gebhart/patrepeval huggingface dataset:
The Nature of Apoptosis of Human Breast Cancer Cells Induced by Three Species of Genus Ganoderma P. Karst. (Aphyllophoromycetideae) Crude Extracts (2008)

The cytotoxic effect of crude extracts of three Ganoderma species (G. lucidum, G. tropicum, and G. tsugae) was screened against the human estrogen-independent cell line, MDA-MB-435 using a microculture tetrazolium (MTT) assay. The crude extract obtained from the fruiting body of Ganoderma lucidum by hot water extraction procedures had IC50 values ranging from 140 to 350 μg mL−1. Acridine-orange/propidium iodine staining, electron microscopy, and transmission electron microscopy showed that the crude extract caused both apoptosis and necrosis. The G. lucidum mycelial crude extract was most effective, with an IC50 value of 148 μg mL−1.
Detection of periodicity in eukaryotic genomes on the basis of power spectrum analysis. (2002)

In the present study, we identified periodic patterns in nucleotide sequence, and characterized nucleotide sequences that confer periodicities to Arabidopsis thaliana and Drosophila melanogaster on the basis of a power spectrum method and frequency of nucleotide sequences. To assign regions that contribute to each periodicity we calculated periodic nucleotide distributions by a parameter proposed in the paper. In A. thaliana, we obtained three periodicities (248 bp-, 167 bp-, and 126 bp) in chromosome 3, three peaks (174 bp-, 88 bp-, and 59 bp-period) in chromosome 4, and four periodicities (356 bp, 174 bp, 88 bp, and 59 bp) in chromosome 5. These are relation to ORF that consists of Gly-rich amino acid sequences including histone protein that consists of Gly-, Ser-, and Ala-rich amino acids residues. For D. melanogaster genome we found that G or C spectral curves have flat region at middle frequency range from f = 10(-4) to 10(-5) (corresponding to cyclic size 1 kb-5 kb), which may be associated with randomness of base sequence composition. This property has not been observed in Saccharomyces cerevisiae, Caenorhabditis elegans, and Homo sapiens yet.
Effects of isolates of ectomycorrhizal fungi and endophytic Mycelium radicis atrovirens that were dominant in soil from disturbed sites on growth of Betula platyphylla var. japonica seedlings (2001)

Effects of ectomycorrhizal fungi and endophytic Mycelium radicis atrovirens Melin (MRA) on growth of Betula platyphylla var. japonica seedlings were investigated under aseptic culture conditions. Three isolates of ectomycorrhizal fungi and two isolates of MRA were used. One MRA isolate was Phialocephala fortinii . Previous field work revealed that these isolates were dominant on the roots of B. platyphylla var. japonica seedlings grown in a mineral subsoil that had been exposed by the removal of surface soil. After a 100‐day incubation, the growth of the seedlings was significantly enhanced by the colonization of these ectomycorrhizal fungal isolates as compared with uninoculated seedlings. In contrast, the growth of seedlings was retarded by the colonization of the MRA isolates. The growth of seedlings that were co‐inoculated with ectomycorrhizal fungi and MRA was similar to that of uninoculated seedlings in most cases. These results suggest that ectomycorrhizal fungi have a beneficial effect on the growth of B. platyphylla var. japonica seedlings and that they suppress the deleterious effect of MRA. Thus, these ectomycorrhizal fungi probably have an important role in establishing B. platyphylla var. japonica seedlings during the initial stage of re‐vegetation following site disturbance by the removal of surface soil.
A Brief Review of the Ah Locus. (1992)

The Ah locus, first described as a functional polymorphism among inbred strains of mice, encodes the Ah receptor--a ligand dependent transcriptional activator. This paper reviews the work on the Ah receptor and its importance in the expression of cytochrome P-450IA1 and the pleiotropic effects of halogenated aromatic hydrocarbons.
Detection of adenovirus DNA in clinical samples by SYBR Green real‐time polymerase chain reaction assay (2005)

SYBR Green real-time PCR is a useful quantitative tool for analysis of adenovirus DNA. The present results for immunocompetent children with adenovirus infections provided basic data for comparison with data obtained from immunocompromised patients.
Design and implementation of the TES science data processing framework (2002)

