gebhart/patrepeval huggingface dataset:
Characterization of A1, a novel hemopoietic-specific early-response gene with sequence similarity to <i>bcl-2</i> . (1993)

Granulocyte-macrophage colony-stimulating factor (GM-CSF) stimulates hemopoietic cell proliferation, differentiation, and functional activation by inducing the expression of specific genes. As part of an investigation of the regulation of gene expression by GM-CSF, we have previously identified a novel murine GM-CSF-inducible gene, A1. In this report, we present the complete nucleotide sequence of the A1 mRNA as well as a portion of the 5' flanking region, and describe the expression pattern of the gene. The results demonstrate that A1 is a hemopoietic tissue-specific gene that is expressed in several hemopoietic cell lineages, including T-helper lymphocytes, macrophages, and neutrophils. In murine bone marrow-derived macrophages, A1 gene expression is rapidly and transiently induced by GM-CSF, and the induction was independent of de novo protein synthesis. In addition to GM-CSF, a transient induction of A1 mRNA accumulation was observed in response to LPS in macrophages. This induction is not mediated by IL-1 alpha or IL-6, neither of which stimulate A1. In the myeloid precursor cell line, 32D cl3, A1 gene expression is stably induced during granulocyte colony-stimulating factor-stimulated myeloid cell differentiation. The A1 message encodes a predicted polypeptide with an M(r) of 20,024 and no signal peptide. The peptide sequence contains a region of 80 amino acids that shows similarity to bcl-2 and to the recently described bcl-2-related gene, MCL1. These data demonstrate that A1 is a novel early-response gene whose expression is associated with a variety of stimuli and occurs in several hemopoietic cell types.
Simple Enzymatic Means to Neutralize DNA Contamination in Nucleic Acid Amplification (2005)

Reverse transcription PCR (RT-PCR) is prone to false positives when contaminating DNA molecules are present at the start of a reaction. Contaminants that derive from earlier work using a given primer pair (carryover PCR products) are of particular concern when those primers are used routinely, as in clinical diagnostics or environmental monitoring. In addition, contamination by genomic DNA can significantly interfere with quantitative and qualitative analysis of RNAs by RT-PCR. Here we describe contaminant restriction (ConR), a method that can be used to neutralize carryover and genomic DNA contamination in RT-PCR studies. Restriction enzymes (REs) added to the amplification cocktail cleave contaminant DNA molecules while sparing the intended target nucleic acid. Restriction, reverse transcription, and amplification steps all take place in the same sealed vessel, thus avoiding any danger of recontamination. ConR eliminates carryover contamination in PCR without compromising target sequence amplification. Because the method is effective against both genomic and carryover contamination, it can be employed routinely in one-step RT-PCR, whatever the RNA target or the nature of the potential DNA contaminant. A variation of this decontamination method, amplicon primer site restriction (APSR), is effective specifically against carryover contamination. APSR, unlike ConR, can be applied during PCR-based amplification of DNA target molecules.
Microsystem 671 nm light source for shifted excitation Raman difference spectroscopy (2009)

We present a compact wavelength stabilized diode laser system at 671 nm on a micro-optical bench as a light source for shifted excitation Raman difference spectroscopy (SERDS). The laser system consists of two broad-area gain media in separate laser cavities using two reflection Bragg gratings with slightly different center wavelengths. A spectral width below 100 pm and a constant wavelength shift of 0.57 +/- 0.06 nm is obtained up to output powers of 250 mW. The suitability of this light source for SERDS is demonstrated using Raman spectra of ethanol with increasing concentrations of Cresyl Violet as the fluorescent contaminant.
Fast wavelet histogram techniques for image indexing (2002)

Image histograms have become very popular in image and video indexing applications because of their low complexity. However, histogram-based techniques are not efficient in retrieving texture images. A histogram technique that exploits the directional properties of a wavelet transform has been proposed in the literature. Although, this technique provides good retrieval performance for texture images, its complexity is very high. We propose fast wavelet histogram techniques that provide superior performance at a substantially reduced complexity.
Phase-based 3D optical flow sensors for motion detection (2011)

