gebhart/patrepeval huggingface dataset:
Extracellular Vesicles Fractionated in Drying Droplet (2019)

We propose a new chromatograph using “coffee-ring effect” and Marangoni recirculation flow in microdroplets to separate extracellular vesicles spatially based on particle size. In this study, EVs were isolated spatially based on particle size in the evaporating droplet. We then find that the size of EVs is correlated with expression levels of certain tetraspanin proteins and confirmed that the possibility of this method can be used for diagnosis. Using this method, we reveal that the level of tetraspanin protein expression depends on the size of the EVs and we find that in the plasma of prostate cancer patients smaller EVs show higher expression of cancer-associated proteins and gene.
Synthesis and Preliminary Studies of a Novel Negative Allosteric Modulator, 7-((2,5-Dioxopyrrolidin-1-yl)methyl)-4-(2-fluoro-4-[11C]methoxyphenyl) quinoline-2-carboxamide, for Imaging of Metabotropic Glutamate Receptor 2 (2017)

Metabotropic glutamate 2 receptors (mGlu<sub>2</sub>) are involved in the pathogenesis of several CNS disorders and neurodegenerative diseases. Pharmacological modulation of this target represents a potential disease-modifying approach for the treatment of substance abuse, depression, schizophrenia, and dementias. While quantification of mGlu<sub>2</sub> receptors in the living brain by positron emission tomography (PET) would help us better understand signaling pathways relevant to these conditions, few successful examples have been demonstrated to image mGlu<sub>2</sub> in vivo, and a suitable PET tracer is yet to be identified. Herein we report the design and synthesis of a radiolabeled negative allosteric modulator (NAM) for mGlu<sub>2</sub> PET tracer development based on a quinoline 2-carboxamide scaffold. The most promising candidate, 7-((2,5-dioxopyrrolidin-1-yl)methyl)-4-(2-fluoro-4-[<sup>11</sup>C]methoxyphenyl) quinoline-2-carboxamide ([<sup>11</sup>C]QCA) was prepared in 13% radiochemical yield (non-decay-corrected at the end of synthesis) with >99% radiochemical purity and >74 GBq/μmol (2 Ci/μmol) specific activity. While the tracer showed limited brain uptake (0.3 SUV), probably attributable to effects on PgP/Bcrp efflux pump, in vitro autoradiography studies demonstrated heterogeneous brain distribution and specific binding. Thus, [<sup>11</sup>C]QCA is a chemical probe that provides the basis for the development of a new generation mGlu<sub>2</sub> PET tracers.
ELLIPTICITY OF LARGE SPOTS IN CMB ANISOTROPY MAPS (2005)

We have measured the ellipticity of several degree scale anisotropies in the BOOMERanG maps of the Cosmic Microwave Background (CMB) at 150 GHz. The average ellipticity is around 2.6–2.7. The biases of the estimator of the ellipticity and for the noise are small in this case. Large spot elongation had been detected also for COBE-DMR and WMAP maps. If this effect is due to geodesic mixing, it would indicate a non-precisely zero curvature of the Universe which is among the discussed reasons of the WMAP low multipole anomaly.
The Natural Progression of Synovial Fluid White Blood-Cell Counts and the Percentage of Polymorphonuclear Cells After Primary Total Knee Arthroplasty (2013)

The synovial fluid WBC count and PMN percentage changed at different rates over the first two years after total knee arthroplasty, with the WBC count exhibiting an initially more rapid decrease and the PMN percentage demonstrating a more linear decrease. Hence, the total neutrophil count, which combines these two parameters, may provide a better method to identify patients with a periprosthetic joint infection. Values for the synovial fluid WBC count, PMN percentage, and total neutrophil count were all significantly elevated in the early postoperative period, and the use of standard cutoff values for the diagnosis of periprosthetic joint infection can lead to false-positive results.
Real-time objects on the bare metal: an efficient hardware realization of the Java/sup TM/ Virtual Machine (2002)

Combining the design-time efficiency of object oriented development with the runtime efficiency of direct hardware support for object oriented execution, aJile Systems has developed a low-power hardware implementation of the Java Virtual Machine for real time and embedded applications. AJile's hardware provides direct support for the entire JVM instruction set and thread model, obviating the need for a Java interpreter or Just-in-Time (JIT) compiler, as well as the traditional Real-Time Operating System (RTOS). AJile's hardware technology also supports multiple JVM contexts executing on the same CPU, enhancing safety and security by guaranteeing space and time allotments for multiple Java applications. Combined with a Java 2 Micro Edition (J2ME) runtime and a back-end target build tool, these technologies constitute an efficient platform for the development of real time embedded applications entirely in Java.
Generation and Partial Characterization of Rabbit Monoclonal Antibody to Pyroglutamate Amyloid-β3-42 (pE3-Aβ) (2018)

