gebhart/patrepeval huggingface dataset:
Symposium: Nanoclustering of Membranes and Membrane Proteins (2015)

Bioscience,University of Utah, Salt Lake City, UT, USA.TheESCRTpathway mediatesa series of importantcellular membraneremod-eling and ﬁssion events, including cytokinetic abscission. During these pro-cesses, ESCRT-III family proteins, including CHMP1B and IST1, formﬁlaments that appear to constrict membranes and facilitate ﬁssion. Here, wereport the ﬁrst structure of ‘‘open’’ and assembled ESCRT-III proteins. Near-atomic resolution electron cryomicroscopy reveals that ﬁlaments comprise acopolymericassemblyofanopenconformationinnerstrandand,unexpectedly,a closed conformation outer strand.1797-SympIn Vivo-Studies of GPCR Conformational Changes using Fluorescence-Based AssaysMartin Lohse.Institute of Pharmacology and Toxicology and Rudolf Virchow Center,University of Wurzburg, Wurzburg, Germany.Activation of and signaling by GPCRs involves conformational changes in thereceptors themselves as well as downstream signaling proteins and also the re-arrangement of protein complexes. We have developed a number of optical as-says based on ﬂuorescence resonance energy transfer (FRET) which allow themeasurement and imaging of GPCR activation and signaling in intact cells.These assays are based on ﬂuorescently labeled receptors and/or downstreamsignaling proteins and can be used in intact cells as well as in entire organismssuch as Drosophila larvae. They permit the analysis of GPCR activation mech-anisms, their amplitudes and kinetics, as well as an analysis of the spatio-temporalpatterningofreceptoractivationandsignaling.Wehavealsousedsin-gle particle tracking to elucidate the movements of these proteins on the cellsurface and the monitoring of their interactions. Our data show that these pro-cesses are highly dynamic and that they can occur in temporally and spatiallyrestricted patterns. This dynamic behavior begins with the high mobility of thecomponents in the cell membrane and their dynamic and reversible interactionand ends with temporallyand spatially regulated activationand signaling. Sup-ported by grants from the Deutsche Forschungsgemeinschaft (SFB487 andSFB688), the European Research Council (Grants ‘‘Topas’’ and Fresco), theHumboldt Foundation and the European Molecular Biology Organization(EMBO).1798-SympLipid Organization of the Plasma MembraneHelgi I. Ingolfsson
De‐migration‐based supervised learning for interpolation and regularization of 3D offset classes (2022)

ABSTRACT Regularization and interpolation of 3D offset classes prior to imaging are an important and challenging step in the marine seismic data processing flow. Here we describe how to perform this task using a deep neural network, and we explain how to overcome the challenge of creating a suitable training data set. The training data set is generated by de‐migrating stacked pre‐stack depth migration images. For each offset class volume, we de‐migrate the pre‐stack depth migrated stacked image into two configurations: (i) the original survey configuration consisting of the recorded source/receiver positions and (ii) an ‘Ideal’ survey configuration with constant offset and azimuth for each 3D offset class. The training creates a 3D convolutional encoder–decoder model that will regularize and interpolate seismic data. The convolutional encoder–decoder is trained on 3D sliding windows in each 3D offset cube to map from (i) to (ii), i.e. to map the original survey configuration with irregular and sparse sampling into the fully sampled regular offset cubes suitable for offset‐based migration, such as Kirchhoff migration. Such migration algorithms rely on regular and sufficiently dense sampling to achieve constructive interference to image the structures and destructive interference to suppress migration noise. We test the new method on one synthetic and one field data example and show that it performs better than a standard regularization/interpolation method based on anti‐leakage Fourier transform, especially for the smallest offset classes. On the synthetic data, we also demonstrate that the convolutional encoder–decoder method preserves the amplitude versus offset as well as the standard method.
Guillain–BarrÉ Syndrome After Immunization in Canadian Children (1996–2012) (2015)

Guillain-Barré syndrome (GBS) cases admitted to Canadian pediatric tertiary care centers were ascertained through active surveillance. From 1996 to 2012, 246 cases were identified, and 24 (10%) had onset ≤30 days after immunization. Annual rate of postimmunization GBS was 2.0 per 100,000 hospitalizations. Postimmunization GBS was an infrequent cause of pediatric hospitalization.
Long‐term durability of antibody responses after SARS‐CoV‐2 vaccination and influencing factors (2023)

