gebhart/patrepeval huggingface dataset:
Phthalimide neovascular factor 1 (PNF1) modulates MT1‐MMP activity in human microvascular endothelial cells (2009)

We are creating synthetic pharmaceuticals with angiogenic activity and potential to promote vascular invasion. We previously demonstrated that one of these molecules, phthalimide neovascular factor 1 (PNF1), significantly expands microvascular networks in vivo following sustained release from poly(lactic-co-glycolic acid) (PLAGA) films. In addition, to probe PNF1 mode of action, we recently applied a novel pathway-based compendium analysis to a multi-timepoint, controlled microarray data set of PNF1-treated (vs. control) human microvascular endothelial cells (HMVECs), and we identified induction of tumor necrosis factor-alpha (TNF-alpha) and, subsequently, transforming growth factor-beta (TGF-beta) signaling networks by PNF1. Here we validate this microarray data set with quantitative real-time polymerase chain reaction (RT-PCR) analysis. Subsequently, we probe this data set and identify three specific TGF-beta-induced genes with regulation by PNF1 conserved over multiple timepoints-amyloid beta (A4) precursor protein (APP), early growth response 1 (EGR-1), and matrix metalloproteinase 14 (MMP14 or MT1-MMP)-that are also implicated in angiogenesis. We further focus on MMP14 given its unique role in angiogenesis, and we validate MT1-MMP modulation by PNF1 with an in vitro fluorescence assay that demonstrates the direct effects that PNF1 exerts on functional metalloproteinase activity. We also utilize endothelial cord formation in collagen gels to show that PNF1-induced stimulation of endothelial cord network formation in vitro is in some way MT1-MMP-dependent. Ultimately, this new network analysis of our transcriptional footprint characterizing PNF1 activity 1-48 h post-supplementation in HMVECs coupled with corresponding validating experiments suggests a key set of a few specific targets that are involved in PNF1 mode of action and important for successful promotion of the neovascularization that we have observed by the drug in vivo.
TEM Observation of Precipitates in Ag‐Added Al‐Mg‐Si Alloys (2012)

This chapter contains sections titled: Introduction Experimental procedure Results and discussions Conclusions Acknowledgement
Public Policy Instrumentation in the EU (2008)

Over the years, and in order to bypass the limits associated to the characteristics of the EU (budget limitations for instance), the Commission has put forward new modes of governance. In part, the EU’s legitimacy discourse relies upon systematic innovation around new modes of governance promoted by the newly enlarged EU for the new millennium (...).
Comparison of free breathing and respiratory triggered diffusion-weighted imaging sequences for liver imaging (2019)

Compared to FB-DWI, both PACE-DWI and SMS-DWI provide better image quality and decreased quantitative variability in the measurement of ADC values of liver lesions.
Benefit of Computed Tomography Enterography in Crohnʼs Disease: Effects on Patient Management and Physician Level of Confidence§† (2011)

CTE is a clinically useful examination, altering management plans in nearly half of patients with CD, while increasing physician LOC for the detection of small bowel inflammation and penetrating disease. These findings further support the use of CTE in CD management algorithms.
Direct detection based optical transceiver for 100 Gb/s systems (2012)

Modulation format plays a critical role for 100G transmission, and there have been extensive works on searching suitable modulation format. We review direct detection based 100G modulation formats, and introduce a novel optical transceiver with DC-DQPSK modulation format for metro networks.
Using metal complex-labeled peptides for charge transfer-based biosensing with semiconductor quantum dots (2009)

Luminescent colloidal semiconductor quantum dots (QDs) have unique optical and photonic properties and are highly sensitive to charge transfer in their surrounding environment. In this study we used synthetic peptides as physical bridges between CdSe-ZnS core-shell QDs and some of the most common redox-active metal complexes to understand the charge transfer interactions between the metal complexes and QDs. We found that QD emission underwent quenching that was highly dependent on the choice of metal complex used. We also found that quenching traces the valence or number of metal complexes brought into close proximity of the nanocrystal surface. Monitoring of the QD absorption bleaching in the presence of the metal complex provided insight into the charge transfer mechanism. The data suggest that two distinct charge transfer mechanisms can take place. One directly to the QD core states for neutral capping ligands and a second to surface states for negatively charged capping ligands. A basic understanding of the proximity driven charge-transfer and quenching interactions allowed us to construct proteolytic enzyme sensing assemblies with the QD-peptide-metal complex conjugates.
Berichtigung: Strategic Utilization of Multifunctional Carbene for Direct Synthesis of Carboxylic—Phosphinic Mixed Anhydride from CO2 (2017)

