gebhart/patrepeval huggingface dataset:
Diversity of Human Monocyte Subsets Revealed by CyTOF Mass Cytometry (2017)

Abstract Background To date, 3 distinct human monocyte subsets have been identified based primarily on their expression of the surface markers CD14 and CD16. With the emerging knowledge of myeloid-derived suppressor cells and other myeloid subsets, we hypothesized that these monocytes were likely more heterogeneous in composition. Therefore, we set out to use the high dimensionality of mass cytometry to accurately identify and define monocyte subsets in blood of healthy humans. Methods Heparinized blood from 12 healthy humans was obtained and analyzed by CyTOF mass cytometry. We employed the Phenograph algorithm to cluster and identify all monocyte subsets based on their phenotypes using a 40-marker mass cytometry panel. Results Phenograph identified a total of 15 monocyte clusters based on cell phenotype. By performing hierarchical clustering, we were able to group the 15 clusters into 6 larger meta-clusters and found that most of these meta-clusters fall within the CD14hi classical monocyte population, illustrating significant heterogeneity among the classical CD14hi monocyte population in humans. We also identified two subsets of nonclassical monocytes of which one was high for both CD61 and CD9 expression, pointing to a possible role in cell adhesion/migration and platelet activation. Conclusion Monocytes are highly diverse with the conventional classical subset showing the most diversity. Studies of these new subsets should lead to greater understanding of functions of monocyte subsets in diseases.
A Robust Adaptive Estimator for Filtering Noise in Images (1995)

Provides three new methods for storing images corrupted by additive noise. One is the adaptive mean median filter for preserving the details of images when restored from additive Gaussian noise. Another is the minimum-maximum method for moving outlier noise. The third method, the robust adaptive mean p-median filter, is based on a combination of the previous two methods. In the past, proposed restoration methods have generally proven to be inadequate for both detail preservation and noise suppression, but the new adaptive mean p-median filter is shown to be good at both of these tasks, while the robust adaptive mean p-median filter can give good performance even in the presence of outliers. Degraded images are processed by the proposed algorithms, with the results compared with a selection of other median-based algorithms that have been proposed in the literature.
Profiling Primary Metabolites of Tomato Fruit with Gas Chromatography/Mass Spectrometry (2011)

Metabolite profiling is a rapidly expanding technology which aims to quantify the entire metabolome of biological samples. Gas Chromatography Mass Spectrometry (GC-MS) is one of the most widely used analytical tools for profiling highly complex mixtures of primary metabolites, such as organic and amino acids, sugars, sugars alcohols, phosphorylated intermediates, and lipophilic compounds. This chapter summarizes all of the preparatory steps for metabolite profiling of polar compounds by GC-MS in tomato fruit, from the sampling of plant material to the derivatization procedures required to render the metabolites volatile.
Use of ion pairing reagents for sensitive detection and separation of phospholipids in the positive ion mode LC-ESI-MS (2011)

Phospholipids make up one of the more important classes of biological molecules. Because of their amphipathic nature and their charge state (e.g., negatively charged or zwitterionic) detection of trace levels of these compounds can be problematic. Electrospray ionization mass spectrometry (ESI-MS) is used in this study to detect very small amounts of these analytes by using the positive ion mode and pairing them with fifteen different cationic ion pairing reagents. The phospholipids used in this analysis were phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), phosphatidylserine (PS), phosphatidylinositol (PI), phosphatidic acid (PA), 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC), cardiolipin (CA) and sphingosyl phosphoethanolamine (SPE). The analysis of these molecules was carried out in the single ion monitoring (SIM) positive mode. In addition to their detection, a high performance liquid chromatography and mass spectrometry (HPLC-MS) method was developed in which the phospholipids were separated and detected simultaneously within a very short period of time. Separation of phospholipids was developed in the reverse phase mode and in the hydrophilic interaction liquid chromatography (HILIC) mode HPLC. Their differences and impact on the sensitivity of the analytes are compared and discussed further in the paper. With this technique, limits of detection (LODs) were very easily recorded at low ppt (ng L(-1)) levels with many of the cationic ion pairing reagents used in this study.
Modeling chlorine dioxide bleaching of chemical pulp (2010)

