98 research outputs found
∗ corresponding author
No full textThe DNA motif discovery problem abstracts the task of discovering short, conserved sites in genomic DNA. Pevzner and Sze recently described a precise combinatorial formulation of motif discovery that motivates the following algorithmic challenge: find twenty planted occurrences of a motif of length fifteen in roughly twelve kilobases of genomic sequence, where each occurrence of the motif differs from its consensus in four randomly chosen positions. Such “subtle ” motifs, though statistically highly significant, expose a weakness in existing motif finding algorithms, which typically fail to discover them. Pevzner and Sze introduced new algorithms to solve their (15,4)-motif challenge, but these methods do not scale efficiently to more difficult problems in the same family, such as the (14,4)-, (16,5)-, and (18,6)-motif problems. We introduce a novel motif discovery algorithm, Projection, designed to enhance the perfor-mance of existing motif finders using random projections of the input’s substrings. Experiments on synthetic data demonstrate that Projection remedies the weakness observed in existing algo-rithms, typically solving the difficult (14,4)-, (16,5)-, and (18,6)-motif problems. Our algorithm is robust to nonuniform background sequence distributions and scales to larger amounts of sequence than that specified in the original challenge. A probabilistic estimate suggests that related motif-finding problems that Projection fails to solve are in all likelihood inherently intractable. We also test the performance of our algorithm on realistic biological examples, including transcription factor binding sites in eukaryotes and ribosome binding sites in prokaryotes. 1
Simplicity in Eulerian circuits : Uniqueness and safety
No full textFunding Information: We are very grateful to the anonymous reviewers who helped improved the presentation of this paper. This work was partially funded by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 851093 , SAFEBIO) and partially by the Academy of Finland (grants No. 322595 , 328877 , 314284 and 335715 ). Publisher Copyright: © 2023 The Author(s)An Eulerian circuit in a directed graph is one of the most fundamental Graph Theory notions. Detecting if a graph G has a unique Eulerian circuit can be done in polynomial time via the BEST theorem by de Bruijn, van Aardenne-Ehrenfest, Smith and Tutte (1941–1951) [15,16] (involving counting arborescences), or via a tailored characterization by Pevzner, 1989 (involving computing the intersection graph of simple cycles of G), both of which thus rely on overly complex notions for the simpler uniqueness problem. In this paper we give a new linear-time checkable characterization of directed graphs with a unique Eulerian circuit. This is based on a simple condition of when two edges must appear consecutively in all Eulerian circuits, in terms of cut nodes of the underlying undirected graph of G. As a by-product, we can also compute in linear-time all maximal safe walks appearing in all Eulerian circuits, for which Nagarajan and Pop proposed in 2009 [12] a polynomial-time algorithm based on Pevzner characterization.Peer reviewe
metaSPAdes: a new versatile metagenomic assembler
No full textWhile metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amplifying the challenge of metagenomic assembly. metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational ideas that proved to be useful in assemblies of single cells and highly polymorphic diploid genomes. We benchmark metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in high-quality assemblies across diverse data sets.</jats:p
Generating Sustainable Wealth from Mozambique's Natural Resource Boom
No full textThis policy note aims to contribute to a
national debate on the management of natural resource
revenues. This policy note, part of a broader analytical
program that seeks to inform macroeconomic and fiscal policy
making in Mozambique to maximize the benefits from natural
resource extraction, presents a series of recommendations on
managing natural resource revenues. It assumes that the
Government of Mozambique will chose to frontload public
investments and spend a large share of the revenue from
natural resources to meet the country's vast
development needs. The policy note is divided in three
sections. Section one discusses some of the challenges
involved in responsibly managing resource revenues and key
factors to consider in developing the fiscal policy
framework. Section two presents a simulation exercise to
illustrate how a fiscal policy framework that frontloads
public spending can be implemented in Mozambique. Section
three concludes the discussion and summarizes
recommendations for enhancing fiscal and resource management
in Mozambique
Shallow Geology of the CO2CRC Otway Site: Evidence for Previously Undetected Neotectonic Features?
