Assessing restoration potential of a critically endangered vegetation type following alien acacia removal

The Fynbos vegetation of the Cape Lowlands is ecologically distinct from mountain Fynbos within the Cape Region of South Africa, but has been highly impacted by agriculture and urban development, while alien plants have invaded most of the remaining natural habitats. Cape Flats Sand Fynbos is a critically endangered lowland vegetation type containing many endemic and threatened species. 100 ha of this vegetation type which was invaded by alien Acacia saligna was cleared in 2012. The standard clearing methods utilised in Lowland Fynbos have resulted in poor native vegetation recovery. Therefore this study aimed to test novel passive (burning) and active (seed sowing) treatments on recovery of native vegetation. After two years all treatments resulted in different recovery trajectories, and modelling treatment responses showed these trajectories to be maintained in the long-term. The passive clearing without burning treatment resulted in herbaceous vegetation dominating, while the active treatment resulted in higher cover, species richness and density of non-sprouting shrubs. A follow-up sowing treatment involving seed pre-treated with smoke and heat improved shrub species richness and seedling density of certain species, especially Thamnochortus punctatus, a dominant structural component species. Therefore an active treatment involving sowing pre-treated seeds after clearing and burning results in best Fynbos recovery compared to either of the passive treatments tested. These restoration methods should be adaptable to other lowland vegetation types within the Fynbos region as well as other Mediterranean climate regions

Active seed sowing can overcome constraints to passive restoration of a critically endangered vegetation type

Invasive alien plants negatively impact ecosystems, but recovery of native vegetation may fail following standard methods of alien species removal alone. Alternative management actions may thus be required. Cape Flats Sand Fynbos is a critically endangered vegetation type in the Cape Floristic Region of South Africa which is threatened by Acacia saligna invasion, but standard clearing methods have failed to restore native vegetation structure. A restoration study was performed comparing passive treatments i.e. clearing without burning (stack-block) versus clearing and burning (burn-block), as well as active intervention by sowing seeds of native species, either initially after burning or a year later, in which seeds were either not pre-treated or pre-treated with smoke and heat exposure before sowing. After two years all treatments resulted in different recovery trajectories, although none resembled the reference condition. Clearing without burning facilitated recovery in less degraded areas with higher initial native shrub cover, but otherwise resulted in limited vegetation recovery. Limited recovery facilitated secondary invasion by herbaceous weeds. Active seed sowing resulted in the highest recovery of native shrub cover and diversity. These findings suggest that passive restoration is constrained by seed limitation, due to the lack of recovery of vegetation components under passive clearing treatment. Active sowing was able to partially overcome this constraint through improved recovery of total shrub cover. However, non-sprouting shrub cover was higher while resprouting shrubs and species of Restionaceae were lower compared to the reference condition. Pre-treatment of seeds before sowing improved establishment of some species. Active treatment involving sowing pre-treated seeds after clearing and burning therefore resulted in best fynbos recovery compared to either of the passive treatments tested. A decision tree has been developed based on these findings in order to guide best protocol for managers

Classification using distance nearest neighbours

This paper proposes a new probabilistic classification algorithm using a Markov random field approach. The joint distribution of class labels is explicitly modelled using the distances between feature vectors. Intuitively, a class label should depend more on class labels which are closer in the feature space, than those which are further away. Our approach builds on previous work by Holmes and Adams (2002, 2003) and Cucala et al. (2008). Our work shares many of the advantages of these approaches in providing a probabilistic basis for the statistical inference. In comparison to previous work, we present a more efficient computational algorithm to overcome the intractability of the Markov random field model. The results of our algorithm are encouraging in comparison to the k-nearest neighbour algorithm.Comment: 12 pages, 2 figures. To appear in Statistics and Computin

Mapping the unique and shared functions of oncogenic KRAS and RIT1 with proteome and transcriptome profiling

Aberrant activation of RAS oncogenes is prevalent in lung adenocarcinoma, with somatic mutation of KRAS occurring in ∼30% of tumors. Recently, we identified somatic mutation of the RAS-family GTPase RIT1 in lung adenocarcinoma, but relatively little is known about the biological pathways regulated by RIT1 and how these relate to the oncogenic KRAS network. Here we present quantitative proteomic and transcriptomic profiles from KRAS-mutant and RIT1-mutant isogenic lung epithelial cells and globally characterize the signaling networks regulated by each oncogene. We find that both mutant KRAS and mutant RIT1 promote S6 kinase, AKT, and RAF/MEK signaling, and promote epithelial-to-mesenchymal transition and immune evasion via HLA protein loss. However, KRAS and RIT1 diverge in regulation of phosphorylation sites on EGFR, USO1, and AHNAK proteins. The majority of the proteome changes are related to altered transcriptional regulation, but a small subset of proteins are differentially regulated by both oncoproteins at the post-transcriptional level, including intermediate filament proteins, metallothioneins, and MHC Class I proteins. These data provide the first global, unbiased characterization of oncogenic RIT1 network and identify the shared and divergent functions of oncogenic RIT1 and KRAS GTPases in lung cancer

