gebhart/patrepeval huggingface dataset:
Mass Spectrometric Imaging for Biomedical Tissue Analysis (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTMass Spectrometric Imaging for Biomedical Tissue AnalysisKamila Chughtai and Ron M. A. Heeren*View Author Information FOM-Institute for Atomic and Molecular Physics, Science Park 104, 1098 XG Amsterdam, The Netherlands* Corresponding author. Telephone: +31-20-7547 100. Fax: +31-20-7547 290. E-mail address: [email protected]Cite this: Chem. Rev. 2010, 110, 5, 3237–3277Publication Date (Web):April 28, 2010Publication History Received13 January 2010Published online28 April 2010Published inissue 12 May 2010https://pubs.acs.org/doi/10.1021/cr100012chttps://doi.org/10.1021/cr100012creview-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views9661Altmetric-Citations527LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Ions,Lipids,Mass spectrometry,Peptides and proteins,Rodent models Get e-Alerts
Polyphenol Coating as an Interlayer for Thin-Film Composite Membranes with Enhanced Nanofiltration Performance (2016)

Thin-film composite (TFC) nanofiltration membranes are prepared via interfacial polymerization with a polyphenol coating as an interlayer for the thin and smooth polyamide selective layer. The polyphenol interlayer is simply fabricated by the codeposition of tannic acid and diethylenetriamine without changing the surface morphology of the polysulfone ultrafiltration substrate. An interfacial polymerization is conducted from piperazidine and trimesoyl chloride on the polyphenol interlayer to construct the polyamide selective layer. The as-prepared TFC nanofiltration membranes show nearly tripled fold of water permeation flux as compared with those prepared at the same condition without an interlayer. They also exhibit a high rejection to Na<sub>2</sub>SO<sub>4</sub> (>98%) because the thin and defect-free polyamide selective layer is formed on the polyphenol interlayer. These nanofiltration properties have high reproducibility, which means the TFC nanofiltration membranes are suitable for scale-up industrial applications.
Dynamic Combination of Automatic Speech Recognition Systems by Driven Decoding (2013)

Combining automatic speech recognition (ASR) systems generally relies on the posterior merging of the outputs or on acoustic cross-adaptation. In this paper, we propose an integrated approach where outputs of secondary systems are integrated in the search algorithm of a primary one. In this driven decoding algorithm (DDA), the secondary systems are viewed as observation sources that should be evaluated and combined to others by a primary search algorithm. DDA is evaluated on a subset of the ESTER I corpus consisting of 4 hours of French radio broadcast news. Results demonstrate DDA significantly outperforms vote-based approaches: we obtain an improvement of 14.5% relative word error rate over the best single-systems, as opposed to the the 6.7% with a ROVER combination. An in-depth analysis of the DDA shows its ability to improve robustness (gains are greater in adverse conditions) and a relatively low dependency on the search algorithm. The application of DDA to both and beam-search-based decoder yields similar performances.
Visualization for knowledge discovery (1992)

Although the fields of data visualization and automated knowledge discovery (AKD) share many goals, workers in each field have been reluctant to adopt the tools and methods of the other field. Many AKD researchers discourage the use of visualization tools because they believe that dependence on human steering will impede the development of numerical or analytical descriptions of complex data. Many visualization researchers are concerned that their present platforms are being pushed to the limits of their performance by the most advanced visualization techniques and are therefore unwilling to incur the perceived overhead of having a database system mediate access to the data. We argue that these attitudes are somewhat short-sighted and that the techniques of these two communities are complementary. We discuss a specific visualization system that we have developed and describe the obstacles that must be overcome in integrating it into an AKD system. © 1992 John Wiley & Sons, Inc.
Understanding Features And Distance Functions For Music Sequence Alignment. (2010)

[TODO] Add abstract here.
Evidence for primordial water in Earth’s deep mantle (2015)

The hydrogen-isotope [deuterium/hydrogen (D/H)] ratio of Earth can be used to constrain the origin of its water. However, the most accessible reservoir, Earth's oceans, may no longer represent the original (primordial) D/H ratio, owing to changes caused by water cycling between the surface and the interior. Thus, a reservoir completely isolated from surface processes is required to define Earth's original D/H signature. Here we present data for Baffin Island and Icelandic lavas, which suggest that the deep mantle has a low D/H ratio (δD more negative than -218 per mil). Such strongly negative values indicate the existence of a component within Earth's interior that inherited its D/H ratio directly from the protosolar nebula.
Recurrence after surgery in patients with NSCLC. (2014)

