gebhart/patrepeval huggingface dataset:
Thioredoxin and glutaredoxin-mediated redox regulation of ribonucleotide reductase (2014)

Ribonucleotide reductase (RNR), the rate-limiting enzyme in DNA synthesis, catalyzes reduction of the different ribonucleotides to their corresponding deoxyribonucleotides. The crucial role of RNR in DNA synthesis has made it an important target for the development of antiviral and anticancer drugs. Taking account of the recent developments in this field of research, this review focuses on the role of thioredoxin and glutaredoxin systems in the redox reactions of the RNR catalysis.
Answering approximate queries over autonomous web databases (2009)

To deal with the problem of empty or too little answers returned from a Web database in response to a user query, this paper proposes a novel approach to provide relevant and ranked query results. Based on the user original query, we speculate how much the user cares about each specified attribute and assign a corresponding weight to it. This original query is then rewritten as an approximate query by relaxing the query criteria range. The relaxation order of all specified attributes and the relaxed degree on each specified attribute are varied with the attribute weights. For the approximate query results, we generate users' contextual preferences from database workload and use them to create a priori orders of tuples in an off-line preprocessing step. Only a few representative orders are saved, each corresponding to a set of contexts. Then, these orders and associated contexts are used at query time to expeditiously provide ranked answers. Results of a preliminary user study demonstrate that our query relaxation and results ranking methods can capture the user's preferences effectively. The efficiency and effectiveness of our approach is also demonstrated by experimental result.
Performance analysis of an innovative multimode, multisalt and multieffect chemisorption refrigeration system (2007)

Abstract The conceptual design of an innovative multimode, multisalt and multieffect solid‐gas chemisorption refrigeration system with evaporation and resorption processes is presented. In the proposed system, both the evaporation heat of the refrigerant during adsorption process and the reaction heat of the low‐temperature salt during resorption process are employed to provide useful cooling. The reaction heat of the high‐temperature salt is recovered for the regeneration process of the middle temperature salt. The presented system has the distinct advantage of larger cooling capacity per unit of heat input in comparison with other types of sorption refrigeration systems, based exclusively on evaporation or resorption. To identify the expected COP of the proposed system, two groups of working pairs containing metal chlorides and ammonia were analyzed. The ideal coefficient of performance (COP) can be improved by more than 59 to 169% if compared to the COP obtained with other kinds of cycle. When the sensible heats of the reactant, the refrigerant and the metallic part of the reactors are considered in the calculation of the COP, this figure can reach values between 0.91 and 1.80, according to the salts employed and the mass ratio between the metallic part of the reactor and the salt. © 2007 American Institute of Chemical Engineers AIChE J, 2007
Intranigral fetal dopamine grafts induce behavioral compensation in the rat Parkinson model (1994)

Neural transplantation in experimental Parkinsonism has so far focused on the ectopic placement of fetal ventral mesencephalic (VM) neurons into the dopamine-denervated caudate-putamen. VM grafts are effective in restoring dopamine neurotransmission in the grafted caudate-putamen and in partial amelioration of behavioral deficits. Recent pharmacological and physiological data have provided strong evidence that dopamine released from dendrites of the substantia nigra pars compacta (SNc) neurons within the pars reticulata (SNr) plays an important role in the regulation of the basal ganglia output pathways. Using a novel microtransplantation approach, multiple small cell suspension grafts (250 nl) derived from the VM of E14 rat embryos were implanted into the SNr of unilaterally 6-hydroxydopamine-lesioned rats. Behavioral changes in drug-induced rotation asymmetry were monitored for up to 14 weeks postgrafting, followed by a quantitative assessment and correlation of tyrosine hydroxylase (TH)-positive cell survival. The reduction in rotational asymmetry caused by the intranigral VM grafts was 64% for SKF 38393 (D1 agonist), 54% for apomorphine (mixed D1 and D2 agonist), and 67% for quinpirole (D2 agonist) when compared to a control spinal cord graft group. By contrast, amphetamine-induced rotation was completely unaffected. The correlation between number of TH-positive cells and behavioral compensation was highest for the D1 agonist (R = -0.729), though clear-cut also for the mixed D1/D2 agonist apomorphine (R = -0.664) and the D2 agonist quinpirole (R = -0.642). Favorable morphological features of the VM micrografts included extensive migration of the dopaminergic neurons into the host SNr and the formation of dense patches of dendrite-like TH-positive terminal networks within the SNr. The results demonstrate a novel pattern of behavioral recovery induced by intranigral VM transplants in the rat Parkinson model. This may have important implications for the understanding of how the nigrostriatal dopamine system influences motor control in the basal ganglia as well as for the development of optimal transplantation strategies in Parkinson's disease.
Optimal training design for linearly time-varying MIMO/OFDM channels modelled by a complex exponential basis expansion (2007)

