gebhart/patrepeval huggingface dataset:
The role of RNF149 in the pre-emptive quality control substrate ubiquitination (2023)

Protein quality control is a process in which a protein's folding status is constantly monitored. Mislocalized proteins (MLP), are processed by the various quality control pathways, as they are often misfolded due to inappropriate cellular surroundings. Polypeptides that fail to translocate into the ER due to an inefficient signal peptide, mutations or ER stress are recognized by the pre-emptive ER associated quality control (pEQC) pathway and degraded by the 26 S proteasome. In this report we reveal the role of RNF149, a membrane bound E3 ligase in the ubiquitination of known pEQC substrates. We demonstrate its selective binding only to non-translocated proteins and its association with known pEQC components. Impairment in RNF149 function increases translocation flux into the ER and manifests in a myeloproliferative neoplasm (MPN) phenotype, a pathological condition associated with pEQC impairment. Finally, the dynamic localization of RNF149 may provide a molecular switch to regulate pEQC during ER stress.
Performance Evaluation of SiC JBS Diodes Rated for 6.5kV Applications (2018)

This paper presents an investigation into the performance of SiC JBS diodes rated for 6.5kV applications. For the active area layout, two hexagonal cell designs with different A Schottky /A Total ratios have been considered. For completeness, the JBS performance is compared to that of SiC PiN diodes, fabricated on the same wafer. A benchmark against state of the art PiN diodes in Si technology is also provided.
Molecular mass distribution of polycations and dextrans by high‐performance size exclusion chromatography (2002)

Abstract A high‐performance size exclusion chromatographic (HPSEC) method for molecular mass distribution (MMD) was developed for polycations. Results obtained from HPSEC using UV and RI detectors were compared with the viscosity measurements. Pullulan standards were used for M w calibration. It is concluded that HPSEC with a UV detector offers a sensitive and simple method that has the required accuracy. Degradation studies following this method indicate that dextrans are stable at a temperature of 55 °C and at different pH solutions for up to 7 days. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Relationship of 11.BETA.-hydroxysteroid dehydrogenase type 1 and hexose-6-phosphate dehydrogenase gene polymorphisms with metabolic syndrome and type 2 diabetes (2011)

11β-Hydroxysteroid dehydrogenase type 1 (HSD11B1), which converts inactive glucocorticoid to active glucocorticoid, plays a critical role in the pathogenesis of visceral obesity, metabolic syndrome, and diabetes. Hexose-6-phosphate dehydrogenase (H6PD) supplies a crucial cofactor, reduced nicotinamide adenine dinucleotide phosphate (NADPH), which allows HSD11B1 to maintain reductase activity. The association of common SNPs in HSD11B1 [IVS3-29G/T (rs12086634), IVS4-11120A/G (rs1000283)] and H6PD [R453Q (rs6688832), P554L (rs17368528)], either separately or combined, with type 2 diabetes and metabolic syndrome was examined in 427 Korean subjects with type 2 diabetes and in 358 nondiabetic Korean subjects. HSD11B1 polymorphisms (rs12086634 and rs1000283) were associated with metabolic syndrome among type 2 diabetic subjects and an H6PD polymorphism (rs17368528) was a risk factor for metabolic syndrome in nondiabetic subjects. However, no significant association of these SNPs with type 2 diabetes and metabolic syndrome was found after considering the multiple comparisons in the total study population. In conclusion, HSD11B1 and H6PD polymorphisms may not be associated with type 2 diabetes and metabolic syndrome. Further investigation of the role of these gene polymorphisms on the pathogenesis of metabolic syndrome is required.
A surface enhanced hyper-Raman scattering study of pyridine adsorbed onto silver: Experiment and theory (1988)

