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Phytoliths in dicotyledons occurring in North-western Europe: Establishing a baseline
<div> <div> <div> <div> </div> </div> </div> </div> <div> <div> <div> <div> <div> <div> <p>This repository contains raw data tables, the R analysis script, plant tissue sample images, and 964 labeled microphotographs as part of the study "Phytoliths in dicotyledons occurring in North-western Europe: Establishing a baseline" published in Annals of Botany. </p> <p>The 964 microphotographs are labeled (metadata) using morphotype codes that can be found in table 2 in the paper (e.g., M-1, AMO_TUB, Tra-1...). </p> </div> </div> </div> </div> </div> </div>
Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources
<p>Knowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9,309 SNPs localised in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to determine the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual / interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (FST = 0.0240; P < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental drivers suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome, suggestive of selective sweeps. Two main genetic groups were identified, northwards and southwards of French Brittany, in accordance with the larval dispersal modelling, which suggested a barrier for larval dispersal linked to the Ushant front. Further genetic subdivision was observed using outlier loci and considering larval behaviour. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for management of cockles, designing conservation strategies, founding broodstock for depleted beds, and producing suitable seed for aquaculture production.</p>
Considerations on baseline generation for Imaging AI studies illustrated on the CT-based prediction of empyema and outcome assessment.
<p><strong>Considerations on baseline generation for Imaging AI studies illustrated on the CT-based prediction of empyema and outcome assessment.</strong></p> <p><strong>Introduction</strong>: For AI-based classification tasks in computed tomography, a reference standard for evaluating the clinical diagnostic accuracy of individual classes is essential. To enable the implementation of an AI tool in clinical practice, this should be drawn from clinical routine data, using State-of-the-art scanners, evaluated in a blinded manner, and verified with a reference test.</p> <p><strong>Methods: </strong>2659 consecutive CTs performed between 01/2016 and 01/2021 with reported pleural effusion were retrospectively included. Pathology reports from thoracocentesis or biopsy within 7 days of CT were used as reference standard (n = 335). Two radiologists (4 and 10 PGY) blindly assessed chest CTs (n=335, 81 empyemas) for pleural CT features and ICC was determined. In addition, both pleural CT features and radiological diagnosis were extracted from written radiological reports. If needed, consensus was achieved using an experienced radiologist's opinion (29 PGY). We assessed the correlation of these findings with the following patient outcomes: mortality and median hospital stay.</p> <p><strong>Results: </strong>Specificity and sensitivity for clinical detection of empyema (N=81) were 90.94 (95%-CI 86.55-94.05) and 72.84 (95%-CI: 61.63-81.85%) in all effusions, with moderate to almost perfect interrater agreement for all pleural findings associated with empyema (Cohen's kappa = 0.41-0.82). Features describing pleural enhancement or thickening achieved the highest accuracy with 87.02% and 81.49%, respectively. Empyema was associated with a longer hospital stay (median= 20 versus 14 days), and findings consistent with pleural carcinosis impacted mortality. </p>
Oncorhynchus kisutch genetic stock ID SNP baseline
