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opencc-by-4.0Sep 2024View details →

Data for Figure 1 in "High-fidelity and polarization insensitive universal photonic processors fabricated by femtosecond laser writing"

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openmit-licenseOct 2024View details →

A High-Performance Code for Analyzing Loss Transport Equations in High-Fidelity Simulations - velocity field data

Velocity field to be processed by the methodology described in  Biassoni, D, Russo, M, Viviani, P, Vitali, G, & Lengani, D. "A High-Performance Code for Analyzing Loss Transport Equations in High-Fidelity Simulations." Proceedings of the ASME Turbo Expo 2024: Turbomachinery Technical Conference and Exposition. Volume 12C: Turbomachinery — Design Methods and CFD Modeling for Turbomachinery; Ducts, Noise, and Component Interactions. London, United Kingdom. June 24–28, 2024. V12CT32A039. ASME. <a href="https://doi.org/10.1115/GT2024-127953" target="_blank" rel="noopener">https://doi.org/10.1115/GT2024-127953</a> and with the code provided at  <a href="https://gitlab.linksfoundation.com/across-public/aeronautics-workflows/asme-turboexpo-2024">https://gitlab.linksfoundation.com/across-public/aeronautics-workflows/asme-turboexpo-2024</a> <h3> </h3>

Fig. 7 in Habitat use and site fidelity of Irrawaddy dolphins (Orcaella brevirostris) in the coastal waters of Bago-Pulupandan, Negros Occidental, Philippines

Fig. 7. Activity Index showing proportion of each behavioural activity (foraging; socialising; traveling; resting) per sector.

Fig. 8 in Habitat use and site fidelity of Irrawaddy dolphins (Orcaella brevirostris) in the coastal waters of Bago-Pulupandan, Negros Occidental, Philippines

Fig. 8. Monthly (N=25) and yearly (N=8) sighting rate (please see Material and Methods) for 19 identified Irrawaddy dolphins from Bago-Pulupandan (includes entire period of the sightings of these identified dolphins).

Fig. 3 in Habitat use and site fidelity of Irrawaddy dolphins (Orcaella brevirostris) in the coastal waters of Bago-Pulupandan, Negros Occidental, Philippines

Fig. 3. Discovery curve of marked individual dolphins in the study area over 25 survey months from 2010 to 2016.

Fig. 1 in Habitat use and site fidelity of Irrawaddy dolphins (Orcaella brevirostris) in the coastal waters of Bago-Pulupandan, Negros Occidental, Philippines

Fig. 1. Coastal waters of Bago City and the Municipality of Pulupandan in Guimaras Strait; Left inset: location of Western Visayas Region in the Philippines; Right inset: Guimaras Strait located between Negros Island and Guimaras Island.

Fig. 4. A in Habitat use and site fidelity of Irrawaddy dolphins (Orcaella brevirostris) in the coastal waters of Bago-Pulupandan, Negros Occidental, Philippines

Fig. 4. A, sightings of Irrawaddy dolphins (in yellow dots) relative to sectors; B, minimum convex polygon (MCP) of all sightings in Bago-Pulupandan coastal waters.

opencc-by-4.0Sep 2021View details →

Flow Cytometry data from: "The EMT transcription factor Zeb1 is essential for HSPC differentiation that acts synergistically with Zeb2 in fine-tuning hematopoietic lineage fidelity"

