gebhart/patrepeval huggingface dataset:
Analysis of starch structure using fluorophore‐assisted carbohydrate electrophoresis (1998)

The analysis of the fine structure of starches is important to the investigation of linkages between starch structure and function and to the investigation of the properties and roles of starch biosynthetic, modifying and degradation enzymes. Fluorophore-assisted carbohydrate electrophoresis has recently been introduced as a method for the analysis of the oligosaccharide populations released by the enzymatic digestion of starches, which has advantages in resolution and sensitivity over previously used methods, and provides the capacity for the facile analysis of oligosaccharide populations on either a molar or mass basis. The use of fluorophore-assisted carbohydrate electrophoresis for the analysis of oligosaccharides is reviewed with particular reference to the choice of label, efficiency of labeling and separation techniques. Examples of separations using slab gel electrophoresis, DNA sequencer analysis and capillary electrophoresis are presented and we conclude that on the basis of resolution and reproducibility, capillary electrophoresis is the method of choice for the separation of oligosaccharides of degree of polymerization from 1 to 100. Examples of isoamylase-debranched starches and glycogens analyzed by capillary electrophoresis are presented. The capillary electrophoresis analysis of starch structure through the analysis of oligosaccharides released by the debranching of limit dextrins derived from starches and glycogens is introduced as a useful diagnostic of starch structure. The potential for future development of novel diagnostics for starch structure using fluorophore-assisted carbohydrate electrophoresis is discussed.
α-Galactosidase A deficient mice: A model of Fabry disease (1997)

Fabry disease is an X-linked inherited metabolic disorder that is caused by a deficiency of alpha-galactosidase A (alpha-Gal A). Progressive deposition of neutral glycosphingolipids that have terminal a-linked galactosyl moieties in vascular endothelial cells causes renal failure along with premature myocardial infarctions and strokes in patients with this condition. No specific treatment is available for patients with this disorder at this time. An animal model of this condition would be valuable for exploring therapeutic strategies for patients with Fabry disease. We report here the generation of alpha-Gal A deficient mice by gene targeting and an analysis of the resulting phenotype. The knockout mice display a complete lack of alpha-Gal A activity. The mice, however, appeared clinically normal at 10 weeks of age. Ultrastructural analysis revealed concentric lamellar inclusions in the kidneys, and confocal microscopy using a fluorescent-labeled lectin specific for alpha-D-galactosyl residues showed accumulation of substrate in the kidneys as well as in cultured fibroblasts. Lipid analysis revealed a marked accumulation of ceramidetrihexoside in the liver and the kidneys. These findings indicate the similarity of the pathophysiological process in the mutant mice and in patients with Fabry disease. The deficiency of alpha-Gal A activity and the accumulation of material containing terminal alpha-galactosyl residues in cultured embryonic fibroblasts derived from alpha-Gal A(-/0) mice were corrected by transducing these cells with bicistronic multidrug resistance retroviruses containing human alpha-Gal A cDNA.
High antitumor activity of RLI, an interleukin-15 (IL-15)–IL-15 receptor α fusion protein, in metastatic melanoma and colorectal cancer (2009)

Interleukin (IL)-15 has an important role in tumor immunosurveillance and has a contemplated use in tumor immunotherapy. We have previously engineered the fusion protein RLI, composed of the NH(2)-terminal (amino acids 1-77, sushi+) domain of IL-15 receptor alpha coupled via a linker to IL-15, and shown that it displayed far better efficacy than IL-15 in vitro. In this report, we investigated in vivo whether RLI would be a better alternative than IL-15 and IL-2 for cancer treatment using two distinct animal models. B16F10 mouse melanoma cells were injected in C57BL/6 mice either i.v. or intrasplenically for lung or liver metastasis, respectively. HCT-116 human colorectal cancer cells were injected in the cecum of nude mice. We show that RLI has a higher efficiency than IL-15 or IL-2 to reduce lung and liver metastasis and enhance survival in the mouse B16F10 melanoma model, a result that was associated with a higher half-life in vivo. We also found that the antitumoral effect of RLI was completely abolished by in vivo depletion of natural killer cells using anti-asialoGM1 antibody. Moreover, RLI was also efficient to reduce by 50% tumor growth and the progression of metastasis of human colon carcinoma cells in an orthotopic nude mouse model. The fusion protein RLI has revealed strong anticancer effect in two different cancer models overcoming the limited effect of IL-15 by increasing its bioavailability and efficiency. These findings hold significant importance for the use of RLI as a potential adjuvant/therapeutic.
<title>Model of an instrumented optoelectronic transmission system in HDL-A and VHDL-AMS</title> (1999)