In Schema 3dieser Zuschrift wird die Struktur von 2g' flschlicherweise als Oligomer postuliert. Eine neuerliche Untersuchung [1] belegt jedoch, dass 2g' monomer vorliegt. Diese Strukturdarstellung und der zugehrige Absatz im Text (beginnend auf S. 16310, links unten) mssen daher wie folgt korrigiert werden: "PoxIm 1g containing bis-N-phosphine oxide groups did not react with carbon dioxide under the ambient conditions, although 1g was totally consumed in toluene at 80 8 8C after 1h(Scheme 3). The quantitative formation of 2gwas confirmed when the product was dissolved in CD 3 CN at 22 8 8C; however,amixture of 2gand 2g' was given in yields of 58 and 42 %, respectively,after changing the solvent from CD 3 CN to C 6 D 6 .Replacement of the solvent from C 6 D 6 to CD 3 CN again afforded 2gas the sole product in > 99 %yield. Treatment of amixture of 2g and 2g' in C 6 D 6 with B(C 6 F 5 ) 3 (1.0 equiv) resulted in the quantitative formation of 2gB(C 6 F 5 ) 3 as the sole product (Scheme 3)."
ShapeMask: Learning to Segment Novel Objects by Refining Shape Priors (2019)

Instance segmentation aims to detect and segment individual objects in a scene. Most existing methods rely on precise mask annotations of every category. However, it is difficult and costly to segment objects in novel categories because a large number of mask annotations is required. We introduce ShapeMask, which learns the intermediate concept of object shape to address the problem of generalization in instance segmentation to novel categories. ShapeMask starts with a bounding box detection and gradually refines it by first estimating the shape of the detected object through a collection of shape priors. Next, ShapeMask refines the coarse shape into an instance level mask by learning instance embeddings. The shape priors provide a strong cue for object-like prediction, and the instance embeddings model the instance specific appearance information. ShapeMask significantly outperforms the state-of-the-art by 6.4 and 3.8 AP when learning across categories, and obtains competitive performance in the fully supervised setting. It is also robust to inaccurate detections, decreased model capacity, and small training data. Moreover, it runs efficiently with 150ms inference time and trains within 11 hours on TPUs. With a larger backbone model, ShapeMask increases the gap with state-of-the-art to 9.4 and 6.2 AP across categories. Code will be released.
Blood oxygen level-dependent magnetic resonance imaging at 3 Tesla in coronary artery disease: validation using quantitative coronary angiography and cardiovascular magnetic resonance perfusion imaging (2010)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
Thromboembolic events associated with lenalidomide. A review after the EMA alert (2012)

<h3>Background</h3> Lenalidomide is an immunomodulator agent authorised in 2007 by EMA for treatment of multiple myeloma (MM), also used as off-label treatment for myelodysplastic syndrome (MS). In December 2010 EMA communicated the association between lenalidomide and an increased risk of arterial and venous thromboembolic events (AVTEs), recommending the administration of antithrombotic prophylaxis (AP) and to avoid erythropoietic agents, especially when other risk factors (RFs) were present. <h3>Purpose</h3> To assess the incidence of AVTEs and the presence of RFs in patients treated with lenalidomide. To assess treatments with lenalidomide in relation to the EMA9s warning. <h3>Materials and methods</h3> Observational retrospective study involving the treatments with lenalidomide started between May 2008 and September 2010 in a regional hospital. <h3>Results</h3> Sixteen patients required lenalidomide, 14 with MM and 2 with MS. Male/female ratio was 8/8, with a median age of 68.3 years (CI 95% 63.1 to 73.4). The average number of cycles administered per patient was six (2–21). The most frequent RFs were: administration of erythropoietic factors (93.8%), tobacco smoking (75.0%) and prior thrombosis (68.8%). More than 85% of patients had at least two RF. The mean value of maximum haemoglobin levels (Hb) was 12.5 g/dl (CI 95% 11.0 to 14.0). 81.3% of patients received AP with low molecular weight heparins (LMWH) or oral anticoagulants. In this period, three AVTEs occurred (during the second, third and seventh cycle, respectively). These cases presented between three and four RFs but none had Hb&gt;13 g/dl. One of these patients had not previously received AP and the treatment with LMWH was started after the AVTE. Treatment with erythropoietic factors was not discontinued in any case. Lenalidomide treatment was spaced out in one case and stopped in another one. <h3>Conclusions</h3> All the patients presented thromboembolism risk factors and most received antithrombotic prophylaxis. The relation between the number of risk factors and thromboembolism events was not found, probably due to the limited size of the population.
In situ Parallel Training of Analog Neural Network Using Electrochemical Random-Access Memory (2021)

