scholarly journals The data of the Swedish Malaise Trap Project, a countrywide inventory of Sweden's insect fauna

2020 ◽  
Vol 8 ◽  
Author(s):  
Dave Karlsson ◽  
Mattias Forshage ◽  
Kevin Holston ◽  
Fredrik Ronquist

Despite Sweden's strong entomological tradition, large portions of its insect fauna remain poorly known. As part of the Swedish Taxonomy Initiative, launched in 2002 to document all multi-cellular species occurring in the country, the first taxonomically-broad inventory of the country's insect fauna was initiated, the Swedish Malaise Trap Project (SMTP). In total, 73 Malaise traps were deployed at 55 localities representing a wide range of habitats across the country. Most traps were run continuously from 2003 to 2006 or for a substantial part of that time period. The total catch is estimated to contain 20 million insects, distributed over 1,919 samples (Karlsson et al. 2020). The samples have been sorted into more than 300 taxonomic units, which are made available for expert identification. Thus far, more than 100 taxonomists have been involved in identifying the sorted material, recording the presence of 4,000 species. One third of these had not been recorded from Sweden before and 700 have tentatively been identified as new to science. Here, we describe the SMTP dataset, published through the Global Biodiversity Information Facility (GBIF). Data on the sorted material are available in the "SMTP Collection Inventory" dataset. It currently includes more than 130,000 records of taxonomically-sorted samples. Data on the identified material are published using the Darwin Core standard for sample-based data. That information is divided up into group-specific datasets, as the sample set processed for each group is different and in most cases non-overlapping. The current data are divided into 79 taxonomic datasets, largely corresponding to taxonomic sorting fractions. The orders Diptera and Hymenoptera together comprise about 90% of the specimens in the material and these orders are mainly sorted to family or subfamily. The remaining insect taxa are mostly sorted to the order level. In total, the 79 datasets currently available comprise around 165,000 specimens, that is, about 1% of the total catch. However, the data are now accumulating rapidly and will be published continuously. The SMTP dataset is unique in that it contains a large proportion of data on previously poorly-known taxa in the Diptera and Hymenoptera.

Author(s):  
Arturo H. Ariño ◽  
Mónica González-Alonso ◽  
Anabel Pérez de Zabalza

With more than one billion primary biodiversity data records (PBR), the Global Biodiversity Information Facility (GBIF) is the largest and, arguably, most comprehensive and accurate resource about the biodiversity data on the planet. Yet, its gaps (taxonomical, geographical or chronological, among others) have often been brought to attention (Gaijy et al. 2013) and efforts are continuously made to ensure more uniform coverage. Especially as data obtained through this resource are increasingly being used for science, policy, and conservation (Ariño et al. 2018), drawing on every possible source of information to complement already existing data opens new opportunities for supplying the integrative knowledge required for global endeavors, such as understanding the global patterns of ecosystem and environment changes. One such potential source that exists, but so far has experienced little integration, is the vast body of data acquired through airborne particle monitoring systems (for example, the European Aeroallergen Network, EAN). A large portion of pollen data is comprised of quantitative sampling of airborne pollen collected through semi-automated spore traps throughout the world. Its main use is clinical, as it forms the basis of the widespread allergen forecast bulletins. While geolocating the source of airborne pollen is fraught with obviously large uncertainty radii, the time and taxon components of the PBR remain highly precise and are therefore fit for many other uses (Hill et al. 2010). Presence data, and under certain circumstances, frequency data inferred from pollen counts have been often proposed as an excellent proxy for past climate change assessments as far back as the start of the Holocene (Mauri et al. 2015) and might therefore also be possibly used for current climate change detection. We call for a concerted effort throughout the palynological community to first increase harmonizing, and then eventually standardizing, pollen data acquisition through the adoption of Darwin Core (DwC) and, eventually, DwC extensions to mine current data and pipeline future airborne pollen data as PBR. mine current data and pipeline future airborne pollen data as PBR. Success in this endeavor may contribute to a better understanding of global change.


