gebhart/patrepeval huggingface dataset:
DNA REPAIR DEFECT IN SMOOTH MUSCLE CELL REPRODUCES FEATURES OF AGE-RELATED VASCULAR DISEASE IN MICE (2021)

Objective: DNA damage and repair responses have been implicated in age-related vascular disease. Evidence in mice shows that deletion of the Ercc1 gene, encoding an endonuclease that participates in several DNA repair systems, leads to features of accelerated ageing. It is not known from which cell type the vascular aging effect of Ercc1 deletion originates. A possibility is local DNA damage in vascular smooth muscle cells (VSMC). We determined features of vascular aging in a mouse model with specific Ercc1 deletion in smooth muscle cells (SMC-KO). Design and method: 12 SMC-KO and 13 Wild-type (WT) littermates were generated using alpha SM22-Cre driven cre-lox deletion of Ercc1. Blood pressure (BP) and in vivo vasodilation (reactive hyperemia: RH) were measured at the age of 22 and 23 weeks respectively. Mice were sacrificed at 24 weeks. Thoracic aorta and iliac artery endothelium-dependent (ED) and –independent (EI) relaxation were assessed (wire myograph). Results: There was no significant difference in BP between WT and SMC-KO. RH was decreased in SMC-KO vs. WT by 73% (P = 0.008). In SMC-KO mice maximal relaxation in iliac arteries to acetylcholine (ED) and sodium nitroprusside donor (EI) were decreased as compared to WT (ED: 48.04 ± 6.80 vs. 86.16 ± 3.68, P = 0.001; EI: 79.84 ± 4.04 vs. 93.78 ± 2.13, P = 0.022). In aorta similar observations were made (ED: 17.11 ± 2.29 vs. 73.42 ± 4.29, P = 0.0001; EI 55.87 ± 4.77 vs. 69.01 ± 5.17, p = 0.007). When added in the organ bath ITI-214 acutely increased aortic EI relaxation both in WT (from 69.01 ± 5.17 to 80.53 ± 2.05, P = 0.006) and SMC-KO (from 55.87 ± 4.77 to 67.17 ± 3.70, P = 0.084). Conclusions: Local DNA damage in SMC causes a decrease of vasodilator responses. This effect is blood pressure-independent. Given that responses to sodium nitroprusside, a nitric oxide (NO) donor, and PDE1, a cGMP-metabolising enzyme, were both involved, most probably a decline of NO-cGMP signalling is involved.
Microfluidic resonant waveguide grating biosensor system for whole cell sensing (2011)

We report on a fluidic resonant waveguide grating (RWG) biosensor system that enables medium throughput measurements of cellular responses under microfluidics in a 32-well format. Dynamic mass redistribution assays under microfluidics differentiate the cross-desensitization process between the β2-adrenoceptor agonist epinephrine and the adenylate cyclase activator forskolin mediated signaling. This system opens new possibility to study cellular processes that are otherwise difficult to achieve using conventional RWG configurations.
Iron-Mediated Radical Nitro-Cyclization Reaction of 1,6-Dienes (2009)

Sequential steps that involved radical addition of a nitro group to 1,6-dienes promoted by the thermal decomposition of iron nitrate(III) nonahydrate, cyclization, and trapping of the resulting terminal radicals by a chlorine atom in the presence of chloride salt afforded five-membered-ring compounds. The present reaction provides a practical method for the synthesis of nitro compounds due to its simple experimental procedure and its use of nontoxic and inexpensive iron reagents.
Characterization of carbonaceous materials using extraction with supercritical pentane (1980)

The use of carbonaceous adsorbents is limited by irreversible adsorption of some compounds so the use of supercritical pentane as an extracting solvent was examined. Carbon black appeared to be broken down slowly, but continuously, by the penane. To see if other types of carbon behaved similarly, high purity graphite, technical grade graphites, active carbons, and charcoals were examined. The extracts were characterized by uv spectroscopy, packed column chromatography using flame ionization and flame photometric detectors, and capillary GC/MS. The extracts were characteristic for each class of carbonaceous material. The high purity graphite yielded large, polycyclic aromatic compounds; the technical grade graphites yielded alkanes and alkyl-substituted benzenes and naphthalenes; the active carbons yielded alkanes, dienes, and small amounts of alkyl-substituted benzenes; and the charcoals yielded almost entirely alkanes in small amounts.
A 33 Year Time History of the Earth Dynamic Oblateness changes from SLR data (2008)

