gebhart/patrepeval huggingface dataset:
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes (2014)

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the large-scale, flexible, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 minutes using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.
Liquid phase silylation process for 248-nm lithography using EL IR photoresist (1994)

The goal of this investigation was to develop a 0.3 micron silylation process for 248 nm exposure, using a commercial photoresist material. Presented are results from investigation into liquid silylation of 248 nm exposure of Dynachem EL IR<SUP>TM</SUP>, a non-melamine image reversal novalac material designed for i-line application. A GCA BOLD 0.42 NA, 248 nm excimer laser projection system was used for exposure. A process has been developed utilizing a silylation solution of hexamethyl- cyclotrisilazane (HMCTS), propylene-glycol-methyl-ether-acetate (PGMEA), and xylene mixtures. Using a 15 run Box-Behnken statistically designed experiment, dry development in 0<SUB>2</SUB> RIE has been optimized with chamber pressure, flow rate, and 0<SUB>2</SUB> flow as process factors. Process responses optimized were selectivity, etch rate, and anisotropy. Results show capabilities and sensitivities of the process. Response surfaces are presented, along with resist image results of 0.3 microns at 5:1 aspect ratio.
Leveraging contextual data for multifactor authentication in the mobile web (2015)

Identify and authentication in the mobile web are important for many types of applications that benefit users, including payments. The mobile web today has several traditional approaches to authentication that allow for sensitive applications to take place. However, moving forward the use of contextual data can have a place in the area of authentication, Use of sensor information available on smartphones can provide information about user context that can serve either to augment existing authentication techniques or even provide additional authentication factors in their own right.
Growth hormone-releasing peptides and the cardiovascular system. (2000)

Growth Hormone (GH)-releasing peptides (GHRPs) and their non peptidyl analogues are synthetic molecules which exhibit strong, dosedependent and reproducible GH-releasing activity but also significant PRL- and ACTH/cortisol-releasing effects. An influence of these compounds on food intake and sleep pattern has been also shown. The neuroendocrine activities of GHRPs are mediated by specific receptors subtypes that have been identified in the pituitary gland, hypothalamus and various extra-hypothalamic brain regions with (125)I-Tyr-Ala-hexarelin, an octapeptide of the GHRP family. In addition, GHRP receptors were also present in different peripheral tissues such as heart, adrenal, ovary, testis, lung and skeletal muscle, with a density significantly higher than that found in the hypothalamo-pituitary -system. A remarkable specific (125)I-Tyr-Ala-hexarelin binding was observed in the human cardiovascular system where the highest binding levels were detected in ventricles, followed by atria, aorta, coronaries, carotid, endocardium and vena cava. The binding of the radioligand to cardiac membranes was inhibited by unlabeled Tyr Ala hexare lin and hexarelin as well as by GHRP-6, GHRP-1 and GHRP-2 but not by MK-677, a non peptidyl GHRP analog. In other experiments on H9c2 myocytes, a fetal cardiomyocytes-derived cell line, specific GHRP binding was found and hexarelin showed an anti-apoptotic activity. On the other hand, in vivo studies in animals and in humans showed that GHRPs possess direct cardiotropic actions. In fact, hexarelin protects from ischemia-induced myocardial damage in aged and GH deficient rats while hexarelin shows a positive inotropic effect in normal subjects as well as in patients with GH deficiency. In conclusion, GHRPs possess extra--neuroendocrine biological activity and, particularly, show direct GH-independent cardiotropic effects.
Poly(<i>N</i>-isopropylacrylamide) Thin Films Densely Grafted onto Gold Surface: Preparation, Characterization, and Dynamic AFM Study of Temperature-Induced Chain Conformational Changes (2008)

Thermally responsive poly(N-isopropylacrylamide) (PNIPAM) films are attracting considerable attention since they offer the possibility to achieve reversible control over surface wettability and biocompatibility. In this paper, we first report a new and simple method for the grafting under melt of amine-terminated PNIPAM chains onto gold surfaces modified with a self-assembled monolayer (SAM) of reactive thiols. The formation of homogeneous tethered PNIPAM films, whose thickness can be tuned by adjusting polymer molecular weight or SAM reactivity, is evidenced by using the combination of ellipsometry, X-ray photon spectroscopy, infrared spectroscopy (PM-IRRAS), and atomic force microscopy. The calculation of grafting parameters from experimental measurements indicated the synthesis of densely grafted PNIPAM films and allowed us to predict a "brushlike" regime for the chains in good solvent. In a second part, the temperature-induced responsive properties are studied in situ by conducting dynamic AFM measurements using the amplitude modulation technique. Imaging in water environment first revealed the reversible modification of surface morphology below and above the theoretical lower critical solution temperature (LCST) of PNIPAM. Then, the determination of amplitude and phase approach curves at various temperatures provided direct measurement of the evolution of the damping factor, or similarly the dissipated energy, as a function of the probe indentation into the PNIPAM film. Most interestingly, we clearly showed the subtle and progressive thermally induced chain conformational change occurring at the scale of several nanometers around the expected LCST.
Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations (2009)

