pinecone/core-2020-05-10-deduplication huggingface dataset:
Absolute geostrophic velocity inverted from World Ocean Atlas 2013 (WOAV13) with the P-vector method

The article of record as published may be found at http://dx.doi.org/10.1002/gdj3.31The World Ocean Atlas-2013 (WOAV13) dataset comprises 3D global gridded climatological fields of absolute geostrophic velocity inverted from WOA13 temperature and salinity fields using the P-vector method. It provides a climatological velocity field that is dynamically compatible to the WOA13 (T, S) fields. The WOAV13 has the same spatial resolution and temporal variation (annual, monthly, seasonal) as WOA13 (T, S) fields, but does not cover the equatorial zone (5°S–5°N) due to the geostrophic balance being the theoretical basis for the P-vector inverse method.Office of Naval Researc
Climatological diurnal variability in sea surface temperature characterized from drifting buoy data

Drifting buoy sea-surface temperature (SST) records have been used to characterize the diurnal variability of ocean temperature at a depth of order 20 cm. We use measurements covering the period 1986–2012 from the International Comprehensive Ocean-Atmosphere Data Set (ICOADS) version 2.5, which is a collection of marine surface observations that includes individual SST records from drifting buoys. Appropriately transformed, this dataset is well suited for estimation of the diurnal cycle, since many drifting buoys have high temporal coverage (many reports per day), and are globally distributed. For each drifter for each day, we compute the local-time daily SST variation relative to the local-time daily mean SST. Climatological estimates of subdaily SST variability are found by averaging across various strata of the data: in 10° latitudinal bands as well as globally; and stratified with respect to season, wind speed and cloud cover. A parameterization of the diurnal variability is fitted as a function of the variables used to stratify the data, and the coefficients for this fit are also provided with the data. Results are consistent with expectations based on the previous work: the diurnal temperature cycle peaks in early afternoon (circa 2 pm local time); there is an increase in amplitude and a decrease in seasonality towards the equator. Generally, the ocean at this depth cools on windy days and warms on calm days, so that a component of subdaily variability is the SST tendency on slower timescales. By not ‘closing’ the diurnal cycle when stratified by environmental conditions, this dataset differs from previously published diurnal-cycle parameterizations. This thorough characterization of the SST diurnal cycle will assist in interpreting SST observations made at different local times of day for climatological purposes, and in testing and constraining models of the diurnal-cycle and air-sea interaction at high temporal resolution
GB3D : a framework for the bedrock geology of Great Britain

In 2011, the British Geological Survey (BGS) decided to begin the assembly of a National Geological Model (NGM) from its existing and on-going geological framework models comprising integrated national crustal, bedrock, and Quaternary models. The bedrock component is the most advanced of these themes and comprises both the calculated models and a complementary network of cross sections that provide a fence diagram for the bedrock geology of Great Britain. This fence diagram, the GB3D_v2012 dataset, is the subject of this article and is available in a variety of formats from the BGS website (www.bgs.ac.uk) as free downloads. It complements the existing 1:625 000 scale map sheets published by BGS utilizing the same colour schema and geological classification. The 121 component cross sections extend to depths between 1.5 and 6 km; they have an aggregate length of over 20 000 km, and they are snapped together at their intersections to ensure total consistency. The sections are guided by the existing BGS geological framework models where they cut through them; they also take account of the vast wealth of published data on the subsurface structure of Britain both from BGS and in the literature. Much of this is in the form of cross sections, contour maps of surfaces, and thicknesses (isopachs). The fence diagram has been built in the Geological Surveying and Investigation in 3D (GSI3D) software. Utilizing the cross sections and the coverages of the geological units simple 3D volumes can be calculated for the less deformed sedimentary strata. It is envisaged that this dataset will form a useful educational resource for geoscience students and the general public, and also provide the bedrock geology context and structure for regional and catchment scale studies
The Accumulation of Stone Age Lithic Artifacts in Rock Fragment Mulches in Northern Ethiopia

Lithic artifacts buried in the soil profile may be transported to the surface during tillage-induced
kinetic sieving, differential erosion, or swell–shrink cycles of clays and become part of a rock fragment mulch. Archaeologically, these manifestations are recognized as surface scatters. Although artifacts at the soil surface are difficult to relate to the local stratigraphic context, surface assemblages may provide information on lithic industries and the archaeological significance of sparsely
explored regions. Through in situ investigation of surface material in 60 1x1m2 plots in the Tembien district in the northern Ethiopian highlands, we show that rock fragment mulches can contain a significant number of lithic artifacts and we provide evidence for mid-Pleistocene occupation of a site. Considering that severe rill and gully erosion may be a threat to the archaeological
heritage and that well-dated African Middle Stone Age sites are rare, we conclude that the region deserves more attention for archaeological research.status: publishe
Quantitative WD-XRF calibration for small ceramic samples and their source material

