gebhart/patrepeval huggingface dataset:
Bioorthogonal Probes for Polo‐like Kinase 1 Imaging and Quantification (2011)

Ein Zellkernprotein, die Polo-like-Kinase 1 (PLK1), wurde mithilfe einer biokompatiblen bioorthogonalen Ligation zwischen einem spezifischen Wirkstoff und einem Fluoreszenzfarbstoff in lebenden Zellen abgebildet. Die Colokalisation des Farbstoffs und Proteins wurde durch Antikörperfärbung und Expression eines GFP-Konstrukts der PLK1 bestätigt. Die zweistufige Prozedur wurde genutzt, um Expressionsspiegel von PLK1 in Krebszell-Linien aus verschiedenen Geweben zu quantifizieren.
Pan-sharpening of multispectral images: a critical review and comparison (2004)

This paper critically reviews state of the art and advanced methods for multispectral (MS) and panchromatic (Pan) image fusion based on either intensity-hue-saturation (IHS) transformation, or redundant multiresolution analysis (MRA). In either case, lower-resolution MS bands are sharpened by injecting details taken from the higher-resolution Pan image. Crucial point is modeling the relationships between detail coefficients of a generic MS band and the Pan image at the same resolution. Once calculated at the coarser resolution, where both types of data are available, such a model shall be extended to the finer resolution to weight the Pan details to be injected. Two injection models embedded in an "a trous" wavelet decomposition will be compared on a test set of very high resolution QuickBird MS+Pan data. One works on approximations and provides a partial unmixing of coarse MS pixels via high-resolution Pan. Another is based on spectral fidelity of original and merged MS data. Fusion comparisons on spatially degraded data, whose high-resolution MS originals are available for reference, show that the former performs better than the latter, in terms of both spatial and spectral fidelity
Probability of detection analysis in multi-hit flaw detection (2021)

Current approaches to qualification or reliability assessment of NDE procedures by traditional probability of detection (POD) testing per MIL-HDBK-1823A require significant number of specimens with known size real or simulated flaws. For many practical applications in aerospace industry, either it is difficult to produce or it is economically not feasible to fabricate the necessary flaw specimens in required quantity. Thus, there is a strong need for alternative methodologies to provide assessments of reliability of NDE procedures using fewer flaw specimens. The paper provides an alternate NDE reliability assessment approach using dependence of the probability of detection (POD) and probability of false positive (POF), on the contrast-to-noise ratio (CNR) and decision threshold-to-noise ratio (TNR) for selected POD and POF models. The NDE reliability assessment approach is termed as limited sample (LS) POD assessment. Current work assumes a multi-hit flaw detection methodology i.e. the flaw detection calls are mapped to form an indication with cluster of pixels in a 2D image. In LS POD approach, the signal response from a fixed size flaw of interest is assumed to follow a normal distribution. The approach uses statistical tolerances computed using signal response sample data and k<sub>1</sub>-factor. Similar to traditional POD analysis, a flaw size with chosen POD and confidence is determined. Alternately, POD/Conf. can be determined for a chosen decision threshold for the flaw size used in the analysis. The POF is also estimated in the analysis. Noise is assumed to follow either a normal or lognormal distribution. For reliable detection of the target size flaw, minimum POD/Conf. of 90/95% and maximum POF of 1% are assumed. The sample of signal responses is assumed to be representative of the assumed population of signal responses. Similarly, the noise measurements are assumed to be representative of those expected in the inspection of real hardware. If representative flaw sample and noise measurements are used, LS POD results pose no risk in the POD and POF estimation. Risk to meeting NDE flaw size detection requirements can be assessed based on how representative the flaw sample and noise measurements are and based on positive margin between LS POD results and procedure reliability requirements.
Design and proof of high quality HfAlO/sub x/ film formation for MOSCAPs and nMOSFETs through Layer-by-Layer Deposition and Annealing process (2004)

