bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Elevation and Suppression of Star Formation within Galaxies
Authors: Wang Enci , Lilly Simon J. , Pezzulli Gabriele , Matthee Jorryt
Published: June 2019

To understand star formation in galaxies, we investigate the star formation rate (SFR) surface density (

) profiles for galaxies, based on a well-defined sample of 976 star-forming MaNGA galaxies. We find that the typical

profiles within 1.5

of normal SF galaxies can be well described by an exponential function for different stellar mass intervals, while the sSFR profile shows positive gradients, especially for more massive SF galaxies. This is due to the more pronounced central cores or bulges, rather than the onset of a “quenching” process. While galaxies that lie significantly above (or below) the star formation main sequence show overall an elevation (or suppression) of

at all radii, this central elevation (or suppression) is more pronounced in more massive galaxies. The degree of central enhancement and suppression is quite symmetric, suggesting that both the elevation and suppression of star formation are following the same physical processes. Furthermore, we find that the dispersion in

within and across the population is found to be tightly correlated with the inferred gas depletion time, whether based on the stellar surface mass density or the orbital dynamical time. This suggests that we are seeing the response of a simple gas-regulator system to variations in the accretion rate. This is explored using a heuristic model that can quantitatively explain the dependence of σ(

) on gas depletion timescale. Variations in accretion rate are progressively more damped out in regions of low star formation efficiency, leading to a reduced amplitude of variations in star formation.
Rocky Planetesimal Formation Aided by Organics
Authors: Homma Kazuaki A. , Okuzumi Satoshi , Nakamoto Taishi , Ueda Yuta
Published: June 2019

The poor stickiness of silicate dust grains is a major obstacle to the formation of rocky planetesimals. In this study, we examine the possibility that silicate grains with an organic mantle, which we call Organic-mantled Grains (OMGs), form planetesimals through direct coagulation. Organic mantles are commonly found in interplanetary dust particles, and laboratory experiments show that they are softer than silicates, in particular in warm environments. This, combined with the theory of particle adhesion, implies that OMGs are stickier than bare silicate grains. Because organic mantles can survive up to 400 K, silicate grains inside the water snow line in protoplanetary disks can in principle hold such mantles. We construct a simple grain adhesion model to estimate the threshold collision velocity below which aggregates of OMGs can grow. The model shows that aggregates of 0.1 μm-sized OMGs can overcome the fragmentation barrier in protoplanetary disks if the mantles are as thick as those in interplanetary dust particles and if the temperature is above ∼200 K. We use this adhesion model to simulate the global evolution of OMG aggregates in the inner part of a protoplanetary disk, demonstrating that OMG aggregates can indeed grow into planetesimals under favorable conditions. Because organic matter is unstable at excessively high temperatures, rocky planetesimal formation by the direct sticking of OMGs is expected to occur in a disk annulus corresponding to the temperature range ∼200–400 K. The organic-rich planetesimals may grow into carbon-poor rocky planetesimals by accreting a large amount of carbon-poor chondrules.
Origin of the CEMP-no Group Morphology in the Milky Way
Authors: Yoon Jinmi , Beers Timothy C. , Tian Di , Whitten Devin D.
Published: June 2019

The elemental-abundance signatures of the very first stars are imprinted on the atmospheres of CEMP-no stars, as various evidence suggests they are bona fide second-generation stars. It has recently been recognized that the CEMP-no stars can be subdivided into at least two groups, based on their distinct morphology in the A(C)–[Fe/H] space, indicating the likely existence of multiple pathways for their formation. In this work, we compare the halo CEMP-no group morphology with that of stars found in satellite dwarf galaxies of the Milky Way—a very similar A(C)–[Fe/H] pattern is found, providing clear evidence that halo CEMP-no stars were indeed accreted from their host mini-halos, similar in nature to those that formed in presently observed ultra-faint dwarfs (UFDs) and dwarf spheroidal (dSph) galaxies. We also infer that the previously noted “anomalous” CEMP-no halo stars (with high A(C) and low [Ba/Fe] ratios) that otherwise would be associated with Group I may have the same origin as the Group III CEMP-no halo stars, by analogy with the location of several Group III CEMP-no stars in the UFDs and dSphs and their distinct separation from that of the CEMP-s stars in the A(Ba)–A(C) space. Interestingly, CEMP-no stars associated with UFDs include both Group II and Group III stars, while the more massive dSphs appear to have only Group II stars. We conclude that understanding the origin of the CEMP-no halo stars requires knowledge of the masses of their parent mini-halos, which is related to the amount of carbon dilution prior to star formation, in addition to the nature of their nucleosynthetic origin.
The Effective Surface Area of Amorphous Solid Water Measured by the Infrared Absorption of Carbon Monoxide
Authors: He Jiao , Clements Aspen R. , Emtiaz SM , Toriello Francis , Garrod Robin T. , Vidali Gianfranco
Published: June 2019

