cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4871756.v1
title: Data for "Long-range temporal correlations in neural narrowband time-series arise due to critical dynamics"

description: Full data to "Long-range temporal correlations in neural narrowbandtime-series arise due to critical dynamics," 2017, PLOSone.Duncan Blythe and Vadim Nikulin
DOI: 10.6084/m9.figshare.4869041
title: Code for wall following in Xenopus laevis

description: These files are the analysis scripts to analyse the data for 'Wall following in <i>Xenopus leaves</i>'; the manuscript can be found on bioRxiv (see below).<br><br>The README file describes the packages and the versions used.<br><br>About half of the scripts (tankCornersLoop, trackingLoop, aviTrackingUtilities, findTankCorners, newThigmoTrackingFunctions, openCVtutorialUtils) were used to track the animals in the videos. Note, though, that the accompanying dataset contains tracked coordinates rather than the video files, because the video files are very large.<br><br>The other half of the scripts (plottingUtilities, tankSizeComparisons, saveExampleWarps, plotValuesSeveralAnimals, tentsComparison, bwComparison, frameCorrectionDictionary, IRcomparison, plottingLoop) concerns the analysis of the data after the x-y coordinates of the animals were obtained. Note that the accompanying dataset contains the x-y coordinates.<br>Finally, there are two Matlab scripts that were used to read out the timestamps written into the first 4 pixels of the TIFF files by the camera.<br><br>Specifically, the graphs shown in the manuscript were generated using the following scripts:<br>- The panels in Figure 3 were produced from the plotValuesSeveralAnimals script.<br>- The panels in Figure 4 were produced from the tentsComparison script.<br>- The panels in Figure 5 were produced from the bwComparison and IRcomparison script.<br>- The panels in Figure 6 were produced from the tankSizeComparisons script.<br><br>For details and permissions please refer to the manuscript. <br>
DOI: 10.6084/m9.figshare.4869041.v1
title: Code for wall following in Xenopus laevis

description: These files are the analysis scripts to analyse the data for 'Wall following in <i>Xenopus leaves</i>'; the manuscript can be found on bioRxiv (see below).<br><br>The README file describes the packages and the versions used.<br><br>About half of the scripts (tankCornersLoop, trackingLoop, aviTrackingUtilities, findTankCorners, newThigmoTrackingFunctions, openCVtutorialUtils) were used to track the animals in the videos. Note, though, that the accompanying dataset contains tracked coordinates rather than the video files, because the video files are very large.<br><br>The other half of the scripts (plottingUtilities, tankSizeComparisons, saveExampleWarps, plotValuesSeveralAnimals, tentsComparison, bwComparison, frameCorrectionDictionary, IRcomparison, plottingLoop) concerns the analysis of the data after the x-y coordinates of the animals were obtained. Note that the accompanying dataset contains the x-y coordinates.<br>Finally, there are two Matlab scripts that were used to read out the timestamps written into the first 4 pixels of the TIFF files by the camera.<br><br>Specifically, the graphs shown in the manuscript were generated using the following scripts:<br>- The panels in Figure 3 were produced from the plotValuesSeveralAnimals script.<br>- The panels in Figure 4 were produced from the tentsComparison script.<br>- The panels in Figure 5 were produced from the bwComparison and IRcomparison script.<br>- The panels in Figure 6 were produced from the tankSizeComparisons script.<br><br>For details and permissions please refer to the manuscript. <br>
DOI: 10.6084/m9.figshare.4868993
title: Convex data and code for Wall following in Xenopus laevis

description: The CSV table contains the data from the 'Wall following in <i>Xenopus laevis</i>' manuscript obtained from swimming in a convex tank. Tadpoles and froglets of <i>Xenopus laevis</i> were observed while freely swimming in a tank with convex curves. Whenever the animal swam along the wall towards the convex curve, an observer scored whether the animal went straight and left the wall at the curve or whether the animal turned to follow the wall. The python code then plots these trials as the proportion of times the animal went straight and left the wall.These data are shown in Figure 7 of the manuscript.<br><br>For details and permissions please refer to the manuscript which can be found on bioRxiv (see link below).<br>
DOI: 10.6084/m9.figshare.4869026
title: Data for Wall following in Xenopus laevis

