gebhart/patrepeval huggingface dataset:
Metabolomics‐assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade (2014)

Steroidal glycoalkaloids (SGAs) are nitrogen-containing secondary metabolites of the Solanum species, which are known to have large chemical and bioactive diversity in nature. While recent effort and development on LC/MS techniques for SGA profiling have elucidated the main pathways of SGA metabolism in tomato, the problem of peak annotation still remains due to the vast diversity of chemical structure and similar on overlapping of chemical formula. Here we provide a case study of peak classification and annotation approach by integration of species and tissue specificities of SGA accumulation for provision of comprehensive pathways of SGA biosynthesis. In order to elucidate natural diversity of SGA biosynthesis, a total of 169 putative SGAs found in eight tomato accessions (Solanum lycopersicum, S. pimpinellifolium, S. cheesmaniae, S. chmielewskii, S. neorickii, S. peruvianum, S. habrochaites, S. pennellii) and four tissue types were used for correlation analysis. The results obtained in this study contribute annotation and classification of SGAs as well as detecting putative novel biosynthetic branch points. As such this represents a novel strategy for peak annotation for plant secondary metabolites.
OESTROGENIC, ANTI‐OESTROGENIC AND FERTILITY EFFECTS OF SOME TRIPHENYLETHANES AND TRIPHENYLETHYLENES RELATED TO ETHAMOXYTRIPHETOL (MER 25) (1976)

Five triphenylethylenes, a triphenylethane and a triphenylethanol, carrying methyl substituents ortho to one or both of the ring oxygen functions, have been examined for oestrogenic, and antioestrogenic activity in mice, and three of the compounds, alpha-[4-(beta-diethylaminoethoxy)-3, 5-xylyl]-alpha-phenyl-beta-4-methoxyphenyl-ethanol (IV), alpha'-[4-(beta-diethylaminoethoxy)-3, 5-xylyl]-4-methoxy-bibenzyl (V) and alpha'-[4-(beta-diethylaminoethoxy)-3, 5-xylyl]-4-methoxy-stilbene (VI), were tested for their effects on fertility in mice. 2 Orthomethylation reduces oestrogenic and/or anti-oestrogenic activity compared with the reported activities of non-methylated analogues. 3 The anti-oestrogenic ethamoxytriphetol (MER 25) reduced fertility in mice whereas its inactive dimethylated analogue (IV) was ineffective. The weakly active anti-oestrogens, V and VI, did not affect fertility in mice.
Simulation Study of Active Noise Control in Wind Turbines Using FxLMS Adaptation Algorithm (2017)

Utility scale wind turbines produce a significant amount of noise which has been identified as one of the most critical challenges to the widespread use of wind energy. Aerodynamic noise caused primarily by the interaction of the boundary layer and (or) the upstream atmospheric turbulence with the trailing edge of the blade has been identified as the most dominant source of noise in wind turbines. The authors here propose an active noise control system based on the FxLMS algorithm which can achieve suppression of noise from a modern wind turbine. Two types of noise sources have been simulated: monopole and dipole. The results of the active noise control algorithm are validated with simulations in MATLAB. The agreement between the results shows the far impact of active noise control techniques will have in future wind turbines.
CD137 stimulation of natural killer cells to enhance the antilymphoma activity of rituximab. (2010)

