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Figure 7 in Systematic revision of the living species of Bullidae (Mollusca: Gastropoda: Cephalaspidea), with a molecular phylogenetic analysis
Figure 7. Inner lateral teeth of radula of Bulla striata. A, B, Ria Formosa, Portugal (BMNH 20050338; H = 30.1, 32.5 mm). C, Naples, Italy (BMNH 20030775; H = 23.5 mm). D, Siné-Saloum, Senegal (BMNH 20030781; H = 15.6 mm). E, F, Siné-Saloum, Senegal (BMNH 20030781; H = 16.4 mm). Scale bars: A–F = 100 Mm.
Figure 5 in Systematic revision of the living species of Bullidae (Mollusca: Gastropoda: Cephalaspidea), with a molecular phylogenetic analysis
Figure 5. Involute spire and visible part of protoconch of Bulla striata (A, G), B. occidentalis (B, I–J), B. mabillei (C), B. solida (D), B. gouldiana (E), and B. punctulata (F, H). A, Siné-Saloum, Senegal (BMNH 20030781; H = 15.6 mm). B, Miami, Florida (BMNH 20030045; H = 28.8 mm). C. Tenerife Island, Canary Islands (BMNH 20020457; H = 26.9 mm). D, off Florida (HBOM 62: 281; H = 34.9 mm). E, Baja California, Mexico (CAS 067260; H = 40.6 mm). F, Guanacaste, Costa Rica (INBio 03458490; H = 13.8 mm). G, Ria Formosa, Portugal (BMNH 20050338; H = 30.1 mm). H, Puntarenas, Costa Rica (INBio 01482898; H = 19.6 mm). I–J, São Paulo, Brazil (MZUSP 30009; H = 33.6, 35.1 mm). Scale bars: A–C, E–F, J = 200 Mm; D = 500 Mm; G–I = 50 Mm.
Figure 2 in Systematic revision of the living species of Bullidae (Mollusca: Gastropoda: Cephalaspidea), with a molecular phylogenetic analysis
Figure 2. Live animals of Atlantic and East Pacific species of Bullidae. A, Bulla striata, Ria de Alvor, Portugal; H = 29 mm (photo: M. A. E. Malaquias). B, B. occidentalis, Guanacahabibes, Cuba; H = 20 mm (photo: L. Moro). C, B. occidentalis, Sanibel Island, Florida; H = 18 mm (photo: Á. Valdés). D, B. mabillei, Tenerife, Canary Islands; H = 31 mm (photo: L. Moro). E, B. punctulata, Panama; H = 25 mm (photo: T. Gosliner). F, B. gouldiana, La Jolla, California; H = 45 mm (B. Lloyd).
Data from: Genetic diversity in a long-lived mammal is explained by the past's demographic shadow and current connectivity
<p>Within-species genetic diversity is crucial for the persistence and integrity of populations and ecosystems. Conservation actions require an understanding of factors influencing genetic diversity, especially in the context of global change. Both population size and connectivity are factors greatly influencing genetic diversity; the relative importance of these factors can however change through time. Hence, quantifying the degree to which population size or genetic connectivity are shaping genetic diversity, and at which ecological time scale (past or present), is challenging, yet essential for the development of efficient conservation strategies. In this study, we estimated the genetic diversity of 42 colonies of <i>Rhinolophus hipposideros,</i> a long-lived mammal vulnerable to global change, sampling locations spanning its continental northern range. We present an integrative approach that disentangles and quantifies the contribution of different connectivity measures in addition to contemporary colony size and historic bottlenecks in shaping genetic diversity. In our study, the best model explained 64% of the variation in genetic diversity. It included historic bottlenecks, contemporary colony sizes, connectivity and a negative interaction between the latter two. Contemporary connectivity explained most genetic diversity when considering a 65 km radius around the focal colonies, emphasizing the large geographic scale at which the positive impact of connectivity on genetic diversity is most profound and hence the minimum scale at which conservation should be planned. Our results highlight that the relative importance of the two main factors shaping genetic diversity varies through time, emphasizing the relevance of disentangling them to ensure appropriate conservation strategies.</p>
Skull shape data for 188 species of living Carnivora
<p>There are 5 files. Two include 2D coordinates used to quantify cranium and mandible shape for a sample of 188 averaged Carnivora species. These coordinates are in .NTS format. Another file is the phylogenetic tree employed for this study in nexus format. In Excel there is museum catalog list of all the specimens included in the study while the text file RoutineR.txt include most of the scripts employed in this study with examples on how to run simulations and other analyses. </p>
Data and code from: Reciprocity and interaction effectiveness in generalised mutualisms among free-living species
<p><span>Mutualistic interactions among free-living species generally involve low-frequency interactions and highly asymmetric dependence among partners, yet our understanding of factors behind their emergence is still limited. Using individual-based interactions of a super-generalist fleshy-fruited plant with its frugivore assemblage, we estimated the Resource Provisioning Effectiveness (RPE) and Seed Dispersal Effectiveness (SDE) to assess the balance in the exchange of resources. Plants were highly dependent on a few frugivore species, while frugivores interacted with most individual plants, resulting in strong asymmetries of mutual dependence. Interaction effectiveness was mainly driven by interaction frequency. Despite highly asymmetric dependences, the strong reliance on quantity of fruit consumed determined high reciprocity in rewards between partners (i.e., higher energy provided by the plant, more seedlings recruited), which was not obscured by minor variations in the quality of animal or plant service. We anticipate reciprocity will emerge in low-intimacy mutualisms where the mutualistic outcome largely relies upon interaction frequency.</span></p>
Trapalyzer: A computer program for quantitative analyses in fluorescent live-imaging studies of Neutrophil Extracellular Trap formation.