A wavelength-dispersive X-ray fluorescence (WD-XRF) calibration is developed for small powdered samples (300mg) with the purpose of analyzing ceramic artifacts that might be available only in limited quantity. This is compared to a conventional calibration using a larger sample mass (2g). The comparison of elemental intensities obtained in both calibrations shows that the decrease in analyzed sample mass results in a linear decrease in measured intensity for the analyzed elements. This indicates that the small- and large-sample calibrations are comparable. Moreover, the elemental contents of four ceramic sherds and two potential clay sources fall well within the range of the certified reference materials that are the basis of the calibration curves. The advantage with the analytical method presented here is that it is rapid and requires only a small amount of sample that can easily be re-used for further analyses. This method has great potential in ceramic provenance studies
Societal Stability and Environmental Change : Examining the Archaeology - Soil Erosion Paradox

This paper critically examines the soil-exhaustion and societal collapse hypothesis both theoretically and empirically. The persistence of civilisations, especially in theMediterranean, despite intensive and erosive arable farming, creates what is described here as the archaeology-soil erosion paradox. This paper examines the data used to estimate past erosion and weathering rates, before presenting three case studies which engage with the theoretical arguments. Study 1 shows 5000 years of high slope erosion rates with both soil use and agriculture continuously maintained in the catchment. Study 2 shows how ancient agricultural terraces were constructed as part of integrated agricultural systems which fed the ancient city of Stymphalos - now abandoned. Study 3 presents a recent example of how after the removal of terraces high soil erosion rates result during intense rainstorms but that arable agriculture can still be maintained whilst external costs are borne by other parties. What these case studies have in common is the creation of soil and increased weathering rates whilst productivity is maintained due to a combination of soft bedrocks and/or agricultural terraces. In societal terms this may not be sustainable but it does not necessarily lead to land abandonment or societal collapse – this is the paradox
Sediment micromorphology and site formation processes during the middle to later Stone Ages at the Haua Fteah Cave, Cyrenaica, Libya

Understanding the timing and conditions of the Middle to Later Stone Age (MSA–LSA)\ud
transition in North Africa is, as with many cultural transitions during the Palaeolithic, based\ud
predominantly on archaeological and palaeoenvironmental records preserved within a small\ud
number of deep cave sediment sequences. The sedimentation processes that created these\ud
sequences, however, vary between sites, and impact on the observed cultural and\ud
environmental sequences and their interpretations. To use these sequences as chronological\ud
cornerstones it is vital to develop a robust understanding of the formation processes that\ud
created them. This paper utilises geoarchaeological analyses (field observations, soil\ud
micromorphology, bulk sedimentology) to examine site formation processes during the MSA–\ud
LSA at the Haua Fteah cave, Libya, one of North Africa's longest cultural sequences. The\ud
depositional processes identified vary in mode and energy, from 'dusty'/aeolian deposition to\ud
mass colluvial mudflows. This variability impacts greatly on the understanding of the\ud
sequence, not least in highlighting sporadic colluvial sediment reworking, including in layers\ud
identified as containing the MSA/LSA transition. The sedimentation processes observed are\ud
consistent with caves across the Mediterranean and beyond, highlighting the necessity for\ud
geoarchaeological analyses to fully unravel the limitations and potential of archaeological and\ud
palaeoenvironmental records within key cultural sequences
Dynamic in vivo imaging of postimplantation mammalian embryos using whole embryo culture

Due to the internal nature of mammalian development, much of the research performed is of a static nature and depends on interpolation between stages of development. This approach cannot explore the dynamic interactions that are essential for normal development. While roller culture overcomes the problem of inaccessibility of the embryo, the constant motion of the medium and embryos makes it impossible to observe and record development. We have developed a static mammalian culture system for imaging development of the mouse embryo. Using this technique, it is possible to sustain normal development for periods of 18-24 h. The success of the culture was evaluated based on the rate of embryo turning, heart rate, somite addition, and several gross morphological features. When this technique is combined with fluorescent markers, it is possible to follow the development of specific tissues or the movement of cells. To highlight some of the strengths of this approach, we present time-lapse movies of embryonic turning, somite addition, closure of the neural tube, and fluorescent imaging of blood circulation in the yolk sac and embryo.status: publishe
Picturing the future-conditional: montage and the global geographies of climate change

