Summary: This dataset contains recruitment survey results of Semibalanus balanoides and Chthamalus sp. in southwestern UK, 2015-2016. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/683132

Summary: The Eddies Dynamics, Mixing, Export, and Species composition (EDDIES) mesozooplankton biomass data set includes estimates of mesozooplankton biomass determined from MOCNESS plankton net tows. Zooplankton biomass estimates were determined from 1 m^2, 150 micron mesh MOCNESS (Multiple Opening/Closing Net and Environmental Sensing System) tows. The following discrete depth intervals were sampled on the upcast: 0-50, 50-100, 100-150, 150-200, 200-300, 300-400, 400-500, 500-600, and 600-700 m. Generally paired tows during the day (9:30-15:00 local time) and night (21:30-03:00) were performed at each station. A single tow generally covered 5-15 km. The nominal position (lat_n and lon_n) for each tow is the position at the mid depth 200-300m sampling interval. Table 1 (pg 1362) of Goldthwait and Steinberg (2008) is a sequential list of all MOCNESS mesozooplankton tows and includes eddy identification number and location. Each sample was size-fractionated using nested sieves of 0.15 mm, 0.5 mm, 1 mm, 2mm, and 5 mm mesh. Zooplankton in each size class were transferred onto pre-weighed 0.15 mm nitex mesh filters and rinsed with deionized water. Samples were then dried for 24 hours at 60 degrees C and weighed.

Summary:

This data presents the results of a test series on five identical unreinforced masonry walls built at half-scale that were constructed using hollow clay brick units and standard cement-based mortar. The test units were subjected to
quasi-static cycles of increasing drift demands and the tests differed with regard to the applied axial load and the moment restraint applied at the top of the walls. The walls were tested up to failure. Throughout the loading the deformations of the walls were recorded using a digital photogrammetric measurement system tracking the movement of 312 points per test unit.

Summary:

The GlobalSCAPE project is setting out to investigate the experiences, attitudes, skills, needs, challenges and professional development of science communicators around the world. This is being achieved with a diary survey, a style of survey designed to be repeated on a set interval several times. To assess the clarity of survey questions prepared for the GlobalSCAPE science communicator diary research, a pilot study was conducted with a sample of participants gathered by project partners (N = 23). This pilot research followed a piggyback approach, where follow-up questions were asked of respondents after they completed each step in the survey. Here, we present the dataset from this pilot survey.

For data privacy reasons, open-ended items were excluded from this dataset

Summary:

This directory contains xml files (which in turn contain concatenated alignments), newick, and phylip formatted tree files. Code and scripts used for generating figures, phylogenies and biogeographic models is available on request.

~/trees/ contains tree files and maximum clade credibility trees from the three phylogenetic inferences: 1) Canarieae with a fossil tip; 2) Canarieae with fossil nodes; and 3) Canarieae with fossil nodes, but without the Canarieae fossil node calibration. See the paper and supplemental text for more information.

~/trees/RAxML/ contains the RAXML starter trees used  

~/xml_files/ contains the xml files used for Bayesian phylogenetic inference in BEAST for all three phylogenetic inferences (see above). Concatenated alignments of molecular data can be found within the xml files.

Summary:

Baltic Sea communities consisting of key and endemic species are threatened by climate change. Using Ecological niche modelling, we map predicted distribution patterns under recent and future climate change scenarios (2050) for a food-web consisting of a guild of meso-grazers (Idotea spp.), their host algae (Fucus vesiculosus and F. radicans) and their fish predator (Gasterosteus aculeatus). Brackish water species depend on two important abiotic factors: temperature and salinity. We assess which of these environmental factors determines the distribution limits of the grazers in the Baltic Sea today. For species in a semi-enclosed sea area such as the Baltic Sea, climate-induced changes may lead to dramatic food-web effects. We assess the consequences of the predicted climate-induced habitat range changes for this unique Baltic community.
 

Summary:

supplementary data products, including all sky-subtracted spectra from individual targets, as well as random draws from posterior PDFs for model parameters (see enclosed README file)

Summary:

Dataset comprises tests sampled in the German Chlamydia trachomatis laboratory sentinel during 2008 and 2014.

Summary:

Model, Data, and Analysis Scripts for The Evolution of Cooperation by the Hankshaw Effect as submitted

Summary:

Structural Models (PDB) of SARS-CoV-2 Spike RBD bound to ACE2 receptors of 215 animals.

Structural model of Human TMPRSS2.

Modelled using the FunMod pipeline and referenced in the preprint

SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals

 

Summary:

This database contain protein sequences of aquatic microbial eukaryotes, or protists. The purpose of this is to make a database that is of reasonable quality to serve as resource for both taxonomy and functional interpretation of metagenomic and metatranscriptomic studies of protists. The source of the sequences were mainly from Marine Microbial Eukaryotes Transcriptome Sequencing Project (MMETSP), and supplemented with various genomes and transcriptomes of organisms that were not a part of MMETSP.

