Find research datasets worth reusing

opencc-by-4.0Dec 2023View details →

Fig. 3 in ATP accumulation in early resting cyst formation towards cryptobiosis in Colpoda cucullus

Fig. 3. Measurement of the relative amount of ATP per 10,000 cells in vegetative cells and cells at 12 h after the onset of encystment induction. The columns and attached bars represent the means and standard errors of 9 identical replicates, respectively. Double asterisks represent significant differences at p <0.01.

opencc-by-4.0Dec 2023View details →

Fig. 2 in ATP accumulation in early resting cyst formation towards cryptobiosis in Colpoda cucullus

Fig. 2. Relative gene expression of ATP synthase beta chain by real time PCR analysis. The columns and attached bars represent the means and standard errors of 4 identical replicates, respectively. Double asterisks represent significant differences at p <0.01.

opencc-by-4.0Dec 2023View details →

Fig. 1 in ATP accumulation in early resting cyst formation towards cryptobiosis in Colpoda cucullus

Fig. 1. Visualization of the mitochondrial membrane potential of Colpoda vegetative cells using a Mito PT assay kit; the results from cells at 0 h and cells at 1–24 h after the onset of encystment induction are shown. Differential interference microscopic observation (A) and fluorescence microscopic observation (B). Cells that contain mitochondria with polarized inner membranes show orange fluorescence, whereas those with depolarized mitochondria show green fluorescence. The bar represents 100 μm.

opencc-by-4.0Dec 2019View details →

Fig. 1 in Evidence of Stress Recovery in Free-Living Ciliate Colpoda cucullus: The Repair Capability of Resting Cysts to Damage Caused by Gamma Irradiation

Fig. 1. Excystment assay of Colpoda wet cysts (A) and dry cysts (B). 'Non-irradiated' indicates non-irradiated cysts; 'irradiated' indicates cysts irradiated at 4000 Gy, and 'irradiated-incubated' indicates cysts irradiated at 4000 Gy and incubated for 12 hours before the induction of excystment. Time indicates the number of hours after the induction of excystment. Columns and attached bars correspond to the means and standard errors, respectively, of six measurements. Asterisks and double asterisks represent significant differences at p <0.05 and p <0.01 (Mann-Whitney U test), respectively.

Fig. 6 in A Study on Resting Cysts of an Oxytrichid Soil Ciliate, Rigidohymena quadrinucleata (Dragesco and Njine, 1971) Berger, 2011 (Ciliophora, Hypotrichia), Including Notes on its Encystation and Excystation Process

Fig. 6. Rigidohymena quadrinucleata, the basic scheme of two excystation modes. The standard mode: The beginning of excystation process is connected with formation of a transparent space between cyst wall and excysting cell. A little later, appears the excystation vacuole. The regenerating specimen breaks the cyst wall and escapes within the single, transparent membrane. The transparent membrane is broken by the excystant and resorbed in the enviroment. The rare mode: The beginning of excystation is associated, similarly, as in the standard mode, with formation of a transparent space and excystation vacuole. The regenerating specimen breaks the transparent membrane first, instead of breaking the whole cyst wall. Finally, the rest of the cyst wall is ruptured by the moving cell and the pressure of the excystation vacuole. The cell leaves the resting cyst. The transparent membrane remains in the empty cyst as a residual body.

Figs 4A–I in A Study on Resting Cysts of an Oxytrichid Soil Ciliate, Rigidohymena quadrinucleata (Dragesco and Njine, 1971) Berger, 2011 (Ciliophora, Hypotrichia), Including Notes on its Encystation and Excystation Process

Figs 4A–I. Rigidohymena quadrinucleata, resting cysts and excystants in the light microscope, the standard mode of excystation. A–F – the beginning of excystation with formation of excystation vacuole and the cyst wall ruptures under the pressure of excystant and excystation vacuole (circular area marks the individual protuberances that were separated from the cyst wall); G–I – during the standard mode, the excystant breaks the cyst wall within the thin, transparent membrane. CW – cyst wall, EV – excystation vacuole, EX – excystant, TM – transparent membrane. Scale bars: 30 μm.

