Achievable Rate Regions for Two-Way Relay Channel using Nested Lattice Coding

This paper studies Gaussian Two-Way Relay Channel where two communication nodes exchange messages with each other via a relay. It is assumed that all nodes operate in half duplex mode without any direct link between the communication nodes. A compress-and-forward relaying strategy using nested lattice codes is first proposed. Then, the proposed scheme is improved by performing a layered coding : a common layer is decoded by both receivers and a refinement layer is recovered only by the receiver which has the best channel conditions. The achievable rates of the new scheme are characterized and are shown to be higher than those provided by the decode-and-forward strategy in some regions.Comment: 27 pages, 13 figures, Submitted to IEEE Transactions on Wireless Communications (October 2013

Finite Dimension Wyner-Ziv Lattice Coding for Two-Way Relay Channel

International audienceTwo-way relay channel (TWRC) models a cooperative communication situation performing duplex transmission via a relay station. For this channel, we have shown previously that a lattice-based physical layer network coding strategy achieves, at the limit of arbitrarily large dimension, the same rate as that offered by the random coding-based regular compress-and-forward. In this paper, we investigate a practical coding scheme using finite dimension lattices and offering a reasonable performance-complexity trade-off. The algorithm relies on lattice based quantization for Wyner-Ziv coding. We characterize the rate region allowed by our coding scheme, discuss the design criteria, and illustrate our results with some numerical examples

HOLOCENE ENVIRONMENT CHANGES IN THE HACHICHINA WETLAND (GULF OF GABES, TUNISIA) EVIDENCED BY FORAMINIFERA AND OSTRACODA, GEOCHEMICAL PROXIES AND SEDIMENTOLOGICAL ANALYSES

Four sediment cores, drilled at Younga and Ouadrane Sebkhas (Hachichina wetland), were selected for micropalaeontological, sedimentological, geochronological and geochemical investigation coupled to hierarchical cluster and correspondence analysis. Our research aimed at reconstructing the past biodiversity, the Holocene palaeoenvironmental evolution and the responsible forcing. Subsurface sediments record four major phases: i) the first one is characterized by poorly to very poorly sorted silts, the dominance of the lagoonal/estuarine ostracod and the lagoonal/marine foraminifera and high values of terrestrial geochemical element ratios, such as K/Al and Fe/Al, which indicate an estuarine lagoon; ii) two major marine transgressions, TR1 and TR2, allowing the settlement of widely opened lagoons towards 7160-8680 and 5070-5520 cal yr BP, are marked by the enhancement of the marine/brackish ostracods and marine foraminifera, the improvement of species number, individuals number and H and E index values and of the marine element ratios such as Cl/Al and Sr/Al; iii) the opening of the lagoon is hampered by the action of drift currents allowing the genesis of sand spit and the settlement of a closed lagoon, towards 2610-3610 cal yr BP, characterized by the enhancement of lagoonal/estuarine ostracods and lagoonal/marine foraminifera and the increase of the individuals number; iv) the dominance of the lagoonal/estuarine ostracods and the lagoonal/marine foraminifera and the decline of the species number and density mark a brackish lagoon, also characterized by very poorly sorted silts transported by uniform suspension, which evolves to the actual sebkha. This evolution, within a global climate alteration context, from an estuarine environment to the present sebkha passing by an opened lagoon, is linked to the complex hydrographic setting of the sebkhas and of the Ouadrane Wadi outlet discharging in the Hachichina wetland

Ostracods distribution in the subsurface sediments of El-Guettiate Sebkha (Skhira, gulf of Gabes). Interest for Holocene palaeoenvironmental reconstruction