In-memory computing based on non-volatile resistive memory can significantly improve the energy efficiency of artificial neural networks. However, accurate <i>in situ</i> training has been challenging due to the nonlinear and stochastic switching of the resistive memory elements. One promising analog memory is the electrochemical random-access memory (ECRAM), also known as the redox transistor. Its low write currents and linear switching properties across hundreds of analog states enable accurate and massively parallel updates of a full crossbar array, which yield rapid and energy-efficient training. While simulations predict that ECRAM based neural networks achieve high training accuracy at significantly higher energy efficiency than digital implementations, these predictions have not been experimentally achieved. In this work, we train a 3 × 3 array of ECRAM devices that learns to discriminate several elementary logic gates (AND, OR, NAND). We record the evolution of the network's synaptic weights during parallel <i>in situ</i> (on-line) training, with outer product updates. Due to linear and reproducible device switching characteristics, our crossbar simulations not only accurately simulate the epochs to convergence, but also quantitatively capture the evolution of weights in individual devices. The implementation of the first <i>in situ</i> parallel training together with strong agreement with simulation results provides a significant advance toward developing ECRAM into larger crossbar arrays for artificial neural network accelerators, which could enable orders of magnitude improvements in energy efficiency of deep neural networks.
Dose Reconstruction from PET Images in Carbon Ion Therapy: A Deconvolution Approach Using an Evolutionary Algorithm (2017)

Dose monitoring and range verification are important tools in carbon ion therapy. For their implementation, positron emission tomography (PET) can be used to image the β <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -activation of tissue during treatment. Predictions of these β <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -activity distributions are usually obtained from Monte Carlo simulations, which demands high computational time and thus limits the applicability of this technique in clinical scenario. Nevertheless, it is desirable to explore faster approaches able to give such a prediction, since only its comparison with the measured distributions allows a definite assessment of potential range deviations from the planned treatment. For the first time, we present an approach to perform deconvolution from PET data in carbon ion therapy and reconstruct the dose. A filtering method is used to predict positron emitter profiles from dose profiles in short time. In order to reverse the convolution and estimate a dose distribution from a positron emitter distribution, we apply an evolutionary algorithm. Filters are obtained from either a library or are created in advance for a specific problem, assuming that a prediction of the positron emitter distribution is available. To perform the latter method and find the best filter for a specific problem, we use another evolutionary algorithm, hence optimizing the filter on-the-fly for the given treatment scheme. The application of our method is shown for dose and positron emitter distributions in homogeneous phantoms using simulated and newly measured online PET data. Carbon ion ranges can be predicted within 2 mm and the shape of the dose distribution is reconstructed with an overall promising agreement.
Reports of the AAAI 2010 Fall Symposia (2011)

The Association for the Advancement of Artificial Intelligence was pleased to present the 2010 Fall Symposium Series, held Thursday through Saturday, November 11–13, at the Westin Arlington Gateway in Arlington, Virginia. The titles of the eight symposia are as follows: (1) Cognitive and Metacognitive Educational Systems; (2) Commonsense Knowledge; (3) Complex Adaptive Systems: Resilience, Robustness, and Evolvability; (4) Computational Models of Narrative; (5) Dialog with Robots; (6) Manifold Learning and Its Applications; (7) Proactive Assistant Agents; and (8) Quantum Informatics for Cognitive, Social, and Semantic Processes. The highlights of each symposium are presented in this report.
Pyrococcus furiosus Prolyl Oligopeptidase: A Dynamic Supramolecular Host for Peptidase and Dirhodium Catalysis (2018)

