gebhart/patrepeval huggingface dataset:
Virtual screening for inhibitors of the human TSLP:TSLPR interaction (2017)

The pro-inflammatory cytokine thymic stromal lymphopoietin (TSLP) plays a pivotal role in the pathophysiology of various allergy disorders that are mediated by type 2 helper T cell (Th2) responses, such as asthma and atopic dermatitis. TSLP forms a ternary complex with the TSLP receptor (TSLPR) and the interleukin-7-receptor subunit alpha (IL-7Rα), thereby activating a signaling cascade that culminates in the release of pro-inflammatory mediators. In this study, we conducted an in silico characterization of the TSLP:TSLPR complex to investigate the drugability of this complex. Two commercially available fragment libraries were screened computationally for possible inhibitors and a selection of fragments was subsequently tested in vitro. The screening setup consisted of two orthogonal assays measuring TSLP binding to TSLPR: a BLI-based assay and a biochemical assay based on a TSLP:alkaline phosphatase fusion protein. Four fragments pertaining to diverse chemical classes were identified to reduce TSLP:TSLPR complex formation to less than 75% in millimolar concentrations. We have used unbiased molecular dynamics simulations to develop a Markov state model that characterized the binding pathway of the most interesting compound. This work provides a proof-of-principle for use of fragments in the inhibition of TSLP:TSLPR complexation.
Genes Associated with Fatty Acid Composition of Beef (2012)

Fatty acid composition has become recognized as an important trait in beef because of its relationship with beef quality, including beef flavor and tenderness. Our laboratory attempted to identify genes responsible for the fatty acid composition of cattle. We found several such genes and developed genetic markers of fatty acid composition. The findings were as follows. 1) Genetic polymorphisms of the stearoyl-CoA desaturase (SCD) gene are associated with fatty acid composition. The effects of SCD type A gene substitution on the percentage of monounsaturated fatty acid (MUFA) and the melting point of intramuscular fat were on average approximately +1.0% and −1.0°C, respectively. 2) Intron polymorphisms of sterol regulatory element binding protein-1 (SREBP-1) also affected MUFA. 3) No effect of SCD or SREBP-1 genotypes on any representative carcass traits of Japanese Black cattle was observed in the field population. 4) Additional genetic markers, adipocytes fatty acid binding protein 4 (FABP4) and liver X receptor α, also affected the fatty acid composition. 5) SCD and FABP4 significantly affected fatty acid composition of Holstein steers. These findings bring new insights into the fat-related carcass traits of beef cattle. In addition, the developed DNA makers will contribute to improved meat quality of beef.
The Use of Rate Enhancers in Supercritical Water Oxidation (1995)

The initiation of supercritical water oxidation was dramatically enhanced when small amounts of strong oxidizing agents, such as H2O2 and HNO3, were added to a simulated waste stream. Tests were performed in a 6.2 meter pipe reactor where oxidation was initiated by mixing the cold aqueous/organic feed with a hot supercritical water/oxidant stream. Without rate enhancers, an inlet mix temperature of 362 C resulted in the incomplete oxidation of isopropanol. When the feed contained 0.75, 1.5 and 3.0 wt% H2O2 oxidation was essentially completed at 5.1, 4.0 and 2.8 meters, respectively. When initiated at 380 C, without rate enhancers, isopropanol reacted completely in 5.6 meters. This length was reduced to ~ 2 meters when the feed contained 2.0 wt % HNO3.
On the application of embedded digit training to speaker independent connected digit recognition (1984)

