Find research datasets worth reusing

opencc-zeroDec 2021View details →

BdSL47: A complete dataset of sign alphabet and digits of Bangla Sign Language (BdSL) using depth information via MediaPipe

BdSL47 is the first open-access complete dataset in Bangla Sign Language that contains hand signs from both 10 sign digits (from sign ০ to sign ৯) and 37 sign alphabet (from sign অ to sign ँ). Dataset summary : <ul> <li>100 RGB images per sign (total 47 signs) from each of 10 users</li> <li>Total input images : 100×47×10 = 47000</li> <li>Input images are processed via MediaPipe, which provided <ul> <li>an output image with hand key-points being detected</li> <li>3D coordinate values of 21 predefined key-points</li> <li>Total 63 coordinate values for each sample</li> </ul> </li> <li>The values are stored in csv files</li> <li>1 CSV file contains values from 100 samples of 1 sign from 1 user</li> <li>Total CSV files : 47×10 = 470</li> </ul> The dataset has been made public for further research purposes. It is also available upon request <a href="https://drive.google.com/drive/u/8/folders/1wmJUlgWUrWNnOvzuL8Ci82Hm3zUx4wS-" rel="noopener">here</a>.

opencc-zeroSep 2022View details →

Remote sensing and field information aid in predicting the presence of the terrestrial orchid Cyclopogon lute-albus

Tropical montane cloud forest is one of the most threatened ecosystems, in central Veracruz, Mexico. Within this ecosystem, terrestrial orchids are strongly dependent on forest conditions and may be sensitive to environmental change. We applied field surveys of abiotic and biotic factors associated with the presence of the terrestrial orchid Cyclopogon luteo-albus and combined this with correlative niche modeling approaches to evaluate its potential distribution under two different environmental sets and two different extents. Layers of environmental information were obtained from Landsat imagery and interpolated bioclimatic and soil property layers. Existing species records were used as training data by sampling five forest fragments in central Veracruz, utilizing herbarium and global biodiversity information facility databases. The resulting predictions were tested by sampling at 15 sites of potential distribution. The model predicted the presence of C. luteo-albus with a reliability of 80%. The most important variables of models derived from interpolated layers coincide with site-relevant parameters suggesting the utility of these tools to further explore species suitabilities at larger geographic extents. Potential distribution mapping is an important tool to identify key areas for conservation and priority areas for future studies of species and partially resolves the lack of records of many orchid species.

Forecasting 24-hour-averaged PM2.5concentration in the Aburrá Valley using tree-based ML models, global forecasts, and satellite information: Dataset

Data necessary for the training and evaluating the 24-hourly-averaged PM2.5 forecast over 19 stations within the Aburrá Valley, Colombia, is included here.

opencc-zeroSep 2022View details →

Data from: Effect of information about the benefits and harms of mammography on women's decision making: the InforMa randomised controlled trial

Background: In Spain, women invited to breast screening are not usually informed about potential harms of screening. The objective of the InforMa study is to assess the effect of receiving information about the benefits and harms of breast screening on informed choice and other decision making outcomes, in women approaching the age of invitation to mammography screening. Methods: Two-stage randomised controlled trial. In the first stage, 40 elementary territorial units of the public healthcare system were selected and randomised to intervention or control. In the second stage, women aged 49-50 years were randomly obtained. The target sample size was 400 women. Women in the intervention arm received a decision aid (DA) with detailed information on the benefits and harms of screening. Women in the control arm received a standard leaflet that did not mention harms and recommended accepting the invitation to participate in the Breast Cancer Screening Program (BCSP). The primary outcome was informed choice, defined as adequate knowledge and intentions consistent with attitudes. Secondary outcomes included decisional conflict, worry about breast cancer, time perspective, opinions about the DA, and participation in the BCSP. Results: In the intervention group, 23.2% of 203 women made an informed choice compared to only 0.5% of 197 women in the control group (p < 0.001). Attitudes and intentions were similar in both study groups with a high frequency of women intending to be screened, 82.8% vs 82.2% (p=0.893). Decisional conflict was significantly lower in the intervention group. No differences were observed in confidence in the decision, anxiety, and participation in BCSP. Conclusions: Women in Spain lack knowledge on the benefits and harms of breast screening. Providing quantitative information on benefits and harms has produced a considerable increase on knowledge and informed choice, with a high acceptance of the informative materials.

