An efficient pseudomedian filter for tiling microrrays

<p>Abstract</p> <p>Background</p> <p>Tiling microarrays are becoming an essential technology in the functional genomics toolbox. They have been applied to the tasks of novel transcript identification, elucidation of transcription factor binding sites, detection of methylated DNA and several other applications in several model organisms. These experiments are being conducted at increasingly finer resolutions as the microarray technology enjoys increasingly greater feature densities. The increased densities naturally lead to increased data analysis requirements. Specifically, the most widely employed algorithm for tiling array analysis involves smoothing observed signals by computing pseudomedians within sliding windows, a <it>O</it>(<it>n</it>²log<it>n</it>) calculation in each window. This poor time complexity is an issue for tiling array analysis and could prove to be a real bottleneck as tiling microarray experiments become grander in scope and finer in resolution.</p> <p>Results</p> <p>We therefore implemented Monahan's HLQEST algorithm that reduces the runtime complexity for computing the pseudomedian of <it>n </it>numbers to <it>O</it>(<it>n</it>log<it>n</it>) from <it>O</it>(<it>n</it>²log<it>n</it>). For a representative tiling microarray dataset, this modification reduced the smoothing procedure's runtime by nearly 90%. We then leveraged the fact that elements within sliding windows remain largely unchanged in overlapping windows (as one slides across genomic space) to further reduce computation by an additional 43%. This was achieved by the application of skip lists to maintaining a sorted list of values from window to window. This sorted list could be maintained with simple <it>O</it>(log <it>n</it>) inserts and deletes. We illustrate the favorable scaling properties of our algorithms with both time complexity analysis and benchmarking on synthetic datasets.</p> <p>Conclusion</p> <p>Tiling microarray analyses that rely upon a sliding window pseudomedian calculation can require many hours of computation. We have eased this requirement significantly by implementing efficient algorithms that scale well with genomic feature density. This result not only speeds the current standard analyses, but also makes possible ones where many iterations of the filter may be required, such as might be required in a bootstrap or parameter estimation setting. Source code and executables are available at <url>http://tiling.gersteinlab.org/pseudomedian/</url>.</p

Material Strength Effect in the Shock Compression of Alumina

The Hugoniot elastic limits (HEL) of a high-density aluminum oxide ceramic (Lucalox) and a slightly lower-density ceramic (porosity approximately 4%) were determined to be 112±13 and 83±5 kbar, respectively. Above the HEL, the shock-stress-volume Hugoniot curves for both materials are offset by 40 kbar or more above their hydrostatic-pressure-volume curves. These results indicate that shear stresses with magnitudes of about 30–40 kbar persist in aluminum oxide to shock-pressure levels of at least 300 kbar

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification

A generic DNA microarray design applicable to any species would greatly benefit comparative genomics. We have addressed the feasibility of such a design by leveraging the great feature densities and relatively unbiased nature of genomic tiling microarrays. Specifically, we first divided each Homo sapiens Refseq-derived gene's spliced nucleotide sequence into all of its possible contiguous 25 nt subsequences. For each of these 25 nt subsequences, we searched a recent human transcript mapping experiment's probe design for the 25 nt probe sequence having the fewest mismatches with the subsequence, but that did not match the subsequence exactly. Signal intensities measured with each gene's nearest-neighbor features were subsequently averaged to predict their gene expression levels in each of the experiment's thirty-three hybridizations. We examined the fidelity of this approach in terms of both sensitivity and specificity for detecting actively transcribed genes, for transcriptional consistency between exons of the same gene, and for reproducibility between tiling array designs. Taken together, our results provide proof-of-principle for probing nucleic acid targets with off-target, nearest-neighbor features

Synthesis, Electrochemistry, and Excited-State Properties of Three Ru(II) Quaterpyridine Complexes

The complexes [Ru(qpy)LL′]2+ (qpy = 2,2′:6′,2″:6″,2‴-quaterpyridine), with 1: L = acetonitrile, L′= chloride; 2: L = L′= acetonitrile; and 3: L = L′= vinylpyridine, have been prepared from [Ru(qpy) (Cl)2]. Their absorption spectra in CH3CN exhibit broad metal-to-ligand charge transfer (MLCT) absorptions arising from overlapping 1A1 → 1MLCT transitions. Photoluminescence is not observed at room temperature, but all three are weakly emissive in 4:1 ethanol/methanol glasses at 77 K with broad, featureless emissions observed between 600 and 1000 nm consistent with MLCT phosphorescence. Cyclic voltammograms in CH3CN reveal the expected RuIII/II redox couples. In 0.1 M trifluoroacetic acid (TFA), 1 and 2 undergo aquation to give [RuII(qpy)(OH2)2]2+, as evidenced by the appearance of waves for the couples [RuIII(qpy)(OH2)2]3+/[RuII(qpy)(OH2)2]2+, [RuIV(qpy)(O)(OH2)]2+/[RuIII(qpy)(OH2)2]3+, and [RuVI(qpy)(O)2]2+/[RuIV(qpy)(O)(OH2)]2+ in cyclic voltammograms

