Forgotten forests - issues and prospects in biome mapping using Seasonally Dry Tropical Forests as a case study

<p>Abstract</p> <p>Background</p> <p>South America is one of the most species diverse continents in the world. Within South America diversity is not distributed evenly at both local and continental scales and this has led to the recognition of various areas with unique species assemblages. Several schemes currently exist which divide the continental-level diversity into large species assemblages referred to as biomes. Here we review five currently available biome maps for South America, including the WWF Ecoregions, the Americas basemap, the Land Cover Map of South America, Morrone's Biogeographic regions of Latin America, and the Ecological Systems Map. The comparison is performed through a case study on the Seasonally Dry Tropical Forest (SDTF) biome using herbarium data of habitat specialist species.</p> <p>Results</p> <p>Current biome maps of South America perform poorly in depicting SDTF distribution. The poor performance of the maps can be attributed to two main factors: (1) poor spatial resolution, and (2) poor biome delimitation. Poor spatial resolution strongly limits the use of some of the maps in GIS applications, especially for areas with heterogeneous landscape such as the Andes. Whilst the Land Cover Map did not suffer from poor spatial resolution, it showed poor delimitation of biomes. The results highlight that delimiting structurally heterogeneous vegetation is difficult based on remote sensed data alone. A new refined working map of South American SDTF biome is proposed, derived using the Biome Distribution Modelling (BDM) approach where georeferenced herbarium data is used in conjunction with bioclimatic data.</p> <p>Conclusions</p> <p>Georeferenced specimen data play potentially an important role in biome mapping. Our study shows that herbarium data could be used as a way of ground-truthing biome maps <it>in silico</it>. The results also illustrate that herbarium data can be used to model vegetation maps through predictive modelling. The BDM approach is a promising new method in biome mapping, and could be particularly useful for mapping poorly known, fragmented, or degraded vegetation. We wish to highlight that biome delimitation is not an exact science, and that transparency is needed on how biomes are used as study units in macroevolutionary and ecological research.</p

Fine-grained Recognition in the Noisy Wild: Sensitivity Analysis of Convolutional Neural Networks Approaches

In this paper, we study the sensitivity of CNN outputs with respect to image transformations and noise in the area of fine-grained recognition. In particular, we answer the following questions (1) how sensitive are CNNs with respect to image transformations encountered during wild image capture?; (2) how can we predict CNN sensitivity?; and (3) can we increase the robustness of CNNs with respect to image degradations? To answer the first question, we provide an extensive empirical sensitivity analysis of commonly used CNN architectures (AlexNet, VGG19, GoogleNet) across various types of image degradations. This allows for predicting CNN performance for new domains comprised by images of lower quality or captured from a different viewpoint. We also show how the sensitivity of CNN outputs can be predicted for single images. Furthermore, we demonstrate that input layer dropout or pre-filtering during test time only reduces CNN sensitivity for high levels of degradation. Experiments for fine-grained recognition tasks reveal that VGG19 is more robust to severe image degradations than AlexNet and GoogleNet. However, small intensity noise can lead to dramatic changes in CNN performance even for VGG19.Comment: BMVC 2016 Pape

Large-scale phylogeography of the disjunct Neotropical tree species Schizolobium parahyba (Fabaceae-Caesalpinioideae).

Neotropical rainforests exhibit high levels of endemism and diversity. Although the evolutionary genetics of plant diversification has garnered increased interest, phylogeographic studies of widely distributed species remain scarce. Here we describe chloroplast and nuclear variation patterns in Schizolobium parahyba (Fabaceae), a widespread tree in Neotropical rainforests that harbor two varieties with a disjunct distribution. Chloroplast and nuclear sequence analyses yielded 21 and 4 haplotypes, respectively. Two genetic diversity centers that correlate with the two known varieties were identified: the Southeastern Atlantic forest and the Amazonian basin. In contrast, the populations from southern and northeastern Atlantic forests and Andean-Central American forests exhibited low levels of genetic diversity and divergent haplotypes, likely related to historical processes that impact the flora and fauna in these regions, such as a founder's effect after dispersion and demographic expansion. Phylogeographic and demographic patterns suggest that episodes of genetic isolation and dispersal events have shaped the evolutionary history for this species, and different patterns have guided the evolution of S. parahyba. Moreover, the results of this study suggest that the dry corridor formed by Cerrado and Caatinga ecoregions and the Andean uplift acted as barriers to this species' gene flow, a picture that may be generalized to most of the plant biodiversity tropical woodlands and forests. These results also reinforce the importance of evaluating multiple genetic markers for a more comprehensive understanding of population structure and history. Our results provide insight into the conservation efforts and ongoing work on the genetics of population divergence and speciation in these Neotropical rainforests. (C) 2012 Elsevier Inc. All rights reserved

