Singularly Perturbed Monotone Systems and an Application to Double Phosphorylation Cycles

The theory of monotone dynamical systems has been found very useful in the modeling of some gene, protein, and signaling networks. In monotone systems, every net feedback loop is positive. On the other hand, negative feedback loops are important features of many systems, since they are required for adaptation and precision. This paper shows that, provided that these negative loops act at a comparatively fast time scale, the main dynamical property of (strongly) monotone systems, convergence to steady states, is still valid. An application is worked out to a double-phosphorylation ``futile cycle'' motif which plays a central role in eukaryotic cell signaling.Comment: 21 pages, 3 figures, corrected typos, references remove

Context as a non-ontological determinant of semantics

The final publication is available at Springer via http://dx.doi.org/110.1007/978-3-540-92235-3_11Proceedings of Third International Conference on Semantic and Digital Media Technologies, SAMT 2008, Koblenz, Germany, December 3-5, 2008.This paper proposes an alternative to formal annotation for the representation of semantics. Drawing on the position of most of last century’s linguistics and interpretation theory, the article argues that meaning is not a property of a document, but an outcome of a contextualized and situated process of interpretation. The consequence of this position is that one should not quite try to represent the meaning of a document (the way formal annotation does), but the context of the activity of which search is part. We present some general considerations on the representation and use of the context, and a simple example of a technique to encode the context represented by the documents collected in the computer in which one is working, and to use them to direct search. We show preliminary results showing that even this rather simpleminded context representation can lead to considerable improvements with respect to commercial search engines

Acute biphenotypic leukaemia: immunophenotypic and cytogenetic analysis

The incidence of acute biphenotypic leukaemia has ranged from less than 1% to almost 50% in various reports in the literature. This wide variability may be attributed to a number of reasons including lack of consistent diagnostic criteria, use of various panels of antibodies, and the failure to recognize the lack of lineage specificity of some of the antibodies used. The morphology, cytochemistry, immunophenotype and cytogenetics of acute biphenotypic leukaemias from our institution were studied. The diagnostic criteria took into consideration the morphology of the analysed cells, light scatter characteristics, and evaluation of antibody fluorescence histograms in determining whether the aberrant marker expression was arising from leukaemic blasts or differentiated bone marrow elements. Fifty-two of 746 cases (7%) fulfilled our criteria for acute biphenotypic leukaemias. These included 30 cases of acute lymphoblastic leukaemia (ALL) expressing myeloid antigens, 21 cases of acute myelogenous leukaemia (AML) expressing lymphoid markers, and one case of ALL expressing both B- and T-cell associated antigens. The acute biphenotypic leukaemia cases consisted of four major immunophenotypic subgroups: CD2± AML (11), CD19± AML (8), CD13 and/or CD33± ALL (24), CD11b± ALL (5) and others (4). Chromosomal analysis was carried out in 42/52 of the acute biphenotypic leukaemia cases; a clonal abnormality was found in 31 of these 42 cases. This study highlights the problems encountered in the diagnosis of acute biphenotypic leukaemia, some of which may be reponsible for the wide variation in the reported incidence of this leukaemia. We suggest that the use of strict, uniform diagnostic criteria may help in establishing a more consistent approach towards diagnosis of this leukaemic entity. We also suggest that biphenotypic leukaemia is comprised of biologically different groups of leukaemia based on immunophenotypic and cytogenetic findings.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73301/1/j.1365-2141.1993.tb03024.x.pd

Strengthening Biblical Historicity vis-a`-vis Minimalism, 1992–2008 and Beyond. Part 2.3: Some Commonalities in Approaches to Writing Ancient Israel’s History

This series of articles covers scholarly works in English which can, at least potentially, be associated with a generally positive view of biblical historicity regarding periods preceding the Israelites’ return from exile. Part 2 covers works that treat the methodological issues at the center of the maximalist–minimalist debate. Parts 2.1 and 2.2 selectively survey the works of 24 non-minimalist scholars during two decades. In the absence of consensus, this article analyzes the works in Parts 2.1 and 2.2, tracing elements of approach that are held in common, at least among pluralities of non-minimalists (possible majorities are not noted). The first commonality of approach is that history is provisional, not final. The second is that history should become fully multidisciplinary. The third commonality is that historians should receive all historical evidence on an equal footing before examination and cross-examination. The fourth and last is that historians should become increasingly sensitive to cultural aspects and coding in ancient Near Eastern materials

Information and digital literacies; a review of concepts

A detailed literature reviewing, analysing the multiple and confusing concepts around the ideas of information literacy and digital literacy at the start of the millennium. The article was well-received, and is my most highly-cited work, with over 1100 citations

Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on 10^3 pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype

The new dictionary of cultural literacy

In this fast-paced information age, how can Americans know what's really important and what's just a passing fashion? Now more than ever, we need a source that concisely sums up the knowledge that matters to Americans -- the people, places, ideas, and events that shape our cultural conversation. With more than six thousand entries,The New Dictionary of Cultural Literacy is that invaluable source. Wireless technology. Gene therapy. NAFTA. In addition to the thousands of terms described in the original Dictionary of Cultural Literacy, here are more than five hundred new entries to bring Americans' bank of essential knowledge up to date. The original entries have been fully revised to reflect recent changes in world history and politics, American literature, and, especially, science and technology. Cultural icons that have stood the test of time (Odysseus, Leaves of Grass, Cleopatra, the Taj Mahal, D-Day) appear alongside entries on such varied concerns as cryptography, the digital divide, the European Union, Kwanzaa, pheromones, SPAM, Type A and Type B personalities, Web browsers, and much, much more. As our world becomes more global and interconnected, it grows smaller through the terms and touchstones that unite us. As E. D. Hirsch writes in the preface, Community is built up of shared knowledge and values -- the same shared knowledge that is taken for granted when we read a book or newspaper, and that is also taken for granted as part of the fabric that connects us to one another. A delicious concoction of information for anyone who wants to be in the know, The New Dictionary of Cultural Literacy brilliantly confirms once again that it is an excellent piece of work . . . stimulating and enlightening (New York Times) -- the most definitive and comprehensive family sourcebook of its kind