gebhart/patrepeval huggingface dataset:
Ambient Mass Spectrometry Imaging Using Direct Liquid Extraction Techniques (2015)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAmbient Mass Spectrometry Imaging Using Direct Liquid Extraction TechniquesJulia Laskin*† and Ingela Lanekoff*‡View Author Information† Physical Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN K8-88, Richland, Washington 99352, United States‡ Department of Chemistry-BMC, Uppsala University, Box 599, 751 24 Uppsala, Sweden*E-mail: [email protected]*E-mail: [email protected]Cite this: Anal. Chem. 2016, 88, 1, 52–73Publication Date (Web):November 13, 2015Publication History Published online24 November 2015Published inissue 5 January 2016https://doi.org/10.1021/acs.analchem.5b04188Copyright © 2015 American Chemical SocietyRequest reuse permissionsArticle Views5279Altmetric-Citations123LEARN 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 InReddit Read OnlinePDF (9 MB) Get e-AlertscloseSUBJECTS:Extraction,Ionization,Liquids,Metabolism,Molecules Get e-Alerts
Identification of a motif for HLA-DR1 binding peptides using M13 display libraries. (1992)

Oligonucleotides encoding peptides known to bind to HLA-DR1 molecules have been inserted into the gene III of filamentous M13 phages. DR1 molecules purified from human lymphoblastoid cell lines could specifically bind to these peptide sequences expressed on the phage surface. A M13 phage peptide library was next constructed and screened with DR1 molecules. After four rounds of selection, more than 80% of the phages were able to bind to DR1. Competition experiments with both isolated phages and corresponding synthetic peptides showed that the binding was specific. Sequence analysis of the peptide encoding region of 60 phages binding to DR1 molecules and comparison with phages of the original library revealed two potential anchor positions. The first was an aromatic residue (Tyr, Phe, or Trp) at the NH2 terminus of the peptide sequences, and the second was located three residues downstream and consisted of Met or Leu. In addition, the negatively charged amino acids Asp and Glu were mostly excluded from the DR1 binding sequences, and the small amino acid residues Gly and Ala were enriched at position 6. As for DR1, this approach should enable one to easily determine the binding motifs of other MHC class II alleles and isotypes. Furthermore, it could have interesting applications in the design of major histocompatibility complex-specific antagonists.
Opioid Receptors (2004)

Opioid receptors belong to the large superfamily of seven transmembrane-spanning (7TM) G protein-coupled receptors (GPCRs). As a class, GPCRs are of fundamental physiological importance mediating the actions of the majority of known neurotransmitters and hormones. Opioid receptors are particularly intriguing members of this receptor family. They are activated both by endogenously produced opioid peptides and by exogenously administered opiate compounds, some of which are not only among the most effective analgesics known but also highly addictive drugs of abuse. A fundamental question in addiction biology is why exogenous opioid drugs, such as morphine and heroin, have a high liability for inducing tolerance, dependence, and addiction. This review focuses on many aspects of opioid receptors with the aim of gaining a greater insight into mechanisms of opioid tolerance and dependence.
Coordination and decentralized cooperation of multiple mobile manipulators (1996)

Mobile manipulation capabilities are key to many new applications of robotics in space, underwater, construction, and service environments. This article discusses the ongoing effort at Stanford University for the development of multiple mobile manipulation systems and presents the basic models and methodologies for their analysis and control. This work builds on four methodologies we have previously developed for fixed-base manipulation: the Operational Space Formulation for task-oriented robot motion and force control; the Dextrous Dynamic Coordination of Macro/Mini structures for increased mechanical bandwidth of robot systems; the Augmented Object Model for the manipulation of objects in a robot system with multiple arms; and the Virtual Linkage Model for the characterization and control of internal forces in a multi-arm system. We present the extension of these methodologies to mobile manipulation systems and propose a new decentralized control structure for cooperative tasks. The article also discusses experimental results obtained with two holonomic mobile manipulation platforms we have designed and constructed at Stanford University. © 1996 John Wiley & Sons, Inc.
The Integrin Ligand Echistatin Prevents Bone Loss in Ovariectomized Mice and Rats (1998)