No full textAustralia's CO2CRC Otway Site hosts a carbon capture and storage (CCS) demonstration facility that has, to date, injected over 80,000 tonnes of CO 2 into two separate geological reservoirs. The reservoir geology is well understood and the site has been the subject of several seismic investigations, though relatively little is known about the near-surface geology and how potential leaks from the injection wells would migrate, particularly within the Port Campbell Limestone. No shallow core has been taken from relevant petroleum wells or water bores, and although there is extensive exposure in the prominent sea cliffs, these are mostly inaccessible. In order to further define the structure and geology of the Port Campbell Limestone at the Otway site, a high-resolution, shallow focused, 3D seismic survey has recently been conducted. The assessment of the near-surface geology described in this paper was used to assist with planning the survey. Using available data, the Port Campbell Limestone is assessed as a series of laterally continuous intercalated limestone, marl, and marly limestones. Interpretation of three previously acquired 3D seismic surveys using a minimum similarity attribute demonstrates evidence for a shallow, steeply east-dipping fault striking approximately NNW-SSE directly below the Otway site. This is observed from approximately 100 m to 380 m depth below surface, where it appears to die out. In the shallow section, the fault is undetectable primarily due to low seismic resolution, and so it is unknown how shallow it propagates. Extrapolation of the fault to the surface projects to between the wells Naylor-1 and CRC-1. A recently acquired high-resolution 3D seismi c survey over the study area will allow for this fault to be further delineated
Интеграция стилей жизни и потребления сериалов (на примере студентов в г. Санкт-Петербург)
No full textДанная работа посвящена механизмам встраивания просмотра сериалов в стили жизни студентов. В условиях поздней современности стиль жизни индивида становится гибким, подвижным, изменчивым. Формируется проектная жизненная стратегия, которая отличается от линейной возможностью сочетания проектов, которые не обязательно связаны друг с другом. Это затрагивает многие сферы человеческой деятельности, включая досуг. Культуриндустрия является, с одной стороны, продуктивной областью для реализации индивидуального стиля жизни, с другой – источником идей для его конструирования. С развитием технических средств и интернета в последние годы заметен рост актуальности сериалов, о чем свидетельствуют крупные бюджеты, высокие рейтинги и заинтересованность жанром признанных актеров, сценаристов и режиссеров. Из примитивного телевизионного жанра сериал превращается в культурный продукт, предлагающий зрителям качественный и содержательный контент. Он представляет собой крупный нарратив, состоящий из фрагментов, но цельный по своей логике. Причиной востребованности сериала представляются его свойства, органично дополняющие «текучий» стиль жизни современного человека. На основании результатов проведенного автором эмпирического исследования, состоящего из онлайн-опроса и глубинных интервью, были выявлены следующие модели интеграции потребления сериалов в стили жизни студентов в г. Санкт-Петербурге: компенсаторная, ориентационная, образовательная. Важным механизмом при этом является гибридизация, означающая возможность совмещать реализацию разных жизненных проектов в один момент времени. Данный механизм может проявляться как содержательно, так и на уровне практики, когда сериал используется как фон для другой деятельности. Важным фактором, влияющим на потребление сериалов, является формирование дискурсивного поля, из которого зрители узнают об актуальных трендах в жанре. По результатам проведенного исследования можно сделать вывод о том, что выбор сериала и стиля его просмотра ситуативен и зависит от приоритетных для индивида проектов в каждом конкретном случае.The work reviews the mechanisms of TV series consumption integration into students’ lifestyles. Lifestyle of late modernity is flexible, changeable, mobile. Project life strategy appears in the modern society and it differs from the linear one by the opportunity to combine various projects. This refers to many spheres of human activities, including leisure. Culture industry is a productive sphere to fulfill individual lifestyles and also a source of ideas for their construction. Lately along with the development of technologies and the internet TV series has become more popular, their budgets and ratings grow, the best actors, screenwriters and directors turn to this genre. It is not a primitive genre anymore and appears to be a cultural product which offers high-quality content. It is a grand whole narrative and still consists of many fragments. The relevance of TV series can be explained with their qualities, that naturally supplement with modern liquid lifestyle. Based on the results of the empirical research made by the author, which included an online survey and in-depth interviews, the following models of TV series consumption integration into different lifestyles among students in Saint-Petersburg were derived: compensatory, orientational, educational. Along with that hybridization is an important mechanism, which means a possibility to combine the realization of various life projects at a time. Hybridization may show itself both substantially and in practice, when TV series is used as a background for other activities. Another important factor of TV series consumption is the field of discourse, which provides news about this genre. Thus, the research shows that the choice of TV series and a way of its’ consumption is situational and depends on individual’s priorities in every case
