gebhart/patrepeval huggingface dataset:
Simultaneous high crystallinity and sub-bandgap optical absorptance in hyperdoped black silicon using nanosecond laser annealing (2015)

Hyperdoped black silicon fabricated with femtosecond laser irradiation has attracted interest for applications in infrared photodetectors and intermediate band photovoltaics due to its sub-bandgap optical absorptance and light-trapping surface. However, hyperdoped black silicon typically has an amorphous and polyphasic polycrystalline surface that can interfere with carrier transport, electrical rectification, and intermediate band formation. Past studies have used thermal annealing to obtain high crystallinity in hyperdoped black silicon, but thermal annealing causes a deactivation of the sub-bandgap optical absorptance. In this study, nanosecond laser annealing is used to obtain high crystallinity and remove pressure-induced phases in hyperdoped black silicon while maintaining high sub-bandgap optical absorptance and a light-trapping surface morphology. Furthermore, it is shown that nanosecond laser annealing reactivates the sub-bandgap optical absorptance of hyperdoped black silicon after deactivation by thermal annealing. Thermal annealing and nanosecond laser annealing can be combined in sequence to fabricate hyperdoped black silicon that simultaneously shows high crystallinity, high above-bandgap and sub-bandgap absorptance, and a rectifying electrical homojunction. Such nanosecond laser annealing could potentially be applied to non-equilibrium material systems beyond hyperdoped black silicon.
Narrow-Band WGM Optical Filters With Tunable FSRs (2007)

Optical resonators of the whispering-gallery-mode (WGM) type featuring DC-tunable free spectral ranges (FSRs) have been demonstrated. By making the FSR tunable, one makes it possible to adjust, during operation, the frequency of a microwave signal generated by an optoelectronic oscillator in which an WGM optical resonator is utilized as a narrow-band filter.
Mirtazapine is effective in the prophylactic treatment of chronic tension-type headache (2004)

Mirtazapine reduced AUC by 34% more than placebo in difficult-to-treat patients. This finding is clinically relevant and may stimulate the development of prophylactic treatments with increased efficacy and fewer side effects for tension-type headache and other types of chronic pain.
Maintaining and evolving GUI-directed test scripts (2009)

Since manual black-box testing of GUI-based applications (GAPs) is tedious and laborious, test engineers create test scripts to automate the testing process. These test scripts interact with GAPs by performing actions on their GUI objects. An extra effort that test engineers put in writing test scripts is paid off when these scripts are run repeatedly. Unfortunately, releasing new versions of GAPs with modified GUIs breaks their corresponding test scripts thereby obliterating benefits of test automation. We offer a novel approach for maintaining and evolving test scripts so that they can test new versions of their respective GAPs. We built a tool to implement our approach, and we conducted a case study with forty five professional programmers and test engineers to evaluate this tool. The results show with strong statistical significance that users find more failures and report fewer false positives (p < 0.02) in test scripts with our tool than with a flagship industry product and a baseline manual approach. Our tool is lightweight and it takes less than eight seconds to analyze approximately 1KLOC of test scripts.
BIST-based diagnosis of FPGA interconnect (2003)

We present a Built-In Self-Test (BIST)-based diagnostic approach for the programmable interconnect resources in Field Programmable Gate Arrays (FPGAs) that can be used for either on-line or off-line testing. The technique was originally intended for on-line diagnosis of faulty interconnect to support fault-tolerant applications. However, the technique has been proven to be an excellent approach for off-line testing and diagnosis as well, providing high-resolution diagnostics with the ability to identify the faulty wire segment or programmable switch. We have implemented this BIST-based diagnostic approach on the ORCA series FPGA and present the results of testing and diagnosing known defective FPGAs.
Wafer-Level packaging technology for optical sensor devices (2017)

Many optical sensors require a packaging that admits light from a defined range of angles, and blocks light from any unwanted sources (e.g., stray light from screen backlighting). To have a narrow angle range on the sensor (filter), but a wide detection range, a preferred solution is to have an aperture and diffuser integrated into the package. In this work, a film-assisted molding process is developed to produce the desired optical packages (including aperture and optional diffuser) for optical sensors on wafer-level. The wafer-level economics would mean that the resulting packages are very small and cheap.
Polyvalent Alphaherpesvirus vectors in veterinary vaccine research. (2010)