In recent years, several algorithms have been proposed for recognizing a string of connected words (typically digits) by optimally piecing together reference patterns corresponding to the words in the string. Although the algorithms differ greatly in details of implementation, storage requirements, etc., they all have essentially the same performance in that their ability to match the unknown string is related to how well words spoken in isolation can match their counterparts in connected speech. For low rates of articulation (i.e., about 100-130 words per minute) the performance of such connected word recognition systems is excellent. However, as the articulation rate approaches that of continuous discourse (180-300 words per minute) the performance of such connected word recognizers falls dramatically. To partially alleviate these problems a modified training procedure was devised in which multiple versions of each reference word were used. The multiple versions included an isolated form for each word, and 2 versions of the word extracted from the middle of 3 word sequences. One of these embedded reference patterns represented a noncontextual token of the word (i.e., spoken in a format where the words on either side had minimal effect on the acoustic properties at the boundaries), and the second represented a highly contextual token of the word. It was shown that a training algorithm could be devised to obtain these embedded reference tokens, and that when using the multiple reference patterns, the performance in a speaker trained system was greatly improved at faster talking rates. In this paper we show how the embedded training technique can be extended to the case of speaker, independent connected word recognizers. In particular, we show that improved recognition performance on connected digit strings is obtained by using standard clustering procedures on the embedded tokens to give a speaker-independent embedded reference set. We also show that the use of the K-nearest neighbor (KNN) rule leads to additional real improvements in performance for recognizing strings of connected digits. A discussion of the types of problems that remain is given.
<title>Erasable Optical Liquid Crystal Disc Memory</title> (1983)

An erasable optical disc memory with smectic liquid crystal (LC) as the active medium has been fabricated and tested. Using appropriate dark field optics, we have demonstrated writing, reading and erasing at data rates of 13.5 MHz with a bit spacing of 1.25 microns. Although not all problems with this memory have been solved, we think the concept is viable with an expanded research effort in materials and system aspects.
Three-Dimensional Optical Coherence Tomography (2009)

Three-dimensional (3D) optical coherence tomography (OCT) is an advanced method of noninvasive infrared imaging of tissues in depth. Heretofore, commercial OCT systems for 3D imaging have been designed principally for external ophthalmological examination. As explained below, such systems have been based on a one-dimensional OCT principle, and in the operation of such a system, 3D imaging is accomplished partly by means of a combination of electronic scanning along the optical (Z) axis and mechanical scanning along the two axes (X and Y) orthogonal to the optical axis. In 3D OCT, 3D imaging involves a form of electronic scanning (without mechanical scanning) along all three axes. Consequently, the need for mechanical adjustment is minimal and the mechanism used to position the OCT probe can be correspondingly more compact. A 3D OCT system also includes a probe of improved design and utilizes advanced signal- processing techniques. Improvements in performance over prior OCT systems include finer resolution, greater speed, and greater depth of field.
High‐throughput screening of chemical exchange saturation transfer MR contrast agents (2010)

A new high-throughput MRI method for screening chemical exchange saturation transfer (CEST) agents is demonstrated, allowing simultaneous testing of multiple samples with minimal attention to sample configuration and shimming of the main magnetic field (B(0)). This approach, which is applicable to diamagnetic, paramagnetic and liposome CEST agents, employs a set of inexpensive glass or plastic capillary tubes containing CEST agents put together in a cheap plastic tube holder, without the need for liquid between the tubes to reduce magnetic susceptibility effects. In this setup, a reference image of direct water saturation spectra is acquired in order to map the absolute water frequency for each volume element (voxel) in the sample image, followed by an image of saturation transfer spectra to determine the CEST properties. Even though the field over the total sample is very inhomogeneous due to air-tube interfaces, the shape of the direct saturation spectra is not affected, allowing removal of susceptibility shift effects from the CEST data by using the absolute water frequencies from the reference map. As a result, quantitative information such as the mean CEST intensity for each sample can be extracted for multiple CEST agents at once. As an initial application, we demonstrate rapid screening of a library of 16 polypeptides for their CEST properties, but in principle the number of tubes is limited only by the available signal-noise-ratio, field of view and gradient strength for imaging.
Reactive evaporation of vanadium dioxide thin films (1985)

