gebhart/patrepeval huggingface dataset:
Memory T Cells in Latent Mycobacterium tuberculosis Infection Are Directed against Three Antigenic Islands and Largely Contained in a CXCR3+CCR6+ Th1 Subset (2013)

An understanding of the immunological footprint of Mycobacterium tuberculosis (MTB) CD4 T cell recognition is still incomplete. Here we report that human Th1 cells specific for MTB are largely contained in a CXCR3(+)CCR6(+) memory subset and highly focused on three broadly immunodominant antigenic islands, all related to bacterial secretion systems. Our results refute the notion that secreted antigens act as a decoy, since both secreted proteins and proteins comprising the secretion system itself are targeted by a fully functional T cell response. In addition, several novel T cell antigens were identified which can be of potential diagnostic use, or as vaccine antigens. These results underline the power of a truly unbiased, genome-wide, analysis of CD4 MTB recognition based on the combined use of epitope predictions, high throughput ELISPOT, and T cell libraries using PBMCs from individuals latently infected with MTB.
Synthesis of β-Hydroxy Ketones and Vinylsilanes from Homopropargylic Alcohols by Intramolecular Hydrosilation (2000)

Catalytic intramolecular hydrosilation of nonracemic homopropargylic alcohols affords the corresponding five-membered cyclic siloxanes regiospecifically. Oxidation or alkylmetal addition converts these intermediates into beta-hydroxy ketones or vinylsilanes under mild conditions.
Suramin inhibits C6 glioma‐induced angiogenesis in vitro (1995)

Aspects of tumor-induced angiogenesis in vitro were examined using an assay involving collagen gel invasion by a surface monolayer of bovine endothelial cells under the influence of serum free conditioned medium produced by C6 cells, an experimentally derived rat glial tumor cell line. The effects of the polyanionic compound suramin, known to interfere with growth factor/cell signaling on this process were evaluated. Collagen gel invasion was quantified by adding C6 conditioned medium with or without various doses of suramin to monolayers of bovine aortic endothelial cells grown on type I collagen gels in transwell inserts. Cultures were monitored with phase-contrast microscopy. After various periods of incubation collagen gels were fixed, embedded in epoxy resin, and 1-micron thick sections were stained with toluidine blue. Additional cultures were used to evaluate the effects of C6 conditioned medium and suramin on endothelial cell proliferation, and on chemotaxis through 8-microns pores. C6 glioma cell conditioned medium induced large vessel endothelial cells to sprout into the underlying collagen matrix and subsequently form networks of capillary like tubes. Conditioned medium was also chemotactic and mitogenic for these cells. The addition of suramin to C6 glioma conditioned medium prevents tube formation in collagen gels, and inhibits both endothelial cell proliferation and chemotaxis in a dose dependent manner. These results suggest that glial tumor cell conditioned medium induces angiogenesis in large vessel endothelial cells in vitro via mechanisms which are disrupted by suramin, most likely involving tumor-derived growth factor release and/or endothelium-mediated matrix proteolysis.
Glossary of medical education terms: Part 5 (2002)

(2002). Glossary of medical education terms: Part 5. Medical Teacher: Vol. 24, No. 6, pp. 658-660.
<i>In vitro</i> hydroxyapatite deposition onto a film surface‐grafted with organophosphate polymer (1994)

To produce a bone-bonding polymer surface that is capable of inducing deposition of a hydroxyapatite (HA) layer in the body fluid, an organophosphate polymer was covalently immobilized onto a high-density polyethylene film by surface graft polymerization of a phosphate-containing monomer. The grafted film was immersed in simulated physiologic solution (SPS). The chemical composition and structure of the formed apatite layer as well as its bonding strength to the polymer surface were investigated. To distinguish the effect of phosphate groups on the deposition of apatite layer from the simple calcium absorption by the anion, a comparative study was done using a polyethylene film with surface immobilized carboxylic groups. Calcium phosphate deposition was observed on all the materials investigated, but the kinetics, composition, deposit amount, and bonding strength of the new phase were found to be significantly different among the modified materials, depending on the density and chemical nature of the surface immobilized ionic groups. It was found that the polymeric materials modified by surface graft polymerization of a phosphate-containing monomer produce a carbonated HA layer firmly bonded with the material upon immersion in SPS. Carboxyl groups in the grafted layer was not enough to activate bonding with the HA layer.
Polysialylation and lipopolysaccharide‐induced shedding of E‐selectin ligand‐1 and neuropilin‐2 by microglia and THP‐1 macrophages (2016)

