gebhart/patrepeval huggingface dataset:
Improving protein extraction and separation methods for investigating the metaproteome of anaerobic benzene communities within sediments (2009)

BTEX compounds such as benzene are frequent soil and groundwater contaminants that are easily biodegraded under oxic conditions by bacteria. In contrast, benzene is rather recalcitrant under anaerobic conditions. The analysis of anoxic degradation is often hampered by difficult sampling conditions, limited amounts of biomass and interference of matrix compounds with proteomic approaches. In order to improve the procedure for protein extraction we established a scheme consisting of the following steps: dissociation of cells from lava granules, cell lysis by ultrasonication and purification of proteins by phenol extraction. The 2D-gels revealed a resolution of about 240 proteins spots and the spot patterns showed strong matrix dependence, but still differences were detectable between the metaproteomes obtained after growth on benzene and benzoate. Using direct data base search as well as de novo sequencing approaches we were able to identify several proteins. An enoyl-CoA hydratase with cross species homology to Azoarcus evansii, is known to be involved in the anoxic degradation of xenobiotics. Thereby the identification confirmed that this procedure has the capacity to analyse the metaproteome of an anoxic living microbial community.
What is the origin of irregular current oscillations in the transfer of ionic surfactants across liquid/liquid interfaces? (2008)

We propose a kinetic description of ionic surfactant transfer across an interface between two immiscible electrolyte solutions that includes interfacial processes (charging of the interface, adsorption, and direct ion transfer) as well as characteristics of the electrical circuit. Our model demonstrates that experimentally observed irregular current oscillations may stem from a dynamical instability of the system which is induced by the interplay between a potential-dependent adsorption and direct ionic transfer across the interface. Calculated temporal patterns exhibit dynamical features which agree well with the experimental observations; in particular, we found that current anomalies occur in a vicinity of the standard ion transfer potential, and the presence of the irregular current oscillations depends on the rate and direction of potential scans.
Compact MOSFET modeling for mixed-signal design (2002)

In this paper, the requirements of a good compact MOSFET model for mixed-signal design are discussed. The model accuracy criteria based on the circuit designer's perspective are given. The issues of statistical modeling, model implementation in a circuit simulator and mixed-signal process characterization are also addressed.
Studies on cyclohexane derivatives: III. A chemical proof of the configurations of the two 1‐isopropyl‐4‐methylcyclohexanes (<i>para</i>‐menthanes) (1962)

Abstract The configurations of the two 1‐isopropyl‐4‐methylcyclohexanes ( para ‐menthanes) were determined by means of syntheses starting from pure cis ‐and pure trans ‐4‐methylcyclohexanecarboxylic acid.
The Origins of Syringomyelia: Numerical Models of Fluid/Structure Interactions in the Spinal Cord (2005)

A two-dimensional axi-symmetric numerical model is constructed of the spinal cord, consisting of elastic cord tissue surrounded by aqueous cerebrospinal fluid, in turn surrounded by elastic dura. The geometric and elastic parameters are simplified but of realistic order, compared with existing measurements. A distal reflecting site models scar tissue formed by earlier trauma to the cord, which is commonly associated with syrinx formation. Transients equivalent to both arterial pulsation and percussive coughing are used to excite wave propagation. Propagation is investigated in this model and one with a central canal down the middle of the cord tissue, and in further idealized versions of it, including a model with no cord, one with a rigid cord, one with a rigid dura, and a double-length untapered variant of the rigid-dura model. Analytical predictions for axial and radial wave-speeds in these different situations are compared with, and used to explain, the numerical outcomes. We find that the anatomic circumstances of the spinal cerebrospinal fluid cavity probably do not allow for significant wave steepening phenomena. The results indicate that wave propagation in the real cord is set by the elastic properties of both the cord tissue and the confining dura mater, fat, and bone. The central canal does not influence the wave propagation significantly.
Comparison of ejection fraction and zonal mean velocity of myocardial fiber shortening. (1975)

