gebhart/patrepeval huggingface dataset:
Ultrasensitive multiplexed miRNA detection based on a self-priming hairpin-triggered isothermal cascade reaction (2021)

We herein describe an ultrasensitive isothermal strategy to detect miRNAs in a multiplexed manner by utilizing a self-priming hairpin-triggered cascade reaction and the adsorption properties of graphene oxide (GO). In principle, a self-priming hairpin probe (SHP) was designed to be opened through binding to the target miRNA and rearranged to serve as a primer. The following extension displaced the target miRNA to be recycled for opening another SHP and produced a double-stranded (ds) SHP with a longer stem region. The nicking enzyme recognition site within the ds SHP was then subjected to continuous repeated nicking and extension reactions, consequently producing a large amount of the trigger sequence. In the second reaction phase, the trigger also transformed another single-stranded (ss) target template probe (TTP) into ds TTP and simultaneously produced numerous target mimic strands (Target') in the same manner, which could activate the first reaction phase, mimicking the target miRNA. Since the ss portions of the two probes were all transformed to the ds forms (ds SHP and ds TTP), they are resistant to the adsorption by graphene oxide (GO) and then emitted intense fluorescence after the application of GO while the ss forms of the two probes produced a negligible fluorescence signal without the target miRNAs. Based on this unique design principle, we were able to simultaneously identify multiple target miRNAs very sensitively down to attomolar levels (42.63 aM for miRNA let-7a, 13.08 aM for miRNA-141, and 10.14 aM for miRNA-98) within 30 min.
Load cell system test experience: Measuring the vibrator ground force on land seismic acquisition (2009)

Many methods have been developed in an attempt to expand the recorded bandwidth associated with Vibroseis surveys, particularly to boost the signal at high frequencies for improving seismic image resolution. However, the dominant frequency band still remains in the range of 10–60Hz and no significant improvement has been achieved at high frequencies in conventional 3D seismic surveys. Ground attenuation is one of possible limitations, and another is that during the course of the seismic acquisition, the vibrator may not actually be generating as much energy at high frequencies as expected. In this paper the letter possibility is addressed by using a Load Cell System to measure the force actually being generated by the servo hydraulic vibrator. We find that these measurements are not consistent with the drive signal from the vibrator electronic controller (weighted‐sum ground force estimate) therefore the conventional weighted‐sum ground force signal is deemed questionable.
Self-Organized Lipid-Porphyrin Bilayer Membranes in Vesicular Form: Nanostructure, Photophysical Properties, and Dioxygen Coordination (2002)

An amphiphilic tetraphenylporphyrin and its iron complex bearing four phospholipid substituents, in which a trimethylolethane residue connects the two acyl chains (lipid-porphyrins), have been synthesized. The free-base lipid-porphyrin 6a self-organizes in aqueous media to form spherical unilamellar vesicles with a diameter of 100 nm and a uniform thickness of 10 nm, which corresponds to twice the length of the molecule. In the visible absorption spectrum, the porphyrin Soret band was significantly red-shifted (12 nm) relative to that of the monomer in benzene/MeOH solution due to the excitonic interaction of the porphyrin chromophores. The [symbol: see text]-A isotherm of 6a gave an area per molecule of 2.2 nm2, which allowed the estimation of the number of molecules in a single vesicle (2.3 x 10(4)). Double-layered Langmuir-Blodgett (LB) films of 6a on a glass surface exhibited an absorption spectrum identical to that of the 6a vesicles in bulk aqueous solution, and this suggests that they contain similar geometric arrangements of the porphyrin moieties. Exciton calculations on the basis of our structural model reproduced the bathochromic shift of the Soret band well. In the photophysical properties of the 6a vesicles, the characteristics of J-aggregated porphyrins substantially predominate: strong fluorescence and extremely short triplet lifetime. The iron complex 6b with a small molar excess of 1-dodecylimidazole (DIm) also formed spherical unilamellar vesicles (100 nm phi). Scanning force microscopy after evaporation on a graphite surface revealed 6b/DIm vesicles with a vertical height of 19.8 nm, which coincided with the thickness of the double bilayer membranes. The ferrous 6c formed a bis(DIm)-coordinated low-spin FeII complex under an N2 atmosphere. Upon addition of O2 to this solution, a kinetically stable O2 adduct was formed at 37 degrees C with a half-life of 17 h. Distinct gel-phase (liquid-crystal) transitions of the lipid-porphyrin membranes were clearly observed; the free base 6a displayed a higher transition temperature (56 degrees C) than the iron complex. Magnetic circular dichroism and infrared spectroscopic studies proved that molecular O2 coordinates to the self-organized lipid-porphyrinatoiron(II) vesicles in aqueous media.
Limitations of a class of binary phase-only filters (1992)

