gebhart/patrepeval huggingface dataset:
Accuracy of Global Positioning System for Determining Driver Performance Parameters (2002)

Global Positioning System (GPS) technology can continuously monitor the time and location of vehicle usage. By recording and analyzing detailed vehicle activity data, researchers can analyze the safety and environmental implications of driver behavior and trip-making patterns. In 2000, NHTSA awarded the Georgia Institute of Technology a contract to equip 1,100 vehicles with a GPS-enhanced device to collect speed and location data. The objective was to acquire more accurate information on the role of excessive speed on crash frequency and severity. GPS technology allows the researcher to continuously measure driver speed, acceleration, and location. When merged with roadway characteristics within a geographic information system (GIS) environment, determinations of driver risk-taking behavior can be made. Second, continuous logging of GPS data allows researchers to capture high-resolution vehicle activity immediately before a crash event, reducing the potential error and bias introduced during determination of precrash speed estimates. Until May 1, 2000, the military degraded the position accuracy of GPS signals for commercial use, known as selective availability. For researchers, life without selective availability is a great improvement. Travel routes can clearly be discerned without the addition of differential correction units. The accuracy of speed, acceleration, and position data obtained from GPS signals for use in determining driver performance parameters without selective availability were tested. The test included four GPS packages, both corrected and uncorrected, simultaneously validated against a distance-measuring instrument. Equipment configuration, data collection methods, and sources of error are reported. The results suggested that non-corrected data can be used to obtain data within a reasonable range of the application requirements. Even without selective availability, GPS accuracy is still problematic in urban canyons and under heavy tree canopies. Although filtering for urban canyon outliers is labor intensive in a continuous monitoring situation, improvements in GIS hold promise for automation of this task.
Discriminant Saliency for Visual Recognition from Cluttered Scenes (2004)

Saliency mechanisms play an important role when visual recognition must be performed in cluttered scenes. We propose a computational definition of saliency that deviates from existing models by equating saliency to discrimination. In particular, the salient attributes of a given visual class are defined as the features that enable best discrimination between that class and all other classes of recognition interest. It is shown that this definition leads to saliency algorithms of low complexity, that are scalable to large recognition problems, and is compatible with existing models of early biological vision. Experimental results demonstrating success in the context of challenging recognition problems are also presented. 1
IL-15 Renders Conventional Lymphocytes Resistant to Suppressive Functions of Regulatory T Cells through Activation of the Phosphatidylinositol 3-Kinase Pathway (2009)

IL-15 drives chronic inflammation in several human diseases. We have recently shown that IL-15 inhibits the immunosuppressive effects of TGF-beta through blockage of the Smad3-signaling pathway. Data pointing to reciprocal interactions between TGF-beta and CD4(+) regulatory T cells led us to investigate the impact of IL-15 on the de novo generation and function of regulatory T cells in humans. Our data indicate that IL-15 does not counteract, but rather promotes the effect of TGF-beta on the de novo generation of regulatory T cells (Treg). Thus, in the presence of TGF-beta, IL-15 enhanced the acquisition of regulatory functions by CD4(+)CD25(-) T cells stimulated by anti-CD3 and anti-CD28 Abs. In contrast, IL-15 impaired the functions of Tregs by acting on effector CD4 and CD8 T cells. Accordingly, in the presence of IL-15, proliferation and IFN-gamma production by peripheral CD4 and CD8 T cells could not be efficiently inhibited by Tregs. IL-15-induced resistance of effector T cells to Tregs resulted from activation of the PI3K signaling pathway but did not involve the rescue of effector T cells from apoptosis. Altogether, these data point to the ambiguous role of IL-15 in the control of Treg functions. This dual role may be instrumental to mount rapid but transient proinflammatory immune responses against pathogens but may become deleterious in situations associated with protracted IL-15 over-expression.
Human-Scale Whole-Organ Bioengineering for Liver Transplantation: A Regenerative Medicine Approach (2012)

