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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jeltsch-Thömmes, Aurich; Tran, Giang; Lienert, Sebastian; Keller, David; +2 Authors
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao

    In memoriam Gerard Pichel (1948-2023), a champion of expert, lay, and tacit knowledge This deposit, having 10.5281/zenodo.7601924 as entry DOI, distributes the sequence of images of a single breaker plunging onto a sandy beach on a windless day. An extended commentary is given in this cover web page. The still frames have been extracted from an impromptu video in the Wikimedia Commons (Vincentz 2013) showing remarkably clearly a shoaling wave that steepens suddenly, grows into a sequence of narrowly spaced plunging breakers, and dissolves in spray and foam. Also clearly visible are the sand stirred and suspended in the foreshore and, upon close inspection, that entrained within the curling wave. Dataset content. This deposit contains: a redistribution of the unprocessed source video (Vincentz 2013); 390 colour distortion-free pictures of 1240x670 pixels, in PNG lossless format, 40ms apart (25 fps); four videos reassembling these processed pictures at different playback speeds (as fast as the physical time, and two-, four- and eightfold slower); they can be viewed in this YouTube playlist; the script used for image extraction and manipulation. Motivation. These images may have informative, didactic and aesthetic value for those intrigued by shore dynamics and wave mechanics, whether initiated or uninitiated. Although the recording concerns a single wave event, even experts risk becoming the least alert to the intricacies of reality. By slow degrees, clinging to unavoidable simplifications may turn expertise into complacency and blunt the genuine appreciation of ground truth (Salt 2008). After all, all research approaches suffer from limitations that make it difficult to distil widely applicable knowledge from complex evidence. For example, experiments are constrained by geometry and by the scaling laws of sand grains; simulations, by modelling three-phase turbulent interactions with very short scales; and parametrizations of field campaigns, by trading off general against locally relevant information. Every avenue of investigation thus leaves us with something to desire. On the upside, appreciating the challenges in foreshore science and engineering does not necessarily require continuous first-hand experience on the beach. Therefore, it is hoped that this dataset stimulates appreciation, contemplation, investigation and/or study. Dataset licensing. (Re-)using the material of this deposit is permitted free of charge under a licence CC BY-SA (attribution and share-alike) 3.0 or 4.0, depending on the file as specified below in the box Files. Dataset description. The ensuing sections describe: the qualitative physics; the procedure of image extraction and manipulation; the content and arrangement of the dataset; the citation format, version information, and vision for this deposit. 1. Physical description An abridged version of this section is also available from the Coastal Wiki. 1.1 Location Vincentz (2013) places the video location at the sandy beach Playa del Matorral. This is in the locality Morro Jable (28.050897°, -14.352003°; municipality of Pájara) in the island of Fuerteventura, Canary Islands, Spain. The precise geolocation of the images is unknown. The Playa del Matorral faces SSW and SE and thus, roughly speaking, the African coast. The region is tidal: the water-level excursion at the nearby Puerto del Rosario is reported to be 2.3 m at springs and 1.6 m at neaps (NGA 2022, p.258). It is hence conceivable but not demonstrable that the flood tide may be have contributed to the wave recorded in the video. The EMODnet bathymetry shows that seabed declines fairly steeply, approximately down to -500 m within 2 km or less from the mean sea level line. The development of a plunging breaker indicates in itself that the beach is behaving as a reflective one. Qualitatively, the closeness to the shore of the breaking line, the narrow shoreface, and the collision of backwash and incoming waves are additional indicators of a steep beach profile (Komar 1998). If present at all, sand bars do not appear to affect the breaking process. Inferences on the local beach profile seem purely speculative, although the particular profile may cause the peculiar behaviour of this one breaker, for example because of a submerged step close to the plunge point. In a steady beach configuration, these plunging waves must bring ashore sufficient sediment to compensate for the offshore transport down the steep slope. 1.2 Calendar The record at Wikimedia Commons only attributes the video the date ‘11 February 2013’. The time stamp of the video file is '16 October 2013'. It is then likely that the former date indicates when the video has been taken. Since the Playa del Matorral faces both east and west, the skylight illumination does not provide clues as for the time of the day. The stage of the tide cannot be estimated either. All in all, the precise time and date are of little relevance for the small-scale development of the single wave seen in the video. 1.3 Description of motion Contemplated in its entirety, the recording conveys the dramatic impression of a prototypical plunging wave dissolving explosively in spray and foam on a natural beach. The onset and development of breakers in the shoreface awes us because of the rapidity, dynamic range, and chaotic and cyclic behaviours embedded in their motion. The scales of motion interleaved within the mixture of water, sand and air in such a sudden and rapid event become clearer thanks to the still frames and to the slowed-down videos. Although inferences about features out of view remain somehow speculative, the qualitative details in the recording reveal distinctive features and stages of development: Waves shoal with long arrival times. A single episode of breaking occurs as if in the isolation of a solitary wave, discounting that here the backrush of each wave feedbacks into the next wave's steepening. Extrapolating the evidence from the recording, this breaking might actually mark a small-amplitude swell, or edge wave, with a period of 13-16 seconds; The recording is taken on a windless day, and no extensive surf zone confuses the nearshore zone seaward of the plunge point; The sand stirred and suspended in the foreshore is visible both in the swash and in the water raised and curled as the wave breaks; The backrush from the previously broken wave has largely returned seawards when a fresh plunger engulfs the foreshore; this emphasises the cycling behaviour expected in a wave, also as far as the sand motion is concerned; The breaking does not unfold as a single wave form seamlessly steepening, curling, and collapsing after a single point of instability has been touched. Instead, while advancing over the small plunge distance, the steep wave face spawns new crests of water that surge ahead and leave behind the previous crest. The trailing crests, nonetheless, impinge on the back of the leading wave face and break behind. The breaking of this 'single breaker' is, in fact, remarkably composite and nonlinear; Because of the considerable steepening, the plunging waves engulf as considerable a volume of air, which produces in turn a dramatic explosion of spray. This evidence on a natural beach can usefully be contrasted with the laboratory studies of Sumer et al (2013) who compare the breaking of a train of plunging waves in a flume with and without a sand bed; and with the laboratory study of Hafsteinsson et al (2017) who organise systematic observations of spilling, plunging and surging breakers in a narrow channel with a uniform bed slope. Finally, the following table comments on some twenty still frames. Selecting these frames entailed the dilemma of choosing times when a process initiates or is already developed enough to be recognisable; the pictures may thus regard both situations. The division into columns reflects fairly loosely a visual separation between either side of a fictional breaker line. I have strived to restrict the commentary to the phenomenological description of the sole free surface (hence avoiding inferences about the underlying flow patterns, however inviting, if self-evident). Please take note that the table only provides orientation and may be revised incrementally without notice later; see, however, §4.2 on versions for notes of substantive edits. Commentary of selected still frames Frame Time (ms) Surf on the foreshore Shoaling and breaking 1 0 The swash of the previously broken wave covers the beach face. Water returns from the limit of wave uprush as a thin sheet of white water. A wide band of foamy water advances shorewards upon that; its front rolls up irregularly, with foamy filaments ejected upwards. Sand in suspension can be inferred from brown-shaded longshore streaks. A wide band of ripple-free water separates the foamy shoreward waters from the incoming shoaling waves. Short-crested wavelets populate the surface seawards of this middle band. 28 1080 [+1080] The thin film on the upper foreshore has retreated significantly. Rolling water marks the edge of the thicker uprush. The ejection of filaments has terminated. The crest of a shoaling wave emerges over the image width; individual short-crested waves ride upon it. To the right, secondary fronts develop within a small cross-shore distance; subsequently, the foremost wave face hides their development from view. 48 1880 [+800] The thin sheet of backrush water is exhausted. The foamy uprush starts to retreat. Extant ripples and wavelets still ride on the wave face as the latter steepens further. 