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Ditrect STORM imaging and image reconstruction of the transcription initiation marker P-S5 and nuclear PI(3,4)P2 indirectly immunolabeled with AF647 (red) and AF555 (green) in control cells.
<p>U-2 OS cells were grown in DMEM with 10% FBS at 37°C and 5% CO<sub>2</sub>. Cells were plated one day before staining in ~50% confluence on the high-precision 12 mm round coverslips treated with Hellmanex, sonicated, washed, dried and sterilized. Cells were control treated with 1:000 DMSO in the culture media.</p> <p>U2OS cells were washed twice with PBS (pH 7.4) and fixed for 30 min in 2% PFA in PBS, washed 3-times for 5 min with PBS, then permeabilized in 0.1% Triton X-100 in PBS for 20 min, washed 3-times for 5 min by PBS and blocked in filtered 5% BSA in PBS for 30 min. Cells were incubated for 45 min with rabbit polyclonal IgG anti-RNAPII CTD P-S5 (Abcam ab5131) 3 µg/mL and mouse monoclonal IgG2 anti-PI(3,4)P2 (Z-P034; Echelon Biosci. Inc., USA) 5 µg/mL in 5% BSA in PBS, washed 3-times for 5 min in PBS and incubated for 30 min with donkey anti-mouse IgG AF555 (Invitrogen A31570) 10 µg/mL and goat anti-rabbit IgG AF647 (Invitrogen A21245) 10 µg/mL diluted in 5% BSA in PBS. Then the cells were washed 3-times for 5 min in PBS, post-fixed for 15 min in 2% PFA in PBS and washed 3-times for 5 min in PBS. All procedures were performed at RT and the cells were stored in PBS in the fridge overnight prior imaging.</p> <p>Coverslips with cells were mounted in the Chamlide chamber (Live Cell Instrument, Korea) and covered with imaging buffer (PBS pH 7.4, 50 mM MEA). Single-molecule localizations (SMLs) data were acquired by Zeiss Elyra PS.1 equipped with HR Diode 642-150 and HR DPSS 561-200 lasers, Alpha Plan-Apochromat 100x/1.46 oil DIC M27 Elyra objective and Andor EM CCD iXon DU 897 camera and Zeiss ZEN Black 2.1 SP3 software (Zeiss). AF647 and AF555 photo-switching was achieved by HiLo illumination and TIRF HP FOV with 100% power of 642nm or 561nm laser, and the signal was acquired via MBS 642 + EF LP 655 and MBS 561 + EF BP 570-620 / LP 750 filters, respectively. Exposure time was 40 ms and EM gain was 300 for both channels.</p> <p>SMLs were calculated in 2D by Zeiss ZEN Black 2.1 SP3 software using x,y 2D Gauss fit with point spread function (PSF) half width 177.9 nm, peak mask size 9 pixels and peak intensity to noise 6 and accounted for overlap in 2D with max cluster size 10. SMLs were rendered in ZEN software with 10 nm/px resolution and 1x PSF expansion factor. The data were model-based drift corrected in ZEN. Two channels were aligned using tetraspec beads fiducial markers for affine calibration. Drift-corrected and aligned localization coordinates were exported as text files. Text files were converted into csv files and imported using self-written macro (Hoboth et al., 2021a) into the ImageJ2 (Rueden et al., 2017) plug-in ThunderSTORM, visualized by normalized Gaussian method (Ovesny et al., 2014).</p>
РИС. 1. Схематичное иЗображение глаЗа наЗемного лёгочного моллюска. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела; L abs – абсолютное расстоЯние между Зрачком и наружной поверхностью хрусталика; D l – продольный диаметр хрусталика; А – абсолютный диаметр Зрачabs ка; D – поперечный диаметр глаЗа. FIG. 1. Schematic drawing of the eye of a terrestrial pulmonate mollusk. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body; L abs – the absolute distance between the pupil and the outer surface of the lens; D l – the longitudinal diameter of the lens; А abs – the absolute diameter of the pupil; D e – the transverse diameter of the eye. in Зрачок камерных глаЗ наЗемных брюхоногих моллюсков (Heterobranchia, Stylommatophora)
РИС. 1. Схематичное иЗображение глаЗа наЗемного лёгочного моллюска. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела; L abs – абсолютное расстоЯние между Зрачком и наружной поверхностью хрусталика; D l – продольный диаметр хрусталика; А – абсолютный диаметр Зрачabs ка; D – поперечный диаметр глаЗа. FIG. 1. Schematic drawing of the eye of a terrestrial pulmonate mollusk. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body; L abs – the absolute distance between the pupil and the outer surface of the lens; D l – the longitudinal diameter of the lens; А abs – the absolute diameter of the pupil; D e – the transverse diameter of the eye.