Integrins that bind RGD (arginine-glycine-aspartic acid) containing peptides, especially the vitronectin receptor alpha(v)beta3, have been implicated in the regulation of osteoclast function. Echistatin, an RGD-containing snake venom peptide with high affinity for beta3 integrins, as well as nonpeptide RGD mimetics, were shown to inhibit osteoclastic bone resorption in vitro and in vivo. To evaluate the role of RGD-binding integrins in bone metabolism, we examined by several methods the effects of echistatin on ovariectomy (OVX)-induced bone loss in mice and rats. First, we confirmed that echistatin binds in vitro with high affinity (Kd, 0.5 nM) to alpha(v)beta3 integrin purified from human placenta and established a competitive binding assay to measure echistatin concentrations in serum. We find that echistatin infused for 2 or 4 weeks at 0.36 microg/h x g body weight (approximately 50 nmol/day x mouse) completely prevents OVX-induced cancellous bone loss in the distal femora of ovariectomized mice. Echistatin has no effect on uterine weight, body weight, and femoral length changes induced by OVX, nor does it cause any apparent changes in major organs other than bone. In OVX rats, echistatin infusion at 0.26 microg/h x g for 4 weeks effectively prevents bone loss, evaluated by dual energy x-ray absorptiometry of the femur, by femoral ash weight, and by bone histomorphometry of the proximal tibia. At effective serum concentrations of 20-30 nM, measured at the end of the infusion period, echistatin maintains histomorphometric indices of bone turnover at control levels but does not decrease osteoclast surface. In conclusion, these results provide in vivo evidence, at the level of bone histology, that RGD-binding integrins, probably alpha(v)beta3, play a rate-limiting role in osteoclastic bone resorption and suggest a therapeutic potential for integrin ligands in the suppression of bone loss.
Tribeca: a system for managing large databases of network traffic (1998)

The engineers who analyze traffic on high bandwidth networks must filter and aggregate either recorded traces of network packets or live traffic from the network itself. These engineers perform operations similar to database queries, but cannot use conventional data managers because of performance concerns and a semantic mismatch between the analysis operations and the operations supported by commercial DBMSs. Traffic analysis does not require fast random access, transactional update, or relational joins. Rather, it needs fast sequential access to a stream of traffic records and the ability to filter, aggregate, define windows, demultiplex, and remultiplex the stream. Tribeca is an extensible, stream-oriented DBMS designed to support network traffic analysis. It combines ideas from temporal and sequence databases with an implementation optimized for databases stored on high speed ID-1 tapes or arriving in real time from the network. The paper describes Tribeca&amp;apos;s query language, executo...
Characterization of a neu/c-erbB-2 protein-specific activating factor. (1991)

The neu oncogene encodes a tyrosine kinase with growth factor receptor-like properties. A neu protein-specific activating factor (NAF) was partially purified from medium conditioned by the transformed human T-cell line ATL-2. NAF was able to stimulate the tyrosine-specific kinase activity of the neu protein (p185neu), induce dimerization and internalization, and increase the growth of cells bearing the neu protein. The effects of NAF were mediated by an interaction with the p185neu extracellular domain. NAF had no effect on the epidermal growth factor receptor kinase activity and no effect on cells that express that receptor. Further analysis of NAF and of other recently described neu protein-activating activities should help clarify the role of the neu protein in cell growth and transformation.
α-Helical Linker of an Artificial 6-Zinc Finger Peptide Contributes to Selective DNA Binding to a Discontinuous Recognition Sequence (2007)

