gebhart/patrepeval huggingface dataset:
Nanoplasmonic Sensing of Materials for Energy Applications (2016)

Sensors are omnipresent in our daily life. They are used in many applications ranging from the touch screen in our smartphones to more critical contexts such as pollution monitoring. Although sensors have been developed for a long time, the demands are continuously increasing and many sensors still suffer from insufficient selectivity and/or sensitivity. The development of nanosensors has been suggested as one solution to push sensor performance boundaries further by exploiting the unique phenomena occurring at the nanoscale. One of the nanotechnology subareas of particular interest for sensing applications is nanoplasmonics, which explores the localized surface plasmon resonance (LSPR) phenomenon occurring in metal nanoparticles.In this thesis, nanoplasmonic sensing is developed and utilized in the context of the current challenges in the energy and environmental fields, or more specifically, the hydrogen economy, Carbon Capture and Storage (CCS) and solar energy harvesting technologies. In the first part, direct nanoplasmonic sensing based on AuPd alloy nanoparticles is explored for use as next-generation hydrogen sensors. To facilitate the nanofabrication of such alloy nanostructures, a bottom-up nanofabrication strategy for producing supported alloy nanoparticles with excellent control of their composition is developed. The performance of the fabricated AuPd alloy hydrogen sensors is then assessed and favorably compared to the performance targets set for hydrogen sensors to be used in fuel cell vehicles. In the second part, indirect nanoplasmonic sensing is established as an analytical tool to assess key properties of energy related materials for CCS and organic photovoltaics. The first study constitutes an investigation of CO2 adsorption in a microporous polymer, and the optical determination of the CO2 isosteric heat of adsorption. The second study addresses the thickness dependence of the glass transition temperature of a polymer:fullerene blend used as light absorber layer in organic photovoltaic devices. These two studies establish indirect nanoplasmonic sensing as a reliable and important analytical tool for the quantitative assessment of material properties of systems highly relevant for energy applications.
myCircos: Facilitating the Creation and Use of Circos Plots Online (2016)

Abstract Circos plots were designed to display large amounts of processed genomic information on a single graphical representation. The creation of such plots remains challenging for less technical users as the leading tool requires command-line proficiency. Here, we introduce myCircos, a web application that facilitates the generation of Circos plots by providing an intuitive user interface, adding interactive functionalities to the representation and providing persistence of previous requests. myCircos is available at: http://mycircos.iric.ca . Non registered users can explore the application through the Guest user. Source code (for local server installation) is available upon request.
Clinical Outcomes of Virologically-Suppressed Patients with Pre-existing HIV-1 Drug Resistance Mutations Switching to Rilpivirine/Emtricitabine/Tenofovir Disoproxil Fumarate in the SPIRIT Study* (2016)

Virologic success rates were high among virologically-suppressed patients with pre-existing NRTI and NNRTI resistance-associated mutations who switched to RPV/FTC/TDF in the SPIRIT study. While plasma RNA genotyping remains preferred, proviral DNA genotyping may provide additional value in virologically-suppressed patients for whom historical resistance data are unavailable.
Proteolysis of microtubule associated protein 2 and sensitivity of pancreatic tumours to docetaxel (2000)

We have studied the state of microtubule associated protein 2 (MAP2) in the pancreatic ductal adenocarcinomas P03 and P02 (sensitive and refractory to docetaxel respectively) since they express the corresponding mRNA and MAP2-related peptides. Immunohistochemical localization showed that in tumour P03 the MAP2-related peptides are highly expressed and confined to the epithelial malignant cells while in P02 the Intensity of the immunostaining is lower. However, anti alpha-tubulin staining followed a similar pattern suggesting that the net amount of macromolecular structures in the sensitive tumour is higher than in the refractory one. This may explain its higher sensitivity to docetaxel, because tubulin assembled into microtubules is the target of the drug. We found that protein extracts from both tumours differed in their proteolytic activity on rat brain MAP2. Since the proteolysis pattern obtained was similar to the one produced by Cathepsin D, we studied the effect of MAP2 proteolysed by this enzyme on microtubule formation in vitro. Proteolysis was found to increase the tendency of tubulin to assemble into macromolecular structures (microtubules and aggregates) in the presence of docetaxel. This suggests that in vivo proteolysis of MAP2 might increase microtubule alterations and potentiate the antitumour effect of docetaxel.
Cooperative simulation of lithography and topography for three-dimensional high-aspect-ratio etching (2018)

