Find research datasets worth reusing

Figure 41 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 41 Scintilla cf. violescens Kuroda & Taki, 1961, Haifa, Israel: right (A) and left (B) valve outer views, left (C) and right (D) valve inner views, hinge of left (E, G) and right (F, H) valve. Scale bars: 2 mm (A–D); 0.5 mm (E–H).

Figure 15 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 15 Hypermastus sp., Tel Aviv, Israel, HELM project (sample S67_3F): front (A, B), side (C, D) and back (E) views, apex with optical microscope (F) and SEM (G) showing the protoconch-teleoconch transition (the shell had a different orientation in images F and G). The arrow marks the constriction between protoconch and teleoconch that is a diagnostic character for this species. Scale bars: 0.5 mm (A–E); 0.2 mm (F, G).

Figure 14 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 14 Vitrinella aff. Vitrinella sp. 1 (sensu Blatterer 2019), Ashdod, Israel, APM DAN project (sample 10B): apical (A, B), umbilical (C, D), front (E) and side (F) views, protoconch (G) and back view (H). Scale bars: 0.3 mm (A–F, H); 0.1 mm (G).

Figure 13 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 13 Iravadia aff. elongata (Hornung & Mermod, 1928) A–F Ashqelon, Israel, HELM project (sample S58_2F): front (A, B) and back (C, D) views, protoconch (E) and detail of sculpture on the body whorl (F) G, H Arusa (near Port Sudan), Sudan: front view of an adult (G) and juvenile (H) shell. Scale bars: 1 mm (A–D, G, H); 0.2 mm (E); 0.3 mm (F).

Figure 12 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 12 Comparison between Elachisina sp. and Elachisina robertsoni Kay, 1979 A–EElachisina sp., west of Rosh HaNikra Islands, Israel, HELM project (sample S13_3L): front (A, B), side (C) and back (D, E) views F–HElachisina robertsoni, BPBM 9754 (holotype), Maunalua Bay, Oahu, Hawaii: front (F), side (G) and back (H) views (photograph courtesy N. Young). Scale bars: 0.5 mm.

Figure 1 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 1 Unidentified gastropod (Caenogastropoda), Haifa Bay, Israel (sample HM27(c)): front (A, B), side (C) and back (D, E) views, protoconch (F, G). Scale bars: 1 mm (A–E); 0.3 mm (F–G).

Figure 11 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 11 Joculator problematicus Albano & Steger, sp. nov., holotype, NHMW-MO-113580, Ashqelon, Israel, HELM project (sample S58_3F): front (A, B), left side (C), right side (D, E) and back (F) views, protoconch (G, H), microsculpture (I) and base and siphonal canal (J). Scale bars: 0.5 mm (A–F); 0.2 mm (G, H); 0.3 mm (I); 0.4 mm (J).

Figure 10 from: Albano PG, Steger J, Bakker PAJ, Bogi C, Bošnjak M, Guy-Haim T, Huseyinoglu MF, LaFollette PI, Lubinevsky H, Mulas M, Stockinger M, Azzarone M, Sabelli B (2021) Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification. ZooKeys 1010: 1-95. https://doi.org/10.3897/zookeys.1010.58759

Figure 10 Cerithiopsis sp., Shiqmona Beach, Israel: front (A, B), side (C) and back (D) views, protoconch oriented to highlight the transition to the teleoconch (E, F), microsculpture (G). Scale bars: 1 mm (A–D); 0.2 mm (E, F); 0.4 mm (G).

opencc-by-4.0Jan 2017View details →

Bone pose estimation Challenge dataset

<p>This is a comprehensive dataset from the 2016 code challenge. Estimation of the poses of the individual bones from videoradiography is a necessary step towards the evaluation of 3D kinematics. The following comprehensive dataset contains video radiography of knee of ten different subjects captured by a 9” c-arm machine. The poses of the individual bones can be estimated either by generating DRRs from MRI scans or by creating 3D model through segmentation. For more details see www.codemaraphon.ru</p>

Data from: Effects of immune challenge on the oviposition strategy of a noctuid moth

Infections can have detrimental effects on the fitness of an animal. Reproducing females may therefore be sensitive to cues of infection and be able to adaptively change their oviposition strategy in the face of infection. As one possibility, females could make a terminal investment and shift reproductive effort from future to current reproduction as life expectancy decreases. We hypothesized that females of the noctuid moth Heliothis virescens make a terminal investment and adapt their oviposition timing as well as their oviposition site selectivity in response to an immune challenge. We indeed found that females that were challenged with the bacterial entomopathogen Serratia entomophila laid more eggs than control females one night after the challenge. Additionally, bacteria-challenged females were less discriminating between oviposition sites than control females. Whereas control females preferred undamaged over damaged plants, immune-challenged females did not differentiate between the two. These results indicate that terminal investment is part of the life history of H. virescens females. Moreover, our results suggest that the strategy of terminal investment in H. virescens oviposition represents a fitness trade-off for females: in the face of infection, an increase in oviposition rate enhances female fitness, whereas low oviposition site selectivity reduces female fitness.

