gebhart/patrepeval huggingface dataset:
Synthesis and Biological Evaluation of 3-Heterocyclyl-7,8,9,10-tetrahydro-(7,10-ethano)-1,2,4-triazolo[3,4-<i>a</i>]phthalazines and Analogues as Subtype-Selective Inverse Agonists for the GABA<sub>A</sub>α5 Benzodiazepine Binding Site (2004)

The identification of a novel series of 7,8,9,10-tetrahydro-(7,10-ethano)-1,2,4-triazolo[3,4-a]phthalazines as GABA(A)alpha5 inverse agonists, which have both binding and functional (efficacy) selectivity for the benzodiazepine binding site of alpha5- over alpha1-, alpha2-, and alpha3-containing GABA(A) receptor subtypes, is described. Binding selectivity was determined to a large part by the degree of planarity of the fused ring system whereas functional selectivity was dependent on the nature of the heterocycle at the 3-position of the triazolopyridazine ring. 3-Furan and 5-methylisoxazole were shown to be optimal for GABA(A)alpha5 functional selectvity. 3-(5-Methylisoxazol-3-yl)-6-(2-pyridyl)methyloxy-1,2,4-triazolo[3,4-a]phthalazine (43) was identified as a full inverse agonist at the GABA(A)alpha5 subtype with functional selectivity over the other GABA(A) receptor subtypes and good oral bioavailability.
Stability of modulation transfer function calibration of surface profilometers using binary pseudo-random gratings and arrays with nonideal groove shapes (2010)

The major problem of measurement of a power spectral density (PSD) distribution of surface heights with surface profilometers arises due to the unknown Modulation Transfer Function (MTF) of the instruments, which tends to distort the PSD at higher spatial frequencies. The special mathematical properties of binary pseudo-random patterns make them an ideal basis for developing MTF calibration test surfaces. Two-dimensional binary pseudo-random arrays (BPRAs) have been fabricated and used for the MTF calibration of the MicroMap{trademark}-570 interferometric microscope with all available objectives. An investigation into the effects of fabrication imperfections on the quality of the MTF calibration and a procedure for accounting for such imperfections are presented.
Undecimated Wavelet Transforms for Image De-noising (2002)

A few different approaches exist for computing undecimated wavelet transform. In this work we construct three undecimated schemes and evaluate their performance for image noise reduction. We use standard wavelet based de-noising techniques and compare the performance of our algorithms with the original undecimated wavelet transform, as well as with the decimated wavelet transform. The experiments we have made show that our algorithms have better noise removal/blurring ratio.
Application to an EMI Noise Filter of a High-Loss CoZrNb/SiO2 Multilayer Film. (1994)

This study reports the application of a magnetic alloy/nonmagnetic insulator multilayer film to EMI noise filters. The eddy-current skin effect in the magnetic alloy layers was used to realize high-loss properties. In a CoZrNb/SiO2 film, the thickness of each layer and the magnetic anisotropy were designed so that the film would exhibit high-loss properties in the 30∼1000 MHz frequency range. A large impedance and noise attenuation for common-mode noise in this frequency range were confirmed in a noise filter tube incorporating the high loss film. In comparison with a ferrite core, a miniaturization of ∼1/102 was achieved in the noise filter tube.
A hypothesis fortheHLA-B27immunedysregulation in spondyloarthropathy: Contributions fromenteric organisms, B27 structure, peptides boundbyB27,andconvergent evolution (1993)

Several humanrheumatic diseases occur pre- dominately inpersons whocarry thehistocompatibility (HLA) class IafleleB27. Theyhavealso beenrelated toGram-negative enteric microorganisms. Inaddition, therecent recovery of peptides boundtoB27hasaflowed anunderstanding ofthe structural requirements fortheir binding. Using theaccumu- lated databaseofprotein sequences, wehavetested aseries of hypotheses. First, wehaveaskedwhether theprimary amino acid sequence ofthehypervariable regions ofHLA-B27shares short sequences withtheproteins ofGram-negative enteric bacteria. Thedatademonstrate that, unique amongtheHLA-B molecules, thehypervariable regions ofHLA-B27unexpectedly share short peptide sequences withproteins fromthese bacte- ria. Second, wehaveaskedwhether theenteric proteins tend tosatisfy thestructural requirements forpeptide binding to B27inthose regions ofthesequence shared withB27.This hypothesis.also tends tobetrue, especially inanaflelically variable partoftheB27sequence whichispredicted tobind B27ifitweretobepresented asafree peptide. Weconclude that HLA-B27andenteric Gram-negative bacteria haveun- dergone apreviously unappreciated formofconvergent evo- lution whichmaybeimportant intheprocess leading tothese rheumatic diseases. Moreover, theregions oftheenteric bac- terial proteins whicharecontiguous withtheshort sequences shared withB27tendtohavestructures whicharealso predicted tobind B27.These observations suggest amechanism forautoimmunity andleadtotheprediction thattheB27- associated diseases aremediated byasubset ofT-cefl receptors, B27,andthepeptides boundbyB27. Ankylosing spondylitis, Reiter syndrome, andother reactive arthritides arereferred toasspondyloarthropathies. They
Anterior Chamber Angle Assessment System (2016)

