gebhart/patrepeval huggingface dataset:
Structurally Similar Woodchuck and Human Hepadnavirus Core Proteins Have Distinctly Different Temperature Dependences of Assembly (2014)

In this paper, we present a cryo-EM structure of a WHV capsid showing its similarity to HBV. We then observe that the assembly properties of the two homologous proteins are very different. Unlike human HBV, the capsid protein of WHV has evolved to function in a nonhomeostatic environment. These studies yield insight into the interplay between core protein self-assembly and the host environment, which may be particularly relevant to plant viruses and viruses with zoonotic cycles involving insect vectors.
Evaluation of a Parallel Architecture and Algorithm for Mapping and Localization (2007)

The Beowulf cluster approach to parallel computation offers a potentially cheap and robust source of computational power for high complexity algorithms in robotics. The challenge is to integrate this approach with the mobility and time critical response constraints of many robotic algorithms. The key contributions of this paper are: (1) introduction of a computational architecture for integrating a cluster into the control architecture of one or more robots, (2) a cluster implementation of Thrun et al's Concurrent Localization and Mapping (CML) algorithm, and (3) presentation of results to illustrate the performance of the implemented CML algorithm and validate the architectural approach.
Utilisation de l'essai des comètes pour la surveillance des milieux aquatiques-problématique de la conservation des échantillons (2018)

Les milieux aquatiques constituent le réceptacle d’un grand nombre de contaminants, anthropiques et naturels, pouvant être dangereux pour les organismes qui y vivent.
Monolithic InGaAs/GaAs multi-QWs DFB nano-ridge laser directly grown on 300 mm Si Wafer (2017)

Ultra-large-volume and low-cost-per-chip CMOS photonics integrated circuit has been searching for high-performance, Si-compatible laser sources that can be directly integrated on Si wafer for mass production. III-V semiconductor, the considered efficient light generation material, unfortunately has big lattice mismatch and thermal expansion contrast with Si, extremely difficult to be epitaxially grown on Si. Here we demonstrate an optically pumped monolithic InGaAs/GaAs multi-QWs single-mode DFB nano-ridge laser which is directly grown from 300 mm Si wafer by using aspect ratio defect trapping technique.
Quantitative live-cell imaging of secretion activity reveals dynamic immune responses (2022)

Abstract The measurement of cytokine secretions has contributed to the development of immunology; however, new methods that enable highly sensitive and efficient analysis are required for the precise characterisation of dynamic secretion activity when using rare cells or limited human specimens. Here, we report a new technology for quantitative live-cell imaging of secretion activity (qLCI-S), that enables high-throughput and dual-colour detection of prolonged secretion activity at the single-cell level, followed by transcriptome analysis for individual cells based on their phenotype. The power of the qLCI-S was demonstrated by visualising the individual and longitudinal cytokine secretion patterns of group 2 innate lymphoid cells, which comprised &lt;0.01% human peripheral blood mononuclear cells, and identifying their minor subpopulations. This new technology will provide new insights into the spatiotemporal dynamic nature of various secretory functions and the development of fundamental tools for phenotypic drug discovery and regenerative and precision medicine.
Acoustomicrofluidic separation of tardigrades from raw cultures for\n sample preparation (2019)

Tardigrades are microscopic animals widely known for their survival\ncapabilities under extreme conditions. They are the focus of current research\nin the fields of taxonomy, biogeography, genomics, proteomics, development,\nspace biology, evolution, and ecology. Tardigrades, such as Hypsibius\nexemplaris, are being advocated as a next-generation model organism for genomic\nand developmental studies. The raw culture of H. exemplaris usually contains\ntardigrades themselves, their eggs, and algal food and feces. Experimentation\nwith tardigrades often requires the demanding and laborious separation of\ntardigrades from raw samples to prepare pure and contamination-free tardigrade\nsamples. In this paper, we propose a two-step acousto-microfluidic separation\nmethod to isolate tardigrades from raw samples. In the first step, a passive\nmicrofluidic filter composed of an array of traps is used to remove large algal\nclusters in the raw sample. In the second step, a surface acoustic wave-based\nactive microfluidic separation device is used to continuously deflect\ntardigrades from their original streamlines inside the microchannel and thus\nselectively isolate them from algae and eggs. The experimental results\ndemonstrated the efficient tardigrade separation with a recovery rate of 96%\nand an algae impurity of 4% on average in a continuous, contactless, automated,\nrapid, biocompatible manner.\n
Pharmacologic Profile of CGS 24128, a Potent, Long-Acting Inhibitor of Neutral Endopeptidase 24.11 (1994)

