Find research datasets worth reusing

opencc-by-4.0Jan 2022View details →

A semi-analytical solution for heat transport in rock with parallel fractures and a heat source in both fracture and matrix

In this study, we propose a two-dimensional semi-analytical solution framework based on a Green’s function approach for a flexible heat source definition, including source dimensions, energy delivery strength and duration, and the presence of a heat source in the matrix and/or fracture. The solution fully accounts for heat conduction, advection, dispersion and transient heat exchange between the mobile and immobile phases in a system of parallel fractures. The solution having a strip heat source extending from a fracture into the matrix indicates that one-dimensional heat conduction in the matrix underestimates and overestimates temperature responses at early and later times, respectively. The dataset is for the figures 2-7 in the journal paper.

opencc-by-4.0Jan 2022View details →

Dual chirped microcomb based parallel ranging at megapixel-line rates

Available data for manuscript: "Dual chirped microcomb based parallel ranging at megapixel-line rates" Arxiv version: https://arxiv.org/abs/2101.03952 Execution tested with Matlab 2019a or newer on Windows. Unzip folder to access files. For Figures and SI Figures execute "Figure*.m" files in corresponding subfolders. Contact anton.lukashchuk@epfl.ch or anton.lukashchuk@skolkovotech.ru if problems with matlab code arise.  All matlab code remains under copyright by the authors: Anton Lukashchuk and Johann Riemensberger; the code is provided solely to be used to reproduce the figures of the aforementioned paper. Raw data for the figures is stored in folder .\Data. GDS file of Si3N4 photonic damascene waveguide resonators is stored in folder: GDS_design.

opencc-zeroJan 2022View details →

Historical museum samples enable the examination of divergent and parallel evolution during invasion

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in north-western Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.

opencc-by-4.0Apr 2022View details →

Supplementary files for, 'Developmental morphology and anatomy shed light on both parallel and convergent evolution of the umbellate inflorescence in Monocots, underlied by a new variant of metatopy.'

Supplementary file for forth coming manuscript. Consists of Pre-processed microscopy images, FiJI readable annotated stacks and raw laser ablation tomography video data   File name:  MainFigures.zip  File format: .zip, individual images in .bmp format. Description of data: Picolay output of main figure panels.   File name:  Supplementary_File_1 File format: .MOV (video) Description of data: Movie 1 LAT scan of Butomus umbellatus   File name:  Supplementary_File_2 File format: .AVI (video) Description of data: Three-dimensional reconstruction of Butomus umbellatus inflorescence   File name:  Supplementary_File_3 File format: .MOV (video) Description of data: Movie 3 Three-dimensional reconstruction of Butomus umbellatus vasculature   File name:  Supplementary_File_4 File format: .TIFF (Can be opened in FIJI) Description of data: Butomus umbellatus vasculature composite tiff file   File name:  Supplementary_File_5 File format: .MOV (video) Description of data: LAT scan of Ornithogalum umbellatum   File name:  Supplementary_File_6 File format: .TIFF (Can be opened in FIJI) Description of data: Ornithogalum umbellatum vasculature tiff file (Can be opened in FIJI)   File name: Supplementary_File_7 File format: .MOV (video) Description of data: LAT scan of Allium hollandicum inflorescence

opencc-by-4.0Feb 2022View details →

Model data repository of "Styles of Trench-parallel Mid-ocean Ridge Subduction Affect Cenozoic Geological Evolution in circum-Pacific Continental Margins"

This dataset contains the data used in Wu et al. (2022): "Styles of Trench-parallel Mid-ocean Ridge Subduction Affect Cenozoic Geological Evolution in circum-Pacific Continental Margins".

opencc-by-4.0Apr 2022View details →

MCPNet : A parallel maximum capacity-based genome-scale gene network construction framework