Data from: Evaluating modularity in morphometric data: challenges with the RV coefficient and a new test measure

Modularity describes the case where patterns of trait covariation are unevenly dispersed across traits. Specifically, trait correlations are high and concentrated within subsets of variables (modules), but the correlations between traits across modules are relatively weaker. For morphometric data sets, hypotheses of modularity are commonly evaluated using the RV coefficient, an association statistic used in a wide variety of fields. In this article, I explore the properties of the RV coefficient using simulated data sets. Using data drawn from a normal distribution where the data were neither modular nor integrated in structure, I show that the RV coefficient is adversely affected by attributes of the data (sample size and the number of variables) that do not characterize the covariance structure between sets of variables. Thus, with the RV coefficient, patterns of modularity or integration in data are confounded with trends generated by sample size and the number of variables, which limits biological interpretations and renders comparisons of RV coefficients across data sets uninformative. As an alternative, I propose the covariance ratio (CR) for quantifying modular structure and show that it is unaffected by sample size or the number of variables. Further, statistical tests based on the CR exhibit appropriate type I error rates and display higher statistical power relative to the RV coefficient when evaluating modular data. Overall, these findings demonstrate that the RV coefficient does not display statistical characteristics suitable for reliable assessment of hypotheses of modular or integrated structure and therefore should not be used to evaluate these patterns in morphological data sets. By contrast, the covariance ratio meets these criteria and provides a useful alternative method for assessing the degree of modular structure in morphological data.

opencc-zeroDec 2015View details →

Data from: Actuarial senescence in a long-lived orchid challenges our current understanding of ageing

The dominant evolutionary theory of actuarial senescence—an increase in death rate with advancing age—is based on the concept of a germ cell line that is separated from the somatic cells early in life. However, such a separation is not clear in all organisms. This has been suggested to explain the paucity of evidence for actuarial senescence in plants. We used a 32 year study of Dactylorhiza lapponica that replaces its organs each growing season, to test whether individuals of this tuberous orchid senesce. We performed a Bayesian survival trajectory analysis accounting for reproductive investment, for individuals under two types of land use, in two climatic regions. The mortality trajectory was best approximated by a Weibull model, showing clear actuarial senescence. Rates of senescence in this model declined with advancing age, but were slightly higher in mown plots and in the more benign climatic region. At older ages, senescence was evident only when accounting for a positive effect of reproductive investment on mortality. Our results demonstrate actuarial senescence as well as a survival–reproduction trade-off in plants, and indicate that environmental context may influence senescence rates. This knowledge is crucial for understanding the evolution of demographic senescence and for models of plant population dynamics.

opencc-zeroDec 2017View details →

Data from: The challenges that spatial context present for synthesizing community ecology across scales

Accurately characterizing spatial patterns on landscapes is necessary to understand the processes that generate biodiversity, a problem that has applications in ecological theory, conservation planning, ecosystem restoration, and ecosystem management. However, the measurement of biodiversity patterns and the ecological and evolutionary processes that underlie those patterns is highly dependent on the study unit size, boundary placement, and number of observations. These issues, together known as the modifiable areal unit problem, are well known in geography. These factors limit the degree to which results from different metacommunity and macro-ecological studies can be compared to draw new inferences, and yet these types of comparisons are widespread in community ecology. Using aquatic community datasets, we demonstrate that spatial context drives analytical results when landscapes are sub-divided. Next, we present a framework for using resampling and neighborhood smoothing to standardize datasets to allow for inferential comparisons. We then provide examples for how addressing these issues enhances our ability to understand the processes shaping ecological communities at landscape scales and allows for informative meta-analytical synthesis. We conclude by calling for greater recognition of issues derived from the modifiable areal unit problem in community ecology, discuss implications of the problem for interpreting the existing literature, and identify tools and approaches for future research.

opencc-zeroDec 2015View details →

Data from: Cytokine responses in birds challenged with the human food-borne pathogen Campylobacter jejuni implies a Th17 response

