gebhart/patrepeval huggingface dataset:
Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from <i>Sphingomonas paucimobilis </i>UT26 (2005)

Haloalkane dehalogenases are microbial enzymes that cleave a carbon-halogen bond in halogenated compounds. The haloalkane dehalogenase LinB, isolated from Sphingomonas paucimobilis UT26, is a broad-specificity enzyme. Fifty-five halogenated aliphatic and cyclic hydrocarbons were tested for dehalogenation with the LinB enzyme. The compounds for testing were systematically selected using a statistical experimental design. Steady-state kinetic constants K(m) and k(cat) were determined for 25 substrates that showed detectable cleavage by the enzyme and low abiotic hydrolysis. Classical quantitative structure-activity relationships (QSARs) were used to correlate the kinetic constants with molecular descriptors and resulted in a model that explained 94% of the experimental data variability. The binding affinity of the tested substrates for this haloalkane dehalogenase correlated with hydrophobicity, molecular surface, dipole moment, and volume:surface ratio. Binding of the substrate molecules in the active site pocket of LinB depends nonlinearly on the size of the molecules. Binding affinity increases with increasing substrate size up to a chain length of six carbon atoms and then decreases. Comparative binding energy (COMBINE) analysis was then used to identify amino acid residues in LinB that modulate its substrate specificity. A model with three statistically significant principal components explained 95% of the experimental data variability. van der Waals interactions between substrate molecules and the enzyme dominated the COMBINE model, in agreement with the importance of substrate size in the classical QSAR model. Only a limited number of protein residues (6-8%) contribute significantly to the explanation of variability in binding affinities. The amino acid residues important for explaining variability in binding affinities are as follows: (i) first-shell residues Asn38, Asp108, Trp109, Glu132, Ile134, Phe143, Phe151, Phe169, Val173, Trp207, Pro208, Ile211, Leu248, and His272, (ii) tunnel residues Pro144, Asp147, Leu177, and Ala247, and (iii) second-shell residues Pro39 and Phe273. The tunnel and the second-shell residues represent the best targets for modulating specificity since their replacement does not lead to loss of functionality by disruption of the active site architecture. The mechanism of molecular adaptation toward a different specificity is discussed on the basis of quantitative comparison of models derived for two protein family members.
Two-dimensional electron gas at a Ga0.47In0.53As/ (Al<i>x</i>Ga1−<i>x</i>)0.48In0.52As interface (1988)

We report the first observation of a two-dimensional electron gas in (AlGa) InAs/GaInAs heterostructures. Angular-dependent Shubnikov–de Haas oscillations and quantum Hall effect prove the two dimensionality of the system. We discuss the effect of the barrier composition on the electronic structure of the system. A significant number of electrons remain confined even for the smallest confinement barrier. Persistent photoconductivity was observed at low temperature.
Studies on Carotenoids (1942)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on CarotenoidsJonathan W. White, Jr., Arthur M. Brunson, and F. P. ZscheileCite this: Ind. Eng. Chem. Anal. Ed. 1942, 14, 10, 798–801Publication Date (Print):October 1, 1942Publication History Published online1 May 2002Published inissue 1 October 1942https://pubs.acs.org/doi/10.1021/i560110a015https://doi.org/10.1021/i560110a015research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
In situ design method for multichannel gain of a distributed Raman amplifier with multiwave OTDR (2002)

We demonstrate a novel approach for the measurement of pump/signal waves interaction in the Raman amplifier (RA), with the use of multiwave optical time-domain reflectometry. With the application of obtained pump-evolution profiles to algorithms based on effective length recalibration, the multichannel Raman gain can easily be predicted with excellent accuracy for the undepleted, distributed RA. As a further extension of this algorithm, an in situ semi-analytic Raman-gain design method is also demonstrated.
Platinum-Catalyzed Enzyme Electrodes Immobilized on Gold Using Self-Assembled Layers (1998)

The bonding of enzymes to self-assembled monolayers (SAMs) of alkanethiols onto gold electrode surfaces is exploited to produce an enzyme biosensor. The attachment of glucose oxidase to a SAM of 3-mercaptopropionic acid was achieved using carbodiimide coupling. The resultant biosensor showed good sensitivity to glucose and a large dynamic range when measured amperometrically via the p-benzoquinone mediator. On the other hand, subsequent platinization of the enzyme-SAM electrode allowed hydrogen peroxide produced in the enzyme reaction to be detected directly, thus obviating the need for an artificial redox mediator. The performance of such sensors constructed on bulk gold electrodes was evaluated and finally compared to that of some preliminary thin-film gold electrodes. Biosensors constructed using the two alternative electrode surfaces have quite different sensitivities, thus reflecting the influence of the anchoring surface on the performance of the biosensor.
Effects of DC Current on the Stress-Strain Curve and Hardness of 6061 T6511 Aluminum (2004)

