gebhart/patrepeval huggingface dataset:
Antimicrobial Peptides for Use in Oyster Aquaculture: Effect on Pathogens, Commensals, and Eukaryotic Expression Systems (2008)

Two antimicrobial peptides (AMPs) of marine origin, tachyplesin from the Japanese horseshoe crab, Tachypleus tridentatus, and pleurocidin-amide from the winter flounder, Pseudopleuronectes americanus, were tested for their potential effectiveness in disease treatment in oyster aquaculture. Tachyplesin had a greater antimicrobial effect than pleurocidin-amide against a range of gram-positive and gram-negative bacteria, with minimum inhibitor concentrations in the range of 0.625 to 5 μg mL−1. Tachyplesin (50 μg mL−1) was also more effective than pleurocidin-amide (250 μg mL−1) against the oyster protozoan parasite Perkinsus marinus, reducing its viability to 9% versus 22% in vitro. Both peptides were unaffected by variations in pH and salinity that would be encountered in marine culture conditions. Candidate algal and yeast for expression and feed-based delivery of recombinant AMPs were largely unaffected by tachyplesin and pleurocidin at concentrations that inhibited bacterial growth but were sensitive to concentrations that reduced the viability of P. marinus. Several proteases, including those of oyster and parasitic origin, decreased AMP activity, but tachyplesin was affected to a much lesser degree than pleurocidin-amide. Coincubation of homogenates from oyster digestive tissues with tachyplesin and pleurocidin-amide was found to reduce the abundance of colony forming units in the tissue. Tachyplesin was more effective against gram-negative bacteria present in oyster tissues, whereas pleurocidin-amide was more effective against gram-positive bacteria. Tachyplesin was considered a better candidate than pleurocidin-amide for feed-based delivery applications in oyster aquaculture.
A “Catch and Release” Strategy for the Parallel Synthesis of 2,4,5-Trisubstituted Pyrimidines (2003)

A resin capture and release strategy for making a combinatorial array of 2,4,5-trisubstituted pyrimidines is demonstrated by capturing β-ketoesters and β-ketoamides on a solid-supported piperazine. Through a cyclocondensation reaction, the solid-supported enaminone is reacted with several guanidines under heating or microwave irradiation affording the corresponding pyrimidines in good yield and chemical purity directly on solution. After this final step, the support can be effectively recycled.
Use of carbomethylcellulose to improve the mechanical and handling characteristics of calcium sulfate bone graft material (2003)

Calcium sulfate has a long history of safe and effective use for repair of bone defects. However, the poor mechanical and physical properties have limited its clinical use. This project sought to augment the mechanical and handling characteristics of calcium sulfate cement by addition of either 5 and 10 wt% carboxymethylcellulose. Compared to control calcium sulfate, the augmented samples had lower density, higher workability, increased modulus of elasticity, and greater ultimate strength.
High Speed Photoresponse Mechanism of a GaAs-MESFET (1980)

The high speed photoresponse of a GaAs-MESFET has been demonstrated using a light pulse of about 100 ps duration with a 2 GHz repetition rate generated by a GaAlAs-DH laser diode. The measured current pulse heights through the gate and through the drain as a function of the gate bias voltage confirmed a theory that the photoresponse in MESFETs is caused by the sweepout effect of photogenerated carriers in the depletion layer extending from the gate to the drain, just as in photodiodes with subsequent ordinal FET amplification.
Dynamic thrombosis and thrombolysis. Role of antithrombins. (1991)

