Find research datasets worth reusing

Supplementary material 3 from: Haubrock PJ, Turbelin AJ, Cuthbert RN, Novoa A, Taylor NG, Angulo E, Ballesteros-Mejia L, Bodey TW, Capinha C, Diagne C, Essl F, Golivets M, Kirichenko N, Kourantidou M, Leroy B, Renault D, Verbrugge L, Courchamp F (2021) Economic costs of invasive alien species across Europe. In: Zenni RD, McDermott S, García-Berthou E, Essl F (Eds) The economic costs of biological invasions around the world. NeoBiota 67: 153-190. https://doi.org/10.3897/neobiota.67.58196

Descriptions of socio-economic explanatory variables considered at the country level as potential correlates of invasion costs

Supplementary material 2 from: Kirichenko N, Haubrock PJ, Cuthbert RN, Akulov E, Karimova E, Shneider Y, Liu C, Angulo E, Diagne C, Courchamp F (2021) Economic costs of biological invasions in terrestrial ecosystems in Russia. In: Zenni RD, McDermott S, García-Berthou E, Essl F (Eds) The economic costs of biological invasions around the world. NeoBiota 67: 103-130. https://doi.org/10.3897/neobiota.67.58529

Table S1. Dataset on economic losses associated with biological invasions in terrestrial ecosystems in Russia

Supplementary material 7 from: Haubrock PJ, Turbelin AJ, Cuthbert RN, Novoa A, Taylor NG, Angulo E, Ballesteros-Mejia L, Bodey TW, Capinha C, Diagne C, Essl F, Golivets M, Kirichenko N, Kourantidou M, Leroy B, Renault D, Verbrugge L, Courchamp F (2021) Economic costs of invasive alien species across Europe. In: Zenni RD, McDermott S, García-Berthou E, Essl F (Eds) The economic costs of biological invasions around the world. NeoBiota 67: 153-190. https://doi.org/10.3897/neobiota.67.58196

Coefficients from linear robust regression model considering temporal trends in invasion costs, qualified per annual GDP among European countries

dryad32/100

Supplemental materials of: Ignored biodiversity in acid soil islands in karst areas, South China: Impatiens longlinensis (Balsaminaceae), a new critically endangered species

The karst area in South China is notable for its fragile vegetation and unique flora with many narrow endemics, and is one of the most threatened biodiversity hotspots in the world. However, the biodiversity of acid soil areas scattered in the karst area have previously been underestimated. With a recent increase of new discoveries of plants and animals, the conservation of biodiversity in these acid soil areas has become urgent. This study deals with a new species, Impatiens longlinensis. The new species is similar to I. yui S.H.Huang and I. lasiophyton Hook.f. in having pubescence, two lateral sepals, funnelform lower sepal, and linear capsule. But it can be distinguished by having orbicular to obovate dorsal sepals and oblong to elliptic lower and upper lobes of lateral united petals. Moreover, molecular data and micro-morphological evidence also support that the species is new to science. The new species is only known from a valley near the summit of Mt. Jinzhongshan within an area of less than 5 km2. Based on the Red List Categories and Criteria developed by the International Union for Conservation of Nature, and the threat posed by exploitation for tourism development, we categorize it as Critically Endangered (CR).

Supplementary material 1 from: dos Santos SA, de Britto MR (2021) The ichthyofauna of a poorly known area in the middle-southern Espinhaço mountain range, state of Minas Gerais, Brazil: diagnostics and identification keys. ZooKeys 1054: 25-66. https://doi.org/10.3897/zookeys.1054.67554

Summarizes voucher information and comparative material with institutional acronyms, following Sabaj (2019).

brassica-snps supplementary materials

This repository contains the following files: <ul> <li>brassica-bsa-supplementary.docx - supplementary methods description</li> <li>st1_histogram_flowering_time_Brassica_F1.xlsx - Supplementary Table 1</li> <li>st2_bulk_sequencing_yields.docx - Supplementary Table 2</li> <li>st3_seacompare.html - Supplementary Table 3</li> <li>st4_snpeff.xlsx - Supplementary Table 4</li> <li>st5_seqstats_genome.xlsx - Supplementary Table 5</li> </ul>

