gebhart/patrepeval huggingface dataset:
Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity (2011)

The bioinformatical results and the experiments conducted in yeast and transgenic plants strongly suggest that the previously poorly analyzed NTRs and CTRs of HD-Zip I proteins play an important role in their function, hence potentially constituting a major source of functional diversity among members of this subfamily.
ChemInform Abstract: The Design of Resolving Agents. Chiral Cyclic Phosphoric Acids. (1986)

Abstract Die aus den aromatischen Aldehyden (I) dargestellten Propandiole (II) werden wie angegeben zu den cyclischen Phosphorsäuren (III) umgesetzt.
Immunoaffinity purification of bovine factor VII (1984)

Factor VII has been purified to homogeneity from bovine plasma by a procedure that includes affinity purification on an immunoadsorbent column. Recovery was determined by both coagulant assay and liquid scintillation counting, using 3H-factor VII as an internal standard. The purification factor calculated by both methods was approximately 120,000-fold, with a final yield of approximately 18%. Homogeneity was assessed by sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis. The material migrated as a single polypeptide chain of 53,000 daltons, and following activation by factor Xa, the one-chain zymogen was quantitatively converted to two-chain factor VIIa. Conversion of affinity-purified factor VII to factor VIIa resulted in up to a 119-fold activation of the coagulant activity, which is 2.7–4 times greater than the activatability reported for factor VII prepared by other methods. Zur et al. calculated that pure factor VII, uncontaminated by traces of factor VIIa, would be activated 123-fold upon conversion to factor VIIa. The close agreement between observed activatability of affinity-purified factor VII and the theoretical prediction suggests that we have isolated factor VII essentially free of factor VIIa. The purification data from three lots of bovine plasma yield an estimate for the plasma concentration of factor VII from 10.1 nM to 18.5 nM.
The incorporation of fibrinogen into extracellular matrix is dependent on active assembly of a fibronectin matrix (2002)

Fibrinogen is a soluble protein produced by hepatocytes and secreted into plasma, where it functions in hemostasis. During inflammation, the hepatic synthesis of fibrinogen is induced 2-10 fold. Recent studies demonstrate that after an inflammatory stimulus, fibrinogen gene expression and protein production is upregulated in lung epithelial cells, where it is secreted basolaterally and consequently deposited into the extracellular matrix in fibrils that extensively colocalize with fibronectin fibrils. In this study, we show that the deposition of fibrinogen into the matrix of fibroblasts occurred rapidly and in a Rho-dependent manner in response to serum or lysophosphatidic acid; RhoA GTPase signaling is also required for fibronectin matrix assembly. Using mouse embryonic fibronectin-null cells, we show that incorporation of exogenous fibrinogen into matrix fibrils occurred only in the presence of exogenous fibronectin, which is also assembled into matrix fibrils. Furthermore, treatment of fibroblasts and fibronectin-null cells with an antibody that inhibits fibronectin matrix assembly impaired incorporation of fibrinogen into matrix fibrils. Collectively, these data suggest that incorporation of fibrinogen into the extracellular matrix requires active fibronectin polymer elongation into matrix fibrils. From these data, we hypothesize that fibrinogen deposition rapidly changes the topology of the extracellular matrix to provide a surface for cell migration and matrix remodeling during tissue repair.
Discrete frequency infrared imaging using quantum cascade lasers for biological tissue analysis (2016)

Infrared (IR) spectroscopic imaging is an emerging modality for biological tissue analysis that has traditionally employed an interferometer for spectral discrimination. Recent technology developments have made discrete frequency sources, both lasers and filters, practical for imaging. The use of quantum cascade lasers in particular, presents new opportunities as well as challenges. Here we describe results from a novel point scanning confocal IR microscope and demonstrate the performance imaging several important spectral bands of lung tissue. Results show the possibility of discrete frequency (DF) absorbance measurements with RMS noise levels down to 0.34 mAU in 0.25 ms.
Impact of tumor‐specific targeting and dosing schedule on tumor growth inhibition after intravenous administration of siRNA‐containing nanoparticles (2007)

