gebhart/patrepeval huggingface dataset:
Biochemical and Docking Analysis of Substrate Interactions with Polyisoprenylated Methylated Protein Methyl Esterase (2010)

Polyisoprenylated proteins (PPs) methylation by polyisoprenylated protein methyl transferase (PPMTase) is counteracted by polyisoprenylated methylated protein methyl esterase (PMPMEase). This is the only reversible step of the polyisoprenylation pathway as the relative amounts of the acid and ester forms are determined by the two competing reactions. Since PMPMEase and PPMTase may influence both the structural/functional conformations of PPs, a thorough study of these enzymes is essential to our understanding of the structural/functional features of PPs. PMPMEase has been reported under such pseudonyms as human carboxylesterase 1 (hCE1) because of its apparent broad substrate spectrum. The current study aimed to show the complementarity between its active site and the polyisoprenylated substrates that it metabolizes. Kinetics analysis was conducted with N-, S- and O-substituted substrates using porcine liver PMPMEase and docking analysis using Arguslab. Consistent with the biochemical analysis, the S-ethyl analog yielded an AScore binding energy of -11.32 compared to -13.48, -14.88, -16.15, and -16.81 kcal/mol for S-prenyl (C-5), S-trans-geranyl (C-10), S-trans,trans-farnesyl (C-15) and S-all trans-geranylgeranyl (C-20), respectively. The all trans-geranylgeranyl moiety provides the optimal size for active site interactions. The data reveal that the trans,trans-farnesyl and all trans-geranylgeranyl groups, which are reminiscent of endogenous PPs modifications, have the highest affinity for PMPMEase. Since PPs such as monomeric G-proteins are oncogenic, PMPMEase may be viewed as a viable target for anticancer drug development. The analyses reveal the important structural elements for the design of specific PMPMEase inhibitors to serve in the modulation of oncogenic PPs activities. The results also show that hCE1's repertoire of substrates extends beyond xenobiotics to include PPs as its endogenous substrates.
Fiber-optical acoustic sensor based on a photonic-crystal diaphragm (2009)

This paper reports on a highly sensitive fiber-optical acoustic sensor. The miniature acoustic sensor consists of a Fabry-Perot interferometer made of a photonic-crystal reflector embedded on a compliant silicon diaphragm placed at the tip of a single-mode fiber. A high-reflectivity multilayer dielectric mirror is deposited on the tip of the single-mode fiber. When combined with the high reflection from the photonic-crystal mirror, this second mirror forms a Fabry-Perot with a relatively high finesse (~15), giving rise to a high pressure sensitivity over the 10-50 kHz range. A minimum detectable pressure of 30 muPa/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> at 15 kHz is reported.
Combinational equivalence checking for threshold logic circuits (2007)

Threshold logic is gaining prominence as an alternative to Boolean logic. The main reason for this trend is the availability of devices that implement these circuits efficiently (current mode, differential mode circuits), as well as the promise they hold for the future nanoalldevices (RTDs, SETs, QCAs and other nano devices). This has generated renewed interest in the design automation community to design efficient CAD tools for threshold logic. Recently a lot of work has been done to synthesize threshold logic circuits. So far there has been no efficient method to verify the synthesized circuits. In this work we address the problem of combinational equivalence checking for threshold circuits. We propose a new algorithm, to obtain compact functional representation of threshold elements. We give the proof of correctness, and analyze its runtime complexity. We use this polynomial time algorithm to develop a new methodology to verify threshold circuits. We report the result of our experiments, comparing the proposed methodology to the naive approach. We get up to 189X improvement in the run time (23X on average), and could verify circuits that the naive approach could not.
Smart-seq2 for sensitive full-length transcriptome profiling in single cells (2013)

Single-cell gene expression analyses hold promise for characterizing cellular heterogeneity, but current methods compromise on either the coverage, the sensitivity or the throughput. Here, we introduce Smart-seq2 with improved reverse transcription, template switching and preamplification to increase both yield and length of cDNA libraries generated from individual cells. Smart-seq2 transcriptome libraries have improved detection, coverage, bias and accuracy compared to Smart-seq libraries and are generated with off-the-shelf reagents at lower cost.
Tailoring the Catalytic Performance of Sol–Gel‐Encapsulated Tetra‐<i>n</i>‐propylammonium Perruthenate (TPAP) in Aerobic Oxidation of Alcohols (2003)

