gebhart/patrepeval huggingface dataset:
Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions: Synthesis, Biological Evaluation, and Protein–Ligand X-ray Studies (2015)

Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand-binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f, 25i, and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolution X-ray structures of 25f- and 25g-bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand-binding site interactions are possibly responsible for their potent activity.
Electrodeposition of Refractory Carbide Coatings. (1982)

A novel method for electrodepositing refractory carbide coatings from molten salts is described. It consists of the simultaneous reduction of the appropriate metal species dissolved in the ternary LiF-NaF-KF eutectic and carbonate dissolved in the same melt. The metal and carbon deposit on the cathode where they react to form the carbide. The coatings are hard, abrasion resistant, and resist oxidation in air to 500 C. Carbides of tantalum and tungsten have been plated so far, and the method is applicable to other carbides as well.
Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow (2017)

Bone tissue harbors unique and essential physiological processes, such as hematopoiesis, bone growth, and bone remodeling. To enable visualization of these processes at the cellular level in an intact environment, we developed "Bone CLARITY," a bone tissue clearing method. We used Bone CLARITY and a custom-built light-sheet fluorescence microscope to detect the endogenous fluorescence of Sox9-tdTomato<sup>+</sup> osteoprogenitor cells in the tibia, femur, and vertebral column of adult transgenic mice. To obtain a complete distribution map of these osteoprogenitor cells, we developed a computational pipeline that semiautomatically detects individual Sox9-tdTomato<sup>+</sup> cells in their native three-dimensional environment. Our computational method counted all labeled osteoprogenitor cells without relying on sampling techniques and displayed increased precision when compared with traditional stereology techniques for estimating the total number of these rare cells. We demonstrate the value of the clearing-imaging pipeline by quantifying changes in the population of Sox9-tdTomato-labeled osteoprogenitor cells after sclerostin antibody treatment. Bone tissue clearing is able to provide fast and comprehensive visualization of biological processes in intact bone tissue.
Whispering Gallery Resonators for Studying Orbital Angular Momentum of a Photon (2005)

We propose a simple method for generation and detection of photons with nonzero angular momentum. The method utilizes high-quality factor ring resonators that transform a plane electromagnetic wave into a wave with nonzero angular momentum, and vice versa. We show that the method is especially promising for studying high-order Bessel beams, unreachable by other techniques.
Multipath resistant coherent timing error detector for DS-CDMA applications (2002)

A new coherent timing error detector (TED) for timing/code tracking loops used inside RAKE receivers in CDMA systems is presented. In contrast to the conventional TED it is well suited for the case of multipath propagation channels. In order to accomplish this task a compensation term is introduced inside the tracking loop directly behind the conventional TED. This compensation term is calculated using the knowledge on the relative delays of all paths and their respective channel coefficients. A compensation scheme like the one described here becomes necessary whenever closely spaced paths have to be tracked. This fact makes this algorithm a favorable candidate for indoor scenarios where individual paths can be spaced even more closely than one chip. The performance of the presented scheme is assessed by means of simulation.
Magnetron sputtered boron films and Ti/B multilayer structures (1990)

Boron and Ti/B films have been magnetron sputter deposited and characterized using x-ray diffraction, Auger-depth profiling, and electron microscopy. The amorphous boron films contain no morphological growth features, unlike those characteristically found in thin films prepared by various plasma vapor deposition processes. The use of a high-density boron sputter target prepared by hot isostatic pressing was a major factor in controlling the deposition process. Consequently, the radio frequency sputter deposited boron proves feasible for ultrathin band pass filters as well as the low Z element in high Z/low Z mirrors which enhance reflectivity from grazing to normal incidence.
Novel BVDV-2 mutants as new candidates for modified-live vaccines (2009)

