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opencc-by-4.0Aug 2021View details →

Data Sets and Results for "Improved data sets and evaluation methods for the automatic prediction of DNA-binding proteins"

Data sets and results for "Improved data sets and evaluation methods for the automatic prediction of DNA-binding proteins" The file "dna_binding_protein_sequences.zip" has the training and testing sets from the paper: RLL - "random_<train/test>_full_1000.csv" RSL - "random_<train/test>_40.csv" RS&LL - "random_<train/test>_40_1000.csv" RLL where included positive examples have verified DNA binding activity - "random_<train/test>_hq_1000.csv" The 10 RS&LL data sets - "random_<train/test>_40_1000.csv" + "random_<train/test>_40_1000_cv_<0-8>.csv" The results files are named similarly. See "see_results.ipynb" in the <a href="https://doi.org/10.5281/zenodo.5153683">codebase</a> that supplement these data sets The species data sets are derived from "uniprot_data_bac.tab" and "uniprot_data_not_bac.tab."  See <a href="https://doi.org/10.5281/zenodo.5153683">code</a>.  The ESM embeddings used by the XGBoost model are in "dna_binding_protein_esm.zip"

opencc-by-4.0Dec 2020View details →

Dataset: Quantitative Evaluation of Enhanced multi-plane clinical fetal diffusion MRI with a crossing-fiber phantom

This dataset provides MRI acquisitions of a customized crossing phantom for fetal brain. It contains: 1) High Resolution acquisitions of 1.5 mm3 isotropic and 61 directions (with b-vectors/b-values) 2) Six low resolution acquisitions of 1x1x4 mm3 and 9-16-25 directions (with respective b-vectors/b-values) 3) A structural T2-w acquisition

opencc-by-4.0Jan 2013View details →

FIG. 3 in Evaluation of Linnaeus' concept of Santolina rosmarinifolia L. (Asteraceae, Anthemideae) and its interpretation

FIG. 3. — Lectotype of S. chamaecyparissus L. subsp. viridis Rouy var. β subintegrifolia Rouy (LY-ROUY).

opencc-by-4.0Jul 2021View details →

Evaluation of the shucking of certain species of scallops contaminated with domoic acid with a view to the production of edible parts meeting the safety requirements foreseen in the Union legislation - Summary statistics on occurrence and consumption data and exposure assessment results

DomoicAcid_Raw_Occurrence_Data.CSV contains the raw occurrence dataset on Domoic Acid contaminant in scallops as extracted from EFSA DWH on the 9 June 2020, 16,369 samples presented in the opinion as described in its section 1.3.2. Occurrence data submitted to EFSA. The data is provided in .csv format. This dataset is compliant with EFSA SSD model and contains two additional columns documenting issues identified in the cleaning process (column: issue) and the action taken (column: outcome) to address the issue (e.g. delete record or update values in specific fields). The link to the catalogues of controlled terminologies can be found under "Related identifiers”. Annex_ DomoicAcid Table of contents Table A1 Description of FoodEx2 codes used to describe scallop species and their anatomical parts Table A2 Data cleaning steps applied to occurrence data on domoic acid in scallops Table A3 Percentage of Left-Censored data and descriptive statistics for Limits of detection (LODs) and Limits of quantification (LOQs) for domoic acid in scallops (mg/kg) Table A4 Descriptive statistics for domoic acid in scallops (mg/kg) as reported in the cleaned database (statistics weighted by number of units per sample) Table A5 Descriptive statistics  of body tissue weights (g) of scallops as submitted by data providers

opencc-by-4.0Aug 2021View details →

An Open-access Database for the Evaluation of Cardio-mechanical Signals from Patients with Valvular Heart Diseases

This dataset is for the paper "An Open-access Database for the Evaluation of Cardio-mechanical Signals from Patients with Valvular Heart Diseases" published to Frontiers in Physiology. Please cite "Yang C, Fan F, Aranoff N, Green P, Li Y, Liu C and Tavassolian N (2021) An Open-Access Database for the Evaluation of Cardio-Mechanical Signals From Patients With Valvular Heart Diseases. Front. Physiol. 12:750221. doi: 10.3389/fphys.2021.750221" when using this database. The archive comprises SCG and GCG recordings sourced from and processed at multiple sites worldwide, including Columbia University Medical Center and Stevens Institute of Technology in the USA, as well as Southeast University, Nanjing Medical University, and the first affiliated hospital of Nanjing Medical University in China. It includes electrocardiogram (ECG), SCG, and GCG recordings collected from 100 patients with various conditions of valvular heart diseases, such as aortic and mitral stenosis. The recordings were collected from clinical environments with the same types of wearable sensor patch. Besides the raw recordings of ECG, SCG and GCG signals, a set of hand-corrected fiducial point annotations is provided by manually checking the results of the annotated algorithm. The database also includes relevant echocardiogram parameters associated with each subject such as ejection fraction, valve area, and mean gradient pressure.

