gebhart/patrepeval huggingface dataset:
Proteomic Analysis of Schistosoma mansoni Cercarial Secretions (2005)

Schistosomiasis is a global health problem caused by several species of schistosome blood flukes. The initial stage of infection is invasion of human skin by a multicellular larva, the cercaria. We identified proteins released by cercariae when they are experimentally induced to exhibit invasive behavior. Comparison of the proteome obtained from skin lipid-induced cercariae (the natural activator), a cleaner mechanical induction procedure, and an uninduced proteomic control allowed identification of protein groups contained in cercarial acetabular gland secretion versus other sources. These included a group of proteins involved in calcium binding, calcium regulation, and calcium-activated functions; two proteins (paramyosin and SPO-1) implicated in immune evasion; and protease isoforms implicated in degradation of host skin barriers. Several other protein families, traditionally found as cytosolic proteins, appeared concentrated in secretory cells. These included proteins with chaperone activity such as HSP70, -86, and -60. Comparison of the three experimental proteomes also allowed identification of protein contaminants from the environment that were identified because of the high sensitivity of the MS/MS system used. These included proteins from the intermediate host snail in which cercariae develop, the investigator, and the laboratory environment. Identification of proteins secreted by invasive larvae provides important new information for validation of models of skin invasion and immune evasion and aids in rational development of an anti-schistosome vaccine.
Low‐Cost Serum‐Free Medium for the BTI‐Tn5B1–4 Insect Cell Line (1998)

Abstract The BTI‐Tn5B1–4 insect cell line, commercially available as the High Five cell line (Invitrogen), supports higher levels of recombinant protein production compared to existing insect cell lines. Proprietary serum‐free media such as ExCell 405 (JRH Biosciences), Express Five (Life Technologies), IS BAC (Irvine Scientific), and CCM3 (HyClone) are available which were developed specifically for a suspension culture of High Five cells. While these media are highly optimized, a lower cost alternative is desirable for large‐scale protein production which is also serum‐free and supports good cell growth (>5 × 10 6 cells/mL) and recombinant protein production (>50 mg/L of secreted protein). The amino acid and carbohydrate metabolism of the Tn5B1–4 cells was first examined. It was found that asparagine was nearly depleted during batch growth in Ex‐Cell 405, without limitations in glutamine, other amino acids, or glucose. Alanine also accumulated to about 35 mM during growth. We then extended the formulation techniques for medium development used for Spodoptera cell lines to the Tn5B1–4 cell line. A medium based on IPL‐41 basal medium, Hy‐Soy protein hydrolysate (Quest, International), yeastolate ultrafiltrate, a lipid−sterol emulsion, and Pluronic F‐68 was developed. Dextran sulfate (100 μg/mL) was used to induce a single cell suspension culture. This medium is denoted as ISYL and performs best when supplemented with a 2.5% lipid−Pluronic F‐68 mixture. Supplementation with additional aspargine in a 1.5% lipid−Pluronic F‐68 mixture did not improve growth, suggesting that a lipid was growth‐limiting and not an amino acid. Ex‐Cell 405 and ISYL with 2.5% lipid−Pluronic F‐68 supplement supported virtually identical growth rates, extent of growth (ca. 6.0 × 10 6 cells/mL) in an 80% oxygen atmosphere, and supported production of SEAP (secreted human alkaline phosphatase) at a volumetric level of about 65−70 mg/L. Thus, the less expensive ISYL medium can deliver acceptable performance and may be suitable for large‐scale insect cell cultures.
miR-9 inhibits Schwann cell migration by targeting CTHRC1 following sciatic nerve injury (2014)