Sol-gel nanohybrid silica particles organically modified and doped with the ruthenium species tetra-n-propylammonium perruthenate (TPAP) are highly efficient catalysts for the selective oxidation of alcohols to carbonyl groups with O(2) at low pressure in toluene. The materials are easily prepared by a one-step sol-gel process, and their catalytic performance can be optimised by tailoring the conditions of their synthesis by hydrolytic co-polycondensation of tetramethoxysilane (TMOS) and alkyltrimethoxysilanes R-Si(OMe)(3) in the presence of TPAP. Eventually, heterogeneous catalysts considerably more active than the unsupported perruthenate were obtained, while also being leach-proof and recyclable. The correlation between the materials' activity, surface polarity and textural properties suggests valuable information on the chemical behaviour of sol-gel catalytic materials in oxidation catalysis; this is of interest in view of the importance of efficient solid catalysts for the selective oxidation of alcohols with O(2).
Plasma N-Glycans as Emerging Biomarkers of Cardiometabolic Risk: A Prospective Investigation in the EPIC-Potsdam Cohort Study (2020)

OBJECTIVE Plasma protein N-glycan profiling integrates information on enzymatic protein glycosylation, which is a highly controlled ubiquitous posttranslational modification. Here we investigate the ability of the plasma N-glycome to predict incidence of type 2 diabetes and cardiovascular diseases (CVDs; i.e., myocardial infarction and stroke). RESEARCH DESIGN AND METHODS Based on the prospective European Prospective Investigation of Cancer (EPIC)-Potsdam cohort (n = 27,548), we constructed case-cohorts including a random subsample of 2,500 participants and all physician-verified incident cases of type 2 diabetes (n = 820; median follow-up time 6.5 years) and CVD (n = 508; median follow-up time 8.2 years). Information on the relative abundance of 39 N-glycan groups in baseline plasma samples was generated by chromatographic profiling. We selected predictive N-glycans for type 2 diabetes and CVD separately, based on cross-validated machine learning, nonlinear model building, and construction of weighted prediction scores. This workflow for CVD was applied separately in men and women. RESULTS The N-glycan–based type 2 diabetes score was strongly predictive for diabetes risk in an internal validation cohort (weighted C-index 0.83, 95% CI 0.78–0.88), and this finding was externally validated in the Finland Cardiovascular Risk Study (FINRISK) cohort. N-glycans were moderately predictive for CVD incidence (weighted C-indices 0.66, 95% CI 0.60–0.72, for men; 0.64, 95% CI 0.55–0.73, for women). Information on the selected N-glycans improved the accuracy of established and clinically applied risk prediction scores for type 2 diabetes and CVD. CONCLUSIONS Selected N-glycans improve type 2 diabetes and CVD prediction beyond established risk markers. Plasma protein N-glycan profiling may thus be useful for risk stratification in the context of precisely targeted primary prevention of cardiometabolic diseases.
Influence of serotype and virus strain on synergism between Marek's disease vaccine viruses (1992)

The enhanced protective effect (synergism) when certain Marek's disease (MD) vaccine viruses are combined has been widely used in the development of improved vaccines, but the mechanism is poorly understood. To better characterize the basis for synergism among MD vaccine viruses, three vaccine viruses from each of the three MD viral serotypes were evaluated alone and in various combinations for protection against early challenge with very virulent MD viruses in four replicate trials. Synergism seemed to be influenced by viral serotype because significant enhancement occurred frequently between viruses of serotypes 2 and 3 (five of nine bivalent vaccines positive), but rarely between viruses of serotypes 1 and 3 (one of nine bivalent vaccines positive) and 1 and 2 (one of nine bivalent vaccines positive), and was not detectable between viruses of the same serotype (none of nine bivalent vaccines positive). With some exceptions, the degree of synergism tended to vary inversely with the mean protective efficacy of the most protective component virus. Little effect of virus dose, virus dose ratio or type and route of viral challenge was noted. The combination of strains 281MI/1 (serotype 2) and WTHV-1/1 (serotype 3), both poorly protective as monovalent vaccines, consistently demonstrated high levels of synergism (over 300%) in antibody-positive chickens challenged 5 days post-vaccination with Md5 virus. This protocol may be a useful model system for further studies on mechanisms of synergism. However, mixtures that optimize synergism are not necessarily as protective as commercial vaccines.
Adaptive environment classification system for hearing aids (2010)

