gebhart/patrepeval huggingface dataset:
Engineering V-Type Nerve Agents Detoxifying Enzymes Using Computationally Focused Libraries (2013)

VX and its Russian (RVX) and Chinese (CVX) analogues rapidly inactivate acetylcholinesterase and are the most toxic stockpile nerve agents. These organophosphates have a thiol leaving group with a choline-like moiety and are hydrolyzed very slowly by natural enzymes. We used an integrated computational and experimental approach to increase Brevundimonas diminuta phosphotriesterase's (PTE) detoxification rate of V-agents by 5000-fold. Computational models were built of the complex between PTE and V-agents. On the basis of these models, the active site was redesigned to be complementary in shape to VX and RVX and to include favorable electrostatic interactions with their choline-like leaving group. Small libraries based on designed sequences were constructed. The libraries were screened by a direct assay for V-agent detoxification, as our initial studies showed that colorimetric surrogates fail to report the detoxification rates of the actual agents. The experimental results were fed back to improve the computational models. Overall, five rounds of iterating between experiment and model refinement led to variants that hydrolyze the toxic SP isomers of all three V-agents with kcat/KM values of up to 5 × 10(6) M(-1) min(-1) and also efficiently detoxify G-agents. These new catalysts provide the basis for broad spectrum nerve agent detoxification.
Comparison of a DNA Hybridization Probe and ELISA for the Detection of<i>Clavibacter michiganensis</i>subsp.<i>sepedonicus</i>in Field-Grown Potatoes (1993)

Clavibacter michiganensis subsp. sepedonicus, the causal agent of bacterial ring rot, was detected in field-grown potatoes using a 1.078-kb repeated C. m. sepedonicus sequence as a probe in DNA hybridizations. Stem and petiole samples from susceptible and tolerant cultivars (Russet Burbank and Belrus, respectively), inoculated with 10 mM phosphate buffer (pH 7.2) or 10 2 or 10 9 cfu of either an aggressive or a less aggressive C. m. sepedonicus strain, were processed by directly blotting cut tissue sections on nylon membranes, macerating frozen tissues, and applying xylem fluid collected by centrifugation to nylon membranes (stems only)
Hybridization Behavior of Mixed DNA/Alkylthiol Monolayers on Gold:  Characterization by Surface Plasmon Resonance and <sup>32</sup>P Radiometric Assay (2006)

Nucleic acid assay from a complex biological milieu is attractive but currently difficult and far from routine. In this study, DNA hybridization from serum dilutions into mixed DNA/mercaptoundecanol (MCU) adlayers on gold was monitored by surface plasmon resonance (SPR). Immobilized DNA probe and hybridized target densities on these surfaces were quantified using 32P-radiometric assays as a function of MCU diluent exposure. SPR surface capture results correlated with radiometric analysis for hybridization performance, demonstrating a maximum DNA hybridization on DNA/MCU mixed adlayers. The maximum target surface capture produced by MCU addition to the DNA probe layer correlates with structural and conformational data on identical mixed DNA/MCU adlayers on gold derived from XPS, NEXAFS, and fluorescence intensity measurements reported in a related study (Lee, C.-Y.; Gong, P.; Harbers, G. M.; Grainger, D. W.; Castner, D. G.; Gamble, L. J. Anal. Chem. 2006, 78, 3316-3325.). MCU addition into the DNA adlayer on gold also improved surface resistance to both nonspecific DNA and serum protein adsorption. Target DNA hybridization from serum dilutions was monitored with SPR on the optimally mixed DNA/MCU adlayers. Both hybridization kinetics and efficiency were strongly affected by nonspecific protein adsorption from a complex milieu even at a minimal serum concentration (e.g., 1%). No target hybridization was detected in SPR assays from serum concentrations above 30%, indicating nonspecific protein adsorption interference of DNA capture and hybridization from complex milieu. Removal of nonsignal proteins from nucleic acid targets prior to assay represents a significant issue for direct sample-to-assay nucleic acid diagnostics from food, blood, tissue, PCR mixtures, and many other biologically complex sample formats.
Observation of noncovalent complexes to the avidin tetramer by electrospray ionization mass spectrometry (1994)