Summary: We compared the pharmacologic profiles of thiorphan, a neutral endopeptidase (NEP) inhibitor which is cleared rapidly from the circulation, and CGS 24128, an inhibitor with a much longer half-life (t½). Thiorphan and CGS 24128 inhibited NEP in vitro with IC50 values of 5.0 ± 0.2 and 4.3 ± 0.2 nM, respectively. After administration at 10 mg/kg intravenously (i.v.), the concentrations of CGS 24128 in the plasma were >500 nM for 4 h but plasma thiorphan was detectable for only 60 min. Thiorphan 3 mg/kg administered intraarterially (i.a.) increased plasma atrial natriuretic peptide immunoreactivity (ANPir) levels by 58 ± 12% in rats administered exogenous ANP(99-126). This response lasted <60 min, whereas the same dose of CGS 24128 produced an average increase of 191 ± 19% in ANPir concentrations that persisted for 4 h. ANP-induced (1 μg/kg i.v.) natriuresis was significantly potentiated in anesthetized rats pretreated (60 min) with a bolus of CGS 24128 10 mg/kg i.v. The change in urinary sodium excretion (UNaV) produced by ANP was 28.8 ± 4.0 and 15.8 ± 1.8 μEq/kg/min in CGS 24128- and vehicle-treated rats, respectively. ANP-induced natriuresis was also greater during continuous infusion of thiorphan (5 mg/kg bolus + 0.1 mg/kg/min i.v.; Δ UNaV = 29.2 ± 5.8 and 13.8 ± 3.2 μEq/kg/min in drug- and vehicle-treated rats, respectively) but not when thiorphan was administered as a bolus (10 mg/kg i.v.) 60 min before the ANP challenge. Similarly, continuous infusion of thiorphan (0.5 mg/kg/min i.v.) or CGS 24128, given as a bolus (10 mg/kg i.v.), decreased mean arterial pressure (MAP) by 26 ± 7 and 31 ± 6 mm Hg, respectively, in DOCA-salt hypertensive rats. This antihypertensive effect was not observed after i.v. bolus injection of thiorphan 30 mg/kg. These data indicate that potent NEP inhibitors can potentiate the biologic actions of endogenous and exogenous ANP, but the efficacy of some compounds is significantly limited by their rate of clearance in vivo.
Comparison of imaging biomarkers for Alzheimer's disease: amyloid imaging with [18F]florbetapir positron emission tomography and magnetic resonance imaging voxel‐based analysis for entorhinal cortex atrophy (2014)

This is the first study to compare [(18)F]florbetapir PET and MRI voxel-based analysis of entorhinal cortex atrophy for AD. Both [(18)F]florbetapir PET and MRI detected changes in AD compared with OHC. Considering that entorhinal cortex atrophy correlated well with cognitive decline only among subjects with beta-amyloid, [18F]florbetapir PET makes it possible to detect AD pathology in the early stage, whereas MRI morphometry for subjects with beta-amyloid provides a good biomarker to assess the severity of AD in the later stage.
Self-assembling Manifolds in Single-cell RNA Sequencing Data (2018)

Abstract Single-cell RNA sequencing has spurred the development of computational methods that enable researchers to classify cell types, delineate developmental trajectories, and measure molecular responses to external perturbations. Many of these technologies rely on their ability to detect genes whose cell-to-cell variations arise from the biological processes of interest rather than transcriptional or technical noise. However, for datasets in which the biologically relevant differences between cells are subtle, identifying these genes is a challenging task. We present the self-assembling manifold (SAM) algorithm, an iterative soft feature selection strategy to quantify gene relevance and improve dimensionality reduction. We demonstrate its advantages over other state-of-the-art methods with experimental validation in identifying novel stem cell populations of Schistosoma , a prevalent parasite that infects hundreds of millions of people. Extending our analysis to a total of 56 datasets, we show that SAM is generalizable and consistently outperforms other methods in a variety of biological and quantitative benchmarks.
Axisymmetric Swirling Vortical Wakes Modulated by a Control Disk (2003)