Coryphaeus of the railway track science (on the occasion to the 100th anniversary of the birth of Doctor of Technical Sciences O. P. Ershkov)
No full text2017 marks the 100th anniversary of the birth of Oleg Petrovich Ershkov - one of the leading scientists of VNIIZhT (currently JSC “VNIIZhT”), Doctor of Technical Sciences. All his scientific work was devoted to the problems of the interaction of rolling stock and the track in curves. The generalized analytical method developed by him to determine the transverse forces in curves and the graphs of the lateral effect of locomotives on the track constructed by this method made it possible to find the values of these forces practically at any radius of the curves, the elevations of the outer rail and the speeds of motion. And today the direction of the scientific activity of O. P. Ershkov is in demand taking into account changing operating conditions. On the basis of experimental studies and generalization of foreign experience, Cand. Tech. Sci. V. Ya. Kartsev was able to determine, under the conditions of traffic safety and comfortable driving of passengers, the propagation to a speed of 250 km/h of the rate of increment of the unprecedented acceleration of 0.6 m/s3 and an increase in the rate of lifting of the wheel along the elevation to 50 mm/s. The new “Guidelines for determining the elevation of the outer rail and the speed of movement in curves” was approved. O. P. Ershkov is the author of more than 100 publications. At the present time, the order of the structure of curves is being developed taking into account the specialization of the lines. The modern generation of scientists and young researchers of VNIIZhT, based on the experience and knowledge of the older generation, adequately continues the scientific traditions of VNIIZhT in this field of knowledge
Factors related to the offer of HIV testing and known HIV status in persons with tuberculosis
No full textObjective: Describe how year of report, substance use, residential setting, demographic characteristics, and provider type are related to the offer of HIV testing and known HIV status in persons with tuberculosis (TB) in New Jersey. Methods: 1) Surveillance data (2000-2013) were analyzed for persons with TB, and associations with offer of HIV testing and known HIV status by the study variables. Models, stratified by provider type, were developed with two HIV outcomes. Interactions by year were added. 2) Thirty-one providers were interviewed about HIV testing in persons with TB. Transcripts were coded and themes identified. Results: 1) HIV testing was offered to 70.4% and HIV status was known in 62.7% of individuals with TB. The odds of HIV testing offer and known HIV status increased two-four times (p<0.0001) after 2006, when opt-out HIV testing was recommended. Differences in HIV testing offer and known HIV status were identified in all age groups compared to 25-44 year olds (OR=0.11-0.81; p<0.0010). Females had lower odds of HIV testing offer and known HIV status than males (OR=0.67-0.73; p<0.0002). Substance users had greater odds of HIV testing offer and known HIV status than non-users (OR=1.85-2.62; p<0.0001). Homeless persons had higher odds of known HIV status (OR=2.49; p=0.0432) than non-homeless person under community care. Black, non-Hispanics (OR=2.07-3.13; p<0.0001) had higher odds of HIV testing offer and known HIV status than White, non-Hispanics. Hispanics under community care (OR=1.62; p=0.0026) had higher known HIV status and Asians under community care had lower odds of known HIV status and offer of HIV testing (OR=0.69-0.71, p<0.0051) compared to White, non-Hispanic. 2) Interview codes fell under four themes: basis of provider’s testing decision, perceived patient barriers, provider testing barriers, and provider testing opportunities. Providers corroborated that the opt-out recommendation has made it easier for offering HIV testing. Barriers to HIV testing included limited time, patient stigma, low access to testing facilities, not knowing/remembering to test, and hesitation to test all persons with TB without risk factors. Conclusion: Interventions are needed to educate providers about HIV testing recommendations for all persons with TB, as well as training on patient support for the process and results.Ph.D.Includes bibliographical referencesby Rajita Bhavaraj
Additional file 4 of viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data
No full textAdditional file 4 Review history
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