The need to characterize ices coating dust grains in dense interstellar clouds arises from the importance of ice morphology in facilitating the diffusion and storage of radicals and reaction products in ices, a well-known place for the formation of complex molecules. Yet, there is considerable uncertainty about the structure of interstellar medium ices, their ability to store volatiles, and under what conditions. We measured the infrared absorption spectra of CO on the pore surface of porous amorphous solid water (ASW), and quantified the effective pore surface area of ASW. Additionally, we present results obtained from a Monte Carlo model of ASW in which the morphology of the ice is directly visualized and quantified. We found that 200 ML of ASW annealed to 20 K has a total pore surface area that is equivalent to 46 ML. This surface area decreases linearly with temperature to about 120 K. We also found that (1) dangling OH bonds only exist on the surface of pores; (2) almost all of the pores in the ASW are connected to the vacuum–ice interface, and are accessible for adsorption of volatiles from the gas phase; there are few closed cavities inside ASW at least up to a thickness of 200 ML; (3) the total pore surface area is proportional to the total three-coordinated water molecules in the ASW in the temperature range 60–120 K. We also discuss the implications on the structure of ASW and surface reactions in the ice mantle in dense clouds.
Public Release of RELXILL_NK: A Relativistic Reflection Model for Testing Einstein’s Gravity
Authors: Abdikamalov Askar B. , Ayzenberg Dimitry , Bambi Cosimo , Dauser Thomas , García Javier A. , Nampalliwar Sourabh
Published: June 2019

We present the public release version of relxill_nk, an X-ray reflection model for testing the Kerr hypothesis and general relativity. This model extends the relxill model that assumes the black hole (BH) spacetime is described by the Kerr metric. We also present relxilllp_nk, the first non-Kerr X-ray reflection model with a lamppost corona configuration, as well as all other models available in the full relxill_nk package. In all models the relevant relativistic effects are calculated through a general relativistic ray-tracing code that can be applied to any well-behaved, stationary, axisymmetric, and asymptotically flat BH spacetime. We show that the numerical error introduced by using a ray-tracing code is not significant compared with the observational error present in current X-ray reflection spectrum observations. In addition, we present the reflection spectrum for the Johannsen metric as calculated by relxill_nk.
How Bright Are Fast Optical Bursts Associated With Fast Radio Bursts?
Authors: Yang Yuan-Pei , Zhang Bing , Wei Jian-Yan
Published: June 2019

The origin of fast radio bursts (FRBs) is still unknown. Multiwavelength observations during or shortly after the FRB phase would be essential to identify the counterpart of an FRB and to constrain its progenitor and environment. In this work, we investigate the brightness of the “fast optical bursts” (FOBs) associated with FRBs and the prospects of detecting them. We investigate several inverse Compton (IC) scattering processes that might produce an FOB, including both the one-zone and two-zone models. We also investigate the extension of the same mechanism of FRB emission to the optical band. We find that a detectable FOB with the current and forthcoming telescopes is possible under the IC scenarios with very special conditions. In particular, the FRB environment would need to invoke a neutron star with an extremely strong magnetic field and an extremely fast spin, or an extremely young supernova remnant surrounding the FRB source. Furthermore, most electrons in the source are also required to have a fine-tuned energy distribution such that most of the IC energy is channeled in the optical band. We conclude that the prospect of detecting FOBs associated with FRBs is low. On the other hand, if FOBs are detected from a small fraction of FRBs, these FOBs would reveal extreme physical conditions in the FRB environments.
The Effect of Minor and Major Mergers on the Evolution of Low-excitation Radio Galaxies
Authors: Gordon Yjan A. , Pimbblet Kevin A. , Kaviraj Sugata , Owers Matt S. , O’Dea Christopher P. , Walmsley Mike , Baum Stefi A. , Crossett Jacob P. , Fraser-McKelvie Amelia , Lintott Chris J. , Pierce Jonathon C. S.
Published: June 2019

We use deep, μ

r
 ≲ 28 mag arcsec−2, r-band imaging from the Dark Energy Camera Legacy Survey to search for past, or ongoing, merger activity in a sample of 282 low-excitation radio galaxies (LERGs) at z < 0.07. Our principal aim is to assess the the role of mergers in the evolution of LERGs. Exploiting the imaging depth, we classify tidal remnants around galaxies as both minor and major morphological disturbances for our LERG sample and 1622 control galaxies matched in redshift, stellar mass, and environment. In groups and in the field, the LERG minor merger fraction is consistent with the control population. In galaxy clusters, 8.8 ± 2.9% of LERGs show evidence of recent minor mergers in contrast to 23.0 ± 2.0% of controls. This ∼4σ deficit of minor mergers in cluster LERGs suggests these events may inhibit this type of nuclear activity for galaxies within the cluster environment. We observe a >4σ excess of major mergers in the LERGs with M
* ≲ 1011 M⊙, with 10 ± 1.5% of these active galactic nuclei involved in such large-scale interactions compared to 3.2 ± 0.4% of control galaxies. This excess of major mergers in LERGs decreases with increasing stellar mass, vanishing by M
* > 1011.3 M⊙. These observations show that minor mergers do not fuel LERGs, and are consistent with typical LERGs being powered by accretion of matter from their halo. Where LERGs are associated with major mergers, these objects may evolve into more efficiently accreting active galactic nuclei as the merger progresses and more gas falls on to the central engine.
A Physical Basis for the H-band Blue-edge Velocity and Light-curve Shape Correlation in Context of Type Ia Supernova Explosion Physics
Authors: Ashall C. , Hoeflich P. , Hsiao E. Y. , Phillips M. M. , Stritzinger M. , Baron E. , Piro A. L. , Burns C. , Contreras C. , Davis S. , Galbany L. , Holmbo S. , Kirshner R. P. , Krisciunas K. , Marion G. H. , Morrell N. , Sand D. J. , Shahbandeh M. , Suntzeff N. B. , Taddia F.
Published: June 2019

