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Fig. 3. Kincaidiana hexatheca Altman, 1936, reproductive organs. A–B in On Kincaidiana Altman, 1936 and Guestphalinus Michaelsen, 1933 (Annelida, Clitellata, Lumbriculidae), with the descriptions of three new species
Fig. 3. Kincaidiana hexatheca Altman, 1936, reproductive organs. A–B. From Hoh River, WA; (A) segments IX-XI; (B) atrium and spermathecae with expanded ampullae in IX-X. C–D. From Rogue River, OR; (C) reproductive organs in IX-XI from an atypical worm with long atria; (D) atrium and spermatheca in IX, from a typical worm.
Consensus QSAR models estimating acute aquatic toxicity for three trophic levels organisms: Algae, Daphnia and Fish
<p>We report new consensus models estimating acute toxicity for algae, daphnia and fish endpoints. We assembled a large collection of 3680 public unique compounds annotated by, at least, one experimental value for the given endpoint. Support Vector Machine models were internally and externally validated following the OECD principles. Reasonable predictive performances were achieved (RMSE<sub>ext</sub> = 0.56 – 0.78) which are in line with those of state-of-the-art models. The known structural alerts are compared with analysis of the atomic contributions to these models obtained using the ISIDA/<em>ColorAtom</em> utility. A benchmarking against existing tools has been carried out on a set of compounds considered more representative and relevant for the chemical space of the current chemical industry. Our model scored one of the best accuracies and data coverage.</p> <p>Nevertheless, industrial data performances were noticeably lower than those on public data, indicating that existing models fail to meet the industrial needs. Thus, final models were updated with the inclusion of new industrial compounds, extending applicability domain and relevance for application in an industrial context. Generate models and collected public data are made freely available.</p> <p><strong>Available fields in the SDF file:</strong></p> <ul> <li>SMILES_Canonical: canonical SMILES code</li> <li>DB: source of the data, "Litterature set" means that the data is originated from an article (see the companion article of the dataset for details).</li> <li>endpoint: organism for which endpoint is available</li> <li>CASRN: CAS registration number</li> <li>98-81-7</li> <li>pEC50 - DAPHNIA: Daphnia, mortality, which is evaluated by the immobilization of the invertebrate is recorded at 48 hours and expressed as the log median effective concentration (pEC50)</li> <li>mg/L - DAPHNIA: Daphnia, mortality, which is evaluated by the immobilization of the invertebrate is recorded at 48 hours and expressed as the median effective concentration (EC50)</li> <li>pLC50 - FISH: Fish, the log median lethal concentration measured at 96 hours is considered (pLC50)</li> <li>mg/L - FISH: Fish, the log median lethal concentration measured at 96 hours is considered (LC50)</li> <li>pEC50 - ALGA: Algae, the purpose is to determine the substance’s growth inhibition effect, expressed as the log median effective concentration (pEC50) measured at 72 hours</li> <li>mg/L - ALGA: Algae, the purpose is to determine the substance’s growth inhibition effect, expressed as the median effective concentration (EC50) measured at 72 hours</li> </ul>
Volatile organic compound analysis, a new tool in the quest for preterm birth prediction – an observational cohort study
<p>Vaginal swabs were taken in pregnancy in high risk asymptomatic women attending a preterm prevention clinic. Women in the study attended the clinical due to a history of preterm birth or midtrimester pregnancy loss, or due to a history of cervical surgery. Individualised management plans were made depending upon individual patient risk factors. During their attendance to the clinic vaginal swabs were taken for VOC analysis. Swabs were taken between 15 and 28 weeks gestation. Women consented to vaginal swabs at each of their visits to the clinic. The dataset contains GC-IMS VOC data from a G.A.S. GC-IMS and includes a Spreadsheet of demographics.</p>
Figure 10. Spheniopsis brasiliensis. A in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 10. Spheniopsis brasiliensis. A transverse section through the heart. AM, Amoebocyte; AU, auricle; PE, pericardium; PEG, pericardial gland; R, rectum; SM, suspensory membrane; V, ventricle.
Figure 3. Spheniopsis brasiliensis. A in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 3. Spheniopsis brasiliensis. A ventral view of the septum, foot and mouth. BG, Byssal groove; F, foot; F(T), 'toe' of foot; M, mouth; SE, septum; SEM, margin of septal membrane; SEP(1),(2),(3),(4), septal pores.
Figure 1 in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 1. Spheniopsis brasiliensis. SEM views of the siphonal apparatus. (A) Posterior view of the exhalant and inhalant siphons, with three and four siphonal papillae, respectively. (B) Higher magnification view of a single siphonal papilla with a terminal array of sensory cilia. CI, Cilia; ES, exhalant siphon; IS, Inhalant siphon; SP, sensory papilla; SPB, base of sensory papillae.
Figure 9. Spheniopsis brasiliensis. A in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 9. Spheniopsis brasiliensis. A transverse section through the pedal ganglia and the statocysts. PEGA, Pedal ganglia; STAT, statocyst; STL, statolith.
