gebhart/patrepeval huggingface dataset:
Biocatalytic aldehyde reduction using tailor‐made whole‐cell catalysts: a novel synthesis of the aroma chemical cinnamyl alcohol (2007)

Abstract A biocatalytic method for the synthesis of the aroma chemical cinnamyl alcohol by means of a wholecell‐catalysed reduction of cinnamyl aldehyde has been developed. As a biocatalyst, recombinant whole cells overexpressing an alcohol dehydrogenase from Lactobacillus kefir and a glucose dehydrogenase from Thermoplasma acidophilum have been used in combination with d‐ glucose as co‐substrate. The reduction process proceeds with a conversion of 98%, even at a high substrate input of 166 g/l cinnamyl aldehyde, and gives a yield of 77% of the desired product, cinnamyl alcohol. In addition to high product concentrations, further advantages of this approach are the use of a low‐cost whole‐cell catalyst, the high purity of the product, as well as the fact that there is no need for the addition of external co‐factor in the biotransformation step. Copyright © 2007 John Wiley &amp; Sons, Ltd.
5-O-Alkylated derivatives of 5-hydroxy-2'-deoxyuridine as potential antiviral agents. Anti-herpes activity of 5-propynyloxy-2'-deoxyuridine (1978)

Alkylation of 5-hydroxyuridine or 5-hydroxy-2'-deoxyuridine with various activated alkylating agents in the presence of 1 equiv of NaOH gave a series of new nucleoside analogues which were evaluated for antiviral activity against vaccinia virus, herpes simplex-1 virus, and vesicular stomatitis virus in both primary rabbit kidney cells and human skin fibroblasts. One of these analogues, 5-propynyloxy-2'-deoxyuridine, was a potent inhibitor of herpes simplex virus. Structure-activity considerations suggest that the anti-herpes activity is dependent on the integrity of the acetylene group since substitution of phenyl, p-nitrophenyl, vinyl, carboxamido, or carboxyl for the triple bond led to diminished antiviral activity.
Evaluating Cellular Drug Uptake with Fluorescent Sensor Proteins (2017)

We are introducing a new approach to evaluate cellular uptake of drugs and drug candidates into living cells. The approach is based on converting the protein target of a given class of compounds into a fluorescent biosensor. By measuring the binding of different compounds to their cognate biosensor in live cells and comparing these values to those measured in vitro, their cellular uptake and concentrations can be ranked. We demonstrate that our strategy enables the evaluation of the cellular uptake into the cytosol of 2 classes of inhibitors using two different sensor designs; first, sensors comprising the self-labeling protein SNAP conjugated with a chemically modified inhibitor shown for inhibitors of the enzyme human carbonic anhydrase II; and a label-free sensor for inhibitors of protein-protein interactions demonstrated for the protein pair p53-HDM2.
Using immunotherapy to enhance the response of a C3H mammary carcinoma to proton radiation (2023)

Checkpoint inhibitors enhanced the response of this C3H mammary carcinoma to proton irradiation. However, this enhancement depended on the checkpoint inhibitor and radiation dose.
RICK/RIP2 Promotes Inflammation and Lethality after Gram-Negative Bacterial Infection in Mice Stimulated with Lipopolysaccharide (45.4) (2009)

Abstract RICK, a serine-threonine kinase, functions downstream of the pattern-recognition receptors Nod1 and Nod2 to mediate NF-kB and MAPK activation in response to specific microbial stimuli. However, the function of RICK in the recognition and host defense of Gram-negative bacteria remains poorly understood. We report here that infection of wild-type and RICK-deficient macrophages with Pseudomonas aeruginosa and Escherichia coli, elicited comparable activation of NF-kB and MAPKs as well as secretion of pro-inflammatory cytokines. However, production of IL-6 and IL-1b induced by these Gram-negative bacteria was impaired in RICK-deficient macrophages when the cells were previously stimulated with LPS or E. coli. The diminished pro-inflammatory response of RICK-deficient macrophages to bacteria was associated with reduced activation of NF-kB and MAPKs. Importantly, mutant mice deficient in RICK were less susceptible than wild-type mice to P. aeruginosa infection when the animals were previously stimulated with LPS. The reduced lethality of RICK-deficient mice infected with P. aeruginosa was independent of pathogen clearance, but was associated with diminished production of pro-inflammatory molecules in vivo. These results demonstrate that RICK contributes to the induction of pro-inflammatory responses and susceptibility to Gram-negative bacteria after exposure to LPS, a condition that is associated with reduced TLR signaling.
The Effect of Live Yeast and Yeast Extracts on Growth Performance of Nursery Pigs Weaned from Sows Fed Diets with or without Yeast Additives (2021)

