gebhart/patrepeval huggingface dataset:
Molecular signature of highly conductive metal-molecule-metal junctions (2009)

The simplicity of single-molecule junctions based on direct bonding of a small molecule between two metallic electrodes makes them an ideal system for the study of fundamental questions related to molecular electronics. Here we study the conductance properties of six different types of molecules by suspending individual molecules between Pt electrodes. All the molecular junctions show a typical conductance of about $1{G}_{0}$ which is ascribed to the dominant role of the Pt contacts. However, despite the metalliclike conductivity, the individual molecular signature is well expressed by the effect of molecular vibrations in the inelastic contribution to the conductance.
On the extraction of dead-time controllers and estimators from delay-free parametrizations (2003)

An approach to control design for dead-time (DT) systems is proposed. The underlying idea is to treat the DT element not as a part of the generalized plant, but rather as a (causality) constraint imposed upon the controller (estimator). This enables one to use well-understood parametrizations of all delay free controllers in the DT design. In particular, DT controllers can be extracted from such delay-free parametrizations. In the paper, the extraction procedures are developed in both H/sup 2/ and H/sup /spl infin// settings. It is shown that the proposed approach yields simple solution procedures and new transparent and intuitively appealing structures for the resulting controllers and estimators.
Study of hydrodynamic behavior of a laboratory scale upflow anaerobic fixed film fixed bed reactor. (2006)

Application of anaerobic fixed film fixed bed reactor (AFFFB), containing mixed population of bacteria, helps in bacterial immobilization as biofilm on a support medium in the reactor overcoming the problem of biomass washout. Knowledge of hydrodynamics characteristics helps in better understanding and evaluating the performance of any reactor. This paper presents residence time distribution (RTD) studies carried out to investigate the hydrodynamic behavior of AFFFB reactor under the influence of varied hydraulic loading resulting in HRTs in range 24 hrs to 6 hrs. Results have demonstrated that the flow pattern is more close to a plug flow type and vary with varying intensity of dispersion and the extent of dispersion increases with decrease in HRTs.
Attenuation of the Febrile Response in Guinea Pigs by Fish Oil Enriched Diets (1989)

The influence of dietary lipid manipulation on the fever response to an injection of murine recombinant Interleukin-1 (rIL-1) in guinea pigs was examined. The animals were fed diets identical except for the lipid source for periods of 5 and 6 wk. In vitro thromboxane B2/B3 (TxB2/B3) production in collagen-stimulated whole blood was also measured. One diet was enriched with menhaden oil, high in the omega-3 series of fatty acids. The other diet contained safflower oil, consisting primarily of the omega-6 fatty acid linoleic acid (74%). Animals fed the fish oil-enriched diet for 6 wk not 5 week had a blunted fever response after rIL-1 injection. This was associated with a 27% increase (p less than 0.05) in total omega-3 fatty acids in plasma phospholipids between weeks 5 and 6 in fish oil-fed animals. Safflower oil-fed animals produced a "normal" febrile response regardless of the duration of feeding. Safflower-fed guinea pigs demonstrated a significant increase in TxB2/B3 production in whole blood after 6 wks that was associated with a 25% increase (p less than 0.05) in plasma phospholipid arachidonic acid levels between weeks 5 and 6. Despite significant reductions in phospholipid linoleic acid in animals fed fish oil, arachidonic acid levels remained unchanged. In the guinea pig model used, long-term menhaden oil feeding can significantly blunt the febrile response induced by exogenous Interleukin-1. Also, a high intake of linoleic acid as seen in safflower oil feeding can significantly increase thromboxane production in stimulated whole blood.(ABSTRACT TRUNCATED AT 250 WORDS)
Clutter rejection filters in color flow imaging: a theoretical approach (1997)

A general class of linear clutter rejection filters is described, covering the commonly used filter types including FIR/IIR filters with linear initialization, as well as regression filters, where the clutter component is estimated by least square curve fitting. The filter can be described by a complex valued matrix, and a frequency response is defined. However, in contrast to a time invariant filter, the general linear filter may create frequency components which are not present in the input signal. This produces bias in the velocity and velocity spread estimates. It is shown that the clutter filter effect on the autocorrelation estimates can be described by a frequency domain transfer function, but unlike time invariant filters, the transfer function is different for each temporal lag of the autocorrelation function. Using a two dimensional (axial and temporal dimension) model of the received signal, the bias in velocity and velocity spread is quantified, both for the autocorrelation algorithm and the time shift cross-correlation estimator. Theoretical expressions, as well as numerical examples are given.
Prevalence of bronchial asthma in schoolchildren in Oslo, Norway (1995)

