Recent Submissions

  • Supplementary data to the article: Impact of fracture geometry and topology on the connectivity and flow properties of stochastic fracture networks

    Zhu, Weiwei; Khirevich, Siarhei; Patzek, Tadeusz (2020-05-26) [Dataset]
    From the shared data, you can: 1. Find the data to reproduce Fig. 7 and 8 in the paper. Those data are averaged by 6000 random realizations for each case; 2. Find the data to plot 2D fracture networks and its graph representation; 3. Find the data to plot 3D fracture networks and its graph representation; 4. Find the data to plot the pressure distribution in 2D fracture networks; 5. Find the data to plot the pressure distribution in 3D fracture networks; 6. Find the corresponding Matlab code to help you visualize the result; To have a better visualization, the system size of 2D ad 3D fracture networks are modified. Those modifications are only for visualization purpose and will not change the results we have in the paper. 
  • SARS-COV-2 Virus Mesoscale Model

    Nguyen, Ngan; Strnad, Ondrej; Klein, Tobias; Luo, Deng; Alharbi, Ruwayda; Wonka, Peter; Maritan, Martina; Mindek, Peter; Autin, Ludovic; Goodsell, David; Viola, Ivan (2020-05-06) [Dataset]
    The dataset contains SARS-COV-2 virus mesoscale atomistic model created as a part of "Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models" paper.
  • Polarization Image Dataset

    Fu, Qiang; Qiu, Simeng; Wang, Congli; Heidrich, Wolfgang (KAUST Research Repository, 2020-02-23) [Dataset]
    [Update on 2020/02/20] Uploaded the raw intensity images at 0, 45, 90 and 135 degrees. This is to facilitate research work for other users. Previous .mat files were deleted because they can be generated with these raw images. Corresponding code was updated in main.m. This polarization image dataset is a collection of 40 high resolution color polarization data, with four raw intensity images with polarization angles at 0, 45, 90 and 135 degrees for each scene. They were captured with a rotating polarizer in front of a point grey color camera. For each polarization angle, 100 images were captured successively and then averaged to output one single image at that angle to suppress noise. They are stored in .png format. Various visualization methods are provided along with the polarization data. The code to generate these visualizations are in the zipped file "_code.zip". To run the code, MATLAB version2018b or higher is required. If you find this dataset useful for your work, please kindly cite our paper Simeng Qiu, Qiang Fu, Congli Wang, Wolfgang Heidrich. Polarization Demosaicking for Monochrome and Color Polarization Focal Plane Arrays. The 24th International Symposium on Vision, Modeling and Visualization. Proceedings of the Conference on Vision, Modeling, and Visualization, 2019. Contact: qiang.fu@kaust.edu.sa
  • HiRM input files

    Raj, Jerry (2020-01-01) [Dataset]
  • Experiments on ocean acidification effects on mussel calcification, supplement to: Wahl, Martin; Schneider Covachã, Sabrina; Saderne, Vincent; Hiebenthal, Claas; Müller, Jens Daniel; Pansch, Christian; Sawall, Yvonne (2018): Macroalgae may mitigate ocean acidification effects on mussel calcification by increasing pH and its fluctuations. Limnology and Oceanography, 63(1), 3-21

    Wahl, M.; Schneider Covachã, S.; Saderne, Vincent; Hiebenthal, C.; Müller, J. D.; Pansch, C.; Sawall, Y. (PANGAEA - Data Publisher for Earth & Environmental Science, 2020) [Dataset]
    Ocean acidification (OA) is generally assumed to negatively impact calcification rates of marine organisms. At a local scale however, biological activity of macrophytes may generate pH fluctuations with rates of change that are orders of magnitude larger than the long-term trend predicted for the open ocean. These fluctuations may in turn impact benthic calcifiers in the vicinity. Combining laboratory, mesocosm and field studies, such interactions between OA, the brown alga Fucus vesiculosus, the sea grass Zostera marina and the blue mussel Mytilus edulis were investigated at spatial scales from decimetres to 100s of meters in the western Baltic. Macrophytes increased the overall mean pH of the habitat by up to 0.3 units relative to macrophyte- free, but otherwise similar, habitats and imposed diurnal pH fluctuations with amplitudes ranging from 0.3 to more than 1 pH unit. These amplitudes and their impact on mussel calcification tended to increase with increasing macrophyte biomass to bulk water ratio. At the laboratory and mesocosm scales, biogenic pH fluc- tuations allowed mussels to maintain calcification even under acidified conditions by shifting most of their calcification activity into the daytime when biogenic fluctuations caused by macrophyte activity offered temporal refuge from OA stress. In natural habitats with a low biomass to water body ratio, the impact of biogenic pH fluctuations on mean calcification rates of M. edulis was less pronounced. Thus, in dense algae or seagrass habitats, macrophytes may mitigate OA impact on mussel calcification by raising mean pH and providing temporal refuge from acidification stress.
  • CCDC 1969089: Experimental Crystal Structure Determination

