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Figure 2 in "One is the loneliest number"; are we witnessing the death throes of the single-author research paper in the field of biological invasions?
Figure 2. Changes in % of research papers published over time by single-authors (white circles and grey line) and four or more authors (black circles and black line) in issues of (a) BioInvasions Records, (b) Aquatic Invasions and (c) Management of Biological Invasions.
Figure 1 in "One is the loneliest number"; are we witnessing the death throes of the single-author research paper in the field of biological invasions?
Figure 1. Mean (± SE) % of research papers published in each issue of BioInvasions Records, Aquatic Invasions and Management of Biological Invasions categorised by number of authors.
Death anxiety scale (DAS): internal structure and factorial invariance in Peruvian adults
<p><span>Este material forma parte del artículo: "Death<span> </span>anxiety<span> </span>scale<span> </span>(DAS): internal Structure <span>and</span><span> </span>factorial<span> </span><span>invariance</span><span> </span>in Peruvian<span> </span>adults", afiliación del primer autor: Universidad César Vallejo.</span></p> <p> </p>
Рис. 2. Пересохший участок протоки, гΔе быΛи найΔены погибшие рыбы Fig. 2. The dried-up section of the subchannel where the dead fish were found in The death of fish in the Bureya River system during autumn migration
Рис. 2. Пересохший участок протоки, гΔе быΛи найΔены погибшие рыбы Fig. 2. The dried-up section of the subchannel where the dead fish were found
Рис. 1. Часть погибших рыб, найΔенных на пересохшем участке протоки Fig. 1. Part of the dead fish found in the dried-up section of the subchannel in The death of fish in the Bureya River system during autumn migration
Рис. 1. Часть погибших рыб, найΔенных на пересохшем участке протоки Fig. 1. Part of the dead fish found in the dried-up section of the subchannel
Рис. 5. Общая схема Δинамики эпизоотии в приамурской попуΛяции коΛьчатого шеΛкопряΔа. ВертикаΛьно: коΛичество погибших гусениц (% от чисΛа собранных за весь периоΔ иссΛеΔований в 2019 г. гусениц). ГоризонтаΛьно: Δата сбора гусениц на территории УПН. — гибеΛь от вируса яΔерного поΛиэΔроза; — гибеΛь от бактериоза Fig. 5. General scheme of the Lackey moth epizootic dynamics for the Cisamurian population. Vertical: number of the deaths, (percentage from the total number of caterpillars collected in 2019 (578 caterpillars)); horizontal: dates of laboratory controls. — death from the NPV; — death from the bacteriosis in Lackey Moth (Malacosoma Neustria L., Lasiocampidae, Lepidoptera) Population During The Eruptive Phase
Рис. 5. Общая схема Δинамики эпизоотии в приамурской попуΛяции коΛьчатого шеΛкопряΔа. ВертикаΛьно: коΛичество погибших гусениц (% от чисΛа собранных за весь периоΔ иссΛеΔований в 2019 г. гусениц). ГоризонтаΛьно: Δата сбора гусениц на территории УПН. — гибеΛь от вируса яΔерного поΛиэΔроза; — гибеΛь от бактериоза Fig. 5. General scheme of the Lackey moth epizootic dynamics for the Cisamurian population. Vertical: number of the deaths, (percentage from the total number of caterpillars collected in 2019 (578 caterpillars)); horizontal: dates of laboratory controls. — death from the NPV; — death from the bacteriosis
Рис. 3. Снижение чисΛенности гусениц при возΑействии разΛичных географических штаммов ВЯП. СтоΛбцы: коΛичество погибших во время эксперимента гусениц поΑ опреΑеΛенной инфекционной нагрузкой. ПоказатеΛи (в процентах) привеΑены в Λевой части табΛицы. СтреΛки: минимаΛьное и максимаΛьное коΛичество погибших во время очереΑного учета гусениц и крестообразные маркеры: среΑнее коΛичество погибших во время очереΑного учета гусениц. ПоказатеΛи (в абсоΛютных значениях) в правой части табΛицы. По горизонтаΛи: номер титра, от боΛьшего к меньшему Fig. 3. Decrease in the number of caterpillars under the influence of various geographical strains of NPV. Columns: number of caterpillars killed during the experiment under a certain infectious load. Indicators (in percent) are shown on the left side of the table. Arrows: the minimum and maximum number of deaths during the next track count and cross markers: the average number of deaths during the next track count. Indicators (in absolute values) on the right side of the table. Horizontal: titre, from highest to lowest in Sensitivity of caterpillars of the gypsy moth (Lymantria dispar, Erebidae) from the South of Khabarovsk Territory to various strains of nuclear polyhedrosis virus