Microglia are tissue macrophages and mediators of innate immune responses in the brain. The protein-modifying glycan polysialic acid (polySia) is implicated in modulating microglia activity. Cultured murine microglia maintain a pool of Golgi-confined polySia, which is depleted in response to lipopolysaccharide (LPS)-induced activation. Polysialylated neuropilin-2 (polySia-NRP2) contributes to this pool but further polySia protein carriers have remained elusive. Here, we use organotypic brain slice cultures to demonstrate that injury-induced activation of microglia initiates Golgi-confined polySia expression in situ. An unbiased glycoproteomic approach with stem cell-derived microglia identifies E-selectin ligand-1 (ESL-1) as a novel polySia acceptor. Together with polySia-NRP2, polySia-ESL-1 is also detected in primary cultured microglia, in brain slice cultures and in phorbol ester-induced THP-1 macrophages. Induction of stem cell-derived microglia, activated microglia in brain slice cultures and THP-1 macrophages by LPS, but not interleukin-4, causes polySia depletion and, as shown for stem cell-derived microglia, a metalloproteinase-dependent release of polySia-ESL-1 and polySia-NRP2. Moreover, soluble polySia attenuates LPS-induced production of nitric oxide and proinflammatory cytokines. Thus, shedding of polySia-ESL-1 and polySia-NRP2 after LPS-induced activation of microglia and THP-1 macrophages may constitute a mechanism for negative feedback regulation. GLIA 2016 GLIA 2016;64:1314-1330.
Transmission maximum-likelihood reconstruction with ordered subsets for cone beam CT (1995)

An iterative algorithm is presented for accelerated reconstruction of cone beam transmission CT data (CBCT). CBCT supplies an attenuation map for SPECT attenuation compensation and anatomical correlation. Iterative algorithms are necessary to reduce truncation artifacts and 3D reconstruction artifacts. An existing transmission maximum-likelihood algorithm (TRML) is accurate but the reconstruction time is too long. The new algorithm is a modified EM algorithm, based on ordered subsets (OSEM). OSEM was evaluated in comparison to TRML using a thorax phantom and a 3D Defrise phantom. A wide range of image measures were evaluated, including spatial resolution, noise, log likelihood, region quantification, truncation artifact removal, and 3D artifact removal. For appropriate subset size, OSEM produced essentially the same image as TRML, but required only one-tenth as many iterations. Thus, adequate images were available in two to four iterations (20-30 min on a SPARC 2 workstation). Further, OSEM still approximately maximizes likelihood: divergence occurs only for very high (and clinically irrelevant) iterations. Ordered subsets are likely to be useful in other geometries (fan and parallel) and for emission CT as well. Therefore, with ordered subsets, high-quality iterative reconstruction is now available in clinically practical reconstructions times.
CrowdSelect (2016)

Crowdsourcing allows many people to complete tasks of various difficulty with minimal recruitment and administration costs. However, the lack of participant accountability may entice people to complete as many tasks as possible without fully engaging in them, jeopardizing the quality of responses. In this paper, we present a dynamic and time efficient solution to the task assignment problem in crowdsourcing platforms. Our proposed approach, CrowdSelect, offers a theoretically proven algorithm to assign workers to tasks in a cost efficient manner, while ensuring high accuracy of the overall task. In contrast to existing works, our approach makes minimal assumptions on the probability of error for workers, and completely removes the assumptions that such probability is known apriori and that it remains consistent over time. Through experiments over real Amazon Mechanical Turk traces and synthetic data, we find that CrowdSelect has a significant gain in term of accuracy compared to state-of-the-art algorithms, and can provide a 17.5\% gain in answers' accuracy compared to previous methods, even when there are over 50\% malicious workers.
Curved edge modification of compact range reflector (1987)

For many years, the compact range has successfully been used to design and evaluate many electromagnetic radiation and scattering systems. However, it has had limited use for large structures because of the large discrepancy between the reflector and target zone sizes. The limitation results from the large edge diffracted signal which emanates from the termination of the reflector. Previous attempts to solve this problem have involved using serrated edges to diffuse the diffracted field. While this reduces the edge diffracted field in the target zone, it is not eliminated. In addition, one has introduced many new corners which also diffract into the target zone. A curved edge modification is presented which reduces the edge diffraction by an order of magnitude or more and in the process does not create new mechanisms which perturb the plane wave in the target zone. Using this curved modification, one is able to design a compact range reflector whose target zone cross section approaches the size of the reflector parabolic surface. This makes the compact range ideal for scale model measurements since larger targets (antennas) can be measured. It also makes it more practical to consider systems which can measure full scale vehicles.
Fibrin Detected in Plasma of Patients with Disseminated intravascuiar Coagulation by Fibrin-specific Antibodies Consists Primarily of High Molecular Weight Factor XIIIa-crosslinked and Plasmin-modified Complexes Partially Containing Fibrinopeptide A (1997)

