gebhart/patrepeval huggingface dataset:
Guanidinium chloride denaturation of the dimeric Bacillus licheniformis BlaI repressor highlights an independent domain unfolding pathway (2004)

The Bacillus licheniformis 749/I BlaI repressor is a prokaryotic regulator that, in the absence of a beta-lactam antibiotic, prevents the transcription of the blaP gene, which encodes the BlaP beta-lactamase. The BlaI repressor is composed of two structural domains. The 82-residue NTD (N-terminal domain) is a DNA-binding domain, and the CTD (C-terminal domain) containing the next 46 residues is a dimerization domain. Recent studies have shown the existence of the monomeric, dimeric and tetrameric forms of BlaI in solution. In the present study, we analyse the equilibrium unfolding of BlaI in the presence of GdmCl (guanidinium chloride) using different techniques: intrinsic and ANS (8-anilinonaphthalene-l-sulphonic acid) fluorescence, far- and near-UV CD spectroscopy, cross-linking, analytical ultracentrifugation, size exclusion chromatography and NMR spectroscopy. In addition, the intact NTD and CTD were purified after proteolysis of BlaI by papain, and their unfolding by GdmCl was also studied. GdmCl-induced equilibrium unfolding was shown to be fully reversible for BlaI and for the two isolated fragments. The results demonstrate that the NTD and CTD of BlaI fold/unfold independently in a four-step process, with no significant co-operative interactions between them. During the first step, the unfolding of the BlaI CTD occurs, followed in the second step by the formation of an 'ANS-bound' intermediate state. Cross-linking and analytical ultracentrifugation experiments suggest that the dissociation of the dimer into two partially unfolded monomers takes place in the third step. Finally, the unfolding of the BlaI NTD occurs at a GdmCl concentration of approx. 4 M. In summary, it is shown that the BlaI CTD is structured, more flexible and less stable than the NTD upon GdmCl denaturation. These results contribute to the characterization of the BlaI dimerization domain (i.e. CTD) involved in the induction process.
Experience using mTOR inhibitors for subependymal giant cell astrocytoma in tuberous sclerosis complex at a single facility (2021)

The Post-group underwent surgery significantly less often than the Pre-group. Since the treatment option to use mTORi in the treatment of SEGA in TSC became available, opportunities for surgical resection have decreased in our facility.
Substrate-bound CCL21 and ICAM1 combined with soluble IL-6 collectively augment the expansion of antigen-specific murine CD4+ T cells (2017)

Immune processes within the complex microenvironment of the lymph node involve multiple intercellular, cell-matrix, and paracrine interactions, resulting in the expansion of antigen-specific T cells. Inspired by the lymph node microenvironment, we aimed to develop an ex vivo "synthetic immune niche" (SIN), which could effectively stimulate the proliferation of antigen-activated CD4<sup>+</sup> T cells. This engineered SIN consisted of surfaces coated with the chemokine C-C motif ligand 21 (CCL21) and with the intercellular adhesion molecule 1 (ICAM1), coupled with the soluble cytokine interleukin 6 (IL-6) added to the culture medium. When activated by ovalbumin-loaded dendritic cells, OT-II T cells growing on regular uncoated culture plates form nonadherent, dynamic clusters around the dendritic cells. We found that functionalization of the plate surface with CCL21 and ICAM1 and the addition of IL-6 to the medium dramatically increases T-cell proliferation and transforms the culture topology from that of suspended 3-dimensional cell clusters into a firm, substrate-attached monolayer of cells. Our findings demonstrate that the components of this SIN collectively modulate T-cell interactions and augment both the proliferation and survival of T cells in an antigen-specific manner, potentially serving as a powerful approach for expanding immunotherapeutic T cells.
Resveratrol Enhances Airway Surface Liquid Depth in Sinonasal Epithelium by Increasing Cystic Fibrosis Transmembrane Conductance Regulator Open Probability (2013)

Resveratrol is a potent chloride secretagogue from the mucosal surface of sinonasal epithelium, and hydrates airway surface liquid by increasing CFTR channel open probability. The foundation for a clinical trial utilizing resveratrol as a therapeutic intervention to increase mucociliary transport and airway surface liquid hydration in sinus disease is strongly supported by these findings.
Monitoring methods for Diaphorina citri Kuwayama (Hemiptera: Liviidae) on citrus groves with different insecticide application programmes (2017)

