gebhart/patrepeval huggingface dataset:
Machine-generated Explanations of Engineering Models: A Compositional Modeling Approach. (1993)

We describe a method for generating causal explanations, in natural language, of the simulated behavior of physical devices. The method is implemented in DME, a system that helps formulate mathematical simulation models from a library of model fragments using a Compositional Modeling approach. Because explanations are generated from models that are dynamically constructed from modular pieces, several of the limitations of conventional explanation techniques are overcome. Since the explanation system has access to the derivation of mathematical equations from the original model specification, the system can explain low-level quantitative behavior predicted by conventional simulation techniques in terms of salient behavioral abstractions such as physical processes, idealized components, and operating modes. Instead of relying on ad hoc causal models, crafted specifically for the explanation task, the program infers causal relationships among parameters in a constraint-ba...
An Integrated-Circuit Approach to Extracellular Microelectrodes (1970)

This paper describes a new multielectrode microprobe which utilizes integrated-circuit fabrication techniques to overcome many of the problems associated with conventional microelectrodes. The probe structure consists of an array of gold electrodes which are supported on a silicon carrier and which project beyond the carrier for a distance of about 50 μ to allow a close approach to active neurons. These electrodes are covered with a thin (0.4-μ) layer of silicon dioxide which is selectively removed at the electrode tips using high-resolution photoengraving techniques to define the recording areas precisely. The processing sequence described permits any two-dimensional electrode array to be realized. Interelectrode spacings can be accurately controlled in the range from 10 to 20 μ or larger, and electrode-tip diameters can be as small as 2 μ.
Immunodominance of Antigenic Site B in the Hemagglutinin of the Current H3N2 Influenza Virus in Humans and Mice (2018)

The hemagglutinin protein of H3N2 influenza viruses is the major target of neutralizing antibodies induced by infection and vaccination. However, the virus frequently escapes antibody-mediated neutralization due to mutations in the globular head domain. Five topologically distinct antigenic sites in the head domain of H3 hemagglutinin, A to E, have been previously described by mapping the binding sites of monoclonal antibodies, yet little is known about the contribution of each site to the immunogenicity of modern H3 hemagglutinins, as measured by hemagglutination inhibition activity, which is known to correlate with protection. To investigate the hierarchy of antibody immunodominance, five Δ1 recombinant influenza viruses expressing hemagglutinin of the A/Hong Kong/4801/2014 (H3N2) strain with mutations in single antigenic sites were generated. Next, the Δ1 viruses were used to determine the hierarchy of immunodominance by measuring the hemagglutination inhibition reactivity of mouse antisera and plasma from 18 human subjects before and after seasonal influenza vaccination in 2017-2018. In both mice and humans, mutations in antigenic site B caused the most significant decrease in hemagglutination inhibition titers compared to wild-type hemagglutinin. This study revealed that antigenic site B is immunodominant in the H3N2 influenza virus strain included in the current vaccine preparations.<b>IMPORTANCE</b> Influenza viruses rapidly evade humoral immunity through antigenic drift, making current vaccines poorly effective and antibody-mediated protection short-lived. The majority of neutralizing antibodies target five antigenic sites in the head domain of the hemagglutinin protein that are also the most sequence-variable regions. A better understanding of the contribution of each antigenic site to the overall antibody response to hemagglutinin may help in the design of improved influenza virus vaccines.
The primary structure of Aspergillus niger acid proteinase A. (1991)

The complete amino acid sequence of the acid proteinase A, a non-pepsin type acid proteinase from the fungus Aspergillus niger var. macrosporus, was determined by protein sequencing. The enzyme was first dissociated at pH 8.5 into a light (L) chain and a heavy (H) chain, and the L chain was sequenced completely. Further sequencing was performed with the reduced and pyridylethylated or aminoethylated derivative of the whole protein, using peptides obtained by digestions with Staphylococcus aureus V8 protease, trypsin, chymotrypsin, and lysylendopeptidase. The location of the two disulfide bonds was determined by analysis of cystine-containing peptides obtained from a chymotryptic digest of the unmodified protein. These results established that the protein consists of a 39-residue L chain and a 173-residue H chain that associate noncovalently to form the native enzyme of 212 residues (Mr 22,265). This is, to our knowledge, the first time that such a protein with a rather short peptide chain associated noncovalently has been found. No sequence homology is found with other acid or aspartic proteinases, except for Scytalidium lignicolum acid proteinase B, an enzyme unrelated to pepsin by sequence, which has about 50% identity with the present enzyme. These two enzymes, however, are remarkably different from each other in some structural features.
Measurement and prediction of radiological progression in early rheumatoid arthritis. (1994)

