gebhart/patrepeval huggingface dataset:
Dietary regulation of nuclear receptors in obesity-related metabolic syndrome. (2008)

In Western culture, excess visceral fat accumulation or obesity has reached epidemic proportions, resulting in metabolic syndrome. However, more than 10 years of research has shown that adipocytes also function as endocrine cells that release various bioactive substances, so called "adipocytokines or adipokines", that play a major role in the regulation of food intake, insulin sensitivity, energy metabolism, and the vascular microenvironment. Adiponectin, an adipocytokine, is considered to improve insulin sensitivity. Recently, monocyte chemoattractant protein (MCP)-1 has been reported to be a novel adipocytokine involved in the development of obesity-associated insulin resistance and atherosclerosis. Nuclear receptors, especially peroxisome proliferator-activated receptor-alpha (PPAR alpha) and PPAR gamma are ligand-activated transcription factors that regulate the metabolism of glucose and lipids. PPAR gamma is strongly expressed in adipocytes and plays a significant role in the transcriptional activation of adipocytokines including adiponectin. PPAR alpha, another PPAR isoform, is involved in the control of lipid metabolism in the liver and skeletal muscle. PPAR alpha activation causes lipid clearance via beta-oxidation enhancement. We showed that various dietary terpenoids and other natural ingredients regulate the transcription of PPAR target genes, induces the expression and secretion of adiponectin, and inhibits those of MCP-1 in adipocytes and beta-oxidation in liver. These findings indicate that dietary factor acts as an agonist of PPARs and is a valuable medical and food component for the gradual improvement of metabolic syndrome.
Laryngeal necrosis after combined chemotherapy and radiation therapy (1997)

Post-radiation necrosis of the larynx is a major complication after irradiation and has become rare. Recently, combined chemotherapy and radiation therapy has been introduced for head and neck tumours. The authors report a case of laryngeal necrosis after combination therapy for a patient with cervical lymph node metastases of nasopharyngeal carcinoma and review the literature on late laryngeal necrosis. Although radiation-induced laryngeal necrosis has become a rare complication, the combination of chemotherapy and radiation therapy may increase its incidence. We should always consider it as a possible late complication and treat it appropriately.
The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments (2006)

As much of the focus of genetics and molecular biology has shifted toward the systems level, it has become increasingly important to accurately extract biologically relevant signal from thousands of related measurements. The common property among these high-dimensional biological studies is that the measured features have a rich and largely unknown underlying structure. One example of much recent interest is identifying differentially expressed genes in comparative microarray experiments. We propose a new approach aimed at optimally performing many hypothesis tests in a high-dimensional study. This approach estimates the optimal discovery procedure (ODP), which has recently been introduced and theoretically shown to optimally perform multiple significance tests. Whereas existing procedures essentially use data from only one feature at a time, the ODP approach uses the relevant information from the entire data set when testing each feature. In particular, we propose a generally applicable estimate of the ODP for identifying differentially expressed genes in microarray experiments. This microarray method consistently shows favorable performance over five highly used existing methods. For example, in testing for differential expression between two breast cancer tumor types, the ODP provides increases from 72% to 185% in the number of genes called significant at a false discovery rate of 3%. Our proposed microarray method is freely available to academic users in the open-source, point-and-click EDGE software package.
Scaffold design and fabrication technologies for engineering tissues — state of the art and future perspectives (2001)