The Tropospheric Emission Spectrometer (TES) Science Data Processing System (SDPS) is being designed and implemented using a Framework to encapsulate common components, provide abstract interfaces to hardware-dependent features, increase maintainability and greatly reduce the burden on science algorithm development teams. The requirements and architectural design of the TES SDPS Framework were initially presented at-the IEEE Aerospace 2000 conference in A Framework-Based Approach to Science Software Development (2000). This paper reviews the Framework, outlines the detailed designs derived from the architectural design, and discusses the major components which have been implemented to date. We also discuss various tools and techniques used during implementation, including our extensive use of the Unified Modeling Language (UML), round-trip engineering, and the inclusion of 3/sup rd/-party software libraries. Finally, we present our observations on the processes and results to date, and our near- and long-term future plans and goals for the TES SDPS Framework.
Lysosome lipid storage disorder in NCTR-BALB/c mice. I. Description of the disease and genetics. (1982)

We describe a strain of BALB/c mice, designated NCTR-BALB/c, carrying a new genetic disorder characterized by excessive tissue deposition of cholesterol and phospholipid. The mice exhibit progressive incoordination, grow less rapidly, and die 80-120 days after birth. In comparison with control animals of the same age, organ weights in the affected animals are lower in absolute value but higher relative to body weight, except for the thymus, which is atrophied, and for the lung and testes, whose absolute weights are not changed. Vacuolated cells are found in many tissues, and large foam cells are present in reticuloendothelial system (RES)-rich organs. Compared with those of BALB/c controls, serum lipoproteins migrate more slowly on electrophoresis; the amount of beta-lipoproteins is increased, while alpha-lipoprotein content is decreased. Serum total cholesterol remains normal. The serum activities of aspartate aminotransferase, creatine phosphokinase, and N-acetyl-beta-glucosaminidase are elevated. Free cholesterol levels are increased 8-10-fold in liver, spleen, and thymus, and about 2-fold in other tissues; but esterified cholesterol levels are normal. The phospholipid content of several tissues is increased 50-100%, largely as a result of an increase in sphingomyelin content. Significant increases in phosphatidylcholine occur also in spleen and lung. The disorder is inherited, affecting both sexes equally, and appears to be transmitted as an autosomal recessive mutation.
Graph Fourier Transform for directed graphs based on Lovász extension of min-cut (2017)

A key tool to analyze signals defined over a graph is the so called Graph Fourier Transform (GFT). Alternative definitions of GFT have been proposed, based on the eigen-decomposition of either the graph Laplacian or adjacency matrix. In this paper, we introduce an alternative approach, valid for the general case of directed graphs, that builds the graph Fourier basis as the set of orthonormal vectors that minimize a well-defined continuous extension of the graph cut size, known as Lovász extension. To cope with the non-convexity of the problem, we exploit a recently developed method devised for handling orthogonality constraints, with provable convergence properties.
Shale Resource Development: Optimised Exploitation of Natural & Induced Hydraulic Fractures (2011)

No two shale reservoirs are the same; however, deployment of a sound life cycle approach to shale gas development can lead to incremental return on investment. In the exploration phase some of the critical issues to address include the use of seismic attributes to identify potential high TOC (total organic content) and levels of Vitrinite reflectance. Acoustic impedance has been correlated to levels of TOC.
Influence of Polymer End-Group Chemistry and Segment—Substrate Interactions on Polymer Adsorption Kinetics (1996)

The role of molecular architecture and segment-substrate interactions in polymer adsorption is investigated with a combination of dispersion-generated isotherms and Total Internal Reflectance Fluorescence (TIRF) adsorption kinetic studies on the plateau of the isotherm. The work focuses on the water-soluble system of end-modified polyethylene oxide (PEO) and silica and polystyrene substrates. A correlation was found between the rate of adsorption from gentle shearing flow and the apparent adsorption energy of the polymer. Competitive adsorption experiments for two modified PEO's adsorbing onto PS revealed that the more hydrophobic of the PEO samples was preferred on the surface, with the order of introduction having little influence on the ultimate coverage. A convection-diffusion analysis of the TIRF experiments with non-adsorbing polymer agreed with dynamic light scattering results, and revealed that all PEO solutions were dominated by aggregates, ranging in size from 150-300 nm.
Analysis of a common inheritable idiotype in IgA-deficient sera using monoclonal antibodies. (1988)