To determine the extent of cardiac involvement until a diminished ejection fraction (EF) is present, zonal mean velocity of circumferential fiber shortening (Vcf) was measured from the left ventriculogram in 36 patients. The longitudinal axis (apex to mid-point of the aortic valve plane) in right anterior oblique view was divided into four equal parts by three perpeendicular chords. Zonal Vct and percent shortening along the proximal, middle and distal chords were measured. The results of this study indicate that a normal EF is frequently associated with a reduced Vct in one or even two zones. A reduced EF is generally accompanied by a diminished Vct in all three zones of the heart. In addition, a close correlation was found between zonal Vct and percent shortening. Hence the latter, which is much simpler to measure, can be instead of Vct Ejection fraction as a measure of myocardial performance is not as sensitive as Vct, especially in hearts with asynchrony of contraction.
Impaired phagocyte responses to lipopolysaccharide in paroxysmal nocturnal hemoglobinuria (1993)

Bone marrow-derived cells from patients suffering from paroxysmal nocturnal hemoglobinuria (PNH) show a defect in the expression of phosphatidylinositol-anchored membrane proteins, including the CD14 molecule. Blocking experiments with anti-CD14 monoclonal antibodies have shown that lipopolysaccharide (LPS)-induced tumor necrosis factor alpha production by monocytes depends on the interaction between CD14 and a complex formed by LPS and LPS-binding protein. We used a whole-blood model to examine the LPS-induced production of tumor necrosis factor alpha and interleukin-6 in PNH patients and healthy volunteers. At low endotoxin concentrations (1 ng/ml), PNH patients displayed a marked defect in the production of both cytokines, whereas at high LPS concentrations (100 ng/ml), cytokine production was similar to that in healthy volunteers. Using flow cytometry, we also studied the expression of the adhesion molecules Mac-1 (CD11b/CD18) and ICAM-1 (CD54) by monocytes and granulocytes after LPS stimulation. Compared with phagocytes from healthy volunteers, CD14-deficient cells showed poor Mac-1 and ICAM-1 upregulation when whole blood was stimulated with LPS (1 ng/ml), whereas their response to higher LPS doses (100 and 1,000 ng/ml) was essentially normal. The importance of the CD14 molecule in the activation of phagocytes by low LPS concentrations was confirmed by the inhibitory effect of an anti-CD14 antibody both in healthy volunteers and in PNH patients. Since these patients produce the soluble form of the CD14 molecule, these data suggest that soluble CD14 could play a role in phagocyte responses to LPS. We conclude that, in whole blood, phagocytes from PNH patients show impaired responsiveness to LPS and this phenomenon is most probably related to their defect in expression of membrane CD14.
Multivariate sequence stratigraphy: Tackling complexity and uncertainty with stratigraphic forward modeling, multiple scenarios, and conditional frequency maps (2006)

Sequence-stratigraphic conceptual models typically focus on accommodation as a dominant control. Although useful in many ways, this approach may not address the full range of possible controls on stratal patterns, nor is it likely to fully address uncertainty in the identification and quantification of controlling processes. Consequently, predictions from sequence-stratigraphic conceptual models may be more limited than generally stated. Progress in addressing this problem can be achieved by applying the latest generation three-dimensional stratigraphic forward modeling to (1) investigate and include more of the parameters that may control stratal architectures and (2) consider multiple scenarios to help determine the impact of uncertainty in operating processes and their parameter values. Results from a three-dimensional diffusional stratigraphic forward model illustrate this approach, suggesting that relative sea level change, shelf width, and sediment-transport efficiency are important large-scale controls on the spatial and temporal distribution of deep-marine stratal volumes. If this result is sufficiently independent of model assumptions and can be replicated in other models, it suggests that all three controlling factors should be included in interpretations and predictions of outcrop and subsurface deep-marine strata. Modeling results also suggest that combining multiple forward-model scenarios to form conditional frequency maps may be a useful, practical method to present and analyze multiple scenarios. The use of multiple forward-modeling scenarios to consider multiple controls on stratal architecture could begin to account more fully for uncertainty in controlling processes and parameter values, in sequence stratigraphy generally, and evaluation of subsurface uncertainty specifically.
Importin-α7 Is Involved in the Formation of Ebola Virus Inclusion Bodies but Is Not Essential for Pathogenicity in Mice (2015)

Ebola virus (EBOV) protein 24 antagonizes the host interferon (IFN) response by hijacking select nuclear importin-α isoforms. Thereby, it blocks STAT1-mediated IFN-α/β and IFN-γ synthesis. However, owing to the lack of importin-α knockout animal models in the past, their role in EBOV pathogenesis remained largely unknown. Here, we demonstrate that importin-α7 is involved in the formation of EBOV inclusion bodies and replication. However, deletion of the gene encoding importin-α7 was not sufficient to increase survival rates among mice infected with EBOV.
Discovery and Design of Novel Vasopresses Hypotensive Pepitide Agonists (1999)