Today, tissue engineers are attempting to engineer virtually every human tissue. Potential tissue-engineered products include cartilage, bone, heart valves, nerves, muscle, bladder, liver, etc. Tissue engineering techniques generally require the use of a porous scaffold, which serves as a three-dimensional template for initial cell attachment and subsequent tissue formation both in vitro and in vivo. The scaffold provides the necessary support for cells to attach, proliferate, and maintain their differentiated function. Its architecture defines the ultimate shape of the new grown soft or hard tissue. In the early days of tissue engineering, clinically established materials such as collagen and polyglycolide were primarily considered as the material of choice for scaffolds. The challenge for more advanced scaffold systems is to arrange cells/tissue in an appropriate 3D configuration and present molecular signals in an appropriate spatial and temporal fashion so that the individual cells will grow and form the desired tissue structures--and do so in a way that can be carried out reproducibly, economically, and on a large scale. This paper is not intended to provide a general review of tissue engineering, but specifically concentrate on the design and processing of synthetic polymeric scaffolds. The material properties and design requirements are discussed. An overview of the various fabrication techniques of scaffolds is presented, beginning with the basic and conventional techniques to the more recent, novel methods that combine both scaffold design and fabrication capabilities.
Functionalized Carbon Nanotubes for Molecular Hydrogen Sensors (2001)

Excellent sensors for molecular hydrogen,to be used, e.g., for leakage control in H2-based energy sources, are fabricated by functionalization of single-walled carbon nanotubes (SWNTs) with a non-continuous coating of palladium. These sensors, with large electrical conductivity modulation in the presence of small H2 concentrations in air, show fast response and high sensitivity even at room temperature. The Figure presents an AFM image of a Pd-coated SWNT.
Development of analytical methods for multiplex bio-assay with inductively coupled plasma mass spectrometry (2008)

Advances in the development of highly multiplexed bio-analytical assays with inductively coupled plasma mass spectrometry (ICP-MS) detection are discussed. Use of novel reagents specifically designed for immunological methods utilizing elemental analysis is presented. The major steps of method development, including selection of elements for tags, validation of tagged reagents, and examples of multiplexed assays, are considered in detail. The paper further describes experimental protocols for elemental tagging of antibodies, immunostaining of live and fixed human leukemia cells, and preparation of samples for ICP-MS analysis. Quantitative analysis of surface antigens on model cell lines using a cocktail of seven lanthanide labeled antibodies demonstrated high specificity and concordance with conventional immunophenotyping.
Response of plasma lipids to dietary cholesterol and wine polyphenols in rats fed polyunsaturated fat diets (2000)

This experiment was designed to evaluate the effects of dietary red wine phenolic compounds (WP) and cholesterol on lipid oxidation and transport in rats. For 5 wk, weanling rats were fed polyunsaturated fat diets (n-6/n-3 = 6.4) supplemented or not supplemented with either 3 g/kg diet of cholesterol, 5 g/kg diet of WP, or both. The concentrations of triacylglycerols (TAG, P < 0.01) and cholesterol (P < 0.0002) were reduced in fasting plasma of rats fed cholesterol despite the cholesterol enrichment of very low density lipoprotein + low density lipoprotein (VLDL + LDL). The response was due to the much lower plasma concentration of high density lipoprotein (HDL) (-35%, P < 0.0001). In contrast, TAG and cholesteryl ester (CE) accumulated in liver (+120 and +450%, respectively, P < 0.0001). However, the cholesterol content of liver microsomes was not affected. Dietary cholesterol altered the distribution of fatty acids mainly by reducing the ratio of arachidonic acid to linoleic acid (P < 0.0001) in plasma VLDL + LDL (-35%) and HDL (-42%) and in liver TAG (-42%), CE (-78%), and phospholipids (-28%). Dietary WP had little or no effect on these variables. On the other hand, dietary cholesterol lowered the alpha-tocopherol concentration in VLDL + LDL ( -40%, P < 0.003) and in microsomes (-60%, P < 0.0001). In contrast, dietary WP increased the concentration in microsomes (+21%, P < 0.0001), but had no effect on the concentration in VLDL + LDL. Cholesterol feeding decreased (P < 0.006) whereas WP feeding increased (P < 0.0001) the resistance of VLDL + LDL to copper-induced oxidation. The production of conjugated dienes after 25 h of oxidation ranged between 650 (WP without cholesterol) and 2,560 (cholesterol without WP) micromol/g VLDL + LDL protein. These findings show that dietary WP were absorbed at sufficient levels to contribute to the protection of polyunsaturated fatty acids in plasma and membranes. They could also reduce the consumption of alpha-tocopherol and endogenous antioxidants. The responses suggest that, in humans, these substances may be beneficial by reducing the deleterious effects of a dietary overload of cholesterol.
Penetration-controlled reactions in organized monolayer assemblies. 2. Aqueous permanganate interaction with self-assembling monolayers of long-chain surfactants (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPenetration-controlled reactions in organized monolayer assemblies. 2. Aqueous permanganate interaction with self-assembling monolayers of long-chain surfactantsRivka Maoz and Jacob SagivCite this: Langmuir 1987, 3, 6, 1045–1051Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/la00078a028https://doi.org/10.1021/la00078a028research-articleACS PublicationsRequest reuse permissionsArticle Views246Altmetric-Citations51LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Mechanisms of action of docosahexaenoic acid in the nervous system (2001)