Our recent work demonstrates a correlation between the high-velocity blue edge, v
edge, of the iron-peak Fe/Co/Ni H-band emission feature and the optical light-curve (LC) shape of normal, transitional and subluminous SNe Ia. We explain this correlation in terms of SN Ia physics. v
edge corresponds to the sharp transition between the complete and incomplete silicon burning regions in the ejecta. It measures the point in velocity space where the outer 56Ni mass fraction, X
Ni, falls to the order of 0.03–0.10. For a given 56Ni mass, M(56Ni), v
edge is sensitive to the specific kinetic energy E
kin(M(56Ni)/M
WD) of the corresponding region. Combining v
edge with LC parameters (i.e., s

BV
,

in B and V) allows us to distinguish between explosion scenarios. The correlation between v
edge and light-curve shape is consistent with explosion models near the Chandrasekhar limit. However, the available sub-M
Ch WD explosion model based on SN 1999by exhibits velocities that are too large to explain the observations. Finally, the subluminous SN 2015bo exhibits signatures of a dynamical merger of two WDs demonstrating diversity among explosion scenarios at the faint end of the SNe Ia population.
The Effect of Drug-Related Problems on Blood Glucose Level in the Treatment of Patients with Type 2 Diabetes Mellitus
Authors: Hartuti Silvy , Nasution Azizah , Syafril Santi
Published: June 2019

AIM: The study aimed to investigate the effect of drug-related problems (DRPs) on changes in blood glucose level (BGL) in the treatment of type 2 diabetes mellitus (T2DM) patients.METHODS: This three-month prospective cross-sectional study was conducted to patients of T2DM with complications hospitalised in Haji Adam Malik (HAM) Hospital, Medan, Indonesia period from July to October 2018. DRPs were identified and classified by using Cipolle DRP classification and trustable literature. The data obtained were analysed by Chi-Square test (p < 0.05 implied that there was a significant relationship).RESULTS: This study involved 81 T2DM patients, 52 (64.2%) of the patients were male, and 29 (35.8%) of them were female. Most (30.9%) of patients were at the age of 51-60 years. Combination of rapid-acting and long-acting insulin was the most frequently provided antidiabetic drugs (69.1%). There were 68 DRPs experienced by 32 (39.5%) of the patients. Percentage of DRP experienced by the 32 patients by number: 1 DRP, 53.1; 2 DRPs, 28.1; 3 DRPs, 3.1; 4 DRPs, 3.1; 5 DRPs, 3.1; 7 DRPs, 9.3. This study showed that 27.2% and 12.3 % of the patients had hyperglycemia and hypoglycemia, respectively. There was no significant relationship between BGL and indication without drug therapy (p = 0.064), ineffective provided drug (p = 0.079), and there was a significant relationship between BGL and irrational dose (p = 0.000). Furthermore, there was a significant relationship between hypoglycemia and adverse drug reaction (p = 0.000).CONCLUSION: DRPs are common among T2DM patients and still required the attention and appropriate actions of healthcare providers.
First record of Viminella sp. (Anthozoa: Alcyonacea: Ellisellidae) in the Persian Gulf
Authors: Shahbazi Shemshad , Sakhaei Nasrin , Zolgharnein Hossein , McFadden Catherine
Published: June 2019

This paper presents the first record ofViminellaGray 1870 from the Persian Gulf. This genus has a global distribution and its largest distribution is in the Indo-Pacific region. A single specimen was collected by a local fisherman from south Hengam Island (the north Persian Gulf) from 60-70 m depth. Colony morphology characteristics were examined by stereomicroscope and optical microscope. Descriptions of the colony and other taxonomic characteristics are provided. The colony is unbranched with a height of 12 cm and its basal diameter is approximately 1.63 mm. The sclerites of the coenenchyme comprise a variety of symmetrical double heads and capstan-like forms (0.05-0.11 mm). In the wall of calyces, slightly elongated double heads, capstans and spindles (about 0.08-0.19 mm) are present. Our finding extends the known geographical distribution of this genus in the Indo-Pacific region to the Persian Gulf.
New records of bats and terrestrial small mammals from the Seli River in Sierra Leone before the construction of a hydroelectric dam
Authors: Weber Natalie , Wistuba Ricarda , Astrin Jonas , Decher Jan
Published: June 2019

