gebhart/patrepeval huggingface dataset:
Zinc folds the N-terminal domain of HIV-1 integrase, promotes multimerization, and enhances catalytic activity (1996)

The N-terminal domain of HIV-1 integrase contains a pair of His and Cys residues (the HHCC motif) that are conserved among retroviral integrases. Although His and Cys residues are often involved in binding zinc, the HHCC motif does not correspond to any recognized class of zinc binding domain. We have investigated the binding of zinc to HIV-1 integrase protein and find that it binds zinc with a stoichiometry of one zinc per integrase monomer. Analysis of zinc binding to deletion derivatives of integrase locates the binding site to the N-terminal domain. Integrase with a mutation in the HHCC motif does not bind zinc, consistent with coordination of zinc by these residues. The isolated N-terminal domain is disordered in the absence of zinc but, in the presence of zinc, it adopts a secondary structure with a high alpha helical content. Integrase bound by zinc tetramerizes more readily than the apoenzyme and is also more active than the apoenzyme in in vitro integration assays. We conclude that binding of zinc to the HHCC motif stabilizes the folded state of the N-terminal domain of integrase and bound zinc is required for optimal enzymatic activity.
Monomères dipyrroliques à caractère hydrophobe : étude électrochimique et polymérisation en milieu aqueux via des molécules cages (1998)

L'étude du mode de polymérisation de monomères constitués de deux entités electropolymérisables espacées par des liens de taille et de rigidité différentes a été réalisée. Nous montrons que les deux entités polymérisables sont impliqL'étude du mode de polymérisation de monomères constitués de deux entités electropolymérisables espacées par des liens de taille et de rigidité différentes a été réalisée. Nous montrons que les deux entités polymérisables sont impliquées dans le processus de formation de films organiques. L'utilisation de tels monomères peut donc être proposée pour l'obtention de polymères bidimensionnels à interactions interchaînes contrôlées. Par ailleurs la formation de complexes d'inclusion entre de tels monomères et la cyclodextrine permet de réaliser l'électrosynthèse de ces matériaux, en milieu aqueux. uées dans le processus de formation de films organiques. L'utilisation de tels monomères peut donc être proposée pour l'obtention de polymères bidimensionnels à interactions interchaînes contrôlées. Par ailleurs la formation de complexes d'inclusion entre de tels monomères et la cyclodextrine permet de réaliser l'électrosynthèse de ces matériaux, en milieu aqueux.
Genetic Determinants of Japanese Encephalitis Virus Vaccine Strain SA14-14-2 That Govern Attenuation of Virulence in Mice (2015)

The live-attenuated JEV SA14-14-2 vaccine has been vital for controlling the incidence of disease caused by JEV, particularly in rural areas of Asia where it is endemic. The vaccine was developed >25 years ago by passaging wild-type JEV strain SA14 in tissue cultures and rodents, with intermittent tissue culture plaque purifications, to produce a virus clone that had adequate levels of attenuation and immunogenicity. The vaccine and parent virus sequences were later compared, and mutations were identified throughout the vaccine virus genome, but their contributions to attenuation were never fully elucidated. Here, using reverse genetics, we comprehensively defined the impact of JEV SA14-14-2 mutations on attenuation of virulence and immunogenicity in mice. These results are relevant for quality control of new lots of the current live-attenuated vaccine and provide insight for the rational design of second-generation, live-attenuated, recombinant JEV vaccine candidates.
Getting a lift (2012)

With inquiries from customers remaining strong, manufacturers are seeing improvements in their order books. Geoff Adam looks at what is on the horizon.
Voltage-Controlled Gating at the Intracellular Entrance to a Hyperpolarization-Activated Cation Channel (2002)

