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Inlists for the paper "Mixed-mode coupling in the Red Clump: I. Standard single star models"
<p>This repository contains the inlists and run_star_extras used for the paper "Mixed-mode coupling in the Red Clump: I. Standard single star models" by Walter E. van Rossem, Andrea Miglio, and Josefina Montalban for use with MESA-11701. The grid cycles through masses first (0.7, 1.0, 1.5, 2.3, 3.0 msol) and then metallicity ([Fe/H] = -1.0, -0.5, 0.0, 0.25, 0.4).</p> <p>Runs 0000-0004 have initial [Fe/H] = -1.0 and masses 0.7, 1.0, 1.5, 2.3, 3.0 solar masses respectively. The next five runs (0005-0009) have [Fe/H] = -0.5 and the same order of masses, and so on.</p> <p>The previous version had an error in the calculation for the non-parallel approximation and was missing a squareroot in the subroutine <code>calc_dlnc_ds_s0_part_ap</code> when calculating <code>Nred_km1</code> and <code>Nred_k</code>.</p>
Data from Red Sea damselfish and coral growth rates study
<p>Data sets for Asynchronous effects of heat stress on growth rates of massive corals and damselfishes in the Red Sea paper. These data are derived from coral cores and damselfish otoliths from the farasan banks in the Red Sea. The data includes 2 meta data sets for each species (coral_perfect & fish.2_copy), along with the raw data sets of untreated growth rates of both species, information for the coral reefs/environmental parameters that were used to build models in SPSS. </p>
Fig. 1 in The identity of the carrageenophyte red alga Sarcothalia radula (Gigartinaceae, Rhodophyta)
Fig. 1. Lectotype of Fucus radula: Esper (1802: pl. CXIII).
Table 1 in The identity of the carrageenophyte red alga Sarcothalia radula (Gigartinaceae, Rhodophyta)
<p><b>Table 1.</b> Specimens sequenced in this study. Samples are ordered by species name and then by collection date. All vouchers are lodged at the herbarium of the Museum of New Zealand Te Papa Tongarewa (WELT). Sequences downloaded from GenBank are available in Appendix 1.</p><table><tbody><tr><th>Species</th><th>Location</th><th>Coordinates</th><th>Date</th><th>Collector</th><th>Voucher no.</th><th>GenBank no.</th></tr></tbody><tbody><tr><th>‘ <i>Gigartina</i> ’ <i>atropurpurea</i></th><td>Island Bay, Wellington, North Island, NZ</td><td>41.3508°S, 174.7727°E</td><td>26 Nov 2000</td><td><i>G. Williams ASA414</i></td><td>A024821A-B</td><td>OP086042</td></tr><tr><td>Blackfellows Caves, South Australia, AU</td><td>37.9245°S, 140.4516°E</td><td>6 Apr 2002</td><td><i>L.E. Phillips ASZ097</i></td><td>A034567</td><td>OP086043</td></tr><tr><td>Henderson Point, Great Exhibition Bay, NZ</td><td>34.7341°S, 173.1111°E</td><td>27 Oct 2003</td><td><i>W.A. Nelson, T.J. Farr, J. Sutherland ASD237</i></td><td>A023789A-B</td><td>OP086044</td></tr><tr><td>Bicheno Wharf, Tasmania, AU</td><td>41.8737°S, 148.3109°E</td><td>2 Dec 2007</td><td><i>J. Buchanan ASZ311</i></td><td>A034594</td><td>OP086045</td></tr><tr><th><i>Sarcothalia circumcincta</i></th><td>Stewart Island/Ringaringa, NZ</td><td>46.9035°S, 168.1435°E</td><td>17 Oct 2001</td><td><i>W.A. Nelson, T.J. Farr, J. Sutherland ASB425</i></td><td>A026351</td><td>OP086046</td></tr><tr><td>Epigwait, Auckland Island, NZ</td><td>50.7905°S, 166.0565°E</td><td>13 Feb 2012</td><td><i>S. Wilcox ASM067</i></td><td>A034569</td><td>OP086047</td></tr><tr><th><i>Sarcothalia radula</i></th><td>Charleston, Constant Bay, NZ</td><td>41.9033°S, 171.4333°E</td><td>10 Mar 2000</td><td><i>W.A. Nelson, T.J. Farr, L. Russell ASA148</i></td><td>A024951</td><td>OP086048</td></tr><tr><td>Chancet Rocks, NZ</td><td>41.8447°S, 174.1858°E</td><td>18 Dec 2000</td><td><i>W.A. Nelson, T.J. Farr, G. Williams ASA453</i></td><td>A024825A-D</td><td>OP086049</td></tr><tr><td>The Neck, Stewart Island/ Ringaringa, NZ</td><td>46.951°S, 168.1755°E</td><td>19 Oct 2001</td><td><i>W.A. Nelson, T.J. Farr, J. Sutherland ASB501</i></td><td>A026296</td><td>OP086050</td></tr><tr><td>Musgrave Inlet, Auckland Island, NZ</td><td>50.6686°S, 166.1782°E</td><td>10 Feb 2004</td><td><i>F. Smith ASE311</i></td><td>A031680</td><td>OP086051, OP086052</td></tr><tr><td>Masked Island, Auckland Islands, NZ</td><td>50.8433°S, 166.0264°E</td><td>13 Feb 2004</td><td><i>F. Smith ASE316</i></td><td>A031679</td><td>OP086053</td></tr><tr><td>Beeman Point, Campbell Island, NZ</td><td>52.5506°S, 169.1523°E</td><td>13 Feb 2013</td><td><i>W.A. Nelson ASF042</i></td><td>A034573/A</td><td>OP086054</td></tr><tr><td>Chalky Inlet, Fiordland, NZ</td><td>45.9767°S, 166.5862°E</td><td>14 Dec 2019</td><td><i>G. Keeler-May AST503</i></td><td>A034575</td><td>OP086055</td></tr></tbody></table>
