gebhart/patrepeval huggingface dataset:
An expanded glutamine repeat destabilizes native ataxin-3 structure and mediates formation of parallel β-fibrils (2001)

The protein ataxin-3 contains a polyglutamine region; increasing the number of glutamines beyond 55 in this region gives rise to the neurodegenerative disease spinocerebellar ataxia type 3. This disease and other polyglutamine expansion diseases are characterized by large intranuclear protein aggregates (nuclear inclusions). By using full-length human ataxin-3, we have investigated the changes in secondary structure, aggregation behavior, and fibril formation associated with an increase from the normal length of 27 glutamines (Q27 ataxin-3) to a pathogenic length of 78 glutamines (Q78 ataxin-3). Q78 ataxin-3 aggregates strongly and could be purified only when expressed with a solubility-enhancing fusion-protein partner. A marked decrease in alpha-helical secondary structure accompanies expansion of the polyglutamine tract, suggesting destabilization of the native protein. Proteolytic removal of the fusion partner in the Q78 protein, but not in the Q27 protein, leads to the formation of SDS-resistant aggregates and Congo-red reactive fibrils. Infrared spectroscopy of fibrils reveals a high beta-sheet content and suggests a parallel, rather than an antiparallel, sheet conformation. We present a model for a polar zipper composed of parallel polyglutamine beta-sheets. Our data show that intact ataxin-3 is fully competent to form aggregates, and posttranslational cleavage or other processing is not necessary to generate a misfolding event. The data also suggest that the protein aggregation phenotype associated with glutamine expansion may derive from two effects: destabilization of the native protein structure and an inherent propensity for beta-fibril formation on the part of glutamine homopolymers.
Breathing Time Warp (1993)

Time Warp and Breathing Time Buckets are two general-purpose optimistic synchronization strategies for supporting parallel discrete-event simulations. However, each one of these approaches has potential fatal shortcomings. Time Warp may exhibit rollback explosions that can cause an avalance of antimessages. Breathing Time Buckets, on the other hand, may not be able to process enough events per synchronization cycle to remain efficient.
Simulation of Life Testing Procedures for Estimating Long-Term Degradation and Lifetime of AlGaN/GaN HEMTs (2008)

Finite element 3-D thermal simulations of long-term degradation in AlGaN/GaN HEMTs for high-power applications are reported on, in which temperature evolves over time as the local degradation rate varies within the modeled device based on the local temperature of the degrading region (i.e., the channel). Specifically, hotter regions within a device are modeled as degrading faster due to a thermal component to the degradation rate equation. This allows self-consistent simulation of life testing, commonly used to estimate long-term reliability by extrapolating failure times seen at elevated channel temperatures to a lower "use" temperature. We find that it is necessary to consider the entire distribution of temperatures within the device instead of at one characteristic location to get the most accurate estimates for long-term device life. The effect of device geometry, assumed degradation mode, incorrect thermal resistance data, and dissipated power level on this lifetime estimation error is investigated. It is found that the error in the extrapolated failure time is greatly increased when both the thermal resistance is in error and the dissipated power of the life test does not match the expected power during operation, compared to when only one of these is off.
Towards a Generic Governance Model for Service Oriented Architectures (2008)

Over the past years, Service-oriented Architecture (SOA) Systems have been recognized more and more as a serious alternative to common monolithic systems for Enterprise Architectures (EA). An SOA provides a flexible means of effectively mapping business processes to IT processes. However, large IT systems require consistent leadership â IT Governance. For SOAs, governance faces new challenges. A number of different approaches for SOA Governance Frameworks exist, which differ extensively in scope and capability, as most of them are product-driven and developed by software companies. In this paper, we outline and compare existing SOA Governance approaches and present our approach - a Generic Governance Model for SOA.
A Finite Temperature Multiscale Interphase Zone Model and Simulations of Fracture (2012)