A total of 340 weaned pigs (241 × 600, DNA; initially 11.2 lb BW) were used in a 45-d study to evaluate previous sow treatment (control vs. yeast additives) and nursery diets with or without added yeast-based pre- and probiotics (Phileo by Lesaffre, Milwaukee, WI) on growth performance. At placement in the nursery, pigs were housed by pen based on previous sow treatment and randomly assigned to 1 of 2 dietary treatments with 5 pigs per pen and 17 replications per treatment. Treatments were arranged in a 2 × 2 factorial with main effects of sow treatment (control vs. yeast-based pre- and probiotic diet; 0.10% ActiSaf Sc 47 HR+ and 0.025% SafMannan) and nursery treatment (control vs. yeast-based pre- and probiotic diet; 0.10% ActiSaf Sc 47 HR+, 0.05% SafMannan, and 0.05% NucleoSaf from d 0 to 7, then concentrations were lowered by 50% from d 7 to 24). All pigs were fed a common diet from d 24 to 45 post-weaning. Progeny from sows fed diets with yeast additives had increased (P < 0.05) ADG, ADFI, and BW from d 0 to 24 and d 0 to 45. However, pigs that were fed yeast additives in the nursery had an overall (d 0 to 45) tendency for reduced ADG (P = 0.079) and lighter ending BW (P = 0.086). In conclusion, offspring from sows fed a live yeast and yeast additives had increased ADG, ADFI, and BW. However, feeding live yeast and yeast additives only in the nursery tended to reduce ADG and ending BW.
[Vertical Distribution Characteristics of Dissolved Organic Matter in Groundwater and Its Cause]. (2016)

Dissolved organic matter (DOM) can change the species, migration and transformation of foreign pollutants in groundwater, and the investigations of its composition and distribution characteristics play a role in environment protection. The groundwater DOMs were obtained at the depths of 1.2, 1.5 and 1.8 m, and its origin, composition, concentration, distribution characteristics and influencing factors were studied using UV-Vis and fluorescence spectra combined with parallel factor analysis and principle components analysis. The results showed that, DOM in the groundwater originated from both terrigenous input and microbial activities, and was comprised of humic-like matter, heterogeneous component, and protein-like matter. Humic-like matter and heterogeneous components showed a high concentration at 1.5 m and a low one at 1.2 m, whereas the protein-like matter exhibited a low concentration at 1.5 m and a high one at 1.2 m. The groundwater DOM at 1.5 m exhibited the highest aromaticity, humification, molecular weight and polar functional group content, while that at 1.2 m depth showed the lowest aromaticity, humification, molecular weight and polar functional group content. The vertical distribution of DOM in groundwater was related to aromaticity, humification, molecular weight and polar functional group, and the DOM with high aromaticity, humification, molecular weight and polar functional group resisted to biodegradation, and could easily enter into the bottom layer groundwater.
100 Gb/s optical packet network architecture (2002)

Two major architectural challenges of creating ultrafast optical time division multiplexed (OTDM) multi-access networks are that they operate with long propagation delays relative to packet transmission times (i.e. there are many packets in flight in the network) and there is limited processing that can be performed at the 100 Gb/s or higher transmission rates. HLAN is an OTDM network architecture that we believe is suitable for implementing a ultrafast integrated services network capable of operating over the distances that short pulse optical signals can propagate (<1000 km).
A Patterned-TiO<sub>2</sub>/SnO<sub>2</sub> Bilayer Type Photocatalyst (2000)

A major challenge in heterogeneous photocatalysis is the need to increase charge separation efficiency of a photocatalyst, under illumination, without any applied electrical potential. Regularly patterned TiO2 films were formed on a SnO2-film coated soda lime glass substrate by using an organically modified sol−gel method. This bilayer-type photocatalyst exhibited a very high photocatalytic activity for gas-phase reactions. Efficient interfacial electron transfer from the TiO2 overlayer to the SnO2 underlayer was demonstrated by labeling and visualizing the reduction sites with Ag particles.
SPIRE: A Methodology for Sequential to Parallel Intermediate Representation Extension (2014)

