gebhart/patrepeval huggingface dataset:
Mutational Analysis of Endonuclease V from <i>Thermotoga maritima</i> (2002)

Endonuclease V nicks damaged DNA at the second phosphodiester bond 3' to inosine, uracil, mismatched bases, or abasic (AP) sites. Alanine scanning mutagenesis was performed in nine conserved positions of Thermotoga maritima endonuclease V to identify amino acid residues involved in recognition or endonucleolytic cleavage of these diverse substrates. Alanine substitution at D43, E89, and D110 either abolishes or substantially reduces inosine cleavage activity. These three mutants gain binding affinity for binding to double-stranded or single-stranded inosine substrates in the absence of a metal ion, suggesting that these residues may be involved in coordinating catalytic metal ion(s). Y80A, H116A, and, to a lesser extent, R88A demonstrate reduced affinities for double-stranded or single-stranded inosine substrates or nicked products. The lack of tight binding to a nicked inosine product accounts for the increased rate of turnover of inosine substrate since the product release is less rate-limiting. Y80A, R88A, and H116A fail to cleave AP site substrates. Their activities toward uracil substrates are in the following order: H116A > R88A > Y80A. These residues may play a role in substrate recognition. K139A maintains wild-type binding affinity for binding to double-stranded and single-stranded inosine substrate, but fails to cleave AP site and uracil substrate efficiently, suggesting that K139 may play a role in facilitating non-inosine substrate cleavage.
On Auctions as the Negotiation Paradigm of Electronic Markets (2000)

Until recently, electronic markets were dominated by the combination of static offer schemes and fixed pricing. Static offer schemes such as online catalogues apparently bear the risk of not matching the requirements of all potential buyers. But fixing a price also imposes another risk to the seller - the price might not always reflect the current market balance of supply and demand and the specific valuation of a single buyer. Whereas static offer schemes today are still prevalent, electronic auctions address the risk related to fixed pricing with an easy way of price discovery and differentiation by soliciting a wide range of bids from multiple parties. In this paper reasons for the recent success of the auction paradigm in electronic markets are identified. But we will also illustrate one fundamental limitation: the price-based bidding of today's auctions supports only distributive negotiations and does not provide a model for integrative negotiations where differences in the valuations of consumers and providers are exploited in order to achieve joint gains. Several solutions have been suggested to address this issue. We review critically these approaches and outline directions for future research.
Very simple approach for high performance DFB laser-electroabsorptionmodulator monolithic integration (1994)

A novel and very simple approach is demonstrated for distributed feedback laser-electroabsorption modulator monolithic integration. This uses the same strained multiquantum well active layer for both optical functions. Very high performance (13.6 dB extinction ratio at 1.5 V operating voltage for a 70 µm long modulator) is reported at 1.5 µm.
Intramolecular Hydroamination Reactions Catalyzed by Neutral and Cationic Group IV Pyridylamido Complexes (2012)

Abstract Zr IV and Hf IV benzyl (neutral or cationic) and amido catalysts stabilized by pyridylamido ligands are found to be good candidates for the intramolecular hydroamination/cyclization of primary and secondary aminoalkenes. In particular, cationic monobenzyl derivatives have shown remarkable catalytic activity for the production of five and six‐membered N‐containing heterocycles from secondary amino alkenes. In addition, Zr IV and Hf IV amido derivatives that are produced by a temperature‐controlled prototropic rearrangement have provided evidence of the central role played by the metal coordination sphere in promoting such catalytic transformations efficiently.
Band Alignment Between ZnO-Based and Cu(In,Ga)Se2 Thin Films for High Efficiency Solar Cells (2006)