    Cadiau, Amandine; Lee, Ji Sun; Damasceno Borges, Daiane; Fabry, Paul; Devic, Thomas; Wharmby, Michael T.; Martineau, Charlotte; Foucher, Damien; Taulelle, Francis; Jun, Chul-Ho; Hwang, Young Kyu; Stock, Norbert; De Lange, Martijn F.; Kapteijn, Freek; Gascon, Jorge; Maurin, Guillaume; Chang, Jong-San; Serre, Christian (Cambridge Crystallographic Data Centre, 2019-11-29) [Dataset]
  • Genome assembly and annotation datasets of the plant growth promoting bacterium Cellulosimicrobium sp. JZ28 isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Saad, Maged; Hirt, Heribert (2019-11-19) [Dataset]
    The files associated with this dataset are the Genbank, GFF and protein coding-sequence (CDSs) files of a plant growth promoting bacterium isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia. Genome annotation was carried out using the Automatic Annotation of Microbial Genomes (AAMG) which is an integrated module in the in-house INDIGO-Desert v1.1 pipeline (Alam et al., 2013).
  • Genome assembly and annotation datasets of the plant growth promoting bacterium Microbacterium sp. JZ31 isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Saad, Maged; Hirt, Heribert (2019-11-18) [Dataset]
    The files associated with this dataset are the Genbank, GFF and protein coding-sequence (CDSs) files of a plant growth promoting bacterium isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia. Genome annotation was carried out using the Automatic Annotation of Microbial Genomes (AAMG) which is an integrated module in the in-house INDIGO-Desert v1.1 pipeline (Alam et al., 2013).
  • Genome assembly and annotation datasets of the plant growth promoting bacterium Cronobacter mutyjensii JZ38 isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Saad, Maged; Hirt, Heribert (2019-11-17) [Dataset]
    The files associated with this dataset are the Genbank, GFF and protein coding-sequence (CDSs) files of a plant growth promoting bacteria isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia. Genome annotation was carried out using the Automatic Annotation of Microbial Genomes (AAMG) which is an integrated module in the in-house INDIGO-Desert v1.1 pipeline (Alam et al., 2013).
  • Genome assembly and annotation datasets of the plant growth promoting bacterium Paenibacillus sp. JZ16 isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia

    Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab; Saad, Maged; Hirt, Heribert (2019-11-17) [Dataset]
    The files associated with this dataset are the GenBank, GFF and protein coding-sequence (CDSs-FASTA) files of a plant growth promoting bacteria isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia. Genome annotation was carried out using the Automatic Annotation of Microbial Genomes (AAMG) which is an integrated module in the in-house INDIGO-Desert v1.1 pipeline (Alam et al., 2013).
  • VCC-LF dataset

    Li, Rui; Heidrich, Wolfgang (2019-09-01) [Dataset]
    This is readme for VCC-LF dataset. This dataset provides light field mat files that capture by Lytro I. The light field resolusion is [h,w,u,v,d]. If you use these data or our toolkit code, please cite our paper properly @inproceedings{ lirsiggraphasia2019, title={Hierarchical and View-invariant Light Field Segmentation by Maximizing Entropy Rate on 4D Ray Graphs}, author={Li, Rui and Heidrich, Wolfgang}, booktitle={ACM Transactions on Graphics (Proc. SIGGRAPH Asia)}, year={2019}, publisher={ACM} }
  • Fast and selective organocatalytic ring-opening polymerization by fluorinated alcohol without a cocatalystm

    Zhao, Wei; Lv, Yanfeng; Li, Ji; Feng, Zihao; Ni, Yonghao; Hadjichristidis, Nikos (Figshare, 2019-07-10) [Dataset]
    source data for -
  • NASA GISS ModelE modelling framework and supporting data for the study of the role of the SO2 radiative effect in sustaining the volcanic winter and soothing the Toba impact on climate

    Osipov, Sergey; Stenchikov, Georgiy L.; Tsigaridis, Kostas; Legrande, Allegra; Bauer, Susanne E. (KAUST Research Repository, 2019-07-10) [Dataset]
    This dataset is the supporting information for the article Osipov et. al., The role of the SO2 radiative effect in sustaining the volcanic winter and soothing the Toba impact on climate, Journal of Geophysical Research: Atmospheres, https://doi.org/10.1029/2019JD031726. It includes the model, rundecks, auxiliary information and other data necessary to reproduce the simulations described in the paper.
  • Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1

    Calì, Corrado; Wawrzyniak, Marta; Becker, Carlos; Maco, Bohumil; Cantoni, Marco; Jorstad, Anne; Nigro, Biagio; Grillo, Federico; De Paola, Vincenzo; Fua, Pascal; Knott, Graham William (Dryad, 2019-05-17) [Dataset]
    This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase in their size such that the total amount of synaptic surface, per unit length of axon, and per unit volume of neuropil, stayed the same. There was also a greater reduction of inhibitory synapses than excitatory, particularly those found on dendritic spines, resulting in an increase in the excitatory/inhibitory balance. The close correlations, that exist in young and adult neurons, between spine volume, bouton volume, synaptic size, and docked vesicle numbers are all preserved during aging. These comparisons display features that indicate a reduced plasticity of cortical circuits, with fewer, more transient, connections, but nevertheless an enhancement of the remaining connectivity that compensates for a generalized synapse loss.
  • Data from: The effects of aging on neuropil structure in mouse somatosensory cortex—A 3D electron microscopy analysis of layer 1

