gebhart/patrepeval huggingface dataset:
Dynamics of circulating TNF during adalimumab treatment using a drug-tolerant TNF assay (2019)

Patients with rheumatoid arthritis (RA) can be successfully treated with tumor necrosis factor (TNF) inhibitors, including the monoclonal antibody adalimumab. Once in remission, a proportion of patients can successfully discontinue treatment, indicating that blocking TNF is no longer required for disease control. To explore the dynamics of circulating TNF during adalimumab treatment, we developed a competition enzyme-linked immunosorbent assay that can quantify TNF in the presence of large amounts of TNF inhibitor, i.e., a "drug-tolerant" assay. In 193 consecutive adalimumab-treated patients with RA, we demonstrated that circulating TNF increased in average of >50-fold upon treatment and reached a stable concentration in time for most patients. A similar increase in TNF was found in 30 healthy volunteers after one dose of adalimumab. This implies that TNF in circulation during anti-TNF treatment is not primarily associated with disease activity. During treatment, TNF was in complex with adalimumab and could be recovered as inactive 3:1 adalimumab-TNF complexes. No quantitative association was found between TNF and adalimumab concentrations. Low TNF concentrations at week 4 were associated with a higher frequency of antidrug antibodies (ADAs) at subsequent time points, less frequent methotrexate use at baseline, and less frequent remission after 52 weeks. Also in healthy volunteers, early low TNF concentrations are associated with ADAs. In conclusion, longitudinal TNF concentrations are mostly stable during adalimumab treatment and may therefore not predict successful treatment discontinuation. However, early low TNF is strongly associated with ADA formation and may be used as timely predictor of nonresponse toward adalimumab treatment.
Analysis of Genetic Elements Controlling<i>Staphylococcus aureus lrgAB</i>Expression: Potential Role of DNA Topology in SarA Regulation (2000)

Penicillin-induced killing and murein hydrolase activity in Staphylococcus aureus are dependent on a variety of regulatory elements, including the LytSR two-component regulatory system and the virulence factor regulators Agr and Sar. The LytSR effects on these processes can be explained, in part, by the recent finding that a LytSR-regulated operon, designated lrgAB, affects murein hydrolase activity and penicillin tolerance. To examine the regulation of lrgAB expression in greater detail, we performed Northern blot and promoter fusion analyses. Both methods revealed that Agr and Sar, like LytSR, positively regulate lrgAB expression. A mutation in the agr locus reduced lrgAB expression approximately sixfold, while the sar mutation reduced lrgAB expression to undetectable levels. cis-acting regulatory elements involved in lrgAB expression were identified by fusing various fragments of the lrgAB promoter region to the xylE reporter gene and integrating these constructs into the chromosome. Catechol 2,3-dioxygenase assays identified DNA sequences, including an inverted repeat and intrinsic bend sites, that contribute to maximal lrgAB expression. Confirmation of the importance of the inverted repeat was achieved by demonstrating that multiple copies of the inverted repeat reduced lrgAB promoter activity, presumably by titrating out a positive regulatory factor. The results of this study demonstrate that lrgAB expression responds to a variety of positive regulatory factors and suggest that specific DNA topology requirements are important for optimal expression.
Poxytrins, a class of oxygenated products from polyunsaturated fatty acids, potently inhibit blood platelet aggregation (2010)

