gebhart/patrepeval huggingface dataset:
Real-time Engine Control Parameters Optimization Method for Small Diesel Engine by Multi Objective Genetic Algorithm (2009)

&lt;div class="htmlview paragraph"&gt;Diesel fuel injection control systems, which are one of the expected solutions for meeting emission regulations, and achieving economical fuel consumption, consist of many parameters. To optimize this system, we have developed an adaptive multi-objective genetic algorithm (MOGA) method for real-time optimization. This method provides Pareto approximation set for the required objectives. Thus engine specifications can be precisely measured and minimize evaluation time. Pre-selection, which is an acceleration method for MOGA, is employed. By using this method we achieved the faster search of three-stage injection sets and PID controller gain.&lt;/div&gt;
Supplementary Figure 1 from Isoform-Specific Phosphoinositide 3-Kinase Inhibitors Exert Distinct Effects in Solid Tumors (2023)

Supplementary Figure 1 from Isoform-Specific Phosphoinositide 3-Kinase Inhibitors Exert Distinct Effects in Solid Tumors
Data Supplement from The Lipid Kinase PI4KIIIβ Is Highly Expressed in Breast Tumors and Activates Akt in Cooperation with Rab11a (2023)

&lt;p&gt;Supplementary Figure 3&lt;/p&gt;
Data from Increased Expression of HER2, HER3, and HER2:HER3 Heterodimers in HPV-Positive HNSCC Using a Novel Proximity-Based Assay: Implications for Targeted Therapies (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; In other cancer types, HPV infection has been reported to coincide with overexpression of HER2 (ERBB2) and HER3 (ERBB3); however, the association between HER2 or HER3 expression and dimer formation in HNSCC has not been reported. Overexpression of HER2 and HER3 may contribute to resistance to EGFR inhibitors, including cetuximab, although the contribution of HPV in modulating cetuximab response remains unknown. Determination of heterodimerization of HER receptors is challenging and has not been reported in HNSCC. The present study aimed to determine the expression of HER proteins in HPV&lt;sup&gt;+&lt;/sup&gt; versus HPV&lt;sup&gt;−&lt;/sup&gt; HNSCC tumors using a proximity-based protein expression assay (VeraTag), and to determine the efficacy of HER-targeting agents in HPV&lt;sup&gt;+&lt;/sup&gt; and HPV&lt;sup&gt;−&lt;/sup&gt; HNSCC cell lines.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Expression of total HER1, HER2, and HER3, p95HER2, p-HER3, HER1:HER1 homodimers, HER2:HER3 heterodimers, and the HER3–PI3K complex in 88 HNSCC was determined using VeraTag, including 33 baseline tumors from individuals treated in a trial including cetuximab. Inhibition of cell growth and protein activation with cetuximab and afatinib was compared in HPV&lt;sup&gt;+&lt;/sup&gt; and HPV&lt;sup&gt;−&lt;/sup&gt; cetuximab-resistant cell lines.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Expression of total HER2, total HER3, HER2:HER3 heterodimers, and the HER3:PI3K complex were significantly elevated in HPV&lt;sup&gt;+&lt;/sup&gt; HNSCC. Total EGFR was significantly increased in HPV&lt;sup&gt;−&lt;/sup&gt; HNSCC where VeraTag assay results correlated with IHC. Afatinib significantly inhibited cell growth when compared with cetuximab in the HPV&lt;sup&gt;+&lt;/sup&gt; and HPV&lt;sup&gt;−&lt;/sup&gt; cetuximab-resistant HNSCC cell lines.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These findings suggest that agents targeting multiple HER proteins may be effective in the setting of HPV&lt;sup&gt;+&lt;/sup&gt; HNSCC and/or cetuximab resistance. &lt;i&gt;Clin Cancer Res; 21(20); 4597–606. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Activation of Complement Following Total Hip Replacement (2016)