We demonstrate a computationally efficient technique for sensing optical flow using angle sensitive pixels. Angle-sensitive pixels function as spatial Gabor filters as a result of their periodic response to angle. Measuring temporal derivatives in the phase response of quadrature filters recovers information about object motion. These sensors work without a lens for global motion, or, with a lens to create a 3D map of object motion under ambient light.
Soil Heating for Enhanced Remediation of Chlorinated Solvents:  A Laboratory Study on Resistive Heating and Vapor Extraction in a Silty, Low-Permeable Soil Contaminated with Trichloroethylene (1998)

Thermally enhanced remediation of trichloroethylene (TCE) from a 50 cm deep silty soil was demonstrated in a two-dimensional laboratory tank. Volatilized TCE was captured by vapor extraction in an overlaying coarse sand layer. Soil vapor extraction was first tested alone at 23 °C, showing very little efficiency due to the low-permeable layer and an estimated cleanup time of more than 1 year. By injecting electric current, the temperature was increased to 85 and 100 °C in steps, and the fluxes of TCE increased by factors of 2.6 and 19, respectively. After 37 days of heating, the mass of TCE in the soil was reduced from 35 to 0.072 g, corresponding to 99.8% mass removal. Average soil TCE concentrations were reduced from 273 to 0.6 mg/kg. Steam production by boiling of pore water and a 9-fold increase in the Henry's law constant of TCE were identified as the major mechanisms for overcoming mass-transfer limitations. The silty soil did not dry out due to water addition at the current electrodes, which is promising for the use of thermal enhancements forremediation of water-saturated clay layers and in shallow groundwater. In-situ thermal cleanups can be done in a few months, at costs typically below $100/m3, and with very high removal efficiency for volatile and semivolatile organ ics.
ChemInform Abstract: Synthetic Methods (1986)

Abstract Review: (155 refs.
3D Molecular Representations Based on the Wave Transform for Convolutional Neural Networks (2018)

Convolutional neural networks (CNN) have been successfully used to handle three-dimensional data and are a natural match for data with spatial structure such as 3D molecular structures. However, a direct 3D representation of a molecule with atoms localized at voxels is too sparse, which leads to poor performance of the CNNs. In this work, we present a novel approach where atoms are extended to fill other nearby voxels with a transformation based on the wave transform. Experimenting on 4.5 million molecules from the Zinc database, we show that our proposed representation leads to better performance of CNN-based autoencoders than either the voxel-based representation or the previously used Gaussian blur of atoms and then successfully apply the new representation to classification tasks such as MACCS fingerprint prediction.
3-D description of normal moveout in anisotropic inhomogeneous media (1998)

Abstract We present a new equation for normal-moveout (NMO) velocity that describes azimuthally dependent reflection traveltimes of pure modes from both horizontal and dipping reflectors in arbitrary anisotropic inhomogeneous media. With the exception of anomalous areas such as those where common-midpoint (CMP) reflection time decreases with offset, the azimuthal variation of NMO velocity represents an ellipse in the horizontal plane, with the orientation of the axes determined by the properties of the medium and the direction of the reflector normal. In general, a minimum of three azimuthal measurements is necessary to reconstruct the best-fit ellipse and obtain NMO velocity in all azimuthal directions. This result provides a simple way to correct for the azimuthal variation in stacking velocity often observed in 3-D surveys. Even more importantly, analytic expressions for the parameters of the NMO ellipse can be used in the inversion of moveout data for the anisotropic coefficients of the medium. For homogeneous transversely isotropic media with a vertical axis of symmetry (VTI media), our equation for azimuthally dependent NMO velocity from dipping reflectors becomes a relatively simple function of phase velocity and its derivatives. We show that the zero-dip NMO velocity Vnmo(0) and the anisotropic coefficient η are sufficient to describe the P-wave NMO velocity for any orientation of the CMP line with respect to the dip plane of the reflector. Using our formalism, Vnmo(0) and ? (the only parameters needed for time processing) can be found from the dip-dependent NMO velocity at any azimuth or, alternatively, from the azimuthally dependent NMO for a single dipping reflector. We also apply this theory to more complicated azimuthally anisotropic models with the orthorhombic symmetry used to describe fractured reservoirs. For reflections from horizontal interfaces in orthorhombic media, the axes of the normal moveout ellipse are aligned with the vertical symmetry planes. Therefore, azimuthal P-wave moveout measurements can be inverted for the orientation of the symmetry planes (typically determined by the fracture direction) and the NMO velocities within them. If the vertical velocity is known, symmetry-plane NMO velocities make it possible to estimate two anisotropic parameters equivalent to Thomsen's coefficient δ for transversely isotropic media.
The electrical behavior of the fundamental high frequency (150 MHz) quartz crystal unit in the plasmatic environment (2002)

