gebhart/patrepeval huggingface dataset:
Measurement of protein‐DNA interaction parameters by electrophoresis mobility shift assay (1989)

Native gel electrophoresis (mobility shift) assays may be used to obtain quantitative information about the site distribution, equilibria and kinetics of protein-DNA interactions. These applications depend on the ability of the electrophoretic system to resolve the reaction components, and on their stabilities during the separation process. Factors which affect the lifetimes and mobilities of protein-DNA complexes during electrophoresis include reaction and electrophoresis buffer composition, pH, and ionic strength; the presence of low molecular weight effectors and enzymatic substrates; the nature and concentration of the gel matrix; the temperature; the molecular weights of protein and DNA; the stoichiometric ratios of their complexes; and the possibility of conformational and configurational isomerization of reaction components. We discuss how these factors influence the acquisition of quantitative data from electrophoretic patterns and band intensities, and present formulas for the estimation of equilibrium constants and rate constants for prototypical DNA-protein interactions.
Zur Benzhydrylierung des Hydroxylamins (1970)

Abstract Die Umsetzung von Hydroxylamin mit Benzhydrylbromid führt zu N‐, O‐, N.N‐Di‐ und N.O‐Di‐benzhydryl‐hydroxylamin ( 1 bzw. 2 bzw. 3 bzw. 4 ), die durch Addition an Isocyansäureester als Harnstoffe ( 5, 6, 9, 10 ) bzw. als Urethane ( 7 ) charakterisiert werden.
Thermodynamic analysis of high pressure hydrogen gas refueling system with turbo-expanders (2019)

This paper introduces a new hydrogen refueling system with a micro-scale hydrogen turbo-expander that enables us to replace a conventional low temperature refrigerator. From the process simulation of hydrogen refueling to the tank of a typical Fuel Cell Vehicle (FCV), the system is thermodynamically verified to be capable of refueling 5 kg-H2 within 3 minutes by the direct expansion in the micro-scale hydrogen turbo-expander. For the realization of this new concept, a process design approach of a high pressure hydrogen refueling system with the micro-scale hydrogen turbo-expander is described. In this process design, a turbine-compressor type is adopted to the micro-scale hydrogen turbo-expander unit, and an extracted power from the turbine side is consumed as a compressor power which is equipped on the opposite side of the turbine rotor. As a consequence of the thermodynamic analysis and simulation for the proposed system including the turbo-expander with adiabatic efficiency around65 %, it reveals that the new system provides some significant advantages compared with the conventional process. From a feasible investigation of this system, several advantageous features such as 1) high energy conservation, 2) compactness, 3) initial cost and operation cost, and, 4) system expandability (modification for shorter time refueling) are also described when it is compared with the existing system.
Minireview: Genomics Versus Orphan Nuclear Receptors—A Half-Time Report (2002)

Following the successful cloning of the orphan nuclear receptors during the 1990s we entered the 21st century with knowledge of the full complement of human nuclear receptors. Many of these proteins are ligand-activated transcription factors that act as the cognate receptors for steroid, retinoid, and thyroid hormones. In addition to these well characterized endocrine hormone receptors, there are a large number of orphan receptors of which less is known about the nature and function of their ligands. The task of deciphering the physiological function of these orphan receptors has been aided by a new generation of genomic technologies. Through application of chemical, structural, and functional genomics, several orphan nuclear receptors have emerged as pharmaceutical drug targets for the treatment of important human diseases. The significant progress that has been made in the functional analysis of more than half of the nuclear receptor gene family provides an opportunity to review the impact of genomics in this endeavor.
CELLULAR REACTIVITY TO THE P. FALCIPARUM PROTEIN TRAP IN ADULT KENYANS: NOVEL EPITOPES, COMPLEX CYTOKINE PATTERNS, AND THE IMPACT OF NATURAL ANTIGENIC VARIATION (2006)

