gebhart/patrepeval huggingface dataset:
Intrinsic resistance switching in amorphous silicon oxide for high performance SiOx ReRAM devices (2017)

In this paper, we present a study of intrinsic bipolar resistance switching in metal-oxide-metal silicon oxide ReRAM devices. Devices exhibit low electroforming voltages (typically − 2.6 V), low switching voltages (± 1 V for setting and resetting), excellent endurance of > 107 switching cycles, good state retention (at room temperature and after 1 h at 260 °C), and narrow distributions of switching voltages and resistance states. We analyse the microstructure of amorphous silicon oxide films and postulate that columnar growth, which results from sputter-deposition of the oxide on rough surfaces, enhances resistance switching behavior.
Mutational Analysis of Plant Cap-Binding Protein eIF4E Reveals Key Amino Acids Involved in Biochemical Functions and Potyvirus Infection (2008)

The eukaryotic translation initiation factor 4E (eIF4E) (the cap-binding protein) is involved in natural resistance against several potyviruses in plants. In lettuce, the recessive resistance genes mo1(1) and mo1(2) against Lettuce mosaic virus (LMV) are alleles coding for forms of eIF4E unable, or less effective, to support virus accumulation. A recombinant LMV expressing the eIF4E of a susceptible lettuce variety from its genome was able to produce symptoms in mo1(1) or mo1(2) varieties. In order to identify the eIF4E amino acid residues necessary for viral infection, we constructed recombinant LMV expressing eIF4E with point mutations affecting various amino acids and compared the abilities of these eIF4E mutants to complement LMV infection in resistant plants. Three types of mutations were produced in order to affect different biochemical functions of eIF4E: cap binding, eIF4G binding, and putative interaction with other virus or host proteins. Several mutations severely reduced the ability of eIF4E to complement LMV accumulation in a resistant host and impeded essential eIF4E functions in yeast. However, the ability of eIF4E to bind a cap analogue or to fully interact with eIF4G appeared unlinked to LMV infection. In addition to providing a functional mutational map of a plant eIF4E, this suggests that the role of eIF4E in the LMV cycle might be distinct from its physiological function in cellular mRNA translation.
Circulating branched‐chain amino acid concentrations are associated with obesity and future insulin resistance in children and adolescents (2012)

Elevations in the concentrations of circulating BCAAs are significantly associated with obesity in children and adolescents, and may independently predict future insulin resistance.
Plasmid-based gene delivery to target tissues in vivo: the intravascular approach. (2003)

Over the past several years, significant progress has been made in the development of non-viral methodologies that can effectively deliver genes to target tissues in vivo. One of the most surprising successes has been the discovery that naked plasmid DNA (pDNA) can be delivered into tissues such as liver and muscle with high efficiency using the vascular system. The key breakthrough involved the realization that pDNA could be injected rapidly into blood vessels (using increased volumes) in a manner that facilitates extravasation of the DNA solution outside the blood vessel wall. The extravasation process places the DNA in contact with the plasma membranes of the underlying parenchymal cells of the target organ. This intravascular delivery technique, termed 'hydrodynamic delivery', has become established as the primary non-viral methodology for delivering pDNA expression constructs to target tissues in vivo. This review highlights many of the most recent studies in which increased volume/rapid injection procedures have been used. These include studies in which the technology was used as a new and powerful tool to address in vivo gene expression questions, as well as numerous studies that were designed to better understand or improve the methodology. It is these scientific efforts that have served to fuel the development of this delivery technology from simply an interesting phenomenon to a highly useful and broadly used gene delivery methodology.
Design and characterization of decoy oligonucleotides containing locked nucleic acids (2002)