An adaptive sound classification framework is proposed for hearing aid applications. The long-term goal is to develop fully trainable instruments in which both the acoustical environments encountered in daily life and the hearing aid settings preferred by the user in each environmental class could be learned. Two adaptive classifiers are described, one based on minimum distance clustering and one on Bayesian classification. Through unsupervised learning, the adaptive systems allow classes to split or merge based on changes in the ongoing acoustical environments. Performance was evaluated using real-world sounds from a wide range of acoustical environments. The systems were first initialized using two classes, speech and noise, followed by a testing period when a third class, music, was introduced. Both systems were successful in detecting the presence of an additional class and estimating its underlying parameters, reaching a testing accuracy close to the target rates obtained from best-case scenarios derived from non-adaptive supervised versions of the classifiers (about 3% lower performance). The adaptive Bayesian classifier resulted in a 4% higher overall accuracy upon splitting adaptation than the minimum distance classifier. Merging accuracy was found to be the same in the two systems and within 1%-2% of the best-case supervised versions.
Film formation of poly (p-phenylene terephthalamide) from sulphuric acid solution. (1992)

A novel process for the formation of poly (p-phenylene terephthalamide) (PPTA) film from liquid crystalline sulphuric acid solution was developed. A homogeneous and transparent PPTA film is very difficult to obtain from sulphuric acid solution owing to the highly anisotropic flow properties of the solution. A biaxially balanced PPTA film could be formed by using the optically anisotropic to isotropic transition appeared in the phase diagram of the PPTA sulphuric acid solution. The phase transition was generated by controlling temperature and/or polymer concentration of the solution. The anisotropic solution was cast on a flat glass plate. The cast dope was carried into a conditioning chamber (air oven) in which the phase transition occurred before it was immersed into the coagulation bath. The isotropic cast dope was coagulated and dried holding dimensions constant. The adjustment of temperature and water content of the cast dope plays an important role in the process and directly affects the properties of the film obtained. The conditioning at 100°C was suitable for the film properties in a series of experiments. The Young's modulus of 14 GPa and tensile strength of 450 MPa were obtained for the film heat-treated at 350°C during 20min. This process can be applied to a continuous large scale process.
Optofluidic flow meter for sub–nanoliter per minute flow measurements (2021)

Performance improvements in microfluidic systems depend on accurate measurement and control of fluids on the micro- and nanoscale, and new applications are continuously moving the needle to lower volumetric flow rates. This work focuses on improving an optofluidic system for the measurement and calibration of microflows to the sub-nanoliter per minute range. The experimental measurements rely on an optofluidic system that delivers excitation light and records fluorescence in a precise interrogation region of a microfluidic channel. Using a scaling relationship between flow rate and the fluorescence emission after photobleaching, the system enables real-time determination of flow rates. Here we demonstrate improved calibration of a flow controller to 1 % uncertainty and improved resolution of the optofluidic flow meter to less than 1 nL/min using molecules with lower diffusion coefficients.
AN AUTOMATED SAMPLING SYSTEM FOR MEASURING SOIL pH (1999)

Within the scope of precision farming there is a need for improved methods of assessing and managing soilvariability. The site-specific management of soil pH is one application that has potential benefits for crop production.However, current grid sampling and mapping techniques to estimate lime requirement may not be adequate. For thisreason, an automated soil sampling system for measuring soil pH on-the-go has been created. The system includes acomputer-operated soil sampling mechanism mounted in a shank, a global positioning unit, and a pH meter with a flatsurface electrode. The system measures soil pH directly on a sample. The automated soil sampling system can determinepH while taking soil samples at a selected depth (0-20 cm) every 8 s. A simple linear regression was used to calibrate theelectrode mV output against soil pH obtained via a standard laboratory method. Field testing yielded an r2of 0.83 and astandard error of prediction of 0.45 pH.
Silicon smelting in a closed furnace (1991)

