gebhart/patrepeval huggingface dataset:
An improved algorithm to accelerate regular expression evaluation (2007)

Modern network intrusion detection systems need to perform regular expression matching at line rate in order to detect the occurrence of critical patterns in packet payloads. While deterministic finite automata (DFAs) allow this operation to be performed in linear time, they may exhibit prohibitive memory requirements. In [9], Kumar et al. propose Delayed Input DFAs (D2FAs), which provide a trade-off between the memory requirements of the compressed DFA and the number of states visited for each character processed, which corresponds directly to the memory bandwidth required to evaluate regular expressions.
A computer program for choosing optimal oligonudeotides for filter hybridization, sequencing and<i>in vitro</i>amplification of DNA (1989)

A method is presented for choosing optimal oligodeoxyribonucleotides as probes for filter hybridization, primers for sequencing, or primers for DNA amplification. Three main factors that determine the quality of a probe are considered: stability of the duplex formed between the probe and target nucleic acid, specificity of the probe for the intended target sequence, and self-complementarity. DNA duplex stability calculations are based on the nearest-neighbor thermodynamic values determined by Breslauer et al. [Proc. Natl. Acad. Sci. U.S.A. (1986), 83: 3746]. Temperatures of duplex dissociation predicted by the method described here were within 0.4 degrees C of the values obtained experimentally for ten oligonucleotides. Calculations for specificity of the probe and its self-complementarity are based on a simple dynamic algorithm.
Fast Compaction Algorithms for NoSQL Databases (2015)

Compaction plays a crucial role in NoSQL systems to ensure a high overall read throughput. In this work, we formally define compaction as an optimization problem that attempts to minimize disk I/O. We prove this problem to be NP-Hard. We then propose a set of algorithms and mathematically analyze upper bounds on worst-case cost. We evaluate the proposed algorithms on real-life workloads. Our results show that our algorithms incur low I/O costs and that a compaction approach using a balanced tree is most preferable.
A stochastic control strategy for hybrid electric vehicles (2004)

The supervisory control strategy of a hybrid vehicle coordinates the operation of vehicle sub-systems to achieve performance targets such as maximizing fuel economy and reducing exhaust emissions. This high-level control problem is commonly referred as the power management problem. In the past, many supervisory control strategies were developed on the basis of a few pre-defined driving cycles, using intuition and heuristics. The resulting control strategy was often inherently cycle-beating and lacked a guaranteed level of optimality. In this study, the power management problem is tackled from a stochastic viewpoint. An infinite-horizon stochastic dynamic optimization problem is formulated. The power demand from the driver is modeled as a random Markov process. The optimal control strategy is then obtained by using stochastic dynamic programming (SDP). The obtained control law is in the form of a stationary full-state feedback and can be directly implemented. Simulation results over standard driving cycles and random driving cycles are presented to demonstrate the effectiveness of the proposed stochastic approach. It was found that the obtained SDP control algorithm outperforms a sub-optimal rule-based control strategy trained from deterministic DP results.
Increased T-helper lymphocytes following active specific intralymphatic immunotherapy of cancer. (1986)

Sixteen malignant cancer patients (seven melanoma, three colon, three lung, and three other) who received tumor vaccine therapy--14 autologous and two allogeneic--were studied for T-cell phenotyping changes. Blood samples were obtained prior to therapy, and also at various time intervals following the therapy. A consistent and reproducible elevation of T3 and T4 subsets, as tested on day 21 after the therapy, was observed in 12 patients. The mean percentages of T3 and T4 fractions before and after (21 days) the treatment were 63.8 versus 75.9% (p less than 0.002) and 44.4 versus 57.4% (p less than 0.001), respectively. Kinetic studies of absolute values of three melanoma patients also showed augmentation of T3 and T4 cells following each tumor vaccine. The lymphatic infusion of tumor vaccine did not cause any toxicity, particularly lymphadenopathy. We believe this is the first report demonstrating augmentation of T4 (helper/inducer) cells with tumor cell vaccine therapy.
Identification and Quantification of Nitrogen and Sulfur Compounds in Catalytically Cracked Heavy Gas Oils by Isobutane/CI GC/MS and GC Using Selective Detectors (1988)