Data from: Incorporating explicit geospatial data shows more species at risk of extinction than the current Red List
The IUCN (International Union for Conservation of Nature) Red List classifies species according to their risk of extinction, informing global to local conservation decisions. Unfortunately, important geospatial data do not explicitly or efficiently enter this process. Rapid growth in the availability of remotely sensed observations provides fine-scale data on elevation and increasingly sophisticated characterizations of land cover and its changes. These data readily show that species are likely not present within many areas within the overall envelopes of their distributions. Additionally, global databases on protected areas inform how extensively ranges are protected. We selected 586 endemic and threatened forest bird species from six of the world's most biodiverse and threatened places (Atlantic Forest of Brazil, Central America, Western Andes of Colombia, Madagascar, Sumatra, and Southeast Asia). The Red List deems 18% of these species to be threatened (15 critically endangered, 29 endangered, and 64 vulnerable). Inevitably, after refining ranges by elevation and forest cover, ranges shrink. Do they do so consistently? For example, refined ranges of critically endangered species might reduce by (say) 50% but so might the ranges of endangered, vulnerable, and nonthreatened species. Critically, this is not the case. We find that 43% of species fall below the range threshold where comparable species are deemed threatened. Some 210 bird species belong in a higher-threat category than the current Red List placement, including 189 species that are currently deemed nonthreatened. Incorporating readily available spatial data substantially increases the numbers of species that should be considered at risk and alters priority areas for conservation.
Inferring whole-organism metabolic rate from red blood cells in birds
<p>Metabolic rate is a key ecological variable that quantifies the energy expenditure needed to fuel almost all biological processes in an organism. Metabolic rates are typically measured at the whole-organism level (woMR) with protocols that can elicit stress responses due to handling and confinement, potentially biasing resulting data. Improved, non-stressful methodology would be especially valuable for measures of field metabolic rate, which quantifies the energy expenditure of free-living individuals. Recently, techniques to measure cellular metabolic rate (cMR) in mitochondria of blood cells have become available, suggesting that blood-based cMR can be a proxy of organismal aerobic performance. Aerobic metabolism actually takes place in the mitochondria. Quantifying cMR from blood samples offers several advantages such as direct estimates of metabolism and minimized disturbance of individuals. To our knowledge, the hypothesis that blood-based cMR correlates with woMR has not yet been directly tested.</p> <p>We measured cMR in red blood cells of captive great tits (<i>Parus major</i>), first during their morning activity period and second after subjecting them to a 2.5 h day-time respirometry protocol to quantify woMR. We predicted cMR to decrease as individuals transitioned from an active to a resting state. In the two blood samples we also assessed circulating corticosterone concentrations to determine the perceived disturbance of individuals. From respirometry traces we extracted initial and final woMR measures to test for a predicted positive correlation with cMR measures, while accounting for corticosterone concentrations.</p> <p>Indeed, cMR declined from the first to the second measurement. Furthermore, woMR and cMR were positively related in individuals that had relatively low corticosterone concentrations and displayed little locomotor activity throughout respirometry. By contrast, woMR and cMR covaried negatively in birds that increased corticosterone concentrations and activity levels substantially.</p> <p>Our results show that red blood cell cMR represents a proxy for woMR when birds do not display signs of stress, i.e. either before increases in hormonal or behavioral parameters have occurred or after they have abated. This method represents a valuable tool for obtaining metabolic data repeatedly and in free-living individuals. Our findings also highlight the importance of accounting for individual stress responses when measuring metabolic rate at any level.