This review describes (from both the animal and human literature) the biological consequences of losses in nervous system docosahexaenoate (DHA). It then concentrates on biological mechanisms that may serve to explain changes in brain and retinal function. Brief consideration is given to actions of DHA as a nonesterified fatty acid and as a docosanoid or other bioactive molecule. The role of DHA-phospholipids in regulating G-protein signaling is presented in the context of studies with rhodopsin. It is clear that the visual pigment responds to the degree of unsaturation of the membrane lipids. At the cell biological level, DHA is shown to have a protective role in a cell culture model of apoptosis in relation to its effects in increasing cellular phosphatidylserine (PS); also, the loss of DHA leads to a loss in PS. Thus, through its effects on PS, DHA may play an important role in the regulation of cell signaling and in cell proliferation. Finally, progress has been made recently in nuclear magnetic resonance studies to delineate differences in molecular structure and order in biomembranes due to subtle changes in the degree of phospholipid unsaturation.
Transduction of Human CD34 + Cells That Mediate Long-Term Engraftment of NOD/SCID Mice by HIV Vectors (1999)

Efficient gene transfer into human hematopoietic stem cells (HSCs) is an important goal in the study of the hematopoietic system as well as for gene therapy of hematopoietic disorders. A lentiviral vector based on the human immunodeficiency virus (HIV) was able to transduce human CD34+ cells capable of stable, long-term reconstitution of nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice. High-efficiency transduction occurred in the absence of cytokine stimulation and resulted in transgene expression in multiple lineages of human hematopoietic cells for up to 22 weeks after transplantation.
Generation of transgenic mice with mild and severe retinal neovascularisation (2005)

The authors generated four hVEGF overexpressing transgenic mouse lines with phenotypes ranging from mild to severe neovascularisation. These models are a valuable research tool to study excess VEGF related molecular and cellular changes and provide additional opportunities to test anti-angiogenic therapies.
Thixotropic behavior of clay dispersions: Combinations of scattering and rheometric techniques (1998)

The thixotropic behavior of a colloidal dispersion of clay consisting of disk-shaped particles was studied by means of a combination of rheometric measurements, static light scattering, and small-angle neutron scattering. At rest, the structure of the gel consists of dense micrometer-sized aggregates assembled into a fractal mass of dimension D. Under shear, in the case of volume fractions with (1⩽D⩽1.2) at rest, a butterfly-type light scattering pattern is observed. This is attributed to the formation of rollers within the dispersion, which align themselves on average perpendicular to the direction of shearing. This produces a fall in resistance to flow and in viscosity. The influence of shear rate on this disaggregation process was studied and linked to the rheometric measurements. Under shear flow conditions, the fall in viscosity is due to orientation and disaggregation processes occurring at length scales on the order of 1 μm. During recovery, the two time scales identified correspond, respectively, to a rapid relaxation of the particle orientations and a slow aggregation process. Thixotropic behavior is identified as being mainly a reversible aggregation process, for which large length scales on the order of a micrometer associated with a fractal arrangement play a decisive role.
Replication Vesicles are Load- and Choke-Points in the Hepatitis C Virus Lifecycle (2013)

