gebhart/patrepeval huggingface dataset:
ASIC Design for Wireless Surgical MEMS Device and Instrumentation (2006)

There is an increasing demand on computerized surgical instrumentation and implants that can acquire intra-operative or in-vivo data for surgeons and engineers. The sensory system is gaining complexity in order to obtain more accurate measurements. Although many off-the-shelf components and chips exist, multiple components are often required to achieve the desired function. Since space is limited in biomedical applications, application specific highly compacted integrated circuits are preferable. In this study, a chip is designed to process an array of microcantilever readout used in an intra-operative soft-tissue balancing instrument
Idiom recognition framework using topological embedding (2013)

Modern processors support hardware-assist instructions (such as TRT and TROT instructions on the IBM System z) to accelerate certain functions such as delimiter search and character conversion. Such special instructions are often used in high-performance libraries, but their exploitation in optimizing compilers has been limited. We devised a new idiom recognition technique based on a topological embedding algorithm to detect idiom patterns in the input programs more aggressively than in previous approaches using exact pattern matching. Our approach can detect a pattern even if the code segment does not exactly match the idiom. For example, we can detect a code segment that includes additional code within the idiom pattern. We also propose an instruction simplification for the idiom recognition. This optimization analyzes all of the usages of the output of the optimized code for a specific idiom. If we find that we do not need an actual value for the output but only a value in a subrange, then we can assign a value in that subrange as the output. The code generation can generate faster code with this optimization. We implemented our new idiom recognition approach based on the Java Just-In-Time (JIT) compiler that is part of the J9 Java Virtual Machine, and we supported several important idioms for the special hardware-assist instructions on the IBM System z and on some models of the IBM System p. To demonstrate the effectiveness of our technique, we performed two experiments. The first experiment was to see how many more patterns we can detect compared to the previous approach. The second experiment measured the performance improvements over the previous approaches. For the first experiment, we used the Java Compatibility Kit (JCK) API tests. For the second experiment we used the IBM XML parser, SPECjvm98, and SPCjbb2000. In summary, relative to a baseline implementation using exact pattern matching, our algorithm converted 76% more loops in JCK tests. On a z9, we also observed significant average performance improvement of the XML parser by 54%, of SPECjvm98 by 1.9%, and of SPECjbb2000 by 4.4%. Finally, we observed that the JIT compilation time increased by only 0.32% to 0.44%.
FOLDAMERS, CROWNS, AND WATER: CONNECTIONS BETWEEN ISOLATED MOLECULES AND SOLUTION-PHASE BEHAVIOR (2010)

Author Institution: Department of Chemistry, Purdue University, West Lafayette, IN 47907; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
Decoupling of interacting neuronal populations by time-shifted stimulation through spike-timing-dependent plasticity (2022)

Abstract The synaptic organization of the brain is constantly modified by activity-dependent synaptic plasticity. In several neurological disorders, abnormal neuronal activity and pathological synaptic connectivity may significantly impair normal brain function. Reorganization of neuronal circuits by therapeutic stimulation has the potential to restore normal brain dynamics. Increasing evidence suggests that the temporal stimulation pattern crucially determines the long-lasting therapeutic effects of stimulation. Here, we tested whether a specific pattern of brain stimulations can enable the suppression of pathologically strong inter-population synaptic connectivity through spike-timing-dependent plasticity (STDP). More specifically, we tested how introducing a time shift between stimuli delivered to two interacting populations of neurons can effectively decouple them. To that end, we first used a tractable model, i.e., two bidirectionally coupled leaky integrate-and-fire (LIF) neurons, to theoretically analyze the optimal range of stimulation frequency and time shift for decoupling. We then extended our results to two reciprocally connected neuronal populations (modules) where inter-population delayed connections were modified by STDP. As predicted by the theoretical results, appropriately time-shifted stimulation causes a decoupling of the two-module system through STDP, i.e., by unlearning pathologically strong synaptic interactions between the two populations. Based on the overall topology of the connections, the decoupling of the two modules, in turn, causes a desynchronization of the populations that outlasts the cessation of stimulation. Decoupling effects of the time-shifted stimulation can be realized by time-shifted burst stimulation as well as time-shifted continuous simulation. Our results provide insight into the further optimization of a variety of multichannel stimulation protocols aiming at a therapeutic reshaping of diseased brain networks.
Thick electrodes for high frequency high Q tunable ferroelectric thin film varactors (2001)

