gebhart/patrepeval huggingface dataset:
Lidar scan feature for localization with highly precise 3-D map (2014)

In recent years, automated vehicle researches move on to the next stage, that is auto-driving experiments on public roads. Major challenge is how to robustly drive at complicated situations such as narrow or non-featured road. In order to realize practical performance, some static information should be kept on memory such as road topology, building shape, white line, curb, traffic light and so on. Currently, some measurement companies have already begun to prepare map database for automated vehicles. They are able to provide highly-precise 3-D map for robust automated driving. This study focuses on what kind of data should be observed during automated driving with such precise database. In particular, we focus on the accurate localization based on the use of lidar data and precise 3-D map, and propose a feature quantity for scan data based on distribution of clusters. Localization experiment shows that our method can measure surrounding uncertainty and guarantee accurate localization.
Peptides targeting inflamed synovial vasculature attenuate autoimmune arthritis (2011)

Autoimmune diseases, such as rheumatoid arthritis, frequently target one major tissue/organ despite the systemic nature of the immune response. This is particularly perplexing in the case of ubiquitously distributed antigens invoked in arthritis induction. We reasoned that selective targeting of the synovial joints in autoimmune arthritis might be due in part to the unique attributes of the joint vasculature. We examined this proposition using the adjuvant-induced arthritis model of human rheumatoid arthritis, and profiled the synovial vasculature using ex vivo and in vivo screening of a defined phage peptide-display library. We identified phage that preferentially homed to the inflamed joints. The corresponding synthetic peptides showed binding to the joint-derived endothelial cells, as well as specificity in inhibiting binding of the respective phage to the synovial vasculature. Intriguingly, the treatment of arthritic rats with one such peptide resulted in efficient inhibition of the progression of arthritis. The suppression of arthritis was attributable in part to the peptide-induced reduction of T-cell trafficking into the joints and the inhibition of angiogenesis. This peptide differed in sequence, in receptor binding specificity, and in angiogenesis/inflammation-related cell signaling from the previously characterized arginine-glycine-aspartic acid-containing peptide. Thus, our study reveals joint-homing peptides that can be further exploited for the selective delivery of antiarthritic agents into the inflamed joints to enhance their efficacy while reducing systemic toxicity, and also for examining intricacies of the pathogenesis of arthritis. This approach can be customized for application to other organ-specific autoimmune diseases as well.
The English strain of rat cytomegalovirus (CMV) contains a novel captured CD200 (vOX2) gene and a spliced CC chemokine upstream from the major immediate-early region: further evidence for a separate evolutionary lineage from that of rat CMV Maastricht (2005)

Sequence data for eight genes, together with time-course Northern blotting and 3'- and 5'-RACE (rapid amplification of cDNA ends) analysis for some mRNAs from a 12 kb region upstream from the major immediate-early (MIE) genes of the English isolate of rat cytomegalovirus (RCMV), are presented. The results identified important differences compared to both murine cytomegalovirus (MCMV) and the Maastricht isolate of RCMV. A striking finding is the presence of a highly conserved, rightwards-oriented homologue of the rat cellular CD200 (OX2) gene immediately to the right of the MIE region, which replaces either the leftwards-oriented AAV REP gene of RCMV (Maastricht) or the upstream spliced portions of the immediate-early 2 gene (ie2) in MCMV. From the presence of other homologues of MCMV- and RCMV-specific genes, such as the beta-chemokine MCK-2, SGG1 and an Fcgamma receptor gene, as reported here, the basic architecture of the MIE region (reported previously) and the level of IE2 and DNA polymerase (POL) protein conservation in phylogenetic analyses, it is clear that the English strain of RCMV is also a member of the genus Muromegalovirus, but is a beta-herpesvirus species that is very distinct from both MCMV and RCMV (Maastricht). Both the lack of a CD200 homologue in the other two rodent viruses and the depth of sequence divergence of the rodent CMV IE2 and POL proteins suggest that these three viruses have evolved as separate species in the genus Muromegalovirus since very early in the host rodent lineage.
Code generation in the polytope model (1998)

Automatic parallelization of nested loops, based on a mathematical model, the polytope model, has been improved significantly over the last decade: state-of-the-art methods allow flexible distributions of computations in space and time, which lead to high-quality parallelism. However, these methods have not found their way into practical parallelizing compilers due to the lack of code generation schemes which are able to deal with the new-found flexibility. To close this gap is the purpose of this paper.
Effect of inflammation on central nervous system development and vulnerability: review (2005)

Hypothetically, all of these effects on the CNS triggered by inflammation may have severe consequences for the individual's ability to cope with environmental exposures during childhood and adulthood.
Cytoplasmic Proteome and Secretome Profiles of Differently Stimulated Human Dendritic Cells (2009)

