Tunable high-resolution synthetic aperture radar imaging

We have recently introduced a modification of the multiple signal classification (MUSIC) method for synthetic aperture radar. This method depends on a tunable, user-defined parameter, $\epsilon$, that allows for quantitative high-resolution imaging. It requires however, relative large single-to-noise ratios (SNR) to work effectively. Here, we first identify the fundamental mechanism in that method that produces high-resolution images. Then we introduce a modification to Kirchhoff Migration (KM) that uses the same mechanism to produces tunable, high-resolution images. This modified KM method can be applied to low SNR measurements. We show simulation results that demonstrate the features of this method

‘‘Cryptic’’ group-I introns in the nuclear SSU-rRNA gene of Verticillium dahliae

Group-I introns are widespread—though irregularly distributed—in eukaryotic organisms, and they have been extensively used for discrimination and phylogenetic analyses. Within the Verticillium genus, which comprises important phytopathogenic fungi, a group-I intron was previously identified in the SSU-rRNA (18S) gene of only V. longisporum. In this work, we aimed at elucidating the SSU-located intron distribution in V. dahliae and other Verticillium species, and the assessment of heterogeneity regarding intron content among rDNA repeats of fungal strains. Using conserved PCR primers for the amplification of the SSU gene, a structurally similar novel intron (sub-group IC1) was detected in only a few V. dahliae isolates. However, when intron-specific primers were used for the screening of a diverse collection of Verticillium isolates that originally failed to produce intron-containing SSU amplicons, most were found to contain one or both intron types, at variable rDNA repeat numbers. This marked heterogeneity was confirmed with qRT-PCR by testing rDNA copy numbers (varying from 39 to 70 copies per haploid genome) and intron copy ratios in selected isolates. Our results demonstrate that (a) IC1 group-I introns are not specific to V. longisporum within the Verticillium genus, (b) V. dahliae isolates of vegetative compatibility groups (VCGs) 4A and 6, which bear the novel intron at most of their rDNA repeats, are closely related, and (c) there is considerable intra-genomic heterogeneity for the presence or absence of introns among the ribosomal repeats. These findings underline that distributions of introns in the highly heterogeneous repetitive rDNA complex should always be verified with sensitive methods to avoid misleading conclusions for the phylogeny of fungi and other organisms

Structural and phylogenetic analysis of the rDNA intergenic spacer region of Verticillium dahliae

The nuclear ribosomal intergenic spacer (IGS) region was structurally analyzed and exploited for molecular discrimination and phylogenetic analysis of vegetative compatibility groups (VCGs) of Verticillium dahliae. A structural study of 201 available IGS sequences of the fungus was performed, and four classes of ubiquitous repetitive elements, organized in higher-order repetitive structures or composite blocks, were detected in a variable IGS subregion. This subregion was amplified from an international collection of 59 V. dahliae isolates covering all VCGs, together with nine representative V. albo-atrum and V. longisporum isolates, and sequenced. Structural and phylogenetic analyses of the sequences of this polymorphic IGS subregion were consistently informative and allowed the identification of two main lineages in V. dahliae, that is, clade I including VCGs 1A, 1B, 2A, 4B, and 3 and clade II containing VCGs 2B, 4A, and 6. Analysis of IGS sequences proved a highly suitable molecular tool for (a) rapid interspecific differentiation, (b) intraspecific discrimination among VCGs of V. dahliae, facilitating high-throughput VCG confirmation and prediction/profiling, and (c) phylogenetic analysis within and among V. dahliae VCGs

Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): Implications for the evolution of Amazonian landscapes during the Quaternary

© 2018 John Wiley & Sons Ltd Aim: To test the importance of alternative diversification drivers and biogeographical processes for the evolution of Amazonian upland forest birds through a densely sampled analysis of diversification of the endemic Amazonian genus Rhegmatorhina at multiple taxonomic and temporal scales. Location: Amazonia. Taxon: Antbirds (Thamnophilidae). Methods: We sequenced four mtDNA and nuclear gene regions of 120 individuals from 50 localities representing all recognized species and subspecies of the genus. We performed molecular phylogenetic analyses using both gene tree and species tree methods, molecular dating analysis and estimated population demographic history and gene flow. Results: Dense sampling throughout the distribution of Rhegmatorhina revealed that the main Amazonian rivers delimit the geographic distribution of taxa as inferred from mtDNA lineages. Molecular phylogenetic analyses resulted in a strongly supported phylogenetic hypothesis for the genus, with two main clades currently separated by the Madeira River. Molecular dating analysis indicated diversification during the Quaternary. Reconstruction of recent demographic history of populations revealed a trend for population expansion in eastern Amazonia and stability in the west. Estimates of gene flow corroborate the possibility that migration after divergence had some influence on the current patterns of diversity. Main Conclusions: Based on broad-scale sampling, a clarification of taxonomic boundaries, and strongly supported phylogenetic relationships, we confirm that, first, mitochondrial lineages within this upland forest Amazonian bird genus agree with spatial patterns known for decades based on phenotypes, and second, that most lineages are geographically delimited by the large Amazonian rivers. The association between past demographic changes related to palaeoclimatic cycles and the historically varying strength and size of rivers as barriers to dispersal may be the path to the answer to the long-standing question of identifying the main drivers of Amazonian diversification