Internal versus external motivation in referral of primary care patients with depression to an internet support group: randomized controlled trial

BACKGROUND: Depressive disorders and symptoms affect more than one-third of primary care patients, many of whom do not receive or do not complete treatment. Internet-based social support from peers could sustain depression treatment engagement and adherence. We do not know whether primary care patients will accept referral to such websites nor do we know which methods of referral would be most effective. OBJECTIVE: We conducted a randomized clinical trial to determine whether (1) a simple generic referral card (control), (2) a patient-oriented brochure that provided examples of online postings and experience (internal motivation), or (3) a physician letter of recommendation (external motivation) would generate the greatest participation in a primary care Internet depression treatment support portal focused around an Internet support group (ISG). METHODS: We used 3 offline methods to identify potential participants who had not used an ISG in the past 6 months. Eligibility was determined in part by a brief structured psychiatric interview based on the Patient Health Questionnaire-9 (PHQ-9). After consent and enrollment, participants were randomly assigned to 1 of 3 groups (control, internal motivation, or external motivation). We constructed a portal to connect primary care patients to both fact-based information and an established ISG (Psycho-Babble). The ISG allowed participants to view messages and then decide if they actually wished to register there. Participation in the portal and the ISG was assessed via automated activity tracking. RESULTS: Fifty participants were assigned to the 3 groups: a motivation-neutral control group (n=18), an internal motivation group (n=19), and an external motivation group (n=13). Of these participants, 31 (62%) visited the portal; 27 (54%) visited the ISG itself. The internal motivation group showed significantly greater participation than the control group on several measures. The external motivation group spent significantly less time logged onto the portal than the control group. The internal motivation group showed significantly greater participation than the external motivation group on several measures. CONCLUSIONS: Referral of primary care patients with depressive disorders and symptoms to an ISG is feasible even if they have never previously used one. This may best be accomplished by enhancing their internal motivation. TRIAL REGISTRATION: Clinicaltrials.gov: NCT00886730; http://clinicaltrials.gov/show/NCT00886730 (Archived by WebCite at http://www.webcitation.org/6F4981fDN)

Comparing nuclear power trajectories in Germany and the UK: from ‘regimes' to ‘democracies’ in sociotechnical transitions and Discontinuities

This paper focuses on arguably the single most striking contrast in contemporary major energy politics in Europe (and even the developed world as a whole): the starkly differing civil nuclear policies of Germany and the UK. Germany is seeking entirely to phase out nuclear power by 2022. Yet the UK advocates a ‘nuclear renaissance’, promoting the most ambitious new nuclear construction programme in Western Europe.Here,this paper poses a simple yet quite fundamental question: what are the particular divergent conditions most strongly implicated in the contrasting developments in these two countries. With nuclear playing such an iconic role in historical discussions over technological continuity and transformation, answering this may assist in wider understandings of sociotechnical incumbency and discontinuity in the burgeoning field of‘sustainability transitions’. To this end, an ‘abductive’ approach is taken: deploying nine potentially relevant criteria for understanding the different directions pursued in Germany and the UK. Together constituted by 30 parameters spanning literatures related to socio-technical regimes in general as well as nuclear technology in particular, the criteria are divided into those that are ‘internal’ and ‘external’ to the ‘focal regime configuration’ of nuclear power and associated ‘challenger technologies’ like renewables. It is ‘internal’ criteria that are emphasised in conventional sociotechnical regime theory, with ‘external’ criteria relatively less well explored. Asking under each criterion whether attempted discontinuation of nuclear power would be more likely in Germany or the UK, a clear picture emerges. ‘Internal’ criteria suggest attempted nuclear discontinuation should be more likely in the UK than in Germany– the reverse of what is occurring. ‘External’ criteria are more aligned with observed dynamics –especially those relating to military nuclear commitments and broader ‘qualities of democracy’. Despite many differences of framing concerning exactly what constitutes ‘democracy’, a rich political science literature on this point is unanimous in characterising Germany more positively than the UK. Although based only on a single case,a potentially important question is nonetheless raised as to whether sociotechnical regime theory might usefully give greater attention to the general importance of various aspects of democracy in constituting conditions for significant technological discontinuities and transformations. If so, the policy implications are significant. A number of important areas are identified for future research, including the roles of diverse understandings and specific aspects of democracy and the particular relevance of military nuclear commitments– whose under-discussion in civil nuclear policy literatures raises its own questions of democratic accountability

Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih

Seven mycobacteriophages from distinct geographical locations were isolated, using Mycobacterium smegmatis mc2155 as the host, and then purified and sequenced. All of the genomes are related to cluster A mycobacteriophages, BobSwaget and Lokk in subcluster A2; Fred313, KADY, Stagni, and StepMih in subcluster A3; and MyraDee in subcluster A18, the first phage to be assigned to that subcluster