gebhart/patrepeval huggingface dataset:
Synthesis and Application of Fluorescein-Labeled Pluronic Block Copolymers to the Study of Polymer−Surface Interactions (2000)

We present a novel methodology for the conjugation of Pluronic poly(ethylene oxide)−poly(propylene oxide)−poly(ethylene oxide) block copolymers with a fluorescein derivative, 5-(4,6-dichlorotriazinyl) aminofluorescein (5-DTAF), at room temperature under aqueous conditions. Two Pluronic block copolymers, F68 with molecular weight (MW) 8400 and P105 with MW 6500, were examined. The labeled block copolymers exhibited maximum absorbance at 498 nm, peak fluorescence at 516 nm, and a marked reduction in both absorbance and fluorescence at acidic pH below 7. Flow cytometry was employed to quantify the real-time adsorption kinetics of labeled block copolymers to two types of surfaces: polystyrene microspheres and blood cells, specifically platelets. This methodology allowed detection of Pluronics at low solution concentrations down to 1 μM. In the case of labeled Pluronic F68 and P105 binding to polystyrene beads, a rapid time-dependent adsorption kinetics was observed with 80% adsorption occurring within 30 s and saturation in 2 min. The concentration-dependent adsorption profile for Pluronic F68 binding to polystyrene beads was similar to that of P105, with increasing binding in the range from 1 to 25 μM and saturation at higher concentrations. Surface modification of the polystyrene beads by carboxylation dramatically reduced the binding of both Pluronic F68 and P105. In experiments that examined Pluronic interaction with blood platelets, we observed that Pluronics not only bind the platelets in a dose-dependent fashion but also bind soluble macromolecules in blood plasma. Overall, the labeled block copolymers synthesized in this study were found to exhibit the fluorescence characteristics of the unconjugated 5-DTAF and the binding characteristics of unlabeled Pluronics. Such an approach of labeling hydroxyl-terminated polymers with fluorescein and applying flow cytometry could be used to probe polymer−surface interactions in a variety of chemical and biological systems.
Embryonic Stem Cells for Myocardial Repair (2007)

Cell replacement therapy is emerging as a novel therapuetic paradigm for restoration of the myocardial electromechanical properties. This innovative strategy has been significantly hampered by the paucity of cell sources for human heart cells. The recent establishment of the human embryonic stem cell (hESC) lines may provide a possible solution for this cellsourcing problem. These unique pluripotent cell lines can be propagated in the undifferentiated state in culture and coaxed to differentiate into cell derivatives of all three germ layers, including cardiomyocytes. This chapter will focus on the derivation and properties of hESC and their cardiomyocyte cell derivatives. The potential applications of this unique differentiating system in several research areas will be discussed, with special emphasis on the steps required to fully harness their unique potential in the emerging field of cardiovascular regenerative medicine.
Animal and human studies with the mitochondria‐targeted antioxidant MitoQ (2010)

As mitochondrial oxidative damage contributes to a wide range of human diseases, antioxidants designed to be accumulated by mitochondria in vivo have been developed. The most extensively studied of these mitochondria-targeted antioxidants is MitoQ, which contains the antioxidant quinone moiety covalently attached to a lipophilic triphenylphosphonium cation. MitoQ has now been used in a range of in vivo studies in rats and mice and in two phase II human trials. Here, we review what has been learned from these animal and human studies with MitoQ.
Metal Substitutions and Inhibition of Thermolysin: Spectra of the Cobalt Enzyme (1974)

Removal of zinc from thermolysin results in an inactive, metal-free apoenzyme.Znz+, Co2+, and Mn2+, when added in stoichiometric amounts, restore 100, ZOO, and 10% of the activity of the native enzyme.Fez+ in high molar excess restores about 60% of the native activity.Zinc is bound much more firmly than is cobalt, as shown by mutual displacement and the resultant enzymatic activities.Zinc in excess of that required to induce activity inhibits the enzyme, seemingly by binding to a specific, inhibitory site.The zinc atom
Operational remote sensing of tropospheric aerosol over land from EOS moderate resolution imaging spectroradiometer (1997)

