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Figure 5 in Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

Figure 5. Digital segmentations (top) and graphical reconstructions of rostral canals in select cetaceans (bottom). A, extant toothed odontocete Tursiops truncatus (SDSNH 21212). B, extinct toothed mysticete Aetiocetus weltoni (UCMP 122900). C, extant toothless mysticete Eschrichtius robustus (modified from: Ekdale et al., 2015).

Figure 4 in Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

Figure 4. CT-scan data of Aetiocetus weltoni (UCMP 122900). Slice A–A' taken oblique to the horizontal plane through the skull as indicated on the surface medial in lateral view to image course of infraorbital canal. Slices B–B', C–C' and D–D' taken along the transverse plane (original scan axis) at different positions along the rostrum as indicated on the surface model in dorsal view.

Figure 1 in Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

Figure 1. Hypothesis of baleen evolution. Relationships based on published phylogenetic analyses (Uhen, 2013; Fordyce & Marx, 2018; Peredo et al., 2018). Thick bars represent stratigraphic ranges downloaded from the Paleobiology Database (paleobiodb.org) on 14 February 2020, using the taxonomic name search form for each terminal taxon named on the cladogram. Red branches indicate presence of lateral palatal foramina.

Figure 3 in Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

Figure 3. Digital segmentation of neurovascular canals through rostrum of Aetiocetus weltoni (UCMP 122900). A, rostral canals in ventral view. B, rostral canals in lateral view. Abbreviations: dc, dental/alveolar canal; lpc, lateral palatal canal.

Figure 2 in Neurovascular evidence for a co-occurrence of teeth and baleen in an Oligocene mysticete and the transition to filter-feeding in baleen whales

Figure 2. Neurovascular canals through rostrum of Aetiocetus weltoni (UCMP 122900). A, ventral view of 3D rendering of skull (top), skull rendered semi-transparent to reveal internal canals of rostrum (middle), and digital segmentation of rostral canals (bottom). B, lateral view of 3D rendering of skull (top), skull rendered semi-transparent to reveal internal canals of rostrum (middle), and digital segmentation of rostral canals (bottom).

opencc-by-4.0Nov 2021View details →

Supporting molecular simulations data for "A universal co-solvent dilution strategy enables facile and cost-effective fabrication of perovskite photovoltaics"

Supplementary data for "A universal co-solvent dilution strategy enables facile and cost-effective fabrication of perovskite photovoltaics"

opennotspecifiedOct 2019View details →

Subspecies and Distribution. B.b.barbastellusSchreber,1774—EuropefromIrelandandIberianPeninsulaEtoLaivia,Belarus,Ukraine,andtheCauca-sus;alsomajorMediterraneanIs,Moroc-co,andTurkey(Anatolia);possiblyextinctinBelgium,Netherlands,andNorway. B. b. guanchae Trujillo, Ibanez & Juste, 2002 — Canary Is (Tenerife and La Gomera). in Vespertilionidae

Subspecies and Distribution. B.b.barbastellusSchreber,1774—EuropefromIrelandandIberianPeninsulaEtoLaivia,Belarus,Ukraine,andtheCauca-sus;alsomajorMediterraneanIs,Moroc-co,andTurkey(Anatolia);possiblyextinctinBelgium,Netherlands,andNorway. B. b. guanchae Trujillo, Ibanez & Juste, 2002 — Canary Is (Tenerife and La Gomera).

opencc-by-4.0Apr 2022View details →

Enhanced Weathering Using Basalt Rock Powder: Carbon Sequestration, Co-benefits and Risks in a Mesocosm Study With Solanum tuberosum data

Dataset used in the work: Enhanced Weathering Using Basalt Rock Powder: Carbon Sequestration,Co-benefits and Risks in a Mesocosm Study With Solanum tuberosum authors:  Arthur Vienne, Silvia Poblador , Miguel Portillo-Estrada, Jens Hartmann, Samuel Ijiehon, Peter Wadeand Sara Vicca

opencc-zeroApr 2022View details →

Data for: Plasticity and co-variation of root traits govern phosphorus acquisition among 20 wheat genotypes

Trait plasticity (variation of a trait under environmental variability or gradients) and trait integration are both crucial for plant adaption to environmental change. Variations in different suite of root traits such as biomass allocation, morphology and physiology underlie diverse phosphorus (P) acquisition strategies among plants. Yet, how the intraspecific plasticity and integration of root traits influence plant adaptation to different P supply remains obscure. To characterize diverse adaptive strategies in relation to plant P acquisition, eight root traits were assessed in 20 wheat (Triticum aestivum L.) genotypes grown in a culture room with low and high P supply. High P supply increased shoot P accumulation and biomass of all wheat genotypes. The shoot P accumulation in genotypes with high P sensitivity (PS: calculated as shoot P content at low P / shoot P content at high P supply) was higher with high P supply and lower with low P supply compared with that in the genotypes with low PS. The high-PS genotypes exhibited larger variation in root length, root/shoot ratio and rhizosphere pH across P supplies than the low-PS genotypes, suggesting an integrated response at the whole-plant level. At low P supply, the high-PS genotypes had greater root length and specific root length, but lower acid phosphatase activity than the low-PS genotypes, which suggests contrasting P-acquisition strategies across the genotypes. Strong co-variation of root traits occurred across low-PS genotypes regardless of P supply; conversely, the high-PS genotypes only exhibited strong trait integration at low P supply, whereas high P supply sharply reduced root trait co-variation. Our findings suggest that P stress may strengthen root trait integration in wheat plants, and that both plasticity and integration of root traits drive plant adaptive strategies and tolerance to P-deficiency stress.

