gebhart/patrepeval huggingface dataset:
Diffusion Tensor MR Imaging and Fiber Tractography: Technical Considerations (2008)

This second article of the 2-part review builds on the theoretic background provided by the first article to cover the major technical factors that affect image quality in diffusion imaging, including the acquisition sequence, magnet field strength, gradient amplitude, and slew rate as well as multichannel radio-frequency coils and parallel imaging. The sources of many common diffusion image artifacts are also explored in detail. The emphasis is on optimizing these technical factors for state-of-the-art diffusion-weighted imaging and diffusion tensor imaging (DTI) based on the best available evidence in the literature. An overview of current methods for quantitative analysis of DTI data and fiber tractography in clinical research is also provided.
Macrophages Are Necessary for Maximal Nuclear Factor- κ B Activation in Response to Endotoxin (2002)

To define the role of macrophages in regulating the lung's response to Escherichia coli endotoxin (lipopolysaccharide [LPS]), depletion of macrophages was accomplished by administration of dichloromethylene diphosphonate (clodronate) delivered via intratracheal (i.t.) and/or intravenous (i.v.) routes. Clodronate reduced the number of macrophages in lung lavage 48 h after either i.t. or i.v. administration, but combined i.t. + i.v. clodronate achieved the most profound depletion (90%). Although i.t. clodronate alone had little effect on the evolution of lung inflammation, combined i.t. + i.v. clodronate treatment decreased neutrophilic alveolitis 4 h after exposure to aerosolized LPS by 80% compared with mice treated with empty liposomes. This decrease was associated with impaired activation of nuclear factor (NF)-kappa B and lower concentrations of tumor necrosis factor (TNF)-alpha in lung lavage fluid. Combined i.t. + i.v. clodronate markedly reduced lung NF-kappa B activation and the intensity of neutrophilic alveolitis after intraperitoneal (i.p.) LPS; however, i.v. clodronate alone had no effect on NF-kappa B activation in either liver or lung tissue or the development of neutrophilic alveolitis. We conclude that generalized macrophage depletion reduces NF-kappa B activation, generation of cytokines, and neutrophilic lung inflammation in response to gram negative bacterial endotoxin. These findings define the role of the macrophage as a critical component for initiation of the NF-kappa B-dependent innate immune response.
Magnetization reversal induced by in-plane current in Ta/CoFeB/MgO structures with perpendicular magnetic easy axis (2014)

We investigate in-plane current-induced magnetization reversal under an in-plane magnetic field in Hall bar shaped devices composed of Ta/CoFeB/MgO structures with perpendicular magnetic easy axis. The observed relationship between the directions of current and magnetization switching and Ta thickness dependence of magnetization switching current are accordance with those for magnetization reversal by spin transfer torque originated from the spin Hall effect in the Ta layer.
Manipulations of cholinesterase gene expression modulate murine megakaryocytopoiesis in vitro. (1990)

Megakaryocytopoiesis was selectively inhibited in cultured murine bone marrow cells by a 15-mer oligodeoxynucleotide complementary to the initiator AUG region in butyrylcholinesterase mRNA. Furthermore, conditioned medium from Xenopus oocytes producing recombinant butyrylcholinesterase stimulated megakaryocytopoiesis. These observations implicate butyrylcholinesterase in megakaryocytopoiesis and suggest application of oligodeoxynucleotides for modulating bone marrow development.
MICROFLUIDIC LIPOSOME GENERATION FROM MONODISPERSE DROPLET EMULSION—TOWARDS THE REALIZATION OF ARTIFICIAL CELLS (2003)

We report here for the first time that a hydrodynamically actuated microfluidic device, capable of precisely controlling the liposome self assembly process, has successfully synthesized liposome of defined size with potentially perfect encapsulation efficiency. This microfluidic platform will enable the control of concentrations of solvents, lipids, co-block polymers to alter size, shape, ionic strengths and composition of vesicle membrane to create a artificial cells with desired functional properties. The emulsion generation microfluidic device consists of micro channels with inlet flow rates controlled by the Harvard 2000 pumps. The micro channels are fabricated by molding PDMS in SU-8 mold[1] and is designed to control the local shear forces between the co-flow of organic and aqueous boundary interface to generate monodispersed droplet emulsions. To generate liposomes, naphthol Green dissolved in water and dioleoylphosphatidylcholine with fluorescently labeled dioleoylphosphatidylethanolamine dissolved in ether were infused into the channel (Fig. 1A). Water in lipid emulsions were generated as droplets at the ladder end of the channel (Fig. 1B).
A real-time procedural shading system for programmable graphics hardware (2001)

