gebhart/patrepeval huggingface dataset:
Peptide surface modification of poly(tetrafluoroethylene‐co‐hexafluoropropylene) enhances its interaction with central nervous system neurons (1998)

Poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP) film surfaces were chemically surface modified to introduce one of three laminin adhesive peptides: GYIGSR, GRGDS, or SIKVAV. FEP film surfaces were first reduced with sodium naphthalide to introduce surface carbon–carbon double bonds at two reaction conditions: 20 min at −78°C, and 3 h at 25°C. Scanning electron microscopy and atomic force microscopy indicated that surface topography was unaffected by the reaction conditions. Reduced FEP film surfaces were further modified to introduce hydroxyl groups via hydroboration/oxidation or carboxylic acid groups via oxidation. The hydroxyl (FEP-CHxOH) and carboxylic acid (FEP-COOH) functionalized surfaces provided reactive handles for peptide coupling using tresyl chloride. Surface elemental composition data, determined from X-ray protoelectron spectroscopy, indicated that equivalent amounts of GYIGSR, GRGDS, and SIKVAV were introduced. Two additional coupling reagents, SMCC and TSU, were compared to tresyl chloride for the coupling of radiolabeled tyrosine of GYIGSR. Between 8 and 150 fmol/cm2 of peptide was introduced to the hydroxyl and carboxylic acid functionalized surfaces, with the tresyl coupling reagent showing the greatest amount of peptide incorporated. The tresyl-coupled peptide-modified surfaces were compared in terms of the response of primary, embryonic hippocampal neurons plated from serum-free medium for 4 days. The number and length of neurites extending from the cell bodies were averaged over 50 cells after 1 and 4 days FEP-CHxO-peptide surfaces had either a greater or equivalent hippocampal neuron interaction than the corresponding FEP-COO-peptide surfaces. All peptide-functionalized surfaces had a greater hippocampal neuron interaction than the corresponding FEP-CHxOH, FEP-COOH, and FEP controls after 4 days underlying the importance of the peptides over hydrophilic or hydrophobic surfaces. After 4 days differences in neurite extension were evident among the peptide-functionalized surfaces, with the longest neurites observed on the SIKVAV-functionalized surfaces. © 1998 John Wiley & Sons, Inc. J Biomed Mater Res, 42, 85–95, 1998.
Mechanism of cytochrome P4503A4- and 2D6-catalyzed dehydrogenation of ezlopitant as probed with isotope effects using five deuterated analogs. (2001)

Ezlopitant is metabolized by cytochrome P450 primarily to two metabolites: a benzyl alcohol and a corresponding alkene. The alkene arises as a direct product of metabolism of ezlopitant rather than through dehydration of the benzyl alcohol. The mechanism of this cytochrome P450 (P450)-catalyzed dehydrogenation reaction was probed with five different deuterium-labeled analogs of ezlopitant. At saturating ezlopitant concentrations, deuterium substitution resulted in small differences in reaction velocity. When deuterium was incorporated into the benzylic position ([d(1)]ezlopitant and [d(7)]ezlopitant), low isotope effects on the formation of both the benzyl alcohol and alkene were observed (1.25-1.55 for CYP3A4 and 1.48-2.61 for CYP2D6), suggesting that abstraction of the benzylic hydrogen is obligatory in the formation of both metabolites. A small amount of metabolic switching occurred because isotope effects were slightly higher for alkene and alcohol formation than for ezlopitant consumption. Intramolecular deuterium isotope effects of the dehydrogenation reaction for tri- and tetradeuterated analogs were very low (1.13-1.15) for both CYP3A4 and CYP2D6, whereas intramolecular isotope effects for the chemical dehydration of correspondingly deuterated ezlopitant benzyl alcohol (CJ-12,764) were 3.8 to 5.9. Thus, dehydrogenation does not appear to occur via enzyme-mediated general acid catalysis of the benzyl alcohol. A mechanism for the dehydrogenation of ezlopitant is proposed in consideration of the data presented.
<title>Range and brightness fusion: using radar and electro-optical data association for tracking small objects</title> (2003)