The regulative effects of microRNAs (miRNAs) on responses of Schwann cells to a nerve injury stimulus are not yet clear. In this study, we noted that the expression of eight miRNAs was downregulated at different time points following rat sciatic nerve transection, and found that 368 potential targets of these eight miRNAs were mainly involved in phenotypic modulation of Schwann cells. Of these miRNAs, miR-9 was identified as an important functional regulator of Schwann cell migration that was a crucial regenerative response of Schwann cells to nerve injury. In vitro, upregulated expression of miR-9 inhibited Schwann cell migration, whereas silencing of miR-9 promoted Schwann cell migration. Intriguingly, miR-9 exerted this regulative function by directly targeting collagen triple helix repeat containing protein 1 (CTHRC1), which in turn inactivated downstream Rac1 GTPase. Rac1 inhibitor reduced the promotive effects of anti-miR-9 on Schwann cell migration. In vivo, high expression of miR-9 reduced Schwann cell migration within a regenerative nerve microenvironment. Collectively, our results confirmed the role of miR-9 in regulating Schwann cell migration after nerve injury, thus offering a new approach to peripheral nerve repair.
Ontology-enabled validation of connectivity relationships in a home theater system (2006)

This article describes a vision for team-based synthesis of engineering systems, enhanced by technologies for ontology-based computing, cast in a Semantic Web framework. Our long-term research objective is to fully understand the extent to which relationships and constraints in ontology-based descriptions of problem domains, working together with description logic reasoning engines, can influence and improve system-level design procedures, particularly in the early stages of development where errors may have a significant long-term impact, but if detected early are cheap to correct. As a first step, we develop a port–jack ontology for a home theater system and exercise rule sets for combinations of correct/incorrect connectivity. The model checking procedure begins with the formulation of a port–jack ontology that will describe allowable constraining relationships in the port and jack connectivity. Allowable types of connections are expressed in the form of domain restrictions. © 2006 Wiley Periodicals, Inc. Int J Int Syst 21: 1111–1125, 2006.
Experiments on Surface Wave Propagation along Annular Plasma Columns (1966)

The propagation of surface waves along a plasma column of annular cross section was investigated experimentally. The laboratory plasma used for the experiment was a mercury-vapor dc discharge. The properties of the experimental discharge tube were examined to show some basic differences between the laboratory plasma and the idealized model of the plasma used for the analysis. In particular, a radially non-uniform density distribution and the variation of the distribution with the applied magnetic field was noted. In spite of the radial-density inhomogeneity, the experimentally determined phase constants of the backward-surface wave are in good agreement with values predicted from the uniform density theory. The attenuation in the absence of the magnetic field is consistent with collisional losses, predominantly with the walls of the container. The effect of an axial magnetic field on the surface-wave characteristics is examined. Experimental results show that in the presence of a magnetic field the attenuation of the backward wave is markedly increased; this enhancement of the damping is not consistent with simple collision theory within the framework of the uniform-density model.
A Model-Driven Approach for Biomedical Data Integration (2010)

A core challenge in biomedical data integration is to enable semantic interoperability between its various stakeholders as well as other interested parties. Promoting the adoption of worldwide accepted information standards along with common controlled terminologies is the right path to achieve this. Our paper describes a solution to this fundamental problem by proposing an approach to semantic data integration based on information models serving as a common language to represent health data coupled with technology that is able to represent the data semantics. We used the HL7 v3 Reference Information Model (RIM) [1] to derive a specific data model for the integrated data, the Web Ontology Language (OWL) [2] to build an ontology that harmonizes the metadata from the disparate data sources, the Unified Modeling Language (UML) [3] to model the data representation, and the Object Constraint Language (OCL) [4] to specify UML model constraints. To illustrate the approach, we use the Essential Hypertension Summary CDA document and related models from Hypergenes, a European Commission funded project [5] exploring the Essential Hypertension disease model.
A Modified Philip–Dunne Infiltrometer for Measuring the Field‐Saturated Hydraulic Conductivity of Surface Soil (2014)