Pooled plasma from 40 patients with severe disseminated intravascular coagulation (DIC) secondary to septic conditions was subjected to gel permeation chromatography on Sephacryl S-500 HR after sample pretreatment with KSCN for dissociation of non-covalent fibrin complexes. Fibrin antigen in eluates was detected by an array of ELISA tests, using two monoclonal antibodies against fibrin degradation product D-dimer, a monoclonal antibody against an epitope generated by plasmin cleavage of the D-domain, and an antibody against the neo-N-terminus of the alpha-chain of fibrin exposed by cleavage of fibrinopeptide A. Tag antibodies were a polyclonal antibody against the fibrinogen/ fibrin D-domain, a POD-conjugated version of the monoclonal antibody against fibrin alpha-chain neo-N-terminus, and a polyclonal antibody against fibrinopeptide A. Most fibrin-related material present in the pooled DIC plasma was of higher molecular mass than fibrinogen. Fibrin polymers were reactive with antibodies against D-dimer, plasmin cleaved D-domain, and fibrin alpha-chain neo-N-terminus. Part of the polymers reacted with antibodies against fibrinopeptide A, indicating presence of fibrinogen or desA-fibrin monomer within the covalently linked complex. In conclusion, the primary analytes detected by monoclonal antibodies for D-dimer, plasmin-specific epitopes of fibrin degradation products, as well as sites exposed by fibrinopeptide cleavage in plasma from patients with disseminated intravascular coagulation are high molecular weight factor XIIIa-crosslinked fibrin complexes, containing plasmin-cleaved D-domains, intact fibrin monomer units, and fibrinogen or desA-fibrin monomer.
An efficient manual image annotation approach based on tagging and browsing (2007)

This paper investigates new approaches to improve the efficiency of manual image annotation and help users to produce better annotation results in a given amount of time. Although important in practice, this issue has rarely been studied in a quantitative way before. To achieve this, we first propose two time models to analyze the annotation process for two popular manual annotation approaches, i.e., tagging and browsing. The complementary properties of these approaches have inspired us to merge them to develop a hybrid annotation algorithms called frequency-based annotation. Our experiments on large-scale multimedia collections have shown that the proposed algorithm can achieve an up to 40% annotation time reduction compared with the baseline methods. In other words, it can produce considerably better results using the same annotation time.
Regulation of <i>Arabidopsis thaliana</i> 4‐coumarate:coenzyme‐A ligase‐1 expression by artificial zinc finger chimeras (2005)

The use of artificial zinc finger chimeras to manipulate the expression of a gene of interest is a promising approach because zinc finger proteins can be engineered to bind any given DNA sequence in the genome. We have previously shown that a zinc finger chimera with a VP16 activation domain can activate a reporter gene in transgenic Arabidopsis thaliana (Sánchez, J.P., Ullman, C., Moore, M., Choo, Y. and Chua, N.H. (2002) Regulation of gene expression in Arabidopsis thaliana by artificial zinc finger chimeras. Plant Cell Physiol. 43, 1465-1472). Here, we report the use of artificial zinc finger chimeras to specifically regulate the 4-coumarate:coenzyme-A ligase-1 (At4CL1) gene in A. thaliana. At4CL1 is a key enzyme in lignin biosynthesis and the down-regulation of At4CL1 can lead to a decrease in lignin content, which has a significant commercial value for the paper industry. To this end, we designed zinc finger chimeras containing either an activation or a repression domain, which bind specifically to the At4CL1 promoter region. Transgenic lines expressing a zinc finger chimera with the VP16 activation domain showed an increase in At4CL1 expression and enzyme activity. In contrast, transgenic lines expressing a chimera with the KOX (KRAB) repression domain displayed repression of At4CL1 expression and enzyme activity. The activation of At4CL1 expression produced an increase in lignin content, and transgenic plant stems showed ectopic lignin distribution. Repression of the At4CL1 gene resulted in reduced lignin content, and lignin distribution in transgenic stems was severely diminished. Our results confirm and extend previous studies of gene regulation using various artificial zinc finger chimeras in animal and plant systems, and show that this system can be used to up- and down-regulate the expression of an endogenous plant gene such as At4CL1.
Simple and Improved Procedure for Regioselective Acylation of Aromatic Ethers with Carboxylic Acids on the Solid Surface of Alumina in the Presence of Trifluoroacetic Anhydride (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSimple and Improved Procedure for Regioselective Acylation of Aromatic Ethers with Carboxylic Acids on the Solid Surface of Alumina in the Presence of Trifluoroacetic AnhydrideBrindaban C. Ranu, Keya Ghosh, and Umasish JanaView Author Information Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, IndiaCite this: J. Org. Chem. 1996, 61, 26, 9546–9547Publication Date (Web):December 27, 1996Publication History Received7 August 1996Published online27 December 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo9615413https://doi.org/10.1021/jo9615413brief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views1902Altmetric-Citations52LEARN 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 SUBJECTS:Aromatic compounds,Ethers,Organic acids,Organic reactions,Post-translational modification Get e-Alerts
Historical insights into cytokines (2007)

