Documentation of a public communication project by German-speaking scientists prior to the September 2021 climate demonstrations

English: Documentation of a communication project by German-speaking scientists encouraging their peers to participate in the September 2021 climate demonstrations by means of short statements or appeals (German, with English and French translations).

Deutsch: Dokumentation eines Kommunikationsprojekts deutschsprachiger Wissenschaftler:innen, ihre Kolleg:innen mit kurzen Statements oder Aufrufen zur Teilnahme an den Klimademonstrationen im September 2021 zu ermuntern (deutsch, mit englischer und französischer Übersetzung).

Français: Documentation d'un projet de communication de scientifiques germanophones visant à encourager leurs collègues à participer aux manifestations pour le climat en septembre 2021 par de courtes déclarations ou des appels (en allemand, avec traduction en anglais et en français).

Action needed for the EU Common Agricultural Policy to address sustainability challenges

Making agriculture sustainable is a global challenge. In the European Union (EU), the Common Agricultural Policy (CAP) is failing with respect to biodiversity, climate, soil, land degradation as well as socio-economic challenges.The European Commission's proposal for a CAP post-2020 provides a scope for enhanced sustainability. However, it also allows Member States to choose low-ambition implementation pathways. It therefore remains essential to address citizens' demands for sustainable agriculture and rectify systemic weaknesses in the CAP, using the full breadth of available scientific evidence and knowledge.Concerned about current attempts to dilute the environmental ambition of the future CAP, and the lack of concrete proposals for improving the CAP in the draft of the European Green Deal, we call on the European Parliament, Council and Commission to adopt 10 urgent action points for delivering sustainable food production, biodiversity conservation and climate mitigation.Knowledge is available to help moving towards evidence-based, sustainable European agriculture that can benefit people, nature and their joint futures.The statements made in this article have the broad support of the scientific community, as expressed by above 3,600 signatories to the preprint version of this manuscript. The list can be found here (https://doi.org/10.5281/zenodo.3685632).

Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals.

Database URL

: http://cetaf.org/cetaf-stable-identifiers.

PESI - a taxonomic backbone for Europe

Background

Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.

The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

New information

This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

Community next steps for making globally unique identifiers work for biocollections data

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided.

Trends in access of plant biodiversity data revealed by Google Analytics

The amount of plant biodiversity data available via the web has exploded in the last decade, but making these data available requires a considerable investment of time and work, both vital considerations for organizations and institutions looking to validate the impact factors of these online works. Here we used Google Analytics (GA), to measure the value of this digital presence. In this paper we examine usage trends using 15 different GA accounts, spread across 451 institutions or botanical projects that comprise over five percent of the world's herbaria. They were studied at both one year and total years. User data from the sample reveal: 1) over 17 million web sessions, 2) on five primary operating systems, 3) search and direct traffic dominates with minimal impact from social media, 4) mobile and new device types have doubled each year for the past three years, 5) and web browsers, the tools we use to interact with the web, are changing. Server-side analytics differ from site to site making the comparison of their data sets difficult. However, use of Google Analytics erases the reporting heterogeneity of unique server-side analytics, as they can now be examined with a standard that provides a clarity for data-driven decisions. The knowledge gained here empowers any collection-based environment regardless of size, with metrics about usability, design, and possible directions for future development.

Fauna Europaea - all European animal species on the web

Fauna Europaea is Europe's main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260,000 taxon names, including 145,000 accepted (sub)species, assembled by a large network of (>400) leading specialists, using advanced electronic tools for data collations with data quality assured through sophisticated validation routines. Fauna Europaea started in 2000 as an EC funded FP5 project and provides a unique taxonomic reference for many user-groups such as scientists, governments, industries, nature conservation communities and educational programs. Fauna Europaea was formally accepted as an INSPIRE standard for Europe, as part of the European Taxonomic Backbone established in PESI.

Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.

Open exchange of scientific knowledge and European copyright: The case of biodiversity information

Background. The 7^th Framework Programme for Research and Technological Development is helping the European Union to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme “Horizon 2020” aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights.

