gebhart/patrepeval huggingface dataset:
Genetic drift of human coronavirus OC43 spike gene during adaptive evolution (2015)

Coronaviruses (CoVs) continuously threaten human health. However, to date, the evolutionary mechanisms that govern CoV strain persistence in human populations have not been fully understood. In this study, we characterized the evolution of the major antigen-spike (S) gene in the most prevalent human coronavirus (HCoV) OC43 using phylogenetic and phylodynamic analysis. Among the five known HCoV-OC43 genotypes (A to E), higher substitution rates and dN/dS values as well as more positive selection sites were detected in the S gene of genotype D, corresponding to the most dominant HCoV epidemic in recent years. Further analysis showed that the majority of substitutions were located in the S1 subunit. Among them, seven positive selection sites were chronologically traced in the temporal evolution routes of genotype D, and six were located around the critical sugar binding region in the N-terminal domain (NTD) of S protein, an important sugar binding domain of CoV. These findings suggest that the genetic drift of the S gene may play an important role in genotype persistence in human populations, providing insights into the mechanisms of HCoV-OC43 adaptive evolution.
Genes To Mental Health (G2MH): A Framework to Map the Combined Effects of Rare and Common Variants on Dimensions of Cognition and Psychopathology (2022)

Rare genomic disorders (RGDs) confer elevated risk for neurodevelopmental psychiatric disorders. In this era of intense genomics discoveries, the landscape of RGDs is rapidly evolving. However, there has not been comparable progress to date in scalable, harmonized phenotyping methods. As a result, beyond associations with categorical diagnoses, the effects on dimensional traits remain unclear for many RGDs. The nature and specificity of RGD effects on cognitive and behavioral traits is an area of intense investigation: RGDs are frequently associated with more than one psychiatric condition, and those studied to date affect, to varying degrees, a broad range of developmental and cognitive functions. Although many RGDs have large effects, phenotypic expression is typically influenced by additional genomic and environmental factors. There is emerging evidence that using polygenic risk scores in individuals with RGDs offers opportunities to refine prediction, thus allowing for the identification of those at greatest risk of psychiatric illness. However, translation into the clinic is hindered by roadblocks, which include limited genetic testing in clinical psychiatry, and the lack of guidelines for following individuals with RGDs, who are at high risk of developing psychiatric symptoms. The Genes to Mental Health Network (G2MH) is a newly funded National Institute of Mental Health initiative that will collect, share, and analyze large-scale data sets combining genomics and dimensional measures of psychopathology spanning diverse populations and geography. The authors present here the most recent understanding of the effects of RGDs on dimensional behavioral traits and risk for psychiatric conditions and discuss strategies that will be pursued within the G2MH network, as well as how expected results can be translated into clinical practice to improve patient outcomes.
Anthocyanins from Hibiscus syriacus L. Inhibit Oxidative Stress-Mediated Apoptosis by Activating the Nrf2/HO-1 Signaling Pathway (2020)

<i>Hibiscus syriacus</i> L. is distributed widely throughout Eastern and Southern Asia and considered as the national flower of South Korea. The extraction of several plant parts of <i>H. syriacus</i> L. is currently used as a natural remedy for several diseases, including breast and lung cancer, microbial infection, and chronic inflammation. However, the effect of the anthocyanin extract of <i>H. syriacus</i> L. petals (PS) in oxidative stress conditions has not been studied. In this study, we evaluated the cytoprotective effect of PS against H<sub>2</sub>O<sub>2</sub>-induced oxidative stress in HaCaT keratinocytes. In this study, we found that PS significantly inhibited H<sub>2</sub>O<sub>2</sub>-induced apoptosis of HaCaT keratinocytes. We also revealed that PS mediated-cytoprotective effect was associated with the increased expression of heme oxygenase-1 (HO-1) arising from the activation of nuclear factor erythroid 2-related factor-2 (Nrf2). PS also decreased H<sub>2</sub>O<sub>2</sub>-induced excessive intracellular ROS generation and restored H<sub>2</sub>O<sub>2</sub>-induced mitochondrial depolarization through the downregulation of mitochondrial ROS production. Furthermore, H<sub>2</sub>O<sub>2</sub>-induced Bax and caspase-3 expression was markedly abolished in the presence of PS. The inhibition of HO-1 by zinc protoporphyrin significantly attenuated the cytoprotective effect of PS in H<sub>2</sub>O<sub>2</sub>-treated HaCaT keratinocytes along with ROS generation, indicating that HO-1 crucially affects PS-mediated cytoprotective properties. Collectively, our results suggested that, under H<sub>2</sub>O<sub>2</sub>-mediated oxidative stress conditions, PS sustained a normal level of mitochondrial membrane potential and ROS generation in HaCaT keratinocytes by activating the Nrf2/HO-1 axis, exerting cytoprotective effects against oxidative stress.
50 ch × 250 Gbit/s 32-QAM transmission over a fully integrated 7-core multicore link (2017)

