gebhart/patrepeval huggingface dataset:
Permeability-related changes revealed at endothelial cell borders in inflamed venules by lectin binding (1996)

Plasma leakage in inflammation results from intercellular gaps that form in the endothelium of venules. These gaps and related morphological changes in endothelial cells are not readily seen by light microscopy. In this study we sought to visualize such changes by using the selective binding properties of plant lectins. Acute inflammation was induced in the trachea of pathogen-free F344 rats by injecting substance P intravenously, and 1, 3, or 10 min later the vasculature was perfused with fixative followed by a biotinylated lectin. Lectin binding was localized by avidinbiotin complex-peroxidase histochemistry and viewed in tracheal whole mounts by differential-interference contrast microscopy. The binding patterns of the 20 lectins tested fell into 4 groups. Most of the lectins either bound uniformly to the endothelium of normal and inflamed venules (group 1, e.g., Lycopersicon esculentum lectin) or bound weakly or not at all to venules (group 2, e.g., Maackia amurensis I lectin). The uniform binding of group 1 lectins not only revealed the overall vascular architecture but also made visible intercellular gaps and fingerlike processes at endothelial cell borders in inflamed venules. In postcapillary venules after substance P, the fingerlike processes were present along an average of 32% of the endothelial cell perimeter at 1 min, 25% at 3 min, and 7% at 10 min, compared with a baseline value of 2%. A third group of lectins (group 3, e.g., concanavalin A) bound selectively to focal patches of inflamed venules but bound weakly to normal venules. The fourth group (group 4, e.g., Ricinus communis I lectin) bound preferentially to focal patches in inflamed venules and also bound uniformly to normal venules. The focal binding of group 3 and 4 lectins coincided with sites of plasma leakage marked by extravasation of the particulate tracer monastral blue and was associated with subendothelial components of the vessel wall. We conclude that selected lectins reveal novel features of focal sites of plasma leakage, endothelial gaps, and fingerlike processes at endothelial cell borders in inflamed venules.
Matching amino acid and nucleotide sequences of mouse rheumatoid factor CDRH3-FRH4 segments to other mouse antibodies with known specificities (2000)

Abstract Contact: t-wu@nwu.edu ** To whom correspondence should be addressed. E267, Technological Institute, 2145 Sheridan Road, Evanston, IL 60208, USA.
Solvatochromic Pyrene Analogues of Prodan Exhibiting Extremely High Fluorescence Quantum Yields in Apolar and Polar Solvents (2013)

True colors: Novel pyrene analogues of Prodan exhibit outstanding photophysical properties with remarkably high fluorescence quantum yield (QY) in solvents ranging from apolar hexane to polar methanol (see figure). This is accompanied by strong solvatochromism and large Stokes shifts. These properties have not been previously achieved in enormous solvatochromic dyes, but are quite useful for emitting materials and imaging tools.
Rapid Membrane Effects of Steroids in Neuroblastoma Cells: Effects of Estrogen on Mitogen Activated Protein Kinase Signalling Cascade and c-fos Immediate Early Gene Transcription (1997)

Rapid effects of steroid hormones have been observed in neuronal cells for many years. We show here, that in the human neuroblastoma cell line SK-N-SH, the membrane impermeable conjugated 17beta-estradiol (E2BSA) activates mitogen activated protein kinase kinase (MAPKK or MEK) and induces the phosphorylation and activation of both ERK-1 and ERK-2 (mitogen activated protein kinase or MAPK). Additionally, E2BSA induces the transcription of a reporter gene construct driven by the promoter of the mouse c-fos proto-oncogene. The effects of this membrane impermeable estrogen on c-fos transcription are not inhibited by the estrogen receptor antagonists Tamoxifen or ICI 182,780, further excluding the involvement of the intracellular estrogen receptor. This is also illustrated by the observation that E2BSA does not activate estrogen response element (ERE) mediated transcription. This is the first report of rapid membrane effects of 17beta-estradiol on growth factor related signalling pathways in neuronal cells, and indicates a potential mechanism by which 17beta-estradiol might affect the expression of genes whose promoters do not contain EREs but are responsive to factors acting through other response elements such as AP-1 and SRE sites.
Glycosidase active site mutations in human -L-iduronidase (2001)