In this paper we consider the tracking of small distant objects using Radar and Electro-Optical (EO) sensors. In particular we address the problem of data association after coalescence - this happens when two objects become sufficiently close (in angular terms) that they can no longer be resolved by the EO sensor. Some moments later they de-coalesce and the resulting detections must be associated with the existing tracks in the EO sensor. Traditionally this would be solved by making use of the velocity vectors of the objects prior to coalescence. This approach can work well for crossing objects, but when the objects are largely moving in a direction radial to the sensor it becomes problematic. Here we investigate the use of data fusion to combine Radar range with a brightness measure derived from an EO sensor to enhance the accuracy of data association. We present a number of results on the performance of this approach taking into account target motion, atmospheric conditions and sensor noise.
1/4-J discharge pumped KrF laser (1978)

Over 1/4-joule per pulse is obtained from a cable-fed uv preionized discharge device where a faster energy deposition rate compensates for a slower voltage rise time. These slower voltage rise-time devices may be scalable to high repetition rates using conventional thyratron switching techniques.
Measuring Friedreich ataxia (2006)

The Friedreich Ataxia Rating Scale, performance measures, and performance measure composites provide valid assessments of disease progression in Friedreich ataxia.
Faster Relief Mapping using the Secant Method (2007)

Relief mapping using the secant method offers an efficient method for adding per-pixel displacement based on height fields to an arbitrary polygonal mesh in real time. The technique utilizes an interval-based method in which bounds of the interval are computed in the beginning and are refined at every iteration until the intersection point is reached. The search space defined by the interval reduces and converges to the intersection point rapidly and outperforms the currently popular method based on binary search (relief mapping) used for performing this task. We compute the bounds using a simple ray-segment intersection method. We demonstrate the algorithm and show empirical and explicit evidence of the speed-up. Source code is available online.
Gene Transfer into Marrow Repopulating Cells: Comparison Between Amphotropic and Gibbon Ape Leukemia Virus Pseudotyped Retroviral Vectors in a Competitive Repopulation Assay in Baboons (1997)

Many diseases might be treated by gene therapy targeted to the hematopoietic system, but low rates of gene transfer achieved in humans and large animals have limited the application of this technique. We have developed a competitive hematopoietic repopulation assay in baboons to evaluate methods for improving gene transfer and have used this method to compare gene transfer rates for retroviral vectors having an envelope protein (pseudotype) from amphotropic murine retrovirus with similar vectors having an envelope protein derived from gibbon ape leukemia virus (GALV). We hypothesized that vectors with a GALV pseudotype might perform better based on our previous work with cultured human hematopoietic cells. CD34(+) marrow cells from each of four untreated baboons were divided into two equal portions that were cocultivated for 48 hours with packaging cells producing equivalent titers of either amphotropic or GALV pseudotyped vectors containing the neo gene. The vectors contained small sequence differences to allow differentiation of cells genetically marked by the different vectors. Nonadherent and adherent cells from the cultures were infused into animals after they received a myeloablative dose of total body irradiation. Polymerase chain reaction (PCR) analysis for neo gene-specific sequences in colony-forming unit-granulocyte-macrophage from cell populations used for transplant showed gene transfer rates of 2.7%, 7.1%, <15%, and 3.9% with the amphotropic vectors and 7.1%, 11.3%, <15%, and 26.4% with the GALV pseudotyped vector. PCR analysis of peripheral blood and marrow cells after engraftment showed the neo gene to be present in all four animals analyzed at levels between 0.1% and 5%. Overall gene transfer efficiency was higher with the GALVpseudotyped vector than with the amphotropic vectors. Southern blot analysis in one animal confirmed a gene transfer efficiency of between 1% and 5%. The higher gene transfer efficiency with the GALV-pseudotyped vector correlated with higher levels of GALV receptor RNA compared with the amphotropic receptor in CD34(+) hematopoietic cells. These results show that GALV-pseudotyped vectors are capable of transducing baboon marrow repopulating cells and may allow more efficient gene transfer rates for human gene therapy directed at hematopoietic cells. In addition, our data show considerable differences in gene transfer efficiency between individual baboons, suggesting that a competitive repopulation assay will be critical for evaluation of methods designed to improve gene transfer into hematopoietic stem cells.
Pim‐1 kinase phosphorylates and stabilizes RUNX3 and alters its subcellular localization (2008)

