gebhart/patrepeval huggingface dataset:
The role of O-linked protein glycosylation in beta-cell dysfunction. (2002)

Although only recently described, the pathway of O-linked protein glycosylation is already being implicated in diseases as diverse as cancer and Alzheimer's. Unlike the better known N-linked pathway, O-linked protein glycosylation is a dynamic and regulated event, much like tyrosine phosphorylation. During the process of O-glycosylation, the enzyme O-GlcNAc transferase (OGT) uses the substrate UDP-N-acetylglucosamine (UDP-GlcNAc) to attach a single O-linked N-acetylglucosamine (O-GlcNAc) to nuclear and cytosolic proteins on serine or threonine residues. Conversely, the enzyme O-GlcNAc-selective N-acetyl-beta-D-glucosaminidase (O-GlcNAcase) removes the O-GlcNAc, returning the protein to its baseline state until the cycle repeats itself. Although proving to be of interest in many different tissues, this pathway is especially important in pancreatic beta-cells. The beta-cell is unique in containing much more OGT than any other cell type. This enables beta-cells to respond to physiological increases in the glucose concentration by converting glucose to the OGT substrate UDP-GlcNAc, thereby dynamically coupling intracellular O-linked protein glycosylation to the extracellular glucose concentration. As a result, the beta-cell also appears to be especially susceptible to disruption of the O-glycosylation pathway. The diabetogenic agent streptozotocin (STZ), a UDP-GlcNAc analogue, causes beta-cell toxicity by irreversibly inhibiting O-GlcNAcase, while the diabetogenic agent alloxan (ALX), also a UDP-GlcNAc analog irreversibly inhibits OGT. This review will summarize what is currently known about beta-cell O-glycosylation and expand upon historical observations of chemically-induced beta-cell toxicity in animals to develop a model suggesting how beta-cell O-glycosylation is also involved in the development and progression of type 2 diabetes in humans.
Impacts of Recharge Estimation on Groundwater Modeling for Arid Basins (2003)

Abstract Recharge is important for evaluating groundwater sustainability, and efficiently managing water supplies. In arid areas, especially in areas where the amount of aquifer production outweighs aquifer replenishment, it can be extremely important to quantify recharge and to spatially identify recharge distribution. Field sampling with a Guelph Permeameter helped identify specific recharge areas and the use of the Soil Water Assessment Tool (SWAT) provided meaningful recharge rates for an arid basin in southwest Texas. SWAT modeling for Wild Horse Basin generated an annual amount of recharge into the basin aquifer that was subsequently used in two transient MODFLOW simulations, one with the recharge distributed according to the sediment unit location (distributed zonation), and one with the recharge concentrated in cells adjacent to the front of the mountain chains surrounding the basin (mountain-front zonation). When comparing the results of the two recharge distributions on individual well hydrographs to historic data, mountain-front recharge appeared to improve model calibration efforts. This study indicates that recharge in arid basins cannot be determined solely by calibrating numerical models because it is so small that other simulation errors overwhelm reasonable differences. However, the location of the distribution of recharge appeared significant when calibrating individual well hydrographs. A deterministic analytical model like SWAT is a good way to estimate recharge in arid basins and create meaningful input parameters for numerical models like MODFLOW. MODFLOW was in turn able to evaluate the SWAT recharge estimations for Wild Horse Basin with Calibration and sensitivity analyses.
Anisotropically oriented electrospun matrices with an imprinted periodic micropattern: a new scaffold for engineered muscle constructs (2013)

Engineered muscle constructs provide a promising perspective on the regeneration or substitution of irreversibly damaged skeletal muscle. However, the highly ordered structure of native muscle tissue necessitates special consideration during scaffold development. Multiple approaches to the design of anisotropically structured substrates with grooved micropatterns or parallel-aligned fibres have previously been undertaken. In this study we report the guidance effect of a scaffold that combines both approaches, oriented fibres and a grooved topography. By electrospinning onto a topographically structured collector, matrices of parallel-oriented poly(ε-caprolactone) fibres with an imprinted wavy topography of 90 µm periodicity were produced. Matrices of randomly oriented fibres or parallel-oriented fibres without micropatterns served as controls. As previously shown, un-patterned, parallel-oriented substrates induced myotube orientation that is parallel to fibre direction. Interestingly, pattern addition induced an orientation of myotubes at an angle of 24° (statistical median) relative to fibre orientation. Myotube length was significantly increased on aligned micropatterned substrates in comparison to that on aligned substrates without pattern (436 ± 245 µm versus 365 ± 212 µm; p < 0.05). We report an innovative, yet simple, design to produce micropatterned electrospun scaffolds that induce an unexpected myotube orientation and an increase in myotube length.
Constituents of the leaf essential oil of <i>Persea indica</i> (L.) K. Spreng. (1993)