Real-time graphics hardware is becoming programmable, but this programmable hardware is complex and difficult to use given current APIs. Higher-level abstractions would both increase programmer productivity and make programs more portable. However, it is challenging to raise the abstraction level while still providing high performance. We have developed a real-time procedural shading language system designed to achieve this goal.Our system is organized around multiple computation frequencies. For example, computations may be associated with vertices or with fragments/pixels. Our system's shading language provides a unified interface that allows a single procedure to include operations from more than one computation frequency.Internally, our system virtualizes limited hardware resources to allow for arbitrarily-complex computations. We map operations to graphics hardware if possible, or to the host CPU as a last resort. This mapping is performed by compiler back-end modules associated with each computation frequency. Our system can map vertex operations to either programmable vertex hardware or to the host CPU, and can map fragment operations to either programmable fragment hardware or to multipass OpenGL. By carefully designing all the components of the system, we are able to generate highly-optimized code. We demonstrate our system running in real-time on a variety of hardware.
Significant inhibition by the flavonoid antioxidant silymarin against 12-O-tetradecanoylphorbol 13-acetate-caused modulation of antioxidant and inflammatory enzymes, and cyclooxygenase 2 and interleukin-1? expression in SENCAR mouse epidermis: Implications in the prevention of stage I tumor promotion (1999)

The flavonoid antioxidant silymarin is used clinically in Europe and Asia for the treatment of liver diseases and is sold in the United States and Europe as a dietary supplement. Recently we showed that silymarin possesses exceptionally high cancer-preventive effects in different mouse skin carcinogenesis models and affords strong anticancer effects in human skin, cervical, prostate, and breast carcinoma cells. More recently, we showed that the anti-tumor-promoting effect of silymarin is primarily targeted against stage I tumor promotion in mouse skin (Cancer Res 1999;59:622-632). Based on this recent study, in this report, further investigations were made to identify and define the biochemical and molecular mechanisms of silymarin's effect during stage I tumor promotion in mouse skin. A single topical application of silymarin at 3-, 6-, and 9-mg doses onto SENCAR mouse skin followed 30 min later with 12-O-tetradecanoylphorbol 13-acetate (TPA) at a 3-microg dose resulted in a 76-95% inhibition (P < 0.001) of TPA-caused skin edema. Similarly, these doses of silymarin also showed 39-90%, 29-85%, and 15-67% protection (P < 0.05 or 0.001), against TPA-caused depletion of epidermal superoxide dismutase, catalase, and glutathione peroxidase activity, respectively. Pretreatment of mice with silymarin also produced highly significant inhibition of TPA-caused induction of epidermal lipid peroxidation (47-66% inhibition, P < 0.001) and myeloperoxidase activity (56-100% inhibition, P < 0.001). In additional studies assessing the effect of silymarin on arachidonic acid metabolism pathways involving lipoxygenase and cyclooxygenase (COX), similar doses of silymarin showed highly significant inhibition of TPA-caused induction of epidermal lipoxygenase (49-77% inhibition, P < 0.001) and COX (35-64% inhibition, P < 0.01 or 0.001) activity. Western immunoblot analysis showed that the observed effect of silymarin on COX activity was due to inhibition of TPA-inducible COX-2 with no change in constitutive COX-1 protein levels. In other studies, silymarin also showed dose-dependent inhibition of TPA-caused induction of epidermal interleukin 1alpha (IL-1alpha) protein (39-72% inhibition, P < 0.005 or 0.001) and mRNA expression. Taken together, the results from these biochemical and molecular studies further substantiate our recent observation of silymarin's anti-tumor-promoting effects primarily at stage I tumor promotion. Furthermore, the observed inhibitory effects of silymarin on COX-2 and IL-1alpha should be further explored to develop preventive strategies against those cancers in which these molecular targets play one of the causative roles, such as non-melanoma skin, colon, and breast cancers in humans.
On the Metabolism of Prostaglandins E1 and E2 in Man (1971)