Both photolithography technique and chemical etching process were experimentally employed for producing 150 MHz rectangular AT-cut crystal resonators. A plasma treatment was employed for a frequency adjustment process by etching gold (Au) electrode films. A large frequency shift from a designed frequency was observed. In this paper, the reasons are electrically and chemically explained why the large frequency shifts occurred after a plasma treatment.
Safety Assessment of 1-Aminocyclopropane-1-carboxylic Acid Deaminase Protein Expressed in Delayed Ripening Tomatoes (1996)

Tomato plants with delayed fruit ripening have been produced by stable insertion of the gene encoding the 1-aminocyclopropane-1-carboxylic acid deaminase (ACCd) protein into the tomato chromosome. Two approaches were used to assess the safety of the ACCd protein for human consumption. Purified Escherichia coli-produced ACCd protein, which is chemically and functionally equivalent to the ACCd protein produced in delayed ripening tomato fruit, was used in these studies. First, the ACCd protein was readily degraded under simulated mammalian digestive conditions. Second, the ACCd protein did not have any deleterious effects when administered to mice by acute gavage at a dosage of up to 602 mg/kg of body weight. This dosage correlates to greater than a 5000- fold safety factor relative to the average daily consumption of tomatoes, assuming that all tomatoes consumed contain the ACCd protein. These results, in conjunction with previously published data, establish that ingestion of tomato fruit expressing the ACCd protein does not pose any safety concerns. Keywords: 1-Aminocyclopropane-1-carboxylic acid deaminase; delayed ripening tomato; protein safety; in vitro digestion; acute gavage
Activation of extracellular matrix metalloproteinases in equine laminitis (1998)

Samples of connective tissue obtained from the hoof of six laminitic and eight non-laminitic adult horses were analysed zymographically to investigate whether connective tissue matrix metalloproteinases are activated or induced during laminitis. The activity or matrix metalloproteinases was substantially greater in the tissues from the laminitic horses than in the tissues from the non-laminitic horses. A comparison of the collagenolytic activity in the laminitic and control tissues showed that collagenolytic activities corresponding to the 92 kDa (P < 0.001), 72 kDa (P < 0.01) and 66 kDa (P < 0.01) bands were induced in the laminitic tissues.
First‐in‐class cardiolipin‐protective compound as a therapeutic agent to restore mitochondrial bioenergetics (2013)

A decline in energy is common in aging, and the restoration of mitochondrial bioenergetics may offer a common approach for the treatment of numerous age-associated diseases. Cardiolipin is a unique phospholipid that is exclusively expressed on the inner mitochondrial membrane where it plays an important structural role in cristae formation and the organization of the respiratory complexes into supercomplexes for optimal oxidative phosphorylation. The interaction between cardiolipin and cytochrome c determines whether cytochrome c acts as an electron carrier or peroxidase. Cardiolipin peroxidation and depletion have been reported in a variety of pathological conditions associated with energy deficiency, and cardiolipin has been identified as a target for drug development. This review focuses on the discovery and development of the first cardiolipin-protective compound as a therapeutic agent. SS-31 is a member of the Szeto-Schiller (SS) peptides known to selectively target the inner mitochondrial membrane. SS-31 binds selectively to cardiolipin via electrostatic and hydrophobic interactions. By interacting with cardiolipin, SS-31 prevents cardiolipin from converting cytochrome c into a peroxidase while protecting its electron carrying function. As a result, SS-31 protects the structure of mitochondrial cristae and promotes oxidative phosphorylation. SS-31 represents a new class of compounds that can recharge the cellular powerhouse and restore bioenergetics. Extensive animal studies have shown that targeting such a fundamental mechanism can benefit highly complex diseases that share a common pathogenesis of bioenergetics failure. This review summarizes the mechanisms of action and therapeutic potential of SS-31 and provides an update of its clinical development programme.
Heterogeneous statistical QoS provisioning over 5G mobile wireless networks (2014)