Sierra Leone is situated at the western edge of the Upper Guinean Forests in West Africa, a recognised biodiversity hotspot which is increasingly threatened by habitat degradation and loss through anthropogenic impacts. The small mammal fauna of Sierra Leone is poorly documented, although bats and rodents account for the majority of mammalian diversity. Based on morphological, genetic and echolocation data, we recorded 30 bat (Chiroptera), three shrew (Soricomorpha) and eleven rodent (Rodentia) species at the Seli River in the north of the country in 2014 and 2016, during a baseline study for the Bumbuna Phase II hydroelectric project. In 2016, 15 bat species were additionally documented at the western fringe of the Loma Mountains, a recently established national park and biodiversity offset for the Bumbuna Phase I dam. Three bat species were recorded for the first time in Sierra Leone, raising the total number for the country to 61. Further, two bat species are threatened and endemic to the Upper Guinean Forest and several taxa of small mammals are poorly known or represent undescribed species. Overall, the habitats of the project area supported a species-rich small mammal fauna including species of global conservation concern. Suitable mitigation measures and/or offsets are necessary to maintain biodiversity and ecosystems in a region that is under high human pressure.
A Proposed Metadata Standard for Recording and Sharing Attribution Information in Biodiversity
Authors: Thessen Anne , Shorthouse David , Paul Deborah , Conlon Michael , Woodburn Matt , Koureas Dimitrios , Ramdeen Sarah , Haak Laurel , Cornwell Peter
Published: June 2019

Research collections are an important tool for understanding the Earth, its systems, and human interaction. Despite the importance of collections, many are not maintained or curated as thoroughly as we would like. Part of the reason for this is the lack of professional reward for collection, curation, or maintenance. To address this gap in attribution metadata, the Research Data Alliance (RDA) and the Biodiversity Information Standards (TDWG) organization co-endorsed a Working Group to create recommendations for the representation of attribution metadata. After 18 months, this Working Group recommended a very simple data exchange standard to link people, the curatorial actions they perform, and the digital or physical objects they are curating. These recommendations are discussed in the context of community-developed use cases. Future work includes:

exploration of a Darwin Core extension,

best practices on how to best adopt these recommendations, and

possible solutions to help accelerate the process of connecting people and their activities in legacy and future data.

exploration of a Darwin Core extension,

best practices on how to best adopt these recommendations, and

possible solutions to help accelerate the process of connecting people and their activities in legacy and future data.

To explore options for making collections work more visible and citable, we tested the use of digital annotation tools and person identifiers in curation workflows. The results from this pilot project in collaboration with ORCID and Data Futures to display specimens on an ORCID profile will be presented.
Mangal: An open infrastructure for ecological interactions
Authors: Vissault Steve , Gravel Dominique , Poisot Timothée
Published: June 2019

Interactions among species is at the heart of ecology. Despite their importance, studying ecological interactions remains difficult due to the lack of standard information and the disparity of formats in which ecological interactions are stored (Poisot et al. 2015). Historically, ecologists have used matrices to store interactions, which tend to easily decontextualize interactions from fieldwork when metadata is missing. To overcome these limitations, we designed Mangal - a global ecological interactions database - which serialize ecological interaction matrices into nodes (e.g. taxon, individuals or population) and edges. This database offers the opportunity to store information on traits, environment and homogenized taxonomy through unique taxonomic identifiers such as Encyclopedia of Life (EOL), Catalogue of Life (COL), Global Biodiversity Information Facility (GBIF) and Integrated Taxonomic Information System (ITIS). Here, we present the new release of Mangal including more than 120,000 interactions, 1,300 networks from 172 scientific publications distributed across the globe. We explore the content, illustrate case studies and present templates in order to contribute to this open infrastructure. For this purpose, we developed and maintained two packages/clients from popular scientific languages: R and Julia to facilitate data access, curation and network deposits on the database (Source code).
Next Steps in Data Capture from Specimen Labels and Data Integration: Lessons learnt from the ICEDIG pilots
Authors: Dillen Mathias , Groom Quentin , Phillips Sarah , Spasic Irena
Published: June 2019

The rapid development and refinement of digital technologies in the last two decades has spearheaded a wave of digitization in natural history collections. This has generated a massive number of digitized images and many more are expected with the planned European Distributed Systems of Scientific Collections (DiSSCo) infrastructure. Many of these images will contain labels with data written on them, typed on them or interpretable from them, but capturing these data remains a challenge. Automated as well as manual methods are being investigated and have yielded mixed results. In addition, previously captured data or data to be captured this way will need to be interoperable in order to make digital access and enrichment most effective. Finally, institutions holding the physical specimens will need to remain capable of efficiently curating the digital, potentially annotated, counterparts. This will require compatibility with the diverse data models of local Collection Management Systems (CMS).

In the context of the ICEDIG (Innovation and consolidation for large scale digitisation of natural heritage) project, a benchmark dataset of herbarium specimens was assembled from nine contributing institutions (Dillen et al. 2019). This dataset was used to evaluate automated methods of text recognition, such as OCR (Optical Character Recognition) and HTR (Handwritten Text Recognition), and post-capture classification, such as language identification or NER (Named Entity Recognition). A pipeline from scan to scientifically useful data was drafted and guidelines for selecting appropriate software solutions were provided.