Hepatitis C virus (HCV) infection develops into chronicity in 80% of all patients, characterized by persistent low-level replication. To understand how the virus establishes its tightly controlled intracellular RNA replication cycle, we developed the first detailed mathematical model of the initial dynamic phase of the intracellular HCV RNA replication. We therefore quantitatively measured viral RNA and protein translation upon synchronous delivery of viral genomes to host cells, and thoroughly validated the model using additional, independent experiments. Model analysis was used to predict the efficacy of different classes of inhibitors and identified sensitive substeps of replication that could be targeted by current and future therapeutics. A protective replication compartment proved to be essential for sustained RNA replication, balancing translation versus replication and thus effectively limiting RNA amplification. The model predicts that host factors involved in the formation of this compartment determine cellular permissiveness to HCV replication. In gene expression profiling, we identified several key processes potentially determining cellular HCV replication efficiency.
Regeneration of bovine and octopus opsins in situ with natural and artificial retinals (1989)

We consider the problem of color regulation in visual pigments for both bovine rhodopsin (lambda max = 500 nm) and octopus rhodopsin (lambda max = 475 nm). Both pigments have 11-cis-retinal (lambda max = 379 nm, in ethanol) as their chromophore. These rhodopsins were bleached in their native membranes, and the opsins were regenerated with natural and artificial chromophores. Both bovine and octopus opsins were regenerated with the 9-cis- and 11-cis-retinal isomers, but the octopus opsin was additionally regenerated with the 13-cis and all-trans isomers. Titration of the octopus opsin with 11-cis-retinal gave an extinction coefficient for octopus rhodopsin of 27,000 +/- 3000 M-1 cm-1 at 475 nm. The absorption maxima of bovine artificial pigments formed by regenerating opsin with the 11-cis dihydro series of chromophores support a color regulation model for bovine rhodopsin in which the chromophore-binding site of the protein has two negative charges: one directly hydrogen bonded to the Schiff base nitrogen and another near carbon-13. Formation of octopus artificial pigments with both all-trans and 11-cis dihydro chromophores leads to a similar model for octopus rhodopsin and metarhodopsin: there are two negative charges in the chromophore-binding site, one directly hydrogen bonded to the Schiff base nitrogen and a second near carbon-13. The interaction of this second charge with the chromophore in octopus rhodopsin is weaker than in bovine, while in metarhodopsin it is as strong as in bovine.
Diabetes mellitus decreases the activity of the albumin promoter in vitro. (1991)

Diabetes mellitus (DM) has been shown previously to decrease hepatic synthesis of both albumin and albumin mRNA. These findings prompted us to ask whether decreased albumin expression is due to changes in the rate of gene transcription. A cell-free in vitro transcription assay demonstrated that activity of the albumin promoter in hepatonuclear extracts was diminished 3- to 4-fold in diabetic compared with control animals. This decrease was abolished in extracts prepared from diabetic animals treated with insulin. The potential mechanisms for diminished activity were examined by mixing extracts from normal and diabetic animals prior to incubation with DNA templates. In the presence of limited amounts of albumin promoter DNA, addition of diabetic to control extract caused a reduction in promoter activity, suggesting that an inhibitor or inhibitors of albumin promoter activity is/are present in the liver of diabetic rats.
Transcription-Based Prediction of Response to IFNβ Using Supervised Computational Methods (2004)

