Find research datasets worth reusing

opencc-by-4.0Jan 2023View details →

Replication package for: "WHEN LESS IS MORE: EXPERIMENTAL EVIDENCE ON INFORMATION DELIVERY DURING INDIA'S DEMONETIZATION"

This package contains all data, codes, documentation required to reproduce figures and tables from Banerjee, Breza, Chandrasekhar, & Golub (forthcoming). "When Less is More: Experimental Evidence on Information Delivery During India's Demonetization" Review of Economic Studies.

opencc-by-4.0Apr 2023View details →

COVID-19 PBMC sample information and the VCF file of variants around OAS1 gene.

We investigated our recently published PBMC scRNA-seq data (Stephenson et al. 2021 Nat Med) obtained from 112 donors, including 84 COVID-19 positive individuals, and profiled using the CITE-seq approach, as an independent in vivo validation of OAS1 eQTL colocalisation with GWAS locus for COVID-19 susceptibility. The dataset includes both sample information and genotype information of variants around OAS1 gene (chr12:111906777-113906777) as in VCF format. The whole variant data of the COVID-19 PBMC samples is available upon request.

opencc-by-4.0Apr 2023View details →

SIMARA: a database for key-value information extraction from full-page handwritten documents

We propose a new database for information extraction from historical handwritten documents. The corpus includes 5,393 finding aids from six different series, dating from the 18th-20th centuries. Finding aids are handwritten documents that contain metadata describing older archives. They are stored in the National Archives of France and are used by archivists to identify and find archival documents. Each document is annotated at page-level, and contains seven fields to retrieve. The localization of each field is not available in such a way that this dataset encourages research on segmentation-free systems for information extraction.

opencc-by-4.0Mar 2023View details →

Using environmental DNA to inform decommissioning decisions for offshore oil and gas infrastructure

Abstract Artificial reefs are being utilised globally to aid in natural resource management, conservation, habitat restoration or the creation of unique marine habitats. There is much discussion around the optimal construction materials and designs for artificial reefs, the influences these have on biological communities, and the resulting ecological and social benefits. This discussion also includes the ecological value of repurposed marine infrastructure, such as decommissioned oil and gas platforms. Platforms often have an operational life spanning multiple decades, over which time they can develop extensive and unique community assemblages. The creation of artificial reefs by repurposing oil and gas platforms can have ecological, economic and sociological merit. However, with more than 12,000 platforms requiring decommissioning globally, there is the need for holistic assessment of biological communities associated with these platforms to inform the potential outcomes of different decommissioning options. We use environmental DNA metabarcoding (eDNA) of water, bio-foul and sediment samples to census broad eukaryotic diversity at eight platforms in the Gulf of Thailand (GoT) and five nearby soft sediment habitat locations. From the three depths targeted, we detected 430 taxa at platforms, with higher diversity in shallow (near-surface) samples (313 taxa), compared to mid (30 m collection depth; 261 taxa) and deep (50 m; 273 taxa). Only three percent of taxa were shared among all depths at platforms. Indicator taxa driving differences at platform depths were of the phyla Chordata, Arthropoda and Echinodermata for shallow samples and Cnidaria, Chlorophyta and Porifera for deep. No known introduced species were detected in platform samples. The frameworks supporting eDNA methodologies, such as taxonomy, assay availability and local reference material, particularly in diverse tropical habitats, require improvement for robust taxonomic analysis. This study highlights the versatility and scalability of eDNA metabarcoding in being able to holistically census marine infrastructure and inform the management and potential conservation of extant platform communities.

opencc-by-4.0Mar 2022View details →

Designing single-cell experiments to harvest fluctuation information while rejecting measurement noise

Numerical simulation outputs and model schematic figures for the Python portion (main text 3.1 and Supporting Information) in the preprint Analysis and design of single-cell experiments to harvest fluctuation information while rejecting measurement noise Huy D. Vo, Linda Forero, Luis Aguilera, Brian Munsky bioRxiv doi: https://doi.org/10.1101/2021.05.11.443611

opencc-by-4.0Jul 2011View details →

Information organizing: an evolutionary and development framework

Information behaviour has emerged as an important aspect of human life; however, our knowledge and understanding of it is incomplete and underdeveloped scientifically. Our understanding of information behaviour and the sub-process information organizing behaviour is largely contemporary in focus. In this presentation Professor Spink discusses an evolutionary and developmental framework for information behaviour and information organizing from her recent book Information Behaviour: An Evolutionary Instinct (2010, Springer) by incorporating related findings, theories and models from evolutionary psychology, cognitive archaeology, cognitive neuroscience and developmental psychology. In her presentation, she argues that information behavior and information organizing are important instinctive socio-cognitive abilities for all humans that can only be fully under- stood with an evolutionary and developmental perspective. Professor Spink’s presentation addresses four important research questions. Firstly, what is the evolutionary, biological and developmental basis for information behaviour and information organizing behaviour? Secondly, what is the role of instinct versus environment in shaping information behaviour and information organizing behaviour? Thirdly, how have information behaviour and organizing capabilities evolved and developed over human species? Fourthly, when and how do information behaviour and in particular information organizing abilities emerge in young children? An evolutionary and developmental approach lays the foundation for a more holistic perspective on information behaviour and information organizing behaviour, and opens many new research directions.

