gebhart/patrepeval huggingface dataset:
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018)

eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de.
Synthesis of Dihydroplakortin, 6-<i>epi</i>-Dihydroplakortin, and Their C10-Desethyl Analogues (2010)

The first synthesis of the marine endoperoxide 9,10-dihydroplakortin, of its C10-desethyl analogue, and of their corresponding C6 epimers is described. Stereogenic centers at C4 and at the lateral chain have been stereoselectively synthesized through Evans' chiral auxiliary chemistry. Moreover, the reported synthesis features a one-pot three-step hydroperoxysilylation/cyclization reaction for the construction of the endoperoxide ring system. Homologation of the aldehyde resulting from diol cleavage through a Wittig-based strategy gave access to the ester-containing lateral chain at C3.
Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks (1999)

Dictyostelium discoideum has been suggested as a eukaryotic model organism for glycobiology studies. Presently, the characteristics of acceptor sites for the N-acetylglucosaminyl-transferases in Dictyostelium discoideum, which link GlcNAc in an alpha linkage to hydroxyl residues, are largely unknown. This motivates the development of a species specific method for prediction of O-linked GlcNAc glycosylation sites in secreted and membrane proteins of D. discoideum. The method presented here employs a jury of artificial neural networks. These networks were trained to recognize the sequence context and protein surface accessibility in 39 experimentally determined O-alpha-GlcNAc sites found in D. discoideum glycoproteins expressed in vivo. Cross-validation of the data revealed a correlation in which 97% of the glycosylated and nonglycosylated sites were correctly identified. Based on the currently limited data set, an abundant periodicity of two (positions-3, -1, +1, +3, etc.) in Proline residues alternating with hydroxyl amino acids was observed upstream and downstream of the acceptor site. This was a consequence of the spacing of the glycosylated residues themselves which were peculiarly found to be situated only at even positions with respect to each other, indicating that these may be located within beta-strands. The method has been used for a rapid and ranked scan of the fraction of the Dictyostelium proteome available in public databases, remarkably 25-30% of which were predicted glycosylated. The scan revealed acceptor sites in several proteins known experimentally to be O-glycosylated at unmapped sites. The available proteome was classified into functional and cellular compartments to study any preferential patterns of glycosylation. A sequence based prediction server for GlcNAc O-glycosylations in D. discoideum proteins has been made available through the WWW at http://www.cbs.dtu.dk/services/DictyOGlyc/ and via E-mail to DictyOGlyc@cbs.dtu.dk.
SYNCHRONOUS MC-CDMA IN DISPERSIVE, MOBILE RAYLEIGH CHANNELS (2000)

... This paper evaluates the effect of Doppler and delay spreads on the performance of an MC-CDMA receiver. An MMSE receiver is analyzed for MC-CDMA transmission over a mobile channel with Doppler. A simplified, pseudo MMSE receiver is proposed that does not need to perform real-time inversion of a large matrix. It performance is shown to be better than for (uncoded) OFDM.
Tailoring Macromolecular Structure of Cationic Polymers towards Efficient Contact Active Antimicrobial Surfaces (2018)

The aim of this work is the preparation of contact active antimicrobial films by blending copolymers with quaternary ammonium salts and polyacrylonitrile as matrix material. A series of copolymers based on acrylonitrile and methacrylic monomers with quaternizable groups were designed with the purpose of investigating the influence of their chemical and structural characteristics on the antimicrobial activity of these surfaces. The biocide activity of these systems was studied against different microorganisms, such as the Gram-positive bacteria <i>Staphylococcus aureus</i> and the Gram-negative bacteria <i>Pseudomona aeruginosa</i> and the yeast <i>Candida parapsilosis.</i> The results confirmed that parameters such as flexibility and polarity of the antimicrobial polymers immobilized on the surfaces strongly affect the efficiency against microorganisms. In contrast to the behavior of copolymers in water solution, when they are tethered to the surface, the active cationic groups are less accessible and then, the mobility of the side chain is critical for a good contact with the microorganism. Blend films composed of copolymers with high positive charge density and chain mobility present up to a more than 99.999% killing efficiency against the studied microorganisms.
Potential seed production from a White Spruce clonal seed orchard. (1970)

