gebhart/patrepeval huggingface dataset:
Copper nanoflowers as effective antifungal agents for plant pathogenic fungi (2016)

Flower-shaped copper nanoparticles were synthesised by a green and ecofriendly chemical reduction approach using copper sulphate and cytyltrimethal ammonium bromide. The UV-vis spectrophotometer analysis showed maximum absorption at about 552 nm, which is specifically reported for copper nanoparticles. The crystal lattice structure of copper nanoflowers was confirmed by X-ray diffraction analysis. Further, the transmission electron microscopic studies revealed the flower shape copper nanoparticles in the size range of 100-500 nm. The stability of thus synthesised copper nanoflowers was assessed by zeta potential analysis, which was found to be 35 mV indicating the most stable nature of nanoflowers. The antifungal activity of these copper nanoflowers was evaluated by Kirby-Bauer disk diffusion method against selected common plant pathogenic fungi. It was found that the chemosynthesised copper nanoflowers demonstrated significant inhibitory activity against the plant pathogenic <i>Aspergillus niger</i>, <i>Fusarium moniliforme</i>, <i>F. culmorum</i>, <i>F. oxysporum</i> and <i>F. tricinctum</i>. The maximum antifungal activity was shown against <i>A. niger</i> followed by <i>F. moniliforme</i>, <i>F. oxysporum</i> and <i>F. tricinctum</i>, whereas the minimum activity was reported against <i>F. culmorum</i>. Similarly, the effect of the copper nanoflowers was also evaluated in combination with commercial antifungal agent (ketoconazole), which demonstrated the enhanced activity of antifungal agent.
Gastric emptying in human disease states. (1991)

The application of new radioisotope methods in external in vivo scanning has increased our knowledge of how disease and treatment can effect gastric emptying (GE). Solids leave the stomach more slowly than liquids, and conditions causing gastroparesis affect solids before liquids. Gastric mucosal abnormalities and their treatment can affect GE. Diseases of the gastric musculature, including the inflammatory and endocrine myopathies, muscular dystrophies, and infiltrative disorders, can result in significant gastroparesis. Acute and chronic neuropathy may both affect gastric emptying. The latter neuropathies are now the subject of intense investigation with new prokinetic drugs. Finally, abnormal GE may be a major clinical feature of certain severe psychiatric disorders.
Improved Nickel Anodes for Industrial Water Electrolyzers (1985)

A method of increasing the energy efficiency of hydrogen production by alkaline water electrolysis is described. An ac activation of sintered Ni anodes leads to reductions in the oxygen evolution overpotential of ∼230 mV at 100–250 mA/cm2. The resulting reduction in cell voltage yields an increased energy efficiency and a significantly lowered cost of hydrogen production. Compared with other processes to raise anode efficiency, ac activation provides a fourfold improvement.
Calculation of Relative Binding Free Energy Difference of DHFR Inhibitors by a Finite Difference Thermodynamic Integration (FDTI) Approach (1999)

We have implemented a Finite Difference Thermodynamic Integration (FDTI) approach to estimate the binding free energy relative to methotrexate (MTX) of three unreported inhibitors of DHFR. The validity of the calculation methodology was first proved by evaluating the relative binding free energy difference for two well-known anticancer agents aminopterin and methotrexate. The usefulness of the method in drug design has been demonstrated by the fact that inhibitor 5, designed by us was found to bind more tightly than MTX, by as much 7.5 kcal/mole and is a worthy candidate for further pharmacological investigations.
Quantitative Phosphoproteomic Analysis of the Tumor Necrosis Factor Pathway (2005)

Protein phosphorylation has become a focus of many proteomic studies due to the central role that it plays in biology. We combine peptide-based gel-free isoelectric focusing and immobilized metal affinity chromatography to enhance the detection of phosphorylation events within complex protein samples using LC-MS. This method is then used to carry out a quantitative phosphoproteomic analysis of the tumor necrosis factor (TNF) pathway using HeLa cells metabolically labeled with 15N-containing amino acids, where 145 phosphorylation sites were found to be up-regulated upon the activation of the TNF pathway.
Accessory active site residues of <i>Streptomyces</i> sp. N174 chitosanase (2009)