Abstract. SPIRE is a new methodology for the design of parallel extensions of the intermediate representations used in compilation frameworks of sequential languages. It can be used to leverage existing infrastructures for sequential languages to address both control and data parallel constructs while preserving as much as possible existing analyses for sequential and parallel code. We suggest to view this upgrade process as an “intermediate representation transformer ” at the syntactic and semantic levels; we show this can be done via the introduction of only ten new concepts, collected in three groups, namely execution, synchronization and data distribution, and precisely defined via a formal semantics and rewriting rules. We use the sequential intermediate representation of PIPS, a comprehensive source-to-source compilation platform, as a use case for our approach. We introduce our SPIRE parallel primitives, extend PIPS intermediate representation and show how example code snippets from the OpenCL, Cilk, OpenMP, X10, Habanero-Java, MPI and Chapel parallel programming languages can be represented this way. A formal definition of SPIRE operational semantics is provided, built on top of the one used for the sequential intermediate representation. We assess the generality of our proposal by (1) showing how a different sequential IR, namely LLVM, can be extended to handle parallelism using the SPIRE methodology and (2) providing implementation and run-time performance data of a SPIRE-derived parallelization process. Our primary goal with the development of SPIRE is to provide, at a low cost, powerful parallel program representations that will ease the design of efficient automatic parallelization algorithms. More generally, our work provides a possible roadmap for the compiler designers who need to introduce parallel features into their own infrastructures.
A polycation-chaperoned in-stem molecular beacon system (2011)

In the presence of poly(L-lysine)-graft-dextran, an in-stem molecular beacon involving three perylene-anthraquinone pairs in the stem region had a signal/background ratio of as high as 570. Response speed was also remarkable; equilibrium was attained within 5 minutes after addition of substrate DNA at 20 °C.
A fast hermite transform with applications to protein structure determination (2007)

We discuss algorithms for a fast and stable approximation of the Hermite transform of a compactly supported function on the real line, attainable via an application of a fast algebraic algorithm for computing sums associated to a three-term relation. Trade-offs between approximation in bandwidth (in the Hermite sense) and size of the support region are addressed. Generalizations to any family of orthogonal polynomials are outlined. Applications to the determination of protein structure are discussed.
Two orders of magnitude increase in metal piezoresistor sensitivity through nanoscale inhomogenization (2012)

Metal-based piezoresistive sensing devices could find a much wider applicability if their sensitivity to mechanical strain could be substantially improved. Here, we report a simple method to enhance the strain sensitivity of metal films by over two orders of magnitude and demonstrate it on specially designed microcantilevers. By locally inhomogenizing thin gold films using controlled electromigration, we have achieved a logarithmic divergence in the strain sensitivity with progressive microstructural modification. The enhancement in strain sensitivity could be explained using non-universal tunneling-percolation transport. We find that the Johnson noise limited signal-to-noise ratio is an order of magnitude better than silicon piezoresistors. This method creates a robust platform for engineering low resistance, high gauge factor metallic piezoresistors that may have profound impact on micro and nanoscale self-sensing technology.
Analysis on the Dielectric Characteristics of Various Insulation Gases for Developing a Sub-cooled Liquid Nitrogen Cooling System (2011)

A sub-cooled liquid nitrogen cooling system is known as a most promising method to develop large scale superconducting apparatuses such as superconducting fault current limiters and superconducting cables [1]. Gaseous helium (GHe), gaseous nitrogen (<TEX>$GN_2$</TEX>) and sulfur hexafluoride (<TEX>$SF_6$</TEX>) are commonly used for designing an high voltage applied superconducting device as an injection gaseous medium [2, 3]. In this paper, the analysis on the dielectric characteristics of GHe, <TEX>$GN_2$</TEX> and <TEX>$SF_6$</TEX> are conducted by designing and manufacturing sphere-to-plane electrode systems. The AC withstand voltage experiments on the various gaseous insulation media are carried out and the results are analyzed by using finite element method (FEM) considering field utilization factors (<TEX>${\xi}$</TEX>). It is found that the electric field intensity at sparkover (<TEX>$E_{MAX}$</TEX>) of insulation media exponentially decreases according to <TEX>${\xi}$</TEX> increases. Also, the empirical expressions of the functional relations between <TEX>$E_{MAX}$</TEX> and <TEX>${\xi}$</TEX> of insulation media are deduced by dielectric experiments and computational analyses. It is expected that the electrical insulation design of applied superconducting devices could be performed by using the deduced empirical formulae without dielectric experiments.
Privacy-Preserving Exploration of Genetic Cohorts with i2b2 At Lausanne University Hospital (2016)

