gebhart/patrepeval huggingface dataset:
Quantitative Study of the Effect of Coverage on the Hybridization Efficiency of Surface-Bound DNA Nanostructures (2008)

We demonstrate that, contrary to current understanding, the density of probe molecules is not responsible for the lack of hybridization in high density single-stranded DNA (ss-DNA) self-assembled monolayers (SAMs). To this end, we use nanografting to fabricate well packed ss-DNA nanopatches within a "carpet matrix" SAM of inert thiols on gold surfaces. The DNA surface density is varied by changing the "writing" parameters, for example, tip speed, and number of scan lines. Since ss-DNA is 50 times more flexible than ds-DNA, hybridization leads to a transition to a "standing up" phase. Therefore, accurate height and compressibility measurements of the nanopatches before and after hybridization allow reliable, sensitive, and label-free detection of hybridization. Side-by-side comparison of self-assembled and nanografted DNA-monolayers shows that the latter, while denser than the former, display higher hybridization efficiencies.
The JPEG 2000 still image compression standard (2001)

One of the aims of the standardization committee has been the development of Part I, which could be used on a royalty- and fee-free basis. This is important for the standard to become widely accepted. The standardization process, which is coordinated by the JTCI/SC29/WG1 of the ISO/IEC has already produced the international standard (IS) for Part I. In this article the structure of Part I of the JPFG 2000 standard is presented and performance comparisons with established standards are reported. This article is intended to serve as a tutorial for the JPEG 2000 standard. The main application areas and their requirements are given. The architecture of the standard follows with the description of the tiling, multicomponent transformations, wavelet transforms, quantization and entropy coding. Some of the most significant features of the standard are presented, such as region-of-interest coding, scalability, visual weighting, error resilience and file format aspects. Finally, some comparative results are reported and the future parts of the standard are discussed.
Inhibition of iodothyronine transport into rat liver cells by a monoclonal antibody. (1986)

The role of the rat liver plasma membrane in the regulation of uptake and subsequent deiodination of thyroxine (T4) or the biologically active thyroid hormone 3,3',5-triiodothyronine (T3) was investigated. Here we report on the production of monoclonal antibodies raised against rat hepatocytes. Two antibodies were selected. Antibody ER-22 did bind to a Mr 52,000 membrane protein and inhibited the 1- and 5-min uptake of both T4 and T3 by primary cultured rat hepatocytes in a dose-dependent fashion. As the uptake of T4 and T3 depends on the presence of a sodium gradient over the plasma membrane, the inhibitory potency of ER-22 on the Na+,K+-ATPase activity was investigated. No inhibition of the uptake of 86Rb+ could be determined, indicating that antibody ER-22 is not directed against the Na+,K+-ATPase but probably the carrier protein itself. Clearance of T3 from the medium and concomitant iodide production by cultured rat hepatocytes during a 20-h incubation in the presence of ER-22 were both inhibited by 50% with respect to a control incubation in the absence of monoclonal antibody, pointing to the importance of carrier-mediated transport in cellular uptake and metabolism of T3. A second monoclonal antibody did bind to two other plasma membrane proteins but did not inhibit transport of thyroid hormone.
Nanometer Gold Clusters Protected by Surface-Bound Monolayers of Thiolated Poly(ethylene glycol) Polymer Electrolyte (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTNanometer Gold Clusters Protected by Surface-Bound Monolayers of Thiolated Poly(ethylene glycol) Polymer ElectrolyteW. Peter Wuelfing, Stephen M. Gross, Deon T. Miles, and Royce W. MurrayView Author Information Kenan Laboratories of Chemistry University of North Carolina Chapel Hill, North Carolina 27599-3290 Cite this: J. Am. Chem. Soc. 1998, 120, 48, 12696–12697Publication Date (Web):November 19, 1998Publication History Received8 September 1998Published online19 November 1998Published inissue 1 December 1998https://pubs.acs.org/doi/10.1021/ja983183mhttps://doi.org/10.1021/ja983183mrapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views5114Altmetric-Citations378LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Gold,Ionic conductivity,Ligands,Monolayers,Polymers Get e-Alerts
Purification, Characterization, and Role of Nucleases and Serine Proteases in Streptomyces Differentiation (1999)