The paper presents the model of a complete multidomain system involving two opto-electronic components: the emitter and the receiver. It is written in Anacad Mentor Graphics HDL-A and integrates the propagation environment characteristics and the thermal behavior of each components. First, packages describing electrical, optical, and thermal behavior of each component. First, packages describing electrical, optical, and thermal domains are detailed. Second, the models of the components are explained. They include an electrical, a thermal and an optical part, the latter being particularly developed. Third, the models of the propagation environment, an optical fiber and the related free space, are presented. The components are assembled to build a compete instrumented opto-electronic transmission system. The laser diode emits a digital clock through an optical fiber to a photodiode. The laser diode is thermal controlled through a Peletier module, which can be deactivated as needed. The alignment of the laser diode with the optical fiber can be studied/modified too. The HDL-A resulting models have been simulated in the ELDO environment. Results show that thermal variations influence the quality of the transmission.
Nrf2 protects against pulmonary fibrosis by regulating the lung oxidant level and Th1/Th2 balance (2010)

The results indicated that Nrf2 protects against the development of pulmonary fibrosis by regulating the cellular redox level and lung Th1/Th2 balance. Thus, Nrf2 might be an important genetic factor in the determination of susceptibility to pulmonary fibrosis.
Identification of the GalP galactose transport protein of Escherichia coli. (1983)

Escherichia coli strains have been isolated with a transposon 10 insertion or an amber mutation inactivating the galP gene, which specifies the galactose-H+ (GalP) transport system. Comparison of the membrane proteins between these strains and their GalP+ parents by dual isotope analysis showed that a component of Mr = 34-39,000 was consistently absent from the GalP- mutants. Galactose, methyl-beta-D-galactoside, and talose protected the GalP transport system from inactivation by N-ethylmaleimide. A membrane protein of Mr = 34-38,000 was modified by N-([2-3H]ethyl)maleimide at the binding site of these sugars. Two-dimensional gel electrophoresis of the membrane proteins has resolved a component of Mr = 35-38,000 (average apparent pI = 5.7) present in parent strains (GalP+) but not in the GalP- mutants. These observations identified a protein of apparent Mr = 37,000 as the product of the galP gene of E. coli.
Hypoxia Induces the Expression of Transketolase-Like 1 in Human Colorectal Cancer (2013)

&lt;b&gt;&lt;i&gt;Background and Aims:&lt;/i&gt;&lt;/b&gt; Transketolase-like (TKTL) 1 is one of the key enzymes for anaerobic sugar degradation even in the presence of oxygen (aerobic glycolysis). Transketolase-dependent reactions supply malignant tumors with ribose and NADPH. Therefore, TKTL1 activity could be crucial for tumor proliferation and survival. The aim of the study was to evaluate the expression of TKTL1 in colorectal cancer (CRC) and its regulation under hypoxic conditions. &lt;b&gt;&lt;i&gt;Methods:&lt;/i&gt;&lt;/b&gt; We studied TKTL1 mRNA and protein expression in CRC cell lines and human CRC biopsies by quantitative real-time PCR, Western blotting and immunohistochemistry. Regulation of TKTL1 under oxygen depletion was analyzed by cultivating cells either in a three-dimensional spheroid model or in a hypoxia incubator chamber. &lt;b&gt;&lt;i&gt;Results:&lt;/i&gt;&lt;/b&gt; TKTL1 mRNA was heterogeneously expressed in monolayers of cells with high levels in HT-29 and SW480. TKTL1 protein was also clearly detectable in HT-29 and SW480. Hypoxia-inducible factor (HIF)-1α protein expression correlated with TKTL1 protein expression in SW480 spheroids over time. On the one hand, induction of hypoxia in T84 spheroids did not induce TKTL1; on the other hand, hypoxia by incubation at 1% O&lt;sub&gt;2&lt;/sub&gt; in a hypoxia incubator chamber clearly showed an upregulation of TKTL1. In 50% of CRC patients, TKTL1 protein expression was upregulated in tumor compared to non-tumor tissue. The immunohistochemical staining of TKTL1 in CRC patient samples resulted in 14 positive and 30 negative samples. &lt;b&gt;&lt;i&gt;Conclusions:&lt;/i&gt;&lt;/b&gt; TKTL1 expression correlated with HIF-1α protein expression and was induced upon hypoxic conditions which could facilitate energy supply to tumors under these circumstances.
Microarray-Based Detection of Salmonella enterica Serovar Typhimurium Transposon Mutants That Cannot Survive in Macrophages and Mice (2005)