Abstract Steam‐distilled leaf oils of Persea indica (L.) K. Spreng. were investigated by GC, GC–MS, and NMR spectroscopy. More than fifty components were identified. Monoterpenes, comprising only 5%, were the smallest group, followed by avocadofurans with 37%, and sesquiterpenes with 49%. The most prominent of the latter were β‐caryophyllene with 18% and germacrene‐D with 15%. The most prominent avocadofuran was ( E )‐avocadienofuran with 16%. These furans substituted in the 2‐position seem to be typical of the genus Persea .
[De novo construction of mammalian synthetic inhibitory transcription factor and promoter pairs]. (2018)

Transcriptional regulation is crucial for regulated gene expression. Due to the complexity, it has been difficult to engineer eukaryotic transcription factor (TF) and promoter pairs. The few availabilities of eukaryotic TF and promotor pairs limit their practical use for clinical or industrial applications. Here, we report a de novo construction of synthetic inhibitory transcription factor and promoter pairs for mammalian transcriptional regulation. The design of synthetic TF was based on the fusion of DNA binding domain and Kruppel associated box transcription regulating domain (KRAB). The synthetic promoter was constructed by inserting the corresponding TF response element after SV40 promoter. We constructed and tested five synthetic inhibitory transcription factor and promoter pairs in cultured mammalian cells. The inhibition capability and orthogonality were verified by flow cytometry. In summary, we demonstrate the feasibility of constructing mammalian inhibitory TF and promoter pairs, which could be standardized for advanced gene-circuit design and various applications in the mammalian synthetic biology.
FlexISP (2014)

Conventional pipelines for capturing, displaying, and storing images are usually defined as a series of cascaded modules, each responsible for addressing a particular problem. While this divide-and-conquer approach offers many benefits, it also introduces a cumulative error, as each step in the pipeline only considers the output of the previous step, not the original sensor data. We propose an end-to-end system that is aware of the camera and image model, enforces natural-image priors, while jointly accounting for common image processing steps like demosaicking, denoising, deconvolution, and so forth, all directly in a given output representation (e.g., YUV, DCT). Our system is flexible and we demonstrate it on regular Bayer images as well as images from custom sensors. In all cases, we achieve large improvements in image quality and signal reconstruction compared to state-of-the-art techniques. Finally, we show that our approach is capable of very efficiently handling high-resolution images, making even mobile implementations feasible.
Ultra‐High Capacitance Nitride Films Utilizing Surface Passivation on Rugged Polysilicon (1992)

This paper describes high performance capacitors formed with silicon nitride dielectrics which meet the requirements for advanced stacked storage structures in 64 Mbit DRAM and beyond. A novel combination of a rugged polysilicon bottom electrode and an ultra‐thin nitride deposited with a surface passivation technique was used. We show that these structures can achieve up to 12 fF/μm2 for 3.3 V applications. We demonstrate that 4‐nm thick nitride films which feature low leakage, high capacitance, and excellent reliability can be fabricated. Time‐dependent dielectric breakdown analysis predicts operating lifetime improvements of more than 20 times for passivated films. Secondary ion mass spectroscopy analysis of these nitride dielectrics shows excellent physical properties. The film integrity is sufficient to extend the oxidation punchthrough limitation down to 4 nm. The rugged polysilicon electrode results in an effective area enhancement of more than 80% as compared to standard polysilicon.
Modification of Aldose Reductase by <i>S</i>-Nitrosoglutathione (1997)