This deposit contains the gene expression profile datasets used for the paper titled "MCPNet : A parallel maximum capacity-based genome-scale gene network construction framework".  There are three sets of data: <ul> <li>Simulated yeast data from NetBenchmark, with random noise injected, as well as the ground truth network matrix.  In "SimulatedYeast.zip".</li> <li>Real Yeast dataset and the ground truth network as an adjacency list file.  in "yeast_data.exp" and "yeast_gs1_list_filtered.tsv".  Data acquired from "Castro DM, de Veaux NR, Miraldi ER, Bonneau R (2019) Multi-study inference of regulatory networks for more accurate models of gene regulation. PLoS Comput Biol 15(1): e1006591. https://doi.org/10.1371/journal.pcbi.1006591", <a href="https://github.com/simonsfoundation/multitask_inferelator/tree/AMuSR">https://github.com/simonsfoundation/multitask_inferelator/tree/AMuSR</a>.</li> <li>Real Arabidopsis athaliana datasets for 5 tissues and 1 environmental challenge.  <ul> <li>athaliana_gs_probes.tsv : ground truth as an adjacency list</li> <li>microarray gene expression profiles for "development", "leaf", "seed", "flower", "seedling1week", "hormone-aba-iaa-ga-br".</li> <li>Aathaliana.Datasets-CEL-File-URLs.xlsx: list of SRA accession numbers for the A. athaliana datasets</li> </ul> </li> </ul>

opencc-by-4.0May 2022View details →

Performance results of ARMOSA model parallelized with COMPSs

Scripts and data results to build the performance graph of the LandSupport ARMOSA application parallelized with COMPSs. This results have been published in D3.6 - REPORT ON THE FINAL MODELS IMPLEMENTATION AND OPTIMIZATION. The archive contains the python script to generate the graphs, and the dataset of the times resulting from the execution of the application in the LandSupport platform. The execution times can only be generated on such platform.

opencc-by-4.0Apr 2022View details →

HDF5 datasets and python scripts to generate figures in "Butterfly distribution of relativistic electrons driven by parallel propagating lower band whistler chorus waves"

HDF5 datasets and python scripts to generate figures in "Butterfly distribution of relativistic electrons driven by parallel propagating lower band whistler chorus waves" RBW simulation datasets in HDF5 format: <ul> <li>300pT.h5    The particle dataset to generate the figures.</li> </ul> Python scripts to generate figures in the manuscript. - Environment: Python 3.6.7 :: Anaconda 4.4.0 (64-bit) - Required modules: matplotlib, numpy, h5py <ul> <li>Figure1.py    Generate figure 1.</li> <li>Figure2.py    Generate figure 2.</li> <li>Figure3.py    Generate figure 3.</li> <li>Figure4.py    Generate figure 4.</li> <li>QLDe.py       Calculate bounce averaged diffusion coefficients according to Shprits et al. (2006) (doi: https://doi.org/10.1029/ 2006JA011725).</li> </ul>

opencc-zeroMay 2022View details →

Parallel generation of extensive vascular networks with application to an archetypal human kidney model

Given the relevance of the inextricable coupling between microcirculation and physiology, and the relation to organ function and disease progression, the construction of synthetic vascular networks for mathematical modelling and computer simulation is becoming an increasingly broad field of research. Building vascular networks that mimic in-vivo morphometry is feasible through algorithms such as constrained constructive optimisation (CCO) and variations. Nevertheless, these methods are limited by the maximum number of vessels to be generated due to the whole network update required at each vessel addition. In this work, we propose a CCO-based approach endowed with a domain decomposition strategy to concurrently create vascular networks. The performance of this approach is evaluated by analysing the agreement with the sequentially generated networks and studying the scalability when building vascular networks up to 200,000 vascular segments. Finally, we apply our method to vascularise a highly complex geometry corresponding to the cortex of a prototypical human kidney. The technique presented in this work enables the automatic generation of extensive vascular networks, removing the limitation from previous works. Thus, we can extent vascular networks (e.g., obtained from medical images) to pre-arteriolar level, yielding patient-specific whole-organ vascular models with an unprecedented level of detail.