Enhanced statistical stability in coherent interferometric imaging

http://iopscience.iop.org/0266-5611/International audienc

Global sea turtle conservation successes

We document a tendency for published estimates of population size in sea turtles to be increasing rather than decreasing across the globe. To examine the population status of the seven species of sea turtle globally, we obtained 299 time series of annual nesting abundance with a total of 4417 annual estimates. The time series ranged in length from 6 to 47 years (mean, 16.2 years). When levels of abundance were summed within regional management units (RMUs) for each species, there were upward trends in 12 RMUs versus downward trends in 5 RMUs. This prevalence of more upward than downward trends was also evident in the individual time series, where we found 95 significant increases in abundance and 35 significant decreases. Adding to this encouraging news for sea turtle conservation, we show that even small sea turtle populations have the capacity to recover, that is, Allee effects appear unimportant. Positive trends in abundance are likely linked to the effective protection of eggs and nesting females, as well as reduced bycatch. However, conservation concerns remain, such as the decline in leatherback turtles in the Eastern and Western Pacific. Furthermore, we also show that, often, time series are too short to identify trends in abundance. Our findings highlight the importance of continued conservation and monitoring efforts that underpin this global conservation success story

Tau deletion prevents stress-induced dendritic atrophy in prefrontal cortex: role of synaptic mitochondria

Tau protein in dendrites and synapses has been recently implicated in synaptic degeneration and neuronal malfunction. Chronic stress, awell-known inducer of neuronal/synaptic atrophy, triggers hyperphosphorylation of Tau protein and cognitive deficits. However, the cause–effect relationship between these events remains to be established. To test the involvement of Tau in stress-induced impairments of cognition,we investigated the impact of stress on cognitive behavior, neuronal structure, and the synaptic proteome in the prefrontal cortex (PFC) of Tau knock-out (Tau-KO) and wild-type (WT) mice. Whereas exposure to chronic stress resulted in atrophy of apical dendrites and spine loss in PFC neurons as well as significant impairments in working memory in WT mice, such changes were absent in Tau-KO animals. Quantitative proteomic analysis of PFC synaptosomal fractions, combined with transmission electron microscopy analysis, suggested a prominent role for mitochondria in the regulation of the effects of stress. Specifically, chronically stressed animals exhibit Tau-dependent alterations in the levels of proteins involved in mitochondrial transport and oxidative phosphorylation aswell as in the synaptic localization of mitochondria in PFC. These findings provide evidence for a causal role of Tau in mediating stress-elicited neuronal atrophy and cognitive impairment and indicate that Tau may exert its effects through synaptic mitochondria.This work was funded by the Portuguese Foundation for Science & Technology (FCT, grant number NMC-113934 to I.S.), the EU Consortium Switchbox (grant number Health-FP7-2010-259772 to O.F.X.A. and N.S.), the Deutsche Forschungsgemeinschaft (grant number FI 1895/1-1 to M.D.F.) and the Max Planck Society (M.D.F., G.M., C.W.T., and O.F.X.A.). In addition, this workwas also co-financed by the Portuguese North Regional Operational Program (ON.2 – O Novo Norte) under the National Strategic Reference Framework (QREN), through the European Regional Development Fund (FEDER) (N.S.). S.L. and I.S. are holders of FCT Fellowships. J.V-S. is a recipient of a PhD fellowship (PD/ BD/105938/2014) of the University of Minho MD/PhD Program funded by FCT.info:eu-repo/semantics/publishedVersio

A novel heuristic algorithm for the modeling and risk assessment of the covid-19 pandemic phenomenon

The modeling and risk assessment of a pandemic phenomenon such as COVID-19 is an important and complicated issue in epidemiology, and such an attempt is of great interest for public health decision-making. To this end, in the present study, based on a recent heuristic algorithm proposed by the authors, the time evolution of COVID-19 is investigated for six different countries/states, namely New York, California, USA, Iran, Sweden and UK. The number of COVID-19-related deaths is used to develop the proposed heuristic model as it is believed that the predicted number of daily deaths in each country/state includes information about the quality of the health system in each area, the age distribution of population, geographical and environmental factors as well as other conditions. Based on derived predicted epidemic curves, a new 3D-epidemic surface is proposed to assess the epidemic phenomenon at any time of its evolution. This research highlights the potential of the proposed model as a tool which can assist in the risk assessment of the COVID-19. Mapping its development through 3D-epidemic surface can assist in revealing its dynamic nature as well as differences and similarities among different districts