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opencc-by-4.0Dec 2021View details →

Quantitative in situ measurement of optical force along a strand of cleaved silica optical fiber induced by the light guided therewithin

This dataset is associated with "Quantitative in situ measurement of optical force along a strand of cleaved silica optical fiber induced by the light guided therewithin", by Mikko Partanen, Hyeonwoo Lee, and Kyunghwan Oh, Photonics Res. 9, 2016 (2021) [https://doi.org/10.1364/PRJ.433995]. It includes data files and Matlab (R2017b) scripts to allow for the replication of the figures. The data files give the oscillator mirror position in the units of nanometers measured at the rate of 200 times per second.

Gene expression and splicing counts from 49 tissues from GTEx v8 genome build hg38 - non-strand specific

Dataset description: 49 folders, each corresponding to one tissue from GTEx v8 and containing the following files: <ol> <li> geneCounts: gene-level counts  </li> <li> k_j: split counts spanning from one exon to another. </li> <li> k_theta: non-split counts covering a splice site </li> <li> n_psi3: total split counts from a given acceptor site </li> <li> n_psi5: total split counts from a given donor site </li> <li> n_theta: total split and non-split counts for a given splice site </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol> The gene counts were originated using the GTF file from <a href="https://www.gencodegenes.org/human/release_29.html">release 29 of GENCODE</a>, and the split and non-split counts contain only the annotated junctions from the same release. Statistics are reported only for GENCODE-annotated introns and splice sites, in compliance with the regulations of the GTEx consortium. For a description of the samples, methods, and protocols, see the GTEx publication specified below. Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, the <a href="https://github.com/gagneurlab/drop">Detection of RNA outliers Pipeline (DROP) </a> can be used to compute gene expression and splicing outliers. Organism: Homo sapiens Genome assembly: hg38 Gene annotation: gencode29 Strand specific: FALSE Paired end: TRUE Protocol: poly(A) enrichment Contact: Vicente A. Yepez, yepez at in.tum.de; Christian Mertes, mertes at in.tum.de; Julien Gagneur, gagneur at in.tum.de Citation: Write the following in the "Data availability" section of the manuscript or similar replacing the three citations by the ones from the References section below: <blockquote> The count matrices for the GTEx samples <cite GTEx publication, see below> were downloaded from Zenodo (doi: 10.5281/zenodo.6078397) and were generated through DROP <cite DROP, see below> using the release 29 of the GENCODE annotation <cite GENCODE, see below>. </blockquote> Also, write the following in the Acknowledgements section:   <blockquote> The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. The raw data used for the analyses described in this manuscript were obtained from the GTEx Portal on June 12, 2017, under accession number dbGaP  phs000424.v8.p2. </blockquote>

opencc-by-4.0Jul 2022View details →

Strand-switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA_data_NAR

This document includes data corresponding to the paper entitled :"Strand-switching mechanism of Pif1 helicase induced by its collision with a G-quadruplex embedded in dsDNA" published in Nucleic Acid Research, 2022. The link to the zenodo depository of the homemade software to open the data is given in the readme.txt file as well as the way the data files are organized

opencc-by-4.0Sep 2022View details →

Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq

Hundreds of loci in human genomes have alleles that are methylated differentially according to their parent of origin. These imprinted loci generally show little variation across tissues, individuals, and populations. We show that such loci can be used to distinguish the maternal and paternal homologs for all autosomes, without the need for the parental DNA. We integrate methylation-detecting nanopore sequencing with the long-range phase information in Strand-seq data to determine the parent of origin of chromosome-length haplotypes for both DNA sequence and DNA methylation in five trios with diverse genetic backgrounds.

opencc-by-4.0Mar 2021View details →

Gene expression and splicing counts from the Yepez, Gusic et al study - non strand-specific

File description: <ol> <li> geneCounts: gene-level counts  </li> <li> k_j: split counts spanning from one exon to another. </li> <li> k_theta: non-split counts covering a splice site </li> <li> n_psi3: total split counts from a given acceptor site </li> <li> n_psi5: total split counts from a given donor site </li> <li> n_theta: total split and non-split counts for a given splice site </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol>   The gene counts were originated using the GTF file from release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a>, and the split and non-split counts contain only the annotated junctions from the same release. Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, the DROP can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Number of samples: 154 Tissue: Fibroblast Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease (ICD-10: N): E75: 1, E79: 13, E88: 118, G31: 9, K72: 3, NONE: 10 Strand specific: FALSE Paired end: TRUE Protocol: poly(A) enrichment Dataset contact: Vicente Yepez, yepez@in.tum.de; Julien Gagneur, gagneur@in.tum.de; Holger Prokisch, prokisch@helmholtz-muenchen.de Citation: Cite both the resource using Zenodo's citation and the publication under References

