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Background material: Literature search strings for master's thesis
<p>History of the preliminary searches for the systematic review.</p>
Figures 2-3 from: Leal-Zanchet A, Marques A (2018) Searching for shelter in a ferruginous cave? A new species of Pasipha from a plateau in the Brazilian savanna (Platyhelminthes, Tricladida). ZooKeys 776: 13-25. https://doi.org/10.3897/zookeys.776.26308
Figures 2-3 Pasipha ferrariaphila sp. n., holotype, dorsal view, 2 general view of preserved specimen 3 schematic drawing of the anterior region of body. The arrow indicates the anterior extremity. Eyes were drawn based on observations carried out under both stereomicroscope and microscope.
Figures 4-8 from: Leal-Zanchet A, Marques A (2018) Searching for shelter in a ferruginous cave? A new species of Pasipha from a plateau in the Brazilian savanna (Platyhelminthes, Tricladida). ZooKeys 776: 13-25. https://doi.org/10.3897/zookeys.776.26308
Figures 4-8 Pasipha ferrariaphila sp. n., holotype. 4 anterior region, transverse section 5–7 pre-pharyngeal region, transverse sections 8 pharynx, sagittal section.
Figures 10-14 from: Leal-Zanchet A, Marques A (2018) Searching for shelter in a ferruginous cave? A new species of Pasipha from a plateau in the Brazilian savanna (Platyhelminthes, Tricladida). ZooKeys 776: 13-25. https://doi.org/10.3897/zookeys.776.26308
Figures 10-14 Pasipha ferrariaphila sp. n., holotype, copulatory apparatus in sagittal sections. 10 general view 11 proximal region of prostatic vesicle 12 ejaculatory duct and proximal portion of male atrium 13 proximal portion of female atrium 14 gonoduct. Arrows indicate the strong musculature in female atrium; the arrow head indicates the canal separating proximal and distal regions of prostatic vesicle. Anterior to the left.
Figure 9 from: Leal-Zanchet A, Marques A (2018) Searching for shelter in a ferruginous cave? A new species of Pasipha from a plateau in the Brazilian savanna (Platyhelminthes, Tricladida). ZooKeys 776: 13-25. https://doi.org/10.3897/zookeys.776.26308
Figure 9 Pasipha ferrariaphila sp. n., holotype, sagittal composite reconstruction of copulatory apparatus. The arrow indicates the strong musculature in female atrium. Anterior to the left.
Figure 1 from: Leal-Zanchet A, Marques A (2018) Searching for shelter in a ferruginous cave? A new species of Pasipha from a plateau in the Brazilian savanna (Platyhelminthes, Tricladida). ZooKeys 776: 13-25. https://doi.org/10.3897/zookeys.776.26308
Figure 1 Location of the type locality of Pasipha ferrariaphila sp. n., represented by a ferruginous cave, Conceição do Mato Dentro, state of Minas Gerais, Brazil. The asterisk indicates the cave location; the outline indicates areas impacted by mining exploitation projects.
FIGURE 7 in In search of the real Pseudomallada prasinus (Neuroptera, Chrysopidae)
FIGURE 7. Portrait of a "greenhead" female with a red suture under the antenna.
FIGURE 8 in In search of the real Pseudomallada prasinus (Neuroptera, Chrysopidae)
FIGURE 8. Portrait of a "sulfurhead" female with a reddish brown subantennal suture.
FIGURE 2 in In search of the real Pseudomallada prasinus (Neuroptera, Chrysopidae)
FIGURE 2. Pseudomallada prasinus (marianus morph), female from Agarone, Ticino, Switzerland.
SLR_Search_Results_HBPRs
<p>This document contains the results of a literature search on HBPRs.</p>
Extensive literature search on glycoalkaloids and quinolizidine alkaloids - results of the selection for relevance and study characterisation
<p>This report presents the outcome of extensive literature search on studies related to the chemistry and toxicity of glycoalkaloids and quinolizidine alkaloids in food and feed. The systematic literature search captures available scientific information published since 1950. 3,147 references were identified as potentially related to the chemistry and toxicity of glycoalkaloids in food and feed and 8,287 as potentially related to the chemistry and toxicity of quinolizidine alkaloids in food and feed. Upon screening of titles and abstracts of the candidates concerning glycoalkaloids, 1,645 were regarded as relevant, the number of included potentially relevant studies concerning quinolizidine alkaloids was 1,783. All included studies were characterised according to 10 different areas of interest of EFSA for further investigation.</p> <p>Software needed to open the files: Microsoft Office - Excel; EndNote.</p> <p> </p> <p><strong>This upload supports the risk assessment on Quinolizidine alkaloids in food and feed:</strong> EFSA CONTAM Panel (EFSA Panel on Contaminants in the Food Chain), Schrenk D, Bodin L, Chipman JK, del Mazo J, Grasl-Kraupp B, Hogstrand C, Hoogenboom LR, Leblanc J-C, Nebbia CS, Nielsen E, Ntzani E, Petersen A, Sand S, Schwerdtle T, Vleminckx C, Wallace H, Alexander J, Cottrill B, Dusemund B, Mulder P, Arcella D, Baert K, Cascio C, Steinkellner H and Bignami M, 2019. Scientific opinion on the risks for animal and human health related to the presence of quinolizidine alkaloids in feed and food, in particular in lupins and lupin-derived products. EFSA Journal 2019;17(10):5860, 113 pp. <br> https://doi.org/10.2903/j.efsa.2019.5860</p>
Data to search Lake Baikal viromes against GOV 2.0
<p>Includes reads from "Metagenomic Analysis of Virioplankton from the Pelagic Zone of Lake Baikal" (https://doi.org/10.3390/v11110991). MG-RAST IDs: BVP1 -- mgm4814173.3, BVP2 -- mgm4816981.3.</p> <p>Also, GOV 2.0 viral populations over 10kb from http://datacommons.cyverse.org/browse/iplant/home/shared/iVirus/GOV2.0/GOV2_viral_populations_larger_than_10KB_or_circular.zip. (From Marine DNA Viral Macro- and Microdiversity from Pole to Pole, https://doi.org/10.1016/j.cell.2019.03.040).</p> <p>The data is grouped together here for ease of access.</p>