In vivo thrombosis after deep arterial injury has been experimentally shown by receptor inhibi- tors to be mediated predominantly by thrombin activation of platelets and to a lesser extent by thrombin-related fibrin formation.Thrombosis and thrombolysis are dynamic and simultaneous pro- cesses that may influence each other, depending on the exposure and concentration of thrombin and administered agents and dosages.The dose-depen- dent antithrombotic effect of heparin is mediated by its antithrombin action, but is incomplete even at dosages of 500 units/kg administered over 1 hour.1"2Because of the critical role of thrombin in the thrombotic and lytic processes and the improved inhibition of thrombin in all locations by small molecular and specific thrombin inhibitors, the articles concerning the specific thrombin inhibitors hirudin and argatroban in the previous3 and the present4 issues of Circulation are of interest.Haskel et al,3 in a recent issue of Circulation, compared single doses of antithrombin (hirudin and heparin) with antiplate- let (aspirin and antibody to glycoprotein 1Ib/IIIa platelet membrane receptor) therapy in the acceler- See p 1510 ation of thrombolysis and prevention of reocclusion.In this issue, Clarke et a14 have taken an important step in administering another antithrombin agent, argatroban, to nine normal volunteers with and without aspirin.Role of Thrombin and Platelets in Arterial Thrombosis Specific thrombin inhibition with hirudin or arga- troban-which do not directly block other mediators of platelet aggregation such as thromboxane, seroto- nin, ADP, or collagen -significantly prevent arterial thrombus formation and markedly limit platelet deposition.1'5-7However, neither specific thromboxane A2 inhibitors or serotonin receptor inhibitors, when given alone, prevent arterial thrombosis or reduce platelet
Biophotonic logic devices based on quantum dots and temporally-staggered Förster energy transfer relays (2013)

Integrating photonic inputs/outputs into unimolecular logic devices can provide significantly increased functional complexity and the ability to expand the repertoire of available operations. Here, we build upon a system previously utilized for biosensing to assemble and prototype several increasingly sophisticated biophotonic logic devices that function based upon multistep Förster resonance energy transfer (FRET) relays. The core system combines a central semiconductor quantum dot (QD) nanoplatform with a long-lifetime Tb complex FRET donor and a near-IR organic fluorophore acceptor; the latter acts as two unique inputs for the QD-based device. The Tb complex allows for a form of temporal memory by providing unique access to a time-delayed modality as an alternate output which significantly increases the inherent computing options. Altering the device by controlling the configuration parameters with biologically based self-assembly provides input control while monitoring changes in emission output of all participants, in both a spectral and temporal-dependent manner, gives rise to two input, single output Boolean Logic operations including OR, AND, INHIBIT, XOR, NOR, NAND, along with the possibility of gate transitions. Incorporation of an enzymatic cleavage step provides for a set-reset function that can be implemented repeatedly with the same building blocks and is demonstrated with single input, single output YES and NOT gates. Potential applications for these devices are discussed in the context of their constituent parts and the richness of available signal.
Analytic analysis of load alignment for coning extreme‐scale rotors (2019)

Abstract Extreme‐scale wind turbines (rated powers greater than 10 MW) with large rotor diameters and conventional upwind designs must resist extreme downwind and gravity loads. This can lead to significant structural design challenges and high blade masses that can impede the reduction of levelized cost of wind energy. Herein, the theoretical basis for downwind load alignment is developed. This alignment can be addressed with active downwind coning to reduce/eliminate flapwise bending loads by balancing the transverse components of thrust, centrifugal, and gravitational force. Equations are developed herein that estimates the optimal coning angle that reduces flapwise loads by a specified amount. This analysis is then applied to a 13.2‐MW scale with 100‐m‐level wind turbine blades, where it is found that a load alignment coning schedule can substantially reduce the root flapwise bending moments. This moment reduction in this example can allow the rotor mass to be decreased significantly when compared with a conventional upwind three‐bladed rotor while maintaining structural performance and annual energy output.
Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1 (2011)

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed.
Laser diagnostics for studies of turbulent combustion (2000)