Mucopolysaccharidosis type I (MPS I; McKusick 25280) results from a deficiency in alpha-L-iduronidase activity. Using a bioinformatics approach, we have previously predicted the putative acid/base catalyst and nucleophile residues in the active site of this human lysosomal glycosidase to be Glu182 and Glu299, respectively. To obtain experimental evidence supporting these predictions, wild-type alpha-L-iduronidase and site-directed mutants E182A and E299A were individually expressed in Chinese hamster ovary-K1 cell lines. We have compared the synthesis, processing, and catalytic properties of the two mutant proteins with wild-type human alpha-L-iduronidase. Both E182A and E299A transfected cells produced catalytically inactive human alpha-L-iduronidase protein at levels comparable to the wild-type control. The E182A protein was synthesized, processed, targeted to the lysosome, and secreted in a similar fashion to wild-type alpha-L-iduronidase. The E299A mutant protein was also synthesized and secreted similarly to the wild-type enzyme, but there were alterations in its rate of traffic and proteolytic processing. These data indicate that the enzymatic inactivity of the E182A and E299A mutants is not due to problems of synthesis/folding, but to the removal of key catalytic residues. In addition, we have identified a MPS I patient with an E182K mutant allele. The E182K mutant protein was expressed in CHO-K1 cells and also found to be enzymatically inactive. Together, these results support the predicted role of E182 and E299 in the catalytic mechanism of alpha-L-iduronidase and we propose that the mutation of either of these residues would contribute to a very severe clinical phenotype in a MPS I patient.
A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin–dopamine receptors (2020)

Dihydroorotate dehydrogenase (DHODH) is a key enzyme required for de novo pyrimidine synthesis and it is suggested as a target for COVID19 treatment due to high pyrimidine demand by the virus replication in the infected host cells as well as its proven effect of blocking of cytokine release by the immune cells to prevent inflammation leading to acute respiratory distress. There are a number of clinical trials underway for COVID19 treatment using DHODH inhibitors; however, there are only a small number of known DHODH antagonists available for testing. Here, we have applied a methodology to identify DHODH antagonist candidates, and compared them using in silico target prediction tools. A large set of 7900 FDA-approved and clinical stage drugs obtained from DrugBank were docked against 20 different structures DHODH available in PDB. Drugs were eliminated according to their predicted affinities by Autodock Vina. About 28 FDA-approved and 79 clinical trial ongoing drugs remained. The mode of interaction of these molecules was analyzed by repeating docking using Autodock 4 and DS Visualiser. Finally, the target region predictions of 28 FDA-approved drugs were determined through PASS and SwissTargetPrediction tools. Interestingly, the analysis of in silico target predictions revealed that serotonin-dopamine receptor antagonists could also be potential DHODH inhibitors. Our candidates shared a common attribute, a possible interaction with serotonin-dopamine receptors as well as other oxidoreductases, like DHODH. Moreover, the Bruton Tyrosine Kinase-inhibitor acalabrutunib and serotonin-dopamine receptor inhibitor drugs on our list have been found in the literature that have shown to be effective against Sars-CoV-2, while the path of activity is yet to be identified. Identifying an effective drug that can suppress both inflammation and virus proliferation will play a crucial role in the treatment of COVID. Therefore, we suggest experimental investigation of the 28 FDA-approved drugs on DHODH activity and Sars-CoV-2 virus proliferation. Those who are found experimentally effective can play an important role in COVID19 treatment. Moreover, we suggest investigating COVID19 case conditions in patients using schizophrenia and depression drugs.
The Metabolic and Molecular Bases of Inherited Disease (1995)

I. INTRODUCTION II. PERSPECTIVES III. GENERAL THEMES IV. CANCER V. CHROMOSOMES VI. DIAGNOSTIC APPROACHES VII. CARBOHYDRATES VIII. AMINO ACIDS IX. ORGANIC ACIDS X. DISORDERS OF MITOCHONDRIAL FUNCTION XI. PURINES AND PYRIMIDINES XII. LIPIDS XIII. PORPHYRINS XIV. METALS XV. PEROXISOMES XVI. LYSOSOMAL DISORDERS XVII. VITAMINS XVIII. HORMONES XIX. BLOOD XX. IMMUNE AND DEFENSE SYSTEMS XXI. MEMBRANE TRANSPORT DISORDERS XXII. CONNECTIVE TISSUE XXIII. CARDIOVASCULAR SYSTEM XXIV. KIDNEY XXV. MUSCLE XXVI. LUNG XXVII. SKIN XXVIII. NEUROGENETICS XXIX. EYE XXX. MULTISYSTEM INBORN ERRORS OF DEVELOPMENT
Long-range Coulomb interactions in small Si devices. Part II. Effective electron mobility in thin-oxide structures (2001)