</p> <p>Metabolic rate is a key ecological variable that quantifies the energy expenditure needed to fuel almost all biological processes in an organism. Metabolic rates are typically measured at the whole-organism level (woMR) with protocols that can elicit stress responses due to handling and confinement, potentially biasing resulting data. Improved, non-stressful methodology would be especially valuable for measures of field metabolic rate, which quantifies the energy expenditure of free-living individuals. Recently, techniques to measure cellular metabolic rate (cMR) in mitochondria of blood cells have become available, suggesting that blood-based cMR can be a proxy of organismal aerobic performance. Aerobic metabolism actually takes place in the mitochondria. Quantifying cMR from blood samples offers several advantages such as direct estimates of metabolism and minimized disturbance of individuals. To our knowledge, the hypothesis that blood-based cMR correlates with woMR has not yet been directly tested.</p> <p>We measured cMR in red blood cells of captive great tits (<i>Parus major</i>), first during their morning activity period and second after subjecting them to a 2.5 h day-time respirometry protocol to quantify woMR. We predicted cMR to decrease as individuals transitioned from an active to a resting state. In the two blood samples we also assessed circulating corticosterone concentrations to determine the perceived disturbance of individuals. From respirometry traces we extracted initial and final woMR measures to test for a predicted positive correlation with cMR measures, while accounting for corticosterone concentrations.</p> <p>Indeed, cMR declined from the first to the second measurement. Furthermore, woMR and cMR were positively related in individuals that had relatively low corticosterone concentrations and displayed little locomotor activity throughout respirometry. By contrast, woMR and cMR covaried negatively in birds that increased corticosterone concentrations and activity levels substantially.</p> <p>Our results show that red blood cell cMR represents a proxy for woMR when birds do not display signs of stress, i.e. either before increases in hormonal or behavioral parameters have occurred or after they have abated. This method represents a valuable tool for obtaining metabolic data repeatedly and in free-living individuals. Our findings also highlight the importance of accounting for individual stress responses when measuring metabolic rate at any level.</p>
The burden of size and growth for the juveniles of large mammalian herbivores: structural and functional constraints in the feeding biology of juveniles relative to adults in red kangaroos, Osphranter rufus
<p>Juvenile mammals in their post weaning developmental stages face many challenges in transitioning to adulthood. Among large grazing species such as ruminant bovids and cervids an overarching challenge is acquiring and processing sufficient nutrients to survive and grow, with a gut that may not yet be fully developed. Marsupial kangaroos of Australia face similar challenges; they also digest vegetation by fermentation in a large foregut. In red kangaroos, Osphranter rufus (= Macropus rufus), the dominant species of Australia's arid interior, females may breed continuously; however, juvenile recruitment to the adult population is irregular and coincident with sporadic rainfall. As compared with adult females the nutritional requirements of juvenile O. rufus are high in relation to their body mass (BM), largely due to the cost of their rapid growth. We examined processes that juveniles have in their morphology, physiology and behaviours to meet their elevated nutritional needs, by comparing recently weaned juveniles of both sexes and adult female O. rufus in their desert habitat. Features studied include relative body sizes, relative dimensions and capacities of principal gut regions, the foregut, small intestine, caecum and large intestine with rectum. Also examined were digesta attributes and rates of digesta excretion. Additionally, the rates of change in skull parameters and dental characteristics to maturity were assessed. Field determinations of diet choice were made for both age classes. In juveniles the content masses of major gut structures were related to body mass (BM), as were those of adult females, i. e. ~BM1.0. In both age classes the digesta mass of the foreguts exceeded 75 % of the total digesta mass. Diets of both juvenile and adult O. rufus largely focused on grasses. Juveniles had higher rates of digesta excretion while foraging than adults. In addition, the foregut contents in juveniles