gebhart/patrepeval huggingface dataset:
Parahydrogen‐induced polarization (PHIP) hyperpolarized MR receptor imaging in vivo: a pilot study of 13C imaging of atheroma in mice (2011)

MR techniques using hyperpolarized (13)C have successfully produced examples of angiography and intermediary metabolic imaging, but, to date, no receptor imaging has been attempted. The goal of this study was to synthesize and evaluate a novel hyperpolarizable molecule, 2,2,3,3-tetrafluoropropyl 1-(13)C-propionate-d(2,3,3) (TFPP), for the detection of atheromatous plaques in vivo. TFPP binds to lipid bilayers and its use in hyperpolarized MR could prove to be a major step towards receptor imaging. The precursor, 2,2,3,3-tetrafluoropropyl 1-(13)C-acrylate-d(2,3,3) (TFPA), binds to 1,2-dimyristoylphosphatidylcholine lipid bilayers with a 1.6-ppm chemical shift in the (19)F MR spectrum. This molecule was designed to be hyperpolarized through the addition of parahydrogen to the (13)C-acrylate moiety by parahydrogen-induced polarization. TFPA was hyperpolarized to TFPP to an extent similar to that of the hydroxyethylacrylate to hydroxyethylpropionate transition: 17 ± 4% for TFPP versus 20% for hydroxyethylpropionate; T(1) relaxation times (45 ± 2 s versus 55 ± 2 s) were comparable and the hyperpolarized properties of TFPP were characterized. Hydroxyethylacrylate, like TFPA, has a chemical structure with an acrylate moiety, but does not contain the lipid-binding tetrafluoropropyl functional group. Hyperpolarized TFPP binds to the lipid bilayer, appearing as a second, chemically shifted (13)C hyperpolarized MR signal with a further reduction in the longitudinal relaxation time (T(1) = 21 ± 1 s). In aortas harvested from low-density lipoprotein receptor knock-out mice fed with a high-fat diet for 9 months, and in which atheroma is deposited in the aorta and heart, TFPP showed greater binding to lipid on the intimal surface than in control mice fed a normal diet. When TFPP was hyperpolarized and administered in vivo to atheromatous mice in a pilot study, increased binding was observed on the endocardial surface of the intact heart compared with normally fed controls. Hyperpolarized TFPP has bio-sensing specificity for lipid, coupled with a 42,000-fold sensitivity gain in the MR signal at 4.7 T. Binding of TFPP with lipids results in the formation of a characteristic second peak in MRS. TFPP therefore has the potential to act as an in vivo molecular probe for atheromatous plaque imaging and may serve as a model of receptor-targeted bio-imaging with enhanced MR sensitivity.
Graph Theory and IC Component Design Analysis (2020)

Graph analysis in large integrated circuit (IC) designs is an essential tool for verifying design logic and timing via dynamic timing analysis (DTA). IC designs resemble graphs with each logic gate as a vertex and the conductive connections between gates as edges. Using DTA digital statistical correlations, graph condensation, and graph partitioning, it is possible to identify high-entropy component centers and paths within an IC design. Identification of high-entropy component centers (HECC) enables focused DTA, effectively lowering the computational complexity of DTA on large integrated circuit graphs. In this paper, a devised methodology termed IC layout subgraph component center identification (CCI) is used to identify described. CCI lowers DTA computationally complexity by condensing IC graphs into reduced subgraphs in which dominant logic functions are verified.
Abstract 5417: A novel curcumin derivative DiFiD prevents pancreatic cancer growth in vivo by suppressing Notch-1 (2011)