The aim of this study was to investigate whether complement activation, via the classical and alternative pathways, occurs following a cemented total hip replacement (THR) surgery due to osteoarthritis. Blood samples were collected systematically from 12 patients - six male and six women, with a median age of 75 (range: 59-90 years) - preoperatively, 6 h post-operatively and on the first, second and third post-operative day. Total function of classical (CH50) and alternative pathways (AH50) was evaluated, along with the determination of serum concentrations of the complement proteins C3, C4, C3d, the soluble terminal complement complex (sTCC) sC5b-9, as well as C-reactive protein (CRP) and albumin. Measurements of CRP and albumin levels elucidated a marked inflammatory response following the operation. The CH50, AH50 and C3 and C4 levels were significantly lower 6 h after the surgery compared with the preoperative levels, but elevated above the preoperative levels during the following 3 days. The complement activation product C3d levels increased continually during the whole observation period, from 13.5 AU/ml (range: 8-19 AU/ml) preoperative to 20 AU/ml (range: 12-34 AU/ml) on the third post-operative day. Furthermore, we observed an increase in the sC5b-9 levels between the preoperative and the third post-operative day. These results demonstrate a significant activation of the complement system following cemented THR. Further studies are needed to elucidate the time frame and the pathogenic role of this observed complement activation.
A cMUT linear array used as echographic probe: fabrication, characterization, and images (2005)

We report the design, the fabrication process, and the characterization of a 64-element ultrasonic transducer array based on the electrostatic effect and realized by silicon micromachined technology. These new devices are usually called capacitive micromachined ultrasonic transducers (cMUT). Using this transducer, we developed a probe for application in medical imaging. The probe was used in conjunction with a commercial echographic system to obtain images of echographic phantoms and of in vivo human body. Good echographic images of a test object and of internal organs of the human body were obtained, demonstrating the practical possibility to use the developed technology to make cMUT echographic probes.
Diaminopimelic Acid Content of Feeds and Rumen Bacteria and Its Usefulness as a Rumen Bacterial Marker (1982)

Several feeds were examined and most were devoid of diaminopimelic acid. Small amounts of diaminopimelic acid were in corn silage, sorghum silage, beet pulp, and two samples of alfalfa hay. Nine strains of rumen bacteria were grown in pure culture in rumen fluid media containing three concentrations of carbohydrate. After incubation, bacteria were harvested and analyzed for diaminopimelic acid and total nitrogen. Among bacterial species there were significant differences in the ratio of diaminopimelic acid nitrogen to total bacterial nitrogen when they were grown in media containing different concentrations of carbohydrate. Diaminopimelic acid nitrogen concentration ranged from none in Streptococcus boris to 1.61% in Ruminococcus flavefaciens. Six rumenfistulated cattle were fed either a highroughage (85% hay) or high-concentrate (85% concentrate) diet to study the effect of diet on diaminopimelic acid content of mixed rumen bacteria. Bacteria from cattle fed the high roughage diet contained more diaminopimelic acid nitrogen to total nitrogen (.65%) than those fed the high-concentrate diet (.50%). Time of sampling in relation to feeding had no effect on diaminopimelic acid nitrogen to total nitrogen content of bacteria. We concluded that to use diaminopimelic acid to predict bacterial production in the rumen accurately, it will be necessary to correct for dietary effects on diaminopimelic acid composition of bacteria.
Distinct Mechanisms Regulate Exposure of Neutralizing Epitopes in the V2 and V3 Loops of HIV-1 Envelope (2014)

Conserved neutralizing epitopes are present in the V1V2 and V3 regions of HIV-1 Env, but these epitopes are often occluded from Abs. This study reveals that distinct mechanisms contribute to the masking of V3 epitopes and V2i epitopes in the V1V2 domain. Importantly, V3 MAbs and some V2i MAbs display greater neutralization against relatively resistant HIV-1 isolates when the MAbs interact with the virus for a prolonged period of time. Given their highly immunogenic nature, V3 and V2i epitopes are valuable targets that would augment the efficacy of HIV vaccines.
NMR technique for determining the depth of shallow nitrogen-vacancy centers in diamond (2016)