Supplementary material 1 from: Cumming RT, Tirant SL, Büscher TH (2021) Resolving a century-old case of generic mistaken identity: polyphyly of Chitoniscus sensu lato resolved with the description of the endemic New Caledonia Trolicaphyllium gen. nov. (Phasmatodea, Phylliidae). ZooKeys 1055: 1-41. https://doi.org/10.3897/zookeys.1055.66796

Table S1. Material examined (specimen data and deposition/ observational records) for localities used within the distribution map (Fig. 21) and to accompany the discussion of each species

dryad32/100

Supplementary materials for: Influence of cognitive reserve on cognitive trajectories: role of brain pathologies

Background and Objectives: Evidence on the association of the cognitive reserve (CR) with the cognitive trajectories is limited. We aimed to examine the influence of CR indicator on domain-specific cognitive trajectories taking brain pathologies into account. Methods: Within the Rush Memory and Aging Project, 1,697 dementia-free participants (mean age: 79.6 years) were followed up to 21 years. CR indicator encompassing education, early-life, mid-life, and late-life cognitive activities, and late-life social activity was ascertained at baseline and categorized as tertiles (the lowest, middle, and highest). Global cognition, episodic memory, semantic memory, working memory, visuospatial ability, and perceptual speed were assessed annually with 19 tests, from which composite scores were derived. During the follow-up, 648 died and underwent autopsies to evaluate brain pathologies. Data were analyzed using linear mixed-effect models. Results: Among the participants, the score of the CR indicator ranged from -8.00 to 5.74 (mean: 0.00±2.23). In multi-adjusted mixed-effect models, compared to the lowest CR, the highest was related to a slower decline in global cognition (β=0.028, 95% confidence interval [CI]: 0.012 to 0.043), episodic memory (β=0.028, 95% CI: 0.010 to 0.047) and working memory (β=0.019, 95% CI: 0.005 to 0.033) during the follow-up. In brain pathological data analysis, the association of the highest CR with cognitive function changes remained significant among participants with high Alzheimer's disease pathology or gross infarcts. Discussion: High CR indicator is associated with preserved global cognitive function, episodic memory, and working memory, even in the presence of brain pathologies. Our findings highlight the important role of high CR accumulation in the prevention of cognitive decline.

Figure 8 in On some maerid and melitid material (Crustacea: Amphipoda) collected by the Hourglass Cruises (Florida). Part 2: Genera Dulichiella and Elasmopus, with a key to world Elasmopus

Figure 8. Telson shapes: (A) Elasmopus rapax; (B) Elasmopus alalo male; (C) Elasmopus alalo female; (D) Elasmopus levis; (E) Elasmopus calliactis; (F) Elasmopus spinibasus; (G) Elasmopus ecuadoriensis two shapes; (H) Elasmopus holgurus; (I, J) Elasmopus bastidai male (I, above), female (J, below); (K) E gracilis; (L) Elasmopus steelei; and (M) Elasmopus pseudinteger.

Figure 7 in On some maerid and melitid material (Crustacea: Amphipoda) collected by the Hourglass Cruises (Florida). Part 2: Genera Dulichiella and Elasmopus, with a key to world Elasmopus

Figure 7. Mandible shapes: (A) Elasmopus rapax; (B) Elasmopus pseudinteger; (C) Elasmopus diplonyx; (D) Elasmopus wahine (similar to Elasmopus alalo, Elasmopus elieri); (E) Elasmopus oaxaquensis; (F and G) Elasmopus spinipalpus.

Figure 6 in On some maerid and melitid material (Crustacea: Amphipoda) collected by the Hourglass Cruises (Florida). Part 2: Genera Dulichiella and Elasmopus, with a key to world Elasmopus

Figure 6. Elasmopus cf. magnispinatus P3, P5, P6, P7, pereopods; Ep2, Ep3 of both sexes, epimeral plates; U3, third uropods of both sexes; T, telson of both sexes; slides FSBC I 79921, FSBC I 79922.

Figure 5 in On some maerid and melitid material (Crustacea: Amphipoda) collected by the Hourglass Cruises (Florida). Part 2: Genera Dulichiella and Elasmopus, with a key to world Elasmopus

Figure 5. Elasmopus cf. magnispinatus Gn1 (in male and female identical), Gn2 of both sexes, Gn1′ and Gn2′ of another specimen enlarged; slides FSBC I 79921, FSBC I 79922.

