59 research outputs found
Computing alignment plots efficiently
Dot plots are a standard method for local comparison of biological sequences.
In a dot plot, a substring to substring distance is computed for all pairs of
fixed-size windows in the input strings. Commonly, the Hamming distance is used
since it can be computed in linear time. However, the Hamming distance is a
rather crude measure of string similarity, and using an alignment-based edit
distance can greatly improve the sensitivity of the dot plot method. In this
paper, we show how to compute alignment plots of the latter type efficiently.
Given two strings of length m and n and a window size w, this problem consists
in computing the edit distance between all pairs of substrings of length w, one
from each input string. The problem can be solved by repeated application of
the standard dynamic programming algorithm in time O(mnw^2). This paper gives
an improved data-parallel algorithm, running in time using
vector operations that work on values in parallel and processors.
We show experimental results from an implementation of this algorithm, which
uses Intel's MMX/SSE instructions for vector parallelism and MPI for
coarse-grained parallelism.Comment: Presented at ParCo 200
Genomic plasticity and rapid host switching can promote the evolution of generalism : a case study in the zoonotic pathogen Campylobacter
This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/I02464X/1, the Medical Research Council (MRC) grants MR/M501608/1 and MR/L015080/1, and the Wellcome Trust grant 088786/C/09/Z. GM was supported by a NISCHR Health Research Fellowship (HF-14–13).Peer reviewedPublisher PD
Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants
Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research
Large molecular systems landscape uncovers T cell trapping in human skin cancer
Immune surveillance of tumour cells is an important function of CD8 T
lymphocytes, which has failed in cancer for reasons still unknown in many
respect but mainly related to cellular processes in the tumour
microenvironment. Applying imaging cycler microscopy to analyse the immune
contexture in a human skin cancer we could identify and map 7,000 distinct
cell surface-associated multi-protein assemblies. The resulting combinatorial
geometry-based high-functional resolution led to discovery of a mechanism of T
cell trapping in the epidermis, which involves SPIKE, a network of suprabasal
keratinocyte projections piercing and interconnecting CD8 T cells. It appears
initiated by clusters of infrabasal T and dendritic cells connected via cell
projections across a fractured basal lamina to suprabasal keratinocytes and T
lymphocytes
Ergebnisse der Evaluierung des Bremer Landesaktionsplans zur Umsetzung der UN-Behindertenrechtskonvention
2014 hat das Bundesland Bremen seinen "Aktionsplan zur Umsetzung der UN Behindertenrechtskonvention im Land Bremen" verabschiedet und veröffentlicht. Im letzten Kapitel des Plans, "Ausblick - Fortschreibung des Aktionsplans", wurde bereits festgelegt, eine Evaluation durchzuführen. Mit dieser Evaluation hat die Bremer Senatorin für Soziales, Jugend, Frauen, Integration und Sport im Dezember 2018 das Deutsche Institut für Menschenrechte beauftragt. Der vorliegende Bericht gibt die Ergebnisse dieser Evaluation wieder
A dressed bag model study of the final-state interaction in photoproduction processes off the deuteron
The impact of the short-range interaction on the pion
photoproduction processes off the deuteron in the -resonance region is
studied in the framework of recently proposed dressed-bag model. A common
dressing procedure for bare three- and six-quark states is used to describe
both the pion decay widths of baryon resonances and the effective (or
) interaction at short ranges related to the inner dressed-bag
states. It is shown that the effect of short-range interaction for
the forward-angle photoproduction off the deuteron cannot be
neglected. The prospects for further development of the model to describe the
short-range (or ) correlations in the lightest nuclei are
discussed
Racial differences in systemic sclerosis disease presentation: a European Scleroderma Trials and Research group study
Objectives. Racial factors play a significant role in SSc. We evaluated differences in SSc presentations between white patients (WP), Asian patients (AP) and black patients (BP) and analysed the effects of geographical locations.Methods. SSc characteristics of patients from the EUSTAR cohort were cross-sectionally compared across racial groups using survival and multiple logistic regression analyses.Results. The study included 9162 WP, 341 AP and 181 BP. AP developed the first non-RP feature faster than WP but slower than BP. AP were less frequently anti-centromere (ACA; odds ratio (OR) = 0.4, P < 0.001) and more frequently anti-topoisomerase-I autoantibodies (ATA) positive (OR = 1.2, P = 0.068), while BP were less likely to be ACA and ATA positive than were WP [OR(ACA) = 0.3, P < 0.001; OR(ATA) = 0.5, P = 0.020]. AP had less often (OR = 0.7, P = 0.06) and BP more often (OR = 2.7, P < 0.001) diffuse skin involvement than had WP.AP and BP were more likely to have pulmonary hypertension [OR(AP) = 2.6, P < 0.001; OR(BP) = 2.7, P = 0.03 vs WP] and a reduced forced vital capacity [OR(AP) = 2.5, P < 0.001; OR(BP) = 2.4, P < 0.004] than were WP. AP more often had an impaired diffusing capacity of the lung than had BP and WP [OR(AP vs BP) = 1.9, P = 0.038; OR(AP vs WP) = 2.4, P < 0.001]. After RP onset, AP and BP had a higher hazard to die than had WP [hazard ratio (HR) (AP) = 1.6, P = 0.011; HR(BP) = 2.1, P < 0.001].Conclusion. Compared with WP, and mostly independent of geographical location, AP have a faster and earlier disease onset with high prevalences of ATA, pulmonary hypertension and forced vital capacity impairment and higher mortality. BP had the fastest disease onset, a high prevalence of diffuse skin involvement and nominally the highest mortality
Feasibility studies for the measurement of time-like proton electromagnetic form factors from p¯ p→ μ+μ- at P ¯ ANDA at FAIR
This paper reports on Monte Carlo simulation results for future measurements of the moduli of time-like proton electromagnetic form factors, | GE| and | GM| , using the p¯ p→ μ+μ- reaction at P ¯ ANDA (FAIR). The electromagnetic form factors are fundamental quantities parameterizing the electric and magnetic structure of hadrons. This work estimates the statistical and total accuracy with which the form factors can be measured at P ¯ ANDA , using an analysis of simulated data within the PandaRoot software framework. The most crucial background channel is p¯ p→ π+π-, due to the very similar behavior of muons and pions in the detector. The suppression factors are evaluated for this and all other relevant background channels at different values of antiproton beam momentum. The signal/background separation is based on a multivariate analysis, using the Boosted Decision Trees method. An expected background subtraction is included in this study, based on realistic angular distributions of the background contribution. Systematic uncertainties are considered and the relative total uncertainties of the form factor measurements are presented
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