94 3720 [+1840] The water contour and surface are smooth on the landward edge. Hills and knobs of circulating white water populate the lower foreshore. The shoaling wave advances. Its face has steepened up considerably and cannot support extant ripples any longer; its surface becomes progressively smoother. 107 4240 [+520] The white water retreats farther seawards. An edge with the deeper swash water steepens slightly. The disappearance of foam reveals the sand suspended in the swash. The front wave has travelled a short distance further shoreward and is very nearly vertical. Its crest is nearly horizontal and still sharply delineated; its contour starts to break up just afterwards. 113 4480 [+240] Ditto. The height of the crest varies alongshore; the part to the right attains its summit and its contour starts to break up. 126 5000 [+520] The landward edge of the swash steepens further and its face shows a sand-rich mixture. The white water from the rear swash overtops this steep edge at places. The crest in the middle of the image attains its summit. Its break-up projects spray and translucent streaks of water upwards. Detached water hangs in the air because the crest drops faster than its fall speed. Rear waves catching up with the breaker, hence not on view, may also affect the break-up of the crest. 129 5120 [+120] Ditto. The fragmented fringe previously at the fore is left behind by a new face and crest that have surged forward. The water mass is translucent enough to show patches and streaks of suspended sand raising to the full height of the wave face. Streaks of bubbles dragged upward from the swash indicate that the wave steepening draws water from the foreshore. 141 5600 [+480] The swash front is a dense mixture of sand and water. Much of the white water on top of the rear swash has become rarefied and is dragged seawards by the raising breaker. The contour of the crest is wavy and has several local summits. The fragmentation into streaks, droplets and spray is intense; spray is ejected upwards, up to the level of the horizon. Conceivably, a wave front at the rear impinges the rear of the front wave. 149 5920 [+320] Ditto. The wave base travels shorewards while the crest curls over. Dense clouds of sand entrained in suspension help identify the onset of a definite curling motion, accompanied by the marked lowering of the fringe height. A new crest fringe appears to surge forward from the parent wave, as seen previously. 157 6240 [+320] The foreshore water is rich in suspended sand and poor in entrained air. The water surface is relatively flat. The crest at the front is curling forward. Visible in the background is also the curling of a trailing wave, confirming the composite nature of this breaker. 159 6320 [+80] Ditto. The first foam of the curling water touches down upon the shallow swash water, only to bounce on the beach face immediately afterwards. The same occurs in other positions with a time lag. Spray is still suspended in the air. 168 6680 [+360] The backrush is, to an approximation, at its seaward visible limit. The plunging water has touched down over the image width. The water that is curling over is laden with sand. The splash generated by the rebound is projected shorewards and raises as high as the wave plunging at the same time. Farther seaward, a train of short-crested waves is shoaling. 175 6960 [+280] The swash is a thick layer of sand-rich mixture and has a flat surface. The splash generates pervasive spray and foam, high enough to hide the view of shoaling waves in the littoral. An inconspicuous hole in the wall of spray to the right of the image is a notable exception to that. 186 7400 [+440] The spray of the breaker has engulfed all the sand suspended in the foreshore. White water (foam, bubbles and droplets) is propelled forwards and engulfs the sand-rich backrush on the foreshore, dominating the view. 196 7800 [+400] The bulk of the splash water has collapsed. The surface is highly fragmented with plenty of ejections and rebounds, priming a fresh swash line to run up the beach face. The colour shades in the foreshore indicate abundant sand in suspension. At the rear of the previous plunge point, the trailing plunging wave rolls across the surf zone. Farther behind, to the left of the image, patches of white water erupt through the free surface. Overall, the height of waves and spray does not hinder the view of littoral waters: no shoaling waves are developing as yet. 202 8040 [+240] The white water bounces on the shoreface forming patches of varying height. Foamy filaments break up into large drops. The breakers previously hidden from view are visible as a sequence of troughs. Mixtures of sand and foam are also visible to the left. The uprush advances above the saturated foreshore. Most spray has settled. The trailing waves stay low as they break and undergo eruptions of white water especially under their crests. 250 9960 [+1920] White water runs up the foreshore vigorously. The ejection of filaments has died off almost completely and the water surface is crossed by foamy wavelets. The edge of the swash glides over the wet foreshore and leaps over at times. The seaward boundary of the white water is a sharp ridge moving slowly seawards. No shoaling wave emerges from the rear waters. 291 11600 [+1640] In the upper foreshore a uniform milky film replaces the irregular patches of foam and sediment. In the middle of the surf, ephemeral fronts of white water sweep the foreshore, while rolling up and plunging. Ditto. 336 13480 [+1880] The surf consists of the landward film of white water, sweeping the upper foreshore, and of the thicker seaward water. White water rolls up and breaks at the knobbly edge between these two regions. Qualitatively, this frame shows a remarkable similarity with frame 1, as for the extents of the run-up water and the ripple-free surface in the shoreface. 390 15560 [+2080] The film of backrush water is exhausted almost completely. The edge of the swash is a gently rolling line. The surf area is fairly uniformly smooth. The water seaward of the surf is free of ripples for some distance. Farther seawards, ripples populate the surface; slightly steepened wave forms prelude to the crest of a fresh shoaling waves, like in frame 1. 2. Image manipulation 2.1 Toolbox Four open-source utilities have been used to produce this dataset: (1) `ffprobe version 4.2.7` to determine the video properties; (2) `ffmpeg version 4.2.7`, to extract the stills from the video; (3,4) `convert` and `identify` from the ImageMagick tools version 6.9.10-23 to manipulate the stills and determine an image’s property respectively. The developers of these utilities claim that they run on a variety of operating system. Here all image processing has been carried out with, and proved to run successfully on, Linux. 2.2 Source video: specifications and characteristics The source video is ogv format. The logical size of the image (improperly called resolution) is 1270x720 pixels; this corresponds to a pixel count of 914,400 (commercially presented as 0.9MP) and, approximately, to a 16:9 aspect ratio. The recording lasts (nominally) 15.6 seconds at a frame rate of 25 fps and contains 390 still frames spaced 0.04 s (40 ms) apart. The effective duration is 15.56 s. The operator holds the camera with a firm hand and the images are well lit and sharp. On close inspection, four glitches become apparent: Lens distortion: the sea horizon is slightly curved upwards at the edges of the image, which indicates pincushion distortion (the image-to-object magnification rate increases away from the lens centre); Tilt: the camera view has a small anticlockwise roll angle with respect to the horizontal, whereby the sea horizon slopes slightly downwards to the right; Glare: the brightness of the images increases between approximatively 4 and 8 seconds of the recording; this overall glare is visible in the lightness of the sky and is arguably caused by the camera automatic diaphragm as it adjusts to the light reflected by the wave breaking; Motion: the horizon slightly shifts upwards at the tail of the video: this is most likely caused by the beach sand yielding under the operator’s weight as the uprush arrives and retreats on the foreshore. The first two imperfections are remedied by manipulating the image, as described next. 2.3 Frame extraction with ffmpeg The 390 still frames are extracted to as many stand-alone image files using the `ffmpeg` utility, which preserves the logical