<p>This data set contains a set of fluorescent microscopy images of a co-culture of neutrophil cells and E. coli bacteria used to study the Neutrophil Extracellular Trap (NET) formation stimulated by bacteria. </p> <p>NETs and live cells were visualized with a double fluorescent staining of DNA using Hoechst 33342 and SYTOX Green. </p> <p><strong>Reagents.</strong></p> <p>Roswell Park Memorial Institute (RPMI) 1640 medium, HEPES, SYTOX<sup>TM</sup> Green, and Hoechst 33342 were purchased from Thermo Fisher Scientific (Waltham, USA). LB broth was purchased from Sigma Aldrich (St Louis, MO, USA).</p> <p><strong>Preparation of blood neutrophils.</strong></p> <p>Neutrophils were obtained from peripheral blood of one healthy blood donor. Blood sample was purchased at Local Blood Donation Centre and according to local regulations, the blood donor enabled blood donation center to sell their blood samples for scientific purposes and the consent of bioethical committee was not required. Blood was collected into a citrate tube and processed within 2 hours from collection. Neutrophils were isolated using density gradient centrifugation followed by polyvinyl alcohol sedimentation, exactly as described in [1]. Isolated neutrophils were suspended in RPMI 1640 medium with 10 mM HEPES (RH). </p> <p><strong>Preparation of bacteria.</strong></p> <p><em>Escherichia coli</em> (American Type Culture Collection(ATCC) 25922 strain) were grown overnight in LB broth with shaking. In the morning, an aliquot of bacterial culture was taken, diluted 100 x in a fresh LB medium and grown for subsequent 2-3 hours. Subsequently, bacterial cultures were washed and resuspended in RH medium.</p> <p><strong>Co-culture of neutrophils with bacteria</strong><br> Neutrophils were seeded into the wells of 48-well plates at the density of 2 ⨉ 10<sup>4</sup> cells/well and allowed to settle for 30 minutes at 37°C, 5% CO2. Subsequently, <em>E. coli</em> was added into the appropriate wells at the multiplicity of infection of 4 or 1 (<em>E.coli</em>: neutrophil). Neutrophils incubated without bacteria were used as a control group. A technical duplicate for each condition was prepared. <br> For each intended timepoint (t=0, 60, 90, 120, 180 minutes), a separate 48 well plate was prepared. The plates were centrifuged for 5 minutes at 250 g to allow the contact of bacteria with neutrophils. The plates were incubated at 37°C, 5\% CO2 for a specified time and then the samples were stained with SYTOX<sup>TM</sup> Green (100 nM) and Hoechst 33342 (1.25 μM) for 10 minutes. Four images of each well were taken with Leica DMi8 fluorescent microscope equipped with a 10× magnification objective (Leica, Wetzlar, Germany). Overall, 120 images have been obtained.</p> <p> </p> <p><strong>2019_04_24--ecoli_neu_tiff_channel_merged.zip:</strong> Images in .tif format, each containing 5 channels: channel 1 for SYTOX Green fluorescent stain (green fluorescence), channel 2 for Hoechst 33342 fluorescent stain (blue fluorescence), and three channels for transmission light encoded in RGB values. </p> <p> </p> <p><strong>2019_04_24--ecoli_neu_tiff_raw_exported.zip:</strong> Images split by different light sources: transmission light (_ch00.tif), SYTOX Green fluorescence (_ch01.tif), Hoechst 33342 fluorescence (_ch02.tif).</p> <p> </p> <p>[1] Bystrzycka W, Moskalik A, Sieczkowska S, Manda-Handzlik A, Demkow U, Ciepiela O. The effect of clindamycin and amoxicillin on neutrophil extracellular trap (NET) release. <em>Cent Eur J Immunol</em>. 2016;41(1):1-5. doi:10.5114/ceji.2016.58811</p>
Living links mixed-species behavioural synchrony
<p>Scan data of capuchin and squirrel monkey West and East Living Links groups for mixed-species behavioural synchrony.</p>
Data from: Invasive plants have greater growth than co-occurring natives in live soil subjected to a drought-rewetting treatment
<p>Although several studies indicate that invasive plant species respond more negatively to drought than native plant species, little remains understood of how and whether drought-rewetting events may affect growth of invasive and co-occurring native plant species both directly and indirectly through soil microorganisms. In a fully crossed factorial design, we grew individuals of four congeneric pairs of invasive and native plant species in 2.5 L pots that contained live or sterilized field soil under one of three drought treatments: no-drought, drought, drought-rewetting. Results show that drought caused a significantly greater decline in total biomass of invasive plants than that of native plants regardless of the presence of live soil microorganisms. However, total biomass of the invasive plants exhibited a greater recovery from drought following rewetting than did that of the native plant species. Moreover, the recovery from drought in invasive species tended to be stronger in live soil than in sterilized soil, while for the native plants, recovery from drought was stronger in sterilized soil than in live soil. Overall, these results suggest that soil biota may enable invasive plants to grow larger than co-occurring native plant species in ecosystems that experience cycles of drought and rewetting.</p>
