gebhart/patrepeval huggingface dataset:
Vertically Oriented Germanium Nanowires Grown from Gold Colloids on Silicon Substrates and Subsequent Gold Removal (2007)

A linker-free method to deposit citrate-stabilized Au colloids onto hydrogen-terminated Si by acidifying the Au colloid solution with HF or HCl is presented. This method prevents oxide formation and provides a model system for studying orientation control of nanowires by epitaxy. Conditions are reported that result in vertically oriented Ge nanowires of uniform diameter and length on Si(111). We then present a method to remove Au catalysts from the nanowires with aqueous triiodide and HCl.
Cytoscape 2.8: new features for data integration and network visualization (2010)

Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org.
Identification of cancer stem cells in head and neck squamous cell carcinoma (2006)

Proc Amer Assoc Cancer Res, Volume 47, 2006

3983 

Epithelial cancers, including head and neck squamous cell carcinoma (HNSCC), contain a heterogeneous population of cells. Studies have shown that a subpopulation of tumorigenic breast cancer cells, “cancer stem cells” (CSC), can be isolated based on their expression of cell surface markers. Identification of CSC in breast cancer suggested that other epithelial tumors might contain tumorigenic and non tumorigenic populations of cells. A NOD/SCID mouse model was used to test the tumorigenic potential of cells derived from human HNSCC. Seven specimens from primary HNSCC were analyzed and distinct populations of CD44 positive (CD44+) and CD44 negative (CD44-) cancer cells were identified and isolated in all specimens. Single cell suspensions of CD44+Lineage- and CD44-Lineage- cells were implanted in NOD/SCID mice. CD44+ cells formed tumors in 13/16 implantations, while 0/20 implantations of CD44- cells formed tumors. As few as 5x103 CD44+ tumor cells gave rise to tumors while up to 5x105 CD44- tumor cells failed to form tumors. Tumors resulting from implantation of CD44+ cells reproduced the original tumor heterogeneity even after serial passage in the animal model. In 5/7 samples Epithelial specific antigen (ESA) expression was used to try to enrich the tumorigenic subpopulation of CD44+ HNSCC cells. Single cell suspensions of CD44+ESA+Lineage- and CD44+ESA-Lineage- cells were implanted. ESA expression did not enrich the tumor cells tumorigenic potential. These results are the first demonstration that HNSCC contains a distinct subpopulation of tumorigenic cells, defined by their expression of the cell surface antigen CD44. The CD44+ cell population in the HNSCC specimens had the exclusive ability to produce tumors and recreate the original tumor heterogeneity. ESA expression did not alter the cells tumorigenic potential. CD44 expression allows for the identification of the tumorigenic subpopulation of HNSCC cells and provides a basis to study the mechanisms that drive the self-renewal of these cells. This could lead to innovative CSC directed therapies for HNSCC and other epithelial malignancies.
Noninvasive Acoustic Cell Trapping in a Microfluidic Perfusion System for Online Bioassays (2007)

Techniques for manipulating, separating, and trapping particles and cells are highly desired in today's bioanalytical and biomedical field. The microfluidic chip-based acoustic noncontact trapping method earlier developed within the group now provides a flexible platform for performing cell- and particle-based assays in continuous flow microsystems. An acoustic standing wave is generated in etched glass channels (600x61 microm2) by miniature ultrasonic transducers (550x550x200 microm3). Particles or cells passing the transducer will be retained and levitated in the center of the channel without any contact with the channel walls. The maximum trapping force was calculated to be 430+/-135 pN by measuring the drag force exerted on a single particle levitated in the standing wave. The temperature increase in the channel was characterized by fluorescence measurements using rhodamine B, and levels of moderate temperature increase were noted. Neural stem cells were acoustically trapped and shown to be viable after 15 min. Further evidence of the mild cell handling conditions was demonstrated as yeast cells were successfully cultured for 6 h in the acoustic trap while being perfused by the cell medium at a flowrate of 1 microL/min. The acoustic microchip method facilitates trapping of single cells as well as larger cell clusters. The noncontact mode of cell handling is especially important when studies on nonadherent cells are performed, e.g., stem cells, yeast cells, or blood cells, as mechanical stress and surface interaction are minimized. The demonstrated acoustic trapping of cells and particles enables cell- or particle-based bioassays to be performed in a continuous flow format.
Imaging Gene Expression in Human Mesenchymal Stem Cells: From Small to Large Animals (2009)

