gebhart/patrepeval huggingface dataset:
A comparison of glycosaminoglycans content of human synovial fluid in different disease states (1984)

Conference Article| October 01 1984 A comparison of glycosaminoglycans content of human synovial fluid in different disease states S. C. MALIK; S. C. MALIK *Department of Physiological Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K. Search for other works by this author on: This Site PubMed Google Scholar J. P. PEARSON; J. P. PEARSON *Department of Physiological Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K. Search for other works by this author on: This Site PubMed Google Scholar C. W. DICK C. W. DICK †Department of Rheumatology, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU, U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1984) 12 (5): 874. https://doi.org/10.1042/bst0120874 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation S. C. MALIK, J. P. PEARSON, C. W. DICK; A comparison of glycosaminoglycans content of human synovial fluid in different disease states. Biochem Soc Trans 1 October 1984; 12 (5): 874. doi: https://doi.org/10.1042/bst0120874 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: CPDD, calcium pyrophosphate deposition disease; JCA, juvenile chronic arthritis; OA, osteoarthritis; RA, rheumatoid arthritis This content is only available as a PDF. © 1984 Biochemical Society1984 Article PDF first page preview Close Modal You do not currently have access to this content.
Hydrogels formed by oxo-ester mediated native chemical ligation (2013)

Oxo-ester mediated native chemical ligation (OMNCL) is a variation of the more general native chemical ligation (NCL) reaction that is widely employed for chemoselective ligation of peptide fragments. While OMNCL has been used for a variety of peptide ligations and for biomolecular modification of surfaces, it is typically practiced under harsh conditions that are unsuitable for use in a biological context. In this report we describe the use of OMNCL for polymer hydrogel formation, in-vitro cell encapsulation, and in-vivo implantation. Multivalent polymer precursors containing <i>N</i>-hydroxysuccinimide (NHS) activated oxo-esters and <i>N</i>-cysteine (<i>N</i>-Cys) endgroups were chemically synthesized from branched poly(ethylene glycol) (PEG). Hydrogels formed rapidly at physiologic pH upon mixing of aqueous solutions of NHS and <i>N</i>-Cys functionalized PEGs. Quantitative 1H NMR experiments showed that the reaction proceeds through an OMNCL pathway involving thiol capture to form a thioester intermediate, followed by an S-to-N acyl rearrangement to yield an amide cross-link. pH and temperature were found to influence gelation rate, allowing tailoring of gelation times from a few seconds to a few minutes. OMNCL hydrogels initially swelled before contracting to reach an equilibrium increase in relative wet weight of 0%. This unique behavior impacted the gel stiffness and was attributed to latent formation of disulfide cross-links between network-bound Cys residues. OMNCL hydrogels were adhesive to hydrated tissue, generating a lap shear adhesion strength of 46 kPa. Cells encapsulated in OMNCL hydrogels maintained high viability, and in-situ formation of OMNCL hydrogel by subcutaneous injection in mice generated a minimal acute inflammatory response. OMNCL represents a promising strategy for chemical cross-linking of hydrogels in a biological context and is an attractive candidate for in-vivo applications such as wound healing, tissue repair, drug delivery, and tissue engineering.
A modular approach to virtual view creation for a scalable immersive teleconferencing configuration (2004)

This paper details a new modular approach to virtual view creation that is designed to work in conjunction with a proposed scalable teleconferencing configuration. This scalable system is configured using building blocks defined as stereo camera analysis blocks (SCAB). SCABs consist of axe-parallel narrow baseline stereo cameras. These provide design flexibility and improve the image analysis process. Virtual view creation is modular in such that we can add or remove SCABs based on our particular requirements without having to modify the view synthesis algorithm. A new approach to virtual view creation from multiple images is defined. This contains two separate processes: surface segmentation, which identifies surfaces, and surface selection and merging, which selects and integrates the best view of a required surface into the virtual view. The surfaces are identified via a sampling density function while the surface selection procedure is based on a weighting scheme.
Purification and characterization of predominant G-protein from bovine lung membranes. Biochemical and immunochemical comparison with Gi1 and Go purified from brain (1989)