opencc-by-4.0May 2022View details →

Co-transcriptomic analysis of the maize-western corn rootworm interaction

We used a maize genotype, Mp708, that is resistant to a large guild of herbivore pests to study the underlying plant defense signaling network between below and aboveground tissues. We also evaluated WCR compensatory transcriptome responses. Using RNA-seq, we profiled the transcriptome of roots and leaves that interacted with WCR infestation up to 5 days post infestation (dpi). Our results suggest that several maize defense genes were induced in roots, whereas WCR defense genes were downregulated at 5 dpi. These findings indicate a dynamic transcriptomic dialog between WCR and WCR-infested maize plants.

opencc-by-4.0May 2022View details →

Cyclic fault slip under the magnifier: Co- and postseismic response of the Pamir front to the 2015 Mw7.2 Sarez, Central Pamir, earthquake

The file Alai_GPS_timeseries.zip contents two text files with time series data for GPS observation of the Alai network for the periods from July 2016 to June 2018 and from July 2018 to June 2020. The data were used to determine the velocities of post-seismic displacements of the Earth's surface in the periods from July 2016 to June 2018 and from July 2018 to June 2020. Each of the other 10 zip files ending in baselines.zip includes time series of daily values of the  baselines between one Alay GPS station and Asian stations not affected by the 2015 Sarez earthquake M7.2w, for a period spanning at least 60 days before and after it . The data was used to calculate the coseismic displacements caused by this earthquake.

opencc-zeroMay 2022View details →

Dataset: Co-administration of adjuvanted recombinant Ov-103 and Ov-RAL2 vaccines confer protection against natural challenge in a bovine O. ochengi infection model of human onchocerciasis

[Abstract from accompanying manuscript] Onchocerciasis (river blindness), caused by the filarial nematode Onchocerca volvulus, is a neglected tropical disease endemic to sub-Saharan Africa. Worldwide, an estimated 20.9 million individuals live with infected and a further 205 million are at risk of disease. Current control methods rely on mass drug administration of ivermectin to suppress microfilarial development. Presently, there are no viable treatment options effective against the long-lived adult worms. The identification and development of efficacious vaccine candidates as complementary tools to support ongoing elimination efforts are therefore a major objective of onchocerciasis research. We evaluated the immunogenicity and protective effects of co-administering two leading O. volvulus-derived recombinant vaccine candidates (Ov-103 and Ov-RAL2) in cattle with subsequent natural exposure to Onchocerca ochengi, a close phylogenetic relative of O. volvulus. Immunisation induced strong IgG responses against both vaccine candidates. Following natural exposure to O. ochengi, vaccination status and resulting serum antibody response was associated with delayed nodule development and onset of microfilaridermia. Peptide arrays identified several Ov-103 and Ov-RAL2-specific epitopes recognised by IgG from immunised cattle which warrant further investigation. Our data provide supporting evidence for ongoing development of a recombinant vaccine for control of human onchocerciasis.

opencc-by-4.0Nov 2021View details →

Addiitional Files: The diagrams of population structure, highly divergent regions, GC content and Nanopore reads depth, SNP number and Nanopore reads depth, and analyses of co-linearity against Nipponbare reference genome in 251 accessions.

Additional Files for " A Super Pan-Genomic Landscape of Rice". Addtional File1:  Supplementary File1.Population structure of 251 rice accessions inferred by ADMIXTURE from K=6 to K=15. Additional File2: Supplementary File2.The diagram of co-linearity for assembled genome against Nipponbare refercne genome in 251 rice accessions. Additional File3: Supplementary File3. Highly divergent regions based on SV. Additional File4: Supplementary File4. The diagram of SNP number and Nanopore reads depth per 100kb windows in 251 rice accessions. Additonal File5:Supplementary File5. The diagram of GC content and the Nanopore reads depth per 10kb windows in 251 rice accessions.

opennotspecifiedJun 2022View details →

FIGURE. Authors (or co-authors) of more than five currently accepted specific and infraspecific cycad taxa (author abbreviations follow Calonje et al. 2022). in Etymological compendium of cycad names

FIGURE. Authors (or co-authors) of more than five currently accepted specific and infraspecific cycad taxa (author abbreviations follow Calonje et al. 2022).

opencc-zeroNov 2015View details →

Data from: Dealing with uncertainty in landscape genetic resistance models: a case of three co-occurring marsupials