In 1993, 4521 schoolchildren in Oslo, Norway, participated in a European study on air pollution and respiratory health. Incorporated in the primary questionnaire were five questions taken from a study performed 12 years earlier on 1772 schoolchildren in the same city. The response rate was 85% in 1993 vs 95% in 1981. The current and cumulative prevalences of doctor-diagnosed asthma in 1993 were 4.2% and 8.0%, respectively, compared to 2.2% (P < 0.01) and 3.4% (P < 0.01) in 1981. Attacks of breathlessness during the last 3 years were experienced by 7.1% in 1993 and 3.3% in 1981 (P < 0.05). Wheezing or breathlessness on exposure to pollen in 1993 and 1981 was reported by 6.1% and 3.7% (P < 0.01), respectively; to animals by 4.0% and 2.8% (P < 0.05); and to exercise by 10.2% and 4.8% (P < 0.01). The prevalence of occasional wheezing and the cumulative prevalence of doctor-diagnosed eczema, urticaria, and hay fever were not significantly altered. To summarize, a higher prevalence of both doctor-diagnosed asthma and symptoms of obstructive airways disease was reported by children attending primary school in Oslo in 1993 than 12 years earlier. No increase was observed in the prevalence of other atopic diseases.
miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53 (2009)

The role of miRNAs in regulating megakaryocyte differentiation was examined using bipotent K562 human leukemia cells. miR-34a is strongly up-regulated during phorbol ester-induced megakaryocyte differentiation, but not during hemin-induced erythrocyte differentiation. Enforced expression of miR-34a in K562 cells inhibits cell proliferation, induces cell-cycle arrest in G(1) phase, and promotes megakaryocyte differentiation as measured by CD41 induction. miR-34a expression is also up-regulated during thrombopoietin-induced differentiation of CD34(+) hematopoietic precursors, and its enforced expression in these cells significantly increases the number of megakaryocyte colonies. miR-34a directly regulates expression of MYB, facilitating megakaryocyte differentiation, and of CDK4 and CDK6, to inhibit the G(1)/S transition. However, these miR-34a target genes are down-regulated rapidly after inducing megakaryocyte differentiation before miR-34a is induced. This suggests that miR-34a is not responsible for the initial down-regulation but may contribute to maintaining their suppression later on. Previous studies have implicated miR-34a as a tumor suppressor gene whose transcription is activated by p53. However, in p53-null K562 cells, phorbol esters induce miR-34a expression independently of p53 by activating an alternative phorbol ester-responsive promoter to produce a longer pri-miR-34a transcript.
Determination of azelaic acid in pharmaceuticals and cosmetics by RP-HPLC after pre-column derivatization. (1994)

This paper reports a RP-HPLC method for the determination in topics of azelaic acid, a keratolytic and anti-comedogenic agent widely used in the treatment of all types of acne. A derivatization step was needed prior to chromatographic analysis because the analyte is lacking in chromophore. A sample clean-up procedure by solid-phase extraction was also developed to analyse azelaic acid in complex matrices, such as pharmaceutical and cosmetic formulations.
Automatic facial expression recognition using features of salient facial patches (2014)

Extraction of discriminative features from salient facial patches plays a vital role in effective facial expression recognition. The accurate detection of facial landmarks improves the localization of the salient patches on face images. This paper proposes a novel framework for expression recognition by using appearance features of selected facial patches. A few prominent facial patches, depending on the position of facial landmarks, are extracted which are active during emotion elicitation. These active patches are further processed to obtain the salient patches which contain discriminative features for classification of each pair of expressions, thereby selecting different facial patches as salient for different pair of expression classes. One-against-one classification method is adopted using these features. In addition, an automated learning-free facial landmark detection technique has been proposed, which achieves similar performances as that of other state-of-art landmark detection methods, yet requires significantly less execution time. The proposed method is found to perform well consistently in different resolutions, hence, providing a solution for expression recognition in low resolution images. Experiments on CK+ and JAFFE facial expression databases show the effectiveness of the proposed system.
Identification of the vinculin-binding site in the cytoskeletal protein <i>α</i>-actinin (1994)

