gebhart/patrepeval huggingface dataset:
Key Aspects of the Novartis Compound Collection Enhancement Project for the Compilation of a Comprehensive Chemogenomics Drug Discovery Screening Collection (2005)

The NIBR (Novartis Institutes for BioMedical Research) compound collection enrichment and enhancement project integrates corporate internal combinatorial compound synthesis and external compound acquisition activities in order to build up a comprehensive screening collection for a modern drug discovery organization. The main purpose of the screening collection is to supply the Novartis drug discovery pipeline with hit-to-lead compounds for today's and the future's portfolio of drug discovery programs, and to provide tool compounds for the chemogenomics investigation of novel biological pathways and circuits. As such, it integrates designed focused and diversity-based compound sets from the synthetic and natural paradigms able to cope with druggable and currently deemed undruggable targets and molecular interaction modes. Herein, we will summarize together with new trends published in the literature, scientific challenges faced and key approaches taken at NIBR to match the chemical and biological spaces.
An overview of R&D work in friction stir welding at SMU (2006)

Friction stir welding (FSW) is an innovative solid-state material joining method invented by The Welding Institute (TWI) in 1991 and has been one of the most significant joining technology developments in the last two decades. It has evolved into a process focused on joining arc weldable (5xxx and 6xxx) and unweldable (2xxx and 7xxx) aluminum alloys to a point where it can be implemented by the aerospace and automotive industries for their joining needs.Research towards the further extension of the process to join dissimilar metal combinations like Fe-Al and Al-Cu is currently underway. A few of the important advantages of FSW over conventional joining techniques include improved joint properties and performance, low-deformation of the workpieces, a significant reduction in production costs and the freeing of skilled labor for use in other tasks. Compared to the conventional arc-welding of aluminum alloys, FSW produces a smaller heat affected zone, and it also allows the successful joining of aluminum alloys, steel, titanium, and dissimilar alloys with a stronger joint.
Hyperprolactinemia and erectile dysfunction. (2000)

Hyperprolactinemia from a pituitary adenoma is a rare cause of erectile dysfunction. Men with erectile dysfunction who are found to have a low testosterone level should have a measurement of their prolactin level. Treatment consists of lowering the prolactin level by medication or surgery, or both. Bromocriptine, a dopamine agonist, is efficacious in lowering elevated prolactin levels and can simultaneously shrink these pituitary tumors. With large tumors, transphenoidal surgery may be used to debulk/remove the tumor. Post-treatment prolactin levels can be used to monitor the efficacy of treatment.
Enhanced Modelling Framework for Equivalent Circuit-Based Power System State Estimation (2020)

The equivalent split-circuit formulation is a novel approach that has recently been applied to a range of power system related problems. As a result, a linear and a nonlinear method for power system state estimation with simultaneous treatment of the conventional and synchrophasor measurements have been proposed. In this article, new circuit models are introduced for different combinations of conventional measurements, thus providing a complete modelling framework for these methods. Additionally, handling cases of null injections and buses with no measurements are included. Simulations are performed on several test systems in order to evaluate the performance of both methods with the enhanced modelling framework and to compare them to a hybrid constrained estimator based on the conventional WLS approach.
Proteomic investigation of human skeletal muscle before and after 70 days of head down bed rest with or without exercise and testosterone countermeasures (2019)

HDBR resulted in alterations to skeletal muscle abundances and phosphorylation of several structural and metabolic proteins. Inclusion of exercise alone or in combination with testosterone treatment modulated the proteomic responses towards cellular reorganization and hypertrophy, respectively. Finally, the baseline proteome may aid in the development of personalized countermeasures to mitigate health risks in astronauts as related to loss of muscle mass and function.
Hypertrophic Chondrocytes Produce Immunoreactive Collagenase in Vivo (1989)

