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opencc-by-4.0May 2023View details →

Dataset 2 for "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses"

Dataset with 154 host species (min 45 sampled individuals sampled at 1+ sites) for the second part of the analysis in "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses". One file contains the data table. One file contains a table with descriptions of the columns in the data table.

opencc-by-4.0Jun 2023View details →

Malware Finances and Operations: a Data-Driven Study of the Value Chain for Infections and Compromised Access

Description The datasets demonstrate the malware economy and the value chain published in our paper, <a href="https://doi.org/10.1145/3600160.3605047">Malware Finances and Operations: a Data-Driven Study of the Value Chain for Infections and Compromised Access</a>, at the 12th International Workshop on Cyber Crime (IWCC 2023), part of the ARES Conference, published by the International Conference Proceedings Series of the ACM ICPS. Using the well-documented scripts, it is straightforward to reproduce our findings. It takes an estimated 1 hour of human time and 3 hours of computing time to duplicate our key findings from MalwareInfectionSet; around one hour with VictimAccessSet; and minutes to replicate the price calculations using AccountAccessSet. See the included README.md files and Python scripts. We choose to represent each victim by a single JavaScript Object Notation (JSON) data file. Data sources provide sets of victim JSON data files from which we've extracted the essential information and omitted Personally Identifiable Information (PII). We collected, curated, and modelled three datasets, which we publish under the <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>. 1. MalwareInfectionSet We discover (and, to the best of our knowledge, document scientifically for the first time) that malware networks appear to dump their data collections online. We collected these infostealer malware logs available for free. We utilise 245 malware log dumps from 2019 and 2020 originating from 14 malware networks. The dataset contains 1.8 million victim files, with a dataset size of 15 GB. 2. VictimAccessSet We demonstrate how Infostealer malware networks sell access to infected victims. Genesis Market focuses on user-friendliness and continuous supply of compromised data. Marketplace listings include everything necessary to gain access to the victim's online accounts, including passwords and usernames, but also detailed collection of information which provides a clone of the victim's browser session. Indeed, Genesis Market simplifies the import of compromised victim authentication data into a web browser session. We measure the prices on Genesis Market and how compromised device prices are determined. We crawled the website between April 2019 and May 2022, collecting the web pages offering the resources for sale. The dataset contains 0.5 million victim files, with a dataset size of 3.5 GB. 3. AccountAccessSet The Database marketplace operates inside the anonymous Tor network. Vendors offer their goods for sale, and customers can purchase them with Bitcoins. The marketplace sells online accounts, such as PayPal and Spotify, as well as private datasets, such as driver's licence photographs and tax forms. We then collect data from Database Market, where vendors sell online credentials, and investigate similarly. To build our dataset, we crawled the website between November 2021 and June 2022, collecting the web pages offering the credentials for sale. The dataset contains 33,896 victim files, with a dataset size of 400 MB. Credits Authors <ul> <li>Billy Bob Brumley (Tampere University, Tampere, Finland)</li> <li>Juha Nurmi (Tampere University, Tampere, Finland)</li> <li>Mikko Niemelä (Cyber Intelligence House, Singapore)</li> </ul> Funding This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under project numbers 804476 (SCARE) and 952622 (SPIRS). Alternative links to download: <a href="https://mega.nz/folder/aJwVyIYJ#9SWh-Z3-TpPfjHZeFxbeew">AccountAccessSet</a>, <a href="https://mega.nz/folder/iUQ3RaKB#48ZkXnFYSR0qXLcbkrZLqw">MalwareInfectionSet</a>, and <a href="https://mega.nz/folder/aNYCFCrK#pbDkJL-PNWjn1ABXbtdR4w">VictimAccessSet</a>.

opencc-by-4.0Sep 2022View details →

Data from: Pathogen community composition and co-infection patterns in a wild community of rodents

