1,711 research outputs found
rEMM: Extensible Markov Model for Data Stream Clustering in R
No full textClustering streams of continuously arriving data has become an important application of data mining in recent years and efficient algorithms have been proposed by several researchers. However, clustering alone neglects the fact that data in a data stream is not only characterized by the proximity of data points which is used by clustering, but also by a temporal component. The extensible Markov model (EMM) adds the temporal component to data stream clustering by superimposing a dynamically adapting Markov chain. In this paper we introduce the implementation of the R extension package rEMM which implements EMM and we discuss some examples and applications.
Effects of urea on K-Cl cotransport in sheep red blood cells: evidence for two signals of swelling
No full textThe activation proceeds with a delay, like activation by swelling. Swelling of cells in urea activates K uptake further, but with no delay. Inactivation after removal of urea also proceeds without delay. With cotransport partially activated by reducing intracellular Mg concentration ([Mg]i) or with staurosporine, urea did not activate cotransport further. However, swelling activated cotransport further in these two types of cells. In terms of the three-state process for swelling-activation of K-Cl cotransport (P. B. Dunham, J. Klimczak, and P. J. Logue, J. Gen. Physiol. 101: 733-765, 1993), these results indicate that urea activates the first conversion, A-->B, and does so by inhibiting the reverse reaction promoted by a kinase, just as reducing [Mg]i does. Stimulation of cotransport by urea is nearly completely reversed by shrinkage, whereas activation by reducing [Mg]i is reversed only approximately 35%. Therefore urea inhibits the kinase indirectly, like swelling, by reducing macromolecular crowding of cytoplasmic proteins (A. P. Minton, G. C. Coleclasure, and J. C. Parker. Proc. Natl. Acad. Sci. USA 89: 10504-10506, 1992). Since swelling activates cotransport in two ways, one mimicked by urea and one not, there must be two signals of swelling, one a reduction of macromolecular crowding and the other probably a mechanical signal.</jats:p
Staurosporine, a protein kinase inhibitor, activates K-Cl cotransport in LK sheep erythrocytes
No full textK-Cl cotransport can participate in volume regulation in a number of cell types. Swelling activation of K-Cl cotransport in sheep erythrocytes proceeds by a two-step process, A<-->B<-->C (Dunham et al., J. Gen. Physiol. 101: 733-765, 1993). The A state, with a low flux, predominates at physiological volume. A-->B is rate limiting and can be activated by reducing cell Mg concentration ([Mg]c); complete activation (B-->C) requires cell swelling. Inhibitors of protein kinases and phosphatases were employed in an attempt to identify enzymatic reactions in the activation process. Staurosporine, a kinase inhibitor, activated K-Cl cotransport by approximately sixfold. Swelling of staurosporine-treated cells caused further activation that proceeded without delay. The effects of staurosporine and reducing [Mg]c were not additive. These two results indicate that staurosporine, like reducing [Mg]c, promotes the rate-limiting A-->B conversion. Unlike swelling, staurosporine activated cotransport without delay. Therefore staurosporine activates by promoting the forward reaction in the A<-->B conversions, in contrast to swelling, which activates by inhibiting the reverse reaction. Calyculin A, a phosphatase inhibitor, inhibited K-Cl cotransport but did not inhibit after activation by reducing [Mg]c, confirming earlier proposals that A-->B is promoted by a phosphatase. Calyculin A, added before or after staurosporine, abolished activation by staurosporine, confirming that staurosporine promotes A-->B. It is proposed that the phosphatase promoting this reaction is regulated by an inhibitory kinase, the staurosporine target.</jats:p
A New Framework for the Citation Indexing Paradigm
No full textA new citation indexing paradigm is proposed: the cascading citation indexing framework (c2IF, for short). It improves the way research publications are assessed for their impact in promoting science and technology. Given a collection of articles and their citation graph, citations are considered at the (article, author) level. Each one article is uniquely identified by means of the Digital Object Identifier (DOI, http://www.doi.org). To identify each one author uniquely, a Universal Author Identifier (UAI) scheme is established. In addition to the citations directly made to a given (article, author) pair, citation paths that target each one citing article are also considered. The granularity of the paradigm is further increased by introducing the concept of the chord, whereby a citation path of length one co-exists with paths of length two or higher, involving the same source- and target- articles. The c2IF output emerges in the form
of a medal standings table, analogous to the one that ranks teams at athletic events: when two (article, author) pairs receive the same number of (direct) citations, the one that is cited by more popular articles (i.e. articles that comprise targets to a larger number of paths in the citation graph), is assigned a higher rank value
Mechanism of swelling activation of K-Cl cotransport in inside-out vesicles of LK sheep erythrocyte membranes
No full textStimulation by swelling of K-Cl cotransport was studied in inside-out vesicles (IOVs) made from membranes of LK sheep erythrocytes. The purpose was to understand this stimulation in terms of the three-state process proposed for regulation of the cotransporter (P.B. Dunham, J. Klimczak, and P.J. Logue. J. Gen. Physiol. 101: 733-765, 1993). The first step in this process, A --> B, is rate limiting and controlled by transphosphorylation reactions. The second step, B --> C, is fast; its control is unknown. Predictions were that maximum velocity (Jmax) of cotransport increases with A --> B and concentration at one-half Jmax (K1/2) of K+ as a substrate decreases with B --> C. We tested the hypothesis that most transporters in IOVs are in the B state and that swelling activates cotransport in vesicles by the B --> C conversion. In accordance with this hypothesis, swelling should activate K+ influx with no discernable delay. It did. K1/2 for K+ should decrease with swelling and Jmax should not change. K1/2 decreased 10-fold, and Jmax did not change. Inhibitors of transphosphorylation, reactions of A --> B, should not affect K+ flux into IOVs, and they did not. The results support the hypothesis: swelling activation of K+ flux into IOVs corresponds to B --> C. A mechanical change in the membrane causes a specific change in the cotransporter: an increase in apparent affinity for K+.</jats:p
