gebhart/patrepeval huggingface dataset:
Milk Thistle,Silybum marianum(L.) Gaertn., Flower Head Development and Associated Marker Compound Profile (2003)

ABSTRACT Flower head development and marker compound changes were examined for milk thistle grown under dryland conditions during the 1998 and 1999 growing seasons. Flower heads harvested at the early flowering, mid-flowering, late flowering, and dehiscing (seed development) growth stages had average seed/ovule weights of 5 mg, 13 mg, 21 mg, and 26 mg, respectively. At the time of harvest, the plants contained flower heads at all stages of development. During the 1999 harvest, the average plant produced 2.0 g, 2.9 g, and 3.4 g of dry seeds per flower head, corresponding to mid-flowering, late flowering, and dehiscing development stages of the flower. The silymarin and fixed-oil content for the 1999 seeds were 1 mg, 14 mg, and 24 mg of silymarin and 15 mg, 168 mg, and 252 mg of lipid/g dry weight for mid-flowering, late flowering, and dehiscing development stages, respectively. The highest silymarin yield was obtained from late flowering and dehiscing flower heads in early September of both test years.
Size Control of Gold Nanocrystals in Citrate Reduction:  The Third Role of Citrate (2007)

Growth kinetics and temporal size/shape evolution of gold nanocrystals by citrate reduction in boiling water were studied systematically and quantitatively. Results reveal that the size variation and overall reaction mechanism were mostly determined by the solution pH that was in turn controlled by the concentration of sodium citrate (Na3Ct) in the traditional Frens's synthesis. This conclusion was further confirmed by the reactions with variable pH but fixed concentrations of the two reactants, HAuCl4 and Na3Ct. Two substantially different reaction pathways were identified, with the switching point at pH = 6.2-6.5. The first pathway is for the low pH range and consists of three overlapping steps: nucleation, random attachment to polycrystalline nanowires, and smoothing of the nanowires via intra-particle ripening to dots. The second pathway that occurred above the pH switching point is consistent with the commonly known nucleation-growth route. Using the second pathway, we demonstrated a new synthetic route for the synthesis of nearly monodisperse gold nanocrystals in the size range from 20 to 40 nm by simply varying the solution pH with fixed concentrations of HAuCl4 and Na3Ct. The switching of the reaction pathways is likely due to the integration nature of water as a reaction medium. In the citrate reduction, the solution pH was varied by changing the initial HAuCl4/Na3Ct ratio. Consequently, when pH was higher than about 6.2, the very reactive [AuCl3(OH)]- would be converted to less reactive [AuCl2(OH)2]- and [AuCl(OH)3]-.
Lumican Regulates Collagen Fibril Assembly: Skin Fragility and Corneal Opacity in the Absence of Lumican (1998)

Lumican, a prototypic leucine-rich proteoglycan with keratan sulfate side chains, is a major component of the cornea, dermal, and muscle connective tissues. Mice homozygous for a null mutation in lumican display skin laxity and fragility resembling certain types of Ehlers-Danlos syndrome. In addition, the mutant mice develop bilateral corneal opacification. The underlying connective tissue defect in the homozygous mutants is deregulated growth of collagen fibrils with a significant proportion of abnormally thick collagen fibrils in the skin and cornea as indicated by transmission electron microscopy. A highly organized and regularly spaced collagen fibril matrix typical of the normal cornea is also missing in these mutant mice. This study establishes a crucial role for lumican in the regulation of collagen assembly into fibrils in various connective tissues. Most importantly, these results provide a definitive link between a necessity for lumican in the development of a highly organized collagenous matrix and corneal transparency.
Operator sequences of the aerobactin operon of plasmid ColV-K30 binding the ferric uptake regulation (fur) repressor (1987)