РИС. 2. ГлаЗ Monachoides incarnata. A. ФотографиЯ препарата иЗолированного глаЗа. B. ФотографиЯ продольного полутонкого среЗа глаЗа. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела. FIG. 2. The eye of Monachoides incarnata. A. Photograph of the preparation of the isolated eye. B. Photograph of the longitudinal semithin section of the eye. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body. in Зрачок камерных глаЗ наЗемных брюхоногих моллюсков (Heterobranchia, Stylommatophora)
РИС. 2. ГлаЗ Monachoides incarnata. A. ФотографиЯ препарата иЗолированного глаЗа. B. ФотографиЯ продольного полутонкого среЗа глаЗа. СокраЩениЯ: c – роговица; ec – глаЗнаЯ капсула; r – сетчатка; p – краЯ Зрачка; l – хрусталик, окруженный слоем стекловидного тела. FIG. 2. The eye of Monachoides incarnata. A. Photograph of the preparation of the isolated eye. B. Photograph of the longitudinal semithin section of the eye. Abbreviation: c – cornea; ec – eye capsule; r – retina; p – edges of the pupil; l – lens, surrounded by a layer of the vitreous body.
РИС. 3. Пенисы моллюсков сем. Bithyniidae иЗ водоемов Тюменской области. A. Bithynia tentaculata, B. B. decipiens, C. B. curta, D. B. producta, E. Boreoelona contortrix, F.Opisthorchophorus troscheli, G. O. baudonianus, H. O. abakumovae, I. Boreoelona sibirica, J. Paraelona socialis, K. P. milachevitchi, L. Digyrcidum bourguignati, M. Boreoelona sp., N. Digyrcidum starobogatovi. МасШтабнаЯ линейка 1 мм. Фото: Н.И. Андреев. FIG. 3. The penes of the bithyniid species from Tyumen Region. A. Bithynia tentaculata, B. B. decipiens, C. B. curta, D. B. producta, E. Boreoelona contortrix, F.Opisthorchophorus troscheli, G. O. baudonianus, H. O. abakumovae, I. Boreoelona sibirica, J. Paraelona socialis, K. P. milachevitchi, L. Digyrcidum bourguignati, M. Boreoelona sp., N. Digyrcidum starobogatovi. Scale bars: 1 mm. Photos: N.I. Andreyev. in Моллюски семейства Bithyniidae (Mollusca, Gastropoda) Тюменской области
РИС. 3. Пенисы моллюсков сем. Bithyniidae иЗ водоемов Тюменской области. A. Bithynia tentaculata, B. B. decipiens, C. B. curta, D. B. producta, E. Boreoelona contortrix, F.Opisthorchophorus troscheli, G. O. baudonianus, H. O. abakumovae, I. Boreoelona sibirica, J. Paraelona socialis, K. P. milachevitchi, L. Digyrcidum bourguignati, M. Boreoelona sp., N. Digyrcidum starobogatovi. МасШтабнаЯ линейка 1 мм. Фото: Н.И. Андреев. FIG. 3. The penes of the bithyniid species from Tyumen Region. A. Bithynia tentaculata, B. B. decipiens, C. B. curta, D. B. producta, E. Boreoelona contortrix, F.Opisthorchophorus troscheli, G. O. baudonianus, H. O. abakumovae, I. Boreoelona sibirica, J. Paraelona socialis, K. P. milachevitchi, L. Digyrcidum bourguignati, M. Boreoelona sp., N. Digyrcidum starobogatovi. Scale bars: 1 mm. Photos: N.I. Andreyev.
