gebhart/patrepeval huggingface dataset:
Proposed uniform nomenclature for the proteins and protein domains of the bacterial phosphoenolpyruvate: sugar phosphotransferase system (1992)

The phosphoenolpyruvate:sugar phosphotransferase system (PTS) consists of two general energy-coupling proteins, enzyme I and HPr, as well as the sugar-specific permeases, commonly referred to as the enzyme II complex (15,19,24,26).The system catalyzes the concomitant transport and phosphorylation of its sugar substrates in a process termed group translocation (16, 25).The PTS permeases found in a variety of bacteria may consist of one, two, three, or four distinct polypeptide chains and, in certain instances, some of these sugar-specific proteins are fused to protein domains which serve the general energy-coupling function(s) of en- zyme I and/or HPr (8,31,34) (see Fig. 1 and 2 for schematic depictions).Evidence suggesting that the entire enzyme II complex is required for concomitant sugar transport and phosphorylation but that enzyme I and HPr merely function to phosphorylate this complex has been presented (4, 9).The enzyme II complex should therefore be considered the functional unit designated permease in this paper.Recent sequence comparison studies have shown that most of the PTS permeases are homologous, i.e., derived from a common ancestral protein (13,21,28,33).These group translocators, comprising the major group of the enzyme II complexes, generally have similar molecular weights of about 68,000, corresponding to about 635 total amino acyl residues (31).Most of them consist either of a single polypeptide chain, commonly termed enzyme II, or of two proteins, commonly called an enzyme II-III pair or an enzyme IIB-IIA pair (15, 31).In a few cases, these perme- ases consist of three or four proteins (6,14,22).Regardless of the number of polypeptide chains in each of these perme- ases, there are always at least three well-recognized func- tional domains: a hydrophobic transmembrane domain which binds and transports the sugar substrate (10), a hydrophilic enzyme III-like domain which possesses the first phosphorylation site (always a histidyl residue [31]), and a second hydrophilic protein or protein domain which pos- sesses the second phosphorylation site (either a cysteyl residue, as for the major group of homologous PTS perme- ases [1,18,22] [see Fig. 3], or a histidyl residue, as for a splinter group of three distinct sequenced PTS permeases which catalyze the transport and phosphorylation of mannose in Escherichia coli, fructose [to yield fructose 6-phos- phate] in Bacillus subtilis, and sorbose in Klebsiella pneu- moniae [5, 12a, 14]).These three permeases of the splinter group lack sufficient sequence similarity with the major group of PTS permeases to establish homology with them, but they are clearly homologous to each other.At the present time, well over 12 PTS permeases have been completely sequenced.While the permeases within the
Heparin-binding peptides from the type I repeats of thrombospondin. Structural requirements for heparin binding and promotion of melanoma cell adhesion and chemotaxis. (1992)

Synthetic peptides derived from the type I repeats of human platelet thrombospondin containing a consensus sequence Trp-Ser-Xaa-Trp bind to heparin, promote cell adhesion, and inhibit heparin-dependent interactions of melanoma cells with extracellular matrix components (Guo, N. H., Krutzsch, H. C., Nègre, E., Vogel, T., Blake, D. A., and Roberts, D. D. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 3040-3044). In the present study, we further examined the structural requirements for activity of these peptides. The minimal active sequence for heparin or sulfatide binding based on inhibition studies is Trp-Ser-Pro-Trp, although an octapeptide is required for optimal activity. The 2 Trp residues and the Ser residue are essential. Peptides with more than 2 residues between the Trp residues are inactive. The Pro residue is essential for activity of the pentapeptide Trp-Ser-Pro-Trp-Ser, but some larger peptides with substitutions for the Pro residue are active. For direct high affinity binding to heparin, both the consensus sequence and a flanking sequence of basic amino acids are essential. Peptides containing the consensus sequence promote cell adhesion and act cooperatively with the adjacent basic amino acid sequence to promote cell spreading. Chemical modification of the Trp residues in the peptides with amino-terminal basic amino acids abolished both cell adhesion and heparin-binding. Peptides containing the consensus sequence and basic amino acids are chemotactic for A2058 human melanoma cells. The functional importance of this novel heparin and sulfatide-binding motif is suggested by its conservation in other members of the thrombospondin gene family, complement components, and in many members of the cytokine receptor and transforming growth factor beta superfamilies.
Arrow: Low-Level Augmented Bayesian Optimization for Finding the Best Cloud VM (2018)