DNA microarrays provide an opportunity to combine the principles of signature-tagged mutagenesis (STM) with microarray technology to identify potentially important bacterial virulence genes. The scope of DNA microarrays allows for less laborious screening on a much larger scale than possible by STM alone. We have adapted a microarray-based transposon tracking strategy for use with a Salmonella enterica serovar Typhimurium cDNA microarray in order to identify genes important for survival and replication in RAW 264.7 mouse macrophage-like cells or in the spleens of BALB/cJ mice. A 50,000-CFU transposon library of S. enterica serovar Typhimurium strain SL1344 was serially passaged in cultured macrophages or intraperitoneally inoculated into BALB/cJ mice. The bacterial genomic DNA was isolated and processed for analysis on the microarray. The novel application of this approach to identify mutants unable to survive in cultured cells resulted in the identification of components of Salmonella pathogenicity island 2 (SPI2), which is known to be critical for intracellular survival and replication. In addition, array results indicated that a number of SPI1-associated genes, currently not associated with intracellular survival, are negatively selected. However, of the SPI1-associated mutants individually tested for intracellular survival, only a sirA mutant exhibited reduced numbers relative to those of wild-type bacteria. Of the mutants unable to survive in mice, significant proportions are either components of the SPI2 pathogenicity island or involved in lipopolysaccharide synthesis. This observation is in agreement with results obtained in the original S. enterica serovar Typhimurium STM screen, illustrating the utility of this approach for the high-throughput identification of virulence factors important for survival in the host.
Isolation of Purified and Live Foxp3+ Regulatory T Cells using FACS Sorting on Scatter Plot (2010)

There are no ideal ways to identify and isolate viable and purified Foxp3(+) regulatory T cells so far. Here we developed a novel procedure for the isolation of highly purified Foxp3(+) cells using flow cytometry. This method relies on an identification and sorting of the lymphoblast cell population identified on a scatter plot using flow cytometry. We confirmed that greater than 98% of the cells sorted using this technique expressed Foxp3 and displayed a potent suppressive activity. This method provides a valuable tool for the study of the T regulatory cell biology and their therapeutic manipulation.
Low-Voltage, Low-Loss, Multi-Gb/s Silicon Micro-Ring Modulator based on a MOS Capacitor (2012)

Optical modulation with 8dB extinction ratio and 3dB insertion loss is achieved by applying a 1.5-Vpp drive voltage to a 10-μm ring with embedded MOS capacitor. Open-eye diagrams are obtained at 3Gbps.
Adsorption behavior of fibrinogen to sulfonated polyethyleneoxide-grafted polyurethane surfaces (1993)

Fibrinogen adsorptions to surface modified polyurethanes (PU, PU-PEO, and PU-PEO-SO3) were studied from plasma in vitro. PU and PU-PEO surfaces demonstrated that initial adsorption increases with increasing plasma concentration in kinetic profiles and adsorption time in adsorption profiles as a function of plasma concentration, but after the plateau is reached, its adsorption amount decreases as plasma concentration (0.2-2.0%) and adsorption time (1-120 min) increase, respectively. In contrast, PU-PEO-SO3 showed that initial adsorption is almost same regardless of plasma concentration and adsorption time, which is due to the high affinity of surface sulfonate group to fibrinogen. All the surfaces indicated the Vroman effect at about 0.6% plasma concentration; however, the displacement was relatively low. Adsorbed amount of fibrinogen at steady state decreased in the order: PU > PU-PEO-SO3 > PU-PEO, regardless of adsorption time and plasma concentration. The adsorption behavior of PU-PEO-SO3 is attributed to both effect of low binding affinity of PEO chain and high affinity of pendant sulfonate group toward fibrinogen.
Deficiency of phenotypic cytotoxic-suppressor T lymphocytes in the BB/W rat. (1986)