description: These data are the basis of the manuscript 'Wall following in <i>Xenopus laevis</i>' which can be found on bioRxiv (see link below). <br><br>The CSV file contains a table with one row per video of an animal freely swimming in a square tank for 10 min. Filename, the animal's developmental stage, its length, and parameters of the video are indicated in the different columns; the 'primary' column indicates the videos of animals in the 'standard condition' (see manuscript for methodological details). <br>The timestamps folder contains timestamps for all videos that were saved as TIFF files; these timestamps were written into the first 4 pixels of each image, read out using two Matlab scripts, which can be found in the accompanying code, and were then saved as those CSV files that can be found here. <br><br>The originalDFs folder contains pickle files (which in turn contain pandas data frames) of all the trackings; the correctedDFs folder contains the same but corrected for frames where the tracking did not work; these corrections can be found in a python dictionary described in the corrections.npy file. The pandas data frames contain the tracked x-y coordinates as well as a number of calculated parameters of interest, such as the distance to the nearest wall at each frame. The data frames containing all frames are called 'df', the ones that contain reduced trajectories (obtained through the Ramer-Douglas-Peucker algorithm) are called 'reduced'. <br><br>For details and permissions, please refer to the manuscript.<br>
DOI: 10.6084/m9.figshare.4868993.v1
title: Convex data and code for Wall following in Xenopus laevis

description: The CSV table contains the data from the 'Wall following in <i>Xenopus laevis</i>' manuscript obtained from swimming in a convex tank. Tadpoles and froglets of <i>Xenopus laevis</i> were observed while freely swimming in a tank with convex curves. Whenever the animal swam along the wall towards the convex curve, an observer scored whether the animal went straight and left the wall at the curve or whether the animal turned to follow the wall. The python code then plots these trials as the proportion of times the animal went straight and left the wall.These data are shown in Figure 7 of the manuscript.<br><br>For details and permissions please refer to the manuscript which can be found on bioRxiv (see link below).<br>
DOI: 10.6084/m9.figshare.4869026.v1
title: Data for Wall following in Xenopus laevis

description: These data are the basis of the manuscript 'Wall following in <i>Xenopus laevis</i>' which can be found on bioRxiv (see link below). <br><br>The CSV file contains a table with one row per video of an animal freely swimming in a square tank for 10 min. Filename, the animal's developmental stage, its length, and parameters of the video are indicated in the different columns; the 'primary' column indicates the videos of animals in the 'standard condition' (see manuscript for methodological details). <br>The timestamps folder contains timestamps for all videos that were saved as TIFF files; these timestamps were written into the first 4 pixels of each image, read out using two Matlab scripts, which can be found in the accompanying code, and were then saved as those CSV files that can be found here. <br><br>The originalDFs folder contains pickle files (which in turn contain pandas data frames) of all the trackings; the correctedDFs folder contains the same but corrected for frames where the tracking did not work; these corrections can be found in a python dictionary described in the corrections.npy file. The pandas data frames contain the tracked x-y coordinates as well as a number of calculated parameters of interest, such as the distance to the nearest wall at each frame. The data frames containing all frames are called 'df', the ones that contain reduced trajectories (obtained through the Ramer-Douglas-Peucker algorithm) are called 'reduced'. <br><br>For details and permissions, please refer to the manuscript.<br>
DOI: 10.6084/m9.figshare.4868924
title: Portal Forecasts test

description: This is a test
DOI: 10.6084/m9.figshare.4869038.v2
title: Slides for the consequences of unhappiness while developing software

description: Semotion'17 slides for "Consequences of unhappiness while developing software"ABSTRACT--The growing literature on affect among software developers mostly reports on the linkage between happiness, software quality, and developer productivity. Understanding the positive side of happiness – positive emotions and moods – is an attractive and important endeavor. Scholars in industrial and organizational psychology have suggested that also studying the negative side – unhappiness – could lead to cost-effective ways of enhancing working conditions, job performance, and to limiting the occurrence of psychological disorders. Our comprehension of the consequences of (un)happiness among developers is still too shallow, and is mainly expressed in terms of development productivity and software quality. In this paper, we attempt to uncover the experienced consequences of unhappiness among software developers. Using qualitative data analysis of the responses given by 181 questionnaire participants, we identified 49 consequences of unhappiness while doing software development. We found detrimental consequences on developers’ mental well-being, the software development process, and the produced artifacts. Our classification scheme, available as open data, will spawn new happiness research opportunities of cause-effect type, and it can act as a guideline for practitioners for identifying damaging effects of unhappiness and for fostering happiness on the job.
DOI: 10.6084/m9.figshare.4868924.v2
title: Portal Forecasts test

