gebhart/patrepeval huggingface dataset:
Sodium fluoride disrupts DNA methylation of H19 and Peg3 imprinted genes during the early development of mouse embryo (2013)

Sodium fluoride (NaF) is associated with embryonic and fetal development abnormalities, but the mechanism by which this occurs is unclear. DNA methylation, an important epigenetic reprogramming mechanism, is essential for normal embryonic development. Thus, we investigated the effect of NaF on DNA methylation in early mouse embryos, as well as mouse sperm and liver using bisulfite sequencing and ELISA. Data indicate that H19, a paternally imprinted gene, compared to control embryos, was less methylated in 8-cell embryos from pregnant mice treated with NaF (100 mg/l) in drinking water for 48 h. Peg3, a maternally imprinted gene, and the Line1 repeated sequence were similarly methylated in NaF-treated and control embryos. Oral ingestion of NaF for 35 days did not significantly change Line1 and genomic global DNA methylation in the liver. H19, Rasgrf1, Line1, and genomic global DNA methylation were also similar in NaF-treated and control sperm. Female mice mated with NaF-treated male mice (35 days) had less methylated H19, but Peg3 was significantly more methylated. Line1 was similarly methylated in treated 8-cell embryos, compared to control embryos. NaF treatment of male mice before copulation significantly increased the expression of H19 in blastocysts, whereas H19 expression was not detected in 8-cell embryos. Data suggest that NaF may interact directly with the embryo to disrupt the maintenance of normal gene imprinting during pregnancy. Long-term NaF exposure of males may not directly affect DNA methylation of the sperm and liver, but the sperm may signal to early embryos with abnormal gene imprinting.
Experimental investigations of stimulated Brillouin scattering beam combination (1992)

We conducted an experimental investigation of beam combination of two beams by stimulated Brillouin scattering (SBS) to determine the conditions under which good phase locking, piston conjugation, and aberration correction could be achieved. Test parameters that were varied included bandwidth, f-number, near- and far-field separation between beams, power ratio between beams, beam aberrations, and polarization mismatch between the beams. The experiments were performed at 532 nm with n-hexane as the SBS medium. Piston-conjugation accuracy was measured by using fringe stability with conventional interferometry and by using extinction in a wave-front-reversing interferometer. The best piston conjugation was obtained when we maximized the overlap of the SBS interaction volumes of the two beams by minimizing the beam separation in the near and the far fields.
Sequential detergent fractionation of primary neurons for proteomics studies (2008)

Proteomics studies employing primary neurons are difficult due to the neurons' characteristics. We have developed a detergent-based fractionation method which reduces complexity of the protein extracts, is sufficiently fast to allow differential proteomics analysis after treatments of neurons for short time periods, can be applied to small numbers of cells directly in culture plates, and allows differential extraction of proteins in a compartment-specific manner. The sequential use of detergent-containing buffers on neurons in culture plates yields four extracts enriched in cytosolic, membrane-bound or enclosed, nuclear, and cytoskeletal proteins. Fractionation of neurons was validated by comparison of the distribution of known subcellular marker proteins in the four extracts using Western blotting. Comparison of extracts by DIGE showed a clear difference in protein composition demonstrating significant variations with a fold change (FC) of at least 1.20 for 82% of the detected spots. Using proteins identified in these spots that could be assigned a subcellular localization based on descriptions in the Uniprot database, an extraction efficiency of 85% was calculated for cytosolic proteins in extract 1, 90% for membrane-bound and membrane-enclosed proteins in extract 2, 82% for nuclear proteins in extract 3 and 38% for cytoskeletal and RAFT proteins in extract 4.
Small Molecule ONC201/TIC10 Induces Caspase-Dependent Apoptosis in Acute Lymphoblastic Leukemia Cells Via Modulation of Bcl-2 and IAP Family Proteins (2014)