N-terminally truncated pyroglutamate amyloid-β (Aβ) peptide starting at position 3 represents a significant fraction of Aβ peptides (pE3-Aβ) in amyloid plaques of postmortem brains from patients with Alzheimer's disease (AD) and older persons with Down syndrome (DS). Studies in transgenic mouse models of AD also showed that pE3-Aβ is a major component of plaques, and mouse monoclonal antibody to pE3-Aβ appears to be a desirable therapeutic agent for AD. Since small peptides do not typically elicit a good immune response in mice, but do so favorably in rabbits, our aims were to generate and partially characterize a rabbit monoclonal antibody (RabmAb) to pE3-Aβ. The generated RabmAb was found to be specific for pE3-Aβ, since it showed no reactivity with Aβ16, Aβ40, Aβ42, Aβ3-11, and pE11-17 Aβ peptides in an enzyme linked immunosorbent assay (ELISA). The isotype of the antibody was found to be IgG class. The antibody possesses high affinity to pE3-Aβ with dissociation constant (KD) for the antibody of 1 nM. The epitope of the antibody lies within the sequence of pE3-FRHD. In dot blotting, the optimal detection of pE3-Aβ was at an antibody concentration of 0.5 μg/ml. The threshold of pE3-Aβ detection was 2 fmol. The antibody was sensitive enough to detect 10 pg/ml of pE3-Aβ in sandwich ELISA. pE3-Aβ was detected in AD and DS brain extracts in ELISA and immunoblotting. Immunohistological studies showed immunolabeling of plaques and blood vessels in brains from patients with AD, and DS showing AD pathology. Thus, the antibody can be widely applied in AD and DS research, and therapeutic applications.
Stability and function of adult vasculature is sustained by Akt/Jagged1 signalling axis in endothelium (2016)

The signalling pathways operational in quiescent, post-development vasculature remain enigmatic. Here we show that unlike neovascularization, endothelial Akt signalling in established vasculature is crucial not for endothelial cell (EC) survival, but for sustained interactions with pericytes and vascular smooth muscle cells (VSMCs) regulating vascular stability and function. Inducible endothelial-specific Akt1 deletion in adult global Akt2KO mice triggers progressive VSMC apoptosis. In hearts, this causes a loss of arteries and arterioles and, despite a high capillary density, diminished vascular patency and severe cardiac dysfunction. Similarly, endothelial Akt deletion induces retinal VSMC loss and basement membrane deterioration resulting in vascular regression and retinal atrophy. Mechanistically, the Akt/mTOR axis controls endothelial Jagged1 expression and, thereby, Notch signalling regulating VSMC maintenance. Jagged1 peptide treatment of Akt1ΔEC;Akt2KO mice and Jagged1 re-expression in Akt-deficient endothelium restores VSMC coverage. Thus, sustained endothelial Akt1/2 signalling is critical in maintaining vascular stability and homeostasis, thereby preserving tissue and organ function.
In Vivo Confocal Fluorescence Imaging of the Intratumor Distribution of the Photosensitizer Mono-l-Aspartylchlorin-e6 (2008)

We present an in vivo fluorescence microscopic evaluation of intratumor distribution of the photosensitizer mono-L-aspartylchlorin-e6 (NPe6) in an intradermal mouse EMT6 tumor model. Although the identification of favorable photophysical and pharmacological properties has led to the development of new photosensitizers in photodynamic therapy, their intratumor distribution kinetics have remained relatively understudied. In this study, we used confocal fluorescence microscopy to follow the transport of NPe6 in vivo after systemic administration through the tail vein. Labeling of vasculature using fluorophore-conjugated anti-CD31 antibodies allows visualization of the uptake of NPe6 in tumor and normal vessels and its partitioning kinetics into the adjacent parenchyma for 3 hours after injection. During the initial 60 minutes after injection, the drug is predominantly confined to the vasculature. Subsequently, it significantly redistributes throughout the extravascular regions with no discernable difference in its extravasation rate between tumor and normal tissues. Further, we investigate the sensitizer's altered intratumor distribution in response to photodynamic therapy irradiation and observe that treatment-induced changes in vessel permeability caused enhanced accumulation of NPe6 in the extravascular space. Our findings are of immediate clinical relevance and demonstrate the importance of an in vivo imaging approach to examine the dynamic process of intratumor drug distribution.
Zebrafish Heme Oxygenase 1a Is Necessary for Normal Development and Macrophage Migration (2022)