2020 ◽  
Vol 21 (2) ◽  
pp. 97-109 ◽  
Author(s):  
Ana P. dos Santos ◽  
Tamara G. de Araújo ◽  
Gandhi Rádis-Baptista

Venom-derived peptides display diverse biological and pharmacological activities, making them useful in drug discovery platforms and for a wide range of applications in medicine and pharmaceutical biotechnology. Due to their target specificities, venom peptides have the potential to be developed into biopharmaceuticals to treat various health conditions such as diabetes mellitus, hypertension, and chronic pain. Despite the high potential for drug development, several limitations preclude the direct use of peptides as therapeutics and hamper the process of converting venom peptides into pharmaceuticals. These limitations include, for instance, chemical instability, poor oral absorption, short halflife, and off-target cytotoxicity. One strategy to overcome these disadvantages relies on the formulation of bioactive peptides with nanocarriers. A range of biocompatible materials are now available that can serve as nanocarriers and can improve the bioavailability of therapeutic and venom-derived peptides for clinical and diagnostic application. Examples of isolated venom peptides and crude animal venoms that have been encapsulated and formulated with different types of nanomaterials with promising results are increasingly reported. Based on the current data, a wealth of information can be collected regarding the utilization of nanocarriers to encapsulate venom peptides and render them bioavailable for pharmaceutical use. Overall, nanomaterials arise as essential components in the preparation of biopharmaceuticals that are based on biological and pharmacological active venom-derived peptides.


2016 ◽  
Vol 24 (2) ◽  
Author(s):  
A. I. Sidorenko ◽  
V. D. Siokhin

In Ukraine the Great Cormorant (Phalacrocorax carbo Linnaeus, 1758) uses a rather wide range of habitats for nesting: islands, trees and shrubs, reedbeds and a variety of man-made structures. In general, the strategy of nesting on man-made structures is uncommon both in Ukraine and Europe, and Cormorantsdo this only in the absence of other sites suitable for nesting. Special research onCormorant colonies on technogenic constructions was carried out during the field expeditions by the Research Institute of Biodiversity of Terrestrial and Aquatic Ecosystems of Ukraine in 2002–2003 and 2012–2016. Besides this, we used retrospective and current data from the literature and Internet resources. Most of the field work was carried out by making surveys by boat and on foot. As a result, we found 8 Cormorant colonies on technogenic constructions in Ukraine: gas platforms in the Sea of Azov (near the village Strilkove, Henichesk district of Kherson region); sunken ships – targets for bombing training near the Arabat Spit (these are also known as «ship islands»); electricity pylons of the high-voltage Enerhodar Dnipro Power Line where it crosses the Kakhovka Reservoir; the dock in Yahorlyk Bayk, used in the past as a target for bombing training bombing; artificial island-platforms on Lake Chernine (Kinburn Peninsula); an artificial island on the Sasyk Lagoon (Odessa region); artificial islands, made as navigation markers on the Kremenchuk and Kiev reservoirs. The study found that in most cases the accompanying species was the CaspianGull (Larus cachinnans Pallas, 1811), which actively destroys the Cormorants’ nests and eats their eggs and chicks. The number of nests in the colonies varied greatly (5–30 nests on the navigation marker islands and ca. 2 000–2 300 on the «ship-islands» and gas platforms). This is due, primarily, to the area of the breeding territory. The research found that fierce territorial competition was observed in most of the colonies both with Caspian Gulls and between Cormorants. In addition, we observed anthropogenic interference in the colonies by fishermen and workers conducting routine maintenance work (as happened in the case of electricity pylons and gas platforms). The benefit of this study is that it is the first research in Ukraine conducted at national level onthis type of nesting by Cormorants. Moreover, the study examines the history of emergence of these nesting territories and population dynamics of the Great Cormorant from the time of initial settlement of the breeding sites till the present.


2018 ◽  
Vol 2 ◽  
pp. e25608 ◽  
Author(s):  
Lee Belbin ◽  
Arthur Chapman ◽  
John Wieczorek ◽  
Paula Zermoglio ◽  
Alex Thompson ◽  
...  