The predominant guanine nucleotide-binding protein (G-protein) of bovine lung membranes, termed GL, has been purified and compared biochemically, immunochemically and functionally with Gi and Go purified from rabbit brain. The purified GL appeared to have a similar subunit structure to Gi and Go, being composed of alpha, beta and possibly gamma subunits. On Coomassie Blue-stained SDS/polyacrylamide gels and immunoblots, the alpha subunit of GL (GL alpha) displayed an intermediate mobility (40 kDa) between those of Gi and Go (Gi alpha and Go alpha). GL alpha was [32P]ADP-ribosylated in the presence of pertussis toxin and [32P]NAD+. Analysis of [32P]ADP-ribosylated alpha subunits by SDS/polyacrylamide-gel electrophoresis and isoelectric focusing showed that GL alpha was distinct from Gi alpha and Go alpha, but very similar to the predominant G-protein in neutrophil membranes. Immunochemical characterization also revealed that GL was distinct from Gi and Go, but was indistinguishable from the G-protein of neutrophils, which has been tentatively identified as Gi2 [Goldsmith, Gierschik, Milligan, Unson, Vinitsky, Maleck & Spiegel (1987) J. Biol. Chem. 262, 14683-14688]. In functional studies, higher Mg2+ concentrations were required for guanosine 5'-[gamma-[35S]thio]triphosphate (GTP[35S]) binding to GL than were required for nucleotide binding to Go, whereas Gi showed a Mg2+-dependence similar to that of GL. The kinetics of GTP[35S] binding to GL was quite different from those of Gi and Go; t1/2 values of maximal binding were 30, 15 and 5 min respectively. In contrast, the rate of hydrolysis of [gamma-32P]GTP by GL (t1/2 approximately 1 min) was approx. 4 times faster than that by Gi or Go. These results indicated that the predominant G-protein purified from lung is structurally and functionally distinct from Gi and Go of brain, but structurally indistinguishable from Gi2 of neutrophils.
Data from Characteristics of Lung Cancers Harboring <i>NRAS</i> Mutations (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; We sought to determine the frequency and clinical characteristics of patients with lung cancer harboring &lt;i&gt;NRAS&lt;/i&gt; mutations. We used preclinical models to identify targeted therapies likely to be of benefit against &lt;i&gt;NRAS&lt;/i&gt;-mutant lung cancer cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We reviewed clinical data from patients whose lung cancers were identified at six institutions or reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) to harbor &lt;i&gt;NRAS&lt;/i&gt; mutations. Six &lt;i&gt;NRAS&lt;/i&gt;-mutant cell lines were screened for sensitivity against inhibitors of multiple kinases (i.e., EGFR, ALK, MET, IGF-1R, BRAF, PI3K, and MEK).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Among 4,562 patients with lung cancers tested, &lt;i&gt;NRAS&lt;/i&gt; mutations were present in 30 (0.7%; 95% confidence interval, 0.45%–0.94%); 28 of these had no other driver mutations. 83% had adenocarcinoma histology with no significant differences in gender. While 95% of patients were former or current smokers, smoking-related G:C&gt;T:A transversions were significantly less frequent in &lt;i&gt;NRAS&lt;/i&gt;-mutated lung tumors than &lt;i&gt;KRAS&lt;/i&gt;-mutant non–small cell lung cancer [NSCLC; &lt;i&gt;NRAS&lt;/i&gt;: 13% (4/30), &lt;i&gt;KRAS&lt;/i&gt;: 66% (1772/2733), &lt;i&gt;P&lt;/i&gt; &lt; 0.00000001]. Five of 6 &lt;i&gt;NRAS&lt;/i&gt;-mutant cell lines were sensitive to the MEK inhibitors, selumetinib and trametinib, but not to other inhibitors tested.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt;&lt;i&gt;NRAS&lt;/i&gt; mutations define a distinct subset of lung cancers (∼1%) with potential sensitivity to MEK inhibitors. Although &lt;i&gt;NRAS&lt;/i&gt; mutations are more common in current/former smokers, the types of mutations are not those classically associated with smoking. &lt;i&gt;Clin Cancer Res; 19(9); 2584–91. ©2013 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Paxos Made Simple (2001)

At the PODC 2001 conference, I got tired of everyone saying how difficult it was to understand the Paxos algorithm, published in [122]. Although people got so hung up in the pseudo-Greek names that they found the paper hard to understand, the algorithm itself is very simple. So, I cornered a couple of people at the conference and explained the algorithm to them orally, with no paper. When I got home, I wrote down the explanation as a short note, which I later revised based on comments from Fred Schneider and Butler Lampson. The current version is 13 pages long, and contains no formula more complicated than n1 > n2.
E.coli Lipopolysaccharides로 유도된 사람 호중구중에서 CD14, Toll-Like receptors, cytoskeletal inhibitors 그리고 NF-kB inhibitor가 MMP-8 분비에 미치는 영향 (2005)