Although many zinc finger motifs have been developed to recognize specific DNA triplets, a rational way to selectively skip a particular non-recognized gap in the DNA sequence has never been established. We have now created a 6-zinc finger peptide with an alpha-helix linker, Sp1ZF6(EAAAR)4, which selectively binds to the discontinuous recognition sites in the same phase (10 bp gap) against the opposite phase (5 bp gap) of the DNA helix. The linker peptide (EAAAR)4 forms an alpha-helix structure stabilized by salt bridges, and the helical length is estimated to be about 30 A, corresponding to that of the 10 bp DNA. The gel shift assays demonstrate that Sp1ZF6(EAAAR)4 preferably binds to the 10 bp-gapped target rather than the 5 bp-gapped target. The CD spectra show that the alpha-helical content of the (EAAAR)4 linker is higher in the complex with the 10 bp-gapped target than in the complex with the 5 bp-gapped target. The present results indicate that the alpha-helical linker is suitable for binding to the recognition sites in the same phase and that the linker induces the loss of binding affinity to the recognition sites with the opposite phase. The engineering of a helix-structured linker in the 6-zinc finger peptides should be one of the most promising approaches for selectively targeting discontinuous recognition sites depending on their phase situations.
Using pulsed gradient spin echo NMR for chemical mixture analysis: How to obtain optimum results (2002)

Abstract Pulsed gradient spin echo NMR is a powerful technique for measuring diffusion coefficients. When coupled with appropriate data processing schemes, the technique becomes an exceptionally valuable tool for mixture analysis, the separation of which is based on the molecular size. Extremely fine differentiation may be possible in the diffusion dimension but only with high‐quality data. For fully resolved resonances, components with diffusion coefficients that differ by less than 2% may be distinguished in mixtures. For highly overlapped resonances, the resolved spectra of pure components with diffusion coefficients that differ by less than 30% may be obtained. In order to achieve the best possible data quality one must be aware of the primary sources of artifacts and incorporate the necessary means to alleviate them. The origin of these artifacts are described, along with the methods necessary to observe them. Practical solutions are presented. Examples are shown that demonstrate the effects of the artifacts on the acquired data set. Many mixture analysis problems may be addressed with conventional high resolution pulsed field gradient probe technology delivering less than 0.5 T m −1 (50 G cm −1 ). © 2002 Wiley Periodicals, Inc. Concepts Magn Reson 14: 225–258, 2002.
Simultaneous determination of multiple mRNA levels utilizing MALDI-TOF mass spectrometry and biotinylated dideoxynucleotides (2010)

Here we report an efficient method to simultaneously measure multiple mRNA levels utilizing mass spectrometry (MS) and molecular affinity isolation. In this approach, reverse transcription products of a group of mRNAs are subjected to competitive PCR with competitors and internal standards of known concentrations, and the PCR products are differentiated and quantified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS to determine the mRNA levels. The method provides high accuracy in quantitative MS analysis due to the facilitated purification of oligonucleotides by molecular affinity isolation. Additionally, owing to the molecular affinity isolation, only those oligonucleotides required for expression level determination are introduced into the mass spectrometer, while other irrelevant reaction components that could overlap with peaks of gene transcripts or competitors are removed prior to MS analysis. Thus the approach enhances the parallel analysis of multiple gene transcripts by MS. Utilizing the method we have simultaneously measured mRNA levels of four genes (Rho, Nrl, Hprt, and Lhx2) in mouse retinal tissue.
TLR7 and TLR8 expression increases tumor cell proliferation and promotes chemoresistance in human pancreatic cancer (2015)

Chronic inflammation as an important epigenetic and environmental factor for putative tumorigenesis and tumor progression may be associated with specific activation of Toll-like receptors (TLR). Recently, carcinogenesis has been suggested to be dependent on TLR7 signaling. In the present study, we determined the role of both TLR7 and TLR8 expression and signaling in tumor cell proliferation and chemoresistance in pancreatic cancer. Expression of TLR7/TLR8 in UICC stage I-IV pancreatic cancer, chronic pancreatitis, normal pancreatic tissue and human pancreatic (PANC1) cancer cell line was examined. For in vitro/in vivo studies TLR7/TLR8 overexpressing PANC1 cell lines were generated and analyzed for effects of (un-)stimulated TLR expression on tumor cell proliferation and chemoresistance. TLR expression was increased in pancreatic cancer, with stage-dependent upregulation in advanced tumors, compared to earlier stages and chronic pancreatitis. Stimulation of TLR7/TLR8 overexpressing PANC1 cells resulted in elevated NF-κB and COX-2 expression, increased cancer cell proliferation and reduced chemosensitivity. More importantly, TLR7/TLR8 expression increased tumor growth in vivo. Our data demonstrate a stage-dependent upregulation of both TLR7 and TLR8 expression in pancreatic cancer. Functional analysis in human pancreatic cancer cells point to a significant role of both TLRs in chronic inflammation-mediated TLR7/TLR8 signaling leading to tumor cell proliferation and chemoresistance.
Self-powered deep brain stimulation via a flexible PIMNT energy harvester (2015)