With the advent of big data applications, which tend to have longer execution time, choosing the right cloud VM has significant performance and economic implications. For example, in our large-scale empirical study of 107 different workloads on three popular big data systems, we found that a wrong choice can lead to a 20 times slowdown or an increase in cost by 10 times. Bayesian optimization is a technique for optimizing expensive (black-box) functions. Previous work has only used instance-level information (such as core counts and memory size) which is not sufficient to represent the search space. In this work, we discover that this may lead to the fragility problem-either incurs high search cost or finds only the sub-optimal solution. The central insight of this paper is to use low-level performance information to augment the process of Bayesian Optimization. Our novel low-level augmented Bayesian Optimization is rarely worse than current practices and often performs much better (in 46 of 107 cases). Further, it significantly reduces the search cost in nearly half of our case studies. Based on this work, we conclude that it is often insufficient to use general-purpose off-the-shelf methods for configuring cloud instances without augmenting those methods with essential systems knowledge such as CPU utilization, working memory size and I/O wait time.
Structure-function in Escherichia coli iron superoxide dismutase: Comparisons with the manganese enzyme from Thermus thermophilus (1995)

The crystal structure of dimeric Fe(III) superoxide dismutase (SOD) from Escherichia coli (3006 protein atoms, 2 irons, and 281 solvents) has been refined to an R of 0.184 using all observed data between 40.0 and 1.85 A (34,879 reflections). Features of this structure are compared with the refined structure of MnSOD from Thermus thermophilus. The coordination geometry at the Fe site is distorted trigonal bipyramidal, with axial ligands His26 and solvent (proposed to be OH-), and in-plane ligands His73, Asp156, and His160. Reduction of crystals to the Fe(II) state does not result in significant changes in metal-ligand geometry (R = 0.188 for data between 40.0 and 1.80 A). The arrangement of iron ligands in Fe(II) and Fe(III)SOD closely matches the Mn coordination found in MnSOD from T. thermophilus [Ludwig, M.L., Metzger, A.L., Pattridge, K.A., & Stallings, W.C. (1991) J. Mol. Biol. 219, 335-358]. Structures of the Fe(III) azide (40.0-1.8 A, R = 0.186) and Mn(III) azide (20.0-1.8 A, R = 0.179) complexes, reported here, reveal azide bound as a sixth ligand with distorted octahedral geometry at the metal; the in-plane ligand-Fe-ligand and ligand-Mn-ligand angles change by 20-30 degrees to coordinate azide as a sixth ligand. However, the positions of the distal azide nitrogens are different in the FeSOD and MnSOD complexes. The geometries of the Fe(III), Fe(II), and Fe(III)-azide species suggest a reaction mechanism for superoxide dismutation in which the metal alternates between five- and six-coordination. A reaction scheme in which the ligated solvent acts as a proton acceptor in the first half-reaction [formation of Fe(II) and oxygen] is consistent with the pH dependence of the kinetic parameters and spectroscopic properties of Fe superoxide dismutase.
Learning Convolutional Neural Networks for Graphs (2016)

Numerous important problems can be framed as learning from graph data. We propose a framework for learning convolutional neural networks for arbitrary graphs. These graphs may be undirected, directed, and with both discrete and continuous node and edge attributes. Analogous to image-based convolutional networks that operate on locally connected regions of the input, we present a general approach to extracting locally connected regions from graphs. Using established benchmark data sets, we demonstrate that the learned feature representations are competitive with state of the art graph kernels and that their computation is highly efficient.
Structural Requirements of Oleosin Domains for Subcellular Targeting to the Oil Body (1995)