We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information.

Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation.

Scientific names of organisms: attribution, rights, and licensing

BACKGROUND

As biological disciplines extend into the 'big data' world, they will need a names-based infrastructure to index and interconnect distributed data. The infrastructure must have access to all names of all organisms if it is to manage all information. Those who compile lists of species hold different views as to the intellectual property rights that apply to the lists. This creates uncertainty that impedes the development of a much-needed infrastructure for sharing biological data in the digital world.

FINDINGS

The laws in the United States of America and European Union are consistent with the position that scientific names of organisms and their compilation in checklists, classifications or taxonomic revisions are not subject to copyright. Compilations of names, such as classifications or checklists, are not creative in the sense of copyright law. Many content providers desire credit for their efforts.

CONCLUSIONS

A 'blue list' identifies elements of checklists, classifications and monographs to which intellectual property rights do not apply. To promote sharing, authors of taxonomic content, compilers, intermediaries, and aggregators should receive citable recognition for their contributions, with the greatest recognition being given to the originating authors. Mechanisms for achieving this are discussed.

Biodiversity into your hands - A call for a virtual global natural history 'metacollection'

BACKGROUND

Many scientific disciplines rely on correct taxon delineations and identifications. So does a great part of the general public as well as decision makers. Researchers, students and enthusiastic amateurs often feel frustrated because information about species remains scattered, difficult to access, or difficult to decipher. Together, this affects almost anyone who wishes to identify species or verify identifications. Many remedies have been proposed, but we argue that the role of natural history collections remains insufficiently appreciated. We suggest using state-of-the-art mass imaging technology and to join forces to create a global natural history metacollection on the internet, providing access to the morphology of tens of millions of specimens and making them available for automated digital image analysis.

DISCUSSION

Robotic high-resolution imaging technology and fast (high performance) computer-based image stitching make it now feasible to digitize entire collection drawers typically used for arthropod collections, or trays or containers used for other objects. Resolutions of 500 megapixels and much higher are already utilized to capture the contents of 40x50 cm collection drawers, providing amazing detail of specimens. Flanked by metadata entry, this helps to create access to tens of thousands of specimens in days. By setting priorities and combining the holdings of the most comprehensive collections for certain taxa, drawer digitizing offers the unique opportunity to create a global, virtual metacollection.The taxonomic and geographic coverage of such a collection could never be achieved by a single institution or individual. We argue that by joining forces, many new impulses will emerge for systematic biology, related fields and understanding of biodiversity in general.Digitizing drawers containing unidentified, little-curated specimens is a contribution towards the beginning of a new era of online curation. It also will help taxonomists and curators to discover and process the millions of "gems" of undescribed species hidden in museum accessions.

SUMMARY

Our proposal suggests creating virtual, high-resolution image resources that will, for the first time in history, provide access for expert scientists as well as students and the general public to the enormous wealth of the world's natural history collections. We foresee that this will contribute to a better understanding, appreciation and increased use of biodiversity resources and the natural history collections serving this cause.

Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information

The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a “non-commercial” (NC) condition. Although many people identify “non-commercial” with “non-profit”, detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works.

Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID

Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors.

Description of Colletotrichum lupini comb. nov. in modern terms

Gloeosporium lupini Bondar is transferred to Colletotrichum. The fungus is characterized morphologically and illustrated. The two varieties, Colletotrichum lupini (Bondar) Nirenberg, Feiler & Hagedorn, comb. nov. var. lupini and Colletotrichum lupini var. setosum Nirenberg, Feiler & Hagedorn var. nov. are described. They are compared with additional Colletotrichum species reported from lupins and other hosts by morphological and physiological methods as well as by RAPD-PCR and DNA-sequencing.

Circulating microemboli in patients after aortic valve replacement with pulmonary autografts and mechanical valve prostheses

BACKGROUND

The pulmonary autograft procedure (Ross) is now considered the gold standard for aortic valve replacement. One of its advantages is the freedom from macroemboli without anticoagulation. Whether this holds true for circulating microemboli, detectable as high-intensity transient Doppler signals (HITS), has not yet been verified.

