Effects of light and soil flooding on the growth and photosynthesis of ramin (Gonystylus bancanus) seedlings in Malaysia

We studied the ecophysiology of ramin (Gonystylus bancanus) seedlings in an experimental set up at the Forest Research Centre in Kuching, Sarawak, Malaysia. Ramin seedlings were grown on flooded and drained peat soil under 100, 76, 46 and 23% sunlight, thus simulating effects of different light conditions (canopy gap size) and drainage that occur in natural ramin populations. Seedling growth was highest in partial sunlight (76%) and reduced with reducing light levels. Aboveground productivity and fine root development were significantly higher in seedlings grown on flooded soil compared with those on drained soil. In contrast, investment in coarse root biomass was significantly higher in seedlings grown on drained soil. It appeared that the aboveground growth benefits in flooded conditions were the result of more advantageous conditions for allocation of carbon to leaves, thus enhancing overall relative growth rates through higher light interception rates despite lower photosynthetic capacity. The results of this experiment suggested that drainage of peat swamp forests would seriously hamper natural regeneration of ramin by limiting the growth of seedlings. It is also suggested that selective logging operations which produce medium-size canopy gaps improve ramin regeneration in hydrologically undisturbed mixed swamp forest

Metagenomic evidence for a polymicrobial signature of sepsis

Our understanding of the host component of sepsis has made significant progress. However, detailed study of the microorganisms causing sepsis, either as single pathogens or microbial assemblages, has received far less attention. Metagenomic data offer opportunities to characterize the microbial communities found in septic and healthy individuals. In this study we apply gradient-boosted tree classifiers and a novel computational decontamination technique built upon SHapley Additive exPlanations (SHAP) to identify microbial hallmarks which discriminate blood metagenomic samples of septic patients from that of healthy individuals. Classifiers had high performance when using the read assignments to microbial genera [area under the receiver operating characteristic (AUROC=0.995)], including after removal of species ‘culture-confirmed’ as the cause of sepsis through clinical testing (AUROC=0.915). Models trained on single genera were inferior to those employing a polymicrobial model and we identified multiple co-occurring bacterial genera absent from healthy controls. While prevailing diagnostic paradigms seek to identify single pathogens, our results point to the involvement of a polymicrobial community in sepsis. We demonstrate the importance of the microbial component in characterising sepsis, which may offer new biological insights into the aetiology of sepsis, and ultimately support the development of clinical diagnostic or even prognostic tools

THE ROLE OF FRICTIONAL STRENGTH

[1] At a subduction zone the amount of friction between the incoming plate and the forearc is an important factor in controlling the dip angle of subduction and the structure of the forearc. In this paper, we investigate the role of the frictional strength of sediments and of the serpentinized peridotite on the evolution of convergent margins. In numerical models, we vary thickness of a serpentinized layer in the mantle wedge (15 to 25 km) and the frictional strength of both the sediments and serpentinized mantle (friction angle 1° to 15°, or static friction coefficient 0.017 to 0.27) to control the amount of frictional coupling between the plates. With plastic strain weakening in the lithosphere, our numerical models can attain stable subduction geometry over millions of years. We find that the frictional strength of the sediments and serpentinized peridotite exerts the largest control on the dip angle of the subduction interface at seismogenic depths. In the case of low sediment and serpentinite friction, the subduction interface has a shallow dip, while the subduction zone develops an accretionary prism, a broad forearc high, a deep forearc basin, and a shallow trench. In the high friction case, the subduction interface is steep, the trench is deeper, and the accretionary prism, forearc high and basin are all absent. The resultant free-air gravity and topographic signature of these subduction zone models are consistent with observations. We believe that the low-friction model produces a geometry and forearc structure similar to that of accretionary margins. Conversely, models with high friction angles in sediments and serpentinite develop characteristics of an erosional convergent margin. We find that the strength of the subduction interface is critical in controlling the amount of coupling at the seismogenic zone and perhaps ultimately the size of the largest earthquakes at subduction zones

An Algorithm for Probabilistic Alternating Simulation

In probabilistic game structures, probabilistic alternating simulation (PA-simulation) relations preserve formulas defined in probabilistic alternating-time temporal logic with respect to the behaviour of a subset of players. We propose a partition based algorithm for computing the largest PA-simulation, which is to our knowledge the first such algorithm that works in polynomial time, by extending the generalised coarsest partition problem (GCPP) in a game-based setting with mixed strategies. The algorithm has higher complexities than those in the literature for non-probabilistic simulation and probabilistic simulation without mixed actions, but slightly improves the existing result for computing probabilistic simulation with respect to mixed actions.Comment: We've fixed a problem in the SOFSEM'12 conference versio