opencc-by-4.0Apr 2023View details →

St. Clair-Detroit River Gastropod Counts and Density Information

Spreadsheet with original data for Chapter 5 of Shay Keretz' PhD Dissertation at Central Michigan University: "Freshwater Gastropod (Mollusca: Gastropoda) Assemblages and First Detection of an Invasive Species in Two Large Connecting Rivers."

opencc-zeroMay 2023View details →

Data from: Hominin fossils from Kromdraai and Drimolen inform Paranthropus robustus craniofacial ontogeny

Growth and development provide critical information about the evolutionary history of early hominin adult morphology. Using fossils from the southern African site of Kromdraai, we herein present the digital models of three juvenile specimens that are especially valuable because they shed light on how the distinct adult craniofacial characteristics of Paranthropus robustus developed. We find significant differences in the development of P. robustus and Australopithecus africanus. Additionally, some features of the P. robustus specimens suggest that the iconic SK 54 juvenile calvaria from the southern African site of Swartkrans is more likely an early Homo specimen rather than Paranthropus. The results of this study shed light on the evolutionary relationships between different early hominin species and could help to identify the closest relative to the Paranthropus/Homo clade.

Total estimated number of informal waste pickers or recyclers in Kathmandu Valley, as of December 2022

Using key informants representing different parts of the informal waste management value chain, the RIPL project has produced an updated estimated total number of informal recyclers for Kathmandu Valley, in December 2022. The overview includes methods of calculation and names of key informants.

Project files provided as supporting information to the manuscript "Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations"

README file to the project files provided as supporting information to the manuscript “Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations" Authors: Manuel Micheloni, Lorenzo Petrolli, Gianluca Lattanzi and Raffaello Potestio ================================== The .zip file is structured as follows: ############## 0_DNA_Sequence ############## The folder contains: • DNAsequence.txt: the DNA molecule employed in the study.  • ecseq.txt: the structure of the DNA. Each nucleotide (LAMMPS residue ID) is associated with the chemical type of the nucleic base. ################### 1_DSB_MDSimulations ################### • MDSimulations:  The LAMMPS MD simulation scripts. The subfolders are structured and named after different DSB motifs (folders 0,1, …,3) providing different external forces (folders 1000, 1100, 1200 refers to the respective average end-to-end distance). The latter subfolders provides: I. LMP_script provides the LAMMPS input file. II. the local internal energy contributions from the nucleotides involved with the residual contact interface between broken DNA moieties (data/1.E);  III. coordinates of the nucleotides involved with the residual contact interface between the DNA moieties (data/2.POS); IV. the binary LAMMPS data file, employed as starting coordinates for the DSB MD simulation (/input_structure). • ScriptsAndAnalysis: The scripts employed to analyze the DSB process.  I. /00_GeneralScripts all the MATLAB functions employed for the analysis. II. /1_SigmoidalFitting provides the scripts from a sigmoidal fitting procedure [1] on the internal energy profile of the nucleotides between the strand breaks (Section 2 of the Supplementary Material).  [1] R P (2022). sigm_fit (https://www.mathworks.com/matlabcentral/fileexchange/42641-sigm_fit), MATLAB Central File Exchange. Retrieved July 2, 2022. ################## 2_DNAFreeDiffusion ################## • SIM: It contains the MD simulations of the freely-diffusing DNA. Namely, the MSD of the DNA molecule, the input structure, and the LAMMPS simulation scripts are reported in /data, /input_structure, and /LMP_scripts respectively. • ANALYSIS: It provides the script employed to estimate the diffusion coefficient of the DNA molecule and the time-scaling factor \Gamma(\zeta). ####################### 3_ForceAnalysis ####################### • data It contains the forces computed from the MD simulations of the intact DNA molecules subject to the external force of 0.42, 0.88 and 3.06 pN. All data are stored in pickle format. The README file contains additional information. NOTE1: Most data/scripts are saved according to the format .mat, employed by MATLAB Ⓡ, a numerical computing environment and proprietary programming language developed by MathWorks. NOTE2: For the force data manipulation, we acknowledge the use of LammpsFileManipulation package (https://pypi.org/project/LammpsFileManipulation/)

