gebhart/patrepeval huggingface dataset:
A new system for management of the “Master Oceanographic Observation Data Set” (MOODS) (1987)

The Naval Oceanographic Office (NAVOCEANO) at NSTL, Miss., collects, analyzes, and displays oceanographic and hydrographic data to support naval operations. The Fleet Numerical Oceanography Center (FNOC) in Monterey, Calif., serves as the production center for most analysis and forecast fields of oceanographic and meteorological parameters, including daily environmental tactical support products for the operating forces. Until 1985, FNOC was responsible for the Master Oceanographic Observation Data Set (MOODS). NAVOCEANO has obtained MOODS from FNOC in order to provide for its maintenance and updating. The term “maintenance” in this case means making data contained in MOODS available to investigators at NAVOCEANO and available to other data requestors that NAVOCEANO is obligated to serve. “Updating” means adding to MOODS both recent observations and data not already contained in MOODS, as well as improving the quality of the data in MOODS. NAVOCEANO is in the process of developing a computer‐based system to perform those functions.
A patch antenna with a top dielectric layer (2004)

The paper presents a technique of enhancing the gain of a patch antenna. The enhancement is realized by putting a dielectric layer on top of the patch. The analysis is performed using the finite-difference time domain method, where Yee's rectangular mesh is used with Liao's second order absorbing boundary condition (Taflove, A. "Computational electrodynamics", Artech House, 1995). The assumptions used in the analysis are as follows: the bottom (substrate) and top dielectric layers are lossless; the ground plane is of infinite extent; the patch is infinitesimally thin. As the top dielectric layer thickness, B/sub top/, increases, the input impedance shows oscillatory variations, with a period slightly larger than one-half of the guided-wave length of a plane wave propagating in an unbounded dielectric material. It is also found that, as B/sub top/ increases, the radiation pattern becomes narrower and the gain reaches a maximum value. However, as B/sub top/ further increases, the gain decreases due to rising side-lobe levels. A gain increase of 7.2 dB is obtained at B/sub top/=1.48/spl lambda//sub 8/ for /spl epsiv//sub r/=2.07.
Phosphorylation of insulin receptor substrates (IRS-1 and IRS-2) is attenuated following cecal ligation and puncture in mice (2023)

CLP impaired insulin-induced tyrosine phosphorylation of both IRS-1 in muscle and IRS-2 in liver. These findings suggest that the molecular mechanism underlying CLP-induced insulin resistance involves impaired IRS-1/IRS-2 phosphorylation.
Laccase Gene Expression and Vinasse Biodegradation by Trametes hirsuta Strain Bm-2 (2015)

Vinasse is the dark-colored wastewater that is generated by bioethanol distilleries from feedstock molasses. The vinasse that is generated from molasses contains high amounts of pollutants, including phenolic compounds and melanoindin. The goal of this work was to study the expression of laccase genes in the Trametes hirsuta strain Bm-2, isolated in Yucatan, Mexico, in the presence of phenolic compounds, as well as its effectiveness in removing colorants from vinasse. In the presence of all phenolic compounds tested (guaiacol, ferulic acid, and vanillic acid), increased levels of laccase-encoding mRNA were observed. Transcript levels in the presence of guaiacol were 40 times higher than those in the control. The lcc1 and lcc2 genes of T. hirsuta were differentially expressed; guaiacol and vanillin induced the expression of both genes, whereas ferulic acid only induced the expression of lcc2. The discoloration of vinasse was concomitant with the increase in laccase activity. The highest value of enzyme activity (2543.7 U/mL) was obtained in 10% (v/v) vinasse, which corresponded to a 69.2% increase in discoloration. This study demonstrates the potential of the Bm-2 strain of T. hirsuta for the biodegradation of vinasse.
Beclomethasone Microparticles for Wet Inhalation, Produced by Supercritical Assisted Atomization (2010)