<p>Genetic stock identification (GSI) <span>using genotypes produced from genotyping-by-sequencing of SNP loci</span> has become the gold standard for stock identification in Pacific salmon, which are found in mixed stocks in the ocean. Sequencing platforms currently applied require large batch sizes and multi-day processing in specialized facilities to perform genotyping by the thousands. However, recent advances in third-generation single-molecule sequencing platforms, like the Oxford Nanopore minION, provide base calling on portable, pocket-sized sequencers and promise real-time, in-field stock identification on variable batch sizes. Here we evaluate utility and comparability to established GSI platforms of at-sea stock identification of coho salmon <i>Oncorhynchus kisutch</i> based on targeted SNP amplicon sequencing on the minION platform during a high-sea winter expedition to the Gulf of Alaska. As long read sequencers are not optimized for short amplicons, we concatenate amplicons to increase coverage and throughput. Nanopore sequencing at-sea yielded stock assignment for 50 of the 80 assessed individuals. Nanopore-based SNP calls agreed with Ion Torrent based genotypes in 83.25%, but assignment of individuals to stock of origin only agreed in 61.5% of individuals highlighting inherent challenges of Nanopore sequencing, such as resolution of homopolymer tracts and indels. However, poor representation of assayed coho salmon in the queried baseline dataset contributed to poor assignment confidence on both platforms. Future improvements will focus on lowering turnaround time, accuracy, throughput, and cost, as well as augmentation of the existing baselines. If successfully implemented, Nanopore sequencing will provide an alternative method to the large-scale laboratory approach by providing mobile small batch genotyping to diverse stakeholders.</p>
Functional divergence from ecological baselines on Caribbean coral reefs
<p>Understanding how emergent ecological assemblages have diverged from natural states is fundamental in predicting future functioning and services of ecosystems. Coral reefs are of particular concern due to their high susceptibility to anthropogenic stressors. Yet, little is known about their pre-disturbance ranges of natural states, and most reports of decline are based on a limited number of sites and high levels of uncertainty. Here, we used a novel approach to estimate the physical functionality of reefs across marine ecoregions based on habitat suitability and morpho-functional traits for coral species. We calibrated ecological niche models for 49 reef-building corals of the Greater Caribbean based on occurrence records and environmental predictors, which we combined with species-specific functional coefficients derived from morpho-functional traits reflecting their contribution to the reef three-dimensional structure to estimate the reef functional potential (RFP). We then assessed the degree of divergence of western Caribbean reefs by comparing our physical functionality estimates against recent field data evaluations. We found spatial variability in RFP across the Caribbean, with the highest mean value in the western Caribbean and the lowest in areas with marginal environmental conditions. Hotspots of RFP exist along the coast of Belize and the southeast of Cuba. Overall, 84% of sites along the western Caribbean showed a substantial reduction in their physical functioning, with the highest reductions occurring within hotspots, implying that reefs displaying the greatest changes have high initial RFP. We conclude that combining niche models with species morpho-functional traits is a valuable and promising approach to estimate the large-scale functional potential of communities and the degree of change in the absence of ecological baselines. These findings have important implications and could be used to guide efforts to preserve coral reefs functionality and define priority conservation areas in the Caribbean.</p>
Thermal ecology and baseline energetic requirements of a large-bodied ectotherm suggest resilience to climate change
<p>Most studies on how rising temperatures will impact terrestrial ectotherms have focused on single populations or multiple sympatric species. Addressing the thermal and energetic implications of climatic variation on multiple allopatric populations of a species will help us better elucidate how a species may be impacted by altered climates. We used eight years of thermal and behavioral data collected from four populations of Pacific rattlesnakes (<em>Crotalus oreganus</em>) living in climatically distinct habitat types (inland and coastal) to determine the field-active and lab-preferred body temperatures, thermoregulatory metrics, and maintenance energetic requirements of snakes from each population. Physical models showed that thermal quality was best at coastal sites, but