gebhart/patrepeval huggingface dataset:
Multicolor-FISH Approaches for the Characterization of Human Chromosomes in Clinical Genetics and Tumor Cytogenetics (2002)

A variety of multicolor fluorescence in situ hybridization (FISH) assays have been developed in the last decade. Routine application of such techniques started in 1996 with the simultaneous use of all the 24 human whole chromosome painting probes (i.e. multiplex-FISH = M-FISH and spectral karyotyping = SKY). Since that time different approaches for chromosomal differentiation based on multicolor-FISH (mFISH) assays have been published with the purpose to characterize structurally abnormal chromosomes and supernumerary marker chromosomes of unknown origin after conventional karyotypic analysis. Their characterization is of high clinical impact and is the requisite condition for further molecular investigations aimed at identification of disease related genes. We present an overview of the available different mFISH methods, highlighting their advantages and limitations, as well as their applications in clinical and tumor cytogenetics. Finally, an outlook is given on further possible developments of thi s special field of molecular cytogenetics. Keywords: fish, m-fish, tumor cytogenetics
5G Multi-RAT Integration Evaluations Using a Common PDCP Layer (2017)

5G is expected to operate in a wide frequency range to support new challenging use-cases. Multi- RATs (Radio Access Technologies): NR (New Radio) and evolved LTE (Long Term Evolution) will together constitute 5G. Utilizing NR at high frequencies will have a significant impact on radio propagation conditions with e.g. unfavorable higher path loss and increased outdoor-to-indoor penetration losses. In order to provide a reliable communication from the outset of 5G deployment and to minimize the standardization and implementation complexity, 5G UP (User Plane) instances of 5G AIs (Air Interface) related to evolved LTE and NR need to be aggregated on a certain layer of the protocol stack. This paper sheds light on how to integrate 5G AIs into a single 5G AI framework and explores which protocol stack layer could be used as aggregation layer. Inter-RAT hard handover is the state of the art technique to integrate multiple RATs in order to support mobility and reliability across different RATs. However, the hard handover incurs a transmission interruption which stands as an obstacle along the way of accomplishing 5G design. According to simulation results, a common PDCP (Packet Data Convergence Protocol) layer improves the hard handover functionality and stands out as a basis for tight interworking between evolved LTE and NR. By means of simulation, it is shown that the multi-RAT UP aggregation can achieve three times higher user throughput, when NR is using 28 GHz and LTE 2 GHz, compared to stand-alone NR.
QscR, a modulator of quorum-sensing signal synthesis and virulence in <i>Pseudomonas aeruginosa</i> (2001)

The opportunistic pathogenic bacterium Pseudomonas aeruginosa uses quorum-sensing signaling systems as global regulators of virulence genes. There are two quorum-sensing signal receptor and signal generator pairs, LasR-LasI and RhlR-RhlI. The recently completed P. aeruginosa genome-sequencing project revealed a gene coding for a homolog of the signal receptors, LasR and RhlR. Here we describe a role for this gene, which we call qscR. The qscR gene product governs the timing of quorum-sensing-controlled gene expression and it dampens virulence in an insect model. We present evidence that suggests the primary role of QscR is repression of lasI. A qscR mutant produces the LasI-generated signal prematurely, and this results in premature transcription of a number of quorum-sensing-regulated genes. When fed to Drosophila melanogaster, the qscR mutant kills the animals more rapidly than the parental P. aeruginosa. The repression of lasI by QscR could serve to ensure that quorum-sensing-controlled genes are not activated in environments where they are not useful.
A rule-based tool for gradual granular data aggregation (2011)

