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Figure 3 in The Importance Of Natura 2000 Sites And Their Management For The Conservation Of Freshwater Fish, Lamprey And Crayfish In Latvia
Figure 3. Occurrence of migratory freshwater fish and lamprey species (n=5) in N2000 and outside N2000 at GC5 cells, grouped by 0–10 %; 10–25 %; 25–50 %;>50 % with species numbers 0; 1; 2; 3–5.
Figure 4 in The Importance Of Natura 2000 Sites And Their Management For The Conservation Of Freshwater Fish, Lamprey And Crayfish In Latvia
Figure 4. Occurrence of introduced freshwater fish, lamprey and crayfish species (n=6) in N2000 and outside N2000 at GC5 cells, grouped by 0–10 %; 10–25 %; 25–50 %;>50 % with species numbers 0; 1; 2–3; 4.
Transcription start site analysis for heterogenous CD4+ T cells using 5′ scRNA-seq
<p>These datasets are generated by ReapTEC (read-level pre-filtering and transcribed enhancer call) using 5' single-cell RNA-seq data on human heterogenous CD4+ T cells. By taking advantage of a unique "cap signature" derived from the 5′-end of a transcript, ReapTEC simultaneously profiles gene expression and enhancer activity at nucleotide resolution using 5′-end single-cell RNA-sequencing (5′ scRNA-seq). The detail of ReapTEC pipeline is described in https://github.com/MurakawaLab/ReapTEC.</p>
РИС. 3. Место нахождениЯ Amuranodonta kijaensis в Хабаровском крае: А. Карта-схема краЯ. В. Приустьевый участок р. Амур. С, D. ТопографическаЯ карта и спутниковый снимок с. Чныррах с укаЗанием места сбора. МасШтабные линейки: 200 км (А), 16 км (B), 4 км (C) и 200 м (D). FIG. 3. Locality of Amuranodonta kijaensis in the Khabarovsk Territory: A. Scheme map of the region. B. Amur River mouth area. C, D. Topographic map and satellite image of Chnyrrakh village indicating the collection site. Scale bars: 200 km (А), 16 km (B), 4 km (C), and 200 m (D). in Новые данные об охранЯемом пресноводном двустворчатом моллюске Amuranodonta kijaensis Moskvicheva, 1973 (Unionidae, Anodontinae)
РИС. 3. Место нахождениЯ Amuranodonta kijaensis в Хабаровском крае: А. Карта-схема краЯ. В. Приустьевый участок р. Амур. С, D. ТопографическаЯ карта и спутниковый снимок с. Чныррах с укаЗанием места сбора. МасШтабные линейки: 200 км (А), 16 км (B), 4 км (C) и 200 м (D). FIG. 3. Locality of Amuranodonta kijaensis in the Khabarovsk Territory: A. Scheme map of the region. B. Amur River mouth area. C, D. Topographic map and satellite image of Chnyrrakh village indicating the collection site. Scale bars: 200 km (А), 16 km (B), 4 km (C), and 200 m (D).
РИС. 1. Место нахождениЯ Amuranodonta kijaensis в Зейском районе, АмурскаЯ обл.: А. Карта-схема области. B. Зейское вдхр. С, D. ТопографическаЯ карта и спутниковый снимок Залива в Западной части Зейского вдхр. у пос. Береговой с укаЗанием места сбора. МасШтабные линейки: 300 км (А), 50 км (В), 4 км (С) и 200 м (D). FIG. 1. Locality of Amuranodonta kijaensis in Zeya District, Amur Region: A. Schematic map of the region. B. Zeya Reservoir. C, D. Topographic map and satellite image of the bay in the western part of Zeya Reservoir near Beregovoi village indicating the collection site. Scale bars: 300 km (А), 50 km (В), 4 km (С), and 200 m (D). in Новые данные об охранЯемом пресноводном двустворчатом моллюске Amuranodonta kijaensis Moskvicheva, 1973 (Unionidae, Anodontinae)
РИС. 1. Место нахождениЯ Amuranodonta kijaensis в Зейском районе, АмурскаЯ обл.: А. Карта-схема области. B. Зейское вдхр. С, D. ТопографическаЯ карта и спутниковый снимок Залива в Западной части Зейского вдхр. у пос. Береговой с укаЗанием места сбора. МасШтабные линейки: 300 км (А), 50 км (В), 4 км (С) и 200 м (D). FIG. 1. Locality of Amuranodonta kijaensis in Zeya District, Amur Region: A. Schematic map of the region. B. Zeya Reservoir. C, D. Topographic map and satellite image of the bay in the western part of Zeya Reservoir near Beregovoi village indicating the collection site. Scale bars: 300 km (А), 50 km (В), 4 km (С), and 200 m (D).