Document Liveness Challenge (DLC-2021) - part 3 (cc)
<p>Dataset DLC-2021 consists of 1424 video clips captured in a wide range of real-world conditions and focused on ID document forensics tasks. Each clip was shot vertically and was at least 5 seconds long. Frames extracted at 10 frames per second and for the 50 first extracted frames document position is manually annotated.<br> The novelty of the dataset is that it contains shots from video with color laminated mock ID documents, color unlaminated copies, grayscale unlaminated copies, and screen recaptures of the documents. The proposed dataset complies with the GDPR because it contains images of synthetic IDs with generated owner photos and artificial personal information.</p> <p>Part 1 contains videos, frames and markup for “original” laminated documents from MIDV-2020 collection and unlaminated gray copies. <br> Part 2 contains videos, frames and markup for documents recaptured from device screen<br> Part 3 contains videos, frames and markup for unlaminated color copies.</p> <p><strong>Share and Cite</strong></p> <p><em>MDPI and ACS Style</em></p> <p>Polevoy, D.V.; Sigareva, I.V.; Ershova, D.M.; Arlazarov, V.V.; Nikolaev, D.P.; Ming, Z.; Luqman, M.M.; Burie, J.-C. Document Liveness Challenge Dataset (DLC-2021). <em>J. Imaging</em> <strong>2022</strong>, <em>8</em>, 181. https://doi.org/10.3390/jimaging8070181</p> <p><em>AMA Style</em></p> <p>Polevoy DV, Sigareva IV, Ershova DM, Arlazarov VV, Nikolaev DP, Ming Z, Luqman MM, Burie J-C. Document Liveness Challenge Dataset (DLC-2021). <em>Journal of Imaging</em>. 2022; 8(7):181. https://doi.org/10.3390/jimaging8070181</p> <p><em>Chicago/Turabian Style</em></p> <p>Polevoy, Dmitry V., Irina V. Sigareva, Daria M. Ershova, Vladimir V. Arlazarov, Dmitry P. Nikolaev, Zuheng Ming, Muhammad M. Luqman, and Jean-Christophe Burie. 2022. "Document Liveness Challenge Dataset (DLC-2021)" <em>Journal of Imaging</em> 8, no. 7: 181. https://doi.org/10.3390/jimaging8070181</p>
Document Liveness Challenge (DLC-2021) - part 2 (re)
<p>Dataset DLC-2021 consists of 1424 video clips captured in a wide range of real-world conditions and focused on ID document forensics tasks. Each clip was shot vertically and was at least 5 seconds long. Frames extracted at 10 frames per second and for the 50 first extracted frames document position is manually annotated.<br> The novelty of the dataset is that it contains shots from video with color laminated mock ID documents, color unlaminated copies, grayscale unlaminated copies, and screen recaptures of the documents. The proposed dataset complies with the GDPR because it contains images of synthetic IDs with generated owner photos and artificial personal information.</p> <p>Part 1 contains videos, frames and markup for “original” laminated documents from MIDV-2020 collection and unlaminated gray copies. <br> Part 2 contains videos, frames and markup for documents recaptured from device screen<br> Part 3 contains videos, frames and markup for unlaminated color copies.</p> <p><strong>Share and Cite</strong></p> <p><em>MDPI and ACS Style</em></p> <p>Polevoy, D.V.; Sigareva, I.V.; Ershova, D.M.; Arlazarov, V.V.; Nikolaev, D.P.; Ming, Z.; Luqman, M.M.; Burie, J.-C. Document Liveness Challenge Dataset (DLC-2021). <em>J. Imaging</em> <strong>2022</strong>, <em>8</em>, 181. https://doi.org/10.3390/jimaging8070181</p> <p><em>AMA Style</em></p> <p>Polevoy DV, Sigareva IV, Ershova DM, Arlazarov VV, Nikolaev DP, Ming Z, Luqman MM, Burie J-C. Document Liveness Challenge Dataset (DLC-2021). <em>Journal of Imaging</em>. 2022; 8(7):181. https://doi.org/10.3390/jimaging8070181</p> <p><em>Chicago/Turabian Style</em></p> <p>Polevoy, Dmitry V., Irina V. Sigareva, Daria M. Ershova, Vladimir V. Arlazarov, Dmitry P. Nikolaev, Zuheng Ming, Muhammad M. Luqman, and Jean-Christophe Burie. 2022. "Document Liveness Challenge Dataset (DLC-2021)" <em>Journal of Imaging</em> 8, no. 7: 181. https://doi.org/10.3390/jimaging8070181</p>
Data for: Should I breed or should I go? Manipulating individual state during migration influences breeding decisions in a long-lived bird species
