gebhart/patrepeval huggingface dataset:
SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation (2013)

Mapping reads to a reference genome is a routine yet computationally intensive task in research based on high-throughput sequencing. In recent years, the sequencing reads of the Illumina platform have become longer and their quality scores higher. According to our calculation, this allows perfect k-mer seed match for almost all reads when a close reference genome is available subject to reasonable specificity. Our other observation is that the majority reads contain at most one short INDEL polymorphism. Based on these observations, we propose a fast-mapping approach, referred to as "SEME," which has two core steps: First it scans a read sequentially in a specific order for a k-mer exact match seed; next it extends the alignment on both sides allowing, at most, one short INDEL each using a novel method called "auto-match function." We decompose the evaluation of the sensitivity and specificity into two parts corresponding to the seed and extension step, and the composite result provides an approximate overall reliability estimate of each mapping. We compare SEME with some existing mapping methods on several datasets, and SEME shows better performance in terms of both running time and mapping rates.
Progress in temporal bone histopathology. III. An improved technique for immunohistochemical investigation of the adult human inner ear. (1990)

A new tissue processing technique is described for immunohistochemistry of the adult human inner ear, avoiding the immuno-compromising step of prolonged decalcification. The procedure allows reliable investigation of frozen sections of the chemically fixed, non-decalcified, adult human cochlea and vestibular sense organs. Preservation of immunoreactivity, combined with satisfying tissue morphology, is illustrated by the immunohistochemical localization of the intermediate filament constituents cytokeratins and neurofilament proteins throughout the membranous labyrinth.
Zebrafish studies identify serotonin receptors mediating antiepileptic activity in Dravet syndrome (2019)

Dravet syndrome is a life-threatening early-onset epilepsy not well controlled by antiepileptic drugs. Drugs that modulate serotonin (5-HT) signalling, including clemizole, locaserin, trazodone and fenfluramine, have recently emerged as potential treatment options for Dravet syndrome. To investigate the serotonin receptors that could moderate this antiepileptic activity, we designed and synthesized 28 novel analogues of clemizole, obtained receptor binding affinity profiles, and performed <i>in vivo</i> screening in a <i>scn1lab</i> mutant zebrafish (<i>Danio rerio</i>) model which recapitulates critical clinical features of Dravet syndrome. We discovered three clemizole analogues with 5-HT receptor binding that exert powerful antiepileptic activity. Based on structure-activity relationships and medicinal chemistry-based analysis, we then screened an additional set of known 5-HT receptor specific drug candidates. Integrating our <i>in vitro</i> and <i>in vivo</i> data implicates 5-HT<sub>2B</sub> receptors as a critical mediator in the mechanism of seizure suppression observed in Dravet syndrome patients treated with 5-HT modulating drugs.
Fibroblast Growth Factor-23 and Cardiovascular Events in CKD (2013)

An elevated level of fibroblast growth factor-23 (FGF-23) is the earliest abnormality of mineral metabolism in CKD. High FGF-23 levels promote left ventricular hypertrophy but not coronary artery calcification. We used survival analysis to determine whether elevated FGF-23 is associated with greater risk of adjudicated congestive heart failure (CHF) and atherosclerotic events (myocardial infarction, stroke, and peripheral vascular disease) in a prospective cohort of 3860 participants with CKD stages 2-4 (baseline estimated GFR [eGFR], 44±15 ml/min per 1.73 m(2)). During a median follow-up of 3.7 years, 360 participants were hospitalized for CHF (27 events/1000 person-years) and 287 had an atherosclerotic event (22 events/1000 person-years). After adjustment for demographic characteristics, kidney function, traditional cardiovascular risk factors, and medications, higher FGF-23 was independently associated with graded risk of CHF (hazard ratio [HR], 1.45 per doubling [95% confidence interval (CI), 1.28 to 1.65]; HR for highest versus lowest quartile, 2.98 [95% CI, 1.97 to 4.52]) and atherosclerotic events (HR per doubling, 1.24 [95% CI, 1.09 to 1.40]; HR for highest versus lowest quartile, 1.76 [95% CI, 1.20 to 2.59]). Elevated FGF-23 was associated more strongly with CHF than with atherosclerotic events (P=0.02), and uniformly was associated with greater risk of CHF events across subgroups stratified by eGFR, proteinuria, prior heart disease, diabetes, BP control, anemia, sodium intake, income, fat-free mass, left ventricular mass index, and ejection fraction. Thus, higher FGF-23 is independently associated with greater risk of cardiovascular events, particularly CHF, in patients with CKD stages 2-4.
Practical Insights On Augmented Reality Support for Shop-Floor Tasks (2019)