The promoter region of the pColV-K30-encoded operon specifying biosynthesis and transport of the siderophore aerobactin was subjected to deletion analysis to determine the smallest DNA sequence affording iron regulation of a iucA'-'lacZ gene fusion. A 78-base-pair (bp) region containing the main (P1) promoter retained the character of inducibility under iron starvation. A 250-bp fragment carrying this sequence was examined for protection against DNase I by the Fur protein, the product of a gene (fur) required for negative control of several iron-regulated functions. The DNase I footprints, in the presence of various divalent heavy-metal ions added as corepressors, revealed two contiguous binding sites with different lengths and affinities for Fur. Increased concentrations of the protein appeared to elicit formation of repressor oligomers which bind to the upstream and downstream regions of the P1 promoter in a metal-dependent fashion, but with a presently undefined stoichiometry. The primary site for Fur binding spans 31 bp and contains two overlapping symmetry dyads which share the sequence 5'-TCATT-3'. It also contains extensive homology with a 19-bp consensus sequence for iron-regulated genes as deduced from comparison with the fhuA and fepA putative promoter sequences.
25-Hydroxycholesterol 3-sulfate is an endogenous ligand of DNA methyltransferases in hepatocytes (2021)

The oxysterol sulfate, 25-hydroxycholesterol 3-sulfate (25HC3S), has been shown to play an important role in lipid metabolism, inflammatory response, and cell survival. However, the mechanism(s) of its function in global regulation is unknown. The current study investigates the molecular mechanism by which 25HC3S functions as an endogenous epigenetic regulator. To study the effects of oxysterols/sterol sulfates on epigenetic modulators, 12 recombinant epigenetic enzymes were used to determine whether 25HC3S acts as their endogenous ligand. The enzyme kinetic study demonstrated that 25HC3S specifically inhibited DNA methyltransferases (DNMTs), DNMT1, DNMT3a, and DNMT3b with IC<sub>50</sub> of 4.04, 3.03, and 9.05 × 10<sup>-6</sup> M, respectively. In human hepatocytes, high glucose induces lipid accumulation by increasing promoter CpG methylation of key genes involved in development of nonalcoholic fatty liver diseases. Using this model, whole genome bisulfate sequencing analysis demonstrated that 25HC3S converts the <sup>5m</sup>CpG to CpG in the promoter regions of 1,074 genes. In addition, we observed increased expression of the demethylated genes, which are involved in the master signaling pathways, including MAPK-ERK, calcium-AMP-activated protein kinase, and type II diabetes mellitus pathways. mRNA array analysis showed that the upregulated genes encoded for key elements of cell survival; conversely, downregulated genes encoded for key enzymes that decrease lipid biosynthesis. Taken together, our results indicate that the expression of these key elements and enzymes are regulated by the demethylated signaling pathways. We summarized that 25HC3S DNA demethylation of <sup>5m</sup>CpG in promoter regions is a potent regulatory mechanism.
Binding of Active (57 kDa) Membrane Type 1-Matrix Metalloproteinase (MT1-MMP) to Tissue Inhibitor of Metalloproteinase (TIMP)-2 Regulates MT1-MMP Processing and Pro-MMP-2 Activation (2000)

Previous studies have shown that membrane type 1-matrix metalloproteinase (MT1-MMP) (MMP-14) initiates pro-MMP-2 activation in a process that is tightly regulated by the level of tissue inhibitor of metalloproteinase (TIMP)-2. However, given the difficulty in modulating TIMP-2 levels, the direct effect of TIMP-2 on MT1-MMP processing and on pro-MMP-2 activation in a cellular system could not be established. Here, recombinant vaccinia viruses encoding full-length MT1-MMP or TIMP-2 were used to express MT1-MMP alone or in combination with various levels of TIMP-2 in mammalian cells. We show that TIMP-2 regulates the amount of active MT1-MMP (57 kDa) on the cell surface whereas in the absence of TIMP-2 MT1-MMP undergoes autocatalysis to a 44-kDa form, which displays a N terminus starting at Gly(285) and hence lacks the entire catalytic domain. Neither pro-MT1-MMP (N terminus Ser(24)) nor the 44-kDa form bound TIMP-2. In contrast, active MT1-MMP (N terminus Tyr(112)) formed a complex with TIMP-2 suggesting that regulation of MT1-MMP processing is mediated by a complex of TIMP-2 with the active enzyme. Consistently, TIMP-2 enhanced the activation of pro-MMP-2 by MT1-MMP. Thus, under controlled conditions, TIMP-2 may act as a positive regulator of MT1-MMP activity by promoting the availability of active MT1-MMP on the cell surface and consequently, may support pericellular proteolysis.
Simultaneous extraction of proteins and metabolites from cells in culture (2014)

