gebhart/patrepeval huggingface dataset:
Near infrared imaging with nanoparticles (2010)

Near infrared imaging has presented itself as a powerful diagnostic technique with potential to serve as a minimally invasive, nonionizing method for sensitive, deep tissue diagnostic imaging. This potential is further realized with the use of nanoparticle (NP)-based near infrared (NIR) contrast agents that are not prone to the rapid photobleaching and instability of their organic counterparts. This review discusses applications that have successfully demonstrated the utility of nanoparticles for NIR imaging, including NIR-emitting semiconductor quantum dots (QDs), resonant gold nanoshells, and dye-encapsulating nanoparticles. NIR QDs demonstrate superior optical performance with exceptional fluorescence brightness stability. However, the heavy metal composition and high propensity for toxicity hinder future application in clinical environments. NIR resonant gold nanoshells also exhibit brilliant signal intensities and likewise have none of the photo- or chemical-instabilities characteristic of organic contrast agents. However, concerns regarding ineffectual clearance and long-term accumulation in nontarget organs are a major issue for this technology. Finally, NIR dye-encapsulating nanoparticles synthesized from calcium phosphate (CP) also demonstrate improved optical performances by shielding the component dye from undesirable environmental influences, thereby enhancing quantum yields, emission brightness, and fluorescent lifetime. Calcium phosphate nanoparticle (CPNP) contrast agents are neither toxic, nor have issues with long-term sequestering, as they are readily dissolved in low pH environments and ultimately absorbed into the system. Though perhaps not as optically superior as QDs or nanoshells, these are a completely nontoxic, bioresorbable option for NP-based NIR imaging that still effectively improves the optical performance of conventional organic agents.
Calorie Restriction Increases Muscle Mitochondrial Biogenesis in Healthy Humans (2007)

The observed increase in muscle mitochondrial DNA in association with a decrease in whole body oxygen consumption and DNA damage suggests that caloric restriction improves mitochondrial function in young non-obese adults.
18β-glycyrrhetinic acid suppresses gastric cancer by activation of miR-149-3p-Wnt-1 signaling (2016)

18β-glycyrrhetinic acid (GRA) exerts anti-tumor effects on various types of cancer. In the present study, we found that GRA attenuated the severity of gastritis and suppressed gastric tumorigenesis in transgenic mice. We also discovered that miR-149-3p was downregulated in gastric cancer tissues and cell lines as compared to normal gastric tissues and epithelial cells, but was upregulated by GRA. miR-149-3p expression also correlated negatively with lymphnode metastasis. Our functional assays showed that miR-149-3p overexpression inhibited cell proliferation and cell cycle progression while inducing apoptosis, while inhibition of miR-149-3p had the opposite effects. In addition, we identified Wnt-1 as a direct target of miR-149-3p. These data suggest that GRA inhibits the initiation and progression of gastric tumors by ameliorating the inflammatory microenvironment through downregulation of COX-2 expression and by inhibiting Wnt-1 expression through the upregulation of tumor suppressor miR-149-3p. GRA may thus have the potential to serve as a useful therapeutic agent for the prevention and treatment of gastric cancer.
Characterization of Dispersions (1991)