The use of Augmented Reality (AR) to improve processes in production has a long history and there are various established use cases in industry and research. Nevertheless, barriers to its seamless integration in everyday shop-floor processes still remain. A holistic approach grounded on socio-technical systems theory and a practical use case in a real-world production environment serve to identify the barriers and to provide recommendations for implementing AR in shop-floor processes. As a starting point, an overview of use cases in industry and research is provided focusing on how AR is used to support shop-floor tasks. Based on this, a practical use case, where maintenance engineers were guided by a head-mounted AR device (Microsoft HoloLens), was implemented to gain insights into the current AR-technology. An experiment was carried out consisting of twelve test runs with six maintenance engineers in a real-world production setting in the automotive industry. Semi-structured interviews with the test persons and video recordings of the tests serve as a basis for data analysis. The results consist primarily of specific use case feedback from test persons and video-based observation findings. Based on these findings, we derived recommendations to seamlessly integrate AR into production processes. These results are structured around enterprise IT infrastructure, AR-technology, shop-floor process related and human-centered aspects.
Fusion of <i>luxA</i> and <i>luxB</i> and its expression in <i>E. coli, S. cerevisiae</i> and <i>D. melanogaster</i> (1990)

Luciferase from Vibrio harveyi is encoded by two adjacent genes, luxA and luxB. The two genes were fused by replacing a segment extending from near the end of luxA into the N-terminal end of luxB by a synthetic oligonucleotide. The construction removed the TAA stop codon at the end of luxA, the intervening region of 26 base pairs, and the initial methionine of luxB. A Smal site was included at the junction between the two genes and an AatII site was created near the end of luxA without altering its amino acid sequence. In Escherichia coli the fused luxAB gene could be expressed to produce functional luciferase that gave about 20% of the activity in cells without the fusion. An out-of-frame ATG exists close to and preceding the ATG of the luxA gene. This was removed and the entire fused gene bracketed by several restriction enzyme sites. The fused luxAB gene was successfully expressed in Saccharomyces cerevisiae and Drosophila melanogaster by transferring it to appropriate plasmid vectors.
New class of turbulence in active fluids (2015)

Turbulence is a fundamental and ubiquitous phenomenon in nature, occurring from astrophysical to biophysical scales. At the same time, it is widely recognized as one of the key unsolved problems in modern physics, representing a paradigmatic example of nonlinear dynamics far from thermodynamic equilibrium. Whereas in the past, most theoretical work in this area has been devoted to Navier-Stokes flows, there is now a growing awareness of the need to extend the research focus to systems with more general patterns of energy injection and dissipation. These include various types of complex fluids and plasmas, as well as active systems consisting of self-propelled particles, like dense bacterial suspensions. Recently, a continuum model has been proposed for such "living fluids" that is based on the Navier-Stokes equations, but extends them to include some of the most general terms admitted by the symmetry of the problem [Wensink HH, et al. (2012) Proc Natl Acad Sci USA 109:14308-14313]. This introduces a cubic nonlinearity, related to the Toner-Tu theory of flocking, which can interact with the quadratic Navier-Stokes nonlinearity. We show that as a result of the subtle interaction between these two terms, the energy spectra at large spatial scales exhibit power laws that are not universal, but depend on both finite-size effects and physical parameters. Our combined numerical and analytical analysis reveals the origin of this effect and even provides a way to understand it quantitatively. Turbulence in active fluids, characterized by this kind of nonlinear self-organization, defines a new class of turbulent flows.
Restoring a maize root signal that attracts insect-killing nematodes to control a major pest (2009)

