gebhart/patrepeval huggingface dataset:
ChemVassa: A New Method for Identifying Small Molecule Hits in Drug Discovery (2012)

ChemVassa, a new chemical structure search technology, was developed to allow rapid in silico screening of compounds for hit and hit-to-lead identification in drug development. It functions by using a novel type of molecular descriptor that examines, in part, the structure of the small molecule undergoing analysis, yielding its "information signature." This descriptor takes into account the atoms, bonds, and their positions in 3-dimensional space. For the present study, a database of ChemVassa molecular descriptors was generated for nearly 16 million compounds (from the ZINC database and other compound sources), then an algorithm was developed that allows rapid similarity searching of the database using a query molecular descriptor (e.g., the signature of atorvastatin, below). A scoring metric then allowed ranking of the search results. We used these tools to search a subset of drug-like molecules using the signature of a commercially successful statin, atorvastatin (Lipitor™). The search identified ten novel compounds, two of which have been demonstrated to interact with HMG-CoA reductase, the macromolecular target of atorvastatin. In particular, one compound discussed in the results section tested successfully with an IC50 of less than 100uM and a completely novel structure relative to known inhibitors. Interactions were validated using computational molecular docking and an Hmg-CoA reductase activity assay. The rapidity and low cost of the methodology, and the novel structure of the interactors, suggests this is a highly favorable new method for hit generation.
Downwind pre‐aligned rotors for extreme‐scale wind turbines (2017)

Abstract Downwind force angles are small for current turbines systems (1–5 MW) such that they may be readily accommodated by conventional upwind configurations. However, analysis indicates that extreme‐scale systems (10–20 MW) will have larger angles that may benefit from downwind‐aligned configurations. To examine potential rotor mass reduction, the pre‐alignment concept was investigated a two‐bladed configuration by keeping the structural and aerodynamic characteristics of each blade fixed (to avoids a complete blade re‐design). Simulations for a 13.2 MW rated rotor at steady‐state conditions show that this concept‐level two‐bladed design may yield 25% rotor mass savings while also reducing average blade stress over all wind speeds. These results employed a pre‐alignment on the basis of a wind speed of 1.25 times the rated wind speed. The downwind pre‐aligned concept may also reduce damage equivalent loads on the blades by 60% for steady rated wind conditions. Even higher mass and damage equivalent load savings (relative to conventional upwind designs) may be possible for larger systems (15–20 MW) for which load‐alignment angles become even larger. However, much more work is needed to determine whether this concept can be translated into a practical design that must meet a wide myriad of other criteria. Copyright © 2017 John Wiley &amp; Sons, Ltd.
Cellular and Physiological Effects of Ganoderma lucidum (Reishi) (2004)

In Asia, a variety of dietary products have been used for centuries as popular remedies to prevent or treat different diseases. A large number of herbs and extracts from medicinal mushrooms are used for the treatment of diseases. Mushrooms such as Ganoderma lucidum (Reishi), Lentinus edodes (Shiitake), Grifola frondosa (Maitake), Hericium erinaceum (Yamabushitake), and Inonotus obliquus (Chaga) have been collected and consumed in China, Korea, and Japan for centuries. Until recently, these mushrooms were largely unknown in the West and were considered 'fungi' without any nutritional value. However, most mushrooms are rich in vitamins, fiber, and amino acids and low in fat, cholesterol, and calories. These mushrooms contain a large variety of biologically active polysaccharides with immunostimulatory properties, which contribute to their anticancer effects. Furthermore, other bioactive substances, including triterpenes, proteins, lipids, cerebrosides, and phenols, have been identified and characterized in medicinal mushrooms. This review summarizes the biological effects of Ganoderma lucidum upon specific signaling molecules and pathways, which are responsible for its therapeutic effects.
Detection of Metal Contaminants in Food Using High Tc SQUIDs Magnetometer (2006)