Viruses belonging to the Herpesviridae family are widely distributed in animals of economic importance and are associated with many diseases and infection sequelae. Herpesvirus infections of production animals are of particular importance due to the economic losses incurred by industry and associated animal health and welfare issues. To combat herpesvirus associated disease in important production animals, the use of vaccination is widely applied. To further enhance vaccine efficiency, concerted efforts to develop vaccination systems that provide optimal safety profiles while providing protective immunological responses is an area of intense study. While much of this research has focused on conventional approaches such as the inactivation or attenuation of viruses, an additional avenue of research being explored is the generation of novel viral vector systems that can deliver antigens from both viral and bacterial pathogens in multi-valent viral vector systems. This paper summarises the current development of several species-specific Alpha-herpesvirinae derived vector platforms for use as multi-valent live viral vaccines against pathogens affecting the horse, swine, poultry and cattle industries.
Selection and initial characterization of novel peptide ligands that bind specifically to human blood outgrowth endothelial cells (2007)

Using phage display technology, we have isolated 12-mer peptide ligands that bind to human blood outgrowth endothelial cells (HBOEC). To avoid non-specific binding we apply negative-positive selection approach by pre-incubating the library with non-HBOEC. The selected phage clones bind to their target cell population with high recovery. Moreover, the isolated clones display outstanding cell specificity as no significant binding is observed on a panel of other cell types. We anticipate the findings from this work to be exploited in the development of future cell-based therapeutic revascularization approaches to ischemic disease and endothelial injury or in combination with biomedical devices.
Surface active buffered hydrogen fluoride having excellent wettability for ULSI processing (1990)

By incorporating selected hydrocarbon surfactants, a surface-active BHF (buffered hydrogen fluoride) has been tailored to achieve the following requirements: (1) the same etch rate as that of conventional BHF; (2) low contact angle; (3) nonsegregation; (4) nonfoaming; (5) low particulate count; (6) few impurities (possibility of purification); (7) low particulate adhesion on the wafer surface; (8) no surface residues; (9) excellent surface smoothness; and (10) high SiO/sub 2//Si etching selectivity. In order to satisfy these requirements, surfactants must satisfy the following characteristics: (1) good solubility in BHF; (2) hydrophilic property at the wafer surface, (3) nondecomposition in BHF; (4) nonreaction with BHF; and (5) sufficient lowering of contact angle at the critical micelle concentration (CMC). Aliphatic amines satisfy these requirements but have foaming problems. The requirements have been achieved using a binary surfactant system consisting of a combination of aliphatic amine and aliphatic alcohol or aliphatic acid.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Sequencing of Argentinated Peptides by Means of Matrix-Assisted Laser Desorption/Ionization Tandem Mass Spectrometry (2002)

Argentinated peptide ions are formed in abundance under matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) conditions in the presence of Ag+ ions. These argentinated peptide ions are fragmented facilely under MALDI-MS/MS conditions to yield [b(n) + OH + Ag]+, [b(n) - H + Ag]+ and [a(n) - H + Ag]+ ions that are indicative of the C-terminal sequence. These observations parallel those made earlier under electrospray MS conditions (Chu, I. K; Guo, X.; Lau, T.-C.; Siu, K W. M. Anal. Chem. 1999, 71, 2364-2372). A mixed protonated and argentinated tryptic peptide map was generated from 37 fmol of bovine serum albumin (BSA) using MALDI-MS. MALDI-MS/MS data from four argentinated peptides at a protein amount of 350 fmol unambiguously identified the protein as BSA. Sequence-tag analysis of two argentinated tryptic peptides was used to identify unambiguously myocyte enhancer factor 2A, which had been recombinantly expressed in a bacterial cell line.
Recombinant prostate specific antigen inhibits angiogenesis in vitro and in vivo (2003)

Purified recombinant PSA inhibits angiogenesis, proving the concept that PSA is an anti-angiogenic, and serine protease activity, as determined by synthetic substrate hydrolysis, is distinct from the anti-angiogenic properties of PSA.
Structure–Activity Relationships of GHRP-6 Azapeptide Ligands of the CD36 Scavenger Receptor by Solid-Phase Submonomer Azapeptide Synthesis (2011)