Surgery remains the only potentially curative modality for early-stage non-small cell lung cancer (NSCLC) patients and tissue availability is made possible. However, a proportion of lung cancer patients develop recurrence, even after curative resection. This review discusses the superiority of surgery, the reasons for recurrence, the timing and pattern of recurrence, the identification of factors related to recurrence, current provisions for treatment and perspectives about surgery for patients with NSCLC.
Microtube batch protein crystallization: Applications to human immunodeficiency virus type 2 (HIV‐2) protease and human renin (1994)

For therapeutically relevant targets, the evaluation of enzymes in complex with their inhibitors by cocrystallization and high resolution structural analysis has become a vital component of structure-driven drug design and development. Two approaches, hanging drop vapor diffusion and a novel microtube batch method, were utilized in parallel to grow crystals of recombinant HIV-2 protease and recombinant human renin in complex with inhibitors. In the case of HIV-2 protease in complex with a reduced amide inhibitor, crystallization was achieved only by the microbatch method. In the case of human renin, the addition of precipitant was required for crystal growth. The microbatch method described here is a useful supplementary or alternative approach for screening parameters and generating crystals suitable for high resolution structural analysis.
Involvement of the Cytoplasmic Domain of the Hemagglutinin-Neuraminidase Protein in Assembly of the Paramyxovirus Simian Virus 5 (1999)

Efficient assembly of enveloped viruses at the plasma membranes of virus-infected cells requires coordination between cytosolic viral components and viral integral membrane glycoproteins. As viral glycoprotein cytoplasmic domains may play a role in this coordination, we have investigated the importance of the hemagglutinin-neuraminidase (HN) protein cytoplasmic domain in the assembly of the nonsegmented negative-strand RNA paramyxovirus simian virus 5 (SV5). By using reverse genetics, recombinant viruses which contain HN with truncated cytoplasmic tails were generated. These viruses were shown to be replication impaired, as judged by small plaque size, reduced replication rate, and low maximum titers when compared to those features of wild-type (wt) SV5. Release of progeny virus particles from cells infected with HN cytoplasmic-tail-truncated viruses was inefficient compared to that of wt virus, but syncytium formation was enhanced. Furthermore, accumulation of viral proteins at presumptive budding sites on the plasma membranes of infected cells was prevented by HN cytoplasmic tail truncations. We interpret these data to indicate that formation of budding complexes, from which efficient release of SV5 particles can occur, depends on the presence of an HN cytoplasmic tail.
Molecular Cloning and Nucleotide Sequence of Purine Nucleoside Phosphorylase and Uridine Phosphorylase Genes fromKlebsiella sp. (1995)

Klebsiella sp. LF 1202 was isolated as a bacterium that can assimilate adenosine as a sole source of carbon and nitrogen [F. Ling et al., Agric. Biol. Chem., 55, 573-575 (1991)] from a soil sample. Both the purine nucleoside phosphorylase (PNPase) and uridine phosphorylase (UPase) of this bacterium were induced simultaneously when the bacterium was cultured in a medium containing adenosine or uridine as a sole source of carbon and nitrogen. This induction profile is different from that of Escherichia coli. Here we cloned and sequenced the gene corresponding to each enzyme. The open reading frame (ORF) of the PNPase gene consisted of 717 bp that encoded a polypeptide of 239 amino acids with a molecular weight of 26,198. The ORF of the UPase gene consisted of 834 bp that encoded a polypeptide of 278 amino acids with a molecular weight of 28,912.
Enhanced Th2 Cell-Mediated Allergic Inflammation in Tyk2-Deficient Mice (2003)