The effects of electricity on the mechanical properties of aluminum are investigated with the ultimate goal of establishing a technique by which the mechanical energy associated with cutting a material can be reduced without requiring an increase in the material’s temperature. The effects of the electricity on the mechanical properties of 6061 aluminum are investigated through both tensile and hardness testing. As the electricity is passed through the material, resistive heating occurs within the material. Therefore, the effects of non-stationary temperatures on the stress-strain behavior of 6061 aluminum are investigate with and without the electrical current flowing through the material. How the electrical effect varies based on the aluminum’s temper is also investigated, along with the effects of electrical pre-treatments. The experimental results indicate that the electricity has the potential to substantially reduce the energy required to machine the material without causing significant increases in the workpiece temperature. The testing also indicates that these effects exist regardless of the temper on the material. Finally, the study found that, while not reducing the energy as substantially as when using a continuous current, an electrical pre-treat can be used to reduce the energy below that found from annealing alone.
Behavioral Social Work in Community and Organizational Settings (1984)

Principles and methods of behavioral social work have found little application at the community and organizational levels of intervention. It is the contention of the authors that integration of such content would enhance practice at these levels. Components of behavioral community intervention are indicated and illustrated in micro/macro settings, with advantages to practice specified. Ethical Considerations in using this methodology are discussed.
DNA sequence of the mouse H-2Dd transplantation antigen gene. (1985)

The inbred BALB/c mouse has three transplantation antigens, H2-Kd, H2-Ld, and H2-Dd. We present the complete nucleotide sequence of the H2-Dd gene as well as 777 residues of previously unpublished H-2Dd protein sequence. These data complete the sequences of all the BALB/c transplantation antigen genes and permit detailed comparison with each other and with their counterparts from the inbred C57BL/10 mouse. Transplantation antigens may differ from one another by as much as 5%-15% of their amino acid sequence for the external domains. These extensive differences may arise by gene conversion. The H-2D region of the BALB/c mouse encodes the H2-Dd and the H2-Ld genes. Serologic data suggest that at least two additional transplantation antigen molecules, H2-Rd and H2-Md, are encoded in the H-2D region of the major compatibility complex. Paradoxically, gene cloning studies have only identified the H2-Dd and the H2-Ld genes in the H-2D region. A complete DNA sequence of the H2-Dd gene shows that a variety of alternative splice sites exist throughout the gene, which may lead to additional gene products and may explain the multiplicity of H-2D-encoded polypeptides.
Defining provably-correct escalation policies for multilayer network restoration (2003)

Automatic protection switching (APS) protocols assigned to different layers in wide-area networks require interworking functionality in order to restore a wide variety of services and accommodate an evolving network infrastructure. Without some coordination between restoration mechanisms, an outage duration would be lengthened as methods assigned to different layers interfere with each other, and the network would be locked up in a deadlocked state that never converges to a new topology. A set of control policies can be specified to schedule different restoration mechanisms in a network that spans multiple layers and administrative boundaries. These control policies, which are expressed as if-then rules, are denoted as the escalation strategy. As rules for coordinating between restoration mechanisms are formally expressed in a policy definition language, a mathematical proof could be provided to prove that the agents have consistent knowledge of the network state, allowing individual APS protocols to cooperate with each other.
Activation of B and As in Ultra Shallow Junction with Heating and Cooling Rates Controlled Millisecond Annealing Induced by Thermal Plasma Jet (2009)

2009 International Conference on Solid State Devices and Materials,Activation of B and As in Ultra Shallow Junction with Heating and Cooling Rates Controlled Millisecond Annealing Induced by Thermal Plasma Jet
TIME DOMAIN ANALYSIS OF OCEAN CLUTTER IN HIGH FREQUENCY RADAR (1990)

High frequency (HF) radar has the unique potential for over-the-horizon detection of ocean surface targets. However, ocean waves are also strong reflectors for HF radar and ths high clutter level has limited its apphcatlon for target detection. Results from the time domain analysis of ocean clutter show that it can be modelled as two angle modulated signals; the two 'carrier' frequencies correspond to the theoretically predicted 'Bragg' Doppler frequencies. This characterization oocan clutter makes it possible to adapt eXlstlng tlme domain techniques to estimate and, if desired, suppress the clutter signal. Enhanced target detection will be demonstrated.
Shear stresses in honeycomb sandwich plates: Analytical solution, finite element method and experimental verification (2012)