This paper presents a combined experimental and theoretical study of the hyper-Raman spectrum of pyridine adsorbed onto roughened silver electrodes. The surface enhanced hyper-Raman spectra (SEHRS) were measured using a focused cw mode-locked Nd:YAG laser with a peak power density of approximately 107 W/cm2 . Dominant bands in the pyridine spectra are the same (totally symmetric) bands as have been seen in the corresponding Raman (SERS) spectrum, although the relative intensities are different. To interpret these spectra, we present a semiempirical molecular orbital method for determining excitation energies, polarizability derivatives, and hyperpolarizability derivatives that is based on the π-electron Pariser–Parr–Pople (PPP) method. An empirical molecular force field is used to derive vibrational information, and the accuracy of the spectra is assessed by comparison with normal Raman spectra for liquid pyridine and with SERS spectra. The resulting SEHRS spectra are in good agreement with the measured spectra, particularly with respect to the intensity changes in the dominant lines in going from SERS to SEHRS. In addition, the theoretical/experimental comparisons indicate that SEHRS is more sensitive to adsorbate orientation than is SERS since the nontotally symmetric modes are predicted to be comparable in SEHRS (but not SERS) intensity to the totally symmetric modes for orientations other than perpendicular. Most important, a comparison of theoretical and experimental SEHRS/SERS ratios suggests that the enhancement factor associated with SEHRS is on the order of 1013 which is much larger than the 106 enhancement seen for SERS.
Dynamics of Internalization and Intracellular Interaction of Tau Antibodies and Human Pathological Tau Protein in a Human Neuron-Like Model (2020)

We and others have shown in various <i>in vivo, ex vivo</i> and cell culture models that several tau antibodies interact with pathological tau within neurons. To further clarify this interaction in a dynamic human model, we differentiated SH-SY5Y cells with retinoic acid and BDNF to create a neuron-like model. Therein, tau antibodies were primarily taken up by receptor-mediated endocytosis, and prevented toxicity of human brain-derived paired helical filament-enriched tau (PHF). Subsequently, we monitored in real-time the interaction of antibodies and PHF within endocytic cellular compartments. Cells were pre-treated with fluorescently-tagged PHF and then incubated with tau antibodies, 4E6, 6B2, or non-specific isotype control IgG1 labeled with a pH sensitive dye. The uptake and binding of the efficacious antibody, 4E6, to PHF occurred mainly within the soma, whereas the ineffective antibody, 6B2, and ineffective control IgG1, were visualized via the processes and showed limited colocalization with PHF within this period. In summary, we have developed a neuron-like model that clarifies the early intracellular dynamics of the interaction of tau antibodies with pathological tau, and identifies features associated with efficacy. Since the model is entirely human, it is suitable to verify the therapeutic potential of humanized antibodies prior to extensive clinical trials.
Corrections: Induction of a Chronic Myelogenous Leukemia-Like Syndrome in Mice with v-abl and BCR/ABL (1990)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Integrated Reciprocating Optical Modulator for Optical High-Order Sideband Generation (2004)

We demonstrated optical high-order sideband generation using a reciprocating optical modulator consisting of a pair of fiber Bragg gratings and an optical phase modulator. The reflection band of the fiber Bragg grating had a steep edge of 0.02 nm. A twelfth optical high-order sideband component was generated from a 4.4 GHz electric signal. Millimeter waves generated as beat signals of the optical high-order sideband components were quite stable. Spectrum line widths were less than 300 Hz. The intensity modulation of the generated millimeter waves was also demonstrated by applying a baseband signal to the modulator without using another electric or optical modulator.
Are We Reconstructing the Best Images Using Navigator-Gated 3D Coronary MRA? Multiple-Image Reconstruction Using CLAWS (2009)

A technique is presented which acquires a 3D-whole heart scan in the quickest time possible for any respiratory trace (p=ns) and enables 3 images to be reconstructed: the most-frequent 5mm navigator window, an end-expiratory image and an end-inspiratory image. Previous techniques require manual window selections which may not be optimal for scan efficiency or image quality. This modified CLAWS approach enables multiple-image reconstruction in the same acquisition time as for a single image. It is not possible to predict which image will be best. A multi-image technique is therefore optimal, particularly as there is no scan time loss.
Uniform Expansion of a Polymeric Helical Stent (2012)