7α-Hydroxy-5,11-diketotetranor-prosta-1,16-dioic acid was identified as the major urinary metabolite after intravenous administration of tritium-labeled prostaglandin E2, prostaglandin E1, 11α-hydroxy-9,15-diketoprosta-5,13-dienoic acid, 11α-hydroxy-9,15-diketoprost-5-enoic acid, and 11α-hydroxy-9,15-diketoprostanoic acid to male and female subjects. Injected prostaglandin E2 was rapidly converted initially into 11α-hydroxy-9, 15-diketoprost-5-enoic acid. Kinetic parameters for these two compounds are given. A method for quantitative determination of the major urinary metabolite was developed. In three subjects, 7, 16, and 27 µg/24 hours were excreted.
Glycogen Synthase Kinase-3 (GSK3) in Psychiatric Diseases and Therapeutic Interventions (2006)

Glycogen synthase kinase-3 (GSK3) has recently been linked to mood disorders and schizophrenia, and the neurotransmitter systems and therapeutic treatments associated with these diseases. GSK3 is a widely influential enzyme that is capable of phosphorylating, and thereby regulating, over forty known substrates. Four mechanisms regulating GSK3 (phosphorylation, protein complexes, localization, and substrate phosphorylation) combine to provide substrate-specific regulation of the actions of GSK3. Several intracellular signaling cascades converge on GSK3 to modulate its activity, and several neurotransmitter systems also regulate GSK3, including serotonergic, dopaminergic, cholinergic, and glutamatergic systems. Because of changes in these neurotransmitter systems and the actions of therapeutic drugs, GSK3 has been linked to the mood disorders, bipolar disorder and depression, and to schizophrenia. Inhibition of GSK3 may be an important therapeutic target of mood stabilizers, and regulation of GSK3 may be involved in the therapeutic effects of other drugs used in psychiatry. Dysregulated GSK3 in bipolar disorder, depression, and schizophrenia could have multiple effects that could impair neural plasticity, such as modulation of neuronal architecture, neurogenesis, gene expression, and the ability of neurons to respond to stressful, potentially lethal, conditions. In part because of these key actions of GSK3 and its associations with mood disorders and schizophrenia, much research is currently being devoted to identifying new selective inhibitors of GSK3.
Novel glycogen synthase kinase 3 and ubiquitination pathways in progressive myoclonus epilepsy (2005)

Lafora progressive myoclonus epilepsy, caused by defective laforin or malin, insidiously present in normal teenagers with cognitive decline, followed by rapidly intractable epilepsy, dementia and death. Pathology reveals neurodegeneration with neurofibrillary tangle formation and Lafora bodies (LBs). LBs are deposits of starch-like polyglucosans, insufficiently branched and hence insoluble glycogen molecules resulting from glycogen synthase (GS) overactivity relative to glycogen branching enzyme activity. We previously made the unexpected observation that laforin, in the absence of which polyglucosans accumulate, specifically binds polyglucosans. This suggested that laforin's role is to detect polyglucosan appearances during glycogen synthesis and to initiate mechanisms to downregulate GS. Glycogen synthase kinase 3 (GSK3) is the principal inhibitor of GS. Dephosphorylation of GSK3 at Ser 9 activates GSK3 to inhibit GS through phosphorylation at multiple sites. Glucose-6-phosphate is a potent allosteric activator of GS. Glucose-6-phosphate levels are high when the amount of glucose increases and its activation of GS overrides any phospho-inhibition. Here, we show that laforin is a GSK3 Ser 9 phosphatase, and therefore capable of inactivating GS through GSK3. We also show that laforin interacts with malin and that malin is an E3 ubiquitin ligase that binds GS. We propose that laforin, in response to appearance of polyglucosans, directs two negative feedback pathways: polyglucosan-laforin-GSK3-GS to inhibit GS activity and polyglucosan-laforin-malin-GS to remove GS through proteasomal degradation.
Ageing and telomeres: a study into organ- and gender-specific telomere shortening (2003)

