Find research datasets worth reusing

opencc-zeroFeb 2022View details →

Dataset: Cool birds: First evidence of energy-saving nocturnal torpor in free-living common swifts Apus apus resting in their nests

<a name="_Hlk94722524"></a>Daily torpor is a means of saving energy by controlled lowering of the metabolic rate (MR) during resting, usually coupled with a decrease in body temperature. We studied nocturnal daily torpor under natural conditions in free-living common swifts Apus apus resting in their nests as a family using two non-invasive approaches. First, we monitored nest temperature (Tnest) in up to 50 occupied nests per breeding season in 2010-2015. Drops in Tnest were the first indication of torpor. Among <a name="_Hlk97457770"></a>16,673 observations, we detected 423 events of substantial drops in Tnest of on average 8.6°C. Second, we measured MR of the families inside nest boxes prepared for calorimetric measurements during cold periods in the breeding seasons of 2017 and 2018. We measured oxygen consumption and carbon dioxide production using a mobile indirect respirometer and calculated the percentage reduction in MR. During six torpor events observed, MR was gradually reduced by on average 56% from the reference value followed by a decrease in Tnest of on average 7.6 °C. In contrast, MR only decreased by about 33% on nights without torpor. Our field data gave an indication of daily torpor, which is used as a strategy for energy saving in free-living common swifts.

opencc-by-4.0Feb 2022View details →

Figs 698–705. Crossopriza Simon, 1893, live specimens. 698–701. C in Revisions of Holocnemus and Crossopriza: the spotted-leg clade of Smeringopinae (Araneae, Pholcidae)

Figs 698–705. Crossopriza Simon, 1893, live specimens. 698–701. C. miskin sp. nov., from Oman, Ibri-Rusdaq; male in dorsal and lateral views; female with and without egg-sac. 702–705. C. lyoni (Blackwall, 1867), male from Singapore and courting/mating pair from Guinea.

opencc-by-4.0Feb 2022View details →

Figs 195–202. Maghreba gen. nov., live specimens. 195. M in Revisions of Holocnemus and Crossopriza: the spotted-leg clade of Smeringopinae (Araneae, Pholcidae)

Figs 195–202. Maghreba gen. nov., live specimens. 195. M. saghro gen. et sp. nov., male from Morocco, between Irherm and Tiferki. 196–198. M. stifadma gen. et sp. nov., male and female from Morocco, Setti-Fatma. 199–202. M. nkob gen. et sp. nov., male and female from Morocco, E of Nkob.

opencc-zeroFeb 2022View details →

Hurricane-associated population decrease in a Critically Endangered long-lived reptile

Catastrophic events, like hurricanes, bring lethal conditions that can have population-altering effects. The threatened Caribbean dry forest occurs in a region known for its high-intensity hurricane seasons and high species endemism, highlighting the need to better understand hurricane impacts in combination with habitat fragmentation and loss. However, such studies remain rare, and for reptiles are mostly restricted to Anolis. Here we used single-season occupancy modeling to infer the impact of the intense 2017 Atlantic hurricane season on the critically endangered Lesser Antillean Iguana, Iguana delicatissima. We surveyed 30 transects across eight habitats on St. Eustatius during 2017–2019, which resulted in 344 individual surveys and 98 iguana observations. Analyses of abundance and site occupancy indicated both measures for 2018 and 2019 were strongly reduced compared to the pre-hurricane 2017 state. Iguanas at higher elevations were affected more profoundly, likely due to higher wind speeds, tree damage and extensive defoliation. Overall, our results indicate a decrease in population estimates (23.3-26.5%) and abundance (22-23.8%) for 2018 and 2019, and a 75% reduction in opportunistic sightings of tagged iguanas between 2017–2018. As only small and isolated I. delicatissima populations remain, our study further demonstrates their vulnerability to stochastic events. Considering the frequency and intensity of hurricanes are projected to increase, our results stress the urgent need for population-increasing conservation actions in order to secure the long-term survival of I. delicatissima throughout its range. Given the projected increase and poleward shift of hurricanes, our study provides important insights from a non-model species.