Abstract Thin film barium strontium titanate (BST) shows great promise for voltage tunable dielectric devices for use at RF and microwave frequencies. An MOCVD process has been developed for production of BST, resulting in films with very low losses (as low as 0.002–0.004) and tunabilities over 50% at low operation voltages. With these values of BST loss, overall device quality factors at RF (100 MHz+) frequencies are primarily limited by losses in the thin metal electrodes, such as Pt, normally used for ferroelectric thin films. The bottom electrode in parallel plate capacitor structures is particularly challenging, since it must provide a good growth surface for BST and be stable at high (>600 °C) growth temperatures in an oxidizing atmosphere yet have high conductivity and compatibility with Si or SiO2/Si substrates. These challenges have previously prevented use of Pt thicknesses over 0.1–0.2 urn. Our solution to this problem, involves combinations of adhesion layers at the Pt/SiO2 interface and embedded stabilization layers to make functioning Pt bottom electrodes as thick as 2 μm. Devices with dielectric Q factors over 150 at 100 MHz (tan δ ∼ 0.006 as measured and modeled by S-parameters) and overall device Q factors over 50 at 30 MHz are described. We have also inserted these devices into tunable filters, achieving tunabilities of 50% and low insertion losses (0.3 dB) at RF frequencies.
Performance tradeoffs among beamforming approaches (2006)

Three main criteria for the adaptive beamformer design are discussed: maximal signal-to-interference-plus-noise ratio (MSINR), minimal mean-squared error (MMSE), and minimal least-square error (MLSE). Although in the case of exactly known power and steering vector of the signal-of-interest (SOI), there are beamformers that can simultaneously meet the MMSE and MSINR criteria, this is no longer true when the exact knowledge of the steering vector is unavailable. To account for steering vector errors, a meaningful approach is to model the actual steering vector as random. In this paper, it is shown that in the latter case, the MMSE and MSINR criteria can not be simultaneously attained. We study the achievable region in the MSE-SINR plane and propose a new adaptive beamformer that can attain a frontier of operating points on the boundary of this region and, therefore, provide an optimal performance tradeoff among the MSINR and MMSE criteria. It is also shown that in the random steering vector case, the MLSE and MSINR criteria are simultaneously achievable and a new adaptive beamformer is proposed that satisfies both these criteria.
SynchroTrace (2018)

Trace-driven simulation of chip multiprocessor (CMP) systems offers many advantages over execution-driven simulation, such as reducing simulation time and complexity, allowing portability, and scalability. However, trace-based simulation approaches have difficulty capturing and accurately replaying multithreaded traces due to the inherent nondeterminism in the execution of multithreaded programs. In this work, we present SynchroTrace, a scalable, flexible, and accurate trace-based multithreaded simulation methodology. By recording synchronization events relevant to modern threading libraries (e.g., Pthreads and OpenMP) and dependencies in the traces, independent of the host architecture, the methodology is able to accurately model the nondeterminism of multithreaded programs for different hardware platforms and threading paradigms. Through capturing high-level instruction categories, the SynchroTrace average CPI trace Replay timing model offers fast and accurate simulation of many-core in-order CMPs. We perform two case studies to validate the SynchroTrace simulation flow against the gem5 full-system simulator: (1) a constraint-based design space exploration with traditional CMP benchmarks and (2) a thread-scalability study with HPC-representative applications. The results from these case studies show that (1) our trace-based approach with trace filtering has a peak speedup of up to 18.7× over simulation in gem5 full-system with an average of 9.6× speedup, (2) SynchroTrace maintains the thread-scaling accuracy of gem5 and can efficiently scale up to 64 threads, and (3) SynchroTrace can trace in one platform and model any platform in early stages of design.
Safety and Immunogenicity of a Purified Hepatitis B Virus Vaccine Prepared by Using Recombinant DNA Technology (1987)