This doctoral thesis deals with the phenomenon-based modeling of pulp bleaching. Previous bleaching models typically utilize one or two empirical correlations to predict the kinetics in kappa number development. Empirical correlations are simple to develop, but their parameters are often tied to the validation system. A major benefit of physico-chemical phenomenon models is that they are valid regardless of the reaction environment. Furthermore, modeling the bleaching processes at molecular level provides a new way to examine the relative importance of various phenomena, the validity of theories and the bottlenecks of bleaching applications. \n The first part of the thesis introduces a model for the pulp suspension environment and describes the physico-chemical models in use (reaction kinetics, mass transfer, thermodynamics). The second part deals with inorganic oxychlorine reactions related to chlorine dioxide bleaching. The reaction kinetics and mechanism are documented for iron- mediated chlorite decomposition, chlorous acid self-decomposition, and for the reaction between hypochlorous acid and chlorous acid. The rate coefficient temperature dependency is reported for the two latter reactions. The reaction kinetic models were utilized in assessing the potential chlorate formation routes encountered in pulp bleaching. It was concluded that chlorous acid self-decomposition is unlikely to contribute to chlorate formation in bleaching applications. The iron-mediated chlorite decomposition and the reaction between hypochlorous acid and chlorous acid are expected to produce chlorate. \n The last part introduces a model for chlorine dioxide delignification. Here the pulp suspension model was combined with a broad set of chemical reactions describing the ClO2 bleaching chemistry. The incorporated reactions cover lignin oxidation, lignin chlorination, hexenuronic acid degradation, lignin dissolution, oxidation of extractives and the essential inorganic oxychlorine reactions. The model predictions were compared against experimental delignification results in order to validate the model and obtain the previously unknown reaction rate parameters. The predictions were generally in good agreement with experimental results. Deviations related primarily to hypochlorous acid driven processes: organochlorine formation, hexenuronic acid degrading reactions, chlorite depletion or chlorate formation. The simulation results suggest that organochlorine formation is restricted by the amount of chlorination-susceptible substrates in pulp rather than the availability of chlorine. It was also concluded that, in addition to the fully inorganic reactions, chlorite is also likely to be consumed in reactions with pulp-related compounds, for instance with aldehydes.
Immobilized-enzyme rate-determination method for glucose analysis. (1980)

Abstract We present a rate-determination method for analyzing glucose. A glucose enzyme electrode serves as the sensor and is made by placing a gel-immobilized layer of glucose oxidase over the tip of a Clark-type O2 electrode. The electrode membrane is made of Teflon and is derivatized by etching with a suspension of colloidal sodium metal in organic solvent. The enzyme is coupled to the membrane surface by use of paraformaldehyde. The immobilized-enzyme method is compared with a similar solution-enzyme method and with the National Glucose Reference method. The immobilized enzyme method compares favorably with the solution-enzyme method and offers the advantages of simplicity, economy of enzyme, and linearity over a greater range of concentration.
Marker development, high-throughput and logistics of MAS applications in a large wheat breeding program (2008)

Molecular markers are being increasingly used as a selection tool in wheat breeding programs around the world. The deployment of multiple genes for disease, quality and agronomic traits into breeding lines is the major aim of a breeding program. To effectively utilise molecular markers, breeders require timely delivered accurate and reliable information, and lots of them! This presentation aims to outline; (1) Development of molecular markers for the breeders’ traits and an informative gene map for breeders that includes traits of immediate interest, and (2) discussions about the high-throughput and logistics of MAS applications in a large breeding program.&#13;\nMolecular marker development is fully integrated with the breeding operations, and activities are focused on the traits that breeders prioritise in the program. As the new markers were identified from our work and/or literature these were then integrated into marker cassettes formed for different group of traits (i.e. quality, disease) for their effective use in MAS.&#13;\n&#13;\nBased on the traits that are required by the breeding program we have established a trait based map that serve as a guide to breeders in their daily activities including crossing decisions. The program currently is using marker-assisted selection for 40 traits/genes, for which more than one marker are used for the quantitative traits. To define the needs of three sub-programs and for the timely delivery of the outputs by the molecular lab, we have developed a simple excel based database. This DB has allowed us to keep track the requirements of each of the three sub-programs to make sure that marker laboratory spends its resources equally. Data analysis is one of the limitations of high-throughput marker applications and to overcome this additional analysis tools are being developed.
Evaluating newly approved drugs for multidrug-resistant tuberculosis (endTB): study protocol for an adaptive, multi-country randomized controlled trial (2021)

ClinicalTrials.gov Identifier NCT02754765. Registered on 28 April 2016; the record was last updated for study protocol version 3.3, on 27 August 2019.
Near-field optical storage system using a solid immersion lens with a left-handed material slab (2004)

A new near-field optical storage system utilizing a left-handed material (LHM) is introduced by attaching an LHM slab to the lower surface of a conventional solid immersion lens (SIL). The performance of the present storage system is compared with a conventional SIL system through numerical simulation. The LHM slab in the present storage system can image very well the focused spot at the lower surface of the SIL to the surface of a disc. It allows a large air-gap for the mechanical convenience while keeping a large signal contrast and a high storage density. The tolerance of the air-gap is also improved.
Musical design patterns: an example of a human-centered model of interactive multimedia (1997)