In this paper, we propose an automatic anterior chamber angle assessment system for Anterior Segment Optical Coherence Tomography (AS-OCT). In our system, the automatic segmentation method is used to segment the clinical structures, which are then used to recover standard clinical ACA measurements. Our measurements can not only support clinical assessments, but also be utilized as features for detecting anterior angle closure in automatic glaucoma diagnosis.
Selection, Purification, Characterisation, and Cloning of a Novel Heat-Stable Stereo-Specific Amidase from<i>Klebsiella</i><i>o</i><i>xytoca</i>, and Its Application in the Synthesis of Enantiomerically Pure (<i>R</i>)- and (<i>S</i>)-3,3,3-Trifluoro-2-hydroxy-2-methylpropionic Acids and (<i>S</i>)-3,3,3-Trifluoro-2-hydroxy-2-methylpropionamide (2002)

We isolated, characterised, and cloned an enantio-specific amidase from Klebsiella oxytoca and used it to resolve (R,S)-3,3,3-trifluoro-2-hydroxy-2-methylpropionamide, giving (R)-3,3,3-trifluoro-2-hydroxy-2-methylpropionic acid and (S)-3,3,3-trifluoro-2-hydroxy-2-methylpropionamide. The (S)-amide could then be hydrolysed chemically to (S)-3,3,3-trifluoro-2-hydroxy-2-methylpropionic acid. The process can therefore be adapted to produce both (R)- and (S)-enantiomers of 3,3,3-trifluoro-2-hydroxy-2-methylpropionic acid, or (S)-3,3,3-trifluoro-2-hydroxy-2-methylpropionamide. The biocatalytic step is part of a combined chemical and biocatalytic route that starts from ethyl trifluoroacetoacetate. The products typically have a purity of greater than 98% and ee values of essentially 100% after isolation. The process has been used to produce 100-g amounts of the (S)-acid, and successfully scaled up to produce 100-kg amounts of the (R)-acid, with the biotransformation carried out at the 1500-L scale.
Addressing nanoimprint lithography mix and match overlay using drop pattern compensation (2020)

Imprint lithography is a promising technology for replication of nano-scale features. For semiconductor device applications, Canon deposits a low viscosity resist on a field by field basis using jetting technology. A patterned mask is lowered into the resist fluid, which then quickly flows into the relief patterns in the mask by capillary action. Following this filling step, the resist is crosslinked under UV radiation, and then the mask is removed, leaving a patterned resist on the substrate. Overlay budgets play a large role in defining production readiness. As an example, DRAM devices require overlay on the order of 15-20% of the half pitch. Canon uses a through the mask (TTM) alignment system to measure a Moiré image anywhere in the field. This system can also record alignment errors of all fields and all marks. The data collected by the TTM system correlates very closely with an Archer measurement tool. In addition, a High Order Distortion Correction (HODC) system, which applies a heat input on a field by field basis through the use of a DMD array has been combined with magnification actuators to correct high order distortion terms up to K30. There is an additional distortion term that must also be addressed for the case of nanoimprint lithography. NIL drop patterns are typically designed to minimize resist fill time and create a uniform residual layer beneath the resist pattern. For device wafers, however, it is important to recognize that there are both long wavelength flatness errors coming from the wafer chuck and existing pattern topography from previously patterned levels that cause out of plane errors. When the mask comes in contact with the resist on the wafer, these out of plane errors can then induce mask bending, resulting in an additional distortion term. To minimize this distortion, a Drop Pattern Compensation (DPC) Model has been implemented to minimize the added distortion terms. In this paper we present an updated study and report on nanoimprint mix and match overlay improvements using DPC. In addition, we describe how the mode array and peak to valley thickness of the resist impacts distortion correction.
Selection and Evaluation of Microorganisms for Biocontrol of Fusarium Head Blight of Wheat Incited by <i>Gibberella zeae</i> (2001)