Abstract ONC201/TIC10 is a potent small molecule anti-tumor agent in several types of solid tumors and lymphomas. ONC201/TIC10 is on track to enter clinical trials for patients with advanced cancer in 2014, with IND issued by the FDA in March, 2014. Early trials will evaluate the safety and efficacy of ONC201/TIC10 as a monoagent in hematological malignancies. In the current study, we evaluated the anti-cancer effects of the small molecule in Acute Lymphoblastic Leukemia (ALL). Analysis of cell viability by the CellTiter-Glo method revealed that ONC201/TIC10 treatment reduces the viability of three ALL cell lines (Reh, Jurkat, MOLT-4) in a dose- (2.5/5/10 μM) and time-dependent manner (24/48/72 h). We have previously reported that ONC201/TIC10-mediated reduction in cell viability and apoptosis in various types of solid tumors occurs at 60/72 h. Interestingly, ONC201/TIC10 reduces the viability of ALL cell lines within 24/48 h at the indicated doses. An inactive TIC10 isomer compound synthesized by Medkoo Biosciences with a structure related to the active ONC201/TIC10 compound does not reduce the viability of ALL cells. Sub-G1 analysis indicated that ONC201/TIC10 induces apoptosis in ALL cells and a pan-caspase inhibitor reduces ONC201/TIC10-mediated apoptosis. Western blot analysis was used to further investigate the mechanism of ONC201/TIC10-mediated apoptosis. ONC201/TIC10-mediated apoptosis involves PARP cleavage and caspase-9 activation. Anti-apoptotic Bcl-2 family members Bcl-2 and Bcl-xl are downregulated while the pro-apoptotic Bcl-2 family member Bim is upregulated in response to ONC201/TIC10 treatment. ONC201/TIC10 also downregulates the inhibitor of apoptosis (IAP) family proteins cIAP1 and cIAP2. We have previously shown that the anti-tumor effect of ONC201/TIC10 involves inhibition Akt and ERK phosphorylation resulting in Foxo3a activation and TRAIL-gene transcription. We observed inhibition of Akt phosphorylation upon ONC201/TIC10 treatment of ALL cells. Thus, ONC201/TIC10 holds promise as a novel agent for the treatment of ALL based on its robust activity in preclinical models of the disease. Our ongoing studies are evaluating the impact of this novel therapy on ALL cells with different translocations, and are introducing combination therapy with ONC201/TIC10 for ALL. Figure 1 Figure 1. Disclosures Allen: Oncoceutics: Employment, Equity Ownership, Patents & Royalties. El-Deiry:Oncoceutics, Inc.: Equity Ownership, Patents & Royalties.
Technology and applications of micromachined adaptive mirrors (1999)

The end of the cold war and the introduction of military technologies to the market has created new application fields for many originally military technologies. One of these technologies is adaptive optics, dealing with dynamic control of the quality of an optical system. As for almost any technology `imported' from the military research field, adaptive optics is expensive. Fortunately there are many civil applications for adaptive optics which produce the necessary development thrust.
Adaptive local tone mapping based on retinex for high dynamic range images (2013)

In this paper, we present a new tone mapping technique for high dynamic range images based on the retinex theory. Our algorithm consists of two steps, global adaptation and local adaptation of the human visual system. In the local adaptation process, the Gaussian filter of the retinex algorithms is substituted with a guided filter to reduce halo artifacts. To guarantee good rendition and dynamic range compression, we propose a contrast enhancement factor based on the luminance values of the scene. In addition, an adaptive nonlinearity offset is introduced to deal with the strength of the logarithm function's nonlinearity. Experiments show that our algorithm provides satisfactory results while preserving details and reducing halo artifacts.
Participation of an endogenous inhibitor of fucosyltransferase activities in the developmental regulation of intestinal fucosylation processes (1991)