A monospecific, polyclonal antibody to neutral collagenase purified from rat myometrial cells was used to examine decalcified sections of normal and rachitic rat long bones, including epiphyses, for presence of immunoreactive collagenase in situ. Reactive antigen was uniformly present in hypertrophic chondrocytes of articular and epiphyseal plate cartilage. Preincubation of antibody with excess homogeneously purified antigen blocked the staining, indicating specificity of the staining for the antigen. Reaction was present in the borders of the enlarging lacunae, suggesting functional importance of this enzyme in the process of lacunar enlargement prior to mineralization. No detectable enzyme was observed in osteoblasts, osteocytes, or osteoclasts. No difference between expression of collagenase by bone cells in rachitic or normal bone was seen. Thus, at the level of sensitivity of this procedure, neutral collagenase appears to function in mature rat bone only in enlarging chondrocyte lacunae.
Performance, Energy and NVM Lifetime-Aware Data Structure Refinement and Placement for Heterogeneous Memory Systems (2023)

&lt;p&gt;The need for increased memory capacity, which is also affordable and sustainable, leads to the adoption of heterogeneous memory hierarchies, combining DRAM and NVM technologies. This work proposes a memory management methodology that relies on multi-objective optimization in terms of performance, energy consumption and impact on NVM’s lifetime, for applications deployed on heterogeneous (i.e. DRAM/NVM) memory systems. The evaluation of the methodology was performed both on emulated and real DRAM/NVM hardware for different applications and data placement algorithms. The experimental results show 58.7% lower execution time, 48.3% less energy consumption and 72.6% less NVM write operations compared to the results obtained by the initial versions of the applications. Thorough evaluation shows that the methodology is flexible and scalable, as it can integrate different data placement algorithms and NVM technologies and requires reasonable exploration time.&lt;/p&gt;
Sensory Evaluation Correlates with Flavor Volatile Profiles of Ripe Tomato Fruits (1997)

`Agriset-761' and `CPT-5' tomato fruits were harvested at green stage and subsequently exposed to a postharvest exogenous ethylene-air mixture (100 ppm C 2 H 4 at 20°C). Tomatoes with visual symptoms of ripening (breaker stage = &lt;10% red coloration) were removed from ethylene treatment after 1, 3, and 5 days and were transferred to 20°C and 85% RH. At “table-ripe” stage (full red coloration and 4-mm fruit deformation after 5 sec@9.8N), whole fruit samples were analyzed for difference/discrimination sensory evaluations, aroma volatile profiles, and chemical composition. Flavor of fruits gassed for 1 day was rated significantly different than that of fruits gassed for 3 or 5 days (n = 25 panelists) for both cultivars. Several panelists noted the perception of “rancid” and “metallic” tastes, and “lingering” aftertaste in fruits gassed for 5 days. Chemical composition assays showed that flavor differences could be partially due to a significant increase in pH values between fruits gassed for 1 and 5 days (4.23 and 4.34, respectively for `Agriset-761') and a significant decrease in titratable acidity (0.91% and 0.73%, respectively, for `Agriset-761'; 1.04% and 0.86%, respectively, for `CPT-5'). No significant differences in soluble solids content or total sugars were found in any treatments for either cultivar. `Agriset-761' showed significant increases in the concentrations of acetone, hexanal, 2+3 methylbutanol, and a decrease in 2-isobutylthiazole, whereas, `CPT-5' fruits showed significant increases in hexanal, 2+3 methylbutanol, trans-2-heptenal, 6-methyl-5-hepten-2-one, 2-isobutylthiazole, β-ionone, geranylacetone, and a decrease is ethanol concentration. In both cultivars, these significant differences in important aroma volatile compounds could be of enormous relevance in the perception of off-flavor/off-odors.
Ellipsometric study of Al2O3/Ag/Si and SiO2/Ag/quartz ashed in an oxygen plasma (1989)