The chitosanase from Streptomyces sp. N174 (CsnN174) is an inverting glycoside hydrolase belonging to family 46. Previous studies identified Asp40 as the general base residue. Mutation of Asp40 into glycine revealed an unexpectedly high residual activity. D40G mutation did not affect the stereochemical mechanism of catalysis or the mode of interaction with substrate. To explain the D40G residual activity, putative accessory catalytic residues were examined. Mutation of Glu36 was highly deleterious in a D40G background. Possibly, the D40G mutation reconfigured the catalytic center in a way that allowed Glu36 to be positioned favorably to perform catalysis. Thr45 was also found to be essential. Thr45 is thought to orientate the nucleophilic water molecule in a position to attack the glycosidic link. The finding that expression of heterologous CsnN174 in Escherichia coli protects cells against the antimicrobial effect of chitosan, allowed the selection of active chitosanase variants after saturation mutagenesis. Thr45 could be replaced only by serine, indicating the importance of the hydroxyl group. The newly identified accessory catalytic residues, Glu36 and Thr45 are located on a three-strand beta sheet highly conserved in GH19, 22, 23, 24 and 46, all members of the 'lysozyme superfamily'. Structural comparisons reveal that each family has its catalytic residues located among a small number of critical positions in this beta sheet. The position of Glu36 in CsnN174 is equivalent to general base residue in GH19 chitinases, whereas Thr45 is located similarly to the catalytic residue Asp52 of GH22 lysozyme. These examples reinforce the evolutionary link among these five GH families.
Phase-matched THz frequency upconversion in a GaP crystal (2006)

We have observed THz frequency upconversion in a GaP crystal. Such a parametric process has a potential for THz detections at room temperature.
A Vector Approach to Regression Analysis and Its Application to Heavy-Duty Diesel Emissions (2000)

<div class="htmlview paragraph">An alternative approach is presented for the regression of response data on predictor variables that are not logically or physically separable. The methodology is demonstrated by its application to a data set of heavy-duty diesel emissions. Because of the covariance of fuel properties, it is found advantageous to redefine the predictor variables as <i>vectors</i>, in which the original fuel properties are <i>components</i>, rather than as <i>scalars</i> each involving only a <i>single</i> fuel property. The fuel property vectors are defined in such a way that they are mathematically independent and statistically uncorrelated. The available data set is not considered adequate for the development of a full-fledged emission model. Nevertheless, the data clearly show that only a few basic patterns of fuel-property variation affect emissions and that the number of these patterns is considerably less than the number of variables initially thought to be involved.</div>
Predictable Interrupt Management for Real Time Kernels over conventional PC Hardware (2006)

In this paper we analyze the traditional model of interrupt management and its incapacity to incorporate reliability and the temporal predictability demanded on real-time systems. As a result of this analysis, we propose a model that integrates interrupts and tasks handling. We make a schedulability analysis to evaluate and distinguish the circumstances under which this integrated model improves the traditional model. The design of a flexible and portable kernel interrupt subsystem for this integrated model is presented. In addition, we present the rationale for the implementation of our design over conventional PC interrupt hardware and the analysis of its overhead. Finally, experimental results are conducted to demonstrate the deterministic behavior of our integrated model and to quantify its overhead.
RadH: A Versatile Halogenase for Integration into Synthetic Pathways (2017)

Abstract Flavin‐dependent halogenases are useful enzymes for providing halogenated molecules with improved biological activity, or intermediates for synthetic derivatization. We demonstrate how the fungal halogenase RadH can be used to regioselectively halogenate a range of bioactive aromatic scaffolds. Site‐directed mutagenesis of RadH was used to identify catalytic residues and provide insight into the mechanism of fungal halogenases. A high‐throughput fluorescence screen was also developed, which enabled a RadH mutant to be evolved with improved properties. Finally we demonstrate how biosynthetic genes from fungi, bacteria, and plants can be combined to encode a new pathway to generate a novel chlorinated coumarin “non‐natural” product in E. coli.
Pattern detection in unstructured data: An experience for a virtualized IT infrastructure (2013)

