gebhart/patrepeval huggingface dataset:
Structural and functional conservation of the programmed −1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2) (2020)

Approximately 17 years after the severe acute respiratory syndrome coronavirus (SARS-CoV) epidemic, the world is currently facing the COVID-19 pandemic caused by SARS corona virus 2 (SARS-CoV-2). According to the most optimistic projections, it will take more than a year to develop a vaccine, so the best short-term strategy may lie in identifying virus-specific targets for small molecule-based interventions. All coronaviruses utilize a molecular mechanism called programmed -1 ribosomal frameshift (-1 PRF) to control the relative expression of their proteins. Previous analyses of SARS-CoV have revealed that it employs a structurally unique three-stemmed mRNA pseudoknot that stimulates high -1 PRF rates and that it also harbors a -1 PRF attenuation element. Altering -1 PRF activity impairs virus replication, suggesting that this activity may be therapeutically targeted. Here, we comparatively analyzed the SARS-CoV and SARS-CoV-2 frameshift signals. Structural and functional analyses revealed that both elements promote similar -1 PRF rates and that silent coding mutations in the slippery sites and in all three stems of the pseudoknot strongly ablate -1 PRF activity. We noted that the upstream attenuator hairpin activity is also functionally retained in both viruses, despite differences in the primary sequence in this region. Small-angle X-ray scattering analyses indicated that the pseudoknots in SARS-CoV and SARS-CoV-2 have the same conformation. Finally, a small molecule previously shown to bind the SARS-CoV pseudoknot and inhibit -1 PRF was similarly effective against -1 PRF in SARS-CoV-2, suggesting that such frameshift inhibitors may be promising lead compounds to combat the current COVID-19 pandemic.
Nasopharyngeal carriage of methicillin-resistant Staphylococcus aureus: incidence and outcomes in pregnant women. (2011)

Maternal nasopharyngeal carriage of MRSA was not associated with adverse maternal or neonatal outcomes, including neonatal MRSA carriage. Regional anesthesia was provided less frequently to MRSA-positive individuals. Further studies in larger groups of patients are needed to help determine the optimal management of MRSA-positive patients during pregnancy.
A Technique for Determining the Carrier Phase Differences between Independent GPS Receivers during Scintillation (2018)

A method for recovering the carrier phase differences between\npairs of independent GPS receivers has been developed\nand demonstrated in truth-model simulations. This\neffort is in support of a project that intends to image the disturbed\nionosphere with diffraction tomography techniques\nusing GPS measurements from large arrays of receivers.\nCarrier phase differential GPS techniques, common in surveying\nand relative navigation, are employed to determine\nthe phase relationships between the receivers in the imaging array. Strategies for estimating the absolute carrier phase\ndisturbances at each receiver are discussed. Simulation results\ndemonstrate that the system can rapidly detect the onset\nof scintillation, identify one non-scintillating reference\nsignal, and recover the carrier phase differences accurate to\n0.1 cycles.
On the epipolar geometry between two images with lens distortion (1996)

In order to achieve a 3D, either Euclidean or projective, reconstruction with high precision, one has to consider lens distortion. In almost all work on multiple-views problems in computer vision, a camera is modeled as a pinhole. Lens distortion has usually been corrected off-line. This paper intends to consider lens distortion as an integral part of a camera. We first describe the epipolar geometry between two images with lens distortion. For a point in one image, its corresponding point in the other image should lie on a so-called epipolar curve. We then investigate the possibility of estimating the distortion parameters and the fundamental matrix based on the generalized epipolar constraint. Experimental results with computer simulation show that the distortion parameters can be estimated correctly if the noise in image points is low and the lens distortion is severe. Otherwise, it is better to treat the cameras as being distortion-free.
Multielement flame spectroscopy (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMultielement flame spectroscopyKenneth W. Busch and George H. MorrisonCite this: Anal. Chem. 1973, 45, 8, 712A–722aPublication Date (Print):July 1, 1973Publication History Published online21 September 2008Published inissue 1 July 1973https://pubs.acs.org/doi/10.1021/ac60330a038https://doi.org/10.1021/ac60330a038research-articleACS PublicationsRequest reuse permissionsArticle Views238Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Surface plastic flow in polishing of rough surfaces (2019)