Using low-speed sedimentation equilibrium we have established that vinculin binds to alpha-actinin with a Kd of 1.3 x 10(-5) M. Electron microscopy of negatively stained preparations of vinculin revealed spherical particles (diameter 11.2 nm; S.D. 1.7 nm, n = 21), whereas alpha-actinin appeared as a rod-shaped particle (length 33 nm; S.D. 3.3 nm, n = 23). Mixtures of the two proteins contained both 'lollipop'- and 'dumbell'-shaped particles which we interpret as either one or two spherical vinculin molecules associated with the ends of the alpha-actinin rod. We have further defined the vinculin-binding site in alpha-actinin using 125I-vinculin and a gel-blot assay in which proteolytic fragments of alpha-actinin and fragments of alpha-actinin expressed in Escherichia coli were resolved by SDS/PAGE and blotted to nitrocellulose. 125I-vinculin bound to polypeptides derived from the spectrin-like repeat region of alpha-actinin, but did not bind to the actin-binding domain. Binding was inhibited by a 100-fold molar excess of unlabelled vinculin. Using a series of glutathione S-transferase fusion proteins we have mapped the vinculin-binding site to a region toward the C-terminal end of the molecule (alpha-actinin residues 713-749). 125I-vinculin also bound to fusion proteins containing this sequence which had been immobilized on glutathione-agarose beads. The vinculin-binding site is localized in a highly conserved region of the molecule close to the first of two EF-hand calcium-binding motifs.
Modulation in the Air: Backscatter Communication Over Ambient OFDM Carrier (2017)

Ambient backscatter communication (AmBC) enables radio-frequency (RF) powered backscatter devices (BDs) (e.g., sensors and tags) to modulate their information bits over ambient RF carriers in an over-the-air manner. This technology, also called “modulation in the air,” has emerged as a promising solution to achieve green communication for future Internet of Things. This paper studies an AmBC system by leveraging the ambient orthogonal frequency division multiplexing (OFDM) modulated signals in the air. We first model such AmBC system from a spread-spectrum communication perspective, upon which a novel joint design for BD waveform and receiver detector is proposed. The BD symbol period is designed as an integer multiplication of the OFDM symbol period, and the waveform for BD bit “0” maintains the same state within the BD symbol period, while the waveform for BD bit “1” has a state transition in the middle of each OFDM symbol period within the BD symbol period. In the receiver detector design, we construct the test statistic that cancels out the direct-link interference by exploiting the repeating structure of the ambient OFDM signals due to the use of cyclic prefix. For the system with a single-antenna receiver, the maximum-likelihood detector is proposed to recover the BD bits, for which the optimal threshold is obtained in closed-form expression. For the system with a multi-antenna receiver, we propose a new test statistic which is a linear combination of the per-antenna test statistics and derive the corresponding optimal detector. The proposed optimal detectors require only knowing the strength of the backscatter channel, thus simplifying their implementation. Moreover, practical timing synchronization algorithms are proposed for the designed AmBC system, and we also analyze the effect of various system parameters on the transmission rate and detection performance. Finally, extensive numerical results are provided to verify that the proposed transceiver design can improve the system bit-error-rate performance and the operating range significantly and achieve much higher data rate, as compared with the conventional design.
Nebulization of the acidified sodium nitrite formulation attenuates acute hypoxic pulmonary vasoconstriction (2010)

Nitrite alone and in acidified forms effectively and similarly attenuates HPV. However, acidified nitrite formulations induce a more pronounced increase in nitric oxide exhalation.
A multi-scale, image-based pore network modeling approach to simulate two-phase flow in heterogeneous rocks (2015)