Transfection of cis-element double-stranded oligonucleotides, referred to as decoy ODNs, has been reported to be a powerful tool that provides a new class of antigene strategies for gene therapy. However, one of the major limitations of the decoy approach is the rapid degradation of phosphodiester oligonucleotides by intracellular nucleases. To date, several DNA analogs have been employed to overcome this issue, but insufficient efficacy and/or specificity have limited their in vivo usefulness. In this paper we have investigated the use of conformationally restricted nucleotides in the design of decoy molecules for nuclear transcription factor kappaB (NF-kappaB). Starting from a synthetic double-stranded oligonucleotide, containing the kappaB consensus binding sequence, we designed a panel of decoy molecules modified to various extents and at various positions with locked nucleic acids (LNAs). Our results indicate that the addition of terminal LNA bases, outside the kappaB sequence, to generate LNA-DNA-LNA co-polymers was sufficient to confer appreciable protection towards nuclease digestion, without interfering with transcription factor binding. Conversely, insertion of LNA substitutions in the context of the kappaB-binding site resulted in further increased stability, but caused a loss of affinity of NF-kappaB for the target sequence. However, our results also indicate that this latter effect was apparently dependent not only on the extent but also on strand positioning of the internal LNA substitutions. This observation is of great importance since it provides evidence for the possibility of tuning DNA-LNA duplexes with internal LNAs into decoy agents with improved features in terms of biological stability and inhibitory effect.
A signal quality index for ballistocardiogram recordings based on electrocardiogram RR intervals and matched filtering (2018)

Detection of noisy ballistocardiogram (BCG) measurements with a matched filter is investigated. The BCG signal is segmented by the RR intervals of the concurrently recorded electrocardiogram (ECG). These segments are called BCG heartbeats and are averaged to estimate a parent template and sub-templates of BCG heartbeats leveraging the quasi-periodic nature of the heart. All BCG heartbeats in the measurement are used to estimate the parent template BCG heartbeat. By contrast, sub-templates are estimated using subsets of BCG heartbeats that extend over several breaths to capture the variations in the phase of the BCG heartbeat due to the breathing cycles. The parent template BCG heartbeat in a recording is regarded as the subject-specific matched filter. Finally, the average correlation coefficient between sub-templates and the parent template BCG heartbeat in a recording is proposed as the signal quality index (SQI). A seven-step experiment was performed among thirteen subjects. For reliable parent template estimation, at least 40 BCG heartbeats should be recorded. For detection of noisy BCG measurements, the area under the receiver operating characteristics curve was presented for conditions of motion artifacts, speaking, and deep breathing. Motion artifacts could be detected with lower false positive rates for the same constraint on the detection rate, when compared to speaking and deep breathing cases. This work may facilitate online detection of noisy BCG recordings.
Architectonic Quantum Dot Solids (1999)

Three things largely determine the electronic properties of a crystal: the energy levels of the atoms or lattice sites, the coupling between adjacent sites, and the symmetry of the solid. Imagine being able to control each of these properties separately, and therefore being able to “design” a solid with a prescribed set of electronic properties. For an atomic solid, this would amount to being able to tune the electronegativity of an atom, to control the strength of the covalent interactions within the lattice, and to choose the crystal structure. While the chemistry of the periodic table does not permit such control, the chemistry of “artificial atoms”,1 or quantum dots (QDs), does. In this Account, we will discuss one example of “designing” a unique electronic property into a QD solid. This property, which is the ability of the solid to reversibly pass through a metal−insulator (MI) transition under ambient conditions, is something that has not been previously demonstrated for a more traditional solid. A two-dimensional (2D) hexagonal superlattice of organically passivated silver QDs was fabricated as a Langmuir monolayer. Selecting a particular size of QD controlled the (super)lattice site energies. The coupling between adjacent QDs was coarsely controlled by selection of the organic surface passivant, and precisely controlled by compressing the superlattice using the Langmuir technique. By using the title “Architectonic2 Quantum Dot Solids”, we emphasize that many of the collective properties of the superlattice were rationally designed into the material.
Metal–Organic Frameworks as A Tunable Platform for Designing Functional Molecular Materials (2013)

