gebhart/patrepeval huggingface dataset:
Expression of Transforming Growth Factor α (TGFα) in Differentiated Rat Mammary Tumors: Estrogen Induction of TGFα Production (1987)

Primary well-differentiated dimethylbenzene alpha-anthracene (DMBA)-or nitrosomethylurea (NMU)-induced rat mammary adenocarcinomas that are estrogen dependent possess biologically active and immunoreactive transforming growth factor alpha (TGF alpha), which can be detected in a sort agar growth-promoting assay and by a specific liquid-phase competitive RIA, respectively. In contrast, tissue extracts prepared from transplantable undifferentiated DMBA-I and NMU-II rat mammary carcinomas that are estrogen independent and metastatic exhibit low or undetectable levels of TGF alpha. In addition, the primary DMBA- and NMU-induced rat mammary adenocarcinomas express a specific 4.8-kilobase TGF alpha mRNA species, whereas little or no TGF alpha mRNA can be detected in the transplantable DMBA-I and NMU-II tumors. Primary tumors synthesize type IV basement membrane collagen, whereas the transplantable tumors elaborate very little type IV collagen. Either TGF alpha or estrogens can differentially enhance the synthesis of type IV collagen by 0.5- to 4-fold over total protein synthesis in primary cultures of normal mouse mammary epithelial cells or in primary NMU-induced tumor cells, respectively. Therefore, TGF alpha could function as an estrogen-inducible autocrine growth factor for well differentiated rat mammary tumor cells by its ability to selectively regulate type IV collagen synthesis. Estrogens can modulate TGF alpha production in vivo in primary DMBA-induced rat mammary tumors, because ovariectomy results in a rapid decline (within 6 h) of TGF alpha mRNA levels. This response to estrogens can also be observed in vitro. Primary DMBA- or NMU-induced rat mammary tumor cells cultured in the presence of 17 beta-estradiol (10(-8) M) for 4 days show an increase in the level of TGF alpha mRNA over cells not treated with estrogen. This increase in TGF alpha mRNA is paralleled by a 2- to 3-fold increase in the levels of immunoreactive TGF alpha that can be detected and in the conditioned medium from estrogen-treated cells. These results suggest that TGF alpha may be an adjunct marker for those mammary tumors that are well differentiated adenocarcinomas and estrogen dependent and that estrogen-independent tumors do not constitutively produce TGF alpha or express TGF alpha mRNA.
Elevation of total homocysteine in the serum of patients with cobalamin or folate deficiency detected by capillary gas chromatography-mass spectrometry. (1988)

To determine if levels of serum total homocysteine are elevated in patients with either cobalamin or folate deficiency, we utilized a new capillary gas chromatographic-mass spectrometric technique to measure total homocysteine in the serum of 78 patients with clinically confirmed cobalamin deficiency and 19 patients with clinically confirmed folate deficiency. Values ranged from 11 to 476 mumol/liter in the cobalamin-deficient patients and 77 of the 78 patients had values above the normal range of 7-22 mumol/liter as determined for 50 normal blood donors. In the cobalamin-deficient patients, serum total homocysteine was positively correlated with serum folate, mean corpuscular volume, serum lactate dehydrogenase, serum methylmalonic acid, and the degree of neurologic involvement, and inversely correlated with platelets and hematocrit. In the folate-deficient patients, values for serum total homocysteine ranged from 17 to 185 mumol/liter and 18 of the 19 patients had values above the normal range. Some patients with pernicious anemia who were intermittently treated with cyanocobalamin were found to have elevated serum levels of total homocysteine while they were free of hematologic and neurologic abnormalities. The measurement of serum total homocysteine will help define the incidence of cobalamin deficiency and folate deficiency in various patient populations.
Antiinflammatory Properties of HDL (2004)