Daily distribution of the aerosol optical thickness and columnar mass concentration will be derived over the continents, from the EOS moderate resolution imaging spectroradiometer (MODIS) using dark land targets. Dark land covers are mainly vegetated areas and dark soils observed in the red and blue channels; therefore the method will be limited to the moist parts of the continents (excluding water and ice cover). After the launch of MODIS the distribution of elevated aerosol concentrations, for example, biomass burning in the tropics or urban industrial aerosol in the midlatitudes, will be continuously monitored. The algorithm takes advantage of the MODIS wide spectral range and high spatial resolution and the strong spectral dependence of the aerosol opacity for most aerosol types that result in low optical thickness in the mid‐IR (2.1 and 3.8 μm). The main steps of the algorithm are (1) identification of dark pixels in the mid‐IR; (2) estimation of their reflectance at 0.47 and 0.66 μm; and (3) derivation of the optical thickness and mass concentration of the accumulation mode from the detected radiance. To differentiate between dust and aerosol dominated by accumulation mode particles, for example, smoke or sulfates, ratios of the aerosol path radiance at 0.47 and 0.66 μm are used. New dynamic aerosol models for biomass burning aerosol, dust and aerosol from industrial/urban origin, are used to determine the aerosol optical properties used in the algorithm. The error in the retrieved aerosol optical thicknesses, τ a is expected to be Δτ a = 0.05±0.2τ a . Daily values are stored on a resolution of 10×10 pixels (1 km nadir resolution). Weighted and gridded 8‐day and monthly composites of the optical thickness, the aerosol mass concentration and spectral radiative forcing are generated for selected scattering angles to increase the accuracy. The daily aerosol information over land and oceans [ Tanré et al ., this issue], combined with continuous aerosol remote sensing from the ground, will be used to study aerosol climatology, to monitor the sources and sinks of specific aerosol types, and to study the interaction of aerosol with water vapor and clouds and their radiative forcing of climate. The aerosol information will also be used for atmospheric corrections of remotely sensed surface reflectance. In this paper, examples of applications and validations are provided.
Absence of vaccine-enhanced RSV disease and changes in pulmonary dendritic cells with adenovirus-based RSV vaccine (2011)

The development of a vaccine against respiratory syncytial virus (RSV) has been hampered by the risk for vaccine-enhanced RSV pulmonary disease induced by immunization with formalin-inactivated RSV (FIRSV). This study focuses on the evaluation of vaccine-enhanced pulmonary disease following immunization with AdF.RGD, an integrin-targeted adenovirus vector that expresses the RSV F protein and includes an RGD (Arg-Gly-Asp) motif. Immunization of BALB/c mice with AdF.RGD, resulted in anti-RSV protective immunity and induced increased RSV-specific IFN-γ T cell responses compared to FIRSV. RSV infection 5 wk after immunization with FIRSV induced pulmonary inflammatory responses in the lung, that was not observed with AdF.RGD. Additionally, In the FIRSV-immunized mice following infection with RSV, pulmonary DC increased and Tregs decreased. This suggests that distinct responses of pulmonary DC and Tregs are a features of vaccine-enhanced RSV disease and that immunization with an RGD-modified Ad vaccine does not trigger vaccine-enhanced disease.
Nucleotide-sequence-specific de novo methylation in a somatic murine cell line. (1989)

DNA fragments encoding the mouse steroid 21-hydroxylase (C21 or Cyp21A1) gene are de novo methylated when introduced into the mouse adrenocortical tumor cell line Y1 by DNA-mediated gene transfer. Although CCGG sequences within the C21 gene are de novo methylated, CCGG sites within flanking vector sequences, other mammalian gene sequences driven by the C21 promoter, and the neomycin-resistance gene, which was cotransfected with the C21 gene, do not become methylated. At least two separate signals for de novo methylation are encoded within the gene since three fragments derived from the C21 gene were methylated de novo. Specific de novo methylation of C21-derived sequences does not occur in L cells or Y1 kin8 cells; this suggests that the cellular factors needed for de novo methylation of the C21 gene are not ubiquitous. Most DNA sequences are not de novo methylated when introduced into somatic cells and DNA sequences other than the C21 gene are not de novo methylated when introduced into Y1 cells. Several groups have suggested that de novo methylation occurs in early embryonic cells and that somatic cells strictly maintain their methylation pattern by a semiconservative methyltransferase. Our results suggest that de novo methylation of specific nucleotide sequences can occur in some mammalian somatic cells.
PET-CT image registration in the chest using free-form deformations (2003)