Intact avidin-biotin and avidin-biotin maleimide noncovalent complexes have been observed by electrospray ionization mass spectrometry (ESI-MS) by using an extended mass range quadrupole mass spectrometer. By utilizing mild ES1 interface conditions, the expected solution behavior of four biotin or biotin maleimide molecules noncovalently binding to each avidin tetramer can be preserved in the gas phase. The ESI-MS results show the appropriate mass additions of 973 ± 60 Da for biotin and 1802 ± 40 Da for biotin maleimide to the avidin tetramer species. These results support the hypothesis that substantial retention of higher order structure is possible in the gas phase by using gentle ESI conditions.
The Bioavailability of Morphine in Controlled‐Release 30‐mg Tablets per Rectum Compared With Immediate‐Release 30‐mg Rectal Suppositories and Controlled‐Release 30‐mg Oral Tablets (1992)

The bioavailability of controlled-release morphine 30-mg tablets (MSC) administered orally or rectally and immediate-release morphine (RMS) 30-mg suppositories per rectum, was compared in this 14-subject, randomized, single-dose, analytically blinded, crossover study. Rectal MSC plasma morphine area under the curve from 0-24 hours (AUC0-24) was 50.8% of RMS and was similar for MSC administered by either route (rectal MSC = 90% oral MSC). Rectal MSC had a significantly delayed time to peak plasma level (5.4 vs 1.07 and 2.5 hrs for rectal MSC vs RMS and oral MSC, respectively) and a significantly attenuated time to maximum concentration (6.1 vs 25.4 and 9.7 ng/ml, respectively). Proctoscopy 24 hours after insertion revealed seven instances of mild, transient mucosal erythema or edema with rectal MSC and 12 with RMS. The number of nonlocal adverse effects was 14 with rectal MSC, 19 with RMS, and 18 with oral MSC. Further studies must determine the therapeutic consequences of pharmacokinetic differences and establish guidelines for rectal MSC use. The product is currently not recommended by the manufacturer for rectal administration.
Influence of the Binder on the Mechanical Properties of the Chromite Self-Reducing Pellets (2013)

Cold and hot mechanical strengths of the chromite self-reducing pellets agglomerated using different binders was evaluated by means of compression and repeated falling tests. The behavior of hot strength was evaluated, actually at room temperature, after the pellets were submitted at thermal treatment at 1173, 1273, 1373, 1473 and 1573K (900, 1000, 1100, 1200 and 1300° C). The binders used were: bentonite, hydrated lime, molasses, carboxymethylcellulose (CMC) and sodium silicate. Initially materials (chromite, ferro-silicon, petroleum coke and binders), were characterized by chemical and particle size analysis. After that, the materials were agglomerated in the form of pellets P1, P2, P3, P4, P5, P6, with additions 0, 0.25, 0.5, 0.75, 1% bentonite and 1% bentonite with 0.2% CMC, respectively. Pellets P7, P8, P9, P10, P11, with additions of 0, 0.25, 0.5, 0.75, 1% bentonite with 12% hydrated lime, respectively. Pellets P12, with additions of the 2% molasses and 8% hydrated lime. Pellets P13, P14 and P15 with additions 1, 2 and 4% sodium silicate respectively. The compression test of these green pellets were measured during 28 curing days. After that they were dried and also submitted for the thermal treatments to evaluated the strength behavior after these treatments. The best result was found with the pellet P15, containing 4% sodium silicate as binder, presented a cold compression strength of 5 kgf/pellet and after thermal treatment at temperatures at 1173 and 1273K the compression strengths were of 15 kgf/pellet and did not decrepitate.
NO<sub>2</sub>and humidity sensing characteristics of few-layer graphenes (2009)

Sensing characteristics of few-layer graphenes for NO2 and humidity have been investigated with graphene samples prepared by the thermal exfoliation of graphitic oxide, conversion of nanodiamond (DG) and arc-discharge of graphite in hydrogen (HG). The sensitivity for NO2 is found to be highest with DG. Nitrogen-doped HG (n-type) shows increased sensitivity for NO2 compared with pure HG. The highest sensitivity for humidity is observed with HG. Sensing characteristics of graphene have been examined for different aliphatic alcohols and the sensitivity is found to vary with the chain length and branching.
Acoustical impedance measurements by the two-microphone-three-calibration (TMTC) method (1990)