METHODS AND RESULTS

We investigated 8 patients (2 women, 6 men; mean age, 50.6+/-17.9 years) after the Ross procedure, 9 patients (3 women, 6 men; mean age, 67.2+/-9.46 years) after aortic valve replacement with a mechanical valve prosthesis, and 12 young healthy volunteers by unilateral 1-hour recording of the middle cerebral artery on digital audio tape. Patients with extracranial carotid artery disease were excluded by color duplex sonography. During the off-line evaluation, the investigator was not aware of any patient details. No HITS were detected in healthy volunteers (95% confidence interval [CI], 0% to 26.46%). After the Ross procedure, 1 patient had 11 and 1 patient had 1 HITS (95% CI, 3.19% to 65.09%). All recipients of mechanical valves had HITS, ranging from 2 to 84 per hour (95% CI, 66.7% to 100%). Significantly more recipients of mechanical valves exhibited HITS than recipients of pulmonary autografts (P<.05) or control subjects (P<.05).

CONCLUSIONS

In contrast to mechanical valves, pulmonary autografts are seldom the source of microemboli, confirming the pulmonary autograft as the superior substitute for aortic valve replacement.

Bigated transcranial Doppler for the detection of clinically silent circulating emboli in normal persons and patients with prosthetic cardiac valves

BACKGROUND AND PURPOSE

Detection of clinically silent circulating microemboli by transcranial Doppler sonography is now being widely investigated in the hope of identifying patients at increased risk for stroke. Automatic detection by bigated Doppler, which uses sampling from two different depths in the artery under study and considers the motion of the embolus, may help to define "periods of interest" that can be evaluated off-line.

METHODS

In 12 normal volunteers and 10 patients with prosthetic aortic valves, we performed 1-hour recordings from one middle cerebral artery. In the normal subjects, we produced additional artifacts to use them as false-positives. Detection of microemboli was done off-line from digital audiotapes by an experienced blinded investigator (used as the gold standard) and was compared with on-line detection using specially designed software.

RESULTS

With the setting used, 91.5% of all recorded artifacts could correctly be identified as such with the software. Embolic signals were detected by the software with a specificity of 59.9% and a sensitivity of 74.3%.

CONCLUSIONS

Bigated Doppler adds a new dimension to the definition and detection of microembolic signals. It constitutes an important step forward toward automatic screening of stroke-prone patients. Assessing on-line periods of interest during the recording and going over the recorded data again off-line helps to save time for the discrimination of embolic signals from both the normal Doppler spectrum background and artifacts.

Periodic leg movements are part of the B-wave rhythm and the cyclic alternating pattern

Periodic leg movements (PLM) in sleep are supposed to constitute a frequent cause of insomnia. There is some controversy whether PLM are the cause of insomnia by provoking microarousals or whether they are simply and epiphenomenon not casually related to the insomnia. We examined four patients with PLM by overnight polysomnography and concomitant transcranial Doppler sonography (TCD) monitoring, 13 patients with suspected normal pressure hydrocephalus by concomitant overnight polysomnography and intracranial pressure recording, and 10 healthy volunteers by concomitant overnight polysomnography and TCD monitoring. EEG arousals occurred more frequently before than after the PLM. PLM were associated with increase in heart rate, breathing amplitude, and cerebral blood flow velocity assessed by TCD. PLM occurred with a mean wavelength of 40.5 s. This mean wavelength corresponded to similar values calculated for intracranial pressure B-waves (43.3 s) in 13 patients with suspected normal-pressure hydrocephalus, TCD B-wave equivalents (42.2 s) in 10 healthy young adults and the frequency of the cyclic alternating pattern in EEg recordings (40 s). Our date suggest that these cyclic variations with a wavelength of about 40 s are part of a common endogenous rhythm. PLM seem to be an epiphenomenon of this rhythm and not the cause of insomnia.