Figs 3A–H in A Study on Resting Cysts of an Oxytrichid Soil Ciliate, Rigidohymena quadrinucleata (Dragesco and Njine, 1971) Berger, 2011 (Ciliophora, Hypotrichia), Including Notes on its Encystation and Excystation Process

Figs 3A–H. Rigidohymena quadrinucleata, resting cysts in the TEM. A–C – cross sections showing the cyst wall, the spine-like protuberances and the content of the resting cyst (arrowheads mark the poorly visible group of mitochondria, asterisks mark the surface protuberances); D – detail of the autophagic vacuoles; E, F – detail of the spine-like protuberances in the young and in mature resting cyst (asterisks mark the protuberances); G, H – the cortex of encysted cells with many regularly waved convex ridges. AV – autophagic vacuole, CS – "curious structure", EC – ectocyst, EN – endocyst, M – mitochondria, MC – mesocyst, MT – metacyst. Scale bars: 1 μm (B, C, E, F); 1,5 μm (G, H); 2 μm (A, D).

Figs 2A–I in A Study on Resting Cysts of an Oxytrichid Soil Ciliate, Rigidohymena quadrinucleata (Dragesco and Njine, 1971) Berger, 2011 (Ciliophora, Hypotrichia), Including Notes on its Encystation and Excystation Process

Figs 2A–I. Rigidohymena quadrinucleata, resting cysts in the light microscope and in the SEM. A, B – young resting cysts without surface ornamentation; C, D – mature resting cysts with fully developed cyst wall (arrowhead marks endocyst); E, F – the cyst contents is squeezed out, macronuclear mass is visible; G – full view of cyst; H, I – surface view of the cyst wall showing the spine-like protuberances (asterisks). EC – ectocyst, EN – endocyst, MA – macronucleus, MC – mesocyst. Scale bars: 30 μm (A–F); 20 µm (G); 10 μm (H, I).

opencc-by-4.0Oct 2021View details →

Do Design-Rules have an Impact on the Understandability of RESTful APIs? A Controlled Experiment

This publication contains the artifacts to reproduce a study, that investigated the impact of design-rules on the understandability of REST APIs. For this study the tool limesurvey (https://www.limesurvey.org/) was used. The following files are provided:  <ul> <li>limesurvey_study_archive_final.zip: This archive contains the survey structure (.Iss file), which can be imported in limesurvey</li> <li>API_Following_Rules.yaml: The API description for the version that follows the rules</li> <li>API_Ignoring_Rules.yaml: The API description for the version that ignores the rules</li> <li>Result_Data.csv: The untouched dataset exported from limesurvey</li> <li>Adjustments_to_Result_Data.txt: A description of changes that were made to the result data in order to filter out invalid answers and make the data easier to analyze</li> <li>Result_Data_Adjusted.csv: The adjusted dataset based on the changes described in the above file</li> <li>experiment_analysis_final.R: The analysis script used to get the results of the study. This script only works with the Result_Data_Adjusted.csv, because it was created based on the adjusted dataset </li> </ul>

opencc-by-4.0Mar 2022View details →

Multiple Nuclei HeLa cell ground truth images with four labels (nuclear envelope, nucleus, rest of the cell, and background) for deep learning architecture training.

