scholarly journals Making Parasite-Host Associations Visible using Global Biotic Interactions

2020 ◽  
Vol 4 ◽  
Author(s):  
Katja Seltmann ◽  
Jorrit Poelen ◽  
Kathryn Sullivan ◽  
Jennifer Zaspel
Keyword(s):  
Grey Literature ◽  
Specific Interaction ◽  
Biotic Interactions ◽  
Species Interaction ◽  
Emergent Properties ◽  
Scientific Publications ◽  
Data Archives ◽  
Collection Data ◽  
Association Data ◽  
Occurrence Records

A wealth of information about how parasites interact with their hosts already exists in collections, scientific publications, specialized databases, and grey literature. The US National Science Foundation-funded Terrestrial Parasite Tracker Thematic Collection Network (TPT) project began in 2019 to help build a comprehensive picture of arthropod ectoparasites including the evolution of these parasite-host biotic associations, distributions, and the ecological interactions of disease vectors. TPT is a network of biodiversity collections whose data can assist scientists, educators, land managers, and policymakers to better understand the complex relationship between hosts and parasites including emergent properties that may explain the causes and frequency of human and wildlife pathogens. TPT member collections make their association information easier to access via Global Biotic Interactions (GloBI, Poelen et al. 2014), which is periodically archived through Zenodo to track progress in the TPT project. TPT leverages GloBI's ability to index biotic associations from specimen occurrence records that come from existing management systems (e.g., Arctos, Symbiota, EMu, Excel, MS Access) to avoid having to completely rework existing, or build new, cyber-infrastructures before collections can share data. TPT-affiliated collection managers use collection-specific translation tables to connect their verbatim (or original) terms used to describe associations (e.g., "ex", "found on", "host") to their interpreted, machine-readable terms in the OBO Relations Ontology (RO). These interpreted terms enable searches across previously siloed association record sets, while the original verbatim values remain accessible to help retain provenance and allow for interpretation improvements. TPT is an ambitious project, with the goal to database label data from over 1.2 million specimens of arthropod parasites of vertebrates coming from 22 collections across North America. In the first year of the project, the TPT collections created over 73,700 new records and 41,984 images. In addition, 17 TPT data providers and three other collaborators shared datasets that are now indexed by GloBI, visible on the TPT GloBI project page. These datasets came from collection specimen occurrence records and literature sources. Two TPT data archives that capture and preserve the changes in the data coming from TPT to GloBI were published through Zenodo (Poelen et al. 2020a, Poelen et al. 2020b). The archives document the changes in how data are shared by collections including the biotic association data format and quantity of data captured. The Poelen et al. 2020b report included all TPT collections and biotic interactions from Arctos collections in VertNet and the Symbiota Collection of Arthropods Network (SCAN). The total number of interactions included in this report was 376,671 records (500,000 interactions is the overall goal for TPT). In addition, close coordination with TPT collection data managers including many one-on-one conversations, a workshop, and a webinar (Sullivan et al. 2020) was conducted to help guide the data capture of biotic associations. GloBI is an effective tool to help integrate biotic association data coming from occurrence records into an openly accessible, global, linked view of existing species interaction records. The results gleaned from the TPT workshop and Zenodo data archives demonstrate that minimizing changes to existing workflows allow for custom interpretation of collection-specific interaction terms. In addition, including collection data managers in the development of the interaction term vocabularies is an important part of the process that may improve data sharing and the overall downstream data quality.

scholarly journals Pemanfaatan Publikasi Ilmiah di Perguruan Tinggi

Pustakaloka ◽  
2017 ◽  
Vol 9 (2) ◽  
Author(s):  
Agung Nugrohoadhi
Keyword(s):  
Teaching And Learning ◽  
Grey Literature ◽  
Scientific Publication ◽  
Academic Community ◽  
Assessment Instruments ◽  
Book Market ◽  
Scientific Publications ◽  
Digital Collections ◽  
Local Content ◽  
Process Support