We present experimental evidence for a new mechanism for how smooth surfaces emerge during repetitive sliding contacts, as in polishing. Electron microscopy observations of Ti-6Al-4V surface with a spherical asperity structure-realized via additive manufacturing-during successive polishing stages suggest that asperity-abrasive contacts exhibit viscous behavior, where the asperity material flows in the form of thin (1-10 μm) fluid-like layers. Subsequent bridging of these layers among neighboring asperities results in progressive surface smoothening. Using analytical asperity-abrasive contact temperature modeling and microstructural characterization, we show that the sliding contacts encounter flash temperatures of the order of 700-900 K which is in the range of the dynamic recrystallization temperature of the material considered, thus supporting the experimental observations. Besides providing a new perspective on the long-held mechanism of polishing, our observations provide a novel approach based on graph theory to quantitatively characterize the evolution of surface morphology. Results suggest that the graph representation offers a more efficient measure to characterize the surface morphology emerging at various stages of polishing. The research findings and observations are of broad relevance to the understanding of plastic flow behavior of sliding contacts ubiquitous in materials processing, tribology, and natural geological processes as well as present unique opportunities to tailor the microstructures by controlling the thermomechanics of the asperity-abrasive contacts.
Low power GaAs current-mode 1.2 Gb/s interchip interconnections (1997)

A new GaAs current-mode (CM) chip-to-chip interconnection circuit is presented that provides high signal transfer speed with a 50 /spl Omega/ active termination and reduced input voltage swing. The power dissipation is shown to be 1/8 of an ECL I/O at the same data rate, 4 mW per pin, using a standard 2 V power supply. The driver-receiver operates with a current swing under 1 mA and provides a large noise margin.
Random target method for fast MTF inspection (2004)

A random target method for fast MTF inspection is proposed. The setup includes a random target, lens under test and a CCD camera with focus adjustment. The target consists of a random black and white pattern of a flat spectrum. The MTF of the lens is acquired by imaging the random target on the CCD using the lens under test, and then analyzing the spatial frequency content of the image. Frequency range up to about 50 cycles/mm is possible using commonly available CCD imagers. Measurement speed and precision depend on the sample matrix size used in calculation. A matrix of 128*128 samples per measured field point provides better than 2% precision and a few second's total execution time (ordinary PC-computer) per lens including best focus evaluation and the measurement of tangential and sagittal MTF curves of 5 field points. Thus fast MTF inspection of low to medium quality lenses seems possible.
Helper threads via virtual multithreading on an experimental itanium <sup>®</sup> 2 processor-based platform (2004)

Helper threading is a technology to accelerate a program by exploiting a processor's multithreading capability to run ``assist'' threads. Previous experiments on hyper-threaded processors have demonstrated significant speedups by using helper threads to prefetch hard-to-predict delinquent data accesses. In order to apply this technique to processors that do not have built-in hardware support for multithreading, we introduce virtual multithreading (VMT), a novel form of switch-on-event user-level multithreading, capable of fly-weight multiplexing of event-driven thread executions on a single processor without additional operating system support. The compiler plays a key role in minimizing synchronization cost by judiciously partitioning register usage among the user-level threads. The VMT approach makes it possible to launch dynamic helper thread instances in response to long-latency cache miss events, and to run helper threads in the shadow of cache misses when the main thread would be otherwise stalled.The concept of VMT is prototyped on an Itanium ® 2 processor using features provided by the Processor Abstraction Layer (PAL) firmware mechanism already present in currently shipping processors. On a 4-way MP physical system equipped with VMT-enabled Itanium 2 processors, helper threading via the VMT mechanism can achieve significant performance gains for a diverse set of real-world workloads, ranging from single-threaded workstation benchmarks to heavily multithreaded large scale decision support systems (DSS) using the IBM DB2 Universal Database. We measure a wall-clock speedup of 5.8% to 38.5% for the workstation benchmarks, and 5.0% to 12.7% on various queries in the DSS workload.
Estimation of peroxisomal and mitochondrial fatty acid oxidation in rat hepatocytes using tritiated substrates (1991)

The pathways of peroxisomal and mitochondrial fatty acid oxidation were monitored with the use of substrates which produce NAD3H. I used as marker substrates: D-[3-3H]3-hydroxybutyrate for mitochondrial NAD3H production, [2-3H]glycerol for cytosolic NAD3H production, and [2-3H]acetate to measure carbon-bound 3H which was also generated by the metabolism of the commercial 9,10-3H-labelled fatty acids. The assumption that peroxisomal NAD3H can be considered to be equivalent to cytosolic NAD3H was supported using a specific inhibitor of mitochondrial fatty acid oxidation. The approach involves determination of the specific yields, and the relative distribution on carbons 4 and 6, of 3H in glucose from the marker substrates and the labelled fatty acids. In hepatocytes from clofibrate-treated rats, the amount of palmitate or oleate oxidation which starts in the peroxisomes is comparable with that which starts in the mitochondria.
Effective antibacterial action of tat (47-58) by increased uptake into bacterial cells in the presence of trypsin. (2008)