Proper sample preparation is an integral part of all omics approaches, and can drastically impact the results of a wide number of analyses. As metabolomics and proteomics research approaches often yield complementary information, it is desirable to have a sample preparation procedure which can yield information for both types of analyses from the same cell population. This protocol explains a method for the separation and isolation of metabolites and proteins from the same biological sample, in order for downstream use in metabolomics and proteomics analyses simultaneously. In this way, two different levels of biological regulation can be studied in a single sample, minimizing the variance that would result from multiple experiments. This protocol can be used with both adherent and suspension cell cultures, and the extraction of metabolites from cellular medium is also detailed, so that cellular uptake and secretion of metabolites can be quantified. Advantages of this technique includes:1.Inexpensive and quick to perform; this method does not require any kits.2.Can be used on any cells in culture, including cell lines and primary cells extracted from living organisms.3.A wide variety of different analysis techniques can be used, adding additional value to metabolomics data analyzed from a sample; this is of high value in experimental systems biology.
Relationships of microRNA expression in mouse lung with age and exposure to cigarette smoke and light (2009)

MicroRNAs provide a formidable tool not only in cancer research but also to investigate physiological mechanisms and to assess the effect of environmental exposures in healthy tissues. Collectively, cigarette smoke and sunlight have been estimated to account for 40% of all human cancers, and not only smoke but also, surprisingly, UV light induced genomic and postgenomic alterations in mouse lung. Here we evaluated by microarray the expression of 484 microRNAs in the lungs of CD-1 mice, including newborns, postweanling males and females, and their dams, either untreated or exposed to environmental cigarette smoke and/or UV-containing light. The results obtained highlighted age-related variations in microRNA profiles, especially during the weanling period, due to perinatal stress and postnatal maturation of the lung. UV light alone did not affect pulmonary microRNAs, whereas smoke produced dramatic changes, mostly in the sense of down-regulation, reflecting both adaptive mechanisms and activation of pathways involved in the pathogenesis of pulmonary diseases. Both gender and age affected smoke-related microRNA dysregulation in mice. The data presented provide supporting evidence that microRNAs play a fundamental role in both physiological and pathological changes occurring in mouse lung.
High-Q integrated 3-D inductors and transformers for high frequency applications (2004)

Using a novel 3-D fabrication technology, we have demonstrated, for the first time, very high frequency and high quality factor (Q) inductors and transformers on Si substrate. On high resistivity Si, this technology achieves a quality factor of Q>60 for 1nH inductor at frequencies of 3 to 7 GHz. High efficiency high-Q transformers with coupling factors 0.6<k<0.9 are achieved with very high self-resonance frequencies (8 GHz<f/sub res/<16 GHz). This technology is very simple and is fully compatible with Si and compound-semiconductor fabrication technologies and can be either implemented as a post-processing step or as a part of a vertical chip to inter poser packaging scheme.
Toward a Comprehensive Understanding of the Factors Underlying Multiracial Person Perception (2016)

Young and colleagues’ recent article substantially contributes to the understanding of multiracial perception generally and in the context of affirmative action. Their introduction of socioeconomic status as a relevant factor in the perception of Latino‐White biracials highlights our need for additional research identifying which target characteristics and perceiver motives influence the perception of multiracials and under what conditions these relationships occur. We outline how future research can incorporate and expand on Young et al.’s work to better understand multiracial person perception and specify the most appropriate contexts in which these findings could be applied by practitioners.
Favouring inhibitory synaptic drive mediated by GABAAreceptors in the basolateral nucleus of the amygdala efficiently reduces pain symptoms in neuropathic mice (2016)

