination of the angle of the effective easy axis in dual-gun cosputtered amorphous Tb-Fe shows an unexpected small deviation from the normal to the film. In other respects, the magnetic properties of films prepared by codeposition are quite comparable to those prepared by other means.1 The easy axis is tilted in the plane normal to the film and parallel to the line connecting the two sources during deposition. The tilt angle is a strong function of film thickness, composition, deposition temperature, and the incident angles of the Tb and Fe vapor beams. The most peculiar result found is a large jump in the angle at the compensation composition for thick (5000-Å) samples grown at room temperature. Bright-field transmission electron microscope (TEM) images of the films show them to be smooth and featureless. A comparison of x-ray, TEM, and magnetic measurements on films prepared under a variety of conditions show the relationship between the microstructure and the tilted easy axis.
Роль окисления белка XRCC1 в регуляции процесса репарации ДНК у млекопитающих (2019)

Впервые изучено влияние окисления белка XRCC1 на модификацию белков, катализируемую поли(АДФ‑рибоза) полимеразами (PARP1 и PARP2). XRCC1, PARP1 и PARP2 обеспечивают координацию многоступенчатого процесса репарации самых многочисленных повреждений ДНК в роли организующих платформ. Нами показано, что окисление снижает эффективность АДФ‑рибозилирования XRCC1 и сродство белка к поли(АДФ‑рибозе). Модификация разных форм XRCC1 АДФ‑рибозой усиливается в присутствии ДНК‑полимеразы β (Polβ), образующей стабильный комплекс с XRCC1. Окисление подавляет ингибирующую активность XRCC1 и её комплекса с Polβ в отношении процесса автомодификации PARP1 и PARP2, что может усиливать эффективность репарации. Результаты исследования указывают на роль окисления XRCC1 в тонкой регуляции уровней поли(АДФ‑рибозил)ирования белков и их координирующих функций в репарации ДНК.
Histone hyperacetylation is involved in the quercetin-induced human leukemia cell death. (2008)

Quercetin (QU) is recognized as a promising anticancer drug, but its mechanism remains elusive. Here we found that QU induced human leukemia cell death in a dose-dependent manner. However, it did not show a dose-dependent inhibition on ROS generation (indicated by the level of malondialdehyde, MDA) in the same cells. QU showed similar antioxidant activity at concentrations of 50, 75 and 100 microM. Consistent with that, the antioxidant, N-acetyl-cysteine (NAC) could only further decrease the ROS generation and enhance the cell death triggered by QU at the concentrations less than 50 microM. These results indicate that an additional mechanism is involved in the anticancer activity of high concentrations of QU. When the effect of QU on histone acetylation was studied, QU induced significant histone hyperacetylation at 75 and 100 microM, indicating the possible involvement of histone hyperacetylation in the anticancer activity of high concentrations of QU. This conclusion was supported by the findings that when histone acetylation in the cells treated by QU was increased by different concentrations of TSA, the cell death was significantly enhanced. Our results thus provide the first evidence that QU can induce histone hyperacetylation and this induction of histone hyperacetylation may represent an unrevealed mechanism in its anticancer activity.
Cell lysis on a microfluidic CD (compact disc) (2004)

Cell lysis was demonstrated on a microfluidic CD (Compact Disc) platform. In this purely mechanical lysis method, spherical particles (beads) in a lysis chamber microfabricated in a CD, cause disruption of mammalian (CHO-K1), bacterial (Escherichia coli), and yeast (Saccharomyces cerevisiae) cells. Interactions between beads and cells are generated in the rimming flow established inside a partially filled annular chamber in the CD rotating around a horizontal axis. To maximize bead-cell interactions in the lysis chamber, the CD was spun forward and backwards around this axis, using high acceleration for 5 to 7 min. Investigation on inter-particle forces (friction and collision) identified the following parameters; bead density, angular velocity, acceleration rate, and solid volume fraction as having the most significant contribution to cell lysis. Cell disruption efficiency was verified either through direct microscopic viewing or measurement of the DNA concentration after cell lysing. Lysis efficiency relative to a conventional lysis protocol was approximately 65%. In the long term, this work is geared towards CD based sample-to-answer nucleic acid analysis which will include cell lysis, DNA purification, DNA amplification, and DNA hybridization detection.
High-speed, bi-directional dual-core fiber transmission system for high-density, short-reach optical interconnects (2015)