We report all-atom molecular dynamics simulations following adsorption of gold-binding and non-gold-binding peptides on gold surfaces modeled with dispersive interactions. We examine the dependence of adsorption on both identity of the amino acids and mobility of the peptides. Within the limitations of the approach, results indicate that when the peptides are solvated, adsorption requires both configurational changes and local flexibility of individual amino acids. This is achieved when peptides consist mostly of random coils or when their secondary structural motifs (helices, sheets) are short and connected by flexible hinges. In the absence of solvent, only affinity for the surface is required: mobility is not important. In combination, these results suggest the barrier to adsorption presented by displacement of water molecules requires conformational sampling enabled through mobility.
Morphogenetic Studies with Partially Synchronized Cultures of Carrot Embryos (1964)

Callus tissue, derived from petiole segments of the wild carrot and containing undifferentiated meristems, can be suspended in liquid nutrient media and passed through a series of sieves to separate the meristems by size. The small meristems of fairly uniform size thus obtained will grow on defined media where their controlled differentiation into embryos can be studied.
Systematic formal verification for fault-tolerant time-triggered algorithms (1999)

Many critical real-time applications are implemented as time-triggered systems. We present a systematic way to derive such time-triggered implementations from algorithms specified as functional programs (in which form their correctness and fault-tolerance properties can be formally and mechanically verified with relative ease). The functional program is first transformed into an untimed synchronous system and, then, to its time-triggered implementation. The first step is specific to the algorithm concerned, but the second is generic and we prove its correctness. This proof has been formalized and mechanically checked with the PVS verification system. The approach provides a methodology that can ease the formal specification and assurance of critical fault-tolerant systems.
Variation and Function of Cucurbitacins in Cucurbita: An Examination of Current Hypotheses (1989)

Though few data document the causes of qualitative and quantitative variation in cucurbitacins among Cucurbita species, the spatial and temporal patterns of cucurbitacin distribution within plants and between species are not likely to be fortuitous or satisfactorily explained by defense or non-defense hypotheses alone. Some interspecific differences in cucurbitacin concentration correlate with xeric and mesic characteristics of cucurbit habitats and support the hypothesis that the production of secondary compounds is mediated to some extent by nutrient availability. However, defense hypotheses find support in the Cucurbita system from two fronts. Patterns of foliar response to injury indicate that Cucurbita species produce cucurbitacins in quantities large enough to discourage nonadapted herbivores but small enough to reduce production costs and detection by adapted herbivores. Furthermore, chemical responses in cucurbits against viral, fungal, and bacterial leaf pathogens do not involve cucurbitacins, suggesting that cucurbits do not employ stereotypic responses to all invading organisms. Instead, cucurbits exhibit some ability to "recognize" particular types of biotic stress and to respond through appropriate chemical defenses. We suggest that current interspecific and intraspecific patterns of cucurbitacin variation in the genus Cucurbita reflect an evolutionary compromise between several abiotic determinants of cucurbitacin metabolism and the conflicting pressures of both physiologically nonadapted and adapted cucurbit herbivores.
Galectins as therapeutic targets for hematological malignancies: a hopeful sweetness. (2014)

Galectins are family of galactose-binding proteins known to play critical roles in inflammation and neoplastic progression. Galectins facilitate the growth and survival of neoplastic cells by regulating their cross-talk with the extracellular microenvironment and hampering anti-neoplastic immunity. Here, we review the role of galectins in the biology of hematological malignancies and their promise as potential therapeutic agents in these diseases.
Culture of phenotypically defined hematopoietic stem cells and other progenitors at limiting dilution on Dexter monolayers [see comments] (1991)