In order to keep more detailed data available for longer periods, old data has to be reduced gradually to save space and improve query performance, especially on resource-constrained systems with limited storage and query processing capabilities. In this regard, some hand-coded data aggregation solutions have been developed; however, their actual usage have been limited, for the reason that hand-coded data aggregation solutions have proven themselves too complex to maintain. Maintenance need to occur as requirements change frequently and the existing data aggregation techniques lack flexibility with regards to efficient requirements change management. This paper presents an effective rule-based tool for data reduction based on gradual granular data aggregation. With the proposed solution, data can be maintained at different levels of granularity. The solution is based on high-level data aggregation rules. Based on these rules, data aggregation code can be auto-generated. The solution is effective, easy-to-use and easy-to-maintain. In addition, the paper also demonstrates the use of the proposed tool based on a farming case study using standard database technologies. The results show productivity of the proposed tool-based solution in terms of initial development time, maintenance time and alteration time as compared to a hand-coded solution.
Reverse atom transfer radical polymerization of butyl methacrylate in a miniemulsion stabilized with a cationic surfactant (2006)

Abstract The miniemulsion reverse atom transfer radical polymerization of butyl methacrylate was carried out with cetyltrimethylammonium bromide (CTAB) as the sole surfactant. The polymerizations were initiated with 2,2′‐azobis[2‐(2‐imidazolin‐2‐yl)propane] dihydrochloride and mediated with copper(II) bromide/tris[2‐di(2‐ethylhexyl acrylate)aminoethyl]amine. The living character was demonstrated by the linear increase in the number‐average molecular weight with conversion and the decreasing polydispersity index with conversion. The polymerizations were conducted at 90 °C with 1 wt % CTAB with respect to the monomer and produced a coagulum‐free latex with a mean particle diameter of 155 nm. The resulting latexes exhibited good shelf‐life stability. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 1628–1634, 2006
Treatment of Human Spasticity with Δ<sup>9</sup>‐Tetrahydrocannabinol (1981)

Abstract: Spasticity is a common neurologic condition in patients with multiple sclerosis, stroke, cerebral palsy or an injured spinal cord. Animal studies suggest that THC has an inhibitory effect on polysynaptic reflexes. Some spastic patients claim improvement after inhaling cannabis. We tested muscle tone, reflexes, strength and performed EMGs before and after double‐blinded oral administration of either 10 or 5 mg THC or placebo. The blinded examiner correctly identified the trials in which the patients received THC in seven of nine cases. For the group, 10 mg THC significantly reduced spasticity by clinical measurement ( P < 0.01). Quadriceps EMG interference pattern was reduced in those four patients with primarily extensor spasticity. THC was administered to eight other patients with spasticity and other CNS lesions. Responses varied, but benefit was seen in three of three patients with “tonic spasms.” No benefit was noted in patients with cerebellar disease.
Mycosis fungoides shows concurrent deregulation of multiple genes involved in the TNF signaling pathway: an expression profile study (2003)

Mycosis fungoides (MF) is the most frequent type of cutaneous T-cell lymphoma, whose diagnosis and study is hampered by its morphologic similarity to inflammatory dermatoses (ID) and the low proportion of tumoral cells, which often account for only 5% to 10% of the total tissue cells. cDNA microarray studies using the CNIO OncoChip of 29 MF and 11 ID cases revealed a signature of 27 genes implicated in the tumorigenesis of MF, including tumor necrosis factor receptor (TNFR)-dependent apoptosis regulators, STAT4, CD40L, and other oncogenes and apoptosis inhibitors. Subsequently a 6-gene prediction model was constructed that is capable of distinguishing MF and ID cases with unprecedented accuracy. This model correctly predicted the class of 97% of cases in a blind test validation using 24 MF patients with low clinical stages. Unsupervised hierarchic clustering has revealed 2 major subclasses of MF, one of which tends to include more aggressive-type MF cases including tumoral MF forms. Furthermore, signatures associated with abnormal immunophenotype (11 genes) and tumor stage disease (5 genes) were identified.
Automated solar module assembly line (1979)

The gathering of information that led to the design approach of the machine, and a summary of the findings in the areas of study along with a description of each station of the machine are discussed. The machine is a cell stringing and string applique machine which is flexible in design, capable of handling a variety of cells and assembling strings of cells which can then be placed in a matrix up to 4 ft x 2 ft. in series or parallel arrangement. The target machine cycle is to be 5 seconds per cell. This machine is primarily adapted to 100 MM round cells with one or two tabs between cells. It places finished strings of up to twelve cells in a matrix of up to six such strings arranged in series or in parallel.
Net shaped high performance oxide ceramic parts by selective laser melting (2010)

