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Figure 3 in Nereidid polychaetes (Annelida) inhabiting the inside of decaying fronds of the mangrove palm Nypa fruticans in a tropical estuary in Malaysia, with special reference to the life history of the dominant species, Namalycastis sp.

Figure 3. Coelomic cells in gametogenesis of Namalycastis sp. (a) Oocyte of a female individual collected from Station 6 on 27 November 2015. (b) Round cluster of spermatogonia or spermatocytes of a male individual collected from Station 4 on 28 September 2016. Scale bars: 0.05 mm.

Figure 2 in Nereidid polychaetes (Annelida) inhabiting the inside of decaying fronds of the mangrove palm Nypa fruticans in a tropical estuary in Malaysia, with special reference to the life history of the dominant species, Namalycastis sp.

Figure 2. Map showing seven sampling sites and distributions of three nereidid species along the lagoon of Setiu Wetlands, Terengganu, on the eastern coast of Peninsular Malaysia. M, Station M (Muara Kuala Setiu); 1, Station 1 (Beting Lintang); 2, Station 2 (in front of Pulau Tebing Tinggi); 3, Station 3 (in front of Pulau Che Hing); 4, Station 4 (in front of Pulau Gemia); 5, Station 5 (northern stream in front of Pulau Awang Jin); 6, Station 6 (southern stream in front of Pulau Awang Jin). Filled circles, Namalycastis sp.; open circle, N. rhodochorde; filled triangles, Perinereis aibuhitensis. Arrow indicates the single opening of Setiu Wetlands.

Figure 14 in Nereidid polychaetes (Annelida) inhabiting the inside of decaying fronds of the mangrove palm Nypa fruticans in a tropical estuary in Malaysia, with special reference to the life history of the dominant species, Namalycastis sp.

Figure 14. Perinereis aibuhitensis (UMT-Ann 2191). (a) Anterior end with everted proboscis, dorsal view. (b) Middle body, dorsal view. (c) Posterior end, dorsal view. (d–f) Posterior views of parapodia in chaetigers 25 (d), 65 (e), and 104 (f). (g) Homogomph spiniger in notochaetae, chaetiger 25. (h) Homogomph spiniger in upper neurochaetae, chaetiger 65. (i) Heterogomph spiniger in lower neurochaetae, chaetiger 65. (j) Heterogomph falciger in upper neurochaetae, chaetiger 25. (k) Heterogomph falciger in lower neurochaetae, chaetiger 65. Scale bars: a–c = 1 mm; d–f = 0.2 mm; g–i = 0.1 mm; j, k = 0.05 mm.

Figure 12 in Nereidid polychaetes (Annelida) inhabiting the inside of decaying fronds of the mangrove palm Nypa fruticans in a tropical estuary in Malaysia, with special reference to the life history of the dominant species, Namalycastis sp.

Figure 12. Namalycastis rhodochorde, UMT-Ann 2270. Chaetae in chaetiger 51. (a) Sesquigomph spiniger in upper neurochaetae. (b) Heterogomph falciger in upper neurochaetae. (c) Heterogomph falciger in lower neurochaetae. Scale bars: 0.1 mm.

Figure 11 in Nereidid polychaetes (Annelida) inhabiting the inside of decaying fronds of the mangrove palm Nypa fruticans in a tropical estuary in Malaysia, with special reference to the life history of the dominant species, Namalycastis sp.

Figure 11. Namalycastis rhodochorde, UMT-Ann 2270. Parapodium of chaetiger 101, posterior view. Scale bar: 0.2 mm.

opencc-by-4.0Nov 2024View details →

Table A.12: Bibliographic references and abbreviations in full table

Open the record for dataset details and reuse information.

opencc-by-4.0Dec 2024View details →

Whole genome re-sequencing workshop data: fastq files and reference genomes

Whole genome re-sequencing data analysis workshop datasets. The files are necessary inputs for the workshop in https://github.com/PoODL-CES/Genomics_learning_workshop Tools and scripts listed in the https://github.com/PoODL-CES/Genomics_learning_workshop repository.   These are subsampled fastq files from: Khan, A., Patel, K., Shukla, H., Viswanathan, A., van der Valk, T., Borthakur, U., Nigam, P., Zachariah, A., Jhala, Y.V., Kardos, M. and Ramakrishnan, U., 2021. Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers. Proceedings of the National Academy of Sciences, 118(49), p.e2023018118. The reference genome is from : Shukla, H., Suryamohan, K., Khan, A., Mohan, K., Perumal, R.C., Mathew, O.K., Menon, R., Dixon, M.D., Muraleedharan, M., Kuriakose, B. and Michael, S., 2023. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation. GigaScience, 12, p.giac112.   The reference has been indexed using: bwa index <a target="_blank" rel="noopener noreferrer">GCA_021130815.1_PanTigT.MC.v3_genomic.fna</a>

opencc-by-4.0Jul 2024View details →

A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei) - Pacbio HIFI reads

The critically endangered mountain gorilla Gorilla beringei beringei faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7) and 0% switch errors detected. These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species. This read set is comprised of fastqs from Pacbio HIFI (3 runs). A preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258

opencc-by-4.0Jul 2024View details →

A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei) -Oxford Nanopore reads

The critically endangered mountain gorilla Gorilla beringei beringei faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7) and 0% switch errors detected. These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species. This repository hosts the Oxford Nanopore ultralong reads. The preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258.

opencc-by-4.0Aug 2024View details →

TEFNET24: Reference Packet Optical Network Topology for Edge to Core Transport [Invited]

In this paper, we introduce TEFNET24, a reference multi-layer hierarchical network topology that spans from access to core networks, specifically designed to meet the demands of beyond-5G and and prepared for next-generation 6G communication systems. This topology, inspired by the actual network deployments of Telefónica in medium-sized countries in Europe and America, integrates both IP and optical (DWDM) layers to provide a comprehensive framework for network design, optimization, and analysis. Our primary contribution is the development of an open-source benchmarking network, accessible to both researchers and industry professionals. This resource aims to facilitate the study and advancement of integrated IP and optical networks, allowing researchers to address key challenges such as traffic aggregation, latency reduction, cost efficiency, and support for advanced applications. We provide guidelines for utilizing this benchmark network, enabling users to evaluate and enhance their solutions for AI-driven network management, ultra-reliable low-latency communication, enhanced mobile broadband, and massive machine-type communication. By sharing this detailed and practical benchmarking network, we seek to foster innovation and collaboration within the optical network community, driving forward the capabilities and performance of future communication networks.

opencc-by-4.0Nov 2021View details →

Reference-Sim

Splice graphs constructed by superimposing transcripts from the positive strand in the GRCh.104 homo sapiens reference genome with abundances sampled from the lognormal distribution with mean and variance both equal to -4, and then multiplied by 1000 and rounded to the nearest integer. Transcripts rounded to 0 are excluded. See https://github.com/lgw2/create_transcript_data for code to create.

opennotspecifiedJan 2009View details →

Subspecies and distribution. G. e. elegans Geoffroy Saint-Hilaire, 1837 — E Madagascar (from the region surrounding the Andapa Basin S to Tolagnaro). G. e. dambrensis Tate & Rand, 1941 — N Madagascar (originally described from Montagne d'Ambre