gebhart/patrepeval huggingface dataset:
Retinoic acids exhibit anti‐fibrotic activity through the inhibition of 5‐lipoxygenase expression in scleroderma fibroblasts (2010)

The pathogenesis of systemic sclerosis (SSc) is not fully understood and there is no effective treatment for this disease. Retinoic acid (RA) can modulate connective tissue metabolism, exhibit anti-fibrotic activity, and improve the clinical symptoms of SSc. However, the mechanisms by which RA elicits its anti-fibrotic actions remain to be determined. The aim of this study was to elucidate the underlying mechanisms by which RA exerts beneficial effects on scleroderma. Cultured skin fibroblasts from patients with scleroderma were treated with RA and their effect on the expression of 5-lipoxygenase (LOX), transforming growth factor (TGF)-β1, connective tissue growth factor (CTGF), type I and type III collagen was tested by reverse transcription polymerase chain reaction (RT-PCR) and western immunoblotting. The effect of MK886, a 5-LOX-specific inhibitor, on the expression of TGF-β1, CTGF, type I and type III collagen was also examined by RT-PCR. In cultured scleroderma fibroblasts, the expression of 5-LOX was elevated compared with normal human dermal fibroblasts. RA significantly inhibited the expression of 5-LOX and of TGF-β1, CTGF, type I and type III collagen. We further found that the expression of TGF-β1, CTGF and type I and type III collagen mRNA was inhibited by MK886 in scleroderma fibroblasts. In vitro, RA reduced 5-LOX expression in scleroderma fibroblasts and downregulated TGF-β1 and CTGF expression, leading to the inhibition of type I and type III collagen synthesis. Our results indicate that the clinical effects of RA on scleroderma are, at least in part, attributable to the reduction of 5-LOX expression and the subsequent suppression of TGF-β1 and CTGF expression that results in the blockade of collagenogenesis.
Assembly Of Phospholipids Into Cellular Membranes: Biosynthesis, Transmembrane Movement And Intracellular Translocation (1988)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Double-Blind, Placebo-Controlled Investigation of Amantadine for Weight Loss in Subjects Who Gained Weight With Olanzapine (2005)

Amantadine induced weight stabilization in subjects taking olanzapine and was well tolerated.
Nucleic acid related compounds. 21. Direct fluorination of uracil and cytosine bases and nucleosides using trifluoromethyl hypofluorite. Mechanism, stereochemistry, and synthetic applications (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleic acid related compounds. 21. Direct fluorination of uracil and cytosine bases and nucleosides using trifluoromethyl hypofluorite. Mechanism, stereochemistry, and synthetic applicationsMorris J. Robins, Malcolm MacCoss, S. R. Naik, and G. RamaniCite this: J. Am. Chem. Soc. 1976, 98, 23, 7381–7389Publication Date (Print):October 1, 1976Publication History Published online1 May 2002Published inissue 1 October 1976https://pubs.acs.org/doi/10.1021/ja00439a046https://doi.org/10.1021/ja00439a046research-articleACS PublicationsRequest reuse permissionsArticle Views574Altmetric-Citations69LEARN 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
Accurate and Efficient Method for Smoothly Space-Variant Gaussian Blurring (2010)

This paper presents a computationally efficient algorithm for smoothly space-variant Gaussian blurring of images. The proposed algorithm uses a specialized filter bank with optimal filters computed through principal component analysis. This filter bank approximates perfect space-variant Gaussian blurring to arbitrarily high accuracy and at greatly reduced computational cost compared to the brute force approach of employing a separate low-pass filter at each image location. This is particularly important for spatially variant image processing such as foveated coding. Experimental results show that the proposed algorithm provides typically 10 to 15 dB better approximation of perfect Gaussian blurring than the blended Gaussian pyramid blurring approach when using a bank of just eight filters.
Immunolocalization of Gastrolith Matrix Protein (GAMP) in the Gastroliths and Exoskeleton of Crayfish, Procambarus clarkii (2000)