A topography simulation of high-aspect-ratio etching considering transports of ions and neutrals is performed, and the mechanism of reactive ion etching (RIE) residues in three-dimensional corner patterns is revealed. Limited ion flux and CF2 diffusion from the wide space of the corner is found to have an effect on the RIE residues. Cooperative simulation of lithography and topography is used to solve the RIE residue problem.
Pulsed laser deposition of thin films and superlattices based on ZnO (2005)

The pulsed laser deposition (PLD) technique has been applied for the epitaxial growth of ZnO for more than two decades. The emergence of high-temperature stability of the excitonic lasing was first demonstrated in a microcrystalline ZnO film grown by PLD leading to recent remarkable growth in this field. A number of attempts have been made to improve the crystallinity for realizing p-type materials in the quest for ZnO-based short wavelength light emitting devices (LEDs). In this paper, we describe practical advantages of PLD and currently accomplished intrinsic properties of ZnO films according to the abundant literature. We find that correlation between Hall mobility and lateral grain size captures the effect of grain boundaries for the films grown on sapphire substrates. On the other hand, advantages of the use of lattice-matched ScAlMgO4 substrate are evidenced by the lower residual electron density, higher mobility and sharper exciton peaks in the photoluminescence and absorption spectra. We also focus on the wide-band-gap ternary alloy, MgxZn1−xO, especially in terms of the composition dependence of its lattice parameters and band-gap in two different crystallographic phases, to discuss the stability of this metastable compound. The studies on the PLD growth of multilayer and superlattices are briefly reviewed. We finally present the current capability of electron and hole doping by incorporating Ga and N into films grown on (0001) ScAlMgO4 substrates. We conclude that the PLD technique and related technologies have now mature to meet the requirements for fabricating UV-LEDs.
Spatial coherence measurements from two L-shape arrays in Shallow Water (2009)

In the Shallow Water’ 06 experiment, two L-shape arrays (ARRAY52 and ARRAY32) were deployed. The vertical line array (VLA) components of both ARRAY52 and ARRAY32 were exactly perpendicular to the direction of sound propagation. The horizontal line array (HLA) component of ARRAY52 was exactly perpendicular to the direction of sound propagation. The HLA component of ARRAY32 was exactly parallel to the direction of sound propagation. This configuration offered an opportunity to simultaneously analyze the three dimensional (3-D) spatial coherences: vertical, transverse horizontal and longitudinal horizontal. When the source and the receivers were below the thermocline, both the vertical and longitudinal horizontal coherence lengths in units of wavelength increased with increasing range and frequency. When the source was within the thermocline, the transverse horizontal coherence length in units of wavelength decreased with frequency and exhibited weak range dependence.
Efficient FFT Computation in IFDMA Transceivers (2022)

Interleaved Frequency Division Multiple Access (IFDMA) has the salient advantage of lower Peak-to-Average Power Ratio (PAPR) than its competitors like Orthogonal FDMA (OFDMA). A recent research effort put forth a new IFDMA transceiver design significantly less complex than conventional IFDMA transceivers. The new IFDMA transceiver design reduces the complexity by exploiting a certain correspondence between the IFDMA signal processing and the Cooley-Tukey IFFT/FFT algorithmic structure so that IFDMA streams can be inserted/extracted at different stages of an IFFT/FFT module according to the sizes of the streams. Although the prior work has laid down the theoretical foundation for the new IFDMA transceiver's structure, the practical realization of the transceiver on specific hardware with resource constraints has not been carefully investigated. This paper is an attempt to fill the gap. Specifically, this paper puts forth a heuristic algorithm called multi-priority scheduling (MPS) to schedule the execution of the butterfly computations in the IFDMA transceiver with the constraint of a limited number of hardware processors. The resulting FFT computation, referred to as MPS-FFT, has a much lower computation time than conventional FFT computation when applied to the IFDMA signal processing. Importantly, we derive a lower bound for the optimal IFDMA FFT computation time to benchmark MPS-FFT. Our experimental results indicate that when the number of hardware processors is a power of two: 1) MPS-FFT has near-optimal computation time; 2) MPS-FFT incurs less than 44.13\% of the computation time of the conventional pipelined FFT.
Cleavage of Ether, Ester, and Tosylate C(sp3)–O Bonds by an Iridium Complex, Initiated by Oxidative Addition of C–H Bonds. Experimental and Computational Studies (2013)