Figure 5 in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 5. Spheniopsis brasiliensis. Transverse sections through the (A) oesophagous; (B) crystalline style sac; (C) mid gut; (D) hind gut; and (E) rectum, all drawn to the same scale. CC, Collagen coat; CS, crystalline style.
Figure 8. Spheniopsis brasiliensis. A transverse section through a in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 8. Spheniopsis brasiliensis. A transverse section through a single digestive tubule. AM, Amoebocyte; CRC, crypt cell; DC, digestive cell.
Figure 4. Spheniopsis brasiliensis. A in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 4. Spheniopsis brasiliensis. A transverse section through the stomach in the region of the conjoined style sac and mid gut. CS, Crystalline style; CSMG, conjoined style sac and mid gut; CSS, crystalline style sac; FIPI, fragments of ingested prey; GS, gastric shield; MG, mid gut; SC, secretory cells.
Figure 7 in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 7. Spheniopsis brasiliensis. Histological sections through the visceral mass and ingested prey items. (A) A transverse section through the stomach with ingested prey items inside it. (B, C) The remains of captured and ingested ostracods. (D) The skeletal remains of an unknown prey item. CSS, Crystalline style sac; GS, gastric shield; IPI, ingested prey item; ST, stomach.
Figure 12. Spheniopsis brasiliensis. A section through a in The organs of prey capture and digestion in the miniature predatory bivalve Spheniopsis brasiliensis (Anomalodesmata: Cuspidarioidea: Spheniopsidae) expose a novel life-history trait
Figure 12. Spheniopsis brasiliensis. A section through a portion of a gonadial follicle. C, Cuticle; DN, dividing nucleus; DO, developing oocyte; EO, encapsulated oocyte; GE, germinal epithelium; N, nucleus; RT, regressing testes; STA, stalk; SPZ, spermatozoan; Y, yolk.
Input Data for "Molecular Lignin Solubility and Structure in Organic Solvents"
<p>Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: `tar -zcvf ligninsolvationstudy.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*log" --exclude="*[0-9].out" --exclude="*npz" --exclude="*pkl" --exclude="*npy" --exclude="*png" --exclude="*bmim*" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*txt" --exclude="*state_prev.cpt" LigninSolvation`, which intentionally excludes large files. The full dataset is available upon request.</p> <p><strong>Directory Descriptions</strong></p> <p><strong>BuildSolventBoxes</strong> contains the scripts and inputs needed to make the solvent boxes suitable for use with the VMD solvate plugin.<br> <strong>BuildSystems</strong> assembles the lignin polymers and solvates them into a complete simulation system. Depends on the outputs from [LigninBuilder](https://github.com/jvermaas/LigninBuilder).<br> <strong>Equilibrium</strong> has all the equilibrium trajectories and the scripts needed to set them up.<br> <strong>FEP</strong> has the free energy perturbation calculation key outputs (the fepout files) and the scripts needed to set up the calculation and analyze them.</p> <p>The scripts are <em>mostly</em> python scripts, but some are also in tcl, and have the appropriate file endings. GROMACS run input files (.tpr) and namd configuration files (.namd) may also be of general interest.</p>
Data for: Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia)
<p>Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4–11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.</p>
How Software Organizations are using the ISO/IEC 29110 Standard's Processes: A Survey of the State of the Art and Practice
<p>ISO/IEC 29110 was developed containing a set of industrially validated practices that can potentially be adopted by software Very Small Entities (VSE). VSEs usually have characteristics that differentiate them from organizations of different sizes, such as extremely limited resources and informal project management processes, tending to adopt Agile methods and having an historical resistance to the adoption of standards, that are in general developed for large organizations. In this sense, our research question arises: "How are software organizations using the ISO/IEC 29110 practices?". To answer this question, a Systematic Mapping Study (SM), and a Survey with software organizations were carried out in order to identify the state of the art and the state of the practice in relation to the use of the standard’s practices. The SM identified 21 primary studies reporting the use of the standard in hundreds of software organizations with positive results such as organizational learning, process improvement, improved communication, and also some negative results, such as deployment difficulties in technical areas and the need for additional time and resources. The Survey carried out with 23 software companies identified that, in general, companies do not explicitly know the content of the standard, but partially carry out, in accordance with the standard, practices related to planning, monitoring, control and execution of a project plan, and do not carry out requirements analysis or architecture and detailed design as defined in the standard. </p>
QM7-X: A comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules
<p>Here, we introduce QM7-X, a comprehensive dataset of > 40 physicochemical properties for ~4.2 M equilibrium and non-equilibrium structures of small organic molecules with up to seven non-hydrogen (C, N, O, S, Cl) atoms. To span this fundamentally important region of chemical compound space (CCS), QM7-X includes an exhaustive sampling of (meta-)stable equilibrium structures---comprised of constitutional/structural isomers and stereoisomers, e.g., enantiomers and diastereomers (including cis-trans-and conformational isomers)---as well as 100 non-equilibrium structural variations thereof to reach a total of ~4.2 M molecular structures. Computed at the tightly converged quantum-mechanical PBE0+MBD level of theory, QM7-X contains global (molecular) and local (atom-in-a-molecule) properties ranging from ground state quantities (such as atomization energies and dipole moments) to response quantities (such as polarizability tensors and dispersion coefficients). By providing a systematic, extensive, and tightly converged dataset of quantum-mechanically computed physical and chemical properties, we expect that QM7-X will play a critical role in the development of next-generation machine-learning based models for exploring greater swaths of CCS and performing <em>in silico</em> design of molecules with targeted properties.</p> <p>The dataset is provided in eight HDF5 based files (compressed in .XZ files). One can also find here a README file with technical usage details and examples of how to access the information stored in the dataset (see createDB.py). </p> <p>*The paper explaining the generation of data stored in QM7-X can be found in <em>Sci Data</em> 8, 43 (2021). DOI: 10.1038/s41597-021-00812-2 . arXiv: https://arxiv.org/abs/2006.15139 .</p>
Non-target screening of organic compounds in offshore produced water by GC×GC-MS (associated data)
<p>Associated data for the manuscript titled "<em>Non-target screening of organic compounds in offshore produced water by GC×GC-MS</em>"</p> <p>Preprint doi://10.26434/chemrxiv.13317938</p> <p> </p>
Characterization data for the manuscript "A data-driven perspective on the colours of metal-organic frameworks"
<p>Visualize the data in this dataset: <a href="https://www.c6h6.org/zenodo/record/4044212">open entry</a>. </p>
Collapse and Continuity: A multi-proxy reconstruction of settlement organization and population trajectories in the Northern Fertile Crescent during the 4.2kya Rapid Climate Change event (dataset and R scripts)
<p>The present digital archive is the outcome of the paper: <strong>Lawrence, D., Palmisano, A., and de Gruchy, M.W., 2021. <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244871">Collapse and Continuity: A multi-proxy reconstruction of settlement organization and population trajectories in the Northern Fertile Crescent during the 4.2kya Rapid Climate Change event</a></strong><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244871">.</a> <em><strong>PLoS ONE</strong></em><strong>,</strong> <strong><em>16</em></strong>(1).</p> <p>The dataset included here provides a collection of <strong>920 </strong>radiocarbon dates and <strong>1070</strong> sites from archaeological surveys. In addition, the digital archive related to this paper provides reproducible analyses in the form of three scripts written in R statistical computing language.</p>
Thiosulfonylation of Unactivated Alkenes with Visible-Light Organic Photocatalysis
<p><strong>Origin of the data: </strong>Experimental spectroscopic measurements<br> <strong>Data Type: </strong>experimental measurements, open access supporting information</p> <p>The data are in CSV, DSW and FBSW format. Supporting information are supplied in PDF format.</p> <p>Data <strong>generated </strong>by instruments: </p> <p>Varian Cary 5E-UV-Vis-NIR spectrophotometer for UV-Vis measurements,<br> Varian Cary Eclipse fluorescence spectrophotomer for fluorescence quenching measurements.</p> <p><strong>Analytical and procedural information: </strong>Stern-Volmer fluorescence quenching experiments, UV-Vis measurements and Fluorescent Quantum Yield determination via ferrioxalate actinometry.</p> <p><strong>Definition of variables: </strong>Wavelength, Absorbance, Concentration<br> <strong>Units of measurement: </strong>nanometers (nm), moles-per-litre (mol/l)</p> <p><strong>Abbreviations: </strong><br> File names and data headers use the following abbreviations:</p> <ul> <li><strong>FQY </strong>refers to Fluorescence Quantum Yield determination experiments</li> <li><strong>Light </strong>refers to irradiated samples in the actinometry experiment, as detailed in the procedure in the supporting information.</li> <li><strong>Dark </strong>refers to non-irradiated samples in the actinometry experiment, as detailed in the procedure in the supporting information.</li> <li><strong>SVQuench </strong>refers to Stern-Volmer quenching experiments</li> <li><strong>RAxx </strong>refer to measurements related to allylbenzene. <strong>Xx </strong>is the amount of quencher in mol/l (05 should be intended as 0.5 mol/l and so on).</li> <li><strong>RTxx </strong>refer to measurements related to <em>S</em>-(4-methylphenyl) 4-methylbenzenethiosulfonate. <strong>Xx </strong>is the amount of quencher in mol/l as above.</li> <li><strong>RExx </strong>refer to measurements related to 1,2-dimethoxy-4-(prop-2-en-1-yl)benzene. <strong>Xx </strong>is the amount of quencher in mol/l as above.</li> <li><strong>RSxx </strong>refer to measurements related to styrene. <strong>Xx </strong>is the amount of quencher in mol/l.</li> <li><strong>RTFxx </strong>refer to measurements related to <em>S</em>-(4-fluorophenyl) 4-fluorobenzenethiosulfonate. <strong>Xx </strong>is the amount of quencher in mol/l as above.</li> <li><strong>MesAcrMe Xx </strong>refers to data related to catalyst 9-mesityl-10-methylacridinium. <strong>Xx </strong>is the amount of catalyst in mol/l as above.</li> <li><strong>DMC </strong>for measurements employing dimethylcarbonate as solvent.</li> <li><strong>ACN </strong>for measurements employing acetonitrile as solvent.</li> </ul>
ScienceDex guides
Understand access before you commit
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.