HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research

BACKGROUND: Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distributed in differently organised databases and web sites not well integrated among them. Moreover it is not generally possible for the user to submit and contemporarily analyse its own data comparing them with the content of a given database, both for population genetics and mitochondrial disease data. RESULTS: HmtDB is a well-integrated web-based human mitochondrial bioinformatic resource aimed at supporting population genetics and mitochondrial disease studies, thanks to a new approach based on site-specific nucleotide and aminoacid variability estimation. HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatic tools, able to produce site-specific variability data and to automatically characterize newly sequenced human mitochondrial genomes. A query system for the retrieval of genomes and a web submission tool for the annotation of new genomes have been designed and will soon be implemented. The first release contains 1255 fully annotated human mitochondrial genomes. Nucleotide site-specific variability data and multialigned genomes can be downloaded. Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the 1255 human genomes and 60 mammalian species are also available. HmtDB is freely available, upon registration, at . CONCLUSION: The HmtDB project will contribute towards completing and/or refining haplogroup classification and revealing the real pathogenic potential of mitochondrial mutations, on the basis of variability estimation

Oxygen stable isotope analyses on ameghinomya antiqua shells: A promising tool for palaeoenvironmental reconstruction along the quaternary patagonian Argentina coast?

There are only a few data concerning the Quaternary climate fluctuations in the marine environments of the Atlantic Patagonian coast. In this regard, the aragonitic shell of the Ameghinomya antiqua bivalve offers the possibility to study the climate variability and the seasonal cycles of sea water temperature in the region at different geological times. We compared oxygen isotopic profiles along the shell-growth axis on four well-preserved A. antiqua bivalves collected from marine coastal deposits of Marine Isotope Stage (MIS) 7, MIS 5, Holocene (7.284 ±140 yr cal BP), and from the present-day active beach of Bahia Bustamante (Patagonia Argentina). Shell ontogeny was determined through the annual growth lines recorded along the external region of the shell, and was also verified by cross-section analyses. The fossil bivalves were around 15 years old, while the Present day shell was 10 years old. When the modern climatic data available are compared, the higher δ18Oshell values represent the cold season, while the lower δ18Oshell values indicate the warm season. The δ18Oshell ranges indicate different environmental conditions and seasonal temperature variations between specimens. By assuming, a constant δ18Ow calculated with the limited environmental data available, superficial seawater temperatures are estimated from the specimens. These paleotemperatures may overestimate water temperatures, and shell formation seems to occur with an offset from expected oxygen isotopic equilibrium with the water in which they lived. Meanwhile, A. antiqua shells are suitable bioarchives for the comparison of seasonal patterns throughout the Quaternary, thus constituting another proxy for the evaluation of paleoclimatic and paleoenvironmental changes in the Patagonia region.Fil: Boretto, Gabriella Margherita. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Consoloni, Ilaria. Università degli Studi di Pisa; ItaliaFil: Morán, Ariana Gisela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Regattieri, Eleonora. Consiglio Nazionale delle Ricerche; ItaliaFil: Gordillo, Sandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Fucks, Enrique Eduardo. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; ArgentinaFil: Zanchetta, Giovanni. Università degli Studi di Pisa; ItaliaFil: Dallai, Luigi. Istituto di Geoscienze e Georisorse; Itali

Stable oxygen and carbon isotope composition of holocene mytilidae from the camarones coast (Chubut, argentina): Palaeoceanographic implications

The stable isotope composition of living and of Holocene Mytilidae shells was measured in the area of Camarones (Chubut, Argentina). The most striking results were the high δ18 O values measured in samples older than ca. 6.1 cal ka BP. In the younger samples, the δ18 O values remained substantially stable and similar to those of living specimens. Analysis of the data revealed the possibility for this isotopic shift to be driven mainly by changes in temperature probably accompanied by minor changes in salinity, suggesting cooler seawater before 6.1 cal ka BP, with a maximum possible temperature shift of ca. 5◦ C. A possible explanation of this change can be related to a northward position of the confluence zone of the Falkland and Brazilian currents. This is consistent with the data obtained in marine cores, which indicate a northerly position of the confluence in the first half of the Holocene. Our data are also in line with the changes in wind strength and position of the Southern Westerlies Wind, as reconstructed in terrestrial proxies from the Southernmost Patagonia region.Fil: Boretto, Gabriella Margherita. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Zanchetta, Giovanni. Università degli Studi di Pisa; Italia. Istituto di Geologia Ambientale e Geoingegneria; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Consoloni, Ilaria. Università degli Studi di Pisa; ItaliaFil: Baneschi, Ilaria. Istituto di Geoscienze e Georisorse; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Guidi, Massimo. Istituto di Geoscienze e Georisorse; Italia. Consiglio Nazionale delle Ricerche; ItaliaFil: Isola, Ilaria. Istituto Nazione di Geofisica e Vulcanologia; ItaliaFil: Bini, Monica. Consiglio Nazionale delle Ricerche; Italia. Università degli Studi di Pisa; ItaliaFil: Ragaini, Luca. Università degli Studi di Pisa; ItaliaFil: Terrasi, Filippo. Seconda Universita Degli Studi Di Napoli; ItaliaFil: Regattieri, Eleonora. Istituto di Geoscienze e Georisorse; ItaliaFil: Dallai, Luigi. Istituto di Geoscienze e Georisorse; Italia. Istituto Nazione di Geofisica e Vulcanologia; Italia. Università degli studi di Roma "La Sapienza"; Itali