Gibberella zeae incites Fusarium head blight (FHB), a devastating disease that causes extensive yield and quality losses to wheat and barley. Of over 700 microbial strains obtained from wheat anthers, 54 were able to utilize tartaric acid as a carbon source when the compound was supplied as choline bitartrate in liquid culture. Four tartaric acid-utilizing and three nonutilizing strains reduced FHB in initial tests and were selected for further assays. Antagonists were effective against three different isolates of G. zeae when single wheat florets were inoculated with pathogen and antagonist inoculum. All seven antagonists increased 100-kernel weight when applied simultaneously with G. zeae isolate Z3639 (P ≤ 0.05). Bacillus strains AS 43.3 and AS 43.4 and Cryptococcus strain OH 182.9 reduced disease severity by >77, 93, and 56%, respectively. Five antagonists increased 100-kernel weight of plants inoculated with G. zeae isolate DAOM 180378. All antagonists except one increased 100-kernel weight, and four of seven antagonists reduced disease severity (P ≤ 0.05) when tested against G. zeae isolate Fg-9-96. In spray-inoculation experiments, Bacillus strains AS 43.3 and AS 43.4 and Cryptococcus strains OH 71.4 and OH 182.9 reduced disease severity, regardless of the sequence, timing, and concentration of inoculum application (P ≤ 0.05), though 100-kernel weight did not always increase when antagonists were applied 4 h after inoculum of G. zeae. Overall, 4 of 54 isolates that utilized tartaric acid in vitro were effective against G. zeae versus only 3 of 170 isolates tested that did not utilize tartaric acid (P ≤ 0.05, χ-square test of goodness of fit), demonstrating the potential benefit of prescreening candidate antagonists of FHB for their ability to utilize tartaric acid. Biological control shows promise as part of an integrated pest management program for managing FHB.
Abstract 98: Reducing Mitochondrial, But Not Cytosolic Iron, Protects The Heart Against Ischemia-reperfusion Injury (2014)

Introduction: Iron is essential for the activity of a large number of cellular proteins, but excess free iron can cause cellular damage through production of reactive oxygen species (ROS). Mitochondria are the major site of cellular iron homeostasis, and we recently showed the mitochondrial iron export is mediated by ATP-binding cassette protein-B8 (ABCB8). The role of mitochondrial iron in ischemia-reperfusion (I/R) injury in the heart has not been examined. We hypothesize that mitochondrial iron has a critical role in I/R damage and a reduction of mitochondrial iron is protective against I/R injury through a reduction in ROS. Results: Cardiomyocyte-specific ABCB8 transgenic (TG) mice had significantly lower mitochondrial iron in the heart than nontransgenic (NTG) littermates at baseline, but their cardiac function and the expression of key antioxidant systems were indistinguishable from NTG littermates. To study the role of mitochondrial iron in I/R injury, we subjected ABCB8 TG mice to I/R. TG mice displayed significantly less apoptosis compared to NTG littermates (11.76% vs. 17.63%, p<0.05, n=4-6) and had significantly reduced lipid peroxidation products 48 hours after I/R. To further confirm that our in vivo finding was due to reduced mitochondrial iron, we studied the effect of pharmacological reduction of mitochondrial iron in vitro. 2,2-bipyridyl (BPD) is a mitochondria-accessible iron chelator while deferoxamine (DFO) has poor penetrance into mitochondria. Treating rat cardiomyoblasts H9C2 with BPD but not DFO significantly reduced chelatable mitochondrial iron, as measured by staining cells with rhodamine B-[(1,10-phenanthrolin-5-yl)aminocarbonyl]benzyl ester. In addition, BPD but not DFO pretreatment protected cells against H2O2 induced cell death (p<0.05). BPD treatment in mice decreased baseline mitochondrial iron and significantly preserved cardiac function after I/R. Conclusions: Our findings demonstrate that selective reduction in mitochondrial iron is protective in I/R injury, and show that mitochondrial iron is a source of ROS and cellular damage in I/R. Thus, targeting mitochondrial iron with selective iron chelators, as studied in our system, may provide a novel approach for treatment of ischemic heart disease.
Surface Plasmon Resonance Phase Imaging (2000)