<p>Documentation of Carry-Over Effects (COEs), defined as effects resulting from events that occurred in a previous time period, has largely been observational and understanding of specific mechanisms underlying COEs is still lacking. To investigate this, we simulated an environmental perturbation during the spring migration of a long-lived bird species and looked at the subsequent effects on various breeding parameters. We captured female greater snow geese (<em>Anser caerulescens atlanticus</em>) on their spring staging sites and maintained individuals in captivity for up to four days before releasing them. We re-observed females 3000 km North, on their Arctic breeding grounds, to estimate their breeding propensity (i.e., probability of initiating a reproductive event for a given year), and measure their arrival date, laying date, clutch size, and nesting success. Only proxies of breeding propensity were affected by our manipulation, which decreased as the time spent in captivity increased. However, females were able to overcome the effects of captivity in two out of the three years of experimentation with normal or good environmental conditions at the breeding site. When facing the additional challenge of poor environmental conditions, many individuals manipulated during migration apparently curtailed their reproductive effort by skipping breeding. This experiment is the first to show that breeding propensity is an important parameter affected by COEs resulting from stressful events prior to reproduction in long-lived species.</p>
Data from: Assessing the reproductive consequences of mate retention and pair bond duration in Thorn-tailed Rayadito (Aphrastura spinicauda), a short-lived, socially monogamous Neotropical bird
<p><strong>Description for "PairingData_Aspinicauda.xlsx" file.</strong></p> <p>Data from: Assessing the reproductive consequences of mate retention and pair bond duration in Thorn-tailed Rayadito (Aphrastura spinicauda), a short-lived, socially monogamous Neotropical bird<br> MS Reference Number: IBIS-2022-OA-113.R2<br> Article DOI: 10.1111/ibi.13183</p> <p>Please address questions to:</p> <p>Esteban Botero D.<br> Guest Scientist<br> Max Planck Institute for Ornithology<br> Dep. Behavioural Ecology and Evolutionary Genetics<br> Eberhard-Gwinner-Str. 8<br> 82319 Seewiesen, Germany<br> Telephone: +49 8157 932453<br> http://www.orn.mpg.de/en<br> e-mail: eboterod@gmail.com; ebotero@orn.mpg.de</p> <p>=====================================================================================<br> =====================================================================================</p> <p><br> General information:</p> <p>The whole dataset contains breeding data collected from a population of the furnariid Thorn-tailed rayadito (Aphrastura spinicauda) in north-central Chile (Fray Jorge National Park; 30º38’S, 71º40’W). These data were collected during 2009–2017 as part of a long-term study on the breeding biology of rayaditos. In this study, data were used to evaluate the consequences of mate replacement versus mate retention using 243 breeding attempts made by 159 different breeding pairs. This, in the end, allowed to test whether successive remating conferred reproductive benefits to reunited pairs.</p> <p>The data set is comprised by an Excel file (three spreadsheets) that are explained below.</p> <p>*************************************************************************************</p> <p>Excel file "PairingData_Aspinicauda.xlsx" (created 11-01-2023)</p> <p><br> ********** Spreadsheet "1. AllPairs" **********<br> This spreadsheet contains information from all breeding attempts monitored during the study (n = 243). Each row correspond to a unique breeding attempt. The ring number is used as an ID for each individual. The matrix includes information regarding individual and pair identification, age, previous breeding status (whether an individual is a widow or a divorcee), current pairing status (whether is a newly formed pair or a reunited pair), number of seasons breeding together for each pair, confidence on pairing information for each pair (high: there was absolute confidence on the previous breeding status of both members of a breeding pair; low: when information on previous breeding status was missing for at least one of the members of a pair), and measures of reproductive success (laying day, clutch size, umber of fledglings produced). This dataset can be saved as a *.txt file so that it can be imported into R (R Core Team 2020).</p> <p>The matrix contains the following variables:</p> <p>VARIABLE DESCRIPTION</p> <p>Year Sampling year.<br> Box Nestbox code.<br> FID ID for the breeding female.<br> FMAge Age for each breeding female (yearling: 1; adult: 2).<br> SocMID ID for the breeding male (social father of the clutch).<br> SocMaAge Age for each breeding male.<br> PairID ID for the breeding pair. This is for indexing purposes.