In this work, an atomistic-based finite temperature multiscale interphase finite element method has been developed, and it has been applied to study fracture process of metallic materials at finite temperature. The coupled thermomechanical finite element formulation is derived based on continuum thermodynamics principles. The mesoscale constitutive relations and thermal conduction properties of materials are enriched by atomistic information of the underneath lattice microstructure in both bulk elements and interphase cohesive zone. This is accomplished by employing the Cauchy–Born rule, harmonic approximation, and colloidal crystal approximation. A main advantage of the proposed approach is its ability to capture the thermal conduction inside the material interface. The multiscale finite element procedure is performed to simulate an engineering nickel plate specimen with weak interfaces under uni-axial stretch. The simulation results indicate that the crack propagation is slowed down by thermal expansion, and a cooling region is found in the front of crack tip. These phenomena agree with related experimental results. The effect of different loading rates on fracture is also investigated.
Trained Quantization Thresholds for Accurate and Efficient Fixed-Point Inference of Deep Neural Networks (2019)

We propose a method of training quantization thresholds (TQT) for uniform symmetric quantizers using standard backpropagation and gradient descent. Contrary to prior work, we show that a careful analysis of the straight-through estimator for threshold gradients allows for a natural range-precision trade-off leading to better optima. Our quantizers are constrained to use power-of-2 scale-factors and per-tensor scaling of weights and activations to make it amenable for hardware implementations. We present analytical support for the general robustness of our methods and empirically validate them on various CNNs for ImageNet classification. We are able to achieve near-floating-point accuracy on traditionally difficult networks such as MobileNets with less than 5 epochs of quantized (8-bit) retraining. Finally, we present Graffitist, a framework that enables automatic quantization of TensorFlow graphs for TQT (available at https://github.com/Xilinx/graffitist ).
A novel partner for the GTP‐bound forms of <i>rho</i> and <i>rac</i> (1995)

Using the yeast two hybrid system and overlay assays we identified a putative rholrac effector, citron, which interacts with the GTP-bound forms of rho and rac1, but not with cdc42. Extensive homologies to known proteins were not observed. This 183 kDa protein contains a C6H2 zinc finger, a PH domain, and a long coiled-coil forming region including 4 leucine zippers and the rholrac binding site. We recently identified three others putative rho effectors characterized by a common rho binding motif. Citron does not share this motif and displays a distinctive protein organization, thus defining a separate class of rho partners.
Formulation of Insulin-Loaded Polymeric Nanoparticles Using Response Surface Methodology (2005)

The objective of this work was to formulate new oral insulin-loaded nanoparticules using the response surface methodology. The insulin nanoparticles were prepared by a water-in-oil-in-water emulsification and evaporation method. The polymers used for the encapsulation were blends of biodegradable poly-epsilon-caprolactone (PCL) and of positively-charged, nonbiodegradable polymer (Eudragis RS). A central composite design has been built to investigate the effects of three controlled variables: ratio of polymers (PCL/RS ratio), volume, and pH of the aqueous solution of polyvinyl alcohol. The nanoparticles were characterized by measuring the amount of entrapped insulin, the particle size, the polydispersity of the obtained particles, the zeta potential, and the amount of insulin released after 7 hours. A second-order model was evaluated by multiple regression and was statistically tested for each of the studied controlled variable. The obtained polynomials proved efficient to localize an optimal operating area highlighted by the use of three-dimensional response surfaces and their corresponding isoresponse curves. An interesting formulation given by the models was selected, prepared, and evaluated. The corresponding quantity of entrapped insulin was 25 IU per 100 mg of polymer, and the particle size was 350 nm with a polydispersity of 0.21. The quantity of released insulin was 4.8 IU per 100 mg of polymer after 7 hours and the zeta potential was +44 mV. All these collected values were in perfect accordance with values estimated by the models. Finally, the results suggested that PCL/RS 50/50 nanoparticles might represent a promising formulation for oral delivery of insulin.
Ubiquitous Interactions for Heads-Up Computing: Understanding Users’ Preferences for Subtle Interaction Techniques in Everyday Settings (2021)

