Using automated vegetation cover estimation from close-range photogrammetric point clouds to compare vegetation location properties in mountain terrain

In this paper we present a low-cost approach to mapping vegetation cover by means of high-resolution close-range terrestrial photogrammetry. A total of 249 clusters of nine 1 m2 plots each, arranged in a 3 × 3 grid, were set up on 18 summits in Mediterranean mountain regions and in the Alps to capture images for photogrammetric processing and in-situ vegetation cover estimates. This was done with a hand-held pole-mounted digital single-lens reflex (DSLR) camera. Low-growing vegetation was automatically segmented using high-resolution point clouds. For classifying vegetation we used a two-step semi-supervised Random Forest approach. First, we applied an expert-based rule set using the Excess Green index (ExG) to predefine non-vegetation and vegetation points. Second, we applied a Random Forest classifier to further enhance the classification of vegetation points using selected topographic parameters (elevation, slope, aspect, roughness, potential solar irradiation) and additional vegetation indices (Excess Green Minus Excess Red (ExGR) and the vegetation index VEG). For ground cover estimation the photogrammetric point clouds were meshed using Screened Poisson Reconstruction. The relative influence of the topographic parameters on the vegetation cover was determined with linear mixed-effects models (LMMs). Analysis of the LMMs revealed a high impact of elevation, aspect, solar irradiation, and standard deviation of slope. The presented approach goes beyond vegetation cover values based on conventional orthoimages and in-situ vegetation cover estimates from field surveys in that it is able to differentiate complete 3D surface areas, including overhangs, and can distinguish between vegetation-covered and other surfaces in an automated manner. The results of the Random Forest classification confirmed it as suitable for vegetation classification, but the relative feature importance values indicate that the classifier did not leverage the potential of the included topographic parameters. In contrast, our application of LMMs utilized the topographic parameters and was able to reveal dependencies in the two biomes, such as elevation and aspect, which were able to explain between 87% and 92.5% of variance

Updating known distribution models for forecasting climate change impact on endangered species

To plan endangered species conservation and to design adequate management programmes, it is necessary to predict their distributional response to climate change, especially under the current situation of rapid change. However, these predictions are customarily done by relating de novo the distribution of the species with climatic conditions with no regard of previously available knowledge about the factors affecting the species distribution. We propose to take advantage of known species distribution models, but proceeding to update them with the variables yielded by climatic models before projecting them to the future. To exemplify our proposal, the availability of suitable habitat across Spain for the endangered Bonelli’s Eagle (Aquila fasciata) was modelled by updating a pre-existing model based on current climate and topography to a combination of different general circulation models and Special Report on Emissions Scenarios. Our results suggested that the main threat for this endangered species would not be climate change, since all forecasting models show that its distribution will be maintained and increased in mainland Spain for all the XXI century. We remark on the importance of linking conservation biology with distribution modelling by updating existing models, frequently available for endangered species, considering all the known factors conditioning the species’ distribution, instead of building new models that are based on climate change variables only.Ministerio de Ciencia e Innovación and FEDER (project CGL2009-11316/BOS

Circulating extracellular vesicles release oncogenic miR-424 in experimental models and patients with aggressive prostate cancer

Extracellular vesicles (EVs) are relevant means for transferring signals across cells and facilitate propagation of oncogenic stimuli promoting disease evolution and metastatic spread in cancer patients. Here, we investigated the release of miR-424 in circulating small EVs or exosomes from prostate cancer patients and assessed the functional implications in multiple experimental models. We found higher frequency of circulating miR-424 positive EVs in patients with metastatic prostate cancer compared to patients with primary tumors and BPH. Release of miR-424 in small EVs was enhanced in cell lines (LNCaPabl), transgenic mice (Pb-Cre4;Ptenflox/flox;Rosa26ERG/ERG) and patient-derived xenograft (PDX) models of aggressive disease. EVs containing miR-424 promoted stem-like traits and tumor-initiating properties in normal prostate epithelial cells while enhanced tumorigenesis in transformed prostate epithelial cells. Intravenous administration of miR-424 positive EVs to mice, mimicking blood circulation, promoted miR-424 transfer and tumor growth in xenograft models. Circulating miR-424 positive EVs from patients with aggressive primary and metastatic tumors induced stem-like features when supplemented to prostate epithelial cells. This study establishes that EVs-mediated transfer of miR-424 across heterogeneous cell populations is an important mechanism of tumor self-sustenance, disease recurrence and progression. These findings might indicate novel approaches for the management and therapy of prostate cancer