opencc-zeroMar 2022View details →

Predation release of Texas horned lizards (Phrynosoma cornutum) living in small towns

Texas horned lizards (Phrynosoma cornutum) have a number of ways to avoid predation, including camouflage, sharp cranial horns, flattening of the body, and the ability to squirt blood from the eyes. These characteristics and their relatively low survival rates in the wild suggests these lizards are under high predation pressure. These lizards have been declining in much of their eastern range due to increased urbanization, agriculture, and loss of prey species. However, they can be still be found in some small south Texas towns where they can reach densities that are much higher (~50 lizards/ha) than in natural areas (~4-10 lizards/ha). We hypothesized that one reason for the high densities observed in these towns may be due to reduced predation pressure. We used model Texas horned lizards to test whether predation levels were lower in two south Texas towns than on a nearby ranch. We constructed models from urethane foam, a material that is ideal for preserving marks left behind by predators. Models (n = 126) and control pieces of foam (n = 21) were left in the field for 9 days in each location in early and late summer and subsequent predation marks were categorized by predator taxa. We observed significantly more predation attempts on the models than on controls and significantly fewer attempts in town (n = 1) compared to the ranch (n = 60). On the ranch, avian predation attempts appear to be common especially when the models did not match the color of the soil. Our results suggest that human modified environments that have suitable habitat and food resources may provide a refuge for some prey species like horned lizards from predators.

opencc-zeroMar 2022View details →

Exposure to lysed bacteria can promote or inhibit growth of neighboring live bacteria depending on local abiotic conditions

Abstract Microbial death is extremely common in nature, yet the ecological role of dead bacteria is unclear. Dead cells are assumed to provide nutrients to surrounding microbes, but may also affect them in other ways. We found that adding lysate prepared from dead bacteria to cultures of Escherichia coli in nutrient-rich conditions suppressed their final population density. This is in stark contrast with the notion that the primary role of dead cells is nutritional, although we also observed this type of effect when we added dead bacteria to cultures that were not supplied with other nutrients. We only observed the growth-suppressive effect of our dead-bacteria treatment after they had undergone significant lysis, suggesting a key role for cellular contents released during lysis. Transcriptomic analysis indicated changes in gene expression in response to dead cells in growing populations, particularly in genes involved in motility. This was supported by experiments with genetic knockouts and copy-number manipulation. Because lysis is commonplace in natural and clinical settings, the growth-suppressive effect of dead cells we describe here may be a widespread and previously unrecognized constraint on bacterial population growth.

FIGURE 7. Freyanopterolichus nipponiae Dubinin, 1953, female. A in Redescription of two parasitic feather mites sampled from the last two Crested Ibises, Nipponia nippon (Temminck, 1835) (Pelecaniformes: Threskiornithidae) lived in Japan

FIGURE 7. Freyanopterolichus nipponiae Dubinin, 1953, female. A—ventral view, B—dorsal view.

FIGURE 8. Freyanopterolichus nipponiae Dubinin, 1953, male. A in Redescription of two parasitic feather mites sampled from the last two Crested Ibises, Nipponia nippon (Temminck, 1835) (Pelecaniformes: Threskiornithidae) lived in Japan

FIGURE 8. Freyanopterolichus nipponiae Dubinin, 1953, male. A—ventral view, B—dorsal view.

FIGURE 2. Compressalges nipponiae Dubinin, 1950, female. A in Redescription of two parasitic feather mites sampled from the last two Crested Ibises, Nipponia nippon (Temminck, 1835) (Pelecaniformes: Threskiornithidae) lived in Japan

FIGURE 2. Compressalges nipponiae Dubinin, 1950, female. A—ventral view, B—dorsal view.