Despite the large interest in the multi-phase flow properties of rocks with broad pore size distributions, most digital rock physics approaches struggle with the presence of multiple pore scales. In this work, we present a method to estimate relative permeability (Kr) and resistivity index (RI) curves of such heterogeneous rocks during drainage. In our dual pore network model (DPNM), macropores are represented as pores and throats , while unresolved microporosity is treated as a continuous porous medium. The scales are coupled by including microporosity as symbolic network elements in the DPNM, based on 3D image analysis. The validity of the method is investigated by treating two carbonate rocks (Estaillades and Savonnières limestone). We present a sensitivity analysis of the drainage behaviour of these networks on the microporosity’s petrophysical properties, which are provided as input. While a number of challenges persist, the presented examples show how DPNM can help increase the understanding of two-phase flow in complex carbonate rocks.
A Novel Human Chymotrypsin-like Digestive Enzyme (1997)

The gene of a novel chymotrypsin-like serine protease has been cloned from human pancreas. The chymotrypsin-like enzyme-1 gene is located on chromosome 16q22.1 in a tight cluster with four unrelated genes. The gene has seven exons with the signal and activation peptide and the three main catalytic residues forming the active site encoded by separate exons. Northern blots of pancreatic mRNA showed a major transcript of 1.0 kilobases and a minor transcript of 1.3 kilobases due to alternative polyadenylation. No transcript was found in other tissues. Its presence in pancreatic tissue, duodenal juice, and urine was demonstrated with antisera raised against synthetic peptides from the derived amino acid sequence of the gene. The peptide sequences were chosen for being most dissimilar to chymotrypsin, and the antisera obtained did not react with purified human chymotrypsin. The proteolytically active CTRL-1 has been identified in pancreatic homogenate, duodenal juice, and urine, and a recombinant CTRL-1 has been characterized. Increased pancreatic secretion of CTRL-1 was induced by protease inhibitors indicating that the enzyme is secreted from pancreas upon feedback stimulation. Both native and recombinant CTRL-1 displayed chymotrypsin- and elastase-2-like activities and hydrolyzed the amide bonds of substrates having tyrosine, phenylalanine, or leucine residues at the P1 position. The enzyme was active over a broad pH range (6.5-9. 0), with a maximum at pH 8.0-8.5. CTRL-1 was produced as a zymogen of 264 amino acids as deduced from the gene sequence, with a sequence identity of 54% with human chymotrypsin B. The number and location of intron/exon junctions as well as the sequence similarity to chymotrypsin both at the DNA and protein level and the presence in duodenal juice indicate that this is a novel digestive enzyme of the chymotrypsin superfamily, albeit one with distinct physiological and biochemical features.
Oxidation of Aromatic Pollutants by Lignin-degrading Fungi and Their Extracellular Peroxidases (2024)

Evidence for organopollutant degradation by the lignin-degrading fungi that cause white rot of wood has accumulated in the literature throughout the past 30 years, but heightened interest in the subject dates from around 1985, when cultures of one frequently used experimental organism, Phanerochaete chrysosporium, were reported to oxidize a wide variety of 14C-labeled pollutants to 14CO2. The compounds mineralized in these studies include benzo[a]pyrene [1], lindane [1], 1,1,1-trichloro-2, 2-bis(4-chiorophenyl)ethane (DDT) [1], various chlorinated anilines [2], and a polychlorinated biphenyl mixture [3]. The salient point of all this work is that ligninolytic fungi clearly differ from other eukaryotes (including other fungi), which do not cleave the rings of polycyclic or highly chlorinated aromatics [4], White rot fungi also differ from most bacteria in their approach to xenobiotic metabolism: aromatic pollutants, like lignin, are unable to support fungal cell growth and division; instead, a primary growth substrate such as glucose or cellulose is required. Pollutant degradation appears in fungal cultures at the same time that ligninolytic activity does, and also resembles ligninolysis in that it is usually stimulated by nutrient limitation [1–3]. In short, the xenobiotic oxidations of white rot fungi are evidently fortuitous side reactions of ligninolytic metabolism. To envisage how this process might work, it is first necessary to consider the mechanism for cleavage of the lignin macromolecule in vivo.
<i>EGFR</i> Variant Heterogeneity in Glioblastoma Resolved through Single-Nucleus Sequencing (2014)

We developed a novel single-cell sequencing methodology capable of identifying unique, nonoverlapping subclonal alterations from archived frozen clinical specimens. Using GBM as an example, we validated our method to successfully define tumor cell subpopulations containing distinct genetic and treatment resistance profiles and potentially mutually cooperative combinations of alterations in EGFR and other genes.
Sulfated and unsulfated steroids modulate γ-aminobutyric acidA receptor function through distinct sites (1999)

