gebhart/patrepeval huggingface dataset:
Feature extraction and classification of underwater signals based on Hilbert-Huang transform (2007)

Noise radiated from underwater targets is a typical nonlinear and non-stationary signal.Hilbert-Huang Transform is a good method of analyzing this kind of signals com- pared to other traditional methods.Based on this method,a new feature extraction method is proposed in this paper.The targets are divided into four types:cargo ship, fishing boat,marine life and sea noise,and their characteristics are described.Experi- ments on actual noises of underwater targets are carried out,and the results illustrate the method is effective.
Hybrid<i>ab initio</i>Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems (2008)

A hybrid computational method intended for simulations of biomolecules in solution is described. The ab initio Kohn-Sham (KS) density functional theory (DFT) method is used to describe the chemically active part of the system and its first solvation shells, while a frozen-density orbital-free (FDOF) DFT method is used to treat the rest of the solvent. The molecules in the FDOF method have fixed internal structures and frozen electron densities. The hybrid method provides a seamless description of the boundary between the subsystems and allows for the flow of molecules across the boundary. Tests on a liquid water system show that the total energy is conserved well during molecular dynamics and that the effect of the solvent environment on the KS subsystem is well described. An initial application to copper ion binding to the prion protein is also presented.
Functional Identification of Two Novel Genes from Pseudomonas sp. Strain HZN6 Involved in the Catabolism of Nicotine (2012)

Nicotine is a natural alkaloid produced by tobacco plants, and the mechanisms of its catabolism by microorganisms are diverse. In the present study, we reported the mutation, cloning, and identification of two novel genes involved in nicotine degradation from the newly isolated Pseudomonas sp. strain HZN6. Transposon mutagenesis identified a HZN6 mutant in which the nicotine-degrading pathway was blocked at pseudooxynicotine. A 3,874-bp DNA fragment flanking the transposon insertion site was obtained through self-formed adaptor PCR. Two open reading frames (designated pao and sap) were analyzed, and the deduced amino acid sequences shared 29% identity with 6-hydroxy-l-nicotine oxidase from Arthrobacter nicotinovorans and 49% identity with an aldehyde dehydrogenase from Bartonella henselae. Both pao and sap were cloned and functionally expressed in recombinant Escherichia coli BL21. The pao gene encoded a novel pseudooxynicotine amine oxidase with noncovalently bound flavin adenine dinucleotide (FAD) and exhibited substrate specificity removing the methylamine from pseudooxynicotine with the formation of 3-succinoylsemialdehyde-pyridine and hydrogen dioxide. The sap gene encoded a NADP(+)-dependent 3-succinoylsemialdehyde-pyridine dehydrogenase that catalyzed the dehydrogenation of 3-succinoylsemialdehyde-pyridine to 3-succinoyl-pyridine. Genetic analyses indicated that the pao gene played an essential role in nicotine or pseudooxynicotine mineralization in strain HZN6, whereas the sap gene did not. This study provides novel insight into the nicotine-degrading mechanism at the genetic level in Pseudomonas spp.
The essentail active‐site lysines of clostridial glutamate dehydrogenase (1992)