РИС. 1. ОЗеро Дальнее (А) и место обнаруЖениЯ Beringiana beringiana в оЗере (B, С), песчаный грунт в месте обитаниЯ беЗЗубок (D). Стрелками обоЗначено место сбора моллюсков. FIG. 1. Lake Dalneye (A) with the sampling site (B, C), sandy bottom in the habitat of mollusks (D). The arrows indicate the site of material sampling. in Первые данные о морфологии глохидиев двустворчатых моллюсков Beringiana beringiana (Bivalvia, Unionidae) оЗера Дальнее, Камчатка
РИС. 1. ОЗеро Дальнее (А) и место обнаруЖениЯ Beringiana beringiana в оЗере (B, С), песчаный грунт в месте обитаниЯ беЗЗубок (D). Стрелками обоЗначено место сбора моллюсков. FIG. 1. Lake Dalneye (A) with the sampling site (B, C), sandy bottom in the habitat of mollusks (D). The arrows indicate the site of material sampling.
РИС. 3. ИЗменчивость формы вагины у Monacha cartusiana c Запада Украины. A. ИваноФранковск. B. Брюховичи. C–E. Львов, участок № 3. F–H. Подборцы. Стрелками покаЗано латеральное выпЯчивание вагины. МасШтаб 1 мм. FIG. 3. Variability of the vagina shape in Monacha cartusiana from Western Ukraine. A. Ivano-Frankivsk. B. Briukhovychi. C–E. Lviv, site 3. F–H. Pidbirtsi. The arrows show the lateral bulge of the vagina. Scale bars 1 mm. in Monacha claustralis и M. cartusiana (Gastropoda, Hygromiidae) - два криптических вида антропохорных наЗемных моллюсков на Западе Украины
РИС. 3. ИЗменчивость формы вагины у Monacha cartusiana c Запада Украины. A. ИваноФранковск. B. Брюховичи. C–E. Львов, участок № 3. F–H. Подборцы. Стрелками покаЗано латеральное выпЯчивание вагины. МасШтаб 1 мм. FIG. 3. Variability of the vagina shape in Monacha cartusiana from Western Ukraine. A. Ivano-Frankivsk. B. Briukhovychi. C–E. Lviv, site 3. F–H. Pidbirtsi. The arrows show the lateral bulge of the vagina. Scale bars 1 mm.
NYMPHE Horizon 2020 project Falasarna (GR) Test Sites preliminary data
<p>The dataset is a preliminary vision on the Falasarna (GR) test site for bioremediation action in the EU funded Horizon 2020 project. The data set iwill be used to futher refine the datasets structure and to define the hyerachical data dependences. The distribution of the typical species for phrigana habitat was investigated. The data were obtain prior application of the bioremediation measures. The data collection mission took place in October 2024. The valuee were obtaiing by direct measurement on site, </p>
Рис. 16. Выброшенная друЗа мидий (Crenomytilus grayanus) на пляЖе б. Теляковского с прикрепившимися риЗоидами водорослей. Fig. 16. A stranded mussel druse (Crenomytilus grayanus) with attached algae rhizoids on the beach of Telyakovskogo Bay. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 16. Выброшенная друЗа мидий (Crenomytilus grayanus) на пляЖе б. Теляковского с прикрепившимися риЗоидами водорослей. Fig. 16. A stranded mussel druse (Crenomytilus grayanus) with attached algae rhizoids on the beach of Telyakovskogo Bay.
Рис. 12. Характер фрагментации и повреЖдений створок спиЗулы сахалинской Spisula sachalinensis иЗ раскопа 1. Fig. 12. Fragmentation and preservation patterns of valves of Spisula sachalinensis from excavation 1. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 12. Характер фрагментации и повреЖдений створок спиЗулы сахалинской Spisula sachalinensis иЗ раскопа 1. Fig. 12. Fragmentation and preservation patterns of valves of Spisula sachalinensis from excavation 1.