Supplementary informations of endogenous starter culture and cheese metagenomes

The first description of the virome composition in Brazilian artisanal Canastra cheese and the phage-bacterial interactions in this food system. Here you can access supplemental methods and results (docx) and supplemental data (MAGs contigs, novel 987 group phage contigs, and MAGs spacers).

opencc-by-4.0Jan 2022View details →

Efficiency and suitability when exploring the conformational space of phase transfer catalysts - Supporting information

Supporting information for Efficiency and suitability when exploring the conformational space of phase transfer catalysts. In this study, a complete exploration of the conformational space within phase transfer catalysts by means of computational methods benchmarking is presented. For this particular research work, only the most applied conformational analysis approaches have been chosen to characterise different Cinchona alkaloid-based phase transfer catalysts. This particular benchmarking study aims to rigorously compare the performance of different conformational methods, determining the strengths of each method and to provide recommendations regarding suitable choices of methods for an analysis.

Data from: On-chip distribution of quantum information using traveling phonons

Source data for Figures.

opencc-by-4.0Feb 2022View details →

Predicting emotion from music videos: exploring the relative contribution of visual and auditory information to affective responses.

The dataset to accompany the paper by Phoebe Chua, Dr. Dimos Makris, Prof. Dorien Herremans, Prof. Gemma Roig, and Prof. Kat Agres on Predicting emotion from music videos: exploring the relative contribution of visual and auditory information on affective responses.

opencc-zeroSep 2022View details →

Data from: Choice of prioritization method impacts recommendations for climate-informed bird conservation in the United States

Climate-informed spatial planning is urgently needed to guide initiatives aimed at both conserving biodiversity as a whole (e.g., protection of 30% of lands and waters by 2030) and recovering North American avifauna in particular. Various methods for prioritizing conservation areas exist, yet alternative methods may direct managers to different lands for protection and thus varying recommendations for meeting area-based targets. Here, we used bird species distribution models and landcover projections to systematically evaluate two widely-used methods for prioritizing areas most likely to facilitate the persistence of multiple species under climate change: (1) in situ macrorefugia, identified as areas of high predicted species retention; and (2) complementarity-based optimizations, identified using the Zonation conservation planning software. For 17 biogeographical groups in the continental United States, we compared priority areas for bird conservation derived from these two alternatives with respect to their spatial distributions and consensus (i.e., overlap), expected conservation outcomes (e.g., species and functional diversity), predicted climate change exposure, habitat characteristics, landscape configurations, and degree of formal protection. Spatial distributions of priority areas differed by biogeographical group and method, with 40.5% consensus on average across groups. Consensus was extensive within mountainous and coastal regions and limited at high latitudes (e.g., Alaska) and in flat, interior regions (e.g., grasslands). As expected, complementarity-based optimizations more efficiently represented species than retention-based in situ macrorefugia, especially for forest groups, and had greater overall biodiversity value and better habitat condition. Conversely, in situ macrorefugia encompassed higher elevations and larger contiguous patches and were expected to experience less winter-season warming. Formal protection averaged <50% across biogeographical groups, regardless of prioritization method. Our findings illustrate the value of complementarity-based optimizations for bird conservation under climate change. More broadly, comparing approaches for prioritizing areas for long-term species persistence can reveal critical tradeoffs in recommendations for climate-informed protected area planning.

Size of an interspecific competitor may be a source of information in reproductive decisions

Animals use interspecific cues as a source of information in decision-making, but the full costs and benefits of interspecific information use are unknown. We tested whether pied flycatchers use the body size and clutch size of great tits as cues in their reproductive decisions and what are the possible fitness consequences as a function of great tit size. The size of great tit females was positively associated with flycatchers' probability to settle near a tit nest over a territory further away. Flycatcher egg mass was positively correlated with great tit female size regardless of flycatcher territory choice. However, in flycatchers that had chosen to nest near great tits, the size of nestlings decreased in relation to increasing great tit female size. Our results demonstrate the use of size of interspecifics as a cue in reproductive decisions and the trade-off between the value of information and costs of competition information users face when using interspecific information in decision-making.

opencc-by-4.0Jun 2022View details →

Characterising the stone artefact raw materials at Liang Bua, Indonesia - Supplementary Information

Supplementary Information, including data and R code, for the paper titled "Characterising the stone artefact raw materials at Liang Bua, Indonesia" by Sam Lin, Lloyd White, Jatmiko, I Made Agus Julianto, Matthew Tocheri and Thomas Sutikna.

opencc-by-4.0Oct 2022View details →

Supporting Information for "Investigation of Hikurangi subduction zone slow slip events using onshore and onshore geodetic data" PhD thesis