Changes in cellular functions in response to drug therapy are mediated by specific transcriptional profiles resulting from the induction or repression in the activity of a number of genes, thereby modifying the preexisting gene activity pattern of the drug-targeted cell(s). Recombinant human interferon beta (rIFNbeta) is routinely used to control exacerbations in multiple sclerosis patients with only partial success, mainly because of adverse effects and a relatively large proportion of nonresponders. We applied advanced data-mining and predictive modeling tools to a longitudinal 70-gene expression dataset generated by kinetic reverse-transcription PCR from 52 multiple sclerosis patients treated with rIFNbeta to discover higher-order predictive patterns associated with treatment outcome and to define the molecular footprint that rIFNbeta engraves on peripheral blood mononuclear cells. We identified nine sets of gene triplets whose expression, when tested before the initiation of therapy, can predict the response to interferon beta with up to 86% accuracy. In addition, time-series analysis revealed potential key players involved in a good or poor response to interferon beta. Statistical testing of a random outcome class and tolerance to noise was carried out to establish the robustness of the predictive models. Large-scale kinetic reverse-transcription PCR, coupled with advanced data-mining efforts, can effectively reveal preexisting and drug-induced gene expression signatures associated with therapeutic effects.
Solvent processing of PMMA and COC chips for bonding devices with optical quality surfaces (2010)

Many prototype microfluidic devices are manufactured by some form of micromachining or injection molding which often&#13;\nleaves poor quality surface. This work presents a simple method that both significantly reduces surface roughness of microfluidic chips and at the same time is used to bond devices. The method has been tested on devices made from poly(methyl methacrylate) (PMMA) and cyclic olefin copolymer (COC). The technique uses a solvent vapour exposure process which creates an irreversible bond between two substrates. It also re-flows the material, producing surfaces with optical quality.
Increased Serum Levels of Vascular Endothelial Growth Factor in Patients with Renal Cell Carcinoma (1999)

Neovascularization, an essential event for the growth of solid tumors, is regulated by a number of angiogenic factors. One such factor, vascular endothelial growth factor (VEGF), is considered to exert a potent angiogenic activity, as indicated by immunohistochemical and molecular evidence. In this study we investigated the serum VEGF level (s-VEGF) in patients with renal cell carcinoma (RCC). s-VEGF in peripheral blood samples was analyzed in 40 RCC patients and 40 patients without cancer (controls) using a sandwich enzyme-linked immunoassay. In 20 RCC patients, serum samples were obtained separately from the bilateral renal veins. s-VEGF was also measured before, 4 and 8 weeks after nephrectomy in 11 patients. There were significant differences in s-VEGF between the RCC patients and the controls (207.3+/-32.9 vs. 71.5+/-9.1 pg/ml, mean+/-SE) (P<0.005), between the tumor-bearing renal veins and the contralateral ones (P<0.01), between the pre- and post-nephrectomy situations (P<0.01) and among the various parameters of tumor status such as tumor extent (P<0.001) and existence of metastasis (P<0.001). s-VEGF significantly correlated with the tumor volume obtained by a three-dimensional measurement (r=0.802, P<0.0001). The sensitivity and specificity of s-VEGF at the cut-off level of 100 pg/ml, as determined by the receiver-operating-characteristics curve, were 80.0% and 72.5%, respectively. The results indicate that tumor tissue of RCC liberates VEGF into the systemic blood flow and that s-VEGF is a possible marker for RCC.
Antisense oligonucleotides extend survival and reverse decrement in muscle response in ALS models (2018)

Mutations in superoxide dismutase 1 (SOD1) are responsible for 20% of familial ALS. Given the gain of toxic function in this dominantly inherited disease, lowering SOD1 mRNA and protein is predicted to provide therapeutic benefit. An early generation antisense oligonucleotide (ASO) targeting SOD1 was identified and tested in a phase I human clinical trial, based on modest protection in animal models of SOD1 ALS. Although the clinical trial provided encouraging safety data, the drug was not advanced because there was progress in designing other, more potent ASOs for CNS application. We have developed next-generation SOD1 ASOs that more potently reduce SOD1 mRNA and protein and extend survival by more than 50 days in SOD1G93A rats and by almost 40 days in SOD1G93A mice. We demonstrated that the initial loss of compound muscle action potential in SOD1G93A mice is reversed after a single dose of SOD1 ASO. Furthermore, increases in serum phospho-neurofilament heavy chain levels, a promising biomarker for ALS, are stopped by SOD1 ASO therapy. These results define a highly potent, new SOD1 ASO ready for human clinical trial and suggest that at least some components of muscle response can be reversed by therapy.