Abstract The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), is a major citrus pest that transmits the bacteria Candidatus Liberibacter asiaticus and Ca . L. americanus associated with huanglongbing ( HLB ) disease. Diaphorina citri population densities can affect the effectiveness of its monitoring and sampling methods. Thus, we compared different methods for adult D. citri monitoring in groves with and without insecticide application programmes. Four short‐term experiments were carried out, each one lasting four consecutive weeks. In these experiments, sticky cards with different colours (yellow, light green, green and dark green), sweep net, two suction device models, visual inspection and stem tap sampling were assessed. Two long‐term experiments were conducted for 4.5 and 5 years, in which only yellow sticky card and visual inspection for D. citri monitoring were assessed. For the short‐term experiments, psyllids were detected by all monitoring methods during all sampling periods in areas without chemical control. However, in areas with psyllid control via fortnightly and monthly applications of insecticides, only sticky cards, regardless of their colour, were able to detect the presence of D. citri . Similarly, for the long‐term experiments, yellow sticky cards were more effective than visual inspection for detecting and quantifying D. citri in all areas with or without insecticide application. Therefore, in areas where HLB is present and chemical control of psyllid is required, sticky cards are the most reliable option for monitoring D. citri .
Investigation of NH3 Emissions from New Technology Vehicles as a Function of Vehicle Operating Conditions (2003)

The objective of this study was to measure ammonia (NH3) emissions from modern technology vehicles since information is scarce aboutthis importantsource of particulate matter (PM) precursors. Test variables included the emission level to which the vehicle was certified, the vehicle operating conditions, and catalyst age. Eight vehicles with low-emission vehicle (LEV) to super-ultralow-emission vehicle (SULEV) certification levels were tested over the Federal Test Procedure (FTP75), a US06 cycle, a hot running 505, a New York City Cycle (NYCC), and a specially designed Modal Emissions Cycle (MEC01v7) using both as-received and bench-aged catalysts. NH3 emissions in the raw exhaust were measured by tunable diode laser (TDL) absorption spectroscopy. The results show that NH3 emissions depend on driving mode and are primarily generated during acceleration events. More specifically, high NH3 emissions were found for high vehicle specific power (VSP) events and rich operating conditions. For some vehicles, NH3 emissions formed immediately after catalyst light-off during a cold start.
Honeywords (2013)

We propose a simple method for improving the security of hashed passwords: the maintenance of additional ``honeywords'' (false passwords) associated with each user's account. An adversary who steals a file of hashed passwords and inverts the hash function cannot tell if he has found the password or a honeyword. The attempted use of a honeyword for login sets off an alarm. An auxiliary server (the ``honeychecker'') can distinguish the user password from honeywords for the login routine, and will set off an alarm if a honeyword is submitted.
Aptamer-Mediated Inhibition of Mycobacterium tuberculosis Polyphosphate Kinase 2 (2011)

Inorganic polyphosphate (polyP) plays a number of critical roles in bacterial persistence, stress, and virulence. PolyP intracellular metabolism is regulated by the polyphosphate kinase (PPK) protein families, and inhibition of PPK activity is a potential approach to disrupting polyP-dependent processes in pathogenic organisms. Here, we biochemically characterized Mycobacterium tuberculosis (MTB) PPK2 and developed DNA-based aptamers that inhibit the enzyme's catalytic activities. MTB PPK2 catalyzed polyP-dependent phosphorylation of ADP to ATP at a rate 838 times higher than the rate of polyP synthesis. Gel filtration chromatography suggested MTB PPK2 to be an octamer. DNA aptamers were isolated against MTB PPK2. Circular dichroism revealed that aptamers grouped into two distinct classes of secondary structure; G-quadruplex and non-G-quadruplex. A selected G-quadruplex aptamer was highly selective for binding to MTB PPK2 with a dissociation constant of 870 nM as determined by isothermal titration calorimetry. The binding between MTB PPK2 and the aptamer was exothermic yet primarily driven by entropy. This G-quadruplex aptamer inhibited MTB PPK2 with an IC(50) of 40 nM and exhibited noncompetitive inhibition kinetics. Mutational mechanistic analysis revealed an aptamer G-quadruplex motif is critical for enzyme inhibition. The aptamer was also tested against Vibrio cholerae PPK2, where it showed an IC(50) of 105 nM and insignificant inhibition against more distantly related Laribacter hongkongensis PPK2.
Test observations of the Kyoto Tridimensional Spectrograph II at the University of Hawaii 88-in and Subaru Telescopes (2004)

