gebhart/patrepeval huggingface dataset:
Universal Reference RNA as a standard for microarray experiments (2019)

Abstract Background Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR), developed with the goal of providing hybridization signal at each microarray probe location (spot). Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment. Results Human, mouse and rat URR (UHRR, UMRR and URRR, respectively) were prepared from pools of RNA derived from individual cell lines representing different tissues. A variety of microarrays were used to determine percentage of spots hybridizing with URR and producing signal above a user defined threshold (microarray coverage). Microarray coverage was consistently greater than 80% for all arrays tested. We confirmed that individual cell lines contribute their own unique set of genes to URR, arguing for a pool of RNA from several cell lines as a better configuration for URR as opposed to a single cell line source for URR. Microarray coverage comparing two separately prepared batches each of UHRR, UMRR and URRR were highly correlated (Pearson's correlation coefficients of 0.97). Conclusion Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation. This type of reference provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and laboratories.
20‐4: Dipole Orientation Measurement Method by Time Resolved Photoluminescence (2018)

In this study, we report a new molecular dipole orientation measurement method by simply measuring photolumincence exciton decay rate with time resolved equipment in the film state. Our measurement method is very simple, universal and reliable to measure the dipole orientation in any OLED molecules.
A Model of Cancer Stem Cells Derived from Mouse Induced Pluripotent Stem Cells (2012)

Cancer stem cells (CSCs) are capable of continuous proliferation and self-renewal and are proposed to play significant roles in oncogenesis, tumor growth, metastasis and cancer recurrence. CSCs are considered derived from normal stem cells affected by the tumor microenvironment although the mechanism of development is not clear yet. In 2007, Yamanaka's group succeeded in generating Nanog mouse induced pluripotent stem (miPS) cells, in which green fluorescent protein (GFP) has been inserted into the 5'-untranslated region of the Nanog gene. Usually, iPS cells, just like embryonic stem cells, are considered to be induced into progenitor cells, which differentiate into various normal phenotypes depending on the normal niche. We hypothesized that CSCs could be derived from Nanog miPS cells in the conditioned culture medium of cancer cell lines, which is a mimic of carcinoma microenvironment. As a result, the Nanog miPS cells treated with the conditioned medium of mouse Lewis lung carcinoma acquired characteristics of CSCs, in that they formed spheroids expressing GFP in suspension culture, and had a high tumorigenicity in Balb/c nude mice exhibiting angiogenesis in vivo. In addition, these iPS-derived CSCs had a capacity of self-renewal and expressed the marker genes, Nanog, Rex1, Eras, Esg1 and Cripto, associated with stem cell properties and an undifferentiated state. Thus we concluded that a model of CSCs was originally developed from miPS cells and proposed the conditioned culture medium of cancer cell lines might perform as niche for producing CSCs. The model of CSCs and the procedure of their establishment will help study the genetic alterations and the secreted factors in the tumor microenvironment which convert miPS cells to CSCs. Furthermore, the identification of potentially bona fide markers of CSCs, which will help the development of novel anti-cancer therapies, might be possible though the CSC model.
<title>Perfect color constancy vs. color normalization for object recognition</title> (1999)

Colors recorded in an image depend on the color of the capture illuminant. As such image colors are not stable features for object recognition but we wish they were stable since perceived colors (the colors we see) are illuminant independent and do correlate with object identity. Color constancy algorithms attempt to infer and remove the illuminant color through image analysis. Over the last two decades, various models for color constancy have been developed. Unfortunately, color constancy algorithms are still not good enough to support object recognition. In this paper, we evaluate optimal color constancy procedures against color normalization. Two perfect color constancy algorithms are described. One is perfect color constancy by the scene, which arrives at an estimate of the illuminant not through algorithmic inference, but through measurement: the light source is measured using a spectraradiometer, assuming the reflectances of object surface are known. The other is perfect color color constancy by the illuminant, which arrives at an estimate of the illuminant through measurement, assuming the reflectances of object surface are unknown. Instead of color constancy, color normalization normalizes color images in terms of the context to remove illumination. To remove dependency due to illumination, images in a calibrated dataset are preprocessed using either the color constancy or color invariant normalization. Two experiments are reported in the paper. In the first experiment, the optimal algorithms of perfect color constancy based on measurement were tested using a calibrated image dataset. In the second experiment, the performances of the optimal color constancy algorithms are compared with color invariant normalization. Unfortunately, measurement driven color constancy by the illuminant does not support perfect recognition. However, color constancy preprocessing based on a scene dependent 'effective illuminant' facilitates near-perfect recognition. In comparison the color invariant normalization also deliver near-perfect recognition. The failure of color constancy by the illuminant is understandable because the measured illuminant doesn't correspond to the actual effective illuminant. Rather, we found illumination to depend both on the light source and characteristics of the scene.
Fighting Naphthenate Deposition at the Heidrun Field (2003)

