gebhart/patrepeval huggingface dataset:
Wnt-Ryk Signaling Mediates Axon Growth Inhibition and Limits Functional Recovery after Spinal Cord Injury (2009)

Wnt proteins are a large family of diffusible factors that play important roles in embryonic development, including axis patterning, cell fate specification, proliferation, and axon development. It was recently demonstrated that Ryk (receptor related to tyrosine kinase) is a conserved high-affinity Wnt receptor, and that Ryk-Wnt interactions guide corticospinal axons down the spinal cord during development. Here, we report that the Ryk-Wnt signal mediates the inhibition of corticospinal axon growth in the adult spinal cord. The expression of Wnt-5a is induced in reactive astrocytes around the injury site following a spinal cord injury. In vitro, Wnt-5a inhibits the neurite growth of postnatal cerebellar neurons by activating RhoA/Rho-kinase. In rats with thoracic spinal cord contusion, intrathecal administration of a neutralizing antibody to Ryk resulted in significant axonal growth of the corticospinal tract and enhanced functional recovery. Thus, reexpression of the embryonic repulsive cues in adult tissues contributes to the failure of axon regeneration in the central nervous system.
Construction of Ribonuclease-Antibody Conjugates for Selective Cytotoxicity (2003)

Immunotoxins based on human and humanized ribonuclease may have potential for cancer therapy while exhibiting less toxic side effects and stimulating less of an immune response in humans than immunotoxins based on plant and bacterial toxins (1). Both recombinant RNase fusion proteins (2-4 see also Chapter 6 , this volume) and chemical RNase conjugates have been made and characterized. The cytotoxic potential of targeted ribonuclease was first demonstrated with bovine RNase conjugated to transferrin or an antibody directed against the human transferrin receptor (5). Antibody RNase conjugates have also been shown to have potent anti-tumor activity against human glioma cells in athymic mice (6) and to enhance the activity of vincristine in mdr1 multidrug-resistant colon cancer cells in vitro and in vivo (7). Recently, RNase chemically conjugated to an antibody against CD22 was found to specifically kill Daudi lymphoma cells in cell culture at picomolar concentrations (IC(50), 10-50 pM) and to exhibit potent antitumor activity in SCID mice with disseminated Daudi lymphoma (unpublished data). Methods for linking RNase to specific cell binding ligands are described.
SaarCOR: a hardware architecture for ray tracing (2002)

The ray tracing algorithmis well-known for its ability to generate high-quality images and its flexibility to support advanced rendering and lighting effects. Interactive ray tracing has been shown to work well on clusters of PCs and supercomputers but direct hardware support for ray tracing has been difficult to implement.In this paper, we present a new, scalable, modular, and highly efficient hardware architecture for real-time ray tracing. It achieves high performance with extremely low memory bandwidth requirements by efficiently tracing bundles of rays. The architecture is easily configurable to support a variety of workloads. For OpenGL-like scenes our architecture offers performance comparable to state-of-the-artrasterization chips. In addition, it supports all the usual ray tracing features including exact shadows, reflections, and refraction and is capable of efficiently handling complex scenes with millions of triangles. The architecture and its performance in different configurations is analyzed based on cycle-accurate simulations.
Simian Immunodeficiency Virus (SIV) Envelope-Specific Fabs with High-Level Homologous Neutralizing Activity: Recovery from a Long-Term-Nonprogressor SIV-Infected Macaque (1998)

An antibody phage display library was constructed from RNA extracted from lymph node cells of a simian immunodeficiency virus (SIV)-infected long-term-nonprogressor macaque. Seven gp120-reactive Fabs were obtained by selection of the library against SIV monomeric gp120. Although each of the Fabs was unique in sequence, there were two distinct groups based on epitope recognition, neutralizing activity in vitro, and molecular analysis. Group 1 Fabs did not neutralize SIV and bound to a linear epitope in the V3 loop of the SIV envelope. In contrast, two of the group 2 Fabs neutralized homologous, neutralization-sensitive SIVsm isolates with high efficiency but failed to neutralize heterologous SIVmac isolates. Based on competition enzyme-linked immunosorbent assays with mouse monoclonal antibodies of known specificity, these Fabs reacted with a conformational epitope that includes domains V3 and V4 of the SIV envelope. These neutralizing and nonneutralizing Fabs provide valuable standardized and renewable reagents for studying the role of antibody in preventing or modifying SIV infection in vivo.
Effect of deep levels on semiconductor carrier concentrations in the case of "strong" compensation (1982)

