gebhart/patrepeval huggingface dataset:
Carbonyl sulfide and carbon dioxide as new substrates, and carbon disulfide as a new inhibitor, of nitrogenase (1995)

Nitrogenase is the metalloenzyme responsible for the biological reduction of N2 to NH3. Nitrogenase has been shown to reduce a variety of substrates in addition to N2 and protons. General properties of alternative substrates for nitrogenase are the presence of N-N, N-O, N-C, and C-C triple or double bonds. In the present work, we demonstrate that Azotobacter vinelandii nitrogenase can reduce both C-S and C-O bonds. Nitrogenase was found to reduce carbonyl sulfide (COS), to CO and H2S at a maximum rate of 37.2 +/- 2.0 nmol min-1 (mg of protein)-1 with a Km of 3.1 +/- 0.6 mM. The formation of CO from nitrogenase reduction of COS was monitored spectrophotometrically in real time by following the formation of carboxyhemoglobin. In this assay, the change in the visible absorption spectrum of reduced hemoglobin upon binding CO provided a sensitive way to quantify CO formation and to remove CO, which is a potent inhibitor of nitrogenase, from solution. COS reduction by nitrogenase required the molybdenum-iron protein (MoFeP), the iron protein (FeP), and MgATP. The reduction reaction was inhibited by MgADP, acetylene, and N2, while H2 was not an inhibitor of COS reduction. The pH optimum for COS reduction was 6.5. Nitrogenase was also found to reduce carbon dioxide (CO2) to CO and H2O. CO2 was reduced at a maximum rate of 0.8 +/- 0.07 nmole min-1 (mg of protein)-1 with a calculated Km for CO2 of 23.3 +/- 3.7 mM.(ABSTRACT TRUNCATED AT 250 WORDS)
Optical tomography of tissues (2002)

Methods of optical tomography of biological tissues are considered, which include pulse-modulation and frequency-modulation tomography, diffusion tomography with the use of cw radiation sources, optical coherent tomography, speckle-correlation tomography of nonstationary media, and optoacoustic tomography. The method for controlling the optical properties of tissues is studied from the point of view of increasing a probing depth in optical coherent tomography. The modern state and prospects of the development of optical tomography are discussed.
Robotics-based location sensing using wireless ethernet (2002)

A key subproblem in the construction of location-aware systems is the determination of the position of a mobile device. This paper describes the design, implementation and analysis of a system for determining position inside a building from measured RF signal strengths of packets on an IEEE 802.11b wireless Ethernet network. Previous approaches to location awareness with RF signals have been severely hampered by non-linearity, noise and complex correlations due to multi-path effects, interference and absorption. The design of our system begins with the observation that determining position from complex, noisy and non-linear signals is a well-studied problem in the field of robotics. Using only off-the-shelf hardware, we achieve robust position estimation to within a meter in our experimental context and after adequate training of our system. We can also coarsely determine our orientation and can track our position as we move. By applying recent advances in probabilistic inference of position and sensor fusion from noisy signals, we show that the RF emissions from base stations as measured by off-the-shelf wireless Ethernet cards are sufficiently rich in information to permit a mobile device to reliably track its location.
Data‐Snooping, Technical Trading Rule Performance, and the Bootstrap (1999)

In this paper we utilize White's Reality Check bootstrap methodology (White (1999)) to evaluate simple technical trading rules while quantifying the data‐snooping bias and fully adjusting for its effect in the context of the full universe from which the trading rules were drawn. Hence, for the first time, the paper presents a comprehensive test of performance across all technical trading rules examined. We consider the study of Brock, Lakonishok, and LeBaron (1992), expand their universe of 26 trading rules, apply the rules to 100 years of daily data on the Dow Jones Industrial Average, and determine the effects of data‐snooping.
Congenital macrothrombocytopenia‐linked mutations in the actin‐binding domain of α‐actinin‐1 enhance F‐actin association (2016)