Gastrolith matrix protein (GAMP) is a novel protein purified from gastroliths of the crayfish, Procambarus clarkii, and has been suggested to be associated with calcium carbonate deposition. In the present study, a specific antibody against GAMP was raised and distribution of GAMP immunoreactivity was studied in crayfish gastrolith and exoskeleton. Localization of calcium carbonate in the exoskeleton, determined by silver nitrate staining and energy dispersive X-ray microanalysis, was compared with that of GAMP immunoreactivity. Crystalline forms of calcium carbonate were also determined. SDS-PAGE and Western blotting revealed that the gastrolith extract contained a major band which was GAMP-immunopositive and showed the same mobility as that of purified GAMP. The exoskeleton extract showed smear bands, but no immunoreaction was detected. By using immunohistochemistry, the anti-GAMP antiserum reacted almost uniformly with gastrolith matrix irrespective of gastrolith size. Epithelial cells of the gastrolith disc were also immunopositive. In the exoskeleton, exocuticle was strongly GAMP-immunopositive, whereas the endocuticle and membrane layer was slightly positive. The epicuticle was immunonegative. Calcium carbonate was detected in exocuticle, endocuticle and a part of the membrane layer, but not in the epicuticle. Thus, the distribution of GAMP immunoreactivity roughly corresponded with that of calcium carbonate. X-ray diffraction study showed that calcium carbonate in the gastrolith was amorphous, whereas that in the exoskeleton consisted of calcite crystals. These data indicate that a GAMP-immunoreactive substance is commonly distributed in the mineralized tissues of the crayfish, but may exist in a chemically different form in other tissues.
The HIV manual : a guide to diagnosis and treatment (1996)

I. Basic Principles II. Symptom-Based Approach III. Infectious Complications A. Bacterial B. Fungal C. Parasitic D. Viral IV. Organ System Topics A. Cardiology B. Dermatology C. Endocrinology and Metabolism D. Hematology E. Nephrology F. Neurology G. Oncology H. Oral V. Pharmacology
New phenotype of mutations deficient in glucosylation of the lipid-linked oligosaccharide: cloning of the ALG8 locus. (1994)

Glc3Man9GlcNAc2 is the preferred substrate of the oligosaccharyltransferase of N-linked glycosylation of proteins, but nonglucosylated oligosaccharides can be transferred to proteins in Saccharomyces cerevisiae. Mutations affecting the addition of the three terminal glucose residues lead to accumulation of Man9GlcNAc2 or Glc1Man9GlcNAc2 in vivo but do not show any detectable growth defect. When these mutations were introduced into a strain with reduced oligosaccharyltransferase activity (due to the wbp1-1 mutation), a severe growth defect was observed: accumulation of suboptimal lipid-linked oligosaccharide and reduced oligosaccharyltransferase activity resulted in a severe underglycosylation of secreted proteins. This new synthetic phenotype made it possible to isolate the ALG8 locus, encoding a potential glucosyltransferase of the endoplasmic reticulum. The ALG8 protein is a 63.5-kDa hydrophobic protein that is not essential for the vegetative growth of yeast. However, the lack of this protein resulted in underglycosylation of secreted proteins.
Energy barrier to decoherence (2001)

We propose a ground-state approach to realizing quantum computers. This scheme is time-independent and inherently defends against decoherence by possessing an energy barrier to excitation. We prove that our time-independent qubits can perform the same algorithms as their time-dependent counterparts. Advantages and disadvantages of the time-independent approach are described. A model involving quantum dots is provided for illustration.
Direct Measurement of Single-Molecule Diffusion and Photodecomposition in Free Solution (1997)

Continuous monitoring of submillisecond free-solution dynamics of individual rhodamine-6G molecules and 30-base single-stranded DNA tagged with rhodamine was achieved. Fluorescence images were recorded from the same set of isolated molecules excited either through the evanescent field at the quartz-liquid interface or as a thin layer of solution defined by micron-sized wires, giving diffraction-limited resolution of inter-connected attoliter volume elements. The single-molecule diffusion coefficients were smaller and the unimolecular photodecomposition lifetimes were longer for the dye-DNA covalent complex as compared with those of the dye molecule itself. Unlike bulk studies, stochastic behavior was found for individual molecules of each type, and smaller diffusion coefficients were observed.
Tamper-Evident Digital Signatures: Protecting Certification Authorities Against Malware. (2005)