A PC controlled food contaminant detection system for practical use was designed and constructed. The system we have developed is the High-Tc SQUID based system, which is covered with waterproof stainless steel plates and acceptable to HACCP (Hazard Analysis and Critical Control Point) program. The outer dimension of the system is 1500L mm x 477W mm x 1445H mm and the acceptable object size is 200W mm x 80H mm. This system employed a double-layered permeable metallic shield with thickness of 1 mm as a magnetically shielded box. The distribution of the magnetic field in the box was simulated by FEM; the gap between each shield layer was optimized before fabrication. Then the shielding factor of 732 in Z-component was achieved. This value is good enough to operate the system in a factory. As a result, we successfully detected a steel ball as small as 0.3 mm in diameter with a distance of 75 mm.
Anisotropy in the Viscoelastic Response of Knee Meniscus Cartilage (2016)

Multilevel characterization aims to expand the biomimetic approach from the structure itself, to include the mechanical characteristics that give the meniscus its peculiar properties, thus providing tools for the design of novel, effective scaffolds. An example of modeling of anisotropic open-cell porous material tailored to fulfill the measured requirements is presented, leading to a definition of additional parameters for a better understanding of the load transmission mechanism and for better scaffold functionality.
Demand response implementation in a home area network: A conceptual hardware architecture (2012)

Demand response (DR) is an important demand-side resource that allows for lower electricity consumption when the system is under stress. This paper presents a DR framework that can be implemented within a home area network, as well as a conceptual hardware architecture for a Home Management System (HMS) and appliance interface units that enable in-home DR implementation. The proposed DR strategy allows for controlling energy-intensive loads taking into consideration both consumers' comfort and load priority. The HMS acts as the central monitoring and decision-making unit for all energy-intensive loads within a home. The appliance interface unit communicates with the HMS while capturing electric power consumption data and performing local load control. Standby electric power consumption of each element in the network is also discussed.
The Stimulatory Effect of Canrenoate, a Mineralocorticoid Antagonist, on the Activity of the Hypothalamus-Pituitary-Adrenal Axis Is Abolished by Alprazolam, a Benzodiazepine, in Humans (2002)

Mineralocorticoid receptors (MR) in the hippocampus play a major role in the control of the hypothalamus-pituitary-adrenal (HPA) axis, mediating the proactive feedback of glucocorticoids in the maintenance of basal activity. Intracerebroventricular and intrahippocampal MR blockade stimulates HPA axis in animals; the systemic administration of mineralocorticoid antagonists enhances spontaneous and CRH-stimulated ACTH and cortisol secretion in humans. Benzodiazepines, namely alprazolam, activate central gamma-aminobutyric acid (GABA)ergic receptors, which are mainly distributed in the hippocampus. Alprazolam has a inhibitory effect on HPA axis either in basal conditions or after central nervous system-mediated stimuli. In humans, alprazolam strongly reduces the corticotroph responsiveness to removal of glucocorticoid feedback by metyrapone. We studied the effect of alprazolam (0.02 mg/kg, orally) on the effect of canrenoate (CAN), an MR antagonist (200 mg as an iv bolus, followed by 200 mg infused in 250 ml saline) or placebo on ACTH, cortisol, and dehydroepiandrosterone (DHEA) secretion in six normal young women (aged 25-32 yr; body mass index, 19-23 kg/m(2)). During placebo, ACTH, cortisol, and DHEA secretion showed a progressive decrease (baseline vs. nadir, mean +/- SEM, from 1830-2400 h, 2.6 +/- 0.3 vs. 1.4 +/- 0.3 pmol/liter, 133.2 +/- 16.4 vs. 46.9 +/- 5.2 nmol/liter, and 22.6 +/- 2.3 vs. 18.6 +/- 2.3 nmol/liter, respectively), although statistical significance was obtained for ACTH and cortisol only (P < 0.05). During CAN treatment, ACTH, cortisol, and DHEA secretion showed a progressive rise, which began at approximately 2100 h and peaked between 2300 and 2400 h (2.9 +/- 0.3 pmol/liter, 172.6 +/- 27.9 nmol/liter, and 45.3 +/- 10.7 nmol/liter, respectively; P < 0.05). Alprazolam abolished the CAN-induced increases in ACTH, cortisol, and DHEA levels (1.8 +/- 0.1 pmol/liter, 59.7 +/- 8.6 nmol/liter, and 19.8 +/- 6.7 nmol/liter; P < 0.05), inducing hormonal peaks overlapping with those recorded after placebo in the absence of any treatment. In conclusion, our study demonstrates that the inhibitory effect of GABAergic activation by alprazolam overrides the stimulatory effect of mineralocorticoid blockade by canrenoate on the HPA axis in humans. These findings emphasize the role of GABA in the control of the HPA axis in humans.
Rod–coil block copolymers: An iterative synthetic approach via living free‐radical procedures (2003)