The demands on the quality of velocity, concentration and temperature data from turbulent combustion systems for comparison with numerical predictions are rising with the increasing performance of models for the numerical description of these effects. These demands lead to a high degree of maturity in laser-based methods for concentration, temperature and species information. Laser-based methods are able to give the required information without severely disturbing the observed effects and with the needed accuracy and temporal and spatial resolution. This article reviews the state of the art and recent developments of laser-Doppler velocimetry, Rayleigh spectroscopy, spontaneous Raman spectroscopy, coherent anti-Stokes Raman spectroscopy and laser-induced fluorescence. Emphasis is placed not only on aspects of these measurement techniques connected with spatially and temporally resolved quantitative measurements in turbulent combustion, but also on the interaction of the requirements of these methods on the object with the requirements of the characterized object itself and with demands from methods of numerical prediction on the generated data. New developments and requirements on the reviewed methods originating from new trends in combustion modelling are included.
Fractions: Results and Implications from National Assessment (1981)

Despite the recent introduction of the calculator and emphasis on the metric system, fractions continue to occupy an important place in school mathematics programs. Persuasive arguments for continued emphasis can be made not only because of their social utility but also because of their place in the development and structuring of mathematical ideas to follow. Accordingly, the National Assessment of Educational Processes (NAEP) allocated a substantial portion of the second mathematics assessment to fractions.
A low-overhead fault tolerance scheme for TSV-based 3D network on chip links (2008)

Three-dimensional die stacking integration provides the ability to stack multiple layers of processed silicon with a large number of vertical interconnects. Through Silicon Vias (TSVs) provide a promising area- and power-efficient way to support communication between different stack layers. Unfortunately, low TSV yield significantly impacts design of three-dimensional die stacks with a large number of TSVs. This paper presents a defect-tolerance technique for TSVs-based multi-bit links through an efficient and effective use of redundancy. This technique is ideally suited for three-dimensional network-on-chip (NoC) links. Simulation results demonstrate significant yield improvement, from 66% to 98%, with a low area cost (17% on a vertical link in a NoC switch, which leads a modest 2.1% increase the total switch area) in 130 nm technology, with minimal impact of VLSI design and test flows.
Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers (2015)

The vision of creating accessible, reliable clinical evidence by accessing the clincial experience of hundreds of millions of patients across the globe is a reality. Observational Health Data Sciences and Informatics (OHDSI) has built on learnings from the Observational Medical Outcomes Partnership to turn methods research and insights into a suite of applications and exploration tools that move the field closer to the ultimate goal of generating evidence about all aspects of healthcare to serve the needs of patients, clinicians and all other decision-makers around the world.
Increased platelet and leukocyte activation as contributing mechanisms for thrombosis in essential thrombocythemia and correlation with the JAK2 mutational status. (2006)

These results would support a role for platelet and monocyte activation in the thrombosis of ET. In these patients, the presence of the JAK2 V617F mutation is associated with higher platelet activation.
Structure of the human alpha 2 subunit gene of the glycine receptor--use of vectorette and Alu-exon PCR. (1996)

The alpha subunit of the glycine receptor is encoded by multiple genes that display developmental and tissue-specific expression. The alpha 1 subunit gene is expressed predominantly in the adult brain stem and spinal cord, whereas the alpha 2 subunit gene is expressed in fetal brain and spinal cord. We wished to determine the genomic organization of the human alpha 2 subunit gene as well as to define the 5' ends of the alpha 1 and alpha 2 subunit genes. Gene structure can be defined rapidly from yeast artificial chromosome (YAC) DNA sources by the use of vectorette-exon polymerase chain reaction (PCR). However, YACs frequently contain small deletions that complicate the determination of the complete exon-intron structure of a gene, and this often necessitates the isolation of additional clones. In this study we have used vectorette-exon PCR from YAC DNA to define exons of the glycine receptor alpha 2 subunit gene. To define those exons that were absent in the isolated YACs, we used Alu-exon PCR on genomic DNA, using nested primers to obtain specificity in the PCR reactions. The alpha 2 subunit gene was found to contain nine exons varying in size from 68 bp (exons 3A and 3B) to 581 bp (exon l). All of the intron-exon boundary sequences conform to consensus splice donor and acceptor sites. In addition, we have defined the 5' end of this gene as well as that of the alpha 1 subunit gene by RACE-PCR. The structures of the alpha subunit glycine receptor genes in humans are very similar to each other and to the alpha subunit genes in mice.
The Influence of Orientation on the Fatigue of Directionally Solidified Superalloys (1980)

