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Figure 2 in Identification of early biomarkers in proteomic profiles of the phaeophyteSaccharina japonicaproximal to and beneath the front of bryozoan colonies
Figure 2: Two-dimensional gel electrophoresis profiles of the late-harvested Saccharina japonica. (A) Distal healthy S. japonica tissue. (B) S. japonica thallus tissue proximal to the bryozoan colony. (C) S. japonica tissue at the bryozoan colony front. The separated proteins were visualized by silver staining. Numbers attached to the arrows refer to the spot number listed in Tables 1 and 2.
Vitellogenins level as a biomarker of the honey bee colony seasonal dynamics
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FIGURE. Conlarium sichuanense (HKAS 113024, holotype) a–c Colonies on dead branches. d–k Conidiogenous cells and conidia. l Germinated conidium. m, n Colony on PDA from surface and reverse. Scale bars: d-k = 10 μm, l = 20 μm. in Conlarium sichuanense sp. nov., on Ficus virens from Sichuan Province, China
FIGURE. Conlarium sichuanense (HKAS 113024, holotype) a–c Colonies on dead branches. d–k Conidiogenous cells and conidia. l Germinated conidium. m, n Colony on PDA from surface and reverse. Scale bars: d-k = 10 μm, l = 20 μm.
Colour illustrations. Flowers, fruits, leaves and seeds of Musa itinerans (background photo by D.T. Vu); from top to bottom and left to right: colony on PDA after 14 d at 24 °C in darkness (left = obverse,right = reverse), sporodochia formed on CLA, aerial conidiophore, aerial conidiogenous cells, aerial conidia, sporodochial conidia. Scale bars: black = 20 µm, white = 10 µm. in Fusarium chuoi R. Hill, Gaya, D.T. Vu, Sand.-Den. & Crous, R. Hill, Gaya, D.T. Vu, Sand.-Den. & Crous sp. nov.
Colour illustrations. Flowers, fruits, leaves and seeds of Musa itinerans (background photo by D.T. Vu); from top to bottom and left to right: colony on PDA after 14 d at 24 °C in darkness (left = obverse,right = reverse), sporodochia formed on CLA, aerial conidiophore, aerial conidiogenous cells, aerial conidia, sporodochial conidia. Scale bars: black = 20 µm, white = 10 µm.
Cell orientation characteristics of the natural combs of honey bee colonies
<p>The cell orientation characteristics of the natural combs of honey bees have received much research attention. Although natural combs have been shown to be composed of cells with three orientations—vertical, intermediate (oblique), and horizontal—the proportion of comb cells in these three orientations varies. Knowledge of the comb-building preferences of honey bees is essential for the installation of wax comb foundations, and clarification of the cell orientation characteristics of natural honey bee combs is important for beekeeping. The purpose of this study was to determine the cell orientation characteristics of natural combs of Eastern honey bees (<i>Apis cerana cerana</i>) and Western honey bees (<i>Apis mellifera ligustica</i>). Newly built combs were used to measure the orientation of hexagonal cells and calculate the proportion of cells in different orientations relative to the total number of cells. The number of eggs laid by queens in the cells of different orientations was also determined. The orientation of cells in the natural combs of Eastern and Western honey bees was determined based on the value of the minimum included angle between the pair of parallel cell walls and a vertical line connecting the top and bottom bars of the movable frame in the geometric plane of the comb: 0°≤θ≤10°, 10°<θ≤20°, and 20°<θ≤30° for vertical, intermediate, and horizontal orientations, respectively. Natural combs were composed of cells with at least one orientation (vertical or horizontal), two orientations (vertical + intermediate (oblique) or vertical + horizontal), or three orientations (vertical + intermediate + horizontal), and the proportions of combs with the three aforementioned configurations differed. Both Eastern honey bees and Western honey bees preferred building combs with cells in a vertical orientation. Queens showed no clear preference for laying eggs in cells of specific orientations. The results of this study provide new insight that could aid the production and cutting of wax comb foundations of Eastern and Western honey bees. Our study highlights the importance of installing wax comb foundations compatible with the comb-building preferences of bees.</p>
Exposure to urban heavy metal contamination diminishes bumble bee colony growth