Time- and frequency-selective fading of propagating channels degrades the performance of multiple-input multiple-output/orthogonal frequency-division multiplexing (MIMO/OFDM) systems extensively by introducing double convolutions in both time-domain and frequency-domain. The author addresses the problem of linearly time-varying (LTV) channel estimation of MIMO/OFDM systems. First, the time-varying coefficients of the LTV channel are modelled by complex exponential basis expansions. Secondly, the LTV channel is estimated and the optimal pilot symbols are derived following the minimum mean square error criterion. It is shown that the optimal pilot strategy is to group consecutive pilot tones together as a pilot cluster and to distribute uniformly all pilot clusters in frequency-domain. In addition, the LTV channel estimation is further improved by imposing a window function on received signals. Finally, through simulations, it is shown that the new channel estimator can provide a considerable performance improvement in estimating MIMO-LTV channels, especially for the rapidly time-varying channel of a large Doppler frequency.
Staying in control: Cybersecurity and the modern electric grid (2011)

This article discusses cybersecurity and the modern electric grid. There is an increasing amount of evidence showing that attackers are now focusing on control systems, operating with varying motivations and intentions.
Orthogonal Expression of an Artificial Metalloenzyme for Abiotic Catalysis (2017)

A cytochrome P450 was engineered to selectively incorporate Ir(Me)-deuteroporphyrin IX (Ir(Me)-DPIX), in lieu of heme, in bacterial cells. Cofactor selectivity was altered by introducing mutations within the heme-binding pocket to discriminate the deuteroporphyrin macrocycle, in combination with mutations to the P450 axial cysteine to accommodate a pendant methyl group on the Ir(Me) center. This artificial metalloenzyme was investigated for activity in non-native metallocarbenoid-mediated olefin cyclopropanation reactions and showed enhanced activity for aliphatic and electron-deficient olefins when compared to the native heme enzyme. This work provides a general strategy to augment the chemical functionality of heme enzymes in cells with application towards abiotic catalysis.
Carboxyl ester lipase (2002)

Carboxyl ester lipase (CEL), previously named cholesterol esterase or bile salt-stimulated (or dependent) lipase, is a lipolytic enzyme capable of hydrolyzing cholesteryl esters, tri-, di-, and mono-acylglycerols, phospholipids, lysophospholipids, and ceramide. The active site catalytic triad of serine-histidine-aspartate is centrally located within the enzyme structure and is partially covered by a surface loop. The carboxyl terminus of the protein regulates enzymatic activity by forming hydrogen bonds with the surface loop to partially shield the active site. Bile salt binding to the loop domain frees the active site for accessibility by water-insoluble substrates. CEL is synthesized primarily in the pancreas and lactating mammary gland, but the enzyme is also expressed in liver, macrophages, and in the vessel wall. In the gastrointestinal tract, CEL serves as a compensatory protein to other lipolytic enzymes for complete digestion and absorption of lipid nutrients. Importantly, CEL also participates in chylomicron assembly and secretion, in a mechanism mediated through its ceramide hydrolytic activity. Cell culture studies suggest a role for CEL in lipoprotein metabolism and oxidized LDL-induced atherosclerosis. Thus, this enzyme, which has a wide substrate reactivity and diffuse anatomic distribution, may have multiple functions in lipid and lipoprotein metabolism, and atherosclerosis.
Structure-Preserving Sparsification of Social Networks (2015)

