gebhart/patrepeval huggingface dataset:
Stromal–epithelial cell interactions and alteration of branching morphogenesis in macromastic mammary glands (2014)

True macromastia is a rare but disabling condition characterized by massive breast growth. The aetiology and pathogenic mechanisms for this disorder remain largely unexplored because of the lack of in vivo or in vitro models. Previous studies suggested that regulation of epithelial cell growth and development by oestrogen was dependent on paracrine growth factors from the stroma. In this study, a co-culture model containing epithelial and stromal cells was used to investigate the interactions of these cells in macromastia. Epithelial cell proliferation and branching morphogenesis were measured to assess the effect of macromastic stromal cells on epithelial cells. We analysed the cytokines secreted by stromal cells and identified molecules that were critical for effects on epithelial cells. Our results indicated a significant increase in cell proliferation and branching morphogenesis of macromastic and non-macromastic epithelial cells when co-cultured with macromastic stromal cells or in conditioned medium from macromastic stromal cells. Hepatocyte growth factor (HGF) is a key factor in epithelial-stromal interactions of macromastia-derived cell cultures. Blockade of HGF with neutralizing antibodies dramatically attenuated epithelial cell proliferation in conditioned medium from macromastic stromal cells. The epithelial-stromal cell co-culture model demonstrated reliability for studying interactions of mammary stromal and epithelial cells in macromastia. In this model, HGF secreted by macromastic stromal cells was found to play an important role in modifying the behaviour of co-cultured epithelial cells. This model allows further studies to investigate basic cellular and molecular mechanisms in tissue from patients with true breast hypertrophy.
Cloning and characterization of the A-factor receptor gene from Streptomyces griseus (1995)

A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) and its specific receptor protein control streptomycin production, streptomycin resistance, and aerial mycelium formation in Streptomyces griseus. The A-factor receptor protein (ArpA) was purified from a cell lysate of S. griseus IFO 13350. The NH2-terminal amino acid sequences of ArpA and lysyl endopeptidase-generated fragments were determined for the purpose of preparing oligonucleotide primers for cloning arpA by the PCR method. The arpA gene cloned in this way directed the synthesis of a protein having A-factor-specific binding activity when expressed in Escherichia coli under the control of the T7 promoter. The arpA gene was thus concluded to encode a 276-amino-acid protein with a calculated molecular mass of 29.1 kDa, as determined by nucleotide sequencing. The A-factor-binding activity was observed with a homodimer of ArpA. The NH2-terminal portion of ArpA contained an alpha-helix-turn-alpha-helix DNA-binding motif that showed great similarity to those of many DNA-binding proteins, which suggests that it exerts its regulatory function for the various phenotypes by directly binding to a certain key gene(s). Although a mutant strain deficient in both the ArpA protein and A-factor production overproduces streptomycin and forms aerial mycelium and spores earlier than the wild-type strain because of repressor-like behavior of ArpA, introduction of arpA into this mutant abolished simultaneously its streptomycin production and aerial mycelium formation. All of these data are consistent with the idea that ArpA acts as a repressor-type regulator for secondary metabolite formation and morphogenesis during the early growth phase and A-factor at a certain critical intracellular concentration releases the derepression, thus leading to the onset of secondary metabolism and aerial mycelium formation. The presence of ArpA-like proteins among Streptomyces spp., as revealed by PCR, together with the presence of A-factor-like compounds, suggests that a hormonal control similar to the A-factor system exists in many species of this genus.
Color Calibrated High Dynamic Range Imaging with ICC Profiles (2001)

High dynamic range (HDR) imaging has become a powerful tool in computer graphics, and is being applied to scenarios like simulation of different film responses, motion blur, and image-based illumination. The HDR images for these applications are typically generated by combining the information from multiple photographs taken at different exposure settings.Unfortunately, the color calibration of these images has so far been limited to very simplistic approaches such as a simple white balance algorithm. More sophisticated methods used for device-independent color representations are not easily applicable because they inherently assume a limited dynamic range. In this paper, we introduce a novel approach for constructing HDR images directly from low dynamic range images that were calibrated using an ICC input profile.
Transfer of Two <i>Burkholderia</i> and An <i>Alcaligenes</i> Species to <i>Ralstonia</i> Gen. Nov. (1995)