Supercritical assisted atomization (SAA) was used to produce micronized particles of beclomethasone dipropionate (BDP) to be used for inhalation therapy. Methanol, acetone, acetone + water 9% v/v, and methanol + water 4% v/v were tested as liquid solvents to explore their influence on particle size and crystalline structure of the precipitated powder. Particles with narrow size distributions (PSD) were obtained by changing the SAA process operating conditions. In particular, using acetone + water 9% v/v with a BDP concentration of 90 mg/mL, crystalline particles ranging between 0.2 and 4.7 μm were produced and 70% by volume of these particles ranged between 1and 3 μm. PSD stability analysis in a wet formulation showed that BDP powder obtained by SAA does not modify over a long period of time. The results obtained on the laboratory scale plant were successfully reproduced on a pilot plant and a further refinement of the operating conditions was performed. About 30 g of BDP microparticles were produced per batch and a recovery of about 93 wt % of the micronized powder with respect to the injected quantity was obtained. The largest volumetric fraction of BDP particles falling in the range 1−3 μm was 83% on the pilot scale.
Brown midrib-3 Corn Silage and Heat Extruded Soybeans for Early Lactating Dairy Cows (1981)

Twenty-eight Holstein cows individually were fed brown midrib-3 or normal corn silage in combination with heated or unheated soybeans as complete rations from wk 3 to wk 10 postpartum in a 2 2 factorial arrangement. Each of the four rations contained 65% silage, 31% soybeans, and 4% of a vitamin-mineral supplement (dry basis). Actual milk (kg/day), milk fat, and milk protein for cows fed brown midrib-3 and normal were: 35.4, 2.82%, and 2.96% and 33.1, 3.15%, and 2.89%. The reduced milk fat percent was consistent with reduced tureen pH and acetate:propionate ratio by cows fed brown midrib-3. Cows fed normal showed a high incidence of ketosis, possibly related to a lower energy intake.
Synthesis of Some Glycine Nicotinates and in-vivo Evaluation of Anti-Convulsant Activity for their Brain specific Slow Release Action (2021)

Aim: Purpose of the present work is to synthesize the pro-pro-drugs of Glycine and evaluate for their anticonvulsant activity in albino rats with brain specific sustained release action in various biological fluids. Materials and Methods: Prepared and synthesized propro-drugs of Glycine nicotinate by esterification with different alcohols and admiration with nicotinic acid. In present work pro-pro drug of Glycine nicotinate were synthesized by taking the Dihydropyridine as carrier molecules. The synthesized compounds have been characterized by IR, IH-NMR, C, H, N analysis and Mass spectral techniques and evaluated for their anticonvulsant activity in albino rats by chemo convulsion method as well for oxidation in various biological fluids. All the synthesized compounds were found to be active and stable in biological fluids. Oxidized form of the conjugate inside the brain act as pro-pro-drug, which on hydrolysis yields parent drug in sustained release manner. The significance of the work is to treat neurological disorder implicated by Glycine. Results: Pro-pro-drug of Glycine nicotinate were synthesized effectively and showed anticonvulsant activity in slow release manners. Conclusion: This work has given a new synthetic strategy and result of anticonvulsant screening was found encouraging.
Pharmacological Levels of Withaferin A (Withania somnifera) Trigger Clinically Relevant Anticancer Effects Specific to Triple Negative Breast Cancer Cells (2014)