Heme oxygenase function is highly conserved between vertebrates where it plays important roles in normal embryonic development and controls oxidative stress. Expression of the zebrafish heme oxygenase 1 genes is known to be responsive to oxidative stress suggesting a conserved physiological function. In this study, we generate a knockout allele of zebrafish <i>hmox1a</i> and characterize the effects of <i>hmox1a</i> and <i>hmox1b</i> loss on embryonic development. We find that loss of <i>hmox1a</i> or <i>hmox1b</i> causes developmental defects in only a minority of embryos, in contrast to <i>Hmox1</i> gene deletions in mice that cause loss of most embryos. Using a tail wound inflammation assay we find a conserved role for <i>hmox1a</i>, but not <i>hmox1b</i>, in normal macrophage migration to the wound site. Together our results indicate that zebrafish <i>hmox1a</i> has clearly a partitioned role from <i>hmox1b</i> that is more consistent with conserved functions of mammalian Heme oxygenase 1.
Discs large (Dlg1) complexes in lymphocyte activation (2004)

T cell antigen recognition involves the formation of a structured interface between antigen-presenting and T cells that facilitates the specific transmission of activating and desensitizing stimuli. The molecular machinery that organizes the signaling molecules and controls their disposition in response to activation remains poorly understood. We show here that in T cells Discs large (Dlg1), a PDZ domain-containing protein, is recruited upon activation to cortical actin and forms complexes with early participants in T cell activation. Transient overexpression of Dlg1 attenuates basal and Vav1-induced NFAT reporter activation. Reduction of Dlg1 expression by RNA interference enhances both CD3- and superantigen-mediated NFAT activation. Attenuation of antigen receptor signaling appears to be a complex, highly orchestrated event that involves the mutual segregation of important elements of the early signaling complex.
Two novel disaccharides, rutinose and methylrutinose, are involved in carbon metabolism in Datisca glomerata (2009)

Datisca glomerata forms nitrogen-fixing root nodules in symbiosis with soil actinomycetes from the genus Frankia. Analysis of sugars in roots, nodules and leaves of D. glomerata revealed the presence of two novel compounds that were identified as alpha-L-rhamnopyranoside-(1 --> 6)-D-glucose (rutinose) and alpha-L-rhamnopyranoside-(1 --> 6)-1-O-beta-D-methylglucose (methylrutinose). Rutinose has been found previously as a/the glycoside part of several flavonoid glycosides, e.g. rutin, also of datiscin, the main flavonoid of Datisca cannabina, but had not been reported as free sugar. Time course analyses suggest that both rutinose and methylrutinose might play a role in transient carbon storage in sink organs and, to a lesser extent, in source leaves. Their concentrations show that they can accumulate in the vacuole. Rutinose, but not methylrutinose, was accepted as a substrate by the tonoplast disaccharide transporter SUT4 from Arabidopsis. In vivo (14)C-labeling and the study of uptake of exogenous sucrose and rutinose from the leaf apoplast showed that neither rutinose nor methylrutinose appreciably participate in phloem translocation of carbon from source to sink organs, despite rutinose being found in the apoplast at significant levels. A model for sugar metabolism in D. glomerata is presented.
LTCC balanced filter based on a transformer type balun for WLAN 802.11 a application (2007)

This paper reports on the design of a balanced filter based on a new transformer type balun. The disadvantages and performance drawbacks of simple second order transformer are discussed and new third order balun structure is proposed. The new structure is realized as broadside coupled lines vertically stacked using multilayer low temperature co-fired ceramic (LTCC) technology. The resulting structure exhibits excellent electrical performance, immunity to manufacturing tolerances and compactness, which allows using this balanced filter as a building block of highly integrated WLAN front-end modules.
The Influence of Tungsten (W) on Properties in High Nitrogen Stainless Steels (1999)