Journal Article Identification and Quantification of Nitrogen and Sulfur Compounds in Catalytically Cracked Heavy Gas Oils by Isobutane/CI GC/MS and GC Using Selective Detectors Get access Ismet Dzidic, Ismet Dzidic Shell Development Company, Westhollow Research Center, P.O. Box 1380, Houston, Texas 77251 Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael D. Balicki, Michael D. Balicki Shell Development Company, Westhollow Research Center, P.O. Box 1380, Houston, Texas 77251 Search for other works by this author on: Oxford Academic PubMed Google Scholar Ileana A.L. Rhodes, Ileana A.L. Rhodes Shell Development Company, Westhollow Research Center, P.O. Box 1380, Houston, Texas 77251 Search for other works by this author on: Oxford Academic PubMed Google Scholar Haskell V. Hart Haskell V. Hart Shell Development Company, Westhollow Research Center, P.O. Box 1380, Houston, Texas 77251 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Chromatographic Science, Volume 26, Issue 5, May 1988, Pages 236–240, https://doi.org/10.1093/chromsci/26.5.236 Published: 01 May 1988 Article history Received: 04 March 1988 Published: 01 May 1988
The Nucleotide Exchange Factor Ric-8A Is a Chaperone for the Conformationally Dynamic Nucleotide-Free State of Gαi1 (2011)

Heterotrimeric G protein α subunits are activated upon exchange of GDP for GTP at the nucleotide binding site of Gα, catalyzed by guanine nucleotide exchange factors (GEFs). In addition to transmembrane G protein-coupled receptors (GPCRs), which act on G protein heterotrimers, members of the family cytosolic proteins typified by mammalian Ric-8A are GEFs for Gi/q/12/13-class Gα subunits. Ric-8A binds to Gα•GDP, resulting in the release of GDP. The Ric-8A complex with nucleotide-free Gαi1 is stable, but dissociates upon binding of GTP to Gαi1. To gain insight into the mechanism of Ric-8A-catalyzed GDP release from Gαi1, experiments were conducted to characterize the physical state of nucleotide-free Gαi1 (hereafter referred to as Gαi1[ ]) in solution, both as a monomeric species, and in the complex with Ric-8A. We found that Ric-8A-bound, nucleotide-free Gαi1 is more accessible to trypsinolysis than Gαi1•GDP, but less so than Gαi1[ ] alone. The TROSY-HSQC spectrum of [(15)N]Gαi1[ ] bound to Ric-8A shows considerable loss of peak intensity relative to that of [(15)N]Gαi1•GDP. Hydrogen-deuterium exchange in Gαi1[ ] bound to Ric-8A is 1.5-fold more extensive than in Gαi1•GDP. Differential scanning calorimetry shows that both Ric-8A and Gαi1•GDP undergo cooperative, irreversible unfolding transitions at 47° and 52°, respectively, while nucleotide-free Gαi1 shows a broad, weak transition near 35°. The unfolding transition for Ric-8A:Gαi1[ ] is complex, with a broad transition that peaks at 50°, suggesting that both Ric-8A and Gαi1[ ] are stabilized within the complex, relative to their respective free states. The C-terminus of Gαi1 is shown to be a critical binding element for Ric-8A, as is also the case for GPCRs, suggesting that the two types of GEF might promote nucleotide exchange by similar mechanisms, by acting as chaperones for the unstable and dynamic nucleotide-free state of Gα.
Low-Loss Two-Pole Tunable Filters With Three Different Predefined Bandwidth Characteristics (2008)

Low-loss tunable filters with three different fractional-bandwidth variations were designed and fabricated on epsiv <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</sub> = 2.2, 0.787 mm Duroid substrates for 850-1400-MHz applications. A detailed analysis for realizing predefined bandwidth characteristics is presented, and a design technique to take into account the source and load impedance loading is discussed. It is found that independent electric and magnetic coupling makes it possible to realize three different coupling coefficient variations with the same filter structure. The proposed topology is different from the comb-line design in that all three filters have identical electrical lengths, the same varactors, and the same filter <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> values. Three different filters are built using Schottky varactor diodes with a tuning range from ~ 850 to ~ 1400 MHz. The constant fraction-bandwidth filter has a 1-dB bandwidth of 5.4%plusmn0.3% and an insertion loss of 2.88-1.04 dB. The decreasing fractional-bandwidth filter shows a 1-dB bandwidth decrease from 5.2% to 2.9% with an insertion loss of 2.89-1.93 dB (this is effectively a 40-45-MHz constant absolute-bandwidth filter). The increasing fractional-bandwidth filter shows a 1-dB bandwidth increase from 4.3% to 6.5% with an insertion loss of 3.47-1.18 dB. The measured <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</i> of the filters are between 53-152 from ~ 850 to ~ 1400 MHz. The measured third-order intermodulation intercept point ranges from 11.3 to 20.1 dBm depending on the bias voltage. To our knowledge, these planar tunable filters represent state-of-the art insertion-loss performance at this frequency range.
The role of transforming growth factor-beta in primary brain tumors (2003)