Objective: MMP-8 is a neutrophil enzyme and its level increases in some inflammatory diseases, including periodontal disease. We knew that the lipopolysaccharide of E.coli(E-LPS) induced MMP-8 release from human neutrophils. E-LPS is known to induce the production and release of inflammatory cytokines through CD14, Toll-like receptor(TLR). In the present study, we investigated whether MMP-8 release by E-LPS is induced via CD14-TLR pathway and the cellular mechanism of MMP-8 release in human neutrophils. Material and methods: Human neutrophils were isolated from the peripheral blood of healthy donors and pre-incubated in medium containing antibodies against CD14, anti-TLR2 and anti-TLR4 or several inhibitors of microtubules and microfilaments and then incubated with E-LPS. The cells were treated TPCK and E-LPS simultaneously. The MMP-8amount in the culture medium was determined using ELISA. Results: E-LPS increased MMP-8release from neutrophils and its induction was inhibited by anti-CD14 and anti-TLR4 but not by anti-TLR2 antibodies. The inhibitors of microtubule and microfilament polymerization significantly decreased E-LPS-induced MMP-8release. TPCK inhibited E-LPS-induced MMP-8 release. Conclusion: These results suggest that MMP-8 release is induced by E-LPS via the CD14-TLR4 signal pathway in human neutrophils and may be depedent on microtubule and microfilament systems and pathway.
Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid (2020)

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that methylates histone H3 at Lysine 27. PRC2 is critical for epigenetic gene silencing, cellular differentiation and the formation of facultative heterochromatin. It can also promote or inhibit oncogenesis. Despite this importance, the molecular mechanisms by which PRC2 compacts chromatin are relatively understudied. Here, we visualized the binding of PRC2 to naked DNA in liquid at the single-molecule level using atomic force microscopy. Analysis of the resulting images showed PRC2, consisting of five subunits (EZH2, EED, SUZ12, AEBP2 and RBBP4), bound to a 2.5-kb DNA with an apparent dissociation constant ($K_{\rm{D}}^{{\rm{app}}}$) of 150 ± 12 nM. PRC2 did not show sequence-specific binding to a region of high GC content (76%) derived from a CpG island embedded in such a long DNA substrate. At higher concentrations, PRC2 compacted DNA by forming DNA loops typically anchored by two or more PRC2 molecules. Additionally, PRC2 binding led to a 3-fold increase in the local bending of DNA's helical backbone without evidence of DNA wrapping around the protein. We suggest that the bending and looping of DNA by PRC2, independent of PRC2's methylation activity, may contribute to heterochromatin formation and therefore epigenetic gene silencing.
Expression of HLA class I molecules and the transporter associated with antigen processing in hepatocellular carcinoma (1996)

The expression of the HLA class I molecules on the cell surface was investigated in hepatocellular carcinoma (HCC) cell lines using complement-mediated cytotoxicity (CMC) and flow cytometric analysis. Although HLA-A antigens were detected by CMC in all cell lines tested, HLA-B and -C antigens were not detectable in six of seven HCC cell lines. These results were also confirmed by flow cytometric analysis focusing on HLA-Bw4 and Bw6 public antigens. Furthermore, complementary DNA (cDNA) from each cell line was tested for the expression of HLA-A, -B, -C and the transporter associated with antigen processing genes (TAP1 and TAP2). Two cell lines showed a reduced level of one or both of the TAP messenger RNAs (mRNAs), and one of these showed a reduction of HLA-B and -C gene expression as well, but the others had detectable mRNA levels. These results demonstrate that hepatocellular carcinoma cell lines tested in the current study lose or decrease the expression of HLA-B and -C alleles on the cell surface, even though mRNA encoding these alleles is present, suggesting that the loss of the HLA molecules might be caused by posttranscriptional events or failure to transport and load peptides necessary for HLA expression. The selective loss of HLA-B and -C, but not -A, molecules (which also excludes a beta 2-microglobulin defect) is intriguing, and may be attributable to the ability of some of the HLA-A molecules to load signal peptides not requiring TAP transport, or to natural selection of HLA-B or -C locus-specific immune surveillance.
Seeded Growth of Highly Luminescent CdSe/CdS Nano-Heterostructures with Rod and Tetrapod Morphologies (2008)

