gebhart/patrepeval huggingface dataset:
Ultrahigh Speed Spin-Transfer Magnetization Switching in Magnetic Multilayers (2006)

It has been demonstrated recently that the magnetization of a nano magnet can be switched by spin-transfer effect within 200 ps. This result is promising for the application of spin-transfer effect to magnetic random access memory. Contrary to thermally-assisted reversal, the switching process slows down with increasing temperature. We analyze these results in terms of a phenomenological model which takes into account the incoherent precession of the magnetization. The results suggest that coherent precession is a key to realize ultra fast switching.
Killing Hypoxic Cell Populations in a 3D Tumor Model with EtNBS-PDT (2011)

An outstanding problem in cancer therapy is the battle against treatment-resistant disease. This is especially true for ovarian cancer, where the majority of patients eventually succumb to treatment-resistant metastatic carcinomatosis. Limited perfusion and diffusion, acidosis, and hypoxia play major roles in the development of resistance to the majority of front-line therapeutic regimens. To overcome these limitations and eliminate otherwise spared cancer cells, we utilized the cationic photosensitizer EtNBS to treat hypoxic regions deep inside in vitro 3D models of metastatic ovarian cancer. Unlike standard regimens that fail to penetrate beyond ∼150 µm, EtNBS was found to not only penetrate throughout the entirety of large (>200 µm) avascular nodules, but also concentrate into the nodules' acidic and hypoxic cores. Photodynamic therapy with EtNBS was observed to be highly effective against these hypoxic regions even at low therapeutic doses, and was capable of destroying both normoxic and hypoxic regions at higher treatment levels. Imaging studies utilizing multiphoton and confocal microscopies, as well as time-lapse optical coherence tomography (TL-OCT), revealed an inside-out pattern of cell death, with apoptosis being the primary mechanism of cell killing. Critically, EtNBS-based photodynamic therapy was found to be effective against the model tumor nodules even under severe hypoxia. The inherent ability of EtNBS photodynamic therapy to impart cytotoxicity across a wide range of tumoral oxygenation levels indicates its potential to eliminate treatment-resistant cell populations.
Flexible pillars for displacement compensation in optical chip assembly (2006)

In chip-to-chip optical interconnect systems with surface mounted light-sources and detectors, thermal and mechanical effects can cause lateral displacements of the assembled devices. These displacements can result in optical signal losses that can critically deteriorate the bit-error-rate of the digital system. We demonstrate that, for a given loss budget of 1 dB, the use of flexible optical pillars with 150-μm height and 50-μm diameter can double the lateral displacement tolerance from about 15 to 30 μm. The pillars fabricated from Avatrel polymer form an air-free path between the light source and the substrate and cause maximum optical power losses less than 0.2 dB.
Office of Legacy Management Decision Tree for Solar Photovoltaic Projects - 13317 (2013)

To support consideration of renewable energy power development as a land reuse option, the DOE Office of Legacy Management (LM) and the National Renewable Energy Laboratory (NREL) established a partnership to conduct an assessment of wind and solar renewable energy resources on LM lands. From a solar capacity perspective, the larger sites in the western United States present opportunities for constructing solar photovoltaic (PV) projects. A detailed analysis and preliminary plan was developed for three large sites in New Mexico, assessing the costs, the conceptual layout of a PV system, and the electric utility interconnection process. As a result of the study, a 1,214-hectare (3,000-acre) site near Grants, New Mexico, was chosen for further study. The state incentives, utility connection process, and transmission line capacity were key factors in assessing the feasibility of the project. LM's Durango, Colorado, Disposal Site was also chosen for consideration because the uranium mill tailings disposal cell is on a hillside facing south, transmission lines cross the property, and the community was very supportive of the project. LM worked with the regulators to demonstrate that the disposal cell's long-term performance would not be impacted by the installation of a PV solar system. A number ofmore » LM-unique issues were resolved in making the site available for a private party to lease a portion of the site for a solar PV project. A lease was awarded in September 2012. Using a solar decision tree that was developed and launched by the EPA and NREL, LM has modified and expanded the decision tree structure to address the unique aspects and challenges faced by LM on its multiple sites. The LM solar decision tree covers factors such as land ownership, usable acreage, financial viability of the project, stakeholder involvement, and transmission line capacity. As additional sites are transferred to LM in the future, the decision tree will assist in determining whether a solar PV project is feasible on the new sites. (authors)« less
Hypoxia: Importance in tumor biology, noninvasive measurement by imaging, and value of its measurement in the management of cancer therapy (2006)