Helical coil polymeric stents provide an alternative method of stenting compared to traditional metallic stents, but require additional investigation to understand deployment, expansion, and fixation. A bilayer helical coil stent consisting of PLLA and PLGA was investigated using the finite element model to evaluate performance by uniform expansion and subsequent recoiling. In vitro material characterization studies showed that a preinsertion water-soaking step to mimic body implantation conditions provided the required ductility level expansion. In this case, the mechanical contribution of the outer PLGA layer was negligible since it softened significantly under environmental conditions. The viscoelastic response was not considered in this study since the strain rate during expansion was relatively slow and the material response was primarily plastic. The numerical model was validated with available experimental expansion and recoiling data. A parametric study was then undertaken to investigate the effect of stent geometry and coefficient of friction at the stent-cylinder interface on the expansion and recoiling characteristics. The model showed that helical stents exhibit a uniform stress distribution after expansion, which is important for controlled degradation when using biodegradable materials. The results indicated that increasing stent width, pitch value, and coil thickness resulted in a larger diameter after recoiling, which would improve fixation in the artery. It was also noted that a helical stent should have more than five coils to be stable after recoiling. This work is part of a larger research study focused on the performance of a balloon-inflated polymeric helical stent for artery applications.
NOT ALL CEMENTLESS STEMS ARE CREATED EQUAL (2013)

Cementless fixation has become dominant for THR throughout the world, but are all stem geometries equivalent in results? Registries are the best source for studying this question because they are absent of personal bias. Results at 5 years allow separation of implants so this time frame was used. Comparing the same articulations (ceramic or metal-on- polyethylene), cementless stems with proximal enhancement (elliptical shape), or a tapered stem with rectangular cross section, have performed better than stems with a slim (blade) AP geometry. Almost all cementless stems reported to registries today are broached only tapered in design.
Toward a logical framework for cognitive effects-based operations: some empirical and computational results (2005)

At present, military modeling and simulation technologies do not possess the representational expressivity needed in order to formally capture the notion of a fully functional organization. Collective, robust, purposive behavior which is typically associated with multiple human actors working in concert has been (largely) outside of the grasp of the military modeling and simulation community. In this thesis, the challenge of modeling organizational behavior will be explored in light of the Effects-based Operations (EBO) paradigm. EBO has manifested itself as a paradigmatic shift towards looking at military planning as fully understanding the causal linkages between taking action and the resultant cascading effects (both intended and unintended) which ripple through the battlespace. While a reasonable amount of research has been directed at understanding the dynamics of physical effects, relatively little attention has been paid to the psychological dimension of effects. The research presented here are the first steps toward a computational framework for a full-spectrum (physical and psychological) analysis of effects called CEBO, standing for Cognitive Effects-Based Operations. CEBO will begin to take shape through the exploration of organizations (multi-agent systems) using the machinery of deontic logic; a family of logical languages used to reason about norms. In order to establish the viability of deontic logic as a mechanism for simulating human-like organizational behavior with respect to norms, I have investigated deontic reasoning from the perspective of cognitive psychology, producing results concerning how humans may mentally represent, reason about, and take appropriate action with respect to norms. As the reasonability of deontic logic as an appropriate formalism for laying the foundations for CEBO is established, I present a computational model of socio-cognitive agency which is consistent with modern conceptions of agent-based normative reasoning, implemented using the Athena denotational proof language (DPL) [67]. Athena performs proof checking, inference; model-checking, and model-building (for counterexample generation) allowing us to reason about normative contingencies and requirements between agents within an organization. Finally, I present an extension to this formal language which allows agents to possess multiple, possibly conflicting sets of obligations, and the machinery by which they may be reasoned over.
Flow-Optimized Model for Gas Jet Desorption Sampling Mass Spectrometry (2023)