The cluster of differentiation 36 (CD36) class B scavenger receptor binds a variety of biologically endogenous ligands in addition to synthetic peptides (i.e., growth hormone-releasing peptides, GHRPs), which modulate biological function related to anti-angiogenic and anti-atherosclerotic activities. Affinity labeling had previously shown that GHRP-6 analogues such as hexarelin, [2-Me-W(2)]GHRP-6 (1), bind to the lysine-rich domain of the CD36 receptor. Moreover, the azapeptide analogue [aza-F(4)]GHRP-6, 2, exhibited a characteristic β-turn conformation as described by CD and NMR spectroscopy and a slightly higher CD36 binding affinity relative to hexarelin (1.34 and 2.37 μM, respectively), suggesting receptor binding was mediated by the conformation and the aromatic residues of these peptide sequences. Ligand-receptor binding interactions were thus explored using azapeptides to examine influences of side-chain diversity and backbone conformation. In particular, considering that aromatic cation interactions may contribute to binding affinity, we have explored the potential of introducing salt bridges to furnish GHRP-6 azapeptide ligands of the CD36 receptor. Fifteen aza-glutamic acid analogues related to 2 were prepared by submonomer solid-phase synthesis. The azapeptide side chains were installed by novel approaches featuring alkylation of resin-bound semicarbazone with Michael acceptors and activated allylic acetates in the presence of phosphazene base (BTPP). Moreover, certain Michael adducts underwent intramolecular cyclization during semicarbazone deprotection, leading to novel pyrrazoline and aza-pyroglutamate N-terminal residues. Structural studies indicated that contingent on sequence the [aza-Glu]GHRP-6 analogues exhibited CD spectra characteristic of random coil, polyproline type II and β-turn secondary structures in aqueous media. In covalent competition binding studies with the GHRP-6 prototype hexarelin bearing a radiotracer, certain [aza-Glu]GHRP-6 azapeptides retained relatively high (2-27 μM) affinity for the CD36 scavenger receptor.
Molecular and Biological Properties of an Immunopotentiating Complex Polysaccharide Adjuvant Produced by a Gliding Bacterium. (1985)

A species of the gliding bacteria Cytophaga produces an exopolymer, designated GBA, that potentiates immune reactions. We showed previously that GBA augments primary immune responses in vitro, causes B lymphocytes to proliferate and secrete immunoglobulin, and induces macrophages to secrete Interleukin 1. GBA is prepared from culture supernatants of Cytophaga. Chemical analysis of these molecules indicates that they are large particulate polymers of amino sugars. In the period covered by this report we examined GBA for additional immunomodulatory activities. We found that GBA stimulates cultured human peripheral blood cells to secrete tumor necrotizing factor alpha and that GBA augments endogenous colony forming the pre-B cell line WEHI 231. We also found that GBA augments endogenous colony forming units in radiation-treatment mice and that it protects mice from otherwise lethal infectious doses of selected strains of E. coli. Other experiments showed that GBA is an immunological adjuvant in vivo. Primary humoral responses of mice immunized with protein antigens in combination with GBA were significantly higher than those of mice immunized with antigen alone. Moreover preliminary experiments showed that GBA augments antigen-specific immunological memory. Keywords: Cytophaga; Immunoenhancing; Radiation; Protection; Infection; ELISA (Enzyme Linked Immunosorbent Assay).
Characterization of the Oxidase Activity in Mammalian Catalase (2005)