This workshop yielded recommendations on using hypoxia measurement to identify patients who would respond best to radiation therapy, which would improve treatment planning. This represents a narrow focus, as hypoxia measurement might also prove useful in drug development and in increasing our understanding of tumor biology.
Limits on amplification of picosecond pulses by using semiconductor laser traveling-wave amplifiers (1991)

The limiting factors in picosecond pulse amplification by semiconductor traveling-wave laser amplifiers are investigated, including the effects of the spontaneous emission. For the amplifier with a negligible amount of spontaneous emission, amplification is limited by the energy saturation for low-repetition-rate pulses, while the power saturation is the limiting factor for high-repetition-rate pulses. The spontaneous emission decreases both the signal gain of the amplifier and the signal-to-noise ratio considerably. The effective gain recovery time and the effective saturation energy are strong functions of the input pulse energy, and the amount of the spontaneous emission.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biomarkers of Rotator Cuff Disease Severity and Repair Healing (2018)

* Identifying biomarkers of disease severity and prognostic factors for healing after rotator cuff repair would allow improved clinical decision-making about the treatment of patients with rotator cuff pathologies and possibly identify targets for therapeutic intervention to promote healing. * The state of investigations to identify biomarkers of disease severity or repair success has been neither systematic nor standardized. Clinical studies to date have been largely exploratory, with small sample sizes and univariate analyses. * Current evidence shows that inflammatory biomarkers (interleukin 1 [IL-1β], interleukin 1 receptor antagonist [IL-1ra], tumor necrosis factor alpha [TNF-α], cyclooxygenase-2 [COX-2], inducible nitric oxide synthase [iNOS]) and matrix remodeling biomarkers (biglycan, aggrecan, and members of the collagen and matrix metalloproteinase [MMP] families) were found to be significantly associated with rotator cuff disease severity. Similarly, inflammatory biomarker COX-2 and matrix remodeling biomarkers (biglycan, tissue inhibitor of metalloproteinase [TIMP]-1, and members of the collagen and MMP families) were found to be significantly associated with rotator cuff retears. * Future studies investigating biomarkers of rotator cuff disease severity and healing should be standardized and should employ sample sizes large enough to allow for adequate power and multivariate analyses. Genetic and cellular biomarkers should be investigated, in addition to the more typical biochemical and structural factors. Progress would be greatly facilitated by forming a consortium of experts to define a strategic approach to biomarker research in rotator cuff disease and repair.
Identification of a Selective G1-Phase Benzimidazolone Inhibitor by a Senescence-Targeted Virtual Screen Using Artificial Neural Networks (2015)

Cellular senescence is a barrier to tumorigenesis in normal cells, and tumor cells undergo senescence responses to genotoxic stimuli, which is a potential target phenotype for cancer therapy. However, in this setting, mixed-mode responses are common with apoptosis the dominant effect. Hence, more selective senescence inducers are required. Here we report a machine learning-based in silico screen to identify potential senescence agonists. We built profiles of differentially affected biological process networks from expression data obtained under induced telomere dysfunction conditions in colorectal cancer cells and matched these to a panel of 17 protein targets with confirmatory screening data in PubChem. We trained a neural network using 3517 compounds identified as active or inactive against these targets. The resulting classification model was used to screen a virtual library of ~2M lead-like compounds. One hundred and forty-seven virtual hits were acquired for validation in growth inhibition and senescence-associated β-galactosidase assays. Among the found hits, a benzimidazolone compound, CB-20903630, had low micromolar IC50 for growth inhibition of HCT116 cells and selectively induced senescence-associated β-galactosidase activity in the entire treated cell population without cytotoxicity or apoptosis induction. Growth suppression was mediated by G1 blockade involving increased p21 expression and suppressed cyclin B1, CDK1, and CDC25C. In addition, the compound inhibited growth of multicellular spheroids and caused severe retardation of population kinetics in long-term treatments. Preliminary structure-activity and structure clustering analyses are reported, and expression analysis of CB-20903630 against other cell cycle suppressor compounds suggested a PI3K/AKT-inhibitor-like profile in normal cells, with different pathways affected in cancer cells.
Activation of the glucocorticoid–receptor complex (1982)