In these studies we describe the production of three mAb raised to an idiotype on an IgG anticasein antibody isolated from the serum of one IgA-deficient blood donor. These are IgM kappa and block the binding of casein Ag to anticasein antibody. Sera of unrelated IgA-deficient donors were tested for the presence of the idiotype; 15 of 56 IgA-deficient sera (25%) contain the anticasein idiotype, whereas 1 of 45 normal sera was positive. Anticasein antibodies as a whole were predominantly of the IgG1 and IgG3 subclass; idiotype-positive anticaseins are predominantly of the IgG1 subclass. For IgA-deficient donors, the relative amount of idiotype-positive anticasein antibody was correlated with the level of anticasein present in the serum. Studies were done to investigate the potential inheritance of the idiotype in families; in three of four families the idiotype was inherited in an apparent autosomal dominant pattern. Our data show that a common cross-reactive idiotype can be detected in the sera of IgA-deficient individuals and their family members. This suggests that V region markers may be conserved in this humoral immunodeficiency disease.
The involucrin gene of Old-World monkeys and other higher primates: synapomorphies and parallelisms resulting from the same gene-altering mechanism. (1992)

The involucrin gene of platyrrhines and hominoids contains a segment of 10-codon repeats which were added vectorially at the same site in the coding region. We have now cloned and sequenced the involucrin gene of four cercopithecoid monkeys--two macaques (mulatta and fascicularis) and two Cercopithecus monkeys (aethiops and hamlyni). Each gene contains a similar segment of short repeats; some of these were added in a common anthropoid lineage, others were added in a common catarrhine lineage, and still others were added in a common macaque or Cercopithecus lineage. Repeats added before a lineage diverges become synapomorphies in the sister taxa resulting from the divergence. Repeats added independently in different diverged lineages become parallelisms. The synapomorphies are the result of the action of a targeted duplication mechanism acting in a common ancestral lineage, but the parallelisms are the result of the same duplication mechanism transmitted to successively divergent sublineages and acting independently in each.
Characterization and Energetics of Leuconostoc Oenos ml 34 (1972)

Characteristics of the malo-lactic bacterium <i>Leuconostoc oenos</i> ML 34 are reported indicating that this organism, previously designated <i>L. citrovorum</i> ML 34, should be placed in the new species <i>L. oenos</i> Garvie 1967. Of 26 compounds tested, energy sources for the organism were D-glucose, D-fructose, D-ribose, trehalose, and cellobiose. L-malic and citric acids, not energy sources themselves, provided a slight increase in cell yield in the presence of limited carbohydrate. Production of one of the end products, D-lactic acid, greatly exceeded that expected on the basis of the fermentation of glucose and L-malic acid substrates. It was concluded not only that sugar utilization is required for malo-lactic fermentation, but that malo-lactic fermentation also has a profound influence on the metabolism of the organism and implies a stimulation in utilization of carbon sources. Also discussed are the nomenclature and taxonomy of the wine leuconostocs.
Hybrid optoacoustic and ultrasound biomicroscopy monitors’ laser-induced tissue modifications and magnetite nanoparticle impregnation (2014)

Tissue modification under laser radiation is emerging as one of the advanced applications of lasers in medicine, with treatments ranging from reshaping and regeneration of cartilage to normalization of the intraocular pressure. Laser-induced structural alterations can be studied using conventional microscopic techniques applied to thin specimen. Yet, development of non-invasive imaging methods for deep tissue monitoring of structural alterations under laser radiation is of great importance, especially for attaining efficient feedback during the procedures. We developed a fast scanning biomicroscopy system that can simultaneously deliver both optoacoustic and pulse-echo ultrasound contrast from intact tissues and show that both modalities allow manifesting the laser-induced changes in cartilage and sclera. Furthermore, images of the sclera samples reveal a crater developing around the center of the laser-irradiated spot as well as a certain degree of thickening within the treated zone, presumably due to pore formation. Finally, we were able to observe selective impregnation of magnetite nanoparticles into the cartilage, thus demonstrating a possible contrast enhancement approach for studying specific treatment effects. Overall, the new imaging approach holds promise for development of noninvasive feedback control systems that could guarantee efficacy and safety of laser-based medical procedures.
Identification and phylogenetic characterization of novel Lactobacillus plantarum species and their metabolite profiles in grass silage (2014)