Highly enriched, phenotypically defined hematopoietic stem, Thy-1loLin-Sca-1+, and progenitor cell populations from mouse bone marrow (BM) were tested at limiting dilution for their ability to reconstitute Dexter monolayers. Several classes of BM cells can reconstitute Dexter cultures, first forming discrete "cobblestone" areas which then mature into colonies consisting primarily of maturing myeloid and erythroid cells. Most such colonies have a limited lifespan in culture. Only the Thy-1loLin-Sca-1+ cell fraction gives rise to colonies that survive longer than 3 weeks, which suggests that a limiting-dilution analysis for long-term reconstitution of Dexter cultures can serve as a quantitative measure of stem cell activity. Additional experiments were performed to assess the formation of new progenitor cells in reconstituted Dexter cultures. Again, only cultures seeded with the stem cell-enriched fraction contained expanded numbers of replatable WEHI-3 CM responsive colony-forming cells (CFU-GM). Quantitative analysis indicates that 97% of the replatable CFU-GM of whole BM is contributed by the Thy-1loLin-Sca-1+ cell fraction, again suggesting a potential stem cell-specific assay. Such quantitative in vitro assays might prove useful in characterization and isolation of human stem cells where in vivo assays are lacking.
One-dimensional parametric study of damage detection in a solid material using a Nonlinear Wave Modulation Spectroscopy (NWMS) technique (2015)

Nonlinear Wave Modulation Spectroscopy (NWMS) is one of the most powerful techniques used to detect damage in materials. It consists in simultaneously applying two continuous waves with different frequencies, the one high, f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , and the other low, f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> . When the material is damaged, the frequency spectrum exhibits harmonics and sidebands which are located at (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> + f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ) and (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> - f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> ). This paper presents a parametric simulation study of the nonlinear propagation of elastic waves in solid media, which can be represented by a one dimensional mass-spring system. The system of motion equations is resolved by a fourth order Runge-Kutta iterative method. A quadratic nonlinearity can be introduced locally in the system at any spring. The objective of the paper is to highlight the ability of the nonlinear acoustic methods, especially the NWMS (Nonlinear Wave Modulation Spectroscopy), to detect damages in solid material. The study of the evolution of the sidebands amplitude, according to the low frequency of the wave (pump wave), f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> , in cracked and intact material will be presented. It is shown that this amplitude reaches a maximum when the pump frequency corresponds to a resonance frequency of the system. In addition, the study shows the strong dependency of the resulting frequency spectrum of the received signal upon the nonlinearity magnitude as well as the rigidity of the simulating crack spring.
Velocity of Sound Measurements in Liquid Metals (1965)

The velocity of sound in liquid metals can be determined to ±0.01% using an ultrasonic pulse echo comparison technique. Several corrections must be taken into account due to thermal expansion effects in the apparatus and an apparent phase shifting to be described. The velocity of sound in liquid indium is presented as determined from this apparatus. Finally, a liquid metal cell of fused quartz is suggested which eliminates the thermal expansion effects and other operational problems of the described liquid metal cell.
Joint Time-Frequency Properties of Freak Waves (2004)

In this paper, we discuss the joint time-frequency properties of a transient freak wave in order to distinguish the freak wave from non-freak waves in a quantitative manner. Exploring the use of an alternative to wavelet-based approaches, joint time-frequency distributions (TFDs), we portray the simultaneous timeand frequency-localized nature of freak waves vs. that of non-freak waves. The knowledge of the TFD, which represents the transient energy distribution over time and frequency in a joint manner, is very powerful as it allows one to calculate various moments and conditional moments in the time and frequency domains. Based on the experimental time series data collected at Texas A&M University, we calculate the instantaneous frequency center, frequency bandwidth and time duration. The instantaneous power spectrum of the freak wave, where the second harmonic component is observed, allows one to interpret the abnormal wave elevation of the freak wave in time domain. Also, the freak wave is characterized by impulsive joint time-frequency properties, i.e., wider instantaneous frequency bandwidth and shorter time duration than the non-freak waves.
The two-processor reliability of hierarchical large-scale ring-based networks (1996)