One objective of tree improvement programs is mass production of genetically superior seed. Such seed is usually collected in grafted or in seedling seed orchards from selected trees. White spruce (Picea glauca (Moench) Voss) is widely planted in the Lake States, and seed orchards are now being established to produce genetically superior seed. What will these orchards yield? We present here some early answers to this question. Our results are limited to clonal orchards. Wright (1964) reported that moderate numbers of cones can be found occasionally on 6to 10-year-old white spruce and that most trees produce cones in quantity by the time they are 10 to 15 years old. Planted white spruce in northeastern Wisconsin apparently do not produce moderate cone crops until they are much older. For example, in an unfertilized planting of trees 21 years old from seed, only 10 out of 23 selected trees could be included in a pollination program requiring a minimum of 10 pollination bags per tree .2 There are several reports in the literature on the potential seed production from grafted material of other species. Among these are cone and seed production of 12year-old grafted Scotch pine (Hadders and Ahgren 1958), cone and seed yields from pine seed orchards (Johnsson 1961), and production of Norway spruce seed in orchards (Ruden 1961). Johnsson reported considerable variation among clones of Scotch pine in the number of cones and seed produced per clone. Van Buijtenen (1966) reported on the effect of spacing, fertilization, and cultivation on flowering and seed production in loblolly pine. To our knowledge there are no reports on potential seed production from white spruce clonal orchards.
Effect of surface roughness on fouling of RO and NF membranes during filtration of a high organic surficial groundwater (2006)

Fouling characteristics of various thin film composite polyamide reverse osmosis (RO) and nanofiltration (NF) membranes were systematically investigated using a high organic surficial groundwater obtained from the City of Plantation, Florida. Prior to bench-scale fouling experiments, surface properties of the selected RO and NF membranes were carefully analysed in order to correlate the rate and extent of fouling to membrane surface characteristics, such as roughness, charge and hydrophobicity. More specifically, the surface roughness was characterized by atomic force microscopy, while the surface charge and hydrophobicity of the membranes were evaluated through zeta potential and contact angle measurements, respectively. The results indicated that membrane fouling became more severe with increasing surface roughness, as measured by the surface area difference, which accounts for both magnitude and frequency of surface peaks. Surface roughness was correlated to flux decline; however, surface charge was not. The limited range of hydrophobicity of the flat sheet studies prohibited conclusions regarding the correlation of flux decline and hydrophobicity. © IWA Publishing 2006.
<title>Four-million-pixel CCD image sensor</title> (1990)

An ultra high resolution image sensor has been developed for industrial and scientific applications. The ultra high resolution sensor is a full-frame CCD sensor, consisting of 2048 x 2048 pixels, and its image area measures 18.43 mm x 18.43 mm. The pixel size is 9 x 9 microns. The sensor has dual readout registers to increase the data rate and can be operated in the single or dual readout register mode. The architecture of this imager is suitable for accumulation mode operation, which results in a very low dark current of 10 pA/sq cm at room temperature.
Evaluating an AOP for TCE and PCE removal (1997)

The authors evaluate an AOP by introducing elevated TCE and PCE into groundwater and propose a chemical kinetic model for evaluating AOP performance. A full‐scale evaluation of an advanced oxidation process (AOP) involving the use of ozone (O 3 ) and hydrogen peroxide (H 2 O 2 ) at a 126‐L/s (2,000‐gpm) flow rate was completed in a plug‐flow hydraulic regime by the Los Angeles (Calif.) Department of Water and Power. This facility is the first full‐scale AOP for trichloroethylene (TCE) and tetrachloroethylene (PCE) treatment in the United States, if not the world. The purpose of this study was to challenge the performance of the plant with typical groundwater pollutants, propose a kinetic model for the process, and confirm past laboratory and pilot studies. Groundwater containing up to 447 μg/L TCE and 163 μg/L PCE was treated to below the maximum contaminant (MCL) level of 5 μg/L. The optimum H 2 O 2 /O 3 dose ratio was 0.5–0.6. Removal efficiency of TCE and PCE declined as groundwater alkalinity increased. Investigation of by‐product formation showed formation of assimilable organic carbon and bromate following the treatment process. A kinetic model calibrated using the experimental data predicted the concentration of TCE and PCE in the finished water reasonably well.
Application of Gas for Mobility Control in Chemical EOR in Problematic Carbonate Reservoirs (2010)

Abstract The use of gas for mobility control in chemical enhanced oil recovery is an attractive option to substitute polymer in conditions where its application is not feasible. Especially in carbonate reservoirs, which generally have low permeability and contains vugs and fractures, the use of polymer may result in the loss of permeability and benefits of chemical conformance control. In such conditions, gas is a good alternative. The direct dependence of dispersed gas mobility on rock permeability reduces the likelihood of gas plugging oil-rich low permeable rock matrix in carbonate reservoirs. The mobility of both gas and liquid phases in fractures can be controlled by changing fractional gas and liquid rates in such a manner that the two phases retains their flow characteristics. A series of high performance surfactant-gas corefloods were performed on different core samples having very low to medium permeability values. In each experiment, foamed chemical slug was chased by foamed drive. The main objective of the research work was to determine mobility control characteristic of dispersed flow by evaluating pressure response and oil recovery data obtained from corefloods. All corefloods resulted in oil recoveries above 75% of residual oil to waterflood. No early surfactant and gas breakthrough was observed, indicating absence of viscous fingering and presence of effective mobility control. The scaled pressure gradients remained within the practical limits observed in field EOR applications. Particularly, low pressure gradients observed at relatively high fluid rates indicates a degree of in-situ foaming for favorable injectivity, thus highlighting the potential use of gas in low permeability reservoirs. The beneficial effect of trapped surfactant mobilization on foaming, with the decrease in salinity, was observed in the form of increased foam strength during the drive injection phase. The experimental study provides an insight into the effective application of gas in chemical floods in problematic carbonate formations. Substituting polymer with gas increases the applicability of chemical EOR methods in different types of reservoirs.
A bandwidth reallocation scheme for Ethernet-based real-time communication (2002)