During the rat weaning period (about day 19 after birth) the intestinal maturation is accompanied by a drastic increase in the fucose content of mucosal glycoconjugates, concomitant with an increase in fucosyltransferase activities. The regulation of this fucosylation process appears to be a rather complex phenomenon, which involves several systems controlling fucosyltransferase activity or substrate availability. An endogenous protein inhibitor of the fucosyltransferase activities displays an opposite developmental pattern to that of fucosyltransferase activities, since its activity is high before weaning and is decreased 5-fold after weaning. Similarly, the GDP-fucose pyrophosphatase activity markedly decreases at weaning. The transformation of GDP-mannose into GDP-fucose increases early, at day 18, preceding the increase in fucosyltransferase activities. Before weaning, and especially at days 14 and 18, high levels of GDP-4-dehydro-6-deoxymannose, the product of the GDP-mannose 4,6-dehydratase activity, are produced during the transformation of GDP-mannose into GDP-fucose, even in excess of reduced coenzyme. This fact indicates that the second step of the transformation (epimerase-reductase reaction) could be a limiting factor for GDP-fucose availability before weaning, but not after weaning. The inverse relationship between the mucosal fucose content (or the fucosyltransferase activity) and the endogenous protein inhibitor during normal postnatal development supports the hypothesis of a physiological role for this inhibitor.
Macrolactamization versus Macrolactonization: Total Synthesis of FK228, the Depsipeptide Histone Deacetylase Inhibitor (2008)

The cyclic depsipeptide FK228 is the only natural product histone deacetylase (HDAC) inhibitor that has advanced to clinical trials as an anticancer agent. While currently obtained by fermentation, total synthesis is an attractive alternative that will facilitate the preparation of unnatural analogues. The previous total syntheses of FK228 featured macrocylization by ester bond formation from a seco-hydroxy acid. Such routes are operationally jeopardized by the steric hindrance of the carboxylic acid and the sensitivity of the allylic alcohol toward elimination. We report a strategically different approach whereby the ester bond is formed intermolecularly at an early stage and macrocyclization is efficiently achieved by amide bond formation.
Degradation and applications of polyhydroxyalkanoates (1995)

A series of tests is available to study the biodegradation of plastic materials under either laboratory or field conditions. Most of the standard methods have been published by the American Society for Testing and Materials. All of them describe techniques to investigate the biodegradation of plastics under laboratory conditions. Microbially formed polyhydroxyalkanoates (PHAs) have been marketed recently as biodegradable plastics. However, currently only a few articles made from PHAs (e.g., bottles) are commercially available. A series of microorganisms (prokaryotes as well as eukaryotes) has been characterized as being able to degrade PHAs. With one exception (Ilyobacter delafieldii), all of them were isolated from aerobic environments. So far, over 10 different extracellular PHA depolymerases have been purified and characterized. Depolymerases that preferentially attack PHAs with monomer units other than 3-hydroxybutyrate have been found only in Pseudomonas fluorescens and Pseudomonas lemoignei.Key words: poly(3-hydroxybutyrate), polyhydroxyalkanoates, biodegradation, industrial applications.
Co-optimizing grating couplers for hybrid integration of InP and SOI photonic platforms (2018)

Grating couplers are widely used optical interfaces in integrated photonics, especially on the Silicon-On-Insulator (SOI) platform. Their design has been optimized for coupling light between a Photonic Integrated Circuit (PIC) and a single-mode fiber, a μlens for free space transport, or even a second PIC in the same SOI platform. In this work, we co-design matching pairs of grating-couplers on distinct SOI and InP photonic platforms for optimized PIC-to-PIC coupling. By matching the scattering strengths of the two grating-couplers, we show that a PIC-to-PIC insertion loss of 3dB can be achieved. We also investigate how the design parameters impact the coupling efficiency and the bandwidth, ending up with a tolerance analysis. The proposed coupling approach between two different waveguide materials has prospective applications for the hybrid-integration of SOI and InP photonic platforms for communication technologies.
Self-massage and Autonomic Response: Future Direction (2017)

Self-massage (SM) is an active technique where participants use various instruments to apply pressure to soft tissue with an attempt to mimic manual therapy techniques. Within the literature, there are many techniques associating positive responses to the phenomena controlled by the central nervous system (i.e. stretching and manual therapies). The purpose of this short communication is to present the literature regarding similar techniques to SM and their effects on the central nervous system. Furthermore, there is no research investigating the safety of performing SM techniques prior to performance. Considering SM is non-invasive and practical, findings of such research would be applicable in clinical and performance settings. Thus, the authors encourage further research that satisfies the needs of these gaps.
Detection of ship targets near coastline by using Doppler Beam Sharpening technique (2011)