Hyperpolarization-activated cation (HCN) channels regulate pacemaking activity in cardiac cells and neurons. Our previous work using the specific HCN channel blocker ZD7288 provided evidence for an intracellular activation gate for these channels because it appears that ZD7288, applied from the intracellular side, can enter and leave HCN channels only at voltages where the activation gate is opened (Shin, K.S., B.S. Rothberg, and G. Yellen. 2001. J. Gen. Physiol. 117:91-101). However, the ZD7288 molecule is larger than the Na(+) or K(+) ions that flow through the open channel. In the present study, we sought to resolve whether the voltage gate at the intracellular entrance to the pore for ZD7288 also can be a gate for permeant ions in HCN channels. Single residues in the putative pore-lining S6 region of an HCN channel (cloned from sea urchin; spHCN) were substituted with cysteines, and the mutants were probed with Cd(2+) applied to the intracellular side of the channel. One mutant, T464C, displayed rapid irreversible block when Cd(2+) was applied to opened channels, with an apparent blocking rate of approximately 3 x 10(5) M(-1)s(-1). The blocking rate was decreased for channels held at more depolarized voltages that close the channels, which is consistent with the Cd(2+) access to this residue being gated from the intracellular side of the channel. 464C channels could be recovered from Cd(2+) inhibition in the presence of a dithiol applied to the intracellular side. The rate of this recovery also was reduced when channels were held at depolarized voltages. Finally, Cd(2+) could be trapped inside channels that were composed of WT/464C tandem-linked subunits, which could otherwise recover spontaneously from Cd(2+) inhibition. Thus, Cd(2+) escape is also gated at the intracellular side of the channel. Together, these results are consistent with a voltage-controlled structure at the intracellular side of the spHCN channel that can gate the flow of cations through the pore.
Preparation of petroselinic acid (1960)

Abstract Petroselinic acid of a grade which is suitable for most laboratory applications has been prepared by a single crystallization of the mixed fatty acids of parsley seed oil from 90% ethanol. A product of higher purity has been prepared from this acid by application of urea segregation techniques for the removal of saturated materials. No evidence of the presence of unsaturated fatty acids other than petroselinic acid was found in either of these samples when their ozonolysis products were examined chromatographically. On the basis of iodine values, assuming the absence of other unsaturated materials, the purities of the two preparations are 96.0 and 99.4%.
Nitrogen management and senescence in two maize hybrids differing in the persistence of leaf greenness: agronomic, physiological and molecular aspects (2005)

Here, nitrogen management within the plant was compared in an early-senescing maize hybrid and in a late-senescing maize hybrid, both grown under field conditions with a high fertilisation input involving large quantities of fertiliser. We monitored, in representative leaf stages, the changes in metabolite content, enzyme activities and steady-state levels of transcripts for marker genes of N primary assimilation, N recycling and leaf senescence. The hybrids differed in terms of persistence of leaf greenness, the expression of marker genes and the concentration of enzymes used to describe the transition from N assimilation to N recycling. The transcription of leaf-senescence marker genes did not differ. Agronomic studies confirmed the ability of the late-senescing hybrid to absorb and store more N in shoots. Despite the differences in the mode of N management adopted by the two hybrids, we conclude that leaf senescence occurs independently of the source-to-sink transition at the high level of fertilisation used involving large quantities of fertiliser. The possibility of improving N metabolic efficiency in the latest maize hybrids is discussed.
Studies on the constituents of Aster tataricus L. f. I. Structures of shionosides A and B, monoterpene glycosides isolated from the root. (1988)

Two new monoterpene glycosides shionosides A and B were isolated from root of Aster tataricus L. f. (Compositae), along with shionone, epifriedelinol and phytosterol glucosides.The structures of the shionsides were elucidated based on chemical and spectral evidence as the β-D-apiofuranosyl-(1→6)-β-D-glucopyranoside (shionoside A) and the α-L-rhamnopyranosyl-(1→6)-β-D-glucopyranoside (shionoside B) of L-endo-camphanol[(1R, 2R, 4S)-3, 3-dimethyl-bicyclo-[2.2.1]hept-2-yl-methanol].
Involvement of Protein Kinase C Activation and Cell Survival/ Cell Cycle Genes in Green Tea Polyphenol (−)-Epigallocatechin 3-Gallate Neuroprotective Action (2002)

Studies from our laboratory have demonstrated that the major green tea polyphenol, (-)-epigallocatechin 3-gallate (EGCG), exerts potent neuroprotective actions in the mice model of Parkinson's disease. These studies were extended to neuronal cell culture employing the parkinsonism-inducing neurotoxin, 6-hydroxydopamine (6-OHDA). Pretreatment with EGCG (0.1-10 microm) attenuated human neuroblastoma (NB) SH-SY5Y cell death, induced by a 24-h exposure to 6-OHDA (50 microm). Potential cell signaling candidates involved in this neuroprotective effect were further examined. EGCG restored the reduced protein kinase C (PKC) and extracellular signal-regulated kinases (ERK1/2) activities caused by 6-OHDA toxicity. However, the neuroprotective effect of EGCG on cell survival was abolished by pretreatment with PKC inhibitor GF 109203X (1 microm). Because EGCG increased phosphorylated PKC, we suggest that PKC isoenzymes are involved in the neuroprotective action of EGCG against 6-OHDA. In addition, gene expression analysis revealed that EGCG prevented both the 6-OHDA-induced expression of several mRNAs, such as Bax, Bad, and Mdm2, and the decrease in Bcl-2, Bcl-w, and Bcl-x(L). These results suggest that the neuroprotective mechanism of EGCG against oxidative stress-induced cell death includes stimulation of PKC and modulation of cell survival/cell cycle genes.
Wavelet denoising of signals based on the fourth order moment (2002)