Abstraksi  : Publikasi  merupakan sarana untuk menyampaikan informasi  yang  diharapkan mampu memberikan  kontribusi positif  bagi pengembangan wawasan ilmiah bagi  seseorang. Dalam perguruan tinggi  publikasi ilmiah bisa berbentuk majalah, jurnal,  ataupun  koleksi  digital berupa e-journal dan e-book  yang saat ini sudah menjadi  kebutuhan yang tak terbantahkan untuk digunakan bagi pendukung proses belajar mengajar ataupun sebagai kegiatan proses kreatif segenap civitas akademika untuk memunculkan ide ide segar sebagai pendukung penelitian. Maka tidaklah mengherankan  apabila perpustakaan sebagai perpustakaa riset  dengan menyediakan publikasi ilmiah yang menyediakan beragam informasi . Dalam perkembangan selanjutnya muncul koleksi repository yang lebih mengkhususkan diri untuk mengelola dokumen yang dihasilkan oleh sebuah instansi dalam hal ini perguruan tinggi dengan sebutan literature kelabu (grey literature) yang dapat berupa dokumen yang khas dan , buku-buku yang jarang didapatkan di pasar buku dan juga dokumen yang sering disebut  local content. Publikasi local content  ini saat ini menjadi salah satu ukuran tolok ukur akreditasi perguruan tinggi  sehingga semakin mengokohkan publikasi ilmiah sebagai salah satu instrument penilaian akreditasi perguruan tinggi. ABSTRACT: Publication is a means to convey information that is expected to contribute positively to the development of scientific insight for a person. In college, scientific publications can be in the form of magazines, journals, or digital collections such as e-journals and e-books that are now an indispensable requirement to be used for teaching and learning process support or as creative activities of the entire academic community to generate ideas Fresh as research supporters. So it is not surprising if the library as a library of research by providing scientific publications that provide a variety of information. In subsequent developments appears more specialized repository collection to manage documents produced by an institution in this college with a literature gray literature that can be a typical document and, the books are rarely found in the book market and also Documents that are often called local content. This local content publication is now one of the benchmarks of college accreditation so that it becomes more and more solidifies the scientific publication as one of the accreditation assessment instruments of universities.

scholarly journals GalliForm, a database of Galliformes occurrence records from the Indo-Malay and Palaearctic, 1800–2008

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Elizabeth H. Boakes ◽  
Richard A. Fuller ◽  
Georgina M. Mace ◽  
Changqing Ding ◽  
Tzo Tze Ang ◽  
...  
Keyword(s):  
Species Distribution ◽  
Grey Literature ◽  
Distribution Data ◽  
Historical Aspect ◽  
Term Change ◽  
Control Procedures ◽  
Field Notes ◽  
Over Exploitation ◽  
Local Extirpation ◽  
Occurrence Records

Abstract Historical as well as current species distribution data are needed to track changes in biodiversity. Species distribution data are found in a variety of sources, each of which has its own distinct bias toward certain taxa, time periods or places. We present GalliForm, a database that comprises 186687 galliform occurrence records linked to 118907 localities in Europe and Asia. Records were derived from museums, peer-reviewed and grey literature, unpublished field notes, diaries and correspondence, banding records, atlas records and online birding trip reports. We describe data collection processes, georeferencing methods and quality-control procedures. This database has underpinned several peer-reviewed studies, investigating spatial and temporal bias in biodiversity data, species’ geographic range changes and local extirpation patterns. In our rapidly changing world, an understanding of long-term change in species’ distributions is key to predicting future impacts of threatening processes such as land use change, over-exploitation of species and climate change. This database, its historical aspect in particular, provides a valuable source of information for further studies in macroecology and biodiversity conservation.

scholarly journals The latitudinal gradient in rates of evolution for bird beaks, a species interaction trait