Рис. 11. Характер фрагментации створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 11. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 11. Характер фрагментации створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 11. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1.
Рис. 13. Частотно-раЗмерное распределение створок спиЗулы сахалинской (Spisula sachalinensis) иЗ раковинной кучи (все выборки). Fig. 13. Size-frequency distribution of valves of Spisula sachalinensis from the shell-midden (all samples). in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 13. Частотно-раЗмерное распределение створок спиЗулы сахалинской (Spisula sachalinensis) иЗ раковинной кучи (все выборки). Fig. 13. Size-frequency distribution of valves of Spisula sachalinensis from the shell-midden (all samples).
Рис. 10. Характер повреЖдений створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 10. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 10. Характер повреЖдений створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 10. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1.
Рис. 9. Частотно-раЗмерное распределение створок устрицы (Crassostrea gigas) иЗ раковинной кучи (все выборки). Fig. 9. Size-frequency distribution of valves of the giant oyster (Crassostrea gigas) from the shell-midden (all samples). in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 9. Частотно-раЗмерное распределение створок устрицы (Crassostrea gigas) иЗ раковинной кучи (все выборки). Fig. 9. Size-frequency distribution of valves of the giant oyster (Crassostrea gigas) from the shell-midden (all samples).
Рис. 4. РаЗведочный шурф, виден слой раковин (раковинная куча) и масса створок спиЗулы сахалинской (Spisula sachalinensis) (Желтая стрелка). Fig. 4. A prospecting pit, a layer of shells (shell-midden) and numerous valves of Spisula sachalinensis (yellow arrow) are seen. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 4. РаЗведочный шурф, виден слой раковин (раковинная куча) и масса створок спиЗулы сахалинской (Spisula sachalinensis) (Желтая стрелка). Fig. 4. A prospecting pit, a layer of shells (shell-midden) and numerous valves of Spisula sachalinensis (yellow arrow) are seen.
Рис. 3. Раскоп 2: А – северная стенка, квадраты С–У; В – профиль бровки по линии меЖду квадратами 12–13, квадратами П–Р. Fig. 3. Excavation 3: A – the northern wall, squares С–У; В – the profile of the edge along the line between the squares 12–13, squares П–Р. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 3. Раскоп 2: А – северная стенка, квадраты С–У; В – профиль бровки по линии меЖду квадратами 12–13, квадратами П–Р. Fig. 3. Excavation 3: A – the northern wall, squares С–У; В – the profile of the edge along the line between the squares 12–13, squares П–Р.
Рис. 2. Раскоп 1: А – сектор 5, профиль бровки по линии меЖду квадратами 20–21; В – северная стенка, квадраты 21–22. Fig. 2. Excavation 1: A – sector 5, the profile of the edge along the line between the squares 20–21; B – the northern wall, squares 21–22. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 2. Раскоп 1: А – сектор 5, профиль бровки по линии меЖду квадратами 20–21; В – северная стенка, квадраты 21–22. Fig. 2. Excavation 1: A – sector 5, the profile of the edge along the line between the squares 20–21; B – the northern wall, squares 21–22.
Рис. 1. Карты Приморского края (А) и юЖного Приморья (В) с укаЗанием располоЖения стоянки Теляковского 2 и фотография побереЖья б. Теляковского (С); оранЖевая стрелка укаЗывает на располоЖение стоянки). Fig. 1. Maps of Primorsky Krai (Territory) (A) and its southern area (south Primorye) (B) showing location of Telyakobskogo 2 site and a photograph of the coast of Telyakovskogo Bay (C); orange arrow shows location of the site). in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 1. Карты Приморского края (А) и юЖного Приморья (В) с укаЗанием располоЖения стоянки Теляковского 2 и фотография побереЖья б. Теляковского (С); оранЖевая стрелка укаЗывает на располоЖение стоянки). Fig. 1. Maps of Primorsky Krai (Territory) (A) and its southern area (south Primorye) (B) showing location of Telyakobskogo 2 site and a photograph of the coast of Telyakovskogo Bay (C); orange arrow shows location of the site).
