gebhart/patrepeval huggingface dataset:
Applications in catalysis, photochemistry, and photodetection: general discussion (2019)

Sylwester Gawinkowski opened a general discussion of the paper by Jorge Salmon-Gamboa: Why you are using SiO2 nanoparticles? Do they have any function or are they only the substrate to attach other active nanoparticles to? You have shown that only gold nanoparticles attached to silica nanoparti
Detection of Sprouted and Midge‐Damaged Wheat Kernels Using Near‐Infrared Hyperspectral Imaging (2009)

ABSTRACT Sprout damage which results in poor breadmaking quality due to enzymatic activity of α‐amylase is one of the important grading factors of wheat in Canada. Potential of near‐infrared (NIR) hyperspectral imaging was investigated to detect sprouting of wheat kernels. Artificially sprouted, midge‐damaged, and healthy wheat kernels were scanned using NIR hyperspectral imaging system in the range of 1000–1600 nm at 60 evenly distributed wavelengths. Multivariate image analysis (MVI) technique based on principal components analysis (PCA) was applied to reduce the dimensionality of the hyperspectral data. Three wavelengths 1101.7, 1132.2, and 1305.1 nm were identified as significant and used in analysis. Statistical discriminant classifiers (linear, quadratic, and Mahalanobis) were used to classify sprouted, midge‐damaged, and healthy wheat kernels. The discriminant classifiers gave maximum accuracy of 98.3 and 100% for classifying healthy and damaged kernels, respectively.
Effects of Upconversion Nanoparticles on Polymerase Chain Reaction (2013)

Nanoparticles (NPs) are attractive materials owing to their physical and electrochemical properties, which make them extremely useful in diagnostic applications. Photon upconversion is the phenomenon where high-energy photons are emitted upon excitation of low-energy photons. Nucleic acids detection based on upconversion nanoparticles (UCNPs), which display a high signal-to-noise ratio and no photobleaching, has been widely applied. We evaluated whether UCNPs can improve polymerase chain reaction (PCR) specificity and affect PCR amplification. The effects of UCNPs with a diameter size of 40, 70, and 250 nm were evaluated using 3 PCR kits (AccuPower PCR PreMix, AmpliTaq Gold 360 Master Mix, and HotStarTaq Plus Master Mix) and 3 real-time PCR kits (AccuPower GreenStar qPCR PreMix, SYBR Green PCR Master Mix, and QuantiTect SYBR Green PCR Kit). Quantum dots were used for comparison with the UCNPs. In the presence of an appropriate concentration of UCNPs, PCR specificity was optimized. UCNPs of 40-nm size improved PCR specificity more effectively than did UCNPs sized 70 or 250 nm. As the size and concentrations of the UCNPs were increased, PCR amplification was more severely inhibited. At lower annealing temperatures (25°C-45°C), addition of the 40 nm UCNP (1 µg/µL) to the PCR reagent produced specific PCR products without nonspecific sequence amplification. Therefore, UCNPs of different sizes, with different DNA polymerases used in the commercial kits, showed different inhibitory effects on PCR amplification. These results demonstrate that optimization of UCNPs, added to reaction mixtures at appropriate concentrations, can improve PCR specificity. However, the mechanism underlining UCNPs effect on PCR remains unclear and will require further investigation.
Modeling Hyperacuity Data with a Hierarchical Neural Vision Network and Modified Hebbian Learning (2013)