There is a current and expanding need to measure surface infiltration rate parameters for stormwater infiltration practices used to mitigate the detrimental effects of land development activities on watershed hydrology. We have developed a falling‐head soil surface infiltrometer, termed the modified Philip–Dunne (MPD) infiltrometer, that is inexpensive to construct, easy to use, and requires a minimal water volume per test. Because of these characteristics, many MPD devices can be deployed simultaneously to obtain infiltration rate data at multiple locations within a given infiltration practice. Green–Ampt theory was used to derive the expressions needed for analyzing the falling‐head data to solve for the field‐saturated hydraulic conductivity ( K fs ) and Green–Ampt wetting‐front suction (ψ). The accuracy of the analysis was determined using numerical experiments in which falling‐head data were generated from a computational solution of the axisymmetric form of the three‐dimensional Richards' equation for homogeneous and isotropic porous media with specified input parameters. The falling‐head data were then analyzed using a quasi‐analytical procedure, and the resulting values of K fs and ψ were compared with the input values. The accuracy of K fs and ψ derived from data acquired using the MPD device was then assessed using physical experiments involving three large barrels packed with different types of sand. The K fs values obtained for the media in the barrels using an MPD infiltrometer were, on average, 82% of the values obtained from whole barrel falling‐head tests. The resulting uncertainty in K fs values from the MPD infiltrometer is considered to be small compared with the orders of magnitude of variability commonly observed for K fs values in the field.
A Protect Device of Programmable Semiconductor Surge Suppressor (2005)

Based on the comparison of the features of semiconductor surge suppressor, the operating principle of the 4th semiconductor transient voltage suppressor (P61089) is introduced, and the protection mechanism of for Subscriber Line Interface Circuits (SLIC) on programmable control exchange set is analyzed. The results show that the performance of the P61089 is enhanced remarkably. Lastly, the test methods of two key parameters are given.
Decentralized non-communicating multiagent collision avoidance with deep reinforcement learning (2017)

Finding feasible, collision-free paths for multiagent systems can be challenging, particularly in non-communicating scenarios where each agent's intent (e.g. goal) is unobservable to the others. In particular, finding time efficient paths often requires anticipating interaction with neighboring agents, the process of which can be computationally prohibitive. This work presents a decentralized multiagent collision avoidance algorithm based on a novel application of deep reinforcement learning, which effectively offloads the online computation (for predicting interaction patterns) to an offline learning procedure. Specifically, the proposed approach develops a value network that encodes the estimated time to the goal given an agent's joint configuration (positions and velocities) with its neighbors. Use of the value network not only admits efficient (i.e., real-time implementable) queries for finding a collision-free velocity vector, but also considers the uncertainty in the other agents' motion. Simulation results show more than 26% improvement in paths quality (i.e., time to reach the goal) when compared with optimal reciprocal collision avoidance (ORCA), a state-of-the-art collision avoidance strategy.
Antioxidative Compounds Isolated from Safflower (Cartthamus tinctorius L.) Oil Cake. (1997)

Seven antioxidative serotonin derivatives were isolated from safflower (Carthamus tinctorius L.) oil cake. Their structures were established as N-[2-(5-hydroxy-1H-indol-3-yl)ethyl]ferulamide (1), N-[2-(5-hydroxy-1H-indol-3-yl)ethyl]-p-coumaramide (2), N,N'-[2,2'-(5,5'-dihydroxy-4,4'-bi-1H-indol-3,3'-yl)diethyl]- di-p-coumaramide (3), N-[2-[3'-[2-(p-coumaramido)ethyl]-5,5'-dihydroxy- 4,4'-bi-1H-indol-3-yl]ethyl]ferulamide (4), and N,N'-[2,2'-(5,5'-dihydroxy-4,4'-bi-1H-indol-3,3'-yl)diethyl]- diferulamide (5), N-[2-[5-(beta-D-glucosyloxy)-1H-indol-3-yl)ethyl]- p-coumaramide (6), and N-[2-[5-(beta-D-glucosyloxy)-1H-indol-3-yl)ethyl]ferulamide (7). Antioxidative activities of the compounds were measured by the ferric thiocyanate method and the alpha,alpha-diphenyl-beta-picrylhydrazyl (DPPH) method, and compounds 1-5 were found to have relatively strong antioxidative activity.
Bird‐repellent effects on bait efficacy for control of invasive mammal pests (2014)

