gebhart/patrepeval huggingface dataset:
High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence (2010)

We have demonstrated how next generation sequencing was combined with high-throughput SNP detection assays to quickly discover large numbers of SNPs. Those SNPs were then used to create a high resolution genetic map that assisted in the assembly of scaffolds from the 8x whole genome shotgun sequences into pseudomolecules corresponding to chromosomes of the organism.
The human receptor for T-cell growth factor. Evidence for variable post-translational processing, phosphorylation, sulfation, and the ability of precursor forms of the receptor to bind T-cell growth factor. (1985)

The T-cell growth factor (TCGF) receptor on phytohemagglutinin-activated normal peripheral blood T-cells is characterized as a glycoprotein with an apparent Mr = 55,000 that contains N-linked and O-linked carbohydrate with only approximately 33,000 daltons of peptide structure (p33) as evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. There are two N-linked glycosylated intermediate precursor forms (apparent Mr = 35,000 (p35) and 37,000 (p37]. This receptor differs from the TCGF receptor on HUT-102B2 cells (apparent Mr = 50,000) because of differences in post-translational processing. Experiments with the carboxylic ionophore monensin demonstrate blockade of the transition of the p35 and p37 receptor precursor forms to the mature receptor, presumably secondary to inhibition of Golgi-associated receptor processing. We identify the primary translation product of TCGF receptor mRNA as intermediate in size between the p33 and the p35/p37 forms. We further demonstrate that the p33, p35, and p37 precursor forms, but not the primary translation product, are all capable of binding TCGF. Thus, the removal of the signal peptide and/or conformational changes of the primary translation product are necessary for ligand binding; however, the extensive post-translational modifications are not. Lastly, we demonstrate that at least some TCGF receptors are phosphorylated and sulfated, and that TCGF receptors on phytohemagglutinin-activated normal T-cells are more heavily sulfated than those on HUT-102B2 cells.
Hydrodynamics challenge problem (2011)

The hydrodynamics challenge problem represents a classical HPC physics problem, namely high deformation event modeling via Lagrangian shock hydrodynamics. This challenge problem solves the Sedov blast wave problem for one material in three dimensions. The problem has an analytic solution, and can be scaled to arbitrarily large problem sizes. The reference code is drawn from a production LLNL hydrodynamics code.
Image Warping of Three-Dimensional Body Scan Data (2003)

<div class="htmlview paragraph">This paper details the application of three-dimensional image warping techniques to full body scan data. Borrowed from the toolbox of geometric morphometries—methods commonly used to quantify the size and shape of anatomical objects in biological research— image unwarping transforms a given image such that relevant landmark positions of the starting image coincide with their positions in the consensus or target configuration. This study demonstrates the process of transforming static scan data to any posture, position, or homology for which landmark data is available, enabling detailed human models to be re-postured and examined in design environments widely varied from the one in which they were scanned.</div>
Synthesis of <sup>14</sup>C‐labelled 2‐[2‐cyclohexylcarbonyloxy‐3‐{4‐(2‐pyridyl) piperazin‐1‐yl}propyl]‐3aα, 4β, 7β, 7aα‐tetrahydro‐4, 7‐methano‐isoindole‐1,3(2H)‐dione dihydrochloride (E‐0713) (1985)

Abstract A 14 C‐labelled form of the antidiabetic compound E‐0713 was synthesized for pharmacokinetic and metabolic studies in six steps, using maleic anhydride [2,3‐ 14 C] as the labelled starting meterial.
Composite effects of reflections and ground bounce for signal vias in multi-layer environment (2002)

The signal propagating down the vias in a multi-layer environment will suffer from composite effects of reflected noise by via discontinuity and ground bounce between power/ground planes. An equivalent circuit modeling is proposed to simulate these effects, which consists of transmission line for signal line, lumped inductance and capacitance for via discontinuity, and two-dimensional field solver for the region between the power and ground planes. Simulations are performed for a four-layer structure and three different cases are considered to characterize both effects. Results show that the via discontinuity is dominant for reflected noise in the early time response, while the ground bounce is dominant in the late time response.
Electrospun and solution blown three-dimensional carbon fiber nonwovens for application as electrodes in microbial fuel cells (2011)

Three-dimensional carbon fiber electrodes prepared by electrospinning and solution blowing are shown to be excellent electrode materials for bioelectrochemical systems such as microbial fuel cells or microbial electrolysis cells. The bioelectrocatalytic anode current density is shown to reach values of up to 30 A m−2, which represents the highest reported values for electroactive microbial biofilms.
Digital epiluminescence microscopy in the evaluation of pigmented lesions: a brief review. (1993)