Development of process orientated understanding of cytokine interactions within the gastrointestinal tract during an immune response to pathogens requires experimentation and statistical modelling. The immune response against pathogen challenge depends on the specific threat to the host. Here, we show that broiler chickens mount a breed-dependent immune response to Campylobacter jejuni infection in the caeca by analysing experimental data using frequentist and Bayesian structural equation models (SEM). SEM provides a framework by which cytokine interdependencies, based on prior knowledge, can be tested. In both breeds important cytokines including pro-inflammatory interleukin (IL)-1β, , IL-4, IL-17A, interferon (IFN)-γ and anti-inflammatory IL-10 and transforming growth factor (TGF)-β4 were expressed post-challenge. The SEM revealed a putative regulatory pathway illustrating a T helper (Th)17 response and regulation of IL-10, which is breed-dependent. The prominence of the Th17 pathway indicates the cytokine response aims to limit the invasion or colonization of an extracellular bacterial pathogen but the time-dependent nature of the response differs between breeds.

opencc-zeroDec 2015View details →

Data from: Challenging the conceptual framework of maintenance hosts for influenza A viruses in wild birds

1.The conceptual framework considering Anseriformes and Charadriiformes as the main maintenance hosts for influenza A viruses (IAV) in wild birds has shaped IAV research and surveillance over the last decades. 2.We challenge this framework by reviewing the worldwide surveillance data on non-Anseriformes and non-Charadriiformes (NANC) species, generally considered as playing little role in IAV maintenance, available in literature and online data bases (close to 200 sources). 3.Globally, we found an IAV infection rate of 1.51% (95% CI, 1.44%–1.59%) for c.101 000 birds tested from NANC species. If Anseriformes have, as expected, a higher infection rate than any other bird orders, eight bird orders have an infection rate higher or close to the Charadriiformes infection rate, challenging the status of Charadriiformes. 4.We interpret the attention paid in favour of Charadriiformes by an extrapolation bias from data collected in hotspots of IAV infection in Charadriiformes (e.g. Delaware Bay, USA). 5.The growing data on IAV in wild birds worldwide, summarised here, supports two non-exclusive hypotheses: (i) the quality of the diagnostic tools and techniques used explain the patterns observed; (ii) IAV maintenance is determined by complex multi-host systems composed of multiple bird species, dependent on the ecosystem and its bird diversity and composition. 6.Synthesis and applications. Our results have two main implications. First, new research and surveillance should be designed in order to understand influenza A viruses ecology in wild birds across the world, along with appropriate diagnostic tools and new hypotheses and dedicated protocols. This should be done in line with our new conceptual framework that conveys less a priori than its predecessor. Secondly, our results call for more bridging between biological and epidemiological sciences in order to tackle disease ecology in multi-host systems.

Data from: The double-edged sword of immune defence and damage control: do food availability and immune challenge alter the balance?

1.Animal immune systems must adaptively balance aggressive immune resistance (ability to destroy pathogens) with infection tolerance (ability to withstand the negative effects of infection; e.g., immunopathology or damage due to pathogen metabolism). 2.Insects offer unique insight into this balancing act because phenoloxidase (PO)-mediated melanisation is a key feature of immune resistance, but PO activation obligates the production of non-specific reactive species that can cause self-damage. The antioxidant glutathione (GSH) can provide protection against such reactive molecules, but high levels of GSH can impair melanisation. In support of the hypothesis that GSH can protect insects (e.g., crickets) from self-damage during an immune response, we found that bacterially infected crickets showed a significant positive relationship between GSH haemolymph concentration and fecundity after controlling for bacterial growth rate. That is, GSH may be a mechanism of infection tolerance because it correlated with fecundity despite bacterial proliferation. 3.Next, we factorially manipulated food availability and immune activation in female crickets to examine whether the relative balance between a component of immune resistance (i.e., PO) and protection from self-damage (i.e., GSH) was plastic and sensitive to environmental conditions. 4.Glutathione and PO were positively correlated, and the PO:GSH ratio was robust and not affected by food availability or immune activation. Thus, increased investment in a mechanism of immune resistance may obligate a concomitant increase in GSH to reduce self-damage (i.e., increase infection tolerance). Chronic immune activation led to greater tolerance of oxidative stress suggesting that repeated immune activation up-regulates infection tolerance mechanisms. Food limitation led to reduced PO activity, but not GSH concentration. This result suggests that mechanisms of immune resistance may be more sensitive to resource scarcity than mechanisms of infection tolerance. 5.We demonstrate that some mechanisms of immune resistance and infection tolerance can be correlated, and that they can be affected by food availability or immune activation.