<i>Alteromonas stellipolaris</i> sp. nov., a novel, budding, prosthecate bacterium from Antarctic seas, and emended description of the genus <i>Alteromonas</i>

Seven novel, cold-adapted, strictly aerobic, facultatively oligotrophic strains, isolated from Antarctic sea water, were investigated by using a polyphasic taxonomic approach. The isolates were Gram-negative, chemoheterotrophic, motile, rod-shaped cells that were psychrotolerant and moderately halophilic. Buds were produced on mother and daughter cells and on prosthecae. Prostheca formation was peritrichous and prosthecae could be branched. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the γ-Proteobacteria and are related to the genus Alteromonas, with 98·3 % sequence similarity to Alteromonas macleodii and 98·0 % to Alteromonas marina, their nearest phylogenetic neighbours. Whole-cell fatty acid profiles of the isolates were very similar and included C16 : 0, C16 : 1 ω7c, C17 : 1 ω8c and C18 : 1 ω8c as the major fatty acid components. These results support the affiliation of these isolates to the genus Alteromonas. DNA–DNA hybridization results and differences in phenotypic characteristics show that the strains represent a novel species with a DNA G+C content of 43–45 mol%. The name Alteromonas stellipolaris sp. nov. is proposed for this novel species; the type strain is ANT 69aT (=LMG 21861T=DSM 15691T). An emended description of the genus Alteromonas is given

Supergravity Higgs Inflation and Shift Symmetry in Electroweak Theory

We present a model of inflation in a supergravity framework in the Einstein frame where the Higgs field of the next to minimal supersymmetric standard model (NMSSM) plays the role of the inflaton. Previous attempts which assumed non-minimal coupling to gravity failed due to a tachyonic instability of the singlet field during inflation. A canonical K\"{a}hler potential with \textit{minimal coupling} to gravity can resolve the tachyonic instability but runs into the $\eta$-problem. We suggest a model which is free of the $\eta$-problem due to an additional coupling in the K\"{a}hler potential which is allowed by the Standard Model gauge group. This induces directions in the potential which we call K-flat. For a certain value of the new coupling in the (N)MSSM, the K\"{a}hler potential is special, because it can be associated with a certain shift symmetry for the Higgs doublets, a generalization of the shift symmetry for singlets in earlier models. We find that K-flat direction has $H_u^0=-H_d^{0*}.$ This shift symmetry is broken by interactions coming from the superpotential and gauge fields. This direction fails to produce successful inflation in the MSSM but produces a viable model in the NMSSM. The model is specifically interesting in the Peccei-Quinn (PQ) limit of the NMSSM. In this limit the model can be confirmed or ruled-out not just by cosmic microwave background observations but also by axion searches.Comment: matches the published version at JCA

Is sodium current present in human sinoatrial node cells?

Pacemaker activity of the sinoatrial node has been studied extensively in various animal species, but is virtually unexplored in man. As such, it is unknown whether the fast sodium current (INa) plays a role in the pacemaker activity of the human sinoatrial node. Recently, we had the unique opportunity to perform patch-clamp experiments on single pacemaker cells isolated from a human sinoatrial node. In 2 out of the 3 cells measured, we observed large inward currents with characteristics of INa. Although we were unable to analyze the current in detail, our findings provide strong evidence that INa is present in human sinoatrial node pacemaker cells, and that this INa is functionally available at potentials negative to -60 mV

Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses

T-cell-mediated immunity to SARS-CoV-2-derived peptides in individuals unexposed to SARS-CoV-2 has been previously reported. This pre-existing immunity was suggested to largely derive from prior exposure to ‘common cold’ endemic human coronaviruses (HCoVs). To test this, we characterised the sequence homology of SARS-CoV-2-derived T-cell epitopes reported in the literature across the full proteome of the Coronaviridae family. 54.8% of these epitopes had no homology to any of the HCoVs. Further, the proportion of SARS-CoV-2-derived epitopes with any level of sequence homology to the proteins encoded by any of the coronaviruses tested is well-predicted by their alignment-free phylogenetic distance to SARS-CoV-2 (Pearson's r = −0.958). No coronavirus in our dataset showed a significant excess of T-cell epitope homology relative to the proportion of expected random matches, given their genetic similarity to SARS-CoV-2. Our findings suggest that prior exposure to human or animal-associated coronaviruses cannot completely explain the T-cell repertoire in unexposed individuals that recognise SARS-CoV-2 cross-reactive epitopes