description: This is a test
DOI: 10.6084/m9.figshare.4868873
title: Elevated carbon dioxide level along with phosphorus application and cyanobacterial inoculation enhances nitrogen fixation and uptake in cowpea crop

description: Climate change, as a result of increase in the concentration of greenhouse gases, influences growth and productivity of leguminous crops. A study was carried out to analyse the impacts of elevated carbon dioxide (CO<sub>2</sub>) and cyanobacterial inoculation on growth, N<sub>2</sub> fixation and N availability and uptake in cowpea crop, under different doses of phosphorus. Cowpea crop was grown under ambient (400 µmol mol<sup>−</sup><sup>1</sup>) and elevated (550 ± 20 µmol mol<sup>−</sup><sup>1</sup>) CO<sub>2</sub> levels using Free-Air Carbon dioxide Enrichment facility. Elevated CO<sub>2</sub> level increased chlorophyll content in leaves, improved nodulation and nitrogen fixation by the crop. Increase in P dose up to 16 mg kg<sup>−</sup><sup>1</sup> soil enhanced nodule development and N<sub>2</sub> fixation under high CO<sub>2</sub> condition. Cyanobacterial inoculation increased nodule weight, leghaemoglobin content in nodules and total nitrogenase activity. Although nitrogen concentration in cowpea seeds decreased in high CO<sub>2</sub> treatment, higher N uptake was recorded. Under elevated CO<sub>2</sub> condition, cyanobacterial inoculation and higher P doses led to enhanced root growth and N<sub>2</sub> fixation and availability of soil nitrogen. The study illustrated the synergistic effect of high CO<sub>2</sub> and cyanobacterial inoculation in enhancing crop growth and availability of soil N, mediated by biological N<sub>2</sub> fixation in cowpea under different levels of P.
DOI: 10.6084/m9.figshare.4868924.v1
title: Portal Forecasts test

description: This is a test
DOI: 10.6084/m9.figshare.4868873.v1
title: Elevated carbon dioxide level along with phosphorus application and cyanobacterial inoculation enhances nitrogen fixation and uptake in cowpea crop

description: Climate change, as a result of increase in the concentration of greenhouse gases, influences growth and productivity of leguminous crops. A study was carried out to analyse the impacts of elevated carbon dioxide (CO<sub>2</sub>) and cyanobacterial inoculation on growth, N<sub>2</sub> fixation and N availability and uptake in cowpea crop, under different doses of phosphorus. Cowpea crop was grown under ambient (400 µmol mol<sup>−</sup><sup>1</sup>) and elevated (550 ± 20 µmol mol<sup>−</sup><sup>1</sup>) CO<sub>2</sub> levels using Free-Air Carbon dioxide Enrichment facility. Elevated CO<sub>2</sub> level increased chlorophyll content in leaves, improved nodulation and nitrogen fixation by the crop. Increase in P dose up to 16 mg kg<sup>−</sup><sup>1</sup> soil enhanced nodule development and N<sub>2</sub> fixation under high CO<sub>2</sub> condition. Cyanobacterial inoculation increased nodule weight, leghaemoglobin content in nodules and total nitrogenase activity. Although nitrogen concentration in cowpea seeds decreased in high CO<sub>2</sub> treatment, higher N uptake was recorded. Under elevated CO<sub>2</sub> condition, cyanobacterial inoculation and higher P doses led to enhanced root growth and N<sub>2</sub> fixation and availability of soil nitrogen. The study illustrated the synergistic effect of high CO<sub>2</sub> and cyanobacterial inoculation in enhancing crop growth and availability of soil N, mediated by biological N<sub>2</sub> fixation in cowpea under different levels of P.
DOI: 10.6084/m9.figshare.4868876.v1
title: 2014 05 23 Independent Sighting by a Third Party

description: Notes and discussion of the independent sighting by a third party that occurred at Allaire State Park on 23 May 2014.<br><br>Project order 2a<br>
DOI: 10.6084/m9.figshare.4868765
title: Identification of bacterial contaminants from calcium carbonate filler production lines and an evaluation of biocide based decontamination procedures

