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Netflow data with sampling 500 for test (D5)

NetFlow traffic generated using DOROTHEA (DOcker-based fRamework fOr gaTHering nEtflow trAffic) NetFlow is a network protocol developed by Cisco for the collection and monitoring of network traffic flow data generated. A flow is defined as a unidirectional sequence of packets with some common properties that pass through a network device. NetFlow flows have been captured with sampling 500 at the packet level. A sampling means that 1 out of every X packets is selected to be flow while the rest of the packets are not valued. The version of NetFlow used to build the datasets is 5.

Netflow data with sampling 250 for training (D1)

NetFlow traffic generated using DOROTHEA (DOcker-based fRamework fOr gaTHering nEtflow trAffic) NetFlow is a network protocol developed by Cisco for the collection and monitoring of network traffic flow data generated. A flow is defined as a unidirectional sequence of packets with some common properties that pass through a network device. NetFlow flows have been captured with sampling 250 at the packet level. A sampling means that 1 out of every X packets is selected to be flow while the rest of the packets are not valued. The version of NetFlow used to build the datasets is 5.

Netflow data with sampling 1000 for training (D3)

NetFlow traffic generated using DOROTHEA (DOcker-based fRamework fOr gaTHering nEtflow trAffic) NetFlow is a network protocol developed by Cisco for the collection and monitoring of network traffic flow data generated. A flow is defined as a unidirectional sequence of packets with some common properties that pass through a network device. NetFlow flows have been captured with sampling 1000 at the packet level. A sampling means that 1 out of every X packets is selected to be flow while the rest of the packets are not valued. The version of NetFlow used to build the datasets is 5.

Netflow data with sampling collected from RedCAYLE (D7)

NetFlow traffic generated using DOROTHEA (DOcker-based fRamework fOr gaTHering nEtflow trAffic) NetFlow is a network protocol developed by Cisco for the collection and monitoring of network traffic flow data generated. A flow is defined as a unidirectional sequence of packets with some common properties that pass through a network device. NetFlow flows have been captured with sampling 1000 at the packet level. A sampling means that 1 out of every X packets is selected to be flow while the rest of the packets are not valued. The version of NetFlow used to build the datasets is 5.

Dataset related to article "SMA-miRs (miR-181a-5p, -324-5p, and -451a) are overexpressed in spinal muscular atrophy skeletal muscle and serum samples"

mice survival after treatment with anti-miR-181a-5p; mice weight after treatment with anti-miR-324-5p

Light intensity in reflection mode of PAAO (AJ-5-04-27 sample, 2nd anodization)

Light intensity data recorded during the anodization of aluminum monocrystal. Light source: SLS201L/M (ThorLabs). Spectrometer: USB4000 (OceanOptics). Spectra acquisition software: SpectraSuite (OceanOptics). Integration time: 380 µs. Scans to average: 10. Spectrum is recorded every 500 ms during anodization. ref.txt includes reference spectra just before the start of anodization process. All measurements data is also included in a single "AJ-5-04-27.zip" file. Anodization was performed in 0.3 mol/L oxalic acid at 40 V for 4 min 57 s.

Light intensity in reflection mode of PAAO (AJ-3-04-20 sample, 2nd anodization)

Light intensity data recorded during the anodization of aluminum monocrystal. Light source: SLS201L/M (ThorLabs). Spectrometer: USB4000 (OceanOptics). Spectra acquisition software: SpectraSuite (OceanOptics). Integration time: 380 µs. Scans to average: 10. Spectrum is recorded every 500 ms during anodization. ref.txt includes reference spectra just before the start of anodization process. All measurements data is also included in a single "AJ-3-04-20.zip" file. Anodization was performed in 0.3 mol/L oxalic acid at 40 V for 4 min 8 s.

Light intensity in reflection mode of PAAO (AJ-4-04-20 sample, 2nd anodization)

Light intensity data recorded during the anodization of aluminum monocrystal. Light source: SLS201L/M (ThorLabs). Spectrometer: USB4000 (OceanOptics). Spectra acquisition software: SpectraSuite (OceanOptics). Integration time: 360 µs. Scans to average: 10. Spectrum is recorded every 500 ms during anodization. ref.txt includes reference spectra just before the start of anodization process. All measurements data is also included in a single "AJ-1-04-20.zip" file. Anodization was performed in 0.3 mol/L oxalic acid at 40 V for 4 min 30 s.

Light intensity in reflection mode of PAAO (AJ-2-04-20 sample, 2nd anodization)

Light intensity data recorded during the anodization of aluminum monocrystal. Light source: SLS201L/M (ThorLabs). Spectrometer: USB4000 (OceanOptics). Spectra acquisition software: SpectraSuite (OceanOptics). Integration time: 360 µs. Scans to average: 10. Spectrum is recorded every 500 ms during anodization. ref.txt includes reference spectra just before the start of anodization process. All measurements data is also included in a single "AJ-2-04-20.zip" file. Anodization was performed in 0.3 mol/L oxalic acid at 40 V for 3 min 37 s.

Light intensity in reflection mode of PAAO (AJ-1-04-20 sample, 2nd anodization)

Light intensity data recorded during the anodization of aluminum monocrystal. Light source: SLS201L/M (ThorLabs). Spectrometer: USB4000 (OceanOptics). Spectra acquisition software: SpectraSuite (OceanOptics). Integration time: 330 µs. Scans to average: 10. Spectrum is recorded every 500 ms during anodization. ref.txt includes reference spectra just before the start of anodization process. All measurements data is also included in a single "AJ-1-04-20.zip" file. Anodization was performed in 0.3 mol/L oxalic acid at 40 V for 3 min 16 s.