In many applications the localization of a wireless communications transmitter is important. Localization of a mobile wireless communication unit using the time difference of arrival (TDOA) method is addressed. The localization of a GSM type emitter is enhanced by using denoised time domain signals. Denoising is obtained by thresholding the wavelet detail coefficients in time and the application of a fourth order moment criterion in scale. The performance, as a function of SNR and mean squared error for the TDOA is obtained.
Two <i>Plasmodium falciparum</i> genes express merozoite proteins that are related to <i>Plasmodium vivax</i> and <i>Plasmodium yoelii</i> adhesive proteins involved in host cell selection and invasion (2000)

Two related Plasmodium falciparum genes and their encoded proteins have been identified by comparative analyses with Plasmodium vivax reticulocyte binding protein 2 (PvRBP-2). The P. falciparum genes have a structure which suggests that they may be the result of an evolutionary duplication event, as they share more than 8 kb of closely related nucleotide sequence but then have quite divergent unique 3' ends. Between these shared and unique regions is a complex set of repeats, the nature and number of which differs between the two genes, as well as between different P. falciparum strains. Both genes encode large hydrophilic proteins, which are concentrated at the invasive apical end of the merozoite and are predicted to be more than 350 kDa, with an N-terminal signal sequence and a single transmembrane domain near their C termini. Importantly, they also share gene structure and amino acid homology with the Plasmodium yoelii 235-kDa rhoptry protein family, which is also related to PvRBP-2. Together these Plasmodium proteins define an extended family of proteins that appear to function in erythrocyte selection and invasion. As such, they may prove to be essential components of malaria vaccine preparations.
Continuous liquid level measurement using a linear electrode array (2007)

This paper describes a novel continuous liquid level measurement technique based on a linear electrode array, which is vertically immersed in the liquid to inject an electric current into it and measure the voltage profile at different depths. We develop models that describe the relationship between voltage and liquid level for several vessel geometries of practical interest. Then, an inverse problem iterative algorithm is used to calculate the liquid level from the set of voltage measurements. The level accuracy values are far smaller than the interelectrode spacing and no calibration procedure is required. We describe a prototype measurement system to measure the water level in a 100 cm deep rectangular tank with a level accuracy of 3 mm when the electrodes are 5 cm apart.
An in vitro model of allergen-dependent IgE synthesis by human B lymphocytes: comparison of the response of an atopic and a non-atopic individual to Dermatophagoides spp. (house dust mite). (1989)

An allergen-dependent in vitro model of immunoglobulin E (IgE) synthesis by human B cells is reported. Using this model, it is demonstrated that polyclonal T cells and CD4+ Dermatophagoides spp. (house dust mite)-specific T-cell clones derived from an atopic, house dust mite (HDM)-allergic individual are able to support IgE synthesis by autologous B cells. The helper activity was interleukin-4 (IL-4) dependent as only cloned T cells expressing detectable mRNA for IL-4 were able to induce IgE synthesis without the addition of exogenous IL-4. Peripheral and cloned T cells reactive with HDM could also be identified from a non-atopic individual but neither population was able to support IgE production even in the presence of exogenous IL-4.
A Finite-State Machine for Accommodating Unexpected Large Ground-Height Variations in Bipedal Robot Walking (2012)