We demonstrate a robust experimental method for determining the depth of individual shallow nitrogen-vacancy (NV) centers in diamond with $\ensuremath{\sim}1$ nm uncertainty. We use a confocal microscope to observe single NV centers and detect the proton nuclear magnetic resonance (NMR) signal produced by objective immersion oil, which has well understood nuclear spin properties, on the diamond surface. We determine the NV center depth by analyzing the NV NMR data using a model that describes the interaction of a single NV center with the statistically polarized proton spin bath. We repeat this procedure for a large number of individual, shallow NV centers and compare the resulting NV depths to the mean value expected from simulations of the ion implantation process used to create the NV centers, with reasonable agreement.
Changes in coronal knee-alignment parameters during the osteoarthritis process in the varus knee (2023)

Therapeutic Study, Level III.
A Study on Accuracy Improvement of Gait Analysis using Wearable Force Plates (2017)

The purpose of this study is established the estimation method for accuracy improvement of gait analysis using the wearable force plates. The wearable force plates installing several compact force sensors and inertial and magnetic field sensors, and the reaction force (force and moment), angular velocity, acceleration and magnetic field can be measured. In this study, we established the estimation method of gait velocity and distance using Extended Kalman filter. This method consists of the posture estimation method, the condition of zero velocity in connect on ground and the linear approximation of acceleration error. We indicated the effective gait velocity and distance in the gait analysis using this method. This method can be used the gait analysis using the wearable force plates.
Trusted Big Data Capture and Transport Architecture for Wireless Sensor Network (2014)

As cloud computing developing rapidly, and Internet of Things and social network applying widely, data type and quantity are growing at an amazing speed. The era of big data has come. However, these create various challenges concerning: Capture, transport, storage, sharing, management, analysis, security, etc. How to trustfully and securely capture and transport data, is a very crucial issue for big data. In the paper, this work aims to construct a trusted big data capture and transport architecture. Firstly, the concepts of big data, trust and reputation, and wireless sensor network are discussed. Then a trusted big data capture and transport architecture using wireless sensor network is designed in detail. Moreover, some implementations of this architecture are described. Records and analysis show this trusted architecture is efficient, and can resist internal compromise attack and external attack.
Detection of DNA Damage in Prokaryotes by Terminal Deoxyribonucleotide Transferase-Mediated dUTP Nick End Labeling (2000)

Numerous agents can damage the DNA of prokaryotes in the environment (e.g., reactive oxygen species, irradiation, and secondary metabolites such as antibiotics, enzymes, starvation, etc.). The large number of potential DNA-damaging agents, as well as their diverse modes of action, precludes a simple test of DNA damage based on detection of nucleic acid breakdown products. In this study, free 3'-OH DNA ends, produced by either direct damage or excision DNA repair, were used to assess DNA damage. Terminal deoxyribonucleotide transferase (TdT)-mediated dUTP nick end labeling (TUNEL) is a procedure in which 3'-OH DNA ends are enzymatically labeled with dUTP-fluorescein isothiocyanate using TdT. Cells labeled by this method can be detected using fluorescence microscopy or flow cytometry. TUNEL was used to measure hydrogen peroxide-induced DNA damage in the archaeon Haloferax volcanii and the bacterium Escherichia coli. DNA repair systems were implicated in the hydrogen peroxide-dependent generation of 3'-OH DNA ends by the finding that the protein synthesis inhibitors chloramphenicol and diphtheria toxin blocked TUNEL labeling of E. coli and H. volcanii, respectively. DNA damage induced by UV light and bacteriophage infection was also measured using TUNEL. This methodology should be useful in applications where DNA damage and repair are of interest, including mutant screening and monitoring of DNA damage in the environment.
Comparative metabolic profiling of<i>mce1</i>operon mutant vs wild-type<i>Mycobacterium tuberculosis</i>strains (2015)