The effects of an above-exit circular disk on the flow structures, turbulence properties, and mixing characteristics of swirling jets separated by a large diameter blockage disk at jet exit are studied by using the smoke-wire flow-visualization technique and a two-component laser Doppler velocimeter. A carbon-dioxide tracer-gas experiment is conducted to examine the mixing capability of the flows modulated by the control disk. The smoke-streak flow patterns, characteristic lengths, velocity vectors, streamlines, velocity distributions, turbulence properties, and concentration distributions of the carbon dioxide are presented and discussed. Topological techniques are applied to analyze and interpret the flow patterns. With the variation of the distance between the control and blockage disks and the central jet Reynolds number, the bubble structures in the near field display complex behaviors of extension, escape, and encapsulation. Under the influence of the control disk, the central jet deflects radially, merges with the swirling annular flow, then turns downstream to form a recirculation bubble in the control-disk wake
Performance of Aged, TransFix-Treated Blood in the Guava EasyCD4 and EasyCD8 Assays (2005)

u Use of TransFix as a stabilizer at a 1:10 ratio when added to whole blood shows good compatibility for use with Guava EasyCD4 and EasyCD8 assays to obtain accurate and precise CD4 and CD8 counts. u The staining pattern from TransFixed samples over 15 days is almost identical to the staining pattern at day 0. At 30 days the staining pattern is starting to show signs of deteri-oration, however accurate counts could still be obtained. u Accurate CD4 and CD8 T-cell counts were shown to be obtained from TransFix-treated samples over a period of 0– 15 days (within 10 % of untreated control) when compared to fresh untreated blood on Day 0. The 30-day TransFixed-samples show an increased negative bias compared to samples treated for 15 days or less, however in most cases counts were within 20 % of counts from untreated samples
Galectin 13 (PP13) Facilitates Remodeling and Structural Stabilization of Maternal Vessels during Pregnancy (2019)

Galectins regulate cell growth, proliferation, differentiation, apoptosis, signal transduction, mRNA splicing, and interactions with the extracellular matrix. Here we focus on the galectins in the reproductive system, particularly on a group of six galectins that first appears in anthropoid primates in conjunction with the evolution of highly invasive placentation and long gestation. Of these six, placental protein 13 (PP13, galectin 13) interacts with glycoproteins and glycolipids to enable successful pregnancy. PP13 is related to the development of a major obstetric syndrome, preeclampsia, a life-threatening complication of pregnancy which affects ten million pregnant women globally. Preeclampsia is characterized by hypertension, proteinuria, and organ failure, and is often accompanied by fetal loss and major newborn disabilities. PP13 facilitates the expansion of uterine arteries and veins during pregnancy in an endothelial cell-dependent manner, via the eNOS and prostaglandin signaling pathways. PP13 acts through its carbohydrate recognition domain that binds to sugar residues of extracellular and connective tissue molecules, thus inducing structural stabilization of vessel expansion. Further, decidual PP13 aggregates may serve as a decoy that induces white blood cell apoptosis, contributing to the mother's immune tolerance to pregnancy. Lower first trimester PP13 level is one of the biomarkers to predict the subsequent risk to develop preeclampsia, while its molecular mutations/polymorphisms that are associated with reduced PP13 expression are accompanied by higher rates of preeclampsia We propose a targeted PP13 replenishing therapy to fight preeclampsia in carriers of these mutations.
Characterization of cis‐acting elements in the promoter of the mouse metallothionein‐3 gene (2000)