In order to satisfy users’ information needs while incurring minimum interference to their ongoing activities, previous studies have proposed using Optical Head-mounted Displays (OHMDs) with different input techniques. However, it is unclear how these techniques compare against one another in terms of being comfortable and non-intrusive to a user’s everyday tasks. Through a wizard-of-oz study, we thus compared four subtle interaction techniques (feet, arms, thumb-index-fingers, and teeth) in three daily hands-busy tasks under different settings (giving a presentation–sitting, carrying bags–walking, and folding clothes–standing). We found that while each interaction technique has its niche, thumb-index-finger interaction has the best overall balance and is most preferred as a cross-scenario subtle interaction technique for smart glasses. We provide further evaluation of thumb-index-finger interaction with an in-the-wild study with 8 users. Our results contribute to an enhanced understanding of user preferences for subtle interaction techniques with smart glasses for everyday use.
Charge Storage Behavior of Nanowire Transistors Functionalized with Bis(terpyridine)−Fe(II) Molecules:  Dependence on Molecular Structure (2004)

We studied the influence of three bis(terpyridine)-Fe(II) molecules-(X-tpy)2FeCl2 (X = H (1), SAc (2), and 4-phenyl-SAc (3)-on charge storage of a nanowire transistor. The molecules were assembled on the surface of an indium oxide nanowire that forms the conduction channel of the transistor. We found that the charge storage characteristics of such a device strongly depends on the structure of the terpyridine ligand: both retention time (tau) and threshold voltage shift (DeltaVth) increased in the order of 1 < 2 < 3, with tau of 200 s, 12 h, and 287 h and DeltaVth at 4.8, 12, and 28 V, respectively. Furthermore, when we placed the devices with molecules 1 and 3 in a vacuum and recorded the I-Vg curves in a two-day period, we observed higher hysteresis stability for device with molecule 3. For example, DeltaVth was reduced from 4.8 to 1.7 V for the device with molecule 1, while there was no reduction in DeltaVth for the device with molecule 2. These results suggest that thiolate headgroup and/or longer ligand length raises the charge tunneling barrier and results in longer charge retention and wider, more stable memory window. This work demonstrates the potential of chemical synthesis toward tailored device characteristics.
Studies on the large subunit rRNA genes and their flanking regions of leuconostocs (1998)

The 16S-23S (spacer-1) and 23S-5S (spacer-2) rRNA intergenic spacer regions of Leuconostoc lactis, Leuconostoc mesenteroides, Leuconostoc mesenteroides subsp. dextranicum, and Leuconostoc mesenteroides subsp. cremoris were amplified by polymerase chain reactions and sequenced. The 23S rRNA genes of Leuconostoc lactis, Leuconostoc mesenteroides, and Leuconostoc mesenteroides subsp. dextranicum were also sequenced. The RNase III-like and RNase E processing sites, as well as putative antitermination signals, were identified within the spacer regions. A single tRNA(Ala) gene without the 3'-terminal CCA sequence was found in spacer-1 regions. Secondary structure models are proposed showing interactions between the two spacer regions of leuconostocs. For all strains studied, spacer-1 and spacer-2 were highly conserved and therefore could not be directly used for strain typing. Sequence information on 23S rRNA genes from Leuconostoc species allowed the determination of regions that can be used as targets for diagnostic probes and amplification primers. Secondary structures of variable helical elements of leuconostocs 23S rRNA were constructed and their primary structures were compared with those of several Gram-positive bacteria with low G+C contents. Comparative analysis revealed that restriction analysis of 23S rRNA variable regions appeared to be sufficient for the search for species-specific signatures. Our experimental observations revealed that one form of the rRNA operons was present in leuconostocs. We have also demonstrated the direct linkage between the three species of rRNA genes, which are organized as follows: 5'-16S rRNA-spacer-1-tRNA(Ala)-23S rRNA-spacer-2-5S rRNA-3'.
Bone Marrow Mesenchymal Stem Cells Loaded With an Oncolytic Adenovirus Suppress the Anti-adenoviral Immune Response in the Cotton Rat Model (2010)