The feasibility of using certain types of binary phase-only filter (BPOF) is investigated. A critical aspect of correlation filters is not often addressed in research on BPOF's: how well do they perform as classifiers in the presence of imperfectly matching templates? It is not enough to detect a single given signal in the presence of noise; it is equally critical to make the correct classification among a number of possible templates with a low false-alarm rate. We show that (+1, -1)-valued BPOF's based on the real part of a conventional matched filter can cause misclassification of simple patterns, even in the absence of noise. These are known to be suboptimal, but the seriousness of their limitations illustrates an important design issue. It is therefore concluded that other types of filters must be used for correlator-based neural network implementations and image processing in general. We also include a commentary on the potential for facing this type of problem with general POF's and BPOF's. The theoretical results are supported by computer simulation and optical experiments.
D05 Development and optimisation of a quantigene assay to measure HTT transcripts levels and investigate the efficiency of lowering htt in vivo (2018)

<h3>Background</h3> Huntington’s Disease (HD) is neurodegenerative disorder caused by the expansion of a CAG repeat in the HTT gene. We have recently shown that incomplete splicing of exon 1 to exon 2 of the HTT (human) and Htt (mouse) mRNAs produces a polyadenylated transcript that contains exon 1 and a short sequence of intron 1, that is translated to an exon 1 HTT protein. Measurement of the abundance of these transcripts has relied on quantitative RT-PCR assays (qPCR), which are time consuming and involve many steps (i.e. RNA isolation, reverse transcription and amplification). Assays employing branched DNA technology to detect nucleic acids involve less steps, can be multiplexed and are commercially available. <h3>Aims</h3> The aim of this study was to develop and optimize a Quantigene assay to measure concomitantly all Htt or HTT transcripts in a timely and efficient manner. <h3>Methods/techniques</h3> We designed probes to develop multiplex assays for mouse Htt and human HTT. In each case, the location of the probe sets within exons, introns and the 3’UTR were designed to identify all possible Htt or HTT transcripts. The zQ175 knock-in HD mouse model at 2 months of age was used to validate the mouse multiplex assay and fibroblasts from HD patients and control samples were used for the human assay. <h3>Results/outcome</h3> We optimized our mouse Quantigene assay and show that it generates comparable data to the much more time-consuming qPCRs. We show that transcription of Httexon1 stops after the second polyA site within intron 1. We also measured differences in the Htt 3’UTR transcripts. The human multiplex Quantigene assay needs to be further optimized as to date, only the full length HTT transcript has been detected, in contrast to our qPCR data. <h3>Conclusions</h3> We have developed and optimized a multiplex Quantigene assay to rapidly measure all mouse Htt transcripts directly in tissue lysates. This assay can be used for investigating levels of the Htt transcripts <i>in vivo</i> after administration of therapeutic agents. This work is supported by the CHDI foundation.
Evasion of added isotopic mercury from a northern temperate lake (2006)