Abstract At the Statoil-operated Heidrun-field in the Norwegian Sea, naphthenate deposits were first observed during a maintenance shutdown in September 1996. Thereafter the problem increased, and by the end of 1997 it was recognised as a constant threat against continuous production. The present paper describes both the short-term measures taken to gain control of the problem in the early days, and the quest for a more elegant long-term solution. Statoil is continuously working to increase its fundamental understanding of the naphthenate problems and to improve the naphthenate inhibitors used at the Heidrun field.
Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes (1997)

Map positions have been determined for 42 non-redundant Arabidopsis expressed sequence tags (ESTs) showing similarity to disease resistance genes (R-ESTs), and for three Pto-like sequences that were amplified with degenerate primers. Employing a PCR-based strategy, yeast artificial chromosome (YAC) clones containing the EST sequences were identified. Since many YACs have been mapped, the locations of the R-ESTs could be inferred from the map positions of the YACs. R-EST clones that exhibited ambiguous map positions were mapped as either cleavable amplifiable polymorphic sequence (CAPS) or restriction fragment length polymorphism (RFLP) markers using F8 (Ler x Col-0) recombinant inbred (RI) lines. In all cases but two, the R-ESTs and Pto-like sequences mapped to single, unique locations. One R-EST and one Pto-like sequence each mapped to two locations. Thus, a total of 47 loci were identified in this study. Several R-ESTs occur in clusters suggesting that they may have arisen via gene duplication events. Interestingly, several R-ESTs map to regions containing genetically defined disease resistance genes. Thus, this collection of mapped R-ESTs may expedite the isolation of disease resistance genes. As the cDNA sequencing projects have identified an estimated 63% of Arabidopsis genes, a very large number of R-ESTs (approximately 95), and by inference disease resistance genes of the leucine-rich repeat-class probably occur in the Arabidopsis genome.
Chirp characteristics of optical combs in MZM-based flat comb generator with optical feedback loop (2012)

Chirp characteristics of a comb signal generated by a Mach-Zehnder-modulator-based flat comb generator with an optical feedback loop were investigated. It was found that the comb source is suitable for pulse generation.
Synthesis of Injectable Antifungal Sch 59884 (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Injectable Antifungal Sch 59884Gary M. Lee, Jefrey Eckert, Dinesh Gala, Martin Schwartz, Paul Renton, Edward Pergamen, Michael Whttington, Doris Schumacher, Larry Heimark, and Petia ShipkovaView Author Information Chemical Process Research and Development, Schering-Plough Research Institute, 1011 Morris Avenue, Union, New Jersey 07083, U.S.A. Cite this: Org. Proc. Res. Dev. 2001, 5, 6, 622–629Publication Date (Web):October 12, 2001Publication History Received23 April 2001Published online12 October 2001Published inissue 1 November 2001https://pubs.acs.org/doi/10.1021/op010212whttps://doi.org/10.1021/op010212wreview-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views742Altmetric-Citations8LEARN 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:Antimicrobial agents,Impurities,Reagents,Salts,Sodium Get e-Alerts
Synthesis of Gallium Nitride Nanoparticles by Microwave Plasma‐Enhanced CVD (2010)

Abstract Gallium nitride (GaN) nanoparticles are successfully synthesized via an improved microwave plasma‐enhanced (MPE)CVD method. Optimization of the MPECVD process is achieved by manipulating the plasma operating conditions, such as antenna length, input power, and pressure. The resulting GaN nanoparticles have an average size of around 8.5 nm with a very narrow size distribution, indicating that well‐dispersed nanoparticles can be obtained, due to the negative charge of the particles caused by the collision of electrons in the plasma process. In addition, a satisfactory stoichiometric ratio, high crystallinity, and relatively good photoluminescence (PL) properties of the GaN nanoparticles are achieved, due to the improved process.
Dialog system for mixed initiative one-turn address entry and error recovery (2009)

In this demonstration we present a mixedinitiative dialog system for address recognition that lets users to specify a complete addresses in a single sentence with address components spoken in their natural sequence. Users can also specify fewer address components in several ways, based on their convenience. The system extracts specified address components, prompts for missing information, disambiguates items independently or collectively all the while guiding the user so as to obtain the desired valid address. The language modeling and dialog management techniques developed for this purpose are also briefly described. Finally, several use cases with screen shots are presented. The combined system yields very high task completion accuracy on user tests.
Development of novel inhibitors of swelling‐activated LRRC8 anion channels (2018)