Text-fig. 11. Acer Post Hammer species 1, UF 279-34456. a, b: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. c: Crowded alternate intervessel pits, TLS. d: Simple perforation plates, helical thickenings in vessel elements, TLS. e: Rays 2–3-seriate, gum deposit in vessel element, TLS. Acer Post Hammer species 2. UF 279-34466. f: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. g: Alternate intervessel pits, helical thickenings in vessel elements, TLS. h: Rays 1–4(–5)-seriate, TLS. i: Crystalliferous strand, multiseriate ray, TLS. Trochodendron beckii, UF 279-24558. j, k: Distinct growth rings, abrupt transition from earlywood to latewood, vesselless, wide rays noded at growth ring boundaries, TS. l: Rays of two distinct sizes, uniseriate and multiseriates>10-seriate, TLS. m. Scalariform intertracheary pits. RLS. Scale bars: 500 µm in j; 200 µm in a, f, k, l; 100 µm in b, h; 50 µm in c, d, e, g, i, m. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa

Text-fig. 11. Acer Post Hammer species 1, UF 279-34456. a, b: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. c: Crowded alternate intervessel pits, TLS. d: Simple perforation plates, helical thickenings in vessel elements, TLS. e: Rays 2–3-seriate, gum deposit in vessel element, TLS. Acer Post Hammer species 2. UF 279-34466. f: Diffuse-porous wood with distinct growth rings, marked by marginal parenchyma, vessels solitary and in short radial multiples, TS. g: Alternate intervessel pits, helical thickenings in vessel elements, TLS. h: Rays 1–4(–5)-seriate, TLS. i: Crystalliferous strand, multiseriate ray, TLS. Trochodendron beckii, UF 279-24558. j, k: Distinct growth rings, abrupt transition from earlywood to latewood, vesselless, wide rays noded at growth ring boundaries, TS. l: Rays of two distinct sizes, uniseriate and multiseriates>10-seriate, TLS. m. Scalariform intertracheary pits. RLS. Scale bars: 500 µm in j; 200 µm in a, f, k, l; 100 µm in b, h; 50 µm in c, d, e, g, i, m.

Text-fig. 9. Wataria kvacekii sp. nov., UF 279-24556. a: Wood ring-porous, earlywood with 2–3 rows of wide pores, vessels solitary and in radial multiples of 2, axial parenchyma scanty vasicentric and some apotracheal diffuse-in-aggregates, TS. b: Series of vessel elements with simple perforations, axial parenchyma strands adjacent to vessels, RLS. c: Alternate intervessel pitting, vessel element end walls horizontal, RLS. d: Vessel-axial parenchyma pitting similar to intervessel pitting, RLS. e, f: Rays with tile cells, storied axial parenchyma, some strands chambered crystalliferous, TLS. g: Detail of ray, TLS. h: Storied imperforate elements. Scale bars: 200 µm in a; 100 µm in b, e; 50 µm in c, d, f, h; 20 µm in g. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa

Text-fig. 9. Wataria kvacekii sp. nov., UF 279-24556. a: Wood ring-porous, earlywood with 2–3 rows of wide pores, vessels solitary and in radial multiples of 2, axial parenchyma scanty vasicentric and some apotracheal diffuse-in-aggregates, TS. b: Series of vessel elements with simple perforations, axial parenchyma strands adjacent to vessels, RLS. c: Alternate intervessel pitting, vessel element end walls horizontal, RLS. d: Vessel-axial parenchyma pitting similar to intervessel pitting, RLS. e, f: Rays with tile cells, storied axial parenchyma, some strands chambered crystalliferous, TLS. g: Detail of ray, TLS. h: Storied imperforate elements. Scale bars: 200 µm in a; 100 µm in b, e; 50 µm in c, d, f, h; 20 µm in g.

Text-fig. 5. Lithocarpoxylon ashwillii sp. nov., UF 279-24544. a, b: Semi-ring porous wood, exclusively solitary vessels in a radial/ diagonal arrangement, diffuse axial parenchyma, TS. c: Homocellular rays composed of procumbent cells; vasicentric tracheids; vessel elements with simple perforation plates (PP), TLS. d: Vessel-ray parenchyma pits (VRP) with reduced borders, vertical, RLS. e: Crystalliferous axial parenchyma strand (C) with a single crystal per chamber; ray with procumbent cells, RLS. f: Aggregate ray (right) composed of loosely associated 1–2-seriate rays, TLS. g: Uniseriate rays, thin-walled tyloses in vessels, vasicentric tracheids (VT). Lithocarpoxylon sp., UF 279-84864. h, i: Semi-ring porous wood, exclusively solitary vessels in radial arrangement. j: Aggregate ray and uniseriate rays. k: Scalariform perforation plate with fewer than 10 bars. l: Vessel-ray parenchyma pits with reduced borders to simple, vertical. Scale bars: 200 µm in a, b, f, h, j; 100 µm in c, i; 50 µm in d. e; 20 µm in k, l. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa

Text-fig. 5. Lithocarpoxylon ashwillii sp. nov., UF 279-24544. a, b: Semi-ring porous wood, exclusively solitary vessels in a radial/ diagonal arrangement, diffuse axial parenchyma, TS. c: Homocellular rays composed of procumbent cells; vasicentric tracheids; vessel elements with simple perforation plates (PP), TLS. d: Vessel-ray parenchyma pits (VRP) with reduced borders, vertical, RLS. e: Crystalliferous axial parenchyma strand (C) with a single crystal per chamber; ray with procumbent cells, RLS. f: Aggregate ray (right) composed of loosely associated 1–2-seriate rays, TLS. g: Uniseriate rays, thin-walled tyloses in vessels, vasicentric tracheids (VT). Lithocarpoxylon sp., UF 279-84864. h, i: Semi-ring porous wood, exclusively solitary vessels in radial arrangement. j: Aggregate ray and uniseriate rays. k: Scalariform perforation plate with fewer than 10 bars. l: Vessel-ray parenchyma pits with reduced borders to simple, vertical. Scale bars: 200 µm in a, b, f, h, j; 100 µm in c, i; 50 µm in d. e; 20 µm in k, l.

opencc-by-4.0Dec 2017View details →

Рис. 17. Выброшенная раковина анадары (Anadara broughtonii) на пляЖе б. Теляковского с прикрепившимися риЗоидами водорослей. Fig. 17. A stranded blood cockle shell (Anadara broughtonii) 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. 17. Выброшенная раковина анадары (Anadara broughtonii) на пляЖе б. Теляковского с прикрепившимися риЗоидами водорослей. Fig. 17. A stranded blood cockle shell (Anadara broughtonii) with attached algae rhizoids on the beach of Telyakovskogo Bay.

opencc-by-4.0Dec 2017View details →

Рис. 15. ПляЖи и пляЖевые танатоценоЗы б. Теляковского (июнь 2015 г.): А – северная часть бухты: пляЖ и валунно-глыбовая литораль; В – срединная часть бухты; С – массовые выбросы устриц (Crassostrea gigas), мидий (Crenomytilus grayanus) и модиолусов (Modiolus kurilensis) в северной части бухты; D – выбросы спиЗулы (Spisula sachalinensis) в срединной части бухты. Fig. 15. Beaches and beach thanatocoenoses of Telyakovskogo Bay (June 2015): A – northern part of the bay: a beach and rocky intertidal zone; B – middle part of the bay; C – abundant strandings of oysters (Crassostrea gigas), mussels (Crenomytilus grayanus and Modiolus kurilensis) in the northern part; D – strandings of Spisula sachalinensis in the middle part. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy

Рис. 15. ПляЖи и пляЖевые танатоценоЗы б. Теляковского (июнь 2015 г.): А – северная часть бухты: пляЖ и валунно-глыбовая литораль; В – срединная часть бухты; С – массовые выбросы устриц (Crassostrea gigas), мидий (Crenomytilus grayanus) и модиолусов (Modiolus kurilensis) в северной части бухты; D – выбросы спиЗулы (Spisula sachalinensis) в срединной части бухты. Fig. 15. Beaches and beach thanatocoenoses of Telyakovskogo Bay (June 2015): A – northern part of the bay: a beach and rocky intertidal zone; B – middle part of the bay; C – abundant strandings of oysters (Crassostrea gigas), mussels (Crenomytilus grayanus and Modiolus kurilensis) in the northern part; D – strandings of Spisula sachalinensis in the middle part.

opencc-by-4.0Mar 2015View details →

Fig. 2 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)

Fig. 2. Alignment of HSP90 amino acid sequence of P. citri McGregor and its homologus amino acid sequences from other species (Frankliniella occidentalis, Trialeurodes vaporariorum, Pteromalus puparum, Tetranychus cinabarinus).

opencc-by-4.0Mar 2023View details →

Fig. 1 in Twenty Years of Sea Turtle Strandings in New Caledonia.

Fig. 1. Map of recorded sea turtle strandings per town of New Caledonia between 1999 and 2021. Blue area represents the Loyalty Province, the orange area represents the North Province and the green area represents the South Province.

opencc-by-4.0Mar 2023View details →

Fig. 3 in Twenty Years of Sea Turtle Strandings in New Caledonia.