Protection against Bovine viral diarrhea virus (BVDV) type 2 infection of commercially available vaccines is often limited due to marked genetic and antigenic differences between BVDV types 1 (BVDV-1) and 2 (BVDV-2). Therefore, the immunogenicity of selected BVDV-1 and BVDV-2 mutants derived from infectious full-length cDNA clones and their use as modified-live vaccine candidates against challenge infection with a virulent heterologous BVDV-2 field isolate were investigated. Deletion mutants of BVDV-1 and BVDV-2 lacking a part of the N(pro) gene (BVDV-1DeltaN(pro)/BVDV-2DeltaN(pro)) were used as well as a packaged replicon with a deletion in the structural core protein encoding region (BVDV-2DeltaC-pseudovirions). The 25 calves used in this vaccination/challenge trial were allocated in five groups (n=5/group). One group received BVDV-1DeltaN(pro) (1 shot), one group BVDV-2DeltaN(pro) (1 shot), one group received both, BVDV-1DeltaN(pro) and BVDV-2DeltaN(pro) (1 shot), and one group was immunised with the BVDV-2DeltaC-pseudovirions (2 shots). The fifth group served as non-vaccinated control group. All groups were challenged intranasally with the BVDV-2 strain HI916 and monitored for signs of clinical disease, virus shedding and viremia. All tested BVDV vaccine candidates markedly reduced the outcome of the heterologous virulent BVDV-2 challenge infection showing graduated protective effects. The BVDV-2DeltaN(pro) mutant was able to induce complete protection and a "sterile immunity" upon challenge. Thus it represents a promising candidate for an efficacious future live vaccine.
An integrating structure of EMI filter based on interleaved flexible multi-layer (FML) foils (2009)

A novel integrated EMI filter structure is proposed in this paper, based on FML foils. It integrates common mode inductors and differential mode capacitors and inductors into a single unit. A novel interleaved flexible multi-layer (FML) foil structure is proposed to overcome the difficulty of enlarging the DM capacitance. A prototype is constructed based on this concept and was put into a front-end converter to replace a discrete EMI filter. Testing result presented.
Plenoptic rendering with interactive performance using GPUs (2012)

Processing and rendering of plenoptic camera data requires significant computational power and memory bandwidth. At the same time, real-time rendering performance is highly desirable so that users can interactively explore the infinite variety of images that can be rendered from a single plenoptic image. In this paper we describe a GPU-based approach for lightfield processing and rendering, with which we are able to achieve interactive performance for focused plenoptic rendering tasks such as refocusing and novel-view generation. We present a progression of rendering approaches for focused plenoptic camera data and analyze their performance on popular GPU-based systems. Our analyses are validated with experimental results on commercially available GPU hardware. Even for complicated rendering algorithms, we are able to render 39Mpixel plenoptic data to 2Mpixel images with frame rates in excess of 500 frames per second.
Detection of Bacteremia in Emergency Department Patients at Risk for Infective Endocarditis Using Universal 16S rRNA Primers in a Decontaminated Polymerase Chain Reaction Assay (2002)

Prompt definitive diagnosis of acute bacterial endocarditis in febrile injection drug users (IDUs) remains problematic because of delays associated with blood culture. Rapid detection of bacteremia by polymerase chain reaction (PCR) by use of "universal" primers has been hampered by background bacterial contamination. Broad-range eubacterial primers selected from the 16S rRNA gene were used in a PCR assay coupled with a simple pre-PCR decontamination step. All PCR reagents were pretreated with the restriction enzyme AluI, which has multiple digestion sites in the amplicon but none in the primer sets. When 4 different bacterial species were spiked into healthy human blood specimens, the assay identified each pathogen with an analytic sensitivity of 5 bacteria/PCR reaction. A clinical trial with 51 febrile IDUs revealed that PCR had a sensitivity and specificity of 86.7% and 86.9%, respectively, versus blood culture. Importantly, all (8/8) patients with blood culture-positive infective endocarditis were determined to be positive by PCR. This assay provides a promising diagnostic for rapid identification of bacteremia, particularly valuable in acute care settings.
Immunoproteomics of <i>Aspergillus</i> for the development of biomarkers and immunotherapies (2016)