Cells critically regulate their volume in response to hypoosmotic swelling by transporting chloride and small organic osmolytes out of the cell through so‐called volume‐regulated anion channels (VRACs). The 5 genes encoding VRACs were recently identified in two independent genome‐wide siRNA screens and are named LRRC8 (for Leucine Rich Repeat Containing) A‐E. LRRC8‐containing VRACs have recently been implicated in drug uptake, adipocyte size, and insulin signaling. Unfortunately, the pharmacological tools available to study the physiology and therapeutic potential of LRRC8 channels is limited to low‐affinity small‐molecule inhibitors that exhibit promiscuous activity toward other anion channels, cation channels, and myriad other off‐targets. To circumvent this barrier, we are employing high‐throughput screening (HTS) of small‐molecule libraries and medicinal chemistry to develop more potent and specific inhibitors of LRRC8 channels. HTS will be performed using a fluorescence assay based on halide quenching of a YFP mutant (i.e. F46L, H148Q, I152L) termed Ozzy. Briefly, HEK‐293 cells stably transfected with Ozzy will be plated in black‐walled, clear‐bottomed 384‐well plates, treated with hypotonic solution containing compounds from the Vanderbilt Institute of Chemical Biology library, and then treated with sodium iodide (NaI). Cell swelling opens endogenously expressed VRAC channels, through which iodide enters the cell and quenches Ozzy fluorescence. Small‐molecule inhibitors should block the iodide‐induced quenching of Ozzy. Checkerboard analysis using the best‐in‐class VRAC inhibitor, DCPIB, yielded a Z′ value of 0.74, indicating the assay is reproducible and robust enough to ensure high‐confidence hit‐picking in a large‐scale screen. The assay also reports dose‐dependent inhibition of iodide influx by DCPIB with an IC 50 of 11 micromolar, which is close to values derived from electrophysiological experiments. We are currently using this assay to interrogate an analog library based on the DCPIB scaffold, with the goal of identifying more potent and specific inhibitors of VRAC. Support or Funding Information Department of Anesthesiology Faculty Development Funds This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Incorporation of Bulky and Cationic Cyclam‐Triazole Moieties into Marimastat Can Generate Potent MMP Inhibitory Activity without Inducing Cytotoxicity (2013)

The synthesis and matrix metalloproteinase (MMP) inhibitory activity of a cyclam-marimastat conjugate and its metal complexes are described. The conjugate, synthesized with a copper(I)-catalyzed Huisgen 1,3-dipolar cycloaddition ("click" reaction), contains two zinc-binding groups (ZBGs). The metal complexation behavior with copper(II) and zinc(II) was investigated using UV/Vis spectrophotometry and (1)H NMR spectroscopy, respectively, demonstrating that the first equivalent of the metal ion was chelated by the cyclam-triazole moiety rather than the hydroxamic acid site. Thus, the corresponding mononuclear metal-cyclam complexes were successfully prepared with one equivalent of the metal salt. Both the cyclam-marimastat conjugate and its metal complexes exhibited slightly reduced potency against MMP-1, but essentially identical inhibitory activity against MMP-3. The conjugate and its metal complexes displayed little or no cytotoxicity, further supporting their potential suitability for imaging MMP localization and activity. To the best of our knowledge, this is the first report that describes the incorporation of metal complexes into an MMP inhibitor without influencing the preexisting ZBG, and the first report of the evaluation of structures containing more than one ZBG as MMP inhibitors.
Selective Hartmann-Hahn Transfer in Liquids (2007)

The sections in this article are 1 Introduction 2 Hamiltonian and Coherence Transfer 3 Decoupling and Relaxation Effects 4 One-Dimensional Applications 5 Use in Selective Two-Dimensional Spectroscopy 6 Biographical Sketch Related Articles
Meeting American Diabetes Association diabetes management targets: trends in Mauritius (2017)

Aims: To examine the proportion of people with diabetes in the multi-ethnic country of Mauritius meeting American Diabetes Association targets in 2009 and 2015. Methods: Data from independent population-based samples of 858 and 656 adults with diagnosed diabetes in 2009 and 2015, respectively, were analysed with regard to recommended American Diabetes Association targets for HbA1c, blood pressure and LDL cholesterol. Results: In 2015 compared with 2009, the proportion of people achieving American Diabetes Association targets for glycaemic control in Mauritius was higher in women (P≤0.01) and in those with only a primary education level (P=0.07), but not in men or people with a higher level of education. Achievement of blood pressure &lt;140/90 mmHg was higher in 2015 compared with 2009 (60% vs 42%) in people of South Asian ethnicity (P&lt;0.001), but not in those of African ethnicity (P=0.16). The percentages of people with LDL cholesterol &lt;2.59 mmol/l were 42.1% and 50.4%, in 2009 and 2015, respectively (P=0.27). Better control of HbA1c and blood pressure was observed in groups in which that control was poorest in 2009. The use of glucose-, blood pressure- and LDL cholesterol-lowering medication was higher in 2015 than in 2009. Conclusions: In certain subgroups, namely women, those with poorer education and those of South Asian ethnicity, whose target achievement was the poorest in 2009, control of glycaemia and blood pressure was better in 2015 as compared with 2009. While these findings are encouraging, further work is required to improve outcomes.
Production, crystallization, and preliminary X‐ray analysis of the human MHC class Ib molecule HLA‐E (1998)