8068 Background: Rituximab, a monoclonal antibody (mAb) directed against CD20, has significantly improved the outcome of patients with lymphoma. Antibody-dependant cell-mediated cytotoxicity (ADCC), mediated largely by natural killer (NK) cells, is thought to play an important role in rituximab's efficacy. In the current study, we hypothesized that the antilymphoma activity of rituximab could be enhanced by stimulation of NK cells with an anti-CD137 agonistic mAb. CD137 (4-1BB) is a costimulatory molecule expressed on a variety of activated immune cells, including T and NK cells. Methods: Rituximab-induced upregulation of CD137 on NK cells was assessed using lymphoma cell lines and primary lymphoma patient samples. In vitro NK cell degranulation and cytotoxicity were assessed by CD107a mobilization and chromium release. A murine lymphoma tumor model targeted by mouse anti-mouse CD20 mAb was used to assess in vivo synergy of anti-CD20 and anti-CD137 mAbs. Results: Using human primary lymphoma samples, we found that, while resting human NK cells do not express CD137 at baseline, these cells highly upregulate CD137 when encountering rituximab-coated tumor B cells. Furthermore, anti-CD137 agonistic mAb significantly enhances rituximab-induced NK cell degranulation and cytotoxicity as measured by CD107a mobilization (p=0.006) and chromium release (p=0.01). In a murine lymphoma model, anti-CD137 mAb significantly enhances anti-tumor activity of anti-CD20 mAb leading to complete tumor resolution (p<0.001) and prolonged survival (p=0.048). This synergistic effect is dependent upon sequential administration of anti-CD20 mAb followed by anti-CD137 mAb (p=0.027). Consistent with this observation, we show that in vivo administration of anti-CD20 mAb induces upregulation of CD137 on mouse NK cells (p=0.001), allowing subsequent targeting with anti- CD137 mAb. Additionally, NK cell depletion completely abrogates the therapeutic effect of anti-CD20 plus anti-CD137 mAb combination (p<0.001). Conclusions: Our results support a novel, sequential antibody approach to enhance rituximab's efficacy in patients with B cell malignancies by stimulation of rituximab-activated NK cells with anti-CD137 mAb. No significant financial relationships to disclose.
A functional reconstitution of the .gamma.-aminobutyric acid transporter from synaptic vesicles using artificial ion gradients (1991)

The gamma-aminobutyric acid transporter of rat brain synaptic vesicles was reconstituted in proteoliposomes, and its activity was studied in response to artificially created membrane potentials or proton gradients. Changes of the membrane potential were monitored using the dyes oxonol VI and 3,3'-diisopropylthiodicarbocyanine iodide, and changes of the H+ gradient were followed using acridine orange. An inside positive membrane potential was generated by the creation of an inwardly directed K+ gradient and the subsequent addition of valinomycin. Under these conditions, valinomycin evoked uptake of [3H]GABA which was saturable. Similarly, [3H]glutamate uptake was stimulated by valinomycin, indicating that both transporters can be driven by the membrane potential. Proton gradients were generated by the incubation of K(+)-loaded proteoliposomes in a buffer free of K+ or Na+ ions and the subsequent addition of nigericin. Proton gradients were also generated via the endogenous H+ ATPase by incubation of K(+)-loaded proteoliposomes in equimolar K+ buffer in the presence of valinomycin. These proton gradients evoked nonspecific, nonsaturable uptake of GABA and beta-alanine but not of glycine in proteoliposomes as well as protein-free liposomes. Therefore, transporter activity was monitored using glycine as an alternative substrate. Proton gradients generated by both methods elicited saturable glycine uptake in proteoliposomes. Together, our data confirm that the vesicular GABA transporter can be energized by both the membrane potential and the pH gradient and show that transport can be achieved by artificial gradients independently of the endogenous proton ATPase.
Task modeling for ambient intelligent environments (2005)

The design of interactive systems for an ambient intelligent environment poses many challenges because of the great diversity in devices the user has control of and the user's situation imposed by the environment. Although task-centered interface design is an established approach for traditional form-based and even for multi-device user interfaces, this design approach is, in its current form, not ready for the design of user interfaces for ambient intelligent environments. In this paper we propose a task-centered approach to design interaction mechanisms for ambient intelligent environments by means of visualization and simulation. We focus on three different concepts that are important to support this approach: situated task allocations, user interface distributions and visualization of context influences. Because the execution of a task depends strongly on the situation or context of use, the consequences of a context change on the execution of a task specification should be communicated with the task designer during the design process. The designer should be able to define the possibilities to execute a task while taking into account constraints imposed by the environment of the user. A tool to support this approach using visualization of the environment and simulation of the interface configurations is introduced.
Comprehensive desk reference of polymer characterization and analysis (2004)

This book is a practical manual for those who analyze polymers. Self-contained chapters describe when a technique should be selected, explain its basic priniciples, describe how instruments are constructed and operated, and teach how the data obtained relate to molecular structure and physical properties. Many clear illustrations are included.
Mechanical properties of amorphous anodic alumina and tantala films using nanoindentation (2002)