The data sets included here are those inverted using the TDEFNODE (McCaffrey et al., 2009) inversion code in the PhD thesis "Investigation of Hikurangi subduction zone slow slip events using onshore and onshore geodetic data" to obtain geodetic slip models of the 2013-2016 and February-July 2019 periods at the Hikurangi subduction zone.   The 2013-2016 period captured the 2013 Kāpiti and 2014/2015 Manawatū slow slip events (SSEs), in addition to the 2013 Cook Strait, 2013 Lake Grassmere, and 2014 Eketāhuna earthquakes. The data related to this model are: campaign_gps_2013.ts -campaign GPS time series -columns: Year  East East_sigma North North_sigma Up Up_sigma -input using TDEFNODE command ts1 coseismic_displacements_2013_07_21.ds -coseismic displacements for Cook Strait earthquake (Hamling et al., 2014) -columns: Longitude  Latitude  Disp_East Disp_North Sigma_East Sigma_North Site Disp_Up Sigma_Up Time1 Time2 -input using TDEFNODE command ds2 coseismic_displacements_2013_08_16.ds -coseismic displacements for Lake Grassmere earthquake (Hamling et al., 2014) -columns: Longitude  Latitude  Disp_East Disp_North Sigma_East Sigma_North Site Disp_Up Sigma_Up Time1 Time2 -input using TDEFNODE command ds2 onshore_gnss_kapiti_manawatu_2013_2016.ts -GNSS time series -columns: Year  East East_sigma North North_sigma Up Up_sigma -input using TDEFNODE command ts1 LOS_coseismic_2013_08_16.is -coseismic Line of Sight displacements for Lake Grassmere earthquake (Hamling et al., 2014) -convention: negative displacement equivalent to ground moving towards the satellite -columns: Longitude  Latitude  LineOfSight_disp sigma  Unit_x Unit_y Unit_z -input using TDEFNODE command is1   Data related to the February-July 2019 SSE model are: onshore_gnss_east_coast_sse_2019.ts -GNSS time series -columns: Year  East East_sigma North North_sigma Up Up_sigma -input using TDEFNODE command ts4 seafloor_displacement_gisborne.ts -seafloor pressure time series -convention: positive change equivalent to seafloor uplift -columns: Year  East East_sigma North North_sigma Up Up_sigma -input using TDEFNODE command ts4 seafloor_displacement_hawkebay.ts -seafloor pressure time series -convention: positive change equivalent to seafloor uplift -columns: Year  East East_sigma North North_sigma Up Up_sigma -input using TDEFNODE command ts4 LOS_SSE_2019.is -SSE-related Line of Sight displacement -convention: positive displacement equivalent to ground moving away from satellite -columns: Longitude  Latitude  LineOfSight_disp sigma  Unit_x Unit_y Unit_z -input using TDEFNODE command is1   The TDEFNODE manual can be found here: https://robmccaffrey.github.io/TDEFNODE/manual/tdefnode_manual.html The header lines in the time series files (.ts) take the site inter-SSE rates from the model of Wallace et al. (2012).   References Hamling, I. J., D’Anastasio, E., Wallace, L. M., Ellis, S., Motagh, M., Samsonov, S., Palmer, N., and Hreinsdóttir, S. (2014). Crustal deformation and stress transfer during a propagating earthquake sequence: The 2013 Cook Strait sequence, central New Zealand. Journal of Geophysical Research: Solid Earth, 119(7):6080–6092. McCaffrey, R. (2009). Time-dependent inversion of three-component continuous GPS for steady and transient sources in northern Cascadia. Geophysical Research Letters, 36(L07304). Wallace, L. M., Barnes, P., Beavan, J., Van Dissen, R., Litchfield, N., Mountjoy, J., Langridge, R., Lamarche, G., and Pondard, N. (2012). The kinematics of a transition from subduction to strike-slip: An example from the central New Zealand plate boundary. Journal of Geophysical Research: Solid Earth, 117(B2).

Data from: Which plumage patches provide information about condition and success in a female fairy-wren?

Recent evidence suggests that female ornaments can commonly act as signals. However, how signaling functions might be affected by the tendency for reduced ornament elaboration in relation to males is less well understood. We address this in mutually ornamented purple-crowned fairy-wrens. We investigated putatively ornamental (tail, ear coverts, crown) and non-ornamental (throat, back) plumage patches in females and compared our findings to previous studies in males. Both sexes have brown backs, buff-white throats, and turquoise-blue tails (bluer in males), while ear coverts are rufous in females and black in males. Both sexes also have a seasonal crown (slate-grey in females, black-and-purple in males). Dominant (breeder) females expressed more complete and greyer (more ornamented) crowns, although variation in coloration should not be discriminable by individuals. Unexpectedly, subordinates showed more colorful (saturated) rufous ear coverts, which should be discriminable. Condition dependence was only evident for crown completeness (% slate-grey cover). Females with more reddish-brown backs were more reproductively successful. Variation in plumage characteristics did not explain differential allocation by mates or chances of gaining dominance. Our outcomes were not entirely consistent with findings in males. The most notable disparity was for the crown, a signal used in male-male competition that in females seems to be expressed as an incomplete version of the male crown that is not associated with fitness benefits. Our study shows that in a species, multiple traits can vary in their information content and that female ornaments can sometimes be less informative than in males, even those that are produced seasonally.