ABSTRACT Rodents are major reservoirs of pathogens that can cause disease in humans and livestock. It is therefore important to know what pathogens naturally circulate in rodent populations, and to understand the factors that may influence their distribution in the wild. Here, we describe the incidence and distribution patterns of a range of endemic and zoonotic pathogens circulating among rodent communities in northern France. The community sample consisted of 713 rodents, including 11  host species  from diverse habitats. Rodents were screened for virus exposure (hantaviruses, cowpox virus, Lymphocytic choriomeningitis virus, Tick-borne encephalitis virus) using antibody assays. Bacterial communities were characterized using 16S rRNA amplicon sequencing of splenic samples. Multiple correspondence (MCA), regression and association screening (SCN) analyses were used to determine the degree to which extrinsic factors contributed to pathogen community structure, and to identify patterns of associations between pathogens within hosts. We found a rich diversity of bacterial genera, with 36 known or suspected to be pathogenic. We revealed that host species is the most important determinant of pathogen community composition, and that hosts that share habitats can have very different pathogen communities. Pathogen diversity and co-infection rates also vary among host species. Aggregation of pathogens responsible for zoonotic diseases suggests that some rodent species may be more important for transmission risk than others. Moreover we detected positive associations between several pathogens, including Bartonella, Mycoplasma species, Cowpox virus (CPXV) and hantaviruses, and these patterns were generally specific to particular host species. Altogether, our results suggest that host and pathogen specificity is the most important driver of pathogen community structure, and that interspecific pathogen-pathogen associations also depend on host species. FILE DESCRIPTION: MiSeq raw sequences of the 16Sv4 rRNA gene from spleen rodent samples This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each spleen rodent sample using the MiSeq platform. The 749 multiplexed PCR products were indexed using both forward and reverse indices. Information of the multiplexed samples (n=363 in replicate) and positive (n= 6) & negative controls (n= 17) is provided in the following XLSX file titled: 16S_raw_abundance_data.xlsx File name: MiSeq raw sequences of the V4 region 16S rRNA gene.zip Raw input and output files generated by the mothur program This ZIP file contains all the input and output files generated during the MiSeq sequence analysis with the mothur program. File name: Raw input and output files generated by the mothur program.zip Log file generated by the mothur program This TXT file contains is the history of all the command lines and parameters used during the MiSeq sequence analysis with the mothur program. File name: mothur.1428506786.logfile Raw abundance table of the 16v4 rRNA gene from spleen rodent samples before data filtering This XLSX file contains the number of reads for each distinct Operational Taxonomic Unit (OTU) and each of the PCR products, including the 332 spleen rodent samples analyzed in the study and the negative & positive controls, sequenced in the MiSeq run before the data filtering. This file contains also the following information: Study_site, Study_year, Sample_habitat, Host_species, Host_age, Host_sex, PCR_ID and the taxonomic classification (Kingdom to Genus) of each OTU. File name: 16S_raw_abundance_data.xlsx Occurrence table of the 16v4 rRNA gene from spleen rodent samples after data filtering This XLSX file contains the occurrences (presence: 1 ; absence: 0) after data filtering of each putative pathogenic Operational Taxonomic Unit (OTU) for each of the 332 spleen rodent samples analyzed in the study. File name: 16S_presence_absence_data.xlsx Statistical Analysis Scripts and Data File This ZIP file contains the R scripts for performing statistical analyses reported in the main text and supplemental materials. There is one main file (Analyses.R), as well as two source scripts required for association screening analyses (SCN.txt and FctTestScreenENV.txt). It also includes an R-legible data file containing occurrences (presence: 1 ; absence: 0) for all pathogen exposure variables on which statistical analyses were conducted (PA_DATA.csv) for each of the 332 spleen rodent samples analyzed in the study. The column names for bacterial exposures correspond to the “Pathogen Code” given in the 16S_presence_absence_data.xlsx file. File name: Statistical Analysis Scripts and Data File.zip

opencc-by-4.0Oct 2023View details →

Hepatitis D infection induces IFN-β-mediated NK cell activation and TRAIL-dependent cytotoxicity

The dataset contains bulk RNA-seq read count matrices of NK cells from healthy donors after 48 h of co-culture with hepatitis D virus infected and non-infected HepG2-hNTCP cells. The samples are described in the table RNA-seq_samples.xls that is included with the count matrices. Further details are given in the publication associated with this dataset (Groth et al., Front Immunol, 2023, https://doi.org/10.3389/fimmu.2023.1287367).