This is a data set that contains labelled HeLa cell images, indicating the four different classes - nuclear envelope, nucleus, rest of the cell, and background. Similar ground truth have been published for this data set, but in this case, multiple nuclei have been labelled, whilst previous ones only focused on the central cell (https://doi.org/10.5281/zenodo.3874949) Details of the imaging, preparation and segmentation have been published in: <ul> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Segmentation and Modelling of the Nuclear Envelope of HeLa Cells Imaged with Serial Block Face Scanning Electron Microscopy. J. Imaging 2019, 5(9), 75; <a href="https://doi.org/10.3390/jimaging5090075">https://doi.org/10.3390/jimaging5090075</a></li> <li>Cefa Karabağ, Martin L. Jones, Christopher J. Peddie, Anne E. Weston, Lucy M. Collinson, Constantino Carlos Reyes-Aldasoro. Semantic segmentation of HeLa cells: An objective comparison between one traditional algorithm and four deep-learning architectures, PLOS ONE, 2020;  <a href="https://doi.org/10.1371/journal.pone.0230605">https://doi.org/10.1371/journal.pone.0230605</a></li> <li> Cefa Karabağ, Martin L. Jones, Constantino Carlos Reyes-Aldasoro, Segmentation of the Plasma Membrane of HeLa Cells, J. Imaging 2021, 7(6), 93; <a href="https://doi.org/10.3390/jimaging7060093">https://doi.org/10.3390/jimaging7060093</a> </li> </ul> <ul> <li>The data sets are freely available through EMPIAR: http://dx.doi.org/10.6019/EMPIAR-10094 EMPIAR.</li> </ul>

opencc-by-4.0May 2022View details →

Resting-state EEG simulations

Cortical-level activity was generated using a flexible neural mass model framework, named COALIA. This multi-population neural mass model enables the simulation of brain-scale electrophysiological activity while accounting for the macro- (between regions) and micro-circuitry (within a single region) of the brain, with one neural mass representing the local field potential of one Desikan-Killiany atlas region [for details, readers may refer to <a href="https://paperpile.com/c/vi4R1W/FXx0">(Bensaid et al. 2019)</a>]. The simulated cortical networks (DMN and DAN) each included six regions based on the Desikan-Killiany atlas <a href="https://paperpile.com/c/vi4R1W/Rmev">(Desikan et al. 2006)</a> in terms of region parcellation. The DMN consisted of the right and left posterior cingulate cortex (PCC), medial orbitofrontal (MOF) gyrus, and inferior parietal lobe (IPL). Regarding the DAN, this network consisted of the right and left inferior parietal lobe (IPL), caudal middle frontal gyrus (cMFG), and superior parietal lobe (SPL). Activity in the alpha band ([8-12] Hz) was attributed to the regions belonging to reference RSNs, while background activity was assigned to remaining cortical regions. A variability between simulated data segments was introduced at the subject level, as well as at the level of epochs per subject. Each “virtual subject” had different connectivity matrices provided to the model, while each epoch for the same subject had a different input noise (mean =90, standard deviation = 30)  set within the model. More specifically, for each subject, a different fractional anisotropy matrix of the HCP dataset was used <a href="https://paperpile.com/c/vi4R1W/XVSq">(Van Essen et al. 2013)</a>, and the weights corresponding to a RSN-connection were modified and set to a value of (1 ± 20%). A corresponding scaling of the matrices followed in accordance with COALIA’s requisites and the type of each input matrix (inhibitory/excitatory). A total of 50 “virtual subjects”, 4 epochs per subject (i.e., 200 data segments) were simulated; with a duration of 40 seconds each and a sampling rate of 2048 Hz. The time delay between NMMs was determined by the euclidean distance between the centroids of Desikan-Killainy’s regions divided by the velocity of action potentials propagation, which was set as 100 cm/s. Scalp EEG signals can be estimated from simulated cortical activity by solving the forward problem.   <a href="http://paperpile.com/b/vi4R1W/FXx0">Bensaid, Siouar, Julien Modolo, Isabelle Merlet, Fabrice Wendling, and Pascal Benquet. 2019. “COALIA: A Computational Model of Human EEG for Consciousness Research.” Frontiers in Systems Neuroscience 13: 1–18.</a> <a href="http://paperpile.com/b/vi4R1W/Rmev">Desikan, Rahul S., Florent Ségonne, Bruce Fischl, Brian T. Quinn, Bradford C. Dickerson, Deborah Blacker, Randy L. Buckner, et al. 2006. “An Automated Labeling System for Subdividing the Human Cerebral Cortex on MRI Scans into Gyral Based Regions of Interest.” NeuroImage 31: 968–80.</a> <a href="http://paperpile.com/b/vi4R1W/XVSq">Van Essen, David C., Stephen M. Smith, Deanna M. Barch, Timothy E. J. Behrens, Essa Yacoub, Kamil Ugurbil, and WU-Minn HCP Consortium. 2013. “The WU-Minn Human Connectome Project: An Overview.” NeuroImage 80 (October): 62–79.</a>

opencc-by-4.0Sep 2022View details →

[Supplementary material] Automated Code Generation for Inter-parameter Dependencies in REST APIs