A transmitted distance of 180 km over an integrated multicore link is demonstrated for a C-band 32-QAM WDM system, where the complete usable amplification region of the integrated 7-core amplifiers, supporting 50 channels per core, is exploited.
Amblyopes see true alignment where normal observers see illusory tilt (2000)

Amblyopia ("lazy eye") is an impairment in visual acuity resulting from abnormal neural development in the visual cortex. We tested the responses of ten amblyopic and six normal observers to illusions of perceived orientation in textures of Gabor patches: the "Fraser illusion," the "phase illusion," and a "tilted chain" illusion. The illusory tilt of the stimulus rows was matched by actual tilt in the opposite direction by using the method of constant stimuli. Amblyopes showed a significant increase in the Fraser illusion, a decrease in the phase illusion, and a reversal of the tilted chain illusion. Amblyopic performance could be simulated in normal observers by reducing the length of the rows. These results can be modeled by a theory which places the neural abnormality in amblyopia at the level of second stage grouping processes. Additionally, the illusions might be useful in the early diagnosis of amblyopia without the need for prior refractive correction.
New flexible multi-volume rendering technique for ultrasound imaging (2009)

Multi-volume rendering is a technique that renders and displays multiple volumes simultaneously. In ultrasound imaging, multi-volume rendering is used for mixing 3D anatomical structures from B-mode imaging with blood flow information from power Doppler imaging (PDI) or color Doppler imaging (CDI). A variety of multi-volume rendering techniques have been proposed, such as post fusion (PF), composite fusion (CF) and progressive fusion (PGF). PF, which combines independently-rendered volumes, is unable to depict a spatial relationship between B-mode images (i.e., tissue structure) and PDI/CDI images (i.e., blood flow). The CF technique suffers from color distortion due to intermixing of hue values. In our recent study, the PGF technique was found to better retain and display tissue structures, vasculature and their depth relationship. However, the disadvantages of PGF include its high computational cost due to the requirement of maintaining a separate rendering pipeline for each volume (i.e., B-mode and power/color Doppler) and potential artifacts of depth-order ambiguity. In this paper, we present a new flexible computationally efficient multivolume rendering technique, named volume fusion (VF), and compare it with existing techniques. We have evaluated the VF method and other multi-volume rendering techniques with data acquired from a commercial ultrasound machine and found that the VF technique can preserve the spatial relationships well amongst multiple volumes without color distortion while the same rendering pipeline can be used to support both PDI and CDI volume fusion.
The Synthesis and Preliminary Biological Evaluations of Selected Analogues of the Potent Broad-Spectrum Antiviral Agent Ganciclovir 1',3'-Cyclic Monophosphate1 (2'-Nor-cGMP) (1989)

Abstract The syntheses and antiviral activity of a series of analogues of the potent antiherpetic 2′-nor-cGMP are described. These derivatives contain systematic changes in either the heterocycle, the acyclic moiety, or the phosphate ring.
Polysaccharide composition during cotton seed fibre development: temporal differences between species and in different seasons (2022)

