gebhart/patrepeval huggingface dataset:
Temperature Micro ave Characteristics o s MESFET Devices with AlAs Buffer (1996)

MAS buffers used to reduce the leakage current of high-temperature GaAs MESFET devices are shown to have no detrimental effect on the microwave performance measured to 200°C. The ft values decrease with increasing temperature, but do not appear to be influenced by the AMs buffer. The fmax values also decrease with increasing temperature; however, they are improved with increasing AMs buffer thickness due to a concomitant decrease in the device output conductance. At 200 C ambient temperature, ft and fmax values of 14.5 GHz and 36.7 GHz, respectively, were measured.
Structural Features Required for the Interaction of the Hsp70 Molecular Chaperone DnaK with Its Cochaperone DnaJ (1999)

Hsp70 family members together with their Hsp40 cochaperones function as molecular chaperones, using an ATP-controlled cycle of polypeptide binding and release to mediate protein folding. Hsp40 plays a key role in the chaperone reaction by stimulating the ATPase activity and activating the substrate binding of Hsp70. We have explored the interaction between the Escherichia coli Hsp70 family member, DnaK, and its cochaperone partner DnaJ. Our data show that the binding of ATP, subsequent conformational changes in DnaK, and DnaJ-stimulated ATP hydrolysis are all required for the formation of a DnaK-DnaJ complex as monitored by Biacore analysis. In addition, our data imply that the interaction of the J-domain with DnaK depends on the substrate binding state of DnaK.
Syntheses and Structure−Activity Relationships of Novel Retinoid X Receptor Agonists (1998)

As part of our studies to develop novel retinoids with increased affinity and selectivity for the retinoid X receptor (RXR) subfamily, we have designed and synthesized a series of (E,E,E)-7-(1,2,3, 4-tetrahydroquinolin-6-yl)-7-alkyl-6-fluoro-3-methylhepta-2, 4, 6-trienoic acid derivatives. These tetrahydroquinolines, generated by introducing a polar N atom into the hydrophobic part of the retinoid skeleton, showed high binding affinity to RXRs. Addition of fluorine at the 6-position of the 2,4,6-trienoic acid moiety afforded compounds which elicit potent and selective transactivation of the RXRs. Compound 14b (ER-35794), which possesses an ethyl substituent at the 7-position and fluorine at the 6-position of the triene moiety, is one of the most potent and selective RXR agonists reported to date.
Modification of the 5′ Terminus of Oligonucleotides for Attachment of Reporter and Conjugate Groups (2000)

Reporter and conjugate groups can be added directly to the 5' terminus of oligonucleotides by appropriate modification. Conjugate groups can be used to increase the affinity of complementary strands, induce irreversible modification of target sequences, or enable sequences to recognize and permeate target cell membranes. This overview discusses the 5' modifications that can be used and strategies for the covalent attachment of ligands to the modified oligonucleotides. Step-by-step protocols for attachment of conjugate groups are given elsewhere in the series.
ChemInform Abstract: TRIAZOLO(4,5‐D)PYRIMIDINES. V. THE NUCLEOPHILIC SUBSTITUTION OF 7‐CHLORO‐ AND D 7‐(P‐TOLYLSULFONYL)‐3‐PHENYL‐3H‐1,2,3‐TRIAZOLO(4,5‐D)PYRIMIDINES (1980)

Abstract Triazolo[4,5‐d]pyrimidines.
Heterodyne coherent anti-Stokes Raman scattering (CARS) imaging (2006)

We have achieved rapid nonlinear vibrational imaging free of nonresonant background with heterodyne coherent anti-Stokes Raman scattering (CARS) interferometric microscopy. This technique completely separates the real and imaginary responses of nonlinear susceptibility chi(3) and yields a signal that is linear in the concentration of vibrational modes. We show that heterodyne CARS microscopy permits the detection of weak vibrational resonances that are otherwise overshadowed by the strong interference of the nonresonant background.
A cDNA clone for human glucosamine-6-sulphatase reveals differences between arylsulphatases and non-arylsulphatases (1992)