This study addresses issues of relevance for siRNA nanoparticle delivery by investigating the functional impact of tumor-specific targeting and dosing schedule. The investigations are performed using an experimental system involving a syngeneic mouse cancer model and a theoretical system based on our previously described mathematical model of siRNA delivery and function. A/J mice bearing subcutaneous Neuro2A tumors approximately 100 mm(3) in size were treated by intravenous injection with siRNA-containing nanoparticles formed with cyclodextrin-containing polycations (CDP). Three consecutive daily doses of transferrin (Tf)-targeted nanoparticles carrying 2.5 mg/kg of two different siRNA sequences targeting ribonucleotide reductase subunit M2 (RRM2) slowed tumor growth, whereas non-targeted nanoparticles were significantly less effective when given at the same dose. Furthermore, administration of the three doses on consecutive days or every 3 days did not lead to statistically significant differences in tumor growth delay. Mathematical model calculations of siRNA-mediated target protein knockdown and tumor growth inhibition are used to elucidate possible mechanisms to explain the observed effects and to provide guidelines for designing more effective siRNA-based treatment regimens regardless of delivery methodology and tumor type.
Rapid Detection of Reassortment of Pandemic H1N1/2009 Influenza Virus (2010)

Our results demonstrated that these assays can detect reintroductions of pandemic H1N1/2009 virus in pigs. These assays might be useful screening tools for identifying viral reassortants derived from pandemic H1N1/2009 or its precursors.
Studies on dissolution mechanism of drugs from ethylcellulose microcapsules. (1987)

The dissolution behavior of 4 drugs from ethylcellulose (EC) microcapsules (MC) was examined at various temperatures. From the early dissolution curves, the apparent dissolution rate constants and permeability constants (Pm) were estimated. The permeation across a Millipore filter and an EC cast membrane were also examined for comparison. The values of activation energy of Pm of MC ranged from 4.0 to 7.6 kcal/mol, independently of the drug solubility, and were close to those obtained for permeation through the Millipore filter and EC cast membrane. Pm values of the EC cast membrane (thickness : 10 μm) were small and decreased greatly with increase in the thickness. These results suggested that the drugs were not transported through the polymer phase but through the water channels existing in the MC membrane. Superposition analysis was applied to the dissolution curves measured at various temperatures and it was found that the extent of the superposition was better for less water-soluble drugs. The dependency of drug permeation through MC on wall thickness (from 5 to 20 μm) was examined using isoniazid. Pm values decreased linearly up to about 12 μm and were constant for a thicker wall at all dissolution temperatures. The activation energy of the dissolution rate constants increased with increasing wall thickness. The water.channels were classified into two types, one with fairly large pores or cracks and which was predominant in thinner films, and another with fine and uniformly distributed channels and which was predominant in thicker films.
Integrin modulators: a patent review (2013)

Integrins have been proven to be valuable therapeutic targets in the treatment of several inflammatory and autoimmune diseases, where leukocyte adhesion processes are regulated by them. Furthermore, they play an important role in pathological angiogenesis and tumor metastasis, being a promising target for cancer therapy.
Thermodynamic Analysis of Interacting Nucleic Acid Strands (2007)

Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality.
Experimental reedbed systems for the treatment of airport runoff (1997)