We have investigated the protein domains responsible for the correct subcellular targeting of plant seed oleosins. We have attempted to study this targeting in vivo using "tagged" oleosins in transgenic plants. Different constructs were prepared lacking gene sequences encoding one of three structural domains of natural oleosins. Each was fused in frame to the Escherichia coli uid A gene encoding beta-glucuronidase (GUS). These constructs were introduced into Brassica napus using Agrobacterium-mediated transformation. GUS activity was measured in washed oil bodies and in the soluble protein fraction of the transgenic seeds. It was found that complete Arabidopsis oleosin-GUS fusions undergo correct subcellular targeting in transgenic Brassica seeds. Removal of the C-terminal domain of the Arabidopsis oleosin comprising the last 48 amino acids had no effect on overall subcellular targeting. In contrast, loss of the first 47 amino acids (N terminus) or amino acids 48 to 113 (which make up a lipophilic core) resulted in impaired targeting of the fusion protein to the oil bodies and greatly reduced accumulation of the fusion protein. Northern blotting revealed that this reduction is not due to differences in mRNA accumulation. Results from these measurements indicated that both the N-terminal and central oleosin domain are important for targeting to the oil body and show that there is a direct correlation between the inability to target to the oil body and protein stability.
A Wireless Portable System With Microsensors for Monitoring Respiratory Diseases (2012)

A wireless portable monitoring system for respiratory diseases using microsensors is proposed. The monitoring system consists of two sensor nodes integrating with Bluetooth transmitters that measure user's respiratory airflow, blood oxygen saturation, and body posture. The utility of micro-hot-film flow sensor makes the monitor can acquire comprehensive respiration parameters which are useful for diagnoses of obstructive sleep apnea, chronic obstructive pulmonary disease, and asthma. The system can serve as both sleep recorder and spirometer. Additionally, a mobile phone or a PC connected to the Internet serving as a monitoring and transfer terminal makes telemedicine achievable. Several experiments were conducted to verify the feasibility and effectiveness of the proposed system for monitoring and diagnosing OSA, COPD, and asthma.
Apoproteins B and A-I and coronary artery disease in humans. (1984)

T his review initially will consider the association between premature coronary artery disease and abnormal lipoprotein cholesterol levels, but then focus on recent evidence linking the apoproteins of lipoproteins to atherosclerosis. This evidence suggests that although cholesterol is the major component common to the plasma and the arterial wall, plasma apoproteins may serve as a better marker of risk for atherosclerosis.
Synthesis of poly‐(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) by recombinant Escherichia coli (1996)

Several recombinant Escherichia coli strains, including XL1-Blue, JM109, HB101, and DH5α harboring a stable high-copynumber plasmid pSYL105 containing the Alcaligenes eutrophus polyhydroxyalkanoate (PHA) biosynthesis genes were constructed. These recombinant strains were examined for their ability to synthesize and accumulate poly-(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] copolymer from glucose and either propionate or valerate. All recombinant E. coli strains could synthesize the P(3HB-co-3HV) copolymer in the medium containing glucose and propionate. However, only the homopolymer poly-(3-hydroxybutyrate) [P(3HB)] was synthesized from glucose and valerate. The PHA concentration and the 3HV fraction could be increased by inducing with acetate and/or oleate. When supplemented with oleate, the 3HV fraction increased by fourfold compared with that obtained without induction. Induction with propionate resulted in lower PHA concentration due to the inhibitory effect, but an 3HV fraction of as high as 33.0% could be obtained. These results suggest that P(3HB-co-3HV) can be efficiently produced from propionate by recombinant E. coli by inducing with acetate, propionate, or oleate. © 1996 John Wiley & Sons, Inc.
ChemInform Abstract: Ion‐Neutral Complexes (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Hierarchical Menu Design: Breadth, Depth, and Task Complexity (1996)