<p>As a result of their industrial past, legacy cites often have elevated concentrations of soil heavy metal contamination. Metal pollution can have negative and prolonged ecosystem impacts, and bees that forage in these urban ecosystems are at risk of exposure. Legacy cities are known to support species rich bee communities, which highlights the importance of determining the impact of heavy metal contamination on wild bee health. We examined how oral exposure to concentrations of four metals found within the provisions of bees foraging within Cleveland, Ohio, USA influenced colony growth of <em>Bombus impatiens</em> Cresson (Hymenoptera: Apidae), a common species within legacy cities across the eastern United States. Colony weight and brood survivorship were compared among hives fed uncontaminated sucrose solution (hereafter nectar), nectar spiked with one metal (arsenic, cadmium, chromium, or lead), and nectar containing all metals, after 15 or 30 d of exposure within flight tents. Across both exposure periods, we found a significantly higher proportion of dead brood in metal exposed hives. Additionally, colonies fed all four metals had a significantly higher proportion of dead brood than those fed a single metal. Our findings illustrate that even low, environmentally relevant concentrations of metals collected by B. impatiens in legacy cities can negatively influence bee colony growth. We highlight the need to identify metal exposure routes for bees in contaminated landscapes to minimize risk and bolster conservation habitat initiative success.</p>
The Embodiment of Colonial Strategy
<p>The Egyptian Empire conquered and colonized Nubia, what is today northern Sudan, on multiple occasions. The colonization strategy employed was highly variable through time, ranging from the construction of militarized fortresses (Middle Kingdom 2050-1650 BCE) to an amicable co-existence approach (New Kingdom 1550-1050 BCE). Egyptian tactics also varied spatially, depending on several factors including a colonized community’s utility to the empire and the potential for revolt. Using a large dataset (<em>n</em>=341), this paper compares osteoarthritis between seven Nubian communities to (1) evaluate whether imperial strategy impacted osteoarthritis severity, and (2) assess whether rates of osteoarthritis differed between colonized communities. </p> <p> </p> <p>Age-controlled ANCOVA analysis suggests there was significant variation in the frequency and severity of osteoarthritis throughout the empire. The Middle Kingdom C-Group, an indigenous Nubian population that lived outside the Egyptian built and occupied fortresses, displayed the highest rates of osteoarthritis for nearly all joint systems. Osteoarthritis then decreased during the post-co­lonial Second Intermediate Period (1650-1550 BCE) and again increased during the recolonization of the New Kingdom. However, there is significant variation of osteoarthritis at three New Kingdom sites, each of which experienced a differing colonization approach. This study suggests that the varying imperial strategies utilized by the Egyptian Empire may have impacted the physical activities and daily lives of Nubians and that these tactics were not equal throughout Nubia, but were tailored to commu­nities. It is therefore difficult to discuss a singular outcome of colonization; rather, these interpretations need to be nuanced with community-level archaeological context.</p>
FIGURE. Chrysosporium multiforme (holotype). A. Conidiogenous structures. B. Intercalary conidia. C. Conidia. D–E. Colony (front and reverse) on PDA. Bars: A–C = 20 μm, D–E = 10 mm. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Chrysosporium multiforme (holotype). A. Conidiogenous structures. B. Intercalary conidia. C. Conidia. D–E. Colony (front and reverse) on PDA. Bars: A–C = 20 μm, D–E = 10 mm.
FIGURE. Chrysosporium kaiyangense (holotype). A–C. Conidiogenous structures. D. Conidia. E. Colony on PDA media. Bars: A–D = 10 μm, E = 10 mm. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Chrysosporium kaiyangense (holotype). A–C. Conidiogenous structures. D. Conidia. E. Colony on PDA media. Bars: A–D = 10 μm, E = 10 mm.
FIGURE. Chrysosporium jiangsuense (holotype). A. Conidiogenous structures. B. Conidia. C–D. Colonies (front and reverse) on PDA. Bars: A–B = 20 μm; C–D = 10 mm. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Chrysosporium jiangsuense (holotype). A. Conidiogenous structures. B. Conidia. C–D. Colonies (front and reverse) on PDA. Bars: A–B = 20 μm; C–D = 10 mm.