A self-powered deep brain stimulation has been demonstrated by a flexible piezoelectric PIMNT energy harvester to induce behavioural changes in a mouse.
Inhibition of Efflux Transporter-Mediated Fungicide Resistance in Pyrenophora tritici-repentis by a Derivative of 4′-Hydroxyflavone and Enhancement of Fungicide Activity (2005)

Populations of the causal agent of wheat tan spot, Pyrenophora tritici-repentis, that are collected from fields frequently treated with reduced fungicide concentrations have reduced sensitivity to strobilurin fungicides and azole fungicides (C14-demethylase inhibitors). Energy-dependent efflux transporter activity can be induced under field conditions and after in vitro application of sublethal amounts of fungicides. Efflux transporters can mediate cross-resistance to a number of fungicides that belong to different chemical classes and have different modes of action. Resistant isolates can grow on substrata amended with fungicides and can infect plants treated with fungicides at levels above recommended field concentrations. We identified the hydroxyflavone derivative 2-(4-ethoxy-phenyl)-chromen-4-one as a potent inhibitor of energy-dependent fungicide efflux transporters in P. tritici-repentis. Application of this compound in combination with fungicides shifted fungicide-resistant P. tritici-repentis isolates back to normal sensitivity levels and prevented infection of wheat leaves. These results highlight the role of energy-dependent efflux transporters in fungicide resistance and could enable a novel disease management strategy based on the inhibition of fungicide efflux to be developed.
Mink Lung Epithelial Cells: Unique Cell Line That Supports Influenza A and B Virus Replication (1998)

We have demonstrated for the first time that a mink lung epithelial cell line (Mv1Lu) supports the replication of influenza A and B viruses, including the recently isolated H5N1 avian and human Hong Kong strains, to titers comparable to those in MDCK cells. These results suggest that Mv1Lu cells might serve as an alternative system for the isolation and cultivation of influenza A and B viruses and may be useful for vaccine development.
Rescue of Exocytosis in Botulinum Toxin A-poisoned Chromaffin Cells by Expression of Cleavage-resistant SNAP-25 (1999)

Botulinum neurotoxin (BoNT) types A and B selectively block exocytosis by cleavage of SNAP-25 and synaptobrevin, respectively; in humans, many months are required for full recovery from the resultant neuromuscular paralysis. To decipher the molecular basis for such prolonged poisoning, intoxication in adreno-chromaffin cells was monitored over 2 months. Exocytosis from BoNT/B-treated cells resumed after 56 days because of the appearance of intact synaptobrevin. However, inhibition continued in BoNT/A-treated cells, throughout the same interval, with a continued predominance of cleaved SNAP-25-(1-197) over the intact protein. When recovery from poisoning was attempted by transfection of the latter cells with the gene encoding full-length SNAP-25-(1-206), no restoration of exocytosis ensued even after 3 weeks. To ascertain if this failure was because of the persistence of the toxin's protease activity, the cells were transfected with BoNT/A-resistant SNAP-25 constructs; importantly, exocytosis was rescued. C-terminal truncation of the toxin-insensitive SNAP-25 revealed that residues 1-201, 1-202, 1-203 afforded a significant return of exocytosis, unlike shorter forms 1-197, -198, -199, or -200; accordingly, mutants M202A or L203A of full-length SNAP-25 rescued secretion. These findings give insights into the C-terminal functional domain of SNAP-25, demonstrate the longevity of BoNT/A protease, and provide the prospect of a therapy for botulism.
13C-NMR Studies of Hyaluronan:  Conformational Sensitivity to Varied Environments (1996)