opencc-by-4.0Jun 2022View details →

Codes for "High-throughput parallel optofluidic 3D-imaging flow cytometry"

Codes used in Ugawa & Ota. "High-throughput parallel optofluidic 3D-imaging flow cytometry". Small size data is also included.

opencc-zeroJun 2022View details →

Scan files, 3D reconstructions, data spreadsheet and supplementary files for Heterochrony and parallel evolution of echinoderm, hemichordate and cephalochordate internal bars

Deuterostomes comprise three phyla with radically different body plans. Phylogenetic bracketing of the living deuterostome clades suggests the latest common ancestor of echinoderms, hemichordates and chordates was a bilaterally symmetrical worm with pharyngeal openings, with these characters lost in echinoderms. Early fossil echinoderms with pharyngeal openings have been described, but their interpretation is highly controversial. Here, we critically evaluate the evidence for pharyngeal structures (gill bars) in the extinct stylophoran echinoderms Lagynocystis pyramidalis and Jaekelocarpus oklahomensis using virtual models based on high-resolution X-ray tomography scans of three-dimensionally preserved fossil specimens. Multivariate analyses of the size, spacing and arrangement of the internal bars in these fossils indicate they are substantially more similar to gill bars in modern enteropneust hemichordates and cephalochordates than to other internal bar-like structures in fossil blastozoan echinoderms. The close similarity between the internal bars of the stylophorans L. pyramidalis and J. oklahomensis and the gill bars of extant chordates and hemichordates is strong evidence for their homology. Differences between these internal bars and bar-like elements of the respiratory systems in blastozoans suggest these structures might have arisen through parallel evolution across deuterostomes, perhaps underpinned by a common developmental genetic mechanism.

opencc-zeroJul 2022View details →

Data from: Local adaptation to seasonal cues at the fronts of two parallel, climate-induced butterfly range expansions

Climate change allows species to expand polewards, but non-changing environmental features may limit expansions. Daylength is unaffected by climate and drives life cycle timing in many animals and plants. Because daylength varies over latitudes, poleward-expanding populations must adapt to new daylength conditions. We studied local adaptation to daylength in the butterfly Lasiommata megera, which is expanding northwards along several routes in Europe. Using common garden laboratory experiments with controlled daylengths, we compared diapause induction between populations from the southern-Swedish core range and recently established marginal populations from two independent expansion fronts in Sweden. Caterpillars from the northern populations entered diapause in clearly longer daylengths than those from southern populations, with the exception of caterpillars from one geographically isolated population. The northern populations have repeatedly and rapidly adapted to their local daylengths, indicating that the common use of daylength as seasonal cue need not strongly limit climate-induced insect range expansions.

opencc-by-4.0Dec 2021View details →

Text-fig. 9. a: Arenicolites isp., BK 13, Layer No. 6; b–f: Bifungites isp., a set of specimens showing variability in chamber shape, b – field photograph, Layer No. 23, c – field photograph, Layer No. 23, d – field photograph, Layer No. 23, e – parallel-orientated specimens, field photograph, Layer No. 23, f – field photograph, Layer No. 23; g: Didymaulichnus isp., convex epirelief, field photograph, Layer No. 1. Scale bar = 1 cm. in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic

Text-fig. 9. a: Arenicolites isp., BK 13, Layer No. 6; b–f: Bifungites isp., a set of specimens showing variability in chamber shape, b – field photograph, Layer No. 23, c – field photograph, Layer No. 23, d – field photograph, Layer No. 23, e – parallel-orientated specimens, field photograph, Layer No. 23, f – field photograph, Layer No. 23; g: Didymaulichnus isp., convex epirelief, field photograph, Layer No. 1. Scale bar = 1 cm.