Mycobacterium tuberculosis disrupted in a 13-gene operon (mce1) accumulates free mycolic acids (FM) in its cell wall and causes accelerated death in mice. Here, to more comprehensively analyze differences in their cell wall lipid composition, we used an untargeted metabolomics approach to compare the lipid profiles of wild-type and mce1 operon mutant strains. By liquid chromatography-mass spectrometry, we identified >400 distinct lipids significantly altered in the mce1 mutant compared to wild type. These lipids included decreased levels of saccharolipids and glycerophospholipids, and increased levels of alpha-, methoxy- and keto mycolic acids (MA), and hydroxyphthioceranic acid. The mutant showed reduced expression of mmpL8, mmpL10, stf0, pks2 and papA2 genes involved in transport and metabolism of lipids recognized to induce proinflammatory response; these lipids were found to be decreased in the mutant. In contrast, the transcripts of mmpL3, fasI, kasA, kasB, acpM and RV3451 involved in MA transport and metabolism increased; MA inhibits inflammatory response in macrophages. Since the mce1 operon is known to be regulated in intracellular M. tuberculosis, we speculate that the differences we observed in cell wall lipid metabolism and composition may affect host response to M. tuberculosis infection and determine the clinical outcome of such an infection.
Analysis of Bacillus anthracis Spores in Milk Using Mass Spectrometry (2004)

New approaches for identifying biological threat agents in raw milk using spectroscopy were tested using Bacillus anthracis (BA) Sterne strain spores seeded into unpasteurized bulk tank milk. Direct filtration onto Tyvek membranes provided the optimal filtration approach from raw milk, but detection limits were not ideal. When beads coated with anti-BA antibodies were mixed with spores in raw milk, the beads were capable of concentrating the spores that could be later detected and characterized by MALDI spectroscopy based on presence of previously characterized small acid-soluble proteins (SASP's). This approach could provide a very rapid assessment of whether milk or milk products have been purposefully contaminated with BA spores. This work was fundamentally a proof-of-concept study demonstrating feasibility of the approach in milk. Other parameters could be changed to potentially lower detection limits, and additional studies are currently underway to improve the approach.
Influência das condições de aeração no tratamento de efluentes fenólicos com biofilmes em reator aeróbio (2005)

No presente trabalho foi estudada a influência das condições de aeração no tratamento de efluentes fenólicos com biofilmes. Os ensaios foram realizados com efluente sintético para simular dejetos industriais com elevadas concentrações de fenol. Foram testadas vazões de aeração de 0,7, 1,6, 2,3 vvm na cinética de biodegradação de fenol. Nas melhores condições testadas, quais sejam: reator de leito empacotado, com suporte de esferas de cerâmica e vazão de 2,3 vvm, foi atingida eficiência de remoção de fenol de aproximadamente 96 %.
A Crystallographic Examination of Predisposition versus Preorganization in de Novo Designed Metalloproteins (2016)

Preorganization and predisposition are important molecular recognition concepts exploited by nature to obtain site-specific and selective metal binding to proteins. While native structures containing an MS3 core are often unavailable in both apo- and holo-forms, one can use designed three-stranded coiled coils (3SCCs) containing tris-thiolate sites to evaluate these concepts. We show that the preferred metal geometry dictates the degree to which the cysteine rotamers change upon metal complexation. The Cys ligands in the apo-form are preorganized for binding trigonal pyramidal species (Pb(II)S3 and As(III)S3) in an endo conformation oriented toward the 3SCC C-termini, whereas the cysteines are predisposed for trigonal planar Hg(II)S3 and 4-coordinate Zn(II)S3O structures, requiring significant thiol rotation for metal binding. This study allows assessment of the importance of protein fold and side-chain reorientation for achieving metal selectivity in human retrotransposons and metalloregulatory proteins.
Hybrid integration of modified uni-traveling carrier photodiodes on a multi-layer silicon nitride platform using total reflection mirrors (2017)

We demonstrate hybrid integration of modified uni-traveling carrier photodiodes on a multi-layer silicon nitride platform using total reflection mirrors etched by focused ion beam. The hybrid photodetectors show external responsivity of 0.15 A/W and bandwidth of 3.5 GHz for devices with a diameter of 80 µm. The insertion loss of the waveguide is 3 dB and the coupling efficiency of the total reflection mirror is -3 dB. The highest RF output power is -0.5 dBm measured at 3 GHz with 9 mA photocurrent and -9 V bias.
Performance tradeoffs in cache design (1988)