Thin-film solar cells based on Cu(In,Ga)Se2 contain a thin buffer layer of CdS in their standard configuration. In order to avoid cadmium in the device for environmental reasons, Cd-free alternatives are investigated. In this thesis, ZnO-based films, containing Mg or S, grown by atomic layer deposition (ALD), are shown to be viable alternatives to CdS. The CdS is an n-type semiconductor, which together with the n-type ZnO top-contact layers form the pn-junction with the p-type Cu(In,Ga)Se2. From device modeling it is known that a buffer layer conduction band (CB) position of 0-0.4 eV above that of the Cu(In,Ga)Se2 layer is consistent with high photovoltaic performance. For the Cu(In,Ga)Se2/ZnO interface this position is measured by photoelectron spectroscopy and optical methods to –0.2 eV, resulting in increased interface recombination. By including sulfur into ZnO, a favorable CB position to Cu(In,Ga)Se2 can be obtained for appropriate sulfur contents, and device efficiencies of up to 16.4% are demonstrated in this work. From theoretical calculations and photoelectron spectroscopy measurements, the shift in the valence and conduction bands of Zn(O,S) are shown to be non-linear with respect to the sulfur content, resulting in a large band gap bowing. ALD is a suitable technique for buffer layer deposition since conformal coverage can be obtained even for very thin films and at low deposition temperatures. However, deposition of Zn(O,S) is shown to deviate from an ideal ALD process with much larger sulfur content in the films than expected from the precursor pulsing ratios and with a clear increase of sulfur towards the Cu(In,Ga)Se2 layer. For (Zn,Mg)O, single-phase ZnO-type films are obtained for Mg/(Zn+Mg) &lt; 0.2. In this region, the band gap increases almost linearly with the Mg content resulting in an improved CB alignment at the heterojunction interface with Cu(In,Ga)Se2 and high device efficiencies of up to 14.1%.
A comparative adsorption study: 17β-estradiol onto aerobic granular sludge and activated sludge (2015)

Adsorption plays a significant role in removing hydrophobic 17β-estradiol (E2) from wastewater. Batch experiments were conducted to compare the adsorption of E2 onto activated aerobic granular sludge (AGS) and activated sludge (AS), and features evaluated included the adsorption kinetics, thermodynamics, and influence of other environmental factors. By using a non-chemical wet-heat technique, both AGS and AS were treated to inactivated status. Then, after loading E2, the adsorption equilibrium capacity of the AGS was found to be greater than that of the AS at the same initial concentration of E2. Moreover, both the adsorption processes corresponded to a pseudo-second-order kinetic model; the adsorption rate constant of AGS was found to be higher and the half-adsorption time was shorter than that of AS. Next, evaluations of adsorption isotherms and thermodynamics indicated that the adsorption process was mainly a physical process. Lower temperatures facilitated a higher equilibrium adsorption capacity. However, the adsorption binding sites of AGS were distributed more uniformly at higher temperature, in contrast to the distribution found for AS. Finally, acidic conditions and an appropriate ionic strength (0.4 mol/L) were found to be particularly conducive to the adsorption process. Overall, the results showed that AGS has the potential to adsorb E2 with significant efficiency, thereby offering a new and more efficient means of treating E2 and trace oestrogens in wastewater.
A Spreadsheet Framework for Visual Exploration of Biomedical Datasets (2005)

In this paper, we present our spreadsheet framework, which uses a spreadsheet-like interface for exploring biomedical datasets. The principles and advantages of this class of visualization systems are illustrated, and a case study for the analysis of hip joint congruity is presented. Throughout this use case, we see how end users can compare different datasets, apply parallel operations on data, create analysis templates, and how this helps them in the exploration process.
Multifunctional Structure-Power for Electric Unmanned Systems (2006)

We provide an overview of recent US Naval Research Laboratory research and development on multifunctional structure-power materials/components for enhancing the performance of unmanned systems through reduction of parasitic (unifunctional) structure mass/volume. Design rules and tools for composite multifunctional materials and three multifunctional structure-power concepts: structure-battery, autophagous (self-consuming) structure-fuel, and solar-skin will be examined. The potential benefits and the technical challenges associated with multifunctional structure-power will be highlighted along with current technological thrusts and possible breakthroughs that can significantly advance the state-of-art.
Misconceptions at the bottom of "Hopelessness of all psychology." (1907)

