gebhart/patrepeval huggingface dataset:
Coloidal gold, ferritin and peroxidase as markers for electron microscopic double labeling lectin techniques. (1978)

Three markers, colloidal gold, ferritin and peroxidase, were checked for usefulness in double labeling of lectin-binding sites. The amount of various lectins for the stabilization of good sols of a different particle size was evaluated. Several lectin-gold complexes were prepared for electron microscopic labeling purposes, and the optimal amount of various lectins needed for stabilization of gold solutions of a different particle size was determined. The following combinations were investigated for their usefulness in labeling two different lectin-binding sites: lectin-gold and lectin-gold (different particle size), lectin-gold and lectin-ferritin, as well as lectin-ferritin and lectin-peroxidase. Of these combinations the latter did not give satisfactory results for double labeling. In all single and double labeling techniques with the above mentioned markers the quantitative evaluation of the number of lectin-binding sites is not feasible, but these techniques will be of considerable value for the investigation of the dynamics of different lectin-binding sites on the cell surface.
Influences of buried-oxide interface on inversion-layer mobility in ultra-thin SOI MOSFETs (2002)

This paper reports on a study of the inversion-layer mobility in n-channel Si MOSFETs fabricated on a silicon-on-insulator (SOI) substrate. In order to make clear the influences of the buried-oxide interface on the inversion-layer mobility in ultra-thin film SOI transistors, SOI wafers of different quality at the buried-oxide interface were prepared, and the mobility behaviors were compared quantitatively. The transistors with a relatively thick SOI film exhibited the universal relationship between the effective mobility and the effective normal field, regardless of the buried-oxide interface quality. It was found, however, that Coulomb scattering due to charged centers at the backside interface between SOI films and buried oxides has great influence on the effective mobility in the thin SOI thickness region, depending on the buried-oxide interface quality. This means that Coulomb scattering due to charged centers at the buried-oxide interface can degrade the mobility with decreasing SOI thickness, unless the SOI wafer quality at the buried-oxide interface is controlled carefully.
Theoretical Study of Helix Formation in Substituted Phenylene Ethynylene Oligomers (2003)

Theoretical investigations of the relative stabilities of helical vs extended forms of phenylene ethynylene oligomers established that MMFF molecular mechanics was more useful than AM1 or DFT for calculating helical structures and for estimating relative energies. At the level of MMFF, theory predicts that for o- or m-oligophenylene ethynylenes, helix formation is enthalpically favored for ester and ether-substituted oligomers. In contrast to simple electron-demand predictions, we predict that the position of substituents can make a substantial difference in the tendency to form helices.
SipA Is Required for Pilus Formation in <i>Streptococcus pyogenes</i> Serotype M3 (2007)

Pili are a major surface feature of the human pathogen Streptococcus pyogenes (group A streptococcus [GAS]). The T3 pilus is composed of a covalently linked polymer of protein T3 (formerly Orf100 or Fct3) with an ancillary protein, Cpa, attached. A putative signal peptidase, SipA (also called LepA), has been identified in several pilus gene clusters of GAS. We demonstrate that the SipA2 allele of a GAS serotype M3 strain is required for synthesis of T3 pili. Heterologous expression in Escherichia coli showed that SipA2, along with the pilus backbone protein T3 and the sortase SrtC2, is required for polymerization of the T3 protein. In addition, we found that SipA2 is also required for linkage of the ancillary pilin protein Cpa to polymerized T3. Despite partial conservation of motifs of the type I signal peptidase family proteins, SipA lacks the highly conserved and catalytically important serine and lysine residues of these enzymes. Substitution of alanine for either of the two serine residues closest to the expected location of an active site serine demonstrated that these serine residues are both dispensable for T3 polymerization. Therefore, it seems unlikely that SipA functions as a signal peptidase. However, a T3 protein mutated at the P-1 position of the signal peptide cleavage site (alanine to arginine) was unstable in the presence of SipA2, suggesting that there is an interaction between SipA and T3. A possible chaperone-like function of SipA2 in T3 pilus formation is discussed.
Enzymatic Hydrogelation of Small Molecules (2008)