Epiluminescence microscopy (ELM) is the application of oil followed by compression by a transparent material and examination under tangential illumination with magnification. This technique reduces the reflected light from the irregular surface of the stratum corneum and makes the epidermis more transparent so that structures at the dermal epidermal junction and upper dermis may be visualized. Digital ELM is the capture of ELM images by a television camera attached to a computer. The ELM approach results in improved diagnostic accuracy for pigmented lesions in the order of 20%. Advantages of digital ELM over standard ELM are the ability to capture images in an almost endless array of colors and hues, permanence of recording without degradation over time, the ability to transmit information electronically over long distances, and the ability to enhance certain features through electronic manipulation. Among the potential applications of digital ELM are assistance in establishing the diagnosis of melanoma during screening, maintenance and retrieval of images in patients who are being followed clinically with pigmented lesions, and better understanding of clinical histopathologic correlations.
Controlling aggregation of cholesterol-modified DNA nanostructures (2019)

DNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure-function relationship of membrane-interfacing DNA constructs - a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.
144. Sediment Handling Technologies for Desilting Basins, Tunnel Sand Traps and Reservoirs (2005)

Reliable and efficient systems for sediment control and removal of sediment from withdrawn water will always be one of several preconditions for successful use of water resources. Sediment handling technologies have been developed the past 11 years, which enable efficient suction and transport of sediment through pipelines and thus exclusion of sediment at intakes and waterways and removal of sediment deposits from reservoirs. In addition to hydropower experience, substantial experience is gained from sediment handling in connection with offshore oil and gas industry. The Slotted Pipe sediment Sluicer (SPSS), enables efficient removal of sediment from sand traps and desilting basins. Due its special design the SPSS ensures that an absolute minimum of water is used for transport of sediment. And that a very low head is required. Being able to operate without inspection for nearly four years at Khimti hydropower plant in Nepal the SPSS is also verified to be suitable for open sand traps and desilting basins. Suction heads like the Saxophone Sediment Sluicer (SSS), has made it possible to operate gravity dredging systems from the surface of deep reservoirs without monitoring or special maneuvering. Disintegration of cohesive material can be obtained with water jetting. During the summer of 2004 cohesive clay that had been dried out during the winter season was removed from a small irrigation reservoir in Ethiopia. It is concluded that newly developed technologies have proven reliable in suction and transport of different types of sediment through pipelines and that sediments can be removed from inaccessible places, such as in pressurized tunnel sand traps and in deep reservoirs.
S 2. Fluorescent acylating agents derived from 7-hydroxycoumarin (1949)

W. Baker and C. B. Collis, J. Chem. Soc., 1949, S12 DOI: 10.1039/JR9490000S12
Direct Administration in the Respiratory Tract Improves Efficacy of Broadly Neutralizing Anti-Influenza Virus Monoclonal Antibodies (2015)

The emergence of influenza virus strains resistant to approved neuraminidase inhibitors and the time constrains after infection when these drugs can be effective constitute major drawbacks for this class of drugs. This highlights a critical need to discover new therapeutic agents that can be used for the treatment of influenza virus-infected patients. The use of broadly neutralizing anti-influenza monoclonal antibodies (MAbs) has been sought as an alternative immunotherapy against influenza infection. Here, we tested in mice previously characterized broadly neutralizing anti-hemagglutinin (HA) stalk MAbs prophylactically and therapeutically using different routes of administration. The efficacy of treatment against an influenza H1N1 pandemic virus challenge was compared between two systemic routes of administration, intraperitoneal (i.p.) and intravenous (i.v.), and two local routes, intranasal (i.n.) and aerosol (a.e.). The dose of MAb required for prophylactic protection was reduced by 10-fold in animals treated locally (i.n. or a.e.) compared with those treated systemically (i.p. or i.v.). Improved therapeutic protection was observed in animals treated i.n. on day 5 postinfection (60% survival) compared with those treated via the i.p. route (20% survival). An increase in therapeutic efficacy against other influenza virus subtypes (H5N1) was also observed when a local route of administration was used. Our findings demonstrate that local administration significantly decreases the amount of broadly neutralizing monoclonal antibody required for protection against influenza, which highlights the potential use of MAbs as a therapeutic agent for influenza-associated disease.
Laser beam scanning using a local deflector integrated with an effective mode filter (1987)

Deflection of a diode laser beam using an injection-type deflector monolithically integrated with a very long waveguide is demonstrated. The deflector and the waveguide constitute a laser cavity. The waveguide filters out higher order modes, and only the fundamental-mode light is incident on the deflector. Because the incident light is of a fixed single mode, the deflection of the output beam is very smooth. The deflection mechanism is primarily due to interference between constituent modes for short deflectors, and phase-front tilting of each mode for long deflectors.
Design and Synthesis of a New Class of Membrane-Permeable Triazaborolopyridinium Fluorescent Probes (2011)