Task Group 2 of the TDWG Data Quality Interest Group aims to provide a standard suite of tests and resulting assertions that can assist with filtering occurrence records for as many applications as possible. Currently ‘data aggregators’ such as the Global Biodiversity Information Facility (GBIF), the Atlas of Living Australia (ALA) and iDigBio run their own suite of tests over records received and report the results of these tests (the assertions): there is, however, no standard reporting mechanisms. We reasoned that the availability of an internationally agreed set of tests would encourage implementations by the aggregators, and at the data sources (museums, herbaria and others) so that issues could be detected and corrected early in the process. All the tests are limited to Darwin Core terms. The ~95 tests refined from over 250 in use around the world, were classified into four output types: validations, notifications, amendments and measures. Validations test one of more Darwin Core terms, for example, that dwc:decimalLatitude is in a valid range (i.e. between -90 and +90 inclusive). Notifications report a status that a user of the record should know about, for example, if there is a user-annotation associated with the record. Amendments are made to one or more Darwin Core terms when the information across the record can be improved, for example, if there is no value for dwc:scientificName, it can be filled in from a valid dwc:taxonID. Measures report values that may be useful for assessing the overall quality of a record, for example, the number of validation tests passed. Evaluation of the tests was complex and time-consuming, but the important parameters of each test have been consistently documented. Each test has a globally unique identifier, a label, an output type, a resource type, the Darwin Core terms used, a description, a dimension (from the Framework on Data Quality from TG1), an example, references, implementations (if any), test-prerequisites and notes. For each test, generic code is being written that should be easy for institutions to implement – be they aggregators or data custodians. A valuable product of the work of TG2 has been a set of general principles. One example is “Darwin Core terms are either: literal verbatim (e.g., dwc:verbatimLocality) and cannot be assumed capable of validation, open-ended (e.g., dwc:behavior) and cannot be assumed capable of validation, or bounded by an agreed vocabulary or extents, and therefore capable of validation (e.g., dwc:countryCode)”. Another is “criteria for including tests is that they are informative, relatively simple to implement, mandatory for amendments and have power in that they will not likely result in 0% or 100% of all record hits.” A third: “Do not ascribe precision where it is unknown.” GBIF, the ALA and iDigBio have committed to implementing the tests once they have been finalized. We are confident that many museums and herbaria will also implement the tests over time. We anticipate that demonstration code and a test dataset that will validate the code will be available on project completion.


Author(s):  
Matt Woodburn ◽  
Gabriele Droege ◽  
Sharon Grant ◽  
Quentin Groom ◽  
Janeen Jones ◽  
...  