Malaria vaccines based on thrombospondin-related adhesive protein of Plasmodium falciparum (Pf TRAP) are currently undergoing clinical trials in humans. This study was designed to investigate naturally acquired cellular immunity to Pf TRAP in adults from a target population for future trials of TRAP-based vaccines in Kilifi, Kenya. We first tested reactivity to a panel of 53 peptides spanning Pf TRAP and identified 26 novel T-cell epitopes. A panel of naturally occurring polymorphic variant epitope peptides were made to the most commonly recognized epitope regions and tested for ability to elicit IFN-gamma, IL-4, and IL-10 production. These data provide for the first time a complex cytokine matrix mapping naturally induced T-cell responses to TRAP and suggest that T-cell responses boosted by vaccination with Pf TRAP could stimulate the release of competing pro- and anti-inflammatory cytokines. They further define polymorphic variants able to boost specific Th1, Th2, and possibly Tr1 reactivity.
A Protocol of Secure Multi-party Multi-data Ranking and Its Application in Privacy Preserving Sequential Pattern Mining (2011)

A secure multi-party multi-data ranking protocol was proposed, which was not related to any specific encryption algorithm. And it was shown that the protocol was correct and secure in the semi-honest model. A privacy-preserving sequential pattern mining solution was also designed based on secure multi-party sum protocol and secure multi-party multi-data raking protocol and a simple analysis of this solution was given. This solution can be used in many aspects: privacy-preserving consumptive action analysis of multi-marketplace, privacy-preserving disease diagnose of multi-hospital and so on.
Robust-resistant spectrum estimation (1982)

Conventional spectrum estimates of both the smoothed-periodogram and autoregressive variety lack robustness toward outliers in the original data. Outliers and other local perturbations are modeled by non-Gaussian additive noise, which is zero most of the time. Correspondingly, the lack of robustness of the conventional estimates of the spectrum manifest not only inflated variances but also damaging asymptotic biases. This paper discusses robust-resistant methods of spectrum estimation which do not suffer in this way. The main approach involves "data cleaning" by either one-sided or two-sided outlier interpolators based on autoregressive approximations. The autoregressive coefficients are themselves estimated robustly in an iterative loop along with the data-cleaning operation. The well-cleaned data are then used along with the autoregressive model to form smoothed spectral density estimates via prewhitening. Study of the so-called "linear part" of the nonlinear outlier interpolator algorithm shows that considerable bias reduction is realizable through use of the robust procedure. Some examples of applications of the robust methodology are presented. Special considerations for real-time processing and large data sets are discussed. Extensions of the method to cross-spectrum estimation, missing data, and irregularly spaced data problems are briefly mentioned.
Chemical Modifications of Hyaluronan using DMTMM-Activated Amidation (2013)

An alternative approach to chemically modifying hyaluronan (HA) has been investigated. The triazine derivative 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) has been used to activate carboxylic groups on HA, which react further to form stable amide bonds with primary and secondary amines. The reaction can either be used to couple monoamines to HA or to produce hydrogels by using diamines that form crosslinks between the HA chains. The reaction between HA and DMTMM has been investigated and optimized in regard to degree of substitution (DS). Analysis using SEC-LC-UV demonstrated that the reaction was successful in coupling benzylamine to HA with a DS of 40%. Gel formation was successful using hexamethylene diamine as a crosslinker. Results also show that the reaction can be controlled by either the DMTMM or the amine concentration so that a specific degree of substitution or crosslinking is achieved. The stability of DMTMM has also been examined, and degradation studies of DMTMM in H2O at 50 °C with 1H NMR analysis show that 11% of the starting material remains after 48 hours. The reaction has proven to be an effective alternative to other modification methods with cheap reagents, simple procedures and the ability to control the amount of modification. Further investigations are nonetheless required in order to determine the full potential the DMTMM-activated amidation of HA.
Surface-limited ionic transport in perovskites Sr0.97(Ti,Fe,Mg)O3 − δ (2000)