Glutamate dehydrogenase (GDH) of Clostridium symbiosum, like GDH from other species, is inactivated by pyridoxal 5'-phosphate (pyridoxal-P). This inactivation follows a similar pattern to that for beef liver GDH, in which a non-covalent GDH-pyridoxal-P complex reacts slowly to form a covalent complex in which pyridoxal-P is in a Schiff's-base linkage to lysine residues. [formula: see text] The equilibrium constant of this first-order reaction on the enzyme surface determines the final extent of inactivation observed [S. S. Chen and P. C. Engel (1975) Biochem. J. 147, 351-358]. For clostridial GDH, the maximal inactivation obtained was about 70%, reached after 10 min with 7 mM pyridoxal-P at pH 7. In keeping with the model, (a) inactivation became irreversible after reduction with NaBH4. (b) The NaBH4-reduced enzyme showed a new absorption peak at 325 nm. (c) Km values for NAD+ and glutamate were unaltered, although Vmax values were decreased by 70%. Kinetic analysis of the inactivation gave values of 0.81 +/- 0.34 min-1 for k3 and 3.61 +/- 0.95 mM for k2/k1. The linear plot of 1/(1-R) against 1/[pyridoxal-P], where R is the limiting residual activity reached in an inactivation reaction, gave a slightly higher value for k2/k1 of 4.8 +/- 0.47 mM and k4 of 0.16 +/- 0.01 min-1. NADH, NAD+, 2-oxoglutarate, glutarate and succinate separately gave partial protection against inactivation, the biggest effect being that of 40 mM succinate (68% activity compared with 33% in the control). Paired combinations of glutarate or 2-oxoglutarate and NAD+ gave slightly better protection than the separate components, but the most effective combination was 40 mM 2-oxoglutarate with 1 mM NADH (85% activity at equilibrium). 70% inactivated enzyme showed an incorporation of 0.7 mM pyridoxal-P/mol subunit, estimated spectrophotometrically after NaBH4 reduction, in keeping with the 1:1 stoichiometry for the inactivation. In a sample protected with 2-oxoglutarate and NADH, however, incorporation was 0.45 mol/mol, as against 0.15 mol/mol expected (85% active). Tryptic peptides of the enzyme, modified with and without protection, were purified by HPLC. Two major peaks containing phosphopyridoxyllysine were unique to the unprotected enzyme. These peaks yielded three peptide sequences clearly homologous to sequences of other GDH species. In each case, a gap at which no obvious phenylthiohydantoin-amino-acid was detected, matched a conserved lysine position. The gap was taken to indicate phosphopyridoxyllysine which had prevented tryptic cleavage.(ABSTRACT TRUNCATED AT 400 WORDS)
Gender Difference in Postprandial Lipemia (1999)

Insulin resistance, hyperinsulinemia, hypertriglyceridemia, and low HDL-cholesterol concentrations are common features of a plurimetabolic syndrome, which increases the risk of coronary artery disease. Although it has been proposed that the development of atherosclerosis through alterations in plasma lipid levels could be a postprandial phenomenon, most studies on gender differences in plasma lipoprotein-lipid concentrations have reported fasting levels. Therefore, the aim of our study was to examine the response of postprandial triglyceride-rich lipoproteins to a standardized meal in 63 men and 25 women. In addition to the measurement of fasting and postprandial plasma lipid levels, numerous physical and metabolic variables were assessed, including body composition by underwater weighing and body fat distribution by computed tomography. Although no gender difference was noted in total body fat mass, men were characterized by a preferential accumulation of abdominal adipose tissue as revealed by an increased waist circumference and a greater visceral adipose tissue accumulation (50% difference) compared with women (P<0.001). Men also showed a greater plasma triglyceride response (P<0.005) as well as increased postprandial insulin and free fatty acid levels compared with women (P<0.01). Visceral adipose tissue was significantly associated with the postprandial triglyceride response in both genders (men: r=0.49, P<0. 0001; women: r=0.43, P<0.05). Finally, when men and women were matched for visceral adipose tissue accumulation, the gender difference in postprandial plasma triglyceride response was eliminated. Thus results of the present study suggest that the well known gender difference in visceral adipose tissue accumulation is an important contributing factor involved in the exaggerated postprandial triglyceride-rich lipoprotein response noted in men compared with women.
Oxidoreductases Involved in Cell Carbon Synthesis of <i>Methanobacterium thermoautotrophicum</i> (1977)

