gebhart/patrepeval huggingface dataset:
Ghrelin Inhibits Proinflammatory Responses and Nuclear Factor-κB Activation in Human Endothelial Cells (2004)

Ghrelin inhibits proinflammatory cytokine production, mononuclear cell binding, and nuclear factor-kappaB activation in human endothelial cells in vitro and endotoxin-induced cytokine production in vivo. These novel antiinflammatory actions of ghrelin suggest that the peptide could play a modulatory role in atherosclerosis, especially in obese patients, in whom ghrelin levels are reduced.
A Study of feature extraction algorithms for optical flow tracking (2012)

Sparse optical flow algorithms, such as the Lucas-Kanade approach, provide more robustness to noise than dense optical flow algorithms and are the preferred approach in many scenarios. Sparse optical flow algorithms estimate the displacement for a selected number of pixels in the image. These pixels can be chosen randomly. However, pixels in regions with more variance between the neighbours will produce more reliable displacement estimates. The selected pixel locations should therefore be chosen wisely. In this study, the suitability of Harris corners, Shi-Tomasi's “Good features to track", SIFT and SURF interest point extractors, Canny edges, and random pixel selection for the purpose of frame-by-frame tracking using a pyramidical Lucas-Kanade algorithm is investigated. The evaluation considers the important factors of processing time, feature count, and feature trackability in indoor and outdoor scenarios using ground vehicles and unmanned aerial vehicles, and for the purpose of visual odometry estimation.
Molecular characterization of thesoxRSgenes ofEscherichia coli: two genes control a superoxide stress regulon (1991)

The soxR locus of Escherichia coli K12 mediates transcriptional activation of a complex oxidative stress regulon in response to superoxide-generating (redox-cycling) agents. We have cloned the soxR locus, which is positioned near the uvrA gene at 92.2 min on the genetic map, by monitoring complementation of a delta soxR mutation. Subclones from the soxR region in the delta soxR strain simultaneously restored cellular resistance to the redox-cycling agent phenazine methosulfate and inducibility of at least two of the regulon proteins, glucose-6-phosphate dehydrogenase and endonuclease IV, by paraquat, another redox-cycling agent. DNA sequence analysis revealed the presence of two genes involved in activating the soxR regulon. These genes, named soxR and soxS, are arranged divergently with their 5' ends separated by only 85 bp. The predicted 12.9-kDa SoxS protein is related to the AraC family of one-component gene regulators, but corresponds only to the putative DNA-binding regions of these proteins. The 17.1-kDa SoxR protein bears significant homology only to the MerR family of proteins including a predicted DNA-binding helix-turn-helix and a cluster of cysteine residues positioned similarly to those that regulate the activity of MerR in response to Hg2+. This suggests that SoxR could be a metal-binding gene regulator that acts as the intracellular sensor for superoxide. SoxS is evidently the proximal activator of the regulon genes: antibiotic resistance and high-level expression of at least three of the regulon proteins was effected in vivo by the individual expression of SoxS, but not of SoxR, whether or not the cells were exposed to paraquat. These data, together with the recently reported paraquat-inducibility of the soxS gene (Wu, I., and Weiss, B. (1990) J. Bacteriol. 173, 2864-2871), indicate that SoxR and SoxS may constitute a novel type of two-component regulatory system in which the two proteins act sequentially to activate transcription of the various regulon genes in response to superoxide stress.
Trends and Patterns of Prostate Cancer: What Do They Suggest? (2001)

Prostate cancer is the most commonly diagnosed non-skin cancer in most western countries particularly in the US. Despite the substantial morbidity and mortality the etiology of prostate cancer is still unknown. As such the patterns and trends of prostate cancer in various countries are presented in this article to provide further insights for future epidemiologic studies. According to international comparisons the rates of prostate cancer have risen in every population-based registry around the world despite the very large population variation in incidence. It is noted that factors affecting reported incidence include changes over time in diagnosis and population differences in access to medical care quality of cancer diagnosis and population differences in access to medical care quality of cancer diagnosis completeness and accuracy of cancer reporting and screening. Moreover changes in prevalence of risk factors in the population will also impact the reported and the real incidence. Finally differences in risk among racial and ethnic groups are discussed.
Thermodynamic and structural description of allosterically regulated VEGFR-2 dimerization (2011)

