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Data from: Inflorescence and flower development in Musa velutina H. Wendl. & Drude (Musaceae), with a consideration of developmental variability, restricted phyllotactic direction, and hand initiation
Premise of research. Inflorescence and flower structure in the Musaceae is unique in the Zingiberales. The inflorescence lacks the obvious cincinnus structure that characterizes the order, and the flowers are unisexual. Previous studies were conducted using cultivated varieties and were carried out with sectioned material, which does not permit accurate developmental descriptions. Developmental study of a wild species with modern methods addresses these shortcomings and provides more accurate descriptions. Methodology. Young inflorescences and flowers were collected from botanical gardens in Hawaii and Australia and critical-point dried for observation with a scanning electron microscope. Pivotal results. All shoots and inflorescences have sinistrorse (left-handed) phyllotaxy, and the sequence of flower initiation is usually correlated with this pattern. Initiation begins on the cathodic side of the hand (opposite the direction of phyllotactic rise) and progresses anodically (in the direction of phyllotactic rise). Within this general pattern, the sequence of flower initiation is variable, even within the same inflorescence. Five patterns of initiation are reported, with additional variation within each pattern. Both male and female flowers have similar early developmental patterns but diverge at the time of petal/inner androecial formation. In male flowers the anterior side of the flower develops slightly ahead of the posterior, while in female flowers the posterior side develops slightly ahead of the anterior. While consistently present in the material analyzed here, these differences are not apparent at the time of gynoecial initiation or in the mature flowers. Conclusions. The banana inflorescence is another example of how higher-level phyllotactic patterns can influence the sequence of organ initiation at lower levels. Despite variability in the sequence of flower initiation in a hand, the best interpretation of the hand remains a cincinnus. Variability in inflorescence and floral development is rarely reported and may be more common than currently supposed.
Data from: Portable bacteria-capturing chip for direct surface-enhanced Raman scattering identification of urinary tract infection pathogens
Acute urinary tract infections (UTIs) are one of the most common nosocomial bacterial infections, which affect almost 50% of the population at least once in their lifetime. UTIs may lead to lethal consequences if they are left undiagnosed and untreated properly. Early, rapid and accurate uropathogens detection methods play a pivotal role in clinical process. In this work, a portable bacteria-grasping surface-enhanced Raman scattering (SERS) chip for identification of three species of uropathogens (E. coli CFT 073, P. aeruginosa PAO1, and P. mirabilis PRM1) directly from culture matrix was reported. The chip was firstly modified with a positively-charged NH3+ group, which enable itself grasp the negatively-charged bacterial cells through the electrostatic adsorption principle. After the bacterial cells were captured by the chip, concentrated Ag nanoparticles (NPs) were used to obtain their Raman fingerprint spectra with recognizable characteristic peaks and good reproducibility. With the help of chemometric method such as discriminant analysis (DA), the SERS based chip allows a rapid, successful identification of three species of UTI bacteria with a minimal bacterial concentration (105 cells/mL) required for clinical diagnostics. In addition, this chip could spot the bacterial SERS fingerprints information directly from LB culture medium and artificial urine without sample pre-treatment. The portable bacteria-grasping SERS based chip provides a possibility for fast and easy detection of uropathogens, and viability of future development in healthcare applications.
Data from: Comparison of infinitesimal and finite locus models for long-term breeding simulations with direct and maternal effects at the example of honeybees
Stochastic simulation studies of animal breeding have mostly relied on either the infinitesimal genetic model or finite polygenic models. In this study, we investigated the long-term effects of the chosen model on honeybee breeding schemes. We implemented the infinitesimal model, as well as finite locus models, with 200 and 400 gene loci and simulated populations of 300 and 1000 colonies per year over the course of 100 years. The selection was of a directly and maternally influenced trait with maternal heritability of h²_m = 0.42, direct heritability of h² d = 0.27, and a negative correlation between the effects of r_md = −0.18. Another set of simulations was run with parameters h²_m = 0.53, h²_d = 0.34, and r_md = −0.53. All models showed similar behavior for the first 20 years. Throughout the study, we observed a higher genetic gain in the direct than in the maternal effects and a smaller gain with a stronger negative covariance. In thelong-term, however, only the infinitesimal model predicted sustainable linear genetic progress, while the finite locus models showed sublinear behavior and, after 100 years, only reached between 58% and 62% of the mean breeding values in the infinitesimal model. While the infinitesimal model suggested a reduction of genetic variance by 33% to 49% after 100 years, the finite locus models saw a more drastic loss of 76% to 92%. When designing sustainable breeding strategies, one should, therefore, not blindly trust the infinitesimal model as the predictions may be overly optimistic. Instead, the more conservative choice of the finite locus model should be favored.