A complete single mode dual-core fiber system for short-reach optical interconnects is fabricated and tested for high-speed data transmission. It includes dual-core fibers capable of bi-directional data transmission, dual-core simplex LC connectors, and fan-outs. The transmission system offers simplified bi-directional traffic engineering with integrated bidirectional transceivers and compact system design, utilizing simplex dual-core LC connectors that use half the space while increasing the bandwidth density by a factor of two. The fiber has two cores that are compatible with single mode fiber and conforms to the industry standard outer diameter of 125 &mu;m. This reduces operational complexity by reducing the size and number of fibers, cables and connectors. Measured OTDR loss for both cores was 0.34 dB/km at 1310 nm and 0.19 dB/km at 1550 nm. Crosstalk for a piece of 5.8 km long dual-core fiber was measured to be below -75 dB at 1310 nm, and below -40 dB at 1550 nm. Both free-space optics fan-outs and tapered-fiber-coupler based MCF fan-outs were evaluated for the transmission system. Error-free and penalty-free 25 Gb/s bi-directional transmission performance was demonstrated for three different fiber lengths, 200 m, 2 km and 10 km, using the complete all-fiber-based system including connectors and fan-outs. This single mode, dual-core fiber transmission system adds complementary value to systems where additional increases in bandwidth density can come from wavelength division multiplexing and multiple bits per symbol.
Gamma-radiation imaging system based on the Compton effect (1977)

A novel gamma-ray camera is proposed that is based on the Compton effect. The basis of the device is a segmented semiconductor detector which is able to locate successive interaction points in multicollision trajectories and the associated energy losses. In this way, conic section can be computed on an image plane for each emission from a point source in the object. An overall image can be constructed by summation of the individual ellipses. The effect of measurement errors is investigated theoretically and by simulation, and leads to favourable estimates for the resolution and sensitivity of the camera. The question of image processing to improve performance is briefly discussed.
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction (2016)

Formalin-fixed paraffin embedded tissue (FFPET) represents a valuable, well-annotated substrate for molecular investigations. The utility of FFPET in molecular analysis is complicated both by heterogeneous tissue composition and low yields when extracting nucleic acids. A literature search revealed a paucity of protocols addressing these issues, and none that showed a validated method for simultaneous extraction of RNA and DNA from regions of interest in FFPET. This method addresses both issues. Tissue specificity was achieved by mapping cancer areas of interest on microscope slides and transferring annotations onto FFPET blocks. Tissue cores were harvested from areas of interest using 0.6 mm microarray punches. Nucleic acid extraction was performed using a commercial FFPET extraction system, with modifications to homogenization, deparaffinization, and Proteinase K digestion steps to improve tissue digestion and increase nucleic acid yields. The modified protocol yields sufficient quantity and quality of nucleic acids for use in a number of downstream analyses, including a multi-analyte gene expression platform, as well as reverse transcriptase coupled real time PCR analysis of mRNA expression, and methylation-specific PCR (MSP) analysis of DNA methylation.
A systems approach to hemostasis: 2. Computational analysis of molecular transport in the thrombus microenvironment (2014)