VEGFs activate 3 receptor tyrosine kinases, VEGFR-1, VEGFR-2, and VEGFR-3, promoting angiogenic and lymphangiogenic signaling. The extracellular receptor domain (ECD) consists of 7 Ig-homology domains; domains 2 and 3 (D23) represent the ligand-binding domain, whereas the function of D4-7 is unclear. Ligand binding promotes receptor dimerization and instigates transmembrane signaling and receptor kinase activation. In the present study, isothermal titration calorimetry showed that the Gibbs free energy of VEGF-A, VEGF-C, or VEGF-E binding to D23 or the full-length ECD of VEGFR-2 is dominated by favorable entropic contribution with enthalpic penalty. The free energy of VEGF binding to the ECD is 1.0-1.7 kcal/mol less favorable than for binding to D23. A model of the VEGF-E/VEGFR-2 ECD complex derived from small-angle scattering data provided evidence for homotypic interactions in D4-7. We also solved the crystal structures of complexes between VEGF-A or VEGF-E with D23, which revealed comparable binding surfaces and similar interactions between the ligands and the receptor, but showed variation in D23 twist angles. The energetically unfavorable homotypic interactions in D4-7 may be required for re-orientation of receptor monomers, and this mechanism might prevent ligand-independent activation of VEGFR-2 to evade the deleterious consequences for blood and lymph vessel homeostasis arising from inappropriate receptor activation.
An Introduction to Regenerative Braking of Electric Vehicles as Anti-Lock Braking System (2007)

Anti-lock braking systems (ABS) are well known in the automotive industry as one of the most critical active safety systems. ABS improves vehicle safety by reducing longitudinal breaking distance. This occurs by the control of the wheel slip. In this study, a basic modeling approach has been introduced on a quarter car model by using ANSOFT Simplorer for the following braking modes: hydraulic braking and all electric vehicle regenerative braking concept.
Tissue elasticity reconstruction based on ultrasonic displacement and strain images (1995)

A method is presented to reconstruct the elastic modulus of soft tissue based on ultrasonic displacement and strain images. Incompressible and compressible media are considered separately. Problems arising with this method, as well as applications to real measurements on gel-based, tissue equivalent phantoms, are given. Results show that artifacts present in strain images can be greatly reduced using a hybrid reconstruction procedure based on numerical solution of the partial differential equations describing mechanical equilibrium of a deformed medium.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mung Bean Nuclease Treatment Increases Capture Specificity of Microdroplet-PCR Based Targeted DNA Enrichment (2014)

Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial.
Mechanism and Regulation of the Glutamine‐Dependent Carbamyl Phosphate Synthetase of Escherichia Coli (1989)

This chapter contains sections titled: Introduction Subunit Structure Reactions Catalyzed by the Enzyme Selective Inactivation of the Glutamine-Dependent Activities Reversible Dissociation of the Enzyme into Catalytically Active Subunits Catalytic Mechanism Allosteric Regulation Sequence Studies and Considerations Relating to Liver Mitochondrial Carbamyl Phosphate Synthetase and Other Enzymes
Specific ablation of human immunodeficiency virus Tat-expressing cells by conditionally toxic retroviruses. (1994)