Dramatic therapeutic benefits of targeting specific signal transduction pathways in some cancers have pushed rational molecular targeting to the forefront of cutting-edge cancer therapy. The identification and targeting of pathways critical to the phenotype of cancers offers new hope in the treatment of many patients. Transforming growth factor beta (TGF-beta) is a multifunctional cytokine that is frequently expressed in multiple types of malignant brain tumors. TGF-beta exerts a complex set of effects in cancers with an early tumor suppressive effect through growth inhibition but later effects in cancer development that are tumorigenic - including increased tumor cell motility and invasion, induction of angiogenesis, and immune suppression. Early preclinical and clinical studies have shown promise of anti-TGF-beta strategies in the treatment of malignant gliomas suggesting TGF-beta may be a potential new therapeutic target in neuro-oncology.
P‐145: Optimization of Molybdenum Oxides for Low‐Reflectance Thin Films using Numerical Simulation (2015)

Mo‐oxide thin films were investigated for low‐reflectance applications. Numerical simulation was used to optimize the optical properties (reflectance and color) of the thin films. Reflectance could be considerably reduced to values of 6% (@ 550 nm) maintaining a colorless black film.
Amino acid substitutions determining G3m(g5). (1990)

Amino acid substitutions specific for allotypic G3m(g5) marker were studied by sequence analysis of the C-terminal BrCN peptides of myeloma protein Ba [G3m(g5+)] and Bu [G3m(g5-)]. The results indicate that arginine and tyrosine at position 435 and 436 are responsible for the specificity. Two substitutions of IgG3 Bu [G3m(b1, b3)] and IgG3 Jir [G3m(b3,s,t)] [Matsumoto et al.: J. Immun. 131: 1865, 1983], in the same positions are arginine-phenylalanine and histidine-tyrosine, respectively. Affinity chromatographic data of modified IgG3 proteins show that the tyrosine residue at position 436 associated with phenylalanine at position 124 of protein A-B fragment plays a role in the interaction. The differences in the yields between IgG3s carrying various haplotypes on Protein A-Sepharose affinity chromatography [Ito et al.: Proc. Japan Acad. 56B: 226, 1980] are also explained through this chromatography and also by the configuration of the residues in tertiary structure [Deisenhofer: Biochemistry 20: 2361, 1980].
Patch-based denoising method using low-rank technique and targeted database for optical coherence tomography image (2017)

Image denoising is a crucial step before performing segmentation or feature extraction on an image, which affects the final result in image processing. In recent years, utilizing the self-similarity characteristics of the images, many patch-based image denoising methods have been proposed, but most of them, named the internal denoising methods, utilized the noisy image only where the performances are constrained by the limited information they used. We proposed a patch-based method, which uses a low-rank technique and targeted database, to denoise the optical coherence tomography (OCT) image. When selecting the similar patches for the noisy patch, our method combined internal and external denoising, utilizing the other images relevant to the noisy image, in which our targeted database is made up of these two kinds of images and is an improvement compared with the previous methods. Next, we leverage the low-rank technique to denoise the group matrix consisting of the noisy patch and the corresponding similar patches, for the fact that a clean image can be seen as a low-rank matrix and rank of the noisy image is much larger than the clean image. After the first-step denoising is accomplished, we take advantage of Gabor transform, which considered the layer characteristic of the OCT retinal images, to construct a noisy image before the second step. Experimental results demonstrate that our method compares favorably with the existing state-of-the-art methods.
Traditions of supernatural warfare (2009)

