Practical Evaluation of Lempel-Ziv-78 and Lempel-Ziv-Welch Tries

We present the first thorough practical study of the Lempel-Ziv-78 and the Lempel-Ziv-Welch computation based on trie data structures. With a careful selection of trie representations we can beat well-tuned popular trie data structures like Judy, m-Bonsai or Cedar

Effect of the magnetic order on the room-temperature band-gap of Mn-doped ZnO thin films

Author name used in this publication: Ruotolo A.2012-2013 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Mobile DNA transposition in somatic cells

It had been long assumed that almost all insertions of mobile DNA elements occurred during germ-cell development rather than in somatic-cell development, but solid evidence for transposition in somatic cells is now accumulating. To add to this evidence, a recent paper in Mobile DNA reports the somatic transposition of a site-specific retrotransposon, R2, into its insertion site in 28S ribosomal DNA in Drosophila embryos

Identifying patterns in treatment response profiles in acute bipolar mania: a cluster analysis approach

<p>Abstract</p> <p>Background</p> <p>Patients with acute mania respond differentially to treatment and, in many cases, fail to obtain or sustain symptom remission. The objective of this exploratory analysis was to characterize response in bipolar disorder by identifying groups of patients with similar manic symptom response profiles.</p> <p>Methods</p> <p>Patients (n = 222) were selected from a randomized, double-blind study of treatment with olanzapine or divalproex in bipolar I disorder, manic or mixed episode, with or without psychotic features. Hierarchical clustering based on Ward's distance was used to identify groups of patients based on Young-Mania Rating Scale (YMRS) total scores at each of 5 assessments over 7 weeks. Logistic regression was used to identify baseline predictors for clusters of interest.</p> <p>Results</p> <p>Four distinct clusters of patients were identified: Cluster 1 (n = 64): patients did not maintain a response (YMRS total scores ≤ 12); Cluster 2 (n = 92): patients responded rapidly (within less than a week) and response was maintained; Cluster 3 (n = 36): patients responded rapidly but relapsed soon afterwards (YMRS ≥ 15); Cluster 4 (n = 30): patients responded slowly (≥ 2 weeks) and response was maintained. Predictive models using baseline variables found YMRS Item 10 (Appearance), and psychosis to be significant predictors for Clusters 1 and 4 vs. Clusters 2 and 3, but none of the baseline characteristics allowed discriminating between Clusters 1 vs. 4. Experiencing a mixed episode at baseline predicted membership in Clusters 2 and 3 vs. Clusters 1 and 4. Treatment with divalproex, larger number of previous manic episodes, lack of disruptive-aggressive behavior, and more prominent depressive symptoms at baseline were predictors for Cluster 3 vs. 2.</p> <p>Conclusion</p> <p>Distinct treatment response profiles can be predicted by clinical features at baseline. The presence of these features as potential risk factors for relapse in patients who have responded to treatment should be considered prior to discharge.</p> <p>Trial registration</p> <p>The clinical trial cited in this report has not been registered because it was conducted and completed prior to the inception of clinical trial registries.</p

Rheological Characterization of the Bundling Transition in F-Actin Solutions Induced by Methylcellulose

In many in vitro experiments Brownian motion hampers quantitative data analysis. Therefore, additives are widely used to increase the solvent viscosity. For this purpose, methylcellulose (MC) has been proven highly effective as already small concentrations can significantly slow down diffusive processes. Beside this advantage, it has already been reported that high MC concentrations can alter the microstructure of polymer solutions such as filamentous actin. However, it remains to be shown to what extent the mechanical properties of a composite actin/MC gel depend on the MC concentration. In particular, significant alterations might occur even if the microstructure seems unaffected. Indeed, we find that the viscoelastic response of entangled F-actin solutions depends sensitively on the amount of MC added. At concentrations higher than 0.2% (w/v) MC, actin filaments are reorganized into bundles which drastically changes the viscoelastic response. At small MC concentrations the impact of MC is more subtle: the two constituents, actin and MC, contribute in an additive way to the mechanical response of the composite material. As a consequence, the effect of methylcellulose on actin solutions has to be considered very carefully when MC is used in biochemical experiments

Physical Activity Attenuates the Genetic Predisposition to Obesity in 20,000 Men and Women from EPIC-Norfolk Prospective Population Study