The benchmark dataset was also processed through multiple crowdsourcing platforms, after which the quality and interoperability of the resulting transcriptions was analyzed. The aptitude of local Collection Management Systems to curate these digitized specimens efficiently was investigated, as well as the fitness of data standards in use to ensure and maintain proper interoperability. In addition, available surveys on CMS use and satisfaction were summarized and in-depth assessments of the CMS in use at the ICEDIG partner institutes were performed. A summary of results and recommendations will be presented.
Ecotaxonomy: Linking traits, taxa, individuals and samples in a flexible virtual research environment for ecological studies
Authors: Potapov Anton , Sandmann Dorothee , Scheu Stefan
Published: June 2019

Major research progress in ecology is being achieved through large-scale collaborations across people, groups and countries. In large-scale projects harmonization of data is tedious and time-consuming, but needs to be done reliably and rapidly. This is especially true if projects investigate under-explored organism groups such as tropical invertebrates. To link taxa to their role in ecosystems, functional traits of the taxa need to be considered. However, despite the urgent need for a common database for invertebrate traits, this is yet to be established. We developed an open web platform, Ecotaxonomy (ecotaxonomy.org), that allows traits, taxa, individuals and samples to be linked within research projects. Ecotaxonomy includes a virtual research environment, allowing project members to work jointly online on the data input, integration and retrieval. The taxonomic system of Ecotaxonomy is based on the Global Biodiversity Information Facility (gbif.org), but may be complemented by morphospecies, pictures, literature and other parameters. Any parameters can be customized inside the system and attached either to taxa, individuals, or environmental samples (Fig. 1). As public output, the system provides interactive identification keys and web catalogs of traits and taxa. Ecotaxonomy is implemented on GCore platform, that is being developed by Complex Cloud Solutions (http://ccs.msk.ru/en/). The GCore is based on Node.js, allowing for fast and efficient standardised programming. Thus, custom modules can be implemented in the future by external developers in the framework of the platform. Ecotaxonomy is now open for beta-testing. After a public release (presumably in 2020), our goal is to keep the system and the code open and ensure data interoperability via Darwin core standards. The initial stage of Ecotaxonomy development (2016-2023) is funded in the framework of a DFG-funded project (SFB 990). To ensure long-term sustainability, we are involving ecological laboratories around the world and ultimately seek to establish a permanent funding by governmental or non-governmental organisations. Using and developing Ecotaxonomy, and linking it to existing open repositories will greatly improve the efficiency and integration of research in trait-based ecology.
Transforming Biodiversity Data into Knowledge for Decision-making
Authors: Weatherdon Lauren
Published: June 2019

Ensuring that we have the data and information necessary to make informed decisions is a core requirement in an era of increasing complexity and anthropogenic impact. With cumulative challenges such as the decline in biodiversity and accelerating climate change, the need for spatially-explicit and methodologically-consistent data that can be compiled to produce useful and reliable indicators of biological change and ecosystem health is growing.

Technological advances—including satellite imagery—are beginning to make this a reality, yet uptake of biodiversity information standards and scaling of data to ensure its applicability at multiple levels of decision-making are still in progress. The complementary Essential Biodiversity Variables (EBVs) and Essential Ocean Variables (EOVs), combined with Darwin Core and other data and metadata standards, provide the underpinnings necessary to produce data that can inform indicators. However, perhaps the largest challenge in developing global, biological change indicators is achieving consistent and holistic coverage over time, with recognition of biodiversity data as global assets that are critical to tracking progress toward the UN Sustainable Development Goals and Targets set by the international community (see Jensen and Campbell (2019) for discussion).

Through this talk, I will describe some of the efforts towards producing and collating effective biodiversity indicators, such as those based on authoritative datasets like the World Database on Protected Areas (https://www.protectedplanet.net/), and work achieved through the Biodiversity Indicators Partnership (https://www.bipindicators.net/). I will also highlight some of the characteristics of effective indicators, and global biodiversity reporting and communication needs as we approach 2020 and beyond.
Towards Linked Open Molecular Data: Recommendations for researchers, collections, infrastructures and publishers
Authors: Droege Gabriele , Karsch-Mizrachi Ilene , Barker Katharine , Coddington Jonathan , Seberg Ole
Published: June 2019

The variety of molecular methods used to analyze biosamples is continuously increasing, as is the need for the standardized deposition, documentation and citation of both the samples as well as the methods applied to them. Global initiatives such as the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), Barcode of Life Data System (BOLD, http://www.boldsystems.org), the Global Biodiversity Information Facility (GBIF, http://www.gbif.org) and the Global Genome Biodiversity Network (GGBN, http://www.ggbn.org), in addition to many others, have been working towards standardized access to biological data for many years. Collectively, these biodiversity data management platforms provide a considerable and indispensable infrastructure to the research community. However, cross-linking the massive amounts of protein and DNA sequence data submitted to these databases every year with standardized records of the underlying biological material remains challenging. Best practices for standardized data submissions and data citations are urgently needed.

In the long run, two goals should be achieved above all else:

all sequence data should be linked to natural history collections, and

biological material that was used for molecular research, especially DNA sequencing, should be deposited and, thus, made accessible in public, well curated collections.

all sequence data should be linked to natural history collections, and

biological material that was used for molecular research, especially DNA sequencing, should be deposited and, thus, made accessible in public, well curated collections.

