Find research datasets worth reusing

High-frequency, hourly, and daily measurements from the East Lake Bonney "Blue Box" (ELBBB), McMurdo Dry Valleys, Antarctica (1994-2024, ongoing)

As part of the McMurdo Dry Valleys Long Term Ecological Research program, continuous measurements have been collected from a network of automated lake monitoring platforms in the McMurdo Dry Valleys of Antarctica. These lake-based stations, commonly referred to as “blue boxes” due to their historically blue instrument enclosures, provide high-frequency observations of key limnological variables essential for understanding physical drivers of aquatic ecosystem dynamics in the perennially ice-covered, meromictic lakes of this polar desert environment. This data package includes measurements from the East Lake Bonney “blue box” lake monitoring platform (ELBBB), established during the 1994-1995 austral summer in East Lake Bonney, Taylor Valley. Parameters include air and water temperature, surface and underwater photosynthetically active radiation (PAR), continuous stage (lake level), ice surface ablation, and, beginning in the 2022-2023 austral summer, dissolved oxygen (DO), reported as percent saturation due to the unavailability of continuous salinity measurements required for computing concentration. Data are provided at high frequency (typically 15-minute intervals), along with hourly and daily summaries. Users should note that summary statistics may be affected by periods of missing data. As there is no universally accepted standard for handling gaps in time-series data, users are encouraged to use the high-frequency data and establish their own criteria for acceptable data completeness to minimize potential bias.

High-frequency, hourly, and daily measurements from the Lake Fryxell "Blue Box" (LFBB), McMurdo Dry Valleys, Antarctica (1997-2024, ongoing)

As part of the McMurdo Dry Valleys Long Term Ecological Research program, continuous measurements have been collected from a network of automated lake monitoring platforms in the McMurdo Dry Valleys of Antarctica. These lake-based stations, commonly referred to as “blue boxes” due to their historically blue instrument enclosures, provide high-frequency observations of key limnological variables essential for understanding physical drivers of aquatic ecosystem dynamics in the perennially ice-covered, meromictic lakes of this polar desert environment. This data package includes measurements from the Lake Fryxell “blue box” lake monitoring platform (LFBB), established during the 1996-1997 austral summer in Lake Fryxell, Taylor Valley. Parameters include air and water temperature, surface and underwater photosynthetically active radiation (PAR), continuous stage (lake level), ice surface ablation, and, beginning in the 2022-2023 austral summer, dissolved oxygen (DO), reported as percent saturation due to the unavailability of continuous salinity measurements required for computing concentration. Data are provided at high frequency (typically 15-minute intervals), along with hourly and daily summaries. Users should note that summary statistics may be affected by periods of missing data. As there is no universally accepted standard for handling gaps in time-series data, users are encouraged to use the high-frequency data and establish their own criteria for acceptable data completeness to minimize potential bias.

High-frequency, hourly, and daily measurements from the Lake Hoare "Blue Box" (LHBB), McMurdo Dry Valleys, Antarctica (1997-2024, ongoing)

As part of the McMurdo Dry Valleys Long Term Ecological Research program, continuous measurements have been collected from a network of automated lake monitoring platforms in the McMurdo Dry Valleys of Antarctica. These lake-based stations, commonly referred to as “blue boxes” due to their historically blue instrument enclosures, provide high-frequency observations of key limnological variables essential for understanding physical drivers of aquatic ecosystem dynamics in the perennially ice-covered, meromictic lakes of this polar desert environment. This data package includes measurements from the Lake Hoare “blue box” lake monitoring platform (ELBBB), established during the 1996-1997 austral summer in Lake Hoare, Taylor Valley. Parameters include air and water temperature, surface and underwater photosynthetically active radiation (PAR), continuous stage (lake level), ice surface ablation, and, beginning in the 2022-2023 austral summer, dissolved oxygen (DO), reported as percent saturation due to the unavailability of continuous salinity measurements required for computing concentration. Data are provided at high frequency (typically 15-minute intervals), along with hourly and daily summaries. Users should note that summary statistics may be affected by periods of missing data. As there is no universally accepted standard for handling gaps in time-series data, users are encouraged to use the high-frequency data and establish their own criteria for acceptable data completeness to minimize potential bias.

