gebhart/patrepeval huggingface dataset:
Essential role of mda-5 in type I IFN responses to polyriboinosinic:polyribocytidylic acid and encephalomyocarditis picornavirus (2006)

The innate immune system recognizes viral dsRNA through two distinct pathways; the Toll-like receptor 3 (TLR3) pathway detects dsRNA phagocytosed in endosomes; the helicases retinoic acid-induced protein I (RIG-I) and melanoma differentiation-associated gene-5 (mda-5) detect cytoplasmic dsRNA generated during viral replication. Both RIG-I and mda-5 can bind polyriboinosinic:polyribocytidylic acid (polyI:C), the synthetic analog of viral dsRNA, and mediate type I IFN responses to polyI:C and multiple RNA viruses in vitro. We generated mda-5-deficient mice and showed that mda-5 is the dominant receptor mediating type I IFN secretion in response to polyI:C in vitro and in vivo. Moreover, mda-5-/- mice exhibited a selectively impaired antiviral response to encephalomyocarditis picornavirus, indicating functional specialization of mda-5 in vivo.
Size-Dependent Localization and Quantitative Evaluation of the Intracellular Migration of Silica Nanoparticles in Caco-2 Cells (2011)

Localization and intracellular migration of 32 and 83 nm SiO2 nanoparticles in relation to the nucleus was evaluated in vitro on undifferentiated human colon carcinoma (Caco-2) cells. The fluorescence dye Atto647N was incorporated into the particles, which enabled detection by high resolution, nondiffraction limited stimulated emission depletion (STED) microscopy. The distribution and agglomeration of nanoparticles was measured with STED microscopy after 5, 24, 48, and 72 h. Analyses revealed that only 32 nm silica particles penetrated into the nucleus of Caco-2 cells upon exposure for 24 h. Here, they formed agglomerates up to 300 nm after 72 h of incubation. Quantitative evaluation of the migration of 32 nm compared to 83 nm particles demonstrated that 32 nm particles obviously migrated faster into and through the cell in the beginning (5 h time point). The presence and agglomeration inside the cells and the penetration into the nucleus were considered to potentially activate cytotoxic responses. Therefore, the cytotoxic (WST-1 assay) and genotoxic (comet assay) effects of the silica nanoparticles were evaluated. Even though 32 nm silica particles are penetrating into the nucleus, neither cytotoxic nor genotoxic effects were detected for either particle size.
[Captopril use in pregnancy and its effects on the fetus and the newborn: case report]. (1998)

Angiotensin-converting enzyme (ACE) inhibitors have been widely used to control hypertension, but their use during gestation may result in fetal death, intra-uterine growth retardation, oligoamnium sequence, hypotension, acute renal failure and ductus arteriosus patency in the newborn. The aim of this case report is to highlight the risks of using this drug during gestation. The authors present a case of captopril use during pregnancy, whose newborn developed acute renal failure and ductus arteriosus patency early in the newborn period. This presentation strengthens the importance of not only monitoring amniotic fluid volume and fetal growth, but also, during the newborn period, control the weight gain, diuresis, systemic arterial pressure and renal function, mainly in the first 72 hours of life.
The histone deacetylase inhibitor and chemotherapeutic agent suberoylanilide hydroxamic acid (SAHA) induces a cell-death pathway characterized by cleavage of Bid and production of reactive oxygen species (2001)

Many chemotherapeutic agents induce mitochondrial-membrane disruption to initiate apoptosis. However, the upstream events leading to drug-induced mitochondrial perturbation have remained poorly defined. We have used a variety of physiological and pharmacological inhibitors of distinct apoptotic pathways to analyze the manner by which suberoylanilide hydroxamic acid (SAHA), a chemotherapeutic agent and histone deacetylase inhibitor, induces cell death. We demonstrate that SAHA initiates cell death by inducing mitochondria-mediated death pathways characterized by cytochrome c release and the production of reactive oxygen species, and does not require the activation of key caspases such as caspase-8 or -3. We provide evidence that mitochondrial disruption is achieved by means of the cleavage of the BH3-only proapoptotic Bcl-2 family member Bid. SAHA-induced Bid cleavage was not blocked by caspase inhibitors or the overexpression of Bcl-2 but did require the transcriptional regulatory activity of SAHA. These data provide evidence of a mechanism of cell death mediated by transcriptional events that result in the cleavage of Bid, disruption of the mitochondrial membrane, and production of reactive oxygen species to induce cell death.
Host-Symbiont Interactions (1978)