description: The aim of this study was to analyze the bacterial community in the production line of a calcium carbonate filler production company and to investigate possible causes for bacterial presence. Throughout 2012, 24 carbonate slurry and six groundwater samples were analyzed. <i>Pseudomonas</i> and <i>Microbacterium</i> were the most frequent contaminants in the slurry, whereas <i>Pseudomonas</i> and <i>Brevundimonas</i> dominated the groundwater samples. Of the 43 different bacterial strains isolated, only five were found both in the slurry and the groundwater, indicating that the latter was not a major source of contamination. The efficacy of 54 commercial biocidal formulations was tested against an artificial bacterial consortium composed of selected slurry isolates. A formulation containing 7.5–15% (v v<sup>–1</sup>) bronopol and 1.0–2.5% (v v<sup>–1</sup>) [chloroisothiazolinone (CIT) + methylisothiazolinone (MIT)] exhibited the highest efficacy. Of the possible causes for bacterial presence, sporogenesis and biocide adsorption to carbonate particles were found to be less probable compared to bacterial adsorption to particles, and the acquisition of resistance to biocides.
DOI: 10.6084/m9.figshare.4868765.v1
title: Identification of bacterial contaminants from calcium carbonate filler production lines and an evaluation of biocide based decontamination procedures

description: The aim of this study was to analyze the bacterial community in the production line of a calcium carbonate filler production company and to investigate possible causes for bacterial presence. Throughout 2012, 24 carbonate slurry and six groundwater samples were analyzed. <i>Pseudomonas</i> and <i>Microbacterium</i> were the most frequent contaminants in the slurry, whereas <i>Pseudomonas</i> and <i>Brevundimonas</i> dominated the groundwater samples. Of the 43 different bacterial strains isolated, only five were found both in the slurry and the groundwater, indicating that the latter was not a major source of contamination. The efficacy of 54 commercial biocidal formulations was tested against an artificial bacterial consortium composed of selected slurry isolates. A formulation containing 7.5–15% (v v<sup>–1</sup>) bronopol and 1.0–2.5% (v v<sup>–1</sup>) [chloroisothiazolinone (CIT) + methylisothiazolinone (MIT)] exhibited the highest efficacy. Of the possible causes for bacterial presence, sporogenesis and biocide adsorption to carbonate particles were found to be less probable compared to bacterial adsorption to particles, and the acquisition of resistance to biocides.
DOI: 10.6084/m9.figshare.4868573
title: Bowl-shaped structures from acylphloroglucinols: an <i>ab initio</i> and DFT study

description: Molecular structures containing bowl-shaped cavities are interesting for purposes such as hosting metal ions or a variety of molecules, including drug molecules. This study considers bowl-shaped structures formed from phloroglucinol (1,3,5-trihydroxybenzene) or acylphloroglucinols (its derivatives containing a COR group) and containing 3 or 4 identical monomeric units. The monomeric units are linked in the same way as in naturally occurring trimeric and tetrameric acylphloroglucinols, i.e. by a methylene bridge and two intermonomer hydrogen bonds. The representativeness of the structures considered is pursued by selecting different R chains. Two conformers were identified for each structure, differing by the orientation of the OH in para to the COR group. Calculations were performed at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels with fully relaxed geometry, and were complemented by single point MP2/HF/6-31G(d,p) calculations. Corresponding open structures were also calculated for comparison sake. The results indicate the presence of steric stress in trimeric bowl-shaped structures, whereas the geometry of tetrameric bowl-shaped structures is close to one of the local-minima geometries of corresponding open structures and appears free of steric stress.
DOI: 10.6084/m9.figshare.4868468
title: Zea mays (6) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (6)<br><br>from:<br><br>Impact of contrasted maize root traits at flowering on water stress tolerance. A simulation study Leitner D, Meunier F, Bodner G, Javaux M, Schnepf A Field Crops Research, 165, 125-137, 2014
DOI: 10.6084/m9.figshare.4868573.v1
title: Bowl-shaped structures from acylphloroglucinols: an <i>ab initio</i> and DFT study