Dendritic cells (DCs), the most potent and specialized antigen-presenting cells, play a key role in the regulation of the adaptive immunity. Immature DCs were generated by in vitro culturing of peripheral blood monocytes and functionally activated with the classical pathogen-associated molecular pattern lipopolysaccharide (LPS). Alternative activation resulting in Th-2 polarization was induced with lipid oxidation products derived from 1-palmitoyl-2-arachidoyl-sn-glycerol-3-phosphorylcholin (OxPAPC). Tolerogenic cells were obtained by treating DCs with human rhinovirus (HRV). The aim of this study was the identification of proteome profiles related to the functionally different dendritic cell phenotypes. Cytoplasmic proteins were analyzed by shotgun proteomics resulting in the identification of 1690 proteins. While mature and alternatively activated DCs displayed highly distinct protein expression profiles, HRV-treated DCs showed minor proteome alterations. As DCs exert many specific functions via secretion, we investigated the secretomes by a combination of 2D-PAGE and shotgun proteomics. We successfully identified a broad variety of cytokines (e.g., GM-CSF, TNF-alpha, interleukin-1beta, 6, 12 beta, 28B and 29), chemokines (e.g., CCL3, 5, 8, 17, 18, 19, 24, CXCL1, 2, 9 and 10) and growth factors (growth/differentiation factor 8, C-type lectin domain family 11 member A). The relative composition of secretome profiles, although comprising much less proteins, was found to be much more affected by functional alteration of cells than the cytoplasmic protein composition. In conclusion, we demonstrate that functional distinct subsets of DCs display distinct proteome profiles which comprise biomarker candidates. These proteins may prove useful for the interpretation of complex clinical proteomics data.
ChemInform Abstract: Nucleoside Hydrogenphosphonates in Oligonucleotide Synthesis. (1986)

Abstract Nucleoside alkyl or aryl hydrogenphosphonates such as (III) [obtained from (I) with the Chlorophosphomorpholidite (II)] cannot be used as Starting materials for the preparation of phosphite triesters.
Calicheamicin γ 1 I and DNA: Molecular Recognition Process Responsible for Site-Specificity (1989)

Calicheamicin gamma 1I is a recently discovered diyne-ene-containing antitumor antibiotic that cleaves DNA in a double-stranded fashion, a rarity among drugs, at specific sequences. It is proposed that the cutting specificity is due to a combination of the complementarity of the diyne-ene portion of the aglycone with DNA secondary structures and stabilization by association of the thiobenzoate-carbohydrate tail with the minor groove.
Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation (2002)

A novel histone methyltransferase, termed Set9, was isolated from human cells. Set9 contains a SET domain, but lacks the pre- and post-SET domains. Set9 methylates specifically lysine 4 (K4) of histone H3 (H3-K4) and potentiates transcription activation. The histone H3 tail interacts specifically with the histone deacetylase NuRD complex. Methylation of histone H3-K4 by Set9 precludes the association of NuRD with the H3 tail. Moreover, methylation of H3-K4 impairs Suv39h1-mediated methylation at K9 of H3 (H3-K9). The interplay between the Set9 and Suv39h1 histone methyltransferases is specific, as the methylation of H3-K9 by the histone methyltransferase G9a was not affected by Set9 methylation of H3-K4. Our studies suggest that Set9-mediated methylation of H3-K4 functions in transcription activation by competing with histone deacetylases and by precluding H3-K9 methylation by Suv39h1. Our results suggest that the methylation of histone tails can have distinct effects on transcription, depending on its chromosomal location, the combination of posttranslational modifications, and the enzyme (or protein complex) involved in the particular modification.
Differentiating a Diverse Range of Volatile Organic Compounds with Polyfluorophore Sensors Built on a DNA Scaffold (2010)

Oligodeoxyfluorosides (ODFs) are short DNA-like oligomers in which DNA bases are replaced with fluorophores. A preliminary study reported that some sequences of ODFs were able to respond to a few organic small molecules in the vapor phase, giving a change in fluorescence. Here, we follow up on this finding by investigating a larger range of volatile organic analytes, and a considerably larger set of sensors. A library of tetramer ODFs of 2401 different sequences was prepared by using combinatorial methods, and was screened in air for fluorescence responses to a set of ten different volatile organics, including multiple aromatic and aliphatic compounds, acids and bases, varied functional groups, and closely related structures. Nineteen responding sensors were selected and characterized. These sensors were cross-screened against all ten analytes, and responses were measured qualitatively (by changes in color and intensity) and quantitatively (by measuring ΔR, ΔG, and ΔB values averaged over five to six sensor beads; R=red, G=green, B=blue). The results show that sensor responses were diverse, with a single sensor responding differently to as many as eight of the ten analytes; multiple classes of responses were seen, including quenching, lighting-up, and varied shifts in wavelength. Responses were strong, with raw ΔR, ΔG, and ΔB values of as high as >200 on a 256-unit scale and unamplified changes in many cases apparent to the naked eye. Sensors were identified that could distinguish clearly between even very closely related compounds such as acrolein and acrylonitrile. Statistical methods were applied to select a small set of four sensors that, as a pattern response, could distinguish between all ten analytes with high confidence. Sequence analysis of the full set of sensors suggested that sequence/order of the monomer components, and not merely composition, was highly important in the responses.
Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps (2001)

Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
Finite-element analysis of axisymmetric cavity resonator using a hybrid edge element technique (1993)

A modified finite-element technique for the analysis of axisymmetric cavities is presented. In this analysis an edge element approach is used in conjunction with a nodal approach to represent all electric field components in the cavity. A bilinear functional is formulated from which resonant frequencies and/or field distributions are obtained. Several geometries are investigated and corresponding results are presented as verification of the method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: Evaluation of the nearest‐neighbor stacking interactions in DNA (1992)

Seventeen DNA dumbbells were constructed that have duplex sequences ranging in length from 14 to 18 base pairs linked on the ends by T4 single-strand loops. Fifteen of the molecules have the core duplexes with the sequences 5'G-T-A-T-C-C-(W-X-Y-Z)-G-G-A-T-A-C3', where (W-X-Y-Z) represents a unique combination of A.T, T.A, G.C, and C.G base pairs. The remaining two molecules have the central sequence (W-X-Y-Z) = A-C and A-C-A-C-A-C. These duplex sequences were designed such that the central sequences include different combinations of the 10 possible nearest-neighbor (n-n) stacks in DNA. In this sense the set of molecules is complete and serves as a model system for evaluating sequence-dependent local stability of DNA. Optical melting curves of the samples were collected in 25, 55, 85, and 115 mM [Na+], and showed, regardless of solvent ionic strength, that the transition temperatures of the dumbbells vary by as much as 14 degrees for different molecules of the set. Results of melting experiments analyzed in terms of a n-n sequence-dependent model allowed evaluation of nine independent linear combinations of the n-n stacking interactions in DNA as a function of solvent ionic strength. Although there are in principle 10 possible different n-n interactions in DNA, these 10 are not linearly independent and therefore can not be uniquely determined. For molecules with ends, there are 9 linearly independent combinations, as opposed to circular or semiinfinite repeating copolymers where only 8 linear combinations of the 10 possible n-n interactions are linearly independent. The n-n interactions are presented as combinations of the deviations from average stacking for the 5'-3' base-pair doublets, delta Gi, and reveal several interesting features: (1) Titratable changes in the values of delta Gi with changing salt environment are observed. In all salts the most stable unique combination is delta G4 = (delta GGpC+delta GCpG)/2, and the least stable is the GpG/CpC stack, delta G2 = delta GGpG/CpC. (2) The chi 2 values of the fits of the evaluated delta Gi's to experimental data increased with decreasing [Na+], suggesting that significant interactions beyond nearest neighbors become more pronounced, particularly at 25 nM Na+.(ABSTRACT TRUNCATED AT 400 WORDS)
Amplitude death induced by dynamic coupling (2003)

The present paper shows that dynamic coupling induces amplitude death in coupled identical oscillators. For a simple limit-cycle oscillator, our theoretical analysis provides the necessary and sufficient condition for amplitude death. Furthermore, we guarantee that amplitude death never occurs, if each oscillator satisfies the odd number property that is known in the field of delayed-feedback control of chaos.
Yaba-Like Disease Virus: an Alternative Replicating Poxvirus Vector for Cancer Gene Therapy (2001)

Vaccinia virus is being investigated as a replicating vector for tumor-directed gene therapy. However, the majority of cancer patients have preformed immunologic reactivity against vaccinia virus, as a result of smallpox vaccination, which may limit its use as a vector. The Yaba-like disease (YLD) virus was investigated here as an alternative, replicating poxvirus for cancer gene therapy. We have demonstrated that the YLD virus does not cross-react with vaccinia virus antibodies, and it replicates efficiently in human tumor cells. YLD virus can be expanded and purified to high titer in CV-1 cells under conditions utilized for vaccinia virus. The YLD virus RNA polymerase was able to express genes regulated by a synthetic promoter designed for use in orthopoxviruses. We sequenced the YLD virus TK gene and created a shuttle plasmid, which allowed the recombination of the green fluorescent protein (GFP) gene into the YLD virus. In a murine model of ovarian cancer, up to 38% of cells in the tumor expressed the GFP transgene 12 days after intraperitoneal virus delivery. YLD virus has favorable characteristics as a vector for cancer gene therapy, and this potential should be explored further.
Alternative Fuels for Platelet Storage: A Metabolic Study (1990)