Kinetic and structural changes in recombinant human aldose reductase (AR) due to modification by S-nitrosoglutathione (GSNO) were investigated. Incubation of the enzyme with 10-50 microM GSNO led to a time- and concentration-dependent inactivation of the enzyme, with a second-order rate constant of 0.087 +/- 0.009 M-1 min-1. However, upon exhaustive modification, 30-40% of the enzyme activity was retained. The non-inactivated enzyme displayed a 2-3-fold change in Km for NADPH and Km fordl-glyceraldehyde, whereas the Km for the lipid peroxidation product, 4-hydroxy-2-trans nonenal (HNE), was comparable to that of the untreated enzyme. The residual activity of the enzyme after GSNO treatment was less sensitive to inhibition by the active site inhibitor sorbinil or to activation by sulfate. Significantly higher catalytic activity was retained when the enzyme was modified in the presence of NADPH, suggesting relatively low reactivity of the E-NADPH complex with GSNO. The modification site was identified using site-directed mutants in which each of the solvent-exposed cysteines of the enzyme was replaced individually by serine. The mutant C298S was insensitive to GSNO, whereas the sensitivity of the mutants C303S and C80S was comparable to that of the wild-type enzyme. Electrospray ionization mass spectroscopy of the GSNO-modified enzyme revealed a major modified species (70% of the protein) with a molecular mass that was 306 Da higher than that of the untreated enzyme, which is consistent with the addition of a single glutathione molecule to the enzyme. The remaining 30% of the protein displayed a molecular mass that was not significantly different from that of the native enzyme. No nitrosated forms of the enzyme were observed. These results suggest that inactivation of AR by GSNO is due to the selective formation of a single mixed disulfide between glutathione and Cys-298 located at the NADP(H)-binding site of the enzyme.
Global modeling of microwave applications by combining the FDTD method and a general semiconductor device and circuit simulator (1999)

This paper presents the coupling of two commercially available simulation codes: DESSIS-ISE, a multidimensional semiconductor device and circuit simulator, and EMLAB-ISE, an electromagnetic-field solver based on the finite-difference time-domain (FDTD) method. Full-wave electromagnetics and nonlinear devices are simulated in a coupled self-consistent way using the lumped-element approach. The active region of the device is represented as a lumped element within the FDTD grid, while the packaging and waveguiding structures are modeled in their physical dimensions. For the nonlinear device, multidimensional semiconductor device simulation, as well as standard SPICE models, may be applied. Several examples show the capability of comprehensive analysis of microwave applications and the versatility in the simulation of the active elements. The coupling formalism is explained in detail, including time-step adjustment and biasing of active devices.
Effect of turosteride, a 5α-reductase inhibitor, on the Dunning R3327 rat prostatic carcinoma (1997)

Turosteride has antitumor activity on Dunning prostatic tumor growth and its role in prostatic cancer treatment is worthy of further investigation.
Biosynthesis Enhancement and Antioxidant and Anti-inflammatory Activities of Peanut (<i>Arachis hypogaea</i> L.) Arachidin-1, Arachidin-3, and Isopentadienylresveratrol (2006)

Arachis hypogaea L.; peanut; groundnut; resveratrol; stilbenoids; arachidin; antioxidant; anti-inflammation.
Synthesis of Enantiomerically Pure Cyclopropyl Trifluoroborates (2006)

Enantiomerically pure cyclopropylboronic esters were converted to the corresponding trifluoroborates, versatile inter­mediates for a variety of transformations. The new deprotection conditions allowed the utilization of general building blocks for ­cyclopropyl amines.
Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses (2020)

The emergence of SARS-CoV-2 and the ensuing explosive epidemic of COVID-19 disease has generated a need for assays to rapidly and conveniently measure the antiviral activity of SARS-CoV-2-specific antibodies. Here, we describe a collection of approaches based on SARS-CoV-2 spike-pseudotyped, single-cycle, replication-defective human immunodeficiency virus type-1 (HIV-1), and vesicular stomatitis virus (VSV), as well as a replication-competent VSV/SARS-CoV-2 chimeric virus. While each surrogate virus exhibited subtle differences in the sensitivity with which neutralizing activity was detected, the neutralizing activity of both convalescent plasma and human monoclonal antibodies measured using each virus correlated quantitatively with neutralizing activity measured using an authentic SARS-CoV-2 neutralization assay. The assays described herein are adaptable to high throughput and are useful tools in the evaluation of serologic immunity conferred by vaccination or prior SARS-CoV-2 infection, as well as the potency of convalescent plasma or human monoclonal antibodies.
Experimental cancer of the lung.Inhibition by vitamin A of the induction of tracheobronchial squamous metaplasia and squamous cell tumors (1967)