Allergic inflammation is mediated by Th2 cell-derived cytokines, including IL-4, IL-5, and IL-13, and down-regulated by IFN-gamma and IL-12. Tyk2 is a member of the Janus family of protein tyrosine kinases and is activated by a variety of cytokines: IFN-alphabeta, IL-6, IL-10, IL-12, and IL-13. In this study, we investigated the role of Tyk2 in the regulation of Ag-induced Th cell differentiation and Ag-induced allergic inflammation in the airways using Tyk2-deficient (Tyk2(-/-)) mice. When splenocytes were stimulated with antigenic peptide, IL-12-mediated Th1 cell differentiation was decreased, but IL-4-mediated Th2 cell differentiation was increased in Tyk2(-/-) mice. In vivo, Ag-specific IgE and IgG1 production was increased, but Ag-specific IgG2a production was decreased in Tyk2(-/-) mice as compared with those in control mice. In addition, Ag-induced eosinophil and CD4(+) T cell recruitment, as well as the production of Th2 cytokines in the airways, was increased in Tyk2(-/-) mice. Adoptive transfer experiments revealed that CD4(+) T cells were responsible for the enhanced Ag-induced eosinophil recruitment in Tyk2(-/-) mice. In contrast, although the level of IL-13 was increased in the airways of Tyk2(-/-) mice after Ag inhalation, the number of goblet cells, as well as Muc5ac mRNA expression, was decreased in Tyk2(-/-) mice. Together, these results indicate that Tyk2 plays a bilateral role in the regulation of allergic inflammation in the airways: Tyk2 plays a role in the down-regulation of Th2 cell-mediated Ab production and eosinophil recruitment in the airways by regulating Th1/Th2 balance toward Th1-type, while Tyk2 is necessary for the induction of IL-13-mediated goblet cell hyperplasia in the airways.
Use of Cholecystokinin-Octapeptide for the Prevention of Parenteral Nutrition-Associated Cholestasis (2005)

Use of CCK-OP failed to reduce significantly the incidence of PNAC or levels of CB. CCK-OP had no effect on other secondary measures and should not be recommended for the prevention of PNAC.
Direct classification from compressively sensed images via deep Boltzmann machine (2016)

We examine a potential technique of performing a classification task based on compressively sensed (CS) data, skipping a computationally expensive reconstruction step. A deep Boltzmann machine is trained on a compressive representation of MNIST handwritten digit data, using a random orthoprojector sensing matrix. The network is first pre-trained on uncompressed data in order to learn the structure of the dataset. The outer network layers are then optimized using backpropagation. We find this approach achieves a 1.21% test data error rate at a sensing rate of 0.4, compared to a 0.99% error rate for non-compressive data.
Enhanced single photon fringe visibility in a 10 km-long prototype quantum cryptography channel (1993)

High visibility (V = 0.985) single photon fringe measurements in a 10 km long, optical fibre-based, time- and polarisation-division Mach-Zehnder interferometer are reported. The ability of the system to transmit key data in a quantum cryptography scheme is assessed.
Mobility of electrons in bulk GaN andAlxGa1−xN/GaNheterostructures (2000)

The room-temperature drift mobility of electrons in the channel of a ${\mathrm{Al}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}\mathrm{N}/\mathrm{G}\mathrm{a}\mathrm{N}$ field-effect transistor associated with scattering by optical and acoustic phonons is calculated as a function of areal density taking into account the two-mode nature of the alloy and half-space and interface modes. It is found that the two-dimensional (2D) mobility is significantly greater than the bulk mobility and this means that the mobility goes through a maximum as a function of density corresponding to a transition from bulk to 2D transport. A simple model is used to describe the transition from bulk to 2D transport as the electron density increased. It is shown that for the structure considered the mobility at 300 K goes through a weak maximum at about 2000 ${\mathrm{cm}}^{2}$/V s at a density of about $2\ifmmode\times\else\texttimes\fi{}{10}^{12} {\mathrm{cm}}^{\mathrm{\ensuremath{-}}2}$ dropping to about 1300 ${\mathrm{cm}}^{2}$/V s at ${10}^{13} {\mathrm{cm}}^{\mathrm{\ensuremath{-}}2}.$ Results for the Hall factor and for the temperatures 77 and 600 K are also obtained. The contribution made by interface-roughness scattering is also discussed.
RETRACTED: Suppression of pathogen-inducible NO synthase (iNOS) activity in tomato increases susceptibility to Pseudomonas syringae (2004)