We have implemented and validated an algorithm for three-dimensional positron emission tomography transmission-to-computed tomography registration in the chest, using mutual information as a similarity criterion. Inherent differences in the two imaging protocols produce significant nonrigid motion between the two acquisitions. A rigid body deformation combined with localized cubic B-splines is used to capture this motion. The deformation is defined on a regular grid and is parameterized by potentially several thousand coefficients. Together with a spline-based continuous representation of images and Parzen histogram estimates, our deformation model allows closed-form expressions for the criterion and its gradient. A limited-memory quasi-Newton optimization algorithm is used in a hierarchical multiresolution framework to automatically align the images. To characterize the performance of the method, 27 scans from patients involved in routine lung cancer staging were used in a validation study. The registrations were assessed visually by two expert observers in specific anatomic locations using a split window validation technique. The visually reported errors are in the 0- to 6-mm range and the average computation time is 100 min on a moderate-performance workstation.
Multiple Interactions of HIV-I Tat Protein with Size-defined Heparin Oligosaccharides (1999)

Tat protein, a transactivating factor of the human immunodeficiency virus type I, acts also as an extracellular molecule. Heparin affects the bioavailability and biological activity of extracellular Tat (Rusnati, M., Coltrini, D., Oreste, P., Zoppetti, G., Albini, A., Noonan, D., D'Adda di Fagagna, F., Giacca, M., and Presta, M. (1997) J. Biol. Chem. 272, 11313-11320). Here, a series of homogeneously sized, (3)H-labeled heparin fragments were evaluated for their capacity to bind to free glutathione S-transferase (GST)-Tat protein and to immobilized GST-Tat. Hexasaccharides represent the minimum sized heparin fragments able to interact with GST-Tat at physiological ionic strength. Also, the affinity of binding increases with increasing the molecular size of the oligosaccharides, with large fragments (>/=18 saccharides) approaching the affinity of full-size heparin. 6-Mer heparin binds GST-Tat with a dissociation constant (K(d)) equal to 0.7 +/- 0.4 microM and a molar oligosaccharide:GST-Tat ratio of about 1:1. Interaction of GST-Tat with 22-mer or full-size heparin is consistent instead with two-component binding. At subsaturating concentrations, a single molecule of heparin interacts with 4-6 molecules of GST-Tat with high affinity (K(d) values in the nanomolar range of concentration); at saturating concentrations, heparin binds GST-Tat with lower affinity (K(d) values in the micromolar range of concentration) and a molar oligosaccharide:GST-Tat ratio of about 1:1. In agreement with the binding data, a positive correlation exists between the size of heparin oligosaccharides and their capacity to inhibit cell internalization, long terminal repeat-transactivating activity of extracellular Tat in HL3T1 cells, and its mitogenic activity in murine adenocarcinoma T53 Tat-less cells. The data demonstrate that the modality of heparin-Tat interaction is strongly affected by the size of the saccharide chain. The possibility of establishing multiple interactions increases the affinity of large heparin fragments for Tat protein and the capacity of the glycosaminoglycan to modulate the biological activity of extracellular Tat.
Metabolic Network Analysis of Streptomyces tenebrarius , a Streptomyces Species with an Active Entner-Doudoroff Pathway (2005)