Data and supplementary information: Effects of lithium on locomotor activity and circadian rhythm of honey bees

Data and supplementary files for publication:Erdem, B., Arslan, O.C., Sevin, S. Gozen, A. G., Agosto-Rivera, J. L., Tugrul, G., & Alemdar, H. (2023). Effects of lithium on locomotor activity and circadian rhythm of honey bees. Scientific Reports, 13, 19861. https://doi.org/10.1038/s41598-023-46777-7 AcuteExp_Dark_ActivityData.xlsx - Total LMA counts of acute experiment in dark condition.AcuteExp_Light_ActivityData.xlsx - Total LMA counts of acute experiment in light condition.ChronicExp_ActivityData.xlsx - Total LMA counts of the chronic experiment.ChronicExp_MortalityData.xlsx - Mortality data of the chronic experiment.ChronicExp_PeriodRhytmData.xlsx - Defines rhythmic and arrhythmic individuals and the circadian periods (h) of the rhythmic individuals in chronic experiment.LD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the 12 h light / 12 h dark condition.DD_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant dark condition.LL_doubleplots.pdf - Double-plotted actograms of the individuals in the chronic experiment in the constant light condition. In the double-plotted actograms, NR indicates "non-rhythmic" individuals.

opencc-zeroMay 2023View details →

Use of density-impact functions to inform and improve the environmental outcomes of feral horse management

The available science often demonstrates the need for feral horse population control but not the degree of control required to achieve environmental conservation objectives. To better manage the influence of feral horses, we must first understand the relationship between feral horse density and environmental impact. We recorded vegetation and soil disturbance, and the sign of potential causes of this impact in two parts of the Australian Alps, the Bogong High Plains (BHP) and the Eastern Victorian Alps (EVA). We calculated density-impact functions to assist managers with determining feral horse density targets for control programmes. Minimal sign of feral horse impact was detected on the BHP, with no impact of feral horses observed along 99% of the length of transects. In contrast, impacts assigned to feral horses were significantly higher in the EVA, where a larger, higher-density population of feral horses existed. However, greater than 83% of the walked transect length was still undisturbed by feral horses in the EVA. We detected a threshold of horse impact at ~250 horse faecal piles per ha. Above this threshold, a slight increase in horse density resulted in a disproportionately large increase in impact. In this context, a relatively small population control effort may substantially reduce direct horse impact. But where horse densities exist below this threshold, considerably more expense and control effort (resulting from the difficulties related to control at low density) is likely to make very little difference to an already low level of direct impact. The combined impacts associated with the sign of deer, feral pigs, fire and humans were large compared to that of feral horses. Management of feral horses to reduce their direct impact is unlikely to be beneficial without complementary management to reduce the effects of these other agents of impact.

opencc-zeroMay 2023View details →

Data for: Early radial positional information in the cochlea is optimized by a precise linear BMP gradient and enhanced by SOX2

Positional information encoded in signaling molecules is essential for early patterning in the prosensory domain of the developing cochlea. The sensory epithelium, the organ of Corti, contains an exquisite repeating pattern of hair cells and supporting cells. This requires precision in the morphogen signals that set the initial radial compartment boundaries, but this has not been investigated. To measure gradient formation and morphogenetic precision in developing cochlea, we developed a quantitative image analysis procedure measuring SOX2 and pSMAD1/5/9 profiles in mouse embryos at embryonic day (E)12.5, E13.5, and E14.5. Intriguingly, we found that the pSMAD1/5/9 profile forms a linear gradient up to the medial ~75% of the PSD from the pSMAD1/5/9 peak in the lateral edge during E12.5 and E13.5. This is a surprising activity readout for a diffusive BMP4 ligand secreted from a tightly constrained lateral region since morphogens typically form exponential or power-law gradient shapes. This is meaningful for gradient interpretation because while linear profiles offer the theoretically highest information content and distributed precision for patterning, a linear morphogen gradient has not yet been observed. Furthermore, this is unique to the cochlear epithelium as the pSMAD1/5/9 gradient is exponential in the surrounding mesenchyme. In addition to the information-optimized linear profile, we found that while pSMAD1/5/9 is stable during this timeframe, an accompanying gradient of SOX2 shifts dynamically. Last, through joint decoding maps of pSMAD1/5/9 and SOX2, we see that there is a high-fidelity mapping between signaling activity and position in the regions that will become Kölliker's organ and the organ of Corti. Mapping is ambiguous in the prosensory domain precursory to the outer sulcus. Altogether, this research provides new insights into the precision of early morphogenetic patterning cues in the radial cochlea prosensory domain.