Abstract The methods of pigment dispersion analysis have been reviewed in regard to their application to rubber, plastics, and other vehicle systems. The characteristics of dispersions have been divided into three categories: (1) agglomeration (2) microdispersion (networking) and (3) polymer-phase distribution. Stylus roughness measurements on cut surfaces offer the combination of simplicity and speed of operation with high accuracy and precision for measuring pigment agglomeration in elastomer systems of known composition. This method may also be applied to the surface of thin plastic extrudates. However, optical analyses of thin cryosections are preferred for most plastics or unknown rubber compounds containing high loadings of carbon black. X-radiography is generally preferable for the analysis of inorganic agglomeration in most polymeric vehicle systems. The scanning electron microscope is also applicable for this type of analysis and has the added capability of identifying unknown agglomerates by energy dispersive x-ray analysis. Automated image-analysis techniques may also be utilized in conjunction with microscopical methods for quantifying the agglomeration of most types of pigments. For carbon blacks, the most suitable materials for on-line image analyses with transmitted light are plastics, paints, and inks which contain low black loadings. Higher carbon-black loadings in rubber can be analyzed by incident light using metallographic polishing of sulfur-hardened specimens. The microdispersion of carbon blacks at the primary aggregate level can be measured by means of electrical conductivity. This method is not applicable to inorganic pigments, large-particle-size carbon blacks, or blacks at very high or low loadings. Pigment microdispersion in different vehicle systems may also be assessed by means of scanning electron microscopy of thick cross sections (plasma etched to enhance contrast) or by transmission electron microscopy of thin cryosections. The tendency for the finer pigments to form 3-dimensional network structures in elastomers may also be measured as a function of the augmentation of dynamic modulus from high to low strain amplitudes. Pigment phase distribution in elastomer blends may be studied by scanning electron microscopy or transmission electron microscopy of thin cryosections, in conjunction with a staining or etching procedure to produce contrast between the separate polymer components. Selective staining is applicable to blends of polymers which differ significantly in their relative levels of unsaturation ( e.g. , NR/CIIR). Pyrolytic etching (under vacuum) may be used to produce interzone contrast in blends of polymers which differ significantly in their resistance to thermal degradation ( e.g. , NR/BR, NR/SBR). Pyrolysis GC may be utilized to determine the amount of carbon black in the separate phases of certain elastomer blends. This method is based on the relative intensity of the primary GC peaks for the individual polymers. The chromatographs are obtained from the bound rubber (carbon-polymer gel) that is developed during the mixing of the compound.
Surface Immobilization of Peptides on SiO2 Nanobeads for a Protease Biosensor (2006)

We have been investigating the development of a biosensor that detects medically relevant enzymes. Silica nanobeads were utilized as an optical platform for the development of the protease biosensor. The biosensor uses the chemical transduction method, fluorescence resonance energy transfer, FRET. FRET requires the utilization of special molecular groups termed donor and acceptor, whose combined purpose is to elicit a change in fluorescence in the presence of a given analyte. Donor (AMCA) and acceptor (FITC) fluorophores were covalently attached at either ends of peptide constructs that were synthesized using Fmoc (9-fluorenylmethoxycarbonyl) strategy, a method for solid-phase synthesis of peptides. Two peptide sequences were constructed: CF6 (a positive substrate) and 051-4 (a negative substrate), and were investigated as a prototype trypsin substrate. The peptides were immobilized onto silica nanobeads (15 nm in diameter) using silanization and simple adsorption and then exposed to various concentrations of trypsin. Only the peptides that were immobilized via silanization gave a significant response. When these peptides were cleaved by trypsin, the donor and acceptor fluorophores were separated, resulting in an increase in donor fluorescence. The response time of the sensor was less than 5 minutes and the limit of detection was 13 ng/ml of trypsin in solution.
DnaA-dependent Assembly of the ABC Primosome at the A Site, A Single-stranded DNA Hairpin Containing a DnaA Box (1995)

The ABC primosome is assembled from DnaA, DnaB and DnaC proteins at a stem-and-loop structure containing a dnaA box within its stem (A site), and catalyses primer RNA synthesis for DNA chain elongation. The DnaA protein can bind to the A site and the A-site-DnaA-protein complex can be isolated by gel-filtration chromatography in the absence of nucleotides. Mutations within the dnaA box completely abolish the binding of DnaA protein. Point mutations within the stem region outside the dnaA box also severely reduce the affinity of DnaA protein for the A site. These results indicate that not only the dnaA box but also other nucleotides and/or secondary structure features of the stem are important for proper recognition of the A site by DnaA protein. The preprimosome, which is able to synthesize RNA primers upon addition of primase, can be isolated by gel-filtration chromatography in the presence of ATP or adenosine 5'-[gamma-thio]triphosphate, a non-hydrolyzable analogue of ATP. The preprimosome can translocate along Escherichia coli single-stranded-DNA-binding protein-coated single-stranded DNA, utilizing the energy released by hydrolysis of ATP, as indicated by its helicase activity. dATP, as well as dCTP, can support the helicase activity of the preprimosome to some extent, while they are inert in helicase assays with DnaB protein in the absence of E. coli single-stranded DNA-binding protein. In keeping with this result, the isolated preprimosome, which appears to contain DnaA and DnaB proteins, is capable of hydrolyzing dATP as well as ATP and GTP. In a reconstituted replication assay, addition of excess dATP restores replication activities which have been inhibited by addition of adenosine 5'-[gamma-thio]triphosphate. The ability of dATP to support helicase and replicative activities of the ABC primosome indicates that the formation of the complex somehow modulates the structures of its component(s) so that they can utilize otherwise inert nucleotides. On the basis of these results, a scheme for the assembly of the ABC primosome at the A site is presented.
EXOCELLULAR ALGINIC ACID FROM AZOTOBACTER VINELANDII (1966)

