gebhart/patrepeval huggingface dataset:
Control of lipopolysaccharide-high-density lipoprotein interactions by an acute-phase reactant in human serum (1985)

We have recently described several phenomena involving the interactions of lipopolysaccharides (LPS) from Salmonella minnesota Re595 (Re595-LPS) with rabbit serum, which are different in and unique to acute-phase serum as compared with normal serum (P.S. Tobias and R.J. Ulevitch, J. Immunol. 131:1913-1916, 1983). To determine whether these phenomena could also be observed in acute-phase human serum (APHS), we used APHS obtained from volunteers injected with etiocholanolone. As observed in acute-phase rabbit serum, we found that (i) in APHS, Re595-LPS forms a protein complex with a density of 1.3 g/cm3 which does not form in normal human serum (NHS), (ii) in APHS, the t1/2 for LPS-high-density lipoprotein (HDL) complexation is at least a factor of 10 slower than the t1/2 for LPS-HDL complexation in NHS, (iii) when Re595-LPS serum mixtures are dialyzed against a low salt buffer, Re595-LPS precipitates in less soluble form from APHS than from NHS, and (iv) the precipitate from Re595-LPS-APHS mixtures includes a protein with a molecular weight of approximately 60,000 which does not precipitate from Re595-LPS-NHS mixtures or from NHS or APHS alone. These indications of an altered status of LPS in NHS and APHS suggest that one or more acute-phase reactants interact with Re595-LPS to modify its rate of binding to HDL.
Effect of Some Phenolic Compounds and Quercus Tannins on Lipid Peroxidation (2010)

Abstract: In the present study, the anti-lipoperoxidant activity of some phenolic acids, flavonoids and purified tannins from Quercus sp. was determined. Phenolic acids (10, 25 and 50 µg / ml) inhibited lipid peroxidation by 42 – 51%. Caffeic acid seems to be the most potent inhibitor among phenolic acids. Tannic acid, a commercially available tannin, inhibited lipid peroxidation in the same manner as phenolic acids. The inhibition did not exceed 43%.Catechin and quercetin significantly inhibited lipid peroxidation at all tested concentrations and the percentages of inhibition varied between 38 and 60%. However, flavonoid glycosides (rutin and diosmin) did not behave in the same way. Quercus purified tannins showed high inhibition of lipid peroxidation. The observed inhibition was not significantly related to the concentration. Among the four tested tannins, castalagin gave the smallest rate of inhibition (53.9%) versus acutissimin B (65.5%). Key words: Lipid peroxidation Polyphenols Antioxidants Quercus tannins
Structure and expression of the mRNA encoding urinary stone protein (osteopontin) (1993)

The chemical nature of urinary stone protein is poorly understood. We have sequenced a cDNA of urinary calcium oxalate stone protein extracted with EDTA. cDNA sequences showed complete identity between urinary stone protein and human osteopontin. Osteopontin protein was detected by staining with Stains-All, which specifically stains phosphoproteins, and by digestion with the highly specific protease thrombin, demonstrating that urinary calcium oxalate stones consist of osteopontin protein. We used a technique of in situ hybridization to detect osteopontin mRNA in the kidney. In control rats, distal tubular cells were sporadically positive, and proximal tubular cells and glomeruli were negative for osteopontin mRNA. A rat model of stone formation was induced with glyoxylic acid. In stone-forming rats, staining of distal tubular cells was remarkably increased, but proximal tubular cells and glomeruli were still negative. Immunostaining for the osteopontin protein also revealed that epithelial cells of distal tubules were weakly positive in control rats and significantly increased in stone-forming rats, although proximal tubular cells and glomeruli were negative. Northern blot analysis showed a significant increase of osteopontin mRNA in stone-forming rats in proportion to the dosage and the duration of the stone-inducing drugs. These results show that osteopontin in the kidney is presumably involved in urinary stone formation as the stone matrix.
Impedance Spectroscopy: A Powerful Tool for Rapid Biomolecular Screening and Cell Culture Monitoring (2005)