Visual hyperacuity enables an observer to make accurate judgements of the relative positions of stimuli when the differences are smaller than the size of a single cone in the fovea. Hyperacuity can be used as a gauge for testing various characteristics of the visual system, and it can also be used as a stringent test for models of the visual system. A variant of the Boundary Contour System (BCS) is here used to address previously unexplained psychophysical hyperacuity results involving contrast polarity, stimulus separation, and sinusoidal masking gratings. Two-dot alignment thresholds were studied by Levi & Waugh (1996), who varied the gap between the dots, with same and opposite contrast polarity with respect to the background, and also with and without a broadband sinusoidal grating of different orientations. They found that when the gap between the dots is small (6 arcmin), different patterns of results are obtained for the same and different contrast polarity conditions. However, when the gap is large (24 arcmin), the same pattern was obtained irrespective of contrast polarity. The simulations presented here replicate these findings, producing the same pattern of results when varying the gap between the dots, with same and opposite contrast polarity with respect to the background, and also with and without a broadband sinusoidal grating of different orientations. The vision model used (BCS) is able to produce these results because it includes stages of contrast insensitivity (complex cells), spatial and orientation competition, and long-range completion. A novel aspect of the model is the use of sampled field processing, which simplifies the model’s description in terms of equations. In addition, modified Hebbian learning and a neural decison module are proposed as mechanisms that link the vision model’s outputs to a decision criterion. All model parts are biologically plausible and have physiological correlates. Meeting abstract presented at VSS 2013
Mechanical limitation of pulmonary blood flow facilitates heart transplantation in older infants with hypoplastic left heart syndrome☆ (2003)

Pre-transplant mechanical limitation of pulmonary blood flow simplified management and reduced morbidity for HLHS patients undergoing heart transplantation at ages >or=4 months. This strategy extends the permissible transplant waiting time in older infants with HLHS.
Synthesis of Enantiomerically Pure 4-Substituted Riboses (2007)

An efficient and flexible synthesis of 4-substituted ribose analogues is described. The key step involves the simple addition of a Grignard reagent to a ketone derived from a commercially available ribose. The addition of a range of Grignard reagents proceeded in high yield and with complete stereocontrol, to provide a single enantiomer in every case, the identity of which was confirmed by single-crystal X-ray crystallography. This addition is unaffected by substitution at the 2-position of the starting ribose.
Analysis and Optimization of Closed Loop Geothermal System in Hot Rock Reservoirs. (2021)

Abstract not provided.
Optimal Electrical Design of System Packages and Integrated Components using the M3-Approach (2007)

In this contribution, a novel design approach, the M3-approach (methodologies-≫models-≫measures), for efficient, reliable and cost-effective design of electronic system packages and integrated components is presented and illustrated using a system-in-package (SiP) module as well as a microstrip patch array antenna and an inductor, as examples. The M3-approach entails developing or applying reliable methodologies for efficient and accurate modeling of system packages and integrated components; using the extracted and experimentally validated models to study the impact of different packaging technologies, integration options, component placement/routing possibilities, immediate surroundings as well as manufacturing tolerances on system performance; and finally, based on these studies, extracting reliable design measures. Applying these measures at the prelayout stage leads to the elimination of re-design efforts and place/route iterations. Consequently, time to market as well as cost is considerably reduced while performance is optimized.
Nonlinear prediction for circular filtering using Fourier series (2016)

While nonlinear filtering for circular quantities is closely related to nonlinear filtering on linear domains, the underlying manifold enables the development of novel filters that take advantage of the boundedness of the domain. Previously, we introduced Fourier filters that approximate the density or its square root using Fourier series. For these filters, we proposed filter steps for arbitrary likelihoods and prediction steps for the identity system model with additive noise. This paper adds the capability of handling arbitrary transition densities in the prediction step, which facilitates, e.g., the use of the filters for nonlinear systems with additive noise. In the evaluation, the new prediction steps for the Fourier filters outperform an SIR particle filter, a grid filter, and a nonlinear variant of the von Mises filter.
Auto-tuning of fast fourier transform on graphics processors (2011)

We present an auto-tuning framework for FFTs on graphics processors (GPUs). Due to complex design of the memory and compute subsystems on GPUs, the performance of FFT kernels over the range of possible input parameters can vary widely. We generate several variants for each component of the FFT kernel that, for different cases, are likely to perform well. Our auto-tuner composes variants to generate kernels and selects the best ones. We present heuristics to prune the search space and profile only a small fraction of all possible kernels. We compose optimized kernels to improve the performance of larger FFT computations. We implement the system using the NVIDIA CUDA API and compare its performance to the state-of-the-art FFT libraries. On a range of NVIDIA GPUs and input sizes, our auto-tuned FFTs outperform the NVIDIA CUFFT 3.0 library by up to 38x and deliver up to 3x higher performance compared to a manually-tuned FFT.
Sequence Variants ofToll-Like Receptor 4Are Associated with Prostate Cancer Risk (2004)