Mutations in the actin cross-linking protein actinin-1 were recently linked to dominantly inherited congenital macrothrombocytopenia. Here, we report that several disease-associated mutations that are located within the actinin-1 actin-binding domain cause increased binding of actinin-1 to actin filaments and enhance filament bundling in vitro. These actinin-1 mutants are also more stably associated with the cytoskeleton in cultured cells, as assessed by biochemical fractionation and fluorescence recovery after photobleaching experiments. For two mutations the disruption of contacts between the calponin homology domains within the actinin actin-binding domain may explain increased filament binding--providing mechanistic and structural insights into the basis of actinin-1 dysfunction in congenital macrothrombocytopenia.
Synthesis of Ternary Logic Circuits Using 2:1 Multiplexers (2018)

Traditionally, binary decision diagram (BDD)-based algorithms are used to synthesize binary logic functions. A BDD can be transformed into circuit implementation by replacing each node in the BDD with a 2:1 multiplexer. Similarly, a ternary decision diagram can be transformed into circuit implementation using 3:1 Multiplexers. In this paper, we present a novel synthesis technique to implement ternary logic circuits using 2:1 multiplexers. Initially a methodology, which transforms a ternary logic function into a ternary-transformed binary decision diagram, is presented. This methodology is the basis for the synthesis algorithm that is used to synthesize various ternary functions using 2:1 multiplexers. Results for various ternary benchmark functions indicate that the proposed algorithm results in circuits that have, on an average 79%, and up to 99% fewer transistors when compared with the most recent 3:1 multiplexer-based algorithm available in the literature. Synthesized circuits have been implemented using carbon-nanotube field-effect transistors and simulated in HSPICE.
Enhanced pharmacokinetic properties of a glycoPEGylated recombinant factor IX: a first human dose trial in patients with hemophilia B (2011)

Replacement therapy with factor IX (FIX) concentrates is the recommended treatment for patients with hemophilia B, an X-linked bleeding disorder occurring in 1:25,000 male births. N9-GP is a recombinant FIX molecule with a prolonged half-life which is obtained by site-directed glycoPEGylation where a 40-kDa polyethylene glycol molecule is attached to the activation peptide of FIX. This first human dose trial in patients with hemophilia B investigated the safety and pharmacokinetic properties of a single IV dose of N9-GP. Sixteen previously treated patients received one dose of their previous FIX product followed by one dose of N9-GP at the same dose level (25, 50, or 100 U/kg). None of the patients developed inhibitors. One patient developed transient hypersensitivity symptoms during administration of N9-GP and was excluded from pharmacokinetic analyses. In the remaining 15 patients, N9-GP was well-tolerated. The half-life was 93 hours, which was 5 times higher than the patient's previous product. The incremental recovery of N9-GP was 94% and 20% higher compared with recombinant and plasma-derived products, respectively. These results indicate that N9-GP has the potential to reduce dosing frequency while providing effective treatment of bleeding episodes with a single dose. The trial was registered at www.clinicaltrials.gov as NCT00956345.
Arterial foam cells with distinctive immunomorphologic and histochemical features of macrophages. (1980)

A variable population of fat-filled "foam" cells in diet-induced experimental arterial intimal plaques of rabbits and monkeys were analyzed for several features characteristic of macrophages. These included: 1) surface binding and phagocytosis of antibody-coated or complement-coated erythrocytes to detect specific surface receptors; 2) cytochemical tests and ultrastructural features to evaluate cell function and structure; and 3) rapid adherence to glass, a feature of macrophage activity, to isolate and identify a homogeneous population of fat-filled foam cells from excised and disrupted arterial lesions. Mixed populations of cells grown in culture from explants of lesions were also analyzed and lipid-filled cells were studied in histologic sections of adjacent lesions. Eighty to ninety percent of the easily dislodged glass-adherent cells from lesions had surface receptors for the Fc portion of immunoglobulin G and for the third component of complement. Coated red blood cells were readily phagocytized, but noncoated cells were not. Acid lipase activity was demonstrated in the Fc-receptor-positive cells. These cells were also devoid of ultrastructural features of smooth muscle. Among the cells growing or migrating out of explants, a population of large round foam cells possessed all of the macrophage features found in the glass-adherent cells from lesions and lacked ultrastructural characteristics of smooth muscle. Fusiform lipid vacuolated cells also grew out of the explants but did not exhibit surface receptors, failed to phagocytize coated or noncoated erythrocytes and did not stain for acid lipase activity; these cells showed distinctive morphologic features of smooth muscle. In histologic sections of nearby lesions foam cells that showed macrophage characteristics, ie, acid lipase activity and the presence of lysozymelike antigen, lacked ultrastructural smooth muscle features. Smooth muscle cells in lesion sections often contained lipid but demonstrated no lysozyme or acid lipase activity. The occurrence of a population of cells with several functional and structural features of macrophages among the lipid-laden cells of experimental diet-induced arterial lesions suggests that some foam cells may be derived from monocytes. An alternative explanation, that metabolically altered autochthonous arterial wall cells assume one or more characteristics of mononuclear phagocytes is less likely, since some of the markers used in these experiments are unrelated. Both explanations deserve further careful study.
Conserved sequence elements associated with exon skipping (2003)