FIGURE. Chrysosporium irregularum (holotype). A. Conidiogenous structures. B. Intercalary conidia. C. Conidia. D–E. Colonies (front and reverse) on PDA. Bars: A–C = 20 μm, D–E= 10 mm. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Chrysosporium irregularum (holotype). A. Conidiogenous structures. B. Intercalary conidia. C. Conidia. D–E. Colonies (front and reverse) on PDA. Bars: A–C = 20 μm, D–E= 10 mm.
FIGURE. Chrysosporium guangxiense (holotype). A. Conidiogenous structures. B. Racquet hyphae. C. Intercalary conidia. D–E. Colonies (front and reverse) on PDA. Bars: A–C = 20 μm, D–E = 10 mm. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Chrysosporium guangxiense (holotype). A. Conidiogenous structures. B. Racquet hyphae. C. Intercalary conidia. D–E. Colonies (front and reverse) on PDA. Bars: A–C = 20 μm, D–E = 10 mm.
FIGURE. Chrysosporium gansuense (holotype). A–B. Conidiogenous structures. C. Conidia. D–E. Colonies (front and reverse) on PDA media. Bars A–C = 10 μm, D–E = 10 mm. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Chrysosporium gansuense (holotype). A–B. Conidiogenous structures. C. Conidia. D–E. Colonies (front and reverse) on PDA media. Bars A–C = 10 μm, D–E = 10 mm.
FIGURE. Chrysosporium sichuanense (holotype). A. Conidiogenous structures. B. Arthroconidia. C. Racquet hyphae. D. Conidia. E–F. Colony (front and reverse) on PDA. Bars: A–D = 20 μm, E–F = 10 mm. in Morphological and phylogenetic characterisations reveal nine new species of Chrysosporium (Onygenaceae, Onygenales) in China
FIGURE. Chrysosporium sichuanense (holotype). A. Conidiogenous structures. B. Arthroconidia. C. Racquet hyphae. D. Conidia. E–F. Colony (front and reverse) on PDA. Bars: A–D = 20 μm, E–F = 10 mm.
Honey bee hive covers reduce food consumption and colony mortality during overwintering
<p class="MsoNormal"><span>Beekeepers regularly employ management practices to mitigate losses during the winter, often considered the most difficult time during a colony life cycle. Management recommendations involving covering or wrapping hives in insulation during winter have a long history; over 100 years ago, most recommendations for overwintering in cold climates involved heavy insulation wraps or moving hives indoors. These recommendations began to change in the mid-20<sup>th</sup> century, but hive covers are still considered useful and are described in contemporary beekeeping manuals and cooperative extension materials. However, most of the data supporting their use is published primarily in non-peer reviewed trade journals and was collected >40 years ago. In this time, the beekeeping environment has changed substantially, with new pressures from pathogens, agrochemicals, and land use changes. Here, we provide an update to the historical literature, reporting a randomized experiment testing the effectiveness of a common honey bee hive cover system across eight apiaries in central Illinois, USA, a temperate region dominated by conventional annual agriculture. We found that, when other recommended overwintering preparations are performed, covered colonies consumed less food stores and survived better than uncovered controls (22.5% higher survival). This study highlights the value of hive covers, even in an area not subject to extremely cold winter conditions, and these data can aid the production of evidence-based extension recommendations for beekeepers.</span></p>
Density dependence of clutch size and offspring sex ratio in starling colonies