Pain is an emotion and neuropathic pain symptoms are modulated by supraspinal structures such as the amygdala. The central nucleus of the amygdala is often called the 'nociceptive amygdala', but little is known about the role of the basolateral amygdala. Here, we monitored the mechanical nociceptive thresholds in a mouse model of neuropathic pain and infused modulators of the glutamate/GABAergic transmission in the basolateral nucleus of the amygdala (BLA) via chronically-implanted cannulas. We found that an N-methyl-D-aspartate-type glutamate receptor antagonist (MK-801) exerted a potent antiallodynic effect, whereas a transient allodynia was induced after perfusion of bicuculline, a GABA(A) receptor antagonist. Potentiating GABA(A) receptor function using diazepam or etifoxine (a non-benzodiazepine anxiolytic) fully but transiently alleviated mechanical allodynia. Interestingly, the antiallodynic effect of etifoxine disappeared in animals that were incapable of producing 3α-steroids. Diazepam had a similar effect but of shorter duration. As indicated by patch-clamp recordings of BLA neurons, these effects were mediated by a potentiation of GABA(A) receptor-mediated synaptic transmission. Together with a presynaptic elevation of miniature inhibitory postsynaptic current frequency, the duration and amplitude of GABA(A) miniature inhibitory postsynaptic currents were also increased (postsynaptic effect). The analgesic contribution of endogenous neurosteroid seemed to be exclusively postsynaptic. This study highlights the importance of the BLA and the local inhibitory/excitatory neuronal network activity while setting the mechanical nociceptive threshold. Furthermore, it appears that promoting inhibition in this specific nucleus could fully alleviate pain symptoms. Therefore, the BLA could be a novel interesting target for the development of pharmacological or non-pharmacological therapies.
Efficient Long-Term Coexpression of a Hammerhead Ribozyme Targeted to the U5 Region of HIV-1 LTR by Linkage to the Multidrug-Resistance Gene (1997)

Ribozymes as anti-HIV-1 agents hold promise for the treatment of AIDS. They can be delivered into cells either exogenously or through an expression system. For effective protection against HIV-1, sufficient and sustained amounts of the antiviral ribozymes must be delivered into target cells. The coexpression of a dominant selectable marker with ribozymes would serve to enrich for cells containing the molecular antiviral and facilitate prolonged expression of these ribozymes. The multidrug resistance gene (MDR1) is a potential clinically relevant selectable marker and offers many advantages over other known dominant selectable markers, including the use of diverse pharmacologically characterized drug or drug combinations for selection. Harvey sarcoma-based retroviral vectors encoding the MDR1 multidrug transporter with a hammerhead ribozyme targeted to highly conserved sequences within the HIV-1 U5 LTR segment have been constructed in a bicistronic format. The internal ribosome entry site (IRES) from encephalomyocarditis virus was used to initiate translation of the MDR1 mRNA. The ribozyme remained functional despite being tethered to MDR1. Long-term, high-level expression of both the ribozyme and MDR1, as evident by RT-PCR and FACS analysis, was observed in a human T cell line containing the construct selected with vincristine, a cytotoxic substrate for the multidrug transporter.
Characterization of lectinlike surface components on Capnocytophaga ochracea ATCC 33596 that mediate coaggregation with gram-positive oral bacteria (1987)

The interactions between Capnocytophaga ochracea ATCC 33596 and Streptococcus sanguis H1, Actinomyces naeslundii PK984, or Actinomyces israelii PK16 are dependent on specific recognitions between heat-sensitive adhesins on C. ochracea and heat-stable structures (probably carbohydrate-containing receptors) on the surfaces of these gram-positive coaggregation partners. The coaggregation of C. ochracea with each of these three organisms was inhibited by L-rhamnose and D-fucose and to a lesser extent by beta-methyl-galactoside. The reaction with S. sanguis was the most sensitive, while the coaggregation with A. israelii was the least sensitive and was only partially inhibited by each of the sugars that were considered to be effective inhibitors. A more effective inhibition of the coaggregation between C. ochracea and A. israelii was achieved by adding a combination of the 6-deoxysugars and N-acetylneuraminic acid. To further characterize the coaggregations, naturally occurring coaggregation-defective (Cog-) mutants of C. ochracea were obtained from several different selections. Three phenotypically distinct groups of mutants were were isolated. Type 1 mutants failed to coaggregate with S. sanguis only. Type 2 mutants lost ability to interact with both S. sanguis and A. naeslundii. Type 3 mutants failed to coaggregate with all three coaggregation partners. Characterization of the Cog- mutants by sugar inhibition studies made it possible to distinguish three classes of adhesin activity.
Quantitative Detection of Hepatitis B Virus DNA by Real-Time Nucleic Acid Sequence-Based Amplification with Molecular Beacon Detection (2001)