Satellite Laser Ranging (SLR) data tracked by the ILRS network have recorded the global nature of long-wavelength mass redistribution occurring within the Earth system for more than three decades. The second degree zonal harmonics of the Earth‘s gravity field, or the J2 coefficient is directly related to the Earth dynamic oblateness, or the dynamic shape factor, which represents how much its rounded shape flattens at the poles and widens at the equator. The variations in J2 are the results of imbalance of the climate induced mass changes between the tropical‘ area (in the range of the north and south 35 degree latitude) and the extra tropical area. Studying the variations in J2 has provided a clear vision of the largescale mass redistribution with a long-term signature within the Earth system from analysis of SLR data. Early analysis of 28-year time series of monthly SLR estimates of J2 [Cheng and Tapley, 2004] has indicated that in addition to the secular, 18.6 year tidal and seasonal variations, the J2 has undergone significant interannual variations with time scales of ~4-6 years and a decadal variation with a period of ~21 years. Two large interannual variations are related to the strong El Ninio-Southern Oscillation (ENSO) events during the periods of 1986-1991 and 1996-2002. Recent analysis including an additional five years of data suggests that the Earth has undergone another 3 fluctuations cycles starting from middle of 2002. Because of the significant aliasing effects in the GRACE data derived J2 coefficient and the J2 variations from SLR data is the most accurate measurement for the application of GRACE product to extract the signal of mass variations in ocean and hydrological. This paper presents detail analysis for the variations in J2 from analysis of multiple geodetic satellites over the period from 1976 to 2008, and a comparison with the monthly solutions from GRACE measurements.
<title>Embedded still image coder with rate-distortion optimization</title> (1998)

It is well known that the fixed rate coder achieves optimality when all coefficients are coded with the same rate-distortion (R-D) slope. In this paper, we show that the performance of the embedded coder can be optimized in a rate-distortion sense by coding the coefficients with decreasing R-D slope. We denote such coding strategy as rate-distortion sense by coding the coefficients with decreasing R-D slope. We denote such coding strategy as rate-distortion optimized embedding (RDE). RDE allocates the available coding bits first to the coefficient with the steepest R-D slope, i.e. the largest distortion decrease per coding bit. The resultant coding bitstream can be truncated at any point and still maintain an optimal R-D performance. To avoid the overhead of coding order transmission, we use the expected R-D slope which can be calculated from the coded bits and are available in both the encoder and the decoder. With the probability estimation table of the QM- coder, the calculation of the R-D slope can be just a look- up table operation. Experimental results show that the rate- distortion optimization significantly improves the coding efficiency in a wide range of coding rates.
Cybernetic modeling of microbial growth on multiple substrates (1984)

The internal regulatory processes, which underlie a variety of behavior in microbial growth on multiple substrates, are viewed as a manifestation of an invariant strategy to optimize some goal of the cells. A goal-seeking or cybernetic model is proposed here, with the optimization obased on a short-term perspective of response to the environment. The model parameters are determined from the growth data on single substrates. The model predicts the entire range of microbial growth behavior on multiple substrates from simultaneous utilization of all sugars to sequential utilization with pronounced diauxic lags. It is shown to predict the many variations of the diauxic phenomenon in different growth conditions. The transients in continuous culture growth on mixed substrates caused by varying the feed strategies are easily simulated by this model. The framework of this model can be applied to batch or continuous culture growth of many bacteria on different combinations of substrates.
Penetrating the Oxide Barrier in Situ and Separating Freestanding Porous Anodic Alumina Films in One Step (2005)