J.C.P., E.C.F., and J.L.S. work for Abbott Diagnostics, a company that performed the serological assays on the biospecimens that were collected for this study. G.Y.M. reports consulting fees from Abbvie, Arena, Boehringer–Ingelheim, Bristol–Myers Squibb, Gilead, Janssen, Fresenius Kabi, Ferring, Merck, Pfizer, Prometheus Labs, Samsung Bioepis, Shionogi, Techlab, and Takeda; advisory or leadership roles with Bristol–Myers Squibb and Redhill Biopharma; and royalties/licenses and patents planned, issued, or pending via Aytu Biosciences. K.S. has received speaking honoraria from Abbott Diagnostics and served as a consultant for Sapient Bioanalytics, a company that supported the collection and processing of samples for this study. The remaining authors have no relevant potential conflicts. The data that support the findings of this study are available from the corresponding authors upon reasonable request. The data are not publicly available due to the contents including information that could compromise research participant privacy/consent.
Colloidal Photonic Crystals of Reusable Hydrogel Microparticles for Sensor and Laser Applications (2021)

Although a wide variety of techniques have been developed to date for the fabrication of high-quality colloidal photonic crystals (CPCs) using monodisperse silica and polystyrene microparticles, poly(<i>N</i>-isopropylacrylamide) (PNIPA) hydrogel microparticles have rarely been utilized for the preparation of active CPCs despite the intriguing feature of temperature-responsive volume changes. This report describes the promising potential abilities of PNIPA hydrogel microparticles for sensor and laser applications. Monodisperse PNIPA hydrogel microparticles were synthesized by emulsion polymerization, and the microparticle diameter was finely controlled by adjusting the surfactant concentration. Such hydrogel microparticles spontaneously formed uniform CPCs with visible Bragg reflection even in fluid suspensions. The addition of small amounts of ionic substances into the centrifuged and deionized CPC suspensions enabled the on-demand color switching between Bragg reflection and white turbidity with temperature, leading to temperature- and ion-sensing applications. Moreover, our expanding experiments successfully demonstrated the optically excited laser action with a single and narrow peak from CPC suspensions with light-emitting dyes by the photonic band gap effect. After the light-emitting dyes were simply removed from the CPC suspensions by centrifugation, the purified PNIPA hydrogel microparticles were permanently reusable as the CPC laser microcavities to generate the laser action at other wavelengths using different dyes. This study contributes the circular economy concept using reusable hydrogel microparticles for the realization of a sustainable society.
Renal ischemia-reperfusion injury and adenosine 2A receptor-mediated tissue protection: role of macrophages (2004)

The role of monocytes/macrophages in the pathogenesis of ischemia-reperfusion injury (IRI) is unknown. We sought to determine whether activation of macrophage adenosine 2A (A(2A)) receptors (A(2A)Rs) mediates tissue protection. We subjected C57Bl/6 mice infused with clodronate [dichloromethylene bisphosphonate (Cl(2)MBP)] to IRI (32 min of ischemia followed by 24 h of reperfusion) to deplete them of macrophages. IRI induced an elevation of plasma creatinine that was reduced with Cl(2)MBP (26% of control). Adoptive transfer of murine RAW 264.7 cells reconstituted injury, an effect blocked significantly by A(2A) agonists (27% of plasma creatinine from mice reconstituted with macrophages). Macrophages subjected to A(2A) knockout by small interfering RNA were adoptively transferred to macrophage-depleted mice and reconstituted injury (110% of control mice); however, the increase in plasma creatinine was blocked by A(2A) agonists (20% of vehicle treatment). Finally, the A(2A) agonist effect on IRI was blocked in macrophage-depleted A(2A)-knockout mice reconstituted with wild-type RAW 264.7 cells. RNase protection assays 24 h after IRI demonstrated that macrophages are required for IL-6 and TGF-beta mRNA induction. However, A(2A) agonist-mediated tissue protection is independent of IL-6 and TGF-beta mRNA. We conclude that the full extent of IRI requires macrophages and that A(2A) agonist-mediated tissue protection is independent of activation of macrophage A(2A)Rs.
Centralized Power Control in Cognitive Radio Networks Using Modulation\n and Coding Classification Feedback (2015)