The hardness and Young's modulus of barrier-type, amorphous anodic oxides have been determined by nanoindentation. The procedure used shallow indents, of 55 nm depth, with alumina, tantala and alumina/tantala `mixed oxide' films of about 500 nm thickness. The results revealed respective hardnesses of approximately 7.0, 5.3 and 6.5 GPa, and respective Young's moduli of approximately 122, 140 and 130 GPa. Thus, the hardness and Young's modulus followed opposite trends, with alumina having the highest hardness and lowest modulus, and the `mixed oxide' having intermediate properties. The hardness and Young's modulus of amorphous alumina are factors of about 3.1-3.7 times lower than those of crystalline aluminas.
The transient build-up and phase synchronization of thin magnetic film parametrons (1964)

THE DEVELOPMENT of thin magnetic film parametrons (also termed parametric phase-locked subharmonic oscillators) has been stimulated by their potential as low-cost reliable logic elements for medium- and low-speed computing machines. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1–4</sup> Among the many ways to implement the parametron, the best known consists of a single-domain uniaxial magnetic film coupled to a coil whose axis is directed along the hard magnetization direction of the film; the coil is further shunted by a tuning capacitor to form a tank circuit resonating at the subharmonic frequency. A second winding, orthogonal to the signal coil, produces a bias field and a pump field along the easy direction of the film. <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> The oscillation characteristics and phase bi-stability of this device have been verified.
Role of the intestinal microbiota and fecal transplantation in inflammatory bowel diseases (2014)

Ulcerative colitis and Crohn's disease are the two major types of inflammatory bowel disease (IBD). Despite intensive study, it is still challenging because the precise etiology and pathogenesis remains unclear. Studies have shown that IBD is associated with changes in the composition of intestinal microbiota, as either a cause or a consequence of abnormal host immune response in genetic susceptible population. Two specific microorganisms (Mycobacterium avium subsp. paratuberculosis and Escherichia coli) get more widely studied, but till now no single microorganism has been identified as the only pathogen. Genetic susceptibility data also suggest impaired handling of bacteria as well as an improper immune response to potential pathogens. The microbiota provides new therapeutic methods, and fecal microbiota transplantation may restore the balance of intestinal flora to supplement or optimize the current therapies.
Use of Dithiodiglycolic Acid as a Tether for Cationic Lipids Decreases the Cytotoxicity and Increases Transgene Expression of Plasmid DNA in Vitro (1999)

Two major barriers that limit cationic lipids in gene delivery are low transfection efficiency and toxicity. In the present studies, we used dithiodiglycolic acid as a new tether for the polar and hydrophobic domains of a cationic lipid, cholesteryl hemidithiodiglycolyl tris(aminoethyl)amine (CHDTAEA). We compared the transfection activity and toxicity of CHDTAEA with its nondisulfide analogue and cholesteryl N-(dimethylaminoethyl) carbamate (DC-Chol). The liposomes of CHDTAEA had more than 2 orders of magnitude greater transfection activity than DC-Chol in CHO cells and 7 times greater transfection activity in SKnSH cells. CHDTAEA also demonstrated much less toxicity than the other two lipids. Dithiodiglycolic acid may act as an excellent linker in the application of cationic lipid syntheses.
Fabrication and Microstructure of Metal-Metal Syntactic Foams (1998)

The objective of this paper is to report on the fabrication process and document the microstructure of metal-metal syntactic foams. The composite microstructure consists of thin-wall, hollow Fe-Cr stainless steel spheres cast in various metal matrices including aluminum alloys 6061, 7075, 413, magnesium alloy AZ31B, and unalloyed aluminum and magnesium. Hollow, spheres were formed from slurries of fine particle size iron and chromium oxides via the coaxial nozzle process. The oxides were reduced and sintered in hydrogen to the corresponding Fe-Cr alloy. Spheres were sufficiently uniform to allow arrangement into random or periodic arrays. These arrays were infiltrated by an aspiration casting process, resulting in a structure less dense than the matrix metal.
Increased neurogenesis and brain‐derived neurotrophic factor in neurokinin‐1 receptor gene knockout mice (2003)

