Nanopore sequencing simulator for DNA data storage

The exponential increase of digital data and the limited capacity of current storage devices have made clear the need for exploring new storage solutions. Thanks to its biological properties, DNA has proven to be a potential candidate for this task, allowing the storage of information at a high density for hundreds or even thousands of years. With the release of nanopore sequencing technologies, DNA data storage is one step closer to become a reality. Many works have proposed solutions for the simulation of this sequencing step, aiming to ease the development of algorithms addressing nanopore-sequenced reads. However, these simulators target the sequencing of complete genomes, whose characteristics differ from the ones of synthetic DNA. This work presents a nanopore sequencing simulator targeting synthetic DNA on the context of DNA data storage

Analysis of an efficient parallel implementation of active-set Newton algorithm

[EN] This paper presents an analysis of an efficient parallel implementation of the active-set Newton algorithm (ASNA), which is used to estimate the nonnegative weights of linear combinations of the atoms in a large-scale dictionary to approximate an observation vector by minimizing the Kullback¿Leibler divergence between the observation vector and the approximation. The performance of ASNA has been proved in previous works against other state-of-the-art methods. The implementations analysed in this paper have been developed in C, using parallel programming techniques to obtain a better performance in multicore architectures than the original MATLAB implementation. Also a hardware analysis is performed to check the influence of CPU frequency and number of CPU cores in the different implementations proposed. The new implementations allow ASNA algorithm to tackle real-time problems due to the execution time reduction obtained.This work has been partially supported by Programa de FPU del MECD, by MINECO and FEDER from Spain, under the projects TEC2015-67387- C4-1-R, and by project PROMETEO FASE II 2014/003 of Generalitat Valenciana. The authors want to thank Dr. Konstantinos Drossos for some very useful mind changing discussions. This work has been conducted in Laboratory of Signal Processing, Tampere University of Technology.San Juan-Sebastian, P.; Virtanen, T.; García Mollá, VM.; Vidal Maciá, AM. (2018). Analysis of an efficient parallel implementation of active-set Newton algorithm. The Journal of Supercomputing. 75(3):1298-1309. https://doi.org/10.1007/s11227-018-2423-5S12981309753Raj B, Smaragdis P (2005) Latent variable decomposition of spectrograms for single channel speaker separation. In: Proceedings of the IEEE Workshop on Applications of Signal Processing to Audio and Acoustics (WASPAA 2005), New Paltz, NyBertin N, Badeau R, Vincent E (2010) Enforcing harmonicity and smoothness in Bayesian non-negative matrix factorization applied to polyphonic music transcription. IEEE Trans Audio Speech Lang Process 18(3):538–549Dikmen O, Mesaros A (2013) Sound event detection using non-negative dictionaries learned from annotated overlapping events. In: IEEE Workshop on Applications of Signal Processing to Audio and Acoustics (WASPAA 2013). New Paltz, NYLawson CL, Hanson RJ (1995) Solving least squares problems. Society for Industrial and Applied Mathematics, PhiladelphiaVirtanen T (2007) Monaural sound source separation by nonnegative matrix factorization with temporal continuity and sparseness criteria. IEEE Trans Audio Speech Lang Process 15(3):1066–1074Virtanen T, Gemmeke J, Raj B (2013) Active-set Newton algorithm for overcomplete non-negative representations of audio. IEEE Trans Audio Speech Lang Process 21(11):2277–2289Cemgil AT (2009) Bayesian inference for nonnegative matrix factorisation models. Comput Intell Neurosci 2009:785152Cichocki A, Zdunek R, Phan AH, Amari S (2009) Nonnegative matrix and tensor factorizations. Wiley, New YorkMATLAB (2014) The Mathworks Inc., MATLAB R2014B, Natnick MATuomas Virtanen, Original MATLAB implementation of ASNA algorithm. http://www.cs.tut.fi/~tuomasv/software.htmlCarabias-Orti J, Rodriguez-Serrano F, Vera-Candeas P, Canadas-Quesada F, Ruiz-Reyes N (2013) Constrained non-negative sparse coding using learnt instrument templates for realtime music transcription. Eng Appl Artif Intell 26:1671–1680San Juan P, Virtanen T, Garcia-Molla Victor M, Vidal Antonio M (2016) Efficient parallel implementation of active-set newton algorithm for non-negative sparse representations. In: 16th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2016), Rota, SpainJuan P San, Efficient implementations of ASNA algorithm. https://gitlab.com/P.SanJuan/ASNAOpenMP v4.5 specification (2015). http://www.openmp.org/wpcontent/uploads/openmp-4.5.pdfGemmeke JF, Hurmalainen A, Virtanen T, Sun Y (2011) Toward a practical implementation of exemplar-based noise robust ASR. In: Signal Processing Conference, 19th European, IEEE, pp 1490–149