Abstract Dielectric spectroscopy or Electrochemical impedance spectroscopy (EIS) is traditionally used in corrosion monitoring, coatings evaluation, batteries, and electrodeposition and semiconductor characterization. However, in recent years, it is gaining widespread application in biotechnology, tissue engineering, and characterization of biological cells, disease diagnosis and cell culture monitoring. This article discusses the principles and implementation of dielectric spectroscopy in these bioanalytical applications. It provides examples of EIS as label‐free, mediator‐free strategies for rapid screening of biocompatible surfaces, monitoring pathogenic bacteria, as well as the analysis of heterogeneous systems, especially biological cells and tissues. Descriptions are given of the application of nanoparticles to improve the analytical sensitivities in EIS. Specific examples are given of the detection of base pair mismatches in the DNA sequence of Hepatitis B disease, TaySach's disease and Microcystis spp. Others include the EIS detection of viable pathogenic bacteria and the influence of nanomaterials in enhancing biosensor performance. Expanding applications in tissue engineering such as adsorption of proteins onto thiolated hexa(ethylene glycol)‐terminated (EG6) self‐assembled monolayer (SAM) are discussed.
Development of a GPS multi-antenna system for attitude determination (1995)

A GPS multi-antenna system consisting of multiple off-the-shelf GPS sensors has been successfully developed and extensively tested in operational marine environments. The advantages to use such a system are the flexibility in the selection of GPS sensors, the cost-effectiveness of the system with the emerging low-cost high performance GPS products and the increased productivity of equipment which can be assembled into a multi-antenna system or dissembled for other positioning purposes. The underlying methodologies to integrate multiple GPS sensors into an attitude determination system are presented. Specifically, the observation model and its error sources are analyzed. A direct computation method and a least squares procedure for attitude estimation are given. On-the-fly carrier phase ambiguity resolution methods are investigated with emphasis on the use of baseline constraints, a priori attitude information from other low-cost attitude sensors, and special antenna configurations. A specialized post-processing software package for attitude estimation using raw GPS multi-antenna measurements has been developed. A marine test has shown that the proposed multi-antenna system and processing software give consistent results with those from a commercial dedicated attitude system. When a wide antenna spacing was used on a 52metre long surveying vessel with a four GPS sensor attitude system, an accuracy better than 0.06 degrees at an output rate of 10 Hz for the estimated ship attitude parameters has been achieved, when the ship attitude reference was provided by a high accuracy INS. Such a performance of multiple GPS sensor attitude systems demonstrates an alternative means to provide accurate, cost-effective and reliable attitude information for hydrographic surveys and other applications.
Activation of Signalling by the Activin Receptor Complex (1996)

Activin exerts its effects by simultaneously binding to two types of p rotein serine/threonine kinase receptors, each type existing in various isoforms. Using the ActR-IB and ActR-IIB receptor isoforms, we have investigated the mechanism of activin receptor activation. ActR-IIB are phosphoproteins with demonstrable affinity for each other. However, activin addition strongly promotes an interaction between these two proteins. Activin binds directly to ActR-IIB, and this complex associates with ActR-IB, which does not bind ligand on its own. In the resulting complex, ActR-IB becomes hyperphosphorylated, and this requires the kinase activity of ActR-IIB. Mutation of conserved serines and threonines in the GS domain, a region just upstream of the kinase domain in ActR-IB, abrogates both phosphorylation and signal propagation, suggesting that this domain contains phosphorylation sites required for signalling. ActR-IB activation can be mimicked by mutation of Thr-206 to aspartic acid, which yields a construct, ActR-IB(T206D), that signals in the absence of ligand. Furthermore, the signalling activity of this mutant construct is undisturbed by overexpression of a dominant negative kinase-defective ActR-IIB construct, indicating that ActR-IB(T206D) can signal independently of ActR-IIB. The evidence suggests that ActR-IIB acts as a primary activin receptor and ActR-IB acts as a downstream transducer of activin signals.
Arenes to Anilines and Aryl Ethers by Sequential Iridium-Catalyzed Borylation and Copper-Catalyzed Coupling (2007)

[reaction: see text] N-Alkyl- and N-arylanilines were synthesized from arenes by a two-step sequence of iridium-catalyzed borylation and copper-catalyzed coupling with amines. Diaryl ethers were obtained by a related sequence of arene borylation, followed by coupling with phenols. In particular, 3,5-disubstituted arylamines and aryl ethers were prepared by initiating this sequence with meta-substituted arenes.
Cloning and expression of a novel type (III) of human γ‐glutamyltransferase truncated mRNA (1996)