Enzymes, a class of highly efficient and specific catalysts in Nature, dictate a myriad of reactions that constitute various cascades in biological systems. Self-assembly, a process prevalent in Nature, also plays important roles in biology, from maintaining the integrity of cells to performing cellular functions and inducing abnormalities that cause disease. To explore enzyme-regulated molecular self-assembly in an aqueous medium will help to understand and control those important biological processes. On the other hand, certain small organic molecules self-assemble in water to form molecular nanofibers and result in a hydrogel, which is referred to as a "supramolecular hydrogel" (and the small molecules are referred to as "supramolecular hydrogelators"). Supramolecular hydrogelators share common features, such as amphiphilicity and supramolecular interactions (pi-pi interactions, hydrogen bonding, and charge interactions among the molecules, among others) that result in nanostructures and form the three-dimensional networks as the matrices of hydrogels. In this Account, we discuss the use of enzymes to trigger and control the self-assembly of small molecules for hydrogelation, which takes place in vitro or in vivo, extra- or intracellularly. Using phosphatase, thermolysin, beta-lactamase, and phosphatase/kinase as examples, we illustrate the design and application of enzyme-catalyzed or -regulated formation of supramolecular hydrogels that offer a new strategy for detecting the activity of enzymes, screening for enzyme inhibitors, typing bacteria, drug delivery systems, and controlling the fate of cells. Since the expression and distribution of enzymes differ by the types and states of cells, tissues, and organs, using an enzymatic reaction to convert precursors into hydrogelators that self-assemble into nanofibers as the matrices of the hydrogel, one can control the delivery, function, and response of a hydrogel according to a specific biological condition or environment, thus providing an accessible route to create sophisticated materials for biomedicine. Particularly, intracellular enzymatic hydrogelation of small molecules offers a unique means for scientists to integrate molecular self-assembly with inherent enzymatic reactions inside cells for developing new biomaterials and therapeutics at the supramolecular level and improving the basic understanding of dynamic molecular self-assembly in water.
<i>Shewanella oneidensis</i> MR-1 Fluxome under Various Oxygen Conditions (2006)

ABSTRACT The central metabolic fluxes of Shewanella oneidensis MR-1 were examined under carbon-limited (aerobic) and oxygen-limited (microaerobic) chemostat conditions, using 13 C-labeled lactate as the sole carbon source. The carbon labeling patterns of key amino acids in biomass were probed using both gas chromatography-mass spectrometry (GC-MS) and 13 C nuclear magnetic resonance (NMR). Based on the genome annotation, a metabolic pathway model was constructed to quantify the central metabolic flux distributions. The model showed that the tricarboxylic acid (TCA) cycle is the major carbon metabolism route under both conditions. The Entner-Doudoroff and pentose phosphate pathways were utilized primarily for biomass synthesis (with a flux below 5% of the lactate uptake rate). The anaplerotic reactions (pyruvate to malate and oxaloacetate to phosphoenolpyruvate) and the glyoxylate shunt were active. Under carbon-limited conditions, a substantial amount (9% of the lactate uptake rate) of carbon entered the highly reversible serine metabolic pathway. Under microaerobic conditions, fluxes through the TCA cycle decreased and acetate production increased compared to what was found for carbon-limited conditions, and the flux from glyoxylate to glycine (serine-glyoxylate aminotransferase) became measurable. Although the flux distributions under aerobic, microaerobic, and shake flask culture conditions were different, the relative flux ratios for some central metabolic reactions did not differ significantly (in particular, between the shake flask and aerobic-chemostat groups). Hence, the central metabolism of S. oneidensis appears to be robust to environmental changes. Our study also demonstrates the merit of coupling GC-MS with 13 C NMR for metabolic flux analysis to reduce the use of 13 C-labeled substrates and to obtain more-accurate flux values.
Paraguay : actual and potential regulatory issues relating to groundwater use in Gran Asuncion (2002)