Reporter gene imaging in human MSCs can be translated to large animals. The study highlights the importance of co-administering a "scaffold" for increasing intramyocardial retention of human MSCs.
New Synthesis of Pyrido[2,3-d]pyrimidines. I. Reaction of 6-Alkoxy-5-cyano-3,4-dihydro-2-pyridones with Guanidine and Cyanamide (1985)

The first step of a new synthesis of pyrido[2,3-d]pyrimidines. the aubstitutlon of the enollc alkaxyl group of E-alkoxy-S-cyano-3.4dihydro-2-pyridones ( ?I by guanidine and cyanamrde is described.BY this procedure a series of 2.4-diamlno-5.6-dihydropyrido[2,3-c]pyrimidin-7(8H)-ones16) and E-cyanamino-S-cyano-3,4-dihydro-2-pyridones 13) have been synthesized.Products 3 have been isolated in this work for t h e first time, and tautorneric equilibrium with the cyanimino farm has been detected in every case.
Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions (2009)

Electromobility shift assay is a simple, efficient, and rapid method for the study of specific DNA-protein interactions. It relies on the reduction in the electrophoretic mobility conferred to a DNA fragment by an interacting protein. The technique is suitable to qualitative, quantitative, and kinetic analyses. It can also be used to analyze conformational changes.
Development of a Safe Gene Delivery System Using Biodegradable Polymer, Poly[α-(4-aminobutyl)-l-glycolic acid] (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTDevelopment of a Safe Gene Delivery System Using Biodegradable Polymer, Poly[α-(4-aminobutyl)-l-glycolic acid]Yong-beom Lim, Chang-hwan Kim, Kwan Kim, Sung Wan Kim, and Jong-sang ParkView Author Information School of Chemistry & Molecular Engineering Seoul National University, Seoul 151-742, Korea Center for Controlled Chemical Delivery (CCCD) University of Utah, Salt Lake City, Utah 84112 Cite this: J. Am. Chem. Soc. 2000, 122, 27, 6524–6525Publication Date (Web):June 23, 2000Publication History Received24 March 2000Published online23 June 2000Published inissue 1 July 2000https://pubs.acs.org/doi/10.1021/ja001033hhttps://doi.org/10.1021/ja001033hrapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1493Altmetric-Citations147LEARN 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:Degradation,Gene delivery,Genetics,Polymers,Toxicity Get e-Alerts
Novel Pseudomonas aeruginosa Quorum-Sensing Inhibitors Identified in an Ultra-High-Throughput Screen (2006)

The opportunistic pathogen Pseudomonas aeruginosa has two complete acyl-homoserine lactone (acyl-HSL) signaling systems, LasR-LasI and RhlR-RhlI. LasI catalyzes the synthesis of N-3-oxododecanoyl homoserine lactone (3OC12-HSL), and LasR is a transcription factor that requires 3OC12-HSL as a ligand. RhlI catalyzes the synthesis of N-butanoyl homoserine lactone (C4), and RhlR is a transcription factor that responds to C4. LasR and RhlR control the transcription of hundreds of P. aeruginosa genes, many of which are critical virulence determinants, and LasR is required for RhlR function. We developed an ultra-high-throughput cell-based assay to screen a library of approximately 200,000 compounds for inhibitors of LasR-dependent gene expression. Although the library contained a large variety of chemical structures, the two best inhibitors resembled the acyl-homoserine lactone molecule that normally binds to LasR. One compound, a tetrazole with a 12-carbon alkyl tail designated PD12, had a 50% inhibitory concentration (IC50) of 30 nM. The second compound, V-06-018, had an IC50 of 10 microM and is a phenyl ring with a 12-carbon alkyl tail. A microarray analysis showed that both compounds were general inhibitors of quorum sensing, i.e., the expression levels of most LasR-dependent genes were affected. Both compounds also inhibited the production of two quorum-sensing-dependent virulence factors, elastase and pyocyanin. These compounds should be useful for studies of LasR-dependent gene regulation and might serve as scaffolds for the identification of new quorum-sensing modulators.
Escherichia coliRNase R Has Dual Activities, Helicase and RNase (2009)