In this paper, a centralized Power Control (PC) scheme and an interference\nchannel learning method are jointly tackled to allow a Cognitive Radio Network\n(CRN) access to the frequency band of a Primary User (PU) operating based on an\nAdaptive Coding and Modulation (ACM) protocol. The learning process enabler is\na cooperative Modulation and Coding Classification (MCC) technique which\nestimates the Modulation and Coding scheme (MCS) of the PU. Due to the lack of\ncooperation between the PU and the CRN, the CRN exploits this multilevel MCC\nsensing feedback as implicit channel state information (CSI) of the PU link in\norder to constantly monitor the impact of the aggregated interference it\ncauses. In this paper, an algorithm is developed for maximizing the CRN\nthroughput (the PC optimization objective) and simultaneously learning how to\nmitigate PU interference (the optimization problem constraint) by using only\nthe MCC information. Ideal approaches for this problem setting with high\nconvergence rate are the cutting plane methods (CPM). Here, we focus on the\nanalytic center cutting plane method (ACCPM) and the center of gravity cutting\nplane method (CGCPM) whose effectiveness in the proposed simultaneous PC and\ninterference channel learning algorithm is demonstrated through numerical\nsimulations.\n
Multi-band antenna with coupling feed structure for mobile handset applications (2010)

In this paper, a multi-band antenna with coupling structure for a mobile handset is proposed. The proposed antenna occupies small volume of 0.85cm (=40mmx3mm><;7mm) although the antenna operates in tri-band. Dielectric substance which has relative permittivity (εr) of 3 is used to support metal structures. The proposed antenna is easy to be fabricated and suitable for mass production process with low profile and multi-band operation.
The Potential of <i>Bothrops moojeni</i> Venom in the Field of Hemostasis (2005)

Early studies in the 1930s on the venom of South American Lancehead snakesofthe Bothrops genuslead to the discovery of compounds active in blood coagulation such as batroxobin and botrocetin. The scope of our investigations is to have a deeper look at the crude venom of B. moojeni using state-of-the-art proteomics methods, as well as newly developed bioassays screening for activities in the different fields of application. The proteomics techniques used up to now have included different chromatography methods, mass spectrometry, and bio-computing. The bioassays are focussed on enzymatic and other activities in the field of hemostasis and fibrinolysis. Besides the known activities several new and interesting ones have been found. They still need to be studied and confirmed in more specific supplementary assays.
Mobile Augmented Reality at the Hollywood Walk of Fame (2011)

This work introduces techniques to facilitate large-scale Augmented Reality (AR) experiences in unprepared outdoor environments. We develop a shape-based object detection framework that works with limited texture and can robustly handle extreme illumination and occlusion issues. The contribution of this work is a purely geometric approach for detecting marker-like objects under difficult and realistic outdoor conditions. We demonstrate these techniques for mobile AR experiences by detecting and tracking star-shaped pentagrams embedded in the Hollywood Walk of Fame at 30Hz on a Nokia N900 phone.
The Adjuvants Polyphosphazene (PCEP) and a Combination of Curdlan Plus Leptin Promote a Th17-Type Immune Response to an Intramuscular Vaccine in Mice (2021)

Our aim was to determine whether polyphosphazene (PCEP), Curdlan (β-glucan, a dectin-1 agonist), and Leptin could act as adjuvants to promote a Th17-type adaptive immune response in mice. Mice were vaccinated via the intramuscular route then boosted three weeks later with Ovalbumin plus: PCEP, Leptin, Curdlan, PCEP+Curdlan, Curdlan+Leptin, or saline. Mice vaccinated with OVA+PCEP and OVA+Curdlan+Leptin showed significantly higher frequency of antigen-specific CD4+ T cells secreting IL-17 relative to OVA-vaccinated mice. No formulation increased the frequency of CD4+ T cells secreting IL-4 or IFNγ. Since activation of innate immunity precedes the development of adaptive immunity, we wished to establish whether induction of Th17-type immunity could be predicted from in vitro experiments and/or from the local cytokine environment after immunization with adjuvants alone. Elevated IL-6 and TGFβ with reduced secretion of IL-12 is a cytokine milieu known to promote differentiation of Th17-type immunity. We injected the immunostimulants or saline buffer into murine thigh muscles and measured acute local cytokine production. PCEP induced significant production of IL-6 and reduced IL-12 production in muscle but it did not lead to elevated TGFβ production. Curdlan+Leptin injected into muscle induced significant production of TGFβ and IL-17 but not IL-6 or IL-12. We also stimulated splenocytes with media or PCEP, Leptin, Curdlan, PCEP+Curdlan, Curdlan+Leptin, PCEP+Leptin, and PCEP+Curdlan+Leptin and measured cytokine production. PCEP stimulation of splenocytes failed to induce significant production of IL-6, IL-12, TGFβ, or IL-17 and therefore ex vivo splenocyte stimulation failed to predict the increased frequency of Th17-type T cells in response to the vaccine. Curdlan-stimulated splenocytes produced Th1-type, inducing cytokine, IL-12. Curdlan+/-PCEP stimulated TGF-β production and Curdlan+Leptin+/- PCEP induced secretion of IL-17. We conclude that PCEP as well as Curdlan+Leptin are Th17-type vaccine adjuvants in mice but that cytokines produced in response to these adjuvants in muscle after injection or in ex vivo cultured splenocytes did not predict their role as a Th17-type adjuvant. Together, these data suggest that the cytokine environments induced by these immunostimulants did not predict induction of an antigen-specific Th17-type adaptive immune response. This is the first report of these adjuvants inducing a Th17-type adaptive immune response.
Dissemination of Clonal Groups of Brachyspira hyodysenteriae amongst Pig Farms in Spain, and Their Relationships to Isolates from Other Countries (2012)