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Decomposition of Microstegium vimineum litter, plants grew through the Big Oaks National Wildlife Refuge in 2019. Litter used in this experiment naturally senesced in the fall 2019, decomposition data collected through 2020. Plants were infected or not-infected with the foliar fungal pathogen Bipolaris gigantea during the 2019 growing season.

Decomposition of plant litter, facilitated primarily by microbial decomposers, plays a critical role in biogeochemical cycling and ecosystem function. Emerging pathogens have the potential to impact litter decomposition by altering the chemical composition and associated microbial community of host tissue. Here, we compared litter decomposition of the invasive grass Microstegium vimineum collected from sites with Bipolaris leaf spot symptoms and sites with no apparent disease symptoms in a common garden experiment. Our results revealed that leaf tissue from litter from non-infected sites decomposed more rapidly through the spring than litter from infected sites. Differences in fungal composition between infected and non-infected litter at the start of the experiment largely persisted through the summer. Our work demonstrates that pathogen colonization may facilitate the persistence of infected host litter, potentially slowing the return of nutrients to the environmental pool while also promoting the survival and dispersal of primary inoculum the following season.

openCC (other)Jun 2023View details →

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Stem diameter of trees and shrubs in thinleaf alder sites along the Tanana River floodplains and severity of stem canker infection of alder in 2006.

This dataset includes the stem diameter of each woody plant >2m tall, by species (or genus), found in each of the thinleaf alder sites we established in the Tanana River floodplains in 2006, as well as an assessment of the severity of canker infection in each thinleaf alder stem. Species (or genus), diameter at breast height (dbh), and severity of canker infection are the variables included here. This dataset can be used in conjunction with a dataset of alder size/age relationships (DN_alder_stand_structure2.xls) to estimate the age structure of alder stands.

openOpenMar 2009View details →

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Abundance and parasitoid infection dynamics of Guinardia delicatula on the Northeast U.S. Shelf from 2006 to 2022 determined by Imaging FlowCytobot.

These data include abundances of the diatom, Guinardia delicatula (= Rhizosolenia delicatula), on the Northeast U.S. Shelf from 2006 to 2022 as part of Long-Term Ecological Research (NES-LTER). Abundances are determined from Imaging FlowCytobot (IFCB) deployed in-situ at ~4m depth at the nearshore Martha’s Vineyard Coastal Observatory (MVCO) from 2006 to 2022 and in underway mode (sampling near-surface seawater) on 24 NOAA EcoMon survey cruises from 2013 to 2022. Abundances based on both human and machine learning image classification are provided. Total G. delicatula abundances are divided into two categories based on whether G. delicatula exhibited current or recent infection by the protistan parasitoid, Cryothecomonas aestivalis. Four data tables are provided with abundance values separated by sampling scheme (time series or survey cruise) and image classification approach (human or machine learning).

openCC0May 2023View details →

opencc-by-4.0Jan 2020View details →

Dataset: Knowledge, information needs and behavior regarding HIV and sexually transmitted infections among migrants from sub-Saharan Africa living in Germany: Results of a participatory health research survey.

Dataset for: Koschollek C, Kuehne A, Müllerschön J, Amoah S, Batemona-Abeke H, Dela Bursi T, Mayamba P, Thorlie A, Mputu Tshibadi C, Wangare Greiner V, Bremer V, Santos-Hövener C: Knowledge, information needs and behavior regarding HIV and sexually transmitted infections among migrants from sub-Saharan Africa living in Germany: Results of a participatory health research survey. This dataset has been described in a PLoS One paper and contains all data necessary to replicate the results presented within this paper (10.1371/journal.pone.0227178). Please cite both the paper as well as the DOI of this dataset if you make use of the data.

opencc-by-4.0Mar 2020View details →

Fig. 1 in A new Myxobolus (Cnidaria: Myxosporea) infecting the ornamental catfish Corydoras schwartzi from the Purus River in Brazil

Fig. 1. Corydoras schwartzi Rössel, 1963 infected by Myxobolus adrianoi sp. nov. A. Sampled fish captured in the Purus River near Lábrea Municipality, Amazonas State, Brazil. B. Histological sections of the fish intestine showing large cyst in the serosa layer (black arrow).