We have demonstrated that seeded growth of nanocrystals offers a convenient way to design nanoheterostructures with complex shapes and morphologies by changing the crystalline structure of the seed. By using Use nanocrystals with wurtzite and zinc blende structure as seeds for growth of US nanorods, we synthesized CdSe/CdS heterostructure nanorods and nanotetrapods, respectively. Both of these structures showed excellent luminescent properties, combining high photoluminescence efficiency (similar to 80 and similar to 50percent for nanorods and nanotetrapods, correspondingly), giant extinction coefficients (similar to 2 x 10(7) and similar to 1.5 x 10(8) M-1 cm (-1) at 350 nm for nanorods and nanotetrapods, correspondingly), and efficient energy transfer from the US arms into the emitting CdSe Core.
Physics and applications of optical vortices in fibers (2012)

Polarisation- and phase-vortices are emerging as light-beams of immense interest in several scientific and technological applications. We review recently developed techniques for generating them, as well as manipulating their nonlinear optical properties, with optical fibers.
Fiber Bragg grating arrays for high resolution manometry (2009)

We demonstrate the application of a fiber Bragg grating based sensor system as a distributed pressure sensing catheter for the human esophagus. It allows space-time resolved measurements of the peristaltic waves of the gullet. The sensor system comprises 30 fiber-optic pressure sensors in a single fiber with a spatial distance below 10 mm each. The sensors are fiber Bragg gratings that are manufactured during the drawing process of the fiber and therefore show enhanced mechanical stability compared to fiber Bragg gratings with local recoating. A well designed soft plastic coating wand will be used to convert local pressure variations into strain variations of the optical fiber core.
Influence of boron diffusion on the perpendicular magnetic anisotropy in Ta|CoFeB|MgO ultrathin films (2015)

We have studied structural and magnetic properties of Ta|CoFeB|MgO heterostructures using cross-section transmission electron microscopy (TEM), electron energy loss spectrum (EELS) imaging, and vibrating sample magnetometry. From the TEM studies, the CoFeB layer is found to be predominantly amorphous for as deposited films, whereas small crystallites, diameter of ∼5 nm, are observed in films annealed at 300 °C. We find that the presence of such nanocrystallites is not sufficient for the occurrence of perpendicular magnetic anisotropy. Using EELS, we find that boron diffuses into the Ta underlayer upon annealing. The Ta underlayer thickness dependence of the magnetic anisotropy indicates that ∼0.2 nm of Ta underlayer is enough to absorb the boron from the CoFeB layer and induce perpendicular magnetic anisotropy. Boron diffusion upon annealing becomes limited when the CoFeB layer thickness is larger than ∼2 nm, which coincides with the thickness at which the saturation magnetization MS and the interface magnetic anisotropy KI drop by ∼20%. These results show the direct role which boron plays in determining the perpendicular magnetic anisotropy in CoFeB|MgO heterostructures.
A Cognitive Assistant for Visualizing and Analyzing Exoplanets (2018)

We demonstrate an embodied cognitive agent that helps scientists visualize and analyze exo-planets and their host stars. The prototype is situated in a room equipped with a large display, microphones, cameras, speakers, and pointing devices. Users communicate with the agent via speech, gestures, and combinations thereof, and it responds by displaying content and generating synthesized speech. Extensive use of context facilitates natural interaction with the agent.
Architectural Evolution of Integrated M-Phase High-Q Bandpass Filters (2011)

-phase bandpass filters (BPFs) are analyzed, and variations of the structure are proposed. For values of that are integer multiples of 4, the conventional -phase BPF structure is modified to take complex baseband impedances and frequency-translate their complex impedance response to the local oscillator frequency. Also, it is demonstrated how the -phase BPF can be modified to implement a high quality factor (Q) image-rejection BPF with quadrature RF inputs. In addition, we present high-Q BPFs whose center frequencies are equal to the sum or difference of the RF and IF (intermediate frequency) clocks. Such filters can be useful in heterodyne receiver architectures.
A Compact Chromatic Dispersion Compensator using Unequal and Mutually-Coupled Microring Resonators (2008)