A quantitative and qualitative study of the ostracods from the SG1 and BSC2 cores of El-Guettiate Sebkha of Skhira (southeastern Tunisia) has allowed the identification of different associations and the reconstruction of the Holocene palaeoenvironments. Ostracods, rich in species, provide three associations: (i) a marine association containing Aurila prasina BARBIETO-GONZALEZ, 1971, Cushmanidea elongata (BRADY, 1868), Urocythereis oblonga (BRADY, 1866), U. favosa (ROEMER, 1838) (coastal marine), Basselerites berchoni (BRADY, 1869), Semicytherura incongruens (G.W. MÜLLER, 1894), S. paradoxa (G.W. MÜLLER, 1894), S. sella (SARS, 1866), S. ruggierii (PUCCI, 1955), Carinocythereis carinata (ROEMER, 1838) and Paracytheridea depressa (G.W. MÜLLER, 1894) (open marine); (ii) lagoonal association, of variable salinity, comprising Xestoleberis aurantia (BAIRD, 1838), Leptocythere fabaeformis (G.W. MÜLLER, 1894) and Cytherois fischeri (SARS, 1866); (iii) brackish estuarine association subject to estuarine influence as indicated by Cyprideis torosa (JONES, 1850) and Loxoconcha elliptica BRADY, 1868. The ostracods from El-Guettiate Sebkha allow us to recognize discrete palaeoenvironments that can be grouped in three phases: i) the first (6595 ± 120 - 6055 ± 30 years BP) begins with an open lagoon rich in marine ostracods followed by an estuarine lagoon (towards 6595 years BP) characterized by the richness of brackish ostracods and high energy. In the last lagoonal environment (installed towards 6055 years BP), brackish species are dominant and associated with lagoonal taxa; ii) the second phase (6055 ± 30 years BP - 5150 ± 30 years BP) is an estuarine lagoon, subject to a large marine influence in which brackish marine and lagoonal species are present in the same percentages. In this environment, littoral drift currents were responsible for the genesis of sand spits, the termination of environments and the dominance of brackish-water ostracods; iii) The last phase (5150 ± 50 years BP - recent) represents a restricted lagoon (about 5150 years BP) and finally a brackish lagoon evolved towards the sebkha environment under investigation here. This phase includes an unstable period with washover deposits resulting from an extreme climatic event.L'étude quantitative et qualitative des ostracodes des carottes SG1 et BSC2, prélevées au niveau de la Sebkha El-Guettiate de Skhira (Sud - Est Tunisien), nous a permis de reconnaître les trois associations suivantes : (1) association de milieu marin s.l. composée de Aurila prasina BARBIETO-GON-ZALEZ, 1971, Cushmanidea elongata (BRADY, 1868), Urocythereis oblonga (BRADY, 1866), U. favosa (ROEMER, 1838) (marin côtier), Basselerites berchoni (BRADY, 1869), Semicytherura incongruens (G.W. MÜLLER, 1894), S. paradoxa (G.W. MÜLLER, 1894), S. sella (SARS, 1866), S. ruggierii (PUCCI, 1955), Carinocythereis carinata (ROEMER, 1838) et Paracytheridea depressa (G.W. MÜLLER, 1894) (marin ouvert) ; (2) association de milieu lagunaire, à salinité variable, constituée, de Xestoleberis aurantia (BAIRD, 1838), Leptocythere fabaeformis (G.W. MÜLLER, 1894) et Cytherois fischeri (SARS, 1866), (3) association de milieu saumâtre estuarien où se développent Cyprideis torosa (JONES, 1850) et Loxocon-cha elliptica BRADY, 1868. Ces associations révèlent les caractéristiques des paléo-environnements qui se sont succédés, au cours de l'Holocène supérieur, à l'emplacement de la Sebkha El-Guettiate. Trois phases peuvent être reconnues : i) la première phase à caractère lagunaire estuarien dominant (6595 ± 120 à 6055 ± 30 ans B.P.) comprend un environnement lagunaire ouvert riche en ostracodes marins dominants évoluant brutalement vers un environnement lagunaire estuarien. Ce dernier est caractérisé par un évènement de haute énergie, vers 6595 ± 120 ans B.P., révélé par des apports détritiques riches en galets, synchrones à l'enrichissement des ostracodes saumâtres. Ensuite, une lagune s'instal-le vers 6055 ± 30 ans B.P. permettant le développement des ostracodes principalement saumâtres dominants mais aussi lagunaires. ii) la phase suivante (6055 ± 120 à 5150 ± 50 ans B.P.) se distingue par la réapparition des taxons marins associés aux espèces lagunaires et saumâtres traduisant une lagune estuarienne largement ouverte soumise à l'influence des courants de dérive littorale. Ces cou-rants, en édifiant des cordons littoraux, ont entraîné la fermeture du milieu et la fin de la dominance des ostracodes saumâtres. iii) la dernière phase (5150 ± 50 ans B.P. à l'actuel) comprend un milieu caractérisé par la richesse des taxons lagunaires évoluant vers un milieu laguno-saumâtre recevant le dépôt de washover suite à un événement climatique extrême. La lagune, de plus en plus fermée, évo-luera progressivement vers la sebkha actuelle