РИС. 2. Дистальные отделы половой системы Limacus maculatus иЗ окрестностей г. ГомелЯ: А – атриум; P – пенис; PR – простата; SP – семЯприемник; OV – Яйцевод; SPOV – спермовидукт; SPD – проток семЯприемника; VD – семЯпровод. FIG. 2. Distal parts of the reproductive system of Limacus maculatus from the vicinity of Gomel city: А – atrium; P – penis; PR – prostata; SP – spermatheca (bursa copulatrix); OV – free oviduct; SPOV – spermoviduct; SPD – spermatheca duct (duct of bursa copulatrix); VD – vas deferens. in Новые находки синантропных слиЗней Limacus maculatus и Arion vulgaris (Mollusca, Gastropoda, Stylommatophora) в Беларуси
РИС. 2. Дистальные отделы половой системы Limacus maculatus иЗ окрестностей г. ГомелЯ: А – атриум; P – пенис; PR – простата; SP – семЯприемник; OV – Яйцевод; SPOV – спермовидукт; SPD – проток семЯприемника; VD – семЯпровод. FIG. 2. Distal parts of the reproductive system of Limacus maculatus from the vicinity of Gomel city: А – atrium; P – penis; PR – prostata; SP – spermatheca (bursa copulatrix); OV – free oviduct; SPOV – spermoviduct; SPD – spermatheca duct (duct of bursa copulatrix); VD – vas deferens.
FIG. 3 in A new species of Boreotrophon P. Fischer, 1884 (Gastropoda, Muricidae, Pagodulinae) from the Sea of Japan
FIG. 3. Boreotrophon candelabrum (A–H) Primorye, depth 8–12 m (A–F): A, B – 43.2 mm, C, D – 39.9 mm, E–F – 24.0 mm; Kuril Is., depth 60 m (G–H) – 33.7 mm; B. alborostratus (I–J) Primorye, depth 140 m – 40.0 mm.
FIG.1 in A new species of Boreotrophon P. Fischer, 1884 (Gastropoda, Muricidae, Pagodulinae) from the Sea of Japan
FIG.1. Map of the type material sampling area (black spot). РИС.1. Карта района отбора типового материала (чернаЯ точка).
FIG. 2 in A new species of Boreotrophon P. Fischer, 1884 (Gastropoda, Muricidae, Pagodulinae) from the Sea of Japan
FIG. 2. Boreotrophon oparini sp. nov. A–E. Holotype ZMMU Lc-41237, 46.2 mm: ventral (A) dorsal (C), right (D) and left (E) views, B – aperture with operculum 9.1 mm x 4.8 mm. F–J. Paratype IBSS, 41.1 mm ventral (F) dorsal (H), right (I) and left (J) view, G – aperture with operculum 8.5 mm x 4.6 mm. РИС. 2. Boreotrophon oparini sp. nov. A–E. Голотип ZMMU Lc-41237, 46.2 мм, ракурсы: вентральный (A) дорсальный (C), справа (D), слева (E), B – устье с крыШечкой 9,1 мм x 4,8 мм. F–J. Паратип IBSS, 41,1 мм, ракурсы: вентральный (F), дорсальный (H), справа (I), слева (J), G – устье с крыШечкой 8,5 мм x 4,6 мм.