The last publication of Mobius 1 gives in his usual very clear and smoothly readable style an excellent sketch of that dogmatic dualistic schism between psychology and natural science which is the bulwark of those who have to make a fundamental contrast between biology as physiology or physico-chemical investigation of living organisms, and a psychology serving as the grammar of the Geisteswissenschaften."As far as man can be perceived, he belongs to nature; as he thinks and feels he is something different from nature."Since science has only a physical basis, it cannot be applied to mental life.Such a statement would almost sound archaic if we were not aware of the fact that after all it voices the opinion of many of the foremost -not to say the best -thinkers of the day.Mobius shows up mercilessly the barrenness of our formal psychology and the bulk of laboratory work, and sees in ' metaphysics ' the only salvation, the only spice, that will make psychology acceptable.He gives an interesting critical review of the methods of animal psychology, the psychological rationalism, evolution, the difference of man and animal, the instinctive processes, the sizing up of the sum of instincts (= the character), and the competition of the instinctive processes, perception, voluntary life, thinking, feeling, discrimination, memory, conception, the notion of the unconscious, and importance of unconscious processes -pages of most suggestive and entertaining contemplations; and finally, after having shaken one sham support of traditional psychology after another, and after having given the reader a better taste of the meat of psychology than I have ever seen offered in so small a scope, he leads him into -idealistic monism.The 69 pages are full of valuable material and in many ways an admirable summary of some of the most vital topics of a psychology and really the testament of a serious worker and thinker.There is but one disappointment, viz., that Mobius did not apply his keen critical maxims to his own way of getting square with his conception of science and with what he calls the ' hopelessness of all psychology.' Mobius gives excellent advice." The chief duty of a psychologist seems to me to be that he use the simplest language, avoid traditional 1 Die Hoffnungslosigkeit alter
Anticipatory Vehicle Routing using Delegate Multi-Agent Systems (2007)

This paper presents an agent-based approach, called delegate multi-agent systems, for anticipatory vehicle routing to avoid traffic congestion. In this approach, individual vehicles are represented by agents, which themselves issue lightweight agents that explore alternative routes in the environment on behalf of the vehicles. Based on the evaluation of the alternatives, the vehicles then issue light-weight agents for allocating road segments, spreading the vehicles' intentions and coordinating their behavior. To evaluate the approach, we have developed an initial prototype application. Test results indicate that delegate multi-agent systems are a promising approach for anticipatory vehicle routing.
Controllable Synthesis of Graphene by Plasma‐Enhanced Chemical Vapor Deposition and Its Related Applications (2016)

Graphene and its derivatives hold a great promise for widespread applications such as field-effect transistors, photovoltaic devices, supercapacitors, and sensors due to excellent properties as well as its atomically thin, transparent, and flexible structure. In order to realize the practical applications, graphene needs to be synthesized in a low-cost, scalable, and controllable manner. Plasma-enhanced chemical vapor deposition (PECVD) is a low-temperature, controllable, and catalyst-free synthesis method suitable for graphene growth and has recently received more attentions. This review summarizes recent advances in the PECVD growth of graphene on different substrates, discusses the growth mechanism and its related applications. Furthermore, the challenges and future development in this field are also discussed.
Cell‐Wall Lipopolysaccharides of Ampicillin‐Resistant Mutants of <i>Escherichia coli</i> K‐12 (1976)

The lipopolysaccharides of ampicillin-resistant cell-wall-defective mutants of Escherichia coli K-12 were analyzed. From their lipopolysaccharides the respective core oligosaccharides were obtained. Following dephosphorylation,the core oligosaccharides were methylated and analyzed by gas chromatography/mass spectrometry. From core-defective mutants substructures of the K-12 core were obtained. Analysis of the lipopolysaccharide preparations from wild-type K-12 indicated the presence of several core structures with different degrees of completion. The lipopolysaccharide preparation was degraded and the oligosaccharide mixture was partially resolved by gel filtration chromatography. Methylation, gas chromatography and mass spectrometry of the oligosaccharides permitted the tentative formulation of the K-12 core structure. Alternative interpretations for this heterogeneity are discussed.
Equivalence salting and temporal dominance of sensations analysis for different sodium chloride substitutes in cream cheese (2013)

The purpose of the study was to determine the potency and equivalence of salt substitutes (potassium chloride, magnesium chloride, monosodium glutamate, potassium lactate, calcium lactate and potassium phosphate monobasic) in cream cheese and to evaluate sensory flavour profiles. The methods used were magnitude estimation and temporal dominance of sensations ( TDS ). Equivalent salting of cream cheese containing 1% sodium chloride was obtained using: 1.2% potassium chloride, 2.56% monosodium glutamate, 2.5% magnesium chloride and 2.98% potassium phosphate. The TDS revealed that, other than salty taste, the most significant flavours produced were sour and bitter. The potencies of salt substitutes are much lower than that of sodium chloride.
Stabilized complex downdating in adaptive beamforming (2002)