Catalase is a highly conserved heme-containing antioxidant enzyme known for its ability to degrade hydrogen peroxide into water and oxygen. In low concentrations of hydrogen peroxide, the enzyme also exhibits peroxidase activity. We report that mammalian catalase also possesses oxidase activity. This activity, which is detected in purified catalases, cell lysates, and intact cells, requires oxygen and utilizes electron donor substrates in the absence of hydrogen peroxide or any added cofactors. Using purified bovine catalase and 10-acetyl-3,7-dihydroxyphenoxazine as the substrate, the oxidase activity was found to be temperature-dependent and displays a pH optimum of 7-9. The Km for the substrate is 2.4 x 10(-4) m, and Vmax is 4.7 x 10(-5) m/s. Endogenous substrates, including the tryptophan precursor indole, the neurotransmitter precursor beta-phenylethylamine, and a variety of peroxidase and laccase substrates, as well as carcinogenic benzidines, were found to be oxidized by catalase or to inhibit this activity. Several dietary plant micronutrients that inhibit carcinogenesis, including indole-3-carbinol, indole-3-carboxaldehyde, ferulic acid, vanillic acid, and epigallocatechin-3-gallate, were effective inhibitors of the activity of catalase oxidase. Difference spectroscopy revealed that catalase oxidase/substrate interactions involve the heme-iron; the resulting spectra show time-dependent decreases in the ferric heme of the enzyme with corresponding increases in the formation of an oxyferryl intermediate, potentially reflecting a compound II-like intermediate. These data suggest a mechanism of oxidase activity involving the formation of an oxygen-bound, substrate-facilitated reductive intermediate. Our results describe a novel function for catalase potentially important in metabolism of endogenous substrates and in the action of carcinogens and chemopreventative agents.
Organic semiconductor laser (1997)

Summary form only given. Lasing action has been demonstrated in a vacuum-deposited 3000 /spl Aring/ thick layer of tris-(8-hydroxyquinoline)aluminum (Alq/sub 3/) doped with DCM laser dye. We observed a remarkably low lasing threshold at a pump energy density of 1 /spl mu/J/cm/sup 2/ with a 500 psec excitation pulse. Initial lifetime measurements showed an extremely high photochemical stability of the laser material. The low lasing threshold and high stability are primarily due to an excitation method in which pump light is absorbed by the host material (Alq/sub 3/), and the light emitting DCM molecules are excited by means of an efficient non-radiative energy transfer from the Alq/sub 3/ molecules. We also found that the facets of vacuum-deposited films are optically smooth, providing enough reflection for feedback. Hence, no processing of the material is necessary to fabricate a good optical cavity.
Ultrafast Light and Electrons: Imaging the Invisible (2016)

The concept of the camera obscura as perceived a 1000 years ago by Alhazen (Ibn al-Haytham), who coined the term and experimented with the light rays (see Sec. 3.1). Note the formation of the inverted image through a ray diagram. Adapted from Al-Hassani et al. [1] Chapter 3 Ultrafast Light and Electrons: Imaging the Invisible
Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure–Activity Studies, Biological and X-ray Structural Analysis (2018)

The design, synthesis, and biological evaluation of a new class of HIV-1 protease inhibitors containing stereochemically defined fused tricyclic polyethers as the P2 ligands and a variety of sulfonamide derivatives as the P2' ligands are described. A number of ring sizes and various substituent effects were investigated to enhance the ligand-backbone interactions in the protease active site. Inhibitors 5c and 5d containing this unprecedented fused 6-5-5 ring system as the P2 ligand, an aminobenzothiazole as the P2' ligand, and a difluorophenylmethyl as the P1 ligand exhibited exceptional enzyme inhibitory potency and maintained excellent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The umbrella-like P2 ligand for these inhibitors has been synthesized efficiently in an optically active form using a Pauson-Khand cyclization reaction as the key step. The racemic alcohols were resolved efficiently using a lipase catalyzed enzymatic resolution. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insight into the binding properties of these new inhibitors.
Compressive spectral polarization imaging (2014)

We present a compressive spectral polarization imager driven by a rotating prism and a colored detector with a micropolarizer array. The prism which shears the scene along one spatial axis according to its wavelength components is successively rotated to different angles as measurement shots are taken. With 0°, 45°, 90°, 135° linear micropolarizers randomly distributed, the micropolarizer array is matched to the detector thus the the first three Stokes parameters of the scene are compressively sensed. The four dimensional (4D) data cube is thus projected onto the two dimensional (2D) FPA. Multiple snapshots are obtained for scenes with detailed spatial and spectral content. The 4D spectral-polarization data cube is reconstructed from the 2D measurements via nonlinear optimization with sparsity constraints. Polarization state planes (degree of linear polarization and angle of polarization) for each spectral slice of the hypercube are presented.
Protective and heart-crossreactive epitopes located within the NH2 terminus of type 19 streptococcal M protein. (1988)