In order to investigate the physical conditions of ionized gas in galaxies, as well as its kinematics, we have developed the Kyoto tridimensional spectrograph II (3DII). It is a multi-mode instrument designed for Cassegrain focus, including integral field spectrograph (IFS) and Fabry-Perot imager modes. We have designed it compact so that we can mount it at 2-m class telescopes as well as at 8-m Subaru telescope. We have succeeded in test observations of the 3DII. In the IFS mode the spatial resolution of ~ 0".5 and 0".4 was obtained in 30-minute exposures at University of Hawaii 88-inch (UH88) and Subaru, respectively, in relatively good weather conditions. Each of 37 × 37 microlenses subtends ~ 0".1 in Subaru's case. This samples well the image size. A wider field of view is emphasized in the case of UH88. Because our micropupil spectroscopy is free from a slit effect, we have reached the accuracy of an order of one tenth of a pixel for deriving velocity fields in terms of velocity center while the full width at half maximum of the instrumental profile corresponds to two pixels. At Subaru we have used a container designed in a collaboration with National Astronomical Observatory, Japan: it fits with a robotic instrument exchanger. The containerincludes two heat exchangers to keep its surface cool and void degrading the image quality. We have established effective observational equences by realizing a software interface with Subaru operating system. ome results from target observations are shown.
SMS/GOES cell and battery data analysis report (1977)

The nickel-cadmium battery design developed for the Synchronous Meteorological Satellite (SMS) and Geostationary Operational Environmental Satellite (GOES) provided background and guidelines for future development, manufacture, and application of spacecraft batteries. SMS/GOES battery design, development, qualification testing, acceptance testing, and life testing/mission performance characteristics were evaluated for correlation with battery cell manufacturing process variables.
VEGF A (rs699947 and rs833061) and VEGFR2 (rs2071559) Gene Polymorphisms are not Associated with AMD Susceptibility in a Spanish Population (2013)

Our study shows that VEGFA rs699947 and rs833061 and VEGFR2 rs2071559 polymorphisms do not modify the risk of suffering AMD in a Spanish population.
Impact of transistor noise on high precision parametric matching measurements (2002)

Utilising the correlation of fluctuations of the drain and source currents of a MOSFET, this paper demonstrates that low frequency transistor noise (and random telegraph signals) can be much higher than the noise contribution of bench top DC semiconductor measurement systems. These results provide valuable insights into the limits of high precision parameter fluctuation (matching) measurement methods.
Protection against aspirin‐induced human gastric mucosal injury by bosentan, a new endothelin‐1 receptor antagonist (1999)

Endothelin receptor antagonism by bosentan can protect the gastric mucosa against aspirin damage. After five doses, bosentan levels fell, possibly because of enzyme induction, and protection was no longer evident. Further investigation is needed to assess whether higher doses would be effective.
Dog Leukocyte Antigen Class II–Associated Genetic Risk Testing for Immune Disorders of Dogs: Simplified Approaches Using Pug Dog Necrotizing Meningoencephalitis as a Model (2011)