At this time, the only definitive treatment of hepatic failure is liver transplantation. However, transplantation has been limited by the severely limited supply of human donor livers. Alternatively, a regenerative medicine approach has been recently proposed in rodents that describe the production of three-dimensional whole-organ scaffolds for assembly of engineered complete organs. In the present study, we describe the decellularization of porcine livers to generate liver constructs at a scale that can be clinically relevant. Adult ischemic porcine livers were successfully decellularized using a customized perfusion protocol, the decellularization process preserved the ultrastructural extracellular matrix components, functional characteristics of the native microvascular and the bile drainage network of the liver, and growth factors necessary for angiogenesis and liver regeneration. Furthermore, isolated hepatocytes engrafted and reorganized in the porcine decellularized livers using a human-sized organ culture system. These results provide proof-of-principle for the generation of a human-sized, three-dimensional organ scaffold as a potential structure for human liver grafts reconstruction for transplantation to treat liver disease.
Derivation of Euploid Human Embryonic Stem Cells from Aneuploid Embryos (2008)

Human embryonic stem cells (HESCs) are pluripotent cells derived from the inner cell mass of preimplantation embryos. In this study, to isolate new lines of HESCs, we used blastocyst-stage embryos diagnosed as aneuploid in preimplantation genetic screening (PGS). During in vitro fertilization treatments, PGS is widely applied to identify chromosomal aneuploidies, especially in cases of advanced maternal age. Embryos that are detected as carrying aneuploidies are destined to be discarded unless donated for research. From 74 fresh PGS-defined aneuploid embryos, we derived seven HESC lines. Most of the embryos were left to hatch spontaneously through the hole created for blastomere biopsy and further treated by immunosurgery. The seven HESC lines exhibited morphology and markers typical of HESCs and the capacity for long-term proliferation. The derived HESC lines manifested pluripotent differentiation potential both in vivo and in vitro. Surprisingly, karyotype analysis of the HESC lines that were derived from these aneuploid embryos showed that the cell lines carry a normal euploid karyotype. We show that the euploidy was not achieved through chromosome duplication. Alternatively, we suggest that the euploid HESC lines originated from mosaic embryos consisting of aneuploid and euploid cells, and in vitro selection occurred to favor euploid cells. We assume that aneuploid HESC lines could be isolated mostly from embryos that are uniform for the aneuploidy. These results led us to conclude that the aneuploid mosaic embryos that are destined to be discarded can serve as an alternative source for normal euploid HESC lines.
A narrow photoluminescence linewidth of 21 meV at 1.35 μm from strain-reduced InAs quantum dots covered by In0.2Ga0.8As grown on GaAs substrates (1999)

InAs quantum dots with size fluctuations of less than 4% were grown on GaAs using the self-assembling method. By covering the quantum dots with In0.2Ga0.8As or In0.2Al0.8As, strain in InAs dots can be partly reduced due to relaxation of lattice constraint in the growth direction. This results in low-energy emission (about 1.3 μm) from the quantum dots. The photoluminescence linewidth can be reduced to 21 meV at room temperature. This width is completely comparable to the theoretical limit of a band-to-band emission from a quantum well at room temperature. Because the dots can be uniformly covered by the strain reducing layers, factors that degrade size uniformity during coverage, such as compositional mixing or segregation, will be suppressed, allowing for an almost ideal buried quantum dot structure.
The Lysyl Oxidases LOX and LOXL2 Are Necessary and Sufficient to Repress E-cadherin in Hypoxia (2009)

Hypoxia has been shown to promote tumor metastasis and lead to therapy resistance. Recent work has demonstrated that hypoxia represses E-cadherin expression, a hallmark of epithelial to mesenchymal transition, which is believed to amplify tumor aggressiveness. The molecular mechanism of E-cadherin repression is unknown, yet lysyl oxidases have been implicated to be involved. Gene expression of lysyl oxidase (LOX) and the related LOX-like 2 (LOXL2) is strongly induced by hypoxia. In addition to the previously demonstrated LOX, we characterize LOXL2 as a direct transcriptional target of HIF-1. We demonstrate that activation of lysyl oxidases is required and sufficient for hypoxic repression of E-cadherin, which mediates cellular transformation and takes effect in cellular invasion assays. Our data support a molecular pathway from hypoxia to cellular transformation. It includes up-regulation of HIF and subsequent transcriptional induction of LOX and LOXL2, which repress E-cadherin and induce epithelial to mesenchymal transition. Lysyl oxidases could be an attractive molecular target for cancers of epithelial origin, in particular because they are partly extracellular.
Solution structure of apamin determined by nuclear magnetic resonance and distance geometry (1988)