Telomeres, the non-coding sequences at the ends of chromosomes, in the absence of telomerase, progressively shorten with each cell division. Shortening of telomeres can induce cell cycle arrest and apoptosis. The aim of this study was to investigate age- and gender-related changes in telomere length in the rat and to detect possible tissue- specific rates of telomere shortening. Changes with age in telomere lengths were assessed by Southern blotting in the kidney, pancreas, liver, lung and brain of male and female rats. We determined the percentage of telomeres in various molecular size regions rather than measuring the average telomere length. The latter was unable to detect telomere shortening in the tissues. The percentage of short telomeres increased with age in the kidney, liver, pancreas and lung of both males and females, but not in the brain. Males had shorter telomeres than females in all organs analysed except the brain, where the lengths were similar. These findings indicate that telomeres shorten in the rat kidney, liver, pancreas and the lung in an age-dependent manner. These data also provide a novel mechanism for the gender-related differences in lifespan and suggest a tissue-specific regulation of telomere length during development and ageing in the rat.
Recognition of defects of the surfscan installation TENCOR 7600 depending on the situation and size of the defect (1998)

The Surfscan installation is used to localize defects or irregularities on the surface of wafers. To simplify, particles with an expansion of &gt;= 0.3 micrometers are recognized as a defect. The measuring principle of the installation is based on the comparisons of periodical structures. This means that only components of the same type are allowed on the wafer. A laser beam scans the surface of the wafer in a grid pattern, whereby the light is scattered on the structures and particles are registered by a photo- multiplier which is rotated by 90 degree against the incoming laser beam. As a rule these defects are not altogether spherical-symmetrical, so that the orientation and structure of the defect affect the intensity of the light scatter. As a defect is only illuminated from one side during measurement, various intensity values can be achieved by rotating the wafer. Therefore measurements with various wafer orientations were taken to assure that a possible defect is illuminated from all four sides. By using various intensity values information can be gained about the form, size and situation of a defect. Further the information can be used to obtain an optimal recipe design of a measurement procedure, and to better define the capture rate of the installation. This results in a more effective use of the installation.
Improved Version of the Red Fluorescent Protein (drFP583/DsRed/RFP) (2002)

GFP has established itself as a highly useful tool throughout many areas of modern biology. Recently, the novel fluorescent protein drFP583, also termed DsRed or RFP, was clonedfrom a coral of the Discosoma genus. The protein is only weakly homologous to GFP and has a red emission spectrum, which makes drFP583 an attractive candidate for in vivo double labeling together with GFP variants. However, wildtype drFP583 has several drawbacks, including inefficient folding of the protein, extremely slow maturation of the chromophore, and tetramerization even in dilute solutions. Here we report on important improvements to this reporter that lead to higher levels of fluorescent drFP583 species in the cell. We further characterized our best mutant for applications in yeast and mammalian cell biology.
Integrated Clinical Decision Support Using an Object-Oriented Database Management System (1993)

Clinical decision support systems assist in diagnosis, alert to abnormal conditions, and manage patient data. Such systems tend to emphasize one of these features at the expense of the others and tend to be developed on an ad hoc basis. In this work, a technique is developed for creating an integrated clinical decision support system wholly within a general-purpose object-oriented database management system. The diagnostic and alerting requirements are accomplished with encapsulated methods and a novel use of the object-oriented database management class-hierarchy structure. The patient data management requirement is satisfied by the normal data management capabilities of the object-oriented DBMS.
Influence of Extrusion Processing on Procyanidin Composition and Total Anthocyanin Contents of Blueberry Pomace (2009)