Anthraquinone is not suitable for inclusion in bait for rat control at the concentrations tested, and also presents some risk to efficacy for possum control. D-pulegone would be suitable for inclusion in bait for possums and rats, but problems related to its volatility in bait manufacture and storage would need to be overcome. Further studies should focus on an alternative secondary repellent, or on establishing the maximum anthraquinone concentration that does not reduce efficacy for rats and testing whether or not that concentration is sufficient to repel native birds from baits reliably.
A Systematic Survey of Expression and Function of Zebrafish frizzled Genes (2013)

Wnt signaling is crucial for the regulation of numerous processes in development. Consistent with this, the gene families for both the ligands (Wnts) and receptors (Frizzleds) are very large. Surprisingly, while we have a reasonable understanding of the Wnt ligands likely to mediate specific Wnt-dependent processes, the corresponding receptors usually remain to be elucidated. Taking advantage of the zebrafish model's excellent genomic and genetic properties, we undertook a comprehensive analysis of the expression patterns of frizzled (fzd) genes in zebrafish. To explore their functions, we focused on testing their requirement in several developmental events known to be regulated by Wnt signaling, convergent extension movements of gastrulation, neural crest induction, and melanocyte specification. We found fourteen distinct fzd genes in the zebrafish genome. Systematic analysis of their expression patterns between 1-somite and 30 hours post-fertilization revealed complex, dynamic and overlapping expression patterns. This analysis demonstrated that only fzd3a, fzd9b, and fzd10 are expressed in the dorsal neural tube at stages corresponding to the timing of melanocyte specification. Surprisingly, however, morpholino knockdown of these, alone or in combination, gave no indication of reduction of melanocytes, suggesting the important involvement of untested fzds or another type of Wnt receptor in this process. Likewise, we found only fzd7b and fzd10 expressed at the border of the neural plate at stages appropriate for neural crest induction. However, neural crest markers were not reduced by knockdown of these receptors. Instead, these morpholino knockdown studies showed that fzd7a and fzd7b work co-operatively to regulate convergent extension movement during gastrulation. Furthermore, we show that the two fzd7 genes function together with fzd10 to regulate epiboly movements and mesoderm differentiation.
Membrane-Bound Nitrate Reductase Is Required for Anaerobic Growth in Cystic Fibrosis Sputum (2007)

The autosomal recessive disorder cystic fibrosis (CF) affects approximately 70,000 people worldwide and is characterized by chronic bacterial lung infections with the opportunistic pathogen Pseudomonas aeruginosa. To form a chronic CF lung infection, P. aeruginosa must grow and proliferate within the CF lung, and the highly viscous sputum within the CF lung provides a likely growth substrate. Recent evidence indicates that anaerobic microenvironments may be present in the CF lung sputum layer. Since anaerobic growth significantly enhances P. aeruginosa biofilm formation and antibiotic resistance, it is important to examine P. aeruginosa physiology and metabolism in anaerobic environments. Measurement of nitrate levels revealed that CF sputum contains sufficient nitrate to support significant P. aeruginosa growth anaerobically, and mutational analysis revealed that the membrane-bound nitrate reductase is essential for P. aeruginosa anaerobic growth in an in vitro CF sputum medium. In addition, expression of genes coding for the membrane-bound nitrate reductase complex is responsive to CF sputum nitrate levels. These findings suggest that the membrane-bound nitrate reductase is critical for P. aeruginosa anaerobic growth with nitrate in the CF lung.
La cuestión del cambio de la práctica de la enseñanza y la necesidad de una teoría de la acción en el aula (2009)

En este artículo se trata en primer lugar de destacar la importancia que tiene el conocimiento de la práctica de la enseñanza –entendida como la actividad que alumnos y profesores realizan en el aula– para determinar el papel que realmente cumple el actual modo de escolarización en la formación de niños y jóvenes y, sobre todo, para establecer líneas de actuación que permitan el cambio y la mejora de la educación. Constatando la escasa producción sobre este campo de la investigación educativa, se señalan las dificultades metodológicas y conceptuales que el caso plantea, defendiendo la necesidad de una teoría de la acción en el aula, es decir, de una teoría que nos permita entender la lógica que gobierna el desarrollo habitual de la enseñanza en el aula. A este respecto, se aportan algunas ideas como es el interés de situar el análisis de la práctica de la enseñanza en el campo de las teorías de la acción humana, el de considerar a alumnos y profesores como sujetos histórica y socialmente contextualizados, el de entender la enseñanza, por tanto, como una práctica configurada históricamente y, en definitiva, el de considerarla como una práctica social. Finalmente, a modo de ejemplo, se examina el papel que examen y el control de la conducta de los alumnos juega en la configuración de la práctica de la enseñanza en el aula.
Control of a Chaotic Parametrically Driven Pendulum (1995)