Sparsification reduces the size of networks while preserving structural and statistical properties of interest. Various sparsifying algorithms have been proposed in different contexts. We contribute the first systematic conceptual and experimental comparison of \textit{edge sparsification} methods on a diverse set of network properties. It is shown that they can be understood as methods for rating edges by importance and then filtering globally by these scores. In addition, we propose a new sparsification method (\textit{Local Degree}) which preserves edges leading to local hub nodes. All methods are evaluated on a set of 100 Facebook social networks with respect to network properties including diameter, connected components, community structure, and multiple node centrality measures. Experiments with our implementations of the sparsification methods (using the open-source network analysis tool suite NetworKit) show that many network properties can be preserved down to about 20\% of the original set of edges. Furthermore, the experimental results allow us to differentiate the behavior of different methods and show which method is suitable with respect to which property. Our Local Degree method is fast enough for large-scale networks and performs well across a wider range of properties than previously proposed methods.
Modeling the intact form of the α<sub>1</sub>-proteinase inhibitor (1990)

The structure of the intact form of the serpin alpha 1-proteinase inhibitor has been modeled based on the assumption that the central strand s4A of the six-stranded beta-sheet A of the cleaved inhibitor is not incorporated into the sheet of intact alpha 1-proteinase inhibitor. This strand was removed from its position in the center of the sheet by suitable rotations about the backbone dihedrals of Lys343 using molecular graphics. The resulting structure was then annealed using molecular dynamics (MD) while applying progressive distance restraints to the reactive peptide bond (Met358-Ser359) for 50 ps. During this time, the disrupted beta-sheet reformed to create a five-stranded beta-sheet with strands 3 and 5 in a parallel arrangement. This change and accompanying structural rearrangements are largely confirmed by the X-ray structure of plakalbumin, whose structure reflects the overall structure of intact serpins. The successful modeling experiment demonstrates the utility of MD for making gross structural predictions based on related structures. The binding loop of the intact form is modeled to allow docking with serine proteinases, in particular thrombin, which most highly constrains the possible conformations of the binding loop.
Analysis of eating behavior in restaurants based on leftover food (2010)

Recently in the restaurant businesses, it has become more difficult to design contents of dishes because customers' preferences have become diverse. Leftover meals are good indicators to elucidate customers' satisfaction and eating behaviors. This study examines what causes customers to leave food uneaten-particularly addressing their attributes, motivations, and situations-by conducting interviews of customer groups and measuring their leftovers. Results show that leaving leftovers is significantly influenced by customers' purposes, not by their attributes such as sex or age. Based on the results, this paper presents a discussion of flexible menu design.
Sealing of Thermally Sprayed HVOF Coatings for Boiler Applications (2004)

Abstract Use of high-chlorine and alkali containing fuels such as biomass and refuse is increasing in production of heat and electricity. Fluidized bed boilers experience severe and harsh conditions, in which high temperatures combined with inhomogenous fuel cause severe material wastage to metallic parts in boilers. Thermally sprayed coatings have been reported to provide protection to the boiler tubes. However, thermally sprayed coatings have encountered serious problems, when corrosion has proceeded to the substrate material through voids and oxides in lamella boundaries. Sealing of the coatings can solve these problems. Sealing of coatings with commercial sealants and laser fusion treatment was investigated. Thermally sprayed HVOF metallic coatings were sealed with different commercial sealing agents and diode laser. The coatings were tested in molten salt, simulating condition of fluidized bed boiler superheaters. Optical microscopy (OM), scanning electron microscopy (SEM) and energy dispersive X-ray analysator (EDX) were used for examination of the tested and non-tested specimens. Some of the tested sealants protected the coatings adequately in the short time alkali chloride - alkali sulphate exposure test. Best sealant contained aluminium oxide and aluminium phosphate. Laser treated coatings had good corrosion resistance in a short-term test.
Smart Grid Mesh Network Security Using Dynamic Key Distribution With Merkle Tree 4-Way Handshaking (2013)