A method is discussed for measuring the acoustical impedance of woodwind instruments that is relatively fast and insensitive to the ambient acoustical noise. The apparatus is essentially made of a measurement head, which is an approximately cylindrical cavity fitted with two microphones (in practice often three or more for technical reasons) and, at one of its ends, a loudspeaker; the other end is connected to the acoustical cavity under study (the instrument). The loudspeaker emits acoustical chirps and the signals provided by the microphones are Fourier transformed with the help of a microcomputer, which also extracts from the results the acoustical impedance as a function of frequency. A relatively high dynamic range is needed in order to match the high quality factor of the resonances of musical instruments, especially at low frequencies. To meet this requirement, it was found necessary to take into account the acoustical losses inside the head as well as the mutual perturbation of the microphones or various perturbations arising from geometrical imperfections of the cavity. This can be done automatically and without long calculations by using a calibration method, based on the successive use of three reference cavities, which are described and discussed in detail in this article. The method has been tested with cylindrical cavities and gives satisfactory results in terms of peak positions and heights. Impedance curves of clarinets have also been measured. The three-calibration technique eliminates several sources of systematics and corrects automatically for various perturbations, such as perturbations of the acoustical field by the microphones, and allows the study of instruments of various diameters.
Integrated 1×32 PLC-splitter with 32 WDM couplers for fiber line testing at 1.65 μm (2002)

A novel silica-based PLC-splitter integrated with couplers is proposed for a PDS transmission system with fiber line testing. A 1/spl times/32 splitter with 32 WDM couplers formed using 1.65 /spl mu/m-reflecting thin film filters is demonstrated.
Bearing detection in the presence of two sources of varying coherence using the complex cepstrum (1987)

The effect of the presence of two acoustic sources (one, the primary, whose location is to be detected) of varying coherence on a cepstral bearing finding procedure is experimentally studied. The coherence between the acoustic sources was altered by adding random noise of various SNR (signal-to-noise ratio) to the input signal of the primary source; the same base signal being fed to both sources. The results demonstrate that, when block liftering is used, the primary source bearing is reliably estimated for coherences as low as gamma sup 2 greater than or approx equal to 0.5. The results also imply that background noise (unreflected) of SNR greater than or approx equal to 10 dB will not markedly affect the accuracy of the bearing estimation algorithm.
Induction of Complete Regressions of Oncogene-induced Breast Tumors in Mice (2005)

Over the past decade, mouse models of cancer have come to resemble human disease much more closely than simple subcutaneous or orthotopic systems. Intervention strategies that work on these new model systems are more likely to have an impact clinically. We have shown recently that antiangiogenic stress imposed by loss of Id protein in endothelial progenitor cells results in dramatic central necrosis in breast tumors initiated in mice by overexpression of the her2/neu oncogene. Tumor cells remain viable at the periphery, perhaps via the hypoxic response pathway which allows the lesions to expand. Inhibition of this pathway by the inactivation of the Hif-1alpha chaperone Hsp90 in combination with antiangiogenic stress leads to the first reported complete regression of these aggressive breast tumors.
Analysis of the Efficiency of Thin-Film Magnetic Recording Heads (1971)

Equations for the flux, magnetic field, and current distributions in a single-turn planar magnetic recording head are derived making the assumption that the magnetic material has constant permeability. These equations are solved in the frequency domain and an expression is given for the head efficiency in terms of the head dimensions, permeability, and frequency.
In-Line Electro-Optic Frequency Translator For Fiber-Optic Sensors (1985)

The integrated-optic frequency shifter utilizes electro-optic polarization conversion by a travelling index grating in LiNbO<sub>3</sub>:Ti stripe waveguides. The optical frequency shift is equal to the frequency of two electric phase-quadrature drive voltages. A device operating at a fixed wavelength of 723 nm with an optical bandwidth of ~ 1 nm shows ≥90% conversion efficiency and ≥30 dB suppression of undesired sidebands at frequency shifts up to ± 10 6Hz.
Rapid-onset sildenafil nasal spray carried by microemulsion systems:<i>in vitro</i>evaluation and<i>in vivo</i>pharmacokinetic studies in rabbits (2011)

An oleic acid-based microemulsion system with a member of the Tween series or Cremophor EL as the surfactant and a short-chain alcohol as the cosolvent was developed for rapid-onset intranasal delivery of sildenafil. The phase behaviour and solubilization capacity of the microemulsion system were characterized, and nasal absorption of sildenafil from the microemulsion formulations was investigated in rabbits. Sildenafil displayed a high solubility of 124 mg/mL in the microemulsion consisting of 40% oleic acid, 10% H(2)O, and 50% Tween 80:ethanol (EA) (at a 1:4 weight ratio). Nasal absorption of sildenafil from this microemulsion was found to be fairly rapid. With a 10-mg dose, the onset of action was arrived instantly following intranasal administration and the duration was over 3 h using an in vivo rabbit studies. In addition, nasal ciliotoxicity studies were carried out using in vivo rat nasal mucosa model and showed no ciliotoxicity. Therefore, the prepared systems are no serious nasal ciliotoxicity for intranasal administration. The microemulsion system composed of oleic acid, Tween 80, EA, and water may be a practical approach for the rapid-onset delivery of sildenafil for the treatment of erectile dysfunction.
614. The stabilities of metal complexes of some derivatives of iminodiacetic acid (1963)