This invention relates generally to thin-film technology and more particularly to a method of producing high-quality vanadium dioxide (VO/sub 2/) thin films through a one-step reactive evaporation process. It is generally known that VO/sub 2/ is one of several transition metal oxides which show an abrupt change in certain physical properties such as electrical resistance at a temperature T/sub t/ (transition temperature). In VO/sub 2/, the transition is probably best described as a first-order semiconductor-to-metal transition accompanied by a lattice distortion with T/sub t/ = 68C. Because of this conveniently low transition temperature and large drop in near infrared transmittance experienced by such films, VO/sub 2/ has been used in thermal relays, electrical-switching elements, and optical-storage media.
The wheat <i>wcs120</i> gene family. A useful model to understand the molecular genetics of freezing tolerance in cereals (1997)

Winter, as compared with spring cereals, possess better acclimation mechanisms that allow them to overwinter and survive freezing temperatures. This difference is genetically programmed and involves a complex genetic system. To understand the nature of this system and its regulation by low temperature, genes associated with freezing tolerance in wheat ( Triticum aestivum L.) were identified and characterized. Among these, the wcs120 gene family encodes a group of proteins ranging in size from 12 to 200 kDa. As shown by biochemical, immunohistochemical, molecular and genetic analyses, this gene family is specific to the Poaceae, highly abundant and coordinately regulated by low temperature. Furthermore, accumulation of WCS protein is directly correlated with the development of freezing tolerance. These analyses also revealed a regulatory control of the vernalization process over low temperature gene expression in winter cereals. Recent studies suggest that the molecular mechanisms controlling the expression of these genes involve negative regulatory factors that are modulated by phosphorylation.
Transposon Mutagenesis in Mycobacteria Using Conditionally Replicating Mycobacteriophages (2003)

Genetic analyses of pathogenic mycobacteria such as Mycobacterium tubeculosis and Mycobacterium bovis required improvement of existing methodologies for the generation of large representative libraries of mutants. Two basic methodologies have been used to generate mutant libraries in both fast- and slow-growing mycobacteria: chemical mutagenesis and transposon mutagenesis. Chemical mutagenesis has successfully been used to produce different auxotrophic mutants in the fast growing mycobacteria Mycobacterium phlei (1,2) and Mycobacterium smegmatis (3,4). A detailed chemical mutagenesis protocol for the generation of mutant libraries in the fast-growing mycobacteria can be found in the previous volume of this manual (5). Chemical mutagenesis is not the ideal method for producing large representative mutant libraries for the slow-growing mycobacteria because: (1) the mutation frequency is relatively low,(2) multiple mutations may occur in the same cells,(3) clumping of the mycobacteria makes the identification and purification of the mutant clones very difficult,and (4) no generalized transducing phage has been described for the slow-growing mycobacteria to allow transfer of the point mutations and construction of isogenic strains.
Underspecified harnesses and interleaved bugs (2012)

Static assertion checking of open programs requires setting up a precise harness to capture the environment assumptions. For instance, a library may require a file handle to be properly initialized before it is passed into it. A harness is used to set up or specify the appropriate preconditions before invoking methods from the program. In the absence of a precise harness, even the most precise automated static checkers are bound to report numerous false alarms. This often limits the adoption of static assertion checking in the hands of a user. In this work, we explore the possibility of automatically filtering away (or prioritizing) warnings that result from imprecision in the harness. We limit our attention to the scenario when one is interested in finding bugs due to concurrency. We define a warning to be an interleaved bug when it manifests on an input for which no sequential interleaving produces a warning. As we argue in the paper, limiting a static analysis to only consider interleaved bugs greatly reduces false positives during static concurrency analysis in the presence of an imprecise harness. We formalize interleaved bugs as a differential analysis between the original program and its sequential version and provide various techniques for finding them. Our implementation CBugs demonstrates that the scheme of finding interleaved bugs can alleviate the need to construct precise harnesses while checking real-life concurrent programs.
SERS Nanotags as Novel Optical Reporters (2005)