There are several well-documented functions of high-density lipoprotein (HDL) that may explain the ability of these lipoproteins to protect against atherosclerosis. The best recognized of these is the ability of HDL to promote the efflux of cholesterol from cells. This process may minimize the accumulation of foam cells in the artery wall. However, HDL has additional properties that may also be antiatherogenic. For example, HDL is an effective antioxidant. The major proteins of HDL, apoA-I and apoA-II, as well as other proteins such as paraoxonase that cotransport with HDL in plasma, are well-known to have antioxidant properties. As a consequence, HDL has the capacity to inhibit the oxidative modification of low-density lipoprotein (LDL) in a process that reduces the atherogenicity of these lipoproteins. HDL also possesses other antiinflammatory properties. By virtue of their ability to inhibit the expression of adhesion molecules in endothelial cells, they reduce the recruitment of blood monocytes into the artery wall. These antioxidant and antiinflammatory properties of HDL may be as important as its cholesterol efflux function in terms of protecting against the development of atherosclerosis.
Synthesis and processing of mammalian protamines and transition proteins (1994)

Mouse and rat seminiferous tubule fragment cultures were used to examine synthesis and processing of mammalian protamines and transition proteins. The tubule fragments were incubated with [3H]-arginine, [3H]-histidine, [35S]-cysteine, or [32P]-PO4, and radiolabeled proteins were analyzed by acid/urea polyacrylamide gel electrophoresis and fluorography or autoradiography. Newly synthesized protamines were recovered from sonication-resistant nuclei (SRN) and could not be detected in cytoplasmic fractions, indicating that protamines are deposited into nuclei immediately after synthesis. Newly synthesized mouse protamine 1 (mP1) and the precursor to mouse protamine 2 (pre-mP2) migrated more slowly during electrophoresis than their predominant testicular forms, identified by staining with Coomassie blue R-250. Within 1 hour of synthesis, the electrophoretic mobilities of mP1 and pre-mP2 increased to match those of their predominant forms. These changes are consistent with initial charge-neutralizing modifications of the newly synthesized protamines, followed by removal of at least some of the modifying ligands, to unmask protamine basicity. Steady-state phosphorylation rates were high for rat protamine 1 (rP1) and were independent of phosphate content; both rP1 molecules of low and high phosphate content were rapidly phosphorylated. Pre-mP2-3, a major processing intermediate derived by proteolysis of pre-mP2, was also rapidly phosphorylated. Like the protamines, transition protein 2 (TP2) was rapidly phosphorylated and increased in electrophoretic mobility soon after synthesis. In contrast, transition protein 1 (TP1) was not phosphorylated and did not exhibit multiple electrophoretic forms.
Leukotrienes (2007)

This review of leukotrienes, which are lipid mediators with a broad array of clinical effects, and leukotriene receptors considers the biochemical and physiological aspects of these molecules, examines their roles in asthma and other diseases, and explains the pharmacologic effects of antileukotriene agents.
A high performance precision machine (2005)

In the area of precision engineering industries, high performance positioning precision machines are increasingly employed to improve the productivity and to lower the manufacturing cost. In many applications such as actuaphotonics or biomedical products, there are increasingly demands for machines that have positioning accuracy of several micrometers. In this paper, we present a prototype precision machine that has a positioning accuracy of 1 /spl mu/m and a peak speed above 1 m/s. The precision positioning machine uses a three phase permanent magnet linear motor as the actuator. As it is capable of producing linear motion directly, it eliminates the needs of mechanical transmission from the rotary to the linear motion. High closed loop performance has been achieved by using a state space based model predictive controller and a dynamic friction compensation system. The friction and the control system have been optimally identified and tuned using the genetic algorithm. Experimental results have verified the effectiveness of the developed approach.
Reassembly of S-layer proteins (2014)