Two main findings are reported. The first is an extension to the complex case of the stabilized hyperbolic Householder transformation. The second is a demonstration by computer simulations that this complex stabilized hyperbolic Householder transformation exhibits superior numerical behavior in beamforming applications relative to its conventional counterpart. The problem statement for stabilized complex downdating in adaptive beamforming is given. The complex version of the stabilized hyperbolic Householder transformation is derived, and it is explained why complex processing is necessary in adaptive beamforming. The formulation of the computer simulation is described, together with the result of a simulation example.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Development of intelligent transport systems in Hong Kong (2002)

Attention has recently been given to the development of intelligent transport systems (ITS) in Hong Kong in order to improve the traffic condition and make efficient use of the available resources. Many cities have embarked on efforts to pursue ITS development, but this has proved that various ITS applications are being emphasised in different cities in accordance to the unique nature of the local transport system and the characteristics of the local environment. There is a need for Hong Kong to develop an ITS strategy for long-term deployment plan. This paper provides a review and an evaluation of the potential ITS applications in Hong Kong.
Proteomic Analysis of <i>Trypanosoma cruzi</i> Secretome: Characterization of Two Populations of Extracellular Vesicles and Soluble Proteins (2012)

Microorganisms use specialized systems to export virulence factors into host cells. Secretion of effector proteins into the extracellular environment has been described in Trypanosoma cruzi; however, a comprehensive proteomic analysis of the secretome and the secretion mechanisms involved remain elusive. Here, we present evidence that T. cruzi releases proteins associated with vesicles that are formed by at least two different mechanisms. Transmission electron microscopy showed larger vesicles budding from the plasma membrane of noninfective epimastigotes and infective metacyclic trypomastigotes, as well as smaller vesicles within the flagellar pocket of both forms. Parasite conditioned culture supernatant was fractionated and characterized by morphological, immunochemical, and proteomic analyses. Three fractions were obtained by differential ultracentrifugation: the first enriched in larger vesicles resembling ectosomes, the second enriched in smaller vesicles resembling exosomes, and a third fraction enriched in soluble proteins not associated with extracellular vesicles. Label-free quantitative proteomic analysis revealed a rich collection of proteins involved in metabolism, signaling, nucleic acid binding, and parasite survival and virulence. These findings support the notion that T. cruzi uses different secretion pathways to excrete/secrete proteins. Moreover, our results suggest that metacyclic forms may use extracellular vesicles to deliver cargo into host cells.
Liposomes and Pulmonary Alveolar Macrophages: Functional and Morphologic Interactions (1991)

In vitro toxicity of liposomes and their functional and morphologic interactions with rat pulmonary alveolar macrophage (AMs) were investigated using viability (trypan blue exclusion), phagocytic and killing activity (uptake and digestion of live S. cerevisiae), surface adherence, respiratory burst (nitro-blue tetrazolium reduction), and morphometry (computerized image analysis) as indicators. Liposome stability in physiologic solutions and uptake of liposome-encapsulated carboxyfluorescein (CF) by AMs was assessed by fluorescence spectroscopy and microscopy. Liposomes made from saturated phospholipids and cholesterol were stable, whereas liposomes consisting of unsaturated phospholipids without cholesterol lost 30% to 40% of their content over 24 h. However, CF uptake was highest with unsaturated phospholipid preparations, whereas uptake of the three other formulations was comparable. Although liposome exposure did not affect macrophage viability, a reduction in the number of phagocytizing macrophages to 73% of control was noted after 24-h incubation with the highest lipid concentration tested (10 mumol/ml). Phagocytic killing was similar under all circumstances observed. The fraction of intracellularly killed yeast ranged from 32% to 42% for both control and experimental samples. An increase in cell surface area from 166.1 +/- 39.9 microns 2 on day O (n = 709) to 196.3 +/- 57.6 microns 2 on day 1 (n = 516) and 211.2 +/- 48.0 microns 2 on day 4 (n = 834) was observed after liposome treatment. The corresponding average cell areas of control samples did not change during the observation period. There was no net cell loss of adherence from monolayers as determined by protein assay. The respiratory burst, indicating generation of intracellular superoxide, was also similar--84% to 92% of experimental and control cells under all conditions showed a strong nitro-blue tetrazolium reduction. In summary, in vitro exposure of AMs to large concentrations of liposomes, although producing an increase in macrophage size, was not associated with aberrant macrophage morphologic features, function, or toxicity for the parameters examined.
Insulin-like growth factor-I receptor activity is essential for Kaposi's sarcoma growth and survival (2005)