A new class of fluorescent triazaborolopyridinium compounds was synthesized from hydrazones of 2-hydrazinylpyridine (HPY) and evaluated as potential dyes for live-cell imaging applications. The HPY dyes are small, their absorption/emission properties are tunable through variation of pyridyl or hydrazone substituents, and they offer favorable photophysical characteristics featuring large Stokes shifts and general insensitivity to solvent or pH. The stability, neutral charge, cell membrane permeability, and favorable relative influences on the water solubility of HPY conjugates are complementary to existing fluorescent dyes and offer advantages for the development of receptor-targeted small-molecule probes. This potential was assessed through the development of a new class of cysteine-derived HPY-conjugate imaging agents for the kinesin spindle protein (KSP) that is expressed in the cytoplasm during mitosis and is a promising chemotherapeutic target. Conjugates possessing the neutral HPY or charged Alexa Fluor dyes that function as potent, selective allosteric inhibitors of the KSP motor were compared using biochemical and cell-based phenotypic assays and live-cell imaging. These results demonstrate the effectiveness of the HPY dye moiety as a component of probes for an intracellular protein target and highlight the importance of dye structure in determining the pathway of cell entry and the overall performance of small-molecule conjugates as imaging agents.
Outbreak of Chikungunya on Reunion Island: Early Clinical and Laboratory Features in 157 Adult Patients (2007)

Chikungunya virus can be responsible for explosive outbreaks of disease. Polyarthralgia and fever are the 2 main clinical features. In this era of travel and globalization, chikungunya should be considered in the differential diagnosis of febrile polyarthralgia with an abrupt onset.
Fine-Grained Recognition of Thousands of Object Categories with Single-Example Training (2017)

We approach the problem of fast detection and recognition of a large number (thousands) of object categories while training on a very limited amount of examples, usually one per category. Examples of this task include: (i) detection of retail products, where we have only one studio image of each product available for training, (ii) detection of brand logos, and (iii) detection of 3D objects and their respective poses within a static 2D image, where only a sparse subset of (partial) object views is available for training, with a single example for each view. Building a detector based on so few examples presents a significant challenge for the current top-performing (deep) learning based techniques, which require large amounts of data to train. Our approach for this task is based on a non-parametric probabilistic model for initial detection, CNN-based refinement and temporal integration where applicable. We successfully demonstrate its usefulness in a variety of experiments on both existing and our own benchmarks achieving state-of-the-art performance.
Combining static and dynamic analysis for the detection of malicious documents (2011)

The widespread adoption of the PDF format for document exchange has given rise to the use of PDF files as a prime vector for malware propagation. As vulnerabilities in the major PDF viewers keep surfacing, effective detection of malicious PDF documents remains an important issue. In this paper we present MDScan, a standalone malicious document scanner that combines static document analysis and dynamic code execution to detect previously unknown PDF threats. Our evaluation shows that MDScan can detect a broad range of malicious PDF documents, even when they have been extensively obfuscated.
Recycling of ABS and ABS/PC blends (1999)

The aim of this work within the framework of mechanical recycling of polymers is upgrading recycled engineering plastics by means of a blending technique. Four different plastics from dismantled Volvo cars have been investigated. They are poly(acrylonitrile-butadiene-styrene) (ABS) and ABS-polycarbonate (ABS/PC) as major components and poly(methyl methacrylate) (PMMA) and polyamide (PA) as minor components. Blending recycled ABS and PC/ABS (70/30) with a small amount of methyl methacrylate-butadiene-styrene core-shell impact modifiers gives the mixture better impact properties than any of its individual components. Some 10% of PMMA from tail light housings can follow the PC/ABS blends made. The property profile will rather be improved. However, PA is an incompatible component that should be sorted out from the mixture. Antioxidants and metal deactivators do not help the recyclates show better mechanical properties. Two toughness measurements, Charpy impact strength and J-integral method, show complimentary results for such blends. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 74: 510–515, 1999
The efficacy of local anesthetics in blocking the sensations of itch, burning, and pain in normal and “sunburned” skin (1971)

Satisfactory methods to determine the efficacy of topical anesthetics in relieving cutaneous itch, pricking, burning, and pain in unbroken skin have not been available. A technique with the use of an alternating current of low amperage and voltage that selectively induces these sensations without apparent in;ury to the skin is described. The efficacy of local anesthetics in obtunding itching and pricking induced experimentally and by exposure of the skin to ultraviolet light was evaluated. Studies in 150 volunteers indicate that salts of local anesthetics are ineffective in obtunding itching and burning in intact normal or ultraviolet burned skin; bases in concentrated solutions are effective.
Conjugation of Colloidal Clusters and Chains by Capillary Condensation (2009)