Based on the results of phenotypic characterization, cellular lipid and fatty acid analysis, phylogenetic analysis of 16S rDNA nucleotide sequences and rNA-DNA hybrization, Burkholderia pickettii, Burkholderia solanacearum and Alcaligenes eutrophus are transferred to the new genus Ralstonia, and Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov., and R. eutropha (Davis 1969) comb. nov. are proposed. The type species of the new genus is R. pickettii. Type strain of R. pickettii is ATCC 27511T, of R. solanacearum is ATCC 10696T, and of R. eutropha is ATCC 17697T.
A Comparison of the GroE Chaperonin Requirements for Sequentially and Structurally Homologous Malate Dehydrogenases (2001)

Escherichia coli malate dehydrogenase (EcMDH) and its eukaryotic counterpart, porcine mitochondrial malate dehydrogenase (PmMDH), are highly homologous proteins with significant sequence identity (60%) and virtually identical native structural folds. Despite this homology, EcMDH folds rapidly and efficiently in vitro and does not seem to interact with GroE chaperonins at physiological temperatures (37 degrees C), whereas PmMDH folds much slower than EcMDH and requires these chaperonins to fold to the native state at 37 degrees C. Double jump experiments indicate that the slow folding behavior of PmMDH is not limited by proline isomerization. Although the folding enhancer glycerol (<5 m) does not alter the renaturation kinetics of EcMDH, it dramatically accelerates the spontaneous renaturation of PmMDH at all temperatures tested. Kinetic analysis of PmMDH renaturation with increasing glycerol concentrations suggests that this osmolyte increases the on-pathway kinetics of the monomer folding to assembly-competent forms. Other osmolytes such as trimethylamine N-oxide, sucrose, and betaine also reactivate PmMDH at nonpermissive temperatures (37 degrees C). Glycerol jump experiments with preformed GroEL.PmMDH complexes indicate that the shift between stringent (requires ATP and GroES) and relaxed (only requires ATP) complex conformations is rapid (<3-5 s). The similarity in irreversible misfolding kinetics of PmMDH measured with glycerol or the activated chaperonin complex (GroEL.GroES.ATP) suggests that these folding aids may influence the same step in the PmMDH folding reaction. Moreover, the interactions between glycerol-induced PmMDH folding intermediates and GroEL.GroES.ATP are diminished. Our results support the notion that the protein folding kinetics of sequentially and structurally homologous proteins, rather than the structural fold, dictates the GroE chaperonin requirement.
How Shall We Use the Proteomics Toolbox for Biomarker Discovery? (2007)

Biomarker discovery for clinical purposes is one of the major areas in which proteomics is used. However, despite considerable effort, the successes have been relatively scarce. In this perspective paper, we try to highlight and analyze the main causes for this limited success, and to suggest alternate strategies, which will avoid them, without eluding the foreseeable weak points of these strategies. Two major strategies are analyzed, namely, the switch from body fluids to cell and tissues for the initial biomarker discovery step or, if body fluids must be analyzed, the implementation of highly selective protein selection strategies.
Lunch Speech II. HomePlug Standards for Worldwide Multimedia In-Home Networking and Broadband Powerline Access (2007)

In 2001, the HomePlug Powerline Alliance released the first International high speed powerline communications standard called HomePlug 1.0.1, which operated at a PHY rate of 14 Mbps. Since that time, more than 7 Million HomePlug 1.0 chips have been sold. An updated product based on HomePlug1.0, called HomePlug 1.0 Turbo and operating at 85Mbps was released in 2004. The most recent HomePlug standard is embodied in the HomePlug AV 1.0 specification, and products complying with this specification and operating at 200 Mbps began to appear in 2006. In addition, the HomePlug Alliance and its members, including Intellon Corporation, are actively engaged in the development of HomePlug BPL and HomePlug Command and Control specifications and products. This presentation will first provide an overview of the HomePlug suite of standards including ongoing work towards BPL and Command and Control specifications as well as an overview of HomePlug1.0. The presentation will then focus on HomePlug AV and will describe in detail the HomePlug AV PHY, MAC and Convergence Layers as well as well as the HomePlug AV certification process. The talk will highlight the key technical advantages of the HomePlug AV when compared with other PLC solutions seeking to satisfy the demand for the high data rates and quality of service requirements for distribution of multimedia throughout the home.
Dry etching of through substrate via holes for GaAs MMIC’s (1985)