Text-fig. 4. Charred grass from diatomite of Saint-Bauzile. a: Overview of diatomite slab with one larger specimen of charred grass (left) and several smaller, lath-shaped charcoal fragments; SM.B 22260; scale bar = 1 cm. b: Detail of vein exhibited on split grass blade, with stomata oriented parallel to vein. c: Stomata oriented in rows and bands parallel to veins exposed on split grass blade. d: Surface of grass leaf with rectangular, elongated cells with strongly undulating margins in an intercostal area. in Evidence For Wildfires During Deposition Of The Late Miocene Diatomites Of The Konservat-Lagerstätte Lake Saint-Bauzile (Ardèche, France) - Preliminary Results

Text-fig. 4. Charred grass from diatomite of Saint-Bauzile. a: Overview of diatomite slab with one larger specimen of charred grass (left) and several smaller, lath-shaped charcoal fragments; SM.B 22260; scale bar = 1 cm. b: Detail of vein exhibited on split grass blade, with stomata oriented parallel to vein. c: Stomata oriented in rows and bands parallel to veins exposed on split grass blade. d: Surface of grass leaf with rectangular, elongated cells with strongly undulating margins in an intercostal area.

Text-fig. 3. Juglandaceae. Carya (a–x). Scale bars = 1 cm. a–e: USNM PAL 772346. Micro-CT scan surface rendering. a, b: Lateral, c: apical, d: basal views. e: Virtual equatorial transverse section. f–n: USNM PAL 772347. f: Lateral view, reflected light, showing path of saw cut for transverse section of (i). g: Basal view, reflected light. h: Apical view, micro-CT surface rendering. i: Physical transverse section displaying locule and cellular preservation of parts of wall. j–n: Virtual sections from micro-CT scan data. j: Transverse section at apical 1/3 of nut. Note narrow lacunae (arrows). k: Longitudinal section parallel to primary septum, traversing one of the cotyledon lobes and showing secondary septum at base. l: Longitudinal section in plane at right angles to (k) in plane of primary septum, showing divergent placental bundles arising from base of nut (arrows). m: Equatorial transverse section showing two lobes of locule separated by primary septum. n: Transverse section near base of nut showing primary and secondary septa, creating four basal lobes of locule; note diverging placental bundles (arrows). o–x: USNM PAL 772351. o: Lateral view of broken nut with exposed locule cast, reflected light. p: Same orientation of nut, micro-CT surface rendering. q: Same specimen lateral view, rotated 90° from (p), micro-CT surface rendering. r: Apical view, reflected light. s–x: Virtual sections from micro-CT in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.

Text-fig. 3. Juglandaceae. Carya (a–x). Scale bars = 1 cm. a–e: USNM PAL 772346. Micro-CT scan surface rendering. a, b: Lateral, c: apical, d: basal views. e: Virtual equatorial transverse section. f–n: USNM PAL 772347. f: Lateral view, reflected light, showing path of saw cut for transverse section of (i). g: Basal view, reflected light. h: Apical view, micro-CT surface rendering. i: Physical transverse section displaying locule and cellular preservation of parts of wall. j–n: Virtual sections from micro-CT scan data. j: Transverse section at apical 1/3 of nut. Note narrow lacunae (arrows). k: Longitudinal section parallel to primary septum, traversing one of the cotyledon lobes and showing secondary septum at base. l: Longitudinal section in plane at right angles to (k) in plane of primary septum, showing divergent placental bundles arising from base of nut (arrows). m: Equatorial transverse section showing two lobes of locule separated by primary septum. n: Transverse section near base of nut showing primary and secondary septa, creating four basal lobes of locule; note diverging placental bundles (arrows). o–x: USNM PAL 772351. o: Lateral view of broken nut with exposed locule cast, reflected light. p: Same orientation of nut, micro-CT surface rendering. q: Same specimen lateral view, rotated 90° from (p), micro-CT surface rendering. r: Apical view, reflected light. s–x: Virtual sections from micro-CT