<p><span>Optimal life-history theory predicts that individuals should adjust both the number and the sex of their offspring to maximize fitness in response to environmental and social factors such as breeding density. While reductions in optimal clutch size are well-studied in birds, the evidence for sex ratio adjustments is still equivocal and, so far, we lack a thorough understanding of how these strategies interact to maximize fitness. Here, we investigate how breeding density simultaneously affects brood sex ratio and clutch size in a sexually dimorphic and polygynous bird. We tested the prediction that mothers breeding at a higher density lay smaller clutches and overproduce daughters, the sex with less variable fitness returns and that disperses further away from their natal territory. We distributed nest boxes at either a high (HD) or a low density (LD) and monitored clutch sizes and sex ratios during five years in a wild breeding colony of spotless starlings. While mothers breeding in HD nests produced more daughters than those breeding in LD nests, the density dependence of clutch size varied among years, with a tendency to lay smaller clutches in HD nests. Our results suggest that mothers consistently adjust offspring sex ratio in response to breeding density, whereas adjustments in clutch size varied in a more complex way. These results support the role of sex allocation strategies in response to density and show that further theoretical and empirical research is required to understand the interaction between clutch size and sex ratio adjustments in animals.</span></p>
On following pages: 48. Paraguayan Tuco-tuco (Ctenomys paraguayensis); 49. Pilar Tuco-tuco (Ctenomys pilarensis (Ctenomys coludo); 53. Famatina Tuco-tuco (Ctenomys famosus); 54. Foch's Tuco-tuco (Ctenomys fochi); 55. Jujuy tuconax); 58. Monte Tuco-tuco (Ctenomys viperinus); 59. Santa Fe Tuco-tuco (Ctenomys " yolandae"); 60. Azara's johannis); 63. Osvaldo Reig's Tuco-tuco (Ctenomys osvaldoreigi); 64. Brown Tuco-tuco (Ctenomys pontifex); 65. Rosendo Guaymallen Tuco-tuco (Ctenomys validus); 68. Emilio's Tuco-tuco (Ctenomys emilianus); 69. Colonial Tuco-tuco (Ctenomys); 50. Maule Tuco-tuco (Ctenomys maulinus); 51. Bonetto's Tuco-tuco (Ctenomys bonettol); 52. Puntilla Tuco-tuco Tuco-tuco (Ctenomysjuris); 56. Catamarca Tuco-tuco (Ctenomys knight); 57. Robust Tuco-tuco (Ctenomys Tuco-tuco (Ctenomys azarae); 61. Cordoba Tuco-tuco (Ctenomys berg); 62. San Juan Tuco-tuco (Ctenomys Pascual's Tuco-tuco (Ctenomys rosendopascuali); 66. Sierra Tontal Tuco-tuco (Ctenomys tulduco); 67. sociabilis). in Ctenomyidae
On following pages: 48. Paraguayan Tuco-tuco (Ctenomys paraguayensis); 49. Pilar Tuco-tuco (Ctenomys pilarensis (Ctenomys coludo); 53. Famatina Tuco-tuco (Ctenomys famosus); 54. Foch's Tuco-tuco (Ctenomys fochi); 55. Jujuy tuconax); 58. Monte Tuco-tuco (Ctenomys viperinus); 59. Santa Fe Tuco-tuco (Ctenomys " yolandae"); 60. Azara's johannis); 63. Osvaldo Reig's Tuco-tuco (Ctenomys osvaldoreigi); 64. Brown Tuco-tuco (Ctenomys pontifex); 65. Rosendo Guaymallen Tuco-tuco (Ctenomys validus); 68. Emilio's Tuco-tuco (Ctenomys emilianus); 69. Colonial Tuco-tuco (Ctenomys); 50. Maule Tuco-tuco (Ctenomys maulinus); 51. Bonetto's Tuco-tuco (Ctenomys bonettol); 52. Puntilla Tuco-tuco Tuco-tuco (Ctenomysjuris); 56. Catamarca Tuco-tuco (Ctenomys knight); 57. Robust Tuco-tuco (Ctenomys Tuco-tuco (Ctenomys azarae); 61. Cordoba Tuco-tuco (Ctenomys berg); 62. San Juan Tuco-tuco (Ctenomys Pascual's Tuco-tuco (Ctenomys rosendopascuali); 66. Sierra Tontal Tuco-tuco (Ctenomys tulduco); 67. sociabilis).