Glucosamine-6-sulphatase is an exo-hydrolase required for the lysosomal degradation of heparan sulphate and keratan sulphate. Deficiency of glucosamine-6-sulphatase activity leads to the lysosomal storage of the glycosaminoglycan, heparan sulphate and the monosaccharide sulphate N-acetylglucosamine 6-sulphate and the autosomal recessive genetic disorder mucopolysaccharidosis type IIID. Glucosamine-6-sulphatase can be classified as a non-arylsulphatase since, relative to arylsulphatase B, it shows negligible activity toward 4-methylumbelliferyl sulphate. We have isolated human cDNA clones and derived amino acid sequence coding for the entire glucosamine-6-sulphatase protein. The predicted sequence has 552 amino acids with a leader peptide of 36 amino acids and contains 13 potential N-glycosylation sites, of which it is likely that 10 are used. Glucosamine-6-sulphatase shows strong sequence similarity to other sulphatases such as the family of arylsulphatases, although the degree of similarity is not as high as that between members of the arylsulphatase family. This pattern of inter- and intra-family similarity delineates regions and amino acid residues that may be critical for sulphatase function and substrate specificity.
Hypoxia Promotes Dissemination and Colonization in New Bone Marrow Niches in Waldenström Macroglobulinemia (2014)

This study provides a better understanding of the biology of dissemination of Waldenström macroglobulinemia and opens new windows for investigation of new therapeutic targets in Waldenström macroglobulinemia based on tumor hypoxia mechanisms.
The epidemiology of thyroid cancer in the Czech Republic incomparison with other countries (2013)

Background. Thyroid cancer includes a broad spectrum of tumours
with different prognoses. The global incidence has been
increasing in recent years. Variables affecting its etiology
are dietary, especially iodine intake and to a lesser extent
selenium, environmental, like - ionizing radiation and,
increased TSH level. These factors interplay with epigenetic
and genetic changes within the cell. This review article
presents thyroid cancer epidemiology, describes its main
characteristics and the influence of environmental and
lifestyle risk factors in the Czech Republic in comparison with
other countries. Methods and Results. An epidemiological study
of Czech patients with malignant thyroid carcinoma was made on
the basis of the National Oncologic Registry (NOR) and Czech
Statistical Office data summarized on the web portal SVOD. The
data were compared with international data from the project
GLOBOCAN 2008 Cancer Incidence and Mortality Worldwide. Apart
from risk factors, prognostic factors with effect on patient
survival were also analyzed. The survey showed that the
incidence of thyroid cancer has been steadily growing in the
Czech Republic. Since the beginning of the 1980s, it has
increased 4 fold. It has a higher incidence than most other
European countries but it is ranked with countries with an
average and decreasing mortality. Obviously, the improved
detection methods do not explain the growing incidence. The
highest incidence is found for papillary carcinoma (PTC), now
over 80% of cases. For follicular and medullar cancers, the
incidence has not increased and for anaplastic carcinoma there
is a slight decrease. Women over 40 years of age constitute the
highest risk group. Conclusions. There are a number of reasons
for these trends, such as improved diagnostic techniques using
ultrasound and FNAB and more radical surgery. There are also
dietary/environmental factors (iodine deficiency and to a
lesser extent selenium), nitrates, polychlorinated biphenyls,
increased ionizing radiation, and prolonged increase in TSH.
The prognosis of patients with DTC depends on the age at the
time of diagnosis. A favorable prognosis also depends on timely
detection.
GaAs surface reconstruction obtained using a dry process (1993)

We report attaining Ga-terminated (4×2) surface reconstruction on virgin GaAs substrates using a completely dry process at temperatures below the oxide sublimation temperature and without group V overpressure. The native oxides are removed with an electron cyclotron resonance hydrogen plasma treatment, followed by annealing at 500 °C in ultrahigh vacuum, which yields a reconstructed surface suitable for epitaxial overgrowth. Characterization by secondary ion mass spectroscopy and transmission electron microscopy reveals the complete removal of O, reduced C, and high structural order at the epilayer/substrate interface when this preparation method is used before molecular beam epitaxy. Annealing the substrate at a lower temperature yields a nonreconstructed surface possessing significant impurity concentrations, and leads to dislocation defects at the epilayer/substrate interface.
Identification and Characterization of a Selective Radioligand for ELOVL6 (2009)