Streptomyces tenebrarius is an industrially important microorganism, producing an antibiotic complex that mainly consists of the aminoglycosides apramycin, tobramycin carbamate, and kanamycin B carbamate. When S. tenebrarius is used for industrial tobramycin production, kanamycin B carbamate is an unwanted by-product. The two compounds differ only by one hydroxyl group, which is present in kanamycin carbamate but is reduced during biosynthesis of tobramycin. (13)C metabolic flux analysis was used for elucidating connections between the primary carbon metabolism and the composition of the antibiotic complex. Metabolic flux maps were constructed for the cells grown on minimal medium with glucose or with a glucose-glycerol mixture as the carbon source. The addition of glycerol, which is more reduced than glucose, led to a three-times-greater reduction of the kanamycin portion of the antibiotic complex. The labeling indicated an active Entner-Doudoroff (ED) pathway, which was previously considered to be nonfunctional in Streptomyces. The activity of the pentose phosphate (PP) pathway was low (10 to 20% of the glucose uptake rate). The fluxes through Embden-Meyerhof-Parnas (EMP) and ED pathways were almost evenly distributed during the exponential growth on glucose. During the transition from growth phase to production phase, a metabolic shift was observed, characterized by a decreased flux through the ED pathway and increased fluxes through the EMP and PP pathways. Higher specific NADH and NADPH production rates were calculated in the cultivation on glucose-glycerol, which was associated with a lower percentage of nonreduced antibiotic kanamycin B carbamate.
Wee1 controls genomic stability during replication by regulating the Mus81-Eme1 endonuclease (2011)

Correct replication of the genome and protection of its integrity are essential for cell survival. In a high-throughput screen studying H2AX phosphorylation, we identified Wee1 as a regulator of genomic stability. Wee1 down-regulation not only induced H2AX phosphorylation but also triggered a general deoxyribonucleic acid (DNA) damage response (DDR) and caused a block in DNA replication, resulting in accumulation of cells in S phase. Wee1-deficient cells showed a decrease in replication fork speed, demonstrating the involvement of Wee1 in DNA replication. Inhibiting Wee1 in cells treated with short treatment of hydroxyurea enhanced the DDR, which suggests that Wee1 specifically protects the stability of stalled replication forks. Notably, the DDR induced by depletion of Wee1 critically depends on the Mus81-Eme1 endonuclease, and we found that codepletion of Mus81 and Wee1 abrogated the S phase delay. Importantly, Wee1 and Mus81 interact in vivo, suggesting direct regulation. Altogether, these results demonstrate a novel role of Wee1 in controlling Mus81 and DNA replication in human cells.
Iron Compounds for Food Fortification: Guidelines for Latin America and the Caribbean 2002 (2002)

Iron deficiency is the most prevalent micronutrient deficiency in the world today. It affects millions of individuals throughout the life cycle, particularly infants and pregnant women, but also older children, adolescents, and women of reproductive age. Living organisms require iron for their cells to function normally. Iron is needed for the development of vital tissues - including the brain - and for transporting and storing oxygen in hemoglobin and muscle myoglobin. Iron deficiency anemia is the severe form of iron deficiency. It can result in low resistance to infection, impaired psychomotor development, and cognitive function in children, poor academic performance, as well as fatigue and poor physical/work endurance. In addition to the above, iron deficiency anemia in pregnancy can result in a low-birth-weight infant. Three intervention strategies are available to prevent iron deficiency and, therefore, iron deficiency anemia. These are supplementation, dietary diversification, and both targeted and untargeted food fortification. Nineteen countries in the Americas have a national food fortification program, in which iron and other micronutrients are added to at least one widely consumed food that is often wheat and/or corn flour. Table 1 shows the iron compounds added to the flours. Each iron compound has different properties and characteristics, which influence its bioavailability, as is discussed later. A number of countries also currently implement fortification programs targeted to specific groups of the population, primarily infants and young children age 6 to 24 months and school-age children.
Case Study of the Effectiveness of Nitrogen Foam and Water-Zone Diverting Agents in Multistage Matrix Acid Treatments (1992)

Summary Several oil wells producing water have been stimulated successfully with multistages of mud acid, nitrogen foam, and water-zone diverting agents. This procedure has improved well performance significantly while having little or no effect on post-treatment water production. The diverters’ effectiveness was analyzed with radioactive tracers, gamma spectroscopy logs, and surface pressure equipment. Results indicate that water-zone diverters and nitrogen foam are effective diverters when used in matrix acid stimulations. Case histories and associated data are included in this paper.
DNA immunization as an efficient strategy for vaccination. (2009)