Cytokines affect nearly every biological process; these include embryonic development, disease pathogenesis, non-specific response to infection, specific response to antigen, changes in cognitive functions and progression of the degenerative processes of aging. In addition, cytokines are part of stem cell differentiation, vaccine efficacy and allograft rejection. This short insight focuses on the milestones in cytokine biology and how the various and often contradictory activities of these small, non-structural proteins affected the fields of inflammation and immunology. Multiple biological properties or pleiotropism is the hallmark of a cytokine. Today, the term "cytokine" encompasses interferons, the interleukins, the chemokine family, mesenchymal growth factors, the tumor necrosis factor family and adipokines. As of this writing, 33 cytokines are called interleukins, but many are part of families of related but distinct gene products. There are certainly over 100 separate genes coding for cytokine-like activities, many with overlapping functions and many still unexplored. Also discussed in this overview are the failures and successes of cytokines as therapeutic targets. A recent advance in the field has been that of differential cytokine production, which can be used to classify human disease as being "autoimmune" or "autoinflammatory" thus impacting on therapeutic interventions.
Selectivity and composition dependence of response of gas-sensitive resistors. Part 2.—Hydrogen sulfide response of Cr<sub>2 –x</sub>Ti<sub>x</sub>O<sub>3 +y</sub> (1995)

Titanium-substituted chromium oxides, Cr2 –xTixO3 +y, form solid solutions in the range 0 ⩽x⩽ 0.4, with surface enrichment of Ti. The electrical behaviour of these compounds was consistent with charge compensation by chromium vacancies. The conductance of porous, small-grain-size specimens could be interpreted as surface trap-limited, with Oads– as the surface species. Both molecular and dissociative chemisorption of H2S was observed. Exposure to H2S at low concentration in air resulted in the formation of sulfate groups at the surface as well as surface hydroxylation. There was a range of binding energy of the surface sulfate: strongly bound sulfate caused a permanent, temperature-dependent conditioning of the surface characterized by a permanent change in the air baseline resistance after an initial dose of H2S. The origin of the gas response of the electrical resistance was attributed to the surface reaction of H2S with Oads– to form adsorbed sulfate, which desorbs as sulfur dioxide. The electrical response was repeatable and stable.
Characteristics of the Force Applied to a Pedal During Human Pushing Efforts: Emergent Linearity (2000)

The force seated humans exert on a translationally fixed pedal (foot force) may be directed at any angle because the fixed distance between the seat and the pedal axis kinematically constrains the lower limb. The authors' objective in the present work was to characterize such force. Participants (N = 7) generated force with their lower limb by pushing against the pedal in the most comfortable manner. Pushing efforts were repeated randomly 3 times at each of 97 sagittal-plane pedal axis positions and 10 additional times in 9 of those positions (2,895 total pushes). In 87% of the pushes, the measured sagittal-plane force exerted on the pedal by the foot changed magnitude and direction through time, such that the path of the head of the force vector traced a straight line. The linearity of the foot force paths reflected directional invariance in the changes of the foot force vector as the magnitude of the vector increased. The orientation of those linear force paths varied with limb posture in a similar manner across participants. The authors conclude that the emergent linearity of the force path is consistent with minimization of path length in foot force space. Alternatively, the linearity of the force paths suggests a motor control strategy that simplifies the control to a monoparametric form.
Applying Aspect-Oriented Programming to Intelligent Synthesis (2000)

I discuss a component-centered, aspect-oriented system, the Object Infrastructure Framework (OIF), NASA's initiative on Intelligent Synthesis Environments (ISE), and the application of OIF to the architecture of ISE.
THE EFFECT OF ANTIHISTAMINIC DRUGS ON CONVULSIVE SEIZURES (1949)

Certain antihistaminic drugs are analeptics and produce convulsions in animals. Although the dose required is about a hundred times that used clinically,<sup>1</sup>1 case is on record in which fits were produced.<sup>2</sup>In a study of the effect of several antihistaminic agents on epileptic seizures, we have found that attacks could be evoked in some persons by doses even smaller than those generally used clinically. This observation deserves the consideration of physicians who are prescribing these drugs. The study was undertaken to see if the common action of myanesin®<sup>3</sup>(3-ortho-toloxy-1,2-propanediol), and diphenhydramine (benadryl®)<sup>4</sup>on parkinsonian tremor also applied to an action on convulsive manifestations. We had observed<sup>5</sup>from electroencephalographic records that the first drug abolished petit mal discharges but increased the discharges from focal lesions of the cerebral cortex. A similar study was therefore made of the action of diphenhydramine and tripelennamine (pyribenzamine®) on seizure