Italian ryegrass (IRG), barley, and rye are types of forage that are difficult to ensile with an assurance of good quality. Therefore, the addition of lactic acid bacteria (LAB) is the best way to enhance the preservation of this silage. However, applications of LAB have been impeded due to its poor growth characteristics, the sudden decline in pH, and other non-beneficial microbial growth associated with its presence. To overcome these limitations, a new Lactobacillus sp. KCC-10 and KCC-19 strain was isolated from well-fermented IRG silage samples. Biochemical and physiological studies revealed that the strains were Gram-positive, catalase-negative, and produced gas from glucose, and produced more lactic acid in fermentation. The 16S rRNA gene-based phylogenetic affiliation was determined by using bioinformatic tools that identified Lactobacillus sp. KCC-10 and KCC-19 with 100 % sequence similarity to Lactobacillus plantarum. Novel L. plantarum strains were deposited in the Korean Collection for Type Cultures under the accession numbers KACC 91785P and KACC 91758P, respectively. The shake-flask cultivation of these new strains under aerobic, microaerobic, and anaerobic conditions showed a higher specific growth rate than that achieved using the well-studied L. plantarum KACC 91016 and KACC 91096 on MRS broth and grass juice. Lactic acid was detected as the dominant organic acid in IRG (78.45 mM), barley (51.28 mM), corn (16.28 mM), and rice paddy (11.05 mM), followed by acetic acid and succinic acid. The KCC-10 in the silage was observed to increase from 2.4 × 105 CFU/g per sample at day 0 to 0.58, 0.60, and 0.59 × 109 CFU/g at day 5 for IRG, barley, and rye, respectively. The growth of KCC-10 and KCC-19 in all the silages decreased, as the storage period increased from 5 to 50 days. Whereas, KCC-19 was noted to increase from 2.7 × 105 CFU/g per sample at day 0 to 0.71, 0.72, and 0.711 × 109 CFU/g at day 5 for IRG, barley, and rye. Among the total organic acids, lactic acid was detected as the dominant acid present in IRG, barley, and rye silages. From these results, we concluded that strains KCC-10 and KCC-19 can be used as appropriate inoculants to prolong the stability of silage and fermentation quality.
Negative refraction, subwavelength focusing and beam formation by photonic crystals (2007)

We present a review of our experimental and numerical studies on the negative refraction related phenomena in two-dimensional dielectric photonic crystals (PCs). By employing photonic bands with appropriate dispersion, the propagation of the electromagnetic wave through a PC can be controlled to a large extent, and diverse and completely novel electromagnetic phenomena can be generated. We perform the spectral analysis of the negative refraction arising from a convex TM polarized photonic band of a hexagonal PC. As a consequence of negative refraction, we demonstrate a photonic crystal flat lens, which has the ability to focus electromagnetic waves and provide subwavelength resolution laterally. Finally, a photonic crystal with an embedded source is shown to provide a highly directional beam, which can be utilized in certain antenna applications.
1-Benzhydryl-4-(4-chlorophenylsulfonyl)piperazine (2008)