Text-fig. 2. Salicaceae (a–g), Cannabaceae (h–n), cf. Betulaceae (o–r). a–g: Saxifragispermum, USNM PAL 772341. Scale bar = 5 mm except as indicated. a–b: Lateral, c: apical, and d: basal views of fruit, reflected light, palladium coated; apex at top of (a, b). e: Equatorial transverse section reflected light; arrows indicate presumed seeds, scale bar = 2 mm. f: Detail of locule contents extracted from (e), transmitted light, scale bar = 200 Μm. g: Interwoven trichomes or fibers from locule, transmitted light, scale bar = 5 Μm. h–j: Celtis. h, i: USNM PAL 772342, reflected light, palladium coated, scale bar = 5 mm. h: Lateral view parallel with plane of dehiscence. i: Lateral view perpendicular to plane of dehiscence. j: DMNH EPI.47809, Celtis in lateral view; showing reticulate sculpture and the vertically-oriented, plane of dehiscence (arrow), scale bar = 5 mm. k–m: Aphananthe. USNM PAL 772344, reflected light, palladium coated, scale bar = 5 mm. k: Apical view, note triangular cross section and apical plug (arrow). l: Lateral view, apex up. m: Lateral view at 90° to (l). n: Detail of cellular pattern at surface of endocarp, scale bar = 0.5 mm. o–r: in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.

Text-fig. 2. Salicaceae (a–g), Cannabaceae (h–n), cf. Betulaceae (o–r). a–g: Saxifragispermum, USNM PAL 772341. Scale bar = 5 mm except as indicated. a–b: Lateral, c: apical, and d: basal views of fruit, reflected light, palladium coated; apex at top of (a, b). e: Equatorial transverse section reflected light; arrows indicate presumed seeds, scale bar = 2 mm. f: Detail of locule contents extracted from (e), transmitted light, scale bar = 200 Μm. g: Interwoven trichomes or fibers from locule, transmitted light, scale bar = 5 Μm. h–j: Celtis. h, i: USNM PAL 772342, reflected light, palladium coated, scale bar = 5 mm. h: Lateral view parallel with plane of dehiscence. i: Lateral view perpendicular to plane of dehiscence. j: DMNH EPI.47809, Celtis in lateral view; showing reticulate sculpture and the vertically-oriented, plane of dehiscence (arrow), scale bar = 5 mm. k–m: Aphananthe. USNM PAL 772344, reflected light, palladium coated, scale bar = 5 mm. k: Apical view, note triangular cross section and apical plug (arrow). l: Lateral view, apex up. m: Lateral view at 90° to (l). n: Detail of cellular pattern at surface of endocarp, scale bar = 0.5 mm. o–r:

Text-fig. 4. Juglandaceae Carya (a–w). Scale bars = 1 cm. a–d: USNM PAL 772352, reflected light, palladium coated. a: Obliquelateral view of nut, apex up. b: Basal view with damage to left and clear depiction of meridional grooves. c, d: Two lateral views oriented about 130° from each other and avoiding the area of damage; the meridional grooves clear in (c). e–l: USNM PAL 772350. e: Intact nut, lateral view, apex up, reflected light. f: One half of split nut revealing in situ chalcedony locule cast, reflected light. g–k: Virtual sections from micro-CT data. g: Longitudinal section parallel to the exposed face in (f). h: Longitudinal section at 90° from (g). i: Transverse section in apical 1/3 showing locule bracketed by C-shaped lacunae (arrows). j: Equatorial transverse section showing two lobes of the locule separated by primary septum, lacuna evident below as white line. k: Transverse section near base in The Early Middle Eocene Wagon Bed Carpoflora Of Central Wyoming, U.S.A.