Two exocellular nucleases with molecular masses of 18 and 34 kDa, which are nutritionally regulated and reach their maximum activity during aerial mycelium formation and sporulation, have been detected in Streptomyces antibioticus. Their function appears to be DNA degradation in the substrate mycelium, and in agreement with this proposed role the two nucleases cooperate efficiently with a periplasmic nuclease previously described in Streptomyces antibioticus to completely hydrolyze DNA. The nucleases cut DNA nonspecifically, leaving 5'-phosphate mononucleotides as the predominant products. Both proteins require Mg2+, and the additional presence of Ca2+ notably stimulates their activities. The two nucleases are inhibited by Zn2+ and aurin tricarboxylic acid. The 18-kDa nuclease from Streptomyces is reminiscent of NUC-18, a thymocyte nuclease proposed to have a key role in glucocorticoid-stimulated apoptosis. The 18-kDa nuclease was shown, by amino-terminal protein sequencing, to be a member of the cyclophilin family and also to possess peptidylprolyl cis-trans-isomerase activity. NUC-18 has also been shown to be a cyclophilin, and "native" cyclophilins are capable of DNA degradation. The S. antibioticus 18-kDa nuclease is produced by a proteolytic processing from a less active protein precursor. The protease responsible has been identified as a serine protease that is inhibited by Nalpha-p-tosyl-L-lysine chloromethyl ketone and leupeptin. Inhibition of both of the nucleases or the protease impairs aerial mycelium development in S. antibioticus. The biochemical features of cellular DNA degradation during Streptomyces development show significant analogies with the late steps of apoptosis of eukaryotic cells.
Carumonam enhances reactivity of Escherichia coli with mono- and polyclonal antisera to rough Escherichia coli J5 (1987)

Escherichia coli O111 reacts only slightly with antiserum to its rough mutant E. coli J5 in an enzyme-linked immunosorbent assay. When E. coli O111 was grown in the presence of sub-MICs of the monocyclic beta-lactam antibiotic carumonam, however, the enzyme-linked immunosorbent assay titer increased from 1,280 to 81,920. When the bacteria were grown in the presence of carumonam, the titer that was obtained with antiserum against E. coli O111 was not affected. This reaction was abolished after this antiserum was absorbed with E. coli J5 in the case of the carumonam-treated strain, whereas this absorption did not affect the reaction with E. coli O111. Thus, the O-antigenic side chain of E. coli O111 seems to be affected if this strain is cultured in the presence of carumonam. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed a relative loss of the O polysaccharide in E. coli O111 when this strain was grown in the presence of carumonam. Also, a much stronger reaction of the antibiotic-affected lipopolysaccharide with a monoclonal antibody against E. coli J5 lipopolysaccharide was shown in immunoblots. The results of this study indicate that there is a synergism between certain antibiotics and monoclonal antibodies, something that could have clinical implications.
Metabolic Basis of Visual Cycle Inhibition by Retinoid and Nonretinoid Compounds in the Vertebrate Retina (2008)

In vertebrate retinal photoreceptors, the absorption of light by rhodopsin leads to photoisomerization of 11-cis-retinal to its all-trans isomer. To sustain vision, a metabolic system evolved that recycles all-trans-retinal back to 11-cis-retinal. The importance of this visual (retinoid) cycle is underscored by the fact that mutations in genes encoding visual cycle components induce a wide spectrum of diseases characterized by abnormal levels of specific retinoid cycle intermediates. In addition, intense illumination can produce retinoid cycle by-products that are toxic to the retina. Thus, inhibition of the retinoid cycle has therapeutic potential in physiological and pathological states. Four classes of inhibitors that include retinoid and nonretinoid compounds have been identified. We investigated the modes of action of these inhibitors by using purified visual cycle components and in vivo systems. We report that retinylamine was the most potent and specific inhibitor of the retinoid cycle among the tested compounds and that it targets the retinoid isomerase, RPE65. Hydrophobic primary amines like farnesylamine also showed inhibitory potency but a short duration of action, probably due to rapid metabolism. These compounds also are reactive nucleophiles with potentially high cellular toxicity. We also evaluated the role of a specific protein-mediated mechanism on retinoid cycle inhibitor uptake by the eye. Our results show that retinylamine is transported to and taken up by the eye by retinol-binding protein-independent and retinoic acid-responsive gene product 6-independent mechanisms. Finally, we provide evidence for a crucial role of lecithin: retinol acyltransferase activity in mediating tissue specific absorption and long lasting therapeutic effects of retinoid-based visual cycle inhibitors.
A novel technique for analysis of accuracy of magnetic tracking systems used in image guided surgery (2010)

With the increased use and development of image-guided surgical applications, there is a need for methods of analysis of the accuracy and precision of the components which compose these systems. One primary component of an image-guided surgery system is the position tracking system which allows for the localization of a tool within the surgical field and provides information which is translated back to the images. Previously much work has been done in characterizing these systems for spatial accuracy and precision. Much of this previous work examines single tracking systems or modalities. We have devised a method which allows for the characterization of a novel tracking system independent of modality and location. We describe the development of a phantom system which allows for rapid design and creation of surfaces with different geometries. We have also demonstrated a method of analysis of the data generated by this phantom system, and used it to compare Biosense-Webster's CartoXP<sup>TM</sup>, and Northern Digital's Aurora<sup>TM</sup>magnetic trackers. We have determined that the accuracy and precision of the CartoXP was best, followed closely by the Aurora's dome volume, then the Aurora's cube volume. The mean accuracy for all systems was better than 3mm and decays with distance from the field generator.
Application and Benefits of Degradable Technology in Open-hole Fracturing (2013)