Data-agnostic management of today's virtualized and cloud IT infrastructures motivates statistical inference from unstructured or semi-structured data. We introduce a universal approach to the determination of statistically relevant patterns in unstructured data, and then showcase its application to log data of a Virtual Center (VMware's virtualization management software). The premise of this study is that the unstructured data can be converted into events, where an event is defined by time, source, and a series of attributes. Every event can have any number of attributes but all must have a time stamp and optionally a source of origination (be it a server, a location, a business process, etc.) The statistical relevance of the data can then be made clear via determining the joint and prior probabilities of events using a discrete probability computation. From this we construct a Directed Virtual Graph with nodes representing events and the branches representing the conditional probabilities between two events. Employing information-theoretic measures the graphs are reduced to a subset of relevant nodes and connections. Moreover, the information contained in the unstructured data set is extracted from these graphs by detecting particular patterns of interest.
Experimental study: Neural network based model predictive control of a distributed parameter system (2016)

An experimental set up has been designed for the purpose of spatial property control of a distributed parameter system. The setup consists of a thin metal chip with four temperature sensors along the length of the chip and four electric heaters to regulate the spatial temperature profile of the metal chip. A sequence of random pulse input signals with varying sampling times for the four manipulated inputs were used for live data generation of the transient temperature values at four locations along the metal chip length. Two data-driven models, namely linear state space model and neural network based model are identified and applied for online control. Model predictive control was used to control the spatial temperature profile for set-point tracking and disturbance rejection.
The California State Forest Service: Its Growth and its Objectives (1931)

Abstract The author goes over the history of California's state forestry department and refers to some of its problems. He reports in ten years a manifold increase in public interest in forestry and in state support of forestry activities.
Highly diastereoselective synthesis of (3R,4R)- and (3R,4S)-.BETA.,.GAMMA.-diamino acids from D-phenylalanine. (1988)

(2R, 3S)-N-Boc-2-Amino-3-hydroxy-1-phenylbutane (9a) and (2R, 3S)-N-Boc-2-amino-3-hydroxy-1-phenylpentane (9b) were converted to (3R, 4R)-N3-Boc-3, 4-diaminopentanoic acid (12a) and (3R, 4R)-N3-Boc-3, 4-diaminohexanoic acid (12b) through SN2 type substitution of the hydroxy group to an amino group and oxidation of the phenyl group to a carboxyl group. In a similar way, the (3R, 4S)-isomers (18a, b) were also synthesized from (2R, 3R)-N-Boc-2-amino-3-hydroxy-1-phenylbutane (15a) and (2R, 3R)-N-Boc-2-amino-3-hydroxy-1-phenylpentane (15b), respectively, derived from (2R, 3S)-N-Cbz-2-amino-3-hydroxy-1-phenylbutane (6a) and (2R, 3S)-N-Cbz-2-amino-3-hydroxy-1-phenylpentane (6b) by means of the diastereoconversion reaction.
Development of a Homologous Radioimmunoassay for Rat Relaxin* (1979)

Highly purified rat relaxin has been radioiodinated to specific activities of approximately 100 micro Ci/microgram with the Bolton and Hunter reagent [N-succinimidyl 3-(4-hydroxy-5-[125I]iodophenyl) propionate]. A rabbit antirat relaxin serum, applicable in a final dilution of 1:100,000, was developed in a rabbit using unconjugated highly purified rat relaxin. A specific and precise double antibody RIA for rat relaxin sufficiently sensitive to routinely measure from 32--2000 pg rat relaxin was developed. Using this RIA, relaxin immunoactivity levels in extracts of pregnant rat ovaries were found to rise from 0.8 microgram/geq ovarian fresh tissue on day 8 of pregnancy to 723 microgram/geq ovarian fresh tissue on day 20 of pregnancy and then to drop precipitously to 6 microgram/geq ovarian fresh tissue on day 1 of lactation. Consistent with the occurrence and relative levels of relaxin in the ovarian extracts, levels of relaxin in pregnant rat serum were less than 2 ng/ml on day 10 of pregnancy, approximately 150 ng/ml on days 20 and 22 of pregnancy, and 12 ng/ml on day 2 of lactation.
Comprehensive Video Understanding: Video Summarization with Content-Based Video Recommender Design (2019)