The lipopolysaccharides of three strains each of Rhizobium leguminosarum, R. phaseoli, and trifolii have been purified and partially characterized. The last step in the purification procedure is gel filtration column chromatography using Sepharose 4B with an elution buffer consisting of ethylenediaminetetraacetic acid and triethylamine. Each of the lipopolysaccharides reported in this paper elutes as a symmetrical peak in the partially included volume of this Sepharose 4B column. The ratio of 2-keto-3-deoxyoctonate acid (a sugar which is characteristic of lipopolysaccharides) to hexose is constant throughout the carbohydrate-containing peaks as they elute from the Sepharose 4B. The compositions and immunodominant structures of the purified lipopolysaccharides vary as much among strains of a single Rhizobium species as among the different species of Rhizobium. There is no obvious correlation between the nodulation group to which a Rhizobium belongs and the chemical composition or immunochemistry of the Rhizobium's lipopolysaccharide. There is extensive crosslysis by phage of strains of R. trifolii, R. phaseoli, and R. leguminosarum. This suggests that the receptors for these cross-lysing phage reside either in nonlipopolysaccharide structures or in common structures within the lipopolysaccharide which are not detected by compositional or immunochemical analysis.
Analysis of site-specific N-glycosylation of recombinant Desmodus rotundus salivary plasminogen activator rDSPAα1 expressed in Chinese hamster ovary cells (1997)

The recombinant plasminogen activator (rDSPA alpha 1) from the vampire bat Desmodus rotundus is a promising new thrombolytic agent that exhibits a superior pharmacological profile if compared to tissue-type plasminogen activator (t-PA) or streptokinase. In the present study the structures of the carbohydrate moieties at the two N-glycosylation sites (Asn-117, Asn-362) of rDSPA alpha 1 expressed in Chinese hamster ovary cells were determined. N-Linked glycans were enzymatically released from isolated tryptic glycopeptides by peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F digestion and separated by two-dimensional HPLC. Oligosaccharide structures were characterized by analysis of carbohydrate composition and linkage, by mass spectrometry, and by sequence analysis in which the fluorescently labeled glycans were cleaved with an array of specific exoglycosidases. More than 30 different oligosaccharides were identified. The results revealed that Asn-117 carried a mixture of one high-mannose structure (17% of site-specific glycosylation), three hybrid glycans (26%) and predominantly biantennary complex N-glycans (54%). Glycosylation site Asn-362 was found to comprise complex glycans with biantennary (50%), 2,4- and 2,6-branched triantennary (21%, 11%), and tetraantennary structures (10%), which were fucosylated at the innermost residue of N-acetylglucosamine. Mainly neutral and monosialylated glycans, and smaller quantities of disialylated glycans, were detected at both glycosylation sites. Sialic acid was alpha 2-3 linked to galactose exclusively. As shown in this study the N-glycans attached to Asn-117 of rDSPA alpha 1 are more processed during biosynthesis than the high-mannose structures linked to Asn-117 of t-PA, to which the polypeptide backbone of rDSPA alpha 1 is structurally closely related.
Novel A-ring cleaved analogs of oleanolic and ursolic acids which affect growth regulation in NRP.152 prostate cells (1997)

Syntheses of eight novel A-ring cleaved oleanane and ursane analogs are described. These compounds were assessed for their ability to inhibit cell proliferation in NRP.152 prostate cells. Four A-ring cleaved derivatives showed significant activity; 5β-(1-methyl-2-ethyl)-10α-(3-aminopropyl)-des-A-urs-12-en-28-oic acid was the most active compound, (IC50, 0.3μM).
Therapeutic Strategies for HIV Infection — Time to Think Hard (1998)

