gebhart/patrepeval huggingface dataset:
Dynamic Active-Site Protection by the <i>M. tuberculosis</i> Protein Tyrosine Phosphatase PtpB Lid Domain (2010)

The Mycobacterium tuberculosis protein tyrosine phosphatase PtpB shows resistance to the oxidative conditions that prevail within an infected host macrophage, but the mechanism of this molecular adaptation is unknown. Crystal structures of PtpB revealed previously that a closed, two-helix lid covers the active site. By measuring single-molecule Forster-type resonance energy transfer to probe the dynamics of two helices that constitute the lid, we obtained direct evidence for large, spontaneous opening transitions of PtpB with the closed form of both helices favored approximately 3:1. Despite similar populations of conformers, the two helices move asynchronously as demonstrated by different opening and closing rates under our experimental conditions. Assuming that lid closure excludes oxidant, the rates of opening and closing quantitatively accounted for the slow observed rate of oxidative inactivation. Increasing solvent viscosity using glycerol but not PEG8000 resulted in higher rates of oxidative inactivation due to an increase in the population of open conformers. These results establish that the rapid conformational gating of the PtpB lid constitutes a reversible physical blockade that transiently masks the active site and retards oxidative inactivation.
Alkylguanidine‐catalyzed heterogeneous transesterification of soybean oil (1999)

Abstract Transesterification of soybean oil with methanol has been carried out in the presence of heterogenized alkylguanidines as catalysts. The alkylguanidines were anchored to modified polystyrene or siliceous MCM‐41, encapsulated in the supercages of zeolite Y, or entrapped in SiO 2 sol‐gel matrices. The catalytic activity of these catalysts was compared with that of their homogeneous counterparts, showing that the yields of methyl esters obtained in the homogeneous phase can be obtained with the guanidines anchored to the supports after longer reaction times. The catalysts prepared by immobilization of alkylguanidines in microporous systems showed diffusion restrictions for the vegetable oil as well as the low stability of the inorganic framework.
Anti-p53 and anti-heat shock proteins antibodies in patients with malignant or pre-malignant lesions of the oral cavity. (2001)

The presence of anti-p53 antibodies in both SCC-bearing patients and in patients with pre-malignant lesions support the notion that p53 gene mutation is an early event in oral tumorigenesis and suggest that this assay could be useful for diagnostic screening of pre-neoplastic lesions at high risk of recurrence and/or transition towards overt malignancy.
Concurrent updates on striped data streams in clustered server systems (2005)

Data Striping is widely used and well-understood in Redundant Arrays of Independent Disks (RAID), whereby an array of disks is controlled by a single device controller. By striping and adding parity information, distribution of I/O load and fault tolerance can be assured. This study focuses the problem of update/read consistency of files that are striped among several nodes, e.g. in a clustered server for media streaming applications. Common RAID systems offer a single entry point so that a read operation delivers either the content before an update or the updated content. This property is not present when arbitrary nodes may access data stripes without a centralized access facility. Thus, coordination is necessary among updates and concurrent read operations. A common solution is to lock files or blocks that are currently being updated. We propose an alternative solution to ensure delivery of valid content during updates without locking blocks globally. This can be used for instance to update the original content of video servers, without the need of temporary copies and access limitations.
Development of a Novel Vaccine Delivery System Based on Gantrez Nanoparticles (2006)

The adjuvant capacity of a novel vaccine vector "Gantrez-nanoparticles" (NP) towards coated or encapsulated ovalbumin (OVA) was investigated. OVA nanoparticles were prepared by a solvent displacement method previously described. The protein was incorporated during the manufacturing process (OVA-encapsulated nanoparticles) or after the preparation (OVA-coated nanoparticles). The mean size of the different nanoparticle formulations was lower than 300 nm, and the OVA content ranged approximately from 67 microg/mg nanoparticles (for OVA-coated nanoparticles) to 30 microg/mg nanoparticles (for OVA-encapsulated nanoparticles). All the OVA-NP formulations were capable of amplifying the antibodies titres (IgG1 and IgG2a) in mice after a single subcutaneous inoculation with respect free OVA or OVA adsorbed to Alum. Furthermore, the elicited response was, for some formulations, predominantly Th1 subtype. Thus, the formulation that contained mainly the antigen inside, and with a low concentration of cross-linking agent, displayed the best potential to induce a Th1 response after 35 days post-immunisation. These results are highly suggestive for the use of Gantrez nanoparticles as an efficient antigen delivery system, especially when a long lasting Th1 cytokine response is required.
Fluorometric detection of deoxyribonucleic acid synthesis; possibilities for interfacing bromodeoxyuridine dye techniques with flow fluorometry. (1977)