occupies proportionally less of the total gut than in adult females. Together, the higher excretion rate and smaller relative foregut of juveniles suggests that they necessarily focus on forage that can be rapidly digested, such as young, green grasses or herbage. Comparison of the skulls of juveniles and adults revealed how this harvest can occur. Relative to BM juveniles had skulls of larger volume than adults. Additionally, during growth the skull lengthens proportionally faster than increasing. By weaning the dimensions of the incisor bite of juveniles neared those of adult females. The area of wear on premolars/molars increased only slowly relative to the development of incisors, further pointing to juveniles selecting more digestible forage than adults. The intermittent availability of such forage, principally young grasses, appears key to the significant recruitment into the O. rufus population in their arid habitat.</p>
Shifting roles of the East China Sea in the phylogeography of red nanmu in East Asia
<p>This dataset contains one README file and two raw data files on the distribution and genetic data described in the paper: Jiang et al. (2021) Shifting roles of the East China Sea in the phylogeography of <em>Machilus thunbergii</em> (Lauraceae) in East Asia. Journal of Biogeography.</p> <p>Ecological niche modeling was employed to predict the potential distribution of <em>M. thunbergii</em> during the Last Glacial Maximum (LGM) and the last interglacial period. Nuclear microsatellite and chloroplast markers were used to reveal the phylogeographic pattern and infer the population history of 33 <em>M. thunbergii</em> populations.</p> <p>The ecological niche models suggested that the ECS provided potentially suitable habitats for <em>M. thunbergii</em> during the LGM. A sharp change in cpDNA haplotypes was found along the eastern China coasts, while microsatellites revealed a clinal pattern for genetic composition from eastern China to central Japan. The divergent lineages formed an admixture on the Zhoushan Archipelago of China and Kyushu Island of Japan. The estimated divergent and admixture times were <em>c</em>. 68 kyr and <em>c</em>. 15 kyr, corresponding to the periods where there were rising sea levels after the MIS4 glaciation and falling sea levels during the LGM, respectively. </p> <p><em>Machilus thunbergii </em>probably underwent alternating population isolation during interglacial periods and connection during glacial maxima across the ECS, but such periodicity of isolation and connection seems not to have promoted diversification as suggested by the species pump hypothesis. Incipient divergence has been periodically wiped out due to frequent coalescence, rendering the ECS more like a "species vacuum", particularly for species with relatively long generation lengths.</p>
QM/MM models of 11 red fluorescent proteins
<p>Geometry configurations on the ground state potential energy surface are obtained at the QM(PBE0-D3/cc-pvdz)/MM(AMBER) level. The list of fluorescent proteins is as follows:</p> <ol> <li>mRojoA</li> <li>mRojo-THSL</li> <li>mRojo-VFAV</li> <li>mRojo-TFAL</li> <li>mRojo-VYGV</li> <li>mRojo-VYGL</li> <li>mRojo-TYGV</li> <li>RDSmCherry0.2</li> <li>RDSmCherry0.5</li> <li>mKeima</li> <li>eqFP670</li> </ol>
Fig. 106. Red Tilapia, 132.0 in The non-native freshwater fishes of Singapore: an annotated compilation
Fig. 106. Red Tilapia, 132.0 mm SL, Pangsua Pond.
Fig. 5 in First record of the nesting biology of the red-vented barbet, Megalaima lagrandieri (Aves: Piciformes: Megalaimidae), an Indochinese endemic
Fig. 5. Fourteen-day-old nestling of the red-vented barbet.
FIGURE 3 in Contrasted Ecological Repartition Of The Northern Fowl Mite Ornithonyssus Sylviarum (Mesostigmata: Macronyssidae) And The Chicken Red Mite Dermanyssus Gallinae (Mesostigmata: Dermanyssidae)
FIGURE 3: COI-based phylogenetic topologie involving all haplotypes isolated in Roy et al. (2009b), plus sequences newly obtained from French and North American Ornithonyssus sylviarum and from North American Dermanyssus individuals. Maximum-likelihood (PHYML). Numbers at nodes represent aLRT values.
FIGURE 2 in Contrasted Ecological Repartition Of The Northern Fowl Mite Ornithonyssus Sylviarum (Mesostigmata: Macronyssidae) And The Chicken Red Mite Dermanyssus Gallinae (Mesostigmata: Dermanyssidae)
FIGURE 2: Percentage of samples containing identified hematophagous mites, according to the type of environment. Solid bar: wild avifauna (n=166), grey bar: industrial fowl (layer and chicken farms) (n=132), open bar: other domestic birds (n=12).