Cell-free extracts of Methanobacterium thermoautotrophicum were found to contain high activities of the following oxidoreductases (at 60 degrees C): pyruvate dehydrogenase (coenzyme A acetylating), 275 nmol/min per mg of protein; alpha-ketoglutarate dehydrogenase (coenzyme A acylating), 100 nmol/min per mg; fumarate reductase, 360 nmol/min per mg; malate dehydrogenase, 240 nmol/min per mg; and glyceraldehyde-3-phosphate dehydrogenase, 100 nmol/min per mg. The kinetic properties (apparent V(max) and K(M) values), pH optimum, temperature dependence of the rate, and specificity for electron acceptors/donors of the different oxidoreductases were examined. Pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase were shown to be two separate enzymes specific for factor 420 rather than for nicotinamide adenine dinucleotide (NAD), NADP, or ferredoxin as the electron acceptor. Both activities catalyzed the reduction of methyl viologen with the respective alpha-ketoacid and a coenzyme A-dependent exchange between the carboxyl group of the alpha-ketoacid and CO(2). The data indicate that the two enzymes are similar to pyruvate synthase and alpha-ketoglutarate synthase, respectively. Fumarate reductase was found in the soluble cell fraction. This enzyme activity coupled with reduced benzyl viologen as the electron donor, but reduced factor 420, NADH, or NADPH was not effective. The cells did not contain menaquinone, thus excluding this compound as the physiological electron donor for fumarate reduction. NAD was the preferred coenzyme for malate dehydrogenase, whereas NADP was preferred for glyceraldehyde-3-phosphate dehydrogenase. The organism also possessed a factor 420-dependent hydrogenase and a factor 420-linked NADP reductase. The involvement of the described oxidoreductases in cell carbon synthesis is discussed.
Helicos Single-Molecule Sequencing of Bacterial Genomes (2011)

With the advent of high-throughput sequencing technologies, multiple bacterial genomes can be sequenced in days. While the ultimate goal of de novo assembly of bacterial genomes is progressing, changes in the genomic sequence of closely related bacterial strains and isolates are now easily monitored by comparison of their sequences to those of a reference genome. Such studies can be applied to the fields of bacterial evolution, epidemiology, and diagnostics. We present a protocol for single-molecule sequencing of bacterial DNA whose end result is the identification of single nucleotide variants, and various size insertions and deletions relative to a reference genome. The protocol is characterized by the simplicity of sample preparation and the lack of amplification-related sequencing bias.
Serum perfluorooctanoic acid and hepatic enzymes, lipoproteins, and cholesterol: A study of occupationally exposed men (1996)

Perfluorooctanoic acid (PFOA) produces marked hepatic effects, including hepatomegaly, focal hepatocyte necrosis, hypolipidemia, and alteration of hepatic lipid metabolism in a number of animal species. In rodents, PFOA is a peroxisome proliferator, an inducer of members of the cytochrome P450 superfamily and other enzymes involved in xenobiotic metabolism, an uncoupler of oxidative phosphorylation, and may not be a cancer promoter. Although PFOA is the major organofluorine compound found in humans, little information is available concerning human responses to PFOA exposure. This study of 115 occupationally exposed workers examined the cross-sectional associations between PFOA and hepatic enzymes, lipoproteins, and cholesterol. The findings indicate that there is no significant clinical hepatic toxicity at the PFOA levels observed in this study. PFOA may modulate the previously described hepatic responses to obesity and xenobiotics.
Thermal and mechanical properties of polyurethane-diacetylene segmented copolymers. I. Molecular weight and annealing effects (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThermal and mechanical properties of polyurethane-diacetylene segmented copolymers. I. Molecular weight and annealing effectsR. A. Nallicheri and Michael F. RubnerCite this: Macromolecules 1990, 23, 4, 1005–1016Publication Date (Print):February 1, 1990Publication History Published online1 May 2002Published inissue 1 February 1990https://pubs.acs.org/doi/10.1021/ma00206a018https://doi.org/10.1021/ma00206a018research-articleACS PublicationsRequest reuse permissionsArticle Views453Altmetric-Citations16LEARN 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
X-Ray Evidence on the Nature of the Surface Layers of Thin Ground Quartz Crystals Secured with the Cauchois Spectrograph (1938)