The utopian vision is of a future where a digital representation of each object in our collections is accessible through the internet and sustainably linked to other digital resources. This is a long term goal however, and in the meantime there is an urgent need to share data about our collections at a higher level with a range of stakeholders (Woodburn et al. 2020). To sustainably achieve this, and to aggregate this information across all natural science collections, the data need to be standardised (Johnston and Robinson 2002). To this end, the Biodiversity Information Standards (TDWG) Collection Descriptions (CD) Interest Group has developed a data standard for describing collections, which is approaching formal review for ratification as a new TDWG standard. It proposes 20 classes (Suppl. material 1) and over 100 properties that can be used to describe, categorise, quantify, link and track digital representations of natural science collections, from high-level approximations to detailed breakdowns depending on the purpose of a particular implementation. The wide range of use cases identified for representing collection description data means that a flexible approach to the standard and the underlying modelling concepts is essential. These are centered around the ‘ObjectGroup’ (Fig. 1), a class that may represent any group (of any size) of physical collection objects, which have one or more common characteristics. This generic definition of the ‘collection’ in ‘collection descriptions’ is an important factor in making the standard flexible enough to support the breadth of use cases. For any use case or implementation, only a subset of classes and properties within the standard are likely to be relevant. In some cases, this subset may have little overlap with those selected for other use cases. This additional need for flexibility means that very few classes and properties, representing the core concepts, are proposed to be mandatory. Metrics, facts and narratives are represented in a normalised structure using an extended MeasurementOrFact class, so that these can be user-defined rather than constrained to a set identified by the standard. Finally, rather than a rigid underlying data model as part of the normative standard, documentation will be developed to provide guidance on how the classes in the standard may be related and quantified according to relational, dimensional and graph-like models. So, in summary, the standard has, by design, been made flexible enough to be used in a number of different ways. The corresponding risk is that it could be used in ways that may not deliver what is needed in terms of outputs, manageability and interoperability with other resources of collection-level or object-level data. To mitigate this, it is key for any new implementer of the standard to establish how it should be used in that particular instance, and define any necessary constraints within the wider scope of the standard and model. This is the concept of the ‘collection description scheme,’ a profile that defines elements such as: which classes and properties should be included, which should be mandatory, and which should be repeatable; which controlled vocabularies and hierarchies should be used to make the data interoperable; how the collections should be broken down into individual ObjectGroups and interlinked, and how the various classes should be related to each other. which classes and properties should be included, which should be mandatory, and which should be repeatable; which controlled vocabularies and hierarchies should be used to make the data interoperable; how the collections should be broken down into individual ObjectGroups and interlinked, and how the various classes should be related to each other. Various factors might influence these decisions, including the types of information that are relevant to the use case, whether quantitative metrics need to be captured and aggregated across collection descriptions, and how many resources can be dedicated to amassing and maintaining the data. This process has particular relevance to the Distributed System of Scientific Collections (DiSSCo) consortium, the design of which incorporates use cases for storing, interlinking and reporting on the collections of its member institutions. These include helping users of the European Loans and Visits System (ELViS) (Islam 2020) to discover specimens for physical and digital loans by providing descriptions and breakdowns of the collections of holding institutions, and monitoring digitisation progress across European collections through a dynamic Collections Digitisation Dashboard. In addition, DiSSCo will be part of a global collections data ecosystem requiring interoperation with other infrastructures such as the GBIF (Global Biodiversity Information Facility) Registry of Scientific Collections, the CETAF (Consortium of European Taxonomic Facilities) Registry of Collections and Index Herbariorum. In this presentation, we will introduce the draft standard and discuss the process of defining new collection description schemes using the standard and data model, and focus on DiSSCo requirements as examples of real-world collection descriptions use cases.


2018 ◽  
Vol 2 ◽  
pp. e26369
Author(s):  
Michael Trizna

As rapid advances in sequencing technology result in more branches of the tree of life being illuminated, there has actually been a decrease in the percentage of sequence records that are backed by voucher specimens Trizna 2018b. The good news is that there are tools Trizna (2017), NCBI (2005), Biocode LLC (2014) to enable well-databased museum vouchers to automatically validate and format specimen and collection metadata for high quality sequence records. Another problem is that there are millions of existing sequence records that are known to contain either incorrect or incomplete specimen data. I will show an end-to-end example of sequencing specimens from a museum, depositing their sequence records in NCBI's (National Center for Biotechnology Information) GenBank database, and then providing updates to GenBank as the museum database revises identifications. I will also talk about linking records from specimen databases as well. Over one million records in the Global Biodiversity Information Facility (GBIF) Trizna (2018a) contain a value in the Darwin Core term "associatedSequences", and I will examine what is currently contained in these entries, and how best to format them to ensure that a tight connection is made to sequence records.


Development ◽  
1977 ◽  
Vol 40 (1) ◽  
pp. 143-157
Author(s):  
Paul S. Burgoyne ◽  
Thomas Ducibella

Mouse embryos (8-cell to early blastocyst) were denuded with pronase, and apposed in pairs which represented a wide range of stage combinations. These pairs either formed aggregates which differentiated into double-sized blastocysts, or they failed to aggregate. The 8–16-cell stages would not envelop late morulae/early blastocysts to form layered aggregates. This must mean that as the embryo differentiates into a blastocyst, the outer surface of the trophoblast loses its capacity for supporting cell spreading. The aggregation data also demonstrate that embryos almost completely lose their potential for aggregation at a very discrete stage in development – namely, between 8 and 9 h before blastocoel formation. It is argued that this is the stage at which the zonular tight junctional seal is completed, and that it is this physical barrier which prevents aggregation. It has been argued previously that the zonular tight junctional seal allows the creation of the special microenvironment which is necessary for the determination of the inner cells as inner cell mass. The completion of this seal 8–9 h before it is required for the formation of a blastocoel would provide a suitable time period for this cell determination to occur. The results obtained also relate to the technique of chimera production. Since the aim of this technique is to generate mice with mixed cell populations, it is important that the blastocyst formed following aggregation should have both cell lines present in the inner cell mass. This can best be assured by using relatively late morula stages (75 h post-HCG injection) since these will have already segregated their inner cells, but the incomplete seal will still allow aggregation to take place.