We have developed a hepatitis B virus (HBV) DNA detection and quantification system based on amplification with nucleic acid sequence-based amplification (NASBA) technology and real-time detection with molecular beacon technology. NASBA is normally applied to amplify single-stranded target RNA, producing RNA amplicons. In this work we show that with modifications like primer design, sample extraction method, and template denaturation, the NASBA technique can be made suitable for DNA target amplification resulting in RNA amplicons. A major advantage of our assay is the one-tube, isothermal nature of the method, which allows high-throughput applications for nucleic acid detection. The homogeneous real-time detection allows a closed-tube format of the assay, avoiding any postamplification handling of amplified material and therefore minimizing the risk of contamination of subsequent reactions. The assay has a detection range of 10(3) to 10(9) HBV DNA copies/ml of plasma or serum (6 logs), with good reproducibility and precision. Compared with other HBV DNA assays, our assay provides good sensitivity, a wide dynamic range, and high-throughput applicability, making it a viable alternative to those based on other amplification or detection methods.
INTEGRATING BUILDING PRODUCT MODELS WITH LIVE VIDEO STREAM (2007)

ABSTRACT: Various Building Information Models (BIMs) are increasingly used for data sharing and communication purposes in real estate and construction sector. This change can be seen as part of more general development where the main target is wide integration infrastructure to handle user interaction, business process, applications and data. Besides of new achievements in BIM technologies the described general development is enabled in an interesting manner by the overall technological integration that is bringing together traditional IT, telecommunication, Internet, TV and radio technologies and entertainment business. The resultant solutions have already changed clearly our working environment, its processes and business, and, more even radical changes are likely to appear. This paper shall present a research project addressing combination of building product models with live video stream applications. The research project named &amp;apos;4D Live &amp;apos; explores hardware, middleware and software platforms for the named purpose whilst the main target is to study emerging new sector specific business processes and changes arising from these solutions. 4D Live project is producing several demonstrative solutions where building models are combined with live video stream from one or several digital video cameras: i) Live internet based 4D, ii) Augmented reality web camera, and iii) Multi-Camera studio for BIM-Human interaction.
Nanobelts of Semiconducting Oxides (2001)

Ultralong beltlike (or ribbonlike) nanostructures (so-called nanobelts) were successfully synthesized for semiconducting oxides of zinc, tin, indium, cadmium, and gallium by simply evaporating the desired commercial metal oxide powders at high temperatures. The as-synthesized oxide nanobelts are pure, structurally uniform, and single crystalline, and most of them are free from defects and dislocations. They have a rectanglelike cross section with typical widths of 30 to 300 nanometers, width-to-thickness ratios of 5 to 10, and lengths of up to a few millimeters. The beltlike morphology appears to be a distinctive and common structural characteristic for the family of semiconducting oxides with cations of different valence states and materials of distinct crystallographic structures. The nanobelts could be an ideal system for fully understanding dimensionally confined transport phenomena in functional oxides and building functional devices along individual nanobelts.
Molecular Beam Epitaxy of III-V Compounds: Application of MBE-Grown Films (1982)

The performance of devices fabricated from materials grown by molecular beam epitaxy (MBE) can ideally be used to judge this new film growth technique. From the beginning, microwave and optoelectronic devices have been fabricated from MBE-grown GaAs and AlxGa1_xAs. Initially this work was done mainly at Bell Telephone Laboratories. Fabrication and performance of various devices obtained from MBE material were summarized in excellent reviews by Cho & Arthur (1) and by Cho (2). In the first decade, emphasis was on the MBE production of standard device structures exhibiting characteristics comparable with or even superior to those fabricated by the more conventional growth and processing techniques. Excellent results were obtained for MBE-grown GaAs devices including varactor diodes (3-5), mixer diodes (5, 6-9), IMPATT diodes (10), Gunn diodes (11), MESFETs (12-17), optical waveguides (18-23), and DH injection lasers (24-46). The unique features of MBE have been further applied to more complex device structures involving novel processing steps such as lateral dimensional control as well as metal-semiconductor and oxide-semiconductor heterojunction formation in a single growth cycle. The limits of the MBE technique for the production of novel device structures have not yet been reached.