Altered Gene Expression in Liver from a Murine Model of Hyperhomocysteinemia

Cystathionine beta-synthase (CBS) deficiency causes severe hyperhomocysteinemia and other signs of homocystinuria syndrome, in particular a premature atherosclerosis with multiple thrombosis. However, the molecular mechanisms by which homocysteine could interfere with normal cell function are poorly understood in a whole organ like the liver, which is central to the catabolism of homocysteine. We used a combination of differential display and cDNA arrays to analyze differential gene expression in association with elevated hepatic homocysteine levels in CBS-deficient mice, a murine model of hyperhomocysteinemia. Expression of several genes was found to be reproducibly abnormal in the livers of heterozygous and homozygous CBS-deficient mice. We report altered expression of genes encoding ribosomal protein S3a and methylthioadenosine phosphorylase, suggesting such cellular growth and proliferation perturbations may occur in homozygous CBS-deficient mice liver. Many up- or down-regulated genes encoded cytochromes P450, evidence of perturbations of the redox potential in heterozygous and homozygous CBS-deficient mice liver. The expression of various genes involved in severe oxidative processes was also abnormal in homozygous CBS-deficient mice liver. Among them, the expression of heme oxygenase 1 gene was increased, concomitant with overexpression of heme oxygenase 1 at the protein level. Commensurate with the difference in hepatic mRNA paraoxonase 1 abundance, the mean hepatic activity of paraoxonase 1, an enzyme that protects low density lipoprotein from oxidation, was 3-fold lower in homozygous CBS-deficient mice. Heterozygous CBS-deficient mice, when fed a hyperhomocysteinemic diet, have also reduced PON1 activity, which demonstrates the effect of hyperhomocysteinemia in the paraoxonase 1 activity

Pyrenophora teres: Profile of an increasingly damaging barley pathogen

Pyrenophora teres, causal agent of net blotch of barley, exists in two forms, designated P. teres f. teres and P. teres f. maculata, which induce net form net blotch (NFNB) and spot form net blotch (SFNB), respectively. Significantly more work has been performed on the net form than on the spot form although recent activity in spot form research has increased because of epidemics of SFNB in barley‐producing regions. Genetic studies have demonstrated that NFNB resistance in barley is present in both dominant and recessive forms, and that resistance/susceptibility to both forms can be conferred by major genes, although minor quantitative trait loci have also been identified. Early work on the virulence of the pathogen showed toxin effector production to be important in disease induction by both forms of pathogen. Since then, several laboratories have investigated effectors of virulence and avirulence, and both forms are complex in their interaction with the host. Here, we assemble recent information from the literature that describes both forms of this important pathogen and includes reports describing the host–pathogen interaction with barley. We also include preliminary findings from a genome sequence survey

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering.Biotechnological and Biological Sciences Research Council (BBSRC). Grant Numbers: BB/K005952/1, BB/L02182X/1 Synthetic Biology Research Centre ‘OpenPlant’ award. Grant Number: BB/L014130/1 Spanish MINECO. Grant Number: BIO2013‐42193‐R Engineering Nitrogen Symbiosis for Africa (ENSA) The Bill & Melinda Gates Foundation US Department of Energy, Office of Biological and Environmental. Grant Number: DE‐AC02‐05CH1123 COST Action. Grant Number: FA100

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century