HLA-E is the first human class Ib major histocompatibility complex molecule to be crystallized. HLA-E is highly conserved and almost nonpolymorphic, and has recently been shown to be the first specialized ligand for natural killer cell receptors. In functional studies, HLA-E is unlike the class Ia MHC molecules in having tightly restricted peptide binding specificity. HLA-E binds a limited set of almost identical leader sequence peptides derived from class Ia molecules and presents these at the cell surface for recognition by natural killer cell receptors. We now show that the extracellular region of HLA-E forms a stable complex with beta2 microglobulin and can be refolded around synthetic peptide. Crystals of this complex formed slowly over four to six months in the presence of ammonium sulphate. The crystals diffract to 2.85 A with space group P3(1)21 and unit cell dimensions a = 182.2 A, b = 182.2 A, c = 88.4 A.
Five-Year Outcomes in Patients With Left Main Disease Treated With Either Percutaneous Coronary Intervention or Coronary Artery Bypass Grafting in the Synergy Between Percutaneous Coronary Intervention With Taxus and Cardiac Surgery Trial (2014)

http://www.clinicaltrials.gov. Unique identifier: NCT00114972.
Co-Rotating Twin-Screw Extruders: Applications (2020)

You have accessCo-Rotating Twin-Screw Extruders: ApplicationsNov 2020Co-Rotating Twin-Screw Extruders: ApplicationsKlemens KohlgrüberKlemens Kohlgrüberhttps://doi.org/10.3139/9781569907825.fmSectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF ShareFacebookTwitterEmailLinkedIn next chapter FiguresReferencesRelatedDetails 2020Pages: I-XVIPrint ISBN: 978-1-56990-781-8eISBN: 978-1-56990-782-5 Copyright & Permissions© 2021 Carl Hanser Verlag GmbH & Co. KGPDF DownloadLoading ...
Phenylenevinylene conjugated oligoelectrolytes as fluorescent dyes for mammalian cell imaging (2014)

Conjugated phenylenevinylene oligoelectrolytes, which consist of a phenylenevinylene core equipped at each end with hydrophilic pendent groups, are shown to be good candidates for mammalian cell membrane staining. When used in the micromolar concentration range, they express low to moderate cell toxicity for selected regular and cancerous cell lines as tested for adherent and suspension cells.
A polymer network liquid crystal poly-CdSe TFT active matrix display (2002)

A polymer network liquid crystal display (PNLCD) with a poly-CdSe thin film transistor (TFT) active matrix is presented. This AM PNLCD combines high brightness and large viewing angles with a low driving voltage capability. Only slight improvements on resistivity are needed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gated pinhole camera imaging of the high-energy ions emitted by a discharge produced Sn plasma for extreme ultraviolet generation (2010)

The origin and nature of the high-energy ions emitted by a dischargeproduced plasma source are studied using gated pinhole camera imaging. Time-of-flight analysis in combination with Faraday cup measurements enables characterization of the high-velocity component of theionic debris. The use of an optional magnetic field allows mass-to-charge analysis of the first part of the Faraday cup signal. It is shown that this consists mainly of oxygen ions emitted from a region near the cathode. Time-resolved images of Sn ions with a kinetic energy of 45 keV visualize the regions in between the electrodes where the high-energy ion generation takes place.
A Randomized Trial of Static and Articulating Spacers for the Treatment of Infection Following Total Knee Arthroplasty (2020)

Therapeutic Level I. See Instructions for Authors for a complete description of levels of evidence.
Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding site (2021)

A vaccine which is effective against the HIV virus is considered to be the best solution to the ongoing global HIV/AIDS epidemic. In the past thirty years, numerous attempts to develop an effective vaccine have been made with little or no success, due, in large part, to the high mutability of the virus. More recent studies showed that a vaccine able to elicit broadly neutralizing antibodies (bnAbs), that is, antibodies that can neutralize a high fraction of global virus variants, has promise to protect against HIV. Such a vaccine has been proposed to involve at least three separate stages: First, activate the appropriate precursor B cells; second, shepherd affinity maturation along pathways toward bnAbs; and, third, polish the Ab response to bind with high affinity to diverse HIV envelopes (Env). This final stage may require immunization with a mixture of Envs. In this paper, we set up a framework based on theory and modeling to design optimal panels of antigens to use in such a mixture. The designed antigens are characterized experimentally and are shown to be stable and to be recognized by known HIV antibodies.