Withaferin A (WA) isolated from Withania somnifera (Ashwagandha) has recently become an attractive phytochemical under investigation in various preclinical studies for treatment of different cancer types. In the present study, a comparative pathway-based transcriptome analysis was applied in epithelial-like MCF-7 and triple negative mesenchymal MDA-MB-231 breast cancer cells exposed to different concentrations of WA which can be detected systemically in in vivo experiments. Whereas WA treatment demonstrated attenuation of multiple cancer hallmarks, the withanolide analogue Withanone (WN) did not exert any of the described effects at comparable concentrations. Pathway enrichment analysis revealed that WA targets specific cancer processes related to cell death, cell cycle and proliferation, which could be functionally validated by flow cytometry and real-time cell proliferation assays. WA also strongly decreased MDA-MB-231 invasion as determined by single-cell collagen invasion assay. This was further supported by decreased gene expression of extracellular matrix-degrading proteases (uPA, PLAT, ADAM8), cell adhesion molecules (integrins, laminins), pro-inflammatory mediators of the metastasis-promoting tumor microenvironment (TNFSF12, IL6, ANGPTL2, CSF1R) and concomitant increased expression of the validated breast cancer metastasis suppressor gene (BRMS1). In line with the transcriptional changes, nanomolar concentrations of WA significantly decreased protein levels and corresponding activity of uPA in MDA-MB-231 cell supernatant, further supporting its anti-metastatic properties. Finally, hierarchical clustering analysis of 84 chromatin writer-reader-eraser enzymes revealed that WA treatment of invasive mesenchymal MDA-MB-231 cells reprogrammed their transcription levels more similarly towards the pattern observed in non-invasive MCF-7 cells. In conclusion, taking into account that sub-cytotoxic concentrations of WA target multiple metastatic effectors in therapy-resistant triple negative breast cancer, WA-based therapeutic strategies targeting the uPA pathway hold promise for further (pre)clinical development to defeat aggressive metastatic breast cancer.
Intertemporal decision-making-related brain states predict adolescent drug abuse intervention responses (2019)

Adolescent drug misuse represents a major risk factor for long-term drug use disorders. However, wide individual differences in responses to first-line behavioral therapies targeting adolescent drug misuse limit critical early intervention. Identifying the neural signatures of those adolescents most likely to respond to an intervention would potentially guide personalized strategies for reducing drug misuse. Prior to a 14-week evidence-based intervention involving combinations of contingency management, motivational enhancement, and cognitive behavioral therapy, thirty adolescent alcohol and/or cannabis users underwent fMRI while performing a reward delay discounting (DD) task tapping an addiction-related cognition. Intervention responses were longitudinally characterized by both urinalysis and self-report measures of the percentage of days used during treatment and in post-treatment follow-up. Group independent component analysis (ICA) of task fMRI data identified neural processing networks related to DD task performance. Separate measures of wholesale recruitment during immediate reward choices and within-network functional connectivity among selective networks significantly predicted intervention-related changes in drug misuse frequency. Specifically, heightened pre-intervention engagement of a temporal lobe "reward motivation" network for impulsive choices on the DD task predicted poorer intervention outcomes, while modes of functional connectivity within the reward motivation network, a prospection network, and a posterior insula network demonstrated robust associations with intervention outcomes. Finally, the pre-intervention functional organization of the prospection network also predicted post-intervention drug use behaviors for up to 6 months of follow-up. Multiple functional variations in the neural processing networks supporting preference for immediate and future rewards signal individual differences in readiness to benefit from an effective behavioral therapy for reducing adolescent drug misuse. The implications for efforts to boost therapy responses are discussed.
Lysozyme Degradation by the Bovine Multicatalytic Proteinase Complex (Proteasome):  Evidence for a Nonprocessive Mode of Degradation (1999)

The multicatalytic proteinase complex (MPC, proteasome) is composed of 28 subunits organized into four rings surrounding a water-filled canal. The catalytic centers face the inner canal confining protein substrates to an enclosed space. Experimental findings obtained with MPC from archaebacteria suggest that degradation of proteins by the complex is processive and have led to the proposal that the lengths of the peptides formed during degradation depend on the distances between active sites in the catalytic chamber. To test whether these postulates are valid for the MPC from a higher organism, we examined the size distributions of products formed early versus late in the course of protein degradation using reduced carboxamidomethylated lysozyme (RCM-lysozyme) and MPC from bovine spleen and pituitary. The majority of final degradation products ranged in length from 6 to 20 amino acids without a clear predilection for peptides of a particular, uniform size. Our observations suggest that selection of cleavage sites is governed by the amino acid sequence specificity of the MPC catalytic sites rather than the distances between the active sites. Early in the course of degradation, peptides with masses between 5 and 10 kDa accumulated in more than 80-fold molar excess over the MPC, indicating dissociation of large, partially degraded intermediates. Initial cleavages occurred at distances between 10 and 44 amino acids from the N- or C-terminus of the molecule and often involved removal of a fragment from both the N- and C-termini of RCM-lysozyme. Our data indicate that degradation of proteins by MPCs from higher organisms involves a nonprocessive mechanism comprised of multiple, independent cleavages with dissociation of degradation intermediates. A general model for protein degradation by the MPC is discussed.
Issues in participative use of an historic city millennial Web site (2002)