As a critical step towards the next new era of mobile wireless networks, recently 5G mobile wireless networks have received significant research attention and efforts from both academia and industry. The 5G mobile wireless networks are expected to provide different delay-bounded QoS guarantees for a wide spectrum of services, applications, and users with extremely diverse requirements. Since the time-sensitive services in 5G multimedia wireless networks may vary dramatically in both a large range from milliseconds to a few seconds and diversity from uniform/ constant delay-bound to different/variable delay-bound guarantees among different wireless links, the delay-bound QoS requirements for different types of services promote the newly emerging heterogeneous statistical delay-bounded QoS provisioning over 5G mobile wireless networks, which, however, imposes many new challenging issues not encountered before in 4G wireless networks. To overcome these new challenges, in this article we propose a novel heterogeneous statistical QoS provisioning architecture for 5G mobile wireless networks. First, we develop and analyze the new heterogeneous statistical QoS system model by applying and extending the effective capacity theory. Then, through the wireless coupling channels, we apply our proposed heterogeneous statistical QoS architecture to efficiently implement the following powerful 5G-candidate wireless techniques: 1) device-to-device networks; 2) full-duplex networks; and 3) cognitive radio networks, respectively, for providing heterogeneous statistical delay-bounded QoS guarantees. Finally, using the simulation experiments we show that our proposed architecture and schemes significantly outperform the existing traditional statistical delay-bounded QoS provisioning schemes in terms of satisfying the heterogeneous delay-bounded QoS requirements while maximizing the aggregate system throughput over 5G mobile wireless networks.
A survey on automatic techniques for enhancement and analysis of digital photography (2013)

Abstract The fast growth in the consumer digital photography industry during the past decade has led to the acquisition and storage of large personal and public digital collections containing photos with different quality levels and redundancy, among other aspects. This naturally increased the difficulty in selecting or modifying those photos. Within the above context, this survey focuses on systematically reviewing the state-of-art on techniques for the enhancement and analysis of digital photos. Nevertheless, it is not within the scope of this survey to review image quality metrics for evaluating degradation due to compression, digital sensor noise, and affine issues. Assuming the photos have good quality in those aspects, this review is centered on techniques that might be useful to automate the task of selecting photos from large collections or to enhance the visual aspect of imperfect photos by using some perceptual measure.
Quality of Experience and Mobility-Aware Green Inter-Radio Access Technology Traffic Offloading (2016)