Forty healthy adult males were given a 20-micrograms intramuscular dose of either a new recombinant hepatitis B virus (HBV) vaccine produced in mammalian cells (rHBsAg) or the currently licensed HBV vaccine derived from human plasma (HEPTAVAX-B), and booster doses were administered one month and six months later. The percentage of vaccinees who seroconverted on the 10th and 30th days after the first vaccination was higher for the rHBsAg vaccinees than for the recipients of plasma-derived vaccine (rHBsAg: 10% on day 10 and 70% on day 30; HEPTAVAX-B: 0% and 25%, respectively). The only statistically significant difference in titers of antibody to HBV surface antigen was noted 30 days after the first vaccination. Both vaccines induced a shift in antibody from the 19S to the 7S fraction and a specific antibody response to the a determinant. The rHBsAg vaccine was not associated with significant reactogenicity or toxicity and was somewhat more immunogenic than the currently licensed product.
The thermophilic bacteria hydrolyzing agar: Characterization of thermostable agarase (2008)

Three strains of anaerobic thermophilic bacteria capable of growing on agarose as a source of energy and carbon were isolated from hot springs near Lake Baikal (Barguzin National Park) and the caldera Uzon (Kamchatka). Cells of all the three strains were spore bacilli with peritrichous flagellation. These isolates grew at a temperature of 55-60 degrees C and pH 6.5-7.0 and fermented a wide range of organic substrates. Analysis of the 16S rRNA sequences allowed us to ascribe the strains B5 and K14 to the genus Thermoanaerobacter and the strain K67 to the genus Caldoanaerobacter. According to the results of DNA-DNA hybridization, B5 was determined as belonging to the species Thermoanaerobacter wiegelii. Agarase was isolated by preparative PAGE and subsequent gel chromatography from the culture liquid of strain B5 grown on the medium containing 0.5% agarose and 0.3% galactose. The molecular weight of this enzyme amounted to 67 kDa and pI, to 4.2. The T. wiegelii B5 agarase was active in the pH range of 3.5 to 7.0 (optimum, 5.2) and temperature range of 50 to 80 degrees C (optimum, 70 degrees C). The preincubation of this enzyme at 90 degrees C for 60 min did not reduce the agarase activity. This activity increased in the presence of metal ions; the maximal effect was observed in the presence of 5 mM Mg2+ and 25 mM Co2+.
Antiproliferative and Tubulin-Destabilising Effects of 3-(Prop-1-en-2-yl)azetidin-2-Ones and Related Compounds in MCF-7 and MDA-MB-231 Breast Cancer Cells (2023)

A series of novel 3-(prop-1-en-2-yl)azetidin-2-one, 3-allylazetidin-2-one and 3-(buta-1,3-dien-1-yl)azetidin-2-one analogues of combretastatin A-4 (CA-4) were designed and synthesised as colchicine-binding site inhibitors (CBSI) in which the ethylene bridge of CA-4 was replaced with a β-lactam (2-azetidinone) scaffold. These compounds, together with related prodrugs, were evaluated for their antiproliferative activity, cell cycle effects and ability to inhibit tubulin assembly. The compounds demonstrated significant in vitro antiproliferative activities in MCF-7 breast cancer cells, particularly for compounds <b>9h, 9q, 9r, 10p, 10r</b> and <b>11h</b>, with IC<sub>50</sub> values in the range 10-33 nM. These compounds were also potent in the triple-negative breast cancer (TBNC) cell line MDA-MB-231, with IC<sub>50</sub> values in the range 23-33 nM, and were comparable with the activity of CA-4. The compounds inhibited the polymerisation of tubulin in vitro, with significant reduction in tubulin polymerization, and were shown to interact at the colchicine-binding site on tubulin. Flow cytometry demonstrated that compound <b>9q</b> arrested MCF-7 cells in the G<sub>2</sub>/M phase and resulted in cellular apoptosis. The antimitotic properties of <b>9q</b> in MCF-7 human breast cancer cells were also evaluated, and the effect on the organization of microtubules in the cells after treatment with compound <b>9q</b> was observed using confocal microscopy. The immunofluorescence results confirm that β-lactam <b>9q</b> is targeting tubulin and resulted in mitotic catastrophe in MCF-7 cells. In silico molecular docking supports the hypothesis that the compounds interact with the colchicine-binding domain of tubulin. Compound <b>9q</b> is a novel potent microtubule-destabilising agent with potential as a promising lead compound for the development of new antitumour agents.
Residual stresses determination in injection molded virgin and recycled HDPE blends: mechanical properties and morphology (2008)