We propose a new method for high-k film growth and demonstrate its usefulness in terms of improvements of electrical characteristics of MOSCAPs and nMOSFETs. Layer-by-Layer Deposition & Annealing (LL-D&A) is a key concept to reduce impurities incorporated in the film through decomposition of precursors. For HfAlO/sub X/ (Hf:75at.%), it is shown that there are big differences in physical and electrical properties between LL-D&A and conventional ALD+PDA. The maximum film thickness for annealing to effectively remove impurities and presumably to cure imperfections should be less than 1.8 nm. The excellent properties for EOT=1.38 nm HfAlO/sub X/ grown through D&A(O/sub 2/) process, such as a very small flatband voltage shift (/spl delta/V/sub FB/) less than 0.06 V for MOSCAP, a well controlled subthreshold swing of 77 mV/dec, a peak mobility of 210 cm/sup 2//Vs and 10-year lifetime at V/sub g/=-1.9 V for poly-Si gate nMOSFET, manifest the superiority of LL-D&A to the conventional ALD+PDA.
Recording of multi-level run-length-limited (ML-RLL) modulation signals on phase-change optical disc (2004)

The writing and reading of 3 level run-length-limited (RLL) modulation signals on optical discs having active (recording) layers comprised of different phase change materials is discussed. These recordings represent a linear storage density enhancement of 50% Vs conventional (2-level) RLL modulation. Thermal simulations of the mark writing process provide a tool that can be used to optimize write strategies for ML-RLL recording.
Inherently Stealthy and Highly Tumor-Selective Gold Nanoraspberries for Photothermal Cancer Therapy (2015)

Owing to their unique optical properties such as large absorption and scattering cross section and large enhancement of electromagnetic field at the surface, plasmonic nanostructures have received extensive attention as a highly promising class of materials for nano-oncology. Most of the existing plasmonic nanostructures require extensive post-synthesis treatments and biofunctionalization routines to mitigate their cytotoxicity and/or make them tumor-specific. Here, we report one-pot synthesis of a novel class of plasmonic nanostructures, namely, gold nanoraspberries (GRBs) with tunable size and localized surface plasmon resonance by using a naturally abundant polysaccharide, chitosan, which acts as a template and capping agent. Significantly, the GRBs, which do not require any further biofunctionalization, exhibit excellent selectivity to tumor cells, thus enabling locoregional therapy at the cellular level. We demonstrate the tumor-selectivity of GRBs by photothermal ablation of tumor cells selectively from their co-culture with normal cells. The simple, scalable and tumor-selective nature of GRBs makes them excellent candidates for translational plasmonics-based nanomedicine.
Common chromosomal fragile site FRA16D sequence: identification of the FOR gene spanning FRA16D and homozygous deletions and translocation breakpoints in cancer cells (2000)

Fluorescence in situ hybridization of a tile path of DNA subclones has previously enabled the cyto-genetic definition of the minimal DNA sequence which spans the FRA16D common chromosomal fragile site, located at 16q23.2. Homozygous deletion of the FRA16D locus has been reported in adenocarcinomas of stomach, colon, lung and ovary. We have sequenced the 270 kb containing the FRA16D fragile site and the minimal homozygously deleted region in tumour cells. This sequence enabled localization of some of the tumour cell breakpoints to regions which contain AT-rich secondary structures similar to those associated with the FRA10B and FRA16B rare fragile sites. The FRA16D DNA sequence also led to the identification of an alternatively spliced gene, named FOR (fragile site FRA16D oxidoreductase), exons of which span both the fragile site and the minimal region of homozygous deletion. In addition, the complete DNA sequence of the FRA16D-containing FOR intron reveals no evidence of additional authentic transcripts. Alternatively spliced FOR transcripts (FOR I, FOR II and FOR III) encode proteins which share N-terminal WW domains and differ at their C-terminus, with FOR III having a truncated oxidoreductase domain. FRA16D-associated deletions selectively affect the FOR gene transcripts. Three out of five previously mapped translocation breakpoints in multiple myeloma are also located within the FOR gene. FOR is therefore the principle genetic target for DNA instability at 16q23.2 and perturbation of FOR function is likely to contribute to the biological consequences of DNA instability at FRA16D in cancer cells.
Towards a Fully Abstract Compiler Using Micro-Policies: Secure Compilation for Mutually Distrustful Components (2015)