A Global Human Settlement Layer from optical high resolution imagery - Concept and first results

A general framework for processing of high and very-high resolution imagery for creating a Global Human Settlement Layer (GHSL) is presented together with a discussion on the results of the first operational test of the production workflow. The test involved the mapping of 24.3 millions of square kilometres of the Earth surface spread over four continents, corresponding to an estimated population of 1.3 billion of people in 2010. The resolution of the input image data ranges from 0.5 to 10 meters, collected by a heterogeneous set of platforms including satellite SPOT (2 and 5), CBERS-2B, RapidEye (2 and 4), WorldView (1 and 2), GeoEye-1, QuickBird-2, Ikonos-2, and airborne sensors. Several imaging modes were tested including panchromatic, multispectral and pan-sharpened images. A new fully automatic image information extraction, generalization and mosaic workflow is presented that is based on multiscale textural and morphological image features extraction. New image feature compression and optimization are introduced, together with new learning and classification techniques allowing for the processing of HR/VHR image data using low-resolution thematic layers as reference. A new systematic approach for quality control and validation allowing global spatial and thematic consistency checking is proposed and applied. The quality of the results are discussed by sensor, by band, by resolution, and eco-regions. Critical points, lessons learned and next steps are highlighted.JRC.G.2-Global security and crisis managemen

Community pre-Release of GHS Data Package (GHS CR2018) in support to the GEO Human Planet Initiative

The GEO Human Planet Initiative is committed to developing a new generation of measurements and information products that provide new scientific evidence and a comprehensive understanding of the human presence on the planet and that can support global policy processes with agreed, actionable and goal-driven metrics. The Human Planet Initiative relies on a core set of partners committed in coordinating the production of the global settlement spatial baseline data, and an enlarged community of partners developing experimental activities on using the new baseline data for derived post-2015 indicators. One of the core partners is the European Commission, Directorate General Joint Research Centre, Global Human Settlement Layer project. The Global Human Settlement Layer project produces global spatial information, evidence-based analytics, and knowledge describing the human presence in the planet. This document describes the Community pre-Release of the GHSL Data Package 2018 - GHS CR2018 - created for the members of the GEO Human Planet Initiative. The data in this data package have the purpose to gather feedbacks from the GEO Human Planet Initiative community, in preparation for the public release of these data. Disclaimer: the data included in the Community Pre-Release of the GHSL Data Package 2018 should be considered preliminary and not yet validated. It may differ substantially with the data that will be included in the public final Release 2018. The JRC data are provided "as is" and "as available" in conformity with the JRC Data Policy1 and the Commission Decision on reuse of Commission documents (2011/833/EU). Although the JRC guarantees its best effort in assuring quality when publishing these data, it provides them without any warranty of warranty of any kind, either express or implied, including, but not limited to, any implied warranty against infringement of third parties' property rights, or merchantability, integration, satisfactory quality and fitness for a particular purpose. The JRC has no obligation to provide technical support or remedies for the data. The JRC does not represent or warrant that the data will be error free or uninterrupted, or that all non-conformities can or will be corrected, or that any data are accurate or complete, or that they are of a satisfactory technical or scientific quality. The JRC or as the case may be the European Commission shall not be held liable for any direct or indirect, incidental, consequential or other damages, including but not limited to the loss of data, loss of profits, or any other financial loss arising from the use of the JRC data, or inability to use them, even if the JRC is notified of the possibility of such damages.JRC.E.1-Disaster Risk Managemen