One of the major forms of alternative splicing, which generates multiple mRNA isoforms differing in the precise combinations of their exon sequences, is exon skipping. While in constitutive splicing all exons are included, in the skipped pattern(s) one or more exons are skipped. The regulation of this process is still not well understood; so far, cis- regulatory elements (such as exonic splicing enhancers) were identified in individual cases. We therefore set to investigate the possibility that exon skipping is controlled by sequences in the adjacent introns. We employed a computer analysis on 54 sequences documented as undergoing exon skipping, and identified two motifs both in the upstream and downstream introns of the skipped exons. One motif is highly enriched in pyrimidines (mostly C residues), and the other motif is highly enriched in purines (mostly G residues). The two motifs differ from the known cis-elements present at the 5' and 3' splice site. Interestingly, the two motifs are complementary, and their relative positional order is conserved in the flanking introns. These suggest that base pairing interactions can underlie a mechanism that involves secondary structure to regulate exon skipping. Remarkably, the two motifs are conserved in mouse orthologous genes that undergo exon skipping.
Hemophilic factor VIII C1- and C2-domain missense mutations and their modeling to the 1.5-angstrom human C2-domain crystal structure (2000)

Abstract Factor VIII C domains contain key binding sites for von Willebrand factor (vWF) and phospholipid membranes. Hemophilic patients were screened for factor VIII C-domain mutations to provide a well-characterized series. Mutated residues were localized to the high-resolution C2 structure and to a homology model of C1. Of 30 families found with mutations in the C domains, there were 14 missense changes, and 9 of these were novel. Of the missense mutations, 10 were associated with reduced vWF binding and 8 were at residues with surface-exposed side chains. Six of the 10 mutants had nearly equivalent factor VIII clotting activity and antigen level, suggesting that reduced vWF binding could cause hemophilia by reducing factor VIII stability in circulation. When the present series was combined with previously described mutations from an online international database, 11 C1 and C2 mutations in patients with mild or moderately severe hemophilia A were associated with antibody-inhibitor development in at least one affected individual. Of these substitutions, 6 occurred at surface-exposed residues. As further details of the C1 structure and its interface with C2 become available, and as binding studies are performed on the plasma of more patients with hemophilic C-domain mutations, prediction of surface binding sites should improve, allowing confirmation by site-specific mutagenesis of surface-exposed residues.
A Script-Based Testbed for Mobile Software Frameworks (2008)

Software testing is essential and takes a large part of resources during software development. This motivates automating software testing as far as possible. Frameworks for automating unit testing are approved and applied for a plethora of programming languages to write tests for small units in the same programming language. Both constraints, unit size and programming language, inhibit automation of software testing in domain of mobile software frameworks. This circumstance has motivated the development of a new testbed for a framework in the domain of mobile systems. In this paper, we describe requirements and challenges in testing mobile software frameworks in general and present a novel testbed for the APOXI framework that addresses these requirements. The main ideas behind this testbed are the usage of a scripting language to specify test cases and to incorporate domain-specific aspects on the language level. The testbed facilitates component and system testing but can be used for unit testing as well.
Effect of probiotic supplementation on serum/yolk cholesterol and on egg shell thickness in layers (1995)