Cryogenic electron ptychographic single particle analysis with wide bandwidth information transfer

Advances in cryogenic transmission electron microscopy have revolutionised the determination of many macromolecular structures at atomic or nearatomic resolution. This method is based on conventional defocused phase contrast imaging. However, it has limitations of weaker contrast for small biological molecules embedded in vitreous ice, in comparison with cryo-ptychography, which shows increased contrast. Here we report a single-particle analysis based on the use of ptychographic reconstruction data, demonstrating that three dimensional reconstructions with a wide information transfer bandwidth can be recovered by Fourier domain synthesis. Our work suggests future applications in otherwise challenging single particle analyses, including small macromolecules and heterogeneous or flexible particles. In addition structure determination in situ within cells without the requirement for protein purification and expression may be possible.

Reproducibility Package for Predictive Limitations of Physics-Informed Neural Networks in Vortex Shedding

This archive contains the repro-pack for the paper at <a href="http://github.com/barbagroup/jcs_paper_pinn">https://github.com/barbagroup/jcs_paper_pinn</a>.

Reproducibility Package (Raw Data) for Predictive Limitations of Physics-Informed Neural Networks in Vortex Shedding

Raw data results from the simulations using PINN methods and PetIBM for the paper at: https://github.com/barbagroup/jcs_paper_pinn

An atomistically informed multiscale approach to the intrusion and extrusion in hydrophobic nanopores

Data from Molecular Dynamics simulations. Files ending in .dat are the "measurement" files and are the files required to compute the free energy and diffusivity from the simulation data. The normal sintax is eqX.dat where X is the imposed filling of the pore. The names of the folders represent the pressure at which the filling was taken (0 MPa, -20 MPa, 60 MPa) We also attach one trajectory file, 0.xyz and one LAMMPS output file, 0.log, which should be enough to reproduce the simulation script, in conjuction with 0.data, the initial condition.

opencc-by-4.0Jun 2023View details →

Supplementary information to Bjørn et al. (2023)

This spreadsheet contains the data behind all figures displayed in the following paper:   Title: Differentiation of greenhouse gases in corporate science-based targets improves alignment with Paris temperature goal Authors: Anders Bjørn1-3*, Shannon Lloyd4, Urs Schenker5, Manuele Margni6,7, Annie Levasseur8, Maxime Agez6 and Damon Matthews2 1 Section for Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark. 2 Department of Geography, Planning and Environment, Concordia University, Montréal, Canada. 3 Centre for Absolute Sustainability, Technical University of Denmark, Kongens Lyngby, Denmark. 4 Department of Management, Concordia University, Montréal, Quebec, Canada. 5 Nestlé Research, Vers-chez-les-Blanc, 1010 Lausanne 26, Switzerland 6 Department of Mathematical and Industrial Engineering, Polytechnique Montréal, Montréal, Canada 7 Institute of Sustainable Energy, School of Engineering, University of Applied Sciences and Arts Western Switzerland, Switzerland 8 Department of Construction Engineering, École de technologie supérieure, Montréal, Canada. *Corresponding author: <a href="mailto:anbjo@dtu.dk">anbjo@dtu.dk</a>.   The paper is currently (June 11th, 2023) under review with Environmental Research Letters

opencc-zeroJun 2023View details →

Microevolutionary processes in a foundation tree inform macrosystem patterns of community biodiversity and structure

Despite an increased focus on multiscale relationships and interdisciplinary integration, few macroecological studies consider the contribution of genetic-based processes to landscape-scale patterns. We tested the hypothesis that tree genetics, climate, and geography jointly drive continental-scale patterns of community structure, using genome-wide SNP data from a broadly distributed foundation tree species (<a>Populus fremontii</a> S. Watson) and two dependent communities (leaf-modifying arthropods and fungal endophytes) spanning southwestern North America. Four key findings emerged: (1) Tree genetic structure was a significant predictor for both communities; however, the strength of influence was both scale- and community-dependent. (2) Tree genetics was the primary driver for endophytes, explaining 17% of variation in continental-scale community structure, whereas (3) climate was the strongest predictor of arthropod structure (24%). (4) Power to detect tree genotype<a>—</a>community phenotype associations changed with scale of genetic organization, increasing from individuals to populations to ecotypes, emphasizing the need to consider nonstationarity (i.e., changes in the effects of factors on ecological processes across scales) when inferring macrosystem properties. Our findings highlight the role of foundation tree species as drivers of macroscale community structure and provide macrosystems ecology with a theoretical framework for linking fine- and intermediate-scale genetic processes to landscape-scale patterns. Management of genetic diversity harbored within foundation species is a critical consideration for conserving and sustaining regional biodiversity.