The loci of the Pim and Runx gene families have been identified as targets for viral insertions in CD2-myc mice. Synergistic cooperation between Pim and RUNX was also found in the CD2-Runx2 transgenic mouse lymphoma model. RUNX genes have come to prominence recently because of their roles as essential regulators of cell fate in development. Paradoxically, they appear to function either as tumor-suppressor genes or dominant oncogenes according to the cellular context. However, the molecular mechanism of the ambiguous roles played by this family of transcription factors in cancer has remained largely uninvestigated. Here we demonstrate that Pim-1 phosphorylates four Ser/Thr residues within the Runt domain and stabilizes RUNX3 protein. In addition, Pim-1 markedly altered the cellular localization of RUNX3 from the nucleus to the cytoplasm. Our results demonstrate that the subcellular localization of RUNX3 is altered by phosphorylation. We propose that RUNX family members may behave as oncogenes if mislocalized to a cellular micro-compartment.
Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes (2009)

To our knowledge, this is the first time that a dual host-symbiont transcriptome sequencing effort has been conducted in a single termite species. This sequence database represents an important new genomic resource for use in further studies of collaborative host-symbiont termite digestion, as well as development of coevolved host and symbiont-derived biocatalysts for use in industrial biomass-to-bioethanol applications. Additionally, this study demonstrates that: (i) phenoloxidase activities are prominent in the R. flavipes gut and are not symbiont derived, (ii) expands the known number of host and symbiont glycosyl hydrolase families in Reticulitermes, and (iii) supports previous models of lignin degradation and host-symbiont collaboration in cellulose/hemicellulose digestion in the termite gut. All sequences in this paper are available publicly with the accession numbers FL634956-FL640828 (Termite Gut library) and FL641015-FL645753 (Symbiont library).
Readthrough activation of early adenovirus E1b gene transcription (1997)

In cells productively infected with adenovirus type 5, transcription is not terminated between the E1a gene and the adjacent downstream E1b gene. Insertion of the mouse beta(maj)-globin transcription termination sequence (GGT) into the E1a coding region dramatically reduces early, but not late, E1b expression (E. Falck-Pedersen, J. Logan, T. Shenk, and J. E. Darnell, Jr., Cell 40:897-905, 1985). In the study described herein, we showed that base substitution mutations in the globin DNA that specifically relieved transcription termination also restored early E1b promoter activity in cis, establishing that maximal early E1b expression requires readthrough transcription originating from the adjacent upstream gene. To identify potential targets of readthrough activation, a series of recombinant viruses with double mutations was constructed. Each double-mutant virus strain had the transcription termination sequences in the first exon of E1a and a deletion within the transcription control region of E1b. Early E1b expression from the double-mutant strains was more defective than that from strains containing either mutation alone, indicating that the deleted regions (positions -362 to -35) are not the target for readthrough activation. Two findings suggested that a cis-dominant property of early viral templates is important for readthrough activation. First, the early E1b defect caused by the GGT insertion was not complemented in trans by factors present in late-infected cells. Second, restoration of E1b transcription at late times occurred concurrently with viral DNA replication. Readthrough activation may help convert virion DNA into a transcriptionally competent template prior to DNA replication and late transcription.
Nucleoside H-phosphonates. 14. Synthesis of nucleoside phosphoroselenoates and phosphorothioselenoates via stereospecific selenization of the corresponding H-phosphonate and H-phosphonothioate diesters with the aid of new selenium-transfer reagent, 3H-1,2-benzothiaselenol-3-one (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleoside H-phosphonates. 14. Synthesis of nucleoside phosphoroselenoates and phosphorothioselenoates via stereospecific selenization of the corresponding H-phosphonate and H-phosphonothioate diesters with the aid of new selenium-transfer reagent, 3H-1,2-benzothiaselenol-3-oneJacek Stawinski and Mats ThelinCite this: J. Org. Chem. 1994, 59, 1, 130–136Publication Date (Print):January 1, 1994Publication History Published online1 May 2002Published inissue 1 January 1994https://pubs.acs.org/doi/10.1021/jo00080a021https://doi.org/10.1021/jo00080a021research-articleACS PublicationsRequest reuse permissionsArticle Views361Altmetric-Citations36LEARN 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
Direct involvement of the CDR3-like domain of CD4 in T helper cell activation (1992)