ELOVL6, a member of the elongation of very long-chain fatty acids (ELOVL) family, has recently been identified as the rate-limiting enzyme for the elongation of palmitoyl-CoA. ELOVL6 deficient mice are protected from high-fat diet induced insulin resistance, suggesting that ELOVL6 might be a promising target for the treatment of metabolic disorders. Despite the increasing interest in Elovl6 as a therapeutic target, the lack of chemical tools for this enzyme has limited further elucidation of the biochemical and pharmacological properties of ELOVL6. We have identified Compound-A, a potent inhibitor for ELOVL6, by screening our company library and subsequently optimizing hit compounds. Compound-A potently inhibited human and mouse ELOVL6 and displayed >100-fold greater selectivity for ELOVL6 over other ELOVL family members. Consistent with its potent and selective inhibitory activity toward ELOVL6, [(3)H]Compound-A bound to ELOVL6 with high affinity while showing no specific binding to other ELOVL enzymes. The observation that [(3)H]Compound-A bound to ELOVL6 in a palmitoyl-CoA-dependent manner in the absence of malonyl-CoA and NADPH suggests that Compound-A might recognize an enzyme-substrate complex, e.g. an acyl-enzyme intermediate. Collectively, these observations demonstrate that Compound-A and its tritiated form are useful tools for biochemical and pharmacological characterization of ELOVL6.
Disrupted autophagy after spinal cord injury is associated with ER stress and neuronal cell death (2015)

Autophagy is a catabolic mechanism facilitating degradation of cytoplasmic proteins and organelles in a lysosome-dependent manner. Autophagy flux is necessary for normal neuronal homeostasis and its dysfunction contributes to neuronal cell death in several neurodegenerative diseases. Elevated autophagy has been reported after spinal cord injury (SCI); however, its mechanism, cell type specificity and relationship to cell death are unknown. Using a rat model of contusive SCI, we observed accumulation of LC3-II-positive autophagosomes starting at posttrauma day 1. This was accompanied by a pronounced accumulation of autophagy substrate protein p62, indicating that early elevation of autophagy markers reflected disrupted autophagosome degradation. Levels of lysosomal protease cathepsin D and numbers of cathepsin-D-positive lysosomes were also decreased at this time, suggesting that lysosomal damage may contribute to the observed defect in autophagy flux. Normalization of p62 levels started by day 7 after SCI, and was associated with increased cathepsin D levels. At day 1 after SCI, accumulation of autophagosomes was pronounced in ventral horn motor neurons and dorsal column oligodendrocytes and microglia. In motor neurons, disruption of autophagy strongly correlated with evidence of endoplasmic reticulum (ER) stress. As autophagy is thought to protect against ER stress, its disruption after SCI could contribute to ER-stress-induced neuronal apoptosis. Consistently, motor neurons showing disrupted autophagy co-expressed ER-stress-associated initiator caspase 12 and cleaved executioner caspase 3. Together, these findings indicate that SCI causes lysosomal dysfunction that contributes to autophagy disruption and associated ER-stress-induced neuronal apoptosis.
A minority-carrier transport model for polysilicon contacts to silicon bipolar devices, including solar cells (1980)

A physical, analytic model for heavily doped polysilicon contacts to silicon bipolar devices is developed. The model defines an effective surface recombination velocity S <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</inf> for minority carriers at the polysilicon-silicon interface in terms of the physical properties of the polysilicon. It thus allows the carrier transport problem in the adjacent silicon region, e.g., the emitter, to be solved and the efficacy of the device, e.g., a transistor or a solar cell, to be characterized, and hence can be an effective design aid. The model is shown to compare well with published experimental data indicating the benefits of polysilicon contacts to bipolar transistors. Such benefits, which result because of the relatively low values of S <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</inf> , might also occur when polysilicon contacts are used on silicon solar cells.
An IC Mixed-Signal Framework for Design, Optimization, and Verification of High-Speed Links (2020)

High-speed serial interfaces are ubiquitous in modern electronic systems; therefore, the design of application specific integrated circuits must often consider their incorporation. This is not a straightforward task since electromagnetic interactions among complex circuits and the influence of off-chip interconnects must be considered. This work presents an automated design, optimization, and pre-silicon verification framework for this type of interfaces, considering a mixed-signal IC environment coupled to a channel simulator through S-parameter models. An application scenario for the optimization of a CTLE stage for USB 3.0 channels is discussed to exemplify the viability of the presented approach.
Multi-path transmission control scheme combining bandwidth aggregation and packet scheduling for real-time streaming in multi-path environment (2010)