size of the frames. The image files are saved in tiff format. This format was chosen so that the tool `convert` does not bump into some memory restrictions encountered when manipulating png files as in next subsection. The output frames have a default pixel resolution of 72 dpi, which determines the expected physical size of the frame when printed. (The tool `convert` can also change this resolution by means of resampling, as described below.) The output file sizes vary slightly in the range 1307kB-1360 kB (base-10 file size) or 1276-1328 KiB (base-2 file size). The output colour format is standard RGB (sRGB), with a colour depth of 8 bit (256 shades available per colour channel). All 390 tiff images take 524MB (or 500MiB) of memory space. They are input for the `convert` utility as described next. They are not distributed with this deposit, but can be recreated with the script provided below as the need be. 2.4 Frame manipulation with convert The sequence of `convert` operations to improve the final still frames is: rotate the image to compensate for the tilt (target: the horizon is symmetric with respect to the vertical axis through the image centre); apply barrel distortion to the image to compensate the pincushion-type lens distortion (target: the horizon is a straight line); crop the image canvas (target: eliminate the vignetting due to the previous manipulations). In theory, the correct order of operations should be 2-1-3. The bias of lens distortion is caused by the camera hardware and affects the entire field of view, regardless of how the camera is held. Determining the parameters of the compensating (barrel) distortion should thus have taken into account the distortion present in the entire field of view. This would have required evaluating the effect of lens distortion with a picture of a test card, such as a chessboard pattern. Here, however, the aim is mainly an aesthetic correction, rather than using the images to extract spatial information from the scene. Straightening up the horizon line is sufficient and can be done after having rotated the image, to the same visual effect obtained in the correct order. The logical size of all 390 manipulated images is 1240x670 pixels (aspect ratio 1.85). Their (default) resolution of 72 dpi (2.834 × 2.834 pixels/mm) means that their print size is 437.5 × 236.4 millimetres. The file sizes in png format vary in the range 750-1168 kB (732-1140 KiB). The complete set of images is 383 MB (365 MiB) large. These files are part of the deposit and their arrangement and naming are explained in Section 3. 2.5 Script The script that performed the image extraction and manipulation is part of the deposit (named script-image-extraction+manipulation.sh). The script is written in GNU bash, version 5.0.17(1). Aside from the image-processing utilities already mentioned, the script also calls standard tools distributed in the GNU coreutils, version 8.30. GNU bash is a standard command-line interpreter in several Linux and MacOS distributions. Windows users could run it after installing the terminal emulator Git for Windows, for example. (Mac users, whose default shell interpreter is zsh, will experience troubles with # indicating comments in bash; please refer to this Apple support article on how to change that to bash.) The comments in the script, beside giving ‘sailing directions’, can serve as pseudocode if one wants to code the same workflow in another scripting language. Do not run this script blindly (some commands delete files). The script is divided into three sections. The first section defines the file paths, command parameters and other flags used in the remaining two sections, which deal with the image extraction and the image manipulation respectively. With this structure, the latter two sections need not to be edited for the script to do its job. The parameters and flags are set to the values used for this deposit and can be adjusted (the input and output paths should, for sure). Also, some commands only display information on the input and output documents before and after the processing. Among the possible usages, for example, one could change the default image resolution (dpi=72) to obtain images with a larger physical size by means of resampling, or change the output image format. Goes without saying: peruse the script and read the helps and manuals of the attending commands first. 3. Data arrangement 3.1 Images The 390 png images are arranged in 15 zip archives, each containing one second worth of motion and hence 25 files (except for the 15 files of the last 0.56 seconds). The archive names indicate the beginning of the respective interval as lapsed time in milliseconds. The name format is t[nnnnn]ms.zip: for example, the archive t05000ms.zip contains the still frames between 5 and 5.96 seconds. The grand total size of the zip archives is 381 MB (363 MiB); the size of the individual archives varies in the range 16-29 MB (15-27 MiB). The name of the files inside the archives indicates the frame progressive number and the lapsed time in milliseconds in the format f[nnn]-t[nnnnn]ms.png. Note that the frame number starts from 1 and the lapsed time from 0. The deposit also includes, outside of the archives, the images at each second (the first file in each archive) in the way of 'covers' that help users pick up the time interval and zipped archive of their interest. The covers name convention is the same as the archives (for example, t05000ms.png shows the first image contained in t05000ms.zip). You can preview these cover images in Zenodo once you accept the CC BY-SA licences: select one cover image from the list in the Files box and look at it in the Preview box that will show up then. 3.2 Videos The original, unprocessed video (Pájara_-_Morro_Jable_-_Playa_del_Matorral_(0)_09.ogv, 73 MB, 70 MiB) is also redistributed with this deposit and should be credited to Vincentz 2013 (see the section Licence for the conditions). Additionally, the processed images have been assembled in a video with the same duration as the original, and then in three more videos whose playback time is two-, four- and eightfold the physical time. These mp4 files have a name patterned as breaker-video1-slow1x.mp4. They are overlain by the frame number, the physical elapsed time, and the playback slow-down so as to help identify especially interesting frames. These slowed-down videos can be viewed in this YouTube playlist. They are 8 (8), 11 (10), 13 (13) and 20 (19) MB (MiB) large respectively; their lengths are 22", 38", 1'9", and 2'11". Take note that making a video out of individual images implies dropping and duplicating frames. In particular, a slowed-down video is created by filling the longer playback time with frames interpolated from the baseline images. A slowed-down video helps gain appreciation of a rapid process, but cannot produce insight into events occurring at a faster rate than 40 ms anyhow. Therefore, the best representation of the ground truth must always be sought in the smallest recording units, that is, the individual 390 images taken at a rate of 25 fps. 4. This deposit 4.1 How to cite this work This commentary and dataset are indexed with a DOI 10.5281/zenodo.7601924. The citation text is available in different styles in the box Share, to the upper right of this web page. (Goes without saying that grey literature should be acknowledged also in peer-reviewed literature.) 4.2 Versions Major numbers indicate changes in the deposit content, minor numbers significant changes in the deposit Description (this web-based document you are reading now). A major version change implies Zenodo issuing a new DOI. The DOI 10.5281/zenodo.7601924 always points to the latest version. The table below displays the history of versions. This deposit has been created on 11 Feb 2023. I adjust the date of publication of the deposit to the latest version, so that the automatic citations provided by Zenodo report consistent date/version information. List of versions v2.4 09/03/2024 Revise §1 https://zenodo.org/record/8070591 v2.3 18/09/2023 Add link to video playlist https://zenodo.org/record/8070591 v2.2 22/07/2023 Complete table in §1.3 https://zenodo.org/record/8070591 v1.2 22/06/2023 Strip description after v2.1 https://zenodo.org/record/7601925 v2.1 22/06/2023 Add videos of dataset https://zenodo.org/record/8070591 v1.1 21/06/2023 Add commentary to §1 https://zenodo.org/record/7601925 v1.0 11/02/2023 Publish images https://zenodo.org/record/7601925 4.3 Next The current wish-list contains: a) linking the script to a GitHub repository if its complexity grows; b) comment the state of the free surface using the terminology of Brocchini and Peregrine (2001), even though their study was prompted by spilling breakers; c) include other videos; d) publish videos in ogv format.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODO; University o...arrow_drop_down
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao ZENODO; University o...arrow_drop_down
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    Authors: Agiadi, Konstantina; Hohmann, Niklas; Gliozzi, Elsa; Thivaiou, Danae; +23 Authors