Hemostatic thrombi formed after a penetrating injury have a heterogeneous architecture in which a core of highly activated, densely packed platelets is covered by a shell of less-activated, loosely packed platelets. In the first manuscript in this series, we show that regional differences in intrathrombus protein transport rates emerge early in the hemostatic response and are preserved as the thrombus develops. Here, we use a theoretical approach to investigate this process and its impact on agonist distribution. The results suggest that hindered diffusion, rather than convection, is the dominant mechanism responsible for molecular movement within the thrombus. The analysis also suggests that the thrombus core, as compared with the shell, provides an environment for retaining soluble agonists such as thrombin, affecting the extent of platelet activation by establishing agonist-specific concentration gradients radiating from the site of injury. This analysis accounts for the observed weaker activation and relative instability of platelets in the shell and predicts that a failure to form a tightly packed thrombus core will limit thrombin accumulation, a prediction tested by analysis of data from mice with a defect in clot retraction.
The major parasite surface antigen associated with human resistance to schistosomiasis is a 37-kD glyceraldehyde-3P-dehydrogenase. (1989)

Schistosomiasis, due to Schistosoma mansoni, is a major health problem in many subtropical countries, and major efforts are being made to define a vaccine. In this regard, we have reported that sera from subjects with low susceptibility to infection by S. mansoni react with a major larval surface antigen (P-37), having an apparent molecular mass of 37 kD, against which sera of susceptible individuals show little reactivity. We have now cloned the cDNA for this antigen by screening a schistosome cDNA expression library with antibodies against the purified protein. The selected cDNAs encode a protein that is specifically identified by immune human sera containing antibodies against P-37, while sera exhibiting low or no reactivity toward P-37 fail to recognize the recombinant protein. The cloned cDNAs hybridize with a 1.2-kb RNA that is the transcript of a single copy gene. This RNA directs the synthesis of a 36.5-kD polypeptide that is precipitated by sera from the most resistant subjects. The amino acid sequence of the encoded polypeptide shows homology with the glycolytic enzyme Glyceraldehyde-3P-dehydrogenase (72.5% of positional identity with human Glyceraldehyde-3P-dehydrogenase). Antibodies against the recombinant protein identified P-37 on the larva. These findings, together with other reports, indicate that a number of conserved proteins may be major targets of host-protective immunity against S. mansoni. The hypothesis is discussed that genetic restriction of the immune response to these antigens may occur in heterogeneous human populations because of the limited number of T cell epitopes carried by these host-like proteins. Such genetic effects might allow parasite transmission through nonresponder (susceptible) individuals. This hypothesis and the protective properties of P-37 can now be tested using the recombinant protein and synthetic peptides derived from selected regions of the polypeptide chain.
How does β-adrenergic signalling affect the transitions from ventricular tachycardia to ventricular fibrillation? (2014)

Changes in APD restitution during βAR activation revealed a novel transient spiral wave dynamics; this spatiotemporal characteristic strongly depends on the protocol of isoproterenol application.
Lifetime Prediction for CMOS Devices with Ultra Thin Gate Oxides Based on Progressive Breakdown (2007)

Progressive breakdown observed in CMOS devices with ultra thin gate oxides can significantly increase the time dependent dielectric breakdown (TDDB) reliability margin of digital CMOS products. The voltage acceleration, the failure distribution of the progressive breakdown and the methodology for quantification of the progressive breakdown is discussed. Extensive experimental data are provided, enabling its implementation
Synthesis of (Methyl 3‐O‐Benzyl‐4,6‐O‐benzylidene‐2‐deoxy‐α‐D‐altropyranosid‐2‐yl) thiophene Derivatives as Precursors of New Iso‐C‐nucleoside Analogues (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Design, Synthesis, and Utility of Defined Molecular Scaffolds (2021)