Abstract A modular approach has been developed for the synthesis of rod–coil block copolymers involving the initial preparation of a macroinitiator based on the rod block followed by the growth of the coil segment with living free‐radical procedures. The key feature of this strategy is the utilization of an alkoxyamine group from the beginning of the synthesis, which serves as a solubilizing group and ensures that each rod block contains a single initiating fragment. Using this approach permits block copolymers based on insoluble biphenyl ester oligomers to be conveniently prepared with coil segments that range from styrenes to acrylates to 1,3‐dienes. The tendency of the rod segments to crystallize is strongly dependent on the weight fraction of the rod segment and the chemical nature of the coil segment. Rod–coil molecules containing at least 25–35 wt % polystyrene or poly( n ‐butyl acrylate) coil segments show a two‐dimensional hexagonal arrangement of rod aggregates, as characterized by transmission electron microscopy and small‐angle X‐ray scattering. Polyisoprene block copolymers exhibit a lamellar microstructure with short rigid domains in which the rod units lie in an interdigitated smectic C arrangement. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 3640–3656, 2003
A uniform metric for anaglyph calculation (2006)

We evaluate a new method for computing color anaglyphs based on uniform approximation in CIE color space. The method depends on the spectral distribution properties of the primaries of the monitor and the transmission functions of the filters in the viewing glasses. We will compare the result of this method with several other methods that have been proposed for computing anaglyphs. To compute the color at a given pixel in the anaglyph image requires solving a linear program. We exploit computational properties of the simplex algorithm to reduce computation time by 72 to 89 percent. After computing the color at a pixel, a depth-first search is performed to collect all neighboring pixels with similar color so that a simple matrix-vector multiplication can be applied. We also parallelize the algorithm and implement it on a cluster environment. We discuss the effects of different data dividing schemes.
Additional file 12: of Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design (2016)

Average drug-specific effects for each guide set (gRNAs directed against the same gene). (XLSX 27 kb)
Control of Vocal Loudness in Young and Old Adults (2001)

This study examined the effect of aging on respiratory and laryngeal mechanisms involved in vocal loudness control. Simultaneous measures of subglottal pressure and electromyographic (EMG) activity from the thyroarytenoid (TA), lateral cricoarytenoid (LCA), and cricothyroid (CT) muscles were investigated in young and old individuals while they attempted to phonate at three loudness levels, "soft," "comfortable," and "loud." Voice sound pressure level (SPL) and fundamental frequency (F ) measures were also obtained. Across loudness conditions, subglottal pressure levels were similar for both age groups. Laryngeal EMG measures tended to be lower and more variable for old compared with young individuals. These differences were most apparent for the TA muscle. Finally, across the three loudness conditions, the old individuals generated SPLs that were lower overall than those produced by the young individuals but modulated loudness levels in a manner similar to that of the young subjects. These findings suggest that the laryngeal mechanism may be more affected than the respiratory system in these old individuals and that these changes may affect vocal loudness levels.
A Model to Optimize a Microwave PBG Accelerator Based on Generic Unit Cell (2007)