<br> FPaSta Previous breeding status of the female (Wid: widow; Div: divorcee; Reu: reunited).<br> MPaSta Previous breeding status of the male (Wid: widow; Div: divorcee; Reu: reunited).<br> PairSta Pairing status for the focal breeding pair (New: newly formed; Reunited: reunited).<br> PairSea No. of seasons breeding together for each pair.<br> Certainty Certainty on previous breeding status (High or Low; see explanation above).<br> LayingD Laying date (number of days in relation to date of first egg in the population).<br> ClutchS Clutch size.<br> NoFle Number of fledging produced.</p> <p><br> ********** Spreadsheet "2. WidowFBre" **********<br> This spreadsheet contains breeding information for females that were monitored in the years before and after mate loss.</p> <p>The matrix contains the following variables:</p> <p>VARIABLE DESCRIPTION</p> <p>Year Sampling year.<br> Box Nestbox code.<br> FID ID for the breeding female.<br> LayingD Laying date during year after mate loss.<br> ClutchS Clutch size during year after mate loss.<br> NoFle Number of fledging produced during year after mate loss.<br> FPaSta Previous breeding status of the female (Wid: widow; Div: divorcee; Reu: reunited).<br> LayingD_x.1 Laying date during year before mate loss (year x-1).<br> ClutchS_x.1 Clutch size during year before mate loss (year x-1).<br> NoFle_x.1 Number of fledging produced during year before mate loss (year x-1).</p> <p><br> ********** Spreadsheet "3. WidowMBre" **********<br> This spreadsheet contains breeding information for males that were monitored in the years before and after mate loss.</p> <p>The matrix contains the following variables:</p> <p>VARIABLE DESCRIPTION</p> <p>Year Sampling year.<br> Box Nestbox code.<br> SocMID ID for the breeding male.<br> LayingD Laying date during year after mate loss.<br> NoFle Number of fledging produced during year after mate loss.<br> MPaSta Previous breeding status of the female (Wid: widow; Div: divorcee; Reu: reunited).<br> LayingD_x.1 Laying date during year before mate loss (year x-1).<br> NoFle_x.1 Number of fledging produced during year before mate loss (year x-1).</p> <p>*************************************************************************************</p> <p><br> =====================================================================================</p> <p><br> Methodological information (for more details, please see the related manuscript):</p> <p>A total of 101–157 nestboxes were installed in Fray Jorge since 2007, and are monitored annually during September–December. We gathered data on reproductive phenology and productivity during 2008–2017 for all nestbox occupants. Nestboxes were initially visited every 3–5 days to detect nest building. Once nestboxes were occupied, we increased the frequency of visits to record data on laying date, clutch size, and the number of hatchlings and fledglings produced (see more details in Botero-Delgadillo et al. 2017). We captured and marked breeding adults and nestlings with numbered aluminium rings when nestlings were 12–14 days old. Additionally, we used mist nets to capture adult birds breeding in natural cavities in our study site. A total of 248 adults (132 females, 116 males) and 730 nestlings were marked. For all nests that were monitored, we marked ~90% of all breeding adults every year.</p> <p>We used data from a total of 243 breeding attempts made by 159 breeding pairs captured during 2009–2017 to describe mating patterns in the study population, including: (i) the duration of social bonds for all breeding pairs formed during the study; (ii) the proportion of newly formed and remated pairs found during the entire study period and during each year; and (iii) the proportion of divorce versus mate loss causing pair dissolution.</p> <p>The consequences of mate retention and successive remating were evaluated by performing mixed-effects models in the lme4 package (Bates et al. 2015) in the free software R 4.0.2 (R Core Team 2020). To assess whether reproductive success was higher for remated pairs than for newly formed pairs, we tested for the effects of pairing status (newly formed vs. remated) on measures of breeding productivity. Linear models were fit for laying date, clutch size, and number of fledglings produced. To control for between-season variation in reproductive output, we calculated Z-scores for all numeric response variables using the mean and standard deviation for each year. All models included age class of both members of a breeding pair as covariates (yearling vs. adult), and female, male and pair ID as random intercepts. First, we performed analyses on the complete set of 243 breeding attempts, and subsequently repeated the analyses on a reduced subset of data that only contained pairs whose previous pairing status was known with certainty (n = 159). This allowed to evaluate potential bias in our results, given that the complete dataset included pairs misclassified as “newly formed”, because the previous pairing status of older individuals that we captured for the first time is unknown.