Inflammation has been implicated as an etiological factor in several human cancers. Growing evidence suggests that chronic inflammation may also play a role in the etiology of prostate cancer. Considering that genetic susceptibility is a major risk factor for this disease, we hypothesize that sequence variants in genes that regulate inflammation may modify individual susceptibility to prostate cancer. The lipopolysaccharide receptor Toll-like receptor 4 (TLR4) is a central player in the signaling pathways of the innate immune response to infection by Gram-negative bacteria and is an important candidate inflammatory gene. We performed a systematic genetic analysis of TLR4 sequence variants by evaluating eight single-nucleotide polymorphisms that span the entire gene among 1383 newly diagnosed prostate cancer patients and 780 age- and residence-matched controls in Sweden. We found an association between a sequence variant (11381G/C) in the 3'-untranslated region of the TLR4 gene and prostate cancer risk. The frequency of the variant genotypes (CG or CC) was significantly higher in the patients (24.1%) than in the controls (19.7%; P = 0.02). The frequency of risk genotypes among patients diagnosed before the age of 65 years was even higher (26.3%). Compared with men who had the wild-type genotype of this single-nucleotide polymorphism (GG), those with GC or CC genotypes had a 26% increased risk for prostate cancer (odds ratio, 1.26; 95% confidence interval, 1.01-1.57) and 39% increased risk increased risk for early onset prostate cancer (before age 65 years; odds ratio, 1.39; 95% confidence interval, 1.02-1.91). The risk attributable to this variant for prostate cancer in Sweden was estimated to be 4.9%. Although the biological mechanism of the observed association remains to be elucidated, our finding supports a role for a bacteria-associated response pathway, possibly acting via inflammation, in the development of prostate cancer.
Development of clone with novel TrpE fusion tag in E. coli for overexpression of trypsin in a bench-scale bioreactor (2020)

Trypsin is a key enzyme under the serine proteases that is found in the pancreas which plays a key role in protein digestion. It cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine. This enzyme has received greater attention mainly due to its increased use in the removal of fusion tags during protein purification and its role in the processing of biosimilars like insulin. The present study was carried out to develop a clone with Novel TrpLE1413(TrpE) Fusion Tag for enhanced expression of trypsin which helps in cost reduction of biosimilar processing. In our experiment we have used a synthetic bovine trypsin gene containing a novel fusion tag TrpE at its N terminus, which was cloned into the pET41b (+) vector and expressed in <i>E. coli</i> BL21 (DE3) in a lab-scale bioreactor. Using the optimized fermentation process with TrpE Fusion Tag, 27.8 g/L inclusion bodies were produced at the end of fermentation, of which 209 mg/L of active trypsin was obtained after purification. In contrast, previous reports have claimed to produce a maximum of 60 mg/L of the enzyme without the fusion tag. Thus based on our findings, the small size (less than 2 kDa) of TrpE tag and its hydrophobicity may reduce the loss incurred during the purification process. Hence, it could be discerned that the use of the TrpE fusion tag along with a robust fermentation process led to 3- 4 fold higher yield making it a commercially viable process facilitating an improved recovery of the enzyme.
Direct Electromagnetic Generation of Compressional Waves in Metals in Static Magnetic Fields (1970)