Secure compilation prevents all low-level attacks on compiled code and allows for sound reasoning about security in the source language. In this work we propose a new attacker model for secure compilation that extends the well-known notion of full abstraction to ensure protection for mutually distrustful components. We devise a compiler chain (compiler, linker, and loader) and a novel security monitor that together defend against this strong attacker model. The monitor is implemented using a recently proposed, generic tag-based protection framework called micro-policies, which comes with hardware support for efficient caching and with a formal verification methodology. Our monitor protects the abstractions of a simple object-oriented language---class isolation, the method call discipline, and type safety---against arbitrary low-level attackers.
Digestion of Ryegrass Pasture in Response to Change in pH in Continuous Culture (2001)

The ruminal pH of dairy cows fed high quality pasture is often below values recommended to optimize digestion. Four continuous culture fermenters were used to determine the pH required for the optimal digestion of pasture. High quality pasture was fermented at four controlled levels of pH (5.4, 5.8, 6.2, and 6.6) according to a 4 x 4 Latin square design. Automatic infusion of 5 M NaOH and 5 M HCl controlled pH to +/- 0.1. Digesta samples were collected during the last 3 d of each of the four 9-d experimental periods. Digestion and synthesis of microbial protein were largely insensitive to pH across a broad range of pH (5.8 to 6.6), but a large reduction in both occurred when pH was 5.4. The digestibility of pasture dry matter and synthesis of microbial protein were optimized at pH 6.35 and 6.13, respectively. The proportions of individual volatile fatty acids were not changed as pH increased. Digestion of high quality pasture in continuous culture was comparable to that predicted by the Cornell Net Carbohydrate and Protein System between pH 6.2 and 6.6. However, the model underpredicted organic matter and fiber digestibility between pH 5.4 and 5.8, compared with values obtained in continuous culture. This suggests that when ruminal pH is less than 6.2, the model may over-predict the production response to supplementation of high quality pasture with an effective fiber source.
Implementing LNS using filtering units of GPUs (2010)

Current GPUs offer specialized graphics hardware in addition to generic floating-point processing units. We propose a method which reuses specialized texture filtering units to perform piecewise polynomial evaluations, which helps accelerate LNS computations and can be used in combination with hardware-based transcendental functions.
WATER HYACINTHS FOR REMOVAL OF CADMIUM AND NICKEL FROM POLLUTED WATERS (1975)

Removal of cadmium and nickel from static water systems utilizing water hyacinths (Eichhornia crassipes (Mart.) Solms) was investigated. This aquatic plant demonstrated the ability to rapidly remove heavy metals from aqueous systems by root absorption and concentration. Water hyacinths demonstrated the ability to absorb and concentrate up to 0.67 mg of cadmium and 0.50 mg of nickel per gram of dry plant material when exposed for a 24-hour period to waters polluted with from 0.578 to 2.00 ppm of these toxic metals. It is found that one hectare of water hyacinths has the potential of removing 300 g of cadmium or nickel from 240,000 liters of water polluted with these metals during a 24-hour period.
Precoder Design for Space-Time Coded Systems Over Correlated Rayleigh Fading Channels Using Convex Optimization (2008)

A class of computationally efficient linear precoders for space-time block coded multiple-input multiple-output wireless systems is derived based on the minimization of the exact symbol error rate (SER) and its upper bound. Both correlations at the transmitter and receiver are assumed to be present, and only statistical channel state information in the form of the transmit and receive correlation matrices is assumed to be available at the transmitter. The convexity of the design based on SER minimization is established and exploited. The advantage of the developed technique is its low complexity. We also find various relationships of the proposed designs to the existing precoding techniques, and derive very simple closed-form precoders for special cases such as two or three receive antennas and constant receive correlation. The numerical simulations illustrate the excellent SER performance of the proposed precoders.
Escherichia coli Flagellar Genes as Target Sites for Integration and Expression of Genetic Circuits (2014)