A growing theme in chemistry is the joining of multiple organic molecular building blocks to create functional molecules. Diverse derivatizable structures—here termed “scaffolds” comprised of “hubs”—provide the foundation for systematic covalent organization of a rich variety of building blocks. This review encompasses 30 tri- or tetra-armed molecular hubs (e.g., triazine, lysine, arenes, dyes) that are used directly or in combination to give linear, cyclic, or branched scaffolds. Each scaffold is categorized by graph theory into one of 31 trees to express the molecular connectivity and overall architecture. Rational chemistry with exacting numbers of derivatizable sites is emphasized. The incorporation of water-solubilization motifs, robust or self-immolative linkers, enzymatically cleavable groups and functional appendages affords immense (and often late-stage) diversification of the scaffolds. Altogether, 107 target molecules are reviewed along with 19 syntheses to illustrate the distinctive chemistries for creating and derivatizing scaffolds. The review covers the history of the field up through 2020, briefly touching on statistically derivatized carriers employed in immunology as counterpoints to the rationally assembled and derivatized scaffolds here, although most citations are from the past two decades. The scaffolds are used widely in fields ranging from pure chemistry to artificial photosynthesis and biomedical sciences.
Absolute Quantification of Specific Nucleic Acids by RT-PCR Using a Nonlinear Mathematical Model for Data Analysis (2003)

I. Introduction...........................................................................................................................235 II. Example ................................................................................................................................236
Heritability and Genome-Wide Association Analyses of Human Gait Suggest Contribution of Common Variants (2015)

Human gait is a complex neurological and musculoskeletal function, of which the genetic basis remains largely unknown. To determine the influence of common genetic variants on gait parameters, we studied 2,946 participants of the Rotterdam Study, a population-based cohort of unrelated elderly individuals. We assessed 30 gait parameters using an electronic walkway, which yielded seven independent gait domains after principal component analysis. Genotypes of participants were imputed to the 1,000 Genomes reference panel for generating genetic relationship matrices to estimate heritability of gait parameters, and for subsequent genome-wide association scans (GWASs) to identify specific variants. Gait domains with the highest age- and sex-adjusted heritability were Variability (h (2) = 61%), Rhythm (37%), and Tandem (32%). For other gait domains, heritability estimates attenuated after adjustment for height and weight. Genome-wide association scans identified a variant on 1p22.3 that was significantly associated with single support time, a variable from the Rhythm domain (rs72953990; N = 2,946; β [SE] = 0.0069 (0.0012), p = 2.30×10(-8)). This variant did not replicate in an independent sample (N = 362; p = .78). In conclusion, human gait has highly heritable components that are explained by common genetic variation, which are partly attributed to height and weight. Collaborative efforts are needed to identify robust single variant associations for the heritable parameters.
Surface functionalization of polystyrene latex particles with a liposaccharide monomer (1995)

Abstract Emulsifier‐free latexes with immobilized carbohydrate residues have been prepared by batch or seed (co)polymerization of styrene in the presence of 11‐(N‐p‐vinylbenzyl)amido undecanoyl maltobionamide (LIMA). The critical micelle concentration and the molecular surface area of LIMA were determined by surface tension and fluorescence measurements. Batch polymerization of LIMA with styrene was first performed using potassium persulfate, proving the efficiency of LIMA as emulsifier. Seed copolymerization was then investigated using polystyrene seed particles with varying experimental conditions (especially the LIMA surface coverage). Material balance of LIMA between aqueous phase and particles was obtained by separating both phases by ultracentrifugation and it was found that the surfaceactive monomer is preferentially on or in the particle (nearly 100% in batch and at most 70% in seed copolymerization). The presence of the carbohydrate residues at the particle surface was directly evidenced by 1 H‐nuclear magnetic resonance, electron spectroscopy for chemical analysis and electrophoretic mobility.
U.S.A.3 UNITED STATES OF AMERICA (1995)

Age discrimination -fact that younger replacement is over 40 years of age is irrelevant HEADNOTES* Facts At age 56, petitioner was fired by respondent corporation and replaced by a 40-year-old worker. He then filed this suit, alleging that his discharge violated the Age Discrimination in Employment Act of 1967 (ADEA). The District Court granted respondent's summary judgment motion, and the Court of Appeals affirmed, holding that petitioner failed to make out a prima facie case of age discrimination under McDonnell Douglas Corp. v Green because he failed to show that he was replaced by someone outside the age group
Palladium-Catalyzed Inter- and Intramolecular α-Arylation of Amides. Application of Intramolecular Amide Arylation to the Synthesis of Oxindoles (1998)