Through substrate via’s are essential in many GaAs monolithic microwave integrated circuits (MMIC’s). They allow for increased circuit complexity and provide low inductance grounding. A dry etch process is described which has been used for etching vias through 0.2 mm thick GaAs substrates. Freon 12 (CCl2F2) is used at high pressure in a RIE mode at 13.6 MHz. Polymer formation has been identified to be the key to controlling the hole profile.
Stimfit: quantifying electrophysiological data with Python (2014)

Intracellular electrophysiological recordings provide crucial insights into elementary neuronal signals such as action potentials and synaptic currents. Analyzing and interpreting these signals is essential for a quantitative understanding of neuronal information processing, and requires both fast data visualization and ready access to complex analysis routines. To achieve this goal, we have developed Stimfit, a free software package for cellular neurophysiology with a Python scripting interface and a built-in Python shell. The program supports most standard file formats for cellular neurophysiology and other biomedical signals through the Biosig library. To quantify and interpret the activity of single neurons and communication between neurons, the program includes algorithms to characterize the kinetics of presynaptic action potentials and postsynaptic currents, estimate latencies between pre- and postsynaptic events, and detect spontaneously occurring events. We validate and benchmark these algorithms, give estimation errors, and provide sample use cases, showing that Stimfit represents an efficient, accessible and extensible way to accurately analyze and interpret neuronal signals.
Anaerobic Respiration of Escherichia coli in the Mouse Intestine (2011)

The intestine is inhabited by a large microbial community consisting primarily of anaerobes and, to a lesser extent, facultative anaerobes, such as Escherichia coli, which we have shown requires aerobic respiration to compete successfully in the mouse intestine (S. A. Jones et al., Infect. Immun. 75:4891-4899, 2007). If facultative anaerobes efficiently lower oxygen availability in the intestine, then their sustained growth must also depend on anaerobic metabolism. In support of this idea, mutants lacking nitrate reductase or fumarate reductase have extreme colonization defects. Here, we further explore the role of anaerobic respiration in colonization using the streptomycin-treated mouse model. We found that respiratory electron flow is primarily via the naphthoquinones, which pass electrons to cytochrome bd oxidase and the anaerobic terminal reductases. We found that E. coli uses nitrate and fumarate in the intestine, but not nitrite, dimethyl sulfoxide, or trimethylamine N-oxide. Competitive colonizations revealed that cytochrome bd oxidase is more advantageous than nitrate reductase or fumarate reductase. Strains lacking nitrate reductase outcompeted fumarate reductase mutants once the nitrate concentration in cecal mucus reached submillimolar levels, indicating that fumarate is the more important anaerobic electron acceptor in the intestine because nitrate is limiting. Since nitrate is highest in the absence of E. coli, we conclude that E. coli is the only bacterium in the streptomycin-treated mouse large intestine that respires nitrate. Lastly, we demonstrated that a mutant lacking the NarXL regulator (activator of the NarG system), but not a mutant lacking the NarP-NarQ regulator, has a colonization defect, consistent with the advantage provided by NarG. The emerging picture is one in which gene regulation is tuned to balance expression of the terminal reductases that E. coli uses to maximize its competitiveness and achieve the highest possible population in the intestine.
A new transformer-coupled differential Armstrong VCO for very low power operation (2010)