The metallothionein (MT)3 gene is expressed predominantly in the brain and the organs of the reproductive system, and fails to respond to metal ions in vivo. A CTG repeat was proposed to function as a potential repressor element in nonpermissive cells, and a sequence similar to the JC virus silencer element was found to function as a negative element in permissive primary astrocytes. The objective of this study was to characterize further the mechanisms governing cell-type specific MT-3 gene transcription. We searched for a suitable cell line expressing the MT-3 gene to be used for determination of MT-3 promoter tissue specificity, and showed that MT-3 expression is activated during neuroectodermal differentiation of P19 cells induced by retinoic acid to levels similar to those found in whole brain. Deletion of the CTG repeat or of the JC virus silencer did not promote MT-3 promoter activity in nonpermissive cells, or enhance expression in permissive cells. We identified MT-3 promoter sequences interacting with liver and brain nuclear proteins, as assayed by DNase I footprinting analyses and electrophoretic mobility shift assay, and assessed the role of these sequences in the regulation of MT-3 expression by cotransfection experiments. We generated stable transfectants in permissive C6 and nonpermissive NIH-3T3 cells, and analysed the methylation status of the MT-3 gene. These studies show that regulation of tissue-specific MT-3 gene expression does not appear to involve a repressor, and suggest that other mechanisms such as chromatin organization and epigenetic modifications could account for the absence of MT-3 gene transcription in nonpermissive cells.
Surface Functionalization of Polyether Dendrimers Using Palladium-Catalyzed Cross-Coupling Reactions (1998)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSurface Functionalization of Polyether Dendrimers Using Palladium-Catalyzed Cross-Coupling ReactionsL. Groenendaal and J. M. J. FréchetView Author Information Department of Chemistry, University of California-Berkeley, Berkeley, California 94720-1460 Cite this: J. Org. Chem. 1998, 63, 16, 5675–5679Publication Date (Web):July 9, 1998Publication History Received2 March 1998Published online9 July 1998Published inissue 1 August 1998https://pubs.acs.org/doi/10.1021/jo980380vhttps://doi.org/10.1021/jo980380vbrief-reportACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views237Altmetric-Citations19LEARN 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 SUBJECTS:Cross coupling reaction,Dendrons,Functionalization,Phenyls,Purification Get e-Alerts
A Comparison of the Conformal Decomposition Finite Element Method to the Level Set Method for Microfluidic Flows. (2013)

Abstract not provided.
Supplementary Data from An Immune Response Enriched 72-Gene Prognostic Profile for Early-Stage Non–Small-Cell Lung Cancer (2023)

Supplementary Data from An Immune Response Enriched 72-Gene Prognostic Profile for Early-Stage Non–Small-Cell Lung Cancer
Scaling-Up of High Pressure Torsion Using Ring Shape (2008)

A 100 mm-diameter ring sample of high purity Al (99.99%) was processed by high-pressure torsion (HPT). It was confirmed that the results of hardness measurements were consistent with those obtained using disk samples and demonstrated that scaling-up the HPT process was feasible using the ring-shaped sample. Evaluating the advantage of using ring sample, the potential for the scaling-up arises from the fact that the ring diameter can be increased by the amount corresponding to the inner central area of disk sample. Furthermore, the applied load is entirely used for the introduction of intense strain and thus for the development of a homogeneous microstrcuture throughout the ring sample.
Photochemical Activation of a Metal–Organic Framework to Reveal Functionality (2010)

Seeing the light: Two highly porous metal–organic frameworks (MOFs) were transformed using UV light to produce MOFs with hydroxy and catechol groups through an unusual postsynthetic deprotection reaction (see scheme).
Energy Efficient Wide Bandgap Devices (2006)

As wide bandgap devices begin to become commercially available, it is becoming clear that electrical efficiency improvement is one of the key drivers for their adoption. For RF applications, GaN HEMTs allow the use of highly efficient class E circuit topologies demonstrating high powers of 63 Watts at 2 GHz with 75% power added efficiency. In broadband WiMax applications, GaN HEMTs offer very wide bandwidths while meeting the IEEE 802.16e standard with >25% drain efficiency. SiC Schottky diodes are allowing up to a 25% reduction in losses in power supplies for computers and servers when used in the power factor correction circuit. Even higher efficiencies can be obtained when the SiC Schottkys are combined with a SiC MOSFET as the switch, resulting in yet another 22% reduction in losses. For motor control, SiC Schottkys allow a >35% reduction in losses, as demonstrated for a 3 HP motor drive
Rates of Microbenthic and Meiobenthic Bacterivory in a Temperate Muddy Tidal Flat Community (1992)