    This is a unified and revised marine fossil record of the Mediterranean covering the Tortonian stage, the pre-evaporitic Messinian and the Zanclean stage and encompassing 22988 occurrences of calcareous nannoplankton, dinoflagellates, foraminifera, corals, ostracods, bryozoans, echinoids, mollusks, fishes, and marine mammals. It consists of three files in .csv format: 1) 'MessinianDB' contains the fossil occurrences; 2) 'coord' has the list of fossiliferous localities with their coordinates and the groups of organisms reported from each one; and 3) 'DBrefs' contains the full citations of the references in the database.

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    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: Datacite
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  • Authors: Dominguez Mantes, Albert; Herrera, Antonio; Khven, Irina; Schlaeppi, Anjalie; +6 Authors

    Fluorescence spot detection datasets used in the paper "Spotiflow: accurate and efficient spot detection for imaging-based spatial transcriptomics with stereographic flow regression". Consists of seven different annotated datasets of synthetic (2), FISH (3) and live-cell imaging (2). 

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    Authors: Morée, Anne L.; Caccavo, Jilda A.; Nissen, Cara;

    Habitat files of 28 Antarctic Toothfish (Dissostichus mawsoni) prey species and the Antarctic Toothfish itself, regridded to the FESOM-REcoM model grid, in NetCDF format. For use in article '21st-century environmental change decreases habitat overlap of Antarctic toothfish (Dissostichus mawsoni) and its prey'. This dataset is a collection of the following: 1) 2-dimensional distribution data for 3 squid species, derived from Raymond et al. (2015) 2) 2-dimensional distribution data for 25 prey species and the Antarctic Toothfish, derived from AquaMaps distribution data 3) the model grid file. A species is present in a certain gridcell when its value is 1, elsewhere the species is considered absent. 1) Original files for the 3 squid species galiteuthis glacialis, kondakovia longimana and mesonychoteuthis hamiltoni are taken from previously published data of Raymond et al. (2015) and regridded to the FESOM-REcoM model grid. These squid species are considered to have their habitat anywhere where habitat suitability in the original Raymond et al. (2015) dataset exceeds the habitat suitability thresholds of 0.228 for Galiteuthis glacialis, 0.281 for Kondakovia longimana and 0.121 for Mesonychoteuthis hamiltoni (threshold values as in Xavier et al. (2016), personal communication with Ben Raymond 16.01.2023 to get exact values). These data have an original resolution of 0.1x0.1 degrees (regular longitude-latitude grid). 2) The 25 files taken from AquaMaps start with Default_* or Reviewed_* and are the native predicted range data as provided by Kaschner et al. (2019). They were shared by Kathleen Kesner-Reyes from AquaMaps in March and April 2023 after being reviewed by her for correctness and actuality. The files that start with Reviewed_* have had adjustments made to the original Default_* based on this review, which is described in more detail on the AquaMaps website. These data have an original resolution of 0.5x0.5 degrees (regular longitude-latitude grid). 3) The model grid file 'Mesh_ancillary_information_v20220919.nc' contains the longitude and latitude data needed for regridding to the FESOM-REcoM model grid. Regridding was done using CDO version 1.9.6 (http://mpimet.mpg.de/cdo; developed by U. Schulzweida) and CDO function 'remaplaf', which performs largest area fraction remapping. References Xavier, J.C., Raymond, B., Jones, D.C. et al. Biogeography of Cephalopods in the Southern Ocean Using Habitat Suitability Prediction Models. Ecosystems 19, 220–247 (2016). https://doi.org/10.1007/s10021-015-9926-1 Raymond, B., Xavier, J., Griffiths, H., Jones, D. (2015) Habitat suitability predictions for 15 species of cephalopods in the Southern Ocean, Ver. 1, Australian Antarctic Data Centre - doi:10.4225/15/563AC33450A28, Accessed: 2023-01-16 Kaschner, K., Kesner-Reyes, K., Garilao, C., Segschneider, J., Rius-Barile, J. Rees, T., & Froese, R. (2019, October). AquaMaps: Predicted range maps for aquatic species. Retrieved from https://www.aquamaps.org.

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    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2024
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: ZENODO
      ZENODO
      Dataset . 2024
      License: CC BY
      Data sources: Datacite
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    Authors: Van Leeuwen, Stefan; Leenders, Liz; Hoogenboom, Ron; Krätschmer, Kerstin; +2 Authors

    On behalf of the Ministry of Agriculture, Nature and Food Quality (LNV), Wageningen Food Safety Research (WFSR) analyses samples of agricultural products of animal origin for dioxins, PCBs, brominated flame retardants (BFRs) and poly- and perfluorinated alkyl substances (PFASs). This includes meat, milk, eggs and fish.The samples are taken at the primary production or processing stage (e.g. in slaughterhouses or raw milk collection services). For dioxin-like compounds, 350 samples are screened first with the DR CALUX® method. Samples giving a signal indicating a level above the lowest action level are regarded as suspected. These samples are further examined using GC/HRMS as confirmatory method. Concerning fish, shellfish and crustaceans, approx. 25 samples are collected at sea by research vessels, at the fish auction, or from whole-sale traders (farmed fish).

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    4TU.ResearchData
    Dataset . 2024
    License: CC BY NC SA
    Data sources: 4TU.ResearchData
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    4TU.ResearchData
    Dataset . 2024
    License: CC BY NC SA
    Data sources: 4TU.ResearchData
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    4TU.ResearchData
    Dataset . 2024
    License: CC BY NC SA
    Data sources: 4TU.ResearchData
    4TU.ResearchData | science.engineering.design
    Dataset . 2024
    License: CC BY NC SA
    Data sources: Datacite
    4TU.ResearchData | science.engineering.design
    Dataset . 2024
    License: CC BY NC SA
    Data sources: Datacite
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      4TU.ResearchData
      Dataset . 2024
      License: CC BY NC SA
      Data sources: 4TU.ResearchData
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      4TU.ResearchData
      Dataset . 2024
      License: CC BY NC SA
      Data sources: 4TU.ResearchData
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      4TU.ResearchData
      Dataset . 2024
      License: CC BY NC SA
      Data sources: 4TU.ResearchData
      4TU.ResearchData | science.engineering.design
      Dataset . 2024
      License: CC BY NC SA
      Data sources: Datacite
      4TU.ResearchData | science.engineering.design
      Dataset . 2024
      License: CC BY NC SA
      Data sources: Datacite
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    Authors: García, María Luján; Birlo, Stella; Zahajska, Petra; Grosjean, Martin; +1 Authors

    XRF measurements in 0.2 to 1 mm increments with an ITRAX XRF core scanner (Cox Analytics) and Cr tube (Croudance et al. 2015, doi:10.1007/978-94-017-9849-5 ). The sediment core HZM19 was collected in 2019, from Holzmaar, West-Eifel Volcanic Field in Germany using a UWITEC Piston Corer. The sediment core was collected to reconstruct environmental and climate changes of Holzmaar for the last 16,000 years cal BP. Particularly in this data set we cover between 2450-2950 cal BP. Funding information:* Georg Forster Research Fellowship for postdoctoral researchers (for the Alexander von Humboldt funding)* Central Research Development Fund (CRDF) of the University of Bremen, 04 Independent Project for Postdocs - Funding objective B

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    PANGAEA
    Dataset . 2024
    Data sources: B2FIND
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      PANGAEA
      Dataset . 2024
      Data sources: B2FIND
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    Authors: Dearing Crampton-Flood, Emily;

    The mid-Piacenzian Warm Period (mPWP, 3264-3025 ka) represents the most recent interval in Earth's history where atmospheric CO2 levels were similar to today. Here, we present a multi-proxy record of Pliocene climate change in the coastal Southern North Sea Basin (SNSB) based on the sedimentary record from borehole Hank, the Netherlands (drilled by TNO, Dutch Geological Survey). We present the stable oxygen and carbon isotope (δ18O and δ13C) measurements of the endobenthic foraminifera species Cassidulina laevigata, and present a new age model for the late Pliocene of the Southern North Sea. This results in a tuned age framework for the SNSB for the Late Pliocene (~3190-2770 ka). Our multi-proxy climate reconstruction for this interval includes biomarker-based SST reconstructions (TEX86, UK37, LDI).

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    PANGAEA
    Dataset . 2024
    Data sources: B2FIND
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    citations0
    popularityAverage
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      PANGAEA
      Dataset . 2024
      Data sources: B2FIND
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    Authors: García, María Luján; Birlo, Stella; Zahajska, Petra; Grosjean, Martin; +1 Authors

    Diatom analyses were done following (Battarbee, 1986; Battarbee et al., 2002; doi:10.2478/s11756-019-00407-8). Including an updated list of names. The sediment core HZM19 was collected in 2019, from Holzmaar, West-Eifel Volcanic Field in Germany using a UWITEC Piston Corer. The sediment core was collected to reconstruct environmental and climate changes of Holzmaar for the last 16,000 years cal BP. Particularly in this data set we cover between 2450-2950 cal BP. An aliquot of each freeze-dried sample was processed with standard procedures (Battarbee, 1986; Battarbee et al., 2002). Only species with >=5% relative abundance in at least two samples were used for further analyses. Species acronyms are listed seperately. Funding information:* Georg Forster Research Fellowship for postdoctoral researchers (for the Alexander von Humboldt funding)* Central Research Development Fund (CRDF) of the University of Bremen, 04 Independent Project for Postdocs– Funding objective B

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    PANGAEA
    Dataset . 2024
    Data sources: B2FIND
    0
    citations0
    popularityAverage
    influenceAverage
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    Authors: Fritz, Michael; Gimsa, Justus; Petzold, Pia; Klein, Konstantin; +7 Authors

    This dataset contains CTD measurements taken in 2015, 2016, 2017, 2018, 2019, 2022, and 2023 during expeditions to Herschel Island - Qikiqtaruk, Yukon, Canada. For the data recording a CTD CastAway was used. The sampling was conducted from a boat from which the CTD was lowered to the sea floor at the specific sampling sites. The sampling information encompasses the GPS position, water depth, pressure, temperature, electrical conductivity, specific conductance, and salinity.