A pincer-ligated iridium complex, (PCP)Ir (PCP = κ(3)-C6H3-2,6-[CH2P(t-Bu)2]2), is found to undergo oxidative addition of C(sp(3))-O bonds of methyl esters (CH3-O2CR'), methyl tosylate (CH3-OTs), and certain electron-poor methyl aryl ethers (CH3-OAr). DFT calculations and mechanistic studies indicate that the reactions proceed via oxidative addition of C-H bonds followed by oxygenate migration, rather than by direct C-O addition. Thus, methyl aryl ethers react via addition of the methoxy C-H bond, followed by α-aryloxide migration to give cis-(PCP)Ir(H)(CH2)(OAr), followed by iridium-to-methylidene hydride migration to give (PCP)Ir(CH3)(OAr). Methyl acetate undergoes C-H bond addition at the carbomethoxy group to give (PCP)Ir(H)[κ(2)-CH2OC(O)Me] which then affords (PCP-CH2)Ir(H)(κ(2)-O2CMe) (6-Me) in which the methoxy C-O bond has been cleaved, and the methylene derived from the methoxy group has migrated into the PCP Cipso-Ir bond. Thermolysis of 6-Me ultimately gives (PCP)Ir(CH3)(κ(2)-O2CR), the net product of methoxy group C-O oxidative addition. Reaction of (PCP)Ir with species of the type ROAr, RO2CMe or ROTs, where R possesses β-C-H bonds (e.g., R = ethyl or isopropyl), results in formation of (PCP)Ir(H)(OAr), (PCP)Ir(H)(O2CMe), or (PCP)Ir(H)(OTs), respectively, along with the corresponding olefin or (PCP)Ir(olefin) complex. Like the C-O bond oxidative additions, these reactions also proceed via initial activation of a C-H bond; in this case, C-H addition at the β-position is followed by β-migration of the aryloxide, carboxylate, or tosylate group. Calculations indicate that the β-migration of the carboxylate group proceeds via an unusual six-membered cyclic transition state in which the alkoxy C-O bond is cleaved with no direct participation by the iridium center.
Relationship between serum cholesterol and indices of erythrocytes and platelets in the US population (2013)

Whereas dyslipidemia has been associated with leukocytosis, the relationship between serum cholesterol and other hematopoietic lineages is poorly defined. Erythrocytes and platelets, anucleate cells relegated to nonspecific diffusional exchange of cholesterol with serum, have been proposed to have a distinct relationship to cholesterol from leukocytes. We examined the relationship between serum cholesterol and circulating erythrocyte/platelet indices in 4,469 adult participants of the National Health and Nutrition Examination Survey (NHANES) 2005-2006. In linear regression analyses, serum non-high density lipoprotein-cholesterol (non-HDL-C) was positively associated with mean erythrocyte number, hematocrit, hemoglobin concentration, platelet count, and platelet crit independently of age, gender, race/ethnicity, smoking, body mass index, serum folate, and C-reactive protein. The magnitude of the relationship was most marked for platelets, with lowest versus highest non-HDL-C quartile subjects having geometric mean platelet counts of 258,000/μl versus 281,000/μl, respectively (adjusted model, P < 0.001 for trend). These associations persisted in a sensitivity analysis excluding several conditions that affect erythrocyte/platelet and/or serum cholesterol levels, and were also noted in an independent analysis of 5,318 participants from NHANES 2007-2008. As non-HDL-C, erythrocytes, and platelets all impact cardiovascular disease risk, there is a need for advancing understanding of the underlying interactions that govern levels of these three blood components.
The Effect of the Amide Substituent on the Biodistribution and Tolerance of Lanthanide(III) DOTA-Tetraamide Derivatives (2008)