E. coli is a model platform for engineering microbes, so genetic circuit design and analysis will be greatly facilitated by simple and effective approaches to introduce genetic constructs into the E. coli chromosome at well-characterised loci. We combined the Red recombinase system of bacteriophage λ and Isothermal Gibson Assembly for rapid integration of novel DNA constructs into the E. coli chromosome. We identified the flagellar region as a promising region for integration and expression of genetic circuits. We characterised integration and expression at four candidate loci, fliD, fliS, fliT, and fliY, of the E. coli flagellar region 3a. The integration efficiency and expression from the four integrations varied considerably. Integration into fliD and fliS significantly decreased motility, while integration into fliT and fliY had only a minor effect on the motility. None of the integrations had negative effects on the growth of the bacteria. Overall, we found that fliT was the most suitable integration site.
Remarkable Activation of an Enzyme by (<i>R</i>)‐Pyrrolidine‐ Substituted Imidazolium Alkyl PEG Sulfate (2008)

Abstract The chiral pyrrolidine‐substituted imidazolium cetyl‐PEG10‐sulfate ( D ‐ProMe) derived from D ‐proline worked as an excellent activating agent of Burkholderia cepacia lipase; it is particularly interesting that the D ‐isomer of the imidazolium salt worked better than the L ‐isomer. This suggests that the imidazolium cation group directly interacts with the enzyme protein and causes preferable modification of the reactivity.
Fast segmentation of range images into planar regions (2002)

A split-and-merge algorithm is proposed for the segmentation of the digitized surface of a range image into planar regions. The geometric data structure used is a triangular tessellation of image domain. This data structure, combined with an adaptive surface approximation technique, allows a better adaptation of the range image segmentation to the surface boundaries. It also provides an efficient neighborhood referencing mechanism, thus resulting in a fast algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Plasmon resonances of gold nanoparticles incorporated inside an optical fibre matrix (2006)

Metallic nanoparticles were incorporated into the core of standard telecommunication grade optical fibres. This creates a simple, yet robust, platform which can be used to investigate the properties of nanoparticles, for sensing, spectroscopy, and optical switching applications. The optical response of gold nanoparticles embedded in the optical fibre matrix was evaluated as a function of temperature and the use of the structure as an inline fibre-optic temperature sensor is described. A redshift in the localized surface plasmon (LSP) resonance related peak, as well as broadening of the plasmon resonance, was observed upon increasing the temperature of the nanoparticle containing fibre. The shift and broadening of the plasmon resonance were attributed to the temperature dependence of dielectric constants of metallic nanoparticles and the silica matrix and to plasmon-phonon interactions.
Ref's eye for the fast guy (2005)

One of the most controversial rules in football is that of offside. However, a possible explanation for this is that the human eye and brain are incapable of processing all the necessary visual information to apply the rule, argues <b>Francisco Belda Maruenda</b>
Sample Multiplexing: Increased Throughput for Quantification of Total Testosterone in Serum by Liquid Chromatography-Tandem Mass Spectrometry (2020)

Sample multiplexing by differential mass tagging of TT increases LC-MS/MS throughput 2-fold without compromising analytical accuracy and sensitivity.
Review of Software to Fit Generalized Estimating Equation Regression Models (1999)

Abstract Researchers are often interested in analyzing data that arise from a longitudinal or clustered design. Although there are a variety of standard likelihood-based approaches to analysis when the outcome variables are approximately multivariate normal, models for discrete-type outcomes generally require a different approach. Liang and Zeger formalized an approach to this problem using generalized estimating equations (GEEs) to extend generalized linear models (GLMs) to a regression setting with correlated observations within subjects. In this article, we briefly review GLM, the GEE methodology, introduce some examples, and compare the GEE implementations of several general purpose statistical packages (SAS, Stata, SUDAAN, and S-Plus). We focus on the user interface, accuracy, and completeness of implementations of this methodology.
The Mechanism of On‐Water Catalysis (2010)