Shengxu Li and colleagues use data from a large prospective observational cohort to examine the extent to which a genetic predisposition toward obesity may be modified by living a physically active lifestyle

Generation and evaluation of a glaesserella (Haemophilus) parasuis capsular mutant

Glaesserella (Haemophilus) parasuis is a commensal bacterium of the upper respiratory tract in pigs and also the causative agent of Glässer’s disease, which causes significant morbidity and mortality in pigs worldwide. Isolates are characterized into 15 serovars by their capsular polysaccharide, which has shown a correlation with isolate pathogenicity. To investigate the role the capsule plays in G. parasuis virulence and host interaction, a capsule mutant of the serovar 5 strain HS069 was generated (HS069Δcap) through allelic exchange following natural transformation. HS069Δcap was unable to cause signs of systemic disease during a pig challenge study and had increased sensitivity to complement killing and phagocytosis by alveolar macrophages. Compared with the parent strain, HS069Δcap produced more robust biofilm and adhered equivalently to 3D4/31 cells; however, it was unable to persistently colonize the nasal cavity of inoculated pigs, with all pigs clearing HS069Δcap by 5 days postchallenge. Our results indicate the importance of the capsular polysaccharide to G. parasuis virulence as well as nasal colonization in pigs

Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution

DNA double-strand breaks (DSBs) are a common form of cellular damage that can lead to cell death if not repaired promptly. Experimental systems have shown that DSB repair in eukaryotic cells is often imperfect and may result in the insertion of extra chromosomal DNA or the duplication of existing DNA at the breakpoint. These events are thought to be a source of genomic instability and human diseases, but it is unclear whether they have contributed significantly to genome evolution. Here we developed an innovative computational pipeline that takes advantage of the repetitive structure of genomes to detect repair-mediated duplication events (RDs) that occurred in the germline and created insertions of at least 50 bp of genomic DNA. Using this pipeline we identified over 1,000 probable RDs in the human genome. Of these, 824 were intra-chromosomal, closely linked duplications of up to 619 bp bearing the hallmarks of the synthesis-dependent strand-annealing repair pathway. This mechanism has duplicated hundreds of sequences predicted to be functional in the human genome, including exons, UTRs, intron splice sites and transcription factor binding sites. Dating of the duplication events using comparative genomics and experimental validation revealed that the mechanism has operated continuously but with decreasing intensity throughout primate evolution. The mechanism has produced species-specific duplications in all primate species surveyed and is contributing to genomic variation among humans. Finally, we show that RDs have also occurred, albeit at a lower frequency, in non-primate mammals and other vertebrates, indicating that this mechanism has been an important force shaping vertebrate genome evolution

Alu pair exclusions in the human genome

<p>Abstract</p> <p>Background</p> <p>The human genome contains approximately one million <it>Alu </it>elements which comprise more than 10% of human DNA by mass. <it>Alu </it>elements possess direction, and are distributed almost equally in positive and negative strand orientations throughout the genome. Previously, it has been shown that closely spaced <it>Alu </it>pairs in opposing orientation (inverted pairs) are found less frequently than <it>Alu </it>pairs having the same orientation (direct pairs). However, this imbalance has only been investigated for <it>Alu </it>pairs separated by 650 or fewer base pairs (bp) in a study conducted prior to the completion of the draft human genome sequence.</p> <p>Results</p> <p>We performed a comprehensive analysis of all (> 800,000) full-length <it>Alu </it>elements in the human genome. This large sample size permits detection of small differences in the ratio between inverted and direct <it>Alu </it>pairs (I:D). We have discovered a significant depression in the full-length <it>Alu </it>pair I:D ratio that extends to repeat pairs separated by ≤ 350,000 bp. Within this imbalance bubble (those <it>Alu </it>pairs separated by ≤ 350,000 bp), direct pairs outnumber inverted pairs. Using PCR, we experimentally verified several examples of inverted <it>Alu </it>pair exclusions that were caused by deletions.</p> <p>Conclusions</p> <p>Over 50 million full-length <it>Alu </it>pairs reside within the I:D imbalance bubble. Their collective impact may represent one source of <it>Alu </it>element-related human genomic instability that has not been previously characterized.</p