The absence of uptake by the liver and spleen indicate that irrespective of the ligand structure and charge, these complexes are not prone to dissociation in vivo. This is in agreement with previously published work that indicates high kinetic inertness for this class of compounds. At low doses, all complexes were well tolerated; however, for applications that require higher doses, the structure and charge of the ligand becomes a fundamentally important parameter. The results reported herein demonstrate the importance of incorporating negatively charged groups on amide substituents if a DOTA-tetraamide complex is to be employed at high doses in vivo.
A multichannel random access protocol for multislot short messages with delay constraints (2004)

A multichannel random access protocol called FMCSA for multislot short messages is proposed in this paper to be used in access networks with large propagation delay. This protocol combines random access with the use of packet level forward error correction coding for new messages and scheduled retransmissions for partially received messages. Analytical and simulation results show that FMCSA can achieve a higher throughput and lower delay than slotted Aloha. When the system is operating at the low load region, the short messages can be delivered in their first attempts with very high probability. With the load increasing, more messages will be received partially in their first attempts and the scheduled retransmission scheme will guarantee the partially received messages to be recovered in their second attempts. Therefore the delay performance of FMCSA is much more robust to the load fluctuation than slot Aloha.
Glossary of Terms Related to Pharmaceutics (2016)

This Glossary of Terms Related to Pharmaceutics is needed by practitioners in the field of pharmaceutics as this field fulfills an important and crucial role, different from the roles of other scientific disciplines involved in the drugmaking process. The glossary contains 168 definitions used in pharmaceutics. These are related to various aspects of this discipline, such as: (1) physicochemical characterization of pharmaceutical preparations and the active ingredients they contain; (2) unit operations used in the practice of pharmaceutics; (3) terms related to the various dosage forms; (4) terms related to the various modes and routes of drug delivery; (5) terms used in pharmacokinetics and biopharmaceutics in general; and additional miscellaneous terms. The field of pharmaceutics itself is of a multidisciplinary nature as its practitioners come from a variety of disciplines, such as chemistry or various biological sciences, thus a glossary containing authoritative definitions would be useful for them. The terms used in pharmaceutics are rarely covered by existing glossaries, and in the cases they are, their definitions are often inappropriate for the field of pharmaceutics and require new or modified definitions to better fit the new context.
ChemInform Abstract: Synthesis and Cytotoxic Activity of 7‐Oxo‐7H‐dibenz[f,ij]isoquinoline and 7‐Oxo‐7H‐benzo[e]perimidine Derivatives. (2001)

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.
Low-Temperature Synthesis of Hollow β-Tricalcium Phosphate Particles for Bone Tissue Engineering Applications (2022)

β-Tricalcium phosphate (β-TCP) has been extensively used in bone tissue engineering in the form of scaffolds, granules, or as reinforcing phase in organic matrices. Solid-state reaction route at high temperatures (>1000 °C) is the most widely used method for the preparation of β-TCP. The high-temperature synthesis, however, results in the formation of hard agglomerates and fused particles which necessitates postprocessing steps such as milling and sieving operations. This, inadvertently, could lead to introducing unwanted trace elements, promoting particle shape irregularity as well as compromising the biodegradability and bioactivity of β-TCP because of the solid microstructure of particles. In this study, we introduce a one-pot wet-chemical method at low temperatures (between 160 and 170 °C) to synthesize hollow β-TCP (hβ-TCP) submicron particles of an average size of 300 nm with a uniform rhombohedral shape. We assessed the cytocompatibility of the hβ-TCP using primary human osteoblasts (HOB), adipose-derived stem cells (ADSC), and antigen-presenting cells (APCs). We demonstrate the bioactivity of the hβ-TCP when cultured with HOB, ADSC, and APCs at a range of particle concentrations (up to 1000 μg/mL) for up to 7 days. hβ-TCP significantly enhances osteogenic differentiation of ADSC without the addition of osteogenic supplements. These findings offer a new type of β-TCP particles prepared at low temperatures, which present various opportunities for developing β-TCP based biomaterials.
Interleukin-18/interferon-γ-inducing factor, a novel cytokine, up-regulates ICAM-1 (CD54) expression in KG-1 cells (1998)