In metal–oxide–semiconductor structures with polycrystalline Si gates, electrons in the inverted channel of the substrate scatter with electrons in the gate via long-range Coulomb interactions. For thin oxides, these interactions can cause a significant transfer of momentum from the channel to the gate, thus reducing the effective mobility of the two-dimensional electron gas in the substrate. We present calculations of the dispersion of the interface plasmons in poly-Si/SiO2/Si structures, comparing the results obtained in the long-wavelength limit to those obtained using the random-phase approximation. Employing the former model, we compute the effect of plasmon scattering on the effective electron mobility in Si inversion layers. We find a significant reduction of the mobility for oxides thinner than about 3 nm.
Fibre-based imaging: new challenges (2015)

A novel minimally invasive micro-endoscopes utilizing disordered light within a standard multimode optical fibre have been introduced recently. The two most important limitations of this exciting technology are (i) the lack of bending flexibility (transformation matrix is only valid as long as the fibre remains stationary) and (ii) high demands on computational power, making the performance of such systems slow. Here we discuss possible routes to address the later one: We introduce a GPU toolbox to make this powerful technique faster and more accessible to bio-medical researchers.
Interleukin-8 is a major component of pleural liquid chemotactic activity in a rabbit model of endotoxin pleurisy (1994)

Gram-negative endotoxin induces production of the potent chemotactic factor interleukin-8 (IL-8) in vitro; however, the importance of IL-8 in endotoxin-induced inflammation in vivo is unknown. We asked whether IL-8 is an important contributor to chemotactic activity in acute inflammatory liquids formed in response to endotoxin, and, if present, what concentrations of IL-8 antigen are generated. For these studies, we cloned and expressed rabbit recombinant IL-8 (rrIL-8), developed specific anti-rabbit IL-8 monoclonal antibodies (mAb), and then used these reagents to develop assays to detect rabbit IL-8 bioactivity and measure rabbit IL-8 antigen. Escherichia coli endotoxin (20 ng/ml, n = 4, or 2,000 ng/ml, n = 4) was instilled into the pleural space of eight rabbits for 6 h. Rabbit IL-8 bioactivity in the endotoxin pleurisy samples was assayed by measuring the migration of rabbit neutrophils toward the pleural liquid under two different conditions: 1) after addition of an anti-IL-8 neutralizing mAb and 2) after desensitization of the neutrophils to rrIL-8. Addition of the anti-IL-8 mAb decreased neutrophil migration toward the pleural liquid by 65 +/- 13 and 75 +/- 22% (mean +/- SE, after 20 and 2,000 ng/ml endotoxin, respectively; P < 0.01 compared with a control mAb). Desensitization of neutrophils to rrIL-8 decreased their migration toward the pleural liquid by 72 +/- 5% (P = 0.03, compared with exposure of neutrophils to buffer alone.(ABSTRACT TRUNCATED AT 250 WORDS)
Epitope-specific antibody-induced cleavage of angiotensin-converting enzyme from the cell surface (2002)

Angiotensin I-converting enzyme (ACE; CD143, EC 3.4.15.1) is a type-1 integral membrane protein that can also be released into extracellular fluids (such as plasma, and seminal and cerebrospinal fluids) as a soluble enzyme following cleavage mediated by an unidentified protease(s), referred to as ACE secretase, in a process known as ‘shedding'. The effects of monoclonal antibodies (mAbs) to eight different epitopes on the N-terminal domain of ACE on shedding was investigated using Chinese hamster ovary cells (CHO cells) expressing an ACE transgene and using human umbilical vein endothelial cells. Antibody-induced shedding of ACE was strongly epitope-specific: most of the antibodies increased the shedding by 20–40%, mAbs 9B9 and 3A5 increased the shedding by 270 and 410% respectively, whereas binding of mAb 3G8 decreased ACE shedding by 36%. The ACE released following mAb treatment lacked a hydrophobic transmembrane domain anchor. The antibody-induced shedding was completely inhibited at 4°C and by zinc chelation using 1,10-phenanthroline, suggesting involvement of a metalloprotease in this process. A hydroxamate-based metalloprotease inhibitor (batimastat, BB-94) was 15 times more efficacious in inhibiting mAb-induced ACE shedding than basal (constitutive) ACE release. Treatment of CHO-ACE cells with BB-94 more effectively prevented elevation in antibody-dependent (but not basal) ACE release induced by 3,4-dichloroisocoumarin and iodoacetamide. These data suggest that different secretases might be responsible for ACE release under basal compared with antibody-induced shedding. Further experiments with more than 40 protease inhibitors suggest that calpains, furin and the proteasome may participate in this process.
Image and Video Matting: A Survey (2008)