A crucial step in the interaction of glucocorticoids with target cells is the activation step, which involves a conformational change in the cytoplasmic glucocorticoid-receptor protein complexes and facilitates their binding to the cell nucleus. Activation can be quantified by measuring the ability of glucocorticoid-receptor complexes to bind to polyanions, such as DNA-cellulose, and unactivated complexes can be separated from activated complexes by rapid ion exchange chromatography using diethylaminoethyl (DEAE)-Sephadex or DEAE-cellulose. Activation occurs in vivo under physiological conditions and the rate of activation of cytoplasmic glucocorticoid-receptor complexes can be enhanced in vitro by physical manipulations (elevated temperature, increased ionic strength, dilution). In vitro studies suggest that activation is a regulated process and a low molecular weight component termed modulator, which has been identified in rat hepatic cytosol, inhibits activation. Additional studies employing phosphatase inhibitors, such as molybdate, and purified calf intestinal alkaline phosphatase suggest that either the receptor protein or a regulatory component is dephosphorylated during activation. Results obtained with specific chemical probes suggest that activation results in the exposure of basic amino acid residues consisting minimally of lysine, arginine, and histidine. Pyridoxal 5'-phosphate, a specific probe for lysine residues, exerts dual effects on glucocorticoid-receptor complexes, since it stimulates the rate of activation and also inhibits the binding of previously activated complexes to nuclei or DNA-cellulose. The ability of 1,10-phenanthroline, a metal chelator, to inhibit the DNA-cellulose binding of activated complexes suggests that a metal ion(s) located at or near the DNA binding site may become exposed as a consequence of activation. Collectively, the results of these various experiments suggest that activation is a regulated biochemical phenomenon with physiological significance.
A novel specific PERK activator reduces toxicity and extends survival in Huntington's disease models (2020)

One of the pathways of the unfolded protein response, initiated by PKR-like endoplasmic reticulum kinase (PERK), is key to neuronal homeostasis in neurodegenerative diseases. PERK pathway activation is usually accomplished by inhibiting eIF2α-P dephosphorylation, after its phosphorylation by PERK. Less tried is an approach involving direct PERK activation without compromising long-term recovery of eIF2α function by dephosphorylation. Here we show major improvement in cellular (STHdh<sup>Q111/111</sup>) and mouse (R6/2) Huntington's disease (HD) models using a potent small molecule PERK activator that we developed, MK-28. MK-28 showed PERK selectivity in vitro on a 391-kinase panel and rescued cells (but not PERK-/- cells) from ER stress-induced apoptosis. Cells were also rescued by the commercial PERK activator CCT020312 but MK-28 was significantly more potent. Computational docking suggested MK-28 interaction with the PERK activation loop. MK-28 exhibited remarkable pharmacokinetic properties and high BBB penetration in mice. Transient subcutaneous delivery of MK-28 significantly improved motor and executive functions and delayed death onset in R6/2 mice, showing no toxicity. Therefore, PERK activation can treat a most aggressive HD model, suggesting a possible approach for HD therapy and worth exploring for other neurodegenerative disorders.
Heterogeneous Electron-Transfer Kinetics for Ruthenium and Ferrocene Redox Moieties through Alkanethiol Monolayers on Gold (2003)