Inducible NO synthase (iNOS) activity is induced upon pathogen inoculation in resistant, but not susceptible, tobacco and Arabidopsis plants. It was shown recently that a variant form of the Arabidopsis P protein (AtvarP) has iNOS activity. P protein is part of the glycine decarboxylase complex (GDC). It is unclear whether P protein also has iNOS activity and, if so, whether AtvarP, P, or both, play a role in plant defense. Here, we show that iNOS activity is induced in both resistant and susceptible tomato leaves upon inoculation with the Pseudomonas syringae pv. tomato strain DC3000. Virus-induced gene-silencing targeting LevarP, a putative tomato ortholog of AtvarP, led to complete suppression of DC3000-induced iNOS activation and an approximately 80% reduction in GDC activity; it also increased disease-symptom severity and DC3000 growth in both resistant and susceptible tomato. To determine whether enhanced susceptibility exhibited by LevarP-silenced, susceptible tomato was due to loss of (i) iNOS activity, (ii) GDC activity, or (iii) both, GDC activity was inhibited with or without concurrent suppression of iNOS. Treatment with methotrexate inhibited both iNOS and GDC activities and resulted in increased susceptibility, comparable with that observed in LevarP-silenced plants. When normal iNOS activity was maintained in the presence of methotrexate by the addition of tetrahydrobiopterin, there was no change in susceptibility, despite a dramatic reduction in GDC activity. Together, these results indicate that iNOS contributes to host defense response against DC3000.
Examination of the role of cGMP in long-term potentiation in the CA1 region of the hippocampus. (1996)

The mechanisms underlying the generation of NMDA receptor-dependent LTP in the CA1 region of the hippocampus continue to receive a great deal of attention because of the postulated importance of LTP as a synaptic mechanism for learning and memory. It is well accepted that the initial induction of LTP occurs in the postsynaptic cell, but the site of expression remains controversial. One prominent hypothesis is that LTP involves the release of one or more retrograde messengers that act on the presynaptic terminal to enhance transmitter release. Recently, evidence has been presented that retrograde messengers function to activate presynaptic guanylyl cyclase and that the resulting rise in presynaptic cGMP levels, when accompanied by presynaptic activity, is responsible for generating an early component of LTP. We have tested this hypothesis by examining whether synaptic strength is increased by coupling tetanic stimulation with application of a membrane-permeable analog of cGMP. The experiments were done in the presence of an NMDA receptor antagonist to block postsynaptic induction mechanisms. Under a variety of experimental conditions, this manipulation failed to generate LTP, suggesting that an increase in cGMP levels accompanied by presynaptic activity is not sufficient to generate LTP in the CA1 region of the hippocampus.
High Frequency and Error-prone DNA Recombination in Ataxia Telangiectasia Cell Lines (1996)

The only specific DNA repair defect found in ataxia telangiectasia (A-T) cells is mis-repair of cleaved DNA. In this report we measured DNA recombination, given its role in DNA repair and genetic instability. Using plasmids containing selectable reporter genes, we found a higher frequency of both chromosomal recombination (>100 times) and extra-chromosomal recombination (27 times) in SV40-transformed A-T cell lines compared with in an SV40-transformed normal fibroblast cell line. Southern analysis of single A-T colonies exhibiting post-integration recombination revealed that 24/27 had undergone aberrant rearrangements; recombination in normal fibroblast colonies was achieved by gene conversion in 8/11 clones and 10/11 clones showed unchanged copies of the plasmid. Using co-transfection of two integrating plasmids, each containing a separate deletion in the xgprt reporter gene, the 27 times difference in extra-chromosomal recombination was found when the plasmids were cleaved at a distance from the reporter gene. When the plasmids were cleaved within the reporter gene, the co-transfection frequency was reduced in A-T, but was increased in normal cells. We conclude that A-T cell lines have not only a high frequency chromosomal and extra-chromosomal recombination, but also exhibit error-prone recombination of cleaved DNA.
Immature joint cartilage and the homograft reaction. (1971)