Supplementary Data for 'Transformers Significantly Improve Splice Site Prediction'
<p><strong>Description:</strong></p> <p>This repository contains supplementary data accompanying the manuscript <strong>"Transformers Significantly Improve Splice Site Prediction"</strong>. The data includes annotations used for training our splice site prediction models and the predictions made by our model and SpliceAI 10k. These datasets are provided to facilitate replication of our results and to support further research in RNA splicing and machine learning applications in genomics.</p> <p><strong>Contents:</strong></p> <ol> <li> <p><strong>Annotations Used for Model Training:</strong></p> <ul> <li> <p><strong>clinvar_splice_variants.tsv</strong></p> <ul> <li><em>Description:</em> Contains detailed information about ClinVar splice variants used in our study.</li> <li><em>Contents Include:</em> Variant identifiers, genomic coordinates, associated clinical significance, and relevant annotations.</li> </ul> </li> <li> <p><strong>splice_site_annotation_gtex.tsv</strong></p> <ul> <li><em>Description:</em> Splice site annotations derived from all tissues in GTEx V8.</li> <li><em>Contents Include:</em> Coordinates of splice sites and transcript information.</li> </ul> </li> <li> <p><strong>splice_site_annotation_icelandic_whole_blood_plus_gtex.tsv</strong></p> <ul> <li><em>Description:</em> Splice site annotations derived from a combination of Icelandic whole blood samples and samples from all tissues in GTEx V8.</li> <li><em>Contents Include:</em> Coordinates of splice sites and transcript information.</li> </ul> </li> </ul> </li> <li> <p><strong>Model Predictions:</strong></p> <p><strong>a. SpliceAI 10k Model Predictions:</strong></p> <ul> <li> <p><strong>spliceai_10k_clinvar_delta.vcf</strong></p> <ul> <li><em>Description:</em> SpliceAI 10k delta scores for ClinVar splice variants.</li> <li><em>Contents Include:</em> Variant Call Format (VCF) file containing delta scores that indicate the predicted impact on splicing for ClinVar variants.</li> </ul> </li> <li> <p><strong>spliceai_10k_no_sqtl_delta.vcf</strong></p> <ul> <li><em>Description:</em> SpliceAI 10k delta scores for variants unlikely to be splicing quantitative trait loci (sQTLs) in Icelandic whole blood.</li> <li><em>Contents Include:</em> VCF file with delta scores for variants not associated with sQTLs.</li> </ul> </li> <li> <p><strong>spliceai_10k_sqtl_delta.vcf</strong></p> <ul> <li><em>Description:</em> SpliceAI 10k delta scores for sQTLs detected in Icelandic whole blood.</li> <li><em>Contents Include:</em> VCF file with delta scores for variants identified as sQTLs.</li> </ul> </li> </ul> <p><strong>b. Transformer 45k Model Predictions:</strong></p> <ul> <li> <p><strong>transformer_45k_clinvar_delta.vcf</strong></p> <ul> <li><em>Description:</em> Transformer 45k delta scores for ClinVar splice variants.</li> <li><em>Contents Include:</em> VCF file with delta scores from our Transformer model, indicating the predicted impact on splicing.</li> </ul> </li> <li> <p><strong>transformer_45k_no_sqtl_delta.vcf</strong></p> <ul> <li><em>Description:</em> Transformer 45k delta scores for variants unlikely to be sQTLs in Icelandic whole blood.</li> <li><em>Contents Include:</em> VCF file with delta scores for variants not associated with sQTLs, as predicted by our model.</li> </ul> </li> <li> <p><strong>transformer_45k_sqtl_delta.vcf</strong></p> <ul> <li><em>Description:</em> Transformer 45k delta scores for sQTLs detected in Icelandic whole blood.</li> <li><em>Contents Include:</em> VCF file with delta scores for variants identified as sQTLs, based on our Transformer model predictions.</li> </ul> </li> </ul> </li> </ol> <p><strong>Additional Information:</strong></p> <ul> <li> <p><strong>Delta Scores and Their Interpretation:</strong></p> <ul> <li>Each variant is assessed for its potential impact on splicing through four delta scores: <ul> <li><strong>Acceptor Site Creation (<code>top_a_creation_delta</code>):</strong> Predicts the likelihood of creating a new acceptor site.</li> <li><strong>Acceptor Site Disruption (<code>top_a_disruption_delta</code>):</strong> Predicts the likelihood of disrupting an existing acceptor site.</li> <li><strong>Donor Site Creation (<code>top_d_creation_delta</code>):</strong> Predicts the likelihood of creating a new donor site.