In Escherichia coli, the cold shock response occurs when there is a temperature downshift from 37 degrees C to 15 degrees C, and this response is characterized by induction of several cold shock proteins, including the DEAD-box helicase CsdA, during the acclimation phase. CsdA is involved in a variety of cellular processes. Our previous studies showed that the helicase activity of CsdA is critical for its function in cold shock acclimation of cells and that the only proteins that were able to complement its function were another helicase, RhlE, an RNA chaperone, CspA, and a cold-inducible exoribonuclease, RNase R. Interestingly, other major 3'-to-5' processing exoribonucleases of E. coli, such as polynucleotide phosphorylase and RNase II, cannot complement the cold shock function of CsdA. Here we carried out a domain analysis of RNase R and showed that this protein has two distinct activities, RNase and helicase, which are independent of each other and are due to different domains. Mutant RNase R proteins that lack the RNase activity but exhibit the helicase activity were able to complement the cold shock function of CsdA, suggesting that only the helicase activity of RNase R is essential for complementation of the cold shock function of CsdA. We also observed that in vivo deletion of the two cold shock domains resulted in a loss of the ability of RNase R to complement the cold shock function of CsdA. We further demonstrated that RNase R exhibits helicase activity in vitro independent of its RNase activity. Our results shed light on the unique properties of RNase R and how it is distinct from other exoribonucleases in E. coli.
Pyrolysis products of untreated and flame retardant‐treated α‐cellulose and levoglucosan (1971)

Abstract A typical gas chromatogram of the volatile pyrolysis products of untreated α‐cellulose contains 39 peaks; however, mass spectral data indicate that at least 59 compounds, with molecular weights less than about 150, are present. A total of 37 compounds have been identified, 13 of which have not been previously reported. Most of the newly identified compounds contain a benzene ring, indicating that these compounds may be products of reactions between initial volatiles. A comparison of the products generated in the temperature range of 330°–440°C indicates that the formation of pyrolysis products is essential independent of temperature. Comparisons of the chromatograms obtained for untreated levoglucosan and cellulose indicate that most of the decomposition of cellulose probably forms levoglucosan which then decomposes to yield the observed pyrolysis products. In addition, the products of flame retardant‐treated levoglucosan are essentially the same as those of cellulose with the same retardant treatment. This suggests that the retardants act on the levoglucosan formed in the decomposition of the cellulose rather than on the cellulose directly.
Localization of the continuous allergenic sites of ragweed allergen Ra3 by a comprehensive synthetic strategy (1985)

A comprehensive synthetic approach, previously introduced by this laboratory for the localization of the full profile of the continuous antigenic sites on proteins, was applied here to localize the continuous sites of ragweed allergen, Ra3, that are recognized by human anti-Ra3 IgE antibodies. The following 10 uniform and overlapping peptides were synthesized and purified: 1-15, 11-25, 21-35, 31-45, 41-55, 51-65, 61-75, 71-85, 81-95 and 91-101. Quantitative radiometric titrations of protein and peptide adsorbents with human IgE, established the full profile of allergenic (IgE binding) sites on Ra3. It was found that Ra3 has four continuous allergenic sites. Antibodies prepared against the IgE binding peptides bound to native Ra3. The findings are briefly discussed in relation to other protein antigenic structures and in terms of design of vaccines using synthetic sites.
Evidence that IgE molecules mediate a spectrum of effects on mast cell survival and activation via aggregation of the FcεRI (2003)

