860 research outputs found
Refinding is Not Finding Again
A challenging problem for Internet users today is how to refind information that they have seen before. We believe that finding and refinding are different user activities and require different types of support. The problem of how to find information on the web is studied extensively---new search algorithms, support for natural language queries, and innovative document indexing techniques are common topics in information retrieval research; visualizations of documents, and task support for finding are topics in human-computer interaction. But refinding has only recently begun to receive attention. In this article, we present evidence to support the claim that information refinding is a different activity than information finding. We present results that show how refinding is different from finding and suggest ways to improve web information seeking tools and designs tosupport refinding information
PICMI: mapping point mutations on genomes
Motivation: Several international collaborations and local projects are producing extensive catalogues of genomic variations that are supplementing existing collections such as the OMIM catalogue. The flood of this type of data will keep increasing and, especially, it will be relevant to a wider user base, including not only molecular biologists, geneticists and bioinformaticians, but also clinical researchers. Mapping the observed variations, sometimes only described at the amino acid level, on a genome, identifying whether they affect a gene and—if so—whether they also affect different isoforms of the same gene, is a time consuming and often frustrating task
Structure in sheared supercooled liquids:Dynamical rearrangements of an effective system of icosahedra
We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics
are correlated with the formation of particles organized into icosahedra under
simple steady state shear. We recast this glassformer as an effective system of
icosahedra [Pinney et al. J. Chem. Phys. 143 244507 (2015)]. From the observed
population of icosahedra in each steady state, we obtain an effective
temperature which is linearly dependent on the shear rate in the range
considered. Upon shear banding, the system separates into a region of high
shear rate and a region of low shear rate. The effective temperatures obtained
in each case show that the low shear regions correspond to a significantly
lower temperature than the high shear regions. Taking a weighted average of the
effective temperature of these regions (weight determined by region size)
yields an estimate of the effective temperature which compares well with an
effective temperature based on the global mesocluster population of the whole
system.Comment: accepted by J. Chehm. Phy
metaSHARK: a WWW platform for interactive exploration of metabolic networks
The metaSHARK (metabolic search and reconstruction kit) web server offers users an intuitive, fully interactive way to explore the KEGG metabolic network via a WWW browser. Metabolic reconstruction information for specific organisms, produced by our automated SHARKhunt tool or from other programs or genome annotations, may be uploaded to the website and overlaid on the generic network. Additional data from gene expression experiments can also be incorporated, allowing the visualization of differential gene expression in the context of the predicted metabolic network. metaSHARK is available at
Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History
Genome-wide protein-protein interaction (PPI) data are readily available
thanks to recent breakthroughs in biotechnology. However, PPI networks of
extant organisms are only snapshots of the network evolution. How to infer the
whole evolution history becomes a challenging problem in computational biology.
In this paper, we present a likelihood-based approach to inferring network
evolution history from the topology of PPI networks and the duplication
relationship among the paralogs. Simulations show that our approach outperforms
the existing ones in terms of the accuracy of reconstruction. Moreover, the
growth parameters of several real PPI networks estimated by our method are more
consistent with the ones predicted in literature.Comment: 15 pages, 5 figures, submitted to ISBRA 201
Lie systems and integrability conditions for t-dependent frequency harmonic oscillators
Time-dependent frequency harmonic oscillators (TDFHO's) are studied through
the theory of Lie systems. We show that they are related to a certain kind of
equations in the Lie group SL(2,R). Some integrability conditions appear as
conditions to be able to transform such equations into simpler ones in a very
specific way. As a particular application of our results we find t-dependent
constants of the motion for certain one-dimensional TDFHO's. Our approach
provides an unifying framework which allows us to apply our developments to all
Lie systems associated with equations in SL(2,R) and to generalise our methods
to study any Lie system
Nonlinearity Management in Higher Dimensions
In the present short communication, we revisit nonlinearity management of the
time-periodic nonlinear Schrodinger equation and the related averaging
procedure. We prove that the averaged nonlinear Schrodinger equation does not
support the blow-up of solutions in higher dimensions, independently of the
strength in the nonlinearity coefficient variance. This conclusion agrees with
earlier works in the case of strong nonlinearity management but contradicts
those in the case of weak nonlinearity management. The apparent discrepancy is
explained by the divergence of the averaging procedure in the limit of weak
nonlinearity management.Comment: 9 pages, 1 figure
Analysis of signalling pathways using continuous time Markov chains
We describe a quantitative modelling and analysis approach for signal transduction networks.
We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable
Senile Systemic Amyloidosis: Clinical Features at Presentation and Outcome
Background Cardiac amyloidosis is a fatal disease whose prognosis and treatment rely on identification of the amyloid type. In our aging population transthyretin amyloidosis (ATTRwt) is common and must be differentiated from other amyloid types. We report the clinical presentation, natural history, and prognostic features of ATTRwt compared with cardiac‐isolated AL amyloidosis and calculate the probability of disease diagnosis of ATTRwt from baseline factors.
Methods and Results All patients with biopsy‐proven ATTRwt (102 cases) and isolated cardiac AL (36 cases) seen from 2002 to 2011 at the UK National Amyloidosis Center were included. Median survival from the onset of symptoms was 6.07 years in the ATTRwt group and 1.7 years in the AL group. Positive troponin, a pacemaker, and increasing New York Heart Association (NYHA) class were associated with worse survival in ATTRwt patients on univariate analysis. All patients with isolated cardiac AL and 24.1% of patients with ATTRwt had evidence of a plasma cell dyscrasia. Older age and lower N‐terminal pro‐B‐type natriuretic peptide (NT pro‐BNP) were factors significantly associated with ATTRwt. Patients aged 70 years and younger with an NT pro‐BNP <183 pmol/L were more likely to have ATTRwt, as were patients older than 70 years with an NT pro‐BNP <1420 pmol/L.
Conclusions Factors at baseline associated with a worse outcome in ATTRwt are positive troponin T, a pacemaker, and NYHA class IV symptoms. The age of the patient at diagnosis and NT pro‐BNP level can aid in distinguishing ATTRwt from AL amyloidosis
- …