Tree-size bounded alternation

AbstractThe size of an accepting computation tree of an alternating Turing machine (ATM) is introduced as a complexity measure. We present a number of applications of tree-size to the study of more traditional complexity classes. Tree-size on ATMs is shown to closely correspond to time on nondeterministic TMs and on nondeterministic auxiliary pushdown automata. One application of the later is a useful new characterization of the class of languages log-space-reducible to context-free languages. Surprising relationships with parallel-time complexity are also demonstrated. ATM computations using at most space S(n) and tree-size Z(n) (simultaneously) can be simulated in alternating space S(n) and time S(n) · log Z(n) (simultaneously). Several well-known simulations, e.g., Savitch's theorem, are special cases of this result. It also leads to improved parallel complexity bounds for many problems in terms of both time and number of “processors.” As one example we show that context-free language recognition in time O(log2 n) is possible on several parallel models. Further, this bound is achievable with only a polynomial number of processors, in contrast to all previously known sub-linear time CFL recognizers

Operational modal analysis of a spar-type floating platform using frequency domain decomposition method

System identification of offshore floating platforms is usually performed by testing small-scale models in wave tanks, where controlled conditions, such as still water for free decay tests, regular and irregular wave loading can be represented. However, this approach may result in constraints on model dimensions, testing time, and costs of the experimental activity. For such reasons, intermediate-scale field modelling of offshore floating structures may become an interesting as well as cost-effective alternative in a near future. Clearly, since the open sea is not a controlled environment, traditional system identification may become challenging and less precise. In this paper, a new approach based on Frequency Domain Decomposition (FDD) method for Operational Modal Analysis is proposed and validated against numerical simulations in ANSYS AQWA v.16.0 on a simple spar-type structure. The results obtained match well with numerical predictions, showing that this new approach, opportunely coupled with more traditional wave tanks techniques, proves to be very promising to perform field-site identification of the model structures

Progress on the experimental set-up for the testing of a floating offshore wind turbine scaled model in a field site

This document describes design and realization of a small-scale field experiment on a 1:30 model of spar floating support structure for offshore wind turbines. The aim of the experiment is to investigate the dynamic behaviour of the floating wind turbine under extreme wave and parked rotor conditions. The experiment has been going on in the Natural Ocean Engineering Laboratory of Reggio Calabria (Italy). In this article, all the stages of the experimental activity are presented, and some results are shown in terms of motions and response amplitude operators. Finally, a comparison with corresponding results obtained using ANSYS AQWA software package is shown, and conclusions are drawn. The presented experimental set-up seems promising to test offshore floating structures for marine renewable energy at a relatively large scale in the Natural Ocean Engineering Laboratory field site

Output-only identification of rigid body motions of floating structures: a case study

In order to identify rigid body motions of floating offshore structures, output-only techniques are very useful for developing low-cost intermediate-scale experimental activities directly into the sea, instead of wave tanks. A crucial parameter, however, is the length of the response records used as input for the identification process, since short records may result in significant loss of accuracy, while long ones may be incompatible with the assumption of stationarity of the sea state. This work presents a sensitivity study conducted on a numerical model of a spar structure, identified by means of Enhanced Frequency Domain Decomposition method. An overview on the efficiency of the method is given for various lengths of response record, along with practical indications on the minimum values acceptable

Compression of next-generation sequencing reads aided by highly efficient de novo assembly

We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based compressor, using a novel de novo assembly algorithm. A probabilistic data structure is used to dramatically reduce the memory required by traditional de Bruijn graph assemblers, allowing millions of reads to be assembled very efficiently. Read sequences are then stored as positions within the assembled contigs. This is combined with statistical compression of read identifiers, quality scores, alignment information, and sequences, effectively collapsing very large datasets to less than 15% of their original size with no loss of information. Availability: Quip is freely available under the BSD license from http://cs.washington.edu/homes/dcjones/quip

Identification and Characterization of Pathogenic Mutations in Neurodevelopmental Disorders Discovered by Next-Generation Sequencing