A simple method for penetrating the barrier layer of an anodic aluminum oxide (AAO) film and for detaching the AAO film from residual Al foil was developed by reversing the bias voltage in situ after the anodization process is completed. With this technique, we have been able to obtain large pieces of free-standing AAO membranes with regular pore sizes of sub-10 nm. By combining Ar ion milling and wetting enhancement processes, Au nanowires were grown in the sub-10 nm pores of the AAO films. Further scaling down of the pore size and extension to the deposition of nanowires and nanotubes of materials other than Au should be possible by further optimizing this procedure.
Menaquinone Biosynthesis in Escherichia coli :  Identification of 2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a Novel Intermediate and Re-Evaluation of MenD Activity (2007)

Menaquinone is an electron carrier in the respiratory chain of Escherichia coli during anaerobic growth. Its biosynthesis involves (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) as an intermediate, which is believed to be derived from isochorismate and 2-ketoglutarate by one of the biosynthetic enzymes-MenD. However, we found that the genuine MenD product is 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic acid (SEPHCHC), rather than SHCHC. This is supported by the following findings: (i) isochorismate consumption and SHCHC formation are not synchronized in the enzymic reaction, (ii) the rate of SHCHC formation is independent of the enzyme concentration, (iii) SHCHC is not formed in weakly acidic or neutral solutions in which the isochorismate substrate is readily consumed by MenD, and (iv) the MenD turnover product, formed under conditions disabling SHCHC formation, possesses spectroscopic characteristics consistent with the structure of SEPHCHC and spontaneously undergoes 2,5-elimination to form SHCHC and pyruvate in weakly basic solutions. Two properties of the intermediate, ultraviolet transparency and chemical instability, provide a rationale for the fact that SHCHC has been consistently mistaken as the MenD product. In accordance with these findings, MenD was rediscovered to be a highly efficient enzyme with a high second-order rate constant and should be renamed SEPHCHC synthase. Intriguingly, the enzymatic activity responsible for conversion of SEPHCHC into SHCHC appears not to associate with any of the known enzymes in menaquinone biosynthesis but is present in the crude extract of E. coli K12, suggesting that a genuine SHCHC synthase remains to be identified to fully elucidate the ubiquitous biosynthetic pathway.
Suppression of Amyloid Deposition Leads to Long-Term Reductions in Alzheimer's Pathologies in Tg2576 Mice (2009)

In amyloid precursor protein (APP) models of amyloid deposition, the amount of amyloid deposits increase with mouse age. At a first approximation, the extent of amyloid accumulation may either reflect small excesses of production over clearance that accumulate over time or, alternatively, indicate a steady-state equilibrium at that age, reflecting the instantaneous excess of production over clearance, which increases as the organism ages. To discriminate between these options, we reversibly suppressed amyloid deposition in Tg2576 mice with the anti-Abeta antibody 2H6, starting at 8 months, just before the first histological deposits can be discerned. Six months later, we stopped the suppression and monitored the progression of amyloid accumulation in control APP mice and suppressed APP mice over the next 3 months. The accumulation hypothesis would predict that the rate of amyloid from 14 to 17 months would be similar in the suppressed and control mice, while the equilibrium hypothesis would predict that the increase would be faster in the suppressed group, possibly catching up completely with the control mice. The results strongly support the accumulation hypothesis, with no evidence of the suppressed mice catching up with the control mice as predicted by equilibrium models. If anything, there was a slower rate of increase in the suppressed APP mice than the control mice, suggesting that a slow seeding mechanism likely precedes a rapid fibrillogenesis in determining the extent of amyloid deposition.
A multichannel distorted wave perturbation treatment applied to molecule–surface scattering (1984)

An approximate quantum mechanical approach to the scattering of systems with several degrees of freedom is developed. It is based on the exact (numerical) solution of the close coupled equations for subsets of the internal states and the coupling of these subsets to each other by perturbation theory. The calculation of the multichannel distorted wave solutions and their perturbative coupling is done simultaneously. Application to diffractive and rotationally inelastic scattering of H2 from a model corrugated surface is given and compared to earlier approximate diffractive sudden close coupled rotation calculations.
Synthesis and evaluation of fluorinated calcium chelators with enhanced relaxation characteristics (1992)