We analyze the carrier concentrations ($\ensuremath{\equiv}p$) resulting from both shallow and deep majority levels. We show that for comparable concentrations of shallow and of compensating levels, a small fraction of deep levels can decrease $p$ by orders of magnitude. Also, a quantitative criterion for obtaining semi-insulating material is derived, and implications for obtaining conducting wide-band-gap materials are discussed. Another result: a steep ("deep") slope of $\mathrm{ln}p$ vs $\frac{1}{T}$ can result even from small percentages of deep levels.
The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics (2015)

P granules and other RNA/protein bodies are membrane-less organelles that may assemble by intracellular phase separation, similar to the condensation of water vapor into droplets. However, the molecular driving forces and the nature of the condensed phases remain poorly understood. Here, we show that the Caenorhabditis elegans protein LAF-1, a DDX3 RNA helicase found in P granules, phase separates into P granule-like droplets in vitro. We adapt a microrheology technique to precisely measure the viscoelasticity of micrometer-sized LAF-1 droplets, revealing purely viscous properties highly tunable by salt and RNA concentration. RNA decreases viscosity and increases molecular dynamics within the droplet. Single molecule FRET assays suggest that this RNA fluidization results from highly dynamic RNA-protein interactions that emerge close to the droplet phase boundary. We demonstrate than an N-terminal, arginine/glycine rich, intrinsically disordered protein (IDP) domain of LAF-1 is necessary and sufficient for both phase separation and RNA-protein interactions. In vivo, RNAi knockdown of LAF-1 results in the dissolution of P granules in the early embryo, with an apparent submicromolar phase boundary comparable to that measured in vitro. Together, these findings demonstrate that LAF-1 is important for promoting P granule assembly and provide insight into the mechanism by which IDP-driven molecular interactions give rise to liquid phase organelles with tunable properties.
Decomposing refinement proofs using assume-guarantee reasoning (2000)

Model-checking algorithms can be used to verify, formally and automatically, if a low-level description of a design conforms with a high-level description. However, for designs with very large state spaces, prior to the application of an algorithm, the refinement-checking task needs to be decomposed into subtasks of manageable complexity. It is natural to decompose the task following the component structure of the design. However, an individual component often does not satisfy its requirements unless the component is put into the right context, which constrains the inputs to the component. Thus, in order to verify each component individually, we need to make assumptions about its inputs, which are provided by the other components of the design. This reasoning is circular: component A is verified under the assumption that context B behaves correctly, and symmetrically, B is verified assuming the correctness of A. The assume-guarantee paradigm provides a systematic theory and methodology for ensuring the soundness of the circular style of postulating and discharging assumptions in component-based reasoning. We give a tutorial introduction to the assume-guarantee paradigm for decomposing refinement-checking tasks. To illustrate the method, we step in detail through the formal verification of a processor pipeline against an instruction set architecture. In this example, the verification of a three-stage pipeline is broken up into three subtasks, one for each stage of the pipeline.
Synthesis and xanthine oxidase inhibitory activity of 4,6‐disubstituted 1‐p‐chlorophenylpyrazolo[3,4‐d]pyrimidines (1982)

Abstract Several 4,6‐disubstituted 1‐ p ‐chlorophenylpyrazolo[3,4‐ d ]pyrimidines were prepared from 4,6‐dichloro‐1‐ p ‐chlorophenylpyrazolo[3,4‐ d ]pyrimidine and their xanthine oxidase inhibitory activity were tested in vitro .
Direct-Injection NMR (DI-NMR):  A Flow NMR Technique for the Analysis of Combinatorial Chemistry Libraries (2000)