DNA-Directed Arrangement of Soft Synthetic Compartments and Their Behavior In Vitro and In Vivo
<p>Data underlying the figures in the publication “DNA-Directed Arrangement of Soft Synthetic Compartments and Their Behavior <em>in Vitro</em> and <em>in Vivo</em>”, published in <em>Nanoscale, </em><strong>2020</strong>, 12, 9786–9799. <a href="https://pubs.rsc.org/en/content/articlelanding/2020/nr/d0nr00361a#!divAbstract">https://pubs.rsc.org/en/content/articlelanding/2020/nr/d0nr00361a#!divAbstract</a></p> <p>Table of contents:</p> <p>It contains four folders with the corresponding datasets for the <em>Figures 1, 2, 3,</em> and <em>5</em>.</p> <p> </p>
Data from: Behavior and nutritional condition buffer a large-bodied endotherm against direct and indirect effects of climate
Temporal changes in net energy balance of animals strongly influence fitness; consequently, natural selection should favor behaviors that increase net energy balance by buffering individuals against negative effects of environmental variation. The relative importance of behavioral responses to climate-induced variation in costs versus supplies of energy, however, is uncertain, as is the degree to which such responses are mediated by current stores of energy. We evaluated relationships among behavior, nutritional condition (i.e., energetic state), and spatiotemporal variation in costs versus supplies of energy available to a large-bodied endotherm, the North American elk (Cervus elaphus), occupying two ecosystems with contrasting climates; 1) a temperate, montane forest; and 2) an arid, high-elevation desert. We hypothesized that during spring through autumn, behavioral responses to the energetic landscape would be both context-dependent (i.e., would vary as a function of the environmental conditions experienced by elk in the forest versus the desert), and state-dependent (i.e., would vary as a function of the energetic state of an individual). We tested several predictions derived from that hypothesis by combining output from a biophysical model of the thermal environment with data on forage quality, animal locations, and nutritional condition of individuals. At the population level, elk in the desert selected areas that reduced costs of thermoregulation over those that provided the highest quality forage. In the forest, however, costs imposed by the thermal environment were less pronounced, and elk selected areas that increased access to high quality forage over those that reduced costs of thermoregulation. At the individual level, nutritional condition did not influence strength of selection for low-cost areas or high quality forage among elk in the forest. In the desert, however, strength of selection for low-cost areas (but not forage quality) was state-dependent - individuals in the poorest condition at the end of winter showed the strongest selection for areas that reduced costs of thermoregulation during spring and summer, and also expended the least amount of energy on locomotion. Our results highlight the importance of understanding the roles of behavior and nutritional condition in buffering endotherms against direct and indirect effects of climate on fitness.
FIGURE 30 in New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation
FIGURE 30. Diasporus diastema from Cerro La Campana, Panama, Panama. Photo by W. E. Duellman.
FIGURE 25 in New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation
FIGURE 25. Distribution of the Subgenus Hylactophryne, Genus Craugastor, Family Craugastoridae.
FIGURE 28 in New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation
FIGURE 28. Haddadus binotatus from Pisinguaba, São Paulo, Brazil. Photo by C. F. B. Haddad.
FIGURE 5 in New World direct-developing frogs (Anura: Terrarana): Molecular phylogeny, classification, biogeography, and conservation
FIGURE 5. Distribution of the taxon Terrarana.
Full year of consistent Direct Normal Irradiance data at 1-min, 10-min and 1-hour time steps.
<p>Full year of consistent Direct Normal Irradiance data at 1-min, 10-min and 1-hour time steps. The consistency is obtained by building the 10-min and 1-hour time step years from the 1-min year. The measurements correspond to the year 2016 and were taken by the meteorological station of the Group of Thermodynamics and Renewable Energy (GTER) of the University ofSeville.</p> <p>The geographical coordinates of the measurement station are: Latitude: 37º24’42’’ North, Longitude: -6º 00’21’’ East.</p> <p>This measurement station measures solar DNI with a sampling and logging frequency of 0.2 Hz and an ISO first class EppleyNIP pyrheliometer mounted on a sun tracker Kipp and Zonen 2AP.</p>
Agility and change-of-direction speed are two different abilities also during the execution of repeated trials and in fatigued conditions. DATASET
<p>Raw dataset for the above-mentioned original research article</p>
Figure 10 in Can hair width and scale pattern and direction of dorsal scapular mammalian hair be a relatively simple means to identify species?