Staff at the University of the West of England (UWE) have been engaged with other agencies in a collaborative process to create a millennial Web site for the citizens and city of Wells. The development of this site on the WWW is a part of a wider investigation which is both an attempt to understand the effective design of Web-based records of localities in terms of content and structure, as well as to set up a method for recording historic sites. The initial goals are to: record the built environment at the turn of the millenium; integrate this with existing records and archives; create a vehicle for the general public to contribute to records; and assist all sections of the community in gaining a richer understanding of their heritage. This paper examines the expectations of the agencies involved, the manner in which these have been implemented on the Web using multimedia, and the feedback and response to date, which has in turn modified the focus of the project.
ChemInform Abstract: REARRANGEMENTS IN LEWIS ACID CATALYZED DIELS‐ALDER REACTIONS. ROUTE TO SUBSTITUTED BICYCLO(2.2.1)HEPTANONES (1979)

Abstract Dimethylbutadien (I) reagiert mit Methacrolein (II) bei 150°C zu einem Addukt (III), das sich mit Zinntetrachlorid zu (IV) umlagert.
AMPK alterations in cardiac physiology and pathology: enemy or ally? (2006)

AMP-activated protein kinase (AMPK) has emerged as a key regulator of energy metabolism in the heart. The high energy demands of the heart are primarily met by the metabolism of both fatty acids and glucose, both processes being regulated by AMPK. During myocardial ischaemia a rapid activation of AMPK occurs, resulting in an activation of both glucose uptake and glycolysis, as well as an increase in fatty acid oxidation. This activation of AMPK has the potential to increase energy production and to inhibit apoptosis, thereby protecting the heart during the ischaemic stress. However, at clinically relevant high levels of fatty acids, ischaemic-induced activation of AMPK also stimulates fatty acid oxidation during and following ischaemia. This can contribute to ischaemic injury secondary to an inhibition of glucose oxidation, which results in a decrease in cardiac efficiency. In a number of other non-cardiac tissues, AMPK has been shown to have pro-apoptotic effects. As a result, the question of whether AMPK activation benefits or harms the ischaemic heart remains controversial. The role of AMPK in cardiac hypertrophy is also controversial. Activation of AMPK inhibits protein synthesis, and may be an adaptive response to pathological cardiac hypertrophy. However, none of mouse models of AMPK deficiency (excluding those that may involve the gamma2 subunit mutations) demonstrate increased cardiac mass, suggesting that AMPK is not essential for restriction of cardiac growth. In addition to the potential effects of AMPK on myofibrillar hypertrophy associated with pressure overload, there is also controversy with respect to the cardiac hypertrophy associated with the gamma2 subunit mutations. In the cardiac hypertrophy associated with glycogen overload, both activating and inactivating mutations of AMPK in mice are associated with a marked cardiac hypertrophy. This review will address the issue of whether AMPK activation acts as an enemy or ally to the ischaemic and hypertrophied heart. Resolving this issue has important implications as to whether therapeutic approaches to protect the ischaemic heart should be developed which either activate or inhibit AMPK.
Phase-change nanoclusters embedded in a memristor for simulating synaptic learning (2019)

A type of memristor with a structure of Pd/Nb : AlNO/Pd was designed and fabricated in this work. Its filaments are embedded by phase-change NbO nanoclusters confirmed by the analysis of cross-sectional profiles. The resistive switching mechanism includes the contribution of oxygen vacancy (VO) migration and the structural evolution of phase-change nanoclusters. The system experiences two types of kinetics under external stimulations to replicate the critical dynamics in real synapses: VO migration corresponding to the dynamics of the Ca2+ flux and transmitter release at the pre-synapse, and the phase change of the NbO nanoclusters corresponding to the ionic flux modulated by the post-synaptic potential (current). It was found that the memristor can respond to a set of pulse stimulations in a pattern containing a slow linear increase term and a periodic oscillation term, suggesting that the output signals might be encoded. The simulation of long-term plasticity indicates that the memristor is suitable for diverse learning protocols, including spike-rate dependent plasticity and spike-timing-dependent plasticity. Our work proposes an elementary cell that closely approximates biological synapses and is usable for brain-like computing.
Antimicrobial activity of four cationic peptides immobilised to poly-hydroxyethylmethacrylate (2016)