An additive manufacturing technique (AM) for ceramics, based on Al2O3–ZrO2 powder by means of Selective Laser Melting (SLM) is presented. Pure ceramic powder is completely melted by a laser beam yielding net-shaped specimens of almost 100% densities without any post-processing. Possible crack formation during the build-up process due to thermal stresses is prevented by a high-temperature preheating of above 1600 ∘C. Specimens with fine-grained nano-sized microstructures and flexural strengths of above 500 MPa are produced. The new technology allows for rapid freeform manufacture of complex net-shaped ceramics, thus, exploiting the outstanding mechanical and thermal properties for high-end medical and engineering disciplines.
A level set‐based parameterization method for structural shape and topology optimization (2007)

Abstract This paper presents an effective parametric approach by extending the conventional level set method to structural shape and topology optimization using the compactly supported radial basis functions (RBFs) and the optimality criteria (OC) method. The structural design boundary is first represented implicitly by embedding into a higher‐dimensional level set function as its zero level set, and the RBFs of a favorable smoothness are then applied to interpolate the level set function. The original initial value problem is thus converted to a parametric optimization, with the expansion coefficients of the interplant posed as the design variables. The OC method is then applied to advance the structure boundary in terms of the velocity field derived from the parametric optimization. Hence, the structural shape and topology optimization is now transformed into a process of iteratively finding coefficients to update the level set function to achieve an optimal configuration. The numerical considerations of the conventional level set method, including upwind schemes, velocity extension, and reinitialization, are eliminated. The proposed scheme is capable of addressing structural shape fidelity and topology change simultaneously and of keeping the boundary smooth during the optimization process. Furthermore, numerical convergence is expected to be improved. A widely investigated example, in the framework of structural stiffness designs, is applied to demonstrate the efficiency and accuracy of the proposed approach. Copyright © 2007 John Wiley & Sons, Ltd.
Generation of Virtual Spectral Color Target and Application to Testing Input Devices (2001)

The spectral sensitivities of image capture devices should be carefully designed to guarantee colorimetric color reproduction. As a standard color test chart, ISO/DIS 12641 is conveniently used for calibrating the scanners or printers. However, its color gamut is not wide enough to evaluate the devices such as digital camera and display systems and the color distributions are not uniform because the chart is a photographic print. This article proposes a virtual color target to estimate the spectral goodness of color devices. A virtual spectrum with given L*a*b* value is generated from the fundamental metamer uniquely obtained by inverse projection of XYZ tristimulus value and an addition of arbitrary metameric black spectrum. The goodness of typical color input sensors is estimated and compared with actual color chips using this virtual spectral target.
Probabilistic multi-class segmentation for the Amazon Picking Challenge (2016)

We present a method for multi-class segmentation from RGB-D data in a realistic warehouse picking setting. The method computes pixel-wise probabilities and combines them to find a coherent object segmentation. It reliably segments objects in cluttered scenarios, even when objects are translucent, reflective, highly deformable, have fuzzy surfaces, or consist of loosely coupled components. The robust performance results from the exploitation of problem structure inherent to the warehouse setting. The proposed method proved its capabilities as part of our winning entry to the 2015 Amazon Picking Challenge. We present a detailed experimental analysis of the contribution of different information sources, compare our method to standard segmentation techniques, and assess possible extensions that further enhance the algorithm's capabilities. We release our software and data sets as open source.
An optically interfaced propulsion management system applied to a commercial transport aircraft (2003)