Research Article| October 01 1997 Experimental reedbed systems for the treatment of airport runoff D. M. Revitt; D. M. Revitt *Urban Pollution Research Centre, Middlesex University, Bounds Green Road, London N11 2NQ, UK Search for other works by this author on: This Site PubMed Google Scholar R. B. E. Shutes; R. B. E. Shutes *Urban Pollution Research Centre, Middlesex University, Bounds Green Road, London N11 2NQ, UK Search for other works by this author on: This Site PubMed Google Scholar N. R. Llewellyn; N. R. Llewellyn *Urban Pollution Research Centre, Middlesex University, Bounds Green Road, London N11 2NQ, UK Search for other works by this author on: This Site PubMed Google Scholar P. Worrall P. Worrall **Penny Anderson Associates, 52 Lower Lane, Chinley, Stockport, Cheshire SK12 6BD, UK Search for other works by this author on: This Site PubMed Google Scholar Water Sci Technol (1997) 36 (8-9): 385–390. https://doi.org/10.2166/wst.1997.0697 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Share Icon Share Facebook Twitter LinkedIn MailTo Tools Icon Tools Cite Icon Cite Permissions Search Site Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsThis Journal Search Advanced Search Citation D. M. Revitt, R. B. E. Shutes, N. R. Llewellyn, P. Worrall; Experimental reedbed systems for the treatment of airport runoff. Water Sci Technol 1 October 1997; 36 (8-9): 385–390. doi: https://doi.org/10.2166/wst.1997.0697 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex The relative efficiencies of pollutant removal from airport runoff by three different designs of pilot scale reedbed treatment systems located at Heathrow airport are described. The sub-surface flow and surface flow systems generally performed more effectively than the rafted systems for reduction of BOD, COD, total ammonia, nitrate, phosphate and metal concentrations. The variable removal efficiencies are explained in terms of the physical, chemical and biological processes which are relevant to each reedbed system. Airport runoff, constructed reedbeds, pollutant removal efficiency This content is only available as a PDF. © IWA Publishing 1997 You do not currently have access to this content.
Corneal thickness measurements in normal and keratoconic eyes: Pentacam comprehensive eye scanner versus noncontact specular microscopy and ultrasound pachymetry (2006)

Results suggest that whereas Pentacam CES and UP may be used interchangeably in normal eyes in the clinical setting for the measurement of CCT, one should be cautious interpreting corneal thickness data from Pentacam CES, UP, and particularly SM in eyes with keratoconus. Whereas, in normal and mildly keratoconic eyes, Pentacam CES and UP demonstrated very high and comparable reproducibility, in moderately keratoconic eyes, Pentacam CES readings showed better reproducibility than UP.
Dendritic Cells Are Required for the Development of Chronic Eosinophilic Airway Inflammation in Response to Inhaled Antigen in Sensitized Mice (1998)

Asthma is characterized by chronic eosinophilic inflammation of the airways, and allergen-specific Th2 lymphocytes are thought to play a major role in the development and maintenance of this type of inflammation in allergic asthma. It is generally accepted that airway dendritic cells (DC) are essential for stimulating naive T cells in a primary immune response to inhaled Ag and for the development of allergic sensitization. We have examined the role of airway DC in stimulating memory T cells in a secondary response to inhaled Ag and the subsequent development of chronic airway inflammation. In our mouse model of asthma, OVA aerosol challenge in OVA-sensitized mice leads to CD4-dependent peribronchial and perivascular eosinophilic inflammation, lung Th2 cytokine production, and systemic IgE production. We have used conditional depletion of airway DC by treatment of thymidine kinase-transgenic mice with the antiviral drug ganciclovir to deplete DC during the secondary exposure to OVA. In sensitized thymidine kinase-transgenic mice, a significant decrease in the number of bronchoalveolar CD4 and CD8 T lymphocytes and B lymphocytes was seen after ganciclovir treatment. In addition, Th2 cytokine-associated eosinophilic airway inflammation was almost completely suppressed. These studies demonstrate for the first time that the DC is essential for presenting inhaled Ag to previously primed Th2 cells in the lung, leading to chronic eosinophilic airway inflammation. Altering the function of airway DC may therefore be an important target for new anti-asthma therapy.
Preferential expression of an alpha-tubulin gene of Arabidopsis in pollen. (1992)