Fluorometric detection of the biosynthetic incorporation of 5-bromodeoxyuridine (BrdU) into deoxyribonucleic acid has permitted cytologic studies of chromosome structure, replication, and repair. Some of these phenomena, previously detected using BrdU-dye techniques on fixed microscopic preparations, should be particularly amenable to analogous experimentation in fluorescence flow systems. Problems involved in interfacing BrdU-dye methodology with flow fluorometry are discussed. The effects of certain chemical modifications of bisbenzimidazole dyes on their spectroscopic properties and potential use for detecting BrdU incorporation into unfixed cells are described. Data on the use and energy transfer characteristics of a pair of deoxyribonucleic acid-binding dyes (33258 Hoechst and ethidium bromide) capable of simultaneously providing information about BrdU substitution and total deoxyribonucleic acid content are presented.
High rate soft output Viterbi decoder (1996)

This paper presents the architecture of a high rate soft output Viterbi decoder (100 Mb/s for worst case process conditions, 8 states, coding rate R=1/2, using a 0.6ym CMOS technology), using the radix trellis method (collapsed trellis) to speed up the rate of a soft output decoder using the Viterbi algorithm and the a posteriori weighting algorithm. The size of this circuit is roughly twice that of the original soft output Viterbi decoder while the speed is increased by a factor of 2. Because of its performances, this circuit is very attractive for satellite digital communication systems and is at the root of turbo-codes, which are a new class of convolutional codes whose performances, in terms of bit error rate, are close to the Shannon limit.
Detecting Photoelectron Images with Semiconductor Arrays for Multichannel Photon Counting (1977)

The number and variety of digicon-type devices has been increasing at a rapid rate in the last year. This paper describes most of those which are new either in type of array used, design of electron optics, photocathodes, faceplates, or unusual applications. New parallel output digicons have been built using large two-dimensional arrays for UV and visible photometry. and spectrophotometry. An intensified charge coupled device with 10,000 channels will be described and test results given. Single photoelectron pulse height distributions for CCDs used in the electron bombardment mode will be shown and the first data on the use of avalanche diodes to detect photoelectrons will be given.
Magnetoelectric coupling of laminated composites under combined thermal and magnetic loadings (2012)

Laminated magnetoelectric (ME) composites are suitable for applications such as magnetic field sensors, transformers, and microwave resonators. Such applications frequently involve environments where the temperature alters. The present work investigates the temperature dependent ME coupling for three kinds of laminates, namely, Terfenol-D/PZT/Terfenol-D, Ni/PZT/Ni, and Metglas/PZT/Metglas. The Terfenol-D/PZT/Terfenol-D is shown to exhibit the best temperature stability. The peak value of the ME coefficient versus temperature curve is predicted for the laminates based on the equivalent circuit model, as well as the measurements of temperature dependent magnetostriction for Terfenol-D, Ni, and Metglas. The predictions agree well with the experimental data, implying that the piezomagnetic coefficient, d11,m, of the magnetic layer plays an important role in the temperature dependent ME coupling of the laminate.
Analysis of density based and fuzzy c-means clustering methods on lesion border extraction in dermoscopy images (2010)

As well as low border error, high precision and recall, visual outcome showed that the DBSCAN effectively delineated targeted lesion, and has bright future; however, the FCM had poor performance especially in border error metric.
Goal-Directed Textured-Image Segmentation (1985)