In this research a relationship between an hierarchical menu's depth and the perceived complexity of a task involving menu retrieval was proposed and validated. 12 subjects were asked to use six different hierarchical menus of varying breadth and depth. The dependent variables were response time and accuracy. The independent variables were depth and breadth of the hierarchy. Subsequent to experimentation, the subjects were asked to complete a questionnaire on users' perceptions of the complexity of the different menu structures. As depth increased, perceived complexity of the menus increased significantly. These phenomena are linked to an existing theory of task complexity. We suggest that the cognitive component influencing users' perceptions of task complexity was short-term memory load.
Micro/Nano Encapsulation via Electrified Coaxial Liquid Jets (2002)

We report a method to generate steady coaxial jets of immiscible liquids with diameters in the range of micrometer/nanometer size. This compound jet is generated by the action of electro-hydrodynamic (EHD) forces with a diameter that ranges from tens of nanometers to tens of micrometers. The eventual jet breakup results in an aerosol of monodisperse compound droplets with the outer liquid surrounding or encapsulating the inner one. Following this approach, we have produced monodisperse capsules with diameters varying between 10 and 0.15 micrometers, depending on the running parameters.
A NADPH Oxidase–Dependent Redox Signaling Pathway Mediates the Selective Radiosensitization Effect of Parthenolide in Prostate Cancer Cells (2010)

Cancer cells are usually under higher oxidative stress compared with normal cells. We hypothesize that introducing additional reactive oxygen species (ROS) insults or suppressing antioxidant capacity may selectively enhance cancer cell killing by oxidative stress-generating agents through stress overload or stress sensitization, whereas normal cells may be able to maintain redox homeostasis under exogenous ROS by adaptive response. Here, we show that parthenolide, a sesquiterpene lactone, selectively exhibits a radiosensitization effect on prostate cancer PC3 cells but not on normal prostate epithelial PrEC cells. Parthenolide causes oxidative stress in PC3 cells but not in PrEC cells, as determined by the oxidation of the ROS-sensitive probe H(2)DCFDA and intracellular reduced thiol and disulfide levels. In PC3 but not PrEC cells, parthenolide activates NADPH oxidase, leading to a decrease in the level of reduced thioredoxin, activation of phosphoinositide 3-kinase/Akt, and consequent FOXO3a phosphorylation, which results in the downregulation of FOXO3a targets antioxidant enzyme manganese superoxide dismutase and catalase. Importantly, when combined with radiation, parthenolide further increases ROS levels in PC3 cells whereas it decreases radiation-induced oxidative stress in PrEC cells, possibly by increasing reduced glutathione levels. Together, the results show that parthenolide selectively activates NADPH oxidase and mediates intense oxidative stress in prostate cancer cells by both increasing ROS generation and decreasing antioxidant defense capacity. The results support the concept of exploiting the intrinsic differences in the redox status of cancer cells and normal cells as targets for selective cancer killing.
Performance of tobacco oil-based bio-diesel fuel in a single cylinder direct injection engine (2010)

In the present investigation, the high viscosity tobacco oil, which has been considered as non-edible oil as a potential alternative fuel for the Compression Ignition Engine (C. I.). Tobacco Methyl Ester (TME) was prepared by transesterification of raw tobacco oil. A two stage transestirification process was developed since tobacco is having higher acidic value. Transesterification was done using NaOH in the presence of sulphuric acid as catalyst and both acid transesterification and base transestirification was performed. Since TME has higher kinematic viscosity, its viscosity has been reduced by blending with neat diesel. The bio-diesel was blended with neat diesel at various volumetric proportions of B2, B5 (denoting 2, 5%) .The performance of this alternate fuel was tested by conducting a series of tests on 4 stroke single cylinder 5.2 kW direct injection diesel engine. The engine was run at different loads like full load, 3/4, 1/2, 1/4 and no load at various speeds and also at constant speed .The tests were conducted by using neat diesel and also diesel fuel blended with TME The combustion characteristics and exhaust emissions like hydrocarbon (HC), carbon (II) oxide (CO) and nitric oxides (NO) were measured. Torque, brake power, specific fuel consumption was also measured and the test was plotted in the graphs. The physical and chemical specifications like flash point, fire point, density, kinematic viscosity and acid number of TME were established. Significant improvement in engine performance was observed. The specific fuel consumption and the exhaust gas temperature reduced due to the decrease in viscosity of TME. From the properties and engine test results it has been established that at lower percentage of blending, TME has improved the engine performance but at higher percentages of blending, the performance and engine emissions were drastically effected. The results show that the TME can be used as an alternate fuel in diesel engines without any engine modifications.