Abstract Background Cotton seed fibres are long single-celled epidermal trichomes that first appear on the surface of the ovule at anthesis and then elongate rapidly over a period of 15–25 days until a secondary cell wall (SCW) begins to develop through a rapid increase in the deposition of microfibrillar cellulose between the plasma membrane and the primary cell wall that eventually terminates elongation. Quantitative measurements of the different polysaccharide components in both wall types over time and how they influence fibre quality can direct studies involved in enhancing fibre properties for yarn quality through cell wall manipulation or molecular breeding. Results A detailed chemical analysis of cell wall composition by differential solvent fractionation was used to identify the range of polysaccharides present in mature cotton fibres and used to validate a simpler total cell wall monosaccharide linkage analysis protocol for wall compositional analysis. Analysis of fibres from 5 days post-anthesis through maturity for three cultivated species, Gossypium hirsutum , G. barbadense , and G. arboreum , showed the dynamic nature of cell wall polysaccharide composition through fibre development and that it progressed differently for each species. Plants grown in the glasshouse during either autumn to winter or spring to summer and within each species had fibre qualities and temporal aspects of cell wall development that were different for each season. Notably, the timing of the deposition of the SCW was delayed in winter grown plants and appeared to influence key fibre quality properties. Conclusions These results suggest that the temporal aspects of cell wall polysaccharide biogenesis during fibre development influence final fibre quality, and this timing is determined by both genetic and environmental factors. The onset of SCW synthesis appears to be a critical factor coinciding with termination of fibre elongation and specifying the duration of wall thickening that then affects fibre length and other wall-associated quality parameters that ultimately determine yarn quality.
ChemInform Abstract: Molecular Design of Novel PGI2 Agonists Without PG Skeleton. Part 1. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Complexity in efflux pump control: cross‐regulation by the paralogues TtgV and TtgT (2007)

Pseudomonas putida DOT-T1E, known for its high tolerance to solvents, possesses three Resistance-Nodulation-Cell Division-type (RND) efflux pumps, namely TtgABC, TtgDEF and TtgGHI, which are involved in the active extrusion of solvents. Expression of the ttgABC and ttgGHI operons was previously shown to be regulated by the adjacently encoded repressors, TtgR and TtgV, respectively. Upstream of the third RND operon, ttgDEF, is located a putative regulator gene, ttgT. In this study, TtgT is shown to bind to the promoter region of the ttgDEF operon, and to be released from DNA in the presence of organic solvents. In vitro studies revealed that TtgV and TtgT bind the same operator sites in both the ttgDEF and the ttgGHI promoters. However, the affinity of TtgV for the ttgDEF operator was higher than that of TtgT, which, together with the fact that the ttgV promoter seems to be almost twice stronger than the ttgT promoter, explains why TtgV takes over in the regulation of the two efflux pump operons. The functional replacement of the cognate, chromosomally encoded TtgT by the plasmid-encoded paralogue TtgV illustrates a new mode of efflux pump regulation of which the physiological relevance is discussed.
Quantum Mechanical Design and Evaluation of Active Sites of Novel Enzymes (2007)

Active sites of enzymes have been designed from quantum mechanical calculations of transition states of reactions catalyzed by the functional side chain and backbone groups of proteins. Theoretical active sites, “theozymes,” have been developed for a variety of aldol, Diels‐Alder, and eliminations reactions. Predictions of the acceleration relative to uncatalyzed have been made from a variety of quantum mechanical methods. Predictions of protein sequences and structures containing this active site were made by David Baker (U. Washington, Seattle). These designs have been evaluated quantum mechanically to determine which are promising for experimental exploration.
Channel-Shuttle Mechanism for the Regulation of Phenylalanine and Tyrosine Synthesis at a Metabolic Branch Point in Pseudomonas aeruginosa (1973)