Intercellular adhesion molecule-1 (ICAM-1, CD54) is a membrane glycoprotein and a member of the immunoglobulin superfamily. It plays a central role in cell to cell-mediated immune responses and is a ligand for leukocyte function-associated antigen-1 (LFA-1). We report here that a newly discovered cytokine, interferon-gamma-inducing factor (IGIF) [H. Okamura et al. (1995) Nature 378, 88] recently proposed to be designated as IL-18, selectively up-regulates ICAM-1 expression in KG-1 cells, a human myelomonocytic cell line, in which IL-18 also enhances interferon-gamma production. IL-18 induced heterotypic aggregation between KG-1 and Peer T cells, which was blocked by anti-ICAM-1 and/or LFA-1 antibodies. Anti-interferon-gamma antibody did not block the IL-18-induced up-regulation of ICAM-1 on KG-1 cells. These results thus show that IGIF/IL-18, enhances ICAM-1 expression in KG-1 cells in an interferon-gamma-independent pathway, up-regulates ICAM-1 functions, and that IL-18 might play a potential role in immunoregulation by mediating immune cell infiltration into the tissues.
Live cell micropatterning reveals the dynamics of signaling complexes at the plasma membrane (2014)

Interactions of proteins in the plasma membrane are notoriously challenging to study under physiological conditions. We report in this paper a generic approach for spatial organization of plasma membrane proteins into micropatterns as a tool for visualizing and quantifying interactions with extracellular, intracellular, and transmembrane proteins in live cells. Based on a protein-repellent poly(ethylene glycol) polymer brush, micropatterned surface functionalization with the HaloTag ligand for capturing HaloTag fusion proteins and RGD peptides promoting cell adhesion was devised. Efficient micropatterning of the type I interferon (IFN) receptor subunit IFNAR2 fused to the HaloTag was achieved, and highly specific IFN binding to the receptor was detected. The dynamics of this interaction could be quantified on the single molecule level, and IFN-induced receptor dimerization in micropatterns could be monitored. Assembly of active signaling complexes was confirmed by immunostaining of phosphorylated Janus family kinases, and the interaction dynamics of cytosolic effector proteins recruited to the receptor complex were unambiguously quantified by fluorescence recovery after photobleaching.
Ultrafast Control of the Optical Transition in Type-II Colloidal Quantum Wells (2023)

Manipulating the optical transition in semiconductors at ultrashort timescales is of both fundamental interest and central importance for emerging photonic applications. Traditionally, this manipulation is realized by electrostatic gating via Stark effects or band-gap renormalizations. Here, we report an ultrafast and all-optical route to engineer an indirect transition in core–crown colloidal quantum wells (CQWs), namely, CdSe/CdTe, with a type-II band alignment. Following the intense laser pulse excitation, the indirect band transition energy exhibits a pronounced blueshift–redshift crossover on the picosecond timescale, stemming from the formation and dissipation of the transient electric field (E-field) that forms upon photoexcitation to compensate for the driving force provided by the band offsets. Both the energy shift and dynamics of the transient E-field can be modulated optically by tuning the laser pulse excitation fluence. Our finding demonstrates a strong analogy between the type-II heterojunction and a p–n junction with respect to carrier equilibrium processes, which holds promise to facilitate the integration of CQWs within optical switching networks.
E47 modulates hepatic glucocorticoid action (2019)

Glucocorticoids (GCs) are effective drugs, but their clinical use is compromised by severe side effects including hyperglycemia, hyperlipidemia and obesity. They bind to the Glucocorticoid Receptor (GR), which acts as a transcription factor. The activation of metabolic genes by GR is thought to underlie these adverse effects. We identify the bHLH factor E47 as a modulator of GR target genes. Using mouse genetics, we find that E47 is required for the regulation of hepatic glucose and lipid metabolism by GR, and that loss of E47 prevents the development of hyperglycemia and hepatic steatosis in response to GCs. Here we show that E47 and GR co-occupy metabolic promoters and enhancers. E47 is needed for the efficient recruitment of GR and coregulators such as Mediator to chromatin. Altogether, our results illustrate how GR and E47 regulate hepatic metabolism, and might provide an entry point for novel therapies with reduced side effects.