Syrian golden hamsters of both sexes received 10 intratracheal instillations each of 3 mg benzo[a]pyrene (BP) and 3 mg hematite suspended in 0.2 ml saline. One group received no further treatment and developed 13 squamous tumors and 13 cases of squamous metaplasia in 53 animals at risk. The second group, one week after the end of the BP treatment, started to receive twice weekly stomach tube feedings of vitamin A palmitate (5 mg or 5000 IU in 0.1 ml corn oil) continued for life. In this group of 46 animals at risk only one developed a microscopic squamous tumor in a bronchus and one developed a patch of squamous metaplasia in the trachea. The incidence of forestomach papillomas was also reduced markedly by vitamin A treatment. The authors suggest that vitamin A has a systemic inhibitory effect on the induction of squamous changes (metaplasia as well as benign and malignant squamous tumors) in the columnar mucous epithelium of the respiratory tract.
Single molecule localization deep within thick cells; a novel super‐resolution microscope (2015)

A novel 3D imaging system based on single-molecule localization microscopy is presented to allow high-accuracy drift-free (<0.7 nm lateral; 2.5 nm axial) imaging many microns deep into a cell. When imaging deep within the cell, distortions of the point-spread function result in an inaccurate and very compressed Z distribution. For the system to accurately represent the position of each blink, a series of depth-dependent calibrations are required. The system and its allied methodology are applied to image the ryanodine receptor in the cardiac myocyte. Using the depth-dependent calibration, the receptors deep within the cell are spread over a Z range that is many hundreds of nanometers greater than implied by conventional analysis. We implemented a time domain filter to detect overlapping blinks that were not filtered by a stringent goodness of fit criterion. This filter enabled us to resolve the structure of the individual (30 nm square) receptors giving a result similar to that obtained with electron tomography.
Off-chip 400 Mbps signal transmission: noise reduction using non-resonant lengths and other techniques (2002)

A 400 Mbps single-ended off-chip link including an open-drain driver and quasi-differential receiver has been designed, simulated, and measured. In this work, the design choices, in particular as related to noise tolerance, are discussed. To reduce the reflections inherent in signal propagation at a 400 Mbps rate, both the data and clock interconnects are restricted to non-resonant lengths. To further improve impedance matching, a daisy-chain termination is evaluated in which the net termination occurs after rather than before, the package pin. Other methods of reducing reflection noise are discussed, such as providing resistor terminations on an SCM or MCM package in order to reduce stub lengths. Measurements indicate good agreement with simulation; when the link is implemented with the noise-reducing features described the measured noise and jitter is sufficiently low for reliable operation at 400 Mbps.
SBL-Based Joint Sparse Channel Estimation and Maximum Likelihood Symbol Detection in OSTBC MIMO-OFDM Systems (2018)

This paper presents sparse Bayesian learning (SBL)-based schemes for approximately sparse channel estimation in an orthogonal space-time block coded (OSTBC) multiple-input multiple-output (MIMO) orthogonal frequency-division multiplexing (OFDM) wireless system. The parameterized prior-based SBL framework is employed to present a pilot scheme for an ill-posed OSTBC MIMO-OFDM channel estimation scenario. Maximum likelihood symbol detection (MLSD) has been incorporated in the expectation-maximization framework for SBL-based channel estimation. This has led to the development of a novel scheme for joint approximately sparse channel estimation and symbol detection. The proposed scheme performs SBL-based channel estimation in the E-step followed by a modified ML decision metric-based symbol detection in the M-step. Bayesian Cramér-Rao bounds are obtained for the genie minimum mean-squared error estimators corresponding to the SBL schemes. Closed-form bit error probability expressions are derived for the MLSD in the presence of SBL-based channel estimation errors. Simulation results are presented towards the end to validate the theoretical bounds and illustrate the performance of the proposed techniques.
Uptime : Strategies for Excellence in Maintenance Management (1995)