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms

Summer CO2 evasion from streams and rivers in the Kolyma River basin, north-east Siberia

Inland water systems are generally supersaturated in carbon dioxide (CO2) and are increasingly recognized as playing an important role in the global carbon cycle. The Arctic may be particularly important in this respect, given the abundance of inland waters and carbon contained in Arctic soils; however, a lack of trace gas measurements from small streams in the Arctic currently limits this understanding.We investigated the spatial variability of CO2 evasion during the summer low-flow period from streams and rivers in the northern portion of the Kolyma River basin in north-eastern Siberia. To this end, partial pressure of carbon dioxide (pCO2) and gas exchange velocities (k) were measured at a diverse set of streams and rivers to calculate CO2 evasion fluxes. We combined these CO2 evasion estimates with satellite remote sensing and geographic information system techniques to calculate total areal CO2 emissions. Our results show that small streams are substantial sources of atmospheric CO2 owing to high pCO2 and k, despite being a small portion of total inland water surface area. In contrast, large rivers were generally near equilibrium with atmospheric CO2. Extrapolating our findings across the Panteleikha-Ambolikha sub-watersheds demonstrated that small streams play a major role in CO2 evasion, accounting for 86% of the total summer CO2 emissions from inland waters within these two sub-watersheds. Further expansion of these regional CO2 emission estimates across time and space will be critical to accurately quantify and understand the role of Arctic streams and rivers in the global carbon budget

Prediction Model to Identify Patients at Risk of 30-Day Treatment Failure in Patients With Staphylococcus aureus Bacteremia

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Opto-mechanical measurement of micro-trap via nonlinear cavity enhanced Raman scattering spectrum

High-gain resonant nonlinear Raman scattering on trapped cold atoms within a high-fineness ring optical cavity is simply explained under a nonlinear opto-mechanical mechanism, and a proposal using it to detect frequency of micro-trap on atom chip is presented. The enhancement of scattering spectrum is due to a coherent Raman conversion between two different cavity modes mediated by collective vibrations of atoms through nonlinear opto-mechanical couplings. The physical conditions of this technique are roughly estimated on Rubidium atoms, and a simple quantum analysis as well as a multi-body semiclassical simulation on this nonlinear Raman process is conducted.Comment: 7 pages, 2 figure

The clinical profile of moderate amblyopia in children younger than 7 years

Objective To describe the demographic and clinical characteristics of a cohort of children with moderate amblyopia participating in the Amblyopia Treatment Study 1, a randomized trial comparing atropine and patching. Methods The children enrolled were younger than 7 years and had strabismic, anisometropic, or combined strabismic and anisometropic amblyopia. Visual acuity, measured with a standardized testing protocol using single-surround HOTV optotypes, was 20/40 to 20/100 in the amblyopic eye, with an intereye acuity difference of 3 or more logMAR lines. There were 419 children enrolled, 409 of whom met these criteria and were included in the analyses. Results The mean age of the 409 children was 5.3 years. The cause of the amblyopia was strabismus in 38%, anisometropia in 37%, and both strabismus and anisometropia in 24%. The mean visual acuity of the amblyopic eyes (approximately 20/60) was similar among the strabismic, anisometropic, and combined groups (P = .24), but visual acuity of the sound eyes was worse in the strabismic group compared with the anisometropic group (P<.001). For the patients randomized into the patching group, 43% were initially treated for 6 hours per day, whereas 17% underwent full-time patching. Patients with poorer visual acuity in the amblyopic eye were prescribed more hours of patching than patients with better acuity (P = .003). Conclusions In the Amblyopia Treatment Study 1, there were nearly equal proportions of patients with strabismic and anisometropic amblyopia. A similar level of visual impairment was found irrespective of the cause of amblyopia. There was considerable variation in treatment practices with regard to the number of hours of initial patching prescribed

Functional diversity of chemokines and chemokine receptors in response to viral infection of the central nervous system.

Encounters with neurotropic viruses result in varied outcomes ranging from encephalitis, paralytic poliomyelitis or other serious consequences to relatively benign infection. One of the principal factors that control the outcome of infection is the localized tissue response and subsequent immune response directed against the invading toxic agent. It is the role of the immune system to contain and control the spread of virus infection in the central nervous system (CNS), and paradoxically, this response may also be pathologic. Chemokines are potent proinflammatory molecules whose expression within virally infected tissues is often associated with protection and/or pathology which correlates with migration and accumulation of immune cells. Indeed, studies with a neurotropic murine coronavirus, mouse hepatitis virus (MHV), have provided important insight into the functional roles of chemokines and chemokine receptors in participating in various aspects of host defense as well as disease development within the CNS. This chapter will highlight recent discoveries that have provided insight into the diverse biologic roles of chemokines and their receptors in coordinating immune responses following viral infection of the CNS