Рис. 3. Снижение чисΛенности гусениц при возΑействии разΛичных географических штаммов ВЯП. СтоΛбцы: коΛичество погибших во время эксперимента гусениц поΑ опреΑеΛенной инфекционной нагрузкой. ПоказатеΛи (в процентах) привеΑены в Λевой части табΛицы. СтреΛки: минимаΛьное и максимаΛьное коΛичество погибших во время очереΑного учета гусениц и крестообразные маркеры: среΑнее коΛичество погибших во время очереΑного учета гусениц. ПоказатеΛи (в абсоΛютных значениях) в правой части табΛицы. По горизонтаΛи: номер титра, от боΛьшего к меньшему Fig. 3. Decrease in the number of caterpillars under the influence of various geographical strains of NPV. Columns: number of caterpillars killed during the experiment under a certain infectious load. Indicators (in percent) are shown on the left side of the table. Arrows: the minimum and maximum number of deaths during the next track count and cross markers: the average number of deaths during the next track count. Indicators (in absolute values) on the right side of the table. Horizontal: titre, from highest to lowest
Data for: "A high-throughput microscopy method for single-cell analysis of event-time correlations in nanoparticle-induced cell death"
<p>Data related to the publication Murschhauser <em>et al.</em>: <a href="https://doi.org/10.1038/s42003-019-0282-0">A high-throughput microscopy method for single-cell analysis of event-time correlations in nanoparticle-induced cell death</a>. It contains fluorescence time traces of single cells marked with cell-event markers and observed by time-lapse microscopy. The cells were treated with nanoparticles at different doses (NP25 and NP100), with staurosporine (sts) or were left untreated for control (ctrl). See the above-mentioned publication for more details.</p> <p>The format of the data is described below.</p> <p>The file <code>Data_A549.zip</code> contains data measured with A549 cells, and the file <code>Data_Huh7.zip</code> contains data measured with Huh7 cells. Both files have the same structure. Each file contains the directories <code>Raw</code> and <code>Fitted</code> as well as a checksum file. The <code>Raw</code> directory contains single-cell fluorescence time courses as obtained by time-lapse microscopy. The <code>Fitted</code> directory contains the results of fitting model functions as well as properties of identified events, such as event times. The checksum file contains SHA256 checksums of all files within these directories and can be used to check file integrity.</p> <p>Both directories contain measurement directories. Each measurement directory contains the data corresponding to one experiment. The name of the measurement directory is the measurement identifier. Each measurement directory contains condition directories. Each condition directory contains data corresponding to one condition measured in the measurement and is named after the condition. Each condition directory contains marker directories. They are named after the fluorescence markers measured and contain files with single-cell data corresponding to the respective markers.</p> <p>The names of those files consist of multiple parts separated by underscores. The first two parts identify a position of the microscope. Since pairs of markers were measured, each position is present in two marker directories. The third part is the measurement identifier. The other parts will be described below.</p> <p>The <code>Raw</code> directory contains only CSV files with the raw fluorescence time courses. The filenames contain no other parts and have the suffix “.txt”. The first row of each CSV file is the time (in units of 10 minutes), and the other rows are the fluorescence time courses of the cells observed at the corresponding position (in arbitrary units). Each file in the <code>Raw</code> directory corresponds to a group of files in the <code>Fitted</code> directory.</p> <p>The <code>Fitted</code> directory contains three types of CSV files. Their names have “ALL” as fourth part, a session identifier as sixth part and the suffix “.csv”. The fifth part indicates the type of file and is one of the following:</p> <ul> <li>“PARAMS” indicates the estimated values for the model parameters. Each row stands for one cell and each column for a parameter of the model function fitted to the data. The model functions are published with the <a href="https://doi.org/10.5281/zenodo.1418465">fitting software</a>.