We have controlled chaos in a pendulum with vertically driven pivot over a range of drive frequencies and damping levels. Using two variations on the OGY method [Ott, Grebogi, and Yorke, Phys. Rev. Lett. 64, 1196 (1990)], and with eddy-current damping as a control parameter, we have stabilized the motion of the pendulum about several of its unstable period-1, -2, and -4 limit cycles. Sampling the angular position at a correct choice of phase within the drive cycle simplified the OGY control rule. A time-proportioning rule was also found to provide robust control.
Quantifying the capability of a new in-situ interferometer (2002)

As design specifications push the limits of optical lithography deep into sub-/spl lambda/ imaging requirements, characterization of imaging tools has become increasingly more important and difficult. The customary Usable Depth of Focus (UDOF) and Distortion testing no longer provide all information necessary to predict the capability of the imaging tools. Process variations and sensitivities convolute the findings of many tool acceptance tests and can mask the true capability of todays High NA imaging tools. A new interferometer imaging tool developed by Litel Instruments (InspecStep/sup TM/ in-situ Interferometer) has been shown to be able to measure the distortion coefficients which are as accurate as conventional Phase Measurement Interferometer (PMI) techniques used by lens manufacturers. We will collect and present data quantifying the capability of this new tool. Repeatability and Reproducibility will be presented in terms of spherical wavefront aberration (rms) as well as comparisons of Zernike coefficients to vendor PMI data. Output configuration compatibility for commercially available lithographic simulators will be demonstrated. Finally a matching study will be presented in which we compared the predictions and calculations of interferometers.
A real options approach to valuing strategic flexibility in uncertain construction projects (2002)

To maximize project value, managers of construction projects must recognize, plan for and strategically manage uncertainty. Current construction planning, estimating, and management practices regarding uncertainty can undervalue projects by failing to exploit opportunities to increase project value, as well as minimize risks. Dynamic uncertainties are described as project conditions that cannot be resolved adequately through improved description or planning for pre-project strategy selection. A real options approach is proposed for proactively using strategic flexibility to recognize and capture project values hidden in dynamic uncertainties. An example of a proposal for a toll road project demonstrates a method of valuing managerial flexibility to evaluate and select strategies. Impacts of real options in other domains, along with this example, are the basis for concluding that using a structured real options approach in construction management can increase returns through improved project planning and management. Potential impacts of the use of real options are discussed, and challenges in valuing real options in construction projects are identified as the basis for future research.
Induction of proliferation and differentiation of cultured urothelial cells on acellular biomaterials (2004)

The mitogenic effects of the extracellular matrix content of biological membranes and fibroblastic inductive factors are synergistic with each other, and can compensate for a low FCS concentration and the absence of other additives. Lowering the FCS concentration to 1% inhibits the proliferation of urothelial cells and permits their terminal differentiation.
Perspective—State of the Art of Rechargeable Aluminum Batteries in Non-Aqueous Systems (2017)

The main challenges to implement sustainable energy storage technologies are the utilization of earth-abundant recyclable materials, low costs, safe cell reactions and high performance, all in a single system. Aluminum batteries seem to cover these requirements. However, their practical performance is still not comparable with the state of the art high performance batteries. A key aspect to further development could be the combination of aluminum with charge storage materials like conductive polymers in non-aqueous electrolytes taking advantage of the properties of each material. This review presents the approaches and perspectives for rechargeable aluminum-based batteries as sustainable high-performance energy storage devices.