Video summarization aims to extract keyframes/shots from a long video. Previous methods mainly take diversity and representativeness of generated summaries as prior knowledge in algorithm design. In this paper, we formulate video summarization as a content-based recommender problem, which should distill the most useful content from a long video for users who suffer from information overload. A scalable deep neural network is proposed on predicting if one video segment is a useful segment for users by explicitly modelling both segment and video. Moreover, we accomplish scene and action recognition in untrimmed videos in order to find more correlations among different aspects of video understanding tasks. Also, our paper will discuss the effect of audio and visual features in summarization task. We also extend our work by data augmentation and multi-task learning for preventing the model from early-stage overfitting. The final results of our model win the first place in ICCV 2019 CoView Workshop Challenge Track.
OWLS (2013)

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Plasmon-Enhanced Upconversion in Single NaYF<sub>4</sub>:Yb<sup>3+</sup>/Er<sup>3+</sup> Codoped Nanocrystals (2009)

In this Letter we report the plasmon-enhanced upconversion in single NaYF(4) nanocrystals codoped with Yb(3+)/Er(3+). Single nanocrystals and gold nanospheres are investigated and assembled in a combined confocal and atomic force microscope setup. The nanocrystals show strong upconversion emission in the green and red under excitation with a continuous wave laser in the near-infrared at 973 nm. By the use of the atomic force microscope, we couple single nanocrystals with gold spheres (30 and 60 nm in diameter) to obtain enhanced upconversion emission. An overall enhancement factor of 3.8 is reached. A comparison of time-resolved measurements on the bare nanocrystal and the coupled nanocrystal-gold sphere systems unveil that faster excitation as well as faster emission occurs in the nanocrystals.
Ankyrin-binding activity of nervous system cell adhesion molecules expressed in adult brain (1993)

A family of ankyrin-binding glycoproteins have been identified in adult rat brain that include alternatively spliced products of the same pre-mRNA. A composite sequence of ankyrin-binding glycoprotein (ABGP) shares 72% amino acid sequence identity with chicken neurofascin, a membrane-spanning neural cell adhesion molecule in the Ig super-family expressed in embryonic brain. ABGP polypeptides and ankyrin associate as pure proteins in a 1:1 molar stoichiometry at a site located in the predicted cytoplasmic domain. ABGP polypeptides are expressed late in postnatal development to approximately the same levels as ankyrin, and comprise a significant fraction of brain membrane proteins. Immunofluorescence studies have shown that ABGP polypeptides are co-localized with ankyrinB. Major differences in developmental expression have been reported for neurofascin in embryos compared with the late postnatal expression of ABGP, suggesting that ABGP and neurofascin represent products of gene duplication events that have subsequently evolved in parallel with distinct roles. Predicted cytoplasmic domains of rat ABGP and chicken neurofascin are nearly identical to each other and closely related to a group of nervous system cell adhesion molecules with variable extracellular domains, including L1, Nr-CAM and Ng-CAM of vertebrates, and neuroglian of Drosophila. A hypothesis to be evaluated is that ankyrin-binding activity is shared by all of these proteins.
Acid and Oxidizing Leaching of Copper Refinery Anodic Slimes in Hexafluorosilicic Acid and Nitric Acid Media (1996)

Abstract Copper refinery anodic slimes containing copper (23.8%), arsenic (2.9%), selenium 8%), tellurium (0.9%), antimony (3.2%), silver (8.3%), and gold (0.3%) were treated by acid leaching using hexafluorosilicic acid (first step) and by acid and oxidizing leaching using a mixture of hexafluorosilicic and nitric acids (second step). This treatment dissolved 99% of the Cu, Se, and Te, 97% of the As, 95% of the Sb, and 85% of the Ag. After these two leaching steps, the final solid leach residue, which represents about 28% in weight of the initial solid, is upgraded in gold (1.11% Au), containing only 0.06% Cu, 0.04% As, 0.3% Se, 0.02% Te, and 0.11% Sb, while still remaining high in silver (4.45%). The leach solutions obtained are concentrated in Cu (24.5 g/L) as the first step, and in Ag (15.3 g/L) and Se (15.5 g/L) as the second step, which is favorable for the selective extraction of metals.
Effects of 2 Slow-Release Fertilizers on the Propagation and Subsequent Growth of 3 Woody Plants (1983)