inland snakes thermoregulated more accurately despite being in more thermally constrained environments. Projected increases of 1 and 2 ºC in ambient temperature result in an increase in overall thermal quality at both coastal and inland sites. Population differences in modeled standard metabolic rate estimates were driven by body size and not field-active body temperature, with inland snakes requiring 1.6x more food annually than coastal snakes. All snakes thermoregulated with high accuracy, suggesting that small increases in ambient temperature are unlikely to impact the maintenance energetic requirements of individual snakes and that some species of large-bodied reptiles may be robust to modest thermal perturbations under conservative climate change predictions.</p>
The baseline immunological and hygienic status of pigs impact disease severity of African swine fever
<p>Primary data of manuscript</p>
Ninety years of coastal monitoring reveals baseline and extreme ocean temperatures are increasing off the Finnish coast
<p>Global marine heatwave assessments often rely on satellite-derived sea surface temperature. However, these data have low accuracy in coastal areas, are unable to measure sub-surface temperatures and have only been available since the 1980s. Here, we analyse 90 years of in situ surface and bottom (30 m) water temperature data from a Finnish coastal monitoring site. Water temperatures were significantly higher between 1991–2020 than 1931–1960 and 1961–1990. We find strong differences between satellite-derived and in situ temperatures, with in situ temperatures being lower in autumn and winter and higher in spring. Measurements at the seafloor indicate marine heatwaves occurred during all seasons between 2016 and 2020, with intensities and durations exceeding previous records. Since the 1990s, we find an upward shift of the baseline temperature and increasingly frequent occurrences of temperatures previously considered as an extreme. Our findings highlight the importance of long-term in situ data and choice of climatological reference periods for assessing change.</p>
Supplementary material 1 from: Touroult J, Stéphane B (2014) Insects of French Guiana: a baseline for diversity and taxonomic effort. ZooKeys 434: 111-130. https://doi.org/10.3897/zookeys.434.7582
How to access, cite and contribute to the TAXREF species database?: Explanation note: This file explains who contributed to the species database and give links for downloading the taxonomic database.
Supplementary material 2 from: Touroult J, Stéphane B (2014) Insects of French Guiana: a baseline for diversity and taxonomic effort. ZooKeys 434: 111-130. https://doi.org/10.3897/zookeys.434.7582
Total species richness estimations for 68 taxonomic groups in French Guiana: Explanation note: Estimated and extrapolated species richness for 68 taxonomic groups in French Guiana and comparative figures for two well-known faunas. These taxa are used to extrapolate the total number of species in French Guiana given in Table 4.
FIGURES 30–33 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURES 30–33. LINe DRAWINgS Of Zygobothrium megacephalum DIeSINg, 1850 fROM Phractocephalus hemioliopterus. 30. PRegRAVID PROgLOTTID, VeNTRAL VIeW (MHNG-PLAT-21854). NOTe: THe UTeRUS IS OMITTeD. 31. GRAVID PROgLOTTID, VeNTRAL VIeW (MHNG-PLAT-85239). 32, 33. CROSS-SeCTIONS AT THe LeVeL Of THe ANTeRIOR AND POSTeRIOR PARTS Of PROgLOTTID, ReSPeCTIVeLY (MHNG-PLAT-18316). Abbreviations: CC—CHROMOPHILIC CeLLS; DO—DORSAL OSMORegULATORY CANAL; DU—DIVeRTICULA Of UTeRUS; LM—INTeRNAL LONgITUDINAL MUSCULATURe; OO—OVARIAN OUTgROWTHS; OV—OVARY; ST—SUbTegUMeNTAL MUSCLe fIbeRS; SU— SUbTegUMeNTAL CeLLS; Te—TeSTeS; Tg—TegUMeNT; UT—UTeRUS; VI—VITeLLINe fOLLICLeS; VO—VeNTRAL OSMORegULATORY CANAL.
FIGURES 10–12 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURES 10–12. LINe DRAWINgS Of Ephedrocephalus microcephalus DIeSINg, 1850 fROM Phractocephalus hemioliopterus. 10. SCOLeX, DORSOVeNTRAL VIeW (MHNG-PLAT-22371) 11. SCOLeX, SAgITTAL SeCTION (MHNG-PLAT-28296). 12. GRAVID PROgLOTTID, VeNTRAL VIeW (MHNG-PLAT-22009). NOTe: THe TeSTeS ARe OMITTeD. Abbreviations: CC—CHROMOPHILIC CeLLS; DO—DORSAL OSMORegULATORY CANALS; gC—gLANDULAR CeLLS; LM—INTeRNAL LONgITUDINAL MUSCULATURe; Me—MeTASCOLeX; OC—OSMORegULATORY CANALS; VO—VeNTRAL OSMORegULATORY CANALS.