This MLST scheme provided sufficient resolution power to unambiguously characterise B. hyodysenteriae isolates, and can be recommended as a routine typing tool that rapidly enables comparisons of isolates. Using this method it was shown that some of the main genetic lineages of B. hyodysenteriae in Spain also occurred in other countries, providing further evidence for international transmission. Finally, analysis of AATs appeared useful for deducing putative ancestral relationships between strains.
Characterization and regulation of H‐K ATPase in intercalated cells of rabbit cortical collecting duct (1997)

K-dependent H+ extrusion was investigated using fluorescence techniques in rabbit cortical collecting tubules (CCTs). Experiments were performed in split-open tubules from normal animals exposed to the intracellular pH indicator 2′,7′-bis(carboxyethyl)-5(6)-carboxyfluorescein (BCECF). This preparation permitted the study of individual intercalated cells (Ics). In the Ics, partial recovery of pHi was observed in response to an acute acid load upon readdition of 5 mM K to the superfusate. This recovery was SCH 28080-inhibitable (10–5 M) and ouabain-insensitive suggesting the process is mediated by a gastric-type H-K ATPase. To see if H-K ATPase plays a role in acid secretion its function was evaluated under chronic metabolic acidosis (CMA) conditions. CMA was induced by replacing drinking water with 75 mM NH4Cl in 5% sucrose for 10–14 days. The SCH 28080-inhibitable K-dependent pHi recovery rate was three-fold higher in CMA ICs compared to controls. To determine the location of the H-K ATPase, CCTs were microperfused and individual peanut lectin binding (PNA) ICs studied. K-dependent pHi recovery was measured in response to an NH4Cl pulse. An apical SCH 28080-inhibited K-dependent pHi recovery process was observed in control and CMA Ics. Taken together these data confirm the existence of a gastric-type H-K ATPase in ICs of rabbit CCT. Based on our findings the H-K ATPase is found on the apical side of the cell and is stimulated under conditions of CMA. J. Exp. Zool. 279:443–455, 1997. © 1997 Wiley-Liss, Inc.
Self-assembly of the simple cubic lattice with an isotropic potential (2006)

Conventional wisdom presumes that low-coordinated crystal ground states require directional interactions. Using our recently introduced optimization procedure to achieve self-assembly of targeted structures [M. C. Rechtsman, Phys. Rev. Lett. 95, 228301 (2005); Phys. Rev. E 73, 011406 (2006)], we present an isotropic pair potential V(r) for a three-dimensional many-particle system whose classical ground state is the low-coordinated simple cubic lattice. This result is part of an ongoing pursuit by the authors to develop analytical and computational tools to solve statistical-mechanical inverse problems for the purpose of achieving targeted self-assembly. The purpose of these methods is to design interparticle interactions that cause self-assembly of technologically important target structures for applications in photonics, catalysis, separation, sensors, and electronics. We also show that standard approximate integral-equation theories of the liquid state that utilize pair correlation function information cannot be used in the reverse mode to predict the correct simple cubic potential. We report in passing optimized isotropic potentials that yield the body-centered-cubic and simple hexagonal lattices, which provide other examples of non-close-packed structures that can be assembled using isotropic pair interactions.
Determinants of TCRα-β chain pairing in generating TCR diversity (2019)