Abstract Background and Aims: Dysregulated Notch signaling plays an important role in the progression of pancreatic cancer. Previous studies have demonstrated that the dietary preventive agent curcumin modulates Notch activity. We have developed a novel curcumin analog DiFiD and determined that it inhibits pancreatic cancer cell growth by affecting proteins that regulate Notch signaling. Methods. Five pancreatic adenocarcinoma cell lines (AsPC-1, MiaPaCa-2, PanC-1, BxPC-3 and Pan02) were used in the study. Cell proliferation was measured for hexosaminidase activity and colony formation assay. Apoptosis was determined by measuring caspase 3/7 activity and western blot analysis for caspase 3. Cell cycle analysis was performed by propidium iodide staining and flow cytometry. Real Time PCR and western blot analyses were used to measure mRNA and protein levels. For in vivo studies, nude mouse xenografts were developed with Pan02 mouse pancreatic tumor cells. Immunohistochemistry was performed for CD31 (surrogate for angiogenesis), COX-2, VEGF and Notch-1. Results. DiFiD treatment resulted in a dose- and time-dependent inhibition of proliferation and in colony formation in all 5 pancreatic cell lines, but not that of normal mouse embryo fibroblasts. Cell cycle analyses demonstrated that DiFiD induced G2/M cell cycle arrest, which was followed by the induction of apoptosis as evidenced by the increased number of cells in the sub-G1 DNA fraction and activated caspase-3. Western blot analyses demonstrated that DiFiD down-regulated the expression of cell cycle related proteins cyclin A, D1 and E, while upregulating p21Waf1. Western blot analyses demonstrated that DiFiD inhibited Notch-1 activation as evidenced by a downregulation in the intracellular domain (NICD) and its downstream targets Hes-1 and Hey1. Expression of the Notch ligand Jagged-1 was also reduced. We further determined that the inhibition of Notch-1 signaling is due to a downregulation in Presenilin-1 and Nicastrin, critical componenst of the gamma-secretase complex. DiFiD also down regulated the expression of COX-2, IL-8 and VEGF. In vivo, nude mice harboring pancreatic cancer cell xenografts showed significant reduction in tumor growth when administered the compound intraperitoneally every day for 21 d. Microvessel density, based on CD31 staining was also significantly lower in DiFiD-treated tumors when compared to in controls. Real Time PCR and immunohistochemistry analyses also demonstrated significant inhibition of COX-2, VEGF, Notch-1, and cyclin D1 expression in the tumors. Conclusion. Together, these data suggest that DiFiD is a novel potent inhibitor of pancreatic tumor growth that targets the Notch-1 activating gamma-secretase complex proteins Presenilin-1 and Nicastrin. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5417. doi:10.1158/1538-7445.AM2011-5417
BNT162b2 Vaccine Encoding the SARS-CoV-2 P2 S Protects Transgenic hACE2 Mice against COVID-19 (2021)

BNT162b2 is a highly efficacious mRNA vaccine approved to prevent COVID-19. This brief report describes the immunogenicity and anti-viral protective effect of BNT162b2 in hACE2 transgenic mice. Prime-boost immunization with BNT162b2 elicited high titers in neutralizing antibodies against SARS-CoV-2, which correlated with viral clearance and alleviated lung lesions in these mice after viral challenge.
Extending materials to systems co-optimizationTM (MSCOTM) modeling to memory array simulation (2021)

In this paper, we describe a framework to enable the memory array simulations for Materials to Systems Cooptimization<sup>TM</sup> (MSCO<sup>TM</sup>) flows. The methodology is applied for projected 3 nm logic FinFET technology node SRAM array. To form the SRAM array, a “tiling” approach is utilized, where neighbor cells are created by copying and mirroring the first cell. Then this process is repeated to create the rest of the array. Electrical pulses are applied to the word-line and bit-line to activate the read and write operations. We demonstrate 128 &times;128 SRAM array simulations and find that the farthest cell from the word-line driver is vulnerable.
A New Surface Plasmon Resonance Assay for In Vitro Screening of Mannose-Binding Lectin Inhibitors (2016)

Mannose-binding lectin (MBL) is a circulating protein that acts as a soluble pattern recognition molecule of the innate immunity. It binds to carbohydrate patterns on the surface of pathogens or of altered self-cells, with activation of the lectin pathway of the complement system. Recent evidence indicates that MBL contributes to the pathophysiology of ischemia-reperfusion injury and other conditions. Thus, MBL inhibitors offer promising therapeutic strategies, since they prevent the interaction of MBL with its target sugar arrays. We developed and characterized a novel assay based on surface plasmon resonance for in vitro screening of these compounds, which may be useful before the more expensive and time-consuming in vivo studies. The assay measures the inhibitor's ability to interfere with the binding of murine MBL-A or MBL-C, or of human recombinant MBL, to mannose residues immobilized on the sensor chip surface. We have applied the assay to measure the IC50 of synthetic glycodendrimers, two of them with neuroprotective properties in animal models of MBL-mediated injuries.
A four-disulphide-bridged toxin, with high affinity towards voltage-gated K+ channels, isolated from Heterometrus spinnifer (Scorpionidae) venom (1997)

