103 research outputs found
Efficient and Compact Representations of Some Non-canonical Prefix-Free Codes
The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-319-46049-9_5[Abstract] For many kinds of prefix-free codes there are efficient and compact alternatives to the traditional tree-based representation. Since these put the codes into canonical form, however, they can only be used when we can choose the order in which codewords are assigned to characters. In this paper we first show how, given a probability distribution over an alphabet of ÏÏ characters, we can store a nearly optimal alphabetic prefix-free code in o(Ï)o(Ï) bits such that we can encode and decode any character in constant time. We then consider a kind of code introduced recently to reduce the space usage of wavelet matrices (Claude, Navarro, and Ordóñez, Information Systems, 2015). They showed how to build an optimal prefix-free code such that the codewordsâ lengths are non-decreasing when they are arranged such that their reverses are in lexicographic order. We show how to store such a code in O(ÏlogL+2Ï”L)O(ÏlogâĄL+2Ï”L) bits, where L is the maximum codeword length and ϔϔ is any positive constant, such that we can encode and decode any character in constant time under reasonable assumptions. Otherwise, we can always encode and decode a codeword of ââ bits in time O(â)O(â) using O(ÏlogL)O(ÏlogâĄL) bits of space.Ministerio de EconomĂa, Industria y Competitividad; TIN2013-47090-C3-3-PMinisterio de EconomĂa, Industria y Competitividad; TIN2015-69951-RMinisterio de EconomĂa, Industria y Competitividad; ITC-20151305Ministerio de EconomĂa, Industria y Competitividad; ITC-20151247Xunta de Galicia; GRC2013/053Chile. NĂșcleo Milenio InformaciĂłn y CoordinaciĂłn en Redes; ICM/FIC.P10-024FCOST. IC1302Academy of Finland; 268324Academy of Finland; 25034
Whole genome mapping of 5' RNA ends in bacteria by tagged sequencing : A comprehensive view in Enterococcus faecalis
Enterococcus faecalis is the third cause of nosocomial infections. To obtain
the first comprehensive view of transcriptional organizations in this
bacterium, we used a modified RNA-seq approach enabling to discriminate primary
from processed 5'RNA ends. We also validated our approach by confirming known
features in Escherichia coli.
We mapped 559 transcription start sites and 352 processing sites in E.
faecalis. A blind motif search retrieved canonical features of SigA- and
SigN-dependent promoters preceding TSSs mapped. We discovered 95 novel putative
regulatory RNAs, small- and antisense RNAs, and 72 transcriptional antisense
organisations.
Presented data constitute a significant insight into bacterial RNA landscapes
and a step towards the inference of regulatory processes at transcriptional and
post-transcriptional levels in a comprehensive manner
Is undernutrition prognostic of infection complications in children undergoing surgery? A systematic review
Background: Healthcare-associated infections are costly and are increasingly viewed as an indicator of the quality of care. Although strategies to reduce infections have become widespread, few studies have formally investigated the role of undernutrition on the development of infection-related complications in children after surgery.
Aim: To perform a systematic review of the literature to determine if undernutrition is prognostic of postoperative infection complications in children.
Methods: Electronic bibliographic and research databases were searched from 1950 to 2014. Inclusion criteria were studies in children (age <18 years) evaluating pre-operative nutritional status and reporting postoperative infection complications. Quality assessment was performed independently by two reviewers, with disagreements resolved by a third reviewer. The quality of the evidence was judged to be low in the majority of studies.
Findings: Ten cohort and two caseecontrol studies met the inclusion criteria. Five studies reported an outcome combining infection-related complications, with the remainder reporting individual infection complications. Six studies reported surgical site infection (SSI) alone or in combination with other infection complications. Direct comparison between studies was difficult due to clinical and diagnostic heterogeneity. Unadjusted analyses (for patient or clinical variables) were suggestive of a relationship between undernutrition and infection complications. In studies controlling for other variables, the analyses did not remain significant for SSI.