If ship targets are near the coastline or islands, it's very difficult for the conventional anti-ship missile to detect them because the echo signal from the land inside the beam-width and same range resolution with the target can hide the target. As the missile approaches the target, the area and RCS of the land patch gets smaller, so that the conventional anti-ship missile can only detect the target at the very short range. The DBS(Doppler Beam Sharpening) technique is known to have been applied to the anti-ship missile to detect the ship target at the long range by discriminating the target from the land by using the difference of Doppler frequency. In this paper we investigate the principle of DBS technique theoretically and analyze the effectiveness by computer simulation.
Environmental impacts of electric vehicles in South Africa : research article (2012)

Electric vehicles have been seen by some policymakers as a tool to target reductions in greenhouse gas emissions. Some researchers have shown that the full environmental impact of electric vehicles depends very much on the cleanliness of the electricity grid. In countries such as the USA and China, where coal-fired power plants still play a very important role in electricity generation, the environmental impact of electric vehicles is equivalent to, or even higher than that of cars running on internal combustion engines. In this study, the environmental impacts of electric vehicles in South Africa were investigated. We found that, as the bulk of South Africa's electricity is generated from relatively low-quality coal and the advanced exhaust clean up technologies are not implemented in the current coal-fired power plants, the use of electric vehicles in South Africa would not help to cut greenhouse gas emissions now (2010) or in the future (in 2030 using the IRP 2010 Revision 2, policy-adjusted IRP scenario), and actually would lead to higher SOx and NOx emissions.
L-valley electrons in SiGe heterostructures: highly anisotropic and tunable Zeeman and Rashba-like spin splittings (2005)

We have conducted a detailed and systematic analysis of Zeeman and Rashba‐like (structure‐asymmetry‐induced) spin splittings in SiGe heterostructures. The calculations were performed in the framework of a relevant kp model, developed specifically for the L point states of the group IV semiconductors. Effects of the alloy composition, crystallographic orientation, spatial confinement, strain, and electric field are accounted for and documented for a realistic structure design. Notable Rashba effect, considerable anisotropy and deviation of the g tensor components from their respective bulk values make the SiGe structures a friendly choice for the effective spin manipulation.
Access control enforcement for conversation-based web services (2006)

Service Oriented Computing is emerging as the main approach to build distributed enterprise applications on the Web. The widespread use of Web services is hindered by the lack of adequate security and privacy support. In this paper, we present a novel framework for enforcing access control in conversation-based Web services. Our approach takes into account the conversational nature of Web services. This is in contrast with existing approaches to access control enforcement that assume a Web service as a set of independent operations. Furthermore, our approach achieves a tradeoff between the need to protect Web service's access control policies and the need to disclose to clients the portion of access control policies related to the conversations they are interested in. This is important to avoid situations where the client cannot progress in the conversation due to the lack of required security requirements. We introduce the concept of k-trustworthiness that defines the conversations for which a client can provide credentials maximizing the likelihood that it will eventually hit a final state.
Approximation algorithms for disjoint paths problems (1996)

The construction of disjoint paths in a network is a basic issue in combinatorial optimization: given a network, and specified pairs of nodes in it, we are interested in finding disjoint paths between as many of these pairs as possible. This leads to a variety of classical NP-complete problems for which very little is known from the point of view of approximation algorithms. It has recently been brought into focus in work on problems such as VLSI layout and routing in high-speed networks; in these settings, the current lack of understanding of the disjoint paths problem is often an obstacle to the design of practical heuristics.
Cleavage of optical fibres following diamond-wedge indentation (1988)