This presentation will trace the serendipitous discovery of novel vasopressin (VP) hypotensive agonists d(CH2)5[D-Tyr(Et)2,X3]VAVP (where X = Arg, Lys). These peptides were uncovered as part of an ongoing program aimed at the design of potent and selective VP antidiuretic (V2 receptor) antagonists. We will also present highlights of our subsequent preliminary studies seeking (i) to design high affinity radioiodinatable ligands for the localization and characterization of the putative VP vasodilatory (V1c?) receptor; (ii) to identify the structural features of selective and non-selective cyclic and linear VP and oxytocin (OT) antagonists of the V2 receptor, the vascular (V1a) receptor and of the uterine (OT) receptor required for hypotensive agonism and; (iii) to enhance hypotensive potency. These novel VP hypotensive agonists could serve as valuable research tools in studies on the roles of VP in blood pressure regulation and may also lead to the development of a new class of therapeutically useful antihypertensives.
ChemInform Abstract: DIMERIZATION OF THE TRYPTOPHYL MOIETY (1977)

Abstract N‐Acetyl‐tryptophan‐methylester (I) ergibt bei der Behandlung mit Fluorwasserstoff und Trifluoressigsäureanhydrid bei 0°C das dimere Produkt (II).
The Cell Biology of Antigen Processing (1991)

T lymphocytes recognize antigen only after a series of intracellular events known as antigen processing. The result of antigen processing is the production of short segments of the primary peptide sequence bound to a polypeptide-binding groove on major histocompatibility complex (MHC) molecules. Antigen originates from one of two sites: intracellular or extracellular. There are two corresponding pathways for antigen processing and two corresponding classes of MHC molecule. Analysis of each pathway has demonstrated that their separation is not purely anatomical, but is maintained by molecular interactions with other molecules. Antigen processing has been shown to regulate the overall immune response, but the mechanisms involved remain obscure.
Efficient endosome-to-Golgi transport of Shiga toxin is dependent on dynamin and clathrin (2004)

It has previously been shown that Shiga toxin, despite being bound to a glycolipid receptor, can be efficiently endocytosed from clathrin-coated pits. However, clathrin-independent endocytosis is also responsible for a proportion of the toxin uptake in some cells. After endocytosis the toxin can be transported in retrograde fashion to the Golgi apparatus and the endoplasmic reticulum, and then to the cytosol, where it exerts its toxic effect by inactivating ribosomes. In order to investigate the role of dynamin and clathrin in endosome-to-Golgi transport of Shiga toxin, we have used HeLa dyn(K44A) and BHK antisense clathrin heavy chain (CHC) cells that, in an inducible manner, express mutant dynamin or CHC antisense RNA, respectively. In these cell lines, one can study the role of dynamin and clathrin on endosome-to-Golgi transport because they, as shown here, still internalize Shiga toxin when dynamin- and clathrin-dependent endocytosis is blocked. Butyric acid has been shown to sensitize A431 cells to Shiga toxin by increasing the proportion of cell-associated toxin that is transported to the Golgi apparatus and the endoplasmic reticulum. Here, we find that, in HeLa and BHK cells also, butyric acid also increased toxin transport to the Golgi apparatus and sensitized the cells to Shiga toxin. We have therefore studied the role of dynamin and clathrin in both untreated and butyric-acid-treated cells by measuring the sulfation of a modified Shiga B fragment. Our results indicate that endosome-to-Golgi transport of Shiga toxin is dependent on functional dynamin in both untreated cells and in cells treated with butyric acid. Interestingly, the regulation of Shiga toxin transport in untreated and butyric-acid-treated cells differs when it comes to the role of clathrin, because only cells that are sensitized to Shiga toxin with butyric acid need functional clathrin for endosome-to-Golgi transport.
Interactions of sterically stabilized particles suspended in a polymer solution (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInteractions of sterically stabilized particles suspended in a polymer solutionAlice P. Gast and Ludwik LeiblerCite this: Macromolecules 1986, 19, 3, 686–691Publication Date (Print):March 1, 1986Publication History Published online1 May 2002Published inissue 1 March 1986https://doi.org/10.1021/ma00157a035RIGHTS & PERMISSIONSArticle Views730Altmetric-Citations120LEARN 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 InReddit PDF (718 KB) Get e-Alerts Get e-Alerts
Antioxidant Capacities of Peel, Pulp, and Seed Fractions of<i>Canarium odontophyllum</i>Miq. Fruit (2010)