Filamentous fungi of the genus Aspergillus play significant roles as pathogens causing superficial and invasive infections as well as allergic reactions in humans. Particularly invasive mycoses caused by Aspergillus species are characterized by high mortality rates due to difficult diagnosis and insufficient antifungal therapy. The application of immunoproteomic approaches has a great potential to identify new targets for the diagnosis, therapy, and vaccine development of diseases caused by Aspergillus species. Serological proteome analyses (SERPA) that combine 2D electrophoresis with Western blotting are still one of the most popular techniques for the identification of antigenic proteins. However, recently a growing number of approaches have been developed to identify proteins, which either provoke an antibody response or which represent targets of T-cell immunity in patients with allergy or fungal infections. Here, we review advances in the studies of immune responses against pathogenic Aspergilli as well as the current status of diagnosis and immunotherapy of Aspergillus infections.
A direct manipulation interface for boolean information retrieval via natural language query (1989)

This paper describes the design of a direct manipulation user interface for Boolean information retrieval. Intended to overcome the difficulties of manipulating explicit Boolean queries as well as the “black box” drawbacks of so-called natural language query systems, the interface presents a two-dimensional graphical representation of a user's natural language query which not only exposes heuristic query transformations performed by the system, but also supports query reformulation by the user via direct manipulation of the representation. The paper illustrates the operation of the interface as implemented in the AI-STARS full-text information retrieval system.
A comparison of on-demand and table driven routing for ad-hoc wireless networks (2002)

We introduce WRP-Lite, which is a table-driven routing protocol that uses non-optimal routes, and compare its performance with the performance of the dynamic source routing (DSR) protocol, which is an on-demand routing protocol for wireless ad-hoc networks. We evaluate the performance of WRP-Lite and DSR for varying degree of mobility and traffic in a 20-node network. The performance parameters are end-to-end delay, control overhead, percentage of packets delivered, and hop distribution. We show that WRP-Lite has much better delay and hop performance while having comparable overhead to DSR.
A low recombination rate indolizine sensitizer for dye-sensitized solar cells (2016)

A sensitizer incorporating a heavily alkylated surface blocking indolizine donor exhibits excellent light absorption and diminished recombination rates in dye-sensitized solar cells (DSCs). DSC device efficiencies (up to 8%) using either I(-)/I3(-) or Co(bpy)3(2+/3+) redox shuttles were obtained, which compare favourably to the known excellent surface coverage co-sensitization dye, .
Synthesis and enzymatic evaluation of 2- and 4-aminothiazole-based inhibitors of neuronal nitric oxide synthase (2009)

Highly potent and selective inhibitors of neuronal nitric oxide synthase (nNOS) possessing a 2-aminopyridine group were recently designed and synthesized in our laboratory and were shown to have significant in vivo efficacy. In this work, analogs of our lead compound possessing 2- and 4-aminothiazole rings in place of the aminopyridine were synthesized. The less basic aminothiazole rings will be less protonated at physiological pH than the aminopyridine ring, and so the molecule will carry a lower net charge. This could lead to an increased ability to cross the blood-brain barrier thereby increasing the in vivo potency of these compounds. The 2-aminothiazole-based compound was less potent than the 2-aminopyridine-based analogue. 4-Aminothiazoles were unstable in water, undergoing tautomerization and hydrolysis to give inactive thiazolones.
Hepatic Progenitors and Strategies for Liver Cell Therapies (2001)

Liver cell therapies, including liver cell transplantation and bioartificial livers, are being developed as alternatives to whole liver transplantation for some patients with severe liver dysfunction. Hepatic progenitors are proposed as ideal cells for use in these liver cell therapies given their ability to expand extensively, differentiate into all mature liver cells, have minimal immunogenicity, be cryopreservable, and reconstitute liver tissue when transplanted. We summarize our ongoing efforts to develop clinical programs of hepatic progenitor cell therapies with a focus on hepatic stem cell biology and strategies that have emerged in analyzing that biology.
Multi‐shot diffusion‐weighted MRI reconstruction with magnitude‐based spatial‐angular locally low‐rank regularization (SPA‐LLR) (2019)