Turbidity and Colony Count of Acinetobacter baumannii suspensions after meropenem-based antibiotic combination exposure
<p class="MsoNormal"><strong><span>Background</span></strong><span>: Carbapenems are the treatment of choice for multidrug-resistant (MDR) <em>A. baumannii</em> infection but are inadequate for carbapenem-resistant <em>A.baumannii </em>(CRAB) infections. Combination therapy came into the spotlight in the last decade. This study compares the colony count reduction after exposure to meropenem-based antibiotics in clinically achieved concentration with the time-kill test.</span></p> <p class="MsoNormal"><strong><span>Results</span></strong><span>: A bactericidal effect was achieved in isolates that were intermediate to ampicillin sulbactam at the administration of meropenem and ampicillin-sulbactam with a 2 MIC + 2 MIC. The combination of meropenem and ampicillin-sulbactam showed a bacteriostatic effect in isolates resistant to both antibiotics. The bactericidal effect was not achieved when meropenem and amikacin were administered to isolates that were intermediate or resistant to meropenem and amikacin.</span></p> <p class="MsoNormal"><strong><span>Conclusion</span></strong><span>: There is a significant difference in the colony count reduction between groups of <em>A. baumannii</em> isolates after exposure to antibiotic combinations.</span></p>
Early postnatal individual vocal recognition in a highly colonial mammal species
<p>Dataset associated with the article entitled 'Early postnatal individual vocal recognition in a highly colonial mammal species'</p>
Nest shape influences colony organization in ants: spatial distribution and connectedness of colony members differs from that predicted by random movement and is affected by nest space
<p><strong>Overview</strong></p> <p>Data used for the manuscript: Nest shape influences colony organization in ants: spatial distribution and connectedness of colony members differs from that predicted by random movement and is affected by available space</p> <p><strong>Purpose of the study</strong></p> <p>Investigating how nest shape influences how <em>Temnothorax rugatulus</em> colonies spatially organize in their nests. This includes physical location of colony members and their distances from the entrance, mobile colony member distance to the brood center, worker distance to the physical center of the nest, and comparing worker distributions with those predicted by a random walk model.</p> <p><strong>Structure of the data</strong></p> <p>EMPIRICAL DATA</p> <p>WORKERS: FullDataCoordWorkers.csv, FullDataCoordWorkersRD2.csv</p> <p>Raw experimental data with worker x and y position in nests</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Day: The experimental day that the observation was collected on</li> <li>ScaledX: X-axis coordinate, scaled from original (px) to (cm) in the software Fiji (Schindelin et al., 2012)</li> <li>ScaledY: Y-axis coordinate, scaled from original (px) to (cm) in the software Fiji</li> <li>ColorID: The unique color marking assigned to an individual worker's head, thorax, abdomen1, abdomen2 (i.e., Yellow, White, Green, Green = Y,W,G,G)</li> <li>Density: The density treatment (High / Low)</li> </ul> <p>BROOD / QUEENS: FullDataCoordBrood.csv, FullDataCoordBroodRD2.csv; FullDataCoordQueen.csv, FullDataCoordQueenRD2.csv</p> <p>Raw experimental data with brood (OR) queen x and y position in nests</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Day: The experimental day that the observation was collected on</li> <li>ScaledX: X-axis coordinate, scaled from original (px) to (cm) in the software Fiji (Schindelin et al., 2012)</li> <li>ScaledY: Y-axis coordinate, scaled from original (px) to (cm) in the software Fiji</li> <li>Density: The density treatment (High / Low)</li> </ul> <p>ALATES: FullDataCoordAlate.csv</p> <p>Raw experimental data with alate (winged reproductive individuals) x and y position in nests</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Day: The experimental day that the observation was collected on</li> <li>ScaledX: X-axis coordinate, scaled from original (px) to (cm) in the software Fiji (Schindelin et al., 2012)</li> <li>ScaledY: Y-axis coordinate, scaled from original (px) to (cm) in the software Fiji</li> <li>SexID: The unique sex assignment and number given to an individual alate: Sex, SexNumber, TotalNumber (i.e., the first male alate observation that came after three queen alates making it the fourth total observation = M,1,4)</li> </ul> <p>NETLOGO SIMULATIONS: ArchitectureMoveModelFull.csv</p> <p>Raw netlogo simulation data with agent x and y positions in nests</p> <ul> <li>RunNumber: The simulation number - 1 to 4000 - there are 1000 simulations for each combination of nest shape and size</li> <li>NestSize: The size of the nest area that agents were allowed to move throughout (Small / Large)</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>TimeStep: The duration of each simulation (should be 50000)</li> <li>xcor: a list of every agent x coordinate position at the end of the simulation</li> <li>ycor: a list of every agent y coordinate position at the end of the simulation</li> </ul> <p>REFERENCE DATA </p> <p>NEST BINS: Empirical</p> <p>BinsNullFull.csv</p> <p>Null data sheet with eight bins for tube and circle nests in every colony</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Bin: Nest section identifier (1-8)</li> </ul> <p>BinCoordFull.csv</p> <p>Reference binning coordinates to group empirical coordinates into nest sections</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>CoordID: The unique coordinate identifier within each colony and nest combination</li> <li>ScaledX: X-axis coordinate, scaled from original (px) to (cm) in the software Fiji (Schindelin et al., 2012)</li> <li>ScaledY: Y-axis coordinate, scaled from original (px) to (cm) in the software Fiji</li> </ul> <p>NEST BINS: Netlogo Simulations</p> <p>BinsNullNetlogo.csv</p> <p>Null data sheet with eight bins for tube and circle nests in each simulation treatment</p> <ul> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>NestSize: The size treatment for simulations (Small / Large)</li> <li>Bin: Nest section identifier (1-8)</li> </ul> <p>BinCoordNetlogo.csv</p> <p>Reference binning coordinates to group Netlogo simulation coordinates into nest sections</p> <ul> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>NestSize: The size treatment for simulations (Small / Large)</li> <li>ScaledX: X-axis coordinate</li> <li>ScaledY: Y-axis coordinate</li> <li>CoordID: The unique coordinate identifier within each colony and nest combination</li> </ul> <p>CORNERS: Empirical</p> <p>CornerFull.csv</p> <p>Whether a nest section has a corner or not</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Bin: Nest section identifier (1-8)</li> <li>Corner: Presence of a corner (Y / N)</li> </ul> <p>CORNERS: Empirical</p> <p>CornerFullSim.csv</p> <ul> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Bin: Nest section identifier (1-8)</li> <li>Corner: Presence of a corner (Y / N)</li> </ul> <p>REFERENCE DATA </p> <p>DISTANCES IN THE NEST: Empirical</p> <p>DistBinsFull.csv</p> <p>Reference coordinates for the entrance of nest sections (Bin) front-to-back and shortest distance to the entrance from each nest section entrance</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Distance: Reference shortest distance from a nest section to the entrance</li> <li>Bin: Nest section identifier (1-8)</li> <li>BinX: X-axis reference coodinate for a nest section entrance</li> <li>BinY: Y-axis reference coodinate for a nest section entrance</li> <li>Xmax: Max X-axis coordinate possible within the nest</li> <li>Ymax: Max Y-axis coordinate possible within the nest</li> <li>MaxDist: Max possible shortest distance from the nest entrance</li> <li>TubeRatio: Ratio of shortest distance to the nest entrance in circle nest / tube nest</li> </ul> <p>DISTANCES IN THE NEST: Netlogo Simulations</p> <p>DistBinsFullNetlogo.csv</p> <p>Reference coordinates for the entrance of nest sections (Bin) front-to-back and shortest distance to the entrance from each nest section entrance</p> <ul> <li>NestSize: The size treatment for simulations (Small / Large)</li> <li>Nest: The nest shape treatment (Tube / Circle)</li> <li>Distance: Reference shortest distance from a nest section to the entrance</li> <li>Bin: Nest section identifier (1-8)</li> <li>BinX: X-axis reference coodinate for a nest section entrance</li> <li>BinY: Y-axis reference coodinate for a nest section entrance</li> <li>Xmax: Max X-axis coordinate possible within the nest</li> <li>Ymax: Max Y-axis coordinate possible within the nest</li> <li>MaxDist: Max possible shortest distance from the nest entrance</li> <li>TubeRatio: Ratio of shortest distance to the nest entrance in circle nest / tube nest</li> </ul> <p>REFERENCE DATA </p> <p>WORKER SITE FIDELITY (SPATIAL FIDELITY & OCCURRENCE ZONE SIZES), ALSO RELATING SIZES TO DISTANCES IN THE NEST</p> <p>ColorRefFull.csv</p> <p>Reference of all possible unique color identifiers paint marked workers</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Head: Head color mark</li> <li>Thorax: Thorax color mark</li> <li>Abd1: Left side abdomen mark</li> <li>Abd2: Right side abdomen mark</li> </ul> <p>NestAreaFull.csv</p> <p>Reference for colony size (number of workers in the colony) and nest area</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Number.ants: Number of workers in the colony after painting</li> <li>Diameter: The diameter of the circle nest</li> <li>Area: The area of the nest</li> </ul> <p>ScalingCircleSFZ.csv</p> <p>Reference to scale the radius of circle nests to make coordinates representing fidelity zone bins</p> <ul> <li>Colony: Unique experimental colony identifiers</li> <li>Scaling: The scaling factor that is applied to the radius of each circle nest</li> </ul>
ScienceDex guides
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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.