Gut-Homing Conventional Plasmablasts and CD27− Plasmablasts Elicited after a Short Time of Exposure to an Oral Live-Attenuated Shigella Vaccine Candidate in Humans

Currently, there is no licensed Shigella vaccine; however, various promising live-attenuated vaccine candidates have emerged, including CVD1208S (ΔguaBA, Δset, Δsen S. flexneri 2a), which was shown to be safe and immunogenic in Phase 1 clinical trials. Here, we report the immune responses elicited in an outpatient Phase 2 clinical trial in which subjects were vaccinated with CVD 1208S. Oral immunization with CVD 1208S elicited high anti-S. flexneri 2a LPS and IpaB antibody responses as well as an acute plasmablast (PB) infiltration in peripheral blood 7 days after immunization. PB sorted based on their expression of homing molecules confirmed that cells expressing integrin α4β7 alone or in combination with CD62L were responsible for antibody production (as measured by ELISpot). Furthermore, using high-color flow-cytometry, on day 7 after immunization, we observed the appearance of conventional PB (CPB, CD19(dim) CD20(−) CD27(+high) CD38(+high) CD3(−)), as well as a PB population that did not express CD27 (CD27(−) PB; pre-plasmablasts). The pattern of individual or simultaneous expression of homing markers (integrin α4β7, CD62L, CXCR3, and CXCR4) suggested that CPB cells homed preferentially to the inflamed gut mucosa. In contrast, ~50% CD27(−) PB cells appear to home to yet to be identified peripheral lymphoid organs or were in a transition state preceding integrin α4β7 upregulation. In sum, these observations demonstrate that strong immune responses, including distinct PB subsets with the potential to home to the gut and other secondary lymphoid organs, can be elicited after a short time of exposure to a shigella oral vaccine

New segregates from the Neotropical genus Stryphnodendron (Leguminosae, Caesalpinioideae, mimosoid clade)

Non-monophyly is a prominent issue in mimosoid legumes, even in some of the less speciose genera such as the neotropical genus Stryphnodendron. This genus includes 35 species occurring from Nicaragua to Southern Brazil mostly in humid forests and savannas. Previous taxonomic studies of Stryphnodendron have highlighted morphologically distinct groups within the genus, recognized by differences on leaves (number of pinnae and size of leaflets), inflorescences (a simple or compound thyrse), and fruit types (legume, nucoid legume or follicle). Recent phylogenetic analyses have confirmed the non-monophyly of Stryphnodendron, supporting the recognition of three independent and morphologically well-delimited genera. Here we re-circumscribe Stryphnodendron and propose the two new genera Gwilymia and Naiadendron. In addition, we also provide an updated taxonomic account of the closely related genus Microlobius, including the proposal of a lectotype for the single species in the genus

The validity and reliability of the CAMDEX-DS for assessing dementia in adults with Down syndrome in Brazil.