Author(s):  
Kyle N. Kunze ◽  
Aidan Haddad ◽  
Alexander E. White ◽  
Matthew R. Cohn ◽  
Robert F. LaPrade ◽  
...  

AbstractInjuries to the menisci of the knee are common in orthopedic sports medicine. Bibliometric studies can identify the core literature on a topic and help further our collective knowledge for both clinical and educational purposes. The purpose of the current study was to (1) identify and describe the 50 most cited articles in meniscus research over an 80-year time period to capture a wide range of influential articles and (2) identify the “citation classics” and milestone articles related to the meniscus of the knee. The Science Citation Index Expanded subsection of the Web of Science Core Collection was systematically searched for the 50 most cited meniscus articles. Data pertaining to bibliometric and publication characteristics were extracted and reported using descriptive statistics. The top 50 articles were published between the years 1941 and 2014 and collectively cited 13,152 times. The median (interquartile [IQR]) number of total citations per article was 203.5 (167.0–261.8), while the median citation rate was 9.6 (7.4–13.9) citations per year. The most cited article was “Knee joint changes after meniscectomy,” published in 1948. The article with the highest citation rate of 78.4 citations per year was “The long-term consequence of anterior cruciate ligaments and meniscus injuries – osteoarthritis,” published in 2007. The majority of articles were clinical outcome studies (n = 28, 56%). The top 50 most cited meniscus articles represent a compilation of highly influential articles which may augment reading curriculums and provide a strong knowledge base for orthopaedic surgery residents and fellows. The decade with the most articles was the 2000s, representing a recent acceleration in meniscus-based research. This is a level IV, cross-sectional study.


Author(s):  
Jacqueline R. deVries

In this volume’s rich survey of women’s print media in the interwar period, it might be surprising to find a chapter on feminist writing in religious periodicals – that is, if one assumes that Britain’s religious traditions were inhospitable contexts for feminist organising during this time period. But that assumption would not be entirely correct. The Anglican, Catholic, and Jewish communities in Britain – the three traditions explored here – certainly clung to theological and institutional structures that prevented women from moving freely or quickly into leadership roles. But these communities were never homogenous and their members expressed a wide range of attitudes about gender, sexuality, and women’s roles, some of which were highly progressive and found their way into print. The changing social and gender norms of the interwar period were much debated topics in Britain’s religious communities, and through their engagement with religious media, women found ways to influence those debates.


1962 ◽  
Vol 17 (4) ◽  
pp. 579-586 ◽  
Author(s):  
Margaret R. Becklake ◽  
C. J. Varvis ◽  
L. D. Pengelly ◽  
S. Kenning ◽  
M. McGregor ◽  
...  

Pulmonary capillary blood flow (Qc) in the exercising subject was calculated from the rate of disappearance of N2O during steady state breathing of an N2O-He-O2 mixture. Measurements were made after alveolar rinsing (reciprocal of N2 washout) had occurred, and up to 30 sec, a time period accompanied by minimal recirculation, since FaNN2O during this period did not rise significantly. Repeatability of the method, judged as the difference of a second estimate from a first on the same subject, was comparable to that reported for the direct Fick technique in resting subjects (31 of 33 paired observations agreed within 20%). Results over a wide range agreed with almost simultaneous measurements by a dye dilution technique (24 of 26 paired observations agreed within 20%), and when related to pulse rate and to Vo2, were comparable to those of the other workers whose subjects were studied in a similar posture. Indeed, this technique (using the indirect Fick principle under “steady state” conditions) probably attains its greatest accuracy during exercise when other methods become less easily applicable. Submitted on December 18, 1961


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