An increasingly important set of tools for life scientists are reagents for multiplexing, the capability to simultaneously detect multiple biological species in the same sample volume at the same time. Optical detection tags are molecules (e.g. fluorescent molecules), or larger entities (e.g. nanoparticles) that are attached to a biological species, and exploit light to quantify the biological species’ presence and/or location. Optical detection tags, the newest of which are 60 years old, have been a central component of such seminal biological tools as the immunoassay, the microarray, and DNA sequencing, and they are omnipresent in the research lab and the clinical lab. For example, current tests for blood groups (ABO/Rh) involve separate tests for each blood type, and additional (separate) tests for pathogens such as syphilis, HIV, West Nile Virus, SARS, etc. Ideally, one would like to carry out all these measurements at once, in the same vial; however, this would take 10+ different tags that can be seen in a whole blood sample. Unfortunately, with existing optical tags, there are neither enough different types, nor are the existing types of the right “color” for whole blood assays. In short, life science bioassays, including diagnostic tests, increasingly require information-rich measurements, but rely on ancient, information-poor technologies.
High average power quasi-CW single-mode green and UV fiber lasers (2015)

Kilowatt-level narrow-linewidth SM ytterbium fiber laser operating in high-repetition-rate QCW regime was used to obtain 700 W average power at 532 nm with single-mode beam quality and wall-plug efficiency of over 23 %. To the best of our knowledge, this is ~60 % higher power than previously reported for single-mode green lasers based on other platforms, and also is ~30 % increase comparing to the previous result obtained by our group on the base of similar fiber laser platform. We have also experimentally proved that the same type of fiber laser can be used for generating of world-record levels of power at other wavelengths of visible and UV spectral ranges by employing cascaded non-linear frequency conversion. Thus, utilizing frequency tripling in 2 LBO crystals, we achieved over 160 W average power of nearly single-mode UV light at 355 nm with THG efficiency of more than 25 %. As far as we know, this is the highest output power ever reported for UV laser with nearly diffraction limited beam quality. We also conducted some preliminary experiments to demonstrate suitability of our approach for generating longer wavelengths of the visible spectrum. By pre-shifting fundamental emission wavelength in fiber Raman converter, followed by frequency doubling in NCPM LBO, we obtained average powers of 36 W at 589 nm and 27 W at 615 nm. These proof-of-concept experiments were performed with low-power pump laser and were not fully optimized with respect to frequency conversion. Our analysis indicates that employing kW-level QCW ytterbium laser with optimized SRS and SHG converters we can achieve hundreds of Watts of average power in red and orange color with single-mode beam quality.
Development of ozonated ultrapure water supplying system using direct-dissolving method (2002)

A new ozonated ultrapure water (O/sub 3/-UPW) supplying system has been established. In the new O/sub 3/-UPW supplying system, a direct dissolving method that can supply O/sub 3/-UPW to many separated points of use from a single unit has been employed. In this system, ozone-containing gas is directly introduced in ultrapure water (direct dissolving) and the water/gas mixture is transported to many points of use through a piping system. At each point of use, bubbles in water/gas mixture are separated and O/sub 3/-UPW without bubbles is supplied to the cleaning equipment. The concentration of dissolved ozone in water rapidly decreases because of self-decomposition. On the other hand ozone in the gas phase is more stable than in the water phase and ozone in the bubbles (gas phase) becomes dissolved in the water while transported through the piping system. As a result; O/sub 3/-UPW with the ozone concentration of higher than 5 ppm is supplied to the cleaning equipment that is installed at distant places as far as 100 m from ozone gas introducing point. We have provided the new system in one of the latest LCD fabrication plants, which is presently in operation.
A Double-sided Z-Impedance Compensated Inductive Power Transfer System (2021)

This paper proposes a highly symmetrical inductive power transfer (IPT) system based on double-sided Z-impedance compensation networks. The double-sided Z-impedance networks are designed with symmetrical configuration and could achieve load-independent CC output with zero-phase angle (ZPA) of input impedance. Compared to the conventional LCC circuit, the proposed Z-network can reduce current stresses on compensation components, which contributes to high-power applications. Meantime, compensation inductors are integrated with main coils to make the whole system compact and eliminate unwanted cross couplings. The proposed IPT system is validated by experiments and 2.3kW power could be transferred with 96.93% dc-dc efficiency across an air gap of 120mm.
Semi-Automatic 3-D Segmentation of Anatomical Structures of Brain MRI Volumes using Graph Cuts (2006)