Abstract: The Zeb2 transcription factor has been demonstrated to play important roles in hematopoiesis and leukemic transformation. Zeb1 is a close family member of Zeb2 but has remained more enigmatic concerning its roles in hematopoiesis. Here we show using conditional loss of function approaches and bone marrow reconstitution experiments that Zeb1 plays cell autonomous role in hematopoietic lineage differentiation, particularly as a positive regulator of monocyte development in addition to its previously reported important role in T-cell differentiation. Analysis of existing single cell RNAseq data of early hematopoiesis has revealed distinctive expression differences between Zeb1 and Zeb2 in HSPC differentiation with Zeb2 being more highly and broadly expressed that Zeb1 except at a key transition point (ST-HSCàMPP1) whereby Zeb1 appears to be the dominantly expressed family member. Inducible deletion of both Zeb1 and Zeb2 using a tamoxifen inducible Cre-mediated approach leads to acute bone marrow failure at this transition point with increased long-term and shortterm hematopoietic stem cell numbers and an accompanying decrease in all hematopoietic lineage differentiation. Bioinformatics analysis of RNAseq data has revealed that Zeb2 acts predominantly as a transcriptional repressor involved in restraining mature hematopoietic lineage gene expression programs from being expressed too early in hematopoietic stem and progenitor cells (HSPCs). Zeb1 appears to fine tune this repressive role during hematopoiesis to ensure hematopoietic lineage fidelity. Analysis of ROSA26 locus based transgenic models has revealed that Zeb1 as well as Zeb2 overexpression within the hematopoietic system can drive extramedullary hematopoiesis/splenomegaly and enhanced monocyte development. Finally, deletion of Zeb2 alone or Zeb1/2 together was found to enhance survival in secondary MLL-AF9 AML models attesting to the oncogenic role of Zeb1/2 in AML.   Flow cytometric and Hematocrit analysis methods:   Cells were stained with antibodies listed in the provided Supplemental Table (Antibodies.xlsx) according to the  manufacturer guidelines. Flow cytometric analyses were performed on the LSRII and Fortessa  X-20 cytometer (BD Biosciences) and the results were analysed by FACSDiva or FlowJo software (BD Biosciences). Cells for MLL-AF9 experiments and RNA-seq were stained and  sorted on Influx or FACSAria Fusion sorters (BD Biosciences) at AMREP Flow Cytometry  Core Facility and FlowCore, Monash University.  Submandibular blood samples were collected into EDTA-coated tubes, and hematology parameters were measured using a HemaVet 950FS automated blood analysis machine (Drew Scientific).

opencc-zeroNov 2022View details →

Rapid evolution of a brood parasite's egg pattern does not lead to large increases in mimetic fidelity

In coevolutionary mimicry systems, mimics evolve to resemble models. When model fitness is reduced by close mimicry (such as when models are hosts and mimics are brood parasites), selection should drive mimics to evolve greater similarity to models over time, and models to evolve away from mimics ('chase-away evolution'), potentially resulting in mimetic fidelity remaining constant over time. Evidence for reciprocal evolution of models and mimics and its effect on mimetic fidelity is limited, however, likely because long-term data are required to observe such trends. Here, we test for these dynamics in an avian brood parasite system. The brood-parasitic cuckoo finch (Anomalospiza imberbis) lays eggs which mimic those of its host, the tawny-flanked prinia (Prinia subflava). In defence, prinias have evolved complex egg patterns which facilitate recognition of parasitic eggs. Prinia egg patterns are more complex than cuckoo finch egg patterns, and so selection should favour elevated complexity in parasite eggs (i.e. mimics evolving towards models) and even greater complexity in host eggs (i.e. models evolving away from mimics). Using a dataset spanning 50 years, we show that egg pattern complexity has indeed increased in both species over this time period, reflecting rapid adaptive evolution of both models and mimics. Both species have evolved at similar rates. Accordingly, we find no detectible increase in mimetic fidelity over time. Thus, host evolution can counteract even rapid parasite evolution, and result in the persistence of imperfect mimicry.

opencc-zeroDec 2022View details →

Combined measures of mimetic fidelity explain imperfect mimicry in a brood parasite–host system

The persistence of imperfect mimicry in nature presents a challenge to mimicry theory. Some hypotheses for the existence of imperfect mimicry make differing predictions depending on how mimetic fidelity is measured. Here, we measure mimetic fidelity in a brood parasite–host system using both trait-based and response-based measures of mimetic fidelity. Cuckoo finches Anomalospiza imberbis lay imperfectly mimetic eggs that lack the fine scribbling characteristic of eggs of the tawny-flanked prinia Prinia subflava, a common host species. A trait-based discriminant analysis based on Minkowski functionals—that use geometric and topological morphometric methods related to egg pattern shape and coverage—reflects this consistent difference between host and parasite eggs. These methods could be applied to quantify other phenotypes including stripes and waved patterns. Furthermore, by painting scribbles onto cuckoo finch eggs and testing their rate of rejection compared to control eggs (i.e. a response-based approach to quantify mimetic fidelity), we show that prinias do not discriminate between eggs based on the absence of scribbles. Overall, our results support relaxed selection on cuckoo finches to mimic scribbles, since prinias do not respond differently to eggs with and without scribbles, despite the existence of this consistent trait difference.