Blueberry juice processing by-products are a rich source of procyanidins, which comprise a group of compounds shown to possess numerous health benefits, including protection against coronary heart disease, type II diabetes, and obesity. Most of the procyanidins present in blueberry pomace, however, are large molecular weight compounds that are poorly absorbed and show weak bioactivity compared to the smaller molecular weight monomers and dimers. The objective of our study was to identify optimal extrusion variables to enhance the contents of monomers and dimers at the expense of large molecular weight procyanidin oligomers and polymers. Extrusion variables temperature (160 and 180 degrees C) and screw speed (150 and 200 rpm) were tested using mixtures of blueberry pomace with decorticated white sorghum flour at a ratio of 30 : 70 and 45% moisture content. Extrudates were analyzed for procyanidin composition and total anthocyanin content. Extrusion of blueberry pomace increased the monomer, dimer, and trimer contents considerably at both temperature and screw speeds. The highest monomer content, obtained at 180 degrees C and 150 rpm screw speed, was 84% higher than the nonextruded control. Significantly higher levels of dimer and trimer contents were also obtained under these conditions. Increases in monomer, dimer, and trimer contents apparently were the result of reduced polymer contents, which was approximately 40% lower for samples extruded at 180 degrees C temperature and 150 rpm screw speed. Extrusion processing reduced total anthocyanin contents by 33% to 42% indicating that additional treatments are needed to retain the pigments. These results demonstrate that extrusion processing can be used to increase procyanidin monomer and dimers in blueberry pomace.
Impaired Bone Morphogenetic Protein Receptor II Signaling in a Transforming Growth Factor-β–Dependent Mouse Model of Pulmonary Hypertension and in Systemic Sclerosis (2015)

We found reduced BMPRII protein in patients with SSc-PAH and a relevant mouse model associated with increased proteasomal degradation of BMPRII. Collectively, these results suggest that impaired BMP signaling, resulting from TGF-β-dependent increased receptor degradation, may promote PAH susceptibility in SSc and provide a unifying mechanism across different forms of PAH.
Phonon-hopping thermal conduction in quantum dot superlattices (2005)

We investigated the thermal conductivity in Ge∕Si quantum dot superlattices both theoretically and experimentally. It is proposed that thermal conduction through the quantum dot superlattices can be described by the phonon-hopping model with the interface transparency obtained from the experiment. Thermal conductivity has been measured as a function of temperature T from 10K to 400K. We have observed an order of magnitude decrease in thermal conductivity value compared to bulk and shift of its peak position to higher temperatures. The thermal conductivity manifests T0.7-T0.9 dependence for T⩽200K. The phonon-hopping model describes the measured thermal conductivity surprisingly well over the wide range of T from ∼40Kto400K. The model allows one to include the specifics of thermal conduction in quantum dot superlattices, such as the dot size, disorder, and interface quality. Our results suggest that the examined quantum dot superlattices are closer to the disordered or polycrystalline materials in terms of thermal transport.
Comparison of In Vivo Efficacy of Different Ocular Lubricants in Dry Eye Animal Models (2014)

Ocular lubricant containing 0.3% SH would be preferable to treat patients with dry eye syndrome.
Cerium oxide nanoparticles: Size-selective formation and structure analysis (2002)

Nanoparticles of cerium oxide with a narrow size distribution (±15%) are prepared by mixing cerium nitrate solution with an ammonium reagent. High-resolution transmission electron microscopy (TEM) indicates that over 99% of the synthesized particles are single crystals. TEM and photon absorption are used to monitor particle size. The lattice parameter increases up to 0.45% as the particle size decreases to 6 nm, as observed with x-ray diffraction. Raman spectra also suggest the particle-size effect and concomitant lattice expansion. The lattice expansion can be explained by increased concentrations of point defects with decreasing particle size.
Intravenous thrombolysis with recombinant tissue plasminogen activator for acute hemispheric stroke. The European Cooperative Acute Stroke Study (ECASS) (1995)

Intravenous thrombolysis in acute ischemic stroke is effective in improving some functional measures and neurologic outcome in a defined subgroup of stroke patients with moderate to severe neurologic deficit and without extended infarct signs on the initial CT scan. However, the identification of this subgroup is difficult and depends on recognition of early major CT signs of early infarction. Therefore, since treating ineligible patients is associated with an unacceptable increase of hemorrhagic complications and death, intravenous thrombolysis cannot currently be recommended for use in an unselected population of acute ischemic stroke patients.