A derivation of the electromagnetic generation of compressional waves in metals in static magnetic fields is given. It is found that the acoustic amplitude varies linearly with the amplitudes of both the incident time-varying electromagnetic field and the static magnetic field, and inversely as the acoustic frequency. An expression is obtained for the fraction of transmitted electromagnetic power converted into acoustic power. I. IKTRODUCTIOS Ll~CTROhlAG~ETIC generation of ultrasonic waves in ttletals has been ol)served under a wide variet,y of experimctntal conditions (l). In a static magnetic field both shear anti compressional waves have heen generated where the direction of polarization de- pends upon the orientation of thc field. Theoretical di+ cussion of this phenomenon with alld without a magnetir field has been given (2). For finite magnetic fields the most gcneral trcatmcnt is tht of Quinn (a). Here, using tt self-consistent semiclassical dcsrription, Quinn explains the gencrat,iorl mechanism on tlw hayis of solutions to equations for the couplctl electron-ion system. 'The ('111- phnsis is on shc:ir-wavc gcncration and propagation. hl- though the treatment is exact,, the generation luechanism may be somewhat, ohscured hy the formalism. The tlasic mechanism for sound generation is, honc~vt~r. un(lcr- shndahle via simple classical concepts. Rlodels of this type have been given and shown to he in quantitative ngreemc.nt, with experiment (3). in the gontwll trcat- ment of Quinn, these discussions were confined to the case of shear waves. It is the purpose of this paper to present a rla4Qsic:d calculation for the generation of com- pressional waves in the presence of a static magnet,ic field (4).
Long‐term evaluation of recombinant interferon α2b in the treatment of patients with hepatitis B e antigen‐negative chronic hepatitis B in Taiwan (2001)

The effect of interferon (IFN) on hepatitis B e antigen (HBeAg)-negative chronic hepatitis B (CHB) has not been fully investigated in Chinese patients. We enrolled 58 HBeAg-negative CHB Chinese patients with hepatitis B viremia in Taiwan to evaluate the response to IFN. 30 patients received recombinant IFN 5 million units 3 times weekly for 6-10 months, and 28 patients who refused IFN treatment served as controls. Rates of virological response and biochemical response were higher in the treated group at the end of treatment (57% vs 18%, P = 0.006, and 73% vs 29%, P = 0.002, respectively). Both effects were superior in the treated group at 6 months after IFN withdrawal (virological: 30% vs 7%, P = 0.06; biochemical: 47% vs 7%, P = 0.002). Improvement of liver histological activities with persistently biochemical response was found in 65% of the treated patients. After a mean of 32 months' follow-up, virological response was rarely maintained (17% vs 4%, P = 0.228) but biochemical response was better in the treated group (27% vs 4%, P = 0.039). None of the treated patients but five controls developed severe complications of CHB during the follow-up period. A larger total IFN dosage or a younger age (< or = 40 years) were associated with 'sustained' virological response. Younger age and higher baseline alanine transaminase values (> or = 120 Ul(-1)) were related to 'sustained' biochemical response.
Smooth second order sliding mode control for reusable launch vehicle in reentry phase (2012)

This paper describes the design of nonlinear robust controller for reusable launch vehicle which is nonlinear, multivariable, strong coupling, and includes uncertain parameters and external disturbance. Firstly, the feasible guidance strategy is introduced to obtain the desired guidance commands. Then, the attitude control model is converted to integral chain system. Next, the continuous finite time convergence second order sliding mode controller is designed for the normal system. In order to improve the robustness, the nonlinear disturbance observer is proposed to suppress the uncertainties and external disturbances. Furthermore, the synthesis of controller and disturbance observer is used to achieve the attitude tracking for reusable in reentry phase. Finally, the six-degree-of-freedom (6-DOF) simulation results verify the effectiveness of the control strategy.
Determination of the conformation of d(GGAAATTTCC)2 in solution by use of proton NMR and restrained molecular dynamics (1990)

The conformation of the putative bent DNA d(GGAAATTTCC)2 in solution was studied by use of 1H NMR and restrained molecular dynamics. Most of the resonances were assigned sequentially. A total of 182 interproton distance restraints were determined from two-dimensional nuclear Overhauser effect spectra with short mixing times. Torsion angle restraints for each sugar moiety were determined by qualitative analysis of a two-dimensional correlated spectrum. Restrained molecular dynamics was carried out with the interproton distances and torsion angles incorporated into the total energy function of the system in the form of effective potential terms. As initial conformations for restrained molecular dynamics, classical A-DNA and B-DNA were adopted. The root mean square deviation (rmsd) between these two conformations is 5.5 A. The conformations obtained by use of restrained molecular dynamics are very similar to each other, the rmsd being 0.8 A. On the other hand, the conformations obtained by use of molecular dynamics without experimental restraints or restrained energy minimization depended heavily on the initial conformations, and convergence to a similar conformation was not attained. The conformation obtained by use of restrained molecular dynamics exhibits a few remarkable features. The second G residue takes on the BII conformation [Fratini, A. V., Kopka, M. L., Drew, H. R., & Dickerson, R. E. (1982) J. Biol. Chem. 257, 14686-14707] rather than the standard BI conformation. There is discontinuity of the sugar puckering between the eighth T and ninth C. The minor groove of the oligo(dA) tract is rather compressed. As a result, d(GGAAATTTCC)2 is bent.
Hydrogen scrambling in non‐covalent complexes of peptides (2012)