FIGURE 3. Compressalges nipponiae Dubinin, 1950, male. A in Redescription of two parasitic feather mites sampled from the last two Crested Ibises, Nipponia nippon (Temminck, 1835) (Pelecaniformes: Threskiornithidae) lived in Japan

FIGURE 3. Compressalges nipponiae Dubinin, 1950, male. A—ventral view, B—dorsal view.

opencc-by-4.0Apr 2022View details →

Keizer et al. "Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics" – Data, software and documentation (10/16)

Data, software and documentation to reproduce the results presented in [<a href="https://www.science.org/doi/10.1126/science.abi9810">Keizer et al. (2022) ‘Live-cell micromanipulation of a genomic locus reveals interphase chromatin mechanics’ Science, 377:6605</a>, DOI: 10.1126/science.abi9810]. <table> <tbody> <tr> <td> Description </td> <td> Location </td> </tr> <tr> <td> Centralized GitHub repository with: <ul> <li>Local copy of all the code and trajectory/force files</li> <li>Jupyter notebooks to make all the graphs in Keizer et al.</li> <li>Pointers to all the datasets also shown in this table</li> </ul> </td> <td> <a href="https://github.com/CoulonLab/Keizer-et-al">Keizer et al.</a> repository </td> </tr> <tr> <td> Raw microscopy data: <ul> <li>Experiments performed with the 30’-PR scheme</li> <li>Experiment performed with the 100”-PR scheme</li> <li>Experiment performed with high frame rate (dt = 0.5”)</li> </ul> </td> <td> <a href="https://zenodo.org/record/4626942">Zenodo 1</a> (30’-PR) <a href="https://zenodo.org/record/4627034">Zenodo 2</a> (30’-PR) <a href="https://zenodo.org/record/4626909">Zenodo 3</a> (30’-PR) <a href="https://zenodo.org/record/4626914">Zenodo 4</a> (30’-PR) <a href="https://zenodo.org/record/4627010">Zenodo 5</a> (30’-PR) <a href="https://zenodo.org/record/4626981">Zenodo 6</a> (100”-PR) <a href="https://zenodo.org/record/6510099">Zenodo 7</a> (30’-PR) <a href="https://zenodo.org/record/6510103">Zenodo 8</a> (30’-PR) <a href="https://zenodo.org/record/6510065">Zenodo 9</a> (dt = 0.5") <a href="https://zenodo.org/record/6510105">Zenodo 10</a> (30’-PR) </td> </tr> <tr> <td> Concatenated TIFFs and timestamp files for all of the 30’-PR data. </td> <td> <a href="https://zenodo.org/record/6510107">Zenodo 11</a> (1/2) <a href="https://zenodo.org/record/6510109">Zenodo 12</a> (2/2) </td> </tr> <tr> <td> Python pipeline to generate (i) concatenated movies, (ii) cropped and rotated movies for each cell, and (iii) force time profiles for each cell. </td> <td> <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository </td> </tr> <tr> <td> <ul> <li>Final registered and rotated TIFF files: <ul> <li>30’-PR experiments: n = 35 cells</li> <li>100”-PR experiment, including time projections & kymograph</li> <li>dt = 0.5” experiments: n = 3 cells</li> <li>no force: n = 11 cells before manipulation, n = 8 cells after manipulation</li> </ul> </li> <li>Data files with trajectories and force time profiles for all analyzed cells</li> <li>Instructions and Fiji/Python scripts to reproduce these files.</li> </ul> </td> <td> <a href="https://zenodo.org/record/6510207">Zenodo 13</a> </td> </tr> <tr> <td> Single-MNPs fluorescence: raw data, Python/Fiji scripts and instructions </td> <td> <a href="https://zenodo.org/record/6510209">Zenodo 14</a> </td> </tr> <tr> <td> <ul> <li>MagSim, Python library for magnetic simulations</li> <li>Jupyter notebook for calibrating and generating maps (Fig. S5 & Fig. S6).</li> </ul> </td> <td> <a href="https://github.com/CoulonLab/MagSim">MagSim</a> repository </td> </tr> <tr> <td> Force calibration – Method 1: Gradient of free GFP-ferritin in solution <ul> <li>Raw microscopy data (6 pillars; Fig. S6B-C)</li> <li>Calculated force maps, with Fiji scripts and instructions to generate them.</li> </ul> </td> <td> <a href="https://zenodo.org/record/4627062">Zenodo 15</a> </td> </tr> <tr> <td> Force calibration – Method 2: Attraction of ferritin-coated beads (Fig. S7) <ul> <li>Raw microscopy data (free diffusion and attraction)</li> <li>Python/Fiji scripts to calculate forces.