Imaging the sediment cover offshore central Chile with surface-wave dispersion and P-wave conversion using DAS
<p>This repository contains codes and data used to reproduce the figures in the paper <em>Vernet, C. et al, "Imaging the sediment cover offshore central Chile with surface-wave dispersion and P-wave conversion using distributed acoustic sensing", 2025, (<a href="https://doi.org/10.1029/2024JB030507">https://doi.org/10.1029/2024JB030507</a>).</em></p>
DATA SET USED IN THE PHYLOGENETIC ANALYSIS ?, condition not preserved. Coding for Paraortygoides based on BMNH PAL A 6217 (holotype of P. radagasti) and SMRME 1303 (holotype of P. messelensis) in The Fossil Galliform Bird Paraortygoides from the Lower Eocene of the United Kingdom
DATA SET USED IN THE PHYLOGENETIC ANALYSIS ?, condition not preserved. Coding for Paraortygoides based on BMNH PAL A 6217 (holotype of P. radagasti) and SMRME 1303 (holotype of P. messelensis)
Table S1. Uncorrected p distance matrix
<p>Uncorrected p distance values for combined COI and 16S sequences from phylogenetic analysis of <em>Helminthoglypta</em> land snails (Mollusca: Gastropoda: Helminthoglyptidae) from northern California and southern Oregon, USA.</p> <p>Note: Specimen numbers marked with * were missing COI sequences.</p> <p>Table in both Excel (*.xlsx) and comma-separated value (*.csv) formats.</p> <p> </p>
Fig. 3. – Kalanchoe darainensis D.-P. Klein & Callm. A in Kalanchoe darainensis (Crassulaceae), a new species from northeastern Madagascar
Fig. 3. – Kalanchoe darainensis D.-P. Klein & Callm. A. Rosulate growth with succulent, bright green to olive leaves; B. Terminal, scarlet red and many-flowered dichasial cymes; C. Leaves entirely covered with short to long glandular hairs. [A–B: Ranirison 749; C: Callmander et al. 241] [Photos: A–B: P. Ranirison; C: M. Callmander]
Fig. 2. – Kalanchoe darainensis D.-P. Klein & Callm. A in Kalanchoe darainensis (Crassulaceae), a new species from northeastern Madagascar
Fig. 2. – Kalanchoe darainensis D.-P. Klein & Callm. A. Habit; B. Basal leaf; C. Dissection of corolla, showing androecium and gynoecium; D. Flower; E. Inflorescence; F. Anther with flattened spheroid connective gland. [Ranirison 749, TEF] [Drawings: R.L. Andriamiarisoa]
nal; E', F', internal, G'-J', Pal. 1341 (peripheral 8); G', H', external; I', J', internal; K'-N', Pal. 1343 (peripheral 9); K', L', external; M', N', internal; O'-R', Pal. 1345 (peripheral 10); O', P', external; Q', R', internal; S'-V', Pal. 1348 (peripheral 11); S', T', external; U', V', internal views; W', reconstruction of carapace Thick lines correspond to scute sulci, dotted lines denote plate sutures, and oblique lines indicate missing plate portions. Abbreviations: Ce, cervical; co, costal; Ma, marginal; ne, neural; nu, nuchal; per, peripheral; Pl, pleural; py, pygal; sp, suprapygal; Spr, supracaudal; Ve, vertebral. Scale bars: A-V', 1 cm; W', 2.5 cm. in Fossil turtles from the early Miocene localities of Mokrá-Quarry (Burdigalian, MN4), South Moravian Region, Czech Republic
nal; E', F', internal, G'-J', Pal. 1341 (peripheral 8); G', H', external; I', J', internal; K'-N', Pal. 1343 (peripheral 9); K', L', external; M', N', internal; O'-R', Pal. 1345 (peripheral 10); O', P', external; Q', R', internal; S'-V', Pal. 1348 (peripheral 11); S', T', external; U', V', internal views; W', reconstruction of carapace Thick lines correspond to scute sulci, dotted lines denote plate sutures, and oblique lines indicate missing plate portions. Abbreviations: Ce, cervical; co, costal; Ma, marginal; ne, neural; nu, nuchal; per, peripheral; Pl, pleural; py, pygal; sp, suprapygal; Spr, supracaudal; Ve, vertebral. Scale bars: A-V', 1 cm; W', 2.5 cm.