Both Sharp and Larsen indices are sensitive to change in the first year of RA, but Sharp has advantages of greater sensitivity and reproducibility: CMC ratio is not useful. Radiological progression rate in the first year correlates only moderately with subsequent rate of progression up to 8 years. This suggests that radiological progression is nonuniform and that different patterns of progression over time may exist.
A New HID Lamp Ballast using Internal LC Resonance and Coupled Inductor Filter (2001)

This paper proposes a new ballast that is ignited by internal LC resonance of buck converter. In order to cancel the steady state current ripple, the proposed ballast utilizes the coupled inductor filter which minimizes the size and weight of the ballast. The operation mode of the proposed ballast is analyzed and the performance of the new ballast is verified by the experimental results from a 150W prototype ballast for metal halide discharge (MHD) lamp.
Regulation of the voltage-gated K+ channel KCNA10 by KCNA4B, a novel β-subunit (2002)

Voltage-gated K+ (Kv) channels are heteromultimeric complexes consisting of pore-forming alpha-subunits and accessory beta-subunits. Several beta-subunits have been identified and shown to interact with specific alpha-subunits to modify their levels of expression or some of their kinetic properties. The aim of the present study was to isolate accessory proteins for KCNA10, a novel Kv channel alpha-subunit functionally related to Kv and cyclic nucleotide-gated cation channels. Because one distinguishing feature of KCNA10 is a putative cyclic nucleotide-binding domain located at the COOH terminus, the entire COOH-terminal region was used to probe a human cardiac cDNA library using the yeast two-hybrid system. Interacting clones were then rescreened in a functional assay by coinjection with KCNA10 in Xenopus oocytes. One of these clones (KCNA4B), when injected alone in oocytes, produced no detectable current. However, when coinjected with KCNA10, it increased KCNA10 current expression by nearly threefold. In addition, the current became more sensitive to activation by cAMP. KCNA4B can be coimmunoprecipitated with the COOH terminus of KCNA10 and full-length KCNA10. It encodes a soluble protein (141 aa) with no amino acid homology to known beta-subunits but with limited structural similarity to the NAD(P)H-dependent oxidoreductase superfamily. KCNA4B is located on chromosome 13 and spans approximately16 kb, and its coding region is made up of five exons. In conclusion, KCNA4B represents the first member of a new class of accessory proteins that modify the properties of Kv channels.
Opsonization Effects onMycobacterium aviumsubsp.paratuberculosis-Macrophage Interactions (2005)

High antibody titers in ruminants infected with Mycobacterium avium subsp. paratuberculosis correlates with disease progression. Effects of humoral responses during mycobacterial infection are not completely understood. This study suggests that activation status may be an important factor in determining macrophage ability to limit proliferation of opsonized M. avium subsp. paratuberculosis.
The SH2/SH3 domain-containing protein Nck is recognized by certain anti-phospholipase C-gamma 1 monoclonal antibodies, and its phosphorylation on tyrosine is stimulated by platelet-derived growth factor and epidermal growth factor treatment. (1992)