The objective of this paper is to develop a bandwidth reallocation scheme for TDMA-implemented Ethernet. The reallocation protocol consists of reporting change, calculating a new schedule, and reliably broadcasting the schedule. We also address the problem of static assignment of allocation vector, validate the essentiality of reallocation scheme, and design the scheme according to its functional requirements. The proposed scheme changes bandwidth allocation during the run-time operation of network system without affecting other traffics, so it can overcome the problem of static allocation. It completes reallocation within a bounded time as long as there are no transmission errors. Using this approach, the network is allowed to adapt to distributed real-time systems where traffic characteristics change dynamically.
Agonist-modulated Regulation of AMP-activated Protein Kinase (AMPK) in Endothelial Cells (2007)

The endothelial isoform of nitric-oxide synthase (eNOS), a key determinant of vascular homeostasis, is a calcium/calmodulin-dependent phosphoprotein regulated by diverse cell surface receptors. Vascular endothelial growth factor (VEGF) and sphingosine 1-phosphate (S1P) stimulate eNOS activity through Akt/phosphoinositide 3-kinase and calcium-dependent pathways. AMP-activated protein kinase (AMPK) also activates eNOS in endothelial cells; however, the molecular mechanisms linking agonist-mediated AMPK regulation with eNOS activation remain incompletely understood. We studied the role of AMPK in VEGF- and S1P-mediated eNOS activation and found that both agonists led to a striking increase in AMPK phosphorylation in pathways involving the calcium/calmodulin-dependent protein kinase kinase beta. Treatment with tyrosine kinase inhibitors or the phosphoinositide 3-kinase inhibitor wortmannin demonstrated differential effects of VEGF versus S1P. Small interfering RNA (siRNA)-mediated knockdown of AMPKalpha1or Akt1 impaired the stimulatory effects of both VEGF and S1P on eNOS activation. AMPKalpha1 knockdown impaired agonist-mediated Akt phosphorylation, whereas Akt1 knockdown did not affect AMPK activation, thus suggesting that AMPK lies upstream of Akt in the pathway leading from receptor activation to eNOS stimulation. Importantly, we found that siRNA-mediated knockdown of AMPKalpha1 abrogates agonist-mediated activation of the small GTPase Rac1. Conversely, siRNA-mediated knockdown of Rac1 decreased the agonist-mediated phosphorylation of AMPK substrates without affecting that of AMPK, implicating Rac1 as a molecular link between AMPK and Akt in agonist-mediated eNOS activation. Finally, siRNA-mediated knockdown of caveolin-1 significantly enhanced AMPK phosphorylation, suggesting that AMPK is negatively regulated by caveolin-1. Taken together, these results suggest that VEGF and S1P differentially regulate AMPK and establish a central role for an agonist-modulated AMPK --> Rac1 --> Akt axis in the control of eNOS in endothelial cells.
Some applications of fuzzy logic in rule–based expert systems (2002)

Fuzzy logic has been used as a means of interpreting vague, incomplete and even contradictory information into a compromised rule base in artificial intelligence such as machine decision–making. Within this context, fuzzy logic can be applied in the field of expert systems to provide additional flexibilities in constructing a working rule base: different experts’ opinions can be incorporated into the same rule base, and each opinion can be modeled in a rather vague notion of human language. As some illustrative application examples, this paper describes how fuzzy logic can be used in expert systems. More precisely, it demonstrates the following applications: (i) a healthcare diagnostic system, (ii) an autofocus camera lens system and (iii) a financial decision system. For each application, basic rules are described, the calculation method is outlined and numerical simulation is provided. These applications demonstrate the suitability and performance of fuzzy logic in expert systems.
Safety, tolerability and immunogenicity of GS-4774, a hepatitis B virus-specific therapeutic vaccine, in healthy subjects: A randomized study (2014)

Clinicaltrials.gov (NCT01779505).
Low-Cost Standard Signatures for Energy-Harvesting Wireless Sensor Networks (2017)