Databases and information systems for research output: digital humanities outlook (DARIAH Bibliographical Data Working Group, September, 30th 2022)

The video recording of the workshop "Databases and information systems for research output: digital humanities outlook" organized by DARIAH Bibliographical Data Working Group.

opencc-zeroJun 2022View details →

Supplementary information for: Monitoring cheese ripening by single-sided NMR

Supplementary information for: Monitoring cheese ripening by single-sided NMR Raw experimental data used to create the manuscript. Data structure: Each folder contains the date of acquisition. Inside folders are CPMG, DT2, and T1T2 experiments with suffix showing the position of the acquired region in micrometers.

opencc-by-4.0Oct 2022View details →

Base de dados pesquisa sobre a aprendizagem informal de crianças da língua inglesa com uso de tecnologias digitais

A coleta de dados foi realizada em três turmas do 3º ano do Ensino Fundamental de uma escola federal brasileira. Todas levaram o termo de autorização de participação para casa e aquelas que o trouxeram assinados pelos responsáveis e aceitaram participar da pesquisa integraram o grupo de participantes. Ao total, 62 famílias responderam o questionário e permitiram que seus filhos participassem da pesquisa. A base de dados inclui os dados dos 62 participantes coletados pelo meio da aplicação de dois instrumentos: a) questionário estruturado com perguntas abertas e fechadas com as famílias. O instrumento foi composto por dezenove questões que buscam caracterizar os sujeitos da pesquisa, seu uso de tecnologias e por quais mídias interagem com a língua inglesa. b) avaliação da língua inglesa baseada no teste de proficiência Cambridge Young Learners (YLE) Pré-A1 Starters. Esses exames são adequados para crianças entre 6 e 12 anos e as habilidades necessárias para realizá-los visam ajudá-los a entender o idioma inglês que encontrou na internet e torná-los melhores usuários do conteúdo em inglês que encontram na mídia. A atividade avaliou as quatro habilidades linguísticas: ler, escrever, falar e ouvir. No total, a avaliação foi composta por 37 questões, sendo 12 de Escuta, 15 de Escrita e Leitura e 10 de Fala.

Comparison of allosteric signaling in DnaK and BiP using mutual information between simulated residue conformations

Molecular Dynamics trajectories of the Hsp70 chaperones DnaK and BiP. System configurations include DnaK or BiP bound to ATP, ATP exchanged to ADP, or the NRLLLTG peptide.

opencc-by-4.0Jul 2022View details →

Project files provided as supporting information to the manuscript "Fast, accurate, and system-specific variable-resolution modelling of proteins"

Project files provided as supporting information to the manuscript "Fast, accurate, and system-specific variable-resolution modelling of proteins". The dataset contains the following files: - RMSD_adk: files containing the root-mean-square deviation computed on the C-alpha atoms/beads in the atomistic and CANVAS simulations of adk (Figure 6). - RMSF_adk: files containing the root-mean-square fluctuations of the C-alpha atoms/beads in the atomistic and CANVAS simulations of adk (Figure 6). - APBS_adk: PQR file of the system and DX file of the surface potential, for both the atomistic and CANVAS systems (Figure 7). - SASA_antibody: files containing the per-residue solvent accessible surface area of the atomistic region of the ake protein, in the atomistic and CANVAS simulations (Figure 8). - RMSF_antibody: files containing the root-mean-square fluctuations of the C-alpha atoms/beads in the atomistic and CANVAS simulations of antibody (Figure 9). - APBS_antibody: PQR file of the system and DX file of the surface potential, for both the atomistic and CANVAS systems (Figure 10). - SASA_antibody: files containing the per-residue solvent accessible surface area of the hinge region of the antibody for each conformational cluster, in the atomistic and CANVAS simulations (Figure 11). - RMSIP_antibody: RMSIP between the essential subspaces computed from the atomistic and CANVAS simulations (Figure S3). - rgyr_antibody: files containing the radii of gyration of the antibody for each conformational cluster, in the atomistic and CANVAS simulations (Figure S4). - ake_AA.mp4: video of the all-atom simulation of adenylate kinase - ake_canvas.mp4: video of the canvas simulation of adenylate kinase

Supplementary information for: Redundancy analysis, genome-wide association studies, and the pigmentation of brown trout (Salmo trutta L.)

The association of molecular variants to phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multi-trait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multi-trait GWAS allowed us to extract 337 independent "colour patterning loci" (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found associated with 218 candidate genes, including 197 genes formerly mentioned in the literature dealing with skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.