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    PANGAEA
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    Authors: Jeltsch-Thömmes, Aurich; Tran, Giang; Lienert, Sebastian; Keller, David; +2 Authors
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    In memoriam Gerard Pichel (1948-2023), a champion of expert, lay, and tacit knowledge This deposit, having 10.5281/zenodo.7601924 as entry DOI, distributes the sequence of images of a single breaker plunging onto a sandy beach on a windless day. An extended commentary is given in this cover web page. The still frames have been extracted from an impromptu video in the Wikimedia Commons (Vincentz 2013) showing remarkably clearly a shoaling wave that steepens suddenly, grows into a sequence of narrowly spaced plunging breakers, and dissolves in spray and foam. Also clearly visible are the sand stirred and suspended in the foreshore and, upon close inspection, that entrained within the curling wave. Dataset content. This deposit contains: a redistribution of the unprocessed source video (Vincentz 2013); 390 colour distortion-free pictures of 1240x670 pixels, in PNG lossless format, 40ms apart (25 fps); four videos reassembling these processed pictures at different playback speeds (as fast as the physical time, and two-, four- and eightfold slower); they can be viewed in this YouTube playlist; the script used for image extraction and manipulation. Motivation. These images may have informative, didactic and aesthetic value for those intrigued by shore dynamics and wave mechanics, whether initiated or uninitiated. Although the recording concerns a single wave event, even experts risk becoming the least alert to the intricacies of reality. By slow degrees, clinging to unavoidable simplifications may turn expertise into complacency and blunt the genuine appreciation of ground truth (Salt 2008). After all, all research approaches suffer from limitations that make it difficult to distil widely applicable knowledge from complex evidence. For example, experiments are constrained by geometry and by the scaling laws of sand grains; simulations, by modelling three-phase turbulent interactions with very short scales; and parametrizations of field campaigns, by trading off general against locally relevant information. Every avenue of investigation thus leaves us with something to desire. On the upside, appreciating the challenges in foreshore science and engineering does not necessarily require continuous first-hand experience on the beach. Therefore, it is hoped that this dataset stimulates appreciation, contemplation, investigation and/or study. Dataset licensing. (Re-)using the material of this deposit is permitted free of charge under a licence CC BY-SA (attribution and share-alike) 3.0 or 4.0, depending on the file as specified below in the box Files. Dataset description. The ensuing sections describe: the qualitative physics; the procedure of image extraction and manipulation; the content and arrangement of the dataset; the citation format, version information, and vision for this deposit. 1. Physical description An abridged version of this section is also available from the Coastal Wiki. 1.1 Location Vincentz (2013) places the video location at the sandy beach Playa del Matorral. This is in the locality Morro Jable (28.050897°, -14.352003°; municipality of Pájara) in the island of Fuerteventura, Canary Islands, Spain. The precise geolocation of the images is unknown. The Playa del Matorral faces SSW and SE and thus, roughly speaking, the African coast. The region is tidal: the water-level excursion at the nearby Puerto del Rosario is reported to be 2.3 m at springs and 1.6 m at neaps (NGA 2022, p.258). It is hence conceivable but not demonstrable that the flood tide may be have contributed to the wave recorded in the video. The EMODnet bathymetry shows that seabed declines fairly steeply, approximately down to -500 m within 2 km or less from the mean sea level line. The development of a plunging breaker indicates in itself that the beach is behaving as a reflective one. Qualitatively, the closeness to the shore of the breaking line, the narrow shoreface, and the collision of backwash and incoming waves are additional indicators of a steep beach profile (Komar 1998). If present at all, sand bars do not appear to affect the breaking process. Inferences on the local beach profile seem purely speculative, although the particular profile may cause the peculiar behaviour of this one breaker, for example because of a submerged step close to the plunge point. In a steady beach configuration, these plunging waves must bring ashore sufficient sediment to compensate for the offshore transport down the steep slope. 1.2 Calendar The record at Wikimedia Commons only attributes the video the date ‘11 February 2013’. The time stamp of the video file is '16 October 2013'. It is then likely that the former date indicates when the video has been taken. Since the Playa del Matorral faces both east and west, the skylight illumination does not provide clues as for the time of the day. The stage of the tide cannot be estimated either. All in all, the precise time and date are of little relevance for the small-scale development of the single wave seen in the video. 1.3 Description of motion Contemplated in its entirety, the recording conveys the dramatic impression of a prototypical plunging wave dissolving explosively in spray and foam on a natural beach. The onset and development of breakers in the shoreface awes us because of the rapidity, dynamic range, and chaotic and cyclic behaviours embedded in their motion. The scales of motion interleaved within the mixture of water, sand and air in such a sudden and rapid event become clearer thanks to the still frames and to the slowed-down videos. Although inferences about features out of view remain somehow speculative, the qualitative details in the recording reveal distinctive features and stages of development: Waves shoal with long arrival times. A single episode of breaking occurs as if in the isolation of a solitary wave, discounting that here the backrush of each wave feedbacks into the next wave's steepening. Extrapolating the evidence from the recording, this breaking might actually mark a small-amplitude swell, or edge wave, with a period of 13-16 seconds; The recording is taken on a windless day, and no extensive surf zone confuses the nearshore zone seaward of the plunge point; The sand stirred and suspended in the foreshore is visible both in the swash and in the water raised and curled as the wave breaks; The backrush from the previously broken wave has largely returned seawards when a fresh plunger engulfs the foreshore; this emphasises the cycling behaviour expected in a wave, also as far as the sand motion is concerned; The breaking does not unfold as a single wave form seamlessly steepening, curling, and collapsing after a single point of instability has been touched. Instead, while advancing over the small plunge distance, the steep wave face spawns new crests of water that surge ahead and leave behind the previous crest. The trailing crests, nonetheless, impinge on the back of the leading wave face and break behind. The breaking of this 'single breaker' is, in fact, remarkably composite and nonlinear; Because of the considerable steepening, the plunging waves engulf as considerable a volume of air, which produces in turn a dramatic explosion of spray. This evidence on a natural beach can usefully be contrasted with the laboratory studies of Sumer et al (2013) who compare the breaking of a train of plunging waves in a flume with and without a sand bed; and with the laboratory study of Hafsteinsson et al (2017) who organise systematic observations of spilling, plunging and surging breakers in a narrow channel with a uniform bed slope. Finally, the following table comments on some twenty still frames. Selecting these frames entailed the dilemma of choosing times when a process initiates or is already developed enough to be recognisable; the pictures may thus regard both situations. The division into columns reflects fairly loosely a visual separation between either side of a fictional breaker line. I have strived to restrict the commentary to the phenomenological description of the sole free surface (hence avoiding inferences about the underlying flow patterns, however inviting, if self-evident). Please take note that the table only provides orientation and may be revised incrementally without notice later; see, however, §4.2 on versions for notes of substantive edits. Commentary of selected still frames Frame Time (ms) Surf on the foreshore Shoaling and breaking 1 0 The swash of the previously broken wave covers the beach face. Water returns from the limit of wave uprush as a thin sheet of white water. A wide band of foamy water advances shorewards upon that; its front rolls up irregularly, with foamy filaments ejected upwards. Sand in suspension can be inferred from brown-shaded longshore streaks. A wide band of ripple-free water separates the foamy shoreward waters from the incoming shoaling waves. Short-crested wavelets populate the surface seawards of this middle band. 28 1080 [+1080] The thin film on the upper foreshore has retreated significantly. Rolling water marks the edge of the thicker uprush. The ejection of filaments has terminated. The crest of a shoaling wave emerges over the image width; individual short-crested waves ride upon it. To the right, secondary fronts develop within a small cross-shore distance; subsequently, the foremost wave face hides their development from view. 48 1880 [+800] The thin sheet of backrush water is exhausted. The foamy uprush starts to retreat. Extant ripples and wavelets still ride on the wave face as the latter steepens further. 