We present a semi-automatic segmentation technique of the anatomical structures of the brain: cerebrum, cerebellum, and brain stem. The method uses graph cuts segmentation with an anatomic template for initialization. First, a skull stripping procedure is applied to remove non-brain tissues. Then, the segmentation is done hierarchically by first, extracting first the cerebrum from the brain, and then from the remaining volume the cerebellum and the brain stem are separated. This method is fast and can separate different anatomical structures of the brain in spite of weak boundaries. We describe our approach and present experimental results demonstrating its usefulness.
Une nouvelle série d'hydrures métalliques ferromagnétiques de type Nd2Fe14BHx(0<x<5) (1984)

A new family of hydrides of intermetallic compounds RE 2 Fe 14 BH x and RE 2 Co 14 BH x has been prepared by hydrogenation of the new magnetic materials of Neomax-type. An increase of magnetization and Curie point is observed in Nd 2 Fe 14 BH 5 Une nouvelle famille d'hydrures de composes intermetalliques Ln 2 Fe 14 BH x et Ln 2 Co 14 BH x a ete preparee par hydruration des nouveaux materiaux magnetiques de type Neomax. Une augmentation de l'aimantation et du point de Curie est observee dans Nd 2 Fe 14 BH 5
Biocatalytic synthesis of polymers. Synthesis of an optically active, epoxy‐substituted polyester by lipase‐catalyzed polymerization (1989)

Abstract The enantioselective polymerization of bis(2,2,2‐trichloroethyl) trans ‐3,4‐epoxyadipate with 1,4‐butanediol using the enzyme porcine pancreatic lipase as a catalyst is described. The polymerization was carried out at ambient temperature in anhydrous ethyl ether. End group analysis provided M N = 5,300 daltons, whereas GPC provided M w = 7,900 daltons for the polymer. The unchanged (+)‐enantiomer of the diester was shown to have an enantiomeric purity of > 95% by proton NMR in the presence of the chiral shift reagent Eu(hfc) 3 . The stereochemical purity of the (−)‐polymer was estimated at > 96% by consideration of the amount of the slower reacting enantiomer that could have been incorporated and still attain the observed degree of polymerization (25) when the starting ratio of racemic diester to diol was 2:1. Direct determination of the stereochemical purity of the polymer using Eu(hfc) 3 was unsuccessful. Similar studies on polymer having random stereochemical orientations of the epoxide showed that such polymers do not behave as if they are racemic in the presence of the shift reagent. The polymer required for the latter studies was prepared by epoxidation of the product from enzyme catalyzed polymerization of bis(2,2,2‐trichloroethyl) trans ‐3‐hexenedioate with 1,4‐butanediol.
An Investigation Into Three Visual Characteristics of Complex Scenes That Evoke Human Emotion (2017)

Prior computational studies have examined hundreds of visual characteristics related to color, texture, and composition in an attempt to predict human emotional responses. Beyond those myriad features examined in computer science, roundness, angularity, and visual complexity have also been found to evoke emotions in human perceivers, as demonstrated in psychological studies of facial expressions, dance poses, and even simple synthetic visual patterns. Capturing these characteristics algorithmically to incorporate in computational studies, however, has proven difficult. Here we expand the scope of previous computer vision work by examining these three visual characteristics in computer analysis of complex scenes, and compare the results to the hundreds of visual qualities previously examined. A large collection of ecologically valid stimuli (i.e., photos that humans regularly encounter on the web), named the EmoSet and containing more than 40,000 images crawled from web albums, was generated using crowdsourcing and subjected to human subject emotion ratings. We developed computational methods to the separate indices of roundness, angularity, and complexity, thereby establishing three new computational constructs. Critically, these three new physically interpretable visual constructs achieve comparable classification accuracy to the hundreds of shape, texture, composition, and facial feature characteristics previously examined. In addition, our experimental results show that color features related most strongly with the positivity of perceived emotions, the texture features related more to calmness or excitement, and roundness, angularity, and simplicity related similarly with both of these emotions dimensions.