The standard heterogeneous electron-transfer rate constants between substrate gold electrodes and either ferrocene or pentaaminepyridine ruthenium redox couples attached to the electrode surface by various lengths of an alkanethiol bridge as a constituent of a mixed self-assembled monolayer were measured as a function of temperature. The ferrocene was either directly attached to the alkanethiol bridge or attached through an ester (CO(2)) linkage. For long bridge lengths (containing more than 11 methylene groups) the rate constants were measured using either chronoamperometry or cyclic voltammetry; for the shorter bridges, the indirect laser induced temperature jump technique was employed to measure the rate constants. Analysis of the distance (bridge length) dependence of the preexponential factors obtained from an Arrhenius analysis of the rate constant versus temperature data demonstrates a clear limiting behavior at a surprisingly small value of this preexponential factor (much lower than would be expected on the basis of aqueous solvent dynamics). This limit is independent of both the identity of the redox couple and the nature of the linkage of the couple to the bridge, and it is definitely different (smaller) from the limit derived from an equivalent analysis of the rate constant (versus temperature) data for the interfacial electron-transfer reaction through oligophenylenevinylene bridges between gold electrodes and ferrocene. There are a number of possible explanations for this behavior including, for example, the possible effects of bridge conformational flexibility upon the electron-transfer kinetics. Nevertheless, conventional ideas regarding electronic coupling through alkane bridges and solvent dynamics are insufficient to explain the results reported here.
Scanning probe microscopy based on magnetoresistive sensing (2011)

Integrated sensors are essential for scanning probe microscopy (SPM) based systems that employ arrays of microcantilevers for high throughput. Common integrated sensors, such as piezoresistive, piezoelectric, capacitive and thermoelectric sensors, suffer from low bandwidth and/or low resolution. In this paper, a novel magnetoresistive-sensor-based scanning probe microscopy (MR-SPM) technique is presented. The principle of MR-SPM is first demonstrated using experiments with magnetic cantilevers and commercial MR sensors. A new cantilever design tailored to MR-SPM is then presented and micromagnetic simulations are employed to evaluate the achievable resolution. A remarkable resolution of 0.84 Å over a bandwidth of 1 MHz is estimated, which would significantly outperform state-of-the-art optical deflection sensors. Due to its combination of high resolution at high bandwidth, and its amenability to integration in probe arrays, MR-SPM holds great promise for low-cost, high-throughput SPM.
Fabrication and Wetting Properties of Metallic Half-Shells with Submicron Diameters (2002)

The deposition of a thin, metal film onto an array of spherical silica colloids, followed by dissolution of the colloidal template, produces metallic half-shells with nanometer-scale dimensions. Half-shells of gold, platinum, and palladium were fabricated, with diameters of the particles ranging from 100 to 500 nm, and shell thicknesses of 8−15 nm. The half-shells have three useful properties because of their geometries: (i) a high ratio of surface area to volume, (ii) a large length of edge relative to size, and (iii) an entropic resistance to assembling into close-packed structures. The surface properties of these half-shells can be modified with self-assembled monolayers (SAMs), formed by adsorption of alkanethiols. The surfaces composed of aggregated gold half-shells are superhydrophobic; the measured contact angle of water on a surface of unmodified gold half-shells was ∼151° and on a surface of gold half-shells functionalized with a hexadecanethiolate SAM was ∼163°. Aggregates of half-shells were patterned using template-assisted self-assembly.
Multifunctional Platform Based on Electroactive Polymers and Silica Nanoparticles for Tissue Engineering Applications (2018)