Directionally solidified (DS) nickel base superalloys were introduced to improve performance of jet engine turbine airfoils. The DS process imparts improved creep-rupture (1) and thermal fatigue (2) resistance in the solidification direction due to preferred crystallographic texture and grain boundary orientation, Figure 1. Although the solidification direction is the prime load bearing direction in turbine airfoils, the actual stress states are in general quite complex as a result of thermal stresses and geometric constraints. This complexity inevitably leads to the generation of stress in directions other than the solidification direction. For satisfactory airfoil performance, the
Co2 Capture And Pumping (2011)

2-3 columns)CO 2 emission ~2.5 Mt CO 2
Efficient Energy Transfer to Achieve Narrow Bandwidth Red Emission from Eu<sup>3+</sup>-Grafting Conjugated Polymers (2002)

A convenient approach to novel Eu3+-grafting conjugated polymers to achieve sharp red emission for polymeric light emitting diodes (PLEDs) has been developed in this contribution. The structure of polymer 1 is verified by FT-IR, 1H, 13C NMR and elemental analysis. The results indicate that efficient intramolecular Föster energy transfer depends on the overlap between the fluorescent spectrum of polymer 1 and absorption spectrum of Eu3+ chelates. Eu(DBM)3 is obviously the best one for accepting energy from polymer 1 among three Eu3+ chelates to exhibit the sharp red emission. The investigation also shows that the efficiency of energy transfer relies on the content of Eu3+ in the complexes. The investigations on the photophysical and electrochemical properties also show that the HOMO and LUMO energy levels and the band gap of complexes have no alteration with the attachment of the Eu3+ chelate in comparison with those of polymer 1 due to the Eu3+ chelate at the side chain of the whole molecule. The pure red electroluminescence is achieved from the fabrication of PLEDs using complex 5 as the active layer with the configuration of ITO/PVK/complex 5/Ba/Al.
Efficient building and placing of gating functions (1995)

In this paper, we present an almost-linear time algorithm for constructing Gated Single Assignment (GSA), which is SSA augmented with gating functions at o-nodes. The gating functions specify the control dependences for each reaching definition at a o-node. We introduce a new concept of gating path, which is path in the control flow graph from the immediate dominator u of a node v to v, such that every node in the path is dominated by u. Previous algorithms start with o-function placement, and then traverse the control flow graph to compute the gating functions. By formulating the problem into gating path construction, we are able to identify not only a o-node, but also a gating path expression which defines a gating function for the o-node.
A New Constitutive Model for Alumina Powder Compaction (1997)

Based on a systematic experimental investigation of the mechanical properties of alumina powder a new general 3-D constitutive model for compaction of powders has been developed. A significant feature of the model is that it describes the time effects on compaction. These effects have been revealed by creep and relaxation phenomena and by the influence of the strain rate. Although the theory is applicable to general 3-D conditions all the parameters involved in the model can be derived from the results of a few number of conventional triaxial drained compression tests. The procedure to identify the model parameters from data is general. Unlike the models available in the literature, the model developed in the present paper accounts for both compressibility and dilatant behavior of powders. Thus it provides a realistic description and a better understanding of the mechanisms of powder pressing. The theory is able to model important aspects of powder behavior with a degree of accuracy which appears to make it useful in FEM analyses of stress and density distribution in a pressed compact.
Mutation of Three Residues in the Third Intracellular Loop of the Dopamine D2 Receptor Creates an Internalization-defective Receptor (2014)