It has previously been shown that chronic treatment with antidepressant drugs increases neurogenesis and levels of brain-derived neurotrophic factor in the hippocampus. These changes have been correlated with changes in learning and long-term potentiation and may contribute to the therapeutic efficacy of antidepressant drug treatment. Recently, antagonists at the neurokinin-1 receptor, the preferred receptor for the neuropeptide substance P, have been shown to have antidepressant activity. Mice with disruption of the neurokinin-1 receptor gene are remarkably similar both behaviourally and neurochemically to mice maintained chronically on antidepressant drugs. We demonstrate here that there is a significant elevation of neurogenesis but not cell survival in the hippocampus of neurokinin-1 receptor knockout mice. Neurogenesis can be increased in wild-type but not neurokinin-1 receptor knockout mice by chronic treatment with antidepressant drugs which preferentially target noradrenergic and serotonergic pathways. Hippocampal levels of brain-derived neurotrophic factor are also two-fold higher in neurokinin-1 receptor knockout mice, whereas cortical levels are similar. Finally, we examined hippocampus-dependent learning and memory but found no clear enhancement in neurokinin-1 receptor knockout mice. These data argue against a simple correlation between increased levels of neurogenesis or brain-derived neurotrophic factor and mnemonic processes in the absence of increased cell survival. They support the hypothesis that increased neurogenesis, perhaps accompanied by higher levels of brain-derived neurotrophic factor, may contribute to the efficacy of antidepressant drug therapy.
“Work-Hardenable” Ductile Bulk Metallic Glass (2005)

Usually, monolithic bulk metallic glasses undergo inhomogeneous plastic deformation and exhibit poor ductility (< 1%) at room temperature. We present a new class of bulk metallic glass, which exhibits high strength of up to 2265 MPa together with extensive "work hardening" and large ductility of 18%. Significant increase in the flow stress was observed during deformation. The "work-hardening" capability and ductility of this class of metallic glass is attributed to a unique structure correlated with atomic-scale inhomogeneity, leading to an inherent capability of extensive shear band formation, interactions, and multiplication of shear bands.
Laser beam surveying, refractive index measurements and the making of a 360° reflection hologram (1995)

Triangulation measurements, using a laser to find the height of a room and of buildings, will be described first. This will be followed by triangulation and laser beam divergence measurements for range finding. The use of a hollow prism to hold liquids, whose refractive indicies are to be found, will then be described. The final topic will describe how a 360° reflection hologram was made at Notre Dame High School, utilizing three lasers and beam spreaders and four lasers and beam spreaders. The 360° hologram, made by a student, will be available for viewing.
Whole blood and serum copper levels in relation to sex and age. (1985)

The zinc content in whole blood and serum was determined in 239 healthy males and 217 healthy females by atomic absorption spectrophotometry. The mean level of zinc obtained in whole human blood from males was 607.0 +/- 105.3 micrograms/100 ml and in females 585.2 +/- 122.9 micrograms/100 ml. The mean level of zinc in serum was 116.6 +/- 55.2 micrograms/100 ml and 105.2 +/- 66.9 micrograms/100 ml in males and females respectively. The zinc concentration in whole blood and serum in males proved to be slightly higher than in females though the difference is not statistically significant. For the males a positive correlation was found between age and the zinc level in whole blood and serum; this is only statistically significant in whole blood. In females, the zinc level in whole blood showed a positive correlation with age which was not statistically significant, while in serum this correlation was negative and statistically significant.
Monitoring of lipid storage in <i>Caenorhabditis elegans</i> using coherent anti-Stokes Raman scattering (CARS) microscopy (2007)