FIGURES 13–18 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURES 13–18. LINe DRAWINgS Of Ephedrocephalus microcephalus DIeSINg, 1850 fROM Phractocephalus hemioliopterus. 13. PRegRAVID PROgLOTTID, DORSAL VIeW (MHNG-PLAT-22009). NOTe: ONLY THe LATeRALMOST VITeLLINe fOLLICLeS IN THe ANTIPORAL AND POSTPORAL SIDeS ARe RePReSeNTeD, bUT THeY OCCUPY THe eNTIRe VeNTRAL SURfACe. 14–16. CROSS-SeCTIONS AT LeVeL Of MIDDLe PART Of PROgLOTTID, CIRRUS-SAC AND OVARY, ReSPeCTIVeLY (MHNG-PLAT-21910). 17. TeRMINAL geNITALIA, DORSAL VIeW (MHNG-PLAT- 22009). 18. EggS IN DISTILLeD WATeR (MHNG-PLAT-21851). Abbreviations: CC—CHROMOPHILIC CeLLS; CI—CIRRUS; CS—CIRRUS-SAC; DO—DORSAL OSMORegULATORY CANAL; eD—ejACULATORY DUCT; eM—eMbRYOPHORe; gA—geNITAL ATRIUM; LM—INTeRNAL LONgITUDINAL MUSCULATURe; LN—LONgITUDINAL NeRVe; Mg—MeHLIS' gLAND; OD—OVIDUCT; ON—ONCOSPHeRe; OV—OVARY; ST—SUbTegUMeNTAL MUSCLe fIbeRS; SU—SUbTegUMeNTAL CeLLS; Te—TeSTeS; Tg—TegUMeNT; UT—UTeRUS; V—VACUOLe; VA—VAS DefeReNS; VC—VAgINAL CANAL; VI—VITeLLINe fOLLICLeS; VO—VeNTRAL OSMORegULATORY CANAL; VS—VAgINAL SPHINCTeR.
FIGURE 29 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURE 29. LINe DRAWINg Of Zygobothrium megacephalum DIeSINg, 1850 fROM Phractocephalus hemioliopterus. SAgITTAL SeCTION Of THe SCOLeX, SHOWINg THe POWeRfUL CIRCULAR MUSCULATURe IN THe ANTeRIOR PART Of SUCKeRS, USeD AS A SPHINCTeR fOR THe HOLDfAST SYSTeM (MHNG-PLAT-21847). Abbreviations: CM—CIRCULAR MUSCULATURe; LM—INTeRNAL LONgITUDINAL MUSCULATURe; OC—OSMORegULATORY CANAL.
FIGURES 19–28 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURES 19–28. SCANNINg eLeCTRON MICROgRAPHS Of Zygobothrium megacephalum DIeSINg, 1850 (MHNG-PLAT-85239) fROM Phractocephalus hemioliopterus. 19. SCOLeX, ANTeRO-DORSOVeNTRAL VIeW. 20. SCOLeX, APICAL VIeW. 21. SCOLeX, LATeRAL VIeW. 22. DeTAIL Of THe SURfACe Of A MATURe PROgLOTTID. NOTe: THe LACINIATION PATTeRN ON THe PROgLOTTID SURfACeS. 23–28. MICROTRICHeS ON THe APeX Of THe SCOLeX, bRIDge-LIKe TISSUe, eXTeRNAL RIM Of SUCKeRS, beTWeeN SUCKeRS, STRObILA AND SURfACe Of LACINIATION, ReSPeCTIVeLY. NOTe: SMALL bLACK NUMbeRS CORReSPOND TO THe fIgUReS SHOWINg HIgHeR MAgNIfICATION IMAgeS Of THeSe SURfACeS.