Fig. 5 in Three New Species of Dendrogaster (Crustacea: Ascothoracida) Infecting Goniasterid Sea-Stars (Echinodermata: Asteroidea) from Japan

Fig. 5. Dendrogaster tobasuii sp. nov., allotype male, total length ca. 6 mm, NSMT-Cr 26861, removed from the main branch of holotype female. A, right lateral view (arrowhead indicating point of breakage of isolated left posterior process); B, isolated left posterior process; C, main body, left lateral view (long setae of thoracic limbs and furca omitted); D, right antennule, medial view; E, left first thoracic limb (thoracopod 2), lateral view. Abbreviations: ab, abdominal segments; bs, basis; cg, claw guard; cl, terminal claw; cx, coxa; en, endopod; ex, exopod; fr, furcal rami; fs, fusion seam; I–IV, segment numbers; mx, second maxillae; sp, rudimentary proximal sensory process; th, thoracomeres.

Fig. 7 in Three New Species of Dendrogaster (Crustacea: Ascothoracida) Infecting Goniasterid Sea-Stars (Echinodermata: Asteroidea) from Japan

Fig. 7. Dendrogaster nagasakimaruae sp. nov., A–D, holotype female, mantle size 22.0 mm, NSMT-Cr 26878, removed from coelomic cavity of Nymphaster euryplax (R 60.0 mm, r 14.6 mm), East China Sea southeast of Danjo Islands, Nagasaki Prefecture (31°51.73′N, 128°29.13′E), 247–257 m depth. A, whole animal, dorsal view; B, linear scheme to indicate a pattern of mantle branching; C, left antennule, medial view; D, second maxillae, posterior view. E–F, allotype male, total length 4.5 mm, NSMT-Cr 26879, removed from the main branch of holotype female. E, whole animal, right lateral view; F, abdomen. Abbreviations: b1a, anterior primary branches; b2a, anterior secondary branches; b3a, anterior tertiary branches; b1p, posterior primary branches; b2p, posterior secondary branches; bl, basal lobe; cg, claw guard; cl, terminal claw; fr, furcal rami; fs, fusion seam; I–IV, segment numbers; mb, main branches; mp, middle piece; pp, posterior processes; sp, rudimentary proximal sensory process.

Fig. 4 in Three New Species of Dendrogaster (Crustacea: Ascothoracida) Infecting Goniasterid Sea-Stars (Echinodermata: Asteroidea) from Japan

Fig. 4. Dendrogaster tobasuii sp. nov., holotype female, mantle size 59.9 mm, NSMT-Cr 26860, removed from coelomic cavity of Mediaster arcuatus (unmeasured), Kumano-nada Sea off Owase, Mie Prefecture, Pacific coast of central Japan, about 300 m depth. A, whole animal, dorsal view; B, linear scheme to indicate a pattern of mantle branching; C, left antennule, medial view; D, fourth segment of right antennule, lateral view; E, second maxillae. Abbreviations: b1a, anterior primary branches; b2a, anterior secondary branches; b3a, anterior tertiary branches; b1p, posterior primary branches; cg, claw guard; cl, terminal claw; fs, fusion seam; I–IV, segment numbers; mb, main branches; mp, middle piece; sp, rudimentary proximal sensory process.

Fig. 3 in Three New Species of Dendrogaster (Crustacea: Ascothoracida) Infecting Goniasterid Sea-Stars (Echinodermata: Asteroidea) from Japan

Fig. 3. Dendrogaster komatsuae sp. nov., nauplius, carapace length 0.87 mm, from holotype female. A, whole animal, ventral view; B, left portion of body, ventral view. Abbreviations: a1, antennule; a2, antenna; md, mandible. Scale bar=0.3 mm.