FIGURE 1 in Contrasted Ecological Repartition Of The Northern Fowl Mite Ornithonyssus Sylviarum (Mesostigmata: Macronyssidae) And The Chicken Red Mite Dermanyssus Gallinae (Mesostigmata: Dermanyssidae)
FIGURE 1: Location of samples collected in France and containing either Dermanyssus. gallinae s. str. (ie non L1) (solid dots) or Ornithonissus sylviarum (open dots). The shape of dots represents environmental information: circle for industrial fowls, triangle for amateur fowl houses, trapezoid for pet bird breeding facilities, square for game bird breeding facilities, 5-branch star for wild avifauna not sampled in orchard/field agroecosystems, 8-branch star for wild avifauna sampled in orchard/field agroecosystems. IF industrial fowl farms, AF amateur breeding facilities, fowl, PB amateur breeding facilities, pet birds, BG amateur breeding facilities, game birds, WA wild avifauna sampled in orchard or field agroecosystems, WNA, wild avifauna not sampled in orchard or field agroecosystem.
FIGURE 2 in Population Trends Of The Red Palm Mite, Raoiella Indica Hirst (Acari: Tenuipalpidae) And Associated Entomopathogenic Fungi In Trinidad, Antigua, St Kitts And Nevis And Dominica
FIGURE 2: Identified material from selected samples in the different islands evaluated. NB. For reference, the population density (mites/cm2) from Trinidad-Icacos (10.69), Trinidad (5.79), Antigua (3.38), St. Kitts and Nevis (6.17) and Dominica (4.94).
Figure 1 in A new genus of red-toothed shrew (Mammalia, Soricidae) from the Early Pleistocene of Gran Dolina (Atapuerca, Burgos, Spain), and a phylogenetic approach to the Eurasiatic Soricinae
Figure 1. Map showing the location of the Sierra de Atapuerca sites in Burgos (Spain).
Figure 8 in The radiation of red colobus monkeys (Primates, Colobinae): morphological evolution in a clade of endangered African primates
Figure 8. Males. Phenogram of the species mean shapes. See Figure 7 for further explanation.
Data from: Inter-annual climate variation influences nest initiation date and nest productivity of the Red-cockaded Woodpecker at the northwestern edge of its range
<p>Climate change, including directional shifts in weather averages and extremes and increased inter-annual weather variation, is influencing demograhy and distributions for many bird species. We examined how temperature and precipitation coinciding with multiple nesting seasons affected overall nesting success and productivity for two red-cockaded woodpecker (<em>Dryobates borealis,</em> RCW) populations at the species' northwestern range periphery. We used 26 years of nesting data (1991-2016) from the two RCW populations to determine if inter-annual weather variation has affected nesting pehnology and productivity. We conducted analyses at both broad nesting periods (30 and 60 days before nesting; 40 days overalpping the nesting period up to fledging) and short windows to capture the effects of temperature and precipitation extremes on individual nests. For both RCW populations, warmer early spring temperatures generally advanced nesting and increased clutch size and fledgling number. However, effects of average precipitation varied depending on amount and duration of precipitation in different time periods. At the nest level, temperature and precipitation extremes were unrelated to nest success and loss of nestlings (brood loss). Our results indicate that RCWs are responding to the effects of climate change in various ways, with warming trends having a positive benefit on the species at its northwestern range periphery.</p>
Coral bleaching due to cold stress on a central Red Sea reef flat
<p>Ocean warming is leading to more frequent coral bleaching events. However, cold stress can also induce bleaching in corals. Here, we report observations of a boreal winter bleaching event in Jan 2020 in the central Red Sea, mainly within a population of the branching coral <em>Stylophora pistillata </em>on an offshore reef flat. Sea surface temperatures rarely fall below 24°C in this region, but data loggers deployed on several nearby reef flats recorded overnight seawater temperatures as low as 18°C just three days before the observations. The low temperatures coincided with an extremely low tide and cool air temperatures, likely resulting in the aerial exposure of the corals during the nighttime low tide event. The risk of aerial exposure is rare in winter months, as the Red Sea exhibits seasonal fluctuations in sea level with winter values typically 0.3-0.4m higher than in summer. These observations are notable for a region typically characterized as a high-temperature sea, and highlight the need for long-term monitoring programs as this rare event may have gone unnoticed.</p>
Travel times of temporary seismic arrays and 3-D Vp and Vs models in the mid-to-south segment of the Red River fault, China
<p>The travel times of the temporary seismic arrays are manually picked. The 3-D Vp and Vs models beneath the mid-to-south segment of the Red River fault are obtained based on the improved double-difference tomography method and abundant data. </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)
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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.