Re-use of patientsâ health records can provide tremendous benefits for clinical research. One of the first essential steps for many research studies, such as clinical trials or population health studies, is to effectively identify, from electronic health record systems, groups of well-characterized patients who meet specific inclusion and exclusion criteria. This procedure is called cohort exploration. Yet, when researchers need to compile specific cohorts of patients, privacy issues represent one of the major obstacles to accessing patientsâ data, especially when sensitive data, such as genomic data, are involved. Because of this, cohort exploration could become extremely difficult and time-consuming. In this joint paper between the Ecole Polytechnique F Â´ edÂ´ erale de Lausanne (EPFL) and the Lausanne University Hospital Â´ (CHUV), we address the challenge of designing and deploying an efficient privacy-preserving explorer for genetic cohorts. Our solution is built on top of i2b2 (informatics for integrating biology and the bedside), the state-of-the-art open-source framework for cohort exploration, and exploits on cutting-edge privacy-enhancing technologies (PETs) such as homomorphic encryption and differential privacy. To the best of our knowledge, our proposed solution is the first of its kind to be successfully deployed in a real operational environment within a hospital. Especially, it has been tested as one of the services of the clinical research data-warehouse of CHUV. Solutions involving homomorphic encryption are often believed to be costly and still immature for use in operational environments. In this paper, we prove the opposite by describing how actually, for specific use cases, this kind of PETs can be very efficient enablers.
(Invited) Insights into the UV-C Optical Absorption of AlN Substrates Grown by PVT (2020)

The structural and optical properties of 2-inch AlN substrates grown by physical vapor transport were assessed. Ultraviolet transmittance and absolute reflectance spectra were measured spectrophotometrically. Accurate absorption coefficients were calculated with a method accounting for reflection losses. Production of high-quality, macrodefect-free AlN substrates possessing absorption coefficients at 265 nm with values from 30 to 50 cm -1 was demonstrated.
Relationship between serum adiponectin levels and age in healthy subjects and patients with type 2 diabetes (2012)

Serum adiponectin levels are significantly and positively associated with age in healthy subjects and in patients with diabetes. This association is independent of renal function, body fat status, glucose metabolism and lipid profiles.
Real-Time Corrosion Monitoring of Aircraft Structures with Prognostic Applications (2012)

This paper presents the theory and experimental validation of a Structural Health Management (SHM) system for monitoring corrosion. Corrosion measurements are acquired using a micro-sized Linear Polarization Resistance (μLPR) sensor. The μLPR sensor is based on conventional macro-sized Linear Polarization Resistance (LPR) sensors with the additional benefit of a reduced form factor making it a viable and economical candidate for remote corrosion monitoring of high value structures, such as buildings, bridges, or aircraft.A series of experiments were conducted to evaluate the μLPR sensor for AA 7075-T6, a common alloy used in aircraft structures. Twelve corrosion coupons were placed alongside twenty-four μLPR sensors in a series of accelerated tests. LPR measurements were sampled once per minute and converted to a corrosion rate using the algorithms presented in this paper. At the end of the experiment, pit-depth due to corrosion was computed from each μLPR sensor and compared with the control coupons.The paper concludes with a feasibility study for the μLPR sensor in prognostic applications. Simultaneous evaluation of twenty-four μLPR sensors provided a stochastic data set appropriate for prognostics. RUL estimates were computed a-posteriori for three separate failure thresholds. The results demonstrate the effectiveness of the sensor as an efficient and practical approach to measuring pit-depth for aircraft structures, such as AA 7075-T6, and provide feasibility for its use in prognostic applications.
Rheological Properties of Cement Pastes Incorporating Polycarboxylate Superplasticizers Containing Different Hydrophobic Groups (2018)