Abstract An experimental study of residual thermal stresses has been carried out in injection molded virgin and recycled high density polyethylene (HDPE) blends. Effects of blend concentrations on residual stresses were investigated under different injection conditions such as melt temperature, mold temperature and cooling time. Layer removal technique was used for measuring residual stresses. In order to determine the relation between the residual stresses and material characteristic of HDPE blends, mechanical and morphological properties of the blends were also investigated. Elastic modulus and impact strength were important key factors for determining the blend characteristics. As a result, it was found that HDPE blends gave higher residual stresses but lower impact strength with higher elastic modulus when recycled concentration was increased. Furthermore, it was seen that shape and size of the crystallites were also effective on residual stresses. Small and spherulitic crystallite structured blends such as 30 % recycled HDPE induced reduction in residual stresses due to easier relaxation with lower elastic modulus and higher impact strength while lamellar crystallite structured blends such as 50 % recycled HDPE gave higher elastic modulus but lower impact strength with higher residual stresses.
Fast detection of both O157 and non-O157 shiga-toxin producing Escherichia coli by real-time optical immunoassay (2015)

This article presents a simple-to-operate immunoassay for the specific detection of Shiga-toxin producing Escherichia coli (STEC). This approach consists in the on-chip assay detection of viable cells on a specifically designed antibody microarray. By skipping any enrichment step and avoiding the use of labelling agent, this approach based on the Surface Plasmon Resonance imaging of the microarrays turns out to be much faster and more cost effective by comparison with standardized methods.
Prediction and Interpretable Visualization of Synthetic Reactions Using Graph Convolutional Networks (2019)

Recently, many research groups have been addressing data-driven approaches for reaction prediction and retrosynthetic analysis. Although the performances of the data-driven approach have progressed due to recent advances of machine learning and deep learning techniques, problems such as improving capability of reaction prediction and the black-box problem of neural networks still persist for practical use by chemists. To expand data-driven approaches to chemists, we focused on two challenges: improvement of reaction prediction and interpretability of the prediction. In this paper, we propose an interpretable prediction framework using Graph Convolutional Networks (GCN) for reaction prediction and Integrated Gradients (IGs) for visualization of contributions to the prediction to address these challenges. As a result, our model showed better performances than the approach using Extended-Connectivity Fingerprint (ECFP). Furthermore, IGs based visualization of the GCN prediction successfully highlighted reaction-related atoms.
A Simple Route Towards Heat Resistant Halide Perovskite-Based Optoelectronics (2018)

Stability of halide perovskite photovoltaics was improved utilizing ultrathin barrier based on atomic layer deposited TiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> .
Modelling the reaction behavior in reactive multilayer systems on substrates used for wafer bonding (2014)