Metal-organic frameworks (MOFs), also known as coordination polymers, represent an interesting class of crystalline molecular materials that are synthesized by combining metal-connecting points and bridging ligands. The modular nature of and mild conditions for MOF synthesis have permitted the rational structural design of numerous MOFs and the incorporation of various functionalities via constituent building blocks. The resulting designer MOFs have shown promise for applications in a number of areas, including gas storage/separation, nonlinear optics/ferroelectricity, catalysis, energy conversion/storage, chemical sensing, biomedical imaging, and drug delivery. The structure-property relationships of MOFs can also be readily established by taking advantage of the knowledge of their detailed atomic structures, which enables fine-tuning of their functionalities for desired applications. Through the combination of molecular synthesis and crystal engineering, MOFs thus present an unprecedented opportunity for the rational and precise design of functional materials.
Solid-Phase Synthetic Strategy and Bioevaluation of a Labeled δ-Opioid Receptor Ligand Dmt-Tic-Lys forIn VivoImaging (2009)

A general solid-phase synthetic strategy is developed to prepare fluorescent and/or lanthanide-labeled derivatives of the delta-opioid receptor (deltaOR) ligand H-Dmt-Tic-Lys(R)-OH. The high delta-OR affinity (K(i) = 3 nM) and desirable in vivo characteristics of the Cy5 derivative 1 suggest its usefulness for structure-function studies and receptor localization and as a high-contrast noninvasive molecular marker for live imaging ex vivo or in vivo.
Pertussis Toxin Treatment in Vivo Is Associated with a Decline in G-protein β-Subunits (1989)

The effects of pertussis toxin on the steady-state levels of G-protein alpha- and beta-subunits were investigated both in vitro and in vivo. The steady-state level Go alpha, a major substrate for pertussis toxin-catalyzed ADP-ribosylation, was unaltered by pertussis toxin treatment for periods up to 100 h for 3T3-L1 cells in culture or up to 3 days in vivo. In 3T3-L1 cells pertussis toxin treatment did not alter levels of Gs alpha-subunits; in S49 cells the level of Gs alpha-subunits declined moderately following by pertussis toxin treatment. The steady-state levels of G beta-subunits, in contrast, were found to decline to less than 50% of the normal cellular complement following pertussis toxin treatment in vitro and in vivo. Inhibitory control of adenylate cyclase, pertussis toxin-catalyzed ADP-ribosylation of Gi alpha and Go alpha, and the GTP-dependent shift in agonist-specific binding to beta-adrenergic receptors were attenuated or abolished within 5 h of pertussis toxin treatment, representing "early" effects of the toxin. Stimulatory regulation of adenylate cyclase, in contrast, displayed a progressive enhancement that was first observed 4 h after pertussis toxin treatment, increasing thereafter up until 100 h, the last time point measured. This progressive enhancement of the stimulatory pathway of adenylate cyclase was not manifest at the level of stimulatory receptors, since the Kd and Bmax for one such receptor, the beta-adrenergic receptor, were shown to be unaltered in toxin-treated cells. Furthermore, the potentiation of stimulation of adenylate cyclase was observed in cells stimulated by the beta-adrenergic agonist isoproterenol and PGE1 alike. The progressive enhancement of the stimulatory pathway correlated best with the decline in G beta-subunit levels that occurs following pertussis intoxication. The changes in both of these parameters occur "late" (12-48 h), as compared to the early events that occur within 5 h. Pertussis toxin action appears to be composed of two, temporally distinct, groups of effects. Pertussis toxin-catalyzed ADP-ribosylation of G alpha-subunits, attenuation of the inhibitory regulation of adenylate cyclase, and attenuation of the ability of GTP to induce an agonist-specific shift in receptor affinity are members of the early group of effects. The second group of late effects includes the decline in G beta-subunit levels and the progressive enhancement of the stimulatory pathway of adenylate cyclase. This enhanced stimulatory control at these later times cannot be explained by the attenuation of the inhibitory pathway occurring early, but rather appears as G beta-subunit levels decline.
Ultrafast vibrational spectroscopy in condensed phases (2002)