In the course of our investigation of phospholipase C (PLC)-gamma 1 phosphorylation by using a set of anti-PLC-gamma 1 monoclonal antibodies (P.-G. Suh, S. H. Ryu, W. C. Choi, K.-Y. Lee, and S. G. Rhee, J. Biol. Chem. 263:14497-14504, 1988), we found that some of these antibodies directly recognize a 47-kDa protein. We show here that this 47-kDa protein is identical to the SH2/SH3-containing protein Nck (J. M. Lehmann, G. Riethmuller, and J. P. Johnson, Nucleic Acids Res. 18:1048, 1990). Nck was found to be constitutively phosphorylated on serine in resting NIH 3T3 cells. Platelet-derived growth factor (PDGF) treatment led to increased Nck phosphorylation on both tyrosine and serine. Nck was also found to be phosphorylated on tyrosine in epidermal growth factor (EGF)-treated A431 cells and in v-Src-transformed NIH 3T3 cells. Multiple sites of serine phosphorylation were detected in Nck from resting cells, and no novel sites were found upon PDGF or EGF treatment. A single major tyrosine phosphorylation site was found in Nck in both PDGF- and EGF-treated cells and in v-Src-transformed cells. This same tyrosine was phosphorylated in vitro by purified PDGF and EGF receptors and also by pp60c-src. We compared the phosphorylation of Nck and PLC-gamma 1 in several cell lines transformed by oncogenes with different modes of transformation. Although PLC-gamma 1 and Nck have significant amino acid identity, particularly in their SH3 regions, and both associate with growth factor receptors in a ligand-dependent manner, they were not always phosphorylated on tyrosine in a coincident manner.
Assessment of Brain Shift Related to Deep Brain Stimulation Surgery (2007)

Deep brain stimulation (DBS) surgery can significantly improve the quality of life for patients suffering from movement disorders, but the success of the procedure depends on the implantation accuracy of the DBS electrode array. Pre-operative surgical planning and navigation are based on the assumption that the brain tissue is rigid between the time of the acquisition of the pre-operative image set and the time of surgery. A shift of deep brain structures by only a few millimeters can potentially increase the number of required microelectrode and/or macroelectrode tracks and decrease implantation accuracy. We studied 25 subjects that underwent DBS surgery and analyzed brain shift between pre-operative and post-operative 3D MRI scans. Brain shift of up to 4 mm was observed in deep brain structures. On average, the recorded shift was in the direction of gravity, with deeper structures experiencing smaller shift than more superficial structures. The main conclusion of the study is that the brain shift is comparable to the size of the targets in deep brain stimulation surgery and should not be ignored. Techniques that minimize the amount of brain shift may therefore lead to increased accuracy of DBS lead implantation.
DAB389EGF Fusion Protein Therapy of Refractory Glioblastoma Multiforme (2003)

Primary brain tumors including anaplastic astrocytomas and glioblastoma multiforme are difficult to treat because of their locally invasive nature and chemoradioresistance. Novel therapies are needed. One class of therapeutics is fusion proteins consisting of peptide toxins fused to brain tumor selective ligands. DAB389EGF is a fusion protein composed of the catalytic and translocation domains of diphtheria toxin fused via a His-Ala linker to human epidermal growth factor (EGF). DAB389EGF is selectively toxic to EGF receptor (EGFR) overexpressing cells. Close to half of all high-grade primary brain tumors have EGFR gene amplification and EGFR overexpression. With the use of convection-enhanced delivery (CED), DAB389EGF may be delivered locally at high concentrations to the brain tumor. CED would avoid many of the pharmacologic and toxicologic barriers which have limited effective use of this agent including rapid clearance from the circulation, high anti-diphtheria toxin antibody titers in the blood and toxicities to the liver and kidney. Both cell lines and animal models are available to assess the potential of this agent for brain tumor therapy. Since significant amounts of clinical grade DAB389EGF are available, some careful additional preclinical efficacy work should lead to testing of this agent in patients within the next few years.
Characters of two North American Chermidae (1924)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Cardiac mass and peripheral vascular structure in hydralazine-treated spontaneously hypertensive rats. (1985)