Acid catalysis by interfacial water: A new mechanism is proposed for on-water catalysis, the acceleration of organic reactions when conducted in aqueous emulsions. It involves the protonation of a substrate by water, driven by the strong adsorption of hydroxide ions at aqueous interfaces with oils. This accounts for the specific role of water, and a deuterium isotope effect, at the interface, on reactions known to be acid-catalysed. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ENZYMATIC DETERMINATION OF 1,3:1,4-β-GLUCANS IN BARLEY GRAIN AND OTHER CEREALS† (1978)

A direct and specific enzymatic method is described for the determination of 1,3:1,4-β-glucans in barley grain and other cereals. In the procedure, purified, amylase-free, bacterial 1,3:1,4-β-glucan hydrolase is used to depolymerize the 1,3:1,4-β-glucan in autoclaved and ethanol-extracted flour prepared from whole grain. The liberated oligoglucosides are extracted with 80% (vol/vol) ethanol and, following acid hydrolysis, measured by the glucose oxidase method. The method can be used to measure total β-glucan and β-glucan in 65°C water-soluble and water-insoluble fractions of cereal grains. The procedure has been applied to barley grains allowed to develop under controlled environmental conditions and to a series of barleys of different geographical origins. The results for Canadian cultivars are compared with estimates based on viscometric data for the same samples. The 1,3:1,4-β-glucan content of a number of other cereals has also been measured.
On the initial velocity of ions generated by matrix-assisted laser desorption ionization and its effect on the calibration of delayed extraction time-of-flight mass spectra (1997)

A novel method was developed to measure the initial velocity of ions generated by matrix-assisted laser desorption ionization (MALDI). It is shown both experimentally and theoretically that with a delayed extraction (DE) technique, the flight time of an ion changes linearly with extraction delay. The initial velocity of the ion, a consequence of the desorption process, can be determined from the slope of this linear curve. Systematic study of the initial velocity was undertaken regarding its dependence on the matrix substance, molecular weight of the analyte, ion polarity, and wavelength of irradiation. It was found that the most important factor was the matrix material. Sinapinic acid and α-cyano-4-hydroxycinnamic acid matrices ejected slower peptide and protein ions than 2,5-dihydroxybenzoic acid or 3-hydroxypicolinic acid: ∼ 300 versus ∼ 550 m/s. Matrix ions themselves exhibited a similar order of initial velocities, but these were 15–40% higher than those of insulin ions. The molecular weight of protein samples (between 5 and 25 ku) was found to have little effect on the initial velocity, but for peptides below 5 ku a gradual transition was noted toward the velocity of the matrix ions. Also decreasing velocity with increasing molecular mass was observed for DNA samples in the 4–14-ku range. In the negative ion mode slightly lower velocities were observed than in the positive ion mode. No difference was found between 337- and 266-nm irradiation. Values of the initial velocities were used to correct systematic errors in the internal calibration observed in mass spectra with delayed extraction. These velocity corrections decrease mass errors substantially in the linear mode, in particular for multicomponent mixtures.
Towards information networks to support composable manufacturing (2008)

Rigid, supply-chain organizational structures are giving way to highly dynamic collaborative partnerships. These partnerships will develop rapidly by composing global manufacturing resources in response to open market opportunities and they will disband just as rapidly when those opportunities disappear. Cooperation, coordination, and distributed decision-making will be critical to the success of these dynamically composable systems. That success, in turn, will depend on the creation of a manufacturing information network that automates as much as possible, the identification, formalization, encoding, and sharing of appropriate manufacturing- and business-related knowledge. In this paper we present some of the issues and requirements associated with the creation of such networks.
Quality of different chondroitin sulfate preparations in relation to their therapeutic activity (2009)

Due to the poor chondroitin sulfate quality of some nutraceuticals, we conclude that stricter regulations regarding their quality control should be introduced to guarantee the manufacture of high quality products for nutraceutical utilization and to protect customers from low-quality, ineffective and potentially dangerous products. There is a need for specific and accurate analytical procedures, which should be enforced to confirm purity and label claims both for raw materials and finished chondroitin sulfate products, and also to govern the origin of ingredients. Until these stricter regulations are in place, then it is strongly recommended that pharmaceutical-grade chondroitin sulfate is used rather than food supplements.