Sulfated and unsulfated neurosteroids such as pregnenolone sulfate, dehydroepiandrosterone sulfate (DHEAS), pregnanolone, and allopregnanolone, modulate ionotropic amino acid neurotransmitter receptors, and may function as endogenous neuromodulators. The gamma-aminobutyric acid type A (GABAA) receptor exhibits both negative and positive modulation by neurosteroids, but the interaction between negative and positive modulators is not well-understood. For a number of neuroactive steroids, sulfation at C-3 reverses the direction of modulation from positive to negative, suggesting that sulfation could be an important control point for the activity of endogenous neurosteroids. Modulation by endogenous and synthetic steroids of the response to exogenous or synaptically released GABA was examined in primary chick spinal cord and rat hippocampal neurons, and in Xenopus laevis oocytes expressing alpha1beta2gamma2S GABAA receptors. Inhibitory activity is retained when hemisuccinate is substituted for sulfate at C-3, suggesting that it is the negative charge, rather than the sulfate group, that confers inhibitory efficacy. The interaction between steroid negative and positive modulators is not competitive, indicating that steroid negative and positive modulators act through distinct sites. Some steroids, such as 11-ketopregnenolone sulfate, appear to act at both negative and positive modulatory sites, as indicated by an 'off-response' upon washout. A similar off-response is also observed after co-application of the negative modulator DHEAS and the positive modulator allopregnanolone. The observation that simultaneous application of sulfated and unsulfated steroids, such as DHEAS and allopregnanolone, act at distinct sites implies that steroid negative and positive modulators can act independently or coordinately to regulate GABA-mediated inhibition in the central nervous system.
Analysis of the effect of bezafibrate on the oxygen dissociation curve of human hemoglobin (1984)

Analysis of the effects of a range of concentrations of the antihyperlipoproteinemia drug, bezafibrate, on the oxygen dissociation curve of dilute hemoglobin solutions indicates a 4:1 binding stoichiometry with a site binding constant of 434 mol-1 for deoxyhemoglobin. Analysis of the combined effects of a range of bezafibrate and 2,3-diphosphoglycerate (DPG) concentrations indicates that 2 of the 4 bezafibrate sites are in the vicinity of the DPG binding site, and competitive with DPG binding, and 2 of the sites are remote from the DPG binding site.
Identification of Unusual Bacterial Glycosylation by Tandem Mass Spectrometry Analyses of Intact Proteins (2005)

The characterization of protein glycosylation can be a complex and time-consuming procedure, especially for prokaryote O-linked glycoproteins, which often comprise unusual oligosaccharide structures with no known glycosylation motif. In this report, we describe a "top-down" approach that provides information on the extent of glycosylation, the molecular masses, and the structure of oligosaccharide residues on bacterial flagella, important structural proteins involved in the motility of pathogenic bacteria. Flagella from four bacterial pathogens, namely, Campylobacter jejuni, Helicobacter pylori, Aeromonas caviae, and Listeria monocytogenes, were analyzed by this top-down mass spectrometry approach. The approach needs minimal sample preparation and can be performed within a few minutes compared to the tedious and often time-consuming "bottom-up" approach involving proteolytic digestion and LC-MS-MS analyses of the suspected glycopeptides. Multiply protonated protein precursor ions subjected to low-energy collisional activation in a quadrupole time-of-flight instrument showed extensive and specific gas-phase deglycosylation resulting in the formation of abundant oxonium ions with very few fragment ions from peptidic bond cleavages. Structural information on individual carbohydrate residues is obtained using a second-generation product ion scan of oxonium ions formed by collisional activation of the intact protein ions in the source region. The four bacterial flagella examined differed not only by the extent of glycosylation but also by the nature of carbohydrate substituents. For example, the flagellin from the Gram-positive bacterium, L. monocytogenes showed O-linked GlcNAc residues at up to 6 sites/protein monomer. In contrast, the three Gram-negative bacterial pathogens C. jejuni, H. pylori and A. caviae displayed up to 19 Ser/Thr O-linked sites modified with residues structurally related to N-acetylpseudaminic acid (Pse5Ac7Ac) and in the case of Campylobacter include a novel N-acetylglutamine substituent on Pse5Am7Ac.