The objective of this study was to immobilise and characterise a variety of antimicrobial peptides (AMPs) onto poly-hydroxyethylmethacrylate (pHEMA) surfaces to achieve an antibacterial effect. Four AMPs, viz. LL-37, melimine, lactoferricin and Mel-4 were immobilised on pHEMA by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) which assisted covalent attachment. Increasing concentrations of AMPs were immobilised to determine the effect on the adhesion of Pseudomonas aeruginosa and Staphylococcus aureus. The AMP immobilised pHEMAs were characterised by X-ray photoelectron spectroscopy (XPS) to determine the surface elemental composition and by amino acid analysis to determine the total amount of AMP attached. In vitro cytotoxicity of the immobilised pHEMA samples to mouse L929 cells was investigated. Melimine and Mel-4 when immobilised at the highest concentrations showed 3.1 ± 0.6 log and 1.3 ± 0.2 log inhibition against P. aeruginosa, and 3.9 ± 0.6 log and 2.4 ± 0.5 log inhibition against S. aureus, respectively. Immobilisation of LL-37 resulted in up to 2.6 ± 1.0 log inhibition against only P. aeruginosa, but no activity against S. aureus. LFc attachment showed no antibacterial activity. Upon XPS analysis, immobilised melimine, LL-37, LFc and Mel-4 had 1.57 ± 0.38%, 1.13 ± 1.36%, 0.66 ± 0.47% and 0.73 ± 0.32% amide nitrogen attached to pHEMA compared to 0.12 ± 0.14% in the untreated controls. Amino acid analysis determined that the total amount of AMP attachment to pHEMA was 44.3 ± 7.4 nmol, 3.8 ± 0.2 nmol, 6.5 ± 0.6 nmol and 48.9 ± 2.3 nmol for the same peptides respectively. None of the AMP immobilised pHEMA surfaces showed any toxicity towards mouse L929 cells. The immobilisation of certain AMPs at nanomolar concentration to pHEMA is an effective option to develop a stable antimicrobial surface.
Power reference tracking of a large-scale industrial freezer system for ancillary service delivery (2013)

This paper outlines the first steps to enable a set of large industrial freezer warehouse units to act as flexible loads in a smart grid setting. We describe the modeling and identification of individual freezer units, focusing on the governing thermal dynamics and corresponding electric-energy consumption. By relying on the model identified, we show how optimal supervisory control inputs can be computed with the goal of tracking a predefined power consumption schedule. Our algorithm is applied to a real freezer warehouse, and its performance with respect to power reference tracking is evaluated and discussed. We show that the freezer system can follow a predefined power schedule despite the currently limited availability of actuators.
Computer applications for prediction of protein&ndash;protein interactions and rational drug design (2009)

In recent years, protein-protein interactions are becoming the object of increasing attention in many different fields, such as structural biology, molecular biology, systems biology, and drug discovery. From a structural biology perspective, it would be desirable to integrate current efforts into the structural proteomics programs. Given that experimental determination of many protein-protein complex structures is highly challenging, and in the context of current high-performance computational capabilities, different computer tools are being developed to help in this task. Among them, computational docking aims to predict the structure of a protein-protein complex starting from the atomic coordinates of its individual components, and in recent years, a growing number of docking approaches are being reported with increased predictive capabilities. The improvement of speed and accuracy of these docking methods, together with the modeling of the interaction networks that regulate the most critical processes in a living organism, will be essential for computational proteomics. The ultimate goal is the rational design of drugs capable of specifically inhibiting or modifying protein-protein interactions of therapeutic significance. While rational design of protein-protein interaction inhibitors is at its very early stage, the first results are promising.