When attacked by herbivorous insects, plants emit volatile compounds that attract natural enemies of the insects. It has been proposed that these volatile signals can be manipulated to improve crop protection. Here, we demonstrate the full potential of this strategy by restoring the emission of a specific belowground signal emitted by insect-damaged maize roots. The western corn rootworm induces the roots of many maize varieties to emit (E)-beta-caryophyllene, which attracts entomopathogenic nematodes that infect and kill the voracious root pest. However, most North American maize varieties have lost the ability to emit (E)-beta-caryophyllene and may therefore receive little protection from the nematodes. To restore the signal, a nonemitting maize line was transformed with a (E)-beta-caryophyllene synthase gene from oregano, resulting in constitutive emissions of this sesquiterpene. In rootworm-infested field plots in which nematodes were released, the (E)-beta-caryophyllene-emitting plants suffered significantly less root damage and had 60% fewer adult beetles emerge than untransformed, nonemitting lines. This demonstration that plant volatile emissions can be manipulated to enhance the effectiveness of biological control agents opens the way for novel and ecologically sound strategies to fight a variety of insect pests.
Technology of Vehicle Identification Based on Laser Radar (2011)

In order to improve driving safety, this paper proposes a Vehicle Identification approach by two-dimensional laser radar. The approach can detect obstacles in front of vehicle and determine whether the obstacles are vehicle. In order to eliminate the effect of system errors generated in the process of Laser radar data collection, Median filtering method is used in radar data processing. In order to determine the number and position of obstacles in front of vehicle, CURE clustering algorithm is proposed to clustering radar data. The clustering algorithm can solve the problem that centroid-based clustering approach is not suitable for non-spherical or arbitrary shaped clusters. Improved the CURE algorithm, the improved algorithm is more suitable for clustering the data of two-dimensional laser radar. The target of vehicle identification is achieved by calculating the width and length of each cluster. The conclusion verified by experiments is this approach can calculate the width and length of obstacle more precisely and recognize vehicle accurately.
<i>p53</i> Mutation Analysis in Breast Tumors by a DNA Microarray Method (2006)

The p53 gene acts as a regulator of cell growth and DNA repair in normal cells; inactivation of the gene seems to lead to cancer. It is the most commonly mutated gene in human cancers, and a high-throughput sequencing method is needed for cancer etiology studies using large sample sets. In our population-based case-control study of breast cancer, the p53 gene was amplified by PCR for 392 subjects from seven hospitals in Western New York using the Affymetrix GeneChip technology. One hundred thirty-eight (35%) of the breast tumors had p53 mutations, of which 88% were located in exons 5 to 8. New hotspots were identified at codons 179, 195, 196, 213, 217, 249, 254, 278, 281, and 298, and previously reported hotspots were found at codons 175, 248, and 273. Manual sequencing for exons 5 to 9 of the p53 gene was done for 139 tumors to validate the Affymetrix assay. The two methods had 100% concordance for mutations detectable by the Affymetrix assay. We also successfully assayed paraffin-embedded breast and lung tumors from as early as 1958 and employed a nested PCR strategy to improve weak PCR amplification. To have statistical power, the investigation of gene environment interactions and cancer requires a large number of tumor analyses, which are frequently only available from archived tissue from multiple sources. We have shown the utility of the Affymetrix GeneChip method under these challenging conditions and provided new data for the mutational spectra of breast cancer in a population-based study.
Humidity-Independent Solid-State Amperometric Sensor for Carbon Monoxide Based on an Electrolyte Prepared by Sol−Gel Chemistry (1998)