Hunting long-lived gluinos at the Pierre Auger Observatory

Eventual signals of split sypersymmetry in cosmic ray physics are analyzed in detail. The study focusses particularly on quasi-stable colorless R-hadrons originating through confinement of long-lived gluinos (with quarks, anti-quarks, and gluons) produced in pp collisions at astrophysical sources. Because of parton density requirements, the gluino has a momentum which is considerable smaller than the energy of the primary proton, and so production of heavy (mass ~ 500 GeV) R-hadrons requires powerful cosmic ray engines able to accelerate particles up to extreme energies, somewhat above 10^{13.6} GeV. Using a realistic Monte Carlo simulation with the AIRES engine, we study the main characteristics of the air showers triggered when one of these exotic hadrons impinges on a stationary nucleon of the Earth atmosphere. We show that R-hadron air showers present clear differences with respect to those initiated by standard particles. We use this shower characteristics to construct observables which may be used to distinguish long-lived gluinos at the Pierre Auger Observatory.Comment: 13 pages revtex, 9 eps figures. A ps version with high resolution figures is available at http://www.hep.physics.neu.edu/staff/doqui/rhadron_highres.p

Effect of Ph and vegetation cover in soil organic matter structure at a high-mountain ecosystem (Sierra Nevada National Park, Granada, Spain)

Poster nº 8246 en EGU General Assembly 2020, Online, 4–8 May 2020During the last decade, soil organic matter dynamics and its determining factors have received increased attention, mainly due to the evident implication of these parameters in climate change understanding, predictions and possible management. High-mountain soil could be considered as hotspot of climate change dynamic since its high carbon accumulation and low organic matter degradation rates could be seriously altered by slight changes in temperature and rainfall regimes associated to climate change effects. In the particular case of Sierra Nevada National Park, this threat could be even stronger due to its Southern character, although its elevated biodiversity could shed some light on how could we predict and manage climate change in the future. In this study, a quantitative and qualitative organic matter characterization was performed and soil microbial activity measured to evaluate the implication of pH and vegetation in soil organic matter dynamics. The sampling areas were selected according to vegetation and soil pH; with distinct soil pH (area A with pH7) and vegetation (high-mountain shrubs and pine reforested area). Soil samples were collected under the influence of several plant species representatives of each vegetation series. Six samples were finally obtained (five replicates each); three were collected in area A under Juniperus communis ssp. Nana (ENE), Genista versicolor (PIO) and Pinus sylvestris (PSI) and other three were collected in area B under Juniperus Sabina (SAB), Astragalus nevadensis (AST) and Pinus sylvestris (PCA). Qualitative and quantitative analyses of soil organic matter were made to establish a possible relationship with microbial activity estimated by respiration rate (alkali trap) and fungi-to-bacteria ratio using a plate count method. Soil easily oxidizable organic carbon content was determined by the Walkley-Black method (SOC %) and organic matter amount was estimated by weight loss on ignition (LOI %). Analytical pyrolysis (Py-GC/MS) was used to analyse in detail the soil organic carbon composition. Our results showed that the microbial and therefore the dynamics of organic matter is influenced by both, soil pH and soil of organic matter. So that the pH in acidic media prevail as a determining factor of microbial growth over soil organic matter composition conditioned by vegetation.Ministerio de Ciencia Innovación y Universidades (MICIU) for INTERCARBON project (CGL2016-78937-R). N.T. Jiménez-Morillo and L. San Emeterio also thanks MICIU for funding FPI research grants (BES-2013-062573 and Ref. BES-2017-07968). Mrs Desiré Monis is acknowledged for technical assistance

J-PLUS: A wide-field multi-band study of the M15 globular cluster. Evidence of multiple stellar populations in the RGB

The Javalambre Photometric Local Universe Survey (J-PLUS) provides wide field-of-view images in 12 narrow, intermediate and broad-band filters optimized for stellar photometry. Here we have applied J-PLUS data for the first time for the study of Galactic GCs using science verification data obtained for the very metal-poor GC M\,15. Our J-PLUS data provide low-resolution spectral energy distributions covering the near-UV to the near-IR, allowing us to search for MPs based on pseudo-spectral fitting diagnostics. J-PLUS CMDs are found to be particularly useful to search for splits in the sequences formed by the upper red giant branch (RGB) and asymptotic giant branch (AGB) stars. We interpret these split sequences as evidence for the presence of MPs. This demonstrates that the J-PLUS survey will have sufficient spatial coverage and spectral resolution to perform a large statistical study of GCs through multi-band photometry in the coming years.Comment: 11 pages, 11 figures. Accepted for publication @ A&