A joint reconstruction method with spatial-angular LLR regularization on magnitude images substantially improves multi-direction DWI reconstruction, simultaneously removes motion-induced phase artifacts, and denoises images.
Stationary chest tomosynthesis using a carbon nanotube x-ray source array: a feasibility study (2014)

Chest tomosynthesis is a low-dose, quasi-3D imaging modality that has been demonstrated to improve the detection sensitivity for small lung nodules, compared to 2D chest radiography. The purpose of this study is to investigate the feasibility and system requirements of stationary chest tomosynthesis (s-DCT) using a spatially distributed carbon nanotube (CNT) x-ray source array, where the projection images are collected by electronically activating individual x-ray focal spots in the source array without mechanical motion of the x-ray source, detector, or the patient. A bench-top system was constructed using an existing CNT field emission source array and a flat panel detector. The tube output, beam quality, focal spot size, system in-plane and in-depth resolution were characterized. Tomosynthesis slices of an anthropomorphic chest phantom were reconstructed for image quality assessment. All 75 CNT sources in the source array were shown to operate reliably at 80 kVp and 5 mA tube current. Source-to-source consistency in the tube current and focal spot size was observed. The incident air kerma reading per mAs was measured as 74.47 uGy mAs(-1) at 100 cm. The first half value layer of the beam was 3 mm aluminum. An average focal spot size of 2.5 × 0.5 mm was measured. The system MTF was measured to be 1.7 cycles mm(-1) along the scanning direction, and 3.4 cycles mm(-1) perpendicular to the scanning direction. As the angular coverage of 11.6°-34°, the full width at half maximum of the artifact spread function improved greatly from 9.5 to 5.2 mm. The reconstructed tomosynthesis slices clearly show airways and pulmonary vascular structures in the anthropomorphic lung phantom. The results show the CNT source array is capable of generating sufficient dose for chest tomosynthesis imaging. The results obtained so far suggest an s-DCT using a distributed CNT x-ray source array is feasible.
A cell culture system for screening human serum for ability to promote cellular cholesterol efflux. Relations between serum components and efflux, esterification, and transfer. (1994)

A cell culture system was employed to test a large number of samples of human serum for the ability to stimulate the efflux of cell cholesterol. The extent of efflux obtained with each specimen was correlated with the serum concentrations of cholesterol, triglycerides, apoprotein (apo) B, apo A-I, apo A-II, and lipoprotein subfractions (ie, high-density lipoprotein2 [HDL2], HDL3, lipoprotein [Lp] A-I, and LpA-I:A-II). In addition, the subsequent esterification of the released cholesterol and the distribution of the synthesized exogenous cholesteryl esters between HDL and low-density lipoprotein/very-low-density lipoprotein provided estimates of the lecithin:cholesterol acyltransferase (LCAT) and cholesteryl ester transfer protein (CETP) activities of each serum. The values for these activities were analyzed for correlations with cell efflux and the various serum parameters. Cell cholesterol efflux best correlated with serum total HDL cholesterol values. HDL2 and HDL3 correlated about equally well with efflux, whereas LpA-I demonstrated a much greater association with efflux than did LpA-I:A-II. Analysis of the data by partial correlation analysis indicated that HDL3 and LpA-I were the HDL subfractions most closely associated with efflux. Esterification of the released radiolabeled cholesterol was strongly and positively correlated with serum triglyceride concentrations and negatively related to the serum concentrations of HDL2. There was no relation between esterification values, which reflect LCAT activity, and efflux. The transfer of the labeled cholesteryl esters between HDL and apoB-containing lipoproteins was used as a measure of CETP activity and demonstrated a pattern in which all apoB-related parameters were positively correlated to transfer of esterified cholesterol, and all HDL associated parameters, particularly HDL3, were negatively related to transfer. No relations were observed between efflux, esterification, and transfer.
Metallurgical Design and Development of High Deformable X100 Line Pipe Steels Suitable for Strain-Based Design (2008)