A bifunctional protein complex was partially purified from Pseudomonas aeruginosa. Catalytic activities for chorismate mutase and prephenate dehydratase coeluted from gel filtration and DEAE-cellulose chromatography columns. The protein complex had a molecular weight of approximately 134,000, as determined by gel filtration. In crude extracts or in partially purified preparations about one-half of the chorismate utilized by the complex is converted to phenylpyruvate, and the other half accumulates as prephenate. The chorismate mutase activity is strongly product-inhibited by prephenate, competitively with chorismate. Accordingly, the first reaction of the complex can be sufficiently retarded by prephenate so that all of the reaction product is phenylpyruvate. Chorismate mutase activity is also competitively inhibited by phenylalanine. Although phenylalanine is effective at low concentrations, maximal inhibition is only 50 to 60%. Inhibition of chorismate mutase by phenylalanine was completely lost after gel filtration. The prephenate dehydratase activity of the protein complex is nearly completely inhibited by 0.1 mm phenylalanine in either crude extracts or partially purified preparations. A second species of prephenate dehydratase was separated from the prephenate dehydratase-chorismate mutase aggregate by gel filtration or anion exchange chromatography. The second prephenate dehydratase had an estimated molecular weight of 76,000, a high affinity for prephenate, and was insensitive to feedback inhibition by phenylalanine. The physiological role of the latter enzyme is uncertain. The other regulatory enzymes of tyrosine and phenylalanine biosynthesis, prephenate mutase aggregate by gel filtration or anion exchange chromatography. The other regulatory enzymes of tyrosine and phenylalanine biosynthesis, prephenate dehydrogenase (molecular weight of 120,000) and 3-deoxy-d-arabino-heptulosonate-7-phosphate synthetase (molecular weight of 52,000), elute from Sephadex G-100 columns as fractions which are distinct from both the chorismate mutase-prephenate dehydratase complex and from the low-molecular-weight species of prephenate dehydratase. A shuttle mechanism governing the metabolic fate of prephenate (to phenylalanine or to tyrosine) is proposed in the context of a model which also accommodates several previously puzzling findings: (i) the dominating role of tyrosine in the control of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthetase and (ii) the lack of feedback control of prephenate dehydrogenase by tyrosine.
Preparing for the Next Generation of Brain-Inspired AI. (2020)

Abstract not provided.
A Facile Solid‐Phase Route to Renewable Aromatic Chemicals from Biobased Furanics (2015)

Renewable aromatics can be conveniently synthesized from furanics by introducing an intermediate hydrogenation step in the Diels-Alder (DA) aromatization route, to effectively block retro-DA activity. Aromatization of the hydrogenated DA adducts requires tandem catalysis, using a metal-based dehydrogenation catalyst and solid acid dehydration catalyst in toluene. Herein it is demonstrated that the hydrogenated DA adducts can instead be conveniently converted into renewable aromatics with up to 80% selectivity in a solid-phase reaction with shorter reaction times using only an acidic zeolite, that is, without solvent or dehydrogenation catalyst. Hydrogenated adducts from diene/dienophile combinations of (methylated) furans with maleic anhydride are efficiently converted into renewable aromatics with this new route. The zeolite H-Y was found to perform the best and can be easily reused after calcination.
Characterization of dielectric and electro-optic properties of PLZT 9/65/35 films on sapphire for electro-optic applications (1998)

Lead lanthanum zirconate titanate (PLZT) thin films were deposited on r-plane sapphire at low temperatures by RF triode magnetron sputtering using lead compensated hot-pressed targets. To obtain fully perovskite phase in the films, two types of post-deposition processing were investigated: rapid thermal annealing (RTA) and furnace annealing (FA). Dielectric and electro-optic properties of PLZT films were found to be strongly dependent on annealing conditions. The peak dielectric constant of the films were 1200 and 2800 with Curie temperatures of 110 degrees C and 190 degrees C after RTA and FA processing, respectively. The dielectric losses in the films were fairly low; tan deltas were less than 0.02 after RTA and less than 0.04 after FA processing. The films showed good optical transmission characteristics after annealing and an anomalously large effective quadratic electro-optic effect was observed in one furnace annealed film.
Native oxide layer effect on polarization cancellation for mirrors over the visible to near-infrared region (2020)