In this paper a numerical method, based on the well known Floquet–Bloch theory, useful to analyze the physical properties of a PBG based accelerator, is presented. The proposed model has been developed to analyze a 2D lattice characterized by a generic inclination angle between the two primitive translation vectors, thus resulting very useful when a periodic structure without an equilateral triangular or square cell has to be investigated. The numerical method has been optimized in order to account several number of space harmonics with a low CPU time and memory consumption. Comparisons with more complex numerical methods demonstrate the accuracy of our model. Several simulations have been performed to find all the geometrical parameters including the inclination angle of the unit cell, filling factor and index contrast. The proposed method, through an optimization procedure of the photonic band structure, allows to obtain a large spectral purity, high order mode suppression and high Q–values.
Development and use of a non-biomaterial model for hands-on training of endoscopic procedures (2017)

Background: Endoscopic submucosal dissection (ESD) and peroral endoscopic myotomy (POEM) are recently developed techniques that have the potential to significantly improve clinical outcomes. However, training opportunities on these techniques remain limited. To address this issue, we developed a novel ex-vivo ESD/POEM training model. Our aim in this paper is to describe the model and provide preliminary evidence of promising feasibility to improve access to ESD/POEM training. Methods: The model was developed using polyvinyl alcohol hydrogel, which can easily be modified to reproduce the stiffness of the different intestinal layers, namely the mucosa, submucosa, and muscle layer. Results: A training workshop, using our ex-vivo model, was held for 28 residents. Satisfaction and feasibility in using the ex-vivo model for endoscopic training were evaluated by using a self-report questionnaire. All participants were satisfied with their training experience (100% satisfaction rate), with 27 of the 28 participants reporting that the model was feasible in replicating all components of the ESD/POEM technique (96.4% feasibility rate). Conclusions: Based on this feedback, we propose that our non-biomaterial model has the feasibility to provide an effective endoscopy education tool and a satisfactory training experience.
A high‐pass/lowpass phase shifter with resistive matching networks (1996)

Abstract This paper proposes a high‐pass/lowpass phase shifter with improved reflection and phase‐shift characteristics using resistive matching networks. The circuit configuration, reflection characteristics, phase‐shift error‐reduction methods, and the design results are described. The relationship between the reflection of the single‐pole, double‐throw (SPDT) switch and the phase‐shift error is discussed in the high‐pass/lowpass phase shifter using filters to switch the SPDT switch. The reflection of the SPDT switch caused by the parasitic resistance of the switching device is investigated, and an impedance matching method using the resistive matching networks is proposed to reduce reflection. The calculation results for an S‐band phase shifter with the resistive matching networks show that the matching can be achieved even for switching devices with resistance and that the phase‐shift error can be reduced. An S‐band, 90° single‐bit phase shifter has been designed and a low return loss of better than 19 dB and a phase‐shift error of less than 4° are achieved, which confirms the usefulness of the resistive matching networks.
Sex-based differences in cardiovascular proteomic profiles and their associations with adverse outcomes in patients with chronic heart failure (2023)

Baseline cardiovascular protein levels differ between women and men. However, the predictive value of repeatedly measured circulating proteins does not seem to differ except for endothelin-1 and somatostatin.
Reduced susceptibility of thin Pseudomonas aeruginosa biofilms to hydrogen peroxide and monochloramine (2001)

Pseudomonas aeruginosa attached to alginate gel beads in sparse, thin biofilms exhibited reduced susceptibility to monochloramine and hydrogen peroxide compared with planktonic cells of the same micro-organism. Disinfection rate coefficients for planktonic bacteria averaged 0.551 mg(-1)min(-1) for monochloramine and 3.1 x 10(-4)l mg(-1) min(-1) for hydrogen peroxide. The corresponding values for 24-h-old biofilm cells were 0.291 mg min(-1) and 9.2 x 10(-5) 1 mg(-1) min(-1) for monochloramine and hydrogen peroxide, respectively. Several pieces of evidence support the interpretation that the reduced susceptibility of biofilm was not due simply to inadequate delivery of the antimicrobial agent to the local environment of the attached cells. No correlation between biofilm susceptibility and biofilm initial areal cell density was observed. Rapid delivery of hydrogen peroxide to the attachment surface, and subsequently to the interior, of the alginate gel beads was visualized by a direct experimental technique. Theoretical analysis of unsteady diffusion and diffusion reaction interactions also argued against any significant delay or barrier to antimicrobial or oxygen delivery. It was hypothesized that new genes are expressed when bacteria attach to a surface and begin to form a biofilm and that some of the resulting gene products reduce the susceptibility of the cell to antimicrobial agents including oxidative biocides such as monochloramine and hydrogen peroxide.
Operation of direct wind generator systems using air-cored axial flux pm technology (2007)