Landscape genetics lacks explicit methods for dealing with the uncertainty in landscape resistance estimation, which is particularly problematic when sample sizes of individuals are small. Unless uncertainty can be quantified, valuable but small datasets may be rendered unusable for conservation purposes. We offer a method to quantify uncertainty in landscape resistance estimates using multi-model inference as an improvement over single-model based inference. We illustrate the approach empirically using co-occurring, woodland-preferring Australian marsupials within a common study area: two arboreal gliders (Petaurus breviceps, and Petaurus norfolcensis) and one ground-dwelling Antechinus (Antechinus flavipes). First, we use maximum-likelihood and a bootstrap procedure to identify the best-supported isolation by resistance (IBR) model out of 56 models defined by linear and non-linear resistance functions. We then quantify uncertainty in resistance estimates by examining parameter selection probabilities from the bootstrapped data. The selection probabilities provide estimates of uncertainty in the parameters that drive the relationships between landscape features and resistance. We then validate our method for quantifying uncertainty using simulated genetic and landscape data showing that for most parameter combinations it provides sensible estimates of uncertainty. We conclude that small datasets can be informative in landscape genetic analyses provided uncertainty can be explicitly quantified. Being explicit about uncertainty in landscape genetic models will make results more interpretable and useful for conservation decision-making, where dealing with uncertainty is critical.

opencc-zeroDec 2014View details →

Data from: Atmospheric N deposition alters co-occurrence, but not functional potential among saprotrophic bacterial communities

The use of co-occurrence patterns to investigate interactions between micro-organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co-occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem-level response occurred concomitantly with compositional changes in saprophytic fungi and bacteria. Here, we investigated the influence of experimental N deposition on biotic interactions among forest floor bacterial assemblages by employing phylogenetic and molecular ecological network analysis. When compared to the ambient treatment, the forest floor bacterial community under experimental N deposition was less rich, more phylogenetically dispersed and exhibited a more clustered co-occurrence network topology. Together, our observations reveal the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. Moreover, they support the hypothesis that nearly two decades of experimental N deposition can modify the organization of microbial communities and provide further insight into why anthropogenic N deposition has reduced decomposition, increased soil C storage and accelerated phenolic DOC production in our field experiment.

opencc-by-4.0Aug 2022View details →

O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas

Molecular dynamics simulations for CODH enzymes studied in "O2-tolerant CO dehydrogenase via tunnel redesign for the removal of CO from industrial flue gas". The repository contains the 10 nanoseconds of NAMD simulation of CODH enzymes.

opencc-by-4.0Aug 2022View details →

hiPSC-CM and co-culture calcium dynamics videos

Note: This version is now redundant - updated videos are available here:  Dvinskikh, Liuba, Sparks, Hugh, Brito, Liliana, MacLeod, Kenneth T, Harding, Sian E, & Dunsby, Chris. (2023, January 29). Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript (Version 1). Zenodo. https://doi.org/10.5281/zenodo.7580163 ---------------------------------------------------------------------------------------------     Supplementary videos for manuscript " Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocyte in co-culture "  The videos included are the following:  Video 1: 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients. Video 2: Widefield transillumination timelapse of hiPSC-CM and adult-CM co-culture. Video 3: Widefield epifluorescence timelapse of hiPSC-CM and adult-CM co-culture Video 4: 3D LSFM timelapse of synchronized transients in hiPSC-CM and adult-CM co-culture. Video 5a: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture, without NBleb. Video 5b: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture, with NBleb.

opencc-zeroAug 2022View details →

The nutritional condition of moose co-varies with climate, but not with density, predation risk, or diet composition

A fundamental question about the ecology of herbivore populations pertains to the relative influence of biotic and abiotic processes on nutritional condition. Nutritional condition is influenced in important, yet poorly understood, ways by plant secondary metabolites (PSMs) which can adversely affect a herbivore's physiology and energetics. Here we assess the relative influence of various abiotic (weather) and biotic (intraspecific competition, predation risk and diet composition) factors on indicators of nutritional condition and the energetic costs of detoxifying PSMs for the moose population in Isle Royale National Park (U.S.A.). Specifically, we observed interannual variation in the ratio of urea nitrogen to creatinine (UN:C), an indicator of nutritional restriction, over 29 years and the ratio of glucuronic acid to creatinine (GA:C), an indicator of energetic investment, in detoxifying PSMs over 19-years. Both UN:C and GA:C were measured in samples of urine-soaked snow. Most importantly, climatic factors explained 66% of the interannual variation in UN:C, with moose being more nutritionally stressed during winters with deep snow and during winters that followed warm summers. None of the biotic factors (density, predation, diet composition) were useful predictors of UN:C or GA:C. The absence of a relationship between diet composition and either UN:C or GA:C suggests that the nutritional ecology of wild herbivores is probably complicated by fine-scale variation in protein content and concentrations of PSMs amongst plants of the same species. UN:C increased with GA:C at both the individual and population-level. That result is consistent with detoxification being energetically costly, such that it impairs nutritional condition and also highlight show spatio-temporal variation in the intake and detoxification of PSMs may influence population dynamics. Lastly, because we observed interannual variation in nutritional condition over three decades and detoxification over two decades these findings are relevant to concerns about how herbivore populations respond to climate change.