Dow Corning has been working towards the advancement of silicon smelting in a closed furnace over the past four years. A 200 kVA closed furnace pilot plant unit was built to investigate the operating parameters for smelting silicon. The single electrode furnace is operated under totally sealed conditions. The feed from the feed hoppers is fed through air locks to the furnace. The off-gas from the furnace, consisting of by-product CO as well as volatiles from the feeds, pass through a venturi scrubber, where water is introduced to scrub out the fume from the furnace and cool the gas. The mixed scrubber water and off-gas pass into a centrifugal mist eliminator where the water and fume disengage from the gas. The fume slurry is passed through bag filters where the fume is separated from the water. The clean off-gas from the furnace was evaluated for its calorific value and evaluated for conversion to useful products. A number of silicon smelting tests were conducted during this program. Various levels of charcoal and coal mixtures were evaluated to determine the optimum mix. A low volatile coal was preferred over typical Blue Gem coal. The coal amount in the mix was maximized without compromising the smelting performance. A raw material mix consisting of 30% charcoal and 70% low volatile coal was determined to be an optimum mix for closed furnace operation. Silicon recoveries in the low nineties were demonstrated using this mix. Four quartz sources were also evaluated in the closed furnace. The closed furnace operation for silicon smelting was identified to offer significant advantages over an open furnace from the standpoint of reduced carbon oxidation losses, electrode consumption, electrical energy consumption and silicon yield improvement. Other advantages in addition to process off-gas recovery included improved safety from reduced heat and fume exposure, and improved pollution control to the environment. 1 ref.
Electroluminescence in alternating copolymers with the acetylene unit (1999)

Abstract 2,7‐diethynyl‐9,9î‐di‐n‐hexylfluorene and 2,7‐dibromo‐9,9î‐di‐n‐hexylfluorene were alternately bonded with each other by a Heck reaction to produce poly(9,9î‐di‐n‐hexyl‐2,7‐fluorenyleneethynylene). The alternating copolymer emitted blue color with the peak maximum at 475 nm on excitation either at 340, 365 or 400 nm. The principal emission maximum shifted to 425 nm on excitation at 340 nm when the polymer was blended with polyvinylcarbazole(PVK). Light‐emitting diodes (LEDs) fabricated with the alternating copolymer sandwiched between indium‐tin oxide glass and Al emitted a light with the peak maximum at 550 nm. The peak maximum shifted to 425 nm when the copolymer was blended with PVK with the blending ratios between 5 to 20% of the emissive copolymer.
An efficient resonant gate drive scheme for high frequency applications (2011)

Gallium Nitride (GaN) and Silicon Carbide (SiC) devices have been found to withstand high voltages without showing degradation [1] and can be switched at high frequencies making them attractive for high power drives. Though GaN/SiC devices can be operated at high temperature and high frequencies, it is important to develop gate drive circuits to turn ON and OFF these devices efficiently at high speeds. This paper proposes a resonant gate drive circuit that aims at reducing the power loss associated with high frequency switching of power IGBT/MOSFETs. The proposed circuit is compared with traditional gate drive circuits from power consumption and switching speed points of view. Experimental results are given to illustrate the concept.
Method of optimizing performance of Rankine cycle power plants. [US DOE Patent] (1980)

A method is described for efficiently operating a Rankine cycle power plant to maximize fuel utilization efficiency or energy conversion efficiency or minimize costs by selecting a turbine fluid inlet state which is substantially on the area adjacent and including the transposed critical temperature line.
LCNN: Lookup-based Convolutional Neural Network (2016)