We report the characterization of a novel human gamma-glutamyltransferase mRNA type. This type III mRNA differs from type I and type II mRNAs previously described by several point mutations and the presence of an unspliced 81 bp intron in the open reading frame. Further, type III mRNAs are truncated ones and are tissue and pathology specifically expressed. In fact, type III mRNAs are present in human placenta, sigmoid, lung and in 50% of acute lymphoblastic leukemia blood cells but they are never found in healthy lymphocytes.
Nickel-catalyzed alkyne annulation by anilines: versatile indole synthesis by C–H/N–H functionalization (2013)

Versatile nickel catalysts enabled the step-economical synthesis of decorated indoles through alkyne annulations with anilines bearing removable directing groups. The C-H/N-H activation strategy efficiently occurred in the absence of any metal oxidants and with excellent selectivities.
Overexpression of Pto Activates Defense Responses and Confers Broad Resistance (1999)

The tomato disease resistance (R) gene Pto specifies race-specific resistance to the bacterial pathogen Pseudomonas syringae pv tomato carrying the avrPto gene. Pto encodes a serine/threonine protein kinase that is postulated to be activated by a physical interaction with the AvrPto protein. Here, we report that overexpression of Pto in tomato activates defense responses in the absence of the Pto-AvrPto interaction. Leaves of three transgenic tomato lines carrying the cauliflower mosaic virus 35S::Pto transgene exhibited microscopic cell death, salicylic acid accumulation, and increased expression of pathogenesis-related genes. Cell death in these plants was limited to palisade mesophyll cells and required light for induction. Mesophyll cells of 35S::Pto plants showed the accumulation of autofluorescent compounds, callose deposition, and lignification. When inoculated with P. s. tomato without avrPto, all three 35S::Pto lines displayed significant resistance and supported less bacterial growth than did nontransgenic lines. Similarly, the 35S::Pto lines also were more resistant to Xanthomonas campestris pv vesicatoria and Cladosporium fulvum. These results demonstrate that defense responses and general resistance can be activated by the overexpression of an R gene.
Single-inductor multiple-output switching converters with time-multiplexing control in discontinuous conduction mode (2003)

An integrated single-inductor dual-output boost converter is presented. This converter adopts time-multiplexing control in providing two independent supply voltages (3.0 and 3.6 V) using only one 1-μH off-chip inductor and a single control loop. This converter is analyzed and compared with existing counterparts in the aspects of integration, architecture, control scheme, and system stability. Implementation of the power stage, the controller, and the peripheral functional blocks is discussed. The design was fabricated with a standard 0.5-μm CMOS n-well process. At an oscillator frequency of 1 MHz, the power conversion efficiency reaches 88.4% at a total output power of 350 mW. This topology can be extended to have multiple outputs and can be applied to buck, flyback, and other kinds of converters.
Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood (2010)

We conclude that about 904 miRNAs are expressed in human leukocytes. Out of these 370 are novel miRNAs. We have identified miRNAs that are differentially regulated in normal PBMC with respect to cancer cells, K562 and HL60. Our results suggest that post - transcriptional processes may play a significant role in regulating levels of miRNAs in tumor cells. The study also provides a customized automated computation pipeline for miRNA profiling and identification of novel miRNAs; even those that are missed out by other existing pipelines. The Computational Pipeline is available at the website: http://mirna.jnu.ac.in/deep_sequencing/deep_sequencing.html.
Fluorometric Evaluation of the Affinities of Isoprenylated Peptides for Lipid Bilayers (1994)