We introduce the notion of tamper-evidence for digital signature generation in order to defend against attacks aimed at covertly leaking secret information held by corrupted network nodes.
Raman Spectroscopic and Light-Induced Kinetic Characterization of a Recombinant Phytochrome of the Cyanobacterium Synechocystis (1997)

A phytochrome-encoding cDNA from the cyanobacterium Synechocystis has been heterologously expressed in Escherichia coli and reconstituted into functional chromoproteins by incubation with either phycocyanobilin (PCB) or phytochromobilin (PPhiB). These materials were studied by Raman spectroscopy and nanosecond flash photolysis. The Raman spectra suggest far-reaching similarities in chromophore configuration and conformation between the Pfr forms of Synechocystis phytochrome and the plant phytochromes (e.g. phyA from oat), but some differences, such as torsions around methine bridges and in hydrogen bonding interactions, in the Pr state. Synechocystis phytochrome (PCB) undergoes a multistep photoconversion reminiscent of the phyA Pr --> Pfr transformation but with different kinetics. The first process resolved is the decay of an intermediate with red-shifted absorption (relative to parent state) and a 25-micros lifetime. The next observable intermediate grows in with 300 (+/-25) micros and decays with 6-8 ms. The final state (Pfr) is formed biexponentially (450 ms, 1 s). When reconstituted with PPhiB, the first decay of this Synechocystis phytochrome is biexponential (5 and 25 micros). The growth of the second intermediate is slower (750 micros) than that in the PCB adduct whereas the decays of both species are similar. The formation of the Pfr form required fitting with three components (350 ms, 2.5 s, and 11 s). H/D Exchange in Synechocystis phytochrome (PCB) delays, by an isotope effect of 2.7, both growth (300 micros) and decay rates (6-8 ms) of the second intermediate. This effect is larger than values determined for phyA (ca. 1.2) and is characteristic of a rate-limiting proton transfer. The formation of the Pfr state of the PCB adduct of Synechocystis phytochrome shows a deuterium effect similar as phyA (ca. 1.2). Activation energies of the second intermediate in the range 0-18 degrees C are 44 (in H2O/buffer) and 48 kJ mol-1 (D2O), with essentially identical pre-exponential factors.
Manipulating Protein Adsorption using a Patchy Protein-Resistant Brush (2010)

Toward the development of surfaces for the precise manipulation of proteins, this study explores the fabrication and protein-interactive behavior of a new type of surface containing extremely small (on the order of 10 nm or less) flat adhesive "patches" or islands embedded in and partially concealed by a protein-repellant PEG (poly(ethylene glycol)) brush. The adsorption of fibrinogen, the model protein chosen to probe the biomaterial interactions of these surfaces, is very sensitive to the surface density of the adhesive patches, occurring only above a threshold. This suggests that two or more adhesive patches are needed to capture each protein. When the average spacing of the adhesive patches exceeds the fibrinogen length, no adsorption occurs because individual patches are too weakly binding for protein capture, as a result of being at least partially obstructed by the brush. The small size of the adhesive patches relative to the 47 nm fibrinogen length thus defines a limiting regime of surface design, distinct from surfaces where larger features can adhere single isolated proteins or multiple proteins together. The restricted protein-surface contact may comprise a means of preserving protein structure and function in the adsorbed state. This article demonstrates several additional interesting features of PEG brushes relevant to biomaterial design. First a moderate amount of adhesive material can be buried at the base of a brush without a measurable impact on the corona density. Second, a different amount of material at the base of a brush can be rendered ineffective to capturing adhesive proteins, despite a modest compromise of the brush corona. From this will follow insight into the design of patterned biomaterial surfaces, the bioactivity of the edges of patterned features, and an understanding of how flaws in brushes compromise protein resistance or allow access to small adhesive sites.
Development and evaluation of a spine biopsy simulator. (1998)

A spine biopsy simulator is being developed to 1) train surgeons on the current method for CT-directed needle biopsy and 2) provide a testbed for developing new image-guided and robot-assist methodologies. A task analysis and function allocation assessment provide the needed information for the first stage of the simulator development and evaluation.
Hybridoma-free generation of monoclonal antibodies (2003)