Kaposi's sarcoma (KS) is a highly vascular tumour and is the most common neoplasm associated with human immunodeficiency virus (HIV-1) infection. Growth factors, in particular vascular endothelial growth factor (VEGF), have been shown to play an important role in its development. The role of insulin-like growth factors (IGFs) in the pathophysiology of different tumours led us to evaluate the role of IGF system in KS. The IGF-I receptors (IGF-IR) were identified by immunohistochemistry in biopsies taken from patients with different AIDS/HIV-related KS stages and on KSIMM cells (an established KS-derived cell line). Insulin-like growth factor-I is a growth factor for KSIMM cells with a maximum increase of 3H-thymidine incorporation of 130 +/- 27.6% (P < 0.05) similar to that induced by VEGF and with which it is additive (281 +/- 13%) (P < 0.05). Moreover, specific blockade of the receptor (either by alpha IR3 antibody or by picropodophyllin, a recently described selective IGF-IR tyrosine phosphorylation inhibitor) induced KSIMM apoptosis, suggesting that IGF-IR agonists (IGF-I and -II) mediate antiapoptotic signals for these cells. We were able to identify an autocrine loop essential for KSIMM cell survival in which IGF-II is the IGF-IR agonist secreted by the cells. In conclusion, IGF-I pathway inhibition is a promising therapeutical approach for KS tumours.
Modeling Anesthetic Drugs' Pharmacodynamic Interaction on the Bispectral Index of the EEG: the Influence of Heart Rate (2007)

The effect of drugs' interaction on the brain signal Bispectral Index (BIS) is of great importance for an anesthesia control drug infusion system. In this study, the objective was to inspect the influence of patient's heart rate on the effect of the drugs on BIS. With this goal, the patient's heart rate was incorporated in an drug interaction model. The model was fitted per patient during anesthesia induction, and tested for prediction under surgery. The results showed that the model with time changing parameters incorporating patient's heart rate has a better performance than a non adjusted model. Three clusters of models were also identified using the fuzzy c-means algorithm. These clusters will help to distinguish between different patients' dynamics.
Weed Management in Spring Seeded Barley, Oats, and Wheat with Prosulfuron (2014)

A limited number of preplant (PP) herbicides are available for spring seeded cereals in Ontario. Six field trials were conducted at the Huron Research Station, Exeter, Ontario, over a two-year period (Exeter, 2010 and 2011) to evaluate glyphosate, prosulfuron, and glyphosate plus prosulfuron applied PP for weed management in spring seeded no-till barley, oats, and wheat. There was no injury in barley, oats, and wheat with glyphosate, prosulfuron, and glyphosate plus prosulfuron applied preplant at the rates evaluated at 1, 2, and 4 weeks after crop emergence. Prosulfuron provided 49–99% control of AMBEL, 28% or less control of CONAR, 31–94% control of POLCO, 49–98% control of SINAR, and 46–79% control of SONAR. Prosulfuron in combination with glyphosate provided 73–98% control of AMBEL, less than 43% control of CONAR, 39–94% control of POLCO, 63–98% control of SINAR, and 60–85% control of SONAR. Prosulfuron reduced density of AMBEL 76% and SINAR 93% but had no significant effect on density of CONAR, POLCO, or SONAR. Prosulfuron in combination with glyphosate reduced biomass of AMBEL as much as 96% and SINAR 98% but had no significant effect on biomass of CONAR, POLCO, or SONAR. Yield of barley, oats, and wheat was not affected with glyphosate, prosulfuron, and glyphosate plus prosulfuron at the rates evaluated.