The pool of tubulin protein in tissues of Arabidopsis is provided by the expression of multiple alpha-tubulin (TUA) and beta-tubulin genes. Whereas most tubulin genes are expressed in many tissues, previous evidence suggested that the TUA1 gene might be expressed primarily in pollen. We now report a detailed analysis of TUA1 expression during Arabidopsis development. In RNA from tissues of dissected flowers, TUA1 transcripts were detected only in stamens and mature pollen. Chimeric genes containing TUA1 5' flanking DNA fused to the beta-glucuronidase (GUS) coding region were used to create transgenic Arabidopsis plants. Plants containing a chimeric gene with 533 bp of 5' flanking sequence were analyzed by histochemical assay to localize GUS expression within the plant. The blue product of GUS enzyme activity accumulated very rapidly in postmitotic pollen grains. Much lower levels of GUS activity were detected in anthers with uninucleate pollen grains, in flower receptacles, and in a few vegetative tissues. Analysis of 5' deletions of the TUA1 promoter suggested that 97 bp of 5' flanking DNA is sufficient to drive GUS expression in pollen and young anthers, whereas at least 380 bp is required to detect GUS expression in the receptacle. Examination of the TUA1 promoter sequence revealed several motifs that are repeated within the TUA1 promoter and are similar to sequences in other pollen-specific promoters.
Thermodynamics of Single Mismatches in RNA Duplexes (1999)

The thermodynamic properties and structures of single mismatches in short RNA duplexes were studied in optical melting and imino proton NMR experiments. The free energy increments at 37 degrees C measured for non-GU single mismatches range from -2.6 to 1.7 kcal/mol. These increments depend on the identity of the mismatch, adjacent base pairs, and the position in the helix. UU and AA mismatches are more stable close to a helix end, but GG mismatch stability is essentially unaffected by the position in the helix. Approximations are suggested for predicting stabilities of single mismatches in short RNA duplexes.
Detection and assignment ofTP53 mutations in tumor DNA using peptide mass signature genotyping (2003)

This report describes the application of a new approach to tumor genotyping called peptide mass signature genotyping (PMSG) that is particularly suited to detecting minority sequences in a DNA sample. Detecting minority sequences is essential for accurate tumor genotyping because tumor resections are generally a mixture of malignant and non-malignant cells, with the mutations of interest often outnumbered by the corresponding wild-type alleles. To explore the suitability of PMSG for tumor genotyping, 25 human squamous cell carcinomas of the head and neck, as well as a set of cell lines derived from those tumors, were analyzed for mutations in exons 5 to 8 of the TP53 gene, the exons that encode the DNA-binding domains of the p53 protein. PMSG identified mutations in 11 tumor DNA samples, whereas dideoxy sequencing of the same samples detected mutations in only four. Currently, PMSG can be used to detect mutations that are present in only 20% of the sample DNA, and we expect that this threshold will be lowered significantly as the PMSG process is improved. Hum Mutat 22:158-165, 2003.
Oxidation of High Density Lipoproteins (1998)

Human high density lipoproteins (HDL) can reduce cholesteryl ester hydroperoxides to the corresponding hydroxides (Sattler W., Christison J. K., and Stocker, R. (1995) Free Radical Biol. & Med. 18, 421-429). Here we demonstrate that this reducing activity extended to hydroperoxides of phosphatidylcholine, was similar in HDL2 and HDL3, was independent of arylesterase and lecithin:cholesteryl acyltransferase activity, was unaffected by sulfhydryl reagents, and was expressed by reconstituted particles containing apoAI or apoAII only, as well as isolated human apoAI. Concomitant with the reduction of lipid hydroperoxides specific oxidized forms of apoAI and apoAII formed in blood-derived and reconstituted HDL. Similarly, specific oxidized forms of apoAI accumulated upon treatment of isolated apoAI with authentic cholesteryl linoleate hydroperoxide. These specific oxidized forms of apoAI and apoAII have been shown previously to contain Met sulfoxide (Met(O)) at Met residues and are also formed when HDL is exposed to Cu2+ or soybean lipoxygenase. Lipid hydroperoxide reduction and the associated formation of specific oxidized forms of apoAI and apoAII were inhibited by solubilizing HDL with SDS or by pretreatment of HDL with chloramine T. The inhibitory effect of chloramine T was dose-dependent and accompanied by the conversion of specific Met residues of apoAI and apoAII into Met(O). Canine HDL, which contains apoAI as the predominant apolipoprotein and which lacks the oxidation-sensitive Met residues Met112 and Met148, showed much weaker lipid hydroperoxide reducing activity and lower extents of formation of oxidized forms of apoAI than human HDL. We conclude that the oxidation of specific Met residues of apoAI and apoAII to Met(O) plays a significant role in the 2-electron reduction of hydroperoxides of cholesteryl esters and phosphatidylcholine associated with human HDL.
Multifunctional Adaptive NS1 Mutations Are Selected upon Human Influenza Virus Evolution in the Mouse (2012)