The identification of human immunodeficiency virus (HIV) as the etiologic agent of AIDS has led to the proposal of novel intervention strategies to block HIV infection and viral replication or eliminate HIV-infected cells. We have produced recombinant retroviruses for a molecular ablation system, whereby a toxin gene can be delivered to hematopoietic cells for the specific elimination of HIV Tat-expressing cells. For this cell-specific ablation, we have coupled the conditional toxin herpes simplex virus type 1 thymidine kinase (tk) gene to the HIV-2 promoter and Tat responsive region (TAR) in order that transcriptional activity be under the absolute control of HIV and simian immunodeficiency virus Tat trans-activator proteins. Since the HIV-2 promoter has a considerable level of basal expression in the absence of Tat, we constructed a number of modifications in the HIV-2 promoter to minimize the risk of cytotoxicity to cells not containing HIV Tat. We demonstrate that certain promoter modifications reduce basal transcription while maintaining high trans-activated levels of expression when transfected or transduced by retroviral vectors into several different cell lines. In mouse and human cells infected with HIV-2 tk retroviruses, we show that Tat-induced expression from the HIV-2 promoter results in differential ablation and a massive reduction in Tat-positive cells after ganciclovir treatment. Thus, the retroviruses produced in these studies may be applicable to HIV ablative therapy.
Identification of Residues on CD40 and Its Ligand Which Are Critical for the Receptor-Ligand Interaction (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIdentification of Residues on CD40 and Its Ligand Which Are Critical for the Receptor-Ligand InteractionJuergen Bajorath, N. Jan Chalupny, John S. Marken, Anthony W. Siadak, John Skonier, Marcia Gordon, Diane Hollenbaugh, Randolph J. Noelle, Hans D. Ochs, and Alejandro AruffoCite this: Biochemistry 1995, 34, 6, 1833–1844Publication Date (Print):February 14, 1995Publication History Published online1 May 2002Published inissue 14 February 1995https://pubs.acs.org/doi/10.1021/bi00006a003https://doi.org/10.1021/bi00006a003research-articleACS PublicationsRequest reuse permissionsArticle Views206Altmetric-Citations64LEARN 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
Deep outdoor illumination estimation (2017)

We present a convolutional neural network-based (CNN-based) technique to estimate high-dynamic range outdoor illumination from a single low dynamic range image. To train the CNN, we leverage a large dataset of outdoor panoramas. We fit a low-dimensional physically-based outdoor illumination model to the skies in these panoramas giving us a compact set of parameters (including sun position, atmospheric conditions, and camera parameters). We extract limited field-of-view images from the panoramas, and train a CNN with this large set of input image–output lighting parameter pairs. Given a test image, this network can be used to infer illumination parameters that can, in turn, be used to reconstruct an outdoor illumination environment map. We demonstrate that our approach allows the recovery of plausible illumination conditions and enables photorealistic virtual object insertion from a single image. An extensive evaluation on both the panorama dataset and captured HDR environment maps shows that our technique significantly outperforms previous solutions to this problem.
Cloning of cDNAs for New Subtypes of Murine Low-Affinity Fc Receptor for IgE (FcεRII/CD23) (1994)

In humans, two subtypes of the low-affinity Fc receptor for IgE, Fc epsilon RIIa and Fc epsilon RIIb, have been identified. The two forms differ only in a short stretch of amino acids at the cytoplasmic amino terminus. On the other hand, only one Fc epsilon RIIa-like receptor was reported in the mouse, although the existence of another subtype of transcript has been suggested. A new cDNA subtype for murine Fc epsilon RII that has amino acid homology to the human subtype b at the amino terminus was cloned by polymerase chain reaction. When expressed transiently in COS cells, the cDNA is capable of generating a functional cell surface protein that is recognized by an anti-Fc epsilon RII antibody and that has affinity to IgE. In the spleen, although the expression level is considerably lower than that of subtype a, the transcript appears in B cells and in non-B cells upon stimulation with IL-4 and LPS, in contrast to the constitutive expression of the conventional Fc epsilon RII transcript. It is also detectable in several cell lines of B- or T-cell lineages. These results suggest that this gene may be the murine counterpart of human Fc epsilon RII subtype b. Another cDNA clone for the distinct Fc epsilon RII transcript has also been isolated. The cDNA also encodes a surface protein functional on COS cells, but its human counterpart has not been found.
Super-Resolution Far-Field Infrared Imaging by Photothermal Heterodyne Imaging (2017)

