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2,235 results for “engineering”
Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision and Reproducibility
<p>This zip contains all input structures for paper the: Alchemical Free<br> Energy Estimators and Molecular Dynamics<br> Engines: Accuracy, Precision and Reproducibility</p> <p>Authors: Alexander D. Wade, Agastya P. Bhati, Shunzhou Wan, Peter V.Coveney</p> <p>The structures of the folders are protein/ligand_transformation/alchemical_leg/input/files</p> <p>The ligand transformation are derived from previous work by wang et al. (https://pubs.acs.org/doi/10.1021/ja512751q)</p> <p>There are two files for the solvent alchemical leg: complex.pdb and complex.prmtop</p> <p>complex.pdb is structure file that also denotes the alchemical atoms in the pdb beta column. complex.prmtop is an AMBER parameter/topology file</p> <p>For the complex alchemical leg there is an additional file constraints.pdb that contains the constraint information in the pdb beta column.</p> <p>These files can be used with TIES_MD (https://ucl-ccs.github.io/TIES_MD/) or other molecular dynamics engiens that take AMBER input.</p>
Engineering of Fully Humanized and Vascularized 3D Bone Marrow Niches Sustaining Undifferentiated Human Cord Blood Hematopoietic Stem and Progenitor Cells
<p>Data underlying the figures in the publication “Engineering of fully humanized and vascularized 3D bone marrow niches sustaining undifferentiated human cord blood hematopoietic stem and progenitor cells”, published in <em>J Tissue Eng., </em><strong>2021</strong>, 12, 2041731421044855.</p> <p>DOI:10.1177/20417314211044855</p> <p> </p> <p>Table of Contents:</p> <p><strong>1. P12-03_TP01_Suppernatant</strong>: Enzyme-linked immunosorbent assay of VEGF concentration in vascularized and not vascularized BM niches.</p> <p><strong>2. P12_WholeNiche</strong>: qPCR data of vascular and osteogenic markers in vascularized and not vascularized BM niches.</p> <p><strong>3. FACs-Overview-SN_relativ</strong>: FACS data showing haematopoietic cell populations in the supernatant after HSC cocoulture in vascularized and not vascularized BM niches.</p> <p><strong>4. FACs-Overview-niche_Relativ</strong>: FACS data showing haematopoietic cell populations in the niche after HSC cocoulture in vascularized and not vascularized BM niches.</p> <p><strong>5. CFU</strong>: Colony formation statistics after HSC cocoulture from vascularized and not vascularized BM niches.</p> <p><strong>6. Cell cycle</strong>: Cell cycle statistics of HSPCs after HSC cocoulture from vascularized and not vascularized BM niches.</p> <p><strong>7. P12_03_AfterHSPC-vs-BeforeHSPCs</strong>: qPCR data of vascular and osteogenic markers in vascularized and not vascularized BM niches after and before HSC cocoulture.</p> <p><strong>8. Scheme</strong>: Vector graphic of experimental setup.</p> <p><strong>9. Images engineered niches</strong>: Folder containing images of engineered niches.</p>
Dataset for "Pop Quiz! Can a Large Language Model Help WIth Reverse Engineering?"
<p>Source files and scripts for the test framework used in evaluating OpenAI's code-davinci-001 (also known as davinci-codex) model for reverse engineering tasks. All results presented in the associated manuscript are preserved in this dataset, or you can use it to perform additional experiments or re-generate the results.</p>
Immunosuppressive niche engineering at the onset of human colorectal cancer
<p>Dataset used in "Immunosuppressive niche engineering at the onset of human colorectal cancer" by Gatenbee et al. 2022. </p>
Social Science Theories in Software Engineering Research - Replication Package
<p>Replication package for the article "Social Science Theories in Software Engineering Research".</p> <p>See README file for additional details.</p>
Topological engineering of terahertz light using electrically tuneable exceptional point singularities
<p>Dataset and codes for the manuscript "Topological engineering of terahertz light using electrically tuneable exceptional point singularities".</p>
The distribution and impact of an invasive plant species (Senecio inaequidens) on a dune building engineer (Calamagrostis arenaria)
<p>These data sets are used to run the analyses in the paper '<em>The distribution and impact of an invasive plant species (</em>Senecio inaequidens<em>) on a dune building engineer (</em>Calamagrostis arenaria<em>)</em>' by Van De Walle et al., 2022, Neobiota (in progress).</p> <p>The presence/absence data (PA) of <em>Senecio inaequidens</em> in European coastal dunes can be found in 'Senecio_PA.xlsx', in the tab 'senecio_PA', together with the country and location where the occurrences were mapped. All coordinates of the samples are available in the tab 'coordinates samples'.</p> <p>'Marram_growth_experiment.xlsx' contains the data gathered during the growth experiment. The origin of the sand is subdivided in 3 columns: 'Location' represents the location along the Belgian coast where sand was gathered, 'senecio' represents whether sand was gathered from underneath a senecio plant or not and 'biota' represents whether biota could affect marram grass growth (biota = 0 thus means that the sand was sterilized).