A new toxin, named HsTX1, has been identified in the venom of Heterometrus spinnifer (Scorpionidae), on the basis of its ability to block the rat Kv1.3 channels expressed in Xenopus oocytes. HsTX1 has been purified and characterized as a 34-residue peptide reticulated by four disulphide bridges. HsTX1 shares 53% and 59% sequence identity with Pandinus imperator toxin1 (Pi1) and maurotoxin, two recently isolated four-disulphide-bridged toxins, whereas it is only 32-47% identical with the other scorpion K+ channel toxins, reticulated by three disulphide bridges. The amidated and carboxylated forms of HsTX1 were synthesized chemically, and identity between the natural and the synthetic amidated peptides was proved by mass spectrometry, co-elution on C18 HPLC and blocking activity on the rat Kv1.3 channels. The disulphide bridge pattern was studied by (1) limited reduction-alkylation at acidic pH and (2) enzymic cleavage on an immobilized trypsin cartridge, both followed by mass and sequence analyses. Three of the disulphide bonds are connected as in the three-disulphide-bridged scorpion toxins, and the two extra half-cystine residues of HsTX1 are cross-linked, as in Pi1. These results, together with those of CD analysis, suggest that HsTX1 probably adopts the same general folding as all scorpion K+ channel toxins. HsTX1 is a potent inhibitor of the rat Kv1.3 channels (IC50 approx. 12 pM). HsTX1 does not compete with 125I-apamin for binding to its receptor site on rat brain synaptosomal membranes, but competes efficiently with 125I-kaliotoxin for binding to the voltage-gated K+ channels on the same preparation (IC50 approx. 1 pM).
QoS-aware joint uplink-downlink scheduling in FDD LTE-Advanced with carrier aggregation (2014)

Efficient resource utilization is of a high importance for LTE/LTE-A network performance and provisioning of user quality of experience. The eNodeB (LTE base station) is responsible for controlling the radio resources between the user and LTE /LTE-A network. The resources can be scheduled in two schemes; either independently or jointly by considering both uplink (UL) and downlink (DL) together. Joint scheduling is an attractive approach for resource utilization and for providing better Quality of Service (QoS), but it adds some computational complexity to the system. This paper aims to provide QoS-aware joint UL-DL scheduling for LTE-A utilizing the functionality of carrier aggregation. The scheme presented enforces the fair sharing of the resources between the UL and DL channels while maintaining good QoS. The work is based on simulation using the MATLAB-based IS-Wireless system level simulator. The key contributions of this work lie in addressing both the joint scheduling and the carrier aggregations while considering the QoS and traffic conditions of the users.
Deep Gaussian process with multitask and transfer learning for performance optimization (2022)

We combine Deep Gaussian Processes with multitask and transfer learning for the performance modeling and optimization of HPC applications. Deep Gaussian processes merge the uncertainty quantification advantage of Gaussian Processes with the predictive power of deep learning. Multitask and transfer learning allow for improved learning efficiency when several similar tasks are to be learned simultaneously and when previous learned models are sought to help in the learning of new tasks, respectively. A comparison with state-of-the-art autotuners shows the advantage of our approach on two application problems.
Realization of a photonic crystal surface emitting laser through GaAs based regrowth (2012)

Recently, there has been much interest in a novel type of device, the 2D photonic crystal surface emitting laser (PCSEL). For commercialization of these devices a robust and high reliability manufacturing method is required. Previous GaAs wafer fusion and GaN regrowth techniques have utilised voids within the photonic crystal which suffer from reliability and reproducibility issues. We demonstrate a GaAs based PCSEL structure which uses epitaxial regrowth to completely infill the etched structure. We discuss the design, epitaxy, and operating characteristics of these devices over a range of temperatures.
Certificate-based Trust Establishment for Airplane Software Distribution (2009)