The demand for natural gas using pipelines and LNG to supply the world gas markets is increasing substituting for oil and coal. The use of high strength line pipe steels provides the reduction of cost of gas transmission pipelines by enabling high-pressure transmission of large volumes of gas. In particular, high strength line pipe materials with a yield strength of X80 or higher have been developed over the last few decades around the world. Long distance gas transmission pipelines from remote areas sometimes pass through discontinuous permafrost, and are subject to ground movements by repeated thaw subsidence and frost heave. In this case, strain-based design has been applied as well as stress-based design. Therefore, high deformable line pipe is required for strain-based design in order to prevent the pipeline from fracturing. Nippon steel has also developed high deformable high strength line pipe material suitable for strain-based design. In recent years, demand for high strength line pipe steels has emerged in which the molybdenum content is reduced because of the high cost of molybdenum. Conventionally, high strength line pipe steel with Mo addition has been developed in order to control the microstructure and to obtain pipe properties such as strength and low temperature toughness. This paper describes the metallurgical design and development of high deformable high strength X100 line pipe with lower Mo content suitable for strain-based design. High deformable X100 line pipe with 16 mm wall thickness as well as good low temperature toughness and seam weld toughness has been developed.
HelpingHand (2012)

Digital painters commonly use a tablet and stylus to drive software like Adobe Photoshop. A high quality stylus with 6 degrees of freedom (DOFs: 2D position, pressure, 2D tilt, and 1D rotation) coupled to a virtual brush simulation engine allows skilled users to produce expressive strokes in their own style. However, such devices are difficult for novices to control, and many people draw with less expensive (lower DOF) input devices. This paper presents a data-driven approach for synthesizing the 6D hand gesture data for users of low-quality input devices. Offline, we collect a library of strokes with 6D data created by trained artists. Online, given a query stroke as a series of 2D positions, we synthesize the 4D hand pose data at each sample based on samples from the library that locally match the query. This framework optionally can also modify the stroke trajectory to match characteristic shapes in the style of the library. Our algorithm outputs a 6D trajectory that can be fed into any virtual brush stroke engine to make expressive strokes for novices or users of limited hardware.
New high-rate automated deposition system for the manufacture of complex multilayer coatings - II. Process control (1997)

In a companion paper, a new fully automated, high rate, deposition system for the fabrication of complex optical coatings was described. In order for this system to accurately deposit complex filters, several conditions have to be met. First, it is important that the deposited films exhibit low absorption and low scatter and have bulk-like reproducible refractive indices. Second, for the accurate optical monitoring of the layer thicknesses, it is critical that the deposited films are homogeneous, have well-defined interfaces and that the refractive indices of the thin film materials are accurately known. In this paper, we will discuss various process control techniques that are necessary to ensure the deposition of high quality SiO 2 and Nb 2 O 5 films so that complex filters based on these materials can be accurately fabricated.
Phenothiazine photosensitizers for onium salt photoinitiated cationic polymerization (2001)

Abstract Phenothiazine compounds bearing a wide range of different substituents are excellent photosensitizers for onium salt cationic photoinitiators. These photosensitizers are generally operative in the mid‐ and long‐range regions of the UV spectrum and are especially useful for enhancing the rate of photoinitiated cationic polymerization carried out utilizing both filtered and broadband UV emission sources. In this article, the syntheses of several different substituted phenothiazines are described and the ability of these compounds to photosensitize the photolysis of different onium salt photoinitiators is evaluated. Attempts were made to correlate the structure and spectral characteristics of the phenothiazines with their efficiency of photosensitization in the cationic photopolymerizations of several typical epoxide and vinyl ether monomers. © 2001 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 39: 1187–1197, 2001