Three woody plants were propagated from cuttings with four levels each of slow-release 27 N-5.2P-0.OK (27-12-0) and 0N-0P-38.2K (0-0-46) fertilizer in factorial combination. Slow-release fertilizer added during propagation had little effect on rooting of cuttings, however, after rooting and before transplanting into larger containers in the spring, the 27-12-0 stimulated both root and top growth of all species. All growth parameters measured for all species grown in 3.8 1 (#1) containers were significantly increased after one growing season when treated with a combination of slow-release N and P during propagation or following transplanting.
LAHEDES: the LAGLIDADG homing endonuclease database and engineering server (2012)

LAGLIDADG homing endonucleases (LHEs) are DNA cleaving enzymes, also termed 'meganucleases' that are employed as gene-targeting reagents. This use of LHEs requires that their DNA specificity be altered to match sequences in genomic targets. The choice of the most appropriate LHE to target a particular gene is facilitated by the growing number of such enzymes with well-characterized activities and structures. 'LAHEDES' (The LAGLIDADG Homing Endonuclease Database and Engineering Server) provides both an online archive of LHEs with validated DNA cleavage specificities and DNA-binding interactions, as well as a tool for the identification of DNA sequences that might be targeted by various LHEs. Searches can be performed using four separate scoring algorithms and user-defined choices of LHE scaffolds. The webserver subsequently provides information regarding clusters of amino acids that should be interrogated during engineering and selection experiments. The webserver is fully open access and can be found at http://homingendonuclease.net.
High-dose dietary<i>myo</i>-inositol supplementation does not alter the ischaemia phenomenon in human diabetics (1989)

Five diabetic patients and 3 non-diabetics were subjected to a dietary supplement of 20 g per day of myo-inositol (40 X the normal ingestion) for 14 days. This amount neither produced toxic side-effects nor changed the peripheral nervefunction expressed by motor conduction velocity or resistance to ischaemia.
Supercritical Fluid Applications in the Design of Novel Antimicrobial Materials (2020)

Bacterial resistance to antibiotics is one of the biggest problems in the modern world. The prevention of bacterial spreading from hospitals to the community and vice versa is an issue we have to deal with. This review presents a vast potential of contemporary high-pressure techniques in the design of materials with antimicrobial activity. Scientists from all over the world came up with ideas on how to exploit extraordinary properties of supercritical fluids in the production of advantageous materials in an environmentally friendly way. The review summarizes reported methods and results.
Mechanical Strain Inhibits Adipogenesis in Mesenchymal Stem Cells by Stimulating a Durable β-Catenin Signal (2008)

The ability of exercise to decrease fat mass and increase bone mass may occur through mechanical biasing of mesenchymal stem cells (MSCs) away from adipogenesis and toward osteoblastogenesis. C3H10T1/2 MSCs cultured in highly adipogenic medium express peroxisome proliferator-activated receptor gamma and adiponectin mRNA and protein, and accumulate intracellular lipid. Mechanical strain applied for 6 h daily inhibited expression of peroxisome proliferator-activated receptor gamma and adiponectin mRNA by up to 35 and 50%, respectively, after 5 d. A decrease in active and total beta-catenin levels during adipogenic differentiation was entirely prevented by daily application of mechanical strain; furthermore, strain induced beta-catenin nuclear translocation. Inhibition of glycogen synthase kinase-3beta by lithium chloride or SB415286 also prevented adipogenesis, suggesting that preservation of beta-catenin levels was important to strain inhibition of adipogenesis. Indeed, mechanical strain inactivated glycogen synthase kinase-3beta, which was preceded by Akt activation, indicating that strain transmits antiadipogenic signals through this pathway. Cells grown under adipogenic conditions showed no increase in osteogenic markers runt-related transcription factor (Runx) 2 and osterix (Osx); subsequent addition of bone morphogenetic protein 2 for 2 d increased Runx2 but not Osx expression in unstrained cultures. When cultures were strained for 5 d before bone morphogenetic protein 2 addition, Runx2 mRNA increased more than in unstrained cultures, and Osx expression more than doubled. As such, mechanical strain enhanced MSC potential to enter the osteoblast lineage despite exposure to adipogenic conditions. Our results indicate that MSC commitment to adipogenesis can be suppressed by mechanical signals, allowing other signals to promote osteoblastogenesis. These data suggest that positive effects of exercise on both fat and bone may occur during mesenchymal lineage selection.