This is the supplementary material of the paper entitled  Automated Code Generation for Inter-parameter Dependencies in REST APIs.

opencc-by-4.0Apr 2024View details →

Yoga Asana Increases Pre-Frontal Cortex Activity and Reduces Resting State Functional Connectivity

This dataset characterizes changes in the prefrontal cortex (PFC) before, during and after Yoga Asana (physical postures) with the mobile neuroimaging technique of functional near-infrared spectroscopy (fNIRS). Measurements were conducted with twenty-seven healthy adults executing four basic Asanas for 23 minutes with each Asana maintained for 25 -30 seconds. All postures significantly increased PFC activity versus baseline and resting state functional connectivity showed a significant decrease post Yoga Asana. Files 8, 15 and 24 were removed due to poor signal quality. During the measurement process of Asana the following stim marks were used to distinguish between postures: Posture A (Tadasana): A Posture B (Uttanasana): B Posture C (Adho Mukah Svasana): C Posture D (Urdhva Muka Svasana): D Results of the repeated measures ANOVA are presented for each combination of Asana. Those showing a significant difference are highlighted in green in the second to last tab of the file (Final Table). Demographics of volunteers are outlined in the last tab of the excel file (Demographics Volunteers).

opencc-by-4.0Aug 2023View details →

EEG recordings during resting-state and the maintenance periods of a spatial working memory task in humans

Scripts used to analyze data for the manuscript submitted for publication in EJN Script_Curve_Fitting_HBM.rtf Dr. Hadj Boumediene Meziane: hbmeziane@gmail.com  We therefore considered this continuous change in power as an extraneous variable yk(x) impacting the measured power spectrum Pow(Ek), and modeled it with a binomial equation that best fit the data, where the coefficients in pi are in descending powers, and the length of p is (n+1), k is trial number (k = 1 to 10): yk(x) = p1 . x2 + p2 . x + p3 In order to statistically compare the topographies between the trials with perfect recall and the trials with failed recall, we subtracted this variable from the mean spectral topographies of each subject and for each electrode by first producing the mean spectral curves of each maintenance trial in the theta and alpha frequency bands, taking into account the IAF, and then calculating the coefficients (p1, p2 and p3) of the binomial equation using the Matlab function polyfit.m. Once the coefficients were determined, this estimate was subtracted from each power spectrum matrix using the following formula: PowFit(Ek) = Pow (Ek) – yk(x)   Script_Perf_Fail_EEG_Power_Spec_HBM.rtf Dr. Hadj Meziane: hbmeziane@gmail.com This script calculates EEG power spectra then compares perf and fail conditions, then plots brain topographies with statical results   Script_Perf_Fail_EEG_Sources_Spec_HBM.rtf Dr. Hadj Boumediene Meziane: hbmeziane@gmail.com This script compares EEG source spectra then compares Perf vs. Fail conditions then plot statistical results (significant voxels) on MRI volume

Figs 5A–I in A Study on Resting Cysts of an Oxytrichid Soil Ciliate, Rigidohymena quadrinucleata (Dragesco and Njine, 1971) Berger, 2011 (Ciliophora, Hypotrichia), Including Notes on its Encystation and Excystation Process

Figs 5A–I. Rigidohymena quadrinucleata, resting cysts and excystants in the light microscope, the rare mode of excystation. A–E – the beginning of excystation with formation of excystation vacuole and the cyst wall ruptures under the pressure of excystant and excystation vacuole (circular area marks the individual protuberances that were separated from the cyst wall, arrowhead marks regenerating ciliature); F–I – during the rare excystation mode, the regenerating excystant breaks the transparent membrane first, inside the resting cyst. CW – cyst wall, EV – excystation vacuole, EX – excystant, MA – macronucleus, TM – transparent membrane, TS – transparent space. Scale bars: 30 μm.