A new tool for analyzing compound libraries by NMR has been developed. Aliquots of solution-state samples (between 120 and 350 microL) are directly injected, using a standard liquids handler, into an NMR (LC-NMR) flow probe. Automated NMR software tracks--and suppresses--intense signals arising from the nondeuterated solvents used (if any) and acquires high-sensitivity one-dimensional 1H NMR spectra. An 88-member combinatorial library, dissolved in DMSO and stored in a 96-well microtiter plate, has been analyzed a number of ways using this technique. This nondestructive technique, which we call direct-injection NMR (DI-NMR) and which is embodied in our versatile automated sample changer (VAST) hardware, has proven to be both routine and robust. Our success in automatically acquiring the NMR data for entire plates of library compounds (within 4-8 h) has caused us to develop new ways to display and analyze the resulting NMR data, as will be shown here.
The ApolloScape Dataset for Autonomous Driving (2018)

Scene parsing aims to assign a class (semantic) label for each pixel in an image. It is a comprehensive analysis of an image. Given the rise of autonomous driving, pixel-accurate environmental perception is expected to be a key enabling technical piece. However, providing a large scale dataset for the design and evaluation of scene parsing algorithms, in particular for outdoor scenes, has been difficult. The per-pixel labelling process is prohibitively expensive, limiting the scale of existing ones. In this paper, we present a large-scale open dataset, ApolloScape, that consists of RGB videos and corresponding dense 3D point clouds. Comparing with existing datasets, our dataset has the following unique properties. The first is its scale, our initial release contains over 140K images - each with its per-pixel semantic mask, up to 1M is scheduled. The second is its complexity. Captured in various traffic conditions, the number of moving objects averages from tens to over one hundred (Figure 1). And the third is the 3D attribute, each image is tagged with high-accuracy pose information at cm accuracy and the static background point cloud has mm relative accuracy. We are able to label these many images by an interactive and efficient labelling pipeline that utilizes the high-quality 3D point cloud. Moreover, our dataset also contains different lane markings based on the lane colors and styles. We expect our new dataset can deeply benefit various autonomous driving related applications that include but not limited to 2D/3D scene understanding, localization, transfer learning, and driving simulation.
Red blood cells as an antigen‐delivery system (1992)

The use of adjuvants is usually required to induce strong immunological responses to protein antigens. However, in many cases these adjuvants cannot be extensively applied in human and veterinary vaccinations because of associated inflammatory reactions or granuloma formation. We show here that protein antigens (bovine serum albumin, hog liver uricase, and yeast hexokinase), coupled to autologous red blood cells by way of a biotin-avidin-biotin bridge, elicit an immunological response in mice similar to or higher than that obtained by the use of Freund's adjuvant. Quantities as low as 0.5 micrograms/mouse are high enough to generate these immunological responses. Furthermore, splenocytes of mice immunized by red blood cell-coupled antigens can be used to generate hybridomas secreting monoclonal antibodies. Thus, the delivery of antigens by autologous red blood cells is an effective way to avoid the use of adjuvants for producing anti-peptide antibodies and possibly to generate peptide vaccines.
Pulse oximeters for the detection of hypoxaemia. (1999)

The main purpose of pulse oximetry is to alert health-care professionals to the early stages of hypoxaemia. Pulse oximetry is an accurate and widely used method of monitoring peripheral saturation. As with any monitoring device, care must be taken to monitor the patient's vital signs. Pulse oximetry measures the saturation of arterial haemoglobin, not the adequacy of ventilation.
Detection of early neuron degeneration and accompanying microglial responses in the retina of a rat model of glaucoma. (2002)

Occlusion of episcleral veins is a reproducible method that mimics human glaucoma, with chronically elevated IOP-induced RGC loss. This study shows that in vivo imaging permits the detection of ganglion cells in the living animal in the early stages of the disease and highlights the importance of in vivo imaging in understanding ophthalmic disorders such as glaucoma. Secondly, activation of intraretinal microglia coincides with degeneration of RGCs in glaucoma.
A New Ring-Forming Methodology for the Synthesis of Conformationally Constrained Bioactive Molecules (2001)