Most multimedia data today is sampled and quantized from analog sources. Even with sophisticated recognition and indexing techniques, it remains difficult to associate human-centered, semantic content and structural information with it. This prohibits many desirable, more advanced interaction metaphors with the data than simple replay. We propose that a human-centered model of both multimedia data and suitable metaphors to directly and instantaneously interact with it is crucial to the design of more interactive and "multimedia-aware" system and application architectures. We show how we implemented such a model for the media type "music" in the WorldBeat system, a highly successful interactive computer-based music exhibit in the Ars Electronica Center in Lint, Austria. The system uses a high-level semantic concept of musical information called "musical design patterns". Interaction with this representation, like spontaneous, computer-supported improvisation, is supported in a novel way, using just a pair of infrared batons to control the entire exhibit. The system and its semantic model offer a technologically and artistically innovative approach that should be of interest to multimedia researchers as well as educators, artists and performers.
Novel valproic acid derivatives with hemoglobin F inducing activity (2006)

Pharmacological induction of hemoglobin F expression may be a promising approach for the treatment of beta-thalassemia and sickle cell disease. Valproic acid, a drug frequently used for the treatment of seizure disorders, has been shown to enhance fetal hemoglobin synthesis in erythroid cells. However, this effect is only modest and requires relative high concentrations. Therefore, the drug appears not to be applicable for the treatment of beta-globin chain disorders. Here, we describe the identification of novel valproic acid derivatives with potent hemoglobin F inducing activities at concentrations that presumably can be obtained in vivo.
Tin Oxide Nanowires, Nanoribbons, and Nanotubes (2002)

Nanowires, sandwiched nanoribbons, and nanotubes of SnO2 are synthesized using elevated temperature synthesis techniques, and their structures are characterized in detail by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). In addition to the normal rutile structured SnO2, it has been possible to form an orthorhombic superlattice-like structure in the present study. The orthorhombic structure can form in a thin nanowire, coexist with the normal rutile structured SnO2 in a sandwiched nanoribbon, or occur in the form of nanotubes. This result is distinct from that for bulk SnO2 where pressures in excess of 150 kbar are required to form the orthorhombic form. The orientation relationship between the orthorhombic SnO2 and the rutile structured SnO2 is determined to be [001]o || [102̄]t and (100)o || (010)t for the nanowires and sandwiched nanoribbons, and [001]o || [3 ]t and (110)o || (451)t for the nanotubes. Although the growth direction of the rutile structured SnO2 nanowires is along [101]t, two growth directions are found to occur in the nanostructures having the orthorhombic SnO2 structure. They are [010]o for nanowires and [1̄10]o for the sandwiched nanoribbons and nanotubes. The results in this study and the observation of orthorhombic SnO2 may result from the formation of the products in an oxygen deficient environment.
Thermal Resistance Measurements for Flexible Straps at Cryogenic Temperatures (2004)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation G. F. Nellis, B. F. Lachner, O. D. Lokken, B. L. Stahl, L. D. Crawford; Thermal Resistance Measurements for Flexible Straps at Cryogenic Temperatures. AIP Conf. Proc. 23 June 2004; 710 (1): 651–658. https://doi.org/10.1063/1.1774739 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 ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Abstract O.23: Lysyl Oxidase Expression In The Patients With Kawasaki Disease (2015)

Background: Histologic study of inflamed coronary arteries from the Kawasaki disease (KD) patients shows infiltration by immune effector cells, IL-17-producing myofibroblasts, and breaks in the internal elastic lamina. Transcripts from genes associated with cell trafficking (e.g. paxillin) are elevated in whole blood from acute KD patients. Lysyl oxidase (LOX) is a multifunctional protein affecting affecting “monocyte and smooth muscle cell migration, elastogenesis, and endothelial-to-mesenchymal transition. LOX promotes cell motility through paxillin phosphorylation, which influences T-cell trafficking via the calcium signaling pathway. We investigated the role of LOX in the pathogenesis of KD. Methods: Agilent microarray data using whole blood were analyzed for differential expression of enzymes in the LOX family (LOX, LOX-like (L)1-4) in acute and convalescent KD samples (n=19). LOXL1 results were validated using RT-PCR in an independent cohort (n=20). LOXL1 transcripts levels were measured in KD whole blood, peripheral blood mononuclear cells (PBMC), T-cell clones, B-cell lines, and myeloid dendritic cells from acute KD patients. Immunohistochemical staining for LOXL1 was performed on coronary arteries from a KD patient who died on illness day 7. Result: LOXL1 expression by microarray was 3.2-fold higher in acute than convalescent samples (p&lt;0.001) and was validated in an independent cohort by RT-PCR (5.4-fold higher, p&lt;0.001). LOXL1 transcripts levels were 2-35 times higher in PBMC compared to whole blood (n=8). KD T cell clones had higher LOXL1 transcript levels than B-cells and dendritic cells. Immunohistochemical staining showed LOXL1-expressing inflammatory cells and smooth muscle cells in the coronary artery walls. Conclusion: LOXL1 may increase inflammation in acute KD by promoting the motility of infiltrating T cells and smooth muscle cells through focal adhesion formation. However, LOXL1 may also participate in arterial wall repair by crosslinking collagen and elastin. Statins inhibit focal adhesion formation and thus cell trafficking but not the crosslinking mediated by LOXL1. Studies of LOXL1 protein levels and paxillin phosphorylation in PBMC may further our understanding of their role in KD pathogenesis.
In situ protein expression of RRM1, ERCC1, and BRCA1 in metastatic breast cancer patients treated with gemcitabine-including chemotherapy (2009)