These days, a wide variety of wireless interfaces are available to connect to Internet. When coverage area of these different technologies overlap, receiver equipped with multiple interfaces can use them simultaneously to improve the performance of its applications in terms of bandwidth rely on bandwidth aggregation. However, specific conditions such as bottleneck bandwidth and end-to-end delay need to be accounted for before using such techniques. If this problem of end-to-end delay and bottleneck bandwidth are not properly addressed, there may be many packets along multiple paths which can arrive late and can lead to a large number of out-of-order packets at the receiver, which can eventually cause serious degradation of video quality at the receiver. For this reason, in this study, the authors propose a multi-path transmission control scheme (MTCS) combining bandwidth aggregation and packet scheduling for real-time streaming in a multi-path environment. In a bandwidth aggregation scheme, the authors propose a mathematical model to find the transmission rate over each path in order to obtain the optimal total throughput. However, the end-to-end delay of each path is not the same. The out-of-order packets problem will become serious in a multi-path environment. Therefore the authors propose a packet scheduling scheme to arrange the transmission sequence in order to effectively minimise the impact of packet reordering at the receiver. Our proposed control scheme not only aggregates the available bandwidth of multiple paths, but also reduces the time of packet reordering at the receiver. Experimental results show with our proposed scheme, the authors not only obtain the optimal transmission throughput but also reduce packet reordering delays under varying drop and delay conditions caused by the underlying network.
Nitrogen Leaching from Cypress Wood Chips (1990)

Columns (4 × 15 cm) of incubated (25C, 7% volumetric moisture) milled cypress [Taxodium distichum (L.) L. Rich] wood chips received 180 mg of each ionic form of N applied to the surface from dry NH 4 NO 3 , KNO 3 , or (NH 4 ) 2 SO 4 and were leached daily with 16 ml deionized water (pH 5.5). After 10 days, &gt;85% of applied N leached from the columns in all treatments. After 25 days, all N leached from the NH 4 NO 3 and KNO 3 treatments, and 93% leached from the (NH 4 ) 2 SO 4 treatment. In subsequent experiments, columns received 360 mg N from NH 4 NO 3 and were leached daily with either 16, 32, 48, or 64 ml of deionized water for 50 days. The rate of N leaching increased with increasing water application rate, although total N leached per column was similar for all water rates after 25 days. Columns that received 45, 90, 180, or 360 mg N/column were leached daily with 16 ml of deionized water. Nitrogen concentrations in the leachate ranged from 3406 ppm -N and 2965 ppm -N at day 5 for the 360-mg rate to 3 and 5 ppm, respectively, at day 35 for the 45-mg rate. In all experiments with NH 4 NO 3 , more -N leached than -N and more -N leached than applied, indicating vitrification occurred. -N and broadcast over cypress wood chips in the landscape would leach quickly into the soil.
A Domain Decomposition Method for Advection-Diffusion Processes with Application to Blood Solutes (2002)

In the present paper we consider a heterogeneous model for the dynamics of a blood solute both in the vascular lumen and inside the arterial wall. In the lumen, we consider an advection-diffusion equation, where the convective field is provided by the velocity of blood, which is in turn obtained by solving the Navier--Stokes equations. Inside the arterial wall we consider a pure diffusive dynamics. Since the endothelial layer at the interface between the lumen and the wall acts as a permeable membrane, whose permeability depends on the shear rate exerted by the blood, the solute concentration is discontinuous across this membrane. A possible approach for the numerical study of this kind of problem is inspired by domain decomposition techniques. In particular, we introduce a splitting in the computation and alternate the solution of the advection-diffusion equation in the lumen with that of the diffusion equation in the wall. We set up an efficient iterative method, based on a suitable reformulation of the problem in terms of a Steklov--Poincaré interface equation. This formulation is a nonstandard one because of the concentration discontinuity at the lumen-wall interface and plays a key role in the proof of convergence of our method. In particular, we prove that the convergence rate performed by the proposed method is independent of the finite element space discretization and provides a criterion for the selection of an acceleration parameter. Several numerical results, referred to as biomedical applications, support our theoretical conclusions and illustrate the efficiency of this algorithm.
Corrigendum: Assessment of wavelets analysis for carrier-phase multipath mitigation (2014)