</p> <p> </p> <p><strong>Abstract</strong></p> <p>Disturbance is thought to enhance the probability of invasive species establishment, a prerequisite for naturalization. Coastal dunes are characterized by disturbance in the form of sand dynamics. We studied the effect of this disturbance on the establishment and spread of an invasive plant species (<em>Senecio inaequidens</em>) in European coastal dunes. Local sand dynamics dictate the spatial configuration of marram grass (<em>Calamagrostis arenaria</em>). Therefore, marram grass configuration was used as a reliable proxy for disturbance. As marram grass plays a crucial role in natural dune formation, we evaluated the possible effects <em>S. inaequidens</em> could have on this process, if it would be able to naturalize in European coastal dunes.</p> <p> We expected the highest probability of <em>S. inaequidens </em>establishment at intermediate marram grass cover because too low cover would increase sand burial, whereas high cover would increase competition. However, our results indicate that <em>S. inaequidens</em> is quite capable of handling higher levels of sand burial. Thus, probability of <em>S. inaequidens</em> establishment was high under low marram cover but slightly lowered when marram cover was high, hinting at the importance of competition.</p> <p>We expected a negative impact of <em>Senecio</em>-altered soils on marram grass growth mediated by soil biota. However, marram grass grew better in sand gathered underneath <em>Senecio</em> plants due to abiotic soil modifications. This enhanced growth may be caused by <em>Senecio</em> leaf litter elevating nutrient concentrations in an otherwise nutrient-poor substrate. If such increased plant growth is a general phenomenon, further expansion of <em>S. inaequidens</em> could accelerate natural succession in European coastal dunes.</p>
Supporting molecular simulations data for "Pseudo-halide anion engineering for α-FAPbI3 perovskite solar cells"
<p>Supporting molecular simulations data for "Pseudo-halide anion engineering for α-FAPbI3 perovskite solar cells"</p>
Optimal Mowing Regime in Enhancing Biodiversity in Seasonal Floodplains along Engineered Channels, Survey data
<p>This is the survey dataset used in the publication " Optimal Mowing Regime in Enhancing Biodiversity in Seasonal Floodplains along Engineered Channels".</p>
Development of Novel Ultra-High Performance Engineered Cementitious Composites (UHP-ECC) for Durable and Resilient Transportation Infrastructure
<p>The objective of this study was to develop novel UHP-ECC materials utilizing readily available ingredients in Region 6 for the construction and repair of transportation infrastructure. Phase one of this study focused on the development of ultra-high strength cementitious matrices by evaluating the effects of ingredient selection and mixture proportioning on the materials’ compressive strength. Variables evaluated included the mass ratios of silica fume to fly ash (SF/FA), supplementary cementitious materials to cement (SCMs/C), and ordinary sand to microsilica sand (OS/MS). Phase two of the study focused on the development of UHP-ECC materials. To this end, based on the knowledge gained from phase one, two ultra-high strength cementitious matrices (one with and one without SF) were formulated and their fracture properties were evaluated through fracture toughness test. Furthermore, fiber-bridging properties of ultra-high-molecular-weight (UHMW) polyethylene (PE) fiber in the developed cementitious matrices were evaluated through single crack tensile test (SCTT). Four different composites were produced by reinforcing the selected cementitious matrices with 1.5 and 2 vol.% UHMW PE fiber. Fresh and hardened properties of the developed composites were assessed by means of flowability test, compressive strength test, uniaxial tensile test, and flexural performance test. Results from phase one showed that SF/FA had the most relevant effect on compressive strength, followed by SCMs/C, and OS/MS. Furthermore, increments in SF/FA produced improvements in strength, whereas increments in SCMs/C and OS/MS reduced strength. Experimental results from phase two indicated that the use of SF and the increase in fiber content generally had a negative effect on the fresh and hardened properties of the composites. These observations were credited to a worsening fiber distribution when using silica fume and/or increasing fiber content. Three UHP-ECC materials utilizing readily available ingredients were successfully developed (i.e., mixtures FA25-f1.5, FA25-f2, and FA20SF5-f2). These materials simultaneously exhibited ultra-high compressive strength (>120 MPa) and ECC-like ductility (tensile strain capacity >2%). The average crack width for all mixtures ranged between 61-131 μm. Mixture FA25-f1.5, which displayed the best mechanical properties, exhibited a compressive strength of 133.1 MPa, flexural strength of 21.4 MPa, tensile strength of 10.3 MPa, tensile strain capacity of 4.3%, and an average crack width of 115.3 μm. Importantly, this mixture did not incorporate silica fume or microsilica sand and used low fiber content (i.e., 1.5 vol.%).</p>