Abstract Advances in next-generation sequencing have allowed insights into the enormous diversity of the human T cell receptor (TCR). Earlier studies have suggested that ~108 unique TRB genes exist at the periphery. In contrast, the factors that determine the pairing of TCRα and TCRβ chains have remained elusive due to the lack of high-throughput single-cell sequencing technology. We have developed a high-throughput single-cell sequencing technology that enables identification of &amp;gt;3×104 paired TRA:TRB sequences per sample and have conducted sequencing of naïve and memory CD4+ and of total T cells from 15 healthy individuals, including six pairs of monozygotic twins. We found that the frequencies of TRAV:TRBV pairing are essentially determined by the frequencies of the individual gene segments, suggesting the absence of structural constraints in the pairing of the α and β chains. Twins are more similar in the frequencies of TRAV and TRBV combinations than are unrelated individuals, but this difference was explained by a genetic influence on AV and BV gene segment frequencies. Twins and unrelated individuals were compared for the sharing of identical TCR sequences. TRA sequence sharing among twins was comparable to that among unrelated individuals, but TRB sharing was significantly higher in twins. Sharing of the entire TCR was regularly found in twins but not detected for naïve CD4+ T cells from unrelated individuals. Results were similar for naïve and memory T cells, with the genetic influence more prominent in memory T cells, suggesting the additional influence of peripheral selection. In support of this interpretation, the sharing of identical TCR sequences in unrelated individuals correlated with the number of shared MHC class II alleles.
Fermented Oyster (Crassostrea gigas) Extract Cures and Prevents Prednisolone-Induced Bone Resorption by Activating Osteoblast Differentiation (2022)

Osteoporosis is a bone resorptive disease characterized by the loss of bone density, causing an increase in bone fragility. In our previous study, we demonstrated that gamma aminobutyric acid-enriched fermented oyster (<i>Crassostrea gigas</i>) extract (FO) stimulated osteogenesis in MC3T3-E1 preosteoblast cells and vertebral formation in zebrafish. However, the efficacy of FO in prednisolone (PDS)-induced bone resorption remains unclear. In this study, we evaluated the osteogenic potential of FO in MC3T3-E1 preosteoblast cells and zebrafish larvae under both PDS-pretreated and PDS-post-treated conditions. We found that FO recovered osteogenic activity by upregulating osteoblast markers, such as alkaline phosphatase (<i>ALP</i>), runt-related transcription factor 2, and osterix, in both PDS-pretreated and post-treated MC3T3-E1 osteoblast cells and zebrafish larvae. In both conditions, PDS-induced decrease in calcification and <i>ALP</i> activity was recovered in the presence of FO. Furthermore, vertebral resorption in zebrafish larvae induced by pretreatment and post-treatment with PDS was restored by treatment with FO, along with the recovery of osteogenic markers and downregulation of osteoclastogenic markers. Finally, whether FO disturbs the endocrine system was confirmed according to the Organization for Economic Cooperation and Development guideline 455. We found that FO did not stimulate estrogen response element-luciferase activity or proliferation in MCF7 cells. Additionally, in ovariectomized mice, no change in uterine weight was observed during FO feeding. These results indicate that FO effectively prevents and treats PDS-induced osteoporosis without endocrine disturbances.
A 660 MHz self-resetting 8 port, 32×64 bits register file and latch in 0.25 μm SOI technology (2002)

Design issues associated with dynamic circuits such as collisions, pulse widening, and noise margins are anticipated to be very sensitive to SOI process and device conditions. Multi-port dynamic register files and latches are important elements in current microprocessors. We designed such a register file and latch for bulk silicon technology, but it can be fabricated in SOI technology without any body contacts. The register file and latch function at frequencies higher than 660 MHz. The salient features are low voltage operability, fully collision-free operation and minimum noise. A robust design is demonstrated with respect to input pulse width variation and skew margins. Charge sharing noise and noise due to leakage coupling and power supply variations are controlled using half latches on the dynamic nodes and by properly optimizing circuits and layouts.
Banyan‐Based Switches (2006)

This chapter contains sections titled: Banyan Networks Batcher-Sorting Network Output Contention Resolution Algorithms The Sunshine Switch Deflection Routing Multicast Copy Networks