M protein was purified to homogeneity from limited pepsin digests of intact type 19 streptococci (pep M19). The purified pep M19 when emulsified in CFA and injected into rabbits evoked type-specific and crossreactive opsonic antibodies, as well as heart-crossreactive antibodies. The NH2-terminal primary structure of pep M19 was determined and a peptide copying the first 24 amino acids [SM19(1-24)C] was chemically synthesized. Rabbits that were immunized with the unconjugated peptide developed antibodies that recognized the native pep M19, as determined by ELISA, and opsonic antibodies against type 19 streptococci, as determined by in vitro opsonophagocytosis tests. The synthetic peptide also evoked antibodies that crossreacted with a 60-kD sarcolemmal membrane protein of human myocardium. By using overlapping synthetic subpeptides as immunoinhibitors, the opsonic and heart-crossreactive epitopes of SM19(1-24)C were localized to SM19(11-24)C. Our data confirm the presence of heart-crossreactive epitopes within the primary structure of pep M19 and show that these potentially harmful autoimmune epitopes may be located in the NH2-terminal regions of certain M proteins. We conclude that continued efforts to identify the primary structures of protective and heart-crossreactive epitopes will be necessary to elucidate the pathogenesis of acute rheumatic heart disease and to develop safe and effective streptococcal vaccines.
Hyperspectral imaging for label-free in vivo identification of myocardial scars and sites of radiofrequency ablation lesions (2017)

HSI based on changes in tissue autofluorescence is a highly effective tool for revealing-in vivo and with high spatial resolution-surface boundaries of myocardial scar and discriminating it from areas of acute necrosis caused by RF ablation.
Cone‐beam volume CT breast imaging: Feasibility study (2002)

X-ray projection mammography, using a film/screen combination, or digital techniques, has proven to be the most effective imaging modality currently available for early detection of breast cancer. However, the inherent superimposition of structures makes a small carcinoma (a few millimeters in size) difficult to detect when it is occult or in dense breasts, leading to a high false-positive biopsy rate. Cone-beam x-ray-projection-based volume imaging using flat panel detectors (FPDs) may allow obtaining three-dimensional breast images, resulting in more accurate diagnosis of structures and patterns of lesions while eliminating the hard compression of breasts. This article presents a novel cone-beam volume computed tomographic breast imaging (CBVCTBI) technique based on the above techniques. Through a variety of computer simulations, the key issues of the system and imaging techniques were addressed, including the x-ray imaging geometry and corresponding reconstruction algorithms, x-ray characteristics of breast tissue and lesions, x-ray setting techniques, the absorbed dose estimation, and the quantitative effect of x-ray scattering on image quality. The preliminary simulation results support the proposed CVBCTBI modality for breast imaging in respect to its feasibility and practicability. The absorbed dose level is comparable to that of current mammography and will not be a prominent problem for this imaging technique. Compared to conventional mammography, the proposed imaging technique with isotropic spatial resolution will potentially provide significantly better low-contrast detectability of breast tumors and more accurate location of breast lesions.
Nanoliter qPCR Platform for Highly Parallel, Quantitative Assessment of Reductive Dehalogenase Genes and Populations of Dehalogenating Microorganisms in Complex Environments (2014)

Idiosyncratic combinations of reductive dehalogenase (rdh) genes are a distinguishing genomic feature of closely related organohalogen-respiring bacteria. This feature can be used to deconvolute the population structure of organohalogen-respiring bacteria in complex environments and to identify relevant subpopulations, which is important for tracking interspecies dynamics needed for successful site remediation. Here we report the development of a nanoliter qPCR platform to identify organohalogen-respiring bacteria and populations by quantifying major orthologous reductive dehalogenase gene groups. The qPCR assays can be operated in parallel within a 5184-well nanoliter qPCR (nL-qPCR) chip at a single annealing temperature and buffer condition. We developed a robust bioinformatics approach to select from thousands of computationally proposed primer pairs those that are specific to individual rdh gene groups and compatible with a single amplification condition. We validated hundreds of the most selective qPCR assays and examined their performance in a trichloroethene-degrading bioreactor, revealing population structures as well as their unexpected shifts in abundance and community dynamics.