Supramolecular catalysis involves the design and characterization of synthetic macromolecules that catalyze chemical reactions. While enzymes are often cited as the inspiration for such catalysts, enzymes can also serve as hosts for non-native catalytic components. Protein-based hosts can be readily produced in E. coli and rapidly evolved for particular applications. Moreover, inherent properties of these systems, including their conformational dynamics, can be exploited for non-native transformations that occur within their interior. Studies on the peptidase activity of a prolyl oligopeptidase from Pyrococcus furiosus (Pfu POP) suggest that its unique two-domain architecture regulates substrate access and specificity. We have established that Pfu POP also serves as an efficient host for asymmetric cyclopropanation upon active-site modification with a dirhodium cofactor. To understand how Pfu POP controls both peptidase and dirhodium catalysis, we determined the crystal structures of this enzyme and its S477C mutant and used these structures as starting points for MD simulations of both the apo structures and systems containing a covalently linked peptidase inhibitor or a dirhodium catalyst. Pfu POP was crystalized in an open conformation, and MD simulations reveal spontaneous transitions between open and closed states, in addition to a number of smaller scale conformational changes, suggesting facile inter-domain movement. Importantly, key aspects of previously reported peptidase kinetics and cyclopropanation selectivity can be rationalized in the context of this inter-domain opening and closing. This finding constitutes a remarkable example in which the conformational dynamics of a supramolecular host affect two different catalytic activities and suggests that Pfu POP could serve as a host for a wide range of non-native catalysts.
Magnetic and structural properties of high rate dual ion-beam sputtered NiFe films (invited) (1987)

NiFe films in the thickness range of 300 Å to 8 μm with excellent magnetic properties and thickness uniformity have been prepared using a newly developed high rate (up to 1000 Å/min) dual ion beam sputtering system. Deposition conditions such as the ion assist voltage, the target orientation and the partial pressure of nitrogen have been optimized to reduce coercivity Hc and stress as well as to improve film adhesion and film thermal stability. The annealing effects on Hc, the anisotropy field Hk, as well as the resistivity of the NiFe films were studied. X-ray diffraction and transmission electron microscopy techniques were used to characterize the microstructures of the films and were correlated with their magnetic properties. These ion-beam sputtered NiFe films have excellent magnetic, electrical, mechanical, and microstructural properties to make them suitable for thin-film head applications.
Distributed Routing Algorithms for Wireless Multihop Networks (2007)

We introduce distributed algorithms to find rate-optimal routes based on local knowledge of the pairwise error probability (reliability) matrix. The distributed algorithms are built by (re)-formulating optimization problems amenable to application of dual decomposition techniques. Convergence of our algorithms to the optimal routing matrix is guaranteed under mild conditions. Many rate-optimality criteria of practical interest can be casted in our framework including maximization of: i)worst user's rate; ii) weighted sum of rates; iii) product of rates; and iv) relay network rate. We test robustness of our algorithms to node mobility.
Increased antigen presenting cell‐mediated T cell activation in mice and patients without the autoimmune regulator (2006)

Patients with autoimmune polyendocrine syndrome type I (APS I)suffer from endocrine and non-endocrine disorders due to mutations in the autoimmune regulator gene (AIRE). Mouse Aire is expressed both in thymic medullary epithelial cells and in peripheral antigen-presenting cells, suggesting a role in both central and peripheral tolerance. We here report that Aire(-/-) dendritic cells (DC) activate naive T cells more efficiently than do Aire(+/+) DC. Expression array analyses of Aire(-/-) DC revealed differential regulation of 68 transcripts, among which, the vascular cell adhesion molecule-1 (VCAM-1) transcript was up-regulated in Aire(-/-) DC. Concurrently, the expression of the VCAM-1 protein was up-regulated on both Aire(-/-) DC and monocytes from APS I patients. Blocking the interaction of VCAM-1 prevented enhanced Aire(-/-) DC stimulation of T cell hybridomas. We determined an increased number of DC in spleen and lymph nodes and of monocytes in the blood from Aire(-/-) mice, and an increased number of blood monocytes in APS I patients. Our findings imply a role for Aire in peripheral DC regulation of T cell activation, and suggest that Aire participates in peripheral tolerance.
Thermalization of electrons in decaying extreme ultraviolet photons induced low pressure argon plasma (2016)