A fly-by-light propulsion management system to transport aircraft under development at Douglas Aircraft Company is described. The system includes an optically interfaced full-authority digital electronic control evaluation system, optical angular position sensors used to sense throttle position, a set of four optical position switches, and an optical ARINC 629 data link. These components, together with a mounting fixture for the sensors, optical cables and connectors, and a data-management unit, are being developed for design into an optical propulsion management system. This system is scheduled to be flight-evaluated on the NASA LaRC 737 ATOPS research aircraft. The objectives of this program are to evaluate the feasibility of using fiber-optic links across the engine/airframe interface and to encourage vendor participation in order to establish a state of vendor technology readiness for the early 1990s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Core glycosylation of cytochrome P-450(arom). Evidence for localization of N terminus of microsomal cytochrome P-450 in the lumen. (1993)

It was found that cytochrome P-450(arom) purified from human placenta microsomes is glycosylated, and the sugar chain was cleaved with endoglycosidase H (Endo H). The core glycosylation of P-450(arom) was examined with two heterologous expression systems, cultured insect cells and in vitro translation system. The P-450(arom) protein expressed in the insect cells was glycosylated, and the sugar chain was sensitive to Endo H. It was also glycosylated when translated with the wheat germ cell-free system in the presence of rough microsomal membrane, and the sugar chain could be removed by Endo H treatment. Since the P-450(arom) molecule has two potential glycosylation sites (Asn-12 and Asn-180), we replaced each of the 2 asparagine residues with alanine by site-directed mutagenesis and examined the glycosylation of the two mutant proteins in the cell-free system. The core glycosylation did not occur when the Asn-12 residue was mutated, whereas the mutant protein with modified Asn-180 residue was glycosylated. These results demonstrated that the potential glycosylation site (Asn-12) in the N-terminal portion of P-450(arom) is the site of glycosylation. We conclude that the N terminus of P-450(arom) is translocated across the endoplasmic reticulum membrane to be glycosylated at the luminal side.
Measurement of Insulin-Like Growth Factor-II in Physiological Fluids and Tissues. II. Extraction and Quantification in Rat Tissues* (1991)

The tissue distribution and developmental patterns of insulin-like growth factor-II (IGF-II) have not been investigated in rat tissues, primarily because of the lack of an efficient extraction method for IGF-II and a sensitive RIA. IGF-II was extracted from rat tissues by formic acid, and the extract was heated at an acidic pH and treated with acetone. The removal of binding proteins was demonstrated by fast protein liquid chromatography size exclusion column and the elimination of a dilutional bias in the RIA. Using rat IGF-II as standard, we optimized a RIA for the quantification of IGF-II in rat tissues. In adult rats, IGF-II was found in all 15 tissues examined, with the highest concentration in the pituitary, followed by kidney, seminal vesicles, intestine, and serum. This distribution is not only different from that of IGF-I, but also differs from that reported for IGF-II mRNA and IGF-II receptors, suggesting that the rates of synthesis and/or metabolism of IGF-II are tissue dependent. Developmentally, IGF-II levels fell postnatally in most tissues, a pattern similar to that of IGF-II mRNA and IGF-II receptor. This developmental pattern supports the hypothesis that IGF-II is important in early growth and development. A relatively homogeneous distribution was observed in the adult rat brain, a distribution also different from that reported for IGF-II mRNA. In the pituitary, the highest concentration was found in the posterior pituitary, followed by the intermediate and anterior pituitary. In conclusion, IGF-II is found in many tissues of adult rats. This observation supports an autocrine and/or paracrine roles for IGF-II.
Establishment and maintenance of planar epithelial cell polarity by asymmetric cadherin bridges: A computer model (2005)

Animal scales, hairs, feathers, and cilia are oriented due to cell polarization in the epithelial plane. Genes involved have been identified, but the signal and mechanism remain unknown. In Drosophila wing polarization, the action of a gradient of Frizzled activity is widely assumed; and cell-cell signalling by cadherins such as Flamingo surely plays a major role. We present a computer model where reading the Frizzled gradient occurs through biased, feedback-reinforced formation of Flamingo-based asymmetric intercellular complexes. Through these complexes neighboring cells are able to compare their Frizzled activity levels. Our computations are highly noise-resistant and reproduce both wild-type and all known mutant wing phenotypes; other phenotypes are predicted. The model puts stringent limits on a Frizzled activation signal, which should exhibit unusual properties: (1) the extracellular Frizzled signalling gradient should be counterdirectional--decreasing from proximal (P) to distal (D), whereas during polarization, the intracellular Frizzled gradient builds up from P to D; (2) the external gradient should be relatively weak and short-lived, lest it prevent inversion of intracellular Frizzled. These features, largely independent of model details, may provide useful clues for future experimental efforts.
Metabolic Oxidative Cleavage of Thioesters: Evidence for the Formation of Sulfenic Acid Intermediates in the Bioactivation of the Antithrombotic Prodrugs Ticlopidine and Clopidogrel (2009)