His hand a sabre; a dagger, his tongue;His finger an arrow; his arm, a spear bright.Kamāl Pāshazāda, Elegy on Sultan Selim (c. 1520)
Hardware-software co-synthesis of partially re-configurable embedded systems optimized for reduced power consumption (2004)

In this paper, we present a scheduling algorithm as part of the hardware-software co-synthesis of low power distributed embedded devices. We used a location priority based algorithm in order to address embedded computer systems consisting of processors, partially reprogrammable FPGAs, and other resources. Our proposed locality emphasized two-dimensional scheduling algorithm prioritizes the unused FPGA locations and chooses a task to match the given position. This is an unusual approach to task scheduling, where the norm is to prioritize the candidate pool of tasks and then decide on a location. The FPGA reconfiguration process consumes large amounts of power. This algorithm is optimized to reduce overall system power consumption and to ensure all tasks meet their respective deadlines. Preliminary experimental results reveal significant reconfiguration overhead reduction while maintaining a low deadline violation rate.
Ca<sup>2+</sup>-induced self-assembly of Bombyx mori silk sericin into a nanofibrous network-like protein matrix for directing controlled nucleation of hydroxylapatite nano-needles (2015)

Bone biomineralization is a well-regulated protein-mediated process where hydroxylapatite (HAP) crystals are nucleated with preferred orientation within self-assembled protein matrix. Mimicking this process is a promising approach to the production of bone-like protein/mineral nanocomposites for bone repair and regeneration. Towards the goal of fabricating such nanocomposites from sericin, a protein spun by <i>Bombyx mori</i> (<i>B.mori</i>) silkworm, and bone mineral HAP, for the first time we investigated the chemical mechanism underpinning the synergistic processes of the conformational change/self-assembly of <i>B.mori</i> sericin ( <b><i>BS</i></b> ) as well as the nucleation of HAP on the resultant self-assembled <b><i>BS</i></b> matrix. We found that <b><i>BS</i></b> , rich in anionic amino acid residues, could bind Ca<sup>2+</sup> ions from the HAP precursor solution through electrostatic attraction. The Ca<sup>2+</sup>binding drove the conformational change of <b><i>BS</i></b> from random coils into β-sheets and its concomitant self-assembly into interconnected nanofibrous network-like protein matrix, which initiated the nucleation and growth of HAP crystals. HAP crystals directed by the resultant self-assembled <b><i>BS</i></b> matrix grew preferentially along their crystallographic c-axis, leading to the formation of HAP nano-needles. The HAP nano-needles in the self-assembled <b><i>BS</i></b> matrix were subsequently aggregated into globules, probably driven by the hydrogen bonding between C=O groups of <b><i>BS</i></b> and O-H groups of HAP nano-needles. The present work sheds light on the chemical mechanisms of <b><i>BS</i></b> self-assembly and the controlled mineralization directed by the self-assembled matrix. We also found that the resultant nanocomposites could promote the osteogenic differentiation of human bone marrow-derived mesenchymal stem cells. Thus our work also generates a biomimetic approach to bone-like silk protein/mineral nanocomposite scaffolds that can find potential applications in bone repair and regeneration.
Colonization of organoapatite–titanium mesh by preosteoblastic cells (2003)

Titanium (Ti) and its alloys continue to serve as successful implant materials for skeletal repair because of their physical properties and biocompatibility. This study investigates the influence of organoapatite (OA), grown directly onto an L-shaped Ti mesh, on preosteoblastic cellular colonization. Unseeded mesh samples were placed on subconfluent layers of MC3T3-E1 murine calvaria cells and cultured for up to 2 weeks. Cells demonstrated accelerated colonization of the three-dimensional OA-Ti mesh substrates over bare Ti controls. Cells also showed significantly increased proliferation on the OA-Ti mesh over bare Ti controls. Cellular differentiation, measured by alkaline phosphatase and osteocalcin expression, was observed at late stages of the experiment with no notable differences between OA-Ti mesh and bare Ti controls. These results suggest that OA grown onto porous Ti substrates is capable of inducing accelerated colonization of unseeded implant structures by osteogenic cells.
Combination of Argentophilic and Perfluorophenyl-Perfluorophenyl Interactions Supports a Head-to-Head [2 + 2] Photodimerization in the Solid State (2014)