The results obtained for the complexes should be similar to those for protein parts spatially close together--hydrogen scrambling between them should be negligible. The knowledge that almost all the scrambling occurs along peptide chains gives a better insight into the mechanism of HDX inside a protein.
Metabolic Redesign of Rhodobacter sphaeroides for Lycopene Production (2018)

Lycopene plays an important role as an antioxidative and anticancer agent, and is an increasingly valuable commodity in the global market. Rhodobacter sphaeroides, a carotenogenic and phototrophic bacterium, is an efficient and practical host for carotenoid production. Herein, we explored the potential of metabolically engineered Rb. sphaeroides as a novel platform to produce lycopene. The basal lycopene-producing strain was generated by introducing an exogenous crtI<sub>4</sub> from Rhodospirillum rubrum to replace the native crtI<sub>3</sub> and deleting crtC in Rb. sphaeroides. Furthermore, knocking out zwf blocked the competitive pentose phosphate pathway and improved the lycopene content by 88%. Finally, the methylerythritol phosphate pathway was reinforced by integration of dxs combined with zwf deletion, which further increased the lycopene content. The final engineered strain produced lycopene to 10.32 mg/g dry cell weight. This study describes a new lycopene producer and provides insight into a photosynthetic bacterium as a host for lycopene biosynthesis.
A Power Efficient Regulated Charge Pump Based on Charge Sharing for Contactless Devices: An Alternative to Four-Phase Charge Pumps (2017)

International audience
Preliminary study of rapid prototype medical models (2001)

Rapid prototype models are directly integrated into non‐engineering applications such as medicine. Medical models are used to plan complex procedures prior to surgery with potential to optimise patient treatment in the operating theatre. This paper presents results following a 12 month National Health Service Executive research project to assess the feasibility of using rapid prototype medical models. A total of 16 medical models were created. Nine anatomical sites were reconstructed from patient data acquired from five London hospitals. The purpose of the models is described and the commissioning surgeons as part of a questionnaire assessed their usefulness. Future developments are discussed and conclusions about the use of medical models are made.
Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments (2004)

We have developed Phylo-VISTA (Shah et al., 2003), an interactive software tool for analyzing multiple alignments by visualizing a similarity measure for DNA sequences of multiple species. The complexity of visual presentation is effectively organized using a framework based upon inter-species phylogenetic relationships. The phylogenetic organization supports rapid, user-guided inter-species comparison. To aid in navigation through large sequence datasets, Phylo-VISTA provides a user with the ability to select and view data at varying resolutions. The combination of multi-resolution data visualization and analysis, combined with the phylogenetic framework for inter-species comparison, produces a highly flexible and powerful tool for visual data analysis of multiple sequence alignments.
A Conceptual Multidimensional Model for Assessing Smart Sustainable Cities (2015)

The concept of Smart Sustainable Cities (SSC) is gaining increasing attention by the countries around the globe, particularly in response to potential future environmental challenges and increased proportion of populations living in cities. Several countries claim to have implemented or in the process of implementing SSCs, and there are many models that can be used to measure how 'smart' the initiatives and cities are. This paper critically evaluates the main models to measure city smartness and identifies deficiencies, namely that they are not sensitive to the needs, resources, priorities and wider context for individual cities. The paper suggests a multidimensional methodological model that assists in evaluating the smartness level of a city while being sensitive to its context. It provides further contribution by combining sustainable and smart attributes of a city.