description: Molecular structures containing bowl-shaped cavities are interesting for purposes such as hosting metal ions or a variety of molecules, including drug molecules. This study considers bowl-shaped structures formed from phloroglucinol (1,3,5-trihydroxybenzene) or acylphloroglucinols (its derivatives containing a COR group) and containing 3 or 4 identical monomeric units. The monomeric units are linked in the same way as in naturally occurring trimeric and tetrameric acylphloroglucinols, i.e. by a methylene bridge and two intermonomer hydrogen bonds. The representativeness of the structures considered is pursued by selecting different R chains. Two conformers were identified for each structure, differing by the orientation of the OH in para to the COR group. Calculations were performed at the HF/6-31G(d,p) and DFT/B3LYP/6-31+G(d,p) levels with fully relaxed geometry, and were complemented by single point MP2/HF/6-31G(d,p) calculations. Corresponding open structures were also calculated for comparison sake. The results indicate the presence of steric stress in trimeric bowl-shaped structures, whereas the geometry of tetrameric bowl-shaped structures is close to one of the local-minima geometries of corresponding open structures and appears free of steric stress.
DOI: 10.6084/m9.figshare.4868456
title: Zea mays (5) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (5).<br><br>from:<br><br>Impact of contrasted maize root traits at flowering on water stress tolerance. A simulation study Leitner D, Meunier F, Bodner G, Javaux M, Schnepf A Field Crops Research, 165, 125-137, 2014
DOI: 10.6084/m9.figshare.4868453
title: Zea mays (4) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (4).<br><br>from:<br><br>Impact of contrasted maize root traits at flowering on water stress tolerance. A simulation study Leitner D, Meunier F, Bodner G, Javaux M, Schnepf A Field Crops Research, 165, 125-137, 2014
DOI: 10.6084/m9.figshare.4868450
title: Zea mays (3) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (3).<br><br>from:<br><br>Root Cortical Aerenchyma Enhances the Growth of Maize on Soils with Suboptimal Availability of Nitrogen, Phosphorus, and Potassium Postma J A, Lynch J P PLANT PHYSIOLOGY, 156, 1190-1201, 2011
DOI: 10.6084/m9.figshare.4868444
title: Zea mays (1) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (1).<br><br>from:<br><br>The algorithmic beauty of plant roots. an L-System model for dynamic root growth simulation Leitner D, Klepsch S, Knie A, Schnepf A Mathematical and Computer Modelling of Dynamical Systems, 16, 575-587, 2010
DOI: 10.6084/m9.figshare.4868447
title: Zea mays (2) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (2).<br><br>from:<br><br>Calibration and evaluation of ArchiSimple, a simple model of root system architecture Pages L, Becel C, Boukcim H, Moreau D, Nguyen C, Voisin A Ecological Modelling, 290, 76-84, 2014
DOI: 10.6084/m9.figshare.4868453.v1
title: Zea mays (4) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (4).<br><br>from:<br><br>Impact of contrasted maize root traits at flowering on water stress tolerance. A simulation study Leitner D, Meunier F, Bodner G, Javaux M, Schnepf A Field Crops Research, 165, 125-137, 2014
DOI: 10.6084/m9.figshare.4868435
title: Sorghum bicolor - CRootBox parameter file

description: CRootbox parameter file for Sorghum bicolor.<br><br>from:<br><br>NA<br>
DOI: 10.6084/m9.figshare.4868447.v1
title: Zea mays (2) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (2).<br><br>from:<br><br>Calibration and evaluation of ArchiSimple, a simple model of root system architecture Pages L, Becel C, Boukcim H, Moreau D, Nguyen C, Voisin A Ecological Modelling, 290, 76-84, 2014
DOI: 10.6084/m9.figshare.4868429
title: Pisum sativum (d) - CRootBox parameter file

description: CRootbox parameter file for Pisum sativum (d).<br><br>from:<br><br>Modelling pea (Pisum sativum) root growth in drying soil. A comparison between observations and model predictions TSEGAYE T, MULLINS C E, DIGGLE A J New Phytologist, 131, 179-189, 1995
DOI: 10.6084/m9.figshare.4868438
title: Triticum aestivum - CRootBox parameter file

description: CRootbox parameter file for Triticum aestivum.<br><br>from:<br><br>Simulation of wheat growth using the 3D root architecture model SPACSYS: Validation and sensitivity analysis Bingham I J, Wu L European Journal of Agronomy, 34, 181-189, 2011
DOI: 10.6084/m9.figshare.4868450.v1
title: Zea mays (3) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (3).<br><br>from:<br><br>Root Cortical Aerenchyma Enhances the Growth of Maize on Soils with Suboptimal Availability of Nitrogen, Phosphorus, and Potassium Postma J A, Lynch J P PLANT PHYSIOLOGY, 156, 1190-1201, 2011
DOI: 10.6084/m9.figshare.4868444.v1
title: Zea mays (1) - CRootBox parameter file

description: CRootbox parameter file for Zea mays (1).<br><br>from:<br><br>The algorithmic beauty of plant roots. an L-System model for dynamic root growth simulation Leitner D, Klepsch S, Knie A, Schnepf A Mathematical and Computer Modelling of Dynamical Systems, 16, 575-587, 2010