A significantly increased risk for a number of autoimmune and infectious diseases in purebred and mixed-breed dogs has been associated with certain alleles or allele combinations of the dog leukocyte antigen (DLA) class II complex containing the DRB1, DQA1, and DQB1 genes. The exact level of risk depends on the specific disease, the alleles in question, and whether alleles exist in a homozygous or heterozygous state. The gold standard for identifying high-risk alleles and their zygosity has involved direct sequencing of the exon 2 regions of each of the 3 genes. However, sequencing and identification of specific alleles at each of the 3 loci are relatively expensive and sequencing techniques are not ideal for additional parentage or identity determination. However, it is often possible to get the same information from sequencing only 1 gene given the small number of possible alleles at each locus in purebred dogs, extensive homozygosity, and tendency for disease-causing alleles at each of the 3 loci to be strongly linked to each other into haplotypes. Therefore, genetic testing in purebred dogs with immune diseases can be often simplified by sequencing alleles at 1 rather than 3 loci. Further simplification of genetic tests for canine immune diseases can be achieved by the use of alternative genetic markers in the DLA class II region that are also strongly linked with the disease genotype. These markers consist of either simple tandem repeats or single nucleotide polymorphisms that are also in strong linkage with specific DLA class II genotypes and/or haplotypes. The current study uses necrotizing meningoencephalitis of Pug dogs as a paradigm to assess simple alternative genetic tests for disease risk. It was possible to attain identical necrotizing meningoencephalitis risk assessments to 3-locus DLA class II sequencing by sequencing only the DQB1 gene, using 3 DLA class II–linked simple tandem repeat markers, or with a small single nucleotide polymorphism array designed to identify breed-specific DQB1 alleles.
Informe sobre la Formación Profesional a distancia en España (2010)

espanolEl presente informe que se entregara en dos articulos, se centra en analizar la implantacion de ensenanzas virtuales en la Formacion Profesional en Espana. Se hace un estudio generalizado de las caracteristicas generales a tener en cuenta a nivel estatal y se realizara un estudio pormenorizado por Comunidades Autonomas de las ensenanzas que se imparten en esta modalidad indicando como se organizan las ensenanzas, que metodologia didactica se aplica y que herramientas software se utilizan. EnglishThis report, divided into two articles, is focused on the analysis of the implementation of the online learning in the Spanish Vocational Training. It makes a general study of the main features to keep in mind in a state-wide scope, and shows a detailed study by regions of the teachings that are developed throughout this method, and points out how the teachings are organized, what didactic methodology is applied and what software tools are used.
Intravascular ultrasonic imaging. (1990)

Because conventional imaging methods are inadequate for evaluating human coronary arteries in vivo, an intravascular ultrasonic imaging catheter was developed that allows the arterial wall to be studied in cross-section from within the artery. The catheter incorporates a mechanically rotating 20-MHz transducer, which is designed so that the ringdown occurs within the catheter and imaging is permitted up to the catheter's surface. The device rotates at 1800-rpm within a plastic sleeve and provides real-time cross-sectional images at 30 frames/sec. Preliminary experimental and clinical studies indicate that the intravascular ultrasonic imaging catheter could play a valuable role in providing preoperative information concerning arterial wall thickness and tissue characteristics, in distinguishing normal from diseased arterial wall structures during therapeutic intervention, and in assessing the results of intervention.
Learning Gradient Fields for Molecular Conformation Generation (2021)

We study a fundamental problem in computational chemistry known as molecular conformation generation, trying to predict stable 3D structures from 2D molecular graphs. Existing machine learning approaches usually first predict distances between atoms and then generate a 3D structure satisfying the distances, where noise in predicted distances may induce extra errors during 3D coordinate generation. Inspired by the traditional force field methods for molecular dynamics simulation, in this paper, we propose a novel approach called ConfGF by directly estimating the gradient fields of the log density of atomic coordinates. The estimated gradient fields allow directly generating stable conformations via Langevin dynamics. However, the problem is very challenging as the gradient fields are roto-translation equivariant. We notice that estimating the gradient fields of atomic coordinates can be translated to estimating the gradient fields of interatomic distances, and hence develop a novel algorithm based on recent score-based generative models to effectively estimate these gradients. Experimental results across multiple tasks show that ConfGF outperforms previous state-of-the-art baselines by a significant margin.
High-electron-mobility AlGaN∕GaN heterostructures grown on Si(001) by molecular-beam epitaxy (2005)

The growth of AlGaN∕GaN heterostructure on Si (001) substrates by molecular-beam epitaxy using ammonia as nitrogen precursor is reported. The structural, optical, and electrical properties of such heterostructures are assessed. It is shown that a two-dimensional electron gas is formed at the Al0.23Ga0.77N∕GaN interface. This type of heterostructure exhibits a sheet carrier density of 4.2×1012cm−2 with a mobility of 730cm2∕Vs at room temperature. Preliminary results concerning high-electron-mobility-transistor static characteristics are presented.
Supplementary Data from K562/GM-CSF Immunotherapy Reduces Tumor Burden in Chronic Myeloid Leukemia Patients with Residual Disease on Imatinib Mesylate (2023)