Contemporary developments in airplane manufacturing and maintenance are motivating the introduction of significant new IT infrastructure, supporting increased communication and data transfer among aircraft and a variety of ground-based information systems operated by airlines and their business partners. A next generation of airplane designs, incorporating wired and wireless network interfaces, will support a wide spectrum of ”eEnabled” or network-enabled applications, including distribution of airplane software, collection and off-board retrieval of airplane health reports, perhaps even participation in advanced collaborative air traffic control. In this context it is clear that airline business viability and even flight safety will come to depend on the security of data transported in these applications. Trust is a fundamental element of security and information assurance in any business context, and must be treated as such in the design of networked IT systems. We consider the establishment and maintenance of trust relations for an application typical of networkenabled airplane applications, namely an Airplane Assets Distribution System (AADS) which affords a capability for on-line distribution of airplane-resident software from suppliers via airlines to airplanes. The AADS involves a large number of parties, among whom explicit and manageable trust relations are essential. In order to achieve integrity and authenticity of software transmitted via the AADS, an infrastructure design solution employing digital signatures and public-key infrastructure must be instantiated and adapted for use in the aviation environment, which has its own architectural peculiarities and stringent assurance requirements. We introduce a protocol for initializing the certificate of an airplane which is used to secure and authenticate data sent by the airplane to its owning airline. We describe the basic protocol and several protection variants, first in an informal discussion and then in a precise formal way, pointing out the differences in security properties of the variants. Finally, we report on the results of model-checking our formalizations using the AVISPA protocol validation tool. The Airplane Certificate Initialization Protocol serves as a concrete example our methodology for modeling, analyzing, and discussing the design of safetyand securitycritical IT systems currently under development in the aerospace industry. Our experience shows this methodology is effective for exploring requirements and design alternatives, surfacing important issues, and giving evidence that the system architecture meets the desired security goals.
Novel tricomponent membranes containing poly(ethylene glycol)/poly(pentamethylcyclopentasiloxane)/poly(dimethylsiloxane) domains (2002)

Abstract The synthesis and characterization of novel tricomponent networks consisting of well‐defined poly(ethylene glycol) (PEG) and poly(dimethylsiloxane) (PDMS) strands crosslinked and reinforced by poly(pentamethylcyclopentasiloxane) (PD 5 ) domains are described. Network synthesis occurred by dissolving α,ω‐diallyl PEG and α,ω‐divinyl PDMS prepolymers in a common solvent (toluene), introducing a stoichiometric excess of pentamethylcyclopentasiloxane (D 5 H) to the charge, inducing the cohydrosilation of the prepolymers by Karstedt's catalyst and completing network formation by the addition of water. Water in the presence of the Pt‐based catalyst oxidizes the SiH groups of D 5 H to SiOH functions that immediately polycondense and bring about crosslinking. The progress of cohydrosilation and polycondensation was followed by monitoring the disappearance of the SiH and SiOH functions by Fourier transform infrared spectroscopy. Because cohydrosilation and polycondensation are essentially quantitative, overall network composition can be controlled by calculating the stoichiometry of the three network constituents. The very low quantities of extractable (sol) fractions corroborate efficient crosslinking. The networks swell in both water and hexanes. Differential scanning calorimetry showed three thermal transitions assigned, respectively, to PEG (melting temperature: 46–60 °C depending on composition), PDMS [glass‐transition temperature ( T g ) = ∼−121 °C], and PD 5 ( T g = ∼−159 °C) and indicated a phase‐separated tricomponent nanoarchitecture. The low T g of the PD 5 phase is unprecedented. The strength and elongation of PEG/PD 5 /PDMS networks can be controlled by overall network composition. The synthesis of networks exhibiting sufficient mechanical properties (tensile stress: 2–5 MPa, elongation: 100–800%) for various possible applications has been demonstrated. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 3093–3102, 2002
Aging and IPF: What Is the Link? (2013)