Azotobactervinelandii produces a partly acetylated exocellular polysaccharide which consists mainly of D-mannuronic acid units and a small proportion of L-guluronic acid units. It resembles alginic acid since it contains 4-O-linked mannuronosyl residues and guluronosyl residues which are 4-O- and (or) 5-O-linked. The specific rotation of bacterial sodium alginate is close to that of its algal counterpart, thus suggesting that the glycosidic configurations are similar.
Intermittent chemotherapy can retain the therapeutic potential of anti‐<scp>CD</scp>137 antibody during the late tumor‐bearing state (2014)

Immunomodulating monoclonal antibodies (mAb) can evoke antitumor T-cell responses, which are attenuated by regulatory T cells (Treg) and myeloid-derived suppressor cells (MDSC). Treatment with cyclophosphamide (CP) and gemcitabine (GEM) can mitigate the immunosuppression by Treg and MDSC, respectively. In the current study, we examined the antitumor effects of a combination of local injection with anti-CD137 mAb and intermittent low-dose chemotherapy using CP and GEM in subcutaneously established CT26 colon carcinoma. Although a significant antitumor effect was observed when local anti-CD137 mAb therapy (5 μg) was started early in the tumor-bearing stage (day 10), no therapeutic efficacy was observed when the mAb therapy was started at a later tumor-bearing stage (day 17). Analyses of the tumor-infiltrating immune cells revealed that the number of Gr-1(high/low) CD11b(+) MDSC started to increase 13 days after tumor inoculation, whereas injection with low-dose (50 mg/kg) CP and GEM mitigated this increase. In addition, although intermittent injections with low-dose CP and GEM on days 10 and 18 suppressed tumor growth significantly, additional local injections of anti-CD137 mAb on days 19, 21, and 23 further augmented the therapeutic efficacy. Cytotoxic T lymphocytes reactive to CT26 and a tumor antigen peptide were induced successfully from the spleen cells of tumor-cured or tumor-stable mice. In a bilateral tumor inoculation model, this combination therapy achieved systemic therapeutic effects and suppressed the growth of mAb-untreated tumors. These results suggest that intermittent immunochemotherapy using CP and GEM could retain the therapeutic potential of anti-CD137 mAb that is normally impaired during the late tumor-bearing stage.
Soluble factors from <i>Lactobacillus GG</i> activate MAPKs and induce cytoprotective heat shock proteins in intestinal epithelial cells (2005)

Conditioned media from the probiotic Lactobacillus GG (LGG-CM) induce heat shock protein (Hsp) expression in intestinal epithelial cells. LGG-CM induces both Hsp25 and Hsp72 in a time- and concentration-dependent manner. These effects are mediated by a low-molecular-weight peptide that is acid and heat stable. DNA microarray experiments demonstrate that Hsp72 is one of the most highly upregulated genes in response to LGG-CM treatment. Real-time PCR and electrophoretic mobility shift assay confirm that regulation of Hsp induction is at least in part transcriptional in nature, involving heat shock factor-1. Although Hsps are not induced for hours after exposure, transient exposure to LGG-CM is sufficient to initiate the signal for Hsp induction, suggesting that signal transduction pathways may be involved. Experiments confirm that LGG-CM modulates the activity of certain signaling pathways in intestinal epithelial cells by activating MAP kinases. Inhibitors of p38 and JNK block the expression of Hsp72 normally induced by LGG-CM. Functional studies indicate that LGG-CM treatment of gut epithelial cells protects them from oxidant stress, perhaps by preserving cytoskeletal integrity. By inducing the expression of cytoprotective Hsps in gut epithelial cells, and by activating signal transduction pathways, the peptide product(s) secreted by LGG may contribute to the beneficial clinical effects attributed to this probiotic.
Patulin Inhibition of Mycovirus Replication in Penicillium stoloniferum (1976)