Thermal gas jet probes, including post-plasma desorption/ionization sources, have not been studied using computational fluid dynamics (CFD) models, as have other ambient mass spectrometry sampling techniques. Two systems were constructed: a heated nitrogen jet probe to establish practical bounds for a sampling/transmission experiment and a CFD model to study trajectories of particles desorbed from a surface through optimization of streamlines and temperatures. The physical model configuration as tested using CFD revealed large losses, transmitting less than 10% of desorbed particles. Different distances between the desorption probe and the transport tube and from the sample surface were studied. The transmission improved when the system was very close to the sample, because the gas jet otherwise creates a region of low pressure that guides the streamlines below the inlet. A baffle positioned to increase pressure in the sample region improves collection efficiency. A Lagrangian particle tracking approach confirms the optimal design leading to a transmission of almost 100%.
Electrochemical Microfluidic Paper-Based Analytical Devices Using a Glucometer for Point-of-Care Detection of Multiple Analytes (2011)

Abstract not Available.
Simultaneous 3 × 10 Gbps optical data transmission in 1-μm, C-, and L-wavebands over a single holey fiber using an ultra-broadband photonic transport system (2010)

An ultra-broadband photonic transport system has been developed to expand the usable wavelength bandwidth for optical communication. Simultaneous 3 x 10-Gbps error-free photonic transmissions are demonstrated in the 1-microm, C-, and L-wavebands by using the ultra-broadband photonic transport system over a 5.4-km-long holey fiber transmission line.
In vitro evidence of a tissue factor-independent mode of action of recombinant factor VIIa in hemophilia (2014)

Successful competition of activated factor VII (FVIIa) with zymogen factor VII (FVII) for tissue factor (TF) and loading of the platelet surface with FVIIa are plausible driving forces behind the pharmacological effect of recombinant FVIIa (rFVIIa) in hemophilia patients. Thrombin generation measurements in platelet-rich hemophilia A plasma revealed competition for TF, which potentially could reduce the effective (r)FVIIa:TF complex concentration and thereby attenuate factor Xa production. However, (auto)activation of FVII apparently counteracted the negative effect of zymogen binding; a small impact was observed at endogenous concentrations of FVII and FVIIa but was virtually absent at pharmacological amounts of rFVIIa. Moreover, corrections of the propagation phase in hemophilia A required rFVIIa concentrations above the range where a physiological level of FVII was capable to downregulate thrombin generation. These data strongly suggest that rFVIIa acts independently of TF in hemophilia therapy and that FVII displacement by rFVIIa is a negligible mechanistic component.
Sparse Convolutional Beamforming for Ultrasound Imaging (2018)

The standard technique used by commercial medical ultrasound systems to form B-mode images is delay and sum (DAS) beamforming. However, DAS often results in limited image resolution and contrast that are governed by the center frequency and the aperture size of the ultrasound transducer. A large number of elements lead to improved resolution but at the same time increase the data size and the system cost due to the receive electronics required for each element. Therefore, reducing the number of receiving channels while producing high-quality images is of great importance. In this paper, we introduce a nonlinear beamformer called COnvolutional Beamforming Algorithm (COBA), which achieves significant improvement of lateral resolution and contrast. In addition, it can be implemented efficiently using the fast Fourier transform. Based on the COBA concept, we next present two sparse beamformers with closed-form expressions for the sensor locations, which result in the same beam pattern as DAS and COBA while using far fewer array elements. Optimization of the number of elements shows that they require a minimal number of elements that are on the order of the square root of the number used by DAS. The performance of the proposed methods is tested and validated using simulated data, phantom scans, and in vivo cardiac data. The results demonstrate that COBA outperforms DAS in terms of resolution and contrast and that the suggested beamformers offer a sizable element reduction while generating images with an equivalent or improved quality in comparison with DAS.
Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 Å resolution (2005)