</li> </ul> </td> <td> <a href="https://zenodo.org/record/6510211">Zenodo 16</a> </td> </tr> <tr> <td> <ul> <li>Python library for force inference using different polymer models</li> </ul> </td> <td> <a href="https://github.com/SGrosse-Holz/rouselib">rouselib</a> repository </td> </tr> </tbody> </table> License: All the code, data and documentation in this repository is under <a href="https://www.gnu.org/licenses/gpl-3.0.en.html">GPLv3</a> license. The <a href="https://hal-cnrs.archives-ouvertes.fr/hal-03740646">Author Accepted Manuscript</a> of the study [Keizer et al. 2022] is under <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY 4.0</a> license. The <a href="https://www.science.org/doi/10.1126/science.abi9810">Final Published Version</a>, published by AAAS, is not (<a href="https://www.science.org/content/page/science-licenses-journal-article-reuse">more information</a>).   Overview of the raw data repositories (Zenodo 1-10) Refer to the Material and Methods section of the article for details on data production. Each Zenodo dataset represents one day of acquisition. It includes the data that was not retained for further downstream analysis. Each dataset contains: <ul> <li>The raw MicroManager folder architecture (one folder contains multiple positions on the coverslip). On occasions where placement or removal of the external magnet led to a loss of focus, the acquisition was stopped and restarted, creating a new MicroManager folder each time. For instance: <ul> <li>The various positions were imaged before injection (folder with the _preInjection, _1-pre-inj or _1-inj_1 suffix)</li> <li>These positions were imaged again after injection (suffix _postInjection, _2-post-inj or _1-inj_2) and before the magnet was added (suffix _beforeexp or _before-attr)</li> <li>They were imaged again with the magnet added (suffix _attraction1). If acquisition was stopped and restarted an extra folder is created (suffix _attraction2)</li> <li>They were then imaged after the magnet was removed (suffix _release1)</li> <li>Finally, the cells were monitored after the experiment (suffix _after-exp or _postexp)</li> </ul> </li> <li>A text file named lab_journal_[...].txt contains extra information the acquisition and experimental procedure</li> <li>Note: the MicroManager metadata in the TIFF file are fully populated</li> </ul>   Overview of the concatenated datasets (Zenodo 11-12) In these Zenodo repository, each position (acquired in different folders), is concatenated into a single TIFF movie using code available in the <a href="https://github.com/CoulonLab/chromag-pipeline">ChroMag-pipeline</a> repository. The folder contains: <ul> <li>One TIFF file per selected position</li> <li>One .xls file per selected position, with one line per frame, and columns with the following information: <ul> <li>path (Relative path): Reference to the original (raw MicroManager) file</li> <li>start_time (Timestamp): Timestamp saved by MicroManager when the acquisition was started (the «acquire » button was pressed).</li> <li>time_in_file (seconds): Number of seconds between start_time and the acquisition of the current timepoint</li> <li>start_time_s (seconds): Variable start_time converted to a number of seconds</li> <li>time (seconds): Sum of start_time and time_in_file</li> <li>timestamp (Timestamp): Variable time, back-converted to a timestamp</li> <li>timeOn (Timestamp): Time(s) when the magnet was added. This timestamp is provided in the datasets.cfg file in the github repository chromag-pipeline</li> <li>timeOff (Timestamp): Time(s) when the magnet was removed. This timestamp is provided in the datasets.cfg file in the github repository chromag-pipeline</li> <li>forceActivated (Boolean): If the magnet is present during the current frame (calculated from timeOn and timeOff)</li> <li>seconds_since_first_magnet_ON (seconds): Number of (relative) seconds since the magnet was added for the first time.</li> <li>Frame (Integer) Frame number (1-indexed)</li> <li>Positions (Integer): The position number</li> </ul> </li> </ul>   Processed datasets (Zenodo 13) and calibration datasets (Zenodo 14-16) These datasets and their analysis are fully described in the Materials and Methods section of the article and in the different README.md files within the various folders of the datasets.