This paper presents a feedback controller that allows MABEL, which is a kneed planar bipedal robot with 1-m-long legs, to accommodate terrain that presents large unexpected increases and decreases in height. The robot is provided no information regarding where the change in terrain height occurs and by how much. A finite-state machine is designed that manages transitions among controllers for flat-ground walking, stepping-up and -down, and a trip reflex. If the robot completes a step, the depth of a step-down or the height of a step-up can be immediately estimated at impact from the lengths of the legs and the angles of the robot’s joints. The change in height can be used to invoke a proper control response. On the other hand, if the swing leg impacts an obstacle during a step, or has a premature impact with the ground, a trip reflex is triggered on the basis of specially designed contact switches on the robot’s shins, contact switches at the end of each leg, and the current configuration of the robot. The design of each control mode and the transition conditions among them are presented. This paper concludes with experimental results of MABEL (blindly) accommodating various types of platforms, including ascent of a 12.5-cm-high platform, stepping-off an 18.5-cm-high platform, and walking over a platform with multiple ascending and descending steps.
STCDG: An Efficient Data Gathering Algorithm Based on Matrix Completion for Wireless Sensor Networks (2012)

Data gathering in sensor networks is required to be efficient, adaptable and robust. Recently, compressive sensing (CS) based data gathering shows promise in meeting these requirements. Existing CS-based data gathering solutions require that a transform that best sparsifies the sensor readings should be used in order to reduce the amount of data traffic in the network as much as possible. As a result, it is very likely that different transforms have to be determined for varied sensor networks, which seriously affects the adaptability of CS-based schemes. In addition, the existing schemes result in significant errors when the sampling rate of sensor data is low (equivalent to the case of high packet loss rate) because CS inherently requires that the number of measurements should exceed a certain threshold. This paper presents STCDG, an efficient data gathering scheme based on matrix completion. STCDG takes advantage of the low-rank feature instead of sparsity, thereby avoiding the problem of having to be customized for specific sensor networks. Besides, we exploit the presence of the short-term stability feature in sensor data, which further narrows down the set of feasible readings and reduces the recovery errors significantly. Furthermore, STCDG avoids the optimization problem involving empty columns by first removing the empty columns and only recovering the non-empty columns, then filling the empty columns using an optimization technique based on temporal stability. Our experimental results indicate that STCDG outperforms the state-of-the-art data gathering algorithms in terms of recovery error, power consumption, lifespan, and network capacity.
DNA‐Origami als Nanometerlineal für die superauflösende Mikroskopie (2009)

Spezifisch fluorophormarkierte rechteckige DNA-Origami werden als Nanometerlineal verwendet. So konnten mit superauflösenden Mikroskopieverfahren, die auf der sukzessiven Lokalisierung von Einzelmolekülen beruhen, zwei Fluorophore mit einem Abstand von ungefähr 90 nm aufgelöst werden. Die Kombination von Mikroskopie jenseits der Beugungsgrenze und DNA-Nanotechnologie eröffnet neue Wege für die Erforschung von Nanostrukturen und deren Dynamik.
The Security Weakness of Block Cipher Piccolo against Fault Analysis (2014)

Piccolo is a 64-bit lightweight block cipher which is able to be implemented in constrained hardware environments such as a wireless sensor network. Fault analysis is a type of side channel attack and cube attack is an algebraic attack finding sufficiently low-degree polynomials in a cipher. In this paper, we show a fault analysis on the Piccolo by using cube attack. We find 16 linear equations corresponding to a round function F by cube attack, which are used to fault analysis. Our attack has the complexity of 2 8.49 and 2 9.21 encryptions with fault injections of target bit positions into Piccolo-80 and Piccolo-128, respectively. And our attack needs 2 20.86 and 2 21.60 encryptions with random 4-bit fault injections for Piccolo-80 and Piccolo-128, respectively.
Specific immunologic recognition of the tumor-specific E2A-PBX1 fusion-point antigen in t(1;19)-positive pre-B cells. (1995)

The t(1;19) translocation is the most commonly observed chromosomal translocation in childhood acute lymphoblastic leukemia (ALL). Its presence among pre-B cell ALL cases, has been associated with a poor prognosis. Two genes, E2A and PBX1, are involved in this t(1;19) translocation. As a consequence, parts of the E2A and PBX1 genes are fused, resulting in a chimeric E2A-PBX1 gene, encoding chimeric E2A-PBX1 proteins. As such, the amino acid sequence at the fusion site represents a unique tumor-specific determinant. We report on the generation of a polyclonal antiserum, termed BP 1/19, raised against the tumor-specific E2A-PBX1 junction of E2A-PBX1 proteins. The specificity of antiserum BP 1/19 for the E2A-PBX1 fusion-point is demonstrated at the peptide and at the protein level. Furthermore, specific binding of antiserum BP 1/19 to t(1;19) positive cells was shown using immunofluorescence techniques. The study shows that: (1) the tumor-specific fusion-point epitope on E2A-PBX1 proteins is presented in an antigenic fashion, and (2) this particular fusion-point epitope can be used in immunological marker analysis using fluorescence microscopy.
Experimental determination of the rate law for charge carrier decay in a polythiophene: Fullerene solar cell (2008)