We have examined the effect of antihypertensive treatment on heart weight and on structural and functional characteristics of isolated mesenteric resistance vessels (internal diameter 170-220 micron) in spontaneously hypertensive rats (SHR) and in Wistar-Kyoto rats (WKY). The SHR and WKY were treated with hydralazine from the age of 4 weeks and were examined at ages 12 to 14 weeks and 23 to 27 weeks. Treated SHR had a mean blood pressure as much as 29% below that of control WKY, which in turn was 25 to 40% less than that of control SHR. In 12- to 14-week-old rats the heart to body weight ratio (which in control SHR was 13% greater than of WKY) was unaffected by treatment. Thereafter, the heart to body weight ratio of treated SHR did not increase as much as usual. At both ages, the media thickness and contractile response of the resistance vessels of the SHR (which were, respectively, 37% and 30% greater than those of vessels of WKY) were unaffected by treatment. However, because treatment caused a small (8%) increase in the lumen diameter of the vessels of the SHR, treatment did cause small, but possibly physiologically important, decreases both in the media to lumen ratio (11%) and in the pressure against which these vessels would have been able to contract (10%). Treatment had little effect on the pharmacological characteristics of vessels of either SHR or WKY. The results suggest that the increased heart weight, media thickness, and contractile response in mesenteric resistance vessels of SHR up to ages 23 to 27 weeks are due primarily to factors other than increased pressure.
12-O-Tetradecanoyl-Phorbol-13-Acetate Induction of the Human Collagenase Gene Is Mediated By an Inducible Enhancer Element Located in the 5′-Flanking Region (1987)

Genomic clones coding for human fibroblast collagenase were isolated. By constructing and transfecting mutants with 5' and 3' deletion mutations of the 5' control region of the gene into human or murine cells, we delimited a 32-base-pair sequence at positions -73 to -42 which is required for the induction of transcription by the tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate. The DNA element behaves as a 12-O-tetradecanoyl-phorbol-13-acetate-inducible enhancer: it mediates the stimulation of transcription to the heterologous herpes simplex virus thymidine kinase promoter and acts in a position- and orientation-independent manner. Differences in enhancer efficiency in different cell lines are interpreted to indicate differences in the activity of a trans-acting factor.
Effect of oral contraceptives (OCS) on drug metabolizing enzymes (DMES) as measured by the validated cooperstown 5+1 cocktail (5+1) (2003)

Clinical Pharmacology &amp; Therapeutics (2003) 73 , P14–P14; doi:
DNA microarrays in lymphoid malignancies. (2003)

Gene expression profiling using cDNA microarrays has the potential to improve current lymphoma classification schemes by establishing a molecular diagnosis of these malignancies. The use of this technology led to the discovery of biologically and clinically distinct subtypes of diffuse large B-cell lymphoma (DLBCL). Gene expression data can also be used to formulate powerful mathematical algorithms that predict the clinical outcome in patients with DLBCL and mantle cell lymphoma. In B-cell chronic lymphocytic leukemia, gene expression profiling identified ZAP70, an important prognostic marker whose expression correlates with the mutational status of the immunoglobulin heavy chain gene and, therefore, with survival in these patients. These examples illustrate that gene expression profiling may pave the way for detailed molecular characterization of lymphoid malignancies that will ultimately lead to tailored, disease-specific therapies.
Memory ordering: a value-based approach (2004)

Value-based replay enforces memory ordering by simply reexecuting load instructions in program order prior to commit, eliminating the need for associative search functionality from the load queue. The load queue can therefore be implemented as a first-in-first-out buffer, like the reorder buffer, which is fundamentally more scalable and power-efficient. In order to mitigate the bandwidth and resource occupancy costs of replay, a set of heuristics filter the set of loads that must be replayed, resulting in negligible performance degradation and data cache bandwidth increases relative to a conventional machine
<title>Global/local motion-compensated frame interpolation for low-bit-rate video</title> (2000)

A new motion-compensated frame interpolation scheme for low bitrate video based on the ITU-T H.263/H.263+ standard is investigated in this research. The proposed scheme works solely on the decoded bitstream with a block-based approach to achieve interpolation results. It is composed of two main modules: the background/foreground segmentation module and the hybrid motion compensated frame interpolation module. The background/foreground segmentation module uses a global motion model to estimate the background motion and an iterative background update to refine the segmentation. The hybrid motion compensated frame interpolation module is employed to reconstruct background and foreground, respectively. Global motion compensation and frame interpolation is applied to background blocks where either the 6-parameter affine or the 8-parameter perspective model is used to reduce the computational complexity and implement perspective correction, while local motion compensation and frame interpolation with localized triangular patch mapping is applied to the foreground area. Experiments show that the proposed scheme can achieve higher overall visual quality compared to conventional block-based frame interpolation schemes.
Folding of Aromatic Amide-Based Oligomers Induced by Benzene-1,3,5-tricarboxylate Anion in DMSO (2009)