</p> <p>We also investigated whether individuals experienced reduced reproductive success after mate replacement. To test this, we compared breeding productivity of individuals in the years before and after mate loss. We focused the analysis on widowed birds, as the frequency of divorced individuals was low in the study population. We used linear mixed-effects models that included data on laying date, clutch size, and number of fledglings produced as response variables. Each sex was tested separately, with clutch size being evaluated only for females. We included the breeding season as predictor (year x vs. x-1), and entered individual ID as a random intercept.</p> <p>Lastly, to evaluate whether successive remating influenced reproductive success, we used data on pairs that bred more than once together during the study (n = 132). Linear mixed-effects models were fitted to assess the effect of the number of seasons breeding together on laying date, clutch size, and number of fledglings produced. Between-season effects were controlled as described above, while the number of seasons breeding together (range: 1–6) was introduced as predictor. Given the skewed distribution of the number of seasons breeding together in this dataset (one = 36%; two = 36%; three = 17%; four = 8%; five = 2%; six = 1%), and the possibility that its effect on reproductive success might not be linear, a dummy variable indicating whether an observation belonged to the first breeding attempt (first attempt vs. after-first attempt) was also entered as predictor. Models included female and male age class as covariates, and pair ID as a random intercept.</p> <p><strong>References:</strong></p> <p>Botero-Delgadillo, E., Quirici, V., Poblete, Y., Cuevas, E., Kuhn, S., Girg, A., Teltscher, K., Poulin, E., Kempenaers, B., & Vásquez, R. A. (2017). Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird. Ecology and Evolution, 7(20), 8363–8378. https://doi.org/10.1002/ece3.3342</p> <p>Bates, D., Maechler, M., Bolker, B., & Walker, S. 2015. Fitting linear mixed-effects models using lme4. J. Stat. Soft. 67: 1–48.</p> <p>R Core Team. (2020). R: a language and environment for statistical computing, version 4.0.2. R Foundation for Statistical Computing, Vienna, Austria, http://www.R.project.org</p> <p><br> =====================================================================================<br> =====================================================================================</p>
Living, working, and shopping patterns
<p><em><strong>In this final Rebalance Dialogue, <a href="https://rebalancemobility.eu/andrea-ricci/">Andrea Ricci</a> moderated the dialogue between <a href="https://rebalancemobility.eu/alain-lhostis/">Alain L’Hostis</a> and <a href="https://rebalancemobility.eu/cristina-marolda/">Cristina Marolda</a> about how living, working and shopping patterns are changing in Europe and transforming our urban context. As ICT-based technology permeates our life, the so-called “smart” solutions become the default option for many people as they supposedly bring time savings and overall efficiency gains. Pandemics have certainly accelerated this change, but a more structural trend was visible even before, which technological innovation alone cannot explain. The implications are far-reaching, they affect urban form, infrastructure requirements, and most importantly basic values such as equality of opportunities.</strong></em></p> <p>REBALANCE wants to know to which of the following four “models” are the aspirations of the majority of citizens – and specifically what the younger generations. First, Suburban dwelling, quiet, more indoor and outdoor space; second, Inner city dwelling, “where the action is”; third, Rural escape, return to nature and fourth the 15-minute city, multi-nodal city</p> <p>One way to predict which of these will be favoured in the long term is to identify robust change factors that support them. The participants identified a surge in rural escape from the city centre, where the real estate market has grown exponentially. Millennials wanted to settle in the inner city but couldn’t afford it. Cities should be balanced between density and green spaces. The 15 min-city model was debated along with it’s multinodal, multicentre characteristics: The Dutch model was also proposed and suggested for further exploration: connected small cities. Currently, there is the question of whether polycentric cities reduce transport injustice or just increase efficiency. Services must be guaranteed for the majority and not just for the elite. The future might offer denser cities because the human population continues to grow. Although digitalisation and gentrification define the city models, these concepts are also defined by the models.