Using monolayer-sensitive variable angle of incidence spectroscopic ellipsometry, the silver oxide growth on a silver mirror, coated with an Al2 O3 or SiO2 protective layer, was investigated. The oxidation was done in a pure oxygen plasma asher. The resulting silver oxide growth was monitored accurately as a function of exposure time in the plasma asher. It was found that silver was converted to silver oxide under the protective coating, during ashing of a sample. The optical constants of a dense silver oxide thin film, created by oxidizing in the asher, were also measured.
Quantum Engineering of Plasmon Modes (2020)

Quantum engineering is used in this work to design unconventional potentials that confine collective plasmonic modes in a semiconductor. Our approach has been enabled by a fully quantum treatment, which goes well beyond commonly employed electromagnetic models as it includes size confinement and tunneling. We have experimentally observed that new mid-infrared resonances of the collective response arise in a step well.
Proposed minimal standards for description of methanogenic archaea (2023)

Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the <i>mcrA</i> gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of <i>Candidatus</i> methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.
Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism (2013)

Lytic polysaccharide monooxygenases (LPMOs) exhibit a mononuclear copper-containing active site and use dioxygen and a reducing agent to oxidatively cleave glycosidic linkages in polysaccharides. LPMOs represent a unique paradigm in carbohydrate turnover and exhibit synergy with hydrolytic enzymes in biomass depolymerization. To date, several features of copper binding to LPMOs have been elucidated, but the identity of the reactive oxygen species and the key steps in the oxidative mechanism have not been elucidated. Here, density functional theory calculations are used with an enzyme active site model to identify the reactive oxygen species and compare two hypothesized reaction pathways in LPMOs for hydrogen abstraction and polysaccharide hydroxylation; namely, a mechanism that employs a η(1)-superoxo intermediate, which abstracts a substrate hydrogen and a hydroperoxo species is responsible for substrate hydroxylation, and a mechanism wherein a copper-oxyl radical abstracts a hydrogen and subsequently hydroxylates the substrate via an oxygen-rebound mechanism. The results predict that oxygen binds end-on (η(1)) to copper, and that a copper-oxyl-mediated, oxygen-rebound mechanism is energetically preferred. The N-terminal histidine methylation is also examined, which is thought to modify the structure and reactivity of the enzyme. Density functional theory calculations suggest that this posttranslational modification has only a minor effect on the LPMO active site structure or reactivity for the examined steps. Overall, this study suggests the steps in the LPMO mechanism for oxidative cleavage of glycosidic bonds.
Heat dissipation and thermometry in nanosystems: When interfaces dominate (2013)

The technological need for characterization of scaled nano-devices is not paralleled with the availability of methods to measure heat flux and temperature on small scales. To measure local temperature and conductance variation we therefore focus on developing measurement tools. These are based on (A) scanning a thermometer across the sample surface region of interest, so called scanning thermal microscopy (SThM), (B) measuring thermal properties directly through self-heating, and (C) measuring directly the heat-flux through 1D-structures.
Silicon monoxide – a convenient precursor for large scale synthesis of near infrared emitting monodisperse silicon nanocrystals (2016)

While silicon nanocrystals (ncSi) embedded in silicon dioxide thin films have been intensively studied in physics, the potential of batch synthesis of silicon nanocrystals from the solid-state disproportionation of SiO powder has not drawn much attention in chemistry. Herein we describe some remarkable effects observed in the diffraction, microscopy and spectroscopy of SiO powder upon thermal processing in the temperature range 850-1100 °C. Quantum confinement effects and structural changes of the material related to the size of the silicon nanocrystals nucleated and grown in this way were established by Photoluminescence (PL), Raman, FTIR and UV-Visible spectroscopy, PXRD and STEM, pinpointing that the most significant disproportionation transformations happened in the temperature range between 900 and 950 °C. With this know-how a high yield synthesis was developed that produced polydispersions of decyl-capped, hexane-soluble silicon nanocrystals predominantly with near infrared (NIR) PL. Using size-selective precipitation, these polydispersions were separated into monodisperse fractions, which allowed their PL absolute quantum yield (AQY) to be studied as a function of silicon nanocrystal size. This investigation yielded volcano-shaped plots for the AQY confirming the most efficient PL wavelength for ncSi to be located at around 820-830 nm, which corresponded to a size of 3.5-4.0 nm. This work provides opportunities for applications of size-selected near infrared emitting silicon nanocrystals in biomedical imaging and photothermal therapy.
Two-dimensional photonic crystals at visible wavelengths (2004)