Resilient 3D-Printed Infrastructure with Engineered Cementitious Composites (ECC)
<p>Conventional construction of reinforced concrete structures is slow, labor-intensive, and expensive. 3D printing holds great potential to assist engineers and architects in constructing fast and economical yet complex representational infrastructures. One of the most significant barriers to the broader adoption of concrete 3D printing in civil infrastructure is the difficulty of providing printed structural components with reinforcement to achieve sound structural performance under different loading conditions. Hence, it is essential to design concrete that can be utilized as a rebar-free material by considering strength and ductility. Recently, the development of Engineered Cementitious Composites (ECC) has neared the possibility to achieve both strength and ductility in the concrete structures without embedding steel reinforcement. ECC has been offered to enhance the problem related to the ductility and low tensile strength of traditional concrete and Fiber Reinforced Composite (FRC). As such, the implementation of intrinsically reinforced cementitious materials has the potential to address this barrier in the reinforcement of 3D-printed concrete and yields significant benefits such as an enhanced structural capacity, durability, and resiliency. This project proposes the development of ECC materials utilizing readily available ingredients in Region 6 with rheological characteristics tailored specifically for 3D printing applications. Furthermore, the project aims to conduct a comprehensive evaluation of the hardened properties of 3D-printed ECC specimens, including mechanical tests.</p>
Insights into the stability of engineered mini-proteins from their dynamic electronic properties
<p>Coordinates and partial charges from GFN2-xTB and wPBEh/cc-pvdz for 20 ps x 20 replicas for two variants of Trp-cage (TC5b and TC10b) as supporting information.</p>
X-ray computed tomography aided engineering approach for non-crimp fabric reinforced composites [Data set]
<p>The finite element models behind the publication</p> <p>Auenhammer, R.M., Jeppesen, N., Mikkelsen, L.P., Dahl, V.A., Blinzler, B.J., Asp, L.E. Robust numerical analysis of fibrous composites from X-ray computed tomography image data enabling low resolutions, <em>Composites Science and Technology, </em><strong>224</strong>, 109458, <a href="https://doi.org/10.1016/j.compscitech.2022.109458">https://doi.org/10.1016/j.compscitech.2022.109458</a>, 2022. </p> <p>The x-ray scan data which the model is based on can be found in the following publication:</p> <p>Jeppesen, N., V.A. Dahl, A.N. Christensen, A.B. Dahl, L.P. Mikkelsen, Characterization of the fiber orientations in non-crimp glass fiber reinforced composites using structure tensor. IOP Conf. Ser.: Mater. Sci. Eng. 942, 012037, <a href="https://doi.org/10.1088/1757-899X/942/1/012037">https://doi.org/10.1088/1757-899X/942/1/012037</a> 2020</p> <p>and data-set</p> <p>Jeppesen N, Dahl V A, Christensen A N, Dahl A B and Mikkelsen L P 2020 Characterization of the fiber orientations in non-crimp glass fiber reinforced composites using structure tensor [data set] Zenodo. <a href="http://dx.doi.org/10.5281/zenodo.3877522">http://dx.doi.org/10.5281/zenodo.3877522.</a></p> <p> </p>
Database of non-target invertebrates recorded in field experiments of genetically engineered Bt maize and corresponding non-Bt maize: data files
<p><span>This database represents a comprehensive collection of experimental field data from all over the world on non-target invertebrates recorded in genetically engineered/modified Bt and non-Bt maize. The three data files deposited here are described by Meissle et al. (2022), BMC Research Notes, <span><a href="https://doi.org/10.1186/s13104-022-06021-3"><span>https://doi.org/10.1186/s13104-022-06021-3</span></a></span><span> </span>.</span></p> <p><span>The database was created for a systematic review with the question if growing Bt maize changes abundance or ecological function of non-target animals compared to growing of non-GM maize, published by Meissle et al. (2022), Environmental Evidence, <a href="https://doi.org/10.1186/s13750-022-00272-0"><span>https://doi.org/10.1186/s13750-022-00272-0</span></a></span>.</p> <p>Data file 1 contains the database with 7279 records of non-target invertebrate abundance, activity density, or predation or parasitism in Bt and non-Bt maize, extracted from 120 publications. Data file 2 includes the list and definitions of variables in the database, and data file 3 represents the critical appraisal questions and answer options.</p>
Data for: Pericytes' Circadian Clock Affects Endothelial Cells' Synchronization and Angiogenesis in a 3D Tissue Engineered Scaffold
<p>Raw data set and analysis files for Mastrullo et al., Frontiers in Pharmacology, 2022 <strong>DOI:</strong> 10.3389/fphar.2022.867070 </p>
Data files for the article "Engineering nanoscale hypersonic phonon transport"