Infrared (IR) imaging provides chemical-specific information without the need for exogenous labels. Conventional far-field IR imaging techniques are diffraction limited, which means an effective spatial resolution of >5 μm with currently available optics. In this article, we present a novel far-field IR imaging technique based on photothermal heterodyne imaging (IR-PHI). In our version of IR-PHI, an IR pump laser excites the sample, causing a small temperature rise that is detected by a counterpropagating visible probe beam. Images and spectra of several different types of soft matter systems (polystyrene beads, thin polymer films, and single Escherichia coli bacterial cells) are presented to demonstrate the sensitivity and versatility of the technique. Importantly, the spatial resolution in the IR-PHI measurements is determined by the visible probe beam: a spatial resolution of 0.3 μm was achieved with a 0.53 μm probe wavelength and a high numerical aperture focusing objective. This is the highest spatial resolution reported to date for far-field IR imaging. Analysis of the experiments shows that for polymer beads in a dry environment, the magnitude of the IR-PHI signal is determined by the scattering cross section of the nano-object at the probe wavelength. This is in contrast to conventional PHI experiments in a heat-transfer medium, where the signal scales as the absorption cross section. This different scaling can be understood through the optical theorem. Our analysis also shows that both thermal expansion and changes in the refractive index of the material are important and that these two effects, in general, counteract each other.
Is raised plasma peptide YY after intestinal resection in the rat responsible for the trophic response? (1985)

The relationship between the adaptive response and plasma PYY concentrations after small bowel resection has been investigated. Seventy five per cent proximal small bowel resection resulted in a rise in plasma PYY at six days from 28 +/- 3.1 to 85 +/- 12.3 pmol/l (p less than 0.001) and this difference was maintained to 48 days. Plasma PYY correlates both with crypt cell production rate (CCPR) in the ileum and with plasma enteroglucagon levels. In a second study, PYY or saline was infused over a 12 day period. There were no significant changes in intestinal wet weight or CCPR in any part of the bowel studied. This indicates that it is unlikely that PYY exerts a major trophic effect on the gastrointestinal tract.
Functional and structural analyses of threonine dehydratase from Corynebacterium glutamicum (1992)

Threonine dehydratase activity is an important element in the flux control of isoleucine biosynthesis. The enzyme of Corynebacterium glutamicum demonstrates a marked sigmoidal dependence of initial velocity on the threonine concentration, a dependence that is consistent with substrate-promoted conversion of the enzyme from a low-activity to a high-activity conformation. In the presence of the negative allosteric effector isoleucine, the K0.5 increased from 21 to 78 mM and the cooperativity, as expressed by the Hill coefficient increased from 2.4 to 3.7. Valine promoted opposite effects: the K0.5 was reduced to 12 mM, and the enzyme exhibited almost no cooperativity. Sequence determination of the C. glutamicum gene for this enzyme revealed an open reading frame coding for a polypeptide of 436 amino acids. From this information and the molecular weight determination of the native enzyme, it follows that the dehydratase is a tetramer with a total mass of 186,396 daltons. Comparison of the deduced polypeptide sequence with the sequences of known threonine dehydratases revealed surprising differences from the C. glutamicum enzyme in the carboxy-terminal portion. This portion is greatly reduced in size, and a large gap of 95 amino acids must be introduced to achieve homology. Therefore, the C. glutamicum enzyme must be considered a small variant of threonine dehydratase that is typically controlled by isoleucine and valine but has an altered structure reflecting a topological difference in the portion of the protein most likely to be important for allosteric regulation.
Natural ligands of the B cell adhesion molecule CD22 beta carry N-linked oligosaccharides with alpha-2,6-linked sialic acids that are required for recognition. (1993)