</p> <blockquote> <p><strong>Awareness of mobility injustice is spreading, especially in regard to the density vs sprawl debate. Long commuting times, in particular, reflect differently on different-economic groups, and attention is growing on “kinetic elites” and other inequality risks. Urban density has been systematically equated with efficiency and quicker accessibility, which leads to a disregard towards urban sprawl. The revision of this dogma could put polycentric cities in the spotlight in the matter of reducing mobility injustice.</strong></p> </blockquote> <p>In societal terms, there could be a possible divide in society between commuters and non-commuters. Also possible a combination of both, with occasional commuting (with longer travel times). There are differences in needs and wishes between generations. Social networks are omnipresent, but is meeting people a driver? For instance, teens in France reduced their mobility for leisure (even before COVID-19). Young people are thought to be more conscious of the environment and sustainability, but this needs to be linked with the awareness of the common good, not as a synonym of freedom reduction.</p> <p>Regarding the debate “comfort vs convenience“, efficiency, in the guise of “individual convenience”, appears to be the main driver of changing patterns. The level of the extent to which efficiency is pursued at the expense of other fundamental values and aspirations, both at the individual level (comfort) and more importantly at the overall community level (equity, conviviality) needs to be explored. Optimisation is not an individual choice and the value of travel time might mean less commuting time (VTT reduces when using ICT), but the value of time is rooted in efficiency. People will travel more when commuting.</p> <p>The discussants stressed that millennials do not put effort into owning the car and that their convenience (efficiency instead of comfort) affects other values such as social sustainability, economic sustainability, and environmental sustainability. And the long term impact of COVID might be the revaluation of the value of personal time and rethinking our priorities.</p> <p>The massive shift towards remote activities (work, learn, shop, etc.) entails that the availability of individual space becomes a prominent concern. The following two extreme alternatives fight to prevail:</p> <ol> <li> <p>Alternative 1: the shift towards remote, virtual life is here to stay. Therefore, it is necessary to redesign our space and the logistics available to ensure comfort and efficiency in the medium/long term. The real estate market undergoes a major structural change, with residential space in higher demand while office space loses value.</p> </li> <li> <p>Alternative 2: confinements and lockdowns have shown that the social/convivial dimensions of most our activities are essential to ensure an acceptable quality of life. Remote work and education are limited to the essentials and most people/families are content with marginal readjusting of their available space.</p> </li> </ol> <p>In this case, the participants raised points such as:</p> <blockquote> <p>“Smart does not equal digital” and the need to be aware of technology, ingrained in society. Things are changing, also the assumptions. Technology must be steered because it is not fair per se.</p> </blockquote> <p><strong>Will urban expansion drive the evolution of transport infrastructure and mobility services or the other way around?</strong></p>
Earthquake catalogs for: A specific earthquake processing workflow for studying long-lived explosive volcanic eruptions with application to the 2008 Okmok eruption