Endogenous myoglobin in human breast cancer is a hallmark of luminal cancer phenotype

BACKGROUND: We aimed to clarify the incidence and the clinicopathological value of non-muscle myoglobin (Mb) in a large cohort of non-invasive and invasive breast cancer cases. METHODS: Matched pairs of breast tissues from 10 patients plus 17 breast cell lines were screened by quantitative PCR for Mb mRNA. In addition, 917 invasive and 155 non-invasive breast cancer cases were analysed by immunohistochemistry for Mb expression and correlated to clinicopathological parameters and basal molecular characteristics including oestrogen receptor-alpha (ERalpha)/progesteron receptor (PR)/HER2, fatty acid synthase (FASN), hypoxia-inducible factor-1alpha (HIF-1alpha), HIF-2alpha, glucose transporter 1 (GLUT1) and carbonic anhydrase IX (CAIX). The spatial relationship of Mb and ERalpha or FASN was followed up by double immunofluorescence. Finally, the effects of estradiol treatment and FASN inhibition on Mb expression in breast cancer cells were analysed. RESULTS: Myoglobin mRNA was found in a subset of breast cancer cell lines; in microdissected tumours Mb transcript was markedly upregulated. In all, 71% of tumours displayed Mb protein expression in significant correlation with a positive hormone receptor status and better prognosis. In silico data mining confirmed higher Mb levels in luminal-type breast cancer. Myoglobin was also correlated to FASN, HIF-2alpha and CAIX, but not to HIF-1alpha or GLUT1, suggesting hypoxia to participate in its regulation. Double immunofluorescence showed a cellular co-expression of ERalpha or FASN and Mb. In addition, Mb levels were modulated on estradiol treatment and FASN inhibition in a cell model. CONCLUSION: We conclude that in breast cancer, Mb is co-expressed with ERalpha and co-regulated by oestrogen signalling and can be considered a hallmark of luminal breast cancer phenotype. This and its possible new role in fatty acid metabolism may have fundamental implications for our understanding of Mb in solid tumours

Ecological Indicator Values for Europe (EIVE) 1.0

Aims: To develop a consistent ecological indicator value system for Europe for five of the main plant niche dimensions: soil moisture (M), soil nitrogen (N), soil reaction (R), light (L) and temperature (T). Study area: Europe (and closely adjacent regions). Methods: We identified 31 indicator value systems for vascular plants in Europe that contained assessments on at least one of the five aforementioned niche dimensions. We rescaled the indicator values of each dimension to a continuous scale, in which 0 represents the minimum and 10 the maximum value present in Europe. Taxon names were harmonised to the Euro+Med Plantbase. For each of the five dimensions, we calculated European values for niche position and niche width by combining the values from the individual EIV systems. Using T values as an example, we externally validated our European indicator values against the median of bioclimatic conditions for global occurrence data of the taxa. Results: In total, we derived European indicator values of niche position and niche width for 14,835 taxa (14,714 for M, 13,748 for N, 14,254 for R, 14,054 for L, 14,496 for T). Relating the obtained values for temperature niche position to the bioclimatic data of species yielded a higher correlation than any of the original EIV systems (r = 0.859). The database: The newly developed Ecological Indicator Values for Europe (EIVE) 1.0, together with all source systems, is available in a flexible, harmonised open access database. Conclusions: EIVE is the most comprehensive ecological indicator value system for European vascular plants to date. The uniform interval scales for niche position and niche width provide new possibilities for ecological and macroecological analyses of vegetation patterns. The developed workflow and documentation will facilitate the future release of updated and expanded versions of EIVE, which may for example include the addition of further taxonomic groups, additional niche dimensions, external validation or regionalisation

Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors.

It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations affecting the substrate-recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancers. The therapeutic implications of these mutations remain incompletely understood. Here we analyzed changes in the ubiquitin landscape induced by endometrial cancer-associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP-CUL3 substrates that are preferentially degraded by endometrial cancer-associated SPOP mutants. The resulting reduction of BET protein levels sensitized cancer cells to BET inhibitors. Conversely, prostate cancer-specific SPOP mutations resulted in impaired degradation of BETs, promoting their resistance to pharmacologic inhibition. These results uncover an oncogenomics paradox, whereby mutations mapping to the same domain evoke opposing drug susceptibilities. Specifically, we provide a molecular rationale for the use of BET inhibitors to treat patients with endometrial but not prostate cancer who harbor SPOP mutations

The genomic evolution of human prostate cancer.