ISOTOPICALLY INVARIANT DUNHAM FIT FOR THE , , AND STATES OF OXYGEN
No full textAuthor Institution: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109; I. Physikalisches Institut, Universitat zu Koln, 50937 Koln, GermanyAt the last meeting, we reported the preliminary results on an isotopically invariant Dunham-type fit of the six oxygen isotopologues including experimental data for in , in , in . At this meeting we report the the results of our complete fit, with additional experimental data for and in . A total of 11879 transitions were collected and fitted with a reduced RMS near unity. We made empirical adjustments to remove apparent offsets between datasets by adding/subtracting individual values based on comparison of repeated measurements and/or our model prediction. It was found that the parameters describing the breakdown of the Born-Oppenheimer approximation were of the expected order of magnitude and showed little variation among the electronic states. Dunham potentials were derived and will be presented. To the best of our knowledge, this is the first analysis that simultaneously fits spectra from all six oxygen isotopologues
THE EFFECT OF THE BREAKDOWN OF THE BORN-OPPENHEIMER APPROXIMATION ON THE EXPRESSIONS FOR THE DUNHAM CO-EFFICIENTS
No full textAuthor Institution: Division of Physics, National Research Council of CanadaExpressions have been derived for the Dunham coefficients (in terms of B, the force constants , and other molecular parameters) after allowing for the breakdown of the Born-Oppenheimer approximation. It will be shown how these expressions lead to an understanding of the deviation between the experimental results and the best theoretical (adiabatic) calculation of the vibrational intervals in the ground electronic states of , HD, and , The effect of allowing for the breakdown of the Born-Oppenheimer approximation on the evaluation of the force c onstants of a diatomic molecule will be discussed. Finally, the use of experimental data for CO and HCL in determining both the isotopic variation of the adiabatic equilibrium internuclear distance, and the isotopically invariant Born-Oppenheimer internuclear distance will be discussed
[3H]bumetanide binding to mouse kidney membranes: identification of corresponding membrane proteins
No full textCrude plasma membranes from whole mouse kidneys have two classes of [3H]bumetanide binding sites. High-affinity sites (K1/2 approximately equal to 0.04 microM; Bmax = 1-2 pmol/mg protein) are similar to those identified on dog kidney membranes (B. Forbush and H.C. Palfrey. J. Biol. Chem. 258: 11787-11792, 1983) both with respect to affinity and in that Na, K, and Cl are required for [3H]bumetanide binding. Low-affinity sites (K1/2 approximately equal to 1 microM; Bmax = 7-14 pmol/mg) are unaffected by removal of these ions; such sites are not seen with dog kidney. When mouse kidney membranes are photolabeled with 4-[3H]benzoyl-5-sulfamoyl-3-(3-thenyloxy)benzoic acid [( 3H]BSTBA), a photoreactive bumetanide analogue, specific incorporation of the label is seen in two regions. As with dog kidney [M. Haas and B. Forbush. Am. J. Physiol. 253 (Cell Physiol. 22): C243-C252, 1987], an approximately 150-kDa protein is labeled with high affinity (K1/2 approximately equal to 0.05 microM). This labeling also requires Na, K, and Cl and appears to correspond to the high-affinity [3H]bumetanide binding sites and to the Na-K-Cl cotransport system. A second peak of [3H]BSTBA photolabeling, centered at approximately 75 kDa, incorporates the label with lower affinity (K1/2 = 2-3 microM). The photolabeling at approximately 75 kDa is unaffected by Na, K, and Cl concentrations and thus may correspond, at least in part, to the low-affinity [3H]bumetanide binding sites. Western blot analysis of [3H]BSTBA-labeled mouse kidney membranes was performed using an antiserum raised to proteins of approximately 82 and approximately 39 kDa isolated from mouse Ehrlich ascites tumor cells using a bumetanide affinity gel (P. B. Dunham, F. Jessen, and E. K. Hoffmann. Proc. Natl. Acad. Sci. USA 87: 6828-6832, 1990). This antiserum cross-reacts with a approximately 150-kDa mouse kidney protein, the staining profile of which on Western blot corresponds very closely to the peak of specific [3H]BSTBA incorporation in this region. The antiserum also reacts with proteins in the range of 65-85 kDa, overlapping the low-affinity peak of [3H]BSTBA incorporation.</jats:p
A GLOBAL FIT OF THE , , AND STATES OF THE SIX ISOTOPOLOGUES OF OXYGEN
No full textAuthor Institution: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109; I. Physikalisches Institut, Universitat zu Koln, 50937 Koln, GermanyA global fit of the six isotopologues of the O molecule has been carried out, with the purpose to support the current and future Earth remote sensing missions. All previously available experimental data from the following systems were collected and used in the analysis: the microwave transitions in the and states, the infared transitions from the , , and systems, the UV transitions from the Schumann-Runge system. For the main O isotopologue, experimental data are available for the following vibrational states: for , for , for , for . A band by band fit was first carried out for these O data to check bad measurements, misassigments and calibration problems. Then all these O data were fitted with a Dunham-type model. It was found that most O data (98\%) could be fitted within 3 times experimental accuracies in the band by band fit; the , , states could be well reproduced with the Dunham-type model; but the vibrational energies for of could not be fitted well with the Dunham-type mode, probably caused by the known perturbations in this state. A band by band fit has been performed for each of the other five minor isotopologues, and a Dunham-type fit is in progress for these data. Eventually data from all the six isotopologues will be simultaneously fitted with a multi-isotopologue Dunham model. We will present the most recent fitting results to date
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