Exothermic self-propagating high-temperature synthesis of intermetallic compounds attain increasing interest in the field of wafer bonding in microelectronics and microsystems technology due to local heat generation. Numerical models of self-sustaining reactions in thin multilayer films can be used to predict velocity and shape of the reaction front. This work deals with heat losses to various substrate materials and material compounds used for wafer bonding as well as the prediction of minimal numbers of bilayers required for a self-propagating reaction front. We introduced a cylindrically symmetric finite element approach. In addition to that, the effect of temperature-dependent specific heat capacities was investigated. Numerical computations were performed for Pd/Al multilayers and are compared to experimental data. It was found that the developed formalism is suitable to determine the mutual influence of heat losses and reaction properties. Furthermore, it was demonstrated that minimal numbers of bilayers can be determined more precisely by including temperature-dependent specific heat capacities.
A Re-assessment of 4CMenB Vaccine Effectiveness Against Serogroup B Invasive Meningococcal Disease in England based on an Incidence Model (2021)

Abstract Background : The four-component serogroup B meningococcal 4CMenB vaccine (Bexsero, GSK) has been routinely given to all infants in the United Kingdom at 2, 4 and 12 months of age since September 2015. After three years, Public Health England (PHE) reported a 75% [95% confidence interval: 64%; 81%] reduction in the incidence of serogroup B invasive meningococcal disease (IMD) in age groups eligible to be fully vaccinated. In contrast, vaccine effectiveness (VE) evaluated in the same immunization program applying the screening method was not statistically significant. We re-analyzed the data using an incidence model and obtained more precise VE estimates. Methods : Aggregate data stratified by age, year and doses received were provided by PHE: serogroup B IMD case counts for the entire population of England (years 2011-2018) and 4CMenB vaccine uptake in infants. We combined uptake with national population estimates to obtain counts of vaccinated and unvaccinated person-time by age and time. We re-estimated VE comparing incidence rates in vaccinated and non-vaccinated using a Bayesian Poisson model for case counts with person-time data as an offset. The model was adjusted for age, time and number of doses received. Results : The incidence model showed that cases decreased until 2013-2014, followed by an increasing trend that continued in the non-vaccinated population during the immunization program. VE in fully vaccinated (three doses) was 80.1% [95% Bayesian credible interval (BCI): 70.3%; 86.7%]. After a single dose, VE was 33.5% [12.4%; 49.7%]95%BCI, and, after two doses, 78.7% [71.5%; 84.5%]95%BCI. We estimated that vaccination has averted 312 cases [252; 368]95%BCI between 2015 and 2018. VE was in line with the previously reported incidence reduction. Conclusions : Our estimates of VE had higher precision than previous estimates based on the screening method, that were not statistically significant. When disease incidence is low and vaccine uptake is high, the screening method applied to cases exclusively from the population eligible to vaccination may not be enough precise and produce misleading point-estimates. Precise and accurate VE estimates are fundamental for informing public health decision making. VE assessment can be enhanced using models that leverage data on subjects not eligible for vaccination.
Physical Reconstruction Function (1987)

This chapter contains sections titled: Grid Geometries, Dot Function and Tone Map, Reflectance and Luminance
Structure of the catalytic core module of theChaetomium thermophilumfamily GH6 cellobiohydrolase Cel6A (2012)

Cellulases, including cellobiohydrolases and endoglucanases, are important enzymes involved in the breakdown of the polysaccharide cellulose. These catalysts have found widescale industrial applications, particularly in the paper and textile industries, and are now finding use in `second-generation' conversion of biomass to biofuels. Despite this considerable biotechnological application, and undoubted future potential, uncertainty remains as to the exact reaction mechanism of the inverting cellulases found in the GH6 family of carbohydrate-active enzymes. In order to gain additional understanding as to how these societally beneficial biocatalysts function, the crystal structure of a GH6 cellobiohydrolase from Chaetomium thermophilum, CtCel6A, has been solved. This structure reveals a distorted α/β-barrel fold comprising a buried tunnel-like active site quite typical of Cel6A enzymes. Analysis of an enzyme-product complex (cellobiose in the -3 and -2 subsites and cellotetraose in subsites +1 to +4) supports the hypothesis that this group of enzymes act via an atypical single-displacement mechanism. Of particular note in this analysis is an active-centre metal ion, Li(+), the position of which matches the position of the positively charged anomeric carbon of the oxocarbenium-ion-like transition state.