Crystalline bacterial cell surface layers (S-layers) represent the outermost cell envelope component in a broad range of bacteria and archaea. They are monomolecular arrays composed of a single protein or glycoprotein species and represent the simplest biological membranes developed during evolution. They are highly porous protein mesh works with unit cell sizes in the range of 3 to 30 nm, and pore sizes of 2 to 8 nm. S-layers are usually 5 to 20 nm thick (in archaea, up to 70 nm). S-layer proteins are one of the most abundant biopolymers on earth. One of their key features, and the focus of this review, is the intrinsic capability of isolated native and recombinant S-layer proteins to form self-assembled mono- or double layers in suspension, at solid supports, the air-water interface, planar lipid films, liposomes, nanocapsules, and nanoparticles. The reassembly is entropy-driven and a fascinating example of matrix assembly following a multistage, non-classical pathway in which the process of S-layer protein folding is directly linked with assembly into extended clusters. Moreover, basic research on the structure, synthesis, genetics, assembly, and function of S-layer proteins laid the foundation for their application in novel approaches in biotechnology, biomimetics, synthetic biology, and nanotechnology.
Mechanical properties of silk fibroin–microcrystalline cellulose composite films (2002)

Abstract Silk fibroin–microcrystalline cellulose (cellulose whisker) composite films with varied compositions were prepared by casting mixed aqueous solution/suspensions of the two components. Silk fibroin was dissolved in 10 M LiSCN followed by dialysis; a cellulose whisker suspension was prepared by sulfuric acid hydrolysis of tunicate cellulose. Macroscopically homogeneous films were obtained at all mixing ratios. While the Young's modulus of the composite films showed a linear, additive dependence on the mixing ratio, the tensile strength and ultimate strain showed a maximum at a 70–80% cellulose content, reaching five times those of fibroin‐alone or cellulose‐alone films. At the same mixing ratio, infrared spectra of the composite films showed a shift of the amide I peak from 1654 to 1625 cm −1 , indicating the conformational change of fibroin from a random coil to a β structure (silk II) at the whisker–matrix interface. This change seems to be induced by contact of fibroin molecules with a highly ordered surface of cellulose whisker. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 3425–3429, 2002
Tandem Metal-Coordination Copolymerization and Organocatalytic Ring-Opening Polymerization via Water To Synthesize Diblock Copolymers of Styrene Oxide/CO2 and Lactide (2012)

Selective transformation of carbon dioxide and epoxides into degradable polycarbonates (CO2-based copolymer) has been regarded as a most promising green polymerization process. Although tremendous progress has been made during the past decade, very few successful examples have been reported to synthesize well-defined block copolymers to expand the scope of these green copolymers. Herein, we report a tandem strategy combining two living polymerization techniques, salenCo(III)X-catalyzed styrene oxide SO/CO2 copolymerization and ring-opening polymerization of lactide with DBU (1,8-diazabicyclo[5.4.0]undec-7-ene), for the synthesis of poly(styrene carbonate-block-lactide) copolymers. The key to the success of this tandem strategy is the judicious choice of water as the chain transfer and/or chain terminator reagent, which is added at the end of the salenCo(III)X-catalyzed SO/CO2 copolymerization to in situ generate hydroxyl groups at the end of the polymer chains. The resulting polycarbonates with −OH end groups can thus be directly used as macroinitiators to subsequently initiate ring-opening polymerization of lactide to synthesize the diblock copolymers. Because of the living polymerization nature of both steps in this tandem strategy, we have demonstrated that the diblock copolymers synthesized possess well-defined structures with narrow molecular weight distributions and controllable lengths of both styrene carbonate and lactide blocks.
Self-curling and -sticking flexible substrate for ECoG electrode array (2013)

We report a flexible electrocorticogram (ECoG) electrode array device with one directionally self-curling and -sticking properties, to solve the difficulty of the handling of thin (<; 10 μm) substrate devices (Fig. 1). As the substrate, we use sandwiched parylene-N/-C which films have different linear expansion coefficients. The thermal dependences of the deflection and curvature radius of the paylene-N/-C system were calculated. Based on the calculations, 2.5-μm parylene-N/2.5-μm paryelen-C “bi-parylene” flexible substrate was prepared. The self-curled substrate with the curvature radius of about 2 mm has been observed. The self-sticking of the curled device has been demonstrated on wet samples, due to the surface tension between the parylene-N and the sample. These results suggest that the bi-parylene substrate becomes a candidate material for easy-to-use flexible thin ECoG devices, enchaining the wrapping property over the brain.
Immunohistologic and functional characterization of a vascular addressin involved in lymphocyte homing into peripheral lymph nodes. (1988)