2A palladium-catalyzed α-arylation of amides is reported. Intermolecular arylation of N,N-dimethylamides and lactams occurs using aryl halides, silylamide base, and a palladium catalyst. Intramolecular arylation of N-(2-halophenyl)amides occurs using alkoxide base and a palladium catalyst. The palladium catalyst was formed in situ from Pd(dba)2 (dba = trans,trans-dibenzylidene acetone) and BINAP (2,2‘-bis(diphenylphosphino)-1,1‘-binaphthalene). Although the intermolecular arylation of amides is less general than that reported previously for ketones, unfunctionalized and electron-rich aryl halides gave α-arylamides in 48−75% yield and N-methyl-α-phenylpyrrolidinone in 49% yield. These reactions provided the highest yields yet reported for regioselective amide arylations. Intramolecular amide arylation of 2-bromoanilides gave oxindoles in 52−82% yield. Mono- and disubstituted acetanilides gave 1,3-di- and 1,3,3-trisubstituted oxindoles. The use of dioxane, rather than THF, solvent was important for some of the amide arylations.
Valorization of glycerol/ethanol-rich wastewater to bioflocculants: recovery, properties, and performance (2019)

Microbial extracellular polymeric substances (EPS) were produced in two membrane bioreactors, each separately treating fresh and saline synthetic wastewater (consisting of glycerol and ethanol), with the purpose of applying them as sustainable bioflocculants. The reactors were operated under nitrogen-rich (COD/N ratios of 5 and 20) and limited (COD/N ratios of 60 and 100) conditions. Under both conditions, high COD removal efficiencies of 87–96% were achieved. However, nitrogen limitation enhanced EPS production, particularly the polysaccharide fraction. The maximum EPS recovery (g EPS−COD/g COD<sub>influent</sub>) from the fresh wastewater was 54% and 36% recovery was obtained from the saline (30 g NaCl/L) wastewater. The biopolymers had molecular weights up to 2.1 MDa and anionic charge densities of 2.3–4.7 meq/g at pH 7. Using kaolin clay suspensions, high flocculation efficiencies of 85–92% turbidity removal were achieved at EPS dosages below 0.5 mg/g clay. Interestingly, EPS produced under saline conditions proved to be better flocculants in a saline environment than the corresponding freshwater EPS in the same environment. The results demonstrate the potential of glycerol/ethanol-rich wastewater, namely biodiesel/ethanol industrial wastewater, as suitable substrates to produce EPS as effective bioflocculants.
A comparison study of EM and physical equivalent circuit modeling for MIM CMOS capacitors (2002)

Abstract In this Letter a new physical model for metal–insulator–metal CMOS capacitors is presented. In the model the parameters of the circuit are derived from the physical structural details. Physical behaviors due to metal skin effect and inductance have been considered. The model has been confirmed by 3D EM simulator and design rules proposed. The model presented is scalable with capacitor geometry, allowing designers to predict and optimize quality factor. The approach has been verified for MIM CMOS capacitors. © 2002 Wiley Periodicals, Inc. Microwave Opt Technol Lett 34: 177–181, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.10409
Noninvasive assessment and classification of human skin burns using images of Caucasian and African patients (2019)

Burns are one of the obnoxious injuries subjecting thousands to loss of life and physical defacement each year. Both high income and Third World countries face major evaluation challenges including but not limited to inadequate workforce, poor diagnostic facilities, inefficient diagnosis and high operational cost. As such, there is need to develop an automatic machine learning algorithm to noninvasively identify skin burns. This will operate with little or no human intervention, thereby acting as an affordable substitute to human expertise. We leverage the weights of pretrained deep neural networks for image description and, subsequently, the extracted image features are fed into the support vector machine for classification. To the best of our knowledge, this is the first study that investigates black African skins. Interestingly, the proposed algorithm achieves state-of-the-art classification accuracy on both Caucasian and African datasets.