Production of monoclonal antibodies requires immortalization of splenocytes by somatic fusion to a myeloma cell line partner (hybridomas). Although hybridomas can be immortal, they may depend on a feeder cell layer and may be genetically unstable. Since the inception of hybridoma technology, efforts to improve efficiency and stability of monoclonal antibody-producing cell lines have not brought about substantial progress. Moreover, suitable human multiple myeloma-derived cell lines for the production of human antibodies have been very difficult to develop. Here we report a strategy that greatly simplifies the generation of antibodies and eliminates the need for hybridomas. We show that splenocytes derived from transgenic mice harboring a mutant temperature-sensitive simian virus 40 large tumor antigen under the control of a mouse major histocompatibility promoter are conditionally immortal at permissive temperatures and produce monoclonal antibodies. This simple approach may become a method of choice for generation and production of both polyclonal and monoclonal antibodies with advantages in high-throughput discovery and antibody-based immunotherapy.
Persistence of polyclonal B cell activation with undetectable parasitemia in late stages of experimental Chagas' disease. (1986)

The polyclonal B cell responses induced by Trypanosoma cruzi infection last for at least 6 mo after the inoculation of the parasites. In the acute phase of the disease, B cells from spleen and lymph nodes are largely stimulated, whereas a decrease in bone marrow PFC is observed. As the disease progresses, the numbers of Ig-secreting cells in the spleen, lymph nodes, and bone marrow are all enhanced. The isotype distribution of PFC, however, remains unvariable along the course of the infection, and it is characterized by the predominance of IgG2a- and IgG2b-secreting cells. No striking difference in the isotype pattern of resistant and susceptible strains of mice was observed. The continuous and long-lasting B cell stimulation generated during the infection may have important consequences in the pathology of Chagas' disease.
Purine Nucleosides. III. Methylation Studies of Certain Naturally Occurring Purine Nucleosides (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurine Nucleosides. III. Methylation Studies of Certain Naturally Occurring Purine NucleosidesJesse W. Jones and Roland K. RobinsCite this: J. Am. Chem. Soc. 1963, 85, 2, 193–201Publication Date (Print):January 1, 1963Publication History Published online1 May 2002Published inissue 1 January 1963https://doi.org/10.1021/ja00885a019RIGHTS & PERMISSIONSArticle Views1224Altmetric-Citations305LEARN 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 InReddit PDF (1 MB) Get e-Alerts Get e-Alerts
DNA Sequence Analysis of a Complementary DNA for Cold-Regulated Arabidopsis Gene cor15 and Characterization of the COR 15 Polypeptide (1992)

Previous studies have indicated that changes in gene expression occur in Arabidopsis thaliana L. (Heyn) during cold acclimation and that certain of the cor (cold-regulated) genes encode polypeptides that share the unusual property of remaining soluble upon boiling in aqueous solution. Here, we identify a cDNA clone for a cold-regulated gene encoding one of the "boiling-stable" polypeptides, COR15. DNA sequence analysis indicated that the gene, designated cor15, encodes a 14.7-kilodalton hydrophilic polypeptide having an N-terminal amino acid sequence that closely resembles transit peptides that target proteins to the stromal compartment of chloroplasts. Immunological studies indicated that COR15 is processed in vivo and that the mature polypeptide, COR 15m, is present in the soluble fraction of chloroplasts. Possible functions of COR 15m are discussed.
Diversity of CRISPR-Cas immune systems and molecular machines (2015)

Bacterial adaptive immunity hinges on CRISPR-Cas systems that provide DNA-encoded, RNA-mediated targeting of exogenous nucleic acids. A plethora of CRISPR molecular machines occur broadly in prokaryotic genomes, with a diversity of Cas nucleases that can be repurposed for various applications.
Handbook of essential fatty acid biology : biochemistry, physiology, and behavioral neurobiology (1997)