Idiopathic pulmonary fibrosis (IPF) is a progressive and usually lethal interstitial lung disease of unknown etiology that is characterized by epithelial cell injury and aberrant activation, expansion of the mesenchymal cell population with the formation of fibroblast/myofibroblast foci, and exaggerated extracellular matrix accumulation. IPF is an aging-related disease, and most patients are over 60 years of age at the time of clinical presentation and diagnosis. Age also influences mortality, and the median survival time is significantly shorter in older individuals compared with younger patients. However, the fundamental mechanisms linking aging to IPF remain unclear. In this chapter, we will discuss some of the modifications naturally occurring in the elderly that may be implicated in the pathogenesis of IPF, including endoplasmic reticulum stress, oxidative stress, mitochondrial dysfunction, dysregulated autophagy, telomere attrition, and a number of epigenetic changes.
ChemInform Abstract: A Short and Efficient Stereoselective Synthesis of the Potent 5‐Lipoxygenase Inhibitor, CMI‐977. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Equilibrium modal power distribution measurement of step-index hard plastic cladding and graded-index silica multimode fibers (2015)

A stable reproducible optical standard source for measuring multimode optical fiber attenuation is required as recent round robin measurements of such fibers at several international companies and national standards organizations showed significant variation when using a source having only the encircled flux in the near field emerging from it defined. The paper presents and compares the far field modal power distributions for (i) 2 km and 3 km step-index multimode Hard Plastic Cladding Fibers, HPCF, (SI-MMF) with 200 μm silica core diameter, 0.37 numerical aperture (NA) and polymer cladding, (ii) a 10 m silica graded-index multimode fiber (GI-MMF) with 50 μm core diameter and 0.2 NA, and (ii) a near field Encircled Flux Mode Convertor or “modcon”. A free space method for measuring the far field using a Lightemitting diode (LED) centered at 850 nm wavelength with 40 nm 10 dB-bandwidth and a charge-coupled device (CCD) camera is compared with a f-theta multi-element lens based far field pattern (FFP) system. Mandrels of different diameter and different numbers of turns of the fiber around them were used to achieve an equilibrium mode distribution (EMD) for the GI-MMF. The paper defines encircled angular flux (EAF) as the fraction of the total optical power radiating from a multimode optical fiber core within a certain solid angle in the far field. The paper calculates the EAF when the solid angle increases from the far field centroid.
Pulsed Electric Fields and Temperature Effects on Drying and Rehydration of Red Beetroots (2008)

The effect of the pulsed electric field (PEF) pretreatment on convective drying of red beetroot tissue was investigated at the drying temperatures Td in the interval 30–100°C. The degree of material damage Z under the PEF and thermal treatment was studied. Dependence of the electrical characteristic damage time τE on the electric field strength E and the thermal characteristic damage time τT on temperature Td is discussed. The drying rate is shown to be maximal for highly disintegrated tissues; PEF pretreatment allowed reduction of the drying temperature by 20–25°C. PEF pretreatment results in greater degree of tissue shrinkage and hence increase in rehydration time; however, the textural properties of rehydrated samples with and without PEF treatment are seen to be similar. The benefit of PEF pretreatment for drying at moderate temperatures with preservation of colorants is also demonstrated.
A 4×40 Gb/s O-band WDM Silicon Photonic Transmitter based on Micro-Ring Modulators (2019)

We present an O-band micro-ring-based silicon-photonic 4-channel WDM transmitter with 6.75 nm-channel spacing for high-speed optical interconnects and demonstrate 4×40 Gb/s data generation operation featuring an energy efficiency of 24.84 fJ/bit/RM under 1.82 Vpp drive.
Benzo[1,2‐d:4,5‐d′]bisimidazoles as a Convenient Platform Towards Dyes that are Capable of Excited‐State Intramolecular Proton Transfer and of Two‐Photon Absorption (2012)

New, strongly fluorescent benzo[1,2-d:4,5-d']bisimidazoles have been prepared by the reaction of Bandrowski's base with various aldehydes. Their structures were carefully designed to achieve efficient excited-state intramolecular proton transfer and good two-photon-absorption (2PA) cross-sections. Functional dyes that possessed both high fluorescence quantum yields and large Stokes shifts were prepared. A π-expanded D-A-D derivative that possessed Φ(fl)=50 % and σ(2)=230 GM in the spectroscopic area of interest for biological imaging is an excellent candidate as a fluorescent probe. Thanks to the presence of two reactive amino groups, such compounds can be easily transformed into probes for bioconjugation. All of these benzo[1,2-d:4,5-d']bisimidazoles were also strongly fluorescent in the solid state.
ChemInform Abstract: Solid‐Phase Synthesis of Biologically Important Indoles (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.