images of flora from nature or of specimens, family Cyperaceae. Only a few of the many sedge spp. are of interest to people in central Mali: Cyperus articulatus (aromatic tubers), Cyperus esculentus (commercialized edible tubers, "pois sucrés"), Cyperus maculatus (rootstocks burned as incense), Cyperus rotundus (edible tubers, not very good and not commercialized).
images of flora from nature or of specimens, family Cucurbitaceae . There are some difficulties involving determinations of wild melons with protrusions (horns), Cucumis pustulatus/metuliferus/prophetarum. Cultivated spp. are Lagenaria (gourd, calabash), Citrullus lanatus (watermelon), and Cucurbita (squash/pumpkin).
images of flora from nature or of specimens, family Cleomaceae. This family was previously part of Capparaceae, and is now sometimes included in Brassicaceae.
images of flora from nature or of specimens, family Burseraceae. Commiphora africana produces a gum (bdellium) known as albarkante in Mali and widely burned as incense.
images of flora from nature or of specimens, family Brassicaceae (formerly Cruciferae). Most of the native plants of this family are Saharan, if Cleomaceae is treated as a separate family as in this collection.
images of plants in nature or specimens, family Annonaceae. Annona reticulata and A. squamosa are planted in courtyards for their fruits (sweetsop). Xylopia is an imported spice ("grains of Selim").
images of plants in nature or specimens, family Anacardiaceae. Includes Anacardium (cashew) and Mangifera (mango). Genus Ozoroa was included in Heeria in the past.
images of plants in nature or specimens, family Amaranthaceae. The ex-Chenopodiaceae are listed as Amaranthaceae_Chenopodioideae. Our specimens of the cultivated amaranth (a sauce vegetable) are listed as Amaranthus_cf._dubius/hybridus.
images of nonflowering plants. file names begin with fl (for "flora") plus "fern", "fungi", or "lichen". The lichen Pseudevernia is imported dry as a spice especially in Timbuktu.
Documentary videos of blacksmiths and carpenters (see also the work "construction and boatbuilding"). Credits are at the end of videos. Additional documentaries from Mali may be added later.
Documentary videos of food and beverage production by Bozo and Dogon people. Credits are at the end of videos. Additional documentaries from Mali may be added later.
Documentary videos showing fishing techniques chiefly of Bozo people (plus some Dogon). Credits are at the end of videos. Additional documentaries from Mali may be added later.
Documentary videos of farming and of foraging for useful native plants. Credits are at the end of videos. Additional documentaries from Mali may be added later.
Documentation of Dogon fox-track divination, a Dogon memorial altar, and a Bozo boat race. Credits are at the end of videos. Additional documentaries from Mali may be added later.
Documentary videos of construction of a granary and building a large skiff (boat). Credits are at the end of videos. Additional documentaries from Mali may be added later.
Videos featuring native plants of Burkina Faso. Credits are at the end of videos. Additional documentaries from Burkina may be added later. Images of native plants will be in a distinct collection.
Occasional videos involving native insects of SW Burkina Faso. Credits are at the end of videos. Additional documentaries from Burkina may be added later. See also the "bees ..." work in this collection.
Documentary videos of metalwork (blacksmiths) and woodwork from Burkina Faso. Credits are at the end of videos. Additional documentaries from Burkina may be added later.
documentary video of small-scale artisanal gold digging in SW Burkina Faso. Credits are at the end of videos. Additional documentaries from Burkina may be added later.
Documentary videos showing food and beverage preparation in SW Burkina Faso. Credits at end of videos. Additional documentaries from Burkina may be added later.
Five-part documentary on making apiaries and collecting honey. Vigué ethnicity, Viemo language. location: near Karangasso-Vigué, southwestern Burkina Faso. credits at end of videos. Other documentaries from Burkina may be added later.
This is data from Wallace, Benyamini et al., 2023, Journal of Neural Engineering. There are two sets of data included:
1. Neural features and error labels used to train error classifiers for each day used in the study
2. Trial data from an example experiment day (Monkey N, Day 6), with runs for offline calibration, online brain control, error monitoring, and error correction.
The purpose of this study was to investigate the use of error signals in motor cortex to improve brain-machine interface (BMI) performance for control of two finger groups. All data is contained in .mat files, which can be opened using MATLAB or the Python SciPy library.