The BB/W rat is currently the best model of type I (insulin dependent diabetes). Even though this rat develops an autoimmune disease, they are immune deficient. In this study we have demonstrated the almost complete absence of the OX 8+, OX 19+ T cytotoxic/suppressor population in diabetes prone and acute diabetic rats. This population is present in the diabetes resistant W line. The diabetes prone and acute diabetic rats have a relative increase in OX 8+, OX 19- natural killer (NK) cells. Our data suggests that virtually all OX 8+ cells in diabetes prone and acute diabetic animals are phenotypic NK cells.
Wavelets, subdivision algorithms, and radial basis functions (1992)

C.K. Chui: Wavelets and spline interpolation N.D. Dyn: Subdivision schemes in computer-aided geometric design M.J.D. Powell: The theory of radial function approximation in 1990.
Characterization of porcine endothelial cell determinants recognized by human natural antibodies (1994)

Abstract: Organs transplanted from pigs to primates are subject to hyperacute rejection. This immunologic reaction is initiated by the recipient's natural antibodies that bind to endothelial cell antigens of the organ, resulting in the activation of the complement system and rapid destruction of the graft. Various lines of evidence, particularly blocking studies, using purified carbohydrates have suggested that the endothelial cell determinant recognized by human natural antibodies is a terminal galactose in an α configuration (α‐Gal). Although these studies are compelling, they fall short of proof because xenoreactive natural antibodies, being polyreactive, might bind to structures other than those used for blocking. Moreover, in vivo evidence that anti‐α‐Gal antibodies participate in hyperacute rejection has not been reported. Here we report that an enzyme specific for α‐Gal, α‐galactosidase, removes α‐galactose residues from both intact porcine aortic endothelial cells and immobilized porcine aortic endothelial cell membrane extracts and that as a result of this, xenoreactive natural antibody binding is lowered by 70 to 80%. This decrease in binding of human IgM causes a corresponding decrease in complement activation. Similar results were obtained using the sera of other Old World primates. Digestion of immobilized porcine aortic endothelial cell membrane extracts with α‐galactosidase produced a similar reduction in human IgM binding to gp 115/135. These results indicate that a terminal α‐galactose is an important component of the gp 115/135 porcine endothelial cell antigen. We also report that perfusion of porcine organs I with primate serum removes anti‐α‐Gal IgM from the serum.
Multidrug resistance proteins QacA and QacB from Staphylococcus aureus: membrane topology and identification of residues involved in substrate specificity. (1996)

The closely related multidrug efflux pumps QacA and QacB, from the bacterial pathogen Staphylococcus aureus, both confer resistance to various toxic organic cations but differ in that QacB mediates lower levels of resistance to divalent cations. Cloning and nucleotide sequencing of the qacB gene revealed that qacB differs from qacA by only seven nucleotide substitutions. Random hydroxylamine mutagenesis of qacB was undertaken, selecting for variants that conferred increased resistance to divalent cations. Both QacA and the QacB mutants capable of conferring resistance to divalent cations contain an acidic residue at either amino acid 322 or 323, whereas QacB contains uncharged residues in these positions. Site-directed mutagenesis of qacA confirmed the importance of an acidic residue within this region of QacA in conferring resistance to divalent cations. Membrane topological analysis using alkaline phosphatase and beta-galactosidase fusions indicated that the QacA protein contains 14 transmembrane segments. Thus, QacA represents the first membrane transport protein shown to contain 14 transmembrane segments, and confirms that the major facilitator superfamily contains a family of proteins with 14 transmembrane segments.
Full Activity From Human β-Globin Locus Control Region Transgenes Requires 5′HS1, Distal β-Globin Promoter, and 3′ β-Globin Sequences (1998)