Oncolytic adenoviral virotherapy is an attractive treatment modality for cancer. However, following intratumoral injections, oncolytic viruses fail to efficiently migrate away from the injection site and are rapidly cleared by the immune system. We have previously demonstrated enhanced viral delivery and replicative persistence in vivo using human bone marrow-derived mesenchymal stem cells (MSCs) as delivery vehicles. In this study, we evaluated the immune response to adenovirus (Ad)-loaded MSCs using the semipermissive cotton rat (CR) model. First, we isolated MSCs from CR bone marrow aspirates. Real-time quantitative PCR analysis revealed that CR MSCs supported the replication of Ads in vitro. Moreover, we observed similar levels of suppression of T-cell proliferation in response to mitogenic stimulation, by MSCs alone and virus-loaded MSCs. Additionally, we found that MSCs suppressed the production of interferon-γ (IFN-γ) by activated T cells. In our in vivo model, CR MSCs enhanced the dissemination and persistence of Ad, compared to virus injection alone. Collectively, our data suggest that the use of MSCs as a delivery strategy for oncolytic Ad potentially offers a myriad of benefits, including improved delivery, enhanced dissemination, and increased persistence of viruses via suppression of the antiviral immune response.
A simple and sensitive pulsed field gel electrophoresis protocol to study 50 kb apoptotic DNA fragmentation in human lymphocytes. (2002)

DNA fragmentation of 50 kb is observed in apoptotic human lymphocytes as measured with pulsed field gel electrophoresis (PFGE). Standard PFGE assay involves embedding of cells into agarose blocks followed by lysis in the presence of proteinase K. In this study, we modified the PFGE protocol by omitting the proteinase K. In this study, we modified the PFGE assay by omitting the proteinase K and changing lysis solution according to the method of anomalous viscosity time dependence (AVTD). The conditions of PFGE were adjusted aiming to compress apoptotic fragments, increasing sensitivity and the number of samples that could be loaded on the same gel. Lymphocytes were irradiated with gamma-rays and apoptotic fragmentation of DNA was determined by PFGE using standard lysis with proteinase K and lysis protocol from AVTD method. Both protocols of lysis resulted in the same pattern of DNA fragments. The yield of radiation-induced apoptotic fragmentation was higher with the AVTD protocol of lysis. The novel PFGE protocol is simple and relatively non-expensive, requires only 7 h running time and gives a possibility to analyse simultaneously up to 69 samples in the same gel. The sensitivity of our protocol provides reproducible detection of 50 kb fragmentation after irradiation of human lymphocytes with 5 cGy of gamma-rays. In 2 of 6 donors tested, this DNA fragmentation was detected at dose on 2 cGy. The novel protocol can be used for quantification of 50 kb apoptotic fragments induced by different agents including low dose ionising radiations, chemicals and electromagnetic fields.
Improvement of magnetic property of GaMnN by codoping of Mg (2003)

GaMnN and Mg-codoped GaMnN films were grown in molecular beam epitaxy using a GaN single precursor. The structural, electrical, and magnetic properties were examined. The Mg-codoped GaMnN layers revealed room-temperature ferromagnetism. Codoping with Mg reduces the Mn incorporation, but increases the conductivity of the GaMnN films. At the same time, the saturation magnetization and coercivity have increased at room temperature. As this improvement was obtained with much reduced Mn concentration of ∼0.3%, the crucial role of the carriers for carrier-induced ferromagnetism in magnetic semiconductors is observed.
A Polarization UWB Receiver with Narrowband Interference Suppression Capability (2007)

A novel polarization receiver for suppressing narrowband interference (NBI) in ultra-wideband (UWB) communication systems is proposed. A null phase-shift polarization (NPSP) filter, consisting of linear polarization vector transformation (PVT), conventional single notch polarization (SNP) filtering, and amplitude and phase compensation (APC), is utilized. The NBI, which has polarized states different from those of the UWB, can be suppressed completely and the UWB signal can be recovered without distortion. Analytical and simulation results indicate that the signal-to-interference ratio and BER performance can be improved effectively after NPSP filtering. The proposed receiver can be implemented in a time-hopping spread spectrum (TH-SS) or a direct-sequence spread spectrum (DS-SS) UWB system.
A versatile microprocessor-based multichannel stimulator for skeletal muscle cardiac assist (1998)

A versatile, microprocessor-based stimulator for skeletal muscle cardiac assist (SMCA) has been designed, constructed, and used in several studies. The stimulator uses multiple bipolar electrodes to deliver arbitrarily specified electrical stimulus sequences to three nerve branches of the latissimus dorsi muscle. The electrodes are electrically isolated to effect regional stimulation of the muscle. The width, amplitude, and interpulse interval of each pulse in the stimulus sequence are independently variable, and the three channels are independently programmable, allowing a wide variety of stimulus patterns. Battery powered units have been used in studies for up to one year. In this paper, the stimulator and sample applications in SMCA are described.
Elevation in the Ratio of Cu/Zn-Superoxide Dismutase to Glutathione Peroxidase Activity Induces Features of Cellular Senescence and This Effect Is Mediated by Hydrogen Peroxide (1996)