Matting refers to the problem of accurate foreground estimation in images and video. It is one of the key techniques in many image editing and film production applications, thus has been extensively studied in the literature. With the recent advances of digital cameras, using matting techniques to create novel composites or facilitate other editing tasks has gained increasing interest from both professionals as well as consumers. Consequently, various matting techniques and systems have been proposed to try to efficiently extract high quality mattes from both still images and video sequences. This survey provides a comprehensive review of existing image and video matting algorithms and systems, with an emphasis on the advanced techniques that have been recently proposed. The first part of the survey is focused on image matting. The fundamental techniques shared by many image matting algorithms, such as color sampling methods and matting affinities, are first analyzed. Image matting techniques are then classified into three categories based on their underlying methodologies, and an objective evaluation is conducted to reveal the advantages and disadvantages of each category. A unique Accuracy vs. Cost analysis is presented as a practical guidance for readers to properly choose matting tools that best fit their specific requirements and constraints. The second part of the survey is focused on video matting. The difficulties and challenges of video matting are first analyzed, and various ways of combining matting algorithms with other video processing techniques for building efficient video matting systems are reviewed. Key contributions, advantages as well as limitations of important systems are summarized. Finally, special matting systems that rely on capturing additional foreground/background information to automate the matting process are discussed. A few interesting directions for future matting research are presented in the conclusion.
Tumor progression—targets for differential therapy (2006)

Differential killing of the patient's cancer cells versus normal cells is a necessity for chemotherapy. Advantage can be taken of close regulations of gene expression and of enzyme activity that are essential for normal cell functioning, and that are altered during tumor progression. Summarized here is our research on four such progression changes of cancer cells; some deregulate proliferation control and others decrease programmed death (apoptosis). These processes will be illustrated with examples of potential chemotherapies based on them. Methods for discovery of such changes include Differential Display and microarrays.
Lunokhod-1 Soviet Lunar Surface Vehicle (1971)

Abstract : Description of the delivery of the Soviet lunar exploration vehicle to the lunar surface in the Sea of Rains on 17 November 1970 by the Luna-17 mission, derived from literature published in the USSR between that date and May 1971. The fact that the Lunokhod-1 has thus far traveled nearly 10 km over rugged terrain and apparently continues to do so indicates success of the concept of a remote drone interacting directly with an unknown and hostile environment. Its sensory equipment comprises narrow-band television systems, mechanical probes, a chemical analysis system, X-ray and cosmic ray detectors, and assorted temperature and pressure gauges.
Induction of Double-strand Breaks Following Neutron Capture by DNA-bound 157 Gd (1988)

Irradiation of plasmid DNA/Gd3+ mixtures with thermal neutrons induces DNA double-strand breaks (dsb). However, the extent of breakage is markedly reduced by sequestering the Gd3+ from DNA by addition of EDTA. Since the 157Gd neutron capture event involves some internal conversion, we suggest that the DNA dsb induction results from Auger electron emission.
(100) Silicon Etch‐Rate Dependence on Boron Concentration in Ethylenediamine‐Pyrocatechol‐Water Solutions (1984)