Text-fig. 4. Juglandaceae Carya (a–w). Scale bars = 1 cm. a–d: USNM PAL 772352, reflected light, palladium coated. a: Obliquelateral view of nut, apex up. b: Basal view with damage to left and clear depiction of meridional grooves. c, d: Two lateral views oriented about 130° from each other and avoiding the area of damage; the meridional grooves clear in (c). e–l: USNM PAL 772350. e: Intact nut, lateral view, apex up, reflected light. f: One half of split nut revealing in situ chalcedony locule cast, reflected light. g–k: Virtual sections from micro-CT data. g: Longitudinal section parallel to the exposed face in (f). h: Longitudinal section at 90° from (g). i: Transverse section in apical 1/3 showing locule bracketed by C-shaped lacunae (arrows). j: Equatorial transverse section showing two lobes of the locule separated by primary septum, lacuna evident below as white line. k: Transverse section near base

opencc-by-4.0Feb 2023View details →

parallel-fibered bone; A5, osteocyte lacunae with well-preserved canaliculi; B3, osteocyte lacunae lacking canaliculi; B4, B5, growth pattern with preserved residuals of the thick annuli and zones (zo I–III) and thin annuli and zones (zo IV–VII); A6, growth pattern with preserved thin annuli and thick zones (zo I–IV), the dotted line marks the border between the perimedullary region and the cortex. Arrows in A5 and B3 indicate osteocyte lacunae; in B4, B5, and A6 indicate the annuli. Growth pattern in B4 figured on the lateral section side, in B5 and A5 on the ventral side; note the cortex thickness variation between B4 and B5. A1, A3, A4, A6, B1, B4, B5 in polarized light and A2, A5, B2, B3 in normal transmitted light. Abbreviations: an, annulus; ec, erosion cavity; pmr, perimedullary region; pos, primary osteon; sos, secondary osteon; zo, zone. in Palaeohistology helps reveal taxonomic variability in exceptionally large temnospondyl humeri from the Upper Triassic of Krasiejów, SW Poland

parallel-fibered bone; A5, osteocyte lacunae with well-preserved canaliculi; B3, osteocyte lacunae lacking canaliculi; B4, B5, growth pattern with preserved residuals of the thick annuli and zones (zo I–III) and thin annuli and zones (zo IV–VII); A6, growth pattern with preserved thin annuli and thick zones (zo I–IV), the dotted line marks the border between the perimedullary region and the cortex. Arrows in A5 and B3 indicate osteocyte lacunae; in B4, B5, and A6 indicate the annuli. Growth pattern in B4 figured on the lateral section side, in B5 and A5 on the ventral side; note the cortex thickness variation between B4 and B5. A1, A3, A4, A6, B1, B4, B5 in polarized light and A2, A5, B2, B3 in normal transmitted light. Abbreviations: an, annulus; ec, erosion cavity; pmr, perimedullary region; pos, primary osteon; sos, secondary osteon; zo, zone.

opencc-zeroMay 2024View details →

Data from: Understanding evolutionary rescue and parallelism in response to environmental stress

Evolutionary rescue, the process by which populations facing environmental stress avoid extinction through genetic adaptation, is a critical area of study in evolutionary biology. The order in which mutations arise and get established will be relevant to the population's rescue. This study investigates the degree of parallel evolution at the genotypic level between independent populations facing environmental stress and subject to different demographic regimes. Under density regulation, two regimes exist: in the former, the population can restore positive growth rates by adjusting its population size or through adaptive mutations, whereas in the second regime, the population is doomed to extinction unless a rescue mutation occurs. Analytical approximations for the likelihood of evolutionary rescue are obtained and contrasted with simulation results. We show that the initial level of maladaptation and the demographic regime significantly affect the level of parallelism. There is an evident transition between these two regimes. Whereas in the first regime, parallelism decreases with the level of maladaptation, it displays the opposite behavior in the rescue/extinction regime. These findings have important implications for understanding population persistence and the degree of parallelism in evolutionary responses as they integrate demographic effects and evolutionary processes.