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A Theory for High-Throughput Genetic Interaction Screening (2022)

Abstract Systematic, genome-scale genetic screens have been instrumental for elucidating genotype-phenotype relationships, but approaches for probing genetic interactions have been limited to at most ∼100 pre-selected gene combinations in mammalian cells. Here, we introduce a theory for high-throughput genetic interaction screens. The theory extends our recently developed Multiplexing using Spectral Imaging and Combinatorics (MuSIC) approach to propose ∼10 5 spectrally unique, genetically-encoded MuSIC barcodes from 18 currently available fluorescent proteins. Simulation studies based on constraints imposed by spectral flow cytometry equipment suggest that genetic interaction screens at the human genome-scale may be possible if MuSIC barcodes can be paired to guide RNAs. While experimental testing of this theory awaits, it offers transformative potential for genetic perturbation technology and knowledge of genetic function. More broadly, the availability of a genome-scale spectral barcode library for non-destructive identification of single-cells could find more widespread applications such as traditional genetic screening and high-dimensional lineage tracing.
Locally stationary random processes (1957)

A new kind of random process, the locally stationary random process, is defined, which includes the stationary random process as a special case. Numerous examples of locally stationary random processes are exhibited. By the generalized spectral density <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\Psi(\omega, \omega \prime)</tex> of a random process is meant the two-dimensional Fourier transform of the covariance of the process; as is well known, in the case of stationary processes, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\Psi(\omega, \omega \prime)</tex> reduces to a positive mass distribution on the line <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\omega = \omega \prime</tex> in the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\omega, \omega \prime</tex> plane, a fact which is the gist of the familiar Wiener-Khintchine relations. In the case of locally stationary random processes, a relation is found between the covariance and the spectral density which constitutes a natural generalization of the Wiener-Khintchine relations.
Generating 510 MW of X-Band Power for Structure-Based Wakefield Acceleration Using a Metamaterial-Based Power Extractor (2021)

We present our recent results generating 510 MW of power at 11.7 GHz using a metamaterial-based metallic power-extractor for application in structure-based wakefield acceleration (SWFA). SWFA is a novel acceleration scheme in which high-charge electron bunches are passed through a power extractor structure to produce a high-intensity wakefield. This wakefield can then be used to accelerate a witness bunch in the same beamline or passed to a separate acceleration beamline. MIT’s approach uses a specialized metamaterial for the power extractor design. By using a metamaterial, we can overcome some of the challenges faced by other SWFA techniques. Here, we discuss the Stage 3 experiment. The Stage 1 and Stage 2 experiments successfully demonstrated the functionality of the metamaterial approach by generating high power RF pulses using the 65 MeV electron beam at the Argonne Wakefield Accelerator (AWA) facility. The 510 MW result from Stage 3 experiment is the highest power generated to-date for SWFA at AWA, and was enable by significant design improvements, including an all-copper structure, fully-symmetric coupler design, and breakdown risk-reduction treatment.
연구논문 : PP가공용 실리콘 유연제의 제조 및 유연최적화 (2004)

An emulsion of octadecamidoethylaminoethyl dodecate (which provides softness) and an emulsion silicone oil KF-96 (which provides lubricity) were separately synthesized. Then PP finishing softeners (SSA-7) was prepared by blending of the synthesized emulsions with beef tallow hardened oil (a softness improving agent). PP finishing treatment was carried out with the prepared SSA-7 and PP finishing resin by a one bath method, and several physical properties were tested. As a result, crease recovery, tear strength, softness, lubricity, and bending resistance were all good, indicating that the prepared SSA-7 is a good PP finishing softener.