Spuriously doubled lines observed in spectra formed by the Cauchois transmission-type curved-crystal focusing spectrograph have been reported by several investigators. B. B. Watson has shown the varying separation of these doublets in several orders to be consistent with the assumption that they are caused by enhanced intensity of reflection in the front and back surface layers of the crystal lamina where its structure has been disturbed by grinding. The enhancement of x-ray reflection by grinding, polishing or other mechanical disturbance is already well known. The present authors note that the more roughly ground of two surfaces on the curved crystal gives rise to the more intense member of the spurious doublet and that heavy etching of the ground quartz surface with hydrofluoric acid suppresses the surface reflection. Cauchois has pointed out that an initially flat crystalline lamina subjected to elastic bending to a circular cylindrical curved form should (approximately) focus the selectively reflected radiation not only from various parts of the arc but also for all regions of the finite thickness of the slab; the second type of focusing is a result of the elastic change in grating constant at points off the neutral axis of the curved slab. The single lines we obtain with curved slabs that have been etched confirm the reality of this type of focusing. We draw the conclusion that the surface layer responsible for the enhanced x-ray reflection must have three interesting properties: (1) The mechanical stress and consequent strain, incident to bending, existing in the main body of the crystal is not shared by this surface layer which thus seems to be differentiated from the rest; (2) the surface layer is crystalline, however, and has the grating constant of unstrained quartz; (3) in spite of their disturbance the atomic planes in this surface layer must have with surprising accuracy the same average orientation as the planes in the main body of the supporting crystal. These properties differing from those to be expected for the amorphous glass-like layers first postulated by Sir George Beilby suggest a recrystallization of the displaced atoms on the underlying crystal foundation such as Finch has proposed.
Preparation and Mechanical Properties of Chitosan/Carbon Nanotubes Composites (2005)

Biopolymer chitosan/multiwalled carbon nanotubes (MWNTs) nanocomposites have been successfully prepared by a simple solution-evaporation method. The morphology and mechanical properties of the chitosan/MWNTs nanocomposites have been characterized with field emission scanning electron microscopy (SEM), bright field transmission electron microscopy (TEM), optical microscopy (OM), wide-angle X-ray diffraction (XRD), and tensile as well as nanoindentation tests. The MWNTs were observed to be homogeneously dispersed throughout the chitosan matrix. When compared with neat chitosan, the mechanical properties, including the tensile modulus and strength, of the nanocomposites are greatly improved by about 93% and 99%, respectively, with incorporation of only 0.8 wt % of MWNTs into the chitosan matrix.
Glucagon acts in the liver to control spontaneous meal size in rats (1993)

To determine the site of origin of pancreatic glucagon's inhibitory effect on spontaneous feeding in rats, glucagon was infused into either the hepatic portal vein or the inferior vena cava during spontaneous meals late in the dark phase. Hepatic portal infusion of 1.7-13.6 micrograms glucagon/meal reduced spontaneous meal size. In contrast, these doses did not significantly affect meal size when delivered via vena caval catheters that ended near the junction of the hepatic vein. This difference indicates that glucagon receptor sites in the liver initiate the satiating action of glucagon during spontaneous meals. The vagal dependency of glucagon satiety was also tested. Hepatic portal infusion of 13.6 micrograms glucagon/meal reduced the size of spontaneous meals both early and late in the dark in neurally intact rats, but not in hepatic-vagotomized rats. Finally, antagonism of endogenous glucagon with hepatic portal infusion of glucagon antibodies in a dose sufficient to neutralize 1 ng glucagon in vitro increased spontaneous meal size in intact rats, but not in hepatic-vagotomized rats. Thus the satiating effects of both exogenous and endogenous glucagon on spontaneous food intake appear to depend on the hepatic branch of the vagus. Taken together, these results are consistent with the hypothesis that glucagon acts in the liver to produce a satiety signal that is transmitted to the brain by the hepatic branch of the abdominal vagus.
Immunologic checkpoints in cancer therapy: focus on the programmed death-1 (PD-1) receptor pathway (2014)

T-lymphocytes have the potential to recognize cancer antigens as foreign and therefore eliminate them. However, immune checkpoints such as cytotoxic T-lymphocyte-associated antigen (CTLA)-4 and programmed cell death (PD)-1 receptor and its ligands (PD-L1, PD-L2) suppress the activity of T-lymphocytes. Advances in the understanding of immunology and its role in cancer have led to the development of immune checkpoint inhibitors that block CTLA-4 and PD-1 and result in durable responses in patients with a wide range of cancers. PD-1 and PD-L1 inhibitors are currently in many stages of clinical investigation, and the anti-PD-1 antibody, pembrolizumab, was recently approved by the US Food and Drug Administration. Many questions remain to be answered, such as the optimal administration schedule, biomarkers that associate with benefit, and potential for use of PD-1 agents in combination approaches. Nonetheless, immunotherapy with PD-1 blocking antibodies is now becoming an integral part in the management of cancer.
Dynamics of laser-induced bubble and nanoparticles generation during ultra-short laser ablation of Pd in liquid (2013)