Wallace, D. M., Benyamini, M., Nason-Tomaszewski, S. R., Costello, J. T., Cubillos, L. H., Mender, M. J., Temmar, H., Willsey, M. S., Patil, P. G., Chestek, C. A., & Zacksenhouse, M. (2023). Error detection and correction in intracortical brain–machine interfaces controlling two finger groups. Journal of Neural Engineering, 20(4), 046037. https://doi.org/10.1088/1741-2552/acef95
This dataset was generated for our work: "Tunable Assembly of Host–Guest Colloidal Crystals". The data set contains data for 5 different binary systems of star particles and convex guests, and one system of only star particles. All simulation were formed at constant pressure. The data set contains GSD files for each of the simulations used in this work along with the corresponding python code used to produce the simulations.
We also include the python code and jupyter notebook to produce the free volume calculations used in this work. and How to use this Data:
Simulation Data:
We include GSD files that can be uploaded into a visualization or analysis software such as Ovito or Freud for independent analysis.
Simulation python scripts (workspaces_for_HPMC_simulations.zip):
We include the python scripts used in this work for simulating host guest systems at constant pressure.
Free Volume Data (Free_volume_calculations_and_analysis.zip):
You can run the jupyter notebook included here to reproduce the free volume analysis for this work.
We also include the python scripts for the free volume calculation python scripts that get the data for these free volume calculations.
The procedure followed while creating this data is summarized in Section II of Chen, Brian, et al. "Behavioral cloning in atari games using a combined variational autoencoder and predictor model." 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2021. This data is not a result of a research but an intermediate product that is used in research.
This dataset is generated to train a behavioral cloning framework from gameplay screen captures and keystrokes of an "expert" player. The RL agent that is trained using "RL Baselines Zoo package" acts as the "expert" player, whose decision making process we desire to learn. In addition to behavioral cloning experiments, this dataset is further used to demonstrate the efficacy of a novel incremental tensor decomposition algorithm on image-based data streams.
Chen, Brian, et al. "Behavioral cloning in atari games using a combined variational autoencoder and predictor model." 2021 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2021., Aksoy, Doruk, et al. "An Incremental Tensor Train Decomposition Algorithm." arXiv preprint arXiv:2211.12487 (2022)., and Chen, Brian, et al. "Low-Rank Tensor-Network Encodings for Video-to-Action Behavioral Cloning", forthcoming
Reconstructed CT slices for tooth in bone fragment of Colognathus obscurus (University of Michigan Museum of Paleontology catalog number UMMP 7506) as a series of TIFF images. Raw projections are not included in this dataset. The reconstructed slice data from the scan are offered here as a series of unsigned 16-bit integer TIFF images. The upper left corner of the first image (*_0000.tif) is the XYZ origin.
This is part of the simulation set of geomagnetic storms from 2010 to 2019. The Space Weather Modeling Framework (SWMF) with the configuration of SWPC v2 was used. The output files can be read by the visualization scripts included in the SWMF or the SpacePy Python package.
Amyloid nanofibers are abundant in microorganisms and are integral components of many biofilms, serving various purposes, from virulent to structural. Nonetheless, the precise characterization of bacterial amyloid nanofibers has been elusive, with incomplete and contradicting results. The present work focuses on the molecular details and characteristics of PSMa1-derived functional amyloids present in Staphylococcus aureus biofilms, using a combination of computational and experimental techniques, to develop a model that can aid the design of compounds to control amyloid formation. Results from molecular dynamics simulations, guided and supported by spectroscopy and microscopy, show that PSMa1 amyloid nanofibers present a helical structure formed by two protofilaments, have an average diameter of about 12 nm, and adopt a left-handed helicity with a periodicity of approximately 72 nm. The chirality of the self-assembled nanofibers, an intrinsic geometric property of its constituent peptides, is central to determining the fibers' lateral growth.
Paolo Elvati, Chloe Luyet, Yichun Wang, Changjiang Liu, J. Scott VanEpps, Nicholas A. Kotov, and Angela Violi ACS Applied Nano Materials 2023 6 (8), 6594-6604 DOI: 10.1021/acsanm.3c00174
A growing body of work has linked key biological activities to the mechanical properties of cellular membranes, and as a means of identification. Here, we present a computational approach to simulate and compare the vibrational spectra in the low-THz region for mammalian and bacterial membranes, investigating the effect of membrane asymmetry and composition, as well as the conserved frequencies of a specific cell. We find that asymmetry does not impact the vibrational spectra, and the impact of sterols depends on the mobility of the components of the membrane. We demonstrate that vibrational spectra can be used to distinguish between membranes and, therefore, could be used in identification of different organisms. The method presented, here, can be immediately extended to other biological structures (e.g., amyloid fibers, polysaccharides, and protein-ligand structures) in order to fingerprint and understand vibrations of numerous biologically-relevant nanoscale structures.