Figure 4 in On some maerid and melitid material (Crustacea: Amphipoda) collected by the Hourglass Cruises (Florida). Part 2: Genera Dulichiella and Elasmopus, with a key to world Elasmopus

Figure 4. Elasmopus cf. magnispinatus A1,2, antennae; Mx2, second maxilla; Md, right and left mandible; slide FSBC I 79921.

Figure 3. Elasmopus levis P3, P5, P6, P7 in On some maerid and melitid material (Crustacea: Amphipoda) collected by the Hourglass Cruises (Florida). Part 2: Genera Dulichiella and Elasmopus, with a key to world Elasmopus

Figure 3. Elasmopus levis P3, P5, P6, P7, pereopods; Ep2, Ep3, epimeral plates; Us, urosome; U3, third uropod; T, telson; slide FSBC I 79919.

Supplementary Materials for paper Evaluating the Rate of Consistency Violation Faults for Self-Stabilizing Programs

Source code and data for the paper Evaluating the Rate of Consistency Violation Faults for Self-Stabilizing Programs Content: + directory src: source code + directory lib: libaries used by source code + directory graphs: input graphs (topology) for programs + directory results-2021: analysis and simulation data + run_analyze_cvf_script.sh: script for running analysis + run_simulation_script.sh: script for running simulation

openother-atAug 2020View details →

Supplementary Material for: 'An impedance pneumography signal quality index: design, assessment and application to respiratory rate monitoring'

This supplementary material accompanies: Charlton P.H. et al., "<a href="https://doi.org/10.1016/j.bspc.2020.102339">An impedance pneumography signal quality index for respiratory rate monitoring: design, assessment and application</a>", Biomedical Signal Processing and Control, 65, 102339, 2021. The Impedance Pneumography Signal Quality Index (SQI) dataset and accompanying scripts (in Matlab format) are provided to facilitate reproduction of the analyses using data from the MIMIC III dataset in this publication. Summary of Publication In this article we developed and assessed the performance of a signal quality index (SQI) for the impedance pneumography signal. The SQI was developed using data from the <a href="http://peterhcharlton.github.io/RRest/listen_dataset.html">Listen dataset</a>, and assessed using data from the <a href="http://peterhcharlton.github.io/RRest/listen_dataset.html">Listen dataset</a> and MIMIC III datasets. The SQI was found to accurately classify segments of impedance pneumography signal as either high or low quality. Furthermore, when it was coupled with a high performance RR algorithm, highly accurate and precise RRs were estimated from those segments deemed to be high quality. In this study performance was assessed in the critical care environment - further work is required to deteremine whether the SQI is suitable for use with wearable sensors. Both the dataset and code used to perform this study are publicly available. Reproducing this Publication The work relating to the MIMIC dataset in this publication can be reproduced as follows:  - Reproducing the analysis These steps can be used to quickly reproduce the analysis using the curated and annotated dataset. *   Download the curated and annotated dataset from <a href="https://doi.org/10.5281/zenodo.3973770">Zenodo</a> using this <a href="https://zenodo.org/record/3973771/files/mimic_imp_sqi_data.mat?download=1">direct download link</a>. *   Run the analysis using the <a href="https://zenodo.org/record/3973771/files/run_imp_sqi_mimic.m?download=1">run_imp_sqi_mimic.m</a> script.  - Full reproduction These steps include downloading the raw data files, extracting data from these files, collating the dataset, manually annotating the data, and performing the analysis. *   Use the <a href="https://zenodo.org/record/3973771/files/ImP_SQI_mimic_data_importer.m?download=1">ImP_SQI_mimic_data_importer.m</a> script to download raw MIMIC data files from PhysioNet, and collate them into a single Matlab file. *   Prepare the dataset for manual annotation by running the <a href="https://zenodo.org/record/3973771/files/run_imp_sqi_mimic.m?download=1">run_imp_sqi_mimic.m</a> script. *   Manually annotate the signals by running the <a href="https://zenodo.org/record/3973771/files/run_imp_sqi_mimic.m?download=1">run_mimic_imp_annotation.m</a> script - the annotations are stored in separate files (the original annotation files are available <a href="https://zenodo.org/record/3974113/files/2019_annotations.zip?download=1">here</a>). *   Import the manual annotations into the collated data file by re-running the <a href="https://zenodo.org/record/3973771/files/ImP_SQI_mimic_data_importer.m?download=1">ImP_SQI_mimic_data_importer.m</a> script. *   Run <a href="https://zenodo.org/record/3973771/files/run_imp_sqi_mimic.m?download=1">run_imp_sqi_mimic.m</a> to perform the analysis described in the publication.  - Submitted manuscript The submitted manuscript is available <a href="https://zenodo.org/record/5211463/files/Impedance%20SQI%20manuscript%20-%20Oct%202020%20revision.docx?download=1">here</a>. The scripts are also stored (alongside details of how to use them) are available in the <a href="http://peterhcharlton.github.io/RRest/">RRest GitHub repository</a> at: <a href="https://github.com/peterhcharlton/RRest/tree/master/RRest_v3.0/Publication_Specific_Scripts/ImP_SQI">https://github.com/peterhcharlton/RRest/tree/master/RRest_v3.0/Publication_Specific_Scripts/ImP_SQI</a> License: The dataset (<a href="https://zenodo.org/record/3974113/files/mimic_imp_sqi_data.mat?download=1">mimic_imp_sqi_data.mat</a>) is distributed under the terms specified in the accompanying LICENSE file. The scripts are distributed under the GNU General Public Licence (as specified towards the start of each file). Version 1.0: This version includes the submitted manuscript.