Supplementary Data from K562/GM-CSF Immunotherapy Reduces Tumor Burden in Chronic Myeloid Leukemia Patients with Residual Disease on Imatinib Mesylate
On the circle polynomials of Zernike and related orthogonal sets (1954)

ABSTRACT The paper is concerned with the construction of polynomials in two variables, which form a complete orthogonal set for the interior of the unit circle and which are ‘invariant in form’ with respect to rotations of axes about the origin of coordinates. It is found that though there exist an infinity of such sets there is only one set which in addition has certain simple properties strictly analogous to that of Legendre polynomials. This set is found to be identical with the set of the circle polynomials of Zernike which play an important part in the theory of phase contrast and in the Nijboer-Zernike diffraction theory of optical aberrations. The results make it possible to derive explicit expressions for the Zernike polynomials in a simple, systematic manner. The method employed may also be used to derive other orthogonal sets. One new set is investigated, and the generating functions for this set and for the Zernike polynomials are also given.
Hyperion, a space-based imaging spectrometer (2003)

The Hyperion Imaging Spectrometer was the first imaging spectrometer to routinely acquire science-grade data from Earth orbit. Instrument performance was validated and carefully monitored through a combination of calibration approaches: solar, lunar, earth (vicarious) and atmospheric observations complemented by onboard calibration lamps and extensive prelaunch calibration. Innovative techniques for spectral calibration of space-based sensors were also tested and validated. Instrument performance met or exceeded predictions including continued operation well beyond the planned one-year program.
Emission of excimer radiation from direct current, high-pressure hollow cathode discharges (1998)

A novel, nonequilibrium, high-pressure, direct current discharge, the microhollow cathode discharge, has been found to be an intense source of xenon and argon excimer radiation peaking at wavelengths of 170 and 130 nm, respectively. In argon discharges with a 100 μm diam hollow cathode, the intensity of the excimer radiation increased by a factor of 5 over the pressure range from 100 to 800 mbar. In xenon discharges, the intensity at 170 nm increased by two orders of magnitude when the pressure was raised from 250 mbar to 1 bar. Sustaining voltages were 200 V for argon and 400 V for xenon discharges, at current levels on the order of mA. The resistive current–voltage characteristics of the microdischarges indicate the possibility to form arrays for direct current, flat panel excimer lamps.
Loss phenomena in single-mode optical fibers: an experimental evaluation (2002)

In this paper we describe the microbend induced loss behaviour and show specific results for several single-mode fibers. Researchers have used complex mathematical developments to describe microbending loss in single mode fibers. We describe a simplified theoretical development to allow prediction of wavelength dependent loss behaviour of single-mode fibers. Single mode fibers subjected to microbending result in narrow bands of attenuation at specific optical wavelengths. This phenomenon is due to coupling of the guided mode power to cladding modes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cloning and Expression of cry11B Gene From a Local Isolate of Bacillus thuringiensis and its Mosquitocidal Activity (2011)

The present paper describes cry11B gene from a local isolate of Bacillus thuringiensis (B.t.). Escherichia coli DH5α was transformed with recombinant DNA comprising pTZ57 and B. t. cry11B gene (1.9kb) amplified from a local B.t. isolate SBS B.t. 48 for cloning. The cloned 1.9kb gene was sequenced and then ligated in the expression vector pT7-7 for transformation of E. coli BL21C + . For expression of the recombinant organism containing cry11B gene, the conditions were optimized with respect to IPTG concentration, time of induction and incubation temperature. The optimized expression was recorded at 1.0mM IPTG incubated at 37 o C for 3.5 h. The toxicity of B.t. spores, recombinant organisms and crude recombinant Cry11B proteins was determined against the third instar larvae of mosquito, Anopheles stephensi. The LC50 of SBS B.t. 48 spores, recombinant organisms and recombinant Cry11B protein was, respectively, 700 µg /ml, 525 µg/ml and 390 ng/ml as against 850, 550 and 470 of HD500 standard B.t. strain. The toxicity of crude Cry11B recombinant protein was 1346 fold higher than that of the recombinant organism.