An amperometric sensor consisting of a film of silica gel over an interdigitated microsensor electrode provided a humidity-independent response to CO over the range of 9%-76% humidity. The residual solvent contents were in the 20%-50% range, depending on the age of the gels and the humidity. Variations in this range did not change the sensitivity. Gaseous CO was quantified in the absence of a contacting liquid phase using either linear scan voltammetry (LSV) or flow injection amperometry (FIamp) at constant applied potential. With LSV after a 2-min exposure to the sample, sensors with gels aged for 28-40 days yielded sensitivities of 0.38, 0.41, and 0.38 nA/ppmv for measurements at 9%, 33%, and 76% humidity, respectively; the corresponding correlation coefficients were 0.992, 0.995, and 0.999. The detection limit with FIamp was 5 ppmv.
REVIEWS MALLARMÉSTÉPHANE: Correspondance. XI. Supplément, errata et addenda aux tomes i à X (1862–1898). Index général. Recueillie, classée et annotée MONDORpar HENRI et AUSTINLLOYD JAMES. Paris: Gallimard. 1985. 459 pp. 260 F. (1985)

Journal Article REVIEWS Get access STÉPHANE MALLARMÉ: Correspondance. XI. Supplément, errata et addenda aux tomes i à X (1862–1898). Index général. Recueillie, classée et annotée par HENRI MONDOR et LLOYD JAMES AUSTIN. Paris: Gallimard. 1985. 459 pp. 260 F. EILEEN SOUFFRIN-LE BRETON EILEEN SOUFFRIN-LE BRETON LONDRES Search for other works by this author on: Oxford Academic Google Scholar French Studies, Volume XXXIX, Issue 4, October 1985, Pages 486–488, https://doi.org/10.1093/fs/XXXIX.4.486 Published: 01 October 1985
The Relationship between the Electronic Packaging Structure Evolution and Microjoining Technology (2014)

Microjoining technology is one of the most important technologies in the production of electronic products. It is not only a important way to realize the performance of chip design, but also the bottleneck which restricts the development of the packaging structure. Microjoining technology determines the feasibility and reliability of packaging structure while the innovation of packaging structure also becomes the motive power of the development of microjoining. This passage tries to explore the relationship between them by studying microjoining technology and the history of packaging structure evolution. It also introduced several kinds of characteristics of common microjoining and chip welding technology and microelectronic welding technology. Finally it predicted the future development of electronic packaging structure and microjoining technology.
An Amperometric Biosensor for Uric Acid Determination Prepared from Uricase Immobilized in Polypyrrole Film (2006)

In order to prepare a biosensor for the determination of uric acid, electropolymerization of pyrrole on Pt surface was carried out with an electrochemical cell containing pyrrole, ferrocene (as a electron mediator) and tetrabutylammonium tetrafluoroborat in acetonitrile by cyclic voltammetry between 0.0 and 1.0 V (vs. Ag/AgCl) at a scan rate of 50 mV/s upon Pt electrode. Uricase was immobilized by a glutaraldehyde/gelatine croslinking procedure on to polypyrrole film after the electropolymerization processes. The response of the biosensor against uric acid was measured after 330 seconds following the application of a constant potential of +0.7 V (vs. Ag/AgCl). The resulting biosensor exhibits excellent electrocatalysis for the uric acid. The amperometric determination is based on the electrochemical detection of H2O2, which is generated in enzymatic reaction of uric acid. The sensor responds to uric acid with a detection limit of 5.0 x 10(-7) M. The sensor remains relatively stable for 5 weeks. Interference effect were investigated on the amperometric response of the biosensor. Determination of uric acid was carried out in the biological fluids by biosensor.
Porous Nickel‐Coated Steel Anodes for Alkaline Water Electrolysis: Corrosion Resistance (1982)