A growing body of work has explored the effects of visual imagery on shifting forms of environmental consciousness and politics. Circulating images of, for example, the ‘whole Earth’ have been ascribed agency in the emergence of new forms of planetary awareness and political globalism. This essay identifies a new form of global environmental image, in the shape of photographic montage depictions of future places transformed by the effects of climate change. Montage enables artists and designers to import the spatial formations of distant places into more familiar locations, in the process producing novel renderings of the interconnections of global environmental change. The future-conditional – ‘if x, then y’ – has become a key register of scientific and artistic engagement with climate change, and practices of visual montage have offered means of reconciling the transformations of space and time in the imagination of putative futures. The essay situates such images within a longer lineage of depictions of the tropical and the ruined, and focuses on contemporary montage depictions of climate-change-induced migration. It argues that many of these ‘global montages’ problematically reinforce extant notions of geographical otherness. Yet montage, as a technique, also renders visible the choices, cuts, juxtapositions and arguments which lie behind any representation, thus offering the seed of a more reflexive mode of future-conditional image-making
(En)visioning place-based adaptation to sea-level rise

This is the final version of the article. Available from the publisher via the DOI in this record.Sustainable climate change adaptation requires an understanding of people’s place attachments, so that potential
impacts and trade-offs are illuminated when making adaptation decisions. Methods are needed that elucidate these
important, but often intangible, place attachments at risk. A study was undertaken to explore place attachment, and
how these person–place bonds might be impacted by flooding and sea-level rise. It engaged with a small town in
coastal Australia that is already highly vulnerable to flooding, and which has been subject to numerous policy
directives intended to reduce climate change-induced flood risk. The town therefore acts as an analogue for climate
change adaptation in other semi-rural coastal communities. Photo-elicitation was found to be highly effective at
elucidating multifarious dimensions of residents’ place attachment. The attachments that were likely to be affected
by flooding (and adapting to flood risk) were encapsulated in: the personal and communal identities associated
with the tourism and fishing industries, the sense of belonging from living and re-living family connections to local
places, and the sense of community and enjoyment derived from diverse recreational activities. The photoelicitation
process provided different outcomes to conventional interviews, focus groups and questionnaires.
Participants sought to both vision (by elucidating their current experiences) and re-envision (in advocating for
different futures) their everyday experiences of adapting to flooding through their photographs and accompanying
narratives. A video introduction to this paper is available at: https://vimeo.com/83484905.The photo-elicitation project forms part of the first author’s
‘Visualising Climate Change’ fellowship research,
funded by the UK’s Economic and Social Research
Council (ES/K001175/1). It builds on the work of the
project ‘Equitable Outcomes in Adaptation to Sea
Level Rise’ led by the University of Melbourne
(Australian Research Council, LP100100586)
Dealing with the deluge of historical weather data: the example of the TEMPEST database

People have long been interested in the history of weather, particularly extremes, and chronologies of past events drawing on information from written records, have been compiled and published throughout history. In recent years, concern over current and future weather and climate has triggered a new level of interest in past weather events and their impacts. This interest, alongside the development of digital humanities research methods has resulted in a rapid growth in the number of online databases relating to historic weather and climate around the world. This paper reviews this expansion with reference to a range of examples, before documenting the design and creation of one such database, TEMPEST, an online repository for extreme weather history in the UK. TEMPEST has been created as the major output of the AHRC funded project ?Spaces of Experience and Horizons of Expectation: Extreme Weather in the UK, Past, Present and Future? (2013-2016). Unlike the majority of existing databases that rely on published materials, TEMPEST?s records are drawn from primary research into original documentary sources held in archives around the UK. The c. 18,000 records that TEMPEST currently contains offer personalised and geo-referenced insights into the relationship between society and extreme weather in the UK spanning a period of over 400 years. We conclude this paper by outlining some potential applications for TEMPEST, and suggesting directions for future research and resources in historical weather. We also consider broader issues for the digital humanities.publishersversionPeer reviewe
Opportunities for biodiversity conservation as cities adapt to climate change.