Antioxidant capacities of ethylacetate, butanol, and water fractions of peel, pulp, and seeds of Canarium odontophyllum Miq. (CO) were determined using various in vitro antioxidant models. Ethylacetate fraction of peel (EAFPE) exhibited the highest total phenolic (TPC), total flavonoid content (TFC), and antioxidant activities compared to pulp, seeds, and other solvent fractions. Antioxidant capacities were assayed by total antioxidant capability, 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical activity, ferric reducing antioxidant power (FRAP), and hemoglobin oxidation assay. Total phenolic content of ethylacetate fractions was positively correlated with the antioxidant activity. This is the first report on the antioxidant activities from CO fruit fractions. Thus, EAFPE can be used potentially as a readily accessible source of natural antioxidants and as a possible pharmaceutical supplement.
Effect of pH on the behavior of duroquinone triplets (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of pH on the behavior of duroquinone tripletsJ. C. Scaiano and P. NetaCite this: J. Am. Chem. Soc. 1980, 102, 5, 1608–1611Publication Date (Print):February 1, 1980Publication History Published online1 May 2002Published inissue 1 February 1980https://pubs.acs.org/doi/10.1021/ja00525a024https://doi.org/10.1021/ja00525a024research-articleACS PublicationsRequest reuse permissionsArticle Views110Altmetric-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
Interconnect fabrication processes and the development of low-cost wiring for CMOS products (1995)

As the cost and performance of integrated circuit (IC) interconnections, or “interconnects,” become increasingly important to the development and manufacturing of successful advanced IC products, so also do underlying metallization and patterning processes. In particular, the goals of achieving product design specifications, low development cost (high and early yield), low manufacturing cost, and portability across products can only result from applying robust unit processes that combine to form integrable and scalable process modules. In this paper, we review the interconnect fabrication processes used to form currently manufactured IBM CMOS products, and describe the materials and process integration issues that motivated their selection. In addition, we identify factors which may inhibit application of the fabrication processes to future products having smaller dimensions. The review suggests that large improvements in cost and scalability can be achieved by forming dual-damascene monolithic studs/wires. Previously, the dual-damascene approach was not generally applicable because of the lack of suitable metal deposition techniques for filling high-aspect-ratio features with highly conductive metal. However, recent advances may provide that capability both for near-term applications using Al-based wiring, and also for future applications using more extendible Cu-based wiring.
Sensors for Using Times of Flight to Measure Flow Velocities (2006)

Thin-film sensors for measuring flow velocities in terms of times of flight are undergoing development. These sensors are very small and can be mounted flush with surfaces of airfoils, ducts, and other objects along which one might need to measure flows. Alternatively or in addition, these sensors can be mounted on small struts protruding from such surfaces for acquiring velocity measurements at various distances from the surfaces for the purpose of obtaining boundary-layer flow-velocity profiles. These sensors are related to, but not the same as, hot-wire anemometers. Each sensor includes a thin-film, electrically conductive loop, along which an electric current is made to flow to heat the loop to a temperature above that of the surrounding fluid. Instantaneous voltage fluctuations in segments of the loop are measured by means of electrical taps placed at intervals along the loop. These voltage fluctuations are caused by local fluctuations in electrical resistance that are, in turn, caused by local temperature fluctuations that are, in turn, caused by fluctuations in flow-induced cooling and, hence, in flow velocity. The differential voltage as a function of time, measured at each pair of taps, is subjected to cross-correlation processing with the corresponding quantities measured at other pairs of taps at different locations on the loop. The cross-correlations yield the times taken by elements of fluid to travel between the pairs of taps. Then the component of velocity along the line between any two pairs of taps is calculated simply as the distance between the pairs of taps divided by the travel time. Unlike in the case of hot-wire anemometers, there is no need to obtain calibration data on voltage fluctuations versus velocity fluctuations because, at least in principle, the correlation times are independent of the calibration data.
Editorial: Challenging the Functional Connectivity Disruption in Neurodegenerative Diseases: New Therapeutic Perspectives Through Non-invasive Neuromodulation and Cutting-Edge Technologies (2018)

EDITORIAL article Front. Neurosci., 08 August 2018 | https://doi.org/10.3389/fnins.2018.00554