H. Irving and J. J. R. F. da Silva, J. Chem. Soc., 1963, 3308 DOI: 10.1039/JR9630003308
General Solid-Phase Method for the Preparation of Mechanism-Based Cysteine Protease Inhibitors (1999)

The first general method has been developed for the expedient solid-phase synthesis of ketone-based cysteine protease inhibitors. The synthesis approach was designed to allow the introduction of diverse functionality at all variable sites about the ketone carbonyl using readily available precursors. The chloromethyl ketone scaffold 7 is attached to the solid support through the newly developed hydrazine linker 6. Successful nucleophilic displacement of the support-bound α-chloro hydrazones 8 with carboxylates, thiolates, and amines provides entry to the acyloxymethyl, mercaptomethyl, and amidomethyl ketone classes of cysteine protease inhibitors. Further transformations followed by cleavage from support provides the fully substituted ketone products in 40−100% overall yields after release from support. Significantly, racemization of the α-stereocenter does not occur during loading onto support, nucleophilic displacement, or cleavage from support.
Plasminogen activator in normal and tumor‐bearing mice (1983)

Abstract The plasminogen activator levels of a series of murine tumors commonly used in cancer drug screening were determined and compared to the levels found in normal mouse tissues. Tumors high in plasminogen activator included the B16 and colon 26. The Lewis lung and M5076 carcinoma showed an intermediate level of activity, while the plasminogen activator activity in the L1210 leukemia and colon 38 was barely elevated above background. The specific activity of the enzyme (per μg protein) in extracts of B16 and colon 26 was three or four times higher than in the most active normal organs surveyed (kidney, lung, brain and intestine). The high level of plasminogen activator activity measured in extracts of the B16 tumor was reflected in a substantial elevation of the levels of fibrin degradation products in the serum of mice carrying this tumor. This result suggests that the tumor‐associated plasminogen activator activity is less subject to inhibitory controls in vivo than is the plasminogen activator of most normal tissues, since the total mass of the tumor was far less than the total mass of the fibrinolytically active tissues, and yet the bulk of the fibrin degradation products were caused by the tumor. We conclude that the high levels of plasminogen activator activity which are observed in many human tumors are found only in some of the transplantable murine tumors. Since this enzyme is active at an increased level in vivo in mice carrying the B16 tumor, plasminogen activator may be a suitable target for selective, enzyme‐activated chemotherapy with this tumor test system.
Expression of selected human HOX-2 genes in B/T acute lymphoid leukemia and interleukin-2/interleukin-1 beta-stimulated natural killer lymphocytes (1992)

Although the key role of human homeobox (HOX) genes in development is well established, their function in adult cells is still under scrutiny. We have analyzed, in normal adult blood cell subpopulations, acute lymphoid leukemia (ALL) cells lines, and primary blasts, the RNA expression of all HOX-2 cluster genes (5'-2.5, 2.4, 2.3, 2.2, 2.1, 2.6, 2.7, 2.8, 2.9, 3') and nine genes in the HOX-1, -3, and -4 cluster by Northern blotting, RNAse protection, and/or reverse transcriptase polymerase chain reaction (RT-PCR). The analyzed HOX-1, -3, and -4 genes were never expressed in all tested cell populations. Natural killer (NK) cells activated in interleukin-2 (IL-2)/IL-1 beta-treated cultures exhibit a gradually increasing, abundant expression of three HOX-2 genes (2.2, 2.6, 2.8), while three other genes (2.3, 2.1, 2.7) are expressed at a lower level at late culture times. However, no HOX-2 gene is expressed in quiescent lymphocytes (NK, B and T [T-cell receptor (TCR) alpha/beta, gamma/delta lymphocytes, thymocytes] cells), granulocytes, and monocytes. In B- and T-ALL cell lines, HOX-2 genes are expressed according to different patterns: (1) widespread transcription (seven of nine genes, including 2.3 and 2.6) in the Peer line bearing the TCR gamma/delta; (2) expression of 2.5, 2.2, and 2.6 in the SEZ 627 line, which derives from an HTLV-1+ T-helper leukemia; (3) transcription of 2.3 and 2.6 in both the T-ALL CEM line and four B-ALL lines (interestingly, CALLA- B-ALL lines are constantly 2.3/2.6 RNA+); (4) no HOX-2 gene expression was detected in one T- and two B-ALL lines. Primary blasts from five T- and five pre-B-ALL showed selective expression of one or more HOX-2 genes, namely 2.5, 2.2, 2.6, and 2.7. Our data are compatible with the hypothesis that selected HOX-2 genes play a role in the IL-2/IL-1 beta-induced activation and/or proliferation of normal NK lymphocytes and possibly in the oncogenetic process of some T- and B-ALL.
Protein Kinase C Inhibition Prevents Upregulation of Vascular ET<sub>B</sub> and 5-HT<sub>1B</sub> Receptors and Reverses Cerebral Blood Flow Reduction after Subarachnoid Haemorrhage in Rats (2006)