Light intensity in reflection mode of PAAO (AJ-3-04-20 sample, 1st anodization)

Light intensity data recorded during the anodization of aluminum monocrystal. Light source: SLS201L/M (ThorLabs). Spectrometer: USB4000 (OceanOptics). Spectra acquisition software: SpectraSuite (OceanOptics). Integration time: 360 us. Scans to average: 10. Spectrum is recorded every 2 s during anodization. ref.txt includes reference spectra just before the start of anodization process. All measurements data is also included in a single "AJ-3-04-20.zip" file. Anodization was performed in 0.3 mol/L oxalic acid at 40 V for 1 hour.

SEM images of PAAO samples (AJ series 1-to-5)

Scanning electron microscopy (SEM) images of porous anodized aluminum oxide (PAAO) samples. The samples were made by anodization of aluminum monocrystal in 0.3 mol/L oxalic acid at 40 V for: 3 min 16 s (AJ-1), 3 min 37 s (AJ-2), 4 min 8 s (AJ-3), 4 min 30 s (AJ-4), 4 min 57 s (AJ-5). The imaging was performed on the surface (top) of the sample, darker parts represent pores. SEM: FEI Quanta 200 FEG (FEI). Vacuum mode: high vacuum (< 6·10-4 Pa). Accelerating voltage: 20 kV. Magnification: 50 000, 100 000, 200 000.

opencc-zeroJan 2022View details →

dryad40/100

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.

Automated Qualitative and Quantitative Analysis of Complex Forensic Drug Samples using 1H NMR

Dataset to accompany the manuscript "Automated Qualitative and Quantitative Analysis of Complex Forensic Drug Samples using 1H NMR"

Sampled ΔH/Δλ and ΔH data from ABFE calculations of 19 ligands bound to MCL-1

Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 19 ligands to bound MCL-1. These ligands are originally detailed by Friberg et al. (https://doi.org/10.1021/jm301448p). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).

Sampled ΔH/Δλ and ΔH data from ABFE calculations (using standard atomic masses) of 10 ligands bound to Cyclophilin D

Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands to bound Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike other datasets in this work, which employed hydrogen mass repartitioning, the ligands here were calculated using standard atomic masses. All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).

Sampled ΔH/Δλ and ΔH data from ABFE calculations of 12 ligands bound to PWWP1

Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 12 ligands to bound PWWP1. These ligands are originally detailed by Böttcher et al. (https://doi.org/10.1038/s41589-019-0310-x). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).

Sampled ΔH/Δλ and ΔH data from ABFE calculations of 10 ligands bound to Cyclophilin D

Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 10 ligands bound to Cyclophilin D. These ligands are originally detailed by Grädler et al. (https://doi.org/10.1016/j.bmcl.2019.126717). Unlike the other Cyclophilin D dataset provided in this work, simulations for these ABFE calculations were carried out using hydrogen mass repartitioning (HMR). The MCL-1, HSP90, and PWWP1 also used HMR. All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).

Sampled ΔH/Δλ and ΔH data from ABFE calculations of 18 ligands bound to HSP90

Supplementary Information: "Evaluating the use of absolute binding free energy in the fragment optimization process" Included are the ABFE raw free energy samples for multiple replicates (labelled by `run` number) of 18 ligands bound to HSP90. These ligands are originally detailed by Murray et al. (https://doi.org/10.1021/jm100059d). All samples are provided as a set of `.xvg` files as generated by GROMACS 2021 (https://doi.org/10.5281/zenodo.5849961). The `.xvg` files are labelled as dhdl.N.xvg where N represents the λ state the free energy values were sampled from. The `.xvg` files contain both ΔH/Δλ and ΔH values, please see the header of each files for more information. Samples detailing the partial decoupling of the ligand from the protein-ligand complex are contained within the `complex` folder. These consist of an orientational restraint addition step (found within the `restraints-xvg` folders), charge annihilation step (found within the `coul-xvg` folders), and Van der Waals decoupling step (found within the `vdw-xvg` folders). Samples detailing the partial decoupling of the ligand from solvent are contained within the `ligand` folder and consist of a charge annihilation step (found within the individual `coul-xvg` folders) and a Van der Waals decoupling step (found within the individual `vdw-xvg` folders).

Imaging of Organic Samples with Megaelectron Volt Time-of-Flight Secondary Ion Mass Spectrometry Capillary Microprobe

Time-of-flight Secondary Ion Mass Spectrometry (TOF SIMS) with MeV primary ions offers a fine balance between secondary ion yield for molecules in the mass range from 100 to 1000 Da and beam spot size, both of which are critical for imaging applications of organic samples. Using conically shaped glass capillaries with an exit diameter of a few micrometers, a high energy heavy primary beam can be collimated to less than 10 μm. In this work, imaging capabilities of such a setup are presented for some organic samples (leucine-evaporated mesh, fly wing section, ink deposited on paper). Lateral resolution measurement and molecular distributions of selected mass peaks are shown. The negative influence of the beam halo, an unavoidable characteristic of primary beam collimation with a conical capillary, is also discussed. A new start trigger for TOF measurements based on the detection of secondary electrons released by the primary ion is presented. This method is applicable for a continuous primary ion beam, and for thick targets that are not transparent to the primary ion beam. The solution preserves the good mass resolution of the thin target setup, where the detection of primary ions with a PIN diode is used for a start trigger, reduces the background, and enables a wide range of samples to be analyzed.