1129 Background: Ribonucleotide reductase 1 (RRM1) is a determinant of gemcitabine efficacy in non-small cell lung cancer (NSCLC) and pancreatic cancer. We investigated the tumoral levels of RRM1 in a population of metastatic breast cancer (MBC) patients treated with gemcitabine-based regimens. The protein levels of the excision repair cross-complementation group 1 (ERCC1) and breast and ovarian cancer susceptibility gene 1 (BRCA1) were also measured. Methods: Fifty-five patients were treated and followed prospectively from September 2004 to December 2007. Treatment consisted of gemcitabine plus a taxane in 46 patients and gemcitabine plus pegylated liposomal doxorubicin in 9 patients. RRM1, ERCC1, and BRCA1 were determined by automated in situ protein quantification (AQUA v1.6) on a tissue microarray containing triplicate tumor specimens. Results: The average scores for RRM1, ERCC1, and BRCA1 ranged from 245.6–2, 774.1, 74.0–410.3, and 54.4–1, 833.1, respectively. A statistically significant correlation between the levels of expression of all three markers (Spearman's rho &gt; .36; P &lt; 0.007) was observed. There was no significant association between RRM1, ERCC1, or BRCA1 levels and disease response, progression free survival, or overall survival. Conclusions: In tumor specimens from patients with MBC, RRM1, and BRCA1 had a range of expression and pattern of distribution that makes these markers potentially suitable for clinical decision making. In contrast, the relatively narrow range of ERCC1 expression might signify that ERCC1 protein levels are not useful predictors of platinum efficacy in MBC. Consistent with what has been shown in NSCLC, RRM1, ERCC1, and BRCA1 levels were significantly correlated, suggesting that the coexpression of such DNA repair proteins may be universal to epithelial malignancies. The lack of correlation between marker levels and clinical outcome may be explained by the specific chemotherapy combinations used. No significant financial relationships to disclose.
Fate of polyoma form IDNA during replication (1975)

The fate of polyoma form IDNA generated during replication was investigated in resting BALB-3T3 cells. The experiments showed that there was extensive re-entry of such molecules into replication. This process took place over a period of several hours and appeared to be random. Progeny form I molecules must, therefore, spend some time in a nonreplicating pool before reinitiating replication. We propose that two factors affect the fate of progeny form IDNA. (i) The rate of reinitiation of progeny molecules is determined by the capacity of the initiation machinery. (ii) The extent of re-entry is determined by the availability of maturation proteins which divert form I from replication.
Extending Natures Leads: The Anticancer Agent Ellipticine (2004)

The natural plant product ellipticine was isolated in 1959 from the Australian evergreen tree of the Apocynaceae family. This compound was found to be an extremely promising anticancer drug. The planar polycyclic structure was found to interact with DNA through intercalation, exhibiting a high DNA binding affinity (10(6) M(-1)). The presence of protonatable ring nitrogens distinguished ellipticine from other simple intercalators. Both monocationic and uncharged species were found to be present under physiological conditions. The positive charge stabilized the binding of ellipticine to nucleic acids, while the more lipophilic uncharged compound was shown to readily penetrate membrane barriers. The structural nature of these compounds offers a plausible basis for the implication of multiple modes of action, including DNA binding, interactions with membrane barriers, oxidative bioactivation and modification of enzyme function; most notably that of topoisomerase II and telomerase. Pharmacologically, a number of toxic side effects have been shown to be problematic, but the amenability of ellipticine towards systematic structural modification has permitted the extensive application of rational drug design. A number of successful ellipticine analogs have been designed and synthesized with improved toxicities and anticancer activities. More recently the synthetic focus has broadened to include the design of hybrid compounds, as well as drug delivery conjugates. Considerable research efforts have been directed towards gaining a greater understanding of the mechanism of action of these drugs that will aid further in the optimization of drug design.
A Low Cost Solution to Digital Tuning of Television Receivers and Citizen Band Transceivers (1976)

A family of LSI frequency synthesizer circuits and their application to television and Citizen Band Radio are described. With a single crystal as the basic frequency reference, these circuits produce tuning accuracy and long term stability for a large number of frequencies at lower cost than for mechanical or crystal multiplexing methods.