Distributed mesh sensor networks provide cost-effective communications for deployment in various smart grid domains, such as home area networks (HAN), neighborhood area networks (NAN), and substation/plant-generation local area networks. This paper introduces a dynamically updating key distribution strategy to enhance mesh network security against cyber attack. The scheme has been applied to two security protocols known as simultaneous authentication of equals (SAE) and efficient mesh security association (EMSA). Since both protocols utilize 4-way handshaking, we propose a Merkle-tree based handshaking scheme, which is capable of improving the resiliency of the network in a situation where an intruder carries a denial of service attack. Finally, by developing a denial of service attack model, we can then evaluate the security of the proposed schemes against cyber attack, as well as network performance in terms of delay and overhead.
Binding of the urokinase-type plasminogen activator to its cell surface receptor is inhibited by low doses of suramin. (1993)

The multipotent drug suramin, which is currently being studied as an anticancer agent, was found to inhibit the interaction between the urokinase-type plasminogen activator (u-PA) and its cellular receptor. 50% inhibition of binding was obtained with a suramin concentration between 30 and 60 micrograms/ml when using U937 cells and a ligand concentration of 0.3 nM. This concentration of the drug is well below the serum levels found in suramin-treated patients. Inhibition of binding was also demonstrated at the molecular level, using chemical cross-linking or an enzyme-linked immunosorbent assay-type technique based on the ligand interaction. The inhibition was not caused by a mere polyanion effect since polysulfates such as heparin, heparan sulfate, and pentosan polysulfate were non-inhibitory or showed only a very weak inhibition. However, polysulfonated compounds with structures resembling suramin (i.e. trypan blue and Evans blue) did prove inhibitory. The inhibition found with suramin showed a concentration dependence consistent with a mixed competitive and noncompetitive mechanism. The off-rate of prebound ligand was accelerated by the drug. It is speculated that the present effect may contribute to the anti-invasive properties of suramin by destroying the cellular potential for localized plasminogen activation and proteolytic matrix degradation.
Studies on the fermentative production of branced-chain amino acids. I. Production of L-leucine by a mutant of Brevibacterium lactofermentum 2256. (1974)

A potent L-leucine producer was screened among mutants of glutamic acid producing bacteria. This strain, No. 218, is one of 2-thiazolealanine resistant mutants derived from a methionine isoleucine double auxotroph of Brevibacterium lactofermentum 2256 by nitrosoguanidine. Strain No. 218 produced 19mg/ml of L-leucine after 72 hr cultivation when 8% glucose and 4% ammonium sulfate were supplied as a carbon and a nitrogen source, respectively, thus giving the yield of 23.1% from glucose. The addition of Fe2+ and Mn2+ in combination gave much more productivity than that of Fe2+ or Mn2+ alone. Effects of amino acids, nucleic acids, vitamins, and the other nutrients on L-leucine production were investigated. The fermentation product was isolated and purified from the culture, and identified as L-leucine.
TGF-β/Smad Signaling in the Injured Liver (2006)

TGF-beta, acting both directly and indirectly, represents a central mediator of fibrogenic remodeling processes in the liver. Besides hepatic stellate cells (HSCs), which are induced by TGF-beta to transdifferentiate to myofibroblasts and to produce extracellular matrix, hepatocytes are also strongly responsive for this cytokine, which induces apoptosis during fibrogenesis and provides growth control in regeneration processes. Based on this, TGF-beta-mediated hepatic responses to injury are the result of a complex interplay between the different liver cell types. In this review we summarize the knowledge about TGF-beta signal transduction in HSCs with special impact on Smad pathways. We further describe a molecular cross-talk between profibrogenic TGF-beta and antifibrogenic IFN-gamma signaling in liver cells. Finally, we introduce hepatocyte plasticity and epithelial-to-mesenchymal transition in the liver, which is well established in tumorigenesis, as a potential feature of fibrogenesis and highlight possible action points of TGF-beta in these contexts.
Attention-reactive user interface for sensemaking (2005)