The purpose of this GW MATE consultancy was to undertake a diagnosis of groundwater conditions, use and status in Gran Asuncion and to identify issues that could influence overall water-sector policy and that need intervention by the newly-constituted regulator ERSSAN (together with other national institutions and/or the proposed new urban water-services concessionaire). The data on which the diagnosis is based was provided mainly in the form of unpublished reports by ERSSAN, Corporacion Nacional de Obras Sanitarias (CORPOSANA) and most especially by Servicio Nacional de Saneamiento Ambiental (SENASA) and the Netherlands Geological Survey (TNO-NITG), but are not cited in detail here.
Malonic Ester Syntheses with Organosilicon Compounds. New Silicon-containing Malonic Esters, Mono- and Dicarboxylic Acids, Barbituric Acids and a Disiloxanetetracarboxylic Acid<sup>1</sup> (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMalonic Ester Syntheses with Organosilicon Compounds. New Silicon-containing Malonic Esters, Mono- and Dicarboxylic Acids, Barbituric Acids and a Disiloxanetetracarboxylic Acid1L. H. Sommer, G. M. Goldberg, G. H. Barnes, and L. S. Stone Jr.Cite this: J. Am. Chem. Soc. 1954, 76, 6, 1609–1612Publication Date (Print):March 1, 1954Publication History Published online1 May 2002Published inissue 1 March 1954https://pubs.acs.org/doi/10.1021/ja01635a043https://doi.org/10.1021/ja01635a043research-articleACS PublicationsRequest reuse permissionsArticle Views429Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Refractive index profiling-state of the art (1989)

Problems associated with different calibration techniques and some instrumental effects that can determine instrumental accuracy are discussed. It is shown how transmission effects can be observed and used to generate a correction curve for refracted near-field instruments. High-quality fiber slices needed for axial interferometry were used to obtain refractive index differences on suitable fibers to +or-1% with the measurements traceable to national standards. Interferometry was used to calibrate a multiple-step fiber which is available in 10-m lengths with a certificate of calibration. The limitations of the technique are discussed, and preliminary results of a study on the effects of residual stress and stress relief on measurements are given. Comparisons are made between measurements made by axial interferometry and refracted near field on a range of fibers. It is shown that commercial profilers can produce reliable measurements of refractive index difference, absolute refractive index, profile shape, and numerical aperture that agree well with measurements by other techniques.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An FPGA family optimized for high densities and reduced routing delay (2002)

The Act-2 family of CMOS field-programmable gate arrays (FPGAs) uses an electrically programmable antifuse and novel architectural and circuit features to obtain higher logic densities while increasing speed and routability. Improvements include: two new logic modules, novel I/O and clock driver circuitry, and more flexible and faster routing paths. New addressing circuitry shortens programming time and speeds complete testing for shorts, opens, and stuck-at faults. Fully automatic placement and complete routing are retrained. Special software tools used for architectural exploration and layout generation are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Crystallization behavior and phase‐transformation mechanism with the use of graphite nanosheets in poly(vinylidene fluoride) nanocomposites (2012)

Abstract Poly(vinylidene fluoride) (PVDF)–graphite nanosheet (GNS) nanocomposites with different contents of GNSs were prepared by the solution‐casting method. The GNSs were produced by the ultrasonic exfoliation of graphite. The effects of GNSs on the crystalline structure, degree of the crystallization, conductivity, and phase‐transformation mechanism of PVDF were investigated. Atomic force microscopy data showed that the GNSs had a flake‐shaped nanostructure. Fourier transform infrared spectroscopy and X‐ray diffraction results revealed that a β phase formed with the addition of GNSs, and the phase‐transformation mechanism from the α phase to the β phase of PVDF was confirmed. Differential scanning calorimetry results indicated that addition of GNSs led to an increased melting temperature and increased degree of crystallization; this implied that the GNSs acted as nucleating agents. © 2012 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
The M2 channel of influenza A virus: a molecular dynamics study (1998)