A variety of ultrafast vibrational excitation and probing methods are first discussed and it is shown that various vibrational spectroscopies can be devised by combining multiple excitation and probing methods. A few ultrafast vibrational spectroscopic methods in condensed phases, which have already been demonstrated and used to study vibrational relaxation phenomena and structural analysis of small polypeptides, are briefly summarized. Then, a number of novel ultrafast vibrational spectroscopies that have been theoretically investigated are discussed by emphasizing their differences from other existing methods. Perspectives on how these ultrafast vibrational spectroscopies in centrosymmetric and non-centrosymmetric condensed phases can be applied to the investigations of chemical reaction dynamics, solvation dynamics, time-dependent structural evolutions of polyatomic molecules such as proteins will be mentioned.
Paramagnetic (Alkene)Rh and (Alkene)Ir Complexes: Metal or Ligand Radicals? (2006)

Abstract In this review a detailed overview is given of the (electronic) structure and reactivity of open‐shell (paramagnetic) alkene rhodium and iridium complexes M x (alkene) (M = Rh, Ir; x = 0, +II). In most cases these species are highly reactive, but some notable exceptions of stable species for which not much reactivity has been described are also included (section 2). Understanding the electronic structure of the reactive nitrogen‐ligand‐based [M II (por)(alkene)] and [M II (alkene)(N‐ligand)] 2+ species (section 3) is complicated by a substantial spin distribution over the metal and the alkene ligand. This dual‐mode metallo‐radical and ligand radical behavior is reflected by their high and diverse reactivity. Metallo‐radical character is demonstrated by a variety of metal‐to‐radical coupling reactions with a series of other radicals, as well as metal‐based allylic hydrogen atom abstractions from M II (α‐alkene) species. On the other hand, (donor induced) ligand radical character is crucial in a variety of M–C and C–C radical coupling reactions, C–O bond formation by oxygenation of M II (alkene) species and alkene “insertions” into (por)M–H bonds. The review concludes with some speculations about possible roles of paramagnetic M(olefin) (M = Rh, Ir) species in catalytic olefin oxygenation and carbene transfer reactions.(© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
DNA vaccines for the prevention and treatment of allergy (2008)

Dendritic cell-based approach has been actively explored to enhance immunogenicity of antiallergy DNA vaccines. Codelivery of hypoallergenic DNA vaccines with potent adjuvants via a desirable delivery mode will help to fulfill the requirements for clinical application of antiallergy DNA vaccines. Activation of TBK1 signaling pathway could be a novel strategy to enhance immunogenicity of DNA vaccines.
Using Gene Expression Ratios to Predict Outcome Among Patients With Mesothelioma (2003)

Gene expression ratio-based analysis accurately predicts treatment-related outcome in mesothelioma samples. This technique could impact the clinical treatment of mesothelioma by allowing the preoperative identification of patients with widely divergent prognoses.
A Java collaborative interface for genetic programming applications: image analysis for scientific inquiry (2002)

Discusses several key issues involved in designing and using a Java collaborative interface for genetic programming applications over the World Wide Web. We present our implementation that has been used in a new system that assists scientists in classifying and extracting novel features in remotely sensed satellite imagery. This paper also identifies issues in developing a class library that facilitates rapid prototyping of such collaborative graphical user interfaces for genetic programming, and suggests how other researchers could benefit from them.
Individually addressable recessed gold microelectrode arrays with monolayers of thio-cyclodextrin nanocavities (2005)

Four, individually addressable 30 microm diameter, e-beam deposited, gold microelectrodes recessed by 6 microm were suitably spaced on a single substrate to avoid diffusional overlap between each microelectrode. The single substrate device was functionalised with thiolated alpha-, beta-, and gamma-cyclodextrin nanocavities without spacer groups to ensure close proximity of the cavities to the electrode surface. The microelectrodes were assessed in two stages. The e-beam deposited micron sized electrodes were characterized using models for recessed and inlaid microdisk electrodes. Subsequently, each individually addressable, atomically flat, micro-patterned gold electrode with thiolated CD ensembles was treated as a nanoporous electrode assembly. Theoretical and experimental results were compared using cyclic voltammetry. Atomic force microscopy was also used to characterise the modified microelectrodes. Comparisons were made with thiolated CDs deposited on macroelectrodes. This is the first report of the behaviour of immobilized CD nanocavities ensembles on atomically flat gold microelectrodes.
Oncostatin M-induced effects on EMT in human proximal tubular cells: differential role of ERK signaling (2007)