Oxygen permeation and faradaic efficiency measurements of perovskite solid solutions Sr0.97Ti1 − x − yFexMgyO3 − δ (x = 0.20–0.40; y = 0–0.10) at 973–1223 K showed that the oxygen transport at membrane thicknesses below 2 mm is limited by both bulk ionic conductivity and the surface exchange kinetics. Incorporation of either iron or magnesium into the B sublattice of strontium titanate results in greater p-type electronic and oxygen ionic conductivities. For Sr0.97(Ti,Fe)O3 − δ solid solutions, the role of the surface exchange as the permeation-determining factor decreases with reducing temperature. In contrast, the limiting effect of the interphase exchange on oxygen transport through Sr0.97Ti0.70Fe0.20Mg0.10O3 − δ membranes is observed to be significant within the studied temperature range, suggesting that doping with magnesium leads to higher ionic conductivity and lower surface exchange rates in comparison with Sr0.97Ti0.60Fe0.40O3 − δ perovskite which exhibit similar permeation fluxes. The ion transference numbers of the solid solutions in air, estimated from the oxygen permeation and faradaic efficiency results, do not exceed 0.14. TGA/DTA results demonstrated the stability of the perovskite phases in CO2-containing atmospheres at temperatures above 770 K. The effect of the surface exchange limitations on the faradaic efficiency results is analysed.
Comparison of UDDI registry replication strategies (2004)

UDDI registries are intended to become the world-wide lookup mechanism for Web-services. As such, the registry has to provide high throughput, low response times, high availability, and access to accurate data. Replication is often used to satisfy such requirements. Various replication strategies exist, favoring different subsets of the above performance metrics. In this paper we have a closer look at two very different replication strategies. One strategy follows the UDDI specification, the second uses a middleware based replication tool. In this paper, we provide a comparison of these two approaches focusing on performance and ease of integration with an existing UDDI implementation.
“Molded” Macroporous Poly(glycidyl methacrylate-<i>co</i>-trimethylolpropane trimethacrylate) Materials with Fine Controlled Porous Properties:  Preparation of Monoliths Using Photoinitiated Polymerization (1997)

A model system has been developed for in situ photopolymerization of glycidyl methacrylate and trimethylolpropane trimethacrylate, leading to macroporous monolithic sorbents. This model system allows the preparation of continuous porous objects intended for applications such as detection, separation, and catalysis. The ease of the preparation, the short time needed for reaction, and the possibility of running the reaction at a low temperature are some of the main advantages of the photoinitiated in situ polymerization compared to a thermally initiated polymerization. Important system variables acting upon the porous properties and flow characteristics of the monoliths have been investigated in an experimental 23 full factorial design. The porous properties of the monoliths are a direct consequence of the quality of the porogenic solvent, as well as the percentage of cross-linking monomer and the ratio between the monomer and porogen phases. The presence of interactive effects between these reaction conditions were verified using multivariate analysis. It was concluded that the pore formation mechanism in an in situ photopolymerization follows rules similar to those found earlier for thermally initiated in situ polymerization of poly(glycidyl methacrylate-co-ethylenedimethacrylate) and poly(styrene-co-divinylbenzene).
Measuring the acceptance of electronic marketplaces: A study based on a used-car trading site (2006)

Electronic marketplaces act as intermediaries between supply and demand. Such forums are often organized by a central operator and are a common form of electronic commerce. The operators are independent entrepreneurs who are competing against one another for business. Their objective is to win over users for their own marketplace in order to generate fees by matching buyers and sellers. This is only possible when the marketplace design is ‘acceptable’ to the users. Using data from an empirical study, the present article analyzes criteria which marketplace users considered important in determining their acceptance of an electronic marketplace. The data were collected from the users (buyers and sellers) of a used-car trading site.
Self-consistent multicomponent envelope function calculation of normal incidence second-harmonic generation in p-type doped symmetric quantum wells (1997)

In a self-consistent multicomponent envelope function approach, we showed that χxxx(2) component of the second-harmonic susceptibility tensor of a symmetric p-type quantum well (QW) exists, because of the valence-band mixing at nonzero values of the in-plane wave vector. For a highly doped narrow GaAs/Al0.3Ga0.7As QW, our calculation indicates that at low temperatures a large value (∼10−7 m/V) of χxxx(2) can be achieved in the far-infrared frequency range without satisfying double resonance conditions. This value is comparable to the experimentally observed value of χzzz(2) in n-type asymmetric QW structures.
Studies on the constituents of Pueraria lobata. III. Isoflavonoids and related compounds in the roots and the voluble stems. (1987)