Part I: Biochemical Properties. Permeability of the Blood-Brain Barrier to Circulating Free Fatty Acids, William A. Banks, Abba J. Kastin, and Stanley I. Rapoport. Fatty Acid Metabolism in Brain in Relation to Development, Membrane Structure, and Signaling, M. Thomas Clandinin and Jacqueline Jumpsen. Abnormalities in Essential Fatty Acid Status in Alcoholism, Norman Salem, Jr. and Nils Urban Olsson. The Biological Properties of Oleic Acid, Elliot M. Berry. n-3 Polyunsaturated Fatty Acids and Human Cytokine Synthesis, Gunther Hartmann and Stefan Endres. Fatty Acid Regulation of Endocrine Activity, Eric P. Widmaier. Part II: Physiology and Health. w3 and w6 Essential Fatty Acid Status in Human Health and Disease, Ralph T. Holman. Visual Function and the Essentiality of a-Linolenic Acid and Docosahexaenoic Acid in Human Infants, Eileen E. Birch, David Birch, and Ricardo Uauy. Neural Function Following Dietary n-3 Fatty Acid Depletion, Andrew J. Sinclair, Harrison S. Weisinger, and Algis J. Vingrys. Polyunsaturated Fats and Learning: Old Data, New Questions, Donald V. Coscina. Fatty Acids, Phospholipids, and Schizophrenia, David F. Horrobin. The Seizing Brain: Phospholipolysis, Oxygen Delivery, and Electrical Activity, Francesco Visioli. Arachidonic Acid, Neurotrauma, and Neurodegenerative Diseases, Akhlaq A. Farooqui, Thad A. Rosenberger, and Lloyd A. Horrocks. Part III: Learning, Cognition, and Complex Behavior. Essential Fatty Acids and Behavior: Is There a Role for the Eicosanoids? Patricia E. Wainwright. Oral and Postingestive Controls of Fat Intake, Danielle Greenberg and Gerard P. Smith. Physiological Role of Fatty Acids in Infancy: Effect of Dietary Fat on Brain Fatty Acids and Learning Ability in Infancy, Akie Yonekubo. Omega-3 Fatty Acid Deficiency and Behavior: A Critical Review and Directions for Future Research, Sydney Reisbick and Martha Neuringer. Effects of Essential Fatty Acid Preparation (SR-3) on Brain Lipids, Biochemistry, and Behavioral and Cognitive Functions, Shlomo Yehuda, Sharon Rabinovitz, and David I. Mostofsky. Index.
Optical‐fiber bundles (2007)

Optical-fiber bundles have been employed as a versatile substrate for the fabrication of high-density microwell arrays. In this minireview, we discuss the application of optical-fiber-bundle arrays for a variety of biological problems. For genomics studies and microbial pathogen detection, individual beads have been functionalized with DNA probes and then loaded into the microwells. In addition, beads differentially responsive to vapors have been employed in an artificial olfaction system. Microwell arrays have also been loaded with living cells to monitor their individual response to biologically active compounds over long periods. Finally, the microwells have been sealed to enclose single enzyme molecules that can be used to measure individual molecule catalytic activity.
Sulfonylureas as Concomitant Insulin Secretagogues and NLRP3 Inflammasome Inhibitors (2017)

Insulin-secretory sulfonylureas are widely used, cost-effective treatments for type 2 diabetes (T2D). However, pancreatic β-cells are continually depleted as T2D progresses, thereby rendering the sulfonylurea drug class ineffective in controlling glycaemia. Dysregulation of the innate immune system via activation of the NLRP3 inflammasome, and the consequent production of interleukin-1β, has been linked to pancreatic β-cell death and multiple inflammatory complications of T2D disease. One proposed strategy for treating T2D is the use of sulfonylurea insulin secretagogues that are also NLRP3 inhibitors. We report the synthesis and biological evaluation of nine sulfonylureas that inhibit NLRP3 activation in murine bone-marrow- derived macrophages in a potent, dose-dependent manner. Six of these compounds inhibited NLRP3 at nanomolar concentrations and can also stimulate insulin secretion from a murine pancreatic cell line (MIN6). These novel compounds possess unprecedented dual modes of action, paving the way for a new generation of sulfonylureas that may be useful as therapeutic candidates and/or tool compounds in T2D and its associated inflammatory complications.