Data from: Effect of host plant and immune challenge on the levels of chemosensory and odorant-binding proteins in caterpillar salivary glands

More than half of the proteome from mandibular glands in caterpillars is represented by chemosensory proteins. Based on sequence similarity, these proteins are putative transporters of ligands to gustatory receptors in sensory organs of insects. We sought to determine whether these proteins are inducible by comparing, both qualitatively and quantitatively, the salivary (mandibular and labial) proteomes from caterpillars (Vanessa cardui) reared on different plants and artificial diet containing either bacteria or bacterial cell-walls. We included a treatment where the caterpillars were switched from feeding on artificial diet to plant material at some point in their development. Additionally, we evaluated the degree of overlap between the proteomes in the hemolymph-filled coelom and salivary glands of caterpillars reared on plant material. We found that the quality and quantity of the identified proteins differed clearly between hemolymph-filled coelom, labial and mandibular glands. Our results indicated that even after molting and two-day feeding on a new diet, protein production is affected by the previous food source used by the caterpillar. Candidate proteins involved in chemosensory perception by insects were detected: three chemosensory (CSPs) and two odorant-binding proteins (OBPs). Using the relative amounts of these proteins across tissues and treatments as criteria for their classification, we detected hemolymph- and mandibular gland-specific CSPs and observed that their levels were affected by caterpillar diet. Moreover, we could compare the protein and transcript levels across tissues and treatment for at least one CSP and one OBP. Therefore, we have identified specific isoforms for testing the role of CSPs and OBPs in plant and pathogen recognition. We detected catalase, immune-related protein and serine proteases and their inhibitors in high relative levels in the mandibular glands in comparison to the labial glands. These findings suggest that the mandibular glands of caterpillars may play an important role protecting the caterpillar from oxidative stress, pathogens and aiding in digestion. Contamination with hemolymph proteins during dissection of salivary glands from caterpillars may occur but it is not substantial since the proteomes from hemolymph, mandibular and labial glands were easily discriminated from each other by principal component analysis of proteomic data.

opencc-zeroDec 2017View details →

Data from: Estimating national population sizes: methodological challenges and applications illustrated in the common nightingale, a declining songbird in the UK

1. Estimation of national population size can be important for setting conservation priorities but its methodology has received little critical attention. Sites for highly aggregated species are often prioritised if they contain 1% of national or biogeographical populations but the utility of this approach for other species is unclear. 2. To make recommendations for study design, we present methods used to estimate the UK population size of the common nightingale Luscinia megarhynchos. We assess the sensitivity of the population estimate to the analytical method used and identify sites of national importance for this territorial songbird. 3. Survey effort was directed by prior knowledge of the species' distribution and the survey design maximised detectability by focussing on the period of greatest song output. We used three different statistical methods to account for detectability, estimating that 55–65% of the national population was detected during surveys. 4. Birds in areas not known to contain the species accounted for 13–23% of the population estimate. Methods to account for these individuals contributed the greatest uncertainty to the results, due to the difficulty of surveying a very large sample of random sites and consequent need to stratify the sample. 5. The 12 derived estimates ranged between 5094 and 5938 territorial males, with the confidence limits ranging from 4764 to 6534. Site delimitation, using clustering based on nearest-neighbour distances, identified one site clearly of national importance and several others potentially nationally important, depending on the population threshold and clustering distance used. 6. Synthesis and applications. National population estimation is difficult and requires that species-specific variability in detectability and individuals present outside surveyed areas are accurately accounted for through survey design and statistical analysis. Accounting for these sources of error will not always be possible and will hamper efforts to assess true population size and consequently to determine whether sites, however defined, exceed critical thresholds of importance. Resources may be better invested in other activities, for example in generating population trends based on relative indices. The latter are generally easier to produce, potentially more robust and arguably more suitable for many conservation applications.

opencc-zeroDec 2016View details →

Data from: Calculating competitive intransitivity: computational challenges

Intransitive, or 'rock-paper-scissors' competition is compelling because it promotes species coexistence and because recent work suggests it may be common in natural systems. One class of intransitivity indices works by considering s, the minimum number of competitive reversals to convert a given competitive community (i.e., a 'tournament') to a hierarchy. The most straightforward example of such 'reversal-based' indices is Petraitis' index, t = 1 - s/M, where M is the maximum s across all possible n-species tournaments. Using exhaustive searches, we prove that Petraitis' formula for M (and, therefore, t) does not hold for n ≥ 7. Furthermore, the determination of s for even moderate values of n may prove difficult, as the equivalent graph-theoretical problem is NP-hard; there is no known computationally feasible way to compute an exact answer for anything but small values of n, let alone a closed-form solution. Petraitis' t is a valuable index of intransitivity; however, at present its use is limited to relatively species-poor systems. More broadly, reversal-based indices, while intuitive, may be problematic because of this computability issue.