The concept of induction therapy followed by maintenance therapy has its origins in the treatment of a number of infectious and neoplastic diseases. Highly potent but toxic and inconvenient treatment is given for several weeks or months to induce a rapid therapeutic response. This period is followed by several months of less intense therapy to consolidate the effect, reduce toxicity, and provide patients with a well-deserved break. In some cancers, reservoirs of disease that are not accessible to systemic therapy are treated in the interim. At the end of the treatment many patients are cured, probably because their immune systems . . .
Activation of Natural Killer T Cells Potentiates or Prevents Experimental Autoimmune Encephalomyelitis (2001)

Natural killer (NK) T cells recognize lipid antigens in the context of the major histocompatibility complex (MHC) class 1-like molecule CD1 and rapidly secrete large amounts of the cytokines interferon (IFN)-gamma and interleukin (IL)-4 upon T cell receptor (TCR) engagement. We have asked whether NK T cell activation influences adaptive T cell responses to myelin antigens and their ability to cause experimental autoimmune encephalomyelitis (EAE), a model for multiple sclerosis. While simultaneous activation of NK T cells with the glycolipid alpha-galactosylceramide (alpha-GalCer) and myelin-reactive T cells potentiates EAE in B10.PL mice, prior activation of NK T cells protects against disease. Exacerbation of EAE is mediated by an enhanced T helper type 1 (Th1) response to myelin basic protein and is lost in mice deficient in IFN-gamma. Protection is mediated by immune deviation of the anti-myelin basic protein (MBP) response and is dependent upon the secretion of IL-4. The modulatory effect of alpha-GalCer requires the CD1d antigen presentation pathway and is dependent upon the nature of the NK T cell response in B10.PL or C57BL/6 mice. Because CD1 molecules are nonpolymorphic and remarkably conserved among different species, modulation of NK T cell activation represents a target for intervention in T cell-mediated autoimmune diseases.
Inertial fusion energy development: what is needed and what will be learned at the National Ignition Facility (2000)

Successful development of inertial fusion energy (IFE) requires that many technical issues be resolved. Separability of drivers, targets, chambers, and other IFE power plant subsystems allows resolution of many of these issues in 'off-line' facilities and programs. Periodically, major 'integrated' facilities give a snapshot of the rate of progress toward the ultimate solutions. The National Ignition Facility (NIF) and Laser Megajoule (LMJ) are just such integrating facilities. This paper reviews the status of IFE development and projects what will be learned from the NIF and LMJ.
Color by correlation: a simple, unifying framework for color constancy (2001)

The paper considers the problem of illuminant estimation: how, given an image of a scene, recorded under an unknown light, we can recover an estimate of that light. Obtaining such an estimate is a central part of solving the color constancy problem. Thus, the work presented will have applications in fields such as color-based object recognition and digital photography. Rather than attempting to recover a single estimate of the illuminant, we instead set out to recover a measure of the likelihood that each of a set of possible illuminants was the scene illuminant. We begin by determining which image colors can occur (and how these colors are distributed) under each of a set of possible lights. We discuss how, for a given camera, we can obtain this knowledge. We then correlate this information with the colors in a particular image to obtain a measure of the likelihood that each of the possible lights was the scene illuminant. Finally, we use this likelihood information to choose a single light as an estimate of the scene illuminant. Computation is expressed and performed in a generic correlation framework which we develop. We propose a new probabilistic instantiation of this correlation framework and show that it delivers very good color constancy on both synthetic and real images. We further show that the proposed framework is rich enough to allow many existing algorithms to be expressed within it: the gray-world and gamut-mapping algorithms are presented in this framework and we also explore the relationship of these algorithms to other probabilistic and neural network approaches to color constancy.
DNA polyintercalating drugs: DNA binding of diacridine derivatives. (1975)