A new optical technique for measuring and visualization of local changes of the order of 10−6 in refractive index in a field of view, based on non-linear phase amplification by surface plasmon resonance is presented. Its application to biological and chemical local bio-sensing and imaging is suggested.
High-performance optical amplifier for WDM communication systems (1998)

Gain equalization of an EDFA is performed by introducing spectrally designed all-fiber filters in the mid-stage of a dual-stage fiber amplifier. Two types of filters are studied: a cascade of narrow-band Bragg gratings for discrete equalization of a finite number of channels and a wide-band Bragg grating performing equalization over the whole 1539 nm to 1557 nm range. In future work, it is planned to use the discrete Bragg grating configuration to simultaneously perform Dispersion compensation (D), Equalization (E) and Stabilization of gain (S) and Channel dropping (C) in a dual-stage EDFA. Integration of these functions will result in a high performance amplifier called the DESC-EDFA.
High Performance Elliptic Curve GF(2m) Crypto-processor (2006)

This study presents a high performance elliptic curve cryptoprocessor architecture over GF(2m). The proposed architecture exploits parallelism at the projective coordinate level to perform parallel field multiplications. Comparisons between the Projective, Jacobian and Lopez-Dahab coordinate systems using sequential and parallel designs are presented. Results show that parallel designs gives better area-time complexity (AT2) than sequential designs by 44-252% which leads to a wide range of design tradeoffs. The results also show that the Projective coordinate system gives the best AT2 in parallel designs with the least number of multiplications levels when using 4 multipliers.
Basic mechanisms of light scattering in tissue (1999)

Tissue strongly scatters light. Therefore, virtually all techniques for probing tissue with light are dependent on the scattering interactions of light with tissue. In particular, noninvasive optical methods for determining tissue morphology are dependent on light scattering. A fundamental understanding of what cellular features scatter light and of how changes internal cellular structures affect the measurement of light transport are needed. In this work, we describe some of the recent progress made towards understanding the basic mechanisms of light scattering in tissue.
The role of chemokines in human immunodeficiency virus infection (2000)

Chemokines that bind to human immunodeficiency virus (HIV) co-receptors are potent and selective inhibitors of HIV infection. Therefore, ever since our discovery of this activity, we have proposed their role in controlling HIV infection as a third arm of the immune response, i.e. in concert with humoral and cellular responses. Research carried out in our laboratory, and performed independently by other groups, has recently strengthened this concept. Here, we critically analyze the evidence indicating the positive contribution of chemokines to HIV infection, their involvement with cognate and innate immunity, and the potential for their use in combating HIV infection.
Ana o 2, a Major Cashew (<i>Anacardium occidentale</i> L.) Nut Allergen of the Legumin Family (2003)

We conclude that this legumin-like protein is a major allergen in cashew nut.
Magnetic Fluid Grinding of Pipe Inner Surface. (1992)

The need to grind the inner surface of a pipe has increased recently, but it is not satisfied by traditional grinding methods. On the other hand, magnetic fluid grinding with a float has been developed as a new method which has more flexible properties than traditional grinding methods. Magnetic fluid was applied to the grinding of a pipe inner surface. The maximum removal rate was 8.9 x 10-12 m3/Nm. Optimum conditions existed in regard to revolution speed of pipe, shape of float, concentration and mean grain size of abrasive grain. The material of the abrasive grain and float influence the removal rate. Therefore, the pipe inner surface was ground effectively for practical usage by magnetic fluid grinding.
Thermal‐Sensing Fiber Devices by Multimaterial Codrawing (2006)

Thermal sensing provides important information on the state of many physiological, chemical, and physical systems. However, the problem of continuously monitoring and detecting a thermal excitation over very large areas (100 m2) with high resolution (1 cm2) still remains. A solution to this problem is presented here in which a fiber (see figure) senses heat along its entire length and generates an electrical signal.
KPPF: Keypoint-Based Point-Pair-Feature for Scalable Automatic Global Registration of Large RGB-D Scans (2017)