Conclusion: There was low-quality evidence that undernutrition may be predictive of postoperative infection complications in children, with the exception of SSI. However, inconsistencies in nutritional and outcome assessments made it difficult to draw conclusions. Larger, high-quality studies are warranted to further investigate a potential prognostic relationship
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition
A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems
Independent Regulation of Reovirus Membrane Penetration and Apoptosis by the ÎŒ1 Ï Domain
Apoptosis plays an important role in the pathogenesis of reovirus encephalitis. Reovirus outer-capsid protein ÎŒ1, which functions to penetrate host cell membranes during viral entry, is the primary regulator of apoptosis following reovirus infection. Ectopic expression of full-length and truncated forms of ÎŒ1 indicates that the ÎŒ1 Ï domain is sufficient to elicit a cell death response. To evaluate the contribution of the ÎŒ1 Ï domain to the induction of apoptosis following reovirus infection, Ï mutant viruses were generated by reverse genetics and analyzed for the capacity to penetrate cell membranes and elicit apoptosis. We found that mutations in Ï diminish reovirus membrane penetration efficiency by preventing conformational changes that lead to generation of key reovirus entry intermediates. Independent of effects on membrane penetration, amino acid substitutions in Ï affect the apoptotic potential of reovirus, suggesting that Ï initiates apoptosis subsequent to cytosolic delivery. In comparison to wild-type virus, apoptosis-defective Ï mutant viruses display diminished neurovirulence following intracranial inoculation of newborn mice. These results indicate that the Ï domain of ÎŒ1 plays an important regulatory role in reovirus-induced apoptosis and disease
Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years
CEERS Key Paper VII: Emission Line Ratios from NIRSpec and NIRCam Wide-Field Slitless Spectroscopy at z>2
We use James Webb Space Telescope Near-Infrared Camera Wide Field Slitless
Spectroscopy (NIRCam WFSS) and Near-Infrared spectrograph (NIRSpec) in the
Cosmic Evolution Early Release survey (CEERS) to measure rest-frame optical
emission-line of 155 galaxies at z>2. The blind NIRCam grism observations
include a sample of galaxies with bright emission lines that were not observed
on the NIRSpec masks. We study the changes of the Ha, [OIII]/Hb, and
[NeIII]/[OII] emission lines in terms of redshift by comparing to lower
redshift SDSS and CLEAR samples. We find a significant (>3) correlation
between [OIII]/Hb with redshift, while [NeIII]/[OII] has a marginal (2)
correlation with redshift. We compare [OIII]/Hb and [NeIII]/[OII] to stellar
mass and Hb SFR. We find that both emission-line ratios have a correlation with
Hb SFR and an anti-correlation with stellar mass across the redshifts 0<z<9.
Comparison with MAPPINGS~V models indicates that these trends are consistent
with lower metallicity and higher ionization in low-mass and high-SFR galaxies.
We additionally compare to IllustriousTNG predictions and find that they
effectively describe the highest [OIII]/Hb ratios observed in our sample,
without the need to invoke MAPPINGS models with significant shock ionizionation
components.Comment: 16 pages, 11 figure
A simple and efficient method to search for selected primary transcripts: non-coding and antisense RNAs in the human pathogen Enterococcus faecalis
Enterococcus faecalis is a commensal bacterium and a major opportunistic human pathogen. In this study, we combined in silico predictions with a novel 5âČRACE-derivative method coined â5âČtagRACEâ, to perform the first search for non-coding RNAs (ncRNAs) encoded on the E. faecalis chromosome. We used the 5âČtagRACE to simultaneously probe and characterize primary transcripts, and demonstrate here the simplicity, the reliability and the sensitivity of the method. The 5âČtagRACE is complementary to tiling arrays or RNA-sequencing methods, and is also directly applicable to deep RNA sequencing and should significantly improve functional studies of bacterial RNA landscapes. From 45 selected loci of the E. faecalis chromosome, we discovered and mapped 29 novel ncRNAs, 10 putative novel mRNAs and 16 antisense transcriptional organizations. We describe in more detail the oxygen-dependent expression of one ncRNA located in an E. faecalis pathogenicity island, the existence of an ncRNA that is antisense to the ncRNA modulator of the RNA polymerase, SsrS and provide evidences for the functional interplay between two distinct toxinâantitoxin modules
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