Face-to-face perfluorophenyl–perfluorophenyl interactions (C6F5···C6F5) are achieved in a disilver metal–organic complex. The C6F5···C6F5 interactions along with argentophilic forces support trans-pentafluorostilbazole to undergo a head-to-head [2 + 2] photodimerization to form a cyclobutane that sustains a fluorinated two-dimensional metal–organic framework.
Multispectral digital colposcopy for in vivo detection of cervical cancer (2003)

We present a multispectral digital colposcope (MDC) to measure multispectral autofluorescence and reflectance images of the cervix by using an inexpensive color CCD camera. The diagnostic ability of the MDC was evaluated by application of MDC spectral response to fluorescence and reflectance spectra measured from a large clinical trial. High diagnostic performance was achieved by use of only two excitation wavelengths: 330 and 440 nm. Good quality autofluorescence images of the human cervix were acquired in vivo with the MDC. Automated diagnostic algorithms correctly identified CIN (cervical intraepithelial neoplasia) lesions from MDC fluorescence images. The MDC has the potential to provide a costeffective alternative to standard colposcopy and better direction of biopsies.
An Improved Preparation of Antibody-Coated Polystyrene Beads for Sandwich Enzyme Immunoassay (1980)

An improved preparation of antibody-coated polystyrene beads for sandwich enzyme immunoassay of human thyroid-stimulating hormone (TSH) was described. Rabbit anti-TSH IgG was purified by eluting at pH 2.5 from a TSH-Sepharose column, diluted 3 or 9 fold with normal rabbit IgG and used for coating polystyrene beads by physical adsorption. In a sandwich enzyme immunoassay of TSH using rabbit (anti-TSH) Fab'-beta-D-galactosidase conjugate, beta-D-galactosidase activities specifically bound to thus prepared polystyrene beads in the presence of TSH was 2.8-6.3 fold higher than those bound to polystyrene beads coated with anti-TSH IgG before purification. A similar effect was observed when guinea pig anti-pork insulin IgG, rabbit (anti-human IgE) IgG and goat (anti-human IgE) IgG were treated at pH 2.5. This improvement may be based on a conformational change of Fc in IgG molecule which was caused by the treatment at pH 2.5. Other sandwich immunoassays such as fluoro- and radio-immunoassays may also be improved in the same way.
LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell‐cell communication (2012)

Leucine-rich repeat-containing 8 (LRRC8) proteins are composed of four transmembrane helices and 17 leucine-rich repeats (LRR). Although LRRC8 proteins have been associated with important processes, like maturation of B cells or adipocyte differentiation, their biology and molecular function are largely unknown. We found that LRRC8 proteins originated from the combination of a pannexin and an LRR domain (most likely related to the SHOC2, LAP, RSU1 and LRRIQ4 protein families) before the diversification of chordates. We propose that, like pannexins, LRRC8 proteins form hexameric channels, which participate in cell-cell communication processes. According to the inferred topological model, and contrary to what was previously assumed, the six LRR domains are located in the cytoplasm, and could participate in the organisation of signalling cascades. By compiling available proteomics and gene expression data, and on the basis of the LRRC8 proposed hexameric channel structure, we present clues to the function of this family.
AUTOMATED EXTRACTION OF SATELLITE TRAILS FROM WIDE ANGLE CCD IMAGERY (2019)

The current UK’s National Space and Security Policy states that the identification of potential on-orbit collisions and warning of re-entries over UK sovereign territory is of high importance, driving requirements for indigenous Space Situational Awareness (SSA) systems capable of delivering these products. The UK’s Defence Science and Technology Laboratory (Dstl) is examining options for the creation of a distributed network of longitudinally distributed, low cost commercial–off-the-shelf electro-optical sensors to support survey work and catalogue maintenance. To effectively exploit this, a robust data handling system is required to autonomously detect satellite trails in a manner that can handle variable target intensities, periodicities and rates of apparent motion, as well as meteors and aircraft. Data captured during the United Kingdom/New Zealand Automated Transfer Vehicle-5 (ATV-5) deorbit observation trial have been employed to inform the development of a prototype processing pipeline for autonomous on-site processing. The approach taken employs pre-existing and documented tools such as Astrometry.NET and DAOPHOT from the astronomical community, together with image processing and orbit determination software developed in-house by Dstl. Some preliminary results from the automated analysis of data collected from wide angle sensors are described, together with an appraisal of the limitations of the proposed system and our plans for future development