The field of vaccinology provides excellent promises to control different infectious and non-infectious diseases. Genetic immunization as a new tool in this area by using naked DNA has been shown to induce humoral as well as cellular immune responses with high efficiency. This demonstrates the enormous potential of this strategy for vaccination purposes. DNA vaccines have been widely used to develop vaccines against various pathogens as well as cancer, autoimmune diseases and allergy. However, despite their successful application in many pre-clinical disease models, their potency in human clinical trials has been insufficient to provide protective immunity. Several strategies have been applied to increase the potency of DNA vaccine. Among these strategies, the linkage of antigens to Heat Shock Proteins (HSPs) and the utilization of different delivery systems have been demonstrated as efficient approaches for increasing the potency of DNA vaccines. The uptake of DNA plasmids by cells upon injection is inefficient. Two basic delivery approaches including physical delivery to achieve higher levels of antigen production and formulation with microparticles to target Antigen-Presenting Cells (APCs) are effective in animal models. Alternatively, different regimens called prime-boost vaccination are also effective. In this regimen, naked DNA is utilized to prime the immune system and either recombinant viral vector or purified recombinant protein with proper adjuvant is used for boosting. In this review, we discuss recent advances in upgrading the efficiency of DNA vaccination in animal models.
Optimizing particle collection for enhanced surface-based biosensors (2003)

In this article, electrode structures that combine dielectrophoretic effects with electrohydrodynamic fluid flow to concentrate particles on active sensor surfaces were presented. To optimize the collection effect on a surface, a novel electrode configuration called zipper electrodes has been developed. The local enrichment effect of these electrodes is such that particles at local concentration of 5/spl times/10/sup 3/ spores/mL can be collected using a single electrode pad. The fluid flow induced in the bulk flow is an efficient mechanism especially for very small particles, since the dielectrophoretic forces working on these particles are normally very small and do not penetrate the liquid as far as the vortex induced by combined dielectrophoresis/fluid flow does. The bulk flow makes it also a very versatile method that can extract a wide range of particles out of the liquid.
Dried Blood Spots - Preparing and Processing for Use in Immunoassays and in Molecular Techniques (2015)

The idea of collecting blood on a paper card and subsequently using the dried blood spots (DBS) for diagnostic purposes originated a century ago. Since then, DBS testing for decades has remained predominantly focused on the diagnosis of infectious diseases especially in resource-limited settings or the systematic screening of newborns for inherited metabolic disorders and only recently have a variety of new and innovative DBS applications begun to emerge. For many years, pre-analytical variables were only inappropriately considered in the field of DBS testing and even today, with the exception of newborn screening, the entire pre-analytical phase, which comprises the preparation and processing of DBS for their final analysis has not been standardized. Given this background, a comprehensive step-by-step protocol, which covers al the essential phases, is proposed, i.e., collection of blood; preparation of blood spots; drying of blood spots; storage and transportation of DBS; elution of DBS, and finally analyses of DBS eluates. The effectiveness of this protocol was first evaluated with 1,762 coupled serum/DBS pairs for detecting markers of hepatitis B virus, hepatitis C virus, and human immunodeficiency virus infections on an automated analytical platform. In a second step, the protocol was utilized during a pilot study, which was conducted on active drug users in the German cities of Berlin and Essen.
Single Image Dehazing by Multi-Scale Fusion (2013)

Haze is an atmospheric phenomenon that significantly degrades the visibility of outdoor scenes. This is mainly due to the atmosphere particles that absorb and scatter the light. This paper introduces a novel single image approach that enhances the visibility of such degraded images. Our method is a fusion-based strategy that derives from two original hazy image inputs by applying a white balance and a contrast enhancing procedure. To blend effectively the information of the derived inputs to preserve the regions with good visibility, we filter their important features by computing three measures (weight maps): luminance, chromaticity, and saliency. To minimize artifacts introduced by the weight maps, our approach is designed in a multiscale fashion, using a Laplacian pyramid representation. We are the first to demonstrate the utility and effectiveness of a fusion-based technique for dehazing based on a single degraded image. The method performs in a per-pixel fashion, which is straightforward to implement. The experimental results demonstrate that the method yields results comparative to and even better than the more complex state-of-the-art techniques, having the advantage of being appropriate for real-time applications.