Capillary condensation was used to establish connections in colloidal clusters and 1D colloidal chains with high regional selectivity. This vapor-phase process produced conjugated clusters and chains with anisotropic functionality. The capillary condensation method is simple and can be applied to a wide range of materials. It can tolerate geometric variations and even permits conjugation of spatially separated particles. The selective deposition was also used to modulate the functionality on the colloid surfaces, producing tip-tethered nanosized building blocks that may be suitable for further assembly via directional interactions.
A dominant role for chemoattractant receptor‐homologous molecule expressed on T helper type 2 (Th2) cells (CRTH2) in mediating chemotaxis of CRTH2<sup>+</sup> CD4<sup>+</sup> Th2 lymphocytes in response to mast cell supernatants (2006)

Human cultured mast cells, immunologically activated with immunoglobuin E (IgE)/anti-IgE, released a factor(s) that promoted chemotaxis of human CRTH2+ CD4+ T helper type 2 (Th2) lymphocytes. Mast cell supernatants collected at 20 min, 1 hr, 2 hr and 4 hr after activation caused a concentration-dependent increase in the migration of Th2 cells. The effect of submaximal dilutions of mast-cell-conditioned media was inhibited in a dose-dependent manner by ramatroban (IC50 = 96 nm), a dual antagonist of both the thromboxane-like prostanoid (TP) receptor and the chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2), but not by the selective TP antagonist SQ29548, implicating CRTH2 in mediating the chemotactic response of these Th2 cells. The effect of mast-cell-conditioned media was mimicked by prostaglandin D2 (PGD2) and this eicosanoid was detected in the conditioned media from activated mast cells in concentrations sufficient to account for the activity of the mast cell supernatants. Treatment of the mast cells with the cyclo-oxygenase inhibitor diclofenac (10 microm) inhibited both the production of PGD2 and the CRTH2+ CD4+ Th2-stimulatory activity, while addition of exogenous PGD2 to conditioned media from diclofenac-treated mast cells restored the ability of the supernatants to promote chemotaxis of these Th2 cells. The degree of inhibition caused by diclofenac treatment of the mast cells was concordant with the degree of inhibition of chemotactic responses afforded by CRTH2 blockade. These data suggest that PGD2, or closely related metabolites of arachidonic acid, produced from mast cells may play a central role in the activation of CRTH2+ CD4+ Th2 lymphocytes through a CRTH2-dependent mechanism.
<title>Ultralightweight low-temperature fused Zerodur mirror</title> (1995)

The performance and utility of optical systems can be significantly improved by using lightweight stable mirror components. Such components have been incorporated into a mirror assembly through a process that utilizes low temperature fusion to bond low CTE faceplates onto a lightweight core structure. The core structure is fabricated using an abrasive waterjet cutting technique that enables the designer to optimize core geometry to enhance the structural performance of the blank. The faceplates are bonded to the lightweight core resulting in a stiff structural mirror. A 15.125 inch Zerodur mirror was fabricated using this unique process and subjected to a test program to measure the optical stability of the mirror in support of either space-based applications. Strength testing was performed to verify the integrity of the fused joints and determine appropriate design allowable stress. A thermal test program was designed to assess performance at various temperature extremes and a mechanical load test was run to verify the capability of the blank to withstand operational loads without degrading the optical surface. The surface figure of the part was measured before, during, and after a 200 degree F temperature cycle with no change in figure quality. In addition, the mirror was subjected to a 10 g load for ten minutes with no change in the figure quality.
The Formation of a Tissue-Engineered Cornea Using Plastically Compressed Collagen Scaffolds and Limbal Stem Cells (2013)

Collagen has excellent biocompatibility, is biodegradable, and possesses low immunogenicity. Therefore, this protein is a very suitable substrate for the formation of a corneal scaffold for therapeutic use. The highly hydrated nature of conventional collagen gels, however, results in a gel that is structurally weak and difficult to manipulate. In this chapter, we describe a novel method to cultivate limbal epithelial cells (LEC) on a compressed collagen scaffold. The compressed collagen scaffold can be rapidly constructed using a cell-independent process, which produces dense and mechanically strong collagen constructs with controllable microscale features.We embedded corneal keratocytes in a collagen gel, which we subsequently compressed and coated with laminin. The resulting construct supported the physiological morphology and stratification of LEC. The expression of a specific marker for differentiated LEC, cytokeratin 3 (CK3), and a marker for undifferentiated LEC, cytokeratin 14 (CK14), were similar in LEC expanded on both the compressed collagen construct and the leading conventional scaffold, denuded amniotic membrane (AM). We therefore demonstrate that a laminin-coated, compressed collagen gel containing keratocytes can support LEC expansion, stratification, and differentiation to a degree that is comparable to denuded AM. Our novel compressed collagen/keratocyte construct has potential for use as a tissue-engineered artificial cornea.