High-frequency, hourly, and daily measurements from the Lake Miers "Blue Box" (LMBB), McMurdo Dry Valleys, Antarctica (2011-2019)

As part of the McMurdo Dry Valleys Long Term Ecological Research program, continuous measurements have been collected from a network of automated lake monitoring platforms in the McMurdo Dry Valleys of Antarctica. These lake-based stations, commonly referred to as “blue boxes” due to their historically blue instrument enclosures, provide high-frequency observations of key limnological variables essential for understanding physical drivers of aquatic ecosystem dynamics in the perennially ice-covered, meromictic lakes of this polar desert environment. This data package includes measurements from the Lake Miers “blue box” lake monitoring platform (ELBBB), established during the 2011-2012 austral summer in Lake Miers, Miers Valley. Parameters include water temperature, surface and underwater photosynthetically active radiation (PAR), continuous stage (lake level), and ice surface ablation. Data are provided at high frequency (typically 15-minute intervals), along with hourly and daily summaries. Users should note that summary statistics may be affected by periods of missing data. As there is no universally accepted standard for handling gaps in time-series data, users are encouraged to use the high-frequency data and establish their own criteria for acceptable data completeness to minimize potential bias. This station was decommissioned during the 2019-2020 austral summer.

High-frequency, hourly, and daily measurements from the West Lake Bonney "Blue Box" (WLBBB), McMurdo Dry Valleys, Antarctica (1996-2024, ongoing)

As part of the McMurdo Dry Valleys Long Term Ecological Research program, continuous measurements have been collected from a network of automated lake monitoring platforms in the McMurdo Dry Valleys of Antarctica. These lake-based stations, commonly referred to as “blue boxes” due to their historically blue instrument enclosures, provide high-frequency observations of key limnological variables essential for understanding physical drivers of aquatic ecosystem dynamics in the perennially ice-covered, meromictic lakes of this polar desert environment. This data package includes measurements from the West Lake Bonney “blue box” lake monitoring platform (WLBBB), established during the 1996-1997 austral summer in West Lake Bonney, Taylor Valley. Parameters include air and water temperature, surface and underwater photosynthetically active radiation (PAR), continuous stage (lake level), ice surface ablation, and, beginning in the 2022-2023 austral summer, dissolved oxygen (DO), reported as percent saturation due to the unavailability of continuous salinity measurements required for computing concentration. Data are provided at high frequency (typically 15-minute intervals), along with hourly and daily summaries. Users should note that summary statistics may be affected by periods of missing data. As there is no universally accepted standard for handling gaps in time-series data, users are encouraged to use the high-frequency data and establish their own criteria for acceptable data completeness to minimize potential bias.

openCC (other)Oct 2023View details →

Chickadee breeding and parasite survey from Boulder, Sugarloaf, and MRS nest boxes, 2019 - 2021.

Between the years 2019 and 2021 chickadees were sampled at the NWT LTER as part of a broader study encompassing multiple projects (The Boulder Chickadee Study). Here we provide data on the presence of infections with haemosporidian parasites for Black-capped Chickadees (Poecile atricapillus) and Mountain Chickadees (P. gambeli). Haemosporidian parasites are a diverse group of apicomplexans that infect vertebrate hosts during a portion of their life cycle (Valkiunas, G. 2004). We screened chickadees for infections with three haemosporidian genera: Leucocytozoon, Plasmodium, and Haemoproteus using a nested PCR protocol (Hellgren et al. 2004). Both nestlings and adults were screened for parasites in 2019 and 2020 but we only screened adults in 2021. Chickadees sampled at NWT LTER did not have detectable infections with Haemoproteus or Plasmodium, however, we found multiple infections with Leucocytozoon. In conjunction with findings at other field sites, infections with Leucocytozoon parasites appear more common for adult chickadees sampled at higher elevation, while Plasmodium parasites were almost exclusively found in the city of Boulder (Theodosopoulos et al. 2023).

opencc-by-4.0Jan 2020View details →

Bounding box coordinates of von Karman vortex street

Those files contain bounding box coordinates of von Karman vortex street annotated by VoTT. The von Karman vortex street is annotated as one object in vortex_street.tar.gz, while each vortex in the von Karman vortex street is annotated as one object in vortices.tar.gz. The original video file is from https://doi.org/10.1063/1.4921683.1 to 1.4921683.9. See also the reference.