<p>Repository for the seismic catalogs from Garza-Giron et al. (2023a,b). These include the catalog with absolute locations using NonLinLoc (Lomax et al., 2001; Lomax and Curtis, 2001), and the relocated catalogs using hypoDD (Waldhauser and Ellsworth, 2000) and GrowClust (Trugman and Shearer, 2017).</p> <p>The header of the CSV files is as follows:</p> <p><strong>Date</strong> (year/month/day), <strong>Time</strong> (hr:min:sec:msec), <strong>Latitude</strong> (decimal degrees), <strong>Longitude</strong> (decimal degrees), <strong>Depth</strong> (km), <strong>Magnitude</strong> (Ml calculated for this study), <strong>Event_type</strong> (VT:vulcano-tectonic;LP:long-period), <strong>Number of stations</strong> where the event was detected, <strong>ID</strong></p> <p>References:</p> <div>Garza‐Giron, R., Brodsky, E. E., Spica, Z. J., Haney, M. M., & Webley, P. W. (2023a). A specific earthquake processing workflow for studying long‐lived, explosive volcanic eruptions with application to the 2008 Okmok Volcano, Alaska, eruption. <em>Journal of Geophysical Research: Solid Earth</em>, e2022JB025882.</div> <div> </div> <div> <div>Garza‐Girón, R., Brodsky, E. E., Spica, Z. J., Haney, M. M., & Webley, P. W. (2023b). Earthquakes record cycles of opening and closing in the enhanced seismic catalog of the 2008 Okmok Volcano, Alaska, eruption. <em>Journal of Geophysical Research: Solid Earth</em>, <em>128</em>(7), e2023JB026893.</div> <div> </div> </div> <p>Lomax A, Curtis A (2001) Fast, probabilistic earthquake location in 3-D models using oct-tree importance sampling. Geophys Res Abstracts, 3:955.</p> <p>Lomax, A., Zollo, A., Capuano, P., and Virieux, J. (2001). Precise, absolute earthquake location under Somma‐Vesuvius volcano using a new 3D velocity model.Geophysical Journal International,146, 313–331.</p> <p>Trugman, D. T., and Shearer, P. M. (2017). GrowClust: A hierarchical clustering algorithm for relative earthquake relocation, with application to the Spanish Springs and Sheldon, Nevada, earthquake sequences. Seismological Research Letters, 88(2A), 379-391.</p> <p>Waldhauser, F., and Ellsworth, W. L. (2000). A double-difference earthquake location algorithm: Method and application to the northern Hayward fault, California. Bulletin of the Seismological Society of America, 90(6), 1353-1368.</p>
BLMtwitter: The Black Lives Matter (BLM) Twitter Corpus
<p>In May 2020, the murder of George Floyd led to protests throughout the United States and around the world. Along with these protests, social media platforms saw a dramatic increase in the volume of discussion regarding Black Lives Matter (BLM). Two years on, online discussion of BLM continues to be lively, not just in the United States but also internationally. This dataset represents one of the most extensive collections of Black Lives Matter tweets available, covering from 2010 through 2022 and including more than 50 million tweets overall. Parallel corpora for All Lives Matter and Blue Lives matter are also included. Monthly updates for 2023 are available on Github (https://github.com/amaurits/BLMtwitter), along with a datasheet and a preprint describing the dataset in more detail.</p>
Live Cells for contour tracking
<p>Pre-processed live cell dataset in tfrecord format. </p> <p>It was used for training and inference of our contour tracking model.</p>
Active cell divisions generate fourfold orientationally ordered phase in living tissue
<p>Morphogenesis, the process through which genes generate form, establishes tissue scale order as a template for constructing the complex shapes of the body plan. The extensive growth required to build these ordered substrates is fuelled by cell proliferation, which, naively, should destroy order. Understanding how active morphogenetic mechanisms couple cellular and mechanical processes to generate order — rather than annihilate it — remains an outstanding question in animal development. We show that cell divisions are the primary drivers of tissue flow leading to a fourfold orientationally ordered phase. Waves of anisotropic cell proliferation propagate across the embryo with precise patterning. Defects introduced into the nascent lattice by cell divisions are moved out of the tissue bulk towards the boundary by subsequent divisions. Specific cell proliferation rates and orientations enable cell divisions to organize rather than fluidize the tissue. We observe this using live imaging and tissue cartography to analyse the dynamics of fourfold tissue ordering in the trunk segmental ectoderm of the crustacean <em>Parhyale hawaiensis</em> beginning 72 hours after egg laying. The result is a robust, active mechanism for generating global orientational order in a non-equilibrium system that sets the stage for the subsequent development of shape and form.</p>
Cost of living by country
<p>This dataset shows the different cost of living per country divided by different categories. This data is the result of scraping from the page <a href="https://www.expatistan.com/cost-of-living">Expatistan.</a></p>
Cost of living by city
<p>This dataset shows the different cost of living per city divided by different categories. This data is the result of scraping from the page <a href="https://www.expatistan.com/cost-of-living">Expatistan.</a></p>
ScienceDex guides
Understand access before you commit
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.