</li> <li><strong>Donor Site Disruption (<code>top_d_disruption_delta</code>):</strong> Predicts the likelihood of disrupting an existing donor site.</li> </ul> </li> <li><strong>Final Delta Score Calculation:</strong> <ul> <li>The overall impact of a variant is determined by taking the maximum of these four delta scores: <div> <div><code>final_delta_score = <span>max</span>(top_a_creation_delta, top_a_disruption_delta, top_d_creation_delta, top_d_disruption_delta) </code></div> </div> </li> <li>A higher final delta score indicates a greater predicted impact on splicing.</li> </ul> </li> <li><strong>Positions:</strong> <ul> <li>The positions (<code>*_pos</code>) indicate the genomic coordinates where the predicted splicing events occur, providing insight into the specific locations affected by the variant.</li> </ul> </li> </ul> </li> </ul> <ul> <li> <ul> <li><strong>Interpreting Delta Scores:</strong> <ul> <li>Delta scores range from 0 to 1.</li> <li>Scores closer to 1 suggest a higher probability of the variant affecting splicing.</li> </ul> </li> </ul> </li> <li> <p><strong>Purpose:</strong></p> <ul> <li>These datasets support the findings reported in our manuscript by providing the raw data used for model training and evaluation.</li> <li>Researchers can use these datasets to replicate our experiments, compare model performances, or conduct further studies on splice site prediction.</li> </ul> </li> </ul> <p> </p> <p><strong>Citation:</strong></p> <p>Please cite this dataset as:</p> <blockquote> <p>B.A. Jónsson, G.H. Halldórsson, S. Árdal, S. Rögnvaldsson, E. Einarsson, P. Sulem, D.F. Guðbjartsson, P. Melsted, K. Stefánsson, M.Ö. Úlfarsson (2023). Supplementary Data for "Transformers Significantly Improve Splice Site Prediction". Zenodo. <a target="_new" rel="noopener">https://doi.org/10.5281/zenodo.14109868</a></p> </blockquote> <p> </p> <p><strong>Contact Information:</strong></p> <p>For questions or further information, please contact:</p> <ul> <li><strong>Benedikt A. Jónsson</strong></li> <li><strong>Affiliation:</strong> deCODE Genetics/Amgen, Inc., Reykjavik, Iceland</li> <li><strong>Email: </strong>benediktj@decode.is</li> </ul>
Assessment of whole-site methane emissions from anaerobic digestion plants: towards establishing emission factors for various plant configurations
<p>This dataset supplements the publication "Assessment of whole-site methane emissions from anaerobic digestion plants: towards establishing emission factors for various plant configurations" by Wechselberger et al. (2025).</p> <p>The dataset contains primary and secondary data underlying the statistical analysis and reported methane emission factors. Emission factors were calculated as described in section 2.3 of the paper. </p> <p>Available files (UTF-8 encoded):</p> <ul> <li>Data.csv (dataset)</li> <li>Glossary.csv (column/variable descriptions of dataset)</li> </ul> <p>The dataset includes plant characteristics and whole-site methane losses of 135 anaerobic digestion plants, covering normal and various other-than-normal operating conditions (155 rows). For statistical analysis, only periods during normal operation and plants with information on the analyzed emission factors and plant characteristics were considered (cf. supplementary information C of the paper). Consequently, the final dataset contained 109 anaerobic digestion plants for statistical analysis on the methane emission factor (% of methane produced) and 28 plants when analyzing the wastewater-specific emission factor (kg methane per population equivalent and year). All but one facility continuously processed feedstock without any post-rotting stages. Plant DE-MH_WP5_1 of the secondary data implemented garage digesters.</p> <p>Data from three plants were collected only after completion of statistical analyses. These data were used to compare methane losses during normal and other-than-normal operating conditions. The respective rows are marked accordingly in the dataset (column “data_collected_after_statistical_analyses”).</p> <p>Version v2 contains the final reference to the publication Wechselberger et al. (2025). The data are the same as in version v1.</p>
ScienceDex guides
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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.