Cache memories have become common across a wide range of computer implementations. To date, most analyses of cache performance have concentrated on time independent metrics, such as miss rate and traffic ratio. This paper presents a series of simulations that explore the interactions between various organizational decisions and program execution time. We investigate the tradeoffs between cache size and CPU/Cache cycle time, set associativity and cycle time, and between block size and main memory speed. The results indicate that neither cycle time nor cache size dominates the other across the entire design space. For common implementation technologies, performance is maximized when the size is increased to the 32KB to 128KB range with modest penalties to the cycle time. If set associativity impacts the cycle time by more than a few nanoseconds, it increases overall execution time. Since the block size and memory transfer rate combine to affect the cache miss penalty, the optimum block size is substantially smaller than that which minimizes the miss rate. Finally, the interdependence between optimal cache configuration and the main memory speed necessitates multi-level cache hierarchies for high performance uniprocessors.
Menadione-dependent alpha glycerophosphate and succinate dehydrogenases in the developing canine retina (1995)

Reducing equivalents for the electron transport chain are generated within the mitochondria by the Krebs cycle and in cytoplasm by processes like lipid metabolism. Two mitochondrial enzymes, succinate dehydrogenase (SDH), a prominent enzyme in the Krebs cycle, and alpha-glycerophosphate dehydrogenase (alpha-GPDH), half of the glycerophosphate shuttle system for bringing reducing equivalents from cytoplasm to mitochondria, were examined enzyme histochemically to assess the contribution of each to metabolism of the developing canine retina. SDH activity, a common marker for oxidative metabolism, was insignificant at birth. By 4 days of age, activity was observed only in developing photoreceptor inner segments. By 21 days of age SDH activity was present throughout the retina, especially in photoreceptor inner segments and plexiform layers, and approached the level observed in the adult dog. Menadione-linked alpha-GPDH (M-alpha-GPDH) activity, however, was prominent in developing vasculature and outermost portion of the neuroblastic layer of the 1 day-old retina. Most notable was localization in vascular precursors, angioblasts, found distant from formed vessels in the peripheral nerve fiber layer. Retinal dependence on an oxidative metabolism in neuronal elements, as represented by SDH activity, occurs only when the vasculature is well established.
Green Zn<sub>2</sub>SiO<sub>4</sub>:Mn thin-film electroluminescence on silicon substrates (1996)

Bright electroluminescence has been achieved on silicon substrates for the first time using Zn 2 SiO 4 :Mn thin films that were RF magnetron sputtered. A brightness of over 16 foot lambert (fL) was observed at 400 Hz and 260 V, with a steep brightness–voltage behaviour characteristic of ZnS electroluminescence. A multiplexed electroluminescent display is now feasible using Zn 2 SiO 4 :Mn.
Integrated Realization of Engineered Materials and Products: A Foundational Problem (2013)

This chapter contains sections titled: A Foundational Problem for ICME Methodologies and Framework Key Requirements for an ICME Methodology Requirements for an ICME Platform Summary Acknowledgments
DNA repair and replication proteins as prognostic markers in melanoma (2012)

Two (XRCC5 and TOP2A) of seven DNA repair and replication proteins studied were prognostic for melanoma.
Subresolution assist feature masks for 0.2-μm window pattern formation (1998)

An assist-feature mask was fabricated for 0.2 micrometers window pattern formations using a dry etching process. Although the mask's assist-features were as small as 0.68 micrometers , mask inspection was successfully carried out using the cell-shift method. In addition, defects in assist-features were repaired by use of a laser mask repair system. The lithographic performance of this assist-feature mask was compared with that of a conventional mask, using a 4x KrF excimer laser exposure tool and a 0.7 micrometers thick positive resist. The numerical aperture (NA) of the exposure tool was 0.55 and annular illumination was used. The depth of focus of the 0.2 micrometers window was improved from 0.4 to 0.6 micrometers . Moreover, it was confirmed that defects in the assist- feature have little influence on the focus latitude of the main pattern. The DOF of patterns repaired with this technique recovered to nearly the same as that of the no- defect pattern.