We present a novel differential Armstrong VCO. The proposed Armstrong VCO adopted a new transformer structure which effectively enhanced the output voltage swing of the VCO. The Armstrong VCO was implemented in 0.13 μm RF CMOS process, and measurement showed the oscillation frequency range from 13 to 14.5 GHz (tuning range of 10.9%). The new Armstrong VCO achieved a measured phase noise performance of -104.6 dBc/Hz at 1 MHz offset from 13.66 GHz carrier. The figure-of-merit (FOM) shows excellent performance and the results demonstrate a potential of the novel Armstrong VCO structure for achieving a good phase noise performance.
On the calculation of binding free energies using continuum methods: Application to MHC class I protein‐peptide interactions (1997)

This paper describes a methodology to calculate the binding free energy (delta G) of a protein-ligand complex using a continuum model of the solvent. A formal thermodynamic cycle is used to decompose the binding free energy into electrostatic and non-electrostatic contributions. In this cycle, the reactants are discharged in water, associated as purely nonpolar entities, and the final complex is then recharged. The total electrostatic free energies of the protein, the ligand, and the complex in water are calculated with the finite difference Poisson-Boltzmann (FDPB) method. The nonpolar (hydrophobic) binding free energy is calculated using a free energy-surface area relationship, with a single alkane/water surface tension coefficient (gamma aw). The loss in backbone and side-chain configurational entropy upon binding is estimated and added to the electrostatic and the nonpolar components of delta G. The methodology is applied to the binding of the murine MHC class I protein H-2Kb with three distinct peptides, and to the human MHC class I protein HLA-A2 in complex with five different peptides. Despite significant differences in the amino acid sequences of the different peptides, the experimental binding free energy differences (delta delta Gexp) are quite small (< 0.3 and < 2.7 kcal/mol for the H-2Kb and HLA-A2 complexes, respectively). For each protein, the calculations are successful in reproducing a fairly small range of values for delta delta Gcalc (< 4.4 and < 5.2 kcal/mol, respectively) although the relative peptide binding affinities of H-2Kb and HLA-A2 are not reproduced. For all protein-peptide complexes that were treated, it was found that electrostatic interactions oppose binding whereas nonpolar interactions drive complex formation. The two types of interactions appear to be correlated in that larger nonpolar contributions to binding are generally opposed by increased electrostatic contributions favoring dissociation. The factors that drive the binding of peptides to MHC proteins are discussed in light of our results.
Effect of alteration of charged residues at the N termini of signal peptides on protein export in Bacillus subtilis (1994)

The role of positively charged residues at the N termini of signal peptides in protein export has been studied in Bacillus subtilis. Bacillus signal peptides (alkaline protease [Apr] and neutral protease [Npr] from Bacillus amyloliquefaciens) were altered and fused to mature levansucrase (Lvs). The effects of the various alterations on the export of Lvs in B. subtilis were determined. The replacement of positively charged residues with neutral residues in both Apr and Npr signal peptides resulted in a slight defect in the export of Lvs from B. subtilis. Introduction of a negatively charged residue (aspartic acid) at the N terminus of Npr signal peptide blocked the export of Lvs. However, Apr signal peptide with a net charge of -3 (three aspartic acid residues) was still functional.
Preparation of oxygen gas barrier poly(ethylene terephthalate) films by deposition of silicon oxide films plasma-polymerized from a mixture of tetramethoxysilane and oxygen (1999)

To prepare silicon oxide (SiOx)-deposited poly(ethylene terephthalate) films with high oxygen gas barrier capability, SiOx deposition by plasma polymerization has been investigated from the viewpoint of chemical composition. Tetramethoxysilane (TMOS) is suitable as a starting material for the synthesis of the SiOx films. The SiOx deposition under self-bias, where the etching action occurs around an electrode surface, is effective in eliminating carbonaceous compounds from the deposited SiOx films. There is no difference in the chemical composition between the SiOx films deposited under self-bias and under no self-bias. The SiOx films are composed of a main component of SiOSi networks and a minor component of carbonized carbons. The SiOx films deposited under no self-bias from the TMOS/O2 mixture show good oxygen gas barrier capability, but the SiOx films deposited under the self-bias show poor capability. The minimum oxygen permeation rate for poly(ethylene terephthalate) films deposited SiOx film is 0.10 cm3 m−2 day−1 atm−1, which corresponds to an oxygen permeability coefficient of 1.4 × 10−17 cm3-cm cm−2 s−1 cm−1 Hg for the SiOx film itself. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 2091–2100, 1999
CMOS logarithmic curvature-corrected voltage reference using a multiple differential structure (2006)