In this work, the dynamics of multiple cavitation bubbles produced by femtosecond laser ablation of a palladium target submerged in acetone is studied by means of time-resolved fast shadowgraphy technique. The data have evidenced the periodic growth and collapse of the bubbles and the consequent emission of material together with the role played by the laser focus position. Comparing the results with the previsions of the Rayleigh–Plesset model a\ngood agreement is found. The nanoparticles obtained under different focusing conditions are characterized by means of TEM analysis. Their dimension and distribution are correlated with the bubbles dynamics.
Contribution of mass spectrometry to the study of the Maillard reaction in food (2004)

The Maillard reaction or non-enzymatic browning corresponds to a set of reactions occurring between amines and carbonyl compounds, especially reducing sugars. The Maillard reaction is known to occur in heated, dried, or stored foods and in vivo in mammalian organisms. In food, the Maillard reaction is responsible for changes in colour, flavor, and nutritive value but also for the formation of stabilizing and mutagenic compounds. Because of the complexity of the Maillard reaction, mass spectrometry, coupled or not to separation techniques, is a key tool in this research area and we will review in this article the contribution of mass spectrometry to the understanding of this reaction. Different steps of Maillard reaction will be described and the importance and the role played by mass spectrometry will be highlighted. In addition, different approaches to investigate the Maillard reaction from the formation of Amadori products (early Maillard reaction product) to the flavor and melanoidin production will also be covered.
Ge-Induced Reversal of Surface Stress Anisotropy on Si(001) (1995)

Using scanning tunneling microscopy, we show that the intrinsic surface stress anisotropy on Si(001) can be tuned through zero and reversed in sign by controlling the coverage of Ge adatoms. Values of the stress anisotropy, obtained by measuring the step separation distributions, range from 1.0 eV $/(1\ifmmode\times\else\texttimes\fi{}1$ cell) for the clean surface to $\ensuremath{-}0.9$ eV $/(1\ifmmode\times\else\texttimes\fi{}1$ cell) for two monolayers of Ge. Absolute values of stresses in directions along and perpendicular to the dimer rows are also extracted.
The Chloroprocaine Controversy: I. A Hypothesis to Explain the Neural Complications of Chloroprocaine Epidural (1984)

Epidural anesthesia using chloroprocaine (especially in the pregnant woman) has recently been associated with a number of persistent serious neurological complications. Fortunately, this occurrence is infrequent but the underlying causes are unknown. We present the thesis that the complications seen (anterior spinal artery syndrome, cauda equina syndrome) are vascular in origin. The basic cause of clinical complications is a “waterfalls phenomenon,” following the introduction of excessive fluid volume intrathecally associated with systemic hypotension. Serious decrease in tissue perfusion results from cerebrospinal fluid hypertension because of low spinal space compliance and decreased vascular perfusion pressure. We suggest a therapeutic regime in the presence of a total spinal following an attempted epidural block.
Densification and Mechanical Behavior of HfC and HfB <sub>2</sub> Fabricated by Spark Plasma Sintering (2008)

Hafnium diboride (HfB 2 )‐ and hafnium carbide (HfC)‐based materials containing MoSi 2 as sintering aid in the volumetric range 1%–9% were densified by spark plasma sintering at temperatures between 1750° and 1950°C. Fully dense samples were obtained with an initial MoSi 2 content of 3 and 9 vol% at 1750°–1800°C. When the doping level was reduced, it was necessary to raise the sintering temperature in order to obtain samples with densities higher than 97%. Undoped powders had to be sintered at 2100°–2200°C. For doped materials, fine microstructures were obtained when the thermal treatment was lower than 1850°C. Silicon carbide formation was observed in both carbide‐ and boride‐based materials. Nanoindentation hardness values were in the range of 25–28 GPa and were independent of the starting composition. The nanoindentation Young's modulus and the fracture toughness of the HfB 2 ‐based materials were higher than those of the HfC‐based materials. The flexural strength of the HfB 2 ‐based material with 9 vol% of MoSi 2 was higher at 1500°C than at room temperature.