The (100) silicon etch‐rate dependence on boron concentration in ethylenediamine‐pyrocatechol‐water (EPW) solutions at 110°C has been measured by successive etching of boron‐diffused silicon. The etch rate begins to decrease near 1019cm−3and decreases approximately as the fourth power of doping over three orders of magnitude in etch rate. The etch‐rate ratio between heavily and lightly doped silicon appears insensitive to pyrazine concentration from 0.01 to 6.0g/liter E, oxygen exposure of the etch solution, and light. The etch‐rate decrease is sensitive to hole concentration and not to atomic concentration of boron or stress. The etch‐rate dependence may be explained by assuming that the hydrogen‐evolution cathodic half‐reaction of the oxidation‐reduction reaction is the rate‐determining step. The reason for the etch‐rate decrease as the hole concentration increases is given in terms of increased Auger recombination of large numbers of electrons chemically produced at the silicon surface during etching. Excellent agreement with experiment is obtained. Similarities of this etch system and the phenomenon of silicon staining are discussed in terms of oxidation‐reduction reactions. Application to control of thickness and uniformity of boron‐doped silicon membranes is discussed.
ChemInform Abstract: Production of Carotenoids by Recombinant DNA Technology. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Effect of Enhanced Glycemic Control with Saxagliptin on Endothelial Nitric Oxide Release and CD40 Levels in Obese Rats (2011)

These findings indicate that enhanced glycemic control with DPP4 inhibition improved NO release and reduced inflammation in a manner not predicted by FG changes alone.
Inherently safe DC/DC converter using a normally-on SiC JFET (2005)

This paper examines the design of an inherently safe DC-DC converter specifically for normally on silicon-carbide based power JFETs. The converter is targeted for ambient temperatures of 225 /spl deg/C. A demonstration converter board has been completed and tested illustrating proof of principle of the self-biased gate driver configuration for deriving a stable 5-V dc output from a 25-V dc input. The converter has also demonstrated conventional "off-line" 120 VAC operation to develop a 12 V dc output.
Effect of 2-Chloro-Substitution of Adenine Moiety in Mixed-Ligand Gold(I) Triphenylphosphine Complexes on Anti-Inflammatory Activity: The Discrepancy between the In Vivo and In Vitro Models (2013)

A series of gold(I) triphenylphosphine (PPh3) complexes (1-9) involving 2-chloro-N6-(substituted-benzyl)adenine derivatives as N-donor ligands was synthesized and thoroughly characterized by relevant methods, including electrospray-ionization (ESI) mass spectrometry and multinuclear NMR spectroscopy. The anti-inflammatory and antiedematous effects of three representatives 1, 5 and 9 were evaluated by means of in vitro model based on the expression of pro- and anti-inflammatory cytokines and influence of the complexes on selected forms of matrix metalloproteinases secreted by LPS-activated THP-1 monocytes and in vivo model evaluating the antiedematous effect of the complexes in the carrageenan-induced rat hind-paw edema model. In addition to the pharmacological observations, the affected hind paws were post mortem subjected to histological and immunohistochemical evaluations. The results of both in vivo and ex vivo methods revealed low antiedematous and anti-inflammatory effects of the complexes, even though the in vitro model identified them as promising anti-inflammatory acting compounds. The reason for this discrepancy lies probably in low stability of the studied complexes in biological environment, as demonstrated by the solution interaction studies with sulfur-containing biomolecules (cysteine and reduced glutathione) using the ESI mass spectrometry.
B Lymphocyte Chemotaxis Regulated in Association with Microanatomic Localization, Differentiation State, and B Cell Receptor Engagement (1998)

Migration of mature B lymphocytes within secondary lymphoid organs and recirculation between these sites are thought to allow B cells to obtain T cell help, to undergo somatic hypermutation, to differentiate into effector cells, and to home to sites of antibody production. The mechanisms that direct migration of B lymphocytes are unknown, but there is evidence that G protein-coupled receptors, and possibly chemokine receptors, may be involved. Stromal cell- derived factor (SDF)-1alpha is a CXC chemokine previously characterized as an efficacious chemoattractant for T lymphocytes and monocytes in peripheral blood. Here we show with purified tonsillar B cells that SDF-1alpha also attracts naive and memory, but not germinal center (GC) B lymphocytes. Furthermore, GC B cells could be converted to respond to SDF-1alpha by in vitro differentiation into memory B lymphocytes. Conversely, the migratory response in naive and memory B cells was significantly reduced after B cell receptor engagement and CD40 signaling. The receptor for SDF-1, CXC chemokine receptor 4 (CXCR4), was found to be expressed on responsive as well as unresponsive B cell subsets, but was more rapidly downregulated on responsive cells by ligand. Finally, messenger RNA for SDF-1 was detected by in situ hybridization in a layer of cells surrounding the GC. These findings show that responsiveness to the chemoattractant SDF-1alpha is regulated during B lymphocyte activation, and correlates with positioning of B lymphocytes within a secondary lymphoid organ.