Abstract A new, general, one pot method for introducing carbocyclic rings alpha to a nitrile moiety is described. Treatment of readily available arylacetonitriles with potassium bis(trimethylsilyl)amide and subsequent alkylation with α, ω-dibromo or dichloroalkanes in tetrahydrofuran under anhydrous conditions at 0 °C produces cycloalkyl adducts in good yields and short reaction times.
The effects of the presence of stored product pests on the microfauna of a flour community (2005)

Stored product pests can alter the bacterial community. Isolated species from this study show a strong genetic relationship to each other, suggesting an isolated evolving system. A unique bacteria was also isolated. GC and sequencing methods of identification are compared.
Have we overestimated the benefit of human(ized) antibodies? (2010)

The infusion of animal-derived antibodies has been known for some time to trigger the generation of antibodies directed at the foreign protein as well as adverse events including cytokine release syndrome. These immunological phenomena drove the development of humanized and fully human monoclonal antibodies. The ability to generate human(ized) antibodies has been both a blessing and a curse. While incremental gains in the clinical efficacy and safety for some agents have been realized, a positive effect has not been observed for all human(ized) antibodies. Many human(ized) antibodies trigger the development of anti-drug antibody responses and infusion reactions. The current belief that antibodies need to be human(ized) to have enhanced therapeutic utility may slow the development of novel animal-derived monoclonal antibody therapeutics for use in clinical indications. In the case of murine antibodies, greater than 20% induce tolerable/negligible immunogenicity, suggesting that in these cases humanization may not offer significant gains in therapeutic utility. Furthermore, humanization of some murine antibodies may reduce their clinical effectiveness. The available data suggest that the utility of human(ized) antibodies needs to be evaluated on a case-by-case basis, taking a cost-benefit approach, taking both biochemical characteristics and the targeted therapeutic indication into account.
A new method for sequencing fully protected oligonucleotides using californium-252 plasma desorption mass spectrometry. 1. Negative ions of dinucleoside monophosphates (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA new method for sequencing fully protected oligonucleotides using californium-252 plasma desorption mass spectrometry. 1. Negative ions of dinucleoside monophosphatesCatherine J. McNeal, Kelvin K. Ogilvie, Nicole Y. Theriault, and Mona J. NemerCite this: J. Am. Chem. Soc. 1982, 104, 4, 972–975Publication Date (Print):February 1, 1982Publication History Published online1 May 2002Published inissue 1 February 1982https://pubs.acs.org/doi/10.1021/ja00368a008https://doi.org/10.1021/ja00368a008research-articleACS PublicationsRequest reuse permissionsArticle Views52Altmetric-Citations34LEARN 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 optionsGet e-Alertsclose Get e-Alerts
Quality of Wet Noodle Prepared with Wheat Flour and Mushroom Powder (1998)

Wet noodles were prepared with wheat flour and mushroom powder (oyster and oak mushrooms), and effects of added mushroom powders on dough rheology and wet noodle quality were examined. Particle size distribution of mushroom powder ranged from 0.04 to , which was different from that of wheat flour. The initial pasting temperature in amylograph, and the water absorption and the dough development time in farinograph increased with the increase of mushroom powder. The peak and final viscosities in amylograph, and dough stability in farinograph decreased with the increase of mushroom powder. Decrease of L value and increase of a and b values were shown with the increase of mushroom powder in wheat flour-mushroom powder composite as well as wet noodles. The cooked weight and volume of cooked noodles were decreased, but the turbidity of soup were increased with the addition of mushroom powder. Most of texture parameters (hardness, cohesiveness, chewiness and cutting force) of cooked noodles decreased with the addition of oyster mushroom powder, but increased with the addition of oak mushroom powder. From the result of sensory evaluation, wet noodles containing 3% oyster mushroom powder and 5% oak mushroom powder were rated as high quality wet noodles.
Oral pulsatile drug delivery systems (2005)