Performing with QuaverSeries Live Coding Environment

<a href="http://webaudioconf.com/posts/2019_27/">http://webaudioconf.com/posts/2019_27/</a>

Live cell imaging data of IRE1a-GFP foci formation

Live cell imaging of XBP1 mRNA and IRE1a-GFP expressing cells.

Live imaging data of XBP1 mRNA under ER stress and IRE1a inhibition

Live microscopy data of XBP1 mRNA transcript in TM and 4u8C.

Live imaging data of XBP1 mRNA under control conditions.

Live imaging data of single XBP1 mRNA transcripts under control conditions.

Live imaging data of XBP1 mRNA under ER stress conditions.

Live microscopy images of single XBP1 mRNA transcripts under ER stress conditions (TM).

[IO Islamic 840] Maâthir-alumarâ, The Second Edition of the Great Biographical Dictionary of the Famous Amîrs, Nawwâbs, and other Noblemen who Lived during the Reign of the Tîmûrides in India

<ul> <li>Another Copy of the Maâthir-alumarâ.</li> <li>This manuscript is now IO Islamic 840 in the India Office collections.</li> <li>[metadata: <a href="https://en.wikipedia.org/wiki/Carl_Hermann_Eth%C3%A9">Hermann Ethé</a>, <a href="http://doi.org/10.5281/zenodo.1323681">Catalogue of Persian Manuscripts in the Library of the India Office, </a><a href="http://doi.org/10.5281/zenodo.1323681">2 vols. (Oxford: India Office, 1903): volume 1,</a> number 626 here with notations and hyperlinks].</li> </ul> 626 An addition to the same. A shorter second or additional volume to the preceding work, serving as supplement to the first, and containing a large number of new biographies, arranged in alphabetical order like those in the first volume. It begins with Isma’îlbeg Dûldî and concludes with Yalankûshkhân Bahâdur. No preface or khâtimah. No date. Mr. Richard Johnson received it from Mîr Muḥammad Ḥusain in Ḥaidarâbâd, A. D. 1788. No. 840, ff. 142, II. 21; careless Nasta’lîḳ; written, as it seems, by the same copyist who transcribed No. 622; size, 151/8 in. by 85/8 in.

opencc-zeroDec 2016View details →

Data from: Phylogenomic analyses of 539 highly informative loci dates a fully resolved time tree for the major clades of living turtles (Testudines)

[No abstract entered]

opencc-zeroDec 2017View details →

Data from: A novel mechanism of gland formation in zebrafish involving transdifferentiation of renal epithelial cells and live cell extrusion

Transdifferentiation is the poorly understood phenomenon whereby a terminally differentiated cell acquires a completely new identity. Here, we describe a rare example of a naturally occurring transdifferentiation in zebrafish in which kidney distal tubule epithelial cells are converted into an endocrine gland known as the Corpuscles of Stannius (CS). We find that this process requires Notch signalling and is associated with the cytoplasmic sequestration of the Hnf1b transcription factor, a master-regulator of renal tubule fate. A deficiency in the Irx3b transcription factor results in ectopic transdifferentiation of distal tubule cells to a CS identity but in a Notch-dependent fashion. Using live-cell imaging we show that CS cells undergo apical constriction en masse and are then extruded from the tubule to form a distinct organ. This system provides a valuable new model to understand the molecular and morphological basis of transdifferentiation and will ad vance efforts to exploit this rare phenomenon therapeutically.