In a previous study, we found an antifungal effect on human pathogenic fungi by the cell-penetrating peptide Tat (47-58) derived from HIV-1. Tat (47-58) immediately entered into the fungal nucleus and affected some physiological changes on the intracellular condition. In this study, Tat (47-58) showed a broad spectrum of antibacterial activity against pathogenic bacteria including bacterial clinical isolates. To improve resistance against proteases for use in vivo, we synthesized an analog of Tat (47-58) by substituting the L-amino acid for the D-amino acid. The D-enantiomer of Tat (47-58) also exhibited a broad spectrum of antibacterial activity at almost the same level of L-Tat (47-58) concentration. Unlike L-Tat (47-58), D-Tat (47-58) showed a significant proteolytic resistance against all proteases tested and antimicrobial activities in the presence of trypsin. Moreover, D-Tat (47-58) inhibited MRSA infection in human HeLa cells whereas L-Tat (47-58) partially allowed MRSA infection, and the results were due to the proteolytic resistance of D-Tat (47-58).
A Novel Dual-Band Zero-Phase True Crossover With Arbitrary Port Impedance (2018)

A novel dual-band true crossover that can match with any impedance presented at its input and output ports is proposed in this letter. To break through the conventional 50-52 reference port impedance constraint, a planar crossover with a zero-phase delay in the transmission is designed first at a single operating frequency. The proposed single-band zero-phase crossover consists of outer branch lines and inner crossed lines, and the design parameters for each line are obtained by applying the even-odd mode analysis method. Second, the dual-band function is implemented on the proposed zero-phase crossover by replacing each line with dual-band transmission line, which has two series sections and one shunt section. A prototype of dual-band zero-phase crossover operating at 2.15 and 4.1 GHz is designed, fabricated, and measured. The simulation and measurement results agree well with each other to prove the design concept.
Efficient cross-correlation via sparse representation in sensor networks (2012)

Cross-correlation is a popular signal processing technique used in numerous localization and tracking systems for obtaining reliable range information. However, a practical efficient implementation has not yet been achieved on resource constrained wireless sensor network platforms. We propose cross-correlation via sparse representation: a new framework for ranging based on l1-minimization. The key idea is to compress the signal samples on the mote platform by efficient random projections and transfer them to a central device, where a convex optimization process estimates the range by exploiting its sparsity in our proposed correlation domain. Through sparse representation theory validation, extensive empirical studies and experiments on an end-to-end acoustic ranging system implemented on resource limited off-the-shelf sensor nodes, we show that the proposed framework, together with the proposed correlation domain achieved up to two order of magnitude better performance compared to naive approaches such as working on DCT domain and downsampling. Furthermore, compared to cross-correlation results, 30-40% measurements are sufficient to obtain precise range estimates with an additional bias of only 2-6cm for high accuracy application requirements, while 5% measurements are adequate to achieve approximately 100cm precision for lower accuracy applications.
Technologies for the Synthesis of mRNA-Encoding Libraries and Discovery of Bioactive Natural Product-Inspired Non-Traditional Macrocyclic Peptides (2013)

In this review, we discuss emerging technologies for drug discovery, which yields novel molecular scaffolds based on natural product-inspired non-traditional peptides expressed using the translation machinery. Unlike natural products, these technologies allow for constructing mRNA-encoding libraries of macrocyclic peptides containing non-canonical sidechains and N-methyl-modified backbones. The complexity of sequence space in such libraries reaches as high as a trillion (>1012), affording initial hits of high affinity ligands against protein targets. Although this article comprehensively covers several related technologies, we discuss in greater detail the technical development and advantages of the Random non-standard Peptide Integration Discovery (RaPID) system, including the recent identification of inhibitors against various therapeutic targets.
Analysis of Incidence Angle and Distance Effects on Terrestrial Laser Scanner Intensity: Search for Correction Methods (2011)

The intensity information from terrestrial laser scanners (TLS) has become an important object of study in recent years, and there are an increasing number of applications that would benefit from the addition of calibrated intensity data to the topographic information. In this paper, we study the range and incidence angle effects on the intensity measurements and search for practical correction methods for different TLS instruments and targets. We find that the range (distance) effect is strongly dominated by instrumental factors, whereas the incidence angle effect is mainly caused by the target surface properties. Correction for both effects is possible, but more studies are needed for physical interpretation and more efficient use of intensity data for target characterization.
Low-Cost Scan Test for IEEE-1500-Based SoC (2008)

In this paper, a reduced-pin-count-testing technique is presented to control the IEEE-1500 wrapper through the IEEE-1149.1 TAP for scan delay test. By using only the IEEE- 1149.1 TAP control pins as test-access pins and by embedding an on-chip test clock generator, low-cost automated test equipment (ATE) can be efficiently utilized to reduce testing costs. Experiments show the effectiveness of our technique in utilizing the ATE channels and scan delay testing.
Microgels in Drug Delivery (2011)

This chapter contains sections titled: Introduction Polymer Gels Polymer Microgels Polymer Microcapsules Swelling, Loading, and Release Kinetics Outlook References
DREAMPlace (2019)