2020 ◽  
Author(s):  
Benjamin G Freeman ◽  
Dolph Schluter ◽  
Joseph A Tobias
Keyword(s):  
Meta Analysis ◽  
Biotic Interactions ◽  
Species Interaction ◽  
Temperate Zone ◽  
Ecological Opportunity ◽  
Evolutionary Diversification ◽  
Diversity Gradient ◽  
Rates Of Evolution ◽  
Speciation Rates ◽  
Beak Size

AbstractWhere is evolution fastest? The biotic interactions hypothesis proposes that greater species richness creates more ecological opportunity, driving faster evolution at low latitudes, whereas the “empty niches” hypothesis proposes that ecological opportunity is greater where diversity is low, spurring faster evolution at high latitudes. Here we tested these contrasting predictions by analyzing rates of bird beak evolution for a global dataset of 1141 sister pairs of birds. Beak size evolves at similar rates across latitudes, while beak shape evolves faster in the temperate zone, consistent with the empty niches hypothesis. We show in a meta-analysis that trait evolution and recent speciation rates are faster in the temperate zone, while rates of molecular evolution are slightly faster in the tropics. Our results suggest that drivers of evolutionary diversification are more potent at higher latitudes, thus calling into question multiple hypotheses invoking faster tropical evolution to explain the latitudinal diversity gradient.

scholarly journals Associations between carabid beetles and fungi in the light of 200 years of published literature

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Gábor Pozsgai ◽  
Ibtissem Ben Fekih ◽  
Markus V. Kohnen ◽  
Said Amrani ◽  
Sándor Bérces ◽  
...  
Keyword(s):  
Large Scale ◽  
Current Knowledge ◽  
Biotic Interactions ◽  
Ground Beetles ◽  
Carabid Beetles ◽  
Ecological Interactions ◽  
Scientific Publications ◽  
Palearctic Region ◽  
Interactive Data ◽  
Unique Dataset

AbstractDescribing and conserving ecological interactions woven into ecosystems is one of the great challenges of the 21st century. Here, we present a unique dataset compiling the biotic interactions between two ecologically and economically important taxa: ground beetles (Coleoptera: Carabidae) and fungi. The resulting dataset contains the carabid-fungus associations collected from 392 scientific publications, 129 countries, mostly from the Palearctic region, published over a period of 200 years. With an updated taxonomy to match the currently accepted nomenclature, 3,378 unique associations among 5,564 records were identified between 1,776 carabid and 676 fungal taxa. Ectoparasitic Laboulbeniales were the most frequent fungal group associated with carabids, especially with Trechinae. The proportion of entomopathogens was low. Three different formats of the data have been provided along with an interactive data digest platform for analytical purposes. Our database summarizes the current knowledge on biotic interactions between insects and fungi, while offering a valuable resource to test large-scale hypotheses on those interactions.

scholarly journals Parasitism in Eukaryota - Reconstruction of Ancestral and Unavailable Extant States

2018 ◽  
Vol 2 ◽  
pp. e25739
Author(s):  
Lydia Buntrock ◽  
Bernhard Renard ◽  
Emanuel Heitlinger
Keyword(s):  
Phylogenetic Trees ◽  
Cross Validation ◽  
Biotic Interactions ◽  
Species Interaction ◽  
State Information ◽  
Large Sets ◽  
Computational Reconstruction ◽  
Important Trait ◽  
Topology Information ◽  
Available Information