Fig. 4 in Taxonomic Re-Evaluation Of Sarika Diadema (Dall, 1897) And S. Asamurai (Panha, 1997), Two Endemic Land Snails From Thailand (Pulmonata: Ariophantidae: Macrochlamydinae)

Fig. 4. Radula morphology. Sarika diadema from Botanic Garden, Trang: A, central tooth with first to third lateral teeth; B, lateral teeth with bicuspid marginal teeth transition; C, outermost marginal teeth. Sarika asamurai from Klong Phanom National Park, Suratthani: D, central tooth with first and second lateral teeth; E, lateral teeth with bicuspid marginal teeth transition; F, outermost marginal teeth. Numbers indicated order of lateral and marginal teeth. Central tooth indicated by 'C'.

Fig. 1 in Taxonomic Re-Evaluation Of Sarika Diadema (Dall, 1897) And S. Asamurai (Panha, 1997), Two Endemic Land Snails From Thailand (Pulmonata: Ariophantidae: Macrochlamydinae)

Fig. 1. The collecting sites of S. diadema (■) and S. asamurai (●) within southern Thailand. Shading represents mountainous areas with an altitude higher than 50 m (light grey) and 500 m (dark grey).

Fig. 2 in Taxonomic Re-Evaluation Of Sarika Diadema (Dall, 1897) And S. Asamurai (Panha, 1997), Two Endemic Land Snails From Thailand (Pulmonata: Ariophantidae: Macrochlamydinae)

Fig. 2. Sarika diadema from Khao Poo-Khao Ya National Park, Pattalung: A, shell morphology; B, body colour in live specimen. Sarika asamurai from Ban Takun, Suratthani: C, shell morphology; D, body colour in live specimen.

Fig. 3 in Taxonomic Re-Evaluation Of Sarika Diadema (Dall, 1897) And S. Asamurai (Panha, 1997), Two Endemic Land Snails From Thailand (Pulmonata: Ariophantidae: Macrochlamydinae)

Fig. 3. Genitalia and jaw of S. diadema and S. asamurai. Sarika diadema from Botanic Garden, Trang: A, whole genital system; B, interior structure of penis; C, single spermatophore with detail of spines between sperm sac and tail filament; D, arrangement of three spermatophores in gametolytic sac; E, jaw. Sarika asamurai from Klong Phanom National Park, Suratthani: F, whole genital system; G, internal structure of penis; H, spermatophore with detail of spines between sperm sac and tail filament and cross section of tail filament; I, jaw. Abbreviations used in the figures are listed under 'anatomical abbreviations' in the materials and methods

Figure 3 in Morphological variability and evaluation of taxonomic characters in the genus Erythemis Hagen, 1861 (Odonata: Libellulidae: Sympetrinae)

Figure 3. PCA diagrams for the first two factors using continuous characters as defined in the present study. a) Biplot shows distribution of morphological characters in M of Erythemis. Numbers represent the following ratio characters: 1) Lab/Lecv-clS3, 2) Lab/LcaS3, 3) LFW/Lnpt, 4) Lab/LclS3, 5) Antr /Lar, 6) Lar/Lba, 7) Acd/lban, 8) AnptHW/LoptHW, 9) Lnpt/Anb, 10) LHW/ Acd, 11) Lban/ Lasa-ca, 12) LHW/Lab, 13) Lban/Anb, 14) LHW/LFW, 15) Las/Ddas, 16) Lba/Lban, 17) LclS3/ LcaS3, 18) Lecv-clS3/LcaS3, 19) Las/Anas, 20) Lab/Las. b) Biplot shows distribution of morphological characters in F of Erythemis. Numbers represent the following characters: 1) Lab/ Lecv-clS3, 2) Lab/LcaS3 3) Lab/LclS3, 4) Lab/Las, 5) LHW/Acd, 6) Lban/Anb, 7) Lecv-clS3/LcaS3, 8) Acd/lban, 9) Lar/Lba, 10) Antr/Lar, 11) LFW/Lnpt, 12) AnptHW/LoptHW, 13) LHW/Lab. See above for abbreviations.

Figure 2 in Morphological variability and evaluation of taxonomic characters in the genus Erythemis Hagen, 1861 (Odonata: Libellulidae: Sympetrinae)

Figure 2. Plots of the first two discriminant functions of the discriminant analysis. a) The first two discriminant functions explain 72.5% in males, the cases in where species are overlapped were analyzed by separated in b. b) The first two discriminant functions explain 88.3% in males, and c) The first two discriminant functions explain 83.7% in F. Polygons define the limits of proposed groups.