The locus control region (LCR) activates high-level human β-globin transgene expression. LCR cassettes composed of 5′HS2-4 linked to the 815 bp β-globin proximal promoter do not express fully. Here, we show that LCR (5′HS2-4) β-globin transgenes that also contain either 5′HS1 or the distal promoter fail to express fully in single- and low-copy transgenic mice. In contrast, full expression is obtained in the presence of both 5′HS1 and the distal promoter. Nine factor binding sites were identified in 5′HS1, using in vitro DNaseI footprint and gel retardation assays, and these include a strong Sp1/Sp3 site, four GATA-1 sites, and two sites that encompass an ACTAAC motif. LCR (5′HS1-4) β-globin transgene constructs with the distal promoter deleted or replaced by spacer DNA show that specific distal promoter sequences are required for full expression. An LCR (5′HS1-4) transgene construct with truncated downstream β-globin gene sequences indicates that 3′ sequences also play an important role. These results show that full expression of the β-globin gene directed by the LCR requires 5′HS1, the distal β-globin promoter, and 3′ sequences, and has implications for gene therapy construct design and models of LCR activation.
Macromolecular Design by Interchange of Xanthates: Background, Design, Scope and Applications (2008)

This chapter contains sections titled: Introduction History of MADIX Polymerization Mechanism of MADIX Polymerization Kinetics of MADIX Polymerization Choice of MADIX Agents Synthesis of MADIX Agents Experimental Conditions in MADIX Monomers Polymerizable by MADIX MADIX Polymerization in Waterborne Dispersed Media Macromolecular Engineering by MADIX Methodologies to Remove the Dithiocarbonate End Groups Applications of MADIX (co)polymers
Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment (2011)

The mucus layer in the colon, acting as a barrier to prevent invasion of pathogens, is thinner and discontinuous in patients with ulcerative colitis (UC). A recent developed in vitro dynamic gut model, the M-SHIME, was used to compare long-term colonization of the mucin layer by the microbiota from six healthy volunteers (HV) and six UC patients and thus distinguish the mucin adhered from the luminal microbiota. Although under the same nutritional conditions, short-chain fatty acid production by the luminal communities from UC patients showed a tendency toward a lower butyrate production. A more in-depth community analysis of those microbial groups known to produce butyrate revealed that the diversity of the Clostridium coccoides/Eubacterium rectale and Clostridium leptum group, and counts of Faecalibacterium prausnitzii were lower in the luminal fractions of the UC samples. Counts of Roseburia spp. were lower in the mucosal fractions of the UC samples. qPCR analysis for butyryl-CoA:acetate CoA transferase, responsible for butyrate production, displayed a lower abundance in both the luminal and mucosal fractions of the UC samples. The M-SHIME model revealed depletion in butyrate producing microbial communities not restricted to the luminal but also in the mucosal samples from UC patients compared to HV.
Coupling evaporation-based, microfluidic concentration and confocal fluorescence spectroscopy (2008)

Detection limits in confocal fluorescence spectroscopy (CFS) have traditionally been restrained by the low molecular detection efficiencies associated with femtoliter probe volumes. In this report, we address this issue by designing a microfluidic evaporator capable of accepting large sample volumes and concentrating biomolecules to a nanoliter-sized, interrogation chamber. Single molecule fluorescence detection within this chamber is enhanced through microfluidic recirculation, enabling single molecule analysis comparable to traditional capillary-based platforms. Proof of concept is demonstrated using a 10X sample concentrator upstream to a 5 nanoliter CFS detection chamber and recording the subsequent increase in single molecule fluorescent bursts. This marriage of active microfluidics and sample processing, and CFS technology offers a novel means of overcoming the limits of single molecule detection in solution.
Design of an 8-wide superscalar RISC microprocessor with simultaneous multithreading (2005)

A 250M transistor microprocessor implements the Alpha instruction set and features 8-wide superscalar issue and simultaneous multithreading in a 0.125/spl mu/m SOI process. Performance is estimated at over three times that of the previous design.