We have studied the metabolism of platelets in vitro using washed platelets. Oxygen uptake and fuel utilization were measured. It was found that glucose is never oxidized to any significant extent and is always converted to lactate, regardless of oxygen availability. Oxidative metabolism fuels 70-100% of the ATP turnover, and oxygen uptake is the same whether the platelet is consuming glucose, acetate or only an unidentified endogenous fuel. When acetate is the added fuel, no endogenous fuel is oxidized, whereas the addition of glucose results in sparing of only 8% of endogenous fuel. Preliminary storage experiments using plasma-free media show that an acetate-containing buffered salt solution provided excellent storage conditions and that a medium without any exogenous fuel is better than one containing glucose. Thus we conclude that a successful storage medium should contain minimal amounts of glucose, and an oxidizable fuel such as acetate, in order to supplement the endogenous one.
Arousal and inhibition of human NK cells (1997)

NK cells express receptors for polymorphic MHC class I molecules that inhibit killing of potential target cells bearing appropriate class I allotypes. Here we review the membrane receptors on human NK cells that are known to initiate cell-mediated cytotoxicity and demonstrate regulation of these responses by the killer cell inhibitory (KIR) receptors.
Feasibility and development of a high-power real accommodating intraocular lens (2005)

Flexible material is capable of being manipulated when placed between a scleral-fixated rigid plane and the ciliary muscles-operated capsular diaphragm. Such manipulation as used by the IOL concept presented here has generated an active change of more than 40.0 D in the monkey eye.
Fabrication and test of polymeric microaxicons (2012)

A digital holographic characterization of Bessel beams produced by polymeric microaxicons is reported. Both intensity and phase of the beam can be numerically reconstructed in whichever point starting from a single acquired hologram. Optical parameters such as the full width at half maximum, the focal length and the depth of focus of the axicon lens are experimentally measured. The Bessel beam exiting from the axicon, with a very large depth of focus with respect to that of a Gaussian beam, is successfully exploited for optical trapping of micrometric objects.
Replacing the Nucleobases in DNA with Designer Molecules (2002)

DNA is not only a carrier of genetic information, but it is also a versatile supramolecular scaffold, arranging smaller organic structures into predesigned geometries. Herein are discussed molecular strategies in which the natural DNA bases on the sugar-phosphate backbone are replaced by other molecules. Some of the base replacements under study include fluorophores, ligands for metals, helix stabilizers, and DNA base shape mimics.
Plasma kallikrein-kinin system and diabetic retinopathy (2013)

Diabetic retinopathy (DR) occurs, to some extent, in most people with at least 20 years' duration of diabetes mellitus. The progression of DR to its sight-threatening stages is usually associated with the worsening of underlying retinal vascular dysfunction and disease. The plasma kallikrein-kinin system (KKS) is activated during vascular injury, where it mediates important functions in innate inflammation, blood flow, and coagulation. Recent findings from human vitreous proteomics and experimental studies on diabetic animal models have implicated the KKS in contributing to DR. Vitreous fluid from people with advanced stages of DR contains increased levels of plasma KKS components, including plasma kallikrein (PK), coagulation factor XII, and high-molecular-weight kininogen. Both bradykinin B1 and B2 receptor isoforms (B1R and B2R, respectively) are expressed in human retina, and retinal B1R levels are increased in diabetic rodents. The activation of the intraocular KKS induces retinal vascular permeability, vasodilation, and retinal thickening, and these responses are exacerbated in diabetic rats. Preclinical studies have shown that the administration of PK inhibitors and B1R antagonists to diabetic rats ameliorates retinal vascular hyperpermeability and inflammation. These findings suggest that components of plasma KKS are potential therapeutic targets for diabetic macular edema.
Recommendations for the management of dyslipidemia and the prevention of cardiovascular disease: summary of the 2003 update. (2003)

Clinical practice guidelines require continual reassessment in response to new information and changes in the pattern of disease. Challenges in Canada, as in all industrialized countries, include the increasing size of the elderly population and the rising prevalence of obesity and diabetes mellitus
Rational design of visible and NIR distyryl-BODIPY dyes from a novel fluorinated platform (2010)

A new series of distyryl-BODIPY has been rationally designed and synthesised from a novel fluorinated platform, 8-pentafluorophenylBODIPY, which has enhanced reactivity in the presence of both electron rich, and for the first time, electron deficient aldehydes. The pentafluorobenzene leads to larger red shifts of absorption and emission compared to previously reported analogues. The reactivity and spectroscopic results have been rationalised with quantum mechanics calculation. The fluorescence sensitivity of one derivative to acidity is also presented.