    Calì, Corrado; Wawrzyniak, Marta; Becker, Carlos; Maco, Bohumil; Cantoni, Marco; Jorstad, Anne; Nigro, Biagio; Grillo, Federico; De Paola, Vincenzo; Fua, Pascal; Knott, Graham William (Dryad, 2019-05-17) [Dataset]
    This study has used dense reconstructions from serial EM images to compare the neuropil ultrastructure and connectivity of aged and adult mice. The analysis used models of axons, dendrites, and their synaptic connections, reconstructed from volumes of neuropil imaged in layer 1 of the somatosensory cortex. This shows the changes to neuropil structure that accompany a general loss of synapses in a well-defined brain region. The loss of excitatory synapses was balanced by an increase in their size such that the total amount of synaptic surface, per unit length of axon, and per unit volume of neuropil, stayed the same. There was also a greater reduction of inhibitory synapses than excitatory, particularly those found on dendritic spines, resulting in an increase in the excitatory/inhibitory balance. The close correlations, that exist in young and adult neurons, between spine volume, bouton volume, synaptic size, and docked vesicle numbers are all preserved during aging. These comparisons display features that indicate a reduced plasticity of cortical circuits, with fewer, more transient, connections, but nevertheless an enhancement of the remaining connectivity that compensates for a generalized synapse loss.
  • Wilson et al 2019_DBA data.xlsx

    Wilson, Rory P; Börger, Luca; Holton, Mark D.; Scantlebury, D. Michael; Gómez-Laich, Agustina; Quintana, Flavio; Rosell, Frank; Graf, Patricia M.; Williams, Hannah; Gunner, Richard; Hopkins, Lloyd; Marks, Nikki; Geraldi, Nathan; Duarte, Carlos M.; Scott, Rebecca; Strano, Michael S.; Robotka, Hermina; Eizaguirre, Christophe; Fahlman, Andreas; Shepard, Emily L. C.; Wilson, Rory P. (Figshare, 2019-05-07) [Dataset]
    Data associated with the paper "Estimates for energy expenditure in free-living animals using acceleration proxies; a reappraisal", accepted for publication in the Journal of Animal Ecology in 2019.
  • Data from: Extra-pair mating in a socially monogamous and paternal mouthbrooding cardinalfish

    Rueger, Theresa; Harrison, Hugo B.; Gardiner, Naomi M.; Berumen, Michael L.; Jones, Geoffrey P. (Dryad, 2019-04-04) [Dataset]
    Many vertebrates form monogamous pairs to mate and care for their offspring. However, genetic tools have increasingly shown that many offspring arise from matings outside of the monogamous pair bond. Social monogamy is relatively common in coral reef fishes, but there have been relatively few studies that have confirmed monogamy or extra-pair reproduction, either for males or females. Here long-term observations and genetic tools were applied to examine the parentage of embryos in a paternally mouthbrooding cardinalfish, Sphaeramia nematoptera. Paternal care in fishes, such as mouth brooding, is thought to be associated with a high degree of confidence in paternity. Two-years of observations confirmed that S. nematoptera form long-term pair bonds within larger groups. However, genetic parentage revealed extra-pair mating by both sexes. Of 105 broods analysed from 64 males, 30.1% were mothered by a female that was not the partner and 11.5% of broods included eggs from two females. Despite the high paternal investment associated with mouthbrooding, 7.5% of broods were fertilised by two males. Extra-pair matings appeared to be opportunistic encounters with individuals from outside the immediate group. We argue that while pair formation contributes to group cohesion, both males and females can maximise lifetime reproductive success by taking advantage of extra-pair mating opportunities. The results contradict the theory that paternal care is associated with a high confidence in paternity.
  • Research data supporting "Investigation of the Thermoelectric Response in Conducting Polymers Doped by Solid-State Diffusion"

    Kang, K.; Schott, S.; Venkateshvaran, D.; Broch, K.; Schweicher, G.; Harkin, D.; Jellett, C.; Nielsen, C.B.; McCulloch, Iain; Sirringhaus, H. (Apollo - University of Cambridge Repository, 2019-03-28) [Dataset]
    Research data supporting the journal publication "Investigation of the Thermoelectric Response in Conducting Polymers Doped by Solid-State Diffusion" is provided, sorted by the figures displaying the underlying data. See the associated README file for further information about this dataset.
  • Data for "grain-displacive gas migration in fine-grained sediments"

    Sun, Zhonghao; Santamarina, Carlos (2019-02-03) [Dataset]

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