94 3720 [+1840] The water contour and surface are smooth on the landward edge. Hills and knobs of circulating white water populate the lower foreshore. The shoaling wave advances. Its face has steepened up considerably and cannot support extant ripples any longer; its surface becomes progressively smoother. 107 4240 [+520] The white water retreats farther seawards. An edge with the deeper swash water steepens slightly. The disappearance of foam reveals the sand suspended in the swash. The front wave has travelled a short distance further shoreward and is very nearly vertical. Its crest is nearly horizontal and still sharply delineated; its contour starts to break up just afterwards. 113 4480 [+240] Ditto. The height of the crest varies alongshore; the part to the right attains its summit and its contour starts to break up. 126 5000 [+520] The landward edge of the swash steepens further and its face shows a sand-rich mixture. The white water from the rear swash overtops this steep edge at places. The crest in the middle of the image attains its summit. Its break-up projects spray and translucent streaks of water upwards. Detached water hangs in the air because the crest drops faster than its fall speed. Rear waves catching up with the breaker, hence not on view, may also affect the break-up of the crest. 129 5120 [+120] Ditto. The fragmented fringe previously at the fore is left behind by a new face and crest that have surged forward. The water mass is translucent enough to show patches and streaks of suspended sand raising to the full height of the wave face. Streaks of bubbles dragged upward from the swash indicate that the wave steepening draws water from the foreshore. 141 5600 [+480] The swash front is a dense mixture of sand and water. Much of the white water on top of the rear swash has become rarefied and is dragged seawards by the raising breaker. The contour of the crest is wavy and has several local summits. The fragmentation into streaks, droplets and spray is intense; spray is ejected upwards, up to the level of the horizon. Conceivably, a wave front at the rear impinges the rear of the front wave. 149 5920 [+320] Ditto. The wave base travels shorewards while the crest curls over. Dense clouds of sand entrained in suspension help identify the onset of a definite curling motion, accompanied by the marked lowering of the fringe height. A new crest fringe appears to surge forward from the parent wave, as seen previously. 157 6240 [+320] The foreshore water is rich in suspended sand and poor in entrained air. The water surface is relatively flat. The crest at the front is curling forward. Visible in the background is also the curling of a trailing wave, confirming the composite nature of this breaker. 159 6320 [+80] Ditto. The first foam of the curling water touches down upon the shallow swash water, only to bounce on the beach face immediately afterwards. The same occurs in other positions with a time lag. Spray is still suspended in the air. 168 6680 [+360] The backrush is, to an approximation, at its seaward visible limit. The plunging water has touched down over the image width. The water that is curling over is laden with sand. The splash generated by the rebound is projected shorewards and raises as high as the wave plunging at the same time. Farther seaward, a train of short-crested waves is shoaling. 175 6960 [+280] The swash is a thick layer of sand-rich mixture and has a flat surface. The splash generates pervasive spray and foam, high enough to hide the view of shoaling waves in the littoral. An inconspicuous hole in the wall of spray to the right of the image is a notable exception to that. 186 7400 [+440] The spray of the breaker has engulfed all the sand suspended in the foreshore. White water (foam, bubbles and droplets) is propelled forwards and engulfs the sand-rich backrush on the foreshore, dominating the view. 196 7800 [+400] The bulk of the splash water has collapsed. The surface is highly fragmented with plenty of ejections and rebounds, priming a fresh swash line to run up the beach face. The colour shades in the foreshore indicate abundant sand in suspension. At the rear of the previous plunge point, the trailing plunging wave rolls across the surf zone. Farther behind, to the left of the image, patches of white water erupt through the free surface. Overall, the height of waves and spray does not hinder the view of littoral waters: no shoaling waves are developing as yet. 202 8040 [+240] The white water bounces on the shoreface forming patches of varying height. Foamy filaments break up into large drops. The breakers previously hidden from view are visible as a sequence of troughs. Mixtures of sand and foam are also visible to the left. The uprush advances above the saturated foreshore. Most spray has settled. The trailing waves stay low as they break and undergo eruptions of white water especially under their crests. 250 9960 [+1920] White water runs up the foreshore vigorously. The ejection of filaments has died off almost completely and the water surface is crossed by foamy wavelets. The edge of the swash glides over the wet foreshore and leaps over at times. The seaward boundary of the white water is a sharp ridge moving slowly seawards. No shoaling wave emerges from the rear waters. 291 11600 [+1640] In the upper foreshore a uniform milky film replaces the irregular patches of foam and sediment. In the middle of the surf, ephemeral fronts of white water sweep the foreshore, while rolling up and plunging. Ditto. 336 13480 [+1880] The surf consists of the landward film of white water, sweeping the upper foreshore, and of the thicker seaward water. White water rolls up and breaks at the knobbly edge between these two regions. Qualitatively, this frame shows a remarkable similarity with frame 1, as for the extents of the run-up water and the ripple-free surface in the shoreface. 390 15560 [+2080] The film of backrush water is exhausted almost completely. The edge of the swash is a gently rolling line. The surf area is fairly uniformly smooth. The water seaward of the surf is free of ripples for some distance. Farther seawards, ripples populate the surface; slightly steepened wave forms prelude to the crest of a fresh shoaling waves, like in frame 1. 2. Image manipulation 2.1 Toolbox Four open-source utilities have been used to produce this dataset: (1) `ffprobe version 4.2.7` to determine the video properties; (2) `ffmpeg version 4.2.7`, to extract the stills from the video; (3,4) `convert` and `identify` from the ImageMagick tools version 6.9.10-23 to manipulate the stills and determine an image’s property respectively. The developers of these utilities claim that they run on a variety of operating system. Here all image processing has been carried out with, and proved to run successfully on, Linux. 2.2 Source video: specifications and characteristics The source video is ogv format. The logical size of the image (improperly called resolution) is 1270x720 pixels; this corresponds to a pixel count of 914,400 (commercially presented as 0.9MP) and, approximately, to a 16:9 aspect ratio. The recording lasts (nominally) 15.6 seconds at a frame rate of 25 fps and contains 390 still frames spaced 0.04 s (40 ms) apart. The effective duration is 15.56 s. The operator holds the camera with a firm hand and the images are well lit and sharp. On close inspection, four glitches become apparent: Lens distortion: the sea horizon is slightly curved upwards at the edges of the image, which indicates pincushion distortion (the image-to-object magnification rate increases away from the lens centre); Tilt: the camera view has a small anticlockwise roll angle with respect to the horizontal, whereby the sea horizon slopes slightly downwards to the right; Glare: the brightness of the images increases between approximatively 4 and 8 seconds of the recording; this overall glare is visible in the lightness of the sky and is arguably caused by the camera automatic diaphragm as it adjusts to the light reflected by the wave breaking; Motion: the horizon slightly shifts upwards at the tail of the video: this is most likely caused by the beach sand yielding under the operator’s weight as the uprush arrives and retreats on the foreshore. The first two