<p>Data files for the article "Engineering nanoscale hypersonic phonon transport". Published in Nature Nanotechnology </p>
Data for "Physically Based Deep Learning Framework to Model Intense Precipitation Events at Engineering Scales"
<p>The dataset consists of high resolution (250 m) and low resolution (0.025 degree) climate model outputs in netCDF format. Each file contains data for one variable and one month.</p> <p>Low resolution files follow the naming scheme: montrealC_0025deg_200x200_ERA5_1m_YYYYMM_VAR.nc</p> <p>High resolution files follow the naming scheme: montrealC_250m_324x324_ERA5_TEB_100_noconv_YYYYMM_VAR.nc</p> <p>YYYYMM stands for the year (first 4 digits) and month (last 2 digits).</p> <p>_VAR indicates the variable contained in the file:</p> <ul> <li>_UU700 stands for the east-west component of wind at a pressure level of 700 hPa (hourly frequency)</li> <li>_VV700 stands for the north-south component of wind at a pressure level of 700 hPa (hourly frequency)</li> <li>When _VAR is omitted, the variable is precipitation at 1-minute temporal resolution</li> </ul>
Supporting Data for Human Factors in Developing Automated Vehicles:A Requirements Engineering Perspective
<p>This data set complements our manuscript in submission with the title:</p> <p>"Human Factors in Developing Automated Vehicles: A Requirements Engineering Perspective"</p> <p>We provide two files:</p> <p>a) the interview guide</p> <p>b) an overview that maps from themes to example quotes and codes derived from particular interview subjects</p>
Exploring Gender Bias in Remote Pair Programming among Software Engineering Students: The Twincode Original Study and First External Replication (datasets)
<p>This repository contains the datasets of the original experiment (University of Seville, December 2021) and its first external replication (University of California, Berkeley, May 2022) of the Twincode exploratory study on the effects of gender bias in remote pair programming among software engineering students.</p>
Supplementary material of the study "Flying over Brazilian Organizations with Zeppelin: A Preliminary Panoramic Picture of Continuous Software Engineering"
<p><strong>Supplementary Material</strong></p> <p><em>Context</em>: Software organizations have faced several challenges, such as the need for faster deliveries, frequent changes in requirements, lower tolerance to failures and the need to adapt to contemporary business models. Agile practices have allowed organizations to shorten development cycles and increase customer collaboration. However, this has not been enough. Organizations should evolve to continuous and data-driven development in a continuous software engineering approach. Continuous Software Engineering (CSE) consists of a set of practices and tools that support a holistic view of software development with the purpose of making it faster, iterative, integrated, continuous and aligned with business. Implementing CSE requires changes in the organization’s culture, practices and structure, which may not be easy. <em>Objective</em>: We aim to provide a preliminary picture of CSE adoption in Brazilian software organizations. <em>Method</em>: We adapted and used Zeppelin, a diagnostic instrument of CSE adoption based on the Stairway to Heaven Model (StH), to perform a survey with 28 Brazilian organizations aiming at investigating the adoption of CSE practices. <em>Results</em>: The results indicate that organizations have better addressed agile and continuous deployment practices than the ones related to continuous integration and continuous experimentation, but this scenario changes a bit depending on the organization type. The results also show that CSE adoption has been heterogeneous, but there are patterns in the adoption of some practices. <em>Conclusion</em>: Although the StH model proposes a sequential and evolutionary path for CSE adoption, organizations have not always followed that path systematically. There are indeed CSE practices that depend on others and thus contribute to sequential implementation. However, organizations tend to adopt the practices gradually, covering different stages, and evolving according to the organization needs.</p> <p>This package contains supplementary material of the study performed to investigate the adoption of CSE practices in Brazilian organizations. It contains:</p> <ul> <li>The questionnaire used to collect data (Google Forms format) – in Portuguese only (available at https://forms.gle/oWpiQ1VJ8oywj4sXA)</li> <li>The questionnaire used to collect data (pdf format) </li> <li>A spreadsheet containing raw data, some tables and graphs</li> <li>Python Notebook files for showing exploratory analysis (using Spearman Coefficient) </li> </ul> <p>Please cite: <em>Paulo Sérgio dos Santos Júnior, Monalessa P. Barcellos, Fabiano B. Ruy, and Moisés S. Omêna. 2022. Flying over Brazilian Organizations with Zeppelin: A Preliminary Panoramic Picture of Continuous Software Engineering. In 36th Brazilian Symposium on Software Engineering (SBES ’22), October 21–23, 2022, Uberlândia, Brazil.</em></p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.