Penicillium stoloniferum NRRL5267 contains two electrophoretically distinct viruses (PsV-F and PsV-S). An in vivo system was developed to test whether a number of fungal metabolites had antiviral properties on PsV-F replication in O.erties on PsV-F replication in P. stoloniferum. Preliminary results indicated that the mycotoxin patulin can block mycovirus replication. Portions of 48 h mycelium were incubated in the presence of varying levels of patulin, and after an additional 48 h incubation, PsV-F content was measured in E260 units by polyacrylamide gel electrophoresis. Patulin at 11, 16 and 20 mug/mg dry wt mycelia blocked PsV-F replication 26, 61 and 71%, respectively, compared with untreated controls. At these levels, host biomass RNA and protein synthesis were minimally affected. No-proliferating fungal mycelium is capable of continued support of PsV-F replication, which is sensitive to patulin. Apparently, inhibitory doses of patulin stimulated PsV-S replication during this 48 h incubation. The preferential action of patulin may arise from metabolite binding to functional enzymes required for virus replication.
A statistical framework for quantifying adaptive behavioural risk for the banking industry (2011)

To remain competitive in the credit industry, financial institutions constantly work to improve their credit scoring systems. This research has developed a new approach for providing early warning of default, using only transaction data for the last month and the 'product' information associated with each transaction. Customers with similar spending patterns are grouped together into clusters and risk is modelled at an individual level within each cluster, allowing customised classifiers to be developed for each cluster. The final model aggregates the customised classifiers using neural network technology, providing a tool which can more accurately predict default than previous methods. It is hoped that this tool will allow banks to use customer behaviour to allow early intervention, averting the escalation of financial problems for their clients.
Collagen Fiber Alignment Does Not Explain Mechanical Anisotropy in Fibroblast Populated Collagen Gels (2007)

Many load-bearing soft tissues exhibit mechanical anisotropy. In order to understand the behavior of natural tissues and to create tissue engineered replacements, quantitative relationships must be developed between the tissue structures and their mechanical behavior. We used a novel collagen gel system to test the hypothesis that collagen fiber alignment is the primary mechanism for the mechanical anisotropy we have reported in structurally anisotropic gels. Loading constraints applied during culture were used to control the structural organization of the collagen fibers of fibroblast populated collagen gels. Gels constrained uniaxially during culture developed fiber alignment and a high degree of mechanical anisotropy, while gels constrained biaxially remained isotropic with randomly distributed collagen fibers. We hypothesized that the mechanical anisotropy that developed in these gels was due primarily to collagen fiber orientation. We tested this hypothesis using two mathematical models that incorporated measured collagen fiber orientations: a structural continuum model that assumes affine fiber kinematics and a network model that allows for nonaffine fiber kinematics. Collagen fiber mechanical properties were determined by fitting biaxial mechanical test data from isotropic collagen gels. The fiber properties of each isotropic gel were then used to predict the biaxial mechanical behavior of paired anisotropic gels. Both models accurately described the isotropic collagen gel behavior. However, the structural continuum model dramatically underestimated the level of mechanical anisotropy in aligned collagen gels despite incorporation of measured fiber orientations; when estimated remodeling-induced changes in collagen fiber length were included, the continuum model slightly overestimated mechanical anisotropy. The network model provided the closest match to experimental data from aligned collagen gels, but still did not fully explain the observed mechanics. Two different modeling approaches showed that the level of collagen fiber alignment in our uniaxially constrained gels cannot explain the high degree of mechanical anisotropy observed in these gels. Our modeling results suggest that remodeling-induced redistribution of collagen fiber lengths, nonaffine fiber kinematics, or some combination of these effects must also be considered in order to explain the dramatic mechanical anisotropy observed in this collagen gel model system.
Effects of varying feeding time on diurnal calving patterns in dairy cows (1985)