Photonic crystal slabs are experimentally demonstrated at visible wavelengths. These consist of freestanding silicon nitride membranes, patterned with square lattices of holes. Measured transmission spectra are in good agreement with finite difference time domain calculations.
Gate Circuits with Feedback in Finite Algebras of Transients (2006)

Simulation of gate circuits is an efficient method of detecting hazards and oscillations that may occur in the presence of gate and wire delays. Ternary simulation, introduced by Eichelberger in 1965, consists of two algorithms, called A and B, and its results are well understood. Ternary simulation has been generalized by Brzozowski and Ésik in 2003 to an infinite algebra C and finite algebras Ck, k ≥ 2, where C2 is ternary algebra. Simulation in C has been studied extensively for feedback-free circuits, for which Algorithm A always terminates and Algorithm B is unnecessary. We study the simulation of gate circuits with feedback in finite algebras Ck, in which Algorithms A and B always terminate. The Boolean functions of the gates are restricted to a set G, where G = H ∪ ˜ H, H = {or, xor}, and ˜ H is the set of functions obtained by complementing any number of inputs and/or the output of functions from H. For gate functions restricted to G, we prove that Algorithm B in Algebra Ck, for k&amp;gt; 2 provides no more information than Algorithm B in ternary algebra. 1
Distinguishing a truncated random permutation from a random function (2015)

An oracle chooses a function $f$ from the set of $n$ bits strings to itself, which is either a randomly chosen permutation or a randomly chosen function. When queried by an $n$-bit string $w$, the oracle computes $f(w)$, truncates the $m$ last bits, and returns only the first $n-m$ bits of $f(w)$. How many queries does a querying adversary need to submit in order to distinguish the truncated permutation from a random function? In 1998, Hall et al. showed an algorithm for determining (with high probability) whether or not $f$ is a permutation, using $O(2^{\frac{m+n}{2}})$ queries. They also showed that if $m &lt; n/7$, a smaller number of queries will not suffice. For $m &gt; n/7$, their method gives a weaker bound. In this manuscript, we show how a modification of the method used by Hall et al. can solve the porblem completely. It extends the result to essentially every $m$, showing that $Ω(2^{\frac{m+n}{2}})$ queries are needed to get a non-negligible distinguishing advantage. We recently became aware that a better bound for the distinguishing advantage, for every $m
<title>Noise measurement technique for document scanners</title> (1996)

Scanner noise is one of the fundamental parameters of image quality. In this paper, we present an algorithm developed to derive the noise of a scanner using the 2D Wiener spectra of the test pattern and the scanner's MTF. The Wiener spectra of the test pattern was measured and its contribution to the measured RMS noise was estimated by integrating the volume under the product of the test pattern Wiener spectra and the scanner's MTF. The test pattern contribution was then removed from the measured noise. The derived noise agrees very well with the noise model for both drum scanner and CCD scanners. The structured 1D noise is also of interest especially when evaluating CCD scanner systems. A method was described to accurately determine 1D structured noise by averaging over fast scan and slow scan directions. Finally an experiment was conducted to verify the noise measurement technique. The true noise of a drum scanner was measured at its analog output terminal, and was compared to the noise estimated with the proposed new noise metric. The agreement between hardware measured noise and the estimated noise is very good with RMS error of less than 0.001 in reflectance unit. With this new technique, we can effectively improve the noise measurement accuracy by a factor of up to 500% for a photographic test pattern.
Re-adhesion control of electric motor coach based on disturbance observer and sensor-less vector control (2003)