The role of the NS1 protein in modulating influenza A virulence and host range was assessed by adapting A/Hong Kong/1/1968 (H3N2) (HK-wt) to increased virulence in the mouse. Sequencing the NS genome segment of mouse-adapted variants revealed 11 mutations in the NS1 gene and 4 in the overlapping NEP gene. Using the HK-wt virus and reverse genetics to incorporate mutant NS gene segments, we demonstrated that all NS1 mutations were adaptive and enhanced virus replication (up to 100 fold) in mouse cells and/or lungs. All but one NS1 mutant was associated with increased virulence measured by survival and weight loss in the mouse. Ten of twelve NS1 mutants significantly enhanced IFN-β antagonism to reduce the level of IFN β production relative to HK-wt in infected mouse lungs at 1 day post infection, where 9 mutants induced viral yields in the lung that were equivalent to or significantly greater than HK-wt (up to 16 fold increase). Eight of 12 NS1 mutants had reduced or lost the ability to bind the 30 kDa cleavage and polyadenylation specificity factor (CPSF30) thus demonstrating a lack of correlation with reduced IFN β production. Mutant NS1 genes resulted in increased viral mRNA transcription (10 of 12 mutants), and protein production (6 of 12 mutants) in mouse cells. Increased transcription activity was demonstrated in the influenza mini-genome assay for 7 of 11 NS1 mutants. Although we have shown gain-of-function properties for all mutant NS genes, the contribution of the NEP mutations to phenotypic changes remains to be assessed. This study demonstrates that NS1 is a multifunctional virulence factor subject to adaptive evolution.
<italic>LC</italic> Passive Wireless Sensors Toward a Wireless Sensing Platform: Status, Prospects, and Challenges (2016)

Inductor-capacitor (LC) passive wireless sensors use a transformer with loose coupling between an external readout coil and an inductor that receives power through this inductive coupling. Changes in the sensor are wirelessly and remotely detected by the readout coil, which makes them highly useful in applications that require the sensor to be powered remotely and to occupy a small volume, such as harsh and sealed environments, where physical access to the sensor is difficult. Although the sensor to accomplish this function dates from the 1960's, its rapid extension over the past decades has benefited from microelectromechanical systems. This paper provides an overview of the status and challenges in the LC passive wireless sensor toward a wireless sensing platform. The basic sensing principles are first categorized into detecting changes of the sensor in response to the capacitance, resistance, inductance, or coupling distance due to the parameter of interest through monitoring the impedance magnitude and phase spectrum. The present state of the art in sensor applications for pressure, strain, temperature, humidity, biochemical, gas, and so on is then reviewed and compared. For emerging applications from many Internet of Things scenarios, geometrical constraints, such as small and non-invasive coils, reduce the magnetic coupling between the sensor and the readout coil, resulting in a limited interrogation distance. Furthermore, an increasing number of applications also require the simultaneous measurement of multiple parameters. Recent efforts to increase the interrogation distance and to extend the measurement of single parameter to multiple parameters are finally outlined.