Supplementary material 1 from: Qu J, Zou X, Cao W, Xu Z, Liang Z (2021) Two new species of Hirsutella (Ophiocordycipitaceae, Sordariomycetes) that are parasitic on lepidopteran insects from China. MycoKeys 82: 81-96. https://doi.org/10.3897/mycokeys.82.66927

Tables S1–S3. A total of 71 taxa were selected to represent the morphological and ecological diversity of Hirsutella asexual morphs and Ophiocordyceps

Supplemental Material: Tectonic Deformation and Volatile Loss in the Formation of Noctis Labyrinthus, Mars

Supplemental text and tables for pending publication

Supplemental Material 2; Large Format Map: Tectonic Deformation and Volatile Loss in the Formation of Noctis Labyrinthus, Mars

Large Format Map of Noctis Labyrinthus, Mars

Supplementary material for "Chick survival and hunting are important drivers for the dynamics of two Alpine black grouse Lyrurus tetrix populations"

Data files, code for all analyses, and an Appendix (with additional figures and tables). The six data files are provided in csv format (Summer counts.csv, TrackingDataSurvival.csv, Occasions.csv, TrackingDataProductivity.csv, SexRatioData.csv, MeteoData.csv). The code file (BlackGrouseCode.txt) is a space delineated text file. The code file is written for R, but some models are run in JAGS from R. The code file also contains the description of the data files, code for data management, code for figures and additional analyses. The Appendix (appendix.pdf) is a pdf. Abstract of the article Alpine black grouse populations are generally declining, but the underlying demographic drivers are largely unknown. We studied the dynamics of two adjacent black grouse populations over a 20 years period in the Italian Alps that differ in hunting pressure to identify the main demographic process affecting these populations and to study the impact of hunting on males. We collected radio-tracking data and conducted population surveys in spring to count displaying cocks and in late summer to determine the breeding success by means of pointing dogs. These different data sets were jointly analysed using a seasonal integrated population model to estimate population sizes and various demographic rates. The two populations fluctuated in size and the number of males from one population increased after hunting intensity was reduced. The main demographic rates did not differ between the populations. Adult survival was relatively low and productivity was high, so the life history shows the feature of a fast turnover species. In both populations, the variability of survival from hatching to the age of five weeks (chick survival) contributed more to the variation of the population growth rates than the variability of survival in later life-history stages, and the former was positively affected by ambient temperatures in July, favouring chick survival. The adult sex ratio of the population where males hunting occurred was shifted towards females, but it evened over time with the reduction of hunting pressure. The adult sex ratio in the population without hunting and the chick sex ratios in both populations were even, suggesting that hunting acted as a mostly additive source of mortality.