In the field of modified release, there has been a growing interest in pulsatile delivery, which generally refers to the liberation of drugs following a programmable lag phase from the time of administration. In particular, the recent literature reports on a variety of pulsatile release systems intended for the oral route, which have been recognised as potentially beneficial to the chronotherapy of widespread diseases, such as bronchial asthma or angina pectoris, with mainly night or early morning symptoms. In addition, time-dependent colon delivery may also represent an appealing related application. The delayed liberation of orally administered drugs has been achieved through a range of formulation approaches, including single- or multiple-unit systems provided with release-controlling coatings, capsular devices and osmotic pumps. Based on these premises, the aim of this review is to outline the rational and prominent design strategies behind oral pulsatile delivery.
But-2-ynylbisoxycarbonyl Chloride:  A Novel C2-Symmetric Reagent for the Protection of Amines and Amino Acids (2005)

[reaction: see text] A novel C2-symmetric protecting group for amines, the but-2-ynylbisoxycarbonyl (Bbc) group, is developed, which can be deblocked with tetrathiomolybdate under neutral conditions. One equivalent of the bischloroformate, BbcCl, is used for the protection of 2 equiv of the amine. Its application in peptide synthesis is established through the synthesis of a tripeptide, and its orthogonality with Cbz, Fmoc, and Boc groups has been studied.
Correlation of the expression of human telomerase subunits with telomerase activity in normal skin and skin tumors (1999)

Activation of telomerase activity in skin tumors is strongly correlated with hTERT expression.
A New Era for Cancer Treatment: Gold‐Nanoparticle‐Mediated Thermal Therapies (2010)

Nanotechnology-based cancer treatment approaches potentially provide localized, targeted therapies that aim to enhance efficacy, reduce side effects, and improve patient quality of life. Gold-nanoparticle-mediated hyperthermia shows particular promise in animal studies, and early clinical testing is currently underway. In this article, the rapidly evolving field of gold nanoparticle thermal therapy is reviewed, highlighting recent literature and describing current challenges to clinical translation of the technology.
Session Initiation Protocol (SIP): Locating SIP Servers (2002)

The Session Initiation Protocol (SIP) uses DNS procedures to allow a client to resolve a SIP Uniform Resource Identifier (URI) into the IP address, port, and transport protocol of the next hop to contact. It also uses DNS to allow a server to send a response to a backup client if the primary client has failed. This document describes those DNS procedures in detail.
Los 10 mandamientos del talento (2004)

We studied the community richness and dynamics of birds in landscapes recently affected by urbanization to test the prediction that biotic communities living in degraded landscapes are increasingly composed of generalist species. We analyzed bird communities in 657 plots monitored by the French Breeding Bird Survey from 2001 to 2005, accounting for the probability of species detection and spatial autocorrelation. We used an independent land-cover program to assess urbanization intensity in each FBBS plot, from 1992 to 2002. We found that urbanization induced community homogenization and that populations of specialist species became increasingly unstable with increasing urbanization of the landscape. Our results emphasize that urbanization has a substantial impact on the spatial component of communities and highlight the destabilizing effect of urbanization on communities over time. These results illustrate that urbanization may be a strong driving force in functional community composition and that measuring community homogenization is a powerful tool in the assessment of the effects of landscape changes and thus aides sustainable urban planning.
Separation of nucleotides by high-voltage capillary electrophoresis. (1984)

A new separation method using high-voltage capillary electrophoresis was applied to the analysis of several nucleotides. This system consisted of a micro-bore glass capillary column of 80-micron i.d., a high-voltage power supply, and a uv detector set at 254 nm. Seven nucleotides (cyclic AMP, AMP, ADP, ATP, GMP, GDP, and GTP) were separated completely from each other in 0.02 M phosphate buffer (pH 7) containing 0.5% ethylene glycol by applying about 150 V/cm. The theoretical plate number for AMP was nearly 45,000. A good separation of nucleotides in biological samples of rat blood, liver, and kidney was attained under the same conditions as above. Concentrations of nucleotides in these biological samples were measured by using pyridoxamine as an internal standard.