We demonstrate that binding of different IgE molecules (IgEs) to their receptor, FcepsilonRI, induces a spectrum of activation events in the absence of a specific antigen and provide evidence that such activation reflects aggregation of FcepsilonRI. Highly cytokinergic IgEs can efficiently induce production of cytokines and render mast cells resistant to apoptosis in an autocrine fashion, whereas poorly cytokinergic IgEs induce these effects inefficiently. Highly cytokinergic IgEs seem to induce more extensive FcepsilonRI aggregation than do poorly cytokinergic IgEs, which leads to stronger mast cell activation and survival effects. These effects of both types of IgEs require Syk tyrosine kinase and can be inhibited by FcepsilonRI disaggregation with monovalent hapten. In hybridoma-transplanted mice, mucosal mast cell numbers correlate with serum IgE levels. Therefore, survival effects of IgE could contribute to the pathogenesis of allergic disease.
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects (2001)

We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative experiments is presented. The analysis is demonstrated via two groups of experiments with 125 and 4129 genes, respectively, in Escherichia coli grown in glucose and acetate.
A Curvature-based Scheme for Improving Road Vehicle Guidance by Computer Vision (1987)

An efficient method for guiding high speed land vehicles along roadways by computer vision has been developed and demonstrated with image sequence processing hardware in a real-time simulation loop <sup>1</sup>. The approach is tailored to a well structured highway environment with good lanemarkings. Contour correlation and high order world models are the basic elements of the method, realised in a special multi-microprocessor (on board) computer system. Perspec-tive projection and dynamical models (Kalman filter) are used in an integrated approach for the design of the visual feedback control system. By determining road curvature explicity from the visual input, previously encountered steady state errors in curves are eliminated. The performance of the system will be demonstrated by a video film. The operation of the image sequence processing system has been tested on a typical Autobahn-scene at velocities up to 100 km/h.
Cutting Edge: Mast Cells Critically Augment Myeloid-Derived Suppressor Cell Activity (2012)

Myeloid-derived suppressor cells (MDSCs) are primarily recognized for their immunosuppressive properties in malignant disease. However, their interaction with other innate immune cells and their regulation of immune responses, such as in parasitic infection, necessitate further characterization. We used our previously published mouse model of MDSC accumulation to examine the immunoregulatory role of MDSCs in B16 melanoma metastasis and Nippostrongylus brasiliensis infection. In this study, we demonstrate that the activity of MDSCs is dependent on the immune stimuli and subset induced. Monocytic MDSCs predictably suppressed antitumor immune responses but granulocytic MDSCs surprisingly enhanced the clearance of N. brasiliensis infection. Intriguingly, both results were dependent on MDSC interaction with mast cells (MCs), as demonstrated by adoptive-transfer studies in MC-deficient (Kit(Wsh)(/)(Wsh)) mice. These findings were further supported by ex vivo cocultures of MCs and MDSCs, indicating a synergistic increase in cytokine production. Thus, MCs can enhance both immunosuppressive and immunosupportive functions of MDSCs.
Extracellular Prolyl Endoprotease from Aspergillus niger and Its Use in the Debittering of Protein Hydrolysates (2005)