The CD4 glycoprotein, a member of the Ig super-family, has long been known to play an important role in the immunologic activation of Th cells. The precise manner in which CD4 participates in this activation process is not yet understood. In an attempt to further define its role in Th cell activation, we modeled the D1 domain of the murine CD4 protein (L3T4) based on the experimentally determined high resolution structure of the human CD4 protein. Because the D1 domain of CD4 strongly resembles the V kappa chain of an antibody, we addressed the question of whether the CDR-like regions of CD4 are also involved in mediating protein-protein interactions. Consequently, we used the modeled L3T4 structure as a template in the design of conformational mimics of the CDR3-like region (residues 86-94). Only the analog designed to mimic both the sequence and conformation of this region exhibited highly specific inhibition of CD4-dependent responses. Because the inhibitory activity could be localized to the Th cell itself, it appears that this analog acts by uncoupling a CD4 association (independent of an APC) critical to generating a proliferative response.
Kinect 3D Point Cloud Live Video Streaming (2015)

We present a live video streaming system using a low cost 3D sensor camera like the Microsoft Kinect. The huge amount of raw point data that Kinect creates has to be stored and transmitted by efficient compact means. Noise and redundancy, however, make the process more difficult to achieve. To overcome these difficulties we propose a live streaming system that streams a 3D video to an Android Mobile phone and to Linux Desktop systems. For Android mobile phone client, the 3D video is filtered before streaming. Filtering stage contains 3 types of filters, Voxel Grid, Statistical Outlier Removal and Histogram-based conditional filters. The video is captured by the Kinect and a 3D point cloud is created. Voxel Grid filter is used since the generated 3D video will have millions of points; a downsampling procedure is applied to minimize the number of points. To reduce outliers and color information, statistical outlier removal and histogram-based conditional filters are used respectively. Conditional filter is customized by the scene histogram for each channel of RGB color to preserve the dominant color information for each scene. For Linux desktop client, the video is filtered by the histogram-based conditional filter and is compressed using an Octree structure that reduces spatial redundancies across the streamed video.
New Vistas on Amygdala Networks in Conditioned Fear (2004)

It is currently believed that the acquisition of classically conditioned fear involves potentiation of conditioned thalamic inputs in the lateral amygdala (LA). In turn, LA cells would excite more neurons in the central nucleus (CE) that, via their projections to the brain stem and hypothalamus, evoke fear responses. However, LA neurons do not directly contact brain stem-projecting CE neurons. This is problematic because CE projections to the periaqueductal gray and pontine reticular formation are believed to generate conditioned freezing and fear-potentiated startle, respectively. Moreover, like LA, CE may receive direct thalamic inputs communicating information about the conditioned and unconditioned stimuli. Finally, recent evidence suggests that the CE itself may be a critical site of plasticity. This review attempts to reconcile the current model with these observations. We suggest that potentiated LA outputs disinhibit CE projection neurons via GABAergic intercalated neurons, thereby permitting associative plasticity in CE. Thus plasticity in both LA and CE would be necessary for acquisition of conditioned fear. This revised model also accounts for inhibition of conditioned fear after extinction.
Winner-Take-All Networks of O(N) Complexity (1988)