We monitored—in the pressure range: 0.5–15 Pa—the electron temperature in decaying plasmas induced in argon gas by pulsed irradiation with extreme ultraviolet (EUV) photons with wavelengths closely around 13.5 nm. For this purpose, temporal measurements of the space-averaged and electric field weighted electron density after pulsed EUV irradiation are combined with an ambipolar diffusion model of the plasma. Results demonstrate that electrons are thermalized to room temperature before the plasma has fully expanded to the chamber walls for pressures of 3 Pa and higher. At pressures below 3 Pa, the electron temperature was found to be up to 0.1 eV above room temperature which is explained by the fact that plasma expansion is too quick for the electrons to fully thermalize. The comparison between plasma expansion duration towards a surface, plasma decay at a surface and time needed for thermalization and cooling of electrons is essential for designers of EUV lithography tools and EUV sources since the temperature of electrons dictates many fundamental physical processes.
Biosynthesis of eriodictyol from tyrosine by Corynebacterium glutamicum (2022)

The biosynthesis of the ortho-hydroxylated flavonoid eriodictyol in C. glutamicum was achieved for the first time via functional expression of E. coli hpaBC, providing a baseline strain for biosynthesis of other complex flavonoids. Our study demonstrates the potential application of C. glutamicum as a host microbe for the biosynthesis of value-added natural compounds from tyrosine.
Abstract 197: Molecular interactions of Globo H ceramide with translin-associated factor X (TRAX) underlie its proangiogenic activities (2019)

Abstract Glycosphingolipids (GSLs) are ubiquitous glycolipids in eukaryotic plasma membranes that consist of a polar glycan chain and a hydrophobic sphingosine- containing ceramide tail. Although GSLs display various diversities and functions, the mechanistic details of GSL interactions with membranous or intracellular components are poorly understood. Globo H ceramide (GHCer), a tumor-associated GSL overexpressed in most types of epithelial cancers, is a potential target of cancer immunotherapy. Previously, we showed that GHCer is shed by cancer cells to mediate immune suppression and promote angiogenesis in the tumor microenvironment. At the cellular level, GHCer from cancer cells binds to translin-associated factor (TRAX), with consequent release of PLCB1 from TRAX to trigger Ca2+ mobilization. Herein, we found that Gb5-ceramide (Gb5Cer), the pentasaccharide precursor of GHCer, could not promote angiogenesis nor Ca2+ mobilization. At the molecular level, ELISA and biacore analysis revealed that GHCer binds to TRAX with a distinct dissociation constant of 4.09×10-8 M, while its precursors, galactosyl-, lactosyl-, Gb4-, and Gb5Cer- showed negligible binding to TRAX. Molecular docking and molecular dynamics indicated that the fucose residue of Globo H is an important contributor to a favorable glycan conformation for interaction with TRAX, consistent with the finding that Gb5Cer had no proangiogenic activities. In addition, GHCer competed with recombinant C-terminus region of phospholipase C β1 (PLCB1) for binding to TRAX, thus providing a molecular mechanism for the proangiogenic effect of GHCer on tumor microenvironment. This study provides the first evidence for interaction of TRAX with a non-protein GSL, deciphered distinct regions of TRAX for interacting with glycan and lipid portions of GHCer, and illustrated the crucial contribution of fucose moiety on GHCer for its interaction with TRAX and angiogenic activity. Citation Format: John Yu, Sheng-Hung Wang, Jing-Yan Cheng, Jung-Tung Hung, Chun-Cheng Lin, Fei-Yun Lo, Chien-Wei Lee, Alice L. Yu. Molecular interactions of Globo H ceramide with translin-associated factor X (TRAX) underlie its proangiogenic activities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 197.
Protective effect ofGlycyrrhiza glabraroots extract on bone mineral density of ovariectomized rats (2019)

Glycyrrhiza glabra root extract notably protected tibial bone mineral density loss in Ovariectomy-plus-Glycyrrhiza rats in comparison with ovariectomized rats, but did not improve biomechanical strength.