The pathogenesis of cerebral ischaemia after subarachnoid haemorrhage (SAH) still remains elusive. The purpose of the present study was to examine whether specific protein kinas C (PKC) inhibition in rats could alter the transcriptional SAH induced Endothelin (ET) type B and 5-hydroxytryptamine type 1B (5-HT(1B)) receptor upregulation and prevent the associated cerebral blood flow (CBF) reduction. The PKC inhibitor RO-31-7549 or vehicle was injected intracisternally after the induced SAH in rats (n=3 to 10 in each groups for each method). The involvement of the PKC isoforms was investigated with Western blot; only PKCdelta and PKCalpha subtypes were increased after SAH RO-31-7549 treatment abolished this. At 2 days after the SAH basilar and middle cerebral arteries were harvested and the contractile response to endothelin-1 (ET-1; ET(A) and ET(B) receptor agonist) and 5-carboxamidotryptamine (5-CT; 5-HT(1) receptor agonist) were investigated with a myograph. The contractile responses to ET-1 and 5-CT were increased (P<0.05) after SAH compared with sham operated rats. In parallel, the ET(B) and 5-HT(1B) receptor mRNA and protein expression were significantly elevated after SAH, as analysed by quantitative real-time polymerase chain reaction and immunohistochemistry, respectively. Administration of RO-31-7549 prevented the upregulated contraction elicited by application of ET-1 and 5-CT in cerebral arteries and kept the ET(B) and 5-HT(1B) receptor mRNA and protein levels at pre-SAH levels. Regional and global CBF evaluated by an autoradiographic technique were reduced by 60%+/-4% after SAH (P<0.05) and prevented by treatment with RO-31-7549. Our study suggests that PKC plays an important role in the pathogenesis of cerebral ischaemia after SAH.
Typing Massive JSON Datasets (2013)

Cloud-specific languages are usually untyped, and no guarantees about the correctness of complex jobs can be statically obtained. Datasets too are usually untyped and no schema information is needed for their manipulation. In this paper we sketch a typing algorithm for JSON datasets. Our approach can be used to infer a succinct type from scratch for a collection of JSON objects, as well as to validate a dataset against a human-designed type and, if necessary, to adapt and improve this type. 1.
Cadmium zinc telluride (CZT) nanowire sensors for detection of low energy gamma-ray detection (2008)

Bulk single crystals of CdZnTe compound semiconductor is used for room temperature radiation detection in commercial radiation sensors. A large volume of detector material with low defect density is required for increasing the detection efficiency. Manufacture of such a bulky detector-quality material with low defect density is expensive. In this communication, synthesis of nanowires arrays of CdZnTe that can be used for detecting low energy radiation is reported for the first time. CdZnTe ternary compound semiconductor, referred as CZT, was electrodeposited in the form of nanowires onto a TiO<sub>2</sub> nanotubular template in non-aqueous electrolytes using a pulse-reverse process at 130 °C. Very high electrical resistivity of the CZT nanowires (in the order of 10<sup>10</sup> Ω-cm) was obtained. Such a high resistivity was attributed to the presence of deep defect states such as cadmium vacancies created by the anodic cycle of the pulse-reverse electrodeposition process. Stacks of series connected CZT nanowire arrays were impressed with different bias potentials. The leakage current was in the order of tens of PicoAmperes. When exposed to a radiation source (Am -241, 60 keV), the current flow in the circuit increased. The preliminary results indicate that the CZT nanowire arrays can be used as radiation detector materials at room temperature with a much low bias potential (0.7 - 2.3 V) as against 300 - 500 V applied to the bulk detector materials.