Two new isoflavone glycosides, the 8-C-apiosyl (1→6) glucosides of daidzein and genistein, were isolated from the roots and the voluble stems of Pueraria lobata (WILLD.) OHWI. Thirteen known isoflavonoids and related compounds were also found.
Inhibition by human T-lymphotropic virus (HTLV-I) of T-lymphocyte mitogenesis: failure of exogenous T-cell growth factor to restore responsiveness to lectin. (1985)

Various retroviruses, including human T-cell lymphotropic virus (HTLV-I) and avian sarcoma virus (ASV), can prevent coincubated human peripheral lymphocytes from responding efficiently to phytohaemagglutinin. Addition of high concentrations of T-cell growth factor (TCGF) activity usually overcomes this inhibition. However, such restoration of responsiveness does not occur in the case of HTLV-coincubated cells.
Comparative evaluation of human leukocyte and fibroblast interferon in the prevention of herpes simplex virus keratitis in a monkey model (1977)

The prophylactic potency of topically applied human leukocyte interferon and human fibroblast interferon was compared in a monkey model with herpes simplex virus type 1-induced keratitis. Both interferons effectively prevented keratitis at 1.9 X 10(6) U of activity per ml but were ineffective at 1.9 X 10(3) U/ml. Slight differences between human leukocyte interferon and human fibroblast interferon observed at the level of 1.9 X 10(5) U/ml were not statistically significant.
A ratiometric fluorescent probe for real-time monitoring of intracellular glutathione fluctuations in response to cisplatin (2020)

Real-time imaging of fluctuations in intracellular glutathione (GSH) concentrations is critical to understanding the mechanism of GSH-related cisplatin-resistance. Here, we describe a ratiometric fluorescence probe based on a reversible Michael addition reaction of GSH with the vinyl-functionalized boron-dipyrromethene (4,4-difluoro-4-bora-3<i>a</i>,4<i>a</i>-diaza-<i>s</i>-indacene or BODIPY) <b>1</b>. The probe was applied for real-time monitoring of the fluctuations in GSH levels in cells under cisplatin treatment. Notably, in cellular cisplatin-sensitive A549 cells, GSH concentrations rose until cell death, while in cisplatin-resistant cell lines, GSH levels first rose to the maximum then fell back to the initial concentration without significant apoptosis. These results indicate that different trends in GSH fluctuation can help distinguish cisplatin-resistant from cisplatin-sensitive cells. As such, this study has shown that probe <b>1</b> may potentially be used for real-time monitoring of intracellular GSH levels in response to therapeutics.
THE REJUVENATING STRATEGIES OF APTN (ABORIGINAL PEOPLES TELEVISION NETWORK) IN CANADA (2014)

Two major mandates for aboriginal TV stations are to pass on traditional cultures and to heal the disruptions in identities between generations. But first the programs must attract young aboriginal audience. This study employs secondary data analysis and in-depth interviews with seven managing officers of APTN and has found the following strategies for reaching youth audience: making people under 35 as target viewers, broadcasting more than 50% of their programs to the youth, obtaining streaming rights and developing online marketing strategies, interacting with younger audience using social media and games, broadcasting aboriginal festivals and music concerts with social media participation from the youth, building a program website and let the youth interact with the TV station and with other viewers, bringing programs into aboriginal communities and let the youth tell their own stories, and avoiding the use of teacher-like educational voices when presenting cultural heritages.
A Phase I/II Trial of Irinotecan Plus Amrubicin Supported with G-CSF for Extended Small-cell Lung Cancer (2013)

The combination of amrubicin and irinotecan with the support of granulocyte colony-stimulation factor produced a potent effect in chemo-naïve extensive-disease small-cell lung cancer patients. The use of biomarkers for this regimen may identify patients who are likely to suffer from treatment-ending severe adverse effects.
Towards wearable cognitive assistance (2014)