We present the reliability analysis of ring-based hierarchical directed networks in the context of large-scale multiprocessors. A wide range of hierarchical structures based on the basic, dual counter-rotating, and braided (skip-a-node) rings are analyzed and compared. We have adopted the two-processor (two-terminal) reliability criteria for our analysis. The results of computing the system reliability for thousands of processors show that hierarchical structures constructed of counter-rotating and braided rings significantly improve the reliability of hierarchical structures constructed of basic rings. For most of the hierarchies the braided structures have better survivability and provide higher reliability than the counter-rotating structures for long mission times. Our results show that uniform hierarchical structures tend to provide better reliability than nonuniform structures. The results are of value in designing real time systems, large-scale architectures and general computer networks. Because Scalable Coherent Interface (SCI) appears to be a promising interface for high speed interconnections, we use it to illustrate both the approach and the applicability of our results. The results apply also to similar ring architectures such as token rings, slotted rings, and other unidirectional ring networks.
Excitation nonlinearities in emission reabsorption laser-induced fluorescence techniques (2004)

The effects of the nonlinear behavior of fluorescent intensity with excitation intensity on emission reabsorption laser-induced fluorescence (ERLIF) are investigated. Excitation nonlinearities arise mainly as a consequence of the depletion of the ground-state population stemming from the finite lifetime of molecules in the excited state. These nonlinearities hinder proper suppression of the excitation intensity information in the fluorescence ratio, degrading measurement accuracy. A method for minimizing this effect is presented. This method is based on the approximation of the fluorescence intensity nonlinearities by a power law. Elevating the two-dimensional fluorescent intensity maps to the appropriate exponent allows for proper suppression of excitation intensity in the fluorescence ratio. An overview of the principles and constitutive equations behind ERLIF film-thickness measurements, along with a characterization of the fluorescence's nonlinear behavior, is presented. The power law approximation and processing scheme used to mitigate this behavior are introduced. Experimental proof of the validity of the approximation and processing scheme is provided.
Chroma Intra Prediction with attention-based CNN architectures (2020)

Neural networks can be used in video coding to improve chroma intra-prediction. In particular, usage of fully-connected networks has enabled better cross-component prediction with respect to traditional linear models. Nonetheless, state-of-the-art architectures tend to disregard the location of individual reference samples in the prediction process. This paper proposes a new neural network architecture for cross-component intra-prediction. The network uses a novel attention module to model spatial relations between reference and predicted samples. The proposed approach is integrated into the Versatile Video Coding (VVC) prediction pipeline. Experimental results demonstrate compression gains over the latest VVC anchor compared with state-of-the-art chroma intra-prediction methods based on neural networks.
An instrument that isn't really (Laboratory Virtual Instrument Engineering Workbench) (1990)

The concept and development of LabVIEW (Laboratory Virtual Instrument Engineering Workbench), a virtual instrument (VI) that provides a simple, graphical way to set up and run numerous instruments on a Mackintosh PC, are described. The first concept basic to LabVIEW had its roots in a large test system comprised of programmable signal sources compatible with IEEE-488 interface specifications, and switching matrices and measurement instruments controlled by a minicomputer. The test system's strength was its flexibility, which it owed to its several levels of user interfaces. This flexible configuration was refined into the notion of instrumentation as a hierarchy of virtual instruments in which all VIs at all levels had the same type of construction. Another characteristic was that each VI have its own user interface. The final conceptual element was the use of loop data-flow structures as the technique used by an engineer to construct and run his or her own VIs. Problems encountered in the development of LabVIEW and the solutions used are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High Gain and High Efficient Stacked Antenna Array with Integrated Horn for 60 GHz Communication Systems (2014)

In order to achieve wide bandwidth and high gain, we propose a stacked antenna structure having a microstrip aperture coupled feeding technique with a mounted Horn integrated on it. With optimized parameters, the single antenna element at a center frequency of 60 GHz, exhibits a wide impedance bandwidth of about 10.58% (58.9–65.25 GHz) with a gain and efficiency of 11.78 dB and 88%, respectively. For improving the gain, we designed a 2 × 2 and 4 × 4 arrays with a corporate feed network. The side lobe levels were minimized and the back radiations were reduced by making use of a reflector at<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mi>λ</mml:mi><mml:mo>/</mml:mo><mml:mn>4</mml:mn></mml:math>distance from the corporate feed network. The<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mn>2</mml:mn><mml:mo>×</mml:mo><mml:mn>2</mml:mn></mml:math>array structure resulted in improved gain of 15.3 dB with efficiency of 83%, while the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M3"><mml:mn>4</mml:mn><mml:mo>×</mml:mo><mml:mn>4</mml:mn></mml:math>array structure provided further gain improvement of 18.07 dB with 68.3% efficiency. The proposed design is modelled in CST Microwave Studio. The results are verified using HFSS, which are found to be in good agreement.