Abstract The introduction of a new technology is critical for operators to expand their completion options, increase efficiency, and drive profitably in challenging environments. For unconventional reservoirs, open-hole fracturing has been key for the economic success of new ventures. With the increase in activity of liquids rich plays, there is a growing need for new technology developments for open-hole fracturing systems that further optimize these completions. Using a combination of open-hole packers and sliding sleeves, open-hole fracturing tools successfully segment horizontal sections of the reservoir to be stimulated individually. In order to achieve isolation, seats of increasing diameters are placed inside the completion at each fracturing sleeve. These seats catch a ball that performs the function of opening the sleeve for fracturing purposes and isolating the completion below the stage. After the stimulation job is performed, the balls should ideally flow back to surface. Unfortunately, as seen in the field and described in the literature, this is often not the case. Balls frequently remain in the completion without coming to surface. In some cases depending on ball and seat material, balls may actually get stuck in the ball seats completely isolating production from the stages below. Many operators have found this to be a root cause of production problems and they are forced to take the added cost and risk of milling out the balls and seats. A new degradable material has been developed for use on frac balls that are used in said open-hole completions. Balls made of this material can handle pressure differentials beyond the current market offering without deformation. After fracturing, these balls degrade away opening up the flow path of the well without intervention. The degradation time is a function of temperature and water chemistry (including brine), but 1 to 4 days is a typical degradation time. No other requirements are needed for the degradation process to occur. This paper discusses a new degradable metal technology and its application in open-hole fracturing.
Release of indomethacin from a novel chitosan microsphere prepared by a naturally occurring crosslinker: Examination of crosslinking and polycation–anionic drug interaction (2001)

Novel chitosan microspheres with lower cytotoxicity were fabricated in this study and their drug release characteristics were investigated. Genipin, a naturally occurring crosslinking reagent that has been used in herbal medicine and in the production of food dye, was used to prepare crosslinked chitosan microspheres by a water-in-oil dispersion method. The crosslinking mechanism examined by FTIR and 13C–NMR suggests that the crosslinking of chitosan by genipin leads to the formation of secondary amide and heterocyclic amino linkage. The polycation–anionic drug interaction between chitosan and indomethacin was pH dependent and could affect the dissolution property of indomethacin. By examination of the release profiles of the crosslinked chitosan microsphere, it was found that the release of indomethacin from the microsphere was sustainable and influenced by factors such as crosslinking of microsphere and chitosan–indomethacin interaction, thus establishing crosslinked chitosan microsphere as a very promising polymeric carrier for drug release. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 81: 1700–1711, 2001
Review of the clinical applications and technological advances of circulating tumor DNA in cancer monitoring (2017)

Circulating cell-free DNA (cfDNA) released by tumor cells, termed ctDNA, closely reflects the heterogeneity of primary cancers and their metastases. As a noninvasive, real-time monitoring biomarker, ctDNA is a promising tool for detecting driver gene mutations, assessing tumor burden and acquired resistance, and early diagnosis. However, isolation and enrichment of cfDNA is a big challenge due to the high degree of DNA fragmentation and its relatively low abundance in the bloodstream. This review aims to provide insights into the recent technological advances in acquisition of optimal quality cfDNA, the use of preservatives, isolation methods, processing timelines, and detection techniques. It also describes clinical applications of ctDNA in cancer patient management.
SPdb – a signal peptide database (2005)

SPdb is a manually curated database constructed to support the understanding and analysis of signal peptides. SPdb tracks the major updates of the two underlying primary databases thereby ensuring that its information remains up-to-date.
Blood transfusion associated lung injury (2019)

Transfusions of blood and blood products are live-saving, but complications may be fatal. Transfusion related lung injury (TRALI) is rare and pathophysiology not yet entirely understood. Diagnosis is difficult due to the usually life-threatening circumstances associated with transfusions and underlying diseases. In this mini-review article, we introduce two cases of TRALI to discuss the problems and controversies associated with different definitions, epidemiology, pathophysiology, blood products, diagnosis, and treatment. Future directions in the field are highlighted.
The role of the chemokine receptor XCR1 in breast cancer cells (2017)