Honeycomb composite structures are used in airplanes, railway cars and vehicles. The sandwich panels consist of two stiff face sheets of aluminium, which are bonded to a very lightweight honeycomb core of aluminium. Compared to normal plates, sandwich panels have a very high stiffness and simultaneously a low weight. The core of these structures is mainly subjected to shear stresses. The shear stresses depend strongly on the angle of the load application. The distribution and the level of the shear stresses are investigated using analytical calculations. The load direction which induces highest stresses in the honeycomb core is derived. This direction is not the W-direction, which is the most compliant one. When doing finite element simulations of honeycomb cores, often the core is homogenized in order to reduce the calculation time. In this article, some equations are derived in order to calculate the real shear stresses from the shear stresses of the homogeneous core. The equations are validated by finite element simulations and partially by tests. Three-point bending tests and additionally some Food Cart Roller Tests were conducted in order to test the panels in different angles.
Regulated subset of G <sub>1</sub> growth-control genes in response to derepression by the Wnt pathway (2003)

Pitx2 is a bicoid-related homeodomain factor that is required for effective cell type-specific proliferation directly activating a specific growth-regulating gene cyclin D2. Here, we report that Pitx2, in response to the Wntbeta-catenin pathway and growth signals, also can regulate c-Myc and cyclin D1. Investigation of molecular mechanisms required for Pitx2-dependent proliferation, in these cases, further supports a nuclear role for beta-catenin in preventing the histone deacetylase 1-dependent inhibitory functions of several DNA-binding transcriptional repressors, potentially including E2F4p130 pocket protein inhibitory complex, as well as lymphoid enhancer factor 1 and Pitx2, by dismissal of histone deacetylase 1 and loss of its enzymatic activity. Thus, beta-catenin plays a signal-integrating role in Wnt- and growth factor-dependent proliferation events in mammalian development by both derepressing several classes of repressors and by activating Pitx2, regulating the activity of several growth control genes.
Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering (2013)

An industrial yeast strain for bioethanol production with lignocellulose hydrolysates has been developed in the genetic background of a strain widely used for commercial bioethanol production. The strain uses glucose and D-xylose with high consumption rates and partial cofermentation in various lignocellulose hydrolysates with very high ethanol yield. The GS1.11-26 strain shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates.
Effect of single amino acid replacements on the thermal stability of the NH2-terminal domain of phage lambda repressor. (1984)

The thermal stabilities of mutant phage lambda repressors that have single amino acid replacements in the NH2-terminal domain have been studied by means of circular dichroism and differential scanning calorimetry. The variations in stability determined by these physical methods correlate with the resistance to proteolysis at various temperatures and can be compared with the temperature-sensitive activity of the mutants in vivo. In general, mutant proteins bearing solvent-exposed substitutions have thermal stabilities identical to wild type, whereas buried substitutions reduce stability. In one case, a single amino acid replacement increases the thermal stability of the repressor.
Type Synthesis of 3-DOF PPR Parallel Manipulators Based on Screw Theory and the Concept of Virtual Chain (2004)

PPR-PMs (parallel manipulators) are the parallel counterparts of the 3-DOF PPR serial robots, which are composed of two P (prismatic) joints and one R (revolute) joint. For a PPR-PM, the moving platform can rotate arbitrarily about an axis undergoing a planar translation. This paper deals with the type synthesis of 3-DOF PPR-PMs. At first, virtual chains are introduced to represent the motion patterns of 3-DOF motions and relevant results from screw theory are recalled. A method is then proposed for the type synthesis of 3-DOF PPR-PMs. Using the proposed approach, the type synthesis of 3-DOF PPR-PMs is performed in three steps, namely, the type synthesis of legs for PPR-PKCs (parallel kinematic chains), the type synthesis of PPR-PKCs, and the selection of actuated joints of PPR-PMs. The three steps are dealt with in detail consequently. The characteristics of the proposed approach is that the type synthesis of legs for PPR-PKCs is reduced to the type synthesis of 3-DOF overconstrained single-loop kinematic chains and thus easy to perform. In addition to all the 3-DOF PPR-PKCs and 3-DOF PPR-PMs proposed in the literature, a number of new 3-DOF PPR-PKCs and 3-DOF PPR-PMs are identified. It is also found that there are no PPR-PMs with identical types of legs.
Proinsulin C-peptide increases nitric oxide production by enhancing mitogen-activated protein-kinase-dependent transcription of endothelial nitric oxide synthase in aortic endothelial cells of Wistar rats (2003)

Our results show that C-peptide increases NO production by increasing eNOS protein contents through ERK-dependent up-regulation of eNOS gene transcription. This could explain some actions of C-peptide on the vasculature, indicating a pivotal role for C-peptide in vascular homeostasis.
Electroactive polymeric sensors in hand prostheses: Bending response of an ionic polymer metal composite (2005)