Superaustenitic stainless steels with about 6% molybdenum (Mo) have now been used successfully for over twenty years because of their high corrosion resistance. Requirements for even better performance have resulted in more highly alloyed superaustenitic steels, also with high nitrogen (N) levels. Substituting W for Mo in stainless steels has been claimed to have both negative and positive effects. To investigate these effects, especially on corrosion resistance in high Mo superaustenitic stainless steels, a series of eight experimental steels was produced. The heats were designed to investigate the effects of substitution of W for Mo in a base alloy containing 24% chromium (Cr), 22% nickel (Ni) and 0.5% nitrogen (N). To achieve this Mo and W were varied between 5 to 7% and 0 to 5% respectively. The microstructures and resistance to localised corrosion were investigated for solution annealed and sensitised samples. Addition of W improved the resistance towards localised corrosion in a similar way as Mo. However, the structural stability was decreased on replacing Mo by W. This negative effect was observed in the whole temperature range studied and had also a negative influence on the crevice corrosion resistance.
Brentuximab vedotin-containing escalated BEACOPP variants for newly diagnosed advanced-stage classical Hodgkin lymphoma: follow-up analysis of a randomized phase II study from the German Hodgkin Study Group (2021)

Patients with advanced-stage Hodgkin lymphoma (HL) receiving intensive treatment with escalated BEACOPP (bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine, prednisone) (eBEACOPP) have excellent outcomes However, late effects such as second primary malignancies (SPM) and infertility represent ongoing concerns Novel approaches using an eBEACOPP backbone, therefore, aim at reducing toxicity without compromising efficacy. The BrECAPP (brentuximab vedotin, etoposide, cyclophosphamide, doxorubicin, procarbazine, prednisone) and BrECADD (brentuximab vedotin, etoposide, cyclophosphamide, doxorubicin, dacarbazine, dexamethasone) protocols were investigated in a randomized phase II study including patients with newly diagnosed advanced-stage classical HL (cHL). Both regimens combine eBEACOPP-based chemotherapy with the CD30-directed antibody-drug conjugate brentuximab vedotin (BV). Response rates were similar to standard eBEACOPP and especially the BrECADD protocol was associated with reduced acute toxicity
On the Relation Between Assessor's Agreement and Accuracy in Gamified Relevance Assessment (2015)

Expert judgments (labels) are widely used in Information Retrieval for the purposes of search quality evaluation and machine learning. Setting up the process of collecting such judgments is a challenge of its own, and the maintenance of judgments quality is an extremely important part of the process. One of the possible ways of controlling the quality is monitoring inter-assessor agreement level. But does the agreement level really reflect the quality of assessor's judgments? Indeed, if a group of assessors comes to a consensus, to what extent should we trust their collective opinion? In this paper, we investigate, whether the agreement level can be used as a metric for estimating the quality of assessor's judgments, and provide recommendations for the design of judgments collection workflow. Namely, we estimate the correlation between assessors' accuracy and agreement in the scope of several workflow designs and investigate which specific workflow features influence the accuracy of judgments the most.
Structural apelin analogues: mitochondrial ROS inhibition and cardiometabolic protection in myocardial ischaemia reperfusion injury (2014)

These data provide the evidence for the potential of the structural apelin analogues in selective reduction of mitochondrial ROS generation and myocardial apoptosis and form the basis for a promising therapeutic strategy in the treatment of oxidative stress-related heart disease.
Mammalian Type I Gonadotropin-Releasing Hormone Receptors Undergo Slow, Constitutive, Agonist-Independent Internalization (2007)