Isotopically enriched Hg (90% 202Hg) was added to a small lake in Ontario, Canada, at a rate equivalent to approximately threefold the annual direct atmospheric deposition rate that is typical of the northeastern United States. The Hg spike was thoroughly mixed into the epilimnion in nine separate events at two-week intervals throughout the summer growing season for three consecutive years. We measured concentrations of spike and ambient dissolved gaseous Hg (DGM) concentrations in surface water and the rate of volatilization of Hg from the lake on four separate, week-long sampling periods using floating dynamic flux chambers. The relationship between empirically measured rates of spike-Hg evasion were evaluated as functions of DGM concentration, wind velocity, and solar illumination. No individual environmental variable proved to be a strong predictor of the evasion flux. The DGM-normalized flux (expressed as the mass transfer coefficient, k) varied with wind velocity in a manner consistent with existing models of evasion of volatile solutes from natural waters but was higher than model estimates at low wind velocity. The empirical data were used to construct a description of evasion flux as a function of total dissolved Hg, wind, and solar illumination. That model was then applied to data for three summers for the experiment to generate estimates of Hg re-emission from the lake surface to the atmosphere. Based on ratios of spike Hg to ambient Hg in DGM and dissolved total Hg pools, ratios of DGM to total Hg in spike and ambient Hg pools, and flux estimates of spike and ambient Hg, we concluded that the added Hg spike was chemically indistinguishable from the ambient Hg in its behavior. Approximately 45% of Hg added to the lake over the summer was lost via volatilization.
Channel Characteristics for Terahertz Wireless Communications (2018)

We investigate channel performances for indoor and outdoor terahertz (THz) wireless links with carrier frequencies of 100, 200, 300 and 400 GHz. Both line-of-sight and non-line-of-sight (specular reflection) data streams off of building walls are demonstrated.
Increased Interstitial Protein Because of Impaired Lymph Drainage Does Not Induce Fibrosis and Inflammation in Lymphedema (2013)

Our data suggest that a high interstitial protein concentration and longstanding edema is not sufficient to induce fibrosis and inflammation characteristic for the human condition and may have implications for our understanding of the pathophysiology of this condition.
Of Mice and Women: A Comparative Tissue Biology Perspective of Breast Stem Cells and Differentiation (2015)

Tissue based research requires a background in human and veterinary pathology, developmental biology, anatomy, as well as molecular and cellular biology. This type of comparative tissue biology (CTB) expertise is necessary to tackle some of the conceptual challenges in human breast stem cell research. It is our opinion that the scarcity of CTB expertise contributed to some erroneous interpretations in tissue based research, some of which are reviewed here in the context of breast stem cells. In this article we examine the dissimilarities between mouse and human mammary tissue and suggest how these may impact stem cell studies. In addition, we consider the differences between breast ducts vs. lobules and clarify how these affect the interpretation of results in stem cell research. Lastly, we introduce a new elaboration of normal epithelial cell types in human breast and discuss how this provides a clinically useful basis for breast cancer classification.
Electron beam writing methods of x-ray masks for eliminating thermal image placement errors (2001)

In this article we describe electron beam writing methods to suppress image placement errors due to the thermal distortion and drift of x-ray masks. Parts of device patterns are written outside of the writing area of a mask before the device pattern writing step to stabilize the temperature of the mask (preparatory writing method). The seesaw writing method, which divides a pattern into many slit parts that are written reciprocally, is used to compensate for the nonuniformity of the heating rate of the mask according to the mask’s position on the stage. The absorber fiducial mark is formed on the mask instead of the cassette or the stage to prevent the drift of the mask, and furthermore, to reduce mask-to-mask overlay errors. The writing is performed by referring to the absorber coordination marks on the mask after the registrations of the marks are measured with an image placement (IP) measurement system (mark-on-the-mask method). The effectiveness of these methods is evaluated through the fabrication of a full-chip mask of a 64 Mbit dynamic random access memory, and an IP accuracy close to 20 nm is obtained.
Concept and Demonstration of Individual Probe Actuation in Two-Dimensional Parallel Atomic Force Microscope System (2007)