1. The effect of probiotic supplementation on egg production, on serum and yolk cholesterol and on egg shell thickness in 24 White Leghorn layers was studied from 28-38 weeks of age. 2. In 3 treatments the diet was supplemented with 0, 100 and 150 mg probiotic/kg food. 3. In the 100 mg probiotic group, egg production improved by 5%, and shell thickness improved slightly, with fewer thin-shelled eggs than in the control (8.6% compared to 18.6%). 4. The initial serum cholesterol concentration of 170.2 mg/dl in control birds remained similar throughout the 10-week experimental period, whereas in the 150 mg group the initial value of 176.5 mg/dl decreased to 114.3 mg by week 10. 5. Yolk cholesterol concentration was 14.69 mg in the control group and 11.28 and 11.37 mg/g in the 100 and 150 mg probiotic groups respectively. Overall mean total egg cholesterol was thus reduced by probiotic supplementation.
Effect of low dose cyclophosphamide on the immune system of cancer patients: depletion of CD4+, 2H4+ suppressor-inducer T-cells. (1988)

We studied peripheral blood lymphocytes (PBL) from 42 patients with metastatic melanoma undergoing treatment with cyclophosphamide (CY) plus melanoma vaccine to determine whether CY immunopotentiation could be related to depletion of T-cells that function as inducers of suppression. Every 28 days, the patients were given CY, 300 mg/m2 i.v., followed 3 days later by the intradermal injection of autologous, irradiated melanoma cells mixed with Bacillus Calmette-Guérin. PBL were separated by density gradient centrifugation and cryopreserved until needed for testing. They were stained with monoclonal antibodies directly conjugated to fluorescein isothiocyanate or phycoerythrin and analyzed by two-color flow cytometry. At no time after the initiation of CY plus vaccine were there any significant changes in the percentages of helper-inducer T-cells (CD4+), suppressor-cytotoxic T-cells (CD8+), or the subpopulation of CD8+ cells expressing Leu 15, a marker for suppressor cells. Treatment of melanoma patients with CY plus vaccine resulted in a progressive fall in the proportion of CD4+ T-cells expressing the 2H4 (CD45) antigen, which identifies inducers of suppression. The reduction of CD4+, 2H4+ T-cells did not become apparent until day 28 after the first dose of CY and reached statistical significance only on days 49 (21 days after the second dose) and 105 (21 days after the fourth dose) (mean changes +/- SE: day 49, -5.4 +/- 1.4%, P less than 0.01; day 105, -9.1 +/- 2.2%, P less than 0.01; t test for nonindependent samples). In contrast, the proportion of CD4+ T-cells expressing the antigen 4B4 (CDw29), which are true helper cells, increased slightly, although not significantly, following the institution of CY plus vaccine (mean changes: day 49, +2.9 +/- 2.1%; day 105, +3.6 +/- 2.4%). Similar results were obtained when absolute numbers of circulating cells, rather than percentages, were analyzed. Thus the number of CD4+, 2H4+ T-cells fell from a mean of 395,000/ml on day 0 to 309,000/ml on day 49 (P less than 0.01) to 256,000/ml on day 105 (P less than 0.05). The absolute number of CD4+, 4B4+ cells remained unchanged at the same time points. These changes were not due to progression of metastatic disease, since a comparison of patients with progressive metastases with those who were rendered disease free by surgery showed no significant differences in the reduction of the percentage of CD4+, 2H4+ T-cells.(ABSTRACT TRUNCATED AT 400 WORDS)
Bilayer Thickness and Membrane Protein Function: An Energetic Perspective (2007)

The lipid bilayer component of biological membranes is important for the distribution, organization, and function of bilayer-spanning proteins. This regulation is due to both specific lipid-protein interactions and general bilayer-protein interactions, which modulate the energetics and kinetics of protein conformational transitions, as well as the protein distribution between different membrane compartments. The bilayer regulation of membrane protein function arises from the hydrophobic coupling between the protein's hydrophobic domains and the bilayer hydrophobic core, which causes protein conformational changes that involve the protein/bilayer boundary to perturb the adjacent bilayer. Such bilayer perturbations, or deformations, incur an energetic cost, which for a given conformational change varies as a function of the bilayer material properties (bilayer thickness, intrinsic lipid curvature, and the elastic compression and bending moduli). Protein function therefore is regulated by changes in bilayer material properties, which determine the free-energy changes caused by the protein-induced bilayer deformation. The lipid bilayer thus becomes an allosteric regulator of membrane function.
Silver/polystyrene-coated hollow glass waveguides for the transmission of terahertz radiation (2007)