We use transient photovoltage and differential charging experiments, complemented by transient absorption data, to determine charge carrier lifetimes and densities in a poly(3-hexylthiophene): methanofullerene solar cell at Voc as a function of white light-bias intensity. For a typical device, the charge carrier decay dynamics are observed to exhibit an approximately third order dependence on charge density (dn∕dt∝n3).
가설 토류벽용 SCW의 미경화 현상 (1991)

본 고는 특정 흙에서의 가설 흙막이용 SCW의 미경화현상 원인을 실험적으로 규명하며 성공적으로 현장 시공한 사례를 소개하고자 한다. 시험은 현장 흙을 채취하여 현장 배합비와 변경된 배합비 및 특정약액의 추가에 따른 SCW의 강도특성 변화를 실내 측정하였다. 그 결과 SCW 미경화 현상의 원인은 현장의 유기질토에 기...
Basic Properties of SS-PARSE Parameter Estimates (2010)

Single shot parameter assessment by retrieval from signal encoding (SS-PARSE) is a recently introduced method to obtain quantitative parameter maps from a single-shot (typically 65 ms) magnetic resonance imaging (MRI) signal. Because it explicitly models local magnetization decay and phase evolution occurring during the signal 1) it can provide quantitative estimates of local transverse magnetization magnitude and phase, frequency, and relaxation rate and 2) it is free of geometric distortion or blurring due to field nonuniformities within the tissues. These properties promise to be advantageous in functional brain MRI (fMRI) and other dynamic imaging applications. In this paper, the basic phenomena underlying the performance of SS-PARSE in practice are discussed. Basic sources of bias errors in the parameter estimates are discussed, and performance of the method is characterized in terms of parameter estimates from simulation, experimental phantoms, and in vivo studies. Characteristics of the sum-of-square-error cost function and the iterative search algorithm are discussed, and their relative roles in determining estimation accuracy are described. Practical guidelines for use of the method are presented and discussed. In vivo parameter maps are also presented.
Direct Conversion of Bio-ethanol to Isobutene on Nanosized Zn<sub><i>x</i></sub>Zr<sub><i>y</i></sub>O<sub><i>z</i></sub> Mixed Oxides with Balanced Acid–Base Sites (2011)

We report the design and synthesis of nanosized Zn(x)Zr(y)O(z) mixed oxides for direct and high-yield conversion of bio-ethanol to isobutene (~83%). ZnO is addded to ZrO(2) to selectively passivate zirconia's strong Lewis acidic sites and weaken Brönsted acidic sites, while simultaneously introducing basicity. As a result, the undesired reactions of bio-ethanol dehydration and acetone polymerization/coking are suppressed. Instead, a surface basic site-catalyzed ethanol dehydrogenation to acetaldehyde, acetaldehyde to acetone conversion via a complex pathway including aldol-condensation/dehydrogenation, and a Brönsted acidic site-catalyzed acetone-to-isobutene reaction pathway dominates on the nanosized Zn(x)Zr(y)O(z) mixed oxide catalyst, leading to a highly selective process for direct conversion of bio-ethanol to isobutene.
Differential Production of IFN-α/β by CSF-1- and GM-CSF-Derived Macrophages (1990)

Mature macrophages, derived in vitro from bone marrow progenitors under the influence of either macrophage colony stimulating factor (CSF-1) or granulocyte-macrophage (GM)-CSF, have been shown to differ morphologically and functionally. The data presented in this report demonstrate that macrophages derived from bone marrow progenitors under the influence of CSF-1 are highly resistant to infection with vesicular stomatitis virus (VSV), and that this refractoriness can be reversed by treatment of cells with anti-IFN-alpha/beta antibody. In contrast, macrophages derived from bone marrow progenitors under the influence of GM-CSF are highly susceptible to the cytopathic effects of VSV, but can be protected by very low concentrations of exogenous IFN-alpha/beta. These findings suggest that CSF-1 derived macrophages have a greater capacity for the production and/or utilization of IFN-alpha/beta than GM-CSF-derived macrophages, which may account for many of the differentiative differences reported previously.