Although reactive oxygen species have been proposed to play a major role in the aging process, the exact molecular mechanisms remain elusive. In this study we investigate the effects of a perturbation in the ratio of Cu/Zn-superoxide dismutase activity (Sod1 dismutases .O2-to H2O2) to glutathione peroxidase activity (Gpx1 catalyses H2O2 conversion to H2O) on cell growth and development. Our data demonstrate that Sod1 transfected cell lines that have an elevation in the ratio of Sod1 activity to Gpx1 activity produce higher levels of H2O2 and exhibit well characterised markers of cellular senescence viz. slower proliferation and altered morphology. On the contrary, Sod1 transfected cell lines that have an unaltered ratio in the activity of these two enzymes, have unaltered levels of H2O2 and fail to show characteristics of senescence. Furthermore, fibroblasts established from individuals with Down syndrome have an increase in the ratio of Sod1 to Gpx1 activity compared with corresponding controls and senesce earlier. Interestingly, cells treated with H2O2 also show features of senescence and/or senesce earlier. We also show that Cip1 mRNA levels are elevated in Down syndrome cells, Sod1 transfectants with an altered Sod1 to Gpx1 activity ratio and those treated with H2O2, thus suggesting that the slow proliferation may be mediated by Cip1. Furthermore, our data demonstrate that Cip1 mRNA levels are induced by exposure of cells to H2O2. These data give valuable insight into possible molecular mechanisms that contribute tribute to cellular senescence and may be useful in the evolution of therapeutic strategies for aging.
Purification and Properties of N-Acetylneuraminate Lyase from Escherichia coli1 (1984)

N-Acetylneuraminate lyase [N-acetylneuraminic acid aldolase EC 4.1.3.3] from Escherichia coli was purified by protamine sulfate treatment, fractionation with ammonium sulfate, column chromatography on DEAE-Sephacel, gel filtration on Ultrogel AcA 44, and preparative polyacrylamide gel electrophoresis. The purified enzyme preparation was homogeneous on analytical polyacrylamide gel electrophoresis, and was free from contaminating enzymes including NADH oxidase and NADH dehydrogenase. The enzyme catalyzed the cleavage of N-acetylneuraminic acid to N-acetylmannosamine and pyruvate in a reversible reaction. Both cleavage and synthesis of N-acetylneuraminic acid had the same pH optimum around 7.7. The enzyme was stable between pH 6.0 to 9.0, and was thermostable up to 60 degrees C. The thermal stability increased up to 75 degrees C in the presence of pyruvate. No metal ion was required for the enzyme activity, but heavy metal ions such as Ag+ and Hg2+ were potent inhibitors. Oxidizing agents such as N-bromosuccinimide, iodine, and hydrogen peroxide, and SH-inhibitors such as p-chloromercuribenzoic acid and mercuric chloride were also potent inhibitors. The Km values for N-acetylneuraminic acid and N-glycolylneuraminic acid were 3.6 mM and 4.3 mM, respectively. Pyruvate inhibited the cleavage reaction competitively; Ki was calculated to be 1.0 mM. In the condensation reaction, N-acetylglucosamine, N-acetylgalactosamine, glucosamine, and galactosamine could not replace N-acetylmannosamine as substrate, and phosphoenolpyruvate, lactate, beta-hydroxypyruvate, and other pyruvate derivatives could not replace pyruvate as substrate. The molecular weight of the native enzyme was estimated to be 98,000 by gel filtration methods. After denaturation in sodium dodecyl sulfate or in 6 M guanidine-HCl, the molecular weight was reduced to 33,000, indicating the existence of 3 identical subunits. The enzyme could be used for the enzymatic determination of sialic acid; reaction conditions were devised for determining the bound form of sialic acid by coupling neuraminidase from Arthrobacter ureafaciens, lactate dehydrogenase, and NADH.