GHSL Data Package 2019

The Global Human Settlement Layer (GHSL) produces new global spatial information, evidence-based analytics and knowledge describing the human presence on the planet Earth. The GHSL operates in a fully open and free data and methods access policy, building the knowledge supporting the definition, the public discussion and the implementation of European policies and the international frameworks as the 2030 Development Agenda and the related thematic agreements. The GHSL supports the GEO Human Planet Initiative (HPI) that is committed to developing a new generation of measurements and information products providing new scientific evidence and a comprehensive understanding of the human presence on the planet and that can support global policy processes with agreed, actionable and goal-driven metrics. The Human Planet Initiative relies on a core set of partners committed in coordinating the production of the global settlement spatial baseline data. One of the core partners is the European Commission, Directorate General Joint Research Centre, Global Human Settlement Layer project. The Global Human Settlement Layer project produces global spatial information, evidence-based analytics, and knowledge describing the human presence in the planet. This document describes the public release of the GHSL Data Package 2019 (GHS P2019).JRC.E.1-Disaster Risk Managemen

Description of the GHS Urban Centre Database 2015

The Global Human Settlement Layer Urban Centres Database (GHS-UCDB) is the most complete database on cities to date, publicly released as an open and free dataset - GHS STAT UCDB2015MT GLOBE R2019A V1.0. The database represents the global status on Urban Centres in 2015 by offering cities location, their extent (surface, shape), and describing each city with a set of geographical, socio-economic and environmental attributes, many of them going back 25 or even 40 years in time. Urban Centres are defined in a consistent way across geographical locations and over time, applying the “Global Definition of Cities and Settlements” developed by the European Union to the Global Human Settlement Layer Built-up (GHS-BUILT) areas and Population (GHS-POP) grids. This report contains the description of the dimensions and the derived attributes that characterise the Urban Centres in the database. The document includes notes about methodology and sources. The GHS-UCDB contains information for more than 10,000 Urban Centres and it is the baseline data of the analytical results presented in the Atlas of the Human Planet 2018.JRC.E.1-Disaster Risk Managemen

The RESET project: constructing a European tephra lattice for refined synchronisation of environmental and archaeological events during the last c. 100 ka

This paper introduces the aims and scope of the RESET project (. RESponse of humans to abrupt Environmental Transitions), a programme of research funded by the Natural Environment Research Council (UK) between 2008 and 2013; it also provides the context and rationale for papers included in a special volume of Quaternary Science Reviews that report some of the project's findings. RESET examined the chronological and correlation methods employed to establish causal links between the timing of abrupt environmental transitions (AETs) on the one hand, and of human dispersal and development on the other, with a focus on the Middle and Upper Palaeolithic periods. The period of interest is the Last Glacial cycle and the early Holocene (c. 100-8 ka), during which time a number of pronounced AETs occurred. A long-running topic of debate is the degree to which human history in Europe and the Mediterranean region during the Palaeolithic was shaped by these AETs, but this has proved difficult to assess because of poor dating control. In an attempt to move the science forward, RESET examined the potential that tephra isochrons, and in particular non-visible ash layers (cryptotephras), might offer for synchronising palaeo-records with a greater degree of finesse. New tephrostratigraphical data generated by the project augment previously-established tephra frameworks for the region, and underpin a more evolved tephra 'lattice' that links palaeo-records between Greenland, the European mainland, sub-marine sequences in the Mediterranean and North Africa. The paper also outlines the significance of other contributions to this special volume: collectively, these illustrate how the lattice was constructed, how it links with cognate tephra research in Europe and elsewhere, and how the evidence of tephra isochrons is beginning to challenge long-held views about the impacts of environmental change on humans during the Palaeolithic. © 2015 Elsevier Ltd.RESET was funded through Consortium Grants awarded by the Natural Environment Research Council, UK, to a collaborating team drawn from four institutions: Royal Holloway University of London (grant reference NE/E015905/1), the Natural History Museum, London (NE/E015913/1), Oxford University (NE/E015670/1) and the University of Southampton, including the National Oceanography Centre (NE/01531X/1). The authors also wish to record their deep gratitude to four members of the scientific community who formed a consultative advisory panel during the lifetime of the RESET project: Professor Barbara Wohlfarth (Stockholm University), Professor Jørgen Peder Steffensen (Niels Bohr Institute, Copenhagen), Dr. Martin Street (Romisch-Germanisches Zentralmuseum, Neuwied) and Professor Clive Oppenheimer (Cambridge University). They provided excellent advice at key stages of the work, which we greatly valued. We also thank Jenny Kynaston (Geography Department, Royal Holloway) for construction of several of the figures in this paper, and Debbie Barrett (Elsevier) and Colin Murray Wallace (Editor-in-Chief, QSR) for their considerable assistance in the production of this special volume.Peer Reviewe