TT1426, from Thermus thermophilus HB8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (PRTase) domain, as revealed by a Pfam database search. The 2.01 A crystal structure of TT1426 has been determined by the multiwavelength anomalous dispersion (MAD) method. TT1426 comprises a core domain consisting of a central five-stranded beta sheet surrounded by four alpha-helices, and a subdomain in the C terminus. The core domain structure resembles those of the type I PRTase family proteins, although a significant structural difference exists in an inserted 43-residue region. The C-terminal subdomain corresponds to the "hood," which contains a substrate-binding site in the type I PRTases. The hood structure of TT1426 differs from those of the other type I PRTases, suggesting the possibility that TT1426 binds an unknown substrate. The structure-based sequence alignment provides clues about the amino acid residues involved in catalysis and substrate binding.
Ethanol Dehydration in HZSM-5 Studied by Density Functional Theory: Evidence for a Concerted Process (2015)

Dehydration over acidic zeolites is an important reaction class for the upgrading of biomass pyrolysis vapors to hydrocarbon fuels or to precursors for myriad chemical products. Here, we examine the dehydration of ethanol at a Brønsted acid site, T12, found in HZSM-5 using density functional theory (DFT). The geometries of both cluster and mixed quantum mechanics/molecular mechanics (QM:MM) models are prepared from the ZSM-5 crystal structure. Comparisons between these models and different DFT methods are conducted to show similar results among the models and methods used. Inclusion of the full catalyst cavity through a QM:MM approach is found to be important, since activation barriers are computed on average as 7 kcal mol(-1) lower than those obtained with a smaller cluster model. Two different pathways, concerted and stepwise, have been considered when examining dehydration and deprotonation steps. The current study shows that a concerted dehydration process is possible with a lower (4-5 kcal mol(-1)) activation barrier while previous literature studies have focused on a stepwise mechanism. Overall, this work demonstrates that fairly high activation energies (∼50 kcal mol(-1)) are required for ethanol dehydration. A concerted mechanism is favored over a stepwise mechanism because charge separation in the transition state is minimized. QM:MM approaches appear to provide superior results to cluster calculations due to a more accurate representation of charges on framework oxygen atoms.
c-myc gene expression and interleukin-2 receptor levels in cloned human CD2+,CD3+ and CD2+,CD3- lymphocytes. (1987)

The levels of c-myc mRNA and interleukin-2 receptors (IL-2 Rec) were studied in human peripheral blood lymphocytes (PBL); mature CD2+,CD3+ T cell clones and CD2+,CD3- natural killer (NK) cell clones, and CD2+,CD3+ and CD2-,CD3- T lymphoma cell lines. A transient induction of the expression of c-myc and IL-2 Rec was observed in PBL after activation with phytohemagglutinin (PHA). Expression of c-myc and IL-2 Rec was also found in the CD2+,CD3+ and CD2+,CD3- clones. The CD2+,CD3+ showed higher levels of c-myc mRNA and IL-2 Rec than the CD2+,CD3- clones. In three T lymphoma cell lines constitutively high levels of c-myc mRNA but no IL-2 Rec were found. Only in JURKAT (CD2+,CD3+), c-myc mRNA levels could be further enhanced by PHA. These results suggest that in the presence of PHA, expression of c-myc and IL-2 Rec is induced via the CD3 receptor, and in the absence of PHA and/or the CD3 receptor alternative routes of induction are involved.
Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties (2000)

In addition to preventing crosstalk among related signaling pathways, scaffold proteins might facilitate signal transduction by preforming multimolecular complexes that can be rapidly activated by incoming signal. In many cases, such as mitogen-activated protein kinase (MAPK) cascades, scaffold proteins are necessary for full activation of a signaling pathway. To date, however, no detailed biochemical model of scaffold action has been suggested. Here we describe a quantitative computer model of MAPK cascade with a generic scaffold protein. Analysis of this model reveals that formation of scaffold-kinase complexes can be used effectively to regulate the specificity, efficiency, and amplitude of signal propagation. In particular, for any generic scaffold there exists a concentration value optimal for signal amplitude. The location of the optimum is determined by the concentrations of the kinases rather than their binding constants and in this way is scaffold independent. This effect and the alteration of threshold properties of the signal propagation at high scaffold concentrations might alter local signaling properties at different subcellular compartments. Different scaffold levels and types might then confer specialized properties to tune evolutionarily conserved signaling modules to specific cellular contexts.