imperfections are remedied by manipulating the image, as described next. 2.3 Frame extraction with ffmpeg The 390 still frames are extracted to as many stand-alone image files using the `ffmpeg` utility, which preserves the logical size of the frames. The image files are saved in tiff format. This format was chosen so that the tool `convert` does not bump into some memory restrictions encountered when manipulating png files as in next subsection. The output frames have a default pixel resolution of 72 dpi, which determines the expected physical size of the frame when printed. (The tool `convert` can also change this resolution by means of resampling, as described below.) The output file sizes vary slightly in the range 1307kB-1360 kB (base-10 file size) or 1276-1328 KiB (base-2 file size). The output colour format is standard RGB (sRGB), with a colour depth of 8 bit (256 shades available per colour channel). All 390 tiff images take 524MB (or 500MiB) of memory space. They are input for the `convert` utility as described next. They are not distributed with this deposit, but can be recreated with the script provided below as the need be. 2.4 Frame manipulation with convert The sequence of `convert` operations to improve the final still frames is: rotate the image to compensate for the tilt (target: the horizon is symmetric with respect to the vertical axis through the image centre); apply barrel distortion to the image to compensate the pincushion-type lens distortion (target: the horizon is a straight line); crop the image canvas (target: eliminate the vignetting due to the previous manipulations). In theory, the correct order of operations should be 2-1-3. The bias of lens distortion is caused by the camera hardware and affects the entire field of view, regardless of how the camera is held. Determining the parameters of the compensating (barrel) distortion should thus have taken into account the distortion present in the entire field of view. This would have required evaluating the effect of lens distortion with a picture of a test card, such as a chessboard pattern. Here, however, the aim is mainly an aesthetic correction, rather than using the images to extract spatial information from the scene. Straightening up the horizon line is sufficient and can be done after having rotated the image, to the same visual effect obtained in the correct order. The logical size of all 390 manipulated images is 1240x670 pixels (aspect ratio 1.85). Their (default) resolution of 72 dpi (2.834 × 2.834 pixels/mm) means that their print size is 437.5 × 236.4 millimetres. The file sizes in png format vary in the range 750-1168 kB (732-1140 KiB). The complete set of images is 383 MB (365 MiB) large. These files are part of the deposit and their arrangement and naming are explained in Section 3. 2.5 Script The script that performed the image extraction and manipulation is part of the deposit (named script-image-extraction+manipulation.sh). The script is written in GNU bash, version 5.0.17(1). Aside from the image-processing utilities already mentioned, the script also calls standard tools distributed in the GNU coreutils, version 8.30. GNU bash is a standard command-line interpreter in several Linux and MacOS distributions. Windows users could run it after installing the terminal emulator Git for Windows, for example. (Mac users, whose default shell interpreter is zsh, will experience troubles with # indicating comments in bash; please refer to this Apple support article on how to change that to bash.) The comments in the script, beside giving ‘sailing directions’, can serve as pseudocode if one wants to code the same workflow in another scripting language. Do not run this script blindly (some commands delete files). The script is divided into three sections. The first section defines the file paths, command parameters and other flags used in the remaining two sections, which deal with the image extraction and the image manipulation respectively. With this structure, the latter two sections need not to be edited for the script to do its job. The parameters and flags are set to the values used for this deposit and can be adjusted (the input and output paths should, for sure). Also, some commands only display information on the input and output documents before and after the processing. Among the possible usages, for example, one could change the default image resolution (dpi=72) to obtain images with a larger physical size by means of resampling, or change the output image format. Goes without saying: peruse the script and read the helps and manuals of the attending commands first. 3. Data arrangement 3.1 Images The 390 png images are arranged in 15 zip archives, each containing one second worth of motion and hence 25 files (except for the 15 files of the last 0.56 seconds). The archive names indicate the beginning of the respective interval as lapsed time in milliseconds. The name format is t[nnnnn]ms.zip: for example, the archive t05000ms.zip contains the still frames between 5 and 5.96 seconds. The grand total size of the zip archives is 381 MB (363 MiB); the size of the individual archives varies in the range 16-29 MB (15-27 MiB). The name of the files inside the archives indicates the frame progressive number and the lapsed time in milliseconds in the format f[nnn]-t[nnnnn]ms.png. Note that the frame number starts from 1 and the lapsed time from 0. The deposit also includes, outside of the archives, the images at each second (the first file in each archive) in the way of 'covers' that help users pick up the time interval and zipped archive of their interest. The covers name convention is the same as the archives (for example, t05000ms.png shows the first image contained in t05000ms.zip). You can preview these cover images in Zenodo once you accept the CC BY-SA licences: select one cover image from the list in the Files box and look at it in the Preview box that will show up then. 3.2 Videos The original, unprocessed video (Pájara_-_Morro_Jable_-_Playa_del_Matorral_(0)_09.ogv, 73 MB, 70 MiB) is also redistributed with this deposit and should be credited to Vincentz 2013 (see the section Licence for the conditions). Additionally, the processed images have been assembled in a video with the same duration as the original, and then in three more videos whose playback time is two-, four- and eightfold the physical time. These mp4 files have a name patterned as breaker-video1-slow1x.mp4. They are overlain by the frame number, the physical elapsed time, and the playback slow-down so as to help identify especially interesting frames. These slowed-down videos can be viewed in this YouTube playlist. They are 8 (8), 11 (10), 13 (13) and 20 (19) MB (MiB) large respectively; their lengths are 22", 38", 1'9", and 2'11". Take note that making a video out of individual images implies dropping and duplicating frames. In particular, a slowed-down video is created by filling the longer playback time with frames interpolated from the baseline images. A slowed-down video helps gain appreciation of a rapid process, but cannot produce insight into events occurring at a faster rate than 40 ms anyhow. Therefore, the best representation of the ground truth must always be sought in the smallest recording units, that is, the individual 390 images taken at a rate of 25 fps. 4. This deposit 4.1 How to cite this work This commentary and dataset are indexed with a DOI 10.5281/zenodo.7601924. The citation text is available in different styles in the box Share, to the upper right of this web page. (Goes without saying that grey literature should be acknowledged also in peer-reviewed literature.) 4.2 Versions Major numbers indicate changes in the deposit content, minor numbers significant changes in the deposit Description (this web-based document you are reading now). A major version change implies Zenodo issuing a new DOI. The DOI 10.5281/zenodo.7601924 always points to the latest version. The table below displays the history of versions. This deposit has been created on 11 Feb 2023. I adjust the date of publication of the deposit to the latest version, so that the automatic citations provided by Zenodo report consistent date/version information. List of versions v2.4 09/03/2024 Revise §1 https://zenodo.org/record/8070591 v2.3 18/09/2023 Add link to video playlist https://zenodo.org/record/8070591 v2.2 22/07/2023 Complete table in §1.3 https://zenodo.org/record/8070591 v1.2 22/06/2023 Strip description after v2.1 https://zenodo.org/record/7601925 v2.1 22/06/2023 Add videos of dataset https://zenodo.org/record/8070591 v1.1 21/06/2023 Add commentary to §1 https://zenodo.org/record/7601925 v1.0 11/02/2023 Publish images https://zenodo.org/record/7601925 4.3 Next The current wish-list contains: a) linking the script to a GitHub repository if its complexity grows; b) comment the state of the free surface using the terminology of Brocchini and Peregrine (2001), even though their study was prompted by spilling breakers; c) include other videos; d) publish videos in ogv format.