Abstract The fluorinated calcium ion chelator 5F BAPTA [1,2‐bis(2‐amino‐5‐fluorophenoxy)ethane‐ N , N , N ′, N ′‐tetra‐acctic acid] was used for the determination of cytosolic Ca 2+ ion levels in cells and tissues by 19 F NMR. The possibility of enhancing the sensitivity of these measurements by modifying the relaxation behavior of the chelator was evaluated. These strategies involved the design of a chelator with reduced T 1 value viz. 5F RBAPTA {1,2‐bis [2‐amino‐4‐(1‐carboxy‐2‐methyl‐2‐propyl)‐5‐fluorophenoxy]ethane‐ N , T , N ′, N ‐tetraacetic acid}, and the evaluation of chelator with slower exchange characteristics, viz 5F BenzEGTA [1‐(2‐amino‐5‐fluorophenoxy)‐2‐(2‐aminoethoxy)ethane‐ N , N , N ′, N ′‐tetraacetic acid]. Both analogs exhibit chemical shift differences on calcium complexation which are similar to those of the parent compound, 5F BAPTA. In the case of BenzEGTA, a considerably greater p H dependence of the apparent calcium, dissociation constant, K D , also results from the presence of a tertiary amine with a p K value above the physioligical range. Additionally, the synthetic approach used for RBAPTA can lead to wide variety of derivatives with variable chemical, biochemical and NMR properties.
Prevalence of retinopathy in Caucasian type 2 diabetic patients from the South of Brazil and relationship with clinical and metabolic factors (2005)

Diabetic retinopathy (DR) is a sight-threatening chronic complication of diabetes mellitus and is the leading cause of acquired blindness in adults. In this cross-sectional study, we investigated the prevalence of and the factors associated with DR in an analysis of 210 consecutive and unrelated Brazilian Caucasians with type 2 diabetes mellitus. Retinopathy was evaluated by ophthalmoscopy and/or biomicroscopy through dilated pupils. The relationship between clinical and metabolic variables and the presence of DR was assessed by logistic regression analysis. DR was detected in 99 of the 210 patients (47%). In the univariate logistic regression analyses, male sex, duration of diabetes, body mass index, glycated hemoglobin, C-peptide, LDL cholesterol, smoking, and albumin excretion rate were found to be associated with the presence of DR. However, the multiple logistic regression analysis showed that only duration of diabetes (odds ratio (OR) = 1.15, 95% CI = 1.09-1.22; P < 0.001), glycated hemoglobin (OR = 1.21, 95% CI = 1.01-1.46; P = 0.047) and albumin excretion rate > 100 microg/min (OR = 12.72, 95% CI = 3.89-41.56; P < 0.001) were independently associated with DR. Although DR was found to be frequent among Brazilian type 2 diabetic patients, its prevalence was within the range observed in other Caucasian populations. Our findings emphasize the need for good glycemic control in order to prevent or delay the onset of DR, since the most well-known risk factors for the development of this complication in type 2 diabetes mellitus, such as duration of diabetes, glycated hemoglobin and albumin excretion rate were independently related to DR.
Handbook of Nutritional Support (1997)

Handbook on the principles of nutritional assessment, recognition of the need for nutritional intervention, and provision of nutritional support. Covers nutrition in pregnancy. In outline format.
GAN-Based Data Augmentation Strategy for Sensor Anomaly Detection in Industrial Robots (2021)

In the current industry world, the industrial robot has emerged as a critical device to make the manufacturing process more efficient through automation. However, abnormal operation of industrial robots caused by sensor failures may interrupt the entire manufacturing process, thereby increasing production costs. In this paper, we first propose a domain-specific framework consisting of offline training and online inference to effectively detect anomalies in the scenario of industrial robotic sensors. In a nutshell, the framework can be identified in three folds: (1) the offline training obtaining historical data from the database to train the time series and anomaly detection models; (2) the online inference deploying the offline trained models for online anomaly detection in real-time; (3) the incremental learning updating the online model for a new type of anomalies. We then propose an improved Generative Adversarial Networks (GANs) named MSGAN with the adaptive update strategy mechanism based on WGAN-GP to generate fake anomaly samples, improving anomaly detection accuracy. Specifically, the Wasserstein distance with the gradient penalty is introduced to improve training stability and sample quality. Moreover, adapting the generator’s complexity in robotic sensors, an adaptive update strategy based on the loss change ratio is adopted to speed up training convergence. Extensive experiments based on real robotic sensor datasets demonstrate the effectiveness of the proposed framework. Moreover, the results demonstrate that the detection accuracy can be improved by the synthetic samples based on the proposed MSGAN algorithm.
Exact NMR simulation of protein-size spin systems using tensor train formalism (2014)