A fluorescence-enhancement assay has been used to monitor the association of a series of fluorescent isoprenylated di- to tetrapeptides, whose sequences represent the carboxyl termini of several isoprenylated proteins (Ki-ras, ral 1, rac 2, and rho C), with phospholipid vesicles. These lipopeptides, containing mainly hydrophilic amino acid residues, all rapidly equilibrate (in seconds or faster) between the aqueous phase and the outer surfaces of lipid vesicles, in a manner that is well-modeled as a simple two-phase partitioning equilibrium. Farnesylated or geranylgeranylated peptides with methylated C-terminal cysteine residues exhibit half-maximal binding to 9:1 phosphatidylcholine (PC)/phosphatidylethanolamine (PE) vesicles at lipid concentrations on the order of 5-40 microM or 200-800 nM, respectively. Removal of the methyl group from the carboxyl-terminal cysteine residue decreases the affinity of a given lipopeptide for neutral (PC/PE) vesicles by 10- to 20-fold and the affinity for vesicles with a physiological surface charge by 40-fold or more. Cysteine-linked farnesyl and geranylgeranyl residues are found to be equivalent to cysteine-linked n-alkyl chains of roughly 11 and 14 carbons, respectively, in the strength of their interactions with lipid bilayers. Variations in vesicle lipid composition (cholesterol or aminophospholipid content) only modestly alter the affinity of isoprenylated peptides for the lipid bilayer. Our data suggest that a C-terminal geranylgeranylcysteine or O-methylated farnesylcysteine residue can by itself confer efficient (but rapidly reversible) membrane binding to proteins bearing these modifications, while an unmethylated C-terminal farnesylcysteine residue by itself would be only marginally efficient as a membrane 'anchor' under physiological conditions.
[Ultrastructural study of fallopian tubes after occlusive sterilization with phenol-mucilage]. (1991)

Tubal biopsy specimens were obtained at the time of tubal reversal in 10 women who had had occlusive sterilization by phenol-mucilage; the interval between sterilization to reversal operation ranged from 1-7 years. Transmission electron microscopy revealed that at the site of the tubal occlusion there were abundant collagen fibrils, a few fibrocytes, and scattered lymphocytes. The mucosal epithelium adjacent to the tubal occlusion showed simple columnar ciliated cells and secretory cells. No pathological changes in these cells were seen. 5 of the 10 patients had become pregnant after 1 year following the reversal procedure. Author evidence suggests that the occlusive sterilization with phenol-mucilage does not induce any malignant changes in tubal tissues even after a long time. It is indicated that this method of sterilization is safe. However, bacteria were found in 1 mucosal epithelial specimen and attention should be paid to this observation. (author's modified)
Unusual Amino Acids: Synthesis and Introduction into Naturally Occurring Peptides and Biologically Active Analogues (2006)

This review covers our recent advances in the synthesis of unusual amino acids in optically pure form, and their introduction into naturally occurring peptides with specific biological properties, or into modified bioactive peptides, aiming to obtain analogues displaying enhanced performances in term of activity, bioavailability and resistance to enzymatic hydrolysis.
Transgenic Plants as Tools to Study the Molecular Organization of Plant Genes (1987)

Transgenic plants are generated in nature by Agrobacterium tumefaciens, a pathogen that produces disease through the transfer of some of its own DNA into susceptible plants. The genes are carried on a plasmid. Much has been learned about how the plasmid is transferred, how the plasmid-borne genes are organized, regulated, and expressed, and how the bacteria's pathogenic effects are produced. The A. tumefaciens plasmid has been manipulated for use as a general vector for the transfer of specific segments of foreign DNA of interest (from plants and other sources) into plants; the activities of various genes and their regulation by enhancer and silencer sequences have been assessed. Future uses of the vector (or others like it that have different host ranges) by the agriculture industry are expected to aid in moving into vulnerable plants specific genes that will protect them from such killers as nonselective herbicides, insects, and viruses.
Influenza A Virus Can Undergo Multiple Cycles of Replication without M2 Ion Channel Activity (2001)

Ion channel proteins are common constituents of cells and have even been identified in some viruses. For example, the M2 protein of influenza A virus has proton ion channel activity that is thought to play an important role in viral replication. Because direct support for this function is lacking, we attempted to generate viruses with defective M2 ion channel activity. Unexpectedly, mutants with apparent loss of M2 ion channel activity by an in vitro assay replicated as efficiently as the wild-type virus in cell culture. We also generated a chimeric mutant containing an M2 protein whose transmembrane domain was replaced with that from the hemagglutinin glycoprotein. This virus replicated reasonably well in cell culture but showed no growth in mice. Finally, a mutant lacking both the transmembrane and cytoplasmic domains of M2 protein grew poorly in cell culture and showed no growth in mice. Thus, influenza A virus can undergo multiple cycles of replication without the M2 transmembrane domain responsible for ion channel activity, although this activity promotes efficient viral replication.
Introduction (1992)