Fig. 3. Recorded sea turtle strandings in New Caledonia a. per species and b. per species and mean Curved Carapace Length (in cm) from 1999 to 2021 with 95% confidence intervals.

opencc-by-4.0Mar 2023View details →

Fig. 2 in Twenty Years of Sea Turtle Strandings in New Caledonia.

Fig. 2. Number of recorded sea turtle strandings in New Caledonia (a) per year, and (b) per month (1999 to 2021).

Fig. 2 in Molecular Identification, Fatty Acid Profile and Trace Elements in a Stranded Fin Whale in Sabah (Borneo, Malaysia): Implications on Migration Routes and Trophic Ecology of Southern Fin Whales.

Fig. 2. (a) The phylogenetic tree showing the stranded baleen whale (Baleen whale KP/Sabah/02082012) clustered together with the fin whale Balaenoptera physalus (U13103, Z18633 and X61145). (b) The phylogenetic analysis of the cytochrome b gene sequence indicating that the stranded fin whale (Baleen whale KP/Sabah/02082012) is closely related to the specimen of fin whales from the southern hemisphere with accession number KC572845, which represents Balaenoptera physalus quoi.

Fig. 1 in Molecular Identification, Fatty Acid Profile and Trace Elements in a Stranded Fin Whale in Sabah (Borneo, Malaysia): Implications on Migration Routes and Trophic Ecology of Southern Fin Whales.

Fig. 1. Stranding site (red-filled triangle) of the fin whale at the Sitompok River (Lat. 05°34'672"N; Long.115°39'710"E) near Kuala Penyu (KP), a coastal town overlooking the South China Sea on the western shores of Sabah (Borneo, Malaysia) (inset map). The approximate location of the sighting of possible fin whales reported by De Boer (2000) is marked with a blue-filled circle. The distribution ranges of rorquals species, including fin whales, in the Philippine waters reported by Slijper et al. (1964) and Acebes (2014) are marked with green-filled circles. The locations of fin whales' migration ranges in Australian waters according to Aulich et al. (2019) are shown using red-filled circles. The stranding site of the unconfirmed fin whale species at Pulau Sugi (Junge 1950) is indicated by a yellow-filled circle.

Fig. 4 in Molecular Identification, Fatty Acid Profile and Trace Elements in a Stranded Fin Whale in Sabah (Borneo, Malaysia): Implications on Migration Routes and Trophic Ecology of Southern Fin Whales.

Fig. 4. (a) Concentrations of trace elements (Mean ± SD) in the skin and blubber of the southern fin whale recorded in the present study compared to (b) the concentrations of trace elements in the skin of southern right whales (Eubalaena australis) extracted from the results of Martino et al. (2013).

Fig. 3 in Molecular Identification, Fatty Acid Profile and Trace Elements in a Stranded Fin Whale in Sabah (Borneo, Malaysia): Implications on Migration Routes and Trophic Ecology of Southern Fin Whales.

Fig. 3. Comparison of the percentages of fatty acid profiles for (a) SFA, (b) MUFA and (c) PUFA in the tissues of adult male (M) and female (F) southern humpback whales during the early and late migrations extracted from the results of Waugh et al. (2012), epipelagic and mesopelagic (i.e., average) fish in the South China Sea (SCS) extracted from the supplementary data of Wang et al. (2019) and the southern fin whale in the present study.

opencc-by-4.0Oct 2017View details →

COMMENTS.— Although not breeding in the Mediterranean, the species forages in Libyan waters (van Dijk et al. 2014). In addition to the single beached record, an individual was pulled from nearshore waters of the Tajura coast in 1996 and died in the rehabilitation facility of the Marine Biology Research Centre (MBRC) at Tajura, where it was subsequently taxidermied at the MBRC Museum (Hamza 2010). Capra's (1949) records were based on a report in "L'Idea Coloniale" for 2 May 1927 (Mongàr) and an unspecified specimen in the Museo Civico di Storia Naturale di Trieste (Sella). IUCN THREAT STATUS.— Vulnerable A2bd. MAP 3. Distribution of Dermochelys coriacea in Libya showing stranding site records. in Atlas of the Reptiles of Libya

COMMENTS.— Although not breeding in the Mediterranean, the species forages in Libyan waters (van Dijk et al. 2014). In addition to the single beached record, an individual was pulled from nearshore waters of the Tajura coast in 1996 and died in the rehabilitation facility of the Marine Biology Research Centre (MBRC) at Tajura, where it was subsequently taxidermied at the MBRC Museum (Hamza 2010). Capra's (1949) records were based on a report in "L'Idea Coloniale" for 2 May 1927 (Mongàr) and an unspecified specimen in the Museo Civico di Storia Naturale di Trieste (Sella). IUCN THREAT STATUS.— Vulnerable A2bd. MAP 3. Distribution of Dermochelys coriacea in Libya showing stranding site records.