Fig. 2 in Three New Species of Dendrogaster (Crustacea: Ascothoracida) Infecting Goniasterid Sea-Stars (Echinodermata: Asteroidea) from Japan

Fig. 2. Dendrogaster komatsuae sp. nov., holotype female, mantle size 46.3 mm, NSMT-Cr 26858, removed from coelomic cavity of Lithosoma japonica (R 50.0 mm, r 25.3 mm), TAMBL-EC10, Kumano-nada Sea off Owase, Mie Prefecture, Pacific coast of central Japan, about 300 m depth. A, whole animal, dorsal view; B, linear scheme to indicate a pattern of mantle branching; C, left anterior branches, unfurled; D, left antennule, medial view; E, third and fourth segments of right antennule (terminal claw missing), lateral view; F, second maxillae. Abbreviations: b1a, anterior primary branches; b2a, anterior secondary branches; bp, posterior branches; b1p, posterior primary branches; cg, claw guard; cl, terminal claw; eb, extra branch; fs, fusion seam; I–IV, segment numbers; mb, main branches; mp, middle piece; sp, rudimentary proximal sensory process; tb, terminal branch.

Fig. 6 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites

Fig. 6. Chiraziulus kaiseri (Mauriès, 1983), female vulva. Scanning electron micrographs. A. Vulva in situ behind second pair of legs, posterior view. B. Details of right vulva behind second pair of legs. C. Detail of microtubular structure under the vulva. D. Vulva in ventral view. E. Vulva in anterior view. Abbreviations: o = operculum; b = bursa. Scale bars: A = 100 μm; B–E = 10 μm.

Fig. 3 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites

Fig. 3. Chiraziulus kaiseri (Mauriès, 1983), paratypes. Scanning electron micrographs. A. Head and first body rings in lateral view. B. Last body rings ("tail") in lateral view. C. Tip of antenna. D. Detail of the limbus; notice lines of beadlike structures between cuticular scutes. E. Detail of labrum in frontal view. F. Gnathochilarium in ventral view; the arrow shows the distomesal setae on stipes. Scale bars: A–B, E–F = 100 μm; C = 10 μm; D = 1 μm.

Fig. 2 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites

Fig. 2. Distribution of species of Chiraziulus Mauriès, 1983 in Iran (Mauriès 1987). C. troglopersicus sp. nov.: red dot (1); C. kaiseri: yellow dots (2–6). 1. Neyneh Cave. 2. "Chiraz" "montagne greseuse au nord de la ville". 3. 19 km W of Shiraz. 4. 5 km N of Persepolis. 5. Oasis 95 km N of Bandarabass. 6. Sarab Cave.

Fig. 9 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites

Fig. 9. Chiraziulus troglopersicus sp. nov., ♂, paratype, gonopods. Scanning electron micrographs. A. Anterior gonopods in posterior view. B. Detail of the process on the tip of an anterior gonopod in posterior view. C. Anterior gonopods in anterior view. D. As C, in apical view. E. Tip of the flagellum. F. Posterior gonopods in lateral view. G. Tip of the long spine-like process of the posterior gonopod. H. Posterior gonopods in posterior view. I. As H, in anterior view. J. Detail of the mesal sternal part of the gonopods. Abbreviations: C = coxal process; T = telepodite; f = flagellum; s = setae; dp = distal process. Scale bars: A–D, F, H–I = 10 μm; E, G, J = 1 μm.

Fig. 8 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites

Fig. 8. Number of podous rings and midbody vertical diameter of the studied specimens. Chiraziulus kaiseri (Mauriès, 1983) in blue; Chiraziulus troglopersicus sp. nov. in red. ▲ = adult ♂♂; ● = juveniles and ♀♀.

Fig. 7 in Highly disjunct and highly infected millipedes - a new cave-dwelling species of Chiraziulus (Diplopoda: Spirostreptida: Cambalidae) from Iran and notes on Laboulbeniales ectoparasites

Fig. 7. Chiraziulus kaiseri (Mauriès, 1983). Comparison of the paratype (A, C, E, G, I and K) and specimen from Ghar Sarab Cave (B, D, F, H, J and L). A–B. Left anterior gonopods, mesal view. C–D. Anterior gonopod, posterior view. E–F. Anterior gonopod, anterior view. G–H. Anterior gonopod, lateral view. I–J. Anterior gonopod, apical view. K–L. Posterior gonopods.