OBJECTIVE: Alzheimer's disease occurs at a higher prevalence and an earlier age in individuals with Down syndrome (DS) than typically developing individuals. However, diagnosing dementia in individuals with intellectual disability remains a challenge due to pre-existing cognitive deficits. The aim of this study was to investigate the validity and reliability of the Brazilian version of the Cambridge Examination for Mental Disorders of Older People with Down's syndrome and Others with Intellectual Disabilities (CAMDEX-DS) for individuals with DS. METHODS: Two psychiatrists, working independently, evaluated 92 adults with DS ≥ 30 years of age. The concurrent validity of the CAMDEX-DS was analyzed in relation to the gold standard of established international criteria. In a subgroup of 20 subjects, the concurrent validity of the CAMDEX-DS was analyzed in relation to an independent objective assessment of cognitive decline over three years. We analyzed the inter-rater reliability of cognitive assessment. RESULTS: The diagnostic accuracy of the CAMDEX-DS compared to the gold standard was 96.7%. CAMDEX-DS-based diagnosis was considered consistent with cognitive decline. The probability of a participant with dementia having cognitive decline was 83%. Inter-rater reliability for the participant assessment was good, with a kappa of > 0.8 for 93% of the CAMDEX-DS items. CONCLUSION: The CAMDEX-DS can be considered the first valid and reliable instrument for evaluating dementia in adults with DS in Brazil. Its use in such individuals could improve clinical practice and research

The Difference of Grammatical Error in Writing Recount Text Between Natural Science and Social Science Students

This study concerned on the difference of grammatical error in writing recount text between natural science and social science students. The objective of this study was to find out the difference of grammatical error in writing recount text between natural science and social science students. This research was conducted by using causal- comparative research. The subject of the study was the students of XI-IPA1 and XI- IPS1 of SMA Swasta Methodist Berastagi. The number of the samples was twenty eight. The techniques for data analysis were quantitative data. The t-result was 2,60 (bigger than t table 1,706). The conclusion is that there is a significant difference of grammatical error in writing recount text between natural science and social science students

The validity and reliability of the CAMDEX-DS for assessing dementia in adults with Down syndrome in Brazil.

OBJECTIVE: Alzheimer's disease occurs at a higher prevalence and an earlier age in individuals with Down syndrome (DS) than typically developing individuals. However, diagnosing dementia in individuals with intellectual disability remains a challenge due to pre-existing cognitive deficits. The aim of this study was to investigate the validity and reliability of the Brazilian version of the Cambridge Examination for Mental Disorders of Older People with Down's syndrome and Others with Intellectual Disabilities (CAMDEX-DS) for individuals with DS. METHODS: Two psychiatrists, working independently, evaluated 92 adults with DS ≥ 30 years of age. The concurrent validity of the CAMDEX-DS was analyzed in relation to the gold standard of established international criteria. In a subgroup of 20 subjects, the concurrent validity of the CAMDEX-DS was analyzed in relation to an independent objective assessment of cognitive decline over three years. We analyzed the inter-rater reliability of cognitive assessment. RESULTS: The diagnostic accuracy of the CAMDEX-DS compared to the gold standard was 96.7%. CAMDEX-DS-based diagnosis was considered consistent with cognitive decline. The probability of a participant with dementia having cognitive decline was 83%. Inter-rater reliability for the participant assessment was good, with a kappa of > 0.8 for 93% of the CAMDEX-DS items. CONCLUSION: The CAMDEX-DS can be considered the first valid and reliable instrument for evaluating dementia in adults with DS in Brazil. Its use in such individuals could improve clinical practice and research

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation

PREMISE Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the “tree of life” are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species‐rich and taxonomically challenging ingoids. METHODS We generated transcriptomes to select low‐copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference. We also evaluate gene tree support and conflict for key internodes and use phylogenetic network analysis to investigate phylogenetic signal across the ingoids. RESULTS Our selection of 964 nuclear genes greatly improves phylogenetic resolution across the mimosoid phylogeny and shows that the ingoid clade can be resolved into several well‐supported clades. However, nearly all loci show lack of phylogenetic signal for some of the deeper internodes within the ingoids. CONCLUSIONS Lack of resolution in the ingoid clade is most likely the result of hyperfast diversification, potentially causing a hard polytomy of six or seven lineages. The gene set for targeted sequencing presented here offers great potential to further enhance the phylogeny of mimosoids and the wider Caesalpinioideae with denser taxon sampling, to provide a framework for taxonomic reclassification, and to study the ingoid radiation