Better understanding of the fundamental mechanisms behind metabolic diseases requires methods to monitor lipid stores on single-cell level in vivo. We have used Caenorhabditis elegans as a model organism to demonstrate the limitations of fluorescence microscopy for imaging of lipids compared with coherent anti-Stokes Raman scattering (CARS) microscopy, the latter allowing chemically specific and label-free imaging in living organisms. CARS microscopy was used to quantitatively monitor the impact of genetic variations in metabolic pathways on lipid storage in 60 specimens of C. elegans. We found that the feeding-defective mutant pha-3 contained a lipid volume fraction one-third of that found in control worms. In contrast, mutants (daf-2, daf-4 dauer) with deficiencies in the insulin and transforming growth factors (IGF and TGF-beta) signaling pathways had lipid volume fractions that were 1.4 and 2 times larger than controls, respectively. This was observed as an accumulation of small-sized lipid droplets in the hypodermal cells, hosting as much as 40% of the total lipid volume in contrast to the 9% for the wild-type larvae. Spectral CARS microscopy measurements indicated that this is accompanied by a shift in the ordering of the lipids from gel to liquid phase. We conclude that the degree of hypodermal lipid storage and the lipid phase can be used as a marker of lipid metabolism shift. This study shows that CARS microscopy has the potential to become a sensitive and important tool for studies of lipid storage mechanisms, improving our understanding of phenomena underlying metabolic disorders.
A model for visual selective attention by two-layered neural network with FitzHugh-Nagumo neurons (2004)

We propose a mathematical model of visual selective attention using a two-layered neural network with spiking neurons described by FitzHugh-Nagumo equation, based on an assumption proposed by Desimone and Duncan. The neural network consists of a layer of hippocampal formation and that of visual cortex. We solve by numerical calculations a set of first-order ordinary differential equations, which describe a time-evolution of each neuron, in order to clarify an attention state, a non-attention state and an attention shift. We find that synchronous phenomena occur not only for a frequency but also for a firing time between the neurons in the hippocampal formation and those in a part of the visual cortex. The visual selective attention is considered as the synchronous phenomena between the firing times of the neurons in the hippocampal formation and those in a part of the visual cortex in the present model.
A review of yield modelling techniques for semiconductor manufacturing (2006)

Abstract Semiconductor manufacturing is a complex multistage manufacturing process, and wafer fabs use complex processes involving billions of dollars worth of equipment to produce integrated circuits. The level of complexities associated with an integrated circuit is increasing in terms of feature size and number of devices. Companies use several performance metrics such as defectiveness, yield, and cycle time to improve manufacturing performance. Maintaining high yield through reliable and accurate quality control measures is one of the key performance criteria used by companies. The intent of this paper is to provide a review of the literature dealing with critical aspects of yield modelling. A review of many topics from simple probabilistic yield models to the incorporation of critical features such as spatial defects and radial yield losses will be provided. We will also assess empirical techniques used to model variations associated with complex interrelated wafer manufacturing processes. We emphasize that yield modelling should not be considered in isolation and system-wide aspects are necessary for integrated yield modelling and analysis. Keywords: Yield modellingSemiconductor manufacturing Acknowledgement This work was supported by NSF/SRC/ISMI grants DMI-0432484 and DMI-0432395.
The role of histone deacetylases in rheumatoid arthritis fibroblast-like synoviocytes (2013)

RA (rheumatoid arthritis) is an inflammatory disease of synovial joints affecting approximately 1% of the population. One of the main cell types involved in damage to RA joint tissue is the FLSs (fibroblast-like synoviocytes). These have a semi-transformed, auto-aggressive phenotype typified by loss of contact inhibition, reduced apoptosis and the production of matrix-degrading enzymes. The mechanisms involved in the development of this phenotype are unclear; however, increasing evidence implicates alterations in the epigenetic regulation of gene expression. Reduced acetylation of amino acids in the tails of histone proteins is an epigenetic mark associated with transcriptional repression and is controlled by the HDAC (histone deacetylase) enzyme family. To date, evidence has implicated HDACs in the auto-aggressive phenotype of FLSs, and administration of HDAC inhibitors to both animal models of RA and individuals with juvenile arthritis has shown efficacy in attenuating inflammation and tissue damage. This highlights a role for HDACs in disease pathogenesis and, more importantly, that HDACs are potential novel therapeutic targets.
Time-over-threshold readout to enhance the high flux capabilities of single-photon-counting detectors (2011)

The MYTHEN single-photon-counting (SPC) detector has been characterized using the time-over-threshold (ToT) readout method, i.e. measuring the time that the signal produced by the detected X-rays remains above the comparator threshold. In the following it is shown that the ToT readout preserves the sensitivity, dynamic range and capability of background suppression of the SPC mode, while enhancing the count-rate capability, which is the main limitation of state-of-the-art SPC systems.