Traffic offloading among coexisting heterogeneous radio access technologies (RATs) (i.e., inter-RAT offloading) is considered an effective strategy for enhancing the capacity of wireless networks and reducing the power consumption of base stations (BSs) and mobile stations (MSs). To fully utilize inter-RAT offloading advantages, a mobility-aware evaluation is needed, which takes into account the combined effects of mobility and MSs/BSs spatial distributions on the performance gains. This thesis develops an analytical mobility-aware evaluation framework that accurately evaluates the performance of inter-RAT offloading while accounting for the MSs/BSs spatial distribution. This framework is then utilized to develop a novel mobility-aware inter-RAT offloading policy, which aims at associating a MS to the best RAT at any time that optimizes a predefined multi-criterion objective. Deploying a power saving mode (PSM) is also considered an effective solution for saving energy. To efficiently exploit the PSM power saving capabilities for voice over IP (VoIP) services, a quality of experience (QoE)-aware PSM performance evaluation is needed. This thesis develops an analytical evaluation framework that assesses the QoE and energy consumption achieved by a fixed PSM. Based on this framework, this thesis develops a novel QoE-aware PSM, which exploits the on-off characteristics of VoIP sessions to further improve the energy saving while accounting for the bursty losses effects on the QoE. Finally, benefits of deploying a PSM can be combined with those of utilizing inter-RAT offloading to maximize the energy saving while guaranteeing a desired level of QoE for VoIP services. This thesis develops an analytical inter-RAT offloading performance evaluation framework that assesses the QoE and energy consumption achieved by an inter-RAT traffic offloading policy taking into account the PSM being used. Based on this framework, this thesis develops a novel QoE/mobility-aware inter-RAT offloading policy that jointly utilizes the inter-RAT offloading and PSM for optimizing a predefined multi-criterion objective. The research in this thesis offers potentials for enhancing performance while reducing computational complexity. The numerical results validate the accuracy of the proposed performance evaluation frameworks and verify the efficacy of the proposed techniques in enhancing the performance compared to their counterparts.
Iterated Integrals of Differential Forms and Loop Space Homology (1973)

We continue to define iterated integrals 5w ... w, where wl, *., w, are 1forms. Such iterated integrals will be defined for forms wi, *-*, w, of arbitrary degrees on a manifold or, more generally, a suitably defined differentiable The space P(X) of piecewise smooth paths on a manifold X turns out to be a space. If wi, *.., w, are forms of respective degrees P1, ..., Pr on X, then the iterated integral Wi .. Wr is a form of degree Pi + * -1+ Prr on P(X). Let P(X; x0, xl) denote the subspace of P(X) consisting of paths from a given point x0 to another given point xl. We are interested in those iterated integrals or linear combinations of iterated integrals, which give rise to de Rham cohomology classes of QSX = P(X; x0, x0) and shall prove an iterated integral version of a loop space de Rham theorem, which includes the following
Preclinical Pharmacokinetics and General Toxicology of Iodixanol (1995)

To document the safety of iodixanol and to assess its pharmacokinetic properties, extensive tests have been performed. Iodixanol was rapidly excreted, mainly via the kidneys, with a plasma half-life in rats and monkeys of 25 and 76 mins, respectively. The pharmacokinetic data were consistent with an extracelleular distribution of iodixanol. During the 24 hours post-dosing, the urinary excretion was from 72 to 100% in rats, and 78% in monkeys. Biliary excretion was 1.5% during the first 4 hours in rats. Fecal excretion was about 7% in rats and 0.8% in monkeys over the first 24 hours after injection. Approximately 0.5 and 1% of the dose was found in the kidneys of rats and monkeys, respectively, 24 hours after dosing. Acute toxicity of iodixanol in rats was low, with an LD(50) greater than 21 g I/kg. In mice the LD(50) was 21 g I/kg and the approximated median lethal dose (ADL(50)) was found to range from 15 to 21 g I/kg. A single dose of 1 and 3 g I/kg was well tolerated in monkeys. As for the other roentgen contrast media, a reversible, dose-related, vacuolation of the proximal tubules in the kidneys was seen in the acute and subacute studies in rats and monkeys. No relationship was seen between the vacuolation and kidney function. Local tolerance studies demonstrated a low irritation potential for iodixanol when injected by a variety of intravascular and extravascular routes. The reproductive capacity of male and female rats was unaffected by iodixanol when administered daily at doses up to 2 g I/kg/day. No teratogenic potential in rats and rabbits of iodixanol was observed. Further, no toxic effects on pups were seen when rats were dosed during the lactation period. Each of 4 standard genotoxicity tests was negative. No antigenic potential of iodixanol was observed when assessed by the passive cutaneous anaphylaxis test and the active systemic anaphylaxis test in guinea pigs. The intravascular tolerability of iodixanol is high, and therefore, iodixanol should be considered as a safe roentgen contrast medium for intravascular use.