Rates of bacterivory in micro- and meiobenthic species were determined by an improved technique in a muddy tidal flat community in Boston Harbor, Mass. The predominant grazers of bacteria were identified, and their rates of grazing were measured in the top 1 cm of the sediment. Grazing rates were measured by a fluorescence-labeled bacteria (FLB) technique. A mixture of two Enterococcus spp. isolates and two isolates of Escherichia coli were prepared as FLB, and they were added to intact sediment cores by replacing the pore water in the upper centimeter of the core. A standard FLB procedure was modified by filtering sediment dilutions onto cellulose membrane filters and processing the filters to render them optically transparent while preserving the physical integrity of the micro- and meiobenthic organisms. Thus, it was possible, on the same microscopic field, to switch from light microscopy for identification of grazers to epifluorescence microscopy for counting FLB present in the gut contents of the same grazers. The majority of benthic organisms present in these sediments consumed FLB, but their consumption rates varied widely. Two ciliate species, a Prorodon sp. and a Chlamidodon sp., and a nematode, a Metoncholaimus sp., consumed fluorescence-labeled coliforms at the highest rates, 126 to 169 FLB per individual per h. Other ciliates and nematodes, as well as microflagellates and harpacticoid copepods, consumed fluorescence-labeled coliforms at lower rates, 1.2 to 26 FLB per individual per h. Foraminiferans and gastrotriches did not contain FLB. Some ciliate grazers discriminated between enterococci and coliforms, consuming the rod-shaped fluorescence-labeled coliforms at 74- to 155-fold-higher rates than did the coccus-shaped fluorescence-labeled enterococci. Other ciliates did not select between fluorescence-labeled enterococci and fluorescence-labeled coliforms. The high rates of bacterivory by some ciliates and nematodes indicated intensive grazing. However, at their low extant densities, the grazers consumed only a small portion of the bacterial standing stock. Major bacterial grazers, e.g., microflagellates, ciliates, and nematodes, could potentially consume, per day, only 0.2, 0.1, and 0.03%, respectively, of the bacterial standing stock (7.5 x 10 bacteria per cm).
Collaborative study of a Supercritical Fluid Chromatography method for the determination of pharmaceutical impurities (2018)

Projet PHARE
Monitoring epoxy and unsaturated polyester reactions under pressure—Reaction rates and mechanical properties (2009)

Abstract The effects of pressure on reaction rates and final mechanical properties were studied for an unsaturated polyester (UP) and epoxy resin. A pressure chamber where reactions can be monitored by use of Raman spectroscopy has been built for these purposes. The chamber allows for pressures up to 13.8 MPa at 200°C. An advanced temperature control system has been adapted to the vessel to precisely control and monitor sample temperature variations and overshoots. It is described how for an accelerated UP reaction increasing pressure will result in a competing effect on the reaction rate where the rate will initially lower, but with increased pressures it may accelerate due to acceleration of the reaction rate constants. The final mechanical properties exhibit a similar behavior slightly increasing with pressure but lowering as pressure is raised further. For epoxy, it was shown that the reaction kinetics were accelerated by pressure although no mechanical property differences could be noted for the pressure ranges tested. POLYM. ENG. SCI., 2009. © 2009 Society of Plastics Engineers.
Iron‐Containing SSZ‐39 (AEI) Zeolite: An Active and Stable High‐Temperature NH3‐SCR Catalyst (2017)

Abstract The preparation of the iron‐containing SSZ‐39 zeolite is described for the first time through two different synthesis methods: post‐synthetic cation exchange and one‐pot synthesis. The nature and stability of the iron species within the different Fe‐SSZ‐39 materials have been studied through different characterization techniques, and their catalytic activity has been evaluated for the selective catalytic reduction (SCR) of NO x with ammonia. The directly synthetized Fe‐SSZ‐39 performs better for the SCR of NO x with ammonia than other related Fe‐zeolites, particularly at elevated reaction temperatures (above 450 °C), and presents improved hydrothermal stability when aged under severe conditions.