The SLICE segmentation system identifies image regions that differ in gray-level distribution, color, spatial texture, or some other local property. This report concentrates on textured-image segmentation using local texture-energy measures and user delimited training regions. Knowledge of target textures or signatures is combined with knowledge of background textures by using histogram-similarity transforms to identify regions that are similar to a target texture and dissimilar to other textures.
Asymmetric Allylic Alkylation of Cyclic Vinylogous Esters and Thioesters by Pd‐Catalyzed Decarboxylation of Enol Carbonate and β‐Ketoester Substrates (2006)

Excellent yields and enantioselectivities were achieved for the palladium-catalyzed asymmetric allylic alkylation of vinylogous thioesters. The close-to-neutral reaction conditions ensure that this reaction can tolerate a wide range of functionalities. Furthermore, this approach provides a convenient protocol for the synthesis of synthetically important α,α- and γ,γ-disubstituted cycloalkenones. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z504421_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Adenovirus-Mediated Gene Transfer to rat Testis in Vivo (1997)

To study transgene expression in the adult rat testis in vivo, an adenovirus vector carrying a lacZ transgene with a nuclear localization signal was used as a marker. The adenovirus vector was first tested on rat Sertoli cell-germ cell cocultures in vitro; it efficiently mediated transgene expression in Sertoli cells but not germ cells. This vector was then delivered to the interstitial compartment of adult rat testes by intratesticular injection, resulting in Leydig cells expressing the transgene. Alternatively, delivering the vector to the intratubular compartment by rete testis injection resulted in expression of the transgene by Sertoli cells of the seminiferous epithelium and principal cells of the epididymis. In vivo, each cell type expressed the transgene by 2 days postinfection, and expression persisted for at least 10 days; however, later time points were associated with a loss of transgene expression and focal interstitial inflammation. This study documents the ability of adenovirus to mediate gene transfer to specific testicular cells, providing a powerful tool to study the short-term effects of specific genes on spermatogenesis in vivo.
Dose‐dependent pharmacokinetics of probenecid in the rat (1988)

The basic pharmacokinetics of probenecid was studied by administration of three different i.v. bolus doses (50, 75, and 100 mg kg-1) to rats. The protein binding of probenecid in pooled rat serum was estimated by equilibrium dialysis. The unbound fraction was found to increase non-linearly with increasing total concentration, yielding a maximum free fraction of 49 per cent. The plasma concentration data obtained were described by a two-compartment model with Michaelis-Menten elimination. The maximal rate of elimination (Vm) remained unchanged between different doses irrespective of whether it was calculated in total or free concentrations (mean 187.2 +/- 8.3 (SD) microgram min-1). The Michaelis-Menten constant (Km) decreased slightly with increasing dose, while the unbound Michaelis-Menten constant (Km,u) did not change between the doses (mean 37.1 +/- 1.3 (SD) microgram ml-1). The volume of distribution of the central compartment (Vc) did not alter when the dose was increased from 50 to 100 mg kg-1 (mean 56.5 +/- 4.3 (SD) ml), but the unbound volume of distribution of the central compartment (Vc,u) decreased from 186.5 +/- 15.6 (SD) to 89.8 +/- 6.9 (SD) ml, which is in accordance with the reduction to be expected for drugs that only distribute in the extracellular fluid.
Speech coding over frame relay networks (2005)

In this paper, the problem of transmitting compressed voice over frame relay networks is addressed. To overcome variable frame delay and frame loss in the networks, an adaptive build out delay mechanism combining silence detection and time-scale modification is described for use in an embedded 8/16 kb/s CELP-MPE speech coder. Vector Linear Prediction (VLP) is then discussed for the purpose of voice frame re-construction. During frame losses, an adaptive energy control mechanism is introduced to suppress sudden energy explosion in the reconstructed frame. Objective and subjective results at random frame error rates are obtained and it is shown that there is virtually no degradation in perceptual quality when the frame loss rate is as high as 1%.
Transient Expression of Genes Transferred <i>In Vivo</i> into Heart Using First-Generation Adenoviral Vectors: Role of the Immune Response (1995)