A concept of an array actuator that is used to control the tip-sample separation of cantilevers in a two-dimensional (2D) probe array scanning system is proposed in this article. The feasibility of the concept is demonstrated with a 10 Ã 10 array actuator with 500 Î¼m xy-pitches. The array actuator is made by slicing a bulk piezoceramic block. The obtained maximum actuation of a single probe was 2.19 Î¼mp_p at Â±168 Vp_p. A major issue for the actuator was the insufficient strength of the frame of the probe array chip. The demonstrated array actuator is highly compatible with previously developed parallel readout modules that use either a parallel optical beam or integrated piezoresistive deflection sensing. A large-scale 2D probe array is our ultimate target. Â© 2007 The Japan Society of Applied Physics.
Role of Platinum in Thermal Barrier Coatings Used in Gas Turbine Blade Applications (2009)

Current technology of thermal barrier coating systems used in gas turbine blade applications relies on the use of a metallic bond coat, which has a twofold function: (i) it develops a thin layer of aluminum oxide enhancing the adhesion of the ceramic top coat and (ii) it provides an additional resistance to oxidation. It was the objective of this study to develop an understanding of the role of platinum in bond coats of the diffusion-type deposited on a nickel-based superalloy. Two Pt-containing bond coats were included in the study: (i) a platinum-aluminide and (ii) a bond coat formed by interdiffusion between an electroplated layer of platinum and the superalloy substrate. In both cases, the top ceramic coat was yttria-stabilized zirconia. For reference purposes, a simple aluminide bond coat free of Pt was also included in the study. Thermal exposure tests at 1150°C with a 24 h cycling period at room temperature were used to compare the coating performance. Microstructural features were characterized by various electron-optical techniques. Experimental results indicated that Pt acts as a “cleanser” of the oxide-bond coat interface by decelerating the kinetics of interdiffusion between the bond coat and superalloy substrate. This was found to promote selective oxidation of Al resulting in a purer Al2O3 scale of a slower growth rate increasing its effectiveness as “glue” holding the ceramic top coat to the underlying metallic substrate. However, the exact effect of Pt was found to be a function of the state of its presence within the outermost coating layer. Of the two bond coats studied, a surface layer of Pt-rich gamma prime phase (L12 superlattice) was found to provide longer coating life in comparison with a mixture of PtAl2 and beta phase. This could be related to the effectiveness of gamma prime phase as a sink for titanium minimizing its detrimental effect on the adherence of aluminum oxide.
Mechanism of Inactivation of Food-borne Pathogens by Pulsed Electric Fields (2001)

Food-borne illnesses, especially
Mechanism of Glucocorticoid-Induced Suppression of Testicular Androgen Biosynthesis In Vitro1 (1982)

The mechanism whereby glucocorticoids directly inhibit gonadotropin-stimulated testosterone production was studied by using primary cultures of testicular cells from adult hypophysectomized rats. Testicular cells were maintained in serum-free media with hormone treatments administered on Day 8 and media collected 48 h later for steroid and cAMP measurement. Highly purified human chorionic gonadotropin (hCG) increased testosterone production relative to controls. Concomitant administration of either natural (cortisone greater than deoxycorticosterone = aldosterone) or synthetic (dexamethasone greater than or equal to prednisolone) corticosteroids inhibited hCG-stimulated testosterone production in a dose-dependent manner. Dexamethasone at 10(-7) M decreased testosterone production by approximately 50-60% and this inhibitory effect was reversible upon removal of the glucocorticoid. In the presence or absence of a phosphodiesterase inhibitor, dexamethasone decreased hCG-stimulated cAMP production by approximately 60%. Dexamethasone also decreased testosterone production induced by cholera toxin and (Bu)2 cAMP by 43 and 63%, respectively. The dexamethasone suppression of testosterone production was accompanied by marked decreases in androstenedione (80% decrease) and 17 alpha-hydroxyprogesterone (57%) production, with a lesser effect on progesterone production (28% decrease) and no effect on pregnenolone production. Exogenous progesterone and 17 alpha-hydroxyprogesterone augmented hCG-stimulated testosterone production. Dexamethasone reduced the conversion of exogenous progesterone to testosterone by 33% but did not affect the conversion of 17 alpha-hydroxyprogesterone to androstenedione and testosterone, suggesting a specific inhibition of 17 alpha-hydroxylase. These results suggest that glucocorticoids directly suppress Leydig cell steroidogenesis by decreasing gonadotropin stimulation of cAMP production and the activity of 17 alpha-hydroxylase.
Composite Structure of Silicon Carbide Fiber Reinforced Metals by Squeeze Casting (1984)