sal; W, visceral; X-Z, Pal. 1308 (costal 5); X, Y, dorsal; Z, visceral; A'-C', Pal. 1309 (costal 6); A', B', dorsal; C', visceral; D'-F', Pal. 1310 (costal 8); D', E', dorsal; F', visceral; G'-J', Pal. 1312 (peripheral 1); G', H', dorsal; I', J', visceral; K'-N', Pal. 1313 (peripheral 7); K', L', dorsal; M', N', visceral; O'-R', Pal. 1314 (peripheral 8); O', P', dorsal; Q', R', visceral views; S', reconstruction of carapace. Thick lines indicate to scute sulci, dotted lines sutures and oblique lines denote missing plate portions. Abbreviations: Ce, cervical; co, costal; Ma, marginal; ne, neural; nu, nuchal; per, peripheral; Pl, pleural; py, pygal; sp, suprapygal; Ve, vertebral. Scale bars: 1 cm. in Fossil turtles from the early Miocene localities of Mokrá-Quarry (Burdigalian, MN4), South Moravian Region, Czech Republic
sal; W, visceral; X-Z, Pal. 1308 (costal 5); X, Y, dorsal; Z, visceral; A'-C', Pal. 1309 (costal 6); A', B', dorsal; C', visceral; D'-F', Pal. 1310 (costal 8); D', E', dorsal; F', visceral; G'-J', Pal. 1312 (peripheral 1); G', H', dorsal; I', J', visceral; K'-N', Pal. 1313 (peripheral 7); K', L', dorsal; M', N', visceral; O'-R', Pal. 1314 (peripheral 8); O', P', dorsal; Q', R', visceral views; S', reconstruction of carapace. Thick lines indicate to scute sulci, dotted lines sutures and oblique lines denote missing plate portions. Abbreviations: Ce, cervical; co, costal; Ma, marginal; ne, neural; nu, nuchal; per, peripheral; Pl, pleural; py, pygal; sp, suprapygal; Ve, vertebral. Scale bars: 1 cm.
Fig. 2. – Aloe gautieri J.-P. Castillon & Nusb. A in Aloe gautieri J.-P. Castillon & Nusb. (Xanthorrhoeaceae), a new species from the northeastern coast of Madagascar
Fig. 2. – Aloe gautieri J.-P. Castillon & Nusb. A. Inflorescence; B. Stem and leaves; C. Whole flowering plant; D. Detail of one flower, stamen and ovary. [A: Ranirison 607, G] [Photos: A: P. Ranirison; B-D: J.-P. Castillon]
Fig. 1. – Aloe gautieri J.-P. Castillon & Nusb. A in Aloe gautieri J.-P. Castillon & Nusb. (Xanthorrhoeaceae), a new species from the northeastern coast of Madagascar
Fig. 1. – Aloe gautieri J.-P. Castillon & Nusb. A. Whole flowering plant; B. Fruit. [A: Gautier & al. 4272, G] [Drawing: C. Chatelain]
Fig. 3 in Aloe gautieri J.-P. Castillon & Nusb. (Xanthorrhoeaceae), a new species from the northeastern coast of Madagascar
Fig. 3. – Living plant of Aloe fragilis Lavranos & Röösli at the type locality of Cap Manambato, near Iharaña (Vohemar). A. Inflorescence; B. Leaves. [Photos: J.-P. Castillon]
Data for figures in Kemp, E M, J W Wegiel, S V Kumar, J V Geiger, D M Mocko, J P Jacob, and C D Peters-Lidard, 2021: A NASA-Air Force precipitation analysis for near-real-time operations. Submitted to _J Hydrometeor_
<p>Tar files containing gridded metrics, domain-wide metric means and confidence intervals, and rain-gauge reports used to generate figures in Kemp et al (2021).<br> <br> Citation:<br> </p> <p>Kemp, E M, J W Wegiel, S V Kumar, J V Geiger, D M Mocko, J P Jacob, and C D Peters-Lidard, 2021: A NASA-Air Force precipitation analysis for near-real-time operations. Submitted to _J Hydrometeor_.</p>
Fig. 2. − Euphorbia neoelliotii J.-P. Castillon & J.-B. Castillon. A in Notes sur Euphorbia sect. Denisophorbia (Euphorbiaceae) à Madagascar: description d'une nouvelle espèce et une nouvelle synonymie
Fig. 2. − Euphorbia neoelliotii J.-P. Castillon & J.-B. Castillon. A. Port général (petits plants); B-C. Rosettes de feuilles; D. Système incyathescentiel; E. Fleur femelle; F. Fleurs mâles; G. Fruit. [Photos: J.-P. Castillon]
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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.