opencc-by-4.0Nov 2020View details →

Human T-box transcription factor T (Brachyury); A Target Enabling Package

Chordoma is a rare cancer occurring along the spinal cord (OMIM: <a href="https://www.omim.org/entry/215400">215400</a>). Chordoma is derived from an embryonic tissue, the notochord, and over-expresses the embryonic transcription factor T-box transcription factor T, the homologue of mouse Brachyury. Chordomas are “genomicaly silent” cancers that do not carry an extensive mutation load. Recent studies indicate that expression of TBXT is essential for persistence and growth of chordoma cells.  As TBXT is not expressed in any post-embryonic tissues, it could be an excellent target for treatment of chordoma. The long-term aim of this project is to test whether TBXT can be targeted with small molecules with sufficient affinity and specificity to be therapeutically useful.  In this TEP we have determined crystal structures of the DNA-binding domain (DBD) of TBXT with and without cognate DNA oligonucleotides. The DNA-free protein crystals were used in a high-throughput fragment screen to identify 29 fragments bound in 6 clusters. The crystal structures of the bound fragments provide starting points for development of stronger binders which could be used to disrupt TBXT activity or to induce the degradation of the protein through a Proteolysis-targeting chimeric molecule (PROTAC) approach.

opencc-by-4.0May 2023View details →

CPACS for Rectangular Box Wing

The Datasets represents a common use case in literature used for composite optimisation. A rectangular profile is defined, greater than the desired structure. Spars, ribs and shell cells define the investigated struture and only for them cells are defined.The following references are build up as CPACS Dataset:<ol><li>Ref3.xml: Marco Picchi Scardaoni and Marco Montemurro. A general global-local modelling framework for the deterministic optimisation of composite structures. Structural and Multidisciplinary Optimization, 62(4):1927–1949, October 2020.</li><li>Ref2.xml: Dianzi Liu, Vassili V. Toroporov, Osvaldo M. Querin, and David C. Barton. Bilevel Optimization of Blended Composite Wing Panels. Journal of Aircraft, 48(1):107–118, January 2011. Publisher: American Institute of Aeronautics and Astronautics.</li><li>Ref1.xml: B. Liu, R.T. Haftka, and M.A. Akg¨un. Two-level composite wing structural optimization using response surfaces.  Structural and Multidisciplinary Optimization, 20(2):87–96, October 2000.</li></ol>Additionally a version with stiffened covers is created based on number 3.

opencc-by-4.0Jul 2021View details →

Unsupervised New Physics detection at 40 MHz: Black Box Dataset

Unsupervised New Physics detection at 40 MHz data challenge Signal Benchmark Dataset consisting of the signal+background Black Box datasets, containing collision events (simulation of LHC 13 TeV proton-proton collisions) pre-filtered by a requirement of a muon or electron with 23 GeV transverse momentum. Data format description available on the data challenge web page: https://mpp-hep.github.io/ADC2021/

opencc-by-4.0Jul 2024View details →

The Delayed Box: Biphenyl Bisimide Cyclophane, a Supramolecular Nano‒environment for Efficient Generation of Delayed Fluorescence

Additional data to report <a title="DOI URL" href="https://doi.org/10.1021/jacs.4c07730">https://doi.org/10.1021/jacs.4c07730</a>: Activating delayed fluorescence emission in a dilute solution via a non-covalent approach is a formidable challenge. In this report, we propose a strategy for efficient delayed fluorescence generation in dilute solution using a non-covalent approach via supramolecularly engineered cyclophane-based nanoenvironments that provide sufficient binding strength to π-conjugated guests and that can stabilize triplet excitons by reducing vibrational dissipation and lowering the singlet–triplet energy gap for efficient delayed fluorescence emission. Toward this goal, a novel biphenyl bisimide-derived cyclophane is introduced as an electron-deficient and efficient triplet-generating host. Upon encapsulation of various carbazole-derived guests inside the nanocavity of this cyclophane, emissive charge transfer (CT) states close to the triplet energy level of the biphenyl bisimide are generated. The experimental results of host–guest studies manifest high association constants up to 104 M–1 as the prerequisite for inclusion complex formation, the generation of emissive CT states, and triplet-state stabilization in a diluted solution state. By means of different carbazole guest molecules, we could realize tunable delayed fluorescence emission in this carbazole-encapsulated biphenyl bisimide cyclophane in methylcyclohexane/carbon tetrachloride solutions with a quantum yield (QY) of up to 15.6%. Crystal structure analyses and solid-state photophysical studies validate the conclusions from our solution studies and provide insights into the delayed fluorescence emission mechanism.