opencc-by-3.0-usJan 2023View details →

Role of eEF2 diphthamide modification in translational fidelity

Supplementary data for the paper : eEF2 Diphthamide Modification Restrains Spurious Frameshifting to Maintain Translational Fidelity In vitro reconstituted elongation assay (MFFFK-invitro.tif), synthetic growth phenotype of REA1 (MDN1) and dph2 deletion mutant (Rea1-dph2.jpg), Western blot to detect full length Mdn1 and Dyn1 (Western_Mdn1.jpg), growth spot assay for WT (DPH2) and dph2-del (WT-dph2-growth.png), and a script for calculating ribosomal drop-off rate from wig file (drop_off_wig.R).

opencc-zeroJan 2023View details →

Multi-fidelity modelling of shark skin denticle flows: Insights into drag generation mechanisms

We investigate the flow over smooth (non-ribletted) shark skin denticles in an open-channel flow using Direct Numerical Simulation (DNS) and two Reynolds Averaged Navier-Stokes (RANS) closures. Large peaks in pressure and viscous drag are observed at the denticle crown edges, where they are exposed to high-speed fluid which penetrates between individual denticles, increasing shear and turbulence. Strong lift forces lead to a positive spanwise torque acting on individual denticles, potentially encouraging bristling if the denticles were not fixed. However, DNS predicts that denticles ultimately increase drag by 58 % compared to a flat plate. Good predictions of drag distributions are obtained by RANS models, although an underestimation of turbulent kinetic energy production leads to an underprediction of drag. Nevertheless, RANS methods correctly predict trends in the drag data and the regions contributing most to viscous and pressure drag. Subsequently, RANS models are used to investigate the dependence of drag on the flow blockage ratio (boundary layer to roughness height ratio), finding that the drag increase due to denticles is halved when the blockage ratio δ /h is increased from 14 to 45. Our results provide an integrated understanding of the drag over non-ribletted denticles, enabling existing diverse drag data to be explained.

opencc-zeroMar 2023View details →

Materials Science Optimization Benchmark Dataset for High-dimensional, Multi-objective, Multi-fidelity Optimization of CrabNet Hyperparameters

Benchmarks are an essential driver of progress in scientific disciplines. Ideal benchmarks mimic real-world tasks as closely as possible, where insufficient difficulty or applicability can stunt growth in the field. Benchmarks should also have sufficiently low computational overhead to promote accessibility and repeatability. The goal is then to win a "Turing test" of sorts by creating a surrogate model that is indistinguishable from the ground truth observation (at least within the dataset bounds that were explored), necessitating a large amount of data. In materials science and chemistry, industry-relevant optimization tasks are often hierarchical, noisy, multi-fidelity, multi-objective, high-dimensional, and non-linearly correlated while exhibiting mixed numerical and categorical variables subject to linear and non-linear constraints. To complicate matters, unexpected, failed simulation or experimental regions may be present in the search space. In this study, 173219 quasi-random hyperparameter combinations were generated across 23 hyperparameters and used to train CrabNet on the Matbench experimental band gap dataset. The results were logged to a free-tier shared MongoDB Atlas dataset. This study resulted in a regression dataset mapping hyperparameter combinations (including repeats) to MAE, RMSE, computational runtime, and model size for CrabNet model trained on the Matbench experimental band gap benchmark task1. This dataset is used to create a surrogate model as close as possible to running the actual simulations by incorporating heteroskedastic noise. Failure cases for bad hyperparameter combinations were excluded via careful construction of the hyperparameter search space, and so were not considered as was done in prior work. For the regression dataset, percentile ranks were computed within each of the groups of identical parameter sets to enable capturing heteroskedastic noise. This contrasts with a more traditional approach that imposes a-priori assumptions such as Gaussian noise, e.g., by providing a mean and standard deviation. A similar approach can be applied to other benchmark datasets to bridge the gap between optimization benchmarks with low computational overhead and realistically complex, real-world optimization scenarios.

openApr 2023View details →

Multi-fidelity Gaussian Process Emulation for Atmospheric Radiative Transfer Models