<p>Neurodevelopmental disorders develop over time and are characterized by a wide variety of mental, behavioral, and physical phenotypes. The categorization of neurodevelopmental disorders encompasses a broad range of conditions including intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, cerebral palsy, schizophrenia, bipolar disorder, and epilepsy, among others. Diagnostic classifications of neurodevelopmental disorders are complicated by comorbidities among these neurodevelopmental disorders, unidentified causal genes, and growing evidence of shared genetic risk factors. </p><p>We sought to identify the genetic underpinnings of a variety of neurodevelopmental disorders, with a particular emphasis on the epilepsies, by employing next&ndash;generation sequencing to thoroughly interrogate genetic variation in the human genome/exome. First, we investigated four families presenting with a seemingly identical and previously undescribed neurodevelopmental disorder characterized by congenital microcephaly, intellectual disability, progressive cerebral atrophy, and intractable seizures. These families all exhibited an apparent autosomal recessive pattern of inheritance. Second, we investigated a heterogeneous cohort of &sim;60 undiagnosed patients, the majority of whom suffered from severe neurodevelopmental disorders with a suspected genetic etiology. Third, we investigated 264 patients with epileptic encephalopathies &mdash; severe childhood epilepsy disorders &mdash; looking specifically at infantile spasms and Lennox&ndash;Gastaut syndrome. Finally, we investigated &sim;40 large multiplex epilepsy families with complex phenotypic constellations and unclear modes of inheritance. The studied neurodevelopmental disorders exhibited a range of genetic complexity, from clear Mendelian disorders to common complex disorders, resulting in varying degrees of success in the identification of clearly causal genetic variants. </p><p>In the first project, we successfully identified the disease&ndash;causing gene. We show that recessive mutations in <italic>ASNS </italic> (encoding asparagine synthetase) are responsible for this previously undescribed neurodevelopmental disorder. We also characterized the causal mutations <italic>in vitro</italic> and studied Asns&ndash;deficient mice that mimicked aspects of the patient phenotype. This work describes ASNS deficiency as a novel neurodevelopmental disorder, identifies three distinct causal mutations in the ASNS gene, and indicates that asparagine synthesis is essential for the proper development and function of the brain.</p><p>In the second project, we exome sequenced 62 undiagnosed patients and their unaffected biological parents (trios). By analyzing all identified variants that were annotated as putatively functional and observed as a novel genotype in the probands (not observed in the unaffected parents or controls), we obtained a genetic diagnosis for 32% (20/62) of these patients. Additionally, we identify strong candidate variants in 31% (13/42) of the undiagnosed cases. We also present additional analysis methods for moving beyond traditional screens, e.g., considering only securely implicated genes, or subjecting qualifying variants from any gene to two unique analysis approaches. This work adds to the growing evidence for the utility of diagnostic exome sequencing, increases patient sizes for rare neurodevelopmental disorders (enabling more detailed analyses of the phenotypic spectrum), and proposes novel analysis approaches which will likely become beneficial as the number of sequenced undiagnosed patients grows. </p><p>In the third project, we again employ a trio&ndash;based exome sequencing design to investigate the role of <italic>de novo</italic> mutations in two classical forms of epileptic encephalopathy. We find a significant excess of <italic>de novo</italic> mutations in the &sim;4,000 genes that are the most intolerant to functional genetic variation in the human population (P = 2.9 x 10<super>&ndash;3</super>, likelihood analysis). We provide clear statistical evidence for two novel genes associated with epileptic encephalopathy &mdash; <italic>GABRB3</italic> and <italic>ALG13</italic>. Together with the 15 well&ndash;established epileptic encephalopathy genes, we statistically confirm the association of an additional ten putative epileptic encephalopathy genes. We show that only &sim;12% of epileptic encephalopathy patients in our cohort are explained by <italic>de novo</italic> mutations in one of these 24 genes, highlighting the extreme locus heterogeneity of the epileptic encephalopathies. </p><p>Finally, we investigated multiplex epilepsy families to uncover novel epilepsy susceptibility factors. Candidate variants emerging from sequencing within discovery families were further assessed by cosegregation testing, variant association testing in a case&ndash;control cohort, and gene&ndash;based resequencing in a cohort of additional multiplex epilepsy families. Despite employing multiple approaches, we did not identify any clear genetic associations with epilepsy. This work has, however, identified a set of candidates that may include real risk factors for epilepsy; the most promising of these is the <italic>MYCBP2</italic> gene. This work emphasizes the extremely high locus and allelic heterogeneity of the epilepsies and demonstrates that very large sample sizes are needed to uncover novel genetic risk factors. </p><p>Collectively, this body of work has securely implicated three novel neurodevelopmental disease genes that inform the underlying pathology of these disorders. Furthermore, in the final three studies, this work has highlighted additional candidate variants and genes that may ultimately be validated as disease&ndash;causing as sample sizes increase.</p>Dissertatio

On intermediate-scale open-sea experiments on floating offshore structures: Feasibility and application on a spar support for offshore wind turbines

Experimental investigation of floating structures represents the most direct way for achieving their dynamic identification and it is particularly valuable for relatively new concepts, such as floating supports for offshore wind turbines, in order to fully understand their dynamic behaviour. Traditional experimental campaigns on floating structures are carried out at small scale, in indoor laboratories, equipped with wave and wind generation facilities. This article presents the results of an open-sea experimental activity on a 1:30 scale model of the OC3-Hywind spar, in parked rotor conditions, carried out at the Natural Ocean Engineering Laboratory (NOEL) of Reggio Calabria (Italy). The aim of the experiment is two-fold. Firstly, it aims to assess the feasibility of low-cost, intermediate-scale, open-sea activities on offshore structures, which are proposed to substitute or complement the traditional indoor activities in ocean basins. Secondly, it provides useful experimental data on damping properties of spar support structures for offshore wind turbines, with respect to heave, roll and pitch degrees of freedom. It is proven that the proposed approach may overcome some limitations of traditional small-scale activities, namely high costs and small scale, and allows to enhance the fidelity of the experimental data currently available in literature for spar floating supports for offshore wind turbines