The solution structure of the bee venom neurotoxin apamin has been determined with a distance geometry program using distance constraints derived from NMR. Twenty embedded structures were generated and refined by using the program DSPACE. After error minimization using both conjugate gradient and dynamics algorithms, six structures had very low residual error. Comparisons of these show that the backbone of the peptide is quite well-defined with the largest rms difference between backbone atoms in these structures of 1.34 A. The side chains have far fewer constraints and show greater variability in their positions. The structure derived here is generally consistent with the qualitative model previously described, with most differences occurring in the loop between the beta-turn (residues 2-5) and the C-terminal alpha-helix (residues 9-17). Comparisons are made with previously derived models from NMR data and other methods.
Chimeric L6 anti-tumor antibody. Genomic construction, expression, and characterization of the antigen binding site. (1992)

We report the cloning of the genomic variable region genes of the human carcinoma reactive murine monoclonal antibody L6 and their genetic linkage to human constant region exons to encode a human IgG1/kappa chimeric antibody. The chimeric protein was produced at levels greater than 20 micrograms/ml (enabling the initiation of clinical trials) and was found to have binding properties identical with that of the murine parent. The nucleic acid sequence of the variable regions was determined and found to be different than that previously reported (1). The deduced amino acid sequence was then used to generate a structural homology based three-dimensional model of the antibody binding site, which was found to share features with antibodies known to interact with a protein surface, but distinct from those that bind to carbohydrate epitopes. Biochemical analysis of binding between antibody and the in vitro-translated product of a cDNA clone that confers L6 immunoreactivity demonstrates that the antibody recognizes a protein epitope encoded by this transcript which requires the presence of membranes, but is unaffected by the removal of carbohydrate side chains.
Antibody-dependent signal amplification in tumor xenografts after pretreatment with biotinylated monoclonal antibody and avidin or streptavidin. (1996)

SAv (2.5 mg/kg) is the preferred "second-step" reagent. At this dose, the number of receptors available for targeting by radiolabeled biotin derivatives is approximately 1.8 times the number of antigen-binding sites accessible for targeting by radiolabeled antibody. Additional targeted-signal amplification should be possible by the successive and repeated administration of such polymeric reagents, each exhibiting high affinity to and forming a specific binding pair with the last-targeted molecule.
A steady state decoupled Kalman filter technique for multiuser detection (2004)

In this paper, we describe a Kalman filter based technique for multiuser detection of asynchronous CDMA systems. Similar to previously proposed techniques, we use a decoupled form of the Kalman filter, which processes each user independently. We then make the further simplifying assumption that the channel statistics are constant over a single symbol allowing us to reduce the Kalman gain to a constant dependent on the current signal to interference plus noise ratio. We study the performance of the constant gain filter and show that by appropriate choice of the gain you can optimize for either minimum bit error rate or maximum interference reduction.
Activity of hammerhead ribozymes containing nonnucleotidic linkers (1993)

Hammerhead ribozymes were synthesized in which the tetranucleotide loop II was replaced by non-nucleotidic linkers of 7, 13, 17 and 19 atoms length. Ribozymes with 17 and 19 atom linkers, in combination with a 4 base pair stem II, had catalytic efficiencies which were 2 fold increased to that of the parent ribozyme with a tetranucleotide loop. Ribozymes with these linkers, but in combination with a 2 base pair stem II, showed a 2 fold decrease in catalytic efficiency when compared to the parent ribozyme. Prolonged preincubation in the presence of MgCl2 was required for hexaethylene glycol linker-modified ribozymes to obtain maximum activity and reproducible kinetic data.
Role of Saliva in Caries Models (1995)

The crucial role played by the actions of saliva in controlling the equilibrium between de- and remineralization in a cariogenic environment is demonstrated by the effects on caries incidence of salivary dysfunction and by the distribution of sites of caries predilection to those were salivary effects are restricted. However, of the several properties of saliva which may confer protective effects, it is not certain which are most important. A distinction can be made between static protective effects, which act continuously, and dynamic effects, which act during the time-course of the Stephan curve. Evidence implicates salivary buffering and sugar clearance as important dynamic effects of saliva to prevent demineralization; of these, the buffering of plaque acids may predominate. Enhanced remineralization of white spot lesions may also be regarded as dynamic protective effects of saliva. Fluoride in saliva (from dentifrices, ingesta, etc.) may promote remineralization and (especially fluoride in plaque) inhibit demineralization. The design of experiments using caries models must take into account the static and dynamic effects of saliva. Some models admit a full expression of these effects, while others may exclude them, restricting the range of investigations possible. The possibility is raised that protective effects of saliva and therapeutic agents may act cooperatively.
Validated Zinc Finger Protein Designs for All 16 GNN DNA Triplet Targets (2002)