Figure 1. a in Morphological variability and evaluation of taxonomic characters in the genus Erythemis Hagen, 1861 (Odonata: Libellulidae: Sympetrinae)

Figure 1. a) Plot showing continuous variation for the character distance between lateral and ventral carinae (dlvc), opposite to meeting point of lateral and medial transverse carinae on S3 (lmt). Numbers represent the following species: 1) E. attala, 2) E. carmelita, 3) E. collocata, 4) E. credula, 5) E. haematogastra, 6) E. mithroides, 7) E. peruviana, 8) E. plebeja, 9) E. simplicicollis, 10) E. vesiculosa. b) S1-3 E. carmelita males showing the measures from Williamson (1923): distance between lateral and ventral carinae (dlvc), divided by the measure of distance between meeting point of lateral and medial transverse carinae and ventral carinae (lmt).

Figures 10–17 in Morphological variability and evaluation of taxonomic characters in the genus Erythemis Hagen, 1861 (Odonata: Libellulidae: Sympetrinae)

Figures 10–17. Discrete characters of vulvar lamina, abdominal appendages, thorax, and femur. Numbers represent the following species: 10) E. peruviana female; 11) E. plebeja female; 12) E. simplicicollis male; 13) E. mithroides male; 14) E. vesiculosa male; 15) E. peruviana female; 16) E. vesiculosa female, 17) E. attala male. Abbreviations indicate the following characters, S 8 -S 9: Abdominal segments 8-9; LV: Vulvar lamina; Pb: Posterior border; Vt: Teeth ventral; Ai: Inferior appendage; As: Antehumeral stripe.

Figures 4–9. Morphometric characters. 4 in Morphological variability and evaluation of taxonomic characters in the genus Erythemis Hagen, 1861 (Odonata: Libellulidae: Sympetrinae)

Figures 4–9. Morphometric characters. 4) S1-3 of E. carmelita male, 5-6) E. simplicicollis male; 7) E. peruviana female; 8) FW of E. vesiculosa male; 9) E. simplicicollis male. Abbreviations indicate the following characters, LFW, LHW: FW or HW length; Lnpt: Nodus-pterostigma length; Antr: Triangle width; Lar: Arculus-second antenodal length; Lba: wing base-arculus length; Lban: Wing base-nodus length; Anpt: Pterostigma width; Lopt: Pterostigma length; Ansbt: Subtriangle width; Acd: HW discoidal field posterior border width; Anb: HW base width; Lasa-ca: Supplementary anal vein-Cu-A crossvein, Lab: Abdomen length; Las: Cercus length; Ddas: reach of teeth on ventral region of cercus; Anas: Anterolateral width of cercus; S: Abdominal segment 3; LclS3: Lateral carina length; LcaS3: 3 Apical carina length; Lecv: Ventral carina length; Lecv-clS3: Basal area between ventral-lateral carinae on S3; Wm: Width medial region of the abdominal segment; S 8: Abdominal segment 8; S 9: Abdominal segment 9; Lal: Female lamina length from base of basal lobe to apex.

Figures 18–25 in Morphological variability and evaluation of taxonomic characters in the genus Erythemis Hagen, 1861 (Odonata: Libellulidae: Sympetrinae)

Figures 18–25. Discrete characters of vesica spermalis. Numbers represent the following species: 18) E. mithroides, dorsal view; 19) E. carmelita, left side view; 20) E. vesiculosa, left side view; 21) E. peruviana, left side view; 22) E. credula, dorsal wiew; 23) E. haematogastra, right side view; 24) E. credula, finger-shaped structures, dorsal view; 25) E. plebeja, dorsal view. Abbreviations indicate the following characters, C: Cornua; L: Lateral lobe; H: Hook; Pb: Posterior border; M: Medial lobe; P: Posterior lobe; NH: Hook not bilobed.

Text-fig. 2. Generalised stratigraphy of the area including the fossil site in Orta-Şabanözü (Sengüler 2007). The coloured formation is Hüyükköy Formation, aged as late Miocene and containing fossil woods. in The First Glyptostroboxylon And Taxodioxylon Descriptions From The Late Miocene Of Turkey And Palaeoclimatological Evaluation

Text-fig. 2. Generalised stratigraphy of the area including the fossil site in Orta-Şabanözü (Sengüler 2007). The coloured formation is Hüyükköy Formation, aged as late Miocene and containing fossil woods.