When the adhesion force coefficient between rail and driving wheel decreases, the electric motor coach has slip phenomena. We have already proposed the anti-slip re-adhesion control system based on a disturbance observer. This system has the fine torque response for one driving wheel driven by one inverter-fed induction motor. However, the bogie of an electric motor coach has four driving wheels driven by two induction motors, which are driven by one inverter. In order to realize the anti-slip re-adhesion control system for the bogie of an electric motor coach, this paper proposes a new anti-slip re-adhesion control based on a disturbance observer and speed sensor-less vector control.
Innate Immunity and Inflammatory Response to Trichomonas vaginalis and Bacterial Vaginosis: Relationship to HIV Acquisition (2010)

Most women contract HIV-1 through sexual intercourse with an infected partner. Highly prevalent, unreported and often asymptomatic lower genital tract infections, including bacterial vaginosis (BV) and trichomoniasis (Trichomonas vaginalis- TV), increase a woman's susceptibility to HIV-1 genital infection, given an exposure. A review of the literature from 1989 to the present was conducted. This article will review potential mechanisms by which BV and TV serve as HIV-1-enhancing cofactors including (i) initiation of a clinical or subclinical mucosal inflammatory response, (ii) alteration of innate mucosal immunity, (iii) alteration of normal vaginal microflora and pH, and (iv) weakening or breach of intact cervico-vaginal mucosa. The transmission of HIV-1, in the absence of cofactors, is poorly efficient. Understanding the mechanisms by which these infections enhance HIV-1 acquisition is important to designing effective, safe and evidence-based prevention modalities.
Crystallization and preliminary X-ray characterization of archaeal group II chaperonin α-subunit fromThermococcusstrain KS-1 (2002)

The archaeal group II chaperonin from Thermococcus strain KS-1 is composed of two kinds of subunits (alpha and beta). Each of the recombinant subunits was individually expressed in Escherichia coli and purified as homo-hexadecamers of each subunit. Both homo-oligomers facilitate the refolding of denatured proteins in vitro in an ATP-dependent manner. A mutant alpha-subunit homo-oligomer with two amino-acid substitutions, which has the ability to capture the unfolded protein but lacks the ability to refold the unfolded protein, was crystallized in two different conditions. One crystal form was obtained from a high-concentration solution of ammonium sulfate and grew to maximum dimensions of 0.15 x 0.15 x 0.4 mm. The crystals of this form belonged to the tetragonal space group P42(1)2, with unit-cell parameters a = b = 209.3, c = 156.1 A, and diffracted X-rays to 2.4 A resolution with synchrotron radiation. The other form was crystallized from a polyethylene glycol 6000 solution and belonged to the tetragonal space group, with unit-cell parameters a = b = 220.8, c = 182.4 A. This form only diffracts X-rays to 6 A resolution. Diffraction data collected from the former crystal enabled initial successful phases to be obtained by the molecular-replacement method.
Spatial separation of parental genomes in hybrids of somatic plant cells (1987)

Chromosome spatial arrangements on metaphase plates of intergeneric intertribal cell hybrids of Nicotiana chinensis and Atropa belladonna as well as interspecific somatic hybrid plants of Nicotiana plumbaginifolia and Nicotiana sylvestris were analyzed. In the metaphases of the first divisions of protoplast fusion products, chromosomes of the two parents were spatially separated (segmented metaphase). In long-term cultured somatic hybrids, the topology of genome separation pattern in both callus cells and plants showed changes in form from "segmental" to "radial." Growing the hybrid cells in the presence of colchicine resulted in random chromosome arrangement both in cells directly exposed to different colchicine concentrations and in colchicine-treated cells grown in colchicine-free media. The degree of genome separation calculated for different cell clones remained constant during in vitro propagation of cells but was significantly lower for subclones derived from colchicine-treated cells. Therefore, it is concluded that spatial chromosome arrangement in metaphase is epigenetically controlled.