Placement for very-large-scale integrated (VLSI) circuits is one of the most important steps for design closure. This paper proposes a novel GPU-accelerated placement framework DREAMPlace, by casting the analytical placement problem equivalently to training a neural network. Implemented on top of a widely-adopted deep learning toolkit PyTorch, with customized key kernels for wirelength and density computations, DREAMPlace can achieve over 30× speedup in global placement without quality degradation compared to the state-of-the-art multi-threaded placer RePlAce. We believe this work shall open up new directions for revisiting classical EDA problems with advancement in AI hardware and software.
G-CSF versus GM-CSF en el tratamiento de la neutropenia de un paciente con síndrome de Felty en hemodiálisis (2000)

espanolDescribimos el caso de un paciente diagnosticado de sindrome de Felty en pro- grama de hemodialisis periodica por amiloidosis secundaria (AA), que presenta episodios repetidos de neutropenia, para la que recibe tratamiento de forma con- secutiva con diferentes factores estimuladores de colonias: granulocitos (G-CSF) y granulocitos macrofagos (GM-CSF). En ambos casos se objetiva una buena res- puesta con una recuperacion rapida de la cifra de granulocitos y ausencia de complicaciones. EnglishWe describe a patient with Felty’s syndrome and chronic renal failure due to se- condary amyloidosis in a periodic haemodialysis programme, who was successfully treated for neutropenia with sequential administration of colony-stimulating factors: granulocyte colony-stimulating factor and granulocyte macrophage colony-stimula- ting factor.
Distribution and quantification of human herpesvirus 6 in multiple sclerosis and control brains (2004)

Multiple sclerosis (MS) is thought to be precipitated by environmental factors, potentially including viruses, in genetically susceptible individuals and recently human herpesvirus 6 (HHV-6) has been associated with the disease. We have analysed post mortem brain for the presence, variant type and quantity of HHV-6 by PCR. A total of 124 samples from seven anatomically defined regions of brain were tested from MS cases and controls. HHV-6 DNA was detected in 41% and 44% of MS case and control samples. The median viral loads were 11 and 9 genome copies/microg DNA in cases and controls respectively and the viral load was not increased in lesions. Except in one instance, the HHV-6 DNA detected was variant B. There was no apparent difference in the distribution of HHV-6 DNA in the brains of MS cases versus controls, nor between normal appearing and lesional tissue in MS cases. Periventricular regions of the brain were more frequently positive for HHV-6 DNA in both MS cases and controls, although this difference was not statistically significant. These studies confirm the neurotropism of HHV-6 but do not demonstrate differences in the distribution, variant type or quantity of HHV-6 in brains from patients with MS versus controls.
GI Epidemiology: nonalcoholic fatty liver disease (2007)

To review the data available on the epidemiology and natural history of NAFLD as well as the risk factors for its development and the areas where future research is necessary. RESULTS /CONCLUSIONS: NAFLD may affect individuals of any age range and race/ethnicity. NAFLD affects one in three adults and one in ten children/adolescents in the United States. Mortality in patients with NAFLD is significantly higher than in the general population of same age and gender with liver-related complications being a common cause of death. Liver-related morbidity and mortality in NAFLD occurs when the disease has progressed to advanced fibrosis and cirrhosis. Further studies are necessary to determine the impact of NAFLD on health-related quality of life and resources utilization, and to the extent to which preventing the development of the metabolic syndrome would prevent NAFLD development and reduce liver-related morbidity and mortality. Lifestyle intervention may improve NAFLD, but medications that increase insulin sensitivity and the antioxidant defenses in the liver deserve evaluation in carefully controlled trials.
Induction of the Maize GapC4 Promoter in Transgenic Potato under Anaerobiosis and in <i>Erwinia carotovora</i>-Inoculated Tuber Tissue (1999)

The induction pattern of the GapC4 promoter from maize in transgenic potato has been analyzed by fusion to the β-glucuronidase (gus) gene. Under anaerobic conditions this promoter confers high level expression not only in leaves, stems, and roots but also in tubers. After inoculation of potato tuber disks with Erwinia carotovora subsp. atroseptica, β-glucuronidase (GUS) activity could be detected in macerated tissue as well as in surrounding intact tissue. In mock controls no induction was detected, ruling out any induction due to an overall limitation in oxygen in the experimental system. In addition, it could be proven that no diffusion of GUS protein from macerated into intact tissue occurred. The promoter was shown to be aerobically induced even in the absence of live bacteria by incubation with purified Erwinia spp. pectolytic enzymes alone. Therefore, promoter induction seems to be mediated by a mobile factor instead of by limitation in oxygen. These results demonstrate that the maize GapC4 promoter is suitable for directing foreign genes encoding antibacterial proteins in transgenic potato.