Deweyan tools for inquiry and the epistemological context of critical pedagogy

This article develops the notion of resistance as articulated in the literature of critical pedagogy as being both culturally sponsored and cognitively manifested. To do so, the authors draw upon John Dewey\u27s conception of tools for inquiry. Dewey provides a way to conceptualize student resistance not as a form of willful disputation, but instead as a function of socialization into cultural models of thought that actively truncate inquiry. In other words, resistance can be construed as the cognitive and emotive dimensions of the ongoing failure of institutions to provide ideas that help individuals both recognize social problems and imagine possible solutions. Focusing on Dewey\u27s epistemological framework, specifically tools for inquiry, provides a way to grasp this problem. It also affords some innovative solutions; for instance, it helps conceive of possible links between the regular curriculum and the study of specific social justice issues, a relationship that is often under-examined. The aims of critical pedagogy depend upon students developing dexterity with the conceptual tools they use to make meaning of the evidence they confront; these are background skills that the regular curriculum can be made to serve even outside social justice-focused curricula. Furthermore, the article concludes that because such inquiry involves the exploration and potential revision of students\u27 world-ordering beliefs, developing flexibility in how one thinks may be better achieved within academic subjects and topics that are not so intimately connected to students\u27 current social lives, especially where students may be directly implicated

Interpreting clinical trial data in multiple myeloma: translating findings to the real-world setting

Substantial improvements in survival have been seen in multiple myeloma (MM) over recent years, associated with the introduction and widespread use of multiple novel agents and regimens, as well as the emerging treatment paradigm of continuous or long-term therapy. However, these therapies and approaches may have limitations in the community setting, associated with toxicity burden, patient burden, and other factors including cost. Consequently, despite improvements in efficacy in the rigorously controlled clinical trials setting, the same results are not always achieved in real-world practice. Furthermore, the large number of different treatment options and regimens under investigation in various MM settings precludes the feasibility of obtaining head-to-head clinical trial data, and there is a temptation to use cross-trial comparisons to evaluate data across regimens. However, multiple aspects, including patient-related, disease-related, and treatment-related factors, can influence clinical trial outcomes and lead to differences between studies that may confound direct comparisons between data. In this review, we explore the various factors requiring attention when evaluating clinical trial data across available agents/regimens, as well as other considerations that may impact the translation of these findings into everyday MM management. We also investigate discrepancies between clinical trial efficacy and real-world effectiveness through a literature review of non-clinical trial data in relapsed/ refractory MM on novel agent−based regimens and evaluate these data in the context of phase 3 trial results for recently approved and commonly used regimens. We thereby demonstrate the complexity of interpreting data across clinical studies in MM, as well as between clinical studies and routine-care analyses, with the aim to help clinicians consider all the necessary issues when tailoring individual patients’ treatment approaches

Improving survey methods in sero-epidemiological studies of injecting drug users: a case example of two cross sectional surveys in Serbia and Montenegro

BACKGROUND: Little is known about the prevalence of HIV or HCV in injecting drug users (IDUs) in Serbia and Montenegro. We measured prevalence of antibodies to HIV (anti-HIV) and hepatitis C virus (anti-HCV), and risk factors for anti-HCV, in community-recruited IDUs in Belgrade and Podgorica, and determined the performance of a parallel rapid HIV testing algorithm. METHODS: Respondent driven sampling and audio-computer assisted survey interviewing (ACASI) methods were employed. Dried blood spots were collected for unlinked anonymous antibody testing. Belgrade IDUs were offered voluntary confidential rapid HIV testing using a parallel testing algorithm, the performance of which was compared with standard laboratory tests. Predictors of anti-HCV positivity and the diagnostic accuracy of the rapid HIV test algorithm were calculated. RESULTS: Overall population prevalence of anti-HIV and anti-HCV in IDUs were 3% and 63% respectively in Belgrade (n = 433) and 0% and 22% in Podgorica (n = 328). Around a quarter of IDUs in each city had injected with used needles and syringes in the last four weeks. In both cities anti-HCV positivity was associated with increasing number of years injecting (eg Belgrade adjusted odds ratio (AOR) 5.6 (95% CI 3.2-9.7) and Podgorica AOR 2.5 (1.3-5.1) for >or= 10 years v 0-4 years), daily injecting (Belgrade AOR 1.6 (1.0-2.7), Podgorica AOR 2.1 (1.3-5.1)), and having ever shared used needles/syringes (Belgrade AOR 2.3 (1.0-5.4), Podgorica AOR 1.9 (1.4-2.6)). Half (47%) of Belgrade participants accepted rapid HIV testing, and there was complete concordance between rapid test results and subsequent confirmatory laboratory tests (sensitivity 100% (95%CI 59%-100%), specificity 100% (95%CI 98%-100%)). CONCLUSION: The combination of community recruitment, ACASI, rapid testing and a linked diagnostic accuracy study provide enhanced methods for conducting blood borne virus sero-prevalence studies in IDUs. The relatively high uptake of rapid testing suggests that introducing this method in community settings could increase the number of people tested in high risk populations. The high prevalence of HCV and relatively high prevalence of injecting risk behaviour indicate that further HIV transmission is likely in IDUs in both cities. Urgent scale up of HIV prevention interventions is needed