Gene therapy for heart diseases requires availability of an efficient vector for gene transfer into myocardium. Recombinant adenovirus expressing the Escherichia coli beta-galactosidase (beta-Gal) gene was shown to infect rat cardiocytes efficiently in vivo. However, a time course of gene expression showed that transgene expression was maximal during the first week following injection, then declined and disappeared by day 21. An immunosuppressive treatment prolonged beta-Gal expression for at least 21 days. On the contrary, a preimmunization of the animals by two intraperitoneal injections of the vector led to a decreased transgene expression 48 hr after intramyocardial injection and to a barely detectable expression at the sixth day. Appearance of adenovirus neutralizing antibodies in preimmunized animals could have contributed to such a refractoriness to further adenoviral infection. Finally, a neonatal intrathymic injection of the vector was able to induce long-term LacZ expression for more than 2 months after heart injection, although neutralizing as well as anti-beta-Gal antibodies were detected in sera of the animals. These results indicate that an immune response against first-generation replication-defective adenoviral vectors is a major cause of transient transgene expression, a cellular response being most probably responsible for ablation of transgene expression in immunocompetent animals.
Research on Ground Source Heat Pump Design (2010)

One of world’s largest uses of energy is the heating and cooling of buildings. Ground Source Heat Pumps (GSHP) provide a more energy efficient way to meet building energy needs than conventional alternatives. At a relatively shallow depth, the ground temperature is nearly constant year round providing a reliable heat source or sink for the operation of a heat pump. The design of such systems is complicated by the short and long term behavior of the ground as well as various options for system configuration and control. The stochastic nature of year-to-year weather variation also influences the design. In this paper the GSHP system is introduced and the system model developed at the UW-Madison is discussed. The impact of weather variation on the optimal design of such a system is examined. Initial validation of the key component in the model, the ground heat exchanger, against experimental data is presented.
Geothermal Energy Production Coupled with CCS: a Field Demonstration at the SECARB Cranfield Site, Cranfield, Mississippi, USA (2013)

A major global research and development effort is underway to commercialize carbon capture and storage (CCS) as a method to mitigate climate change. Recent studies have shown the potential to couple CCS with geothermal energy extraction using supercritical CO2 (ScCO2) as the working fluid. In a geothermal reservoir, the working fluid produces electricity as a byproduct of the CCS process by mining heat out of a reservoir as it is circulated between injector and producer wells. While ScCO2 has lower heat capacity than water, its lower viscosity more than compensates by providing for greater fluid mobility. Furthermore, CO2 exhibits high expansivity and compressibility, which can both help reduce parasitic loads in fluid cycling. Given the high capital costs for developing the deep well infrastructure for geologic storage of CO2, the potential to simultaneously produce geothermal energy is an attractive method to offset some of the costs and added energy requirements for separating and transporting the waste CO2 stream. We present here the preliminary design and reservoir engineering associated with the development of direct-fired turbomachinery for pilot-scale deployment at the SECARB Cranfield Phase III CO2 Storage Project, in Cranfield, Mississippi, U.S.A. The pilot-scale deployment leverages the prior investment in the Cranfield Phase III research site, providing the first ever opportunity to acquire combined CO2 storage/geothermal energy extraction data necessary to address the uncertainties involved in this novel technique. At the SECARB Cranfield Site, our target reservoir, the Tuscaloosa Formation, lies at a depth of 3.0 km, and an initial temperature of 127 °C. A CO2 injector well and two existing observation wells are ideally suited for establishing a CO2 thermosiphon and monitoring the thermal and pressure evolution of the well-pair on a timescale that can help validate coupled models. It is hoped that this initial demonstration on a pre-commercial scale can accelerate commercialization of combined CCS/geothermal energy extraction by removing uncertainties in system modeling.
Synthesis of Fluorine-Containing Sulfonamide Derivatives (1968)