Parasitism can be defined as an interaction between species in which one of the interaction partners, the parasite, lives in or on the other, the host. The parasite draws food from its host and harms it in the process. According to some estimates, over 40% of all eukaryotes are parasites. Nevertheless, it is difficult to obtain information about a particular taxon is a parasite computationally making it difficult to query large sets of taxa. Here we test to what extend it is possible to use the Open Tree of Life (OTL), a synthesis of phylogenetic trees on a backbone taxonomy (resulting in unresolved nodes), to expand available information via phylogenetic trait prediction. We use the Global Biotic Interactions (GloBI) database to categorise 25,992 and 34,879 species as parasites and free-living, respectively, and predict states for over ~2.3 million (97.34%) leaf nodes without state information. We estimate the accuracy of our maximum parsimony based predictions using cross-validation and simulation at roughly 60-80% overall, but strongly varying between clades. The cross-validation resulted in an accuracy of 98.17% which is explained by the fact that the data are not uniformly distributed. We describe this variation across taxa as associated with available state and topology information. We compare our results with several smaller scale studies, which used manual expert curation and conclude that computationally inferred state changes largely agree in number and placement with those. In clades in which available state information is biased (mostly towards parasites, e.g. in Nematodes) phylogenetic prediction is bound to provide results contradicting conventional wisdom. This represents, to our knowledge, the first comprehensive computational reconstruction of the emergence of parasitism in eukaryotes. We argue that such an approach is necessary to allow further incorporation of parasitism as an important trait in species interaction databases and in individual studies on eukaryotes, e.g. in the microbiome.

scholarly journals A national atlas of tsetse and African animal trypanosomosis in Mali

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Boucader Diarra ◽  
Modibo Diarra ◽  
Oumar Diall ◽  
Boubacar Bass ◽  
Youssouf Sanogo ◽  
...  
Keyword(s):  
Animal Health ◽  
Grey Literature ◽  
National Level ◽  
Sub Saharan Africa ◽  
Tsetse Flies ◽  
Scientific Publications ◽  
North East ◽  
The North ◽  
African Animal Trypanosomosis ◽  
Animal Trypanosomosis

Abstract Background Tsetse-transmitted trypanosomosis is a deadly, neglected tropical disease and a major challenge for mixed crop-livestock agriculture in sub-Saharan Africa. It is caused by several species of the genus Trypanosoma. Information on the occurrence of tsetse flies and African animal trypanosomosis (AAT) is available for different areas of Mali. However, these data have never been harmonized and centralized, which prevents the development of comprehensive epidemiological maps and constrains an evidence-based planning of control actions. To address this challenge, we created a dynamic geo-spatial database of tsetse and AAT distribution in Mali. Methods A digital repository containing epidemiological data collected between 2000 and 2018 was assembled. In addition to scientific publications, the repository includes field datasheets, technical reports and other grey literature. The data were verified, harmonized, georeferenced and integrated into a single spatially-explicit database. Results For the tsetse component, approximately 19,000 trapping records, corresponding to 6000 distinct trapping locations and 38,000 flies were included in the database. Glossina palpalis gambiensis was the most widespread and abundant species, and it was found in the southern, southern-central and western parts of the country. Glossina tachinoides was only found in the South. Only a few specimens of Glossina morsitans submorsitans were detected. For the AAT component, approximately 1000 survey records were included, corresponding to 450 distinct survey sites and 37,000 tested bovines. AAT was found in all surveyed regions, although data for the tsetse-free North and North-East are lacking. Trypanosoma vivax and Trypanosoma congolense were the dominant species, while Trypanosoma brucei infections were much less numerous. Conclusions The atlas of tsetse and AAT in Mali provides a synoptic view of the vector and disease situation at the national level. Still, major geographical gaps affect the North, the North-East and the West, and there is also a severe lack of data over the past five years. Trypanosomosis remains a major animal health problem in Mali. However, despite its prevalence and distribution, monitoring and control activities are presently very limited. Efforts should be made to strengthen the progressive control of AAT in Mali, and the atlas provides a new tool to identify priority areas for intervention.