The observation that the bitterest peptides from casein hydrolysates contain several proline residues led us to hypothesize that a proline-specific protease would be instrumental in debittering such peptides. To identify the desired proline-specific activity, a microbiological screening was carried out in which the chromogenic peptide benzyloxycarbonyl-glycine-proline-p-nitroanilide (Z-Gly-Pro-pNA) was used as the substrate. An Aspergillus niger (A. niger) strain was identified that produces an extracellular proline-specific protease with an acidic pH optimum. On the basis of sequence similarities, we conclude that the A. niger-derived enzyme probably belongs to the S28 family of clan SC of serine proteases rather than the S9 family to which prolyl oligopeptidases belong. Incubating the overexpressed and purified enzyme with bitter casein hydrolysates showed a major debittering effect. Reversed phase HPLC analysis revealed that this debittering effect is accompanied by a significant reduction of the number of hydrophobic peptides present.
Immunoglobulin Binding by Mouse Intestinal Epithelial Cell Receptors (1976)

The IgG receptors involved in transporting maternal antibodies to the blood stream of the young mouse were studied by feeding internally labeled mouse myeloma proteins and enzymatically generated specific fragments of these proteins. The data obtained from competition experiments showed the following: 1) intestinal receptors have a single specificity which is directed against IgG Fc determinants; 2) IgG subclass proteins differ in their affinities for the receptors and thus have similar but not identical Fc recognition sites; 3) the order of affinities of the IgG subclass proteins for the receptors correlates with the relative concentrations of the four subclass proteins in mouse milk; and 4) several subfractions of the Fc fragment were inactive in binding to the receptors. In many of their properties the intestinal receptors resemble the Fc receptors on other cell types, but they are apparently unique in their ability to bind tightly non-aggregated IgG molecules.
Comparative quantification of nucleic acids using single-molecule detection and molecular beacons (2005)

This paper reports a highly sensitive homogenous method for comparative quantification of nucleic acids based on single-molecule detection (SMD) and molecular beacons (MBs). Two different color MBs were used to perform a separation-free comparative hybridization assay for simultaneous quantification of both target and control strands. A fluorescent burst, emitted from a single hybrid when it passes through a minuscule laser-focused region, is detected with high signal-to-noise ratio (SNR) by using single-molecule fluorescence spectroscopy. Targets are quantified via counting of discrete fluorescent bursts. The high SNR achieved in both detection channels overcame the complications of fluorescent variability usually observed in dual-color ensemble measurements. In comparison with the conventional ensemble methods, this method improved the detection limit by 3 orders of magnitude and reduced the probe consumption by 6 orders of magnitude, facilitating a highly sensitive approach for comparative quantification of nucleic acids and offering great promise for genomic quantification without amplification.
An illustrated comparison of processing methods for MR phase imaging and QSM: combining array coil signals and phase unwrapping (2016)

Phase imaging benefits from strong susceptibility effects at very high field and the high signal-to-noise ratio (SNR) afforded by multi-channel coils. Combining the information from coils is not trivial, however, as the phase that originates in local field effects (the source of interesting contrast) is modified by the inhomogeneous sensitivity of each coil. This has historically been addressed by referencing individual coil sensitivities to that of a volume coil, but alternative approaches are required for ultra-high field systems in which no such coil is available. An additional challenge in phase imaging is that the phase that develops up to the echo time is "wrapped" into a range of 2π radians. Phase wraps need to be removed in order to reveal the underlying phase distribution of interest. Beginning with a coil combination using a homogeneous reference volume coil - the Roemer approach - which can be applied at 3 T and lower field strengths, we review alternative methods for combining single-echo and multi-echo phase images where no such reference coil is available. These are applied to high-resolution data acquired at 7 T and their effectiveness assessed via an index of agreement between phase values over channels and the contrast-to-noise ratio in combined images. The virtual receiver coil and COMPOSER approaches were both found to be computationally efficient and effective. The main features of spatial and temporal phase unwrapping methods are reviewed, placing particular emphasis on recent developments in temporal phase unwrapping and Laplacian approaches. The features and performance of these are illustrated in application to simulated and high-resolution in vivo data. Temporal unwrapping was the fastest of the methods tested and the Laplacian the most robust in images with low SNR. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.