All result files, searching parameter files, and simulated data sets used in FeasiModel
<p>All result files, searching parameter files, and simulated data sets used in FeasiModel</p>
Database files 1 for network described in "Expanding the scope of a catalogue search to bioisosteric fragment merges using a graph database approach"
<p>Contains part 1/2 of the database files required for running the database described in "Expanding the scope of a catalogue search to bioisosteric fragment merges using a graph database approach" that can be run with https://github.com/stephwills/docker-neo4j.</p>
Database files 2 for network described in "Expanding the scope of a catalogue search to bioisosteric fragment merges using a graph database approach"
<p>Contains part 2/2 of the database files required for running the database described in "Expanding the scope of a catalogue search to bioisosteric fragment merges using a graph database approach" that can be run with https://github.com/stephwills/docker-neo4j.</p>
Appendix - Detailed search terms for database browsing.
Open the record for dataset details and reuse information.
Avoiding searching for outcomes called for additional search strategies
Open the record for dataset details and reuse information.
Data for ICSE 2025 paper "Search-Based LLMs for Code Optimization"
Open the record for dataset details and reuse information.
Data from: An automated approach to identifying search terms for systematic reviews using keyword co-occurrence networks
1. Systematic review, meta-analysis, and other forms of evidence synthesis are critical to strengthen the evidence base concerning conservation issues and to answer ecological and evolutionary questions. Synthesis lags behind the pace of scientific publishing, however, due to time and resource costs which partial automation of evidence synthesis tasks could reduce. Additionally, current methods of retrieving evidence for synthesis are susceptible to bias towards studies with which researchers are familiar. In fields that lack standardized terminology encoded in an ontology, including ecology and evolution, research teams can unintentionally exclude articles from the review by omitting synonymous phrases in their search terms. 2. To combat these problems, we developed a quick, objective, reproducible method for generating search strategies that uses text mining and keyword co-occurrence networks to identify the most important terms for a review. The method reduces bias in search strategy development because it does not rely on a predetermined set of articles and can improve search recall by identifying synonymous terms that research teams might otherwise omit. 3. When tested against the search strategies used in published environmental systematic reviews, our method performs as well as the published searches and retrieves gold-standard hits that replicated versions of the original searches do not. Because the method is quasi-automated, the amount of time required to develop a search strategy, conduct searches, and assemble results is reduced from approximately 17-34 hours to under 2 hours. 4. To facilitate use of the method for environmental evidence synthesis, we implemented the method in the R package litsearchr, which also contains a suite of functions to improve efficiency of systematic reviews by automatically deduplicating and assembling results from separate databases.
Data from: The interaction between ambush predators, search patterns of herbivores and aggregations of plants
<p>While predators benefit from spatial overlap with their prey, prey strive to avoid predators. I used an individual-based simulation comprising sit-and-wait predators, widely-foraging herbivores, and plants, to examine the link between predator ambush location, herbivore movement, and plant aggregation. I used a genetic algorithm to reach the best strategies for all players. The predators could ambush herbivores either inside or outside plant patches. The herbivores could use movement of varying directionality levels, with a change in directionality following the detection of plants. When the predators were fixed outside plant patches, the herbivores were selected to use a directional movement before plant encounter followed by a tortuous movement afterwards. When predators were fixed inside patches, herbivores used a continuous directional movement. Predators maintained within-patch positions when the herbivores were fixed to use the directional-tortuous movement. The predator location inside patches led to higher plant aggregations, by changing the herbivore movement. Finally, I allowed half of the predators to search for herbivores and let them compete with sit-and-wait predators located inside plant patches. When plants were clumped and herbivores used a directional-tortuous movement, with a movement shift after plant detection, ambush predators had a higher success relative to widely-foraging predators. In all other scenarios, widely-foraging predators did much better than ambush predators. The findings from my simulation suggest a behavioral mechanism for several observed phenomena of predator-prey interactions, such as a shorter stay by herbivores in patches when predators ambush them nearby, and a more directional movement of herbivores in riskier habitats.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.