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Catalytic H/D Exchange between Organic Compounds and D<sub>2</sub>O with TpRu(PPh<sub>3</sub>)(CH<sub>3</sub>CN)H (Tp = hydro(trispyrazolyl)borate). Reaction of TpRu(PPh<sub>3</sub>)(CH<sub>3</sub>CN)H with Water to Form Acetamido Complex TpRu(PPh<sub>3</sub>)(H<sub>2</sub>O)(NHC(O)CH<sub>3</sub>) (2007)

Deuteration of organic molecules using D2O as the deuterium source is affected with catalytic systems based on the ruthenium solvento hydride complex TpRu(PPh3)(CH3CN)H. The deuteration reactions can be performed under Ar or H2. In the former case, the hydride ligand is rapidly deuterated by D2O, and in the course of the catalysis, D2O converts TpRu(PPh3)(CH3CN)D into the acetamido complex TpRu(PPh3)(D2O)(NDC(O)CH3), which at the later stage of the reaction generates two additional minor species, one of which is the partially deuterated carbonyl hydride species TpRu(PPh3)(CO)H(or D). All of these complexes are, however, found to be inactive for the H/D exchange reactions between the organic molecules and D2O. In the exchange reactions under H2, a mixture of the HD isotopomers, TpRu(PPh3)H3-xDx, of the dihydrogen hydride complex TpRu(PPh3)(H2)H are the active species. On the basis of our previous work on the TpRu(PPh3)(CH3CN)H-catalyzed H/D exchange reactions between deuterated organic molecules and CH4, it is proposed that TpRu(PPh3)(CH3CN)D and TpRu(PPh3)(H3-x)Dx exchange their deuteride ligands Ru−D with R−H via the intermediacies of the η2-R−H(or D) and η2-H−H(or D) σ-complexes; the Ru−H bonds thus formed after the exchange are deuterated by D2O to regenerate the metal deuterides. The solvento complex TpRu(PPh3)(CH3CN)D under Ar is suggested to be more active than TpRu(PPh3)(H3-x)Dx under H2 for the H/D exchange reactions because the former reacts more readily with the organic molecule R−H to generate the η2-R−H σ-complex due to higher lability of the CH3CN ligand in comparison with the dihydrogen or hydrogen−deuterium ligand of TpRu(PPh3)(H3-x)Dx. The acetamido complex TpRu(PPh3)(H2O)(NHC(O)CH3) was independently prepared by refluxing a THF solution of TpRu(PPh3)(CH3CN)H containing excess water for 24 h, and its molecular structure was determined by X-ray crystallography. Theoretical calculations at the Becke3LYP level of DFT theory have been performed to study the reaction of TpRu(PPh3)(CH3CN)H with H2O that leads to the formation TpRu(PPh3)(H2O)(NHC(O)CH3). It is shown that the hydration reaction is promoted by a Ru−H···H−OH dihydrogen-bonding interaction between the hydride ligand and the attacking water molecule. An explanation for the failure of the chloro analogue TpRu(PPh3)(CH3CN)Cl to react with water to form the acetamido complex is also provided.
Environmentally Friendly Boron-Based Pyrotechnic Delays: An Additive Manufacturing Approach (2019)

Pyrotechnic time delays are reactive systems that burn for a desired period of time at a specified rate and are commonly used in military applications such as grenades and hand-held signals. Typically, they are manufactured by pressing the reactive powder into a metal housing. This rigid design inherently limits configurability, and they have had reliability issues. Additionally, there has been advocacy for environmentally friendly pyrotechnic ignition delays, by removal of barium chromate (BaCrO4). This study has two distinct objectives. First, determine the viability of two possible replacements, strontium molybdate (SrMoO4) and barium molybdate (BaMoO4), for the harmful component, BaCrO4, in the traditional T-10 delay. This includes combustion characteristics such as burning rate, combustion temperature, and gas generation. Furthermore, thermal characteristics are determined through differential scanning calorimetry (DSC), and combustion products are analyzed with X-ray diffraction (XRD). Second, by using a novel approach, these reactive delay systems are integrated into printable ink formulations and deposited onto soapstone substrates. This demonstrates a high degree of configurability and an effort toward a universal delay.