Considerable attention has recently been paid to the application of chemokines to cancer immunotherapy due to their complex role in cell proliferation, invasion, metastasis, and tumorigenesis, which extends beyond the regulation of lymphocyte migration during immune responses. The expression and the function of the chemokine receptor XCR1 on breast cancer have remained elusive to date. In this study, the expressions of XCR1 mRNA were tested by quantitative real-time polymerase chain reaction in one breast epithelial cell line (MCF-10A) and nine breast cancer cell lines (MDA-MB-231, 231HM, 231BO, MDA-MB-468, MCF-7, T47D, Bcap-37, ZR-75-30, and SK-BR-3). We established XCR1-overexpressing breast cancer cell line MDA-MB-231 (231/XCR1) in XCR1 low expression cell line MDA-MB-231 (231). The ability of proliferation, invasion, and metastasis was measured by CCK8, plate cloning formation, and transwell analysis, respectively, in XCR1-overexpressing breast cancer cell lines (231/XCR1) and their parental cell line MDA-MB-231/Vector (simplified as "231/Vector"); 5×10<sup>6</sup>/100 μL cells were inoculated in mammary fat pad of BALB/c nude mice. There were six BALB/c nude mice in the experimental group and control group. Protein expression was analyzed by cell immunofluorescence and Western blot. The growth of XCR1-overexpressing human breast cancer cell line MDA-MB-231 in vitro was restrained and tumorigenesis in vivo was also extenuated, its mechanism may involve in the inhibition of MAPK and PI3K/AKT/mTOR signaling pathway, but increase in LC3 expression. However, the overexpression of XCR1 in human breast cancer cell line MDA-MB-231 in vitro can promote the migration and invasion partially due to decreasing the protein level of β-catenin. Therefore, XCR1 can affect the biological characteristics of some special breast cancer cells through complex signal transduction pathway.
Determination of HID electrode falls in a model lamp I: Pyrometric measurements (2002)

To verify models describing the near-electrode regions electrodes of pure and doped tungsten for high intensity discharge lamps are investigated in a special model lamp. It can be operated with arc currents of 1 A to 10 A, DC or AC with arbitrary waveforms up to a few kHz. Argon and xenon, at pressures from 0.1 MPa to 1 MPa, are used as fill gases. A large variety of electrodes can be inserted. To perform spatially resolved measurements they are displaced reproducibly within the discharge tube during lamp operation.
Novel TMPRSS6 mutations associated with iron-refractory iron deficiency anemia (IRIDA) (2010)

Mutations leading to abrogation of matriptase-2 proteolytic activity in humans are associated with an iron-refractory iron deficiency anemia (IRIDA) due to elevated hepcidin levels. In this paper we describe 12 IRIDA patients belonging to 7 unrelated families and identify 10 (9 novel) TMPRSS6 mutations spread along the gene sequence: 5 missense, 1 non sense and 4 frameshift. The frameshift and non sense mutations are predict to result in truncated protein lacking the catalytic domain. The causal role of missense mutations (Y141C, I212T, R271Q, S304L and C510S) is demonstrated by in silico analysis, their absence in 100 control chromosomes and the high conservation of the involved residues. The C510S mutation in the LDLRA domain in silico model causes an intra-molecular structural imbalance that impairs matriptase-2 activation. We also assessed the in vitro effect on hepcidin promoter and the proteolytic activity of I212T and R271Q variants demonstrating a reduced inhibitory effect for the former mutation, but surprisingly a normal function for R271Q which appears a silent mutation in vitro. Based on mRNA expression studies I212T could also decrease the total amount of protein produced, likely interfering with mRNA stability. Collectively, our results extend the pattern of TMPRSS6 mutations associated with IRIDA and propose a model of causality for some of the novel missense mutation.
Induction of nuclear envelope breakdown, chromosome condensation, and spindle formation in cell-free extracts. (1985)

Incubation of demembranated sperm chromatin in cytoplasmic extracts of unfertilized Xenopus laevis eggs resulted in nuclear envelope assembly, chromosome decondensation, and sperm pronuclear formation. In contrast, egg extracts made with EGTA-containing buffers induced the sperm chromatin to form chromosomes or irregularly shaped clumps of chromatin that were incorporated into bipolar or multipolar spindles. The 150,000 g supernatants of the EGTA extracts could not alone support these changes in incubated nuclei. However, these supernatants induced not only chromosome condensation and spindle formation, but also nuclear envelope breakdown when added to sperm pronuclei or isolated Xenopus liver or brain nuclei that were incubated in extracts made without EGTA. Similar changes were induced by partially purified preparations of maturation-promoting factor. The addition of calcium chloride to extracts containing condensed chromosomes and spindles caused dissolution of the spindles, decondensation of the chromosomes, and re-formation of interphase nuclei. These results indicate that nuclear envelope breakdown, chromosome condensation, and spindle assembly, as well as the regulation of these processes by Ca2+-sensitive cytoplasmic components, can be studied in vitro using extracts of amphibian eggs.