Here we will provide recommendations both for researchers and collections how to cite underlying biological material at INSDC and in publications in a standardized way towards Linked Open Data. We will also address how the global infrastructures and publishers can improve their interoperability.
Using Named Graphs and Knowledge Graph Template Patterns for Efficiently Organizing FAIR Anatomy Data and Metadata
Authors: Vogt Lars , Baum Roman
Published: June 2019

Currently, morphological data and metadata are still mostly published as unstructured free texts, which lack semantic transparency, cannot be parsed by computers, and do not comply with the FAIR (Findable, Accessible, Interoperable, Reusable; Wilkinson et al. (2016) data principles, thus hampering their reuse by non-experts and their integration across many fields in the life sciences. With an ever-increasing amount of available ontologies and the development of adequate semantic technology, however, a solution to this problem becomes available.

Instead of free text descriptions, morphological data and metadata can be recorded, stored, and communicated through the Web in the form of Resource Description Framework (RDF) triple statements that use the ‘Subject – Property – Object’ syntax of RDF and URIs of ontology classes and properties as well as URIs for individual entities as terminology. Since a given URI can take the ‘Subject’ position in one and the ‘Object’ position in another RDF statement, several triples can be linked to form a highly formalized and structured directed graph (semantic graph).

After introducing an instance-based approach of recording morphological descriptions and their accompanying metadata as semantic knowledge graphs (i.e. Anatomy Knowledge Graphs), we propose a knowledge graph template pattern for each type of anatomical observation and a pattern for documenting metadata. The use of template patterns for knowledge graphs provides Interoperability and Reusability of comparable anatomical observations and of their accompanying metadata and a means to meaningfully visualize information contained in semantic graphs in a user-friendly HTML representation. Stored in a tuple store, Anatomy Knowledge Graphs become Findable and Accessible through the store’s SPARQL endpoint. As a consequence, anatomy data and metadata documented as Anatomy Knowledge Graphs in a tuple store are FAIR.

Finally, we suggest a general scheme of how to efficiently organize Anatomy Knowledge Graphs in a tuple store framework based on instances of named graphs, with each individual named graph instantiating an ontology class that relates to a particular type of observation (e.g., weight measurement named graph class). A named graph is a fourth element in an RDF statement (‘Subject – Property – Object – Named Graph’), turning the triple into a quadruple. All RDF statements that share the same URI in the ‘Named Graph’ position belong to the same named graph. The use of named graph resources allows meaningful fragmentation of the contents of an Anatomy Knowledge Graph (Fig. 1), which in turn enables subsequent specification of all kinds of data views for managing and accessing morphological data and metadata. This scheme has been implemented in the description module of the prototype for semantic Morph∙D∙Base.
When Data Management Meets Project Management
Authors: Meyke Evgeniy
Published: June 2019

Complex projects that collect, curate and analyse biodiversity data are often presented with the challenge of accommodating diverse data types, various curation and output workflows, and evolving project logistics that require rapid changes in the applications and data structures. At the same time, sustainability concerns and maintenance overheads pose a risk to the long term viability of such projects.

We advocate the use of flexible, multiplatform tools that adapt to operational, day-to-day challenges while providing a robust, cost efficient, and maintainable framework that serves the needs data collectors, managers and users.

EarthCape is a highly versatile platform for managing biodiversity research and collections data, associated molecular laboratory data (Fig. 1), multimedia, structured ecological surveys and monitoring schemes, and more. The platform includes a fully functional Windows client as well as a web application. The data are stored in the cloud or on-premises and can be accessed by users with various access and editing rights. Ease of customization (making changes to user interface and functionality) is critical for most environments that deal with operational research processes. For active researchers and curators, there is rarely time to wait for a cycle of development that follows a change or feature request. In EarthCape, most of the changes to the default setup can be implemented by the end users with minimum effort and require no programming skills.

High flexibility and a range of customisation options is complemented with mapping to Darwin Core standard and integration with GBIF, Geolocate, Genbank, and Biodiversity Heritage Library APIs. The system is currently used daily for rapid data entry, digitization and sample tracking, by such organisations as Imperial College, University of Cambridge, University of Helsinki, University of Oxford.

Being an operational data entry and retrieval tool, EarthCape sits at the bottom of Virtual Research Environments ecosystem. It is not a software or platform to build data repositories, but rather a very focused tool falling under "back office" software category. Routine label printing, laboratory notebook maintenance, rapid data entry set up, or any other of relatively loaded user interfaces make use of any industry standard relational database back end. This opens a wide scope for IT designers to implement desired integrations within their institutional infrastructure. APIs and developer access to core EarthCape libraries to build own applications and modules are under development.