Abstract A major problem in the fibre-optics and communications area is the coupling of two fibre ends with the minimum of transmission loss across the interface. The fibre end faces need to be flat, smooth and at right angles to the fibre axes. A method of achieving this is described. It involves first adding a short precursor crack to the fibre by indentation with a diamond wedge under carefully controlled conditions and then pulling the fibre along its axis until it fractures. The length of the precursor crack is critical, since if it is too long it, and the associated indentation damage, affect the transmission, and if it is too short the final fracture no longer traverses the fibre smoothly but produces rough fracture surfaces. The angle of the diamond wedge is also important if it is to produce a good precursor crack and be capable of repeated use without suffering damage. Experiments are described which optimize the diamond wedge angle and the loads. A model is developed relating the length of the precursor crack formed by wedge indentation and the applied load and wedge angle.
Elements of naturality in dynamical simulation frameworks for Hamiltonian, thermostatic, and Lindbladian ows on classical and quantum state-spaces (2010)

The practical focus of this work is the dynamical simulation of polarization transport processes in quantum spin microscopy and spectroscopy. The simulation framework is built-up progressively, beginning with state-spaces (configuration manifolds) that are geometrically natural, introducing coordinates that are algebraically natural; and finally specifying dynamical potentials that are physically natural; in each respect explicit criteria are given for naturality. The resulting framework encompasses Hamiltonian flow (both classical and quantum), quantum Lindbladian processes, and classical thermostatic processes. Constructive validation and verification criteria are given for metric and symplectic flows on classical, quantum, and hybrid state-spaces, with particular emphasis to tensor network state-spaces. Both classical and quantum examples are presented, including dynamic nuclear polarization (DNP). A broad span of applications and challenges is discussed, ranging from the design and simulation of quantum spin microscopes to the design and simulation of quantum oracles.
Self-Assembled Peptide Nanotubes Are Uniquely Rigid Bioinspired Supramolecular Structures (2005)

We recently presented a novel class of self-assembled diphenylalanine-based peptide nanotubes. Here, for the first time, we present their mechanical properties, which we directly measured through indentation type experiments using atomic force microscopy. We find that the averaged point stiffness of the nanotubes is 160 N/m, and that they have a correspondingly high Young's modulus of approximately 19 GPa, as calculated by finite element analysis. This high value places these peptide nanotubes among the stiffest biological materials presently known, making them attractive building blocks for the design and assembly of biocompatible nanodevices.
Poly(ADP-Ribose) Polymerase Inhibition Prevents Homocysteine-Induced Endothelial Dysfunction in the Isolated Rat Aorta (2004)

Recent studies have clearly shown that there is a relationship between hyperhomocysteinemia and endothelial dysfunction. However, the effect of poly(ADP-ribose) polymerase (PARP) inhibition on homocysteine (Hcy)-induced endothelial damage has not been investigated. In this study, we investigated whether the loss of endothelial function in rat aortic rings preincubated with Hcy is dependent upon the PARP pathway within the vasculature. Preincubation of rat aortic rings with Hcy (1 mmol/l; 180 min) significantly inhibited endothelium-dependent relaxation in this tissue. This inhibitory effect was significantly reduced in the presence of both superoxide dismutase (100 U ml(-1)) and catalase (100 U ml(-1)) together with Hcy. Similarly, preincubation for 180 min with either N-(6-oxo-5,6-dihydro-phenanthridin-2-yl)-N,N-dimethylacetamide hydrochloride (PJ34; 3 micromol/l) or 3-aminobenzamide (3 mmol/l), structurally different PARP inhibitors, also significantly prevented the development of endothelial dysfunction induced by Hcy. Further incubation of aortic rings with these PARP inhibitors for 60 min after exposure to Hcy for 180 min, at least in part, improved the endothelium-dependent relaxation responses. Thus, our results suggest that intraendothelial PARP activation may be associated with endothelial dysfunction in hyperhomocysteinemic conditions and that inhibition of this pathway may present a novel pharmacological approach to prevent Hcy-induced endothelial damage. Suprisingly, inhibition of the PARP pathway not only prevents the endothelial dysfunction mediated by Hcy, but is also able to rapidly improve it.
Certification of Si powder diffraction standard reference material 640a (1983)

A new lot of high-purity silicon powder with mean crystallite size of about 6 μm has been certified as Standard Reference Material 640a. This SRM can be used as both an external and an internal 2θ calibration standard. The lattice parameter, uncorrected for refraction, is a = 5.430825(11) for λ(Cu Kα1) = 1.5405981 Å at 298.1 K.