</li> <li>“SIMULATED” indicates the fitted traces. The traces are calculated using the model functions and the estimated parameters. The format is the same as for the raw traces, but the time is in units of hours and has a higher resolution.</li> <li>“STATE” indicates additional information extracted from the fitted traces. Each row stands for a cell and each column for a property. The first column is the number of the cell. The second column is the event time found (in hours); non-finite values indicate that no event time was found. The third and fourth columns contain the absolute and relative amplitude of the trace, respectively. The fifth column is the logarithmic likelihood of the best fit. The sixth column indicates an algorithm used for postprocessing, and the seventh column indicates the trace slope at the event. See the fitting software for details.</li> </ul> <p> </p>
Quantitative phase microscopy timelapse dataset of PNT1A, DU-145 and LNCaP cells with annotated caspase 3,7-dependent and independent cell death
<p>Time-lapse dataset of prostatic cell lines (DU-145, PNT1A, LNCaP) exposed to cell death-inducing compounds (staurosporine, doxorubicin) and black phosphorus. The time-lapse dataset is annotated as follows: (1) cell masks and cell numbers, (2) by cell death type and timepoint of death in the attached xlsx file. This dataset is supplementary to the article:</p> <p>Vicar, T., Raudenska, M., Gumulec, J. <em>et al.</em> The Quantitative-Phase Dynamics of Apoptosis and Lytic Cell Death. <em>Sci Rep</em> <strong>10, </strong>1566 (2020). <a href="https://doi.org/10.1038/s41598-020-58474-w">https://doi.org/10.1038/s41598-020-58474-w</a></p> <p>Correlative fluorescence microscopy is in a separate dataset <a href="https://doi.org/10.5281/zenodo.4531900">10.5281/zenodo.4531900</a></p> <p>Code is available at <a href="https://github.com/tomasvicar/CellDeathDetect">https://github.com/tomasvicar/CellDeathDetect</a></p> <p><strong>Methods</strong></p> <p><em>Cell culture and cultured cell conditions</em><br> LNCaP cell line was established from a lymph node metastase of the hormone-refractory patient and contains a mutation in the AR gene. This mutation creates a promiscuous AR that can bind to different types of steroids. LNCaP cells are AR-positive, PSA-positive, PTEN-negative and harbor wild-type p53 {Skjoth, 2006 #150; Mitchell, 2000 #149}. PNT1A is immortalized non-tumorigenic epithelial cell line. PNT1A cells harbour wild-type p53. However, SV40 induced T-antigen expression inhibits the activity of p53. This cell line had lost the expression of androgen receptor (AR) and prostate-specific antigen (PSA) (Raudenska, 2019). DU-145 cell line is derived from the metastatic site in the brain and contains P223L and V274F mutations in p53. This cell line is PSA and AR-negative and androgen independent (Chappell, 2012). All cell lines used in this study were purchased from HPA Culture Collections (Salisbury, UK). and were cultured in RPMI-1640 medium with 10 % FBS. The medium was supplemented with antibiotics (penicillin 100 U/ml and streptomycin 0.1 mg/ml). Cells were maintained at 37°C in a humidified (60%) incubator with 5% CO2 (Sanyo, Japan).</p> <p><em>Correlative time-lapse quantitative phase-fluorescence imaging</em></p> <p>QPI and fluorescence imaging were performed by using multimodal holographic microscope Q-PHASE (TESCAN, Brno, Czech Republic). To determine the amount of caspase-3/7 product accumulation, cells were loaded with 2 µM CellEventTM Caspase-3/7 Green Detection Reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol and visualized using FITC 488 nm filter. To detect the cells with a loss of plasma membrane integrity, cells were stained with 1 ug/ml propidium iodide (Sigma Aldrich Co., St. Louis, MO, USA) and visualized using TRITC 542 nm filter. Nuclear morphology and chromatin condensation were analyzed using Hoechst 33342 nuclear staining (ENZO, Lausen, Switzerland) and visualized using DAPI 461 nm filter. Cells were cultivated in Flow chambers μ-Slide I Lauer Family (Ibidi, Martinsried, Germany). To maintain standard cultivation conditions (37°C, humidified air (60%) with 5% CO2) during time-lapse experiments, cells were placed in the gas chamber H201 - for Mad City Labs Z100/Z500 piezo Z-stages (Okolab, Ottaviano NA, Italy). To image enough cells in one field of view, lens Nikon Plan 10/0.30 were chosen. For each cell line and each treatment, seven fields of view were observed with the frame rate 3 mins/frame for 24 or 48 h respectively. Holograms were captured by CCD camera (XIMEA MR4021 MC-VELETA), fluorescence images were captured using ANDOR Zyla 5.5 sCMOS camera. Complete quantitative phase image reconstruction and image processing were performed in Q-PHASE control software. Cell dry mass values were derived according to {Prescher, 2005 #177} and {Park, 2018 #178} from the phase (eq. (1)), where m is cell dry mass density (in pg/μm2), φ is detected phase (in rad), λ is wavelength in μm (0.65 μm in Q-PHASE), and α is specific refraction increment (≈0.18 μm3/pg). All values in the formula except the Phi are constant. Phi (Phase) is the value measured directly by the microscope. Integrated phase shift through a cell is proportional to its dry mass, which enables studying changes in cell mass distribution (Park et al., 2018).</p> <p><strong>File description</strong></p> <p>There are three archives included for particular cell lines:</p> <ul> <li>QPI_annotated_timelapse_DU145.zip for DU-145 cells</li> <li>QPI_annotated_timelapse_PNT1A.zip for PNT1A cells</li> <li>QPI_annotated_timelapse_LNCaP.zip for LNCaP cells</li> </ul> <p>The archive includes of following files:</p> <ul> <li><strong>Tiff with time-lapse</strong> quantitative phase image (32-bit files 600x600px with values in pg/um2 with framerate 1 frame/3minutes with 1.59 px/um), named <em>QPI_cellline_treatment_FOV.tiff</em></li> <li><strong>Tiff file with segmentation</strong> mask for particular cells named <em>mask_cellline_treatment_FOV.tiff</em></li> <li><strong>xlsx table</strong> with cell death type (1 for apoptosis, 2 for necrosis, 3 for ambiguous/surviving) and time of death for representative cell number from mask, named <em>labels_cellline_treatment_FOV.xlsx</em></li> </ul> <p>file naming has following conventions:</p> <ul> <li>cell names: DU145, PNT1A, LNCaP for particular cell line</li> <li>treatments: st, bp, do for staurosporine, black phosphorus and doxorubicin</li> <li>fields of view: 1 to 7</li> </ul> <p>e.g. QPI_DU145_st_4.tif, mask_DU145_st_4.tif, labels_DU145_st_4.xlsx</p> <p>Note that correlative fluorescence images are available at <a href="https://doi.org/10.5281/zenodo.4531900">10.5281/zenodo.4531900</a></p>
visualization of person entities and their places of birth and death (source: https://kor.uni-frankfurt.de)
<p><strong>Datenexport</strong></p> <ul> <li>es wurden alle Entitäten der Typen „Ort“ und „Person“ exportiert</li> <li>es wurden alle Verknüpfungen zwischen den exportierten Entitäten exportiert <ul> <li>bei den exportierten Verknüpfungen handelt es sich ausschließlich um die Relationen „Geburtsort von“ und „Sterbeort von“</li> </ul> </li> <li>parallele Kanten sind in Gephi nicht möglich. Bei Auftreten paralleler Kanten wurden diese in eine Kante mit einem erhöhten Kantengewicht überführt: g<sub>edge</sub>= n<sub>parallel_edges</sub>, wobei g<sub>edge</sub> das Kantengewicht der im Graph beibehaltenen Kante zwischen einem Start- und Zielknoten und n<sub>parallel_edges</sub> die Anzahl derparallelen Kanten zwischen diesem Start- und Zielknoten ist <ul> <li>Dies tritt beispielsweise auf, wenn ein Personenknoten sowohl über die Relationen „Geburtsort von“ als auch „Sterbeort von“ mit einem Ortsknoten verknüpft ist.</li> </ul> </li> </ul> <p><strong>Datenanalyse</strong></p> <ul> <li>zunächst wurden für jeden Knoten die gewichteten Grade berechnet</li> <li>dann wurden die Knoten, deren gewichteter Grad geringer als 1 sind aus dem Graphen entfernt. <ul> <li>Dies bedeutet, dass alle nicht mit einem anderen Knoten verbundenen Knoten entfernt wurden. Der resultierende Graph enthält danach nur noch 2,91% der Knoten.</li> </ul> </li> <li>Anschließend wurde die Modularität des verbleibenden Graphen berechnet, wobei jeder Knoten in eine Modularitätsklasse eingeordnet wird, innerhalb derer ihre Knoten stärker untereinander verbunden sind als mit Knoten anderer Modularitätsklassen</li> </ul> <p><strong>Visualisierung</strong></p> <ul> <li>der Graph wurde farblich nach Modularitätsklasse partitioniert</li> <li>die Knoten wurden in Bezug auf ihren gewichteten Grad der Größe nach geordnet</li> <li>der Graph wurde anschließend mittels des ForceAtlas-Algorithmus gelayoutet</li> <li>das Layout des Graphen wurde durch das anschließende Durchführen des Noverlap-Algorithmus verbessert</li> </ul>