Text-fig. 6. The riparian/swamp forest structure of the village of Sakarcaören in the late Miocene, location within the east part of GVP, and comparison with the other forest types from early Miocene of GVP (Akkemik et al. 2009, 2016, 2017, Bayam et al. 2018). in The First Glyptostroboxylon And Taxodioxylon Descriptions From The Late Miocene Of Turkey And Palaeoclimatological Evaluation

Text-fig. 6. The riparian/swamp forest structure of the village of Sakarcaören in the late Miocene, location within the east part of GVP, and comparison with the other forest types from early Miocene of GVP (Akkemik et al. 2009, 2016, 2017, Bayam et al. 2018).

Text-fig. 3. Photo of the area where the fossil samples were collected. It is near to Sakarcaören village in the city of Orta, Çankırı Province. Arrows indicate the petrified wood pieces. in The First Glyptostroboxylon And Taxodioxylon Descriptions From The Late Miocene Of Turkey And Palaeoclimatological Evaluation

Text-fig. 3. Photo of the area where the fossil samples were collected. It is near to Sakarcaören village in the city of Orta, Çankırı Province. Arrows indicate the petrified wood pieces.

Text-fig. 1. Sampling areas in Çankırı province: the village of Sakarcaören near to the town of Orta (green circle) in the east of GVP, and the other sites (yellow circles), volcanic centers (red circles) and the border of GVP. The sites marked as yellow circles: ELM, Elmali village; SOG, Soguksu National Park; BUG, Bugralar village; INO, Inozu Valley South Side; INL, Inozu Valley North Side; KAR, Karasar village; MEN, Menceler Plateau; KIR, Kiraluc Site near Nuhhoca village; AGU, Asagiguney village; KUZ, Kuzca village (Bayam et al. 2018); PEL, Pelitcik village (Akkemik et al. 2009); GUD, Gudul (Akkemik et al. 2017); HOC, Hoçaş village and KOZ, Kozyaka village (Akkemik et al. 2016). The sites located in the western part (INO, INL, KAR, MEN, KIR, AGU, KUZ, HOC and KUZ) are from early – middle Burdigalian and Hancili Formation (Altun et al. 2002, Akbaş et al. 2002). The sites in the central part (GUD, BUG, ELM, PEL and SOG) are from middle – late Burdigalian, Pazar Formation (Kazancı 2012, Sen et al. 2017), and finally the fossil site in the east part of GVP is the late Miocene, Hüyükköy Formation (Sengüler 2007). in The First Glyptostroboxylon And Taxodioxylon Descriptions From The Late Miocene Of Turkey And Palaeoclimatological Evaluation

Text-fig. 1. Sampling areas in Çankırı province: the village of Sakarcaören near to the town of Orta (green circle) in the east of GVP, and the other sites (yellow circles), volcanic centers (red circles) and the border of GVP. The sites marked as yellow circles: ELM, Elmali village; SOG, Soguksu National Park; BUG, Bugralar village; INO, Inozu Valley South Side; INL, Inozu Valley North Side; KAR, Karasar village; MEN, Menceler Plateau; KIR, Kiraluc Site near Nuhhoca village; AGU, Asagiguney village; KUZ, Kuzca village (Bayam et al. 2018); PEL, Pelitcik village (Akkemik et al. 2009); GUD, Gudul (Akkemik et al. 2017); HOC, Hoçaş village and KOZ, Kozyaka village (Akkemik et al. 2016). The sites located in the western part (INO, INL, KAR, MEN, KIR, AGU, KUZ, HOC and KUZ) are from early – middle Burdigalian and Hancili Formation (Altun et al. 2002, Akbaş et al. 2002). The sites in the central part (GUD, BUG, ELM, PEL and SOG) are from middle – late Burdigalian, Pazar Formation (Kazancı 2012, Sen et al. 2017), and finally the fossil site in the east part of GVP is the late Miocene, Hüyükköy Formation (Sengüler 2007).

Text-fig. 5. Distribution of Taxodioxylon gypsaceum in the Miocene (solid circles) and distribution (open circles) of its nearest representatives at present (Sequoia sempervirens, Sequoiadendron giganteum and Metasequoia glyptostroboides) (Eckenwalder 2009, Farjon 2010). in The First Glyptostroboxylon And Taxodioxylon Descriptions From The Late Miocene Of Turkey And Palaeoclimatological Evaluation

Text-fig. 5. Distribution of Taxodioxylon gypsaceum in the Miocene (solid circles) and distribution (open circles) of its nearest representatives at present (Sequoia sempervirens, Sequoiadendron giganteum and Metasequoia glyptostroboides) (Eckenwalder 2009, Farjon 2010).