The tissue localization or "homing" of circulating lymphocytes is directed in part by specialized vessels that define sites of lymphocyte exit from the blood. In peripheral lymph nodes, mucosal lymphoid tissues (Peyer's patches and appendix), and sites of chronic inflammation, for example, lymphocytes leave the blood by adhering to and migrating between those endothelial cells lining postcapillary high endothelial venules (HEV). Functional analyses of lymphocyte interactions with HEV have shown the lymphocytes can discriminate between HEV in different tissues, indicating that HEV express tissue-specific determinants or address signals for lymphocyte recognition. We recently described such a tissue-specific "vascular addressin" that is selectively expressed by endothelial cells supporting lymphocyte extravasation into mucosal tissues and that appears to be required for mucosa-specific lymphocyte homing (Streeter, P. R., E. L. Berg, B. N. Rouse, R. F. Bargatze, and E. C. Butcher. 1988. Nature (Lond.). 331:41-46). Here we document the existence and tissue-specific distribution of a distinct HEV differentiation antigen. Defined by monoclonal antibody MECA-79, this antigen is expressed at high levels on the lumenal surface and in the cytoplasm of HEV in peripheral lymph nodes. By contrast, although MECA-79 stains many HEV in the mucosal Peyer's patches, expression in most cases is restricted to the perivascular or ablumenal aspect of these venules. In the small intestine lamina propria, a mucosa-associated site that supports the extravasation of lymphocytes, venules do not stain with MECA-79. Finally, we demonstrate that MECA-79 blocks binding of both normal lymphocytes and a peripheral lymph node-specific lymphoma to peripheral lymph node HEV in vitro and that it also inhibits normal lymphocyte homing to peripheral lymph nodes in vivo without significantly influencing lymphocyte interactions with Peyer's patch HEV in vitro or in vivo. Thus, MECA-79 defines a novel vascular addressin involved in directing lymphocyte homing to peripheral lymph nodes.
Thermosensitivity of Green Fluorescent Protein Fluorescence Utilized to Reveal Novel Nuclear-Like Compartments in a Mutant Nucleoporin NSP11 (1995)

Tagging proteins with the green fluorescent protein (GFP) from Aequorea victoria is a good means of analyzing protein localization in living cells. Nevertheless, GFP and a chimeric protein, GFP-nucleoplasmin, expressed in Saccharomyces cerevisiae were less fluorescent at high culture temperatures. Proteins synthesized at a low temperature retained their fluorescence despite a shift to a higher temperature. Hence, when a temperature-sensitive nsp1 mutant expressing GFP-nucleoplasmin was cultured at 23 degrees C and then shifted to 35 degrees C, we were able to exclusively monitor the localization of the protein synthesized prior to the temperature shift. This protein accumulated in novel nuclear-like compartments devoid of DNA.
Neutrophil elastase up‐regulates human β‐defensin‐2 expression in human bronchial epithelial cells (2003)

Human beta-defensin-2 (HBD-2) gene expression is induced by tumour necrosis factor-alpha, interleukin-1beta and lipopolysaccharide. The objective of this study was to investigate the effect of neutrophil elastase (NE), a major pro-inflammatory protease, on HBD-2 expression. HBD-2 gene expression was assessed by reverse transcription polymerase chain reaction in the human bronchial epithelial cell line 16HBE14o- and primary normal human bronchial epithelial (NHBE) cells. Optimal HBD-2 expression was induced with 100 nM NE. Using a HBD-2-luciferase reporter construct, luciferase activity increased significantly in 16HBE14o- cells following incubation with NE. An increase in HBD-2 protein expression was observed in primary NHBE cells after incubation with NE as assessed by laser scanning cytometry. In conclusion, NE up-regulates HBD-2 expression in bronchial epithelial cells.
Sampling and Analytical Strategies for Biomarker Discovery using Mass Spectrometry (2006)