Poly(vinylidene fluoride) nanocomposites processed with different morphologies, such as porous and non-porous films and fibres, have been prepared with silica nanoparticles (SiNPs) of varying diameter (17, 100, 160 and 300 nm), which in turn have encapsulated perylenediimide (PDI), a fluorescent molecule. The structural, morphological, optical, thermal, and mechanical properties of the nanocomposites, with SiNP filler concentration up to 16 wt %, were evaluated. Furthermore, cytotoxicity and cell proliferation studies were performed. All SiNPs are negatively charged independently of the pH and more stable from pH 5 upwards. The introduction of SiNPs within the polymer matrix increases the contact angle independently of the nanoparticle diameter. Moreover, the smallest ones (17 nm) also improve the PVDF Young's modulus. The filler diameter, physico-chemical, thermal and mechanical properties of the polymer matrix were not significantly affected. Finally, the SiNPs' inclusion does not induce cytotoxicity in murine myoblasts (C2C12) after 72 h of contact and proliferation studies reveal that the prepared composites represent a suitable platform for tissue engineering applications, as they allow us to combine the biocompatibility and piezoelectricity of the polymer with the possible functionalization and drug encapsulation and release of the SiNP.
Human monoclonal Fab fragments from a combinatorial library prepared from an individual with a low serum titer to a virus (1994)

An IgG1k lambda Fab library was generated on the surface of phage beginning with bone marrow RNA from a healthy 22-year-old human donor. The donor had been immunized to measles in his early childhood but had only a low serum titer to a measles antigen preparation. The resulting library of approximately 10(7) clones was panned against the measles antigen preparation and three positive Fab-producing clones identified by ELISA. One of the Fabs was found to be specific to measles and to bind with high apparent affinity (10(8) M-1). The other two bind with lower affinity and show marked cross-reactivity with a number of other antigens. They possess heavy chains derived, with extensive somatic modification, from the single member gene family VH6. The study indicates that both high-affinity specific antibodies and lower affinity polyreactive antibodies can be derived from the library approach under appropriate conditions.
Measurement of Faraday rotation using phase-sensitive low-coherence interferometry (2009)

We report a differential phase sensor capable of measuring Faraday rotation in reflection mode with a single measurement and a small field-depth factor. Based on a polarization-maintaining-fiber low-coherence interferometer, the sensor measures phase difference between two decorrelated and oppositely polarized circular states incident on a sample. Sensitivity of the sensor for the Faraday rotation is 0.31 arcmin, allowing applications on small volumes of liquids. The Verdet constants of various liquids, including clear and turbid samples, are measured at 857 nm.
Organic circuits on flexible substrates (2006)

The technology of flexible integrated circuits based on thin-film field-effect transistors with organic semiconductor layers has advanced quite rapidly over the past few years, and the first commercial applications are beginning to appear. This paper discusses a number of problems and challenges that remain, such as complementary logic, supply voltage, stability, and manufacturing cost
In Vitro Activity of wALADin Benzimidazoles against Different Life Cycle Stages of Plasmodium Parasites (2014)

wALADin1 benzimidazoles are specific inhibitors of δ-aminolevulinic acid dehydratase from Wolbachia endobacteria of filarial nematodes. We report that wALADin1 and two derivatives killed blood stage Plasmodium falciparum in vitro (50% inhibitory concentrations, 39, 7.7, and 12.8 μM, respectively). One of these derivatives inhibited gliding motility of Plasmodium berghei ANKA infectious sporozoites with nanomolar affinity and blocked invasion into hepatocytes but did not affect intrahepatocytic replication. Hence, wALADin1 benzimidazoles are tools to study gliding motility and potential antiplasmodial drug candidates.
ChemInform Abstract: A Novel Baylis—Hillman Protocol for the Synthesis of Functionalized Fused Furans. (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.
Supplementary Figures 1-2 from Polo-like Kinase 1 (Plk1) as a Novel Drug Target in Chronic Myeloid Leukemia: Overriding Imatinib Resistance with the Plk1 Inhibitor BI 2536 (2023)

Supplementary Figures 1-2 from Polo-like Kinase 1 (Plk1) as a Novel Drug Target in Chronic Myeloid Leukemia: Overriding Imatinib Resistance with the Plk1 Inhibitor BI 2536
Formal verification of FIRE (1997)

We present our experiences with the formal verification of an automotivechip used to control the safety features in a car. We useda BDD based model checker in our work. We describe our verificationmethodology for verifying a very complicated property on arelatively large design. We also describe the bugs that were foundand present our views on how to make model checking an effectiveintegrated part of the design flow for complex hardware systems.