Figs 1A–D in A Study on Resting Cysts of an Oxytrichid Soil Ciliate, Rigidohymena quadrinucleata (Dragesco and Njine, 1971) Berger, 2011 (Ciliophora, Hypotrichia), Including Notes on its Encystation and Excystation Process

Figs 1A–D. Rigidohymena quadrinucleata, trophic specimen and schematic illustrations of morphology of resting cysts. A – ventral view of a representative trophic specimen from the studied Slovak population; B – illustration of resting cyst based on transmission electron microscopy investigations; C, D – illustrations of young and mature resting cysts based on light microscopy investigations. 1–6 – six fronto-ventral-transverse cirral rows, AV – autophagic vacuole, AZM – adoral zone of membranelles, CC – caudal cirri, CS – "curious structures", CV – contractile vacuole, CX – cortex, EC – ectocyst, EM – endoral membrane, EN – endocyst, FV – food vacuole, LMR – left marginal cirral row, M – mitochondria, MA – macronucleus, MC – mesocyst, MI – micronucleus, MT – metacyst, PM – paroral membrane, RMR – right marginal cirral rows, SP – spine-like protuberances, TC – transverse cirri. Scale bars: 25 µm (A); 5 µm (B); 25 µm (C, D).

Fig. 2 in Tolerance of Colpoda cucullus Nag-1 Resting Cysts and Presumed Structure for Protection against UV Light

Fig. 2. Nomarski images (A-1−F-1) and their fluorescence photomicrographs (A-2−F-2) showing the formation of the auto-fluorescent cyst wall and NSPs in the encysting cells (wet cysts) after the onset of encystment induction. The cyst age (3 h to 5 days; A–F) is given at the upper right of each photograph. ec/en: ectocyst-endocyst complex, ec: an ectocyst layer, le: lepidosomes, ma: macronucleus, mu: mucus, NSP: nuclei-surrounding particle.

Fig. 2 in Gamma Radiation Tolerance and Protein Carbonylation Caused by Irradiation of Resting Cysts in the Free-living Ciliated Protist Colpoda cucullus

Fig. 2. Analysis of proteins (Left panel) and protein carbonylation by ECL (Right panel) from non-irradiated and 4000 Gy irradiated cells. The samples in the lanes were from non-irradiated cells (NonIR), 4000 Gy irradiated cells (IR), and cells incubated for 12 h after 4000 Gy irradiation (IR incubated). The protein bands and ECL signals were measured and are shown in parentheses for each lane relative to the Non-IR sample.

Fig. 4 in Gamma Radiation Tolerance and Protein Carbonylation Caused by Irradiation of Resting Cysts in the Free-living Ciliated Protist Colpoda cucullus

Fig. 4. Relative viability of Colpoda vegetative cells, wet cysts, and dry cysts after gamma radiation doses of 0 (non-irradiated), 500, 1000, 2000, 3000, and 4000 Gy. The column heights and attached bars are the means and standard errors, respectively, of six measurements at each dose. Double asterisks indicate a significant difference at p <0.01 (Mann-Whitney U test).

Fig. 3 in Gamma Radiation Tolerance and Protein Carbonylation Caused by Irradiation of Resting Cysts in the Free-living Ciliated Protist Colpoda cucullus

Fig. 3. Excystment of Colpoda dry cysts, after gamma irradiation at 0 (non-irradiated), 500, 1000, 2000, 3000, and 4000 Gy, as a function of time after induction of excystment. The points and bars mark the means and standard errors, respectively, of six measurements at each dose. The excystment mean ± SE at 3, 6, 24, and 96 h after the induction of excystment is shown in (a), (b), (c), and (d), respectively. The column heights and attached bars in (a) to (d) are the means and standard errors, respectively, of six measurements at each dose. Asterisks and double asterisks indicate a significant difference at p <0.05 and p <0.01, respectively (Mann-Whitney U test).