We introduce a new method, based on alternating optimization, for compact representation of spin Hamiltonians and solution of linear systems of algebraic equations in the tensor train format. We demonstrate the method's utility by simulating, without approximations, a 15 N NMR spectrum of ubiquitin-a protein containing several hundred interacting nuclear spins. Existing simulation algorithms for the spin system and the NMR experiment in question either require significant approximations or scale exponentially with the spin system size. We compare the proposed method to the SPINACH package that uses heuristic restricted state space techniques to achieve polynomial complexity scaling. When the spin system topology is close to a linear chain (e.g., for the backbone of a protein), the tensor train representation is more compact and can be computed faster than the sparse representation using restricted state spaces.
Edge Detection and Feature Line Tracing in 3D-Point Clouds by Analyzing Geometric Properties of Neighborhoods (2016)

This paper presents an automated and effective method for detecting 3D edges and tracing feature lines from 3D-point clouds. This method is named Analysis of Geometric Properties of Neighborhoods (AGPN), and it includes two main steps: edge detection and feature line tracing. In the edge detection step, AGPN analyzes geometric properties of each query point’s neighborhood, and then combines RANdom SAmple Consensus (RANSAC) and angular gap metric to detect edges. In the feature line tracing step, feature lines are traced by a hybrid method based on region growing and model fitting in the detected edges. Our approach is experimentally validated on complex man-made objects and large-scale urban scenes with millions of points. Comparative studies with state-of-the-art methods demonstrate that our method obtains a promising, reliable, and high performance in detecting edges and tracing feature lines in 3D-point clouds. Moreover, AGPN is insensitive to the point density of the input data.
Electrochemical Performance of a Novel Cathode material &ldquo;LiFeOF&rdquo; for Li-ion Batteries (2015)

Iron-based conversion cathode, FeOF is attractive, because of the low cost and the large specific capacity. However, the synthesis is not easy and it cannot be used as cathode against carbonaceous anode. To overcome these drawbacks, we focused on the LiFeOF phase, which has the same chemical composition as the discharged intermediate product of FeOF cathode. LiFeOF can be easily synthesized from LiF and FeO by the dry ball-milling method at room temperature. The reversible capacity was 292 mAh g−1 with an average voltage of 2.5 V and an energy density over 700 Wh kg−1, which is higher than that of LiFePO4. In addition, we confirmed the feasibility of LiFeOF cathode against Li4Ti5O12 anode.
Fundamentals of heat and mass transfer, 2nd edition (1990)

This text introduces the physical effects underlying heat and mass transfer phenomena and develops methodologies for solving a variety of real-world problems. It emphasizes the importance of conservation principles, particularly the first law of thermodynamics, in heat transfer analysis, and has been expanded to encompass principles and problems in mass transfer. Includes numerous examples and problems.
Epitaxy of Dissimilar Materials (1995)

Differences in crystal structure, bonding, and materials properties play important roles in dissimilar materials epitaxy. Emphasis is placed on how these differences affect the growth of dissimilar materials heterostructures. Examples of the growth of elemental metals and semi-metals (AI, Ag, Sb, Bi); metallic and semi-metal compounds (transition-metal group III compounds with CsCI crystal structure, rare-earth group V compounds with NaCl crystal structure, orthorhombic YbSb2, Fe3AI'_xSix with BiF3 crystal structure); magnetic compounds (tetragonal ,-MnAI, hexagonal �­ MnAs); and insulators (rare-earth trifluorides with tysonite crystal struc­ ture, metal fluorides with the CaF2 crystal structure) on compound semi­ conductors are used to demonstrate the issues involved. The use of tem­ plate layers is crucial in controlling the orientation and crystal quality of the epitaxial layers.