Figure 10. Boxplot of 30 guard hair widths for each species including quartile ranges.
Presence locations (direct and indirect) of blue sheep and livestock in Johar Valley, Uttarakhand, India from years 2015-2017
<p><span>In-depth knowledge of distribution and their factors are important for species conservation and management. Many forms of such data have led to development of new analytical techniques for better interpretation. For mountainous terrains with certain limitations, species data is obtained in presence-only form. Point process model is one of the recent approaches for modelling such data, taking care of pseudo-absences and spatial independence. For conservation of regions with limited resources and species with similar ecological requirements, it is important to properly assess competition extent between wild and domestic species. We attempted to use point process framework to estimate resource selection function of blue sheep (<i>Pseudois nayaur</i>) in pastoralism influenced areas of a western Himalayan landscape. Our study is a first attempt to use this framework to estimate resource selection on a dataset not collected using radio-telemetry. Spatial locations of presence points of blue sheep and livestock and a background sample of random points along with six topographic covariates were used for modelling resource selection probability via intensity function. Blue sheep showed its predicted presence in areas with open vegetation coinciding with alpine meadows, influenced by southern aspect keeping a threshold distance of 600m-1000m from cliffs (escape terrain). Livestock, also showed presence probability in open vegetation but at lower altitudes mainly on valley floors. Our results suggest that though blue sheep continued to use the same habitat type after livestock arrival, they selected different resources based on topographic factors. Livestock were in areas convenient for pastoralists for establishing their campsites and feasibility of grazing along with presence of nutritious grasses. Thus, we assume that probable shift of habitat for blue sheep from optimal areas occurs due to livestock presence, which might disturb their nutritional balance. Our study provides helpful insights for management of rangelands, which when tied with dietary patterns will give wholesome idea for proper conservation measures in future.</span></p>
Figure 2 in Direct development of the bush frog Raorchestes longchuanensis (Yang and Li 1978) under laborary conditions in Southern China
Figure 2. Raorchestes longchuanensis, in nature from Yinjiang, Yunnan, China.
Assortative mating for between-patch dispersal status in a wild bird population: Exploring the role of direct and indirect underlying mechanisms
<p><span>Previous studies have reported functional integration between dispersal and other phenotypic traits allowing individuals to alleviate dispersal costs, and such associations can affect dispersal evolution in return. In sexually reproducing species, assortative mating according to dispersal can shape the maintenance of such trait associations. Despite the potentially crucial consequences of dispersal in natural populations, assortative mating for dispersal and its underlying mechanisms remain largely unexplored. Here, we assessed assortative mating for between-patch dispersal status in a fragmented population of a small passerine bird, the collared flycatcher, and explored whether such assortative mating could result from (i) direct mate choice based on dispersal-related behavioural (aggressiveness and boldness) and morphological traits (tarsus and wing length), (ii) biased mating due to spatio-temporal heterogeneity in the distribution of dispersal phenotypes and/or (iii) post-mating adjustment of dispersal phenotype or dispersal-related traits. We found intrinsic assortative mating (i.e. positive among-pair correlation) for current dispersal status (in the year of mating) but not for natal dispersal status, even though we could not exclude it due to limited power. We also found assortative mating for boldness and age category (yearlings vs. older adults), and the probability for pair members to be assorted for current dispersal status was higher when both pair members were of similar boldness score and of the same age compared to mixed-age pairs. Mate choice based on boldness and age thus appears as a possible mechanism underlying assortative mating for dispersal status. Our analyses however remained correlative and only an experimental manipulation of these traits could allow inferring causal links. Non-random mating for dispersal-related traits may affect the evolution of dispersal syndromes in this population. More work is nevertheless needed to fully assess the evolutionary implications of age- and behaviour-based assortative mating for dispersal.</span></p>
Data for: Direct evidence for increased disease resistance in polyandrous broods exists only in eusocial