CD22 beta is a glycoprotein found on the surface of B cells during restricted stages of development. It is believed to play a role in cell-cell interactions and B cell activation. The accompanying paper (Sgroi, D., Varki, A., Braesch-Andersen, S., and Stamenkovic, I. (1993) J. Biol. Chem. 268, 7011-7018) shows that CD22 beta recognizes multiple glycoproteins on the surfaces of T and B cells and that sialylation of these ligands is essential for binding. To identify the structure(s) of the sialylated oligosaccharide(s) recognized by CD22 beta, [3H]glucosamine-labeled glycoproteins were purified from Daudi cells by adsorption onto a CD22 beta recombinant immunoglobulin (CD22 beta Rg) chimera attached to protein A-Sepharose (PAS), and the N-linked oligosaccharides were released by peptide N-glycosidase F. These released oligosaccharides failed to bind to CD22 beta Rg-PAS under the conditions used initially to adsorb the glycoproteins, but their elution from a column of CD22 beta Rg-PAS was significantly retarded. Populations of oligosaccharides with different affinities could be identified by their order of elution. Specific sialidases were used to determine the content of alpha-2,3- and alpha-2,6-linked sialic acid in these different populations and their contribution to binding. Multiantennary oligosaccharides with one alpha-2,6-linked residue bound marginally, and those with two or more bound more tightly. alpha-2,3-Linked sialic acid residues were without effect. Binding did not require divalent cations and was abrogated by mild periodate oxidation of the outer side chain of sialic acid. No marked differences in size or fucose content were found between the populations of high and low affinity oligosaccharides. However, the low affinity population could be partially converted into higher affinity by treatment with beta-galactoside alpha-2,6 sialyltransferase and CMP-sialic acid. Thus, CD22 beta is a mammalian lectin that can recognize specific N-linked oligosaccharide structures containing alpha-2,6-linked sialic acids.
Anti‐tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC‐dependent vulnerability (2018)

The modulation of pre-mRNA splicing is proposed as an attractive anti-neoplastic strategy, especially for the cancers that exhibit aberrant pre-mRNA splicing. Here, we discovered that T-025 functions as an orally available and potent inhibitor of Cdc2-like kinases (CLKs), evolutionally conserved kinases that facilitate exon recognition in the splicing machinery. Treatment with T-025 reduced CLK-dependent phosphorylation, resulting in the induction of skipped exons, cell death, and growth suppression <i>in vitro</i> and <i>in vivo</i> Further, through growth inhibitory characterization, we identified high CLK2 expression or <i>MYC</i> amplification as a sensitive-associated biomarker of T-025. Mechanistically, the level of CLK2 expression correlated with the magnitude of global skipped exons in response to T-025 treatment. MYC activation, which altered pre-mRNA splicing without the transcriptional regulation of CLKs, rendered cancer cells vulnerable to CLK inhibitors with synergistic cell death. Finally, we demonstrated <i>in vivo</i> anti-tumor efficacy of T-025 in an allograft model of spontaneous, MYC-driven breast cancer, at well-tolerated dosage. Collectively, our results suggest that the novel CLK inhibitor could have therapeutic benefits, especially for MYC-driven cancer patients.
Molecular Fluorescence (2012)

Preface. Prologue. Introduction. Absorption of UV--visible light. Characteristics of Fluorescence Emission. Effects of Intermolecular Photophysical Processes on Fluorescence Emission. Fluorescence polarization: Emission Ansotropy. Principles of steady--state and time--resolved fluorometric techniques. Effect of polarity of fluorescence emission. Polarity probes. Microviscosity, fluidity, molecular mobility. Estimation by means of fluorescent probes. Resonance energy transfer and its applications. Fluorescent molecular sensors of ions and molecules. Advanced techniques in fluorescence spectroscopy. Epilogue. Index.