In stark contrast to the inspiring functionality of the natural hand, limitations of current upper limb prostheses stemming from marginal feedback control, challenges of mechanical design, and lack of sensory capacity, are well-established. This paper provides a critical review of current sensory systems and the potential of a selection of electroactive polymers for sensory applications in hand prostheses. Candidate electroactive polymers are reviewed in terms of their relevant advantages and disadvantages, together with their current implementation in related applications. Empirical analysis of one of the most novel electroactive polymers, ionic polymer metal composites (IPMC), was conducted to demonstrate its potential for prosthetic applications. With linear responses within the operating range typical of hand prostheses, bending angles, and bending rates were accurately measured with 4.4+/-2.5 and 4.8+/-3.5% error, respectively, using the IPMC sensors. With these comparable error rates to traditional resistive bend sensors and a wide range of sensitivities and responses, electroactive polymers offer a promising alternative to more traditional sensory approaches. Their potential role in prosthetics is further heightened by their flexible and formable structure, and their ability to act as both sensors and actuators.
Immune Regulation in the Intestine: A Balancing Act between Effector and Regulatory T Cell Responses (2004)

The immune system in the intestine must respond rapidly to invading pathogens without mounting sustained effector cell responses to the indigenous commensal bacteria. Results from this laboratory using the T cell transfer model of colitis suggest that specialized populations of regulatory T cells control the immune response in the intestine. Regulatory T (Tr) cell activity is enriched within the naturally arising CD4(+) CD25(+) Tr subset that has been shown to prevent a number of inflammatory diseases. CD4(+) CD25(+) Tr cells control intestinal inflammation induced by both innate and adaptive immune responses via IL-10- and TGF-beta-dependent mechanisms. Recent results have shown that CD4(+) CD25(+) Tr cells can cure established colitis, suggesting their utility for the treatment of inflammatory bowel disease.
The Effect of Accelerated Aging Tests on the Optical Properties of Silicone and EVA Encapsulants (2009)

The absorption coefficient of three silicones and EVA is measured before and after exposure to three accelerated aging tests: (i) ~2000 hours under Xe-arc lamp exposure at room temperature, (ii) 1200 hours at 85% relative humidity and 85 °C, and (iii) six months at the focal point of a 30× linear tracker. The first exposure satisfied the IEC’s UV conditioning test but with the samples at room temperature rather than 60 °C, the second satisfied the IEEE’s damp-heat test and the damp-heat component of the UL and IEC’s humidity-freeze tests, and the third is a stringent but non-conventional test available at the Australian National University. The most stable encapsulant was found to be polydimethylsiloxane (PDMS) silicone. The EVA was stable under the UV illumination but yellowed under damp-heat exposure and was decimated by the 30× concentrated sunlight. We found the EVA to have the greatest tendency to absorb moisture, a feature that increases scattering and reduces transmission.
Gene Transfer of Tissue Inhibitor of Metalloproteinases-3 Reverses the Inhibitory Effects of TNF-α on Fas-Induced Apoptosis in Rheumatoid Arthritis Synovial Fibroblasts (2005)

Apart from counteracting matrix metalloproteinases, tissue inhibitor of metalloproteinases-3 (TIMP-3) has proapoptotic properties. These features have been attributed to the inhibition of metalloproteinases involved in the shedding of cell surface receptors such as the TNFR. However, little is known about effects of TIMP-3 in cells that are not susceptible to apoptosis by TNF-alpha. In this study, we report that gene transfer of TIMP-3 into human rheumatoid arthritis synovial fibroblasts and MRC-5 human fetal lung fibroblasts facilitates apoptosis and completely reverses the apoptosis-inhibiting effects of TNF-alpha. Although TNF-alpha inhibits Fas/CD95-induced apoptosis in untransfected and mock-transfected cells, fibroblasts ectopically expressing TIMP-3 are sensitized most strongly to Fas/CD95-mediated cell death by TNF-alpha. Neither synthetic MMP inhibitors nor glycosylated bioactive TIMP-3 are able to achieve these effects. Gene transfer of TIMP-3 inhibits the TNF-alpha-induced activation of NF-kappaB in rheumatoid arthritis synovial fibroblasts and reduces the up-regulation of soluble Fas/CD95 by TNF-alpha, but has no effects on the cell surface expression of Fas. Collectively, our data demonstrate that intracellularly produced TIMP-3 not only induces apoptosis, but also modulates the apoptosis-inhibiting effects of TNF-alpha in human rheumatoid arthritis synovial fibroblast-like cells. Thus, our findings may stimulate further studies on the therapeutic potential of gene transfer strategies with TIMP-3.