Overview of life and death of digital scholarly editions
<p>The dataset is based on the online catalogue for Digital Scholarly Editions (<a href="http://www.digitale-edition.de/">http://www.digitale-edition.de/</a>) on 7/8/2019. Based on the links provided in the catalogue, we queried the Wayback Machine (https://archive.org/web/) for first seen and last seen version of the website and added this information to the dataset. </p>
Fig. 1 in Air sac trematodes: Morishitium polonicum as a newly identified cause of death in the common blackbird (Turdus merula)
Fig. 1. Necropsy of Turdus merula, female. Gross lesions are represented by heavy parasite colonization of coelomic cavity. A. Many trematodes are clearly seen on different serosal membranes. Note the presence of parasites on the liver serosa, air sacs and pericardium (arrow). B. After removal of all the organs of the gastroenteric apparatus, an involvement of kidney and lungs serosa is also evident. Note the presence of an inflammatory focus with exudate at the periphery of the left lung (arrowhead).
Fig. 4 in Air sac trematodes: Morishitium polonicum as a newly identified cause of death in the common blackbird (Turdus merula)
Fig. 4. Maximum likelihood analyses of sequences of mitochondrial DNA loci of the newly isolated Morishitium polonicum and previously sequenced Cyclocoelidae. (A) CO1, (B) ND1. The bars indicate the number of substitutions per nucleotide.
Figure 3 in The lure of hidden death: development of an attract-and-kill strategy against Agriotes obscurus (Coleoptera: Elateridae) combining semiochemicals and entomopathogenic nematodes
Figure 3. Mean number of holes in the potato food source after infection according to nematode populations across time ((S. carpocapsae e-nema: χ2 = 73.62, p <0.001; S. feltiae AM25: χ2 = 5.03, p = 0.02, respectively). Light bars correspond to the treatments without potato extract, and the dark bars correspond to the treatments with addition of potato extract. Error bars represent the standard error of the mean.
Figure 5. Sentinel 3 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 5. Sentinel 3 imagery of the chlorophyll-a concentration in the study area on April 22, 2021.
Figure 3 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 3. Some dead species were collected during sampling. The orange circle indicates Atherina sp., and the yellow square indicates other affected species.
Figure 2 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 2. Regional map and sampling stations in the southern of Sea of Marmara (1: Misakça, 2: Şirinçavuş, 3: Narlı, 4: Tatlısu)
Figure 5 in The lure of hidden death: development of an attract-and-kill strategy against Agriotes obscurus (Coleoptera: Elateridae) combining semiochemicals and entomopathogenic nematodes
Figure 5. Proportion of molting wireworms according to nematode population across time (χ2 = 0.17, p = 0.92). Light bars correspond to the treatments without potato extract, and the dark bars correspond to the treatments with addition of potato extract. Error bars represent 95% confidence intervals.
Figure 1 in Marine mucilage in the Sea of Marmara and its effects on the marine ecosystem: mass deaths
Figure 1. Mucilage aggregation examples on the water surface in the Sea of Marmara, a) on April 23, 2021, on the coast of Misakça and b) on May 25, 2021, in Erdek Harbor.
Figure 1 in The lure of hidden death: development of an attract-and-kill strategy against Agriotes obscurus (Coleoptera: Elateridae) combining semiochemicals and entomopathogenic nematodes
Figure 1. Proportion of dead wireworms over time after the application of different nematode strains (χ2 = 57.76, p <0.001). Hb stands for Heterorhabditis bacteriophora, Sc stands for Steinernema carpocapsae, and Sf stands for Steinernema feltiae. Control corresponds to absence of EPNs. The stars indicate that the concerned strains are responsible for a significantly higher mortality (Tukey HSD; p <0.05).
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.