scholarly journals The Ecology of Plant Interactions: A Giant with Feet of Clay

2021 ◽  
Author(s):  
Ciro Cabal ◽  
Ricardo Martínez-García ◽  
Fernando Valladares
Keyword(s):  
Biotic Interactions ◽  
Phenomenological Approach ◽  
Species Interaction ◽  
Spatial And Temporal Variability ◽  
Plant Interactions ◽  
Individual Level ◽  
Biophysical Processes ◽  
Individual Scale ◽  
The Individual ◽  
The Right

Ecologists use the net biotic interactions among plants as a major factor to predict other ecosystem features, such as species diversity, community structure, or plant atmospheric carbon uptake. By adopting this approach, ecologists have built a giant body of theory founded on observational evidence. However, growing evidence points out that this may not be the right approach. The literature addressing the biophysical mechanisms underlying the plant interactions is much scarcer. A rising number of scientists claim the need for a mechanistic understanding of plant interactions due to the limitations that a phenomenological approach raises both in empirical and theoretical studies. Scattered studies have recently taken such a mechanistic approach, but we still lack a general theoretical framework to study mechanistically plant interactions. In this review, we first recapitulate the elementary units of plant interactions, i.e., all the known biophysical processes affected by the presence of an influencing plant and the possible phenotypic responses of plants influenced by those processes. Second, we discuss how a net interaction between two plants emerges from the simultaneous effect of these elementary units. Third, we touch upon the spatial and temporal variability of the net interaction and discuss the links between this variability and the underlying biophysical processes. We conclude by discussing how to integrate these processes into a mechanistic framework for plant interactions that must necessarily focus on the individual scale and explicitly incorporate the spatial structure of the community and environmental factors: the plant interaction models (PIM). A PIM incorporates a pair or few plants interacting with their physical environment so that the biotic interaction is not imposed but emerges from the model. This type of model can provide concise, mechanistic hypotheses to be tested empirically. This review calls for a paradigm shift in the ecology of plant interactions, from the classic species interaction study towards a more mechanistic individual-level approach. It also presents a comprehensive foundation for studying the mechanisms underpinning the net interaction between two plants.

Libros en abierto de las editoriales universitarias españolas

2021 ◽  
Author(s):  
Rosana López-Carreño ◽  
Ángel M. Delgado-Vázquez ◽  
Francisco-Javier Martínez-Méndez
Keyword(s):  
Open Access ◽  
Public Universities ◽  
Grey Literature ◽  
Open Science ◽  
Open Access Publishing ◽  
Academic Publishing ◽  
Scientific Publications ◽  
Acceso Abierto ◽  
Spanish Public Universities ◽  
Access Policies

This paper analyses the set of scientific publications in open access, other than journals (monographs, conferences proceedings, teaching materials and grey literature), published by Spanish public universities, studying their volume, documentary typology, level of description and open access policies with the aim of measuring their degree of incorporation and compliance with the principles of Open Science. An exhaustive review of the disposed material in open access by these publishers has been carried out, which has allowed to make a diagnosis of their level of open access publishing. Grey literature is the most common documentary type followed by the monograph, in the open publication of these publishers that does not reach even 5% of the average editorial production. The results allow us to conclude that the academic publishing, and more specifically the academic books in open access, still has a very reduced presence within the editorial production of these institutions. Resumen Este trabajo analiza el conjunto de las publicaciones científicas en acceso abierto, distintas de las revistas científicas (monografías, actas de congresos, materiales didácticos y literatura gris), dispuestas para su consulta por las editoriales universitarias públicas, estudiando su volumen, tipología documental, nivel de descripción y políticas de acceso abierto con el objetivo de medir el grado de incorporación y cumplimiento de los principios de Ciencia Abierta. Se ha llevado a cabo una exhaustiva revisión del material publicado en acceso abierto por estas editoriales que ha permitido establecer un diagnóstico de su nivel de edición en acceso abierto. La literatura gris es el tipo documental más frecuente seguido de la monografía, en la publicación en abierto de las editoriales universitarias que no alcanza ni el 5% de la producción editorial universitaria. Los resultados permiten concluir que la publicación académica, y más concretamente el libro en acceso abierto, sigue teniendo una presencia muy reducida dentro de la producción editorial de estas instituciones.