1. Grafts of joint cartilage from immature lambs were used to repair articular cartilage defects in other lambs and in adult sheep. 2. Stability of these grafts in a functional state was found in most for periods up to fourteen months. Although a limited homograft reaction occurred this did not lead to destruction of the cartilage, even though parts of it were well vascularised. 3. The results suggest that the process of endochondral ossification is associated with the liberation of antigenic material leading to sensitisation of the host. Destruction ofthe cartilage is prevented by an inhibitory action which the matrix appears to exert on the destructive elements themselves and which is itself dependent on the vitality of the chondrocytes. 4. The avascularity of cartilage is not a sufficient explanation for its privileged position in relation to the homograft reaction.
Increased Nuclear NAD Biosynthesis and SIRT1 Activation Prevent Axonal Degeneration (2004)

Axonal degeneration is an active program of self-destruction that is observed in many physiological and pathological settings. In Wallerian degeneration slow (wlds) mice, Wallerian degeneration in response to axonal injury is delayed because of a mutation that results in overexpression of a chimeric protein (Wlds) composed of the ubiquitin assembly protein Ufd2a and the nicotinamide adenine dinucleotide (NAD) biosynthetic enzyme Nmnat1. We demonstrate that increased Nmnat activity is responsible for the axon-sparing activity of the Wlds protein. Furthermore, we demonstrate that SIRT1, a mammalian ortholog of Sir2, is the downstream effector of increased Nmnat activity that leads to axonal protection. These findings suggest that novel therapeutic strategies directed at increasing the supply of NAD and/or Sir2 activation may be effective for treatment of diseases characterized by axonopathy and neurodegeneration.
Dynamics of interstitial and intracellular pH in evolving brain infarct (1991)

We examined the relationships between intracellular pH (pHi) and interstitial pH (pHe) in a rat model of focal ischemia. Interstitial pH was measured with pH-sensitive microelectrodes, and the average tissue pH was measured with the [14C]dimethadione method in rats subjected to occlusion of the right middle cerebral and common carotid arteries (MCA-CCAO). In normal cortex, pHe and pHi were 7.24 +/- 0.97 and 7.01 +/- 0.13 (means +/- SD, n = 6), respectively. In the ischemic cortex, pHe fell to 6.43 +/- 0.13, whereas pHi decreased only to 6.86 +/- 0.11 (n = 5) 1 h after MCA-CCAO. After 4 h of ischemia, the pHe was 6.61 +/- 0.09 and pHi was 6.62 +/- 0.20 (n = 4). Treatment with glucose before ischemia markedly lowered the pHe (5.88 +/- 0.17) but not pHi (6.83 +/- 0.03, n = 4) measured 1 h after ischemia. In the ischemic cortex of animals made hypoglycemic by pretreatment with insulin, neither pHe (7.25 +/- 0.06) nor pHi (6.99 +/- 0.13, n = 4) decreased. The demonstrated difference in pHi and pHe indicates that some cells remained sufficiently functional to maintain a plasma membrane gradient of protons within the evolving infarct. If the calculated pHi values accurately reflect the true pHi of cells within zones of severe focal ischemia, then cerebral infarction can proceed at pHi levels not greatly altered from normal.
Labelling of proteins with 2-(4-isothiocyanatobenzyl)-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid and lanthanides and detection by ICP-MS (2008)

The labelling of two different proteins (bovine serum albumin, hen egg white lysozyme) with the commercially available chelating compound 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (p-SCN-Bn-DOTA) has been investigated. The assay described here has been optimised for the application to detect proteins labelled by stable isotopes of Eu, Tb and Ho and separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Detection has been performed by laser ablation ICP-MS after electroblotting of the target proteins onto NC membranes. A range of total protein amounts from 0.015 pmol (BSA) to 105 pmol (lysozyme) has been covered. A calibration was performed for BSA in the range from 0.015 to 15 pmol and a limit of detection below 15 fmol can be estimated. For lysozyme integrated sensitivities of more than 107 cps pmol−1 of protein have been realized. The conditions, once optimised for labelling with Eu, have been applied for other lanthanides (Tb, Ho), too. ESI-MS of the intact and the tryptic digested lysozyme has been used as to provide a better understanding of the reaction chemistry and efficiency. The procedure described here looks promising to develop multielement labelling strategies (multiplexing) for ICP-MS applications in quantitative proteomics.