We have designed, fabricated, and tested a series of compact CMOS integrated circuits that realize the winner-take-all function.These analog, continuous-time circuits use only O(n) of interconnect to perform this function.We have also modified the winner-take-all circuit, realizing a circuit that computes local nonlinear inhibition.Two general types of inhibition mediate activity in neural systems: subtractive inhibition, which sets a zero level for the computation, and multiplicative (nonlinear) inhibition, which regulates the gain of the computation.We report a physical realization of general nonlinear inhibition in its extreme form, known as winner-take-all.We have designed and fabricated a series of compact, completely functional CMOS integrated circuits that realize the winner-take-all function, using the full analog nature of the medium.This circuit has been used successfully as a component in several VLSI sensory systems that perform auditory localization (Lazzaro and Mead, in press) and visual stereopsis (Mahowald and Delbruck, 1988).Winnertake-all circuits with over 170 inputs function correctly in these sensory systems.We have also modified this global winner-take-all circuit, realizing a circuit that computes local nonlinear inhibition.The circuit allows multiple winners in the network, and is well suited for use in systems that represent a feature space topographically and that process several features in parallel.We have designed, fabricated, and tested a CMOS integrated circuit that computes locally the winner-take-all function of spatially ordered input.
CD8+ T-Cell Responses Identify β-Cell Autoimmunity in Human Type 1 Diabetes (2007)

Despite the understanding that type 1 diabetes pathogenesis is mediated by T-cells, detection of these rare lymphocytes remains largely elusive. Suitable T-cell assays are highly needed, since they could offer preclinical diagnoses and immune surrogate end points for clinical trials. Although CD4+ T-cell assays have met with limited success, CD8+ T-cells are increasingly recognized as key actors in the diabetes of the NOD mouse. CD8+ T-cells are likely to play a role also in humans and may provide new markers of β-cell autoimmunity. Taking advantage of a panel of HLA-A2–restricted β-cell epitopes derived from preproinsulin, GAD, and islet glucose-6-phosphatase catalytic subunit-related protein (IGRP), we have implemented an islet-specific CD8+ T-cell interferon-γ enzyme-linked immunospot (ISL8Spot) assay. The ISL8Spot assay is capable of detecting and quantifying β-cell–reactive CD8+ T-cells directly ex vivo, without any preliminary expansion, using either fresh or frozen samples. Positive ISL8Spot responses separate new-onset diabetic and healthy samples with high accuracy (86% sensitivity, 91% specificity), using as few as five immunodominant epitopes. Moreover, sensitivity reaches 100% when the ISL8Spot assay is complemented by antibody determinations. Combination of CD8+ T-cell measurements with immune intervention strategies may open new avenues toward type 1 diabetes prediction and prevention.
Simplified method for polarization-sensitive optical coherence tomography (2001)

We report a method for extracting the birefringence properties of biological samples with micrometer-scale resolution in three dimensions, using a new form of polarization-sensitive optical coherence tomography. The method measures net retardance, net fast axis, and total reflectivity as a function of depth into the sample. Polarization sensing is accomplished by illumination of the sample with at least three separate polarization states during consecutive acquisitions of the same pixel, A scan, or B scan. The method can be implemented by use of non-polarization-maintaining fiber and a single detector. In a calibration test of the system, net retardance was measured with an average error of 7.5 degrees (standard deviation 2.2 degrees ) over the retardance range 0 degrees to 180 degrees , and a fast axis with average error of 4.8 degrees over the range 0 degrees to 180 degrees .