Molecular dynamics simulations have been performed on a tetramer of the 25-residue (SSDPLVVAASIIGILHLILWILDRL) synthetic peptide [1] which contains the transmembrane domain of the influenza A virus M2 coat protein. The peptide bundle was initially assembled as a parallel alpha-helix bundle in the octane portion of a phase separated water/octane system, which provided a membrane-mimetic environment. A 4-ns dynamics trajectory identified a left-handed coiled coil state of the neutral bundle, with a water filled funnel-like structural motif at the N-terminus involving the long hydrophobic sequence. The neck of the funnel begins at V27 and terminates at H37, which blocks the channel. The C-terminus is held together by inter-helix hydrogen bonds and contains water below H37. Solvation of the S23 and D24 residues, located at the rim of the funnel, appears to be important for stability of the structure. The calculated average tilt of the helices in the neutral bundle is 27 +/- 5 degrees, which agrees well with recent NMR data.
<title>Shadow-insensitive material detection/classification with atmospherically corrected hyperspectral imagery</title> (2001)

Shadow-insensitive detection or classification of surface materials in atmospherically corrected hyperspectral imagery can be achieved by expressing the reflectance spectrum as a linear combination of spectra that correspond to illumination by the direct sum and by the sky. Some specific algorithms and applications are illustrated using HYperspectral Digital Imagery Collection Experiment (HYDICE) data.
Dose-dependent roles for canonical Wnt signalling in <i>de novo</i> crypt formation and cell cycle properties of the colonic epithelium (2012)

There is a gradient of β-catenin expression along the colonic crypt axis with the highest levels at the crypt bottom. In addition, colorectal cancers show a heterogeneous subcellular pattern of β-catenin accumulation. However, it remains unclear whether different levels of Wnt signalling exert distinct roles in the colonic epithelium. Here, we investigated the dose-dependent effect of canonical Wnt activation on colonic epithelial differentiation by controlling the expression levels of stabilised β-catenin using a doxycycline-inducible transgenic system in mice. We show that elevated levels of Wnt signalling induce the amplification of Lgr5+ cells, which is accompanied by crypt fission and a reduction in cell proliferation among progenitor cells. By contrast, lower levels of β-catenin induction enhance cell proliferation rates of epithelial progenitors without affecting crypt fission rates. Notably, slow-cycling cells produced by β-catenin activation exhibit activation of Notch signalling. Consistent with the interpretation that the combination of Notch and Wnt signalling maintains crypt cells in a low proliferative state, the treatment of β-catenin-expressing mice with a Notch inhibitor turned such slow-cycling cells into actively proliferating cells. Our results indicate that the activation of the canonical Wnt signalling pathway is sufficient for de novo crypt formation, and suggest that different levels of canonical Wnt activations, in cooperation with Notch signalling, establish a hierarchy of slower-cycling stem cells and faster-cycling progenitor cells characteristic for the colonic epithelium.
On Hardware and Hardware Models for Embedded Real-Time Systems (2001)

When building an embedded real-time systems, the choice of hardware platform is very important to create an analyzable and predictable system. Also, the quality of the models of the hardware used in software tools is very important to the correctness of timing analysis and the integrity of the system.
Loss-of-Function of Human PINK1 Results in Mitochondrial Pathology and Can Be Rescued by Parkin (2007)

Degeneration of dopaminergic neurons in the substantia nigra is characteristic for Parkinson's disease (PD), the second most common neurodegenerative disorder. Mitochondrial dysfunction is believed to contribute to the etiology of PD. Although most cases are sporadic, recent evidence points to a number of genes involved in familial variants of PD. Among them, a loss-of-function of phosphatase and tensin homolog-induced kinase 1 (PINK1; PARK6) is associated with rare cases of autosomal recessive parkinsonism. In HeLa cells, RNA interference-mediated downregulation of PINK1 results in abnormal mitochondrial morphology and altered membrane potential. Morphological changes of mitochondria can be rescued by expression of wild-type PINK1 but not by PD-associated PINK1 mutants. Moreover, primary cells derived from patients with two different PINK1 mutants showed a similar defect in mitochondrial morphology. Human parkin but not PD-associated mutants could rescue mitochondrial pathology in human cells like wild-type PINK1. Our results may therefore suggest that PINK1 deficiency in humans results in mitochondrial abnormalities associated with cellular stress, a pathological phenotype, which can be ameliorated by enhanced expression of parkin.
Binaural Classification for Reverberant Speech Segregation Using Deep Neural Networks (2014)