We have applied techniques developed for IR waveguides to fabricate Ag/polystyrene (PS) -coated hollow glass waveguides (HGWs) for transmission of terahertz radiation. A loss of 0.95 dB/m at 119 microm (2.5 THz) was obtained for a 2 mm bore, 90 cm long Ag/PS HGW. We found that TE modes are supported in HGWs with thin PS films, while hybrid (HE) modes dominate when PS film thickness increases. The lowest losses are obtained for the thicker PS films and the propagation of the HE modes.
Cross-Correlation-Based Structural System Identification Using Unmanned Aerial Vehicles (2017)

Computer vision techniques have been employed to characterize dynamic properties of structures, as well as to capture structural motion for system identification purposes. All of these methods leverage image-processing techniques using a stationary camera. This requirement makes finding an effective location for camera installation difficult, because civil infrastructure (i.e., bridges, buildings, etc.) are often difficult to access, being constructed over rivers, roads, or other obstacles. This paper seeks to use video from Unmanned Aerial Vehicles (UAVs) to address this problem. As opposed to the traditional way of using stationary cameras, the use of UAVs brings the issue of the camera itself moving; thus, the displacements of the structure obtained by processing UAV video are relative to the UAV camera. Some efforts have been reported to compensate for the camera motion, but they require certain assumptions that may be difficult to satisfy. This paper proposes a new method for structural system identification using the UAV video directly. Several challenges are addressed, including: (1) estimation of an appropriate scale factor; and (2) compensation for the rolling shutter effect. Experimental validation is carried out to validate the proposed approach. The experimental results demonstrate the efficacy and significant potential of the proposed approach.
Unrealistic Demands on Science and Medicine (1971)

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Neurotrophic rationale in glaucoma: A TrkA agonist, but not NGF or a p75 antagonist, protects retinal ganglion cellsin vivo (2007)

Glaucoma is a major cause of vision impairment, which arises from the sustained and progressive apoptosis of retinal ganglion cells (RGC), with ocular hypertension being a major risk or co-morbidity factor. Because RGC death often continues after normalization of ocular hypertension, growth factor-mediated protection of compromised neurons may be useful. However, the therapeutic use of nerve growth factor (NGF) has not proven effective at delaying RGC death in glaucoma. We postulated that one cause for the failure of NGF may be related to its binding to two receptors, TrkA and p75. These receptors have distinct cellular distribution in the retina and in neurons they induce complex and sometimes opposing activities. Here, we show in an in vivo therapeutic model of glaucoma that a selective agonist of the pro-survival TrkA receptor was effective at preventing RGC death. RGC loss was fully prevented by combining the selective agonist of TrkA with intraocular pressure-lowering drugs. In contrast, neither NGF nor an antagonist of the pro-apoptotic p75 receptor protected RGCs. These results further a neurotrophic rationale for glaucoma.
318 J integral evaluation of the bending structure with a surface crack by the three-dimensional local hybrid method (2006)

Jintegral evaluation ofthe bending structure
Selective LPCVD Tungsten for Contact Barrier Applications (1986)

This study assesses the use of selective LPCVD tungsten as a contact barrier in VLSI circuits. Measurements of the contact resistance and leakage current are evaluated as a function of variations in W deposition parameters, implant type, implant dosage, and metallization heat‐treatment. Addition of to alter the equilibrium of the displacement reaction is seen to cause minimal erosion and encroachment of the Si contacts as well as produce low and thermally stable contact resistances to both n+ and p+ diffusions. For surface doping concentrations of and , measured values of the contact resistance for 2.0 μm sized vias are near 30Ω. Such values are quite compatible with high performance CMOS device requirements. Further reductions in these values are achieved with use of a self‐aligned contact barrier metallization. The contact resistance for 2.0 μm sized vias are, in this case, near 4 and 15OHgr; for the n+ and p+diffusions, respectively. Sporadic leakage across shallow n+/P‐Tub junctions remains, however, a serious problem associated with this selective LPCVD W process. Understanding the origin of this leakage and eliminating it can lead to numerous applications of this technology in VLSI manufacturing.