scholarly journals Microclimate and resource quality determine resource use in a range-expanding herbivore

2021 ◽  
Vol 17 (8) ◽  
pp. 20210175
Author(s):  
James E. Stewart ◽  
Ilya M. D. Maclean ◽  
Alice J. Edney ◽  
Jon Bridle ◽  
Robert J. Wilson
Keyword(s):  
Climate Change ◽  
Spatial Scales ◽  
Good Condition ◽  
Biotic Interactions ◽  
Egg Laying ◽  
Emergent Properties ◽  
Ecological Communities ◽  
Ambient Temperatures ◽  
Resource Condition ◽  
Range Dynamics

The consequences of climate change for biogeographic range dynamics depend on the spatial scales at which climate influences focal species directly and indirectly via biotic interactions. An overlooked question concerns the extent to which microclimates modify specialist biotic interactions, with emergent properties for communities and range dynamics. Here, we use an in-field experiment to assess egg-laying behaviour of a range-expanding herbivore across a range of natural microclimatic conditions. We show that variation in microclimate, resource condition and individual fecundity can generate differences in egg-laying rates of almost two orders of magnitude in an exemplar species, the brown argus butterfly ( Aricia agestis ). This within-site variation in fecundity dwarfs variation resulting from differences in average ambient temperatures among populations. Although higher temperatures did not reduce female selection for host plants in good condition, the thermal sensitivities of egg-laying behaviours have the potential to accelerate climate-driven range expansion by increasing egg-laying encounters with novel hosts in increasingly suitable microclimates. Understanding the sensitivity of specialist biotic interactions to microclimatic variation is, therefore, critical to predict the outcomes of climate change across species' geographical ranges, and the resilience of ecological communities.

scholarly journals Protocol for evaluating the impact of interventions on the future Burden of Disease in Scotland

2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Grant Wyper ◽  
Ian Grant ◽  
Eilidh Fletcher ◽  
Neil Anand ◽  
Neil Craig ◽  
...  
Keyword(s):  
Risk Factors ◽  
Burden Of Disease ◽  
Grey Literature ◽  
Routine Data ◽  
Years Of Life Lost ◽  
Scientific Publications ◽  
Efficient Manner ◽  
Health Loss ◽  
Life Years ◽  
The Impact

BackgroundRecent evidence shows that after several decades of gains in life expectancy, Scotland has firmly entered a period of slow-down. Trend data show that the prevalence of morbidity continues to increase resulting in a frailer and more vulnerable population. Burden of Disease (BOD) studies measure the causes of health loss and their attribution to risk factor exposure and are essential to tackling current and future population needs for care workforce and services in an efficient manner. AimTo assess the current and projected health loss in Scotland between 2019 and 2040, based on different scenarios for change in risk factors and the impact and cost-effectiveness of evidence-based interventions on those risk factors. Methods and AnalysisEstimates of Years Lived with Disability (YLD), Years of Life Lost (YLL) and DALYs (Disability-adjusted Life Years) will be developed for 132 conditions for Scotland using routine data sources and linkage techniques. These estimates will be linked to risk factors using attributable fractions from the Global Burden of Disease (GBD) 2017 study. Scenario-modelling will be carried out based on three scenarios: continuation; worsening; and improvements of secular trends. Cost-effective interventions will be identified and their results will be assessed in the context of Scottish BOD estimates (current & projected) and evidence on the costs and potential impact of those interventions. Dissemination Findings from Scottish BOD estimates along with information on costs and effectiveness will help direct resources to interventions and policies with the most potential to reduce disease burdens and improve population health. Results will be disseminated through pre-print publications, scientific publications, grey literature, social media and conference or workshop presentations both nationally and internationally throughout the European Burden of Disease Network and associated events.

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