Abstract The presence of native oxide layers on aluminum mirrors can be a nuisance for precision optical design. As the native oxide thickness varies from mirror to mirror, its effect cannot be completely canceled even in the conventional crossed fold mirror geometry. We show how this effect arises and how it can be mitigated, and provide an experimental demonstration in which the residual linear retardance and linear diattenuation are reduced to &lt;0.14° and &lt;0.001, respectively, over the visible and near-infra-red spectral range.
Community-based sero-prevalence of chikungunya and yellow fever in the South Omo Valley of Southern Ethiopia (2020)

High sero-prevalence of IgG antibody to CHIKV shows the circulation of the virus in the present study area. A low sero-prevalence of IgG antibody to YFV in YF vaccine received individuals is highly concerning from a public health point of view as waning of immune response to YFV infection could result in a periodic outbreaks of YF in endemic areas.Nevertheless, the present study has not investigated for possible cross-reactivity of antibody to CHIKV with other alphaviruses like O'nyong-nyong virus and antibody to YFV with other flaviviruses like Dengue fever virus and this warrants further studies in the present study area.
Characterization of PVDF with Raman spectroscopy : from off-line to on-line measurements (2014)

International audience
Robust metastability-based TRNG design in nanometer CMOS with sub-vdd pre-charge and hybrid self-calibration (2012)

In this work, we study the impact of sub-vdd pre-charge operation of metastability-based True Random Number Generator (TRNG) and propose a hybrid self-calibration to improve the statistics of the TRNG in the presence increasing intra-die variation. Circuits designed in deep submicron technologies are susceptible to process variation. The variability may affect the circuit performance, power and reliability. Numerous pre-silicon design methodologies and post-silicon circuit tuning mechanisms have been studied in literature. We propose a sub-vdd pre-charge technique to improve the tolerance of the TRNG to device mismatch. This is followed by a hybrid self-detection and calibration technique based on algorithmic post processing and circuit tuning to mitigate the effects of variability. The cryptographic metric of `bit entropy' is used to validate the proposed techniques. The TRNG circuit and the proposed techniques are implemented using 45nm PDK. Results show that variation in fabrication process affect the reliability of TRNG circuits. Pre-charging the TRNG to 0.7V for a typical supply voltage of 1.1V reduces the impact of device mismatch on the circuit by 2X for device mismatch as large as 4-5%. The hybrid self-calibration further improves the bit entropy by ~120% across a range of 5% intra-die variation. The simple control logic has an estimated area of 128 um <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and results in a negligible energy overhead of 0.82 fJ/bit.
POWER DISTRIBUTION (1998)

Digital logic requires a stable, quiet, DC supply voltage while drawing a large AC current with very high-frequency components comparable to signal rise times. It is not unusual for a high-performance digital circuit board to draw over 200 A from the primary power supply with the derivative at the point of use over 200 GA/s. However, with careful design, a power supply network can tolerate large variations in current draw while holding the supply voltage within a specified range (typically ±10% or less).
Electrochemical Studies and DFT Analysis of Pt Stability and Surface Passivation on NbRuyOz Support (2011)

The suppression of current exchange during the ethanol oxidation reaction on platinum supported on NbRuyOz (mixed metal oxide) has been investigated. 60% Pt/NbRuyOz was synthesized in a single step using aerosol spray pyrolysis, followed by reductive thermal post-treatment. Rapid cyclic voltammetry at a polarization rate of 1 V/s between anodic and cathodic potentials in 0.1M HClO4 and 1M KOH reveals the growth of a thin film of oxygen-rich niobia covering the catalyst and support particles. Step-increase cyclic voltammetry and chronopotentiostatic coulometry approaching, at, and above the oxygen evolution potential suggests that the mechanism of 3D film growth is oxygen-dependent. Density Functional Theory calculations indicate that the rate of oxygen diffusion across the Pt(111) surface is in good agreement with experimental observations of the period of catalyst deactivation (several weeks) when exposed to open atmosphere. This suggests that the mechanism of catalytic deactivation (passivation) could involve the capture and release of oxygen as Nb2O5 breaks down into reduced fragments of NbOx.