Docosahexaenoic acid (DHA), an important component of marine lipids, exhibits anti-inflammatory activity related to some of its oxygenated metabolites, such as neuroprotectin/protectin D1 [NPD1/PD1; 10(R),17(S)-dihydroxy-docosa-4Z,7Z, 11E,13E,15Z,19Z-hexaenoic acid] produced through the 15-lipoxygenase pathway. However, other metabolites from DHA can be produced through this pathway, and other polyunsaturated fatty acids (PUFAs) of nutritional value may be oxygenated as well. Their biological activities remain unknown. Isomers of protectin D1 were synthesized using soybean lipoxygenase and tested for their ability to inhibit human blood platelet aggregation. A geometric isomer called PDX, previously described with the 11E,13Z,15E geometry, instead of 11E,13E,15Z in PD1, inhibited platelet aggregation at submicromolar concentrations when induced by either collagen, arachidonic acid, or thromboxane. The inhibition occurred at the level of both the cyclooxygenase activity and thromboxane receptor site. Interestingly, all the metabolites tested exhibiting the E,Z,E-conjugated triene were active, whereas E,E,Z trienes (as in PD1) or all-trans (E,E,E) trienes were inactive. We conclude that PDX and other oxygenated products from PUFAs of nutritional interest, having the E,Z,E-conjugated triene motif and collectively named poxytrins (PUFA oxygenated trienes), might have antithrombotic potential.
Selective Catalytic Reduction NO by Ammonia Over Ceramic and Active Carbon Based Catalysts (2011)

The need for environmental protection is an indisputable objective. This is particularly important wherever environmental burden has become so high that the environment is no longer capable of self-purification. Such situation exists in our country. A major problem is the protection of the atmosphere. The main pollutants emitted into the atmosphere include carbon monoxide (CO), sulphur dioxide (SO2), nitrogen dioxides (NO2), hydrocarbons (CH), and particulates. Share of individual sectors of the industry in the total emissions is not identical. It is demonstrated by Fig. 1.
Experimental studies of the production of converging cylindrical shock waves (1979)

AN improved experimental technique for the production of cylindrical converging shock waves is presented. This is accomplished with an annular shock tube fitted with an axisymmetric area contraction which redirects an annular incident shock into a cylindrical implosion chamber. The contraction profile is designed in accordance with Whitham's ray-shock theory, and a three-element profile is found to provide the best overall performance on the basis of twodimensional tests. Experiments with a three-element conical contraction demonstrate that highly symmetrical cylindrical implosions may be achieved by this method, and that the cylindrical shock amplification is well predicted by the Chester-Chisnell-Whitham (CCW) area Mach No. rule.
Patients with acute myeloid leukemia and an activating mutation in FLT3 respond to a small-molecule FLT3 tyrosine kinase inhibitor, PKC412 (2004)

Leukemic cells from 30% of patients with acute myeloid leukemia (AML) have an activating mutation in the FLT3 (fms-like tyrosine kinase) gene, which represents a target for drug therapy. We treated 20 patients, each with mutant FLT3 relapsed/refractory AML or high-grade myelodysplastic syndrome and not believed to be candidates for chemotherapy, with an FLT3 tyrosine kinase inhibitor, PKC412 (N-benzoylstaurosporine), at a dose of 75 mg 3 times daily by mouth. The drug was generally well tolerated, although 2 patients developed fatal pulmonary events of unclear etiology. The peripheral blast count decreased by 50% in 14 patients (70%). Seven patients (35%) experienced a greater than 2-log reduction in peripheral blast count for at least 4 weeks (median response duration, 13 weeks; range, 9-47 weeks); PKC412 reduced bone marrow blast counts by 50% in 6 patients (2 of these to < 5%). FLT3 autophosphorylation was inhibited in most of the Corresponding patients, indicating in vivo target inhibition at the dose schedule used in this study. PKC412 is an oral tyrosine kinase inhibitor with clinical activity in patients with AML whose blasts have an activating mutation of FLT3, suggesting potential use in combination with active agents, such as chemotherapy.
Integrated detection and protection schemes for high-impedance faults on distribution systems (2003)

The authors describe two integrated microcomputer-based detection and protection schemes for distribution system faults including high-impedance faults. The main objective of the two schemes is to deal with single-line-to-ground faults of feeders on a distribution substation using delta-delta connection. The first scheme, based on an innovative fault-detection algorithm, identifies a faulty feeder by measuring varied phase angles between phase currents and bus voltages. The second scheme, including several existing detection algorithms, incorporates an expert system for selecting an algorithm suitable for a given application based on their advantages. A simulation software package is built to simulate the implementation of the two schemes and their combination. Using the simulation package and feeder fault data, simulation tests are made to verify the feasibility of the schemes, the algorithms, and the system structures suggested.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Experimentally Measured Input Referred Voltage Offsets and Kickback Noise in RHBD Analog Comparator Arrays (2007)