To use this database, one has to understand the main function of the three files here.

(1) The protein sequences are stored in .faa file. You can build an alignment/search database out of that and search your meta-omics sequences against it. Each sequence in the FASTA file has an ID which always consists of two parts like this: "MMETSP0004_1234567". The text before the first underscore is the source ID of that sequence.

(2) Taxonomy information of each source ID are stored in "EukZoo_taxonomy_table_v_0.2.tsv". One can use the information within in conjunction with database search results to assign taxonomy to sequences.

(3) KEGG annotation of each sequence are stored in "EukZoo_KEGG_annotation_v_0.2.tsv". One can use the information within in conjunction with database search results to assign KEGG functional annotation (KO ID) to sequences.

I also provide scripts to assign taxonomy and KEGG annotation from database search results. You can also find the scripts and explanations on how to use them on the EukZoo GitHub page. You will find details on how the database was created and curated on there as well.

Please contact me at zhenfeng.liu1@gmail.com if you have any questions or requests. Thank you for your interest in EukZoo.

Summary:

This paper presents a publically available data set recorded during the shake-table test of a structure with reinforced concrete (RC) and unreinforced masonry (URM) walls. The shake-table test, performed at the TREES laboratory of EUCENTRE (Pavia, Italy), was part of a larger research initiative at EPFL (Lausanne, Switzerland) that addresses the seismic behaviour of mixed RC-URM structures. The half-scale test unit was subjected to several shakings of different intensity levels. The paper presents the geometry of the test unit, the properties of the construction materials, the instrumentation, and outlines the organization of the recorded data. Two sets of data are available: the unprocessed data and a second set of processed data where conventional and optical measurements are synchronised. This second set contains also some derived data, which allows to quickly plot key quantities such as base shear and top displacement. The aim of the paper is to provide all information required by the reader for analysing the test data and using it for validation purposes of numerical and mechanical models. The performance of the test unit is described in a companion paper.

Summary:

Performance improvements, many bug fixes.

Summary:

Previous test data on unreinforced masonry walls focused on the global response of the wall. A new dataset on six wall tests, which is publically available, allows linking global to local deformations of masonry walls, which can be useful for advancing performance-based design and assessment methods for unreinforced masonry buildings. This data paper presents the
results of a test series on six identical unreinforced masonry walls that were constructed using hollow clay brick units and standard cement-based mortar.
The test units were subjected to quasi-static cycles of increasing drift demands and the tests differed with regard to the applied axial load and the moment restraint applied at the top of the walls. The walls were tested up to failure. Throughout the loading the deformations of the walls were recorded using a digital photogrammetric measurement system tracking the movement of 312 points per test unit.

Summary: Number of new fronds recorded at the kelp mooring (Central CA Macrocystis pyrifera forest, 36° 37.297’ N, 121° 54.102’ W) from July to August 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/822535

Summary: pH measured in situ over depth in the kelp forest (36° 37.3’ N, 121° 54.1’ W) recorded in July 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/826162

Summary: A key tool for investigating the regulation of genes is represented by Bacterial Artificial Chromosomes-reporter constructs (BAC). BACs are large insert libraries, often >>100 kb, which thus capture the genomic sequences surrounding a gene of interest, including all, or nearly all, of the elements underpinning regulation. Recombinant BACs, containing a reporter gene in place of the endogenous coding sequence of genes, can be utilized to drive the expression of reporter genes under the regulatory control of the gene of interest while still embedded within its genomic context. Systematic deletions within the BAC reporter construct can be used to identify the minimal reporter in an unbiased way, avoiding the risk of overlooking regulatory elements that may be many kilobases away from the transcription start-site. Nematostella vectensis (Edwardsiidae, Anthozoa, Cnidaria) has become an important model in regenerative biology, ecology, and especially in studies of evo-devo and gene-regulatory networks due to its interesting phylogenetic position and amenability to molecular techniques. This dataset represents the sequencing of 5 Nematostella vectensis BACs containing the genes of interest: NvDpp, NvChordin, NvFoxa, NvWnta, and NvWnt1.

Summary: Data from moored instruments (pH, dissolved oxygen, temperature, salinity, PAR, pressure) at 9 depths outside (36° 37.342’ N, 121° 54.049’ W) and inside the kelp canopy (36° 37.297’ N, 121° 54.102’ W.) at Hopkins Marine Station, recorded between June and October 2018. The tidal depth of the kelp canopy mooring ranges from 8 to 11 meter. The outside mooring is located 115m north and offshore from the kelp forest, the tidal range is 16 to 9 meters. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/822549

Summary: Surface irradiance measured on the roof of the Monterey Bay Aquarium (36.62 °N, 121.90 °W) from June to October 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/822517

Summary:

Data and Codebook for the HIT-COVID Project