opencc-by-nc-sa-4.0Sep 2022View details →

Cholec80-Boxes: Bounding-Box Labels for Surgical Tools in Five Cholecystectomy Videos

The dataset is descriped in a pending publication titled "Cholec80-Boxes: Bounding-box Labeling Data for Surgical Tools in Cholecystectomy Images". The dataset was used in the following studies titled: <ul> <li>"Surgical tool classification & localisation using attention and multi-feature fusion deep learning approach".</li> <li>"Laparoscopic video analysis using temporal, attention, and multi-feature fusion based-approaches".</li> <li>"Analysing attention convolutional neural network for surgical tool localisation: A feasibility study".</li> </ul> The dataset consists of cholecystectomy images and bounding-box labels for surgical tools. These images were extracted from five videos of the Cholec80 dataset (Twinanda et al., 2016) at a rate of 1 Hz. The images are stored in '.png' format with a resolution of 854*480 pixels. Each video’s images are organized in a separate folder. The labeling data are stored in a CSV file, which contains the region of interest (ROI) labels for each surgical tool visible in the extracted images. Additionally, the CSV file provides information about each labeled image. Table 1 presents a content description of the 'ROI_Labels.csv' file. Table 1: Description of 'ROI_Labels.csv' file. <table> <tbody> <tr> <td>Column Name</td> <td>Description</td> <td>Type</td> </tr> <tr> <td>Surgery_num</td> <td>Procedure number in the Cholec80 dataset from which the image was extracted.</td> <td>Integer</td> </tr> <tr> <td>Dir</td> <td>Directory of the image folder.</td> <td>String</td> </tr> <tr> <td>FrameName</td> <td>Image name in the format 'Video_SS_fffff.png', where SS is the Surgery_num and fffff is the frame number in the video.</td> <td>String</td> </tr> <tr> <td>NumBBox_inFrame</td> <td>The bounding-box number in the image.</td> <td>Integer</td> </tr> <tr> <td>ToolName</td> <td>Name of the surgical tool.</td> <td>String</td> </tr> <tr> <td>BBox_X</td> <td>X-coordinate of the top-left corner.</td> <td>Integer</td> </tr> <tr> <td>BBox_Y</td> <td>Y-coordinate of the top-left corner.</td> <td>Integer</td> </tr> <tr> <td>BBox_Width</td> <td>Bounding box width.</td> <td>Integer</td> </tr> <tr> <td>BBox_Height</td> <td>Bounding box height.</td> <td>Integer</td> </tr> </tbody> </table>   Citing This Dataset: When using this dataset, please cite the following publications: <ul> <li>Jalal, N. A., Alshirbaji, T. A., Docherty, P. D., Arabian, H., Laufer, B., Krueger-Ziolek, S., Neumuth, T. & Moeller, K. (2023). Laparoscopic video analysis using temporal, attention, and multi-feature fusion based-approaches. Sensors, 23(4), 1958. </li> <li>Jalal, N. A., Alshirbaji, T. A., Docherty, P. D., Arabian, H., Neumuth, T., & Möller, K. (2023). Surgical tool classification & localisation using attention and multi-feature fusion deep learning approach. IFAC-PapersOnLine, 56(2), 5626-5631.</li> <li> Abdulbaki Alshirbaji, T., Arabian, H., Jalal, N. A., Battistel, A., Docherty, P. D., Neumuth, T., & Moeller, K.  Cholec80-Boxes: Bounding-box labeling data for surgical tools in cholecystectomy images. (to be submitted).  </li> <li>Twinanda, A. P., Shehata, S., Mutter, D., Marescaux, J., De Mathelin, M., & Padoy, N. (2016). Endonet: a deep architecture for recognition tasks on laparoscopic videos. IEEE transactions on medical imaging, 36(1), 86-97.</li> </ul>

opencc-by-4.0Aug 2024View details →

Brightfield images of cells and spheroids in wells annotated with bounding boxes

The images in this dataset show cells in different developmental stages upon forming spheroids. They can go through several developmental sages: Starting from cells, they turninto compacted objects and then into spheroids. Ultimately, they can die and disintegrate. The objects are annotated with bounding boxes that carry these respective labels. The dataset in its current form can be upload to an OMERO server using the omero-cli-transfer package - simply download the zip file, log into your omero server and use the `omero transfer unpack` command as shown on the <a href="https://github.com/ome/omero-cli-transfer">omero-cli-transfer documentation</a>. The dataset can be used to train object detection models such as a <a href="https://docs.ultralytics.com/models/yolov8/">yolo classifier </a>- the linked repository provides a tutorial on how to do so.