Growing evidence suggests that a proportion of interstitial myofibroblasts detected during renal tubulointerstitial fibrosis originates from tubular epithelial cells by a process called epithelial-mesenchymal transition (EMT). The IL-6-type cytokine oncostatin M (OSM) has been recently implicated in the induction of EMT. We investigated OSM effects on the expression of both cell-cell contact proteins and mesenchymal markers and studied OSM-induced intracellular signaling mechanisms associated with these events in human proximal tubular cells. Human recombinant OSM attenuated the expression of N-cadherin, E-cadherin, and claudin-2 in human kidney-2 (HK-2) cells associated with the induction of HK-2 cell scattering in 3D collagen matrices. Conversely, expression of collagen type I, vimentin, and S100A4 was induced by OSM. OSM-stimulated cell scattering was inhibited by antibodies against gp130. Besides inducing phosphorylation of Stat1 and Stat3, OSM led to a strong concentration- and time-dependent phosphorylation of the mitogen-activated protein kinases ERK1, ERK2, and ERK5. MEK1/2 inhibitor U0126 (10 muM) blocked basal and OSM-induced ERK1/2 phosphorylation but not phosphorylation of either ERK5 or Stat1/3. Both synthetic MEK1/2 inhibitors U0126 and Cl-1040, when used at concentrations which inhibit ERK1/2 phosphorylation but not ERK5 phosphorylation, restored N-cadherin expression in the presence of OSM, inhibited basal claudin-2 expression, but did not affect either basal or OSM-inhibited E-cadherin expression or OSM-induced expression of collagen type I and vimentin. These results suggest that in human proximal tubular cells ERK1/2 signaling represents an important component of OSM's inhibitory effect on N-cadherin expression. Furthermore, functional ERK1/2 signaling is necessary for basal claudin-2 expression.
Microenvironmental Genomic Alterations and Clinicopathological Behavior in Head and Neck Squamous Cell Carcinoma (2007)

Stroma-specific genetic alterations are associated with smoking-related head and neck SCC genesis. These findings suggest novel prognostic or diagnostic biomarkers and identify potential new molecular targets for therapeutic and preventive intervention.
Human monoclonal rheumatoid factors augment arthritis in mice by the activation of T cells (1996)

In order to investigate the in vivo role of rheumatoid factor (RF), the effects of the administration of human monoclonal (m) IgM-RF and IgG-RF on the development of arthritis in mice were examined. The administration of human mRFs into mice immunized with type II collagen (CII) markedly enhanced the clinical score and paw swelling. The severity of arthritic joint disease with a marked infiltration of lymphoid cells, proliferation of synovial membrane, pannus formation and destruction of articular cartilage was significantly enhanced in both groups receiving RF (RF-enhanced arthritis). Skin ulcers were also observed in some of these RF-enhanced arthritis mice, whereas no such signs were observed in CII-immunized mice without mRFs. Both IgM-RF and IgG-RF increased CII-specific IgG antibodies in circulation, and the severity of arthritis correlated with the production of high titres of anti-CII antibodies. In vivo treatment of RF-enhanced arthritis mice with an anti-CD4 MoAb or an anti-CD8 MoAb inhibited the induction and progression of arthritis in these mice. Administration of RF to severe combined immunodeficient (SCID) mice with arthritis developed by the transfer of spleen cells from CII-immunized mice, prolonged the arthritis and enhanced the severity. This murine model of RF-enhanced arthritis may provide a useful tool for analysing the pathogenesis of rheumatoid arthritis in RF-positive patients.
High-accuracy flush-and-scan software diagnostic (2001)

The software technique presented operates over a wide range of defect modes to quickly and accurately diagnose the failing latch in a defective chain without special circuitry or pattern generation. The high-accuracy flush-and-scan software diagnostic technique localizes scan chain defects. Rather than using special tests or circuits, the flush-and-scan technique records the signatures of failures resulting from normal test patterns, and uses software simulations to locate defects. To identify a defective latch, this technique repeatedly simulates different loads (initializations) until the simulation results match those from the tester.