Speech signal degradation in real environments mainly results from room reverberation and concurrent noise. While human listening is robust in complex auditory scenes, current speech segregation algorithms do not perform well in noisy and reverberant environments. We treat the binaural segregation problem as binary classification, and employ deep neural networks (DNNs) for the classification task. The binaural features of the interaural time difference and interaural level difference are used as the main auditory features for classification. The monaural feature of gammatone frequency cepstral coefficients is also used to improve classification performance, especially when interference and target speech are collocated or very close to one another. We systematically examine DNN generalization to untrained spatial configurations. Evaluations and comparisons show that DNN-based binaural classification produces superior segregation performance in a variety of multisource and reverberant conditions.
Eye elongation during accommodation in humans: differences between emmetropes and myopes. (1998)

The detected eye elongation can be explained by the accommodation-induced contraction of the ciliary muscle, which results in forward and inward pulling of the choroid, thus decreasing the circumference of the sclera, and leads to an elongation of the axial eye length. Finally, it was demonstrated that PCI, in contrast to clinical ultrasound, is capable of characterizing eye length changes during accommodation in humans.
Measures of Anxiety among Tennis Players in Singles and Doubles Matches (1996)

Male and female tennis players (N = 100) completed the Competitive State Anxiety. Inventory-2 about 1 hr. before playing singles and doubles matches. Multivariate analysis of variance of anxiety and self-confidence responses by match result indicated that winners of singles matches had significantly lower scores on Cognitive Anxiety and higher ones on Self-confidence scores than losers. Winners of doubles matches had significantly higher Self-confidence scores than losers. Discriminant function analysis indicated that 72% of results for singles matches and 70% of results for doubles matches could be correctly classified from responses to the precompetition measures. A comparison of anxiety responses by playing condition indicated that, irrespective of the match outcome, scores on Cognitive and Somatic Anxiety were higher and scores on Self-confidence were lower before playing singles than before playing doubles. The findings suggest that precompetition scores on measures of anxiety provide significant indicators of performance in tennis but that responses vary for singles and doubles play.
Automatic generation of remediation procedures for malware infections (2010)

Immune checkpoint inhibitors block the checkpoint molecules. Different types of cancer immune checkpoint inhibitors have been approved recently: CTLA-4 monoclonal antibodies (as ipilimumab); anti-PD-1 monoclonal antibodies (as pembrolizumab and nivolumab); and anti-PD-L1 monoclonal antibodies (as atezolizumab, avelumab, and durmalumab). We collect recent published results about autoimmune endocrine dysfunctions associated with cancer antibody immunotherapies. These agents cause a raised immune response leading to immune-related adverse events (irAEs), varying from mild to fatal, based on the organ system and severity. Immune-related endocrine toxicities are usually irreversible in 50% of cases, and include hypophysitis, thyroid dysfunctions, type 1 diabetes mellitus, and adrenal insufficiency. Anti-PD-1-antibodies are more frequently associated with thyroid dysfunctions (including painless thyroiditis, hypothyroidism, thyrotoxicosis, or thyroid storm), while the most frequent irAE related to anti-CTLA-4-antibodies is hypophysitis. The combination of anti-CTLA-4 and anti-PD-1 antibodies is associated with a 30% chance of irAEs. Symptoms and clinical signs vary depending on the target organ. IrAEs are usually managed by an oncological therapist, but in more challenging circumstances (i.e., for new onset insulin-dependent diabetes, hypoadrenalism, gonadal hormones dysfunctions, or durable hypophysitis) an endocrinologist is needed.