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Longitudinal study of the relationship between knee angle and tibiofemoral cartilage volume in subjects with knee osteoarthritis (2004)

Baseline knee angle is associated with the rate of cartilage loss in the knee. Further work will be needed to determine whether therapies aimed at modifying the knee angle will reduce the progression of knee OA.
Rapid and Label-Free Detection of Breast Cancer Biomarker CA15-3 in Clinical Human Serum Samples with Optofluidic Ring Resonator Sensors (2009)

Sensitive and specific detection of breast cancer biomarker CA15-3 in human serum is an important step toward successful evaluation of clinical treatment and prediction of breast cancer recurrence. In this work, we developed an optofluidic ring resonator (OFRR) sensor and the corresponding sensing protocols for label-free CA15-3 detection without any additional signal amplification steps. Nonspecific serum protein adsorption was minimized with effective surface blocking methods. The sensor performance for CA15-3 detection was first characterized in phosphate-buffered saline (PBS) buffer and in fetal calf serum. Then the potential use of the OFRR as a simple clinical laboratory testing device for breast cancer diagnostics was tested by measuring the CA15-3 level in clinical human serum samples, and the results were compared with those of standard clinical lab tests. It was found that the OFRR was capable of detecting approximately 1 unit/mL CA15-3 in both PBS buffer and diluted serum within approximately 30 min. Our work marks the first demonstration of the optical ring resonator biosensor in real clinical applications that features low cost, simple detection procedures, rapid response time, low sample consumption, and high specificity.
Genomic organization and chromosomal localization of three members of the UDP-N-acetylgalactosamine: Polypeptide N-acetylgalactosaminyltransferase family (1998)

A homologous family of UDP- N -acetylgalactosamine: polypeptide N -acetylgalactosaminyltransferases (GalNAc-transferases) initiate O-glycosylation. These transferases share overall amino acid sequence similarities of approximately 45-50%, but segments with higher similarities of approximately 80% are found in the putative catalytic domain. Here we have characterized the genomic organization of the coding regions of three GalNAc-transferase genes and determined their chromosomal localization. The coding regions of GALNT1 , -T2 , and -T3 were found to span 11, 16, and 10 exons, respectively. Several intron/exon boundaries were conserved within the three genes. One conserved boundary was shared in a homologous C. elegans GalNAc-transferase gene. Fluorescence in situ hybridization showed that GALNT1 , -T2 , and -T3 are localized at chromosomes 18q12-q21, 1q41-q42, and 2q24-q31, respectively. These results suggest that the members of the polypeptide GalNAc-transferase family diverged early in evolution from a common ancestral gene through gene duplication.
Mechanism of Activation of the Caenorhabditis elegans ras Homologue let-60 by a Novel, Temperature-Sensitive, Gain-of-Function Mutation (1997)

The Caenorhabditis elegans let-60 gene encodes a Ras protein that mediates induction of the hermaphrodite vulva. To better understand how mutations constitutively activate Ras and cause unregulated cell division, we have characterized ga89, a temperature-sensitive, gain-of-function mutation in let-60 ras. At 25 degrees, ga89 increases let-60 activity resulting in a multivulva phenotype. At 15 degrees, ga89 decreases let-60 activity resulting in a vulvaless phenotype in let-60(ga89)/Df animals. The ga89 mutation causes a leucine (L) to phenylalanine (F) substitution at amino acid 19, a residue conserved in all Ras proteins. We introduced the L19F change into human H-Ras protein and found that the in vitro GTPase activity of H-Ras became temperature-dependent. Genetic experiments suggest that LET-60 (L19F) interacts with GAP and GNEF, since mutations that decrease GAP and GNEF activity affect the multivulva phenotype of let-60(ga89) animals. These results suggest that the L19F mutation primarily affects the intrinsic rate of GTP hydrolysis by Ras, and that this effect may be sufficient to account for the activated-Ras phenotype caused by let-60(ga89). Our results suggest that a mutation in a human ras gene analogous to ga89 might contribute to oncogenic transformation.