This work is motivated by a general question: can micro-scale energy-harvesting techniques be exploited to support low-cost standard security solutions on resource-constrained devices? We focus on guaranteeing integrity and authentication in Internet of Things (IoT) and Wireless Sensor Network (WSN) applications. In this article, we propose techniques to make ECDSA signatures low cost and implementable on resource-constrained devices. By combining precomputation techniques and energy-harvesting capabilities of modern sensor nodes, we achieve significant improvement over prior works. In addition, we show that the cost of ECDSA signatures can be reduced by up to a factor 10 by using harvesting-aware optimizations.
Efficacy and safety of ezetimibe coadministered with statins: randomised, placebo-controlled, blinded experience in 2382 patients with primary hypercholesterolemia (2004)

We assessed pooled safety and lipid-regulating efficacy data from four similarly designed trials of ezetimibe coadministered with statins in 2382 patients with primary hypercholesterolemia. Patients were randomised to one of the following double-blind treatments for 12 weeks: placebo; ezetimibe 10 mg; statin; or statin + ezetimibe. Statin doses tested were 10, 20, 40 mg/day (atorvastatin, simvastatin, pravastatin or lovastatin) or 80 mg/day (atorvastatin, simvastatin). Treatment with ezetimibe + statin led to significantly greater reductions in low-density lipoprotein cholesterol (LDL-C), total cholesterol, triglycerides, non-high-density lipoprotein cholesterol (non-HDL-C), apolipoprotein B and increases in HDL-C, compared to statin alone. At each statin dose, treatment with ezetimibe + statin led to a greater LDL-C reduction compared to the next highest statin monotherapy dose. Ezetimibe + statin had a safety profile similar to statin monotherapy. Coadministration of ezetimibe + statin offers a well-tolerated, highly efficacious new treatment strategy for patients with hypercholesterolemia.
[Cloning of Xenopus laevis major histocompatibility complex class II beta-chain genes]. (1994)

The amphibian Xenopus laevis is the most primitive vertebrate in which the major histocompatibility complex (MHC) has been identified both at the biochemical and functional level. In the present study, cDNA clones for MHC class II beta-chain genes of Xenopus laevis were isolated using the polymerase chain reaction. In partially inbred animals with the MHC f haplotype, two distinct cDNA clones assumed to encode isotypes were identified. The deduced MHC class II beta-chain of Xenopus laevis had structures fundamentally similar to those of their mammalian counterparts. The overall amino acid sequence identity between Xenopus laevis and representative mammalian MHC class II beta-chains was approximately 41-50%. Sequence comparison of cDNA clones isolated from outbred individuals and the partially inbred frog with the MHC f haplotype showed that nucleotide substitutions are located primarily in the beta 1 domain and that non-synonymous substitutions occur more frequently than synonymous substitutions in the putative antigen binding site. This result indicates that, as in mammalian MHC genes, the MHC class II beta-chain genes of Xenopus laevis are under positive Darwinian selection. Despite the fact that Xenopus laevis is a tetraploid species, its MHC, as defined by serology, immunochemistry, and mixed lymphocyte reaction, is diploidized. Family studies showed that all MHC class II beta-chain genes detectable in the genome of Xenopus laevis segregate with serologically defined MHC haplotypes, suggesting that the second, inactivated set of MHC class II beta-chain genes was either deleted or that their sequences diverged too far to be detected by DNA hybridization. Furthermore, a nearly constant number of MHC class II beta-chain genes was detectable in most, if not all, Xenopus species with various degrees of ploidy. Thus, various polyploid species of Xenopus appear to have used a similar strategy to diploidize their MHC genes.
Diffusion Limitation of Lithium Metal and Li–Mg Alloy Anodes on LLZO Type Solid Electrolytes as a Function of Temperature and Pressure (2019)

Abstract The morphological instability of the lithium metal anode is the key factor restricting the rate capability of lithium metal solid state batteries. During lithium stripping, pore formation takes place at the interface due to the slow diffusion kinetics of vacancies in the lithium metal. The resulting current focusing increases the internal cell resistance and promotes fast lithium penetration. In this work, galvanostatic electrochemical impedance spectroscopy is used to investigate operando the morphological changes at the interface by analysis of the interface capacitances. Therewith, the effect of temperature, stack pressure, and chemical modification is investigated. The work demonstrates that introducing 10 at% Mg into the lithium metal anode can effectively prevent contact loss. Nevertheless, a fundamental kinetic limitation is also observed for the Li‐rich alloy, namely the diffusion controlled decrease of the lithium metal concentration at the interface. An analytical diffusion model is used to describe the temperature‐dependent delithiation kinetics of Li–Mg alloys. Overall, it is shown that different electrode design concepts should be considered. Mg alloying can increase lithium utilization, when no external pressure is applied while pure lithium metal is superior for setups that allow stack pressures in the MPa range.