I will talk about an emerging class of user interfaces that if not exactly intelligent are at least attention-reactive. They are being developed to handle "sensemaking" tasks, in which users find, analyze, and creation products or action from large collections of documents. Applications might be expected to develop in law, education, scholarship, security, and medicine. These interfaces have a focus + context visualization on the front end and a semantic contextual computing engine on the back end. Ultimately they can be expected to have mixed initiatives. These interfaces require the development of a supporting science of human information interaction that stresses interaction between the user and information and deemphasizes the platform through which this occurs.
Astroparticle physics with a customized low-background Broad Energy Germanium detector (2010)

We have found that modified Broad Energy Ge detectors produced by CANBERRA have several promising features, including large mass, low electronic noise, and excellent pulse-shape analysis capabilities. Modified BEGe detectors obtain these capabilities due to their low-capacitance “point-contact” electrode configuration. Modified BEGes are also the only point-contact design fabricated on a commercial basis. We have deployed a modified BEGe, named “MALBEK” in a low-background cryostat and shield in the Kimballton Underground Research Facility, located in Ripplemead, Virginia at a depth of 1450 meters water equivalent. We will focus on detector characteristics, data acquisition, and analysis techniques used with MALBEK.
Growth of Mouse Yolk Sac Cells Cultured <i>in Vivo</i> (1976)

The proliferation and differentiation of yolk sac cells from 10 1/2-day-old mouse embryos were studied in diffusion chambers implanted into syngeneic and allogeneic hosts. The most striking observation was the appearance, proliferation and predominance of immature and mature plasma cells. The data suggested that the differentiation into plasma cells and the rate of growth of yolk sac cells cultured in vivo may be dependent on the genetics of the strain of mouse and host. This demonstration of differentiation of plasma cells from yolk sac cells cultured in vivo adds further information to the origin and ontogeny of potentially immunocompetent cells.
Selective CVD tungsten contact plug technology with plasma pre-treatment (2003)

Low-resistance contact plug technology using selective CVD of W by the SiH/sub 4/ reduction of WF/sub 6/ with SF/sub 6/ pretreatment was developed. This technology solved problems such as encroachment, wormholes, Si consumption, and poor adhesion encountered in only the H/sub 2/-reduction system or only the SiH/sub 4/-reduction system without pretreatment. The contact resistance in this system is lower than that in conventional metallization with Al-Si/Si contacts. It is predicted that this technology will become important for improving the reliability of the interconnection for submicron VLSI.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Opportunistic Service Provisioning in the Cloud (2012)

There is an emerging trend to deploy services in cloud environments due to their flexibility in providing virtual capacity and pay-as-you-go billing features. Cost-aware services demand computation capacity such as virtual machines (VMs) from a cloud operator according to the workload (i.e., service invocations) and pay for the amount of capacity used following billing contracts. However, as recent empirical studies show, the performance variability, i.e., non-uniform VM performance, is inherently higher than in private hosting platforms, since cloud platforms provide VMs running on top of typically heterogeneous hardware shared by multiple clients. Consequently, the provisioning of service capacity in a cloud needs to consider workload variability as well as varying VM performance. We propose an opportunistic service replication policy that leverages the variability in VM performance, as well as the on-demand billing features of the cloud. Our objective is to minimize the service provisioning costs by keeping a lower number of faster VMs, while maintaining target system utilization. Our evaluation results on traces collected from in-production systems show that the proposed policy achieves significant cost savings and low response times.
Thermal lens correction in a solid-state laser using a flexible bimorph mirror (1989)

The resonator of a YAG:Nd3+ laser was used as an example to demonstrate the possibility of correcting the lowest aberrations of a thermal lens by an adaptive bimorph mirror. A fivefold reduction in the thermal lens astigmatism and of certain other aberrations was achieved at laser pump currents in the range 10 to 34 A.