The title compound, C(23)H(23)ClN(2)O(2)S, was synthesized by the nucleophilic substitution of 1-benzhydrylpiperazine with 4-chloro-phenyl-sulfonyl chloride. The piperazine ring is in a chair conformation. The geometry around the S atom is that of a distorted tetra-hedron. There is a large range of bond angles around the piperazine N atoms. The dihedral angle between the least-squares plane (p1) defined by the four coplanar C atoms of the piperazine ring and the benzene ring is 81.6 (1)°. The dihedral angles between p1 and the phenyl rings are 76.2 (1) and 72.9 (2)°. The two phenyl rings make a dihedral angle of 65.9 (1)°. Intramolecular C-H⋯O hydrogen bonds are present.
Experimental Bond Critical Point and Local Energy Density Properties Determined for Mn−O, Fe−O, and Co−O Bonded Interactions for Tephroite, Mn2SiO4, Fayalite, Fe2SiO4, and Co2SiO4Olivine and Selected Organic Metal Complexes: Comparison with Properties Calculated for Non-Transition and Transition Metal M−O Bonded Interactions for Silicates and Oxides (2008)

Bond critical point (bcp) and local energy density properties for the electron density (ED) distributions, calculated with first-principle quantum mechanical methods for divalent transition metal Mn-, Co-, and Fe-containing silicates and oxides are compared with experimental model ED properties for tephroite, Mn 2SiO 4, fayalite, Fe 2SiO 4, and Co 2SiO 4 olivine, each determined with high-energy synchrotron single-crystal X-ray diffraction data. Trends between the experimental bond lengths, R(M-O), (M = Mn, Fe, Co), and the calculated bcp properties are comparable with those observed for non-transition M-O bonded interactions. The bcp properties, local total energy density, H( r c), and bond length trends determined for the Mn-O, Co-O, and Fe-O interactions are also comparable. A comparison is also made with model experimental bcp properties determined for several Mn-O, Fe-O, and Co-O bonded interactions for selected organometallic complexes and several oxides. Despite the complexities of the structures of the organometallic complexes, the agreement between the calculated and model experimental bcp properties is fair to good in several cases. The G( r c)/rho( r c) versus R(M-O) trends established for non-transition metal M-O bonded interactions hold for the transition metal M-O bonded interactions with G( r c)/rho( r c) increasing in value as H( r c) becomes progressively more negative in value, indicating an increasing shared character of the interaction as G( r c)/rho( r c) increases in value. As observed for the non-transition metal M-O bonded interactions, the Laplacian, nabla (2)rho( r c), increases in value as rho( r c) increases and as H( r c) decreases and becomes progressive more negative in value. The Mn-O, Fe-O, and Co-O bonded interactions are indicated to be of intermediate character with a substantial component of closed-shell character compared with Fe-S and Ni-S bonded interactions, which show greater shared character based on the | V( r c)|/ G( r c) bond character indicator. The atomic charges conferred on the transition metal atoms for the three olivines decrease with increasing atomic number from Mn to Fe to Co as the average M-O bond lengths decrease from 2.219 to 2.168 to 2.128 A, respectively.
GEN04-1: Cancellation of MR Head Asymmetry in Magnetic Tape Storage Systems (2006)

This paper describes a fully digital approach for pulse-asymmetry estimation and cancellation in magnetic tape storage systems that employ magneto-resistive (MR) read heads. Algorithms are presented for decision-aided and non-decision- aided estimation of pulse asymmetry. The cancellation of asymmetry is based on a quadratic model of the MR head non- linearity. Using read-back waveforms obtained from commercial tape drives, it is shown that a significant improvement in read-channel performance is achieved by the techniques described. Asymmetry estimation and cancellation using a specific pattern defined in the linear tape open (LTO) tape format are also addressed.
Novel interrogation technique for Tilted Fiber Bragg Gratings sensors based on single wavelength time delay measurements (2009)

A novel interrogation scheme for Tilted Fiber Bragg Gratings (TFBGs) sensors is here proposed based on single wavelength time delay measurements. To this aim, the group delay of a weakly tilted TFBG has been characterized by direct time domain measurement. The experimental characterization shows the capability of TFBGs to enable superluminal and subluminal propagation of an optical pulse in optical fibers. The sharp group delay features of the TFBGs are exploited for refractometric applications to detect the SRI variations by single wavelength time delay measurements. The obtained preliminary results demonstrate the possibility to detect SRI changes by means of single wavelength time delay measurements with a sensitivity enhanced in the range 1.33-1.40 with respect to previously reported interrogation techniques.