One of the most important challenges in the field of 3D data processing is to be able to reconstruct a complete 3D scene with a high accuracy from several captures. Usually this process is achieved through two main phases: a coarse, or rough, alignment step then a fine alignment. In this article we propose an automatic scalable global registration method (i.e. without arbitrary pose of the sensor) under the following constraints: markerless, very large scale data (several, potentially many millions of points per scans), little overlap between scans, for more than two or three dozens of scans, without a priori knowledge on the 6 degrees of freedom. Here we only address the coarse alignment, and consider the fine alignment step tackled by dedicated existing approaches such as Iterative Closest Point (ICP) [3]. We evaluate thoroughly our method on our own dataset of 33 real large scale scans of an indoor building. The data presents some pairs of scans with very little overlap, architectural challenges (a patio and a rotunda open through several levels of the buildings, etc), several millions of points per scan. We will make this dataset public as part of a benchmark available for the community. We have thus evaluated the accuracy of our method, the scalability to the initial amount of points and the robustness to occlusions, little scan overlap and architectural challenges.
<title>Kinetics for reversible optical storage in azo polymers</title> (1993)

Optical information can be stored, erased, or overwritten on azo polymer thin films using polarized light. The information is in the form of localized dichroism and birefringence and is read using a low power probe beam. We have investigated this image storage phenomenon on a series of polyacrylates and polymethacrylates containing azo aromatic groups on the side chains. The monomers are obtained from commercially available azo dyes. The polymers are amorphous and have high glass transition temperatures. We present a model for the writing and erasing process and investigate the physical origins of the parameters which influence the properties of the recording medium.
Gellan Gum‐based Hydrogels for Tissue Engineering Applications (2016)

Gellan Gum (GG) is an FDA-approved natural polysaccharide that found applications in the food and cosmetics industry, mainly as a gelling agent and stabilizer. One of the most important suppliers CP Kelco has introduced this technology into the market more than a decade ago. In respect to GG biological performance, different cell types have been shown to not adhere and spread when encapsulated within gels. This chapter discusses the main features of GG and its derivatives, together with blending and chemical modification or functionalization routes for tailoring its physicochemical and biological performances. It reviews the current literature on the GG-based hydrogels as novel biomaterials for finding applications in a wide range of tissue engineering and regenerative medicine (TERM) strategies. Micromolding, lithography-based techniques, emulsification, microfluidics, and bioprinting methods are some of the possible fabrication methods that can be exploited for obtaining microscale GG-based hydrogels.
CpG-conjugated apoptotic tumor cells elicit potent tumor immunity (131.41) (2010)

Abstract Cancer immunotherapy seeks to induce protective immune responses to tumor-associated antigens (TAA), thereby mediating the eradication of tumor cells. While whole tumor cells represent a comprehensive source of TAA (eliminating the need to identify individual Ags on tumors from different individuals), they tend to be poorly immunogenic. To address this concern, we covalently conjugated immunostimulatory CpG oligodeoxynucleotides (ODN) onto apoptotic tumor cells and examined their ability to induce TAA-specific immune responses. Results show that CpG-conjugated tumor cell vaccines are highly immunogenic. CpG-conjugation enhances the uptake of target cell by DC, triggers the up-regulation of co-stimulatory molecules, and promotes the production of immunomodulatory cytokines (such as IL-12). Vaccination with CpG-conjugated tumor cells stimulates the expansion of tumor-specific CTL that reduce the growth of established tumors. These results suggest that the adjuvant properties of CpG ODN can be harnessed to improve cancer immunotherapy.
CRISPR RNA-guided integrases for high-efficiency and multiplexed bacterial genome engineering (2020)

Tn 7 -like transposons are pervasive mobile genetic elements in bacteria that mobilize using heteromeric transposase complexes comprising distinct targeting modules. We recently described a Tn 7 -like transposon from Vibrio cholerae that employs a Type I-F CRISPR–Cas system for RNA-guided transposition, in which Cascade directly recruits transposition proteins to integrate donor DNA downstream of genomic target sites complementary to CRISPR RNA. However, the requirement for multiple expression vectors and low overall integration efficiencies, particularly for large genetic payloads, hindered the practical utility of the transposon. Here, we present a significantly improved INTEGRATE (insertion of transposable elements by guide RNA-assisted targeting) system for targeted, multiplexed, and marker-free DNA integration of up to 10 kilobases at ~100% efficiency. Using multi-spacer CRISPR arrays, we achieved simultaneous multiplex insertions in three genomic loci, and facile multi-loci deletions when combining orthogonal integrases and recombinases. Finally, we demonstrated robust function in other biomedically- and industrially-relevant bacteria, and developed an accessible computational algorithm for guide RNA design. This work establishes INTEGRATE as a versatile and portable tool that enables multiplex and kilobase-scale genome engineering.