We propose ultra-small silicon microring-based dispersion compensators, with −530 ps/nm dispersion over 8.5 μm and power fluctuation of 0.15 dB. Equivalent dispersion is up-to 6.23×1010 ps/nm/km. Dispersion slope compensation is also achieved.
The Role of Neutrophils in Antiviral Defense-in Vitro Studies on the Mechanism of Antiviral Inhibition (1977)

Highly enriched populations of bovine neutrophils were added, in the presence of antiviral antibody, to herpesvirus-infected bovine cell cultures. A cell dose-dependent reduction in virus-induced cytopathology was observed. The mechanism of inhibition was presumed to be mediated by a subcellular neutrophil product and not the result of either direct cytotoxicity or antibody-dependent cell-mediated cytotoxicity (ADCC). Thus, inhibition of comparable magnitude was observed when neutrophils and virus-infected cells were separated by cell impermeable membranes. In addition, plaque reduction occurred when antiviral immunoglobulins or fragments unable to mediate ADCC were used in the assays. Killed neutrophils and sonicates were unable to mediate plaque inhibition. Speculations were made as to the origin of the virus-inhibitory substances and the role that neutrophils might assume in mediating recovery from virus infection.
Reply: (2019)

We appreciate the comments from Drs Lim and Moon on our article entitled, “ Dynamic Contrast-Enhanced MRI Reveals Unique Blood-Brain Barrier Permeability Characteristics in the Hippocampus in the Normal Brain,” and appreciate the opportunity to respond. The first comment is focused on the
Abstract LB-202: The rare, highly malignant small cell carcinoma of the ovary displays common inactivating germline and somatic mutations in the tumor suppressor SMARCA4 (2014)

Abstract Small Cell Carcinoma of the Ovary Hypercalcemic Type (SCCOHT) is a rare and highly aggressive malignancy that affects children and young women at a mean age of 24 (range 14 months - 58 years). SCCOHT is refractory to standard of care therapy for ovarian cancer, with ∼75% mortality within 18 months of diagnosis. The early age of onset of SCCOHT and reports of familial occurrence in some cases, strongly suggest an underlying hereditary etiology. To understand the molecular pathogenesis of SCCOHT, we performed next-generation genomic sequencing on a series of tumor and germline samples from SCCOHT patients. This analysis revealed germline and somatic inactivating mutations in SMARCA4, a subunit of the SWI/SNF chromatin-remodeling complex, in 75% (9/12) of SCCOHT patients. Moreover, immunohistochemical (IHC) analysis of 15 tumors revealed that 87% (13/15) of tumors lacked SMARCA4 protein. The high prevalence of SMARCA4 mutations in SCCOHT has not been previously reported in other, more common ovarian carcinomas. We therefore examined the expression of SMARCA4 protein in 300 ovarian carcinomas of different histologies by IHC and found SMARCA4 protein loss in only 6 tumors. In addition, the BIN-67 SCCOHT cell line, which harbors 2 splice site mutations in SMARCA4, showed complete absence of SMARCA4 protein by Western blot while representative cell lines from 4 other ovarian carcinoma subtypes as well as immortalized granulosa cells (SVOG) and adult granulosa tumor cells (KGN) all maintained SMARCA4 expression. The prevalence of germline and sporadic SMARCA4 mutations as well as frequent SMARCA4 protein loss in SCCOHTs implicates this gene as a tumor suppressor in this cancer and more broadly suggests a role for the SWI/SNF complex in its pathogenesis. In addition to providing evidence to the pathogenesis of SCCOHT, this finding provides the opportunity to develop treatment approaches for SCCOHT based on targeting vulnerabilities of SMARCA4-deficient cells. Citation Format: Pilar Ramos, Anthony Karnezis, David Craig, Aleksandar Sekulic, Megan Russell, William Hendricks, Michael Barrett, Karey Shumansky, Yidong Yang, Sohrab Shah, Leah Prentice, Marco Marra, Jeffrey Kiefer, Victoria Zismann, Troy McEachron, Bodour Salhia, Joseph Pressey, John Farley, Stephen Anthony, Richard Roden, Heather Cunliffe, David Huntsman, Jeffrey Trent. The rare, highly malignant small cell carcinoma of the ovary displays common inactivating germline and somatic mutations in the tumor suppressor SMARCA4. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-202. doi:10.1158/1538-7445.AM2014-LB-202