Hyaluronan (HA) samples ranging in size from small oligosaccharides to high molecular weight polymer have been studied by 13C-NMR spectroscopy. In neutral aqueous solutions, the chemical shifts of carbons directly involved in the β-1,3 glucuronidic linkage are found to be sensitive to (1) residue linkage position in short chains, (2) oligomer degree of polymerization, (3) solvent ionic strength, and (4) monovalent vs divalent counterions. The carbons of the β-1,4-glucosaminidic linkage show less sensitivity to the above conditions. Thus conformational versatility for HA in aqueous solution is correlated with a chemical shift change primarily in carbons of the β-1,3 linkage. We have also compared the 13C spectrum of HA in neutral aqueous salt solutions to spectra observed in dimethyl sulfoxide (DMSO) solution (ordered 2- or 4-fold HA form) or the solid state (Na+ counterion, tetragonal 4-fold helical HA form). The solid state spectrum is similar to that found in DMSO but differs substantially from the aqueous solution spectrum. The differences are attributed to (1) rotation of the acetamido group, with concomitant change in hydrogen bonding and average conformation at the β-1,4 linkage, and (2) loss of hydrogen bonds in aqueous solution and consequent change in average conformation at the β-1,3 linkage.
A common antigenic determinant found in two functionally unrelated toxins. (1984)

The heat-stable enterotoxin ST Ib produced by enterotoxigenic E. coli strains shares a sequence homology with the sea snail neurotoxin, conotoxin GI. Rabbit antisera were raised against synthetic analogs of these toxins and to a six-residue peptide representing the region common to both toxins. Results from enzyme-linked immunosorbent assays indicate that the homologous region of both toxins represents part of their antigenic site. The lack of cross-reactivity exhibited by the six-residue common domain with serum directed against either toxin suggests that this region probably retains a similar conformation in the intact toxins but not in the isolated fragment.
Differential antibody screening of cloned Plasmodium falciparum sequences expressed in Escherichia coli: procedure for isolation of defined antigens and analysis of human antisera. (1984)

We describe a procedure that uses polyspecific human sera for screening Escherichia coli colonies expressing cloned Plasmodium falciparum cDNA sequences in order to detect colonies that react differentially with different sera. This procedure can be used for two distinct purposes. First, it enables the isolation of clones encoding specified antigenic sequences present in the complex mixture, without purification of either antigens or antibodies by conventional procedures. This requires that the antigen can be expressed in E. coli and that antisera are available that differ substantially in their reactivities to the component of interest. To develop the procedure, we used two polyspecific sera that shared many anti-P. falciparum specificities but differed in that only one was reactive to the isolate-specific S antigen of P. falciparum strain FCQ27/PNG (called FC27). Differential screening with the two sera identified 30 cDNA clones, and colony hybridization confirmed that 25 of these express S-antigen sequences. Second, the procedure identifies defined antibody specificities within polyspecific human sera by virtue of their ability to react with any given cDNA clone. The procedure has been used here to identify antibody specificities that increase dramatically in titer between the acute and convalescent phases of malaria in certain individuals and, hence, to isolate clones encoding the corresponding antigens.
Multiple Jets in Electrospinning (2006)

The low fluid throughput in electrospinning may limit the industrial use of single needle system. To meet high liquid throughput requirements and uniform fibers, a special aligned multiple jets setup has been designed in this paper. The needles have been disposed as a regular hexagon. A 7 cm diameter iron ring has been used in one experiment and different heights of the 7 needles have been used in another experiment in order to received uniform fibers from 7 needles. The results demonstrate that the special setup could produce uniform fibers according to SEM images. Electrical field distribution from the spinning nozzle to the collector was also calculated, analyzed and presented in this paper
A transport network layer based on optical network elements (1993)

An approach to the realization of a broadband, flexible, multiwavelength transport network employing an optical network layer. The design methodology for a network demonstrator is presented, and the transmission, switching, line, and management/supervisory subsystems and components are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>