In this paper, we describe the folding of a series of linear arylamide oligomers in DMSO that is induced by benzene-1,3,5-tricarboxylate anion. The oligomers are comprised of naphthalene-2,7-diamine and 1,3,5-benzenetricarboxylic acid segments with two (tert-butoxycarbonylamino) groups at the ends and two to four hydrophilic N,N-bis(2-(2-(2-methoxyethoxy)ethoxy)ethyl)amino groups at one side of the backbones. (2D NOESY) (1)H NMR, fluorescence and UV-vis studies indicate that the oligomers do not adopt defined conformations in DMSO but fold into compact structures in the presence of the anion. It is revealed that the folded conformation is induced by intermolecular hydrogen bonds between the amide and aromatic hydrogen atoms of the oligomers and the oxygen atoms of the anion. (1)H NMR and UV-vis titrations support a 1:1 binding stoichiometry, and the associated constants are determined, which are found to increase with the elongation of the oligomers.
The Cell Cycle (1981)

FIFTEEN years ago it seemed that one could selectively damage cancer cells by exploiting simple differences in the cell-cycle kinetics of normal and neoplastic cells. Although these hopes have not been fulfilled, an increasing understanding of the biology of cell division has clarified concepts of tumor growth and indicated new approaches to more effective treatment.There are two definitions of the cell cycle. In a strict sense, the cell cycle is the interval between the midpoint of mitosis and the midpoint of the subsequent mitosis in one daughter cell or both. By this narrow definition, a review of the cell . . .
Self-aligned enhancement-mode AlGaN/GaN HEMTs using fluoride-based plasma treatment (2005)

Wide bandgap AlGaN/GaN high electron mobility transistors (HEMTs) are emerging as excellent candidates for high power, high frequency and also high temperature applications. Up to now, the focus has been to improve the performance of depletion-mode (D-mode) AlGaN/GaN HEMTs. From the application point of view, enhancement-mode (E-mode) HEMTs have many advantages.
Role of GSK‐3β activation and α7 nAChRs in Aβ1–42‐induced tau phosphorylation in PC12 cells (2008)

Beta-amyloid peptide 1-42 (Abeta(1-42)) and hyperphosphorylated tau are associated with neurodegeneration in Alzheimer's disease. Emerging evidence indicates that Abeta(1-42) can potentiate hyperphosphorylation of tau in cell lines and in transgenic mice, but the underlying mechanism(s) remains unclear. In this study, Abeta(1-42)-induced tau phosphorylation was investigated in differentiated PC12 cells. Treatment of cells with Abeta(1-42) increased phosphorylation of tau at serine-202 as detected by AT8 antibody. This Abeta(1-42)-induced tau phosphorylation paralleled phosphorylation of glycogen synthase kinase-3beta (GSK-3beta) at tyrosine-216 (GSK-3beta-pY216), which was partially inhibited by the GSK-3beta inhibitor, CHIR98023. Abeta(1-42)-induced tau phosphorylation and increase in GSK-3beta-pY216 phosphorylation were also partially attenuated by alpha7 nicotinic acetylcholine receptor (alpha7 nAChR) selective ligands including agonist A-582941 and antagonists methyllycaconitine and alpha-bungarotoxin. The alpha7 nAChR agonist and the GSK-3beta inhibitor had no additive effect. These observations suggest that alpha7 nAChR modulation can influence Abeta(1-42)-induced tau phosphorylation, possibly involving GSK-3beta. This study provides evidence of nAChR mechanisms underlying Abeta(1-42) toxicity and tau phosphorylation, which, if translated in vivo, could provide additional basis for the utility of alpha7 nAChR ligands in the treatment of Alzheimer's disease.