Analog comparator arrays fabricated on a bulk CMOS 130-nm are measured to quantify input-referred offsets due to transistor variation and kickback noise. Comparators using RHBD edgeless and conventional two-edge transistors are compared to determine the impact on the circuit behavior. Both random variation and kickback noise are slightly larger than for an equivalent design using two-edge transistors. The input-referred offsets are shown to be completely systematic.
Angular momentum primitives for human turning: Control implications for biped robots (2008)

Human locomotion involves a number of different complex activities. Humanoid robots, if they are expected to work in a human environment, should be expected to navigate obstacles and transients as well as, or better than a human being. Turning is one aspect of human walking that is poorly understood from the perspective of biomechanics and robotics. It is an important task comprising a large percentage of daily activities through most human environments. During turning the body is subjected to torques that the leave the body unstable. By understanding the contributions of the spin angular momentum about the center of mass we can gain insight on how to design better controllers for bipedal robots. There are several different types of turning; using alternate legs as the stance leg to accomplish the turn and then recover and also, turning can be a steady-state phenomena as well as a more transient behavior depending on speed. The contributions of spin angular momentum to the center of mass is considered in the case of a spin-turn where the inside foot pivots and the opposite foot the direction of the turn returns the body to level ground walking. Motivations for control of human walking bipeds are discussed. Further, a theory is developed that turning is dominated by contributions from the swing leg producing angular momentum about the body during the turn.
Effects of <i>In Vivo</i> Administration of Kainic Acid on the Extracellular Amino Acid Pool in the Rabbit Hippocampus (1983)

The effect of local administration of kainic acid in the rabbit hippocampus was studied; the hippocampus was perfused continuously in the freely moving animal with an implanted 0.3-mm dialysis fiber. The pattern of endogenous amino acids in the perfusate, reflecting extracellular amino acids, was monitored with liquid chromatography separation and fluorimetric detection of amino acid derivatives. Kainic acid was included in the perfusion medium for up to 70 min at 0.1-1.0 mM and, with time, induced epileptiform activity. Endogenous glutamic acid, taurine, and phosphoethanolamine levels were increased selectively at the lower perfusion concentrations of kainic acid. Long perfusion periods with higher concentrations increased the levels of virtually all amino acids. Perfusion of the hippocampus with depolarizing concentrations of potassium gave an amino acid response partly similar to that seen with kainic acid treatment. However, one notable difference between the two responses was that the extracellular concentration of glutamine, although not influenced by kainic acid, was significantly decreased after high potassium concentrations. These results confirm previous notions that kainic acid has a primarily excitatory effect, one manifestation of this effect being the release of glutamic acid.
LPA <sub>1</sub> ‐induced cytoskeleton reorganization drives fibrosis through CTGF‐dependent fibroblast proliferation (2013)

There has been much recent interest in lysophosphatidic acid (LPA) signaling through one of its receptors, LPA1, in fibrotic diseases, but the mechanisms by which LPA-LPA1 signaling promotes pathological fibrosis remain to be fully elucidated. Using a mouse peritoneal fibrosis model, we demonstrate central roles for LPA and LPA1 in fibroblast proliferation. Genetic deletion or pharmacological antagonism of LPA1 protected mice from peritoneal fibrosis, blunting the increases in peritoneal collagen by 65.4 and 52.9%, respectively, compared to control animals and demonstrated that peritoneal fibroblast proliferation was highly LPA1 dependent. Activation of LPA1 on mesothelial cells induced these cells to express connective tissue growth factor (CTGF), driving fibroblast proliferation in a paracrine fashion. Activation of mesothelial cell LPA1 induced CTGF expression by inducing cytoskeleton reorganization in these cells, causing nuclear translocation of myocardin-related transcription factor (MRTF)-A and MRTF-B. Pharmacological inhibition of MRTF-induced transcription also diminished CTGF expression and fibrosis in the peritoneal fibrosis model, mitigating the increase in peritoneal collagen content by 57.9% compared to controls. LPA1-induced cytoskeleton reorganization therefore makes a previously unrecognized but critically important contribution to the profibrotic activities of LPA by driving MRTF-dependent CTGF expression, which, in turn, drives fibroblast proliferation.
Electrical switching behaviour of semiconducting aluminium telluride glasses (1994)