There is an often unspoken truth behind the course of scientific investigation that involves not what is necessarily academically worthy of study, but rather what is scientifically worthy in the eyes of funding agencies. The perception of worthy research is, as cost is driven in the simplest sense in economics, often driven by demand. Presently, the demand for novel diagnostic and therapeutic protein biomarkers that possess high sensitivity and specificity is placing major impact on the field of proteomics. The focal discovery technology that is being relied on is mass spectrometry (MS), whereas the challenge of biomarker discovery often lies not in the application of MS but in the underlying proteome sampling and bioinformatic processing strategies. Although biomarker discovery research has been historically technology-driven, it is clear from the meager success in generating validated biomarkers that increasing attention must be placed at the pre-analytic stage, such as sample retrieval and preparation. As diseases vary, so do the combinations of sampling and sample analyses necessary to discover novel biomarkers. In this review, we highlight different strategies used toward biomarker discovery and discuss them in terms of their reliance on technology and methodology.
Low-Rank Mechanism: Optimizing Batch Queries under Differential Privacy (2012)

Differential privacy is a promising privacy-preserving paradigm for statistical query processing over sensitive data. It works by injecting random noise into each query result, such that it is provably hard for the adversary to infer the presence or absence of any individual record from the published noisy results. The main objective in differentially private query processing is to maximize the accuracy of the query results, while satisfying the privacy guarantees. Previous work, notably the matrix mechanism, has suggested that processing a batch of correlated queries as a whole can potentially achieve considerable accuracy gains, compared to answering them individually. However, as we point out in this paper, the matrix mechanism is mainly of theoretical interest; in particular, several inherent problems in its design limit its accuracy in practice, which almost never exceeds that of naive methods. In fact, we are not aware of any existing solution that can effectively optimize a query batch under differential privacy. Motivated by this, we propose the Low-Rank Mechanism (LRM), the first practical differentially private technique for answering batch queries with high accuracy, based on a low rank approximation of the workload matrix. We prove that the accuracy provided by LRM is close to the theoretical lower bound for any mechanism to answer a batch of queries under differential privacy. Extensive experiments using real data demonstrate that LRM consistently outperforms state-of-the-art query processing solutions under differential privacy, by large margins.
Phylogenies From Molecular Sequences: Inference And Reliability (1988)

PHYLOGENIES FROM MOLECULAR SEQUENCES: INFERENCE AND RELIABILITY, Page 1 of 1 < Previous page | Next page > /docserver/preview/fulltext/genet/22/1/annurev.ge.22.120188.002513-1.gif
Multiband and wideband properties of printedfractal branched antennas (1999)

Multiband and wideband properties of printed fractal branched antennas The presented numerical and experimental results show that the input reflection coefficient relative to 50 Ω of a fractal tree antenna exhibits a multiband behaviour generated by the elements of successive iteration levels as well as a wideband response produced by the large number of elements of the last iteration level.
Competitive Fluorescence Polarization Assays for the Detection of Phosphoinositide Kinase and Phosphatase Activity (2003)

We describe the development and implementation of competitive fluorescence polarization (FP) based assays for determining activity of phosphoinositide 3-kinase (PI 3-K) and the type-II SH2-domain-containing inositol 5-phosphatase (SHIP2). These assays are based on the interaction of specific phosphoinositide binding proteins with fluorophore-labeled phosphoinositide and inositol phosphate tracers. Enzyme reaction products are detected by their ability to compete with the fluorescent tracers for protein binding, leading to an increase in the amount of free tracer and a decrease in polarization (mP) values. A variety of fluorophore-labeled tracers were evaluated, and assay sensitivity and specificity for products of PI 3-K and SHIP2 activity was determined. Assay performance was evaluated using recombinant PI 3-Kalpha and SHIP2 with diC(8)-PI(4,5)P(2) and diC(8)-PI(3,4,5)P(3) as respective substrates. IC(50) values for previously characterized PI 3-K inhibitors were within expected ranges. These assays are homogeneous, sensitive, and rapid, and suitable for HTS applications, and will facilitate screening for novel inhibitors of phosphoinositide kinases and phosphatases in drug development.