Regulatory elements present in the cytoplasmic carboxyl-terminal tails of G protein-coupled receptors contribute to agonist-dependent receptor desensitization, internalization, and association with accessory proteins such as beta-arrestin. The mammalian type I GnRH receptors are unique among the rhodopsin-like G protein-coupled receptors because they lack a cytoplasmic carboxyl-terminal tail. In addition, they do not recruit beta-arrestin, nor do they undergo rapid desensitization. By measuring the internalization of labeled GnRH agonists, previous studies have reported that mammalian type I GnRH receptors undergo slow agonist-dependent internalization. In the present study, we have measured the internalization of epitope-tagged GnRH receptors, both in the absence and presence of GnRH stimulation. We demonstrate that mammalian type I GnRH receptors exhibit a low level of constitutive agonist-independent internalization. Stimulation with GnRH agonist did not significantly enhance the level of receptor internalization above the constitutive level. In contrast, the catfish GnRH and rat TRH receptors, which have cytoplasmic carboxyl-terminal tails, displayed similar levels of constitutive agonist-independent internalization but underwent robust agonist-dependent internalization, as did chimeras of the mammalian type I GnRH receptor with the cytoplasmic carboxyl-terminal tails of the catfish GnRH receptor or the rat TRH receptor. When the carboxyl-terminal Tyr325 and Leu328 residues of the mammalian type I GnRH receptor were replaced with alanines, these two mutant receptors underwent significantly impaired internalization, suggesting a function for the Tyr-X-X-Leu sequence in mediating the constitutive agonist-independent internalization of mammalian type I GnRH receptors. These findings provide further support for the underlying notion that the absence of the cytoplasmic carboxyl-terminal tail of the mammalian type I GnRH receptors has been selected for during evolution to prevent rapid receptor desensitization and internalization to allow protracted GnRH signaling in mammals.
Controlling Cherenkov Angles with Resonance Transition Radiation (2018)

We propose a new mechanism using the constructive interference of resonance transition radiation from photonic crystals to generate Cherenkov radiation into controllable Cherenkov angles with high sensitivity to any desired range of velocities.
Intramolecular Photoaddition of Vinylogous Amides with Allenes:  A Novel Approach to the Synthesis of Pyrroles (2006)

Irradiation of vinylogous amide or imide 5 (R = H, alkyl, or Ac) leads to the selective formation of either crossed photoadduct 7 (R = Ac) or parallel photoadduct 8 (R = H or alkyl) as a function of the nature of the group R. The latter result leads to a novel approach to the synthesis of pyrroles, that is, 8'.
Metal-Coordinated Hydrogels As Efficient Oxygen Evolution Electrocatalysts (2022)

Conductive polymer hydrogels have large surface area and high conductivity. Their properties can easily be tailored further by functionalizing them with metals and nonmetals. However, the potential of metal-conjugated hydrogels for electrocatalysis has rarely been investigated. In this work, we report the synthesis of transition metals-conjugated polyaniline-phytic acid (PANI-PA) hydrogels that show efficient electrocatalytic properties for the oxygen evolution reaction (OER). Among many transition metals studied, Fe is accommodated by the hydrogel the most because of the favorable affinity of the PA groups in the hydrogel for Fe. Meanwhile, those containing both Fe and Co are found to be the most effective for electrocatalysis of OER. The most optimized such hydrogel, NF@Hgel-Fe 0.3 Co 0.1 , which has 3:1 ratio of Fe and Co, needs an overpotential of only 280 mV to catalyze OER with a current density of 10 mV cm -2 in 1 M KOH solution. Furthermore, these metal-doped PANI-PA hydrogels can easily be loaded on nickel foam and carbon cloth via a simple soak-and-dry method to form free-standing electrodes. Overall, the work demonstrates a facile synthesis and fabrication of sustainable OER electrocatalysts and electrodes that are composed of easily processable hydrogels conjugated with various earth-abundant transition metals. Figure R. Schematic illustration of the synthesis of PA-PANI-Metal (Hgel-M x ) hydrogels for electrocatalysis of OER. Figure 1
A Summary of the Special Issue “Emerging Network-on-Chip Architectures for Low Power Embedded Systems” (2017)

The International Technology Roadmap for Semiconductors [1] foresees that the number of processing elements that will be integrated into a system-on-chip will be on the order of thousands by 2020.[...]
Rational design of stealthy hyperuniform two-phase media with tunable order (2018)

Disordered stealthy hyperuniform materials are exotic amorphous states of matter that have attracted recent attention because of their novel structural characteristics (hidden order at large length scales) and physical properties, including desirable photonic and transport properties. It is therefore useful to devise algorithms that enable one to design a wide class of such amorphous configurations at will. In this paper, we present several algorithms enabling the systematic identification and generation of discrete (digitized) stealthy hyperuniform patterns with a tunable degree of order, paving the way towards the rational design of disordered materials endowed with novel thermodynamic and physical properties. To quantify the degree of order or disorder of the stealthy systems, we utilize the discrete version of the τ order metric, which accounts for the underlying spatial correlations that exist across all relevant length scales in a given digitized two-phase (or, equivalently, a two-spin state) system of interest. Our results impinge on a myriad of fields, ranging from physics, materials science and engineering, visual perception, and information theory to modern data science.