Semiconducting chalcogenide glasses, AIxTe100-x with the atomic percentage of aluminium (x) varying between 15 and 25, have been prepared by the vacuum sealed-melt quenching technique. The I-V characteristics of these samples have been measured at four different temperatures using a custom-built PC-based system. All the compositions studied are found to exhibit a current-controlled negative resistance irreversible switching behaviour. Furthermore, it is observed that there is an increase in the switching field 'Et' of AIxTe100-1 glasses with increasing Al content. The threshold field for a given composition is found to decrease with increasing temperature.
High performance hierarchical torus network under matrix transpose traffic patterns (2004)

Interconnection networks play a crucial role in the performance of massively parallel computers. Hierarchical interconnection networks provide high performance at low cost by exploring the locality that exists in the communication patterns of massively parallel computers. A hierarchical torus network (HTN) is a 2D-torus network of multiple basic modules, in which the basic modules are 3D-torus networks that are hierarchically interconnected for higher level networks. The static network performance of the HTN has already been studied and has been shown to be good. Dynamic communication performance has been evaluated under uniform traffic patterns but not under a nonuniform traffic, such as matrix transpose traffic patterns. In this paper, we present a deadlock-free routing algorithm for the HTN using 3 virtual channels and evaluate the network's dynamic communication performance under matrix transpose traffic, using the proposed routing algorithm. We evaluate the dynamic communication performance of HTN, H3D-mesh, TESH, and mesh networks by computer simulation. We find that the dynamic communication performance of HTN is better than that of the H3D-mesh, TESH, and mesh networks.
Structure of the Metal-free γ-Carboxyglutamic Acid-rich Membrane Binding Region of Factor IX by Two-dimensional NMR Spectroscopy (1995)

The gamma-carboxyglutamic acid-rich domain of blood coagulation Factor IX is required for the binding of the protein to phospholipid membranes. To investigate the three-dimensional structure of this domain, a synthetic peptide corresponding to residues 1-47 of Factor IX was studied by 1H NMR spectroscopy. In the absence of metal ions, the proton chemical shift dispersion in the one-dimensional NMR spectrum indicated that the peptide contains regular structural elements. Upon the addition of Ca(II) or Mg(II), large chemical shift changes were observed in the amide proton and methyl proton regions of the spectrum, consistent with the conformational transitions that metal ions are known to induce in native Factor IX. The apopeptide was studied by two-dimensional NMR spectroscopy at 500 MHz to determine its solution structure. Protons were assigned using total correlation spectroscopy, nuclear Overhauser effect spectroscopy, and double quantum-filtered correlation spectroscopy experiments. Intensities of cross-peaks in the nuclear Overhauser effect spectrum were used to generate a set of interproton distance restraints. The structure of the apopeptide was then calculated using distance geometry methods. There are three structural elements in the apopeptide that are linked by a flexible polypeptide backbone. These elements include a short amino-terminal tetrapeptide loop (amino acids 6-9), the disulfide-containing hexapeptide loop (amino acids 18-23), and a carboxyl-terminal alpha helix (amino acids 37-46). Amide hydrogen exchange kinetics indicate that the majority of the peptide is solvent accessible, except in the carboxyl-terminal element. The structured regions in the apopeptide are insufficient to support phospholipid binding, indicating the importance of additional structural features in the Ca(II)-stabilized conformer.
Activation of H-ras Oncogene in Rat Bladder Tumors Induced by N-Butyl-N-(4-hydroxybutyl)nitrosamine1 (1988)