As a first step in the synthesis and the study of DNA polyintercalating drugs, dimers of acridines have been prepared. Their DNA binding properties have been studied. It has been determined that when the chain separating the two aromatic rings is longer than a criticål distance, bisintercalation is actually observed and that the DNA binding affinity becomes quite large (greater than 10(8)-10(9) M-1). It is shown also that the optical characteristics of these molecules are dependent on the sequences of DNA. The fluorescence intensity of one of these dimers when bound to DNA varies as the fourth power of its A+T content. This derivative could be used as a fluorescent probe of DNA sequence.
Biodegradable Porous Silicon Barcode Nanowires with Defined Geometry (2010)

Silicon nanowires are of proven importance in diverse fields such as energy production and storage, flexible electronics, and biomedicine due to the unique characteristics emerging from their one-dimensional semiconducting nature and their mechanical properties. Here we report the synthesis of biodegradable porous silicon barcode nanowires by metal assisted electroless etch of single crystal silicon with resistivity ranging from 0.0008 Ω-cm to 10 Ω-cm. We define the geometry of the barcode nanowiresby nanolithography and we characterize their multicolor reflectance and photoluminescence. We develop phase diagrams for the different nanostructures obtained as a function of metal catalyst, H(2)O(2) concentration, ethanol concentration and silicon resistivity, and propose a mechanism that explains these observations. We demonstrate that these nanowires are biodegradable, and their degradation time can be modulated by surface treatments.
Atomic Structure of Reduced Graphene Oxide (2010)

Using high resolution transmission electron microscopy, we identify the specific atomic scale features in chemically derived graphene monolayers that originate from the oxidation-reduction treatment of graphene. The layers are found to comprise defect-free graphene areas with sizes of a few nanometers interspersed with defect areas dominated by clustered pentagons and heptagons. Interestingly, all carbon atoms in these defective areas are bonded to three neighbors maintaining a planar sp(2)-configuration, which makes them undetectable by spectroscopic techniques. Furthermore, we observe that they introduce significant in-plane distortions and strain in the surrounding lattice.
Channeled-substrate planar structure (AlGa)As injection lasers (1977)

Undesirable nonlinear ’’kinks’’ in light-output–vs–current characteristics of stripe geometry double-heterostructure (DH) injection lasers are significantly reduced by stabilizing the transverse modes along the junction plane. Built-in passive guiding mechanism is introduced by growing planar (AlGa)As/GaAs DH layers on a grooved GaAs substrate.
Deterministic Coupling of Single Quantum Dots to Single Nanocavity Modes (2005)

We demonstrate a deterministic approach to the implementation of solid-state cavity quantum electrodynamics (QED) systems based on a precise spatial and spectral overlap between a single self-assembled quantum dot and a photonic crystal membrane nanocavity. By fine-tuning nanocavity modes with a high quality factor into resonance with any given quantum dot exciton, we observed clear signatures of cavity QED (such as the Purcell effect) in all fabricated structures. This approach removes the major hindrances that had limited the application of solid-state cavity QED and enables the realization of experiments previously proposed in the context of quantum information processing.
Extracellular Matrix-like Cell-Adhesive Hydrogels from RGD-Containing Poly(ethylene glycol) Diacrylate (2006)

ADVERTISEMENT RETURN TO ISSUECommunication to the...Communication to the EditorNEXTExtracellular Matrix-like Cell-Adhesive Hydrogels from RGD-Containing Poly(ethylene glycol) DiacrylateJunmin Zhu, Jeffrey A. Beamish, Chad Tang, Kandice Kottke-Marchant, and Roger E. MarchantView Author Information Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106; Department of Macromolecular Science, Case Western Reserve University, Cleveland, Ohio 44106; and Department of Clinical Pathology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, Ohio 44195 Cite this: Macromolecules 2006, 39, 4, 1305–1307Publication Date (Web):January 24, 2006Publication History Received31 October 2005Revised27 December 2005Published online24 January 2006Published inissue 1 February 2006https://pubs.acs.org/doi/10.1021/ma052333shttps://doi.org/10.1021/ma052333srapid-communicationACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views1347Altmetric-Citations33LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Cell physiology,Cells,Hydrogels,Peptides and proteins Get e-Alerts
Extended survival and broad immune responses following vaccination of patients with metastatic melanoma with peptide-pulsed CD34+ progenitor derived dendritic cells (DCs) (2005)

