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 σσ characters, we can store a nearly optimal alphabetic prefix-free code in o(σ)o(σ) 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 codewords’ 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(σlogL+2ϵL)O(σlog⁡L+2ϵL) bits, where L is the maximum codeword length and ϵϵ 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 ℓℓ bits in time O(ℓ)O(ℓ) using O(σlogL)O(σlog⁡L) bits of space.Ministerio de Economía, Industria y Competitividad; TIN2013-47090-C3-3-PMinisterio de Economía, Industria y Competitividad; TIN2015-69951-RMinisterio de Economía, Industria y Competitividad; ITC-20151305Ministerio de Economía, Industria y Competitividad; ITC-20151247Xunta de Galicia; GRC2013/053Chile. Núcleo Milenio Información y Coordinación 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

Clinical impact of CEUS on non-characterizable observations and observations with intermediate probability of malignancy on CT/MRI in patients at risk for HCC.

BACKGROUND Hepatocellular carcinoma (HCC) is a unique cancer allowing tumor diagnosis with identification of definitive patterns of enhancement on contrast-enhanced imaging, avoiding invasive biopsy. However, it is still unclear to what extent Contrast-Enhanced Ultrasound (CEUS) is a clinically useful additional step when Computed tomography (CT) or Magnetic resonance imaging (MRI) are inconclusive. METHODS A prospective international multicenter validation study for CEUS Liver Imaging Reporting and Data System (LI-RADS) was conducted between January 2018 and August 2021. 646 patients at risk for HCC with focal liver lesions were enrolled. CEUS was performed using an intravenous ultrasound contrast agent within 4 weeks of CT/MRI. Liver nodules were categorized based on LI-RADS (LR) criteria. Histology or one-year follow-up CT/MRI imaging results were used as the reference standard. The diagnostic performance of CEUS was evaluated for inconclusive CT/MRI scan in two scenarios for which the AASLD recommends repeat imaging or imaging follow-up: observations deemed non-characterizable (LR-NC) or with indeterminate probability of malignancy (LR-3). RESULTS 75 observations on CT or MRI were categorized as LR-3 (n = 54) or LR-NC (n = 21) CEUS recategorization of such observations into a different LR category (namely, into one among LR-1, LR-2, LR-5, LR-M, or LR-TIV) resulted in management recommendation changes in 33.3% (25/75) and in all but one (96.0%, 24/25) observation, the new management recommendations were correct. CONCLUSION CEUS LI-RADS resulted in management recommendations change in substantial number of liver observations with initial indeterminate CT/MRI characterization, identifying both non-malignant lesions and HCC, potentially accelerating the diagnostic process and alleviating the need for biopsy or follow-up imaging. CLINICALTRIALS gov number, NCT03318380

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 μ1 ϕ Domain

Apoptosis plays an important role in the pathogenesis of reovirus encephalitis. Reovirus outer-capsid protein μ1, 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 μ1 indicates that the μ1 ϕ domain is sufficient to elicit a cell death response. To evaluate the contribution of the μ1 ϕ domain to the induction of apoptosis following reovirus infection, ϕ mutant viruses were generated by reverse genetics and analyzed for the capacity to penetrate cell membranes and elicit apoptosis. We found that mutations in ϕ 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 ϕ affect the apoptotic potential of reovirus, suggesting that ϕ initiates apoptosis subsequent to cytosolic delivery. In comparison to wild-type virus, apoptosis-defective ϕ mutant viruses display diminished neurovirulence following intracranial inoculation of newborn mice. These results indicate that the ϕ domain of μ1 plays an important regulatory role in reovirus-induced apoptosis and disease

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$\sigma$) correlation between [OIII]/Hb with redshift, while [NeIII]/[OII] has a marginal (2$\sigma$) 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

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