Ras-oncogene activation was investigated in the bladder tumors of F344 male rats given N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) in drinking water. DNA from one of the nine transitional cell carcinomas contained an H-ras oncogene detectable by the NIH/3T3 transfection assay. Analysis of p21 ras proteins suggested that the activating mutation resided within codon 61 of the H-ras gene and that such activating mutations were not present in other tumors. In contrast to mutational activation of ras genes, enhanced expression of p21 was observed in all tumors examined by immunohistochemical techniques with the use of Formalin-fixed paraffin-embedded tissue sections and an anti-ras p21 antibody, RAP-5. Further histochemical analysis of bladder tissues at various stages of the BBN-induced carcinogenic process indicated that the enhanced expression of p21 appeared early; the reactivity with RAP-5 was observed in diffuse hyperplastic epithelia after 5 weeks of exposure to BBN. The frequency of ras oncogenes, activated either by point mutations or overexpression of p21, in BBN-induced rat bladder carcinomas has thus been shown to be similar to that observed in human bladder carcinomas.
Cloudy with high chance of DBMS: A 10-year prediction for Enterprise-Grade ML (2019)

Machine learning (ML) has proven itself in high-value web applications such as search ranking and is emerging as a powerful tool in a much broader range of enterprise scenarios including voice recognition and conversational understanding for customer support, autotuning for videoconferencing, intelligent feedback loops in large-scale sysops, manufacturing and autonomous vehicle management, complex financial predictions, just to name a few. Meanwhile, as the value of data is increasingly recognized and monetized, concerns about securing valuable data and risks to individual privacy have been growing. Consequently, rigorous data management has emerged as a key requirement in enterprise settings. How will these trends (ML growing popularity, and stricter data governance) intersect? What are the unmet requirements for applying ML in enterprise settings? What are the technical challenges for the DB community to solve? In this paper, we present our vision of how ML and database systems are likely to come together, and early steps we take towards making this vision a reality.
Constrained adaptive filtering algorithms based on conjugate gradient techniques for beamforming (2010)

This article proposes constrained adaptive algorithms based on the conjugate gradient (CG) method for adaptive beamforming. The proposed algorithms are derived for the implementation of the beamformer according to the minimum variance and constant modulus criteria subject to a constraint on the array response. A CG-based weight vector strategy is created for enforcing the constraint and computing the weight expressions. The devised algorithms avoid the covariance matrix inversion and exhibit fast convergence with low complexity. A complexity analysis compares the proposed algorithms with the existing ones. The convergence properties of the CCM criterion are studied, conditions for convexity are established and a convergence analysis for the proposed algorithms is derived. Simulation results are conducted for both stationary and non-stationary scenarios, showing the convergence and tracking ability of the proposed algorithms.
Toxic shock syndrome: the effect of solid phase materials on the physiology of Staphylococcus aureus. (1985)

Rayon and chemically modified cotton were compared for their effects in vitro on the physiology of a strain of Staphylococcus aureus isolated from a patient with toxic shock syndrome. Two types of experiment were carried out. The materials were used to pretreat the medium before culturing in the absence of the materials. Chemically modified cotton was either added or removed from three hour cultures and incubation continued. The rayon treated medium had little effect on growth or exoenzyme/toxin production by S. aureus. The chemically modified cotton greatly reduced growth of S. aureus and decreased exoenzyme/toxin production when added to three hour cultures. However, pretreated medium and cultures grown for three hours with the material present followed by incubation in its absence increased the exoenzyme/toxin production by S. aureus. The in vitro data suggests large effects of chemically modified cotton on the physiology of S. aureus by in some way, at present unknown, altering the growth medium.
Fast signature simulation for PPSFP simulators (2003)

This paper presents a novel technique to compute the signatures of multiple-input shift-registers (MISRs) in computer simulation when used in conjunction with parallel pattern single fault propagation (PPSFP) simulators. We first use a look-up table technique similar to compute a set of signatures, one for each input data stream of a MISR, at a common input tap position. Then we present an algorithm that modifies these signatures to reflect their actual input positions and obtain the final signature. Our experimental results show that the proposed signature simulation technique outperforms some existing methods with minimal memory requirements.