2525 Background: Culture of CD34+ blood cells with GM-CSF, Flt-3 ligand and TNF yield distinct dendritic cell (DC) subtypes including Langerhans and interstitial DCs. Such composite DC vaccine was loaded with melanoma peptides (MART-1, tyrosinase, MAGE-3, gp100) and control antigens flu-matrix and KLH, and administered subcutaneously to patients with metastatic melanoma in a Phase I trial. Methods: HLA-A0201+patients received 4 DC vaccinations every 2 weeks followed by additional 4 monthly DC vaccinations. All DCs were pulsed with KLH, 20% of cells were pulsed with flu-matrix peptide and 80% with melanoma peptides. IFN-gamma ELISPOT and tetramer staining were used to measure specific CD8+ T cells. Spearman correlation was used with non-transformed data. Patient survival was calculated using Kaplan-Meier estimation based on log-rank analysis of difference. Results: There were 18 patients: 10 male with median age (range) was 53 (40–73) years. 6 patients had progressive melanoma after 4 vaccines and were removed from study. 12 patients received 5–8 consolidation DC vaccinations. There were no significant adverse events. The median (range) overall survival was 20 (2–69) months. At present there are 5 patients (27.7%, [95% c.i. 19.3–39.6]) who are alive at 55+, 61+, 61+, 61+ and 69+ months after their last vaccine. Production of IFN-gamma determined by ELISPOT to 3–4 melanoma antigens after 4 DC vaccinations correlated with overall survival (p=0.0065). Peptide tetramers of CD8+ T-cells validated Mart-1 and flu ELISPOTS. 5/5 long-term survivors had immunity to greater than 3 melanoma antigens after 4 vaccinations and at least 2 antigens after their last vaccination. Conclusions: Vaccination of patients with metastatic melanoma with melanoma peptide- loaded DCs made from CD34+ progenitor cells resulted in a broad melanoma antigen-specific CD8+ T-cell immune response that correlated with survival in a significant number of patients. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Argos Therapeutics, ODC Therapy
Introduction (Special Health Law Issue) (1989)

This article outlines the topic of affordable health care in the United States. It advocates for citizens who, according to the article, do not receive adequate health care attention. Ultimately, the article demonstrates that the United States has the resources to solve the health care crisis.
Identification of CD71 (transferrin receptor) expressing erythrocytes by multiparameter‐flow‐cytometry (MP‐FCM): correlation to the quantitation of reticulocytes as determined by conventional microscopy and by MP‐FCM using a RNA‐staining dye (1992)

Reticulocytes express the CD71-defined antigen, the transferrin receptor. This report describes how by means of dual-colour immunofluorescence using MP-FCM (multiparameter-flow-cytometry) CD71+ erythrocytes can be detected regularly in blood of healthy adults. Percentages of these CD71+ erythrocytes were compared to the percentages of reticulocytes as determined by conventional microscopy using brilliant cressyl blue, and to the percentages of erythrocytes with high RNA content, as detected by MP-FCM using a RNA-staining dye (thiazole-orange). Only about two-thirds of the percentages determined by the two latter methods were detected by MP-FCM using the CD71 expression for definition of reticulocytes. Studying clinical samples, however, including both specimens with very low and very high numbers of reticulocytes, almost identical percentages were determined by all the three methods described. Studying reticulocytes in vitro, a rapid decline of the expression of the transferrin receptor was observed on reticulocytes. Due to the differential expression of the transferrin receptor on reticulocytes, different subsets of reticulocytes could be identified. The dual-colour MP-FCM method described allows for the characterization and enumeration of immature erythrocytes, representing the major subset of reticulocytes as determined by conventional methods. Furthermore, it allows for subset dissection of reticulocytes.