Normal calvings among 527 cows in a Ruakura Research Station herd (No. 1) were not evenly distributed throughout the 24 hours. They were most frequent in the early morning (0100 h to 0600 h, 39%) and afternoon (1300 h to 1900 h, 29%). ,This diurnal pattern was consistent between years. Altering feeding time from 0700 h to either 1600 h or 1900 h did not increase the frequency of daylight calvings. Feeding at 1900 h did produce 2 periods of intensive grazing each 24 h instead of only one. If a beneficial change in calving pattern is to be produced, it may be necessary to disrupt the period when most cows rest (0100 h to 0600 h) by feeding at around 0300 h.
Role of insulin-like growth factor-1 in reversing catabolism. (1992)

Journal Article Role of insulin-like growth factor-1 in reversing catabolism Get access D R Clemmons D R Clemmons Search for other works by this author on: Oxford Academic Google Scholar The Journal of Clinical Endocrinology & Metabolism, Volume 75, Issue 5, 1 November 1992, Pages 1183–1185, https://doi.org/10.1210/jcem.75.5.1430076 Published: 01 November 1992
Raloxifene Enhances Material-Level Mechanical Properties of Femoral Cortical and Trabecular Bone (2007)

We have previously documented that raloxifene enhances the mechanical properties of dog vertebrae independent of changes in bone mass, suggesting a positive effect of raloxifene on material-level mechanical properties. The goal of this study was to determine the separate effects of raloxifene on the material-level mechanical properties of trabecular and cortical bone from the femur of beagle dogs. Skeletally mature female beagles (n = 12 per group) were treated daily for 1 yr with oral doses of vehicle or raloxifene (0.50 mg/kg d). Trabecular bone mechanical properties were measured at the femoral neck using reduced platen compression, a method that allows the trabecular bone to be tested without coring specimens. Cortical bone properties were assessed on prismatic beam specimens machined from the femoral diaphysis using both monotonic and dynamic (cyclic relaxation) four-point bending tests. Trabecular bone from raloxifene-treated animals had significantly higher ultimate stress (+130%), modulus (+89%), and toughness (+152%) compared with vehicle-treated animals. Cortical bone from raloxifene-treated animals had significantly greater toughness (+62%) compared with vehicle, primarily as a function of increased postyield displacement (+100%). There was no significant difference between groups in the percentage of stiffness loss during cortical bone cyclic relaxation tests. These results are consistent with previous data from the vertebrae of these same animals, showing raloxifene has positive effects on biomechanical properties independent of changes in bone volume/density. This may help explain how raloxifene reduces osteoporotic fractures despite modest changes in bone mass.
Protein Phosphatase-1 Dephosphorylates the C-terminal Domain of RNA Polymerase-II (2002)

Transcription by RNA polymerase-II (RNAPII) is controlled by multisite phosphorylation of the heptapeptide repeats in the C-terminal domain (CTD) of the largest subunit. Phosphorylation of CTD is mediated by the cyclin-dependent protein kinases Cdk7 and Cdk9, whereas protein serine/threonine phosphatase FCP1 dephosphorylates CTD. We have recently reported that human immunodeficiency virus-1 (HIV-1) transcription is positively regulated by protein phosphatase-1 (PP1) and that PP1 dephosphorylates recombinant CTD. Here, we provide further evidence that PP1 can dephosphorylate RNAPII CTD. In vitro, PP1 dephosphorylated recombinant CTD as well as purified RNAPII CTD. HeLa nuclear extracts were found to contain a species of PP1 that dephosphorylates both serine 2 and serine 5 of the heptapeptide repeats. In nuclear extracts, PP1 and FCP1 contributed roughly equally to the dephosphorylation of serine 2. PP1 co-purified with RNAPII by gel filtration and associated with RNAPII on immunoaffinity columns prepared with anti-CTD antibodies. In cultured cells treated with CTD kinase inhibitors, the dephosphorylation of RNAPII on serine 2 was inhibited by 45% by preincubation with okadaic acid, which inhibits phosphatases of PPP family, including PP1 but not FCP1. Our data demonstrate that RNAPII CTD is dephosphorylated by PP1 in vitro and by PPP-type phosphatase, distinct from FCP1, in vivo.