Two unkown aminofluoropyridines, 2-amino-5-fluoropyridine and 2-amino-3-fluoropyridine, were prepared and 16 kinds of new fluorine-containing sulfonamides were synthesized to test their in vitro antibacterial activity.
Anti-human immunodeficiency virus 1 (HIV-1) activities of 3-deazaadenosine analogs: increased potency against 3'-azido-3'-deoxythymidine-resistant HIV-1 strains. (1995)

3-Deazaadenosine (DZA), 3-deaza-(+/-)-aristeromycin (DZAri), and 3-deazaneplanocin A (DZNep) are powerful modulators of cellular processes. When tested against H9 cells infected acutely with two different strains of human immunodeficiency virus 1 (HIV-1) and in the chronically infected monocytoid cell lines U1 and THP-1, the 3-deazanucleosides caused a marked reduction in p24 antigen production. Similar reductions in p24 antigen were seen in phytohemagglutinin-stimulated peripheral blood mononuclear cells infected with clinical HIV-1 isolates. Strikingly, in comparing the therapeutic indices between the paired pre- and post-3'-azido-3'-deoxythymidine (AZT) treatment HIV-1 isolates, DZNep and neplanocin A showed an increase of 3- to 18-fold in their potency against AZT-resistant HIV-1 isolates. In H9 cells treated with DZNep and DZAri, the formation of triphosphate nucleotides of DZNep and DZAri was observed. The mode of action of DZNep and DZAri appears complex, at least in part, at the level of infectivity as shown by decreases in syncytia formation in HIV-1-infected H9 cells and at the level of transcription as both drugs inhibited the expression of basal or tat-induced HIV-1 long terminal repeat chloramphenicol acetyltransferase activity in stably transfected cell lines. Since DZNep induced in H9 cells a rapid expression of nuclear binding factors that recognize the AP-1 transcription site, the anti-HIV-1 activity of the DZA analogs could partly be the induction of critical factors in the host cells. Thus, the 3-deazanucleoside drugs belong to an unusual class of anti-HIV-1 drugs, which may have therapeutic potential, in particular against AZT-resistant strains.
Resistance of seedlings of <i>Nicotiana</i> species to <i>Peronospora tabacina</i> Adam (1962)

Seedlings of Nicotiana species of Australian and American origin were tested for resistance to an Australian strain of P. tabacina. American species were less resistant than Australian species and differences in 12 results of similar tests in both countries could have been due to differences in the pathogen or in the seed lines tested. The data suggest that the pathogen would have difficult in surviving on the highly resistant Australian species of Nicotiana in their natural arid habitat. Field observations have shown that survival occurs on the introduced susceptible species N. tabacum and N. glauca.
Optimum Matching Technique for the Switch Design (2007)

The theoretical background and hardware implementation of optimal matching filters designed to minimize harmonic generation by RF switches and provide harmonic filtering of the PA generated harmonics is presented. The switch with the optimally matched filters shows 5-7 dB improvements in harmonics generated under high VSWR, leading to better than -39dBm harmonics at 35/33 dBm for all phases of VSWR=5:1 for low/high band GSM applications. This technique leads to a fully integrated solution offering both improved harmonics performance and reduced size.
Simultaneous position and reflector estimation (SPRE) by single base-station (2018)

Accurately estimating user's location is an important functionality in mobile communications. In this paper, we propose SPRE algorithm that can simultaneously estimate the positions of both user and reflectors with single base-station (BS). Different from previous work, the BS knows nothing about the surrounding environment and the motion model of the user. All BS knows is the measured time-of-arrivals (TOAs) and angle-of-arrivals (AOAs) of multiple paths. Since signals from different propagation paths are received by the same receiver, the TOA differences between the direct path and the reflection paths have nearly no errors, which provides SPRE with high-accuracy information. The SPRE takes an iterative procedure to estimate the user's location and reflectors' locations. Simulation results show that reflectors can be accurately estimated after couples of iterations, and in return they improve the estimation accuracy of user position. The proposed SPRE method can localize a mobile user with sub-meter accuracy in indoor cases and meter accuracy in outdoor cases. If the locations of reflectors are known a priori, the SPRE method can realize centimeter-level accuracy of positioning.