Porting state of the art deep learning algorithms to resource constrained compute platforms (e.g. VR, AR, wearables) is extremely challenging. We propose a fast, compact, and accurate model for convolutional neural networks that enables efficient learning and inference. We introduce LCNN, a lookup-based convolutional neural network that encodes convolutions by few lookups to a dictionary that is trained to cover the space of weights in CNNs. Training LCNN involves jointly learning a dictionary and a small set of linear combinations. The size of the dictionary naturally traces a spectrum of trade-offs between efficiency and accuracy. Our experimental results on ImageNet challenge show that LCNN can offer 3.2x speedup while achieving 55.1% top-1 accuracy using AlexNet architecture. Our fastest LCNN offers 37.6x speed up over AlexNet while maintaining 44.3% top-1 accuracy. LCNN not only offers dramatic speed ups at inference, but it also enables efficient training. In this paper, we show the benefits of LCNN in few-shot learning and few-iteration learning, two crucial aspects of on-device training of deep learning models.
Plasminogen activator inhibitor in human tears after laser refractive surgery (2008)

The similarity in the general time pattern of PAI-2 after PRK and LASIK suggests commonality in the enzymatic control response to corneal surgical wounding. Taken in the context of previous work, the observed levels of PAI-2 concentration in eyes with and without opacification suggest that in the postsurgical period, PAI-2 is not the controlling mechanism for the later development of corneal opacification and haze.
Cocoa particles for food emulsion stabilisation (2013)

Emulsifying properties of cocoa particles have been investigated in systems containing purified sunflower oil (PSO) and water at varying pH, concentration and source of cocoa particles including cocoa powders (CP), cocoa fibre (CF) and cocoa mass (CM). The effect of cocoa particle source, pH and cocoa particle concentration on emulsion stability was evaluated by following changes in characteristic droplet diameter. Size distributions acquired on the emulsions and aqueous cocoa particle suspensions overlapped. Based on cryo-SEM imaging of the emulsions, isolation of cocoa particle fines and a process of washing the cocoa particles to remove any water soluble molecules, it was concluded that the cocoa particle fines not captured by the small angle laser diffraction method employed for sizing, act as Pickering particles. This research has demonstrated a universal nature of a natural food particle to stabilise oil-in-water emulsions not requiring particle modification or adjusting of the solution properties of the emulsion phases.
Intraocular impedance as a function of the position in the eye, electrode material and electrode size (2005)

A critical element of a retinal prosthesis is the electrode assembly, which is placed on the retina. It is via this interface that the nerve cells are stimulated to produce the perception of light. The electrode impedance is an integral part in determining the design of the stimulating electrode and the attached circuit. The impedances involved are not only the tissue impedance but the electrode itself contributes to the impedance. Further on the electrode impedance depends not only the material of the electrode but also the size of the electrode. This paper discusses the results obtained by the intraocular impedance measurements with varying electrode size, electrode material and position of the electrode within the eye.
Arterial Spin-Label Imaging in Patients with Normal Bolus Perfusion-weighted MR Imaging Findings: Pilot Identification of the Borderzone Sign (2009)

Approximately half of the patients with normal bolus PW imaging findings had abnormal ASL findings-most commonly the borderzone sign. Results of this pilot study suggest that ASL imaging in patients who have this sign and are suspected of having cerebrovascular disease yields additional and complementary hemodynamic information.
Commensal Hafnia alvei strain reduces food intake and fat mass in obese mice—a new potential probiotic for appetite and body weight management (2020)

H.alvei HA4597 strain reduces food intake, body weight and fat mass gain in hyperphagic and obese mice. These data combined with low enterobacterial ClpB gene abundance in the microbiota of obese humans provide the rationale for using H.alvei as a probiotic for appetite and body weight management in overweight and obesity.
Adaptive lens using liquid crystal concentration redistribution (2006)

An adaptive lens using electrically induced liquid crystal (LC)/monomer concentration redistribution is demonstrated. In the absence of an electric field, the LC/monomer mixture is homogeneously distributed. Application of an inhomogeneous electric field causes the LC molecules to diffuse towards the high field region and the liquid monomer towards the low field region. On the other hand, the LC molecules tend to diffuse from high to low concentration direction in order to balance the concentration change. A gradient LC concentration is thus obtained. Using the gradient LC concentration, we demonstrate a tunable-focus lens. Compared with a conventional LC lens, our lens has advantages in small astigmatism and without light scattering, but its response time is slower.