This repository contains several datasets of spectral atmospheric transfer functions (i.e. path radiance, transmittances, spherical albedo) simulated with MODTRAN6 atmospheric radiative transfer model. The simulations are stored in hdf5 files using the Atmospheric Look-up table Generator (ALG) toolbox (<a href="https://doi.org/10.5194/gmd-13-1945-2020">https://doi.org/10.5194/gmd-13-1945-2020</a>). Each dataset has an associated .xml file that includes the configuration of ALG/MODTRAN6 executions. All datasets include the input atmospheric/geometric variables that are summarized in the following table. Each dataset file has a random distribution (based on latin hypercube sampling) these input variables with varying number of points (e.g. train500.h5 contains 500 samples). The reference dataset contains 10000 samples and was used as reference for evaluating Gaussian Processes emulators. <table> <tbody><tr> <th>Input Variables</th> <th>Units</th> <th>Min</th> <th>Max</th> </tr> </tbody><tbody> <tr> <td>O3 column concentration</td> <td>atm-cm</td> <td>0.25</td> <td>0.45</td> </tr> <tr> <td>Columnar Water Vapor</td> <td>g/cm2</td> <td>0.2</td> <td>4</td> </tr> <tr> <td>Aerosol Optical Thickness</td> <td>-</td> <td>0.04</td> <td>0.6</td> </tr> <tr> <td>Asymmetry parameter</td> <td>-</td> <td>0.5</td> <td>0.85</td> </tr> <tr> <td>Angstrom exponent</td> <td>-</td> <td>0.1</td> <td>2</td> </tr> <tr> <td>Single Scattering Albedo</td> <td>-</td> <td>0.8</td> <td>1</td> </tr> <tr> <td>Surface elevation</td> <td>km</td> <td>0</td> <td>2.5</td> </tr> <tr> <td>Solar Zenith Angle</td> <td>deg</td> <td>0</td> <td>70</td> </tr> <tr> <td>Relative Zenith Angle</td> <td>deg</td> <td>0</td> <td>180</td> </tr> </tbody> </table>

opengpl-2.0Aug 2023View details →

Artifact for MobiCom'23: Virtual Device Farms for Mobile App Testing at Scale: A Pursuit for Fidelity, Efficiency, and Accessibility

This dataset contains the anonymized failure data collected from our physical and device farms over a three-month period. The failure data involves 5,918 physical devices as well as 5,918 virtualized devices running on ARM commodity servers. For more details, please visit our website (<a href="https://android-emulation-testing.github.io/">Android-Emulation-Testing.github.io</a>) or read our paper: <ul> <li>[MobiCom'23] Virtual Device Farms for Mobile App Testing at Scale: A Pursuit for Fidelity, Efficiency, and Accessibility</li> </ul> If you use our dataset in your work, please reference it using: <pre><code>@inproceedings {lin2022virtual, author = {Lin, Hao and Qiu, Jiaxing and Wang, Hongyi and Li, Zhenhua and Gong, Liangyi and Gao, Di and Liu, Yunhao and Qian, Feng and Zhang, Zhao and Yang, Ping and Xu, Tianyin}, title = {{Virtual Device Farms for Mobile App Testing at Scale: A Pursuit for Fidelity, Efficiency, and Accessibility}}, booktitle = {The 29th Annual International Conference on Mobile Computing and Networking (ACM MobiCom'23)}, year = {2023}, publisher = {ACM} }</code></pre>

opencc-by-4.0Nov 2023View details →

A Taxonomy of C Decompiler Fidelity Issues

This archive contains the supplementary material and dataset for the USENIX Security paper “A Taxonomy of C Decompiler Fidelity Issues.”   The dataset archive contains all coded examples and a decompiler comparison summary table.   The codebook file contains a detailed description of each code in the taxonomy as well as additional details about the coding process, including a definition of alignment and a list of benign issues.

publicAug 2025View details →

Data from: Clone tracking through repeated malaria reveals high-fidelity CD4+ memory responses

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publicDec 2022View details →

Combined measures of mimetic fidelity explain imperfect mimicry in a brood parasite–host system

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publicJan 2023View details →

Multi-fidelity modelling of shark skin denticle flows: Insights into drag generation mechanisms

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