<p><u>Background</u></p> <p>The 'genetic diversity' hypothesis posits that polyandry evolved as a mechanism to increase genetic diversity within broods. One extension of this hypothesis is the 'genetic diversity for disease resistance' hypothesis (GDDRH). Originally designed for eusocial Hymenoptera, GDDRH states that polyandry will evolve as an effect of lower parasite prevalence in genetically variable broods. However, this hypothesis has been broadly applied to several other taxa. It is unclear how much empirical evidence supports GDDRH specifically, especially outside eusocial Hymenoptera.</p> <p><u>Results</u></p> <p>This question was addressed by conducting a literature review and posteriorly conducting meta-analyses on the data available using Hedges's <i>g</i>. The literature review found 10 direct and 32 indirect studies with both having a strong publication bias towards Hymenoptera. Two meta-analyses were conducted and both found increased polyandry (direct tests; <i>n</i> = 8, <i>g</i> = 0.2283, <i>p</i> = <0.0001) and genetic diversity generated by other mechanisms (indirect tests; <i>n </i> = 10, <i>g</i> = 0.21, <i>p</i> = <0.0001) reduced parasite load. A subsequent moderator analysis revealed that there were no differences among Orders, indicating there may be applicability outside of Hymenoptera. However, due to publication bias and low sample size we must exercise caution with these results. </p> <p><u>Conclusion</u></p> <p>Despite the fact that the GDDRH was developed for Hymenoptera, it is frequently applied to other taxa. This study highlights the low amount of direct evidence supporting GDDRH, particularly outside of eusocial Hymenoptera. It calls for future research to address species that have high dispersal rates and contain mixes of solitary and communal nesting.</p>
Disentangling the direct and indirect effects of canopy and understory vegetation on the foraging habitat selection of the brown bear Ursus arctos
<p>Elucidating the factors affecting the foraging habitat selection of wildlife can further our understanding of the animal– habitat relationships and inform wildlife conservation and management. Canopy and understory vegetation may directly or indirectly affect the foraging habitat selection of carnivores through changes in habitat structure and prey availability, respectively; however, the relative importance of these two effects remains largely unknown. Dwarf bamboo Sasa kurilensis is a predominant understory plant that suppresses regeneration in the forests of northern Japan. The purpose of this study was to disentangle the direct and indirect effects of canopy forest type Larix kaempferi plantation versus natural mixed forest) and dwarf bamboo on foraging habitat selection of a large carnivore, the brown bear Ursus arctos. In the Shiretoko World Heritage, brown bears dig for cicada nymphs during summer. We evaluated the frequency of brown bear foraging on cicadas by investigating traces of digging for cicada nymphs. A structural equation model was used to statistically disentangle the direct and indirect effects of vegetation. Our results demonstrated that canopy and understory vegetation directly and indirectly affected foraging habitat selection of brown bears. Dwarf bamboo negatively affected cicada nymph density, which positively affected brown bear digging. This suggests that dwarf bamboo also had indirect negative effects on brown bears. Forest type had significant direct and indirect effects via change in cicada nymph density on foraging behavior in brown bears. Forestry managers in northern Japan, including the study site, try to remove dwarf bamboo for assisting natural regeneration. Removal of dwarf bamboo by scarification might not only promote natural regeneration, but also provide a beneficial foraging habitat for bears.</p>
Figure 3 from: Deans A, Seltmann K, Yoder M, Miko I, Forshage M, Bertone M, Agosti D, Austin A, Balhoff J, Borowiec M, Brady S, Broad G, Brothers D, Burks R, Buffington M, Campbell H, Dew K, Ernst A, Fernandez-Triana J, Gates M, Gibson G, Jennings J, Johnson N, Karlsson D, Kawada R, Krogmann L, Kula R, Ohl M, Rasmussen C, Ronquist F, Schulmeister S, Sharkey M, Talamas E, Tucker E, Vilhelmsen L, Ward P, Wharton R (2012) A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research 27: 67-88. https://doi.org/10.3897/jhr.27.2961
Figure 3 - The detailed breakdown report from an analyzer report. See Using the "analyzer" tool for explanation.
Figure 2 from: Deans A, Seltmann K, Yoder M, Miko I, Forshage M, Bertone M, Agosti D, Austin A, Balhoff J, Borowiec M, Brady S, Broad G, Brothers D, Burks R, Buffington M, Campbell H, Dew K, Ernst A, Fernandez-Triana J, Gates M, Gibson G, Jennings J, Johnson N, Karlsson D, Kawada R, Krogmann L, Kula R, Ohl M, Rasmussen C, Ronquist F, Schulmeister S, Sharkey M, Talamas E, Tucker E, Vilhelmsen L, Ward P, Wharton R (2012) A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions. Journal of Hymenoptera Research 27: 67-88. https://doi.org/10.3897/jhr.27.2961
Figure 2 - Using and interpreting results from the analyzer. See Using the "analyzer" tool for explanation. A Help link B Input field C CAPTCHA test D Result table E Download link; and F Detailed breakdown link.
A Dynamic MaxSAT-based Approach to Directed Feedback Vertex Sets - Results
<p>The Results for the paper of the same name, published at ALENEX 2023.</p>
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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.
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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
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