Metabolic cleavage of the CO-S bond of some thioesters RCOSR' with the formation of RCOOH requires a monooxygenase-dependent oxidative activation of this bond. The nature of the S-containing product(s) resulting from this cleavage remains unclear in most cases. This communication provides the first evidence for the formation of sulfenic acid intermediates 4a and 4b during the oxidative cleavage of the CO-S bond of thiolactone metabolites 2a and 2b of antithrombotic prodrugs, ticlopidine and clopidogrel, by rat and human liver microsomes. These intermediates have been trapped by dimedone, and the corresponding adducts 5a and 5b have been characterized by mass spectrometry (MS) and (1)H and (13)C NMR spectroscopy. Their formation is monooxygenase-dependent and almost completely inhibited by microsomal cytochrome P450 inhibitors. Moreover, they were also formed upon incubation with microsomes containing recombinant human P450 3A4, 3A5, 2C8, 2C9, 2C19, 2D6, or 1A2. In the presence of thiols such as mercaptoethanol, N-acetylcysteine, or glutathione, microsomal incubations of 2a led to mixed disulfides that have been characterized by MS and should result from reaction of 4a with these thiols. At high thiol concentrations, one observed in HPLC-MS the formation of a product exhibiting the MS expected for the previously described thiol metabolite 3a, a reduction product of 4a that has been reported as the pharmacologically active metabolite of ticlopidine. These data provide the first evidence for the formation of sulfenic acid reactive metabolites upon P450-catalyzed oxidative cleavage of thioesters. They also provide a first detailed mechanism for the previously described formation of pharmacologically active thiols such as 3a upon oxidative metabolism of ticlopidine and clopidogrel.
Active capacitor voltage control of flying capacitor multilevel converters (2004)

A novel control strategy for voltage balancing of flying capacitor multilevel converters controlled with phase shifted SPWM is presented. Based on the polarity of the phase current, a relatively small square wave is added to the nominal modulation signals (typically sinusoidal) controlling the converter switches and in this way the flying capacitor voltages can be directly regulated. A simple algorithm is developed to explore an optimal solution for multiple capacitor voltage regulation. The impact of the proposed control strategy on the flying capacitor voltage variation and converter output voltage is analysed. The effectiveness of the control strategy is validated by simulation results of a five-level converter.
Quantitative morphometric measurements using site selective image cytometry of intact tissue (2008)

Site selective two-photon tissue image cytometry has previously been successfully applied to measure the number of rare cells in three-dimensional tissue specimens up to cubic millimetres in size. However, the extension of this approach for high-throughput quantification of cellular morphological states has not been demonstrated. In this paper, we report the use of site-selective tissue image cytometry for the study of homologous recombination (HR) events during cell division in the pancreas of transgenic mice. Since HRs are rare events, recombinant cells distribute sparsely inside the organ. A detailed measurement throughout the whole tissue is thus not practical. Instead, the site selective two-photon tissue cytometer incorporates a low magnification, wide field, one-photon imaging subsystem that rapidly identifies regions of interest containing recombinant cell clusters. Subsequently, high-resolution three-dimensional assays based on two-photon microscopy can be performed only in these regions of interest. We further show that three-dimensional morphology extraction algorithms can be used to analyse the resultant high-resolution two-photon image stacks providing information not only on the frequency and the distribution of these recombinant cell clusters and their constituent cells, but also on their morphology.