Anodes for alkaline water electrolysis made by sintering porous nickel coatings to mild steel substrates have produced low oxygen evolution overpotentials. Despite the porosity of the nickel coatings, the anodes display a high degree of corrosion resistance in at 80°C. The present work shows that the anodes are stabilized by nickel‐iron alloy formed at the steel substrate surface. The results of metallographic, electron microprobe, and scanning electron microscope studies of the nickel‐iron alloy formation are presented. The alloy is formed by diffusion during the sintering operation which binds the porous coating to the substrate. Rapid grain boundary diffusion produces nickel‐rich veins in the steel, from which bulk diffusion proceeds into the grains, broadening the alloy formation region. The partial contact between the coating and the substrate results in areas of higher nickel concentration directly below the nickel‐steel contact areas.
Detection of Anomaly Temperature Based on ASTER and ETM+ Thermal Infrared Image (2008)

Thermal remote sensing is an important field in research of remote sensing. The authors performed a verification study on the brightness temperature derived from thermal infrared band image data of LANDSAT-7/enhanced thematic mapper plus (ETM+) and advanced spaceborne thermal emission and reflection radiometer (ASTER) for the detection of areas with abnormal high temperatures around Dali city in the southern part of China. As to the thermal infrared band, the functions for converting the digital number (DN) values of satellite imagery into the brightness temperature are introduced. Then, according to the brightness temperatures calculated, generate the density segmentation images and get the areas with high temperature. Finally, as the result of comparison of the density segmentation images derived from the satellite images and the temperature distribution map measured in the filed, the variance shows that the proposed method of high-temperature detection from satellite images is feasible in a way, but there are limitations.
Vino e poesia. Centocinquanta epigrammi greci sul vino (2006)

Lo stretto rapporto tra vino e poesia è un fil rouge che attraversa tutta la letteratura greca. Sia che esso riguardi un influsso diretto del vino sulla produzione poetica sia che si limiti a sottolineare in tutti i modi possibili la fondamentale presenza del vino all'interno del simposio, il nesso indissolubile vino-poesia attraversa tutta la cultura greca, dall'età arcaica fino a quella bizantina, come dimostrano gli epigrammi dell'Antologia Palatina che coprono mille anni di storia letteraria.\nIn centocinquanta epigrammi, non esclusivamente simposiali, lettie tradotti nel rispetto delel loro forme metriche originarie, viene ripercorsa la storia di un simile legame, a dimostrazione del fatto che il vino era un elemento di straordinaria importanza all'interno della società e della cultura greca.
The determination of state of charge based on extended kalman filter using per-unit system and time constant principle (2009)

In order to cope with the parameter variations for aged battery, which result in erroneous SOC estimation, the SOC estimation algorithm of lithium-ion batteries based on extended Kalman filter (EKF) using per-unit system and time constant principle is proposed. In this per-unit system, the absolute values of capacity, voltage and current for aged batteries are converted into relative ones and are applied to dynamic model of the EKF algorithm. Moreover, the parameter values (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Diff</sub> , C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Diff</sub> ) are applied to dynamic and measurement model of EKF algorithm by time constant principle. In comparison with Ah-counting and EKF results, the estimation results using the proposed EKF algorithm have error within ±3%. Few aged batteries (1.3 Ah) for 18650 types are used for verification of the proposed method.
Near-Infrared Molecular Emission from a Gas Fountain (1994)

An electrothermal fountain is used to heat gas-phase samples in the range of 300 to 400°C in order to observe their near-infrared (NIR) emissions. In conjunction with the fountain, a 1/8-m Ebert monochromator and an uncooled PbS detector are shown to be sufficiently sensitive for recording the NIR fingerprints of CH 4 , CO 2 , N 2 O, and C 2 H 6 . At fountain temperatures of approximately 400°C, the molecular emission is confined to the long wavelength NIR region (1600–2500 nm) and yields limits of detection in the range of 4 to 10% v/v (3–10 mg/s). Reproducibilities have relative standard deviations of 3.0%. The calibration curves for the gases examined in this study have small linear dynamic ranges (factors of 2 to 10) and exhibit some degree of upward curvature. Ramifications of the application of NIR molecular emission spectroscopy to the qualitative and quantitative analyses of mixtures are discussed.