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    Authors: Agiadi, Konstantina; Hohmann, Niklas; Gliozzi, Elsa; Thivaiou, Danae; +23 Authors

    This is a unified and revised marine fossil record of the Mediterranean covering the Tortonian stage, the pre-evaporitic Messinian and the Zanclean stage and encompassing 22988 occurrences of calcareous nannoplankton, dinoflagellates, foraminifera, corals, ostracods, bryozoans, echinoids, mollusks, fishes, and marine mammals. It consists of three files in .csv format: 1) 'MessinianDB' contains the fossil occurrences; 2) 'coord' has the list of fossiliferous localities with their coordinates and the groups of organisms reported from each one; and 3) 'DBrefs' contains the full citations of the references in the database.

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    ZENODO
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      ZENODO
      Dataset . 2024
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  • Authors: Dominguez Mantes, Albert; Herrera, Antonio; Khven, Irina; Schlaeppi, Anjalie; +6 Authors

    Fluorescence spot detection datasets used in the paper "Spotiflow: accurate and efficient spot detection for imaging-based spatial transcriptomics with stereographic flow regression". Consists of seven different annotated datasets of synthetic (2), FISH (3) and live-cell imaging (2). 

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    Authors: Morée, Anne L.; Caccavo, Jilda A.; Nissen, Cara;

    Habitat files of 28 Antarctic Toothfish (Dissostichus mawsoni) prey species and the Antarctic Toothfish itself, regridded to the FESOM-REcoM model grid, in NetCDF format. For use in article '21st-century environmental change decreases habitat overlap of Antarctic toothfish (Dissostichus mawsoni) and its prey'. This dataset is a collection of the following: 1) 2-dimensional distribution data for 3 squid species, derived from Raymond et al. (2015) 2) 2-dimensional distribution data for 25 prey species and the Antarctic Toothfish, derived from AquaMaps distribution data 3) the model grid file. A species is present in a certain gridcell when its value is 1, elsewhere the species is considered absent. 1) Original files for the 3 squid species galiteuthis glacialis, kondakovia longimana and mesonychoteuthis hamiltoni are taken from previously published data of Raymond et al. (2015) and regridded to the FESOM-REcoM model grid. These squid species are considered to have their habitat anywhere where habitat suitability in the original Raymond et al. (2015) dataset exceeds the habitat suitability thresholds of 0.228 for Galiteuthis glacialis, 0.281 for Kondakovia longimana and 0.121 for Mesonychoteuthis hamiltoni (threshold values as in Xavier et al. (2016), personal communication with Ben Raymond 16.01.2023 to get exact values). These data have an original resolution of 0.1x0.1 degrees (regular longitude-latitude grid). 2) The 25 files taken from AquaMaps start with Default_* or Reviewed_* and are the native predicted range data as provided by Kaschner et al. (2019). They were shared by Kathleen Kesner-Reyes from AquaMaps in March and April 2023 after being reviewed by her for correctness and actuality. The files that start with Reviewed_* have had adjustments made to the original Default_* based on this review, which is described in more detail on the AquaMaps website. These data have an original resolution of 0.5x0.5 degrees (regular longitude-latitude grid). 3) The model grid file 'Mesh_ancillary_information_v20220919.nc' contains the longitude and latitude data needed for regridding to the FESOM-REcoM model grid. Regridding was done using CDO version 1.9.6 (http://mpimet.mpg.de/cdo; developed by U. Schulzweida) and CDO function 'remaplaf', which performs largest area fraction remapping. References Xavier, J.C., Raymond, B., Jones, D.C. et al. Biogeography of Cephalopods in the Southern Ocean Using Habitat Suitability Prediction Models. Ecosystems 19, 220–247 (2016). https://doi.org/10.1007/s10021-015-9926-1 Raymond, B., Xavier, J., Griffiths, H., Jones, D. (2015) Habitat suitability predictions for 15 species of cephalopods in the Southern Ocean, Ver. 1, Australian Antarctic Data Centre - doi:10.4225/15/563AC33450A28, Accessed: 2023-01-16 Kaschner, K., Kesner-Reyes, K., Garilao, C., Segschneider, J., Rius-Barile, J. Rees, T., & Froese, R. (2019, October). AquaMaps: Predicted range maps for aquatic species. Retrieved from https://www.aquamaps.org.

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    ZENODO
    Dataset . 2024
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    ZENODO
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      ZENODO
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    Authors: Van Leeuwen, Stefan; Leenders, Liz; Hoogenboom, Ron; Krätschmer, Kerstin; +2 Authors

    On behalf of the Ministry of Agriculture, Nature and Food Quality (LNV), Wageningen Food Safety Research (WFSR) analyses samples of agricultural products of animal origin for dioxins, PCBs, brominated flame retardants (BFRs) and poly- and perfluorinated alkyl substances (PFASs). This includes meat, milk, eggs and fish.The samples are taken at the primary production or processing stage (e.g. in slaughterhouses or raw milk collection services). For dioxin-like compounds, 350 samples are screened first with the DR CALUX® method. Samples giving a signal indicating a level above the lowest action level are regarded as suspected. These samples are further examined using GC/HRMS as confirmatory method. Concerning fish, shellfish and crustaceans, approx. 25 samples are collected at sea by research vessels, at the fish auction, or from whole-sale traders (farmed fish).

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    4TU.ResearchData
    Dataset . 2024
    License: CC BY NC SA
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    4TU.ResearchData
    Dataset . 2024
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    4TU.ResearchData
    Dataset . 2024
    License: CC BY NC SA
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    4TU.ResearchData | science.engineering.design
    Dataset . 2024
    License: CC BY NC SA
    Data sources: Datacite
    4TU.ResearchData | science.engineering.design
    Dataset . 2024
    License: CC BY NC SA
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      4TU.ResearchData
      Dataset . 2024
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      4TU.ResearchData
      Dataset . 2024
      License: CC BY NC SA
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      4TU.ResearchData
      Dataset . 2024
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      4TU.ResearchData | science.engineering.design
      Dataset . 2024
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      4TU.ResearchData | science.engineering.design
      Dataset . 2024
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    Authors: García, María Luján; Birlo, Stella; Zahajska, Petra; Grosjean, Martin; +1 Authors

    XRF measurements in 0.2 to 1 mm increments with an ITRAX XRF core scanner (Cox Analytics) and Cr tube (Croudance et al. 2015, doi:10.1007/978-94-017-9849-5 ). The sediment core HZM19 was collected in 2019, from Holzmaar, West-Eifel Volcanic Field in Germany using a UWITEC Piston Corer. The sediment core was collected to reconstruct environmental and climate changes of Holzmaar for the last 16,000 years cal BP. Particularly in this data set we cover between 2450-2950 cal BP. Funding information:* Georg Forster Research Fellowship for postdoctoral researchers (for the Alexander von Humboldt funding)* Central Research Development Fund (CRDF) of the University of Bremen, 04 Independent Project for Postdocs - Funding objective B

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    PANGAEA
    Dataset . 2024
    Data sources: B2FIND
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      PANGAEA
      Dataset . 2024
      Data sources: B2FIND
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    Authors: Dearing Crampton-Flood, Emily;

    The mid-Piacenzian Warm Period (mPWP, 3264-3025 ka) represents the most recent interval in Earth's history where atmospheric CO2 levels were similar to today. Here, we present a multi-proxy record of Pliocene climate change in the coastal Southern North Sea Basin (SNSB) based on the sedimentary record from borehole Hank, the Netherlands (drilled by TNO, Dutch Geological Survey). We present the stable oxygen and carbon isotope (δ18O and δ13C) measurements of the endobenthic foraminifera species Cassidulina laevigata, and present a new age model for the late Pliocene of the Southern North Sea. This results in a tuned age framework for the SNSB for the Late Pliocene (~3190-2770 ka). Our multi-proxy climate reconstruction for this interval includes biomarker-based SST reconstructions (TEX86, UK37, LDI).

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    PANGAEA
    Dataset . 2024
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      PANGAEA
      Dataset . 2024
      Data sources: B2FIND
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    Authors: García, María Luján; Birlo, Stella; Zahajska, Petra; Grosjean, Martin; +1 Authors

    Diatom analyses were done following (Battarbee, 1986; Battarbee et al., 2002; doi:10.2478/s11756-019-00407-8). Including an updated list of names. The sediment core HZM19 was collected in 2019, from Holzmaar, West-Eifel Volcanic Field in Germany using a UWITEC Piston Corer. The sediment core was collected to reconstruct environmental and climate changes of Holzmaar for the last 16,000 years cal BP. Particularly in this data set we cover between 2450-2950 cal BP. An aliquot of each freeze-dried sample was processed with standard procedures (Battarbee, 1986; Battarbee et al., 2002). Only species with >=5% relative abundance in at least two samples were used for further analyses. Species acronyms are listed seperately. Funding information:* Georg Forster Research Fellowship for postdoctoral researchers (for the Alexander von Humboldt funding)* Central Research Development Fund (CRDF) of the University of Bremen, 04 Independent Project for Postdocs– Funding objective B

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    PANGAEA
    Dataset . 2024
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      PANGAEA
      Dataset . 2024
      Data sources: B2FIND
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    Authors: Fritz, Michael; Gimsa, Justus; Petzold, Pia; Klein, Konstantin; +7 Authors

    This dataset contains CTD measurements taken in 2015, 2016, 2017, 2018, 2019, 2022, and 2023 during expeditions to Herschel Island - Qikiqtaruk, Yukon, Canada. For the data recording a CTD CastAway was used. The sampling was conducted from a boat from which the CTD was lowered to the sea floor at the specific sampling sites. The sampling information encompasses the GPS position, water depth, pressure, temperature, electrical conductivity, specific conductance, and salinity.

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    PANGAEA
    Dataset . 2024
    Data sources: B2FIND
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      Dataset . 2024
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