Arrestins mediate desensitization and internalization of G protein-coupled receptors and also direct receptor signaling toward heterotrimeric G protein-independent signaling pathways. We previously identified a four-residue segment (residues 212-215) of the dopamine D2 receptor that is necessary for arrestin binding in an in vitro heterologous expression system but that also impairs receptor expression. We now describe the characterization of additional mutations at that arrestin binding site in the third intracellular loop. Mutating two (residues 214 and 215) or three (residues 213-215) of the four residues to alanine partially decreased agonist-induced recruitment of arrestin3 without altering activation of a G protein. Arrestin-dependent receptor internalization, which requires arrestin binding to β2-adaptin (the β2 subunit of the clathrin-associated adaptor protein AP2) and clathrin, was disproportionately affected by the three-residue mutation, with no agonist-induced internalization observed even in the presence of overexpressed arrestin or G protein-coupled receptor kinase 2. The disjunction between arrestin recruitment and internalization could not be explained by alterations in the time course of the receptor-arrestin interaction, the recruitment of G protein-coupled receptor kinase 2, or the receptor-induced interaction between arrestin and β2-adaptin, suggesting that the mutation impairs a property of the internalization complex that has not yet been identified.
Automation of Radiation Treatment Planning—IV. Derivation of a Mathematical Expression for the per cent Depth Dose Surface of Cobalt 60 Beams and Visualisation of Multiple Field Dose Distributions (1964)

A formula is presented for approximating the per cent depth distribution resulting from any portal size 60Co beam at 80 cm SSD. This equation may be used to obtain computer print-outs of combined multifield dose distributions as described previously (Sterling et al., 1963b), or, in a new programme, can be used to print out the combined isodose curves directly to scale with small error. A distinct geometric property of the per cent depth dose distribution is discovered and described without attempting to explain it.
Adaptive Deep Kernel Learning (2019)

Deep kernel learning provides an elegant and principled framework for combining the structural properties of deep learning algorithms with the flexibility of kernel methods. By means of a deep neural network, we learn a parametrized kernel operator that can be combined with a differentiable kernel algorithm during inference. While previous work within this framework has focused on learning a single kernel for large datasets, we learn a kernel family for a variety of few-shot regression tasks. Compared to single deep kernel learning, our algorithm enables the identification of the appropriate kernel for each task during inference. As such, it is well adapted for complex task distributions in a few-shot learning setting, which we demonstrate by comparing against existing state-of-the-art algorithms using real-world, few-shot regression tasks related to the field of drug discovery.
A functional analysis of imprinting in parthenogenetic embryonic stem cells (1994)

A detailed analysis of the developmental potential of parthenogenetic embryonic stem cells (PGES) was made in vivo and in vitro, and a comparison was made with the development of cells from parthenogenetic embryos (PG). In vivo, in chimeras with normal host cells (N), PGES cells showed a restricted tissue distribution consistent with that of PG cells, suggesting faithful imprinting in PGES cells with respect to genes involved in lineage allocation and differentiation. Restricted developmental potential was also observed in teratomas formed by ectopic transfer under the kidney capsule. In contrast, the classic phenotype of growth retardation normally observed in PG<==>N chimeras was not seen, suggesting aberrant regulation in PGES cells of genes involved in growth regulation. We also analysed the expression of known imprinted genes after ES cell differentiation. Igf2, H19 and Igf2r were all appropriately expressed in the PGES derived cells following induction of differentiation in vitro with all-trans retinoic acid or DMSO, when compared with control (D3) and androgenetic ES cells (AGES). Interestingly, H19 was found to be expressed at high levels following differentiation of the AGES cells. Due to the unexpected normal growth regulation of PGES<==>N chimeras we also examined Igf2 expression in PGES derived cells differentiated in vivo and found that this gene was still repressed. Our studies show that PGES cells provide a valuable in vitro model system to study the effects of imprinting on cell differentiation and they also provide invaluable material for extensive molecular studies on imprinted genes. In addition, the aberrant growth phenotype observed in chimeras has implications for mechanisms that regulate the somatic establishment and maintenance of some imprints. This is of particular interest as aberrant imprinting has recently been invoked in the etiology of some human diseases.