FIGURES 1–9 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURES 1–9. SCANNINg eLeCTRON MICROgRAPHS Of Ephedrocephalus microcephalus DIeSINg, 1850 (MHNG-PLAT-28296) fROM Phractocephalus hemioliopterus. 1. SCOLeX, LATeRAL VIeW, SHOWINg THe DeePLY WRINKLeD MeTASCOLeX. 2. DeTAIL Of THe SUCKeRS, APICAL VIeW. 3. SCOLeX, APICAL VIeW. 4–9. MICROTRICHeS ON THe APeX Of SCOLeX, eXTeRNAL AND INTeRNAL RIM Of SUCKeRS, SURfACe beTWeeN SUCKeRS, MeTASCOLeX AND STRObILA, ReSPeCTIVeLY. NOTe: SMALL bLACK NUMbeRS CORReSPOND TO THe fIgUReS SHOWINg HIgHeR MAgNIfICATION IMAgeS Of THeSe SURfACeS.
FIGURES 38, 39 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURES 38, 39. LINe DRAWINgS Of eggS Of Cangatiella PAVANeLLI & DOS SANTOS, 1991 IN DISTILLeD WATeR. 38. Cangatiella arandasi PAVANeLLI & DOS SANTOS, 1991 (MHNG-PLAT-34751) fROM Trachelyopterus galeatus. 39. Cangatiella macdonaghi (SZIDAT & SORIA, 1951) (MHNG-PLAT-30269) fROM Odontesthes hatcheri. Abbreviations: eM—eMbRYOPHORe; Oe—OUTeR eNVeLOPe; ON—ONCOSPHeRe; PP—POLAR PROjeCTIONS; V—VACUOLe.
FIGURES 34–37 in Towards a robust systematic baseline of Neotropical fish tapeworms (Cestoda: Proteocephalidae): amended diagnoses of two genera from the redtail catfish, Phractocephalus hemioliopterus
FIGURES 34–37. LINe DRAWINgS Of Zygobothrium megacephalum DIeSINg, 1850 fROM Phractocephalus hemioliopterus. 34, 35. CROSS-SeCTIONS AT THe LeVeL Of THe ANTeRIOR AND POSTeRIOR PART Of THe TeRMINAL geNITALIA, ReSPeCTIVeLY. 36. TeRMINAL geNITALIA, VeNTRAL VIeW (MHNG-PLAT-18317). NOTe THe SMALL SPINeS (SPINITRICHeS) ON THe CIRRUS. 37. EggS IN DISTILLeD WATeR (MHNG- PLAT-85239). Abbreviations: AC—ARMeD CIRRUS; CC—CHROMOPHILIC CeLLS; DP—DIgITATe PROjeCTIONS; DO—DORSAL OSMORegULATORY CANAL; eD—ejACULATORY DUCT; eM—eMbRYOPHORe; LA—LACINIATIONS; LM—INTeRNAL LONgITUDINAL MUSCULATURe; Oe—OUTeR eNVeLOPe; ON—ONCOSPHeRe; V—VACUOLe; VA—VAS DefeReNS; VI—VITeLLINe fOLLICLeS; VO—VeNTRAL OSMORegULATORY CANAL; VS—VAgINAL SPHINCTeR.
Parameters and data set for all baseline methods used to formulate and evaluate the ligand NTBs-based strategy
Open the record for dataset details and reuse information.
Supplementary material 1 from: Jażdżewska AM, Corbari L, Driskell A, Frutos I, Havermans C, Hendrycks E, Hughes L, Lörz A-N, Stransky B, Tandberg AHS, Vader W, Brix S (2018) A genetic fingerprint of Amphipoda from Icelandic waters – the baseline for further biodiversity and biogeography studies. In: Brix S, Lörz A-N, Stransky B, Svavarsson J (Eds) Amphipoda from the IceAGE-project (Icelandic marine Animals: Genetics and Ecology). ZooKeys 731: 55–73. https://doi.org/10.3897/zookeys.731.19931
Table S1 : Explanation note: Amphipod and outgroup accession numbers in BOLD, GenBank and station data.
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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.