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Soil respiration in treatment boxes on canopy gradient sites at the Coweeta Hydrologic Laboratory from 1997 to 1998

We tested whether inputs from canopy herbivores would affect soil processes such as respiration, nutrient cycling, and decomposition along an elevation gradient. The five treatments we used were frass additions, throughfall additions, removal of all litter that fell during the study, removal of greenfall that fell during the study, and controls. Soil respiration was significantly reduced on low and mid elevation sites in litter exclusion, greenfall exclusion and throughfall addition treatments (from 0.846 g CO2/m2/h for controls to 0.618, 0.667, and 0.708 g CO2/m2/h, respectively, for the three treatments).

openCustomJan 2020View details →

Fig. 30. Rhopalondendrina tigris igen. et isp. nov. A–B in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)

Fig. 30. Rhopalondendrina tigris igen. et isp. nov. A–B. Planar and lateral views of two specimens illustrating the diagnostic arcuate entrance tunnel and paw-shaped main chamber; SEM of epoxy casts from a bivalve shell sampled off Mauritania. C–D. SEM of specimens in an initial (C, paratype) and a mature (D, holotype) ontogenetic stage, cast in epoxy from experimental bivalve substrates that were deployed at the Great Barrier Reef, Australia. E–F. Lateral and planar views of another specimen (paratype) from the type locality.

Fig. 33. A in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)

Fig. 33. A. Evolutionary trends in dendrinid microborings, considering the known range (based on certain end members only) of the various ichnospecies (light grey) and the number of ichnospecies making their first appearance (dark grey). Numbers are per period, except for the Paleocene to Pleistocene (global series). Relevant evolutionary radiations and extinction events are indicated. B. Same graph for all microbioerosion ichnospecies, but based on actual records only (data from Wisshak et al. 2008; numbers per period). C. Ichnodiversity curve for all bioerosion ichnogenera based on range data (data from Buatois & Mángano 2016; numbers per global series).

Fig. 32 in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)

Fig. 32. Composite and compound trace fossils in Upper Cretaceous belemnite rostra from the "Senonian" of Lüneburg, Germany (A), Upper Campanian of Kronsmoor, Germany (B), Lower Campanian of Misburg (C–D), and Lower Maastrichtian of Rügen, Germany (E–G). A. Nice display of Dendrina dendrina (Morris, 1851), D. belemniticola Mägdefrau, 1937, D. lacerata Hofmann, 1996, Calcideletrix anomala (Mägdefrau, 1937) and C. flexuosa Mägdefrau, 1937, partly in lateral contact or overlapping and partly interconnected by tubular tunnels. B. Several D. dendrina, interconnected by tubular tunnels. C–D. Overview and close-up of a C. anomala connected to several paratypes of D. lacerata. E–G. Large C. flexuosa connected to several D. lacerata at its periphery (close-up in F), as well as to a widened tubular tunnel reminiscent of Filuroda reptans (Clarke, 1908) (close-up in G).

Fig. 29. Rhopalondendrina contra igen. et isp. nov. A–E in Taming an ichnotaxonomical Pandora's box: revision of dendritic and rosetted microborings (ichnofamily: Dendrinidae)

Fig. 29. Rhopalondendrina contra igen. et isp. nov. A–E. Overviews and close-ups of the holotype, illustrating the morphology of the entrance tunnel (arrows in A and D; close-ups in C and E) and the anastomosing plexus, covered with short and spiny protrusions (close-up in B). SEM of epoxy cast of a bivalve shell sampled in Middle Miocene strata at Balcome Bay, Victoria, Australia (same for F–H). F. Juvenile specimen (paratype) with clearly visible entrance tunnel (arrow indicating initial point of entry). G–H. Larger specimen (paratype) with the plexus developed on the opposite surface of the bivalve shell from the initial point of entry (arrow in G).