Cities are investing billions of dollars in climate change adaptation to combat the effects of sea‐level rise, temperature extremes, increasingly intense storm events, flooding and water scarcity. Natural ecosystems have enormous potential to contribute to city resilience, and so, actions that rely on this approach could sustain considerable co‐benefits for biodiversity. In this paper we identify the prevalence of key themes of human adaptation response that could have biodiversity conservation outcomes in cities. We then quantify the area of impact for actions that identify specific targets for greening or green infrastructure that could involve natural ecosystems, providing an indicator of potential co‐benefits to biodiversity. We then extrapolate to explore the total area of land that could benefit from catchment management approaches, the area of waterways that could benefit from nature‐based improvement of these spaces, and finally the number of threatened species that could benefit across these cities. From 80 city climate adaptation plans analysed, we found that urban greening plays a key role in most adaptation strategies, and represents an enormous opportunity for biodiversity conservation, given the diversity of animal and plant species in urban environments. We show that the ranges of at least 270 threatened species overlap with the area covered by just 58 city adaptation plans, including watershed catchments totalling over 28 million km2. However, an analysis of 80 city adaptation plans (of a total 151 found globally) shows that this opportunity is being missed. Just 18% of the plans assessed contained specific intentions to promote biodiversity. We highlight this missed opportunity, as climate adaptation actions undertaken by cities represent an enormous incipient opportunity for nature conservation. Finally, we encourage planners and city governments to incorporate biological conservation into climate adaption plans, for the mutual benefit of urban societies and their biodiversity
Towards a study of information geographies: (im)mutable augmentations and a mapping of the geographies of information

Information has always had geography. It is from somewhere; about somewhere; it evolves and is transformed\ud
somewhere; it is mediated by networks, infrastructures, and technologies: all of which exist in physical, material\ud
places. These geographies of information about places matter because they shape how we are able to find and\ud
understand different parts of the world. Places invisible or discounted in representations are invisible in practice to\ud
many people. In other words, geographic augmentations are much more than just representations of places: they\ud
are part of the place itself; they shape it rather than simply reflect it. This fusing of the spatial and informational\ud
augmentations that are immutable means that annotations of place emerge as sites of political contestation: with\ud
different groups of people trying to impose different narratives on informational augmentations. This paper therefore\ud
explores how information geographies have their own geographic distributions: geographies of access, of\ud
participation, and of representation. The paper offers a deliberately broad survey of a range of key platforms that\ud
mediate, host, and deliver different types of geographic information. It does so using a combination of existing\ud
statistics and bespoke data not previously mapped or analysed. Through this effort, the paper demonstrates that in\ud
addition to the geographies of uneven access to contemporary modes of communication, uneven geographies of\ud
participation and representation are also evident and in some cases are being amplified rather than alleviated. In\ud
other words, the paper comprehensively shows one important facet of contemporary information geographies: that\ud
geographic information itself is characterised by a host of uneven geographies. The paper concludes that there are\ud
few signs that global informational peripheries are achieving comparable levels of participation or representation with\ud
traditional information cores, despite the hopes that the fast-paced spread of the internet to three billion people might change this pattern.Peer-reviewedPublisher Versio
Matched Ascertainment of Informative Families for Complex Genetic Modelling

Family data are used extensively in quantitative genetic studies to disentangle the genetic and environmental contributions to various diseases. Many family studies based their analysis on population-based registers containing a large number of individuals composed of small family units. For binary trait analyses, exact marginal likelihood is a common approach, but, due to the computational demand of the enormous data sets, it allows only a limited number of effects in the model. This makes it particularly difficult to perform joint estimation of variance components for a binary trait and the potential confounders. We have developed a data-reduction method of ascertaining informative families from population-based family registers. We propose a scheme where the ascertained families match the full cohort with respect to some relevant statistics, such as the risk to relatives of an affected individual. The ascertainment-adjusted analysis, which we implement using a pseudo-likelihood approach, is shown to be efficient relative to the analysis of the whole cohort and robust to mis-specification of the random effect distribution.published_or_final_versionSpringer Open Choice, 01 Dec 201
PEL: an unbiased method for estimating age-dependent genetic disease risk from pedigree data unselected for family history.

International audienceProviding valid risk estimates of a genetic disease with variable age of onset is a major challenge for prevention strategies. When data are obtained from pedigrees ascertained through affected individuals, an adjustment for ascertainment bias is necessary. This article focuses on ascertainment through at least one affected and presents an estimation method based on maximum likelihood, called the Proband's phenotype exclusion likelihood or PEL for estimating age-dependent penetrance using disease status and genotypic information of family members in pedigrees unselected for family history. We studied the properties of the PEL and compared with another method, the prospective likelihood, in terms of bias and efficiency in risk estimate. For that purpose, family samples were simulated under various disease risk models and under various ascertainment patterns. We showed that, whatever the genetic model and the ascertainment scheme, the PEL provided unbiased estimates, whereas the prospective likelihood exhibited some bias in a number of situations. As an illustration, we estimated the disease risk for transthyretin amyloid neuropathy from a French sample and a Portuguese sample and for BRCA1/2 associated breast cancer from a sample ascertained on early-onset breast cancer cases