Received 14 April 2014. Accepted 14 April 2014. A.A. El-Ghazouly and N. El-Sheimy. Department of Geomatics Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada. M. Elhabiby. Department of Geomatics Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada; Public Works Department, Faculty of Engineering, Ain Shams University, Cairo, Egypt. Corresponding author: Ahmed A. El-Ghazouly (e-mail: aaelghaz@ucalgary.ca). 668
TheSalmonella entericaSerotype Typhimurium Effector Proteins SipA, SopA, SopB, SopD, and SopE2 Act in Concert To Induce Diarrhea in Calves (2002)

Salmonella enterica serotype Typhimurium requires a functional type III secretion system encoded by Salmonella pathogenicity island 1 (SPI1) to cause diarrhea. We investigated the role of genes encoding secreted target proteins of the SPI1-associated type III secretion system for enteropathogenicity in calves. Salmonella serotype Typhimurium strains having mutations in sptP, avrA, sspH1, or slrP induced fluid secretion in the bovine ligated ileal loop model at levels similar to that of the wild type. In contrast, mutations in sipA, sopA, sopB, sopD, or sopE2 significantly reduced fluid accumulation in bovine ligated ileal loops at 8 h postinfection. A strain carrying mutations in sipA, sopA, sopB, sopD, and sopE2 (sipA sopABDE2 mutant) caused the same level of fluid accumulation in bovine ligated ileal loops as a strain carrying a mutation in sipB, a SPI1 gene required for the translocation of effector proteins into host cells. A positive correlation was observed between the severity of histopathological lesions detected in the ileal mucosa and the levels of fluid accumulation induced by the different mutants. After oral infection of calves, the Salmonella serotype Typhimurium sipAsopABDE2 mutant caused only mild diarrhea and was more strongly attenuated than strains having only single mutations. These data demonstrate that SipA, SopA, SopB, SopD, and SopE2 are major virulence factors responsible for diarrhea during Salmonella serotype Typhimurium infection of calves.
Detection of Large Ions in Time-of-Flight Mass Spectrometry: Effects of Ion Mass and Acceleration Voltage on Microchannel Plate Detector Response (2014)

In time-of-flight mass spectrometry (TOF-MS), ion detection is typically accomplished by the generation and amplification of secondary electrons produced by ions colliding with a microchannel plate (MCP) detector. Here, the response of an MCP detector as a function of ion mass and acceleration voltage is characterized, for singly charged peptide/protein ions ranging from 1 to 290 kDa in mass, and for acceleration voltages from 5 to 25 kV. A nondestructive inductive charge detector (ICD) employed in parallel with MCP detection provides a reliable reference signal to allow accurate calibration of the MCP response. MCP detection efficiencies were very close to unity for smaller ions at high acceleration voltages (e.g., angiotensin, 1046.5 Da, at 25 kV acceleration voltage), but decreased to ~11% for the largest ions examined (immunoglobulin G (IgG) dimer, 290 kDa) even at the highest acceleration voltage employed (25 kV). The secondary electron yield γ (average number of electrons produced per ion collision) is found to be proportional to mv(3.1) (m: ion mass, v: ion velocity) over the entire mass range examined, and inversely proportional to the square root of m in TOF-MS analysis. The results indicate that although MCP detectors indeed offer superlative performance in the detection of smaller peptide/protein species, their performance does fall off substantially for larger proteins, particularly under conditions of low acceleration voltage.
THE HELIOTAIL REVEALED BY THEINTERSTELLAR BOUNDARY EXPLORER (2013)

Recent combined observations from the first three years of Interstellar Boundary Explorer (IBEX) data allow us to examine the heliosphere's downwind region—the heliotail—for the first time. In contrast to a preliminary identification of a narrow "offset heliotail" structure, we find a broad slow solar wind plasma sheet crossing essentially the entire downwind side of the heliosphere at low to mid-latitudes, with fast wind tail regions to the north and south. The slow wind plasma sheet exhibits the steepest ENA spectra in the IBEX sky maps, appears as a two-lobed structure (lobes on the port and starboard sides), and is twisted in the sense of (but at a smaller angle than) the external magnetic field. The overall heliotail structure clearly demonstrates the intermediate nature of the heliosphere's interstellar interaction, where both the external dynamic and magnetic pressures strongly affect the heliosphere.