For all managers, comprehensive, realistic approach for improving asset performance. In uptime, goods and services flow out to customers without obstacles. In today's competitive environment, managers cannot rely on a single strategy to stay on top - they need to integrate the best strategies for asset management. Here's an overview of today's most reliable approaches: total productive maintenance reliability-centered maintenance, maintenance diagnostics and computerized maintenance management. Includes many practical examples for any manager who needs to see the 'big picture' of maintenance management.
A dynamic model for simulating a trip and fall during gait (2002)

The purpose of this study was to develop an analytical model to simulate a trip and fall during gait. The human body was modeled as a 12 degree-of-freedom linkage system. The kinematics of the lower extremity for one cycle of gait were obtained for a healthy subject using an optoelectronic three-dimensional data acquisition system. Inverse dynamics was used to compute the moments about the hip, knee and ankle joints of the lower extremity. These moments were then used as input actuators to the joints in to a forward dynamics model to simulate the swing phase of gait from toe-off to heel-strike. An optimization procedure to minimize errors associated with the computed experimental torque was applied to correct for mathematical instability. An experiment was performed to measure the three-dimensional foot--obstacle contact force for a healthy subject tripping on an obstacle during gait. The contact force was applied to the swing limb of the forward dynamics model for 0.09 s beginning at 0.04 s after toe-off. Tripping on an obstacle followed by a muscle-relaxed fall was simulated. The simulation results were visualized with animation software.
Uracil-DNA Glycosylase in the Extreme Thermophile Archaeoglobus fulgidus (2000)

Uracil-DNA glycosylase (UDG) is an essential enzyme for maintaining genomic integrity. Here we describe a UDG from the extreme thermophile Archaeoglobus fulgidus. The enzyme is a member of a new class of enzymes found in prokaryotes that is distinct from the UDG enzyme found in Escherichia coli, eukaryotes, and DNA-containing viruses. The A. fulgidus UDG is extremely thermostable, maintaining full activity after heating for 1.5 h at 95 degrees C. The protein is capable of removing uracil from double-stranded DNA containing either a U/A or U/G base pair as well as from single-stranded DNA. This enzyme is product-inhibited by both uracil and apurinic/apyrimidinic sites. The A. fulgidus UDG has a high degree of similarity at the primary amino acid sequence level to the enzyme found in Thermotoga maritima, a thermophilic eubacteria, and suggests a conserved mechanism of UDG-initiated base excision repair in archaea and thermophilic eubacteria.
Physical properties of silk fibers treated with ethylene glycol diglycidyl ether by the pad/batch method (1993)

Abstract This paper deals with the epoxide treatment of silk fabrics by the pad/batch method. The optimum reaction conditions, i.e., NaOH concentration, and reaction temperature were 2.5 g/L and 30°C, respectively. A weight gain of 8.5% was attained at a reaction time of 6 h. This value slightly increased to 10% after 24 h. The reactivity of tyrosine and basic amino acid residues was dependent on the reaction time and did not significantly differ from the results of epoxide‐treated silk fiber by the conventional method in tetrachloroethylene. The moisture regain slightly decreased at 4% weight gain and then increased with the epoxide content, exceeding the value of the untreated control. The crease recovery of the epoxide‐treated silk fabrics measured in the wet state was significantly improved, whereas that in the dry state was almost unchanged. The rate of photoyellowing of the epoxide‐treated silk fabrics by the pad/batch method was reduced significantly compared with that of the untreated control. Among the mechanical properties, elongation at break and tensile modulus remained unchanged, whereas the tensile strength slightly increased following the epoxide reaction. The thermal properties were evaluated by DSC and TGA and on the basis of the dynamic viscoelastic measurements. The DSC curve of the epoxide‐treated sample showed a slight increase of the decomposition temperature of silk fibroin. The rate of weight loss determined by TGA remained unchanged regardless of the chemical modification, whereas the peak of loss modulus became broader and shifted to lower temperature. The X‐ray diffractograms showed that the crystalline structure of silk fibers was not affected by the reaction with epoxides. © 1993 John Wiley & Sons, Inc.