We describe the architecture and prototype implementation of an assistive system based on Google Glass devices for users in cognitive decline. It combines the first-person image capture and sensing capabilities of Glass with remote processing to perform real-time scene interpretation. The system architecture is multi-tiered. It offers tight end-to-end latency bounds on compute-intensive operations, while addressing concerns such as limited battery capacity and limited processing capability of wearable devices. The system gracefully degrades services in the face of network failures and unavailability of distant architectural tiers.
A comparison of the dispersion relations for anisotropic elastodynamic finite-difference grids (2011)

Abstract Several staggered grid schemes have been suggested for performing finite-difference calculations for the elastic wave equations. In this paper, the dispersion relationships and related computational requirements for the Lebedev and rotated staggered grids for anisotropic, elastic, finite-difference calculations in smooth models are analyzed and compared. These grids are related to a popular staggered grid for the isotropic problem, the Virieux grid. The Lebedev grid decomposes into Virieux grids, two in two dimensions and four in three dimensions, which decouple in isotropic media. Therefore the Lebedev scheme will have twice or four times the computational requirements, memory, and CPU as the Virieux grid but can be used with general anisotropy. In two dimensions, the rotated staggered grid is exactly equivalent to the Lebedev grid, but in three dimensions it is fundamentally different. The numerical dispersion in finite-difference grids depends on the direction of propagation and the grid type and parameters. A joint numerical dispersion relation for the two grids types in the isotropic case is derived. In order to compare the computational requirements for the two grid types, the dispersion, averaged over propagation direction and medium velocity are calculated. Setting the parameters so the average dispersion is equal for the two grids, the computational requirements of the two grid types are compared. In three dimensions, the rotated staggered grid requires at least 20% more memory for the field data and at least twice as many number of floating point operations and memory accesses, so the Lebedev grid is more efficient and is to be preferred.
Comparison of Three PCR Primer Sets for Identification of <i>vanB</i> Gene Carriage in Feces and Correlation with Carriage of Vancomycin-Resistant Enterococci: Interference by <i>vanB</i> -Containing Anaerobic Bacilli (2004)

We assessed the sensitivities and specificities of three previously described PCR primers on enrichment broth cultures of feces for the accurate detection of fecal carriage of vancomycin-resistant enterococci (VRE). In addition, we investigated specimens that were vanB PCR positive but VRE culture negative for the presence of other vanB-containing pathogens. Feces from 59 patients (12 patients carrying vanB Enterococcus faecium strains and 47 patients negative for VRE carriage) were cultured for 36 h in aerobic brain heart infusion (BHI) broth, anaerobic BHI (AnO(2)BHI) broth, or aerobic Enterococcosel (EC) broth. DNA was extracted from the cultures and tested for the presence of vanB by using the PCR primers of Dutka-Malen et al. (S. Dutka-Malen, S. Evers, and P. Courvalin, J. Clin. Microbiol. 33:24-27, 1995), Bell et al. (J. M. Bell, J. C. Paton, and J. Turnidge, J. Clin. Microbiol. 36:2187-2190, 1998), and Stinear et al. (T. P. Stinear, D. C. Olden, P. D. R. Johnson, J. K. Davies, and M. L. Grayson, Lancet 357:855-856, 2001). The sensitivity (specificity) of PCR compared with the results of culture on BHI, AnO(2)BHI, and EC broths were 67% (96%), 50% (94%), and 17% (100%), respectively, with the primers of Dutka-Malen et al.; 92% (60%), 92% (45%), and 92% (83%), respectively, with the primers of Bell et al.; and 92% (49%), 92% (43%), and 100% (51%) respectively, with the primers of Stinear et al. The primers of both Bell et al. and Stinear et al. were significantly more sensitive than those of Dutka-Malen et al. in EC broth (P = 0.001 and P < 0.001, respectively). The poor specificities for all primer pairs were due in part to the isolation and identification of six anaerobic gram-positive bacilli, Clostridium hathewayi (n = 3), a Clostridium innocuum-like organism (n = 1), Clostridium bolteae (n = 1), and Ruminococcus lactaris-like (n = 1), from five fecal specimens that were vanB positive but VRE culture negative. All six organisms were demonstrated to contain a vanB gene identical to that of VRE. VanB-containing bowel anaerobes may result in false-positive interpretation of PCR-positive fecal enrichment cultures as VRE, regardless of the primers and protocols used.