	 

	Key words: TME (Tobacco Methyl Ester), transesterification, diesel blend Bxx.
The end of Britain?: Thoughts on the future of national sovereignty in a regional Europe (2001)

The twentieth century was a century of revolutions. Some, like those of Russia in 1917, followed the traditional path of drama and violence, yet others equally fundamental to the governance of their countries occurred without the bloodshed that normally accompanies such change. The latter path has been the one followed in western Europe since 1945, where two constitutional revolutions have occurred almost without being noticed. Together these revolutions by stealth have dismantled the traditional nation-state model in western Europe. This is not to say, however, that the nation-states of Europe do not continue to operate and play a significant role on both the European and world stages. The continued importance of the national tier, as a significant and perhaps primary level of governance, obscures a more subtle truth. Although the nation-state continues to play the prominent role in European governance, it is not the same entity that existed in the prewar world. A constitutional revolution from above has seen ever-greater authority removed from the hands of individual nation-state or 'Member-State' governments and placed under the collective authority of the European Union's institutions. In tandem with this, a second, and even less visible, revolution from below has seen the development of policy-making below the nation-state. It is this regional revolution which forms the focus of this paper.
Quasi-planar high-Q millimeter-wave resonators (2006)

Several low-profile 250-/spl mu/m-high Ka-band cavity resonators are demonstrated with resonant frequencies near 26 GHz and unloaded quality (Q) factors greater than 400. The air-filled copper cavity resonators are fabricated on a silicon substrate using a photolithographic process. A microrectangular coaxial transmission-line feed is integrated in the same process. Four resonators with different mechanical support structures are demonstrated. The resonators are designed using the finite-element method and simulation of both the resonant frequency and Q factor agree well with measurements.
Magnetoplasmonic nanostructures: systems supporting both plasmonic and magnetic properties (2009)

We present in this work our current understanding on magnetoplasmonic structures, that is, systems whose constituents exhibit simultaneously magnetic and plasmonic properties. We analyze both the influence of the plasmon resonance on the magneto-optical properties of the&#13;\nsystem and the ability of the magnetic field to modulate the plasmon properties. In particular we show how, in magnetoplasmonic systems sustaining localized or propagating surface plasmons, the associated electromagnetic field enhancement gives rise to an enhancement of the magneto-optical activity. On the other hand, we have analyzed the modulation of the propagating surface plasmon polariton wavevector in noble metal/ferromagnet/noble metal&#13;\ntrilayers by an external magnetic field. These phenomena can be addressed as new concepts for the development of active plasmonic devices.
Selection of a Bacillus pumilus Strain Highly Active against Ceratitis capitata (Wiedemann) Larvae (2009)

Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), the Mediterranean fruit fly (medfly), is one of the most important fruit pests worldwide. The medfly is a polyphagous species that causes losses in many crops, which leads to huge economic losses. Entomopathogenic bacteria belonging to the genus Bacillus have been proven to be safe, environmentally friendly, and cost-effective tools to control pest populations. As no control method for C. capitata based on these bacteria has been developed, isolation of novel strains is needed. Here, we report the isolation of 115 bacterial strains and the results of toxicity screening with adults and larvae of C. capitata. As a result of this analysis, we obtained a novel Bacillus pumilus strain, strain 15.1, that is highly toxic to C. capitata larvae. The toxicity of this strain for C. capitata was related to the sporulation process and was observed only when cultures were incubated at low temperatures before they were used in a bioassay. The mortality rate for C. capitata larvae ranged from 68 to 94% depending on the conditions under which the culture was kept before the bioassay. Toxicity was proven to be a special characteristic of the newly isolated strain, since other B. pumilus strains did not have a toxic effect on C. capitata larvae. The results of the present study suggest that B. pumilus 15.1 could be considered a strong candidate for developing strategies for biological control of C. capitata.