The Cys(2)-His(2)-type zinc finger DNA-binding proteins can be engineered to bind specifically to many different DNA sequences. A single zinc finger typically binds to a 3-4-base pair DNA subsite. One strategy for design is to identify highly specific fingers that recognize each of the 64 possible DNA triplets. We started with a subgroup of the 64 triplets, the GNN-binding fingers. The GNN-binding fingers have been examined in several studies, but previous studies did not produce specific fingers for all of the 16 GNN triplets. These previous studies did not provide any information on the possible positional or context effects on the performance of these fingers. To identify the most specific design and take the possible positional effects into consideration, we did a large-scale site selection experiment on our GNN designs. From this study, we identified very specific fingers for 14 of the 16 GNN triplets, demonstrating for the first time a clear positional dependence for many of the designs. Further systematic specificity study reveals that the in vivo functionality of these zinc finger proteins in a reporter assay depends on their binding affinities to their target sequences, thus giving a better understanding of how these zinc finger proteins might function inside cells.
Photoactivable fluorophores. 3. Synthesis and photoactivation of fluorogenic difunctionalized fluoresceins (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotoactivable fluorophores. 3. Synthesis and photoactivation of fluorogenic difunctionalized fluoresceinsGrant A. Krafft, W. Randall. Sutton, and Richard T. CummingsCite this: J. Am. Chem. Soc. 1988, 110, 1, 301–303Publication Date (Print):January 1, 1988Publication History Published online1 May 2002Published inissue 1 January 1988https://pubs.acs.org/doi/10.1021/ja00209a055https://doi.org/10.1021/ja00209a055research-articleACS PublicationsRequest reuse permissionsArticle Views919Altmetric-Citations78LEARN 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
Dielectric omnidirectional visible reflector (2001)

We demonstrate the fabrication of an all-dielectric omnidirectional mirror for visible frequencies. The dielectric reflector consists of a stack of 19 alternating layers of tin (IV) sulfide and silica. Using a combination of thermal evaporation (for tin sulfide) and thick electron-beam evaporation (for silica), we have achieved a refractive-index contrast of 2.6/1.46 , one of the highest refractive-index contrasts demonstrated in one-dimensional photonic bandgap systems designed for the visible frequency range. The tin sulfide-silica material system developed allowed the formation of a broadband visible reflector with an omnidirectional range greater than 10%. Possible applications of the system include efficient reflectors, high-frequency waveguides for communications and power delivery, and high- Q cavities.
A Quantitative Assay Reveals Ligand Specificity of the DNA Scaffold Repair Protein XRCC1 and Efficient Disassembly of Complexes of XRCC1 and the Poly(ADP-ribose) Polymerase 1 by Poly(ADP-ribose) Glycohydrolase (2014)

The posttranslational modification of proteins with poly(ADP-ribose) (PAR) regulates protein-protein interactions in DNA repair, gene expression, chromatin structure, and cell fate determination. The PAR polymerase PARP1 binds to damaged chromatin and synthesizes PAR chains to signal DNA damage and recruit the DNA repair scaffold, XRCC1. Pharmacological blockade of PARP1 enzymatic activity impairs XRCC1-dependent repair of DNA damage and selectively kills cancer cells lacking other DNA repair functions. As such, PARP inhibitors are promising new therapies for repair-deficient tumors such as BRCA mutated breast cancers. Although the XRCC1-PARP1 complex is relevant to the proposed therapeutic mechanism of PARP inhibitors, the physical makeup and dynamics of this complex are not well characterized at the molecular level. Here we describe a fluorescence-based, real-time assay that quantitatively monitors interactions between PARylated PARP1 and XRCC1. Using this assay, we show that the PAR posttranslational modification by itself is a high affinity ligand for XRCC1, requiring a minimum chain length of 7 ADP-ribose units in the oligo(ADP-ribose) ligand for a stable interaction with XRCC1. This discrete binding interface enables the PAR glycohydrolase (PARG) to completely disassemble the PARP1-XRCC1 complex without assistance from a mono(ADP-ribose) glycohydrolase. Our quantitative, real-time assay of PAR-dependent protein-protein interactions and PAR turnover by PARG is an excellent tool for high-throughput screening to identify pharmacological modulators of PAR metabolism that may be useful therapeutic alternatives to PARP inhibitors.