The present paper deals with microstructures and segregations of silicon-carbide fiber reinforced copper-added aluminium and aluminium-added magnesium alloy composites, fabricated by squeeze casting, as well as refers to the effect of the microstructure on the tensile strength of composites. The results obtained as follows; (1) Microscopic examination showed the solute element rich layer of a semicircle surroundings was locally formed on fibers in the composites, whichever matrix alloy was used. The layer was identified to be a eutectic constitution by EPMA analysis. With the decrease of the percentage of alloying element, the layer decreases in thickness and area fraction, and finally, for the case of 1% copper-aluminium matrix, no copper-rich layer was detected. (2) The appearance of the layer decreases the tensile strength of composites because of its brittleness.
Wind Turbine Blockset in Saber. General Overview and Description of the Model (2004)

This report presents a new developed Saber Toolbox for wind turbine applications. This toolbox has been developed during the research project ?Simulation Platform to model, optimize and design wind turbines?. The report provides a quick overview of the Saber and then explains the structure of this simulation package, which is different than other tools e.g. Matlab/Simulink. Then the structure of the toolbox is shown as well as the description of the developed models. The main focus here is to underline the special structure of the models, which are a mixture of Saber built-in blocks and new developed blocks. Since the developed models are based on Saber built-in blocks, a description of the libraries from Saber is given. Then some simulation results using the developed models are shown. Finally some general conclusions regarding this new developed Toolbox as well as some directions for future work are made.
Carbon nanotube based photocathodes for high frequency amplifiers (2009)

The combination of high frequency, high power, high efficiency capabilities is a feature of vacuum tube technology. For most of applications, large bandwidths are required, and therefore the modulation method should also allow large bandwidth operation. Optically modulated cold cathodes, avoiding the use of resonant cavities, should satisfy this requirement. This is the reason why we have developed carbon nanotube based photocathode.
Isolation, characterization, and hepatoprotective properties of betulinic acid and ricinine fromTetracarpidium conophorumseeds (Euphorbiaceae) (2020)

The present study is to isolate and characterize betulinic acid and ricinine from T. conophorum seeds. Phytochemical investigation on hexane fraction of T. conophorum seeds led to the isolation of two compounds, Betulinic acid (1), and Ricinine (2). Betulinic acid and ricinine were screened against HepG2 cells and tested in vivo in CCl<sub>4</sub> -induced experimental rats model. Results from this study showed that the compounds had hepatoprotective and cytotoxic activities. It was observed that betulinic acid inhibited HepG2 cell with percentage inhibition of 54% compared with standard doxorubicin (64%), while ricinine was inactive against HepG2 cell lines. Furthermore, molecular docking was carried out on betulinic acids and ricinine, with binding energies of -11.2 kcal/mol and -5.4 kcal/mol, respectively, indicating strong binding sites and interactions with Hepatitis B Virus DNA polymerase. Therefore, findings from this study suggest that betulinic acid possess cytotoxic and hepatoprotective properties, while ricinine exhibited hepatoprotection in CCl<sub>4</sub> -induced liver damage. PRACTICAL APPLICATIONS: Medicinal plants contain unrestricted ability to make compounds that intrigue researchers in the quest for novel phyto-therapeutic drugs. The continuous exploration of new compounds in the medicinal plant is an auspicious strategy for the prevention of diseases. Therefore, the purpose of this research is to evaluate the cytotoxic and hepatoprotective compounds (betulinic acid and ricinine) isolated from T. conophorum seeds.
Application of Microfluidic Methodology for the Analysis of DNA (2018)

Over the past 20 years, many of the developments and potential applications of microfluidic methodology have incorporated nucleic acid processes which have, in their own right, undergone a number of innovative changes [...].