A new superior-order curvature-corrected voltage reference will be presented. In order to improve the temperature behavior of the circuit, a double differential structure will be used, implementing the linear and the superior-order curvature corrections. An original CTAT (complementary with absolute temperature) voltage generator will be proposed, using exclusively MOS transistors biased in weak inversion for a low power operation of the voltage reference, having two great advantages: an important reducing of the circuit silicon area and an improved accuracy. The superior-order curvature-correction will be implemented by taking the difference between two gate-source voltages of subthreshold-operated MOS transistors, biased at drain currents having different temperature dependencies: PPAT (proportional with absolute temperature) and PTAT/sup 2/. In order to obtain a low-voltage operation of the circuit, the classical MOS transistor, which implements the zero-order compensated voltage reference, will be replaced by a DTMOS (dynamic threshold MOS) transistor. The SPICE simulations confirm the theoretical estimated results, showing a temperature coefficient under 9.4 ppm/K for an extended input range 173 K < T < 423K and for a supply voltage of 2.5V and a current consumption of about 1/spl mu/A.
Characterization of T cell epitopes restricted by HLA-DP9 in streptococcal M12 protein. (1995)

Interaction of the HLA-DP9 (DPA1*0201/DPB1*0901) molecule and M protein of serotype 12 (SS95/12) streptococci, a main component of the streptococcal cell wall Ag, has been investigated to decipher peptide-binding capacity and T cell activation in the context of the HLA-DP molecule. Seven antigenic peptides (amino acids 19-25) restricted by the HLA-DP9 molecule were identified in M12 protein, using M12 protein- or peptide-specific T cell lines from naturally exposed individuals. The binding affinity of each peptide to the HLA-DP9 molecule was measured by fluorescence intensity of biotinylated peptides bound to L cell transfectants expressing HLA-DP9, followed by treatment with avidin-fluorescence. Binding of biotinylated peptides to the HLA-DP9 molecule was inhibited by an excess amount of corresponding nonbiotinylated peptides and other nonbiotinylated peptides, indicating that the peptides were bound to the HLA-DP9 molecule at a single binding site. Seven synthetic peptides containing the T cell epitopes restricted by the HLA-DP9 molecule had high binding affinity to the HLA-DP9 molecule. Comparison of the amino acid sequences of truncated analogues that could bind to the HLA-DP9 molecule and/or activate T cells suggested an HLA-DP9-specific binding motif, composed of a positively charged residue (R or K) at position 1, a hydrophobic residue (A, G, or L) at position 6, and another hydrophobic residue (L or V) at position 9. Analysis of single amino acid-substituted analogues suggested that the positively charged amino acid in the motif served as a key anchor residue for binding to the HLA-DP9 molecule, which differs from the binding motif to the HLA-DR molecules.
Progressive Western Australian collision with Asia: implications for regional orogography, oceanography, climate and marine biota (2018)

The western margin of Australia has migrated over 30° northward in the last fifty million years. As it progressed, it carried evidence of greenhouse to icehouse climate and ocean transitions in the sedimentary sequences. In the last ten million years Australia collided with the Asian plate to the north, leading to the uplift of the Indonesian archipelago and Papua New Guinea highlands and restricting the interchange between the Indian and Pacific oceans. This created the near “modern” oceanography of the region with the onset of the Indonesian Throughflow and related Leeuwin Current. It also resulted in the ongoing crustal stress along the North West Shelf causing substantial seismicity and faulting. Recent sediment coring by the International Ocean Discovery Program (IODP) and RV Sonne has yielded superb palaeoclimatic and palaeoceanographic archives that will uncover details of the evolution of this margin through the late Neogene to Recent. Knowledge of the past evolution of Australia’s western margin is essential if we are to better predict the consequences of ocean/climate variability for future climate change.