Prostate cancers are highly prevalent in the developed world, with inheritable risk contributing appreciably to tumour development. Genomic heterogeneity within individual prostate glands and between patients derives predominantly from structural variants and copy-number aberrations. Subtypes of prostate cancers are being delineated through the increasing use of next-generation sequencing, but these subtypes are yet to be used to guide the prognosis or therapeutic strategy. Herein, we review our current knowledge of the mutational landscape of human prostate cancer, describing what is known of the common mutations underpinning its development. We evaluate recurrent prostate-specific mutations prior to discussing the mutational events that are shared both in prostate cancer and across multiple cancer types. From these data, we construct a putative overview of the genomic evolution of human prostate cancer

Vegetation of Europe: hierarchical floristic classification system of vascular plant, bryophyte, lichen, and algal communities

Vegetation classification consistent with the Braun-Blanquet approach is widely used in Europe for applied vegetation science, conservation planning and land management. During the long history of syntaxonomy, many concepts and names of vegetation units have been proposed, but there has been no single classification system integrating these units. Here we (1) present a comprehensive, hierarchical, syntaxonomic system of alliances, orders and classes of Braun-Blanquet syntaxonomy for vascular plant, bryophyte and lichen, and algal communities of Europe; (2) briefly characterize in ecological and geographic terms accepted syntaxonomic concepts; (3) link available synonyms to these accepted concepts; and (4) provide a list of diagnostic species for all classes. Location: European mainland, Greenland, Arctic archipelagos (including Iceland, Svalbard, Novaya Zemlya), Canary Islands, Madeira, Azores, Caucasus, Cyprus. Methods: We evaluated approximately 10 000 bibliographic sources to create a comprehensive list of previously proposed syntaxonomic units. These units were evaluated by experts for their floristic and ecological distinctness, clarity of geographic distribution and compliance with the nomenclature code. Accepted units were compiled into three systems of classes, orders and alliances (EuroVegChecklist, EVC) for communities dominated by vascular plants (EVC1), bryophytes and lichens (EVC2) and algae (EVC3). Results: EVC1 includes 109 classes, 300 orders and 1108 alliances; EVC2 includes 27 classes, 53 orders and 137 alliances, and EVC3 includes 13 classes, 24 orders and 53 alliances. In total 13 448 taxa were assigned as indicator species to classes of EVC1, 2087 to classes of EVC2 and 368 to classes of EVC3. Accepted syntaxonomic concepts are summarized in a series of appendices, and detailed information on each is accessible through the software tool EuroVegBrowser. Conclusions: This paper features the first comprehensive and critical account of European syntaxa and synthesizes more than 100 yr of classification effort by European phytosociologists. It aims to document and stabilize the concepts and nomenclature of syntaxa for practical uses, such as calibration of habitat classification used by the European Union, standardization of terminology for environmental assessment, management and conservation of nature areas, landscape planning and education. The presented classification systems provide a baseline for future development and revision of European syntaxonomy.info:eu-repo/semantics/publishedVersio

Ellenberg-type indicator values for European vascular plant species

Aims: Ellenberg-type indicator values are expert-based rankings of plant species according to their ecological optima on main environmental gradients. Here we extend the indicator-value system proposed by Heinz Ellenberg and co-authors for Central Europe by incorporating other systems of Ellenberg-type indicator values (i.e., those using scales compatible with Ellenberg values) developed for other European regions. Our aim is to create a harmonized data set of Ellenberg-type indicator values applicable at the European scale. Methods: We collected European data sets of indicator values for vascular plants and selected 13 data sets that used the nine-, ten- or twelve-degree scales defined by Ellenberg for light, temperature, moisture, reaction, nutrients and salinity. We compared these values with the original Ellenberg values and used those that showed consistent trends in regression slope and coefficient of determination. We calculated the average value for each combination of species and indicator values from these data sets. Based on species’ co-occurrences in European vegetation plots, we also calculated new values for species that were not assigned an indicator value. Results: We provide a new data set of Ellenberg-type indicator values for 8908 European vascular plant species (8168 for light, 7400 for temperature, 8030 for moisture, 7282 for reaction, 7193 for nutrients, and 7507 for salinity), of which 398 species have been newly assigned to at least one indicator value. Conclusions: The newly introduced indicator values are compatible with the original Ellenberg values. They can be used for large-scale studies of the European flora and vegetation or for gap-filling in regional data sets. The European indicator values and the original and taxonomically harmonized regional data sets of Ellenberg-type indicator values are available in the Supporting Information and the Zenodo repository