Basic data visualisation (charts, pivots, dashboards), mapping (full featured desktop GIS module), data outputs (report and label designer) are tailored not only to research analyses, but also for managing logistics and communication when working on (data) papers. The presentation will focus on the software platform featuring most prominent use cases from two areas: ecological research (managing complex network data digitization project) and museum collections management (herbarium and insect collections).
FinBIF: An all-embracing, integrated, cross-sectoral biodiversity data infrastructure
Authors: Schulman Leif , Juslén Aino , Lahti Kari
Published: June 2019

The service model of the Global Biodiversity Information Facility (GBIF) is being implemented in an increasing number of national biodiversity (BD) data services. While GBIF already shares >109 data points, national initiatives are an essential component: increase in GBIF-mediated data relies on national data mobilisation and GBIF is not optimised to support local use. The Finnish Biodiversity Information Facility (FinBIF), initiated in 2012 and operational since late 2016, is one of the more recent examples of national BD research infrastructures (RIs) – and arguably among the most comprehensive. Here, we describe FinBIF’s development and service integration, and provide a model approach for the construction of all-inclusive national BD RIs.

FinBIF integrates a wide array of BD RI approaches under the same umbrella. These include large-scale and multi-technology digitisation of natural history collections; building a national DNA barcode reference library and linking it to species occurrence data; citizen science platforms enabling recording, managing and sharing of observation data; management and sharing of restricted data among authorities; community-driven species identification support; an e-learning environment for species identification; and IUCN Red Listing (Fig. 1).

FinBIF’s aims are to accelerate digitisation, mobilisation, and distribution of biodiversity data and to boost their use in research and education, environmental administration, and the private sector. The core functionalities of FinBIF were built in a 3.5-year project (01/2015–06/2018) by a consortium of four university-based natural history collection facilities led by the Finnish Museum of Natural History Luomus. Close to 30% of the total funding was granted through the Finnish Research Infrastructures programme (FIRI) governed by the national research council and based on scientific excellence. Government funds for productivity enhancement in state administration covered c.40 % of the development and the rest was self-financed by the implementing consortium of organisations that have both a research and an education mission.

The cross-sectoral scope of FinBIF has led to rapid uptake and a broad user base of its functionalities and services. Not only researchers but also administrative authorities, various enterprises and a large number of private citizens show a significant interest in the RI (Table 1).

FinBIF is now in its second construction cycle (2019–2022), funded through the FIRI programme and, thus, focused on researcher services. The work programme includes integration of tools for data management in ecological restoration and e-Lab tools for spatial analyses, morphometric analysis of 3D images, species identification from sound recordings, and metagenomics analyses.
Using Unsupervised Artificial Neural Networks to Detect Sibling Species: A case in Myxomycetes
Authors: Pando Francisco , Heredia Ignacio , Lloret Lara
Published: June 2019

Species distribution modelling (SDM) --i.e. the prediction of species potential geographic distributions based on correlations between known presence records and the environmental conditions at occurrence localities-- is one of the most freqently cited developments in recent years in the realm of biodiversity studies (Web of Science 2019). The reasons for the explosion in SDM studies reside in: a) the pressure to know species distributions (under both present and future climate change scenarios) with precision to satisfy scientific as well as societal objectives; b) the impossibility of knowing every occurrence of all but the most conspicuous and/or special interest species; c) the availability of primary occurrence and environmental data in unprecedented amounts, thanks to initiatives like the Global Biodiversity Information Facility (GBIF); and d) the development of algorithms and software, along with the computing power, which allow inference of species distribution models from the available data.

The standard methods to produce such models are based on environmental feature vectors, and some well-established algorithms such as distance-based machine learning, regression or a combination of these (Tsoar et al. 2007).

In this presentation, we explore deep learning techniques (LeCun et al. 2015), particularly how those developed in recent years could contribute to the study of species distribution (see also Botella et al. 2018; Deneu et al. 2018). In this contribution we aim to identify sibling species on the basis of their ecological preferences. In this exercise, we prepare an image-based environmental representation space using an unsupervised classification approach, instead of a set of environmental feature vectors. For our case study, we chose a well-known cosmopolitan myxomycete (i.e., mycetozoan) species: Hemitrichia serpula (Scop.) Rostaf., whose ecological preferences --involving several biomes-- may suggest that it could comprise several sibling species.
Different Approaches between First and Second Mass Digitisation Project for the Herbarium (BR) at Meise Botanic Garden
Authors: De Smedt Sofie , Bogaerts Ann , Engledow Henry , Groom Quentin
Published: June 2019

The Herbarium of Meise Botanic Garden is in the top 15 herbaria worldwide. The collection comprises some four million specimens, which are important for scientific research.

Digitisation of specimens includes imaging, transcription of label information, linking data and making the results publicly accessible online. In addition to facilitating researchers’ access to specimens, digitisation also brings new possibilities for analysis and discovery of new data, such as the vast amount of information on handwritten labels.

In the DOE! project (Digitale Ontsluiting Erfgoedcollecties), funded by the Flemish Government, 1.2 million herbarium sheets from the African and Belgian collections were digitised. We have received additional funding to digitise a further 1.4 million specimens for the remaining vascular plants and macro-algae collections, by October 2021. These include the historic collections of Von Martius and Van Heurck.

Carl Friedrich Philipp von Martius (1794–1868) was a pioneering explorer whose expeditions led to the discovery of many species. He amassed over 300,000 specimens, some of which were used to compile the first Flora of Brazil.

Henri Van Heurck (1838–1909) also gathered herbarium specimens from all over the world, including a specimen originally from the collection of Linnaeus.

Despite this being our second mass digitisation project, there are significant differences in our approach. This is partly due to lessons learned from the first project and partly to the nature of the collections themselves. The differences in the tendering process, specimen preparation, workflow and data capture will be explained.

Making these specimens openly available online through www.botanicalcollections.be is valuable to scientific research as well as valorising of our collections. Currently, the site attracts 7000 users a year, which adds up to 15,000 sessions a year and the average session is more than 8 minutes. This means that people are actively using our website and these numbers can be expected to grow as we add more specimens and functionality.
Chromosome numbers for the Italian flora: 7
Authors: Astuti Giovanni , Liu Lijuan , Peruzzi Lorenzo
Published: June 2019

In this contribution, new chromosome data obtained on material collected in Italy are presented. It includes a total of 105 chromosome counts for three populations of PulmonariavallarsaeA.Kern.subsp.apennina (Cristof. & Puppi) Cecchi & Selvi and for three populations of P.hirta L.
Solanum plastisexum, an enigmatic new bush tomato from the Australian Monsoon Tropics exhibiting breeding system fluidity
Authors: McDonnell Angela J. , Wetreich Heather B. , Cantley Jason T. , Jobson Peter , Martine Christopher T.
Published: June 2019

A bush tomato that has evaded classification by solanologists for decades has been identified and is described as a new species belonging to the Australian “Solanumdioicumgroup” of the Ord Victoria Plain biogeographic region in the monsoon tropics of the Northern Territory. Although now recognised to be andromonoecious,S.plastisexumMartine & McDonnell,sp. nov.exhibits multiple reproductive phenotypes, with solitary perfect flowers, a few staminate flowers or with cymes composed of a basal hermaphrodite and an extended rachis of several to many staminate flowers. When in fruit, the distal rachis may abcise and drop. A member of SolanumsubgenusLeptostemonum,Solanumplastisexumis allied to theS.eburneumSymon species group. Morphometric analyses presented here reveal thatS.plastisexumdiffers statistically from all of its closest relatives includingS.eburneum,S.diversiflorumF. Meull.,S.jobsoniiMartine, J.Cantley & L.M.Lacey,S.succosumA.R.Bean & Albr. andS.watneyiMartine & Frawley in both reproductive and vegetative characters. We present evidence supporting the recognition ofS.plastisexumas a distinctive entity, a description of the species, representative photographs, a map showing the distribution of members of theS.eburneumspecies group and a key to the andromonoeciousSolanumspecies of the Northern Territory of Australia. This new species is apparently labile in its reproductive expression, lending to its epithet, and is a model for the sort of sexual fluidity that is present throughout the plant kingdom.
Origin of the Diplazium hachijoense complex (Athyriaceae)
Authors: Hori Kiyotaka , Murakami Noriaki
Published: June 2019

We analyzed the phylogeny of theDiplaziumhachijoensecomplex using plastidtrnL-Fand low-copy nuclear markerAK1DNA sequences. Based on allele constitution, triploid apogamous species of theD.hachijoensecomplex appeared to have originated from the hybridization of triploid apogamous species and diploid sexual species by recurrent hybridization events. These results suggested that triploid apogamous ferns can achieve hybridization with diploid sexual species by producing diploid spores with irregular meiosis in sporogenesis. Furthermore, the present study predicted the involvement of several unknown species associated with hybridization. More sampling ofCallipterisspecies from China and adjacent areas is required to determine the relationships among unknown species and theD.hachijoensecomplex.
Au croisement de l’histoire culturelle et des sciences de l’information et de la communication. Une approche transdisciplinaire des transferts culturels dans les Alpes Occidentales tardo-médiévales
Authors: Cailloux Marianne
Published: June 2019

Cette communication propose une réflexion sur les nouvelles orientations de l’histoire culturelle pour l’objet-image des périodes anciennes (médiévale et moderne). Les modalités de médiation, de processus en dynamique et en flux conduisent à réinterpréter l’analyse de l’image comme objet d’étude global, dans la lignée des travaux d’Hans Belting, en convoquant des auteurs plus récents comme Yves Jeanneret. Il s’agit d’observer comment les théories et concepts des sciences de l’information et de la communication permettent potentiellement une ouverture transdisciplinaire dans l’étude des transferts culturels, ici à travers des exemples pris dans les Alpes occidentales.
De la patria à la Franche-Comté : bâtisseurs et stucateurs de la Valsesia dans la province comtoise entre la fin du xviie siècle et le début du xixe siècle
Authors: Zito Mickaël
Published: June 2019

À la charnière entre les xviie et xviiie siècles, une communauté de bâtisseurs et de stucateurs originaires de la Valsesia, une vallée du nord de l’Italie, arrive en Franche-Comté, province en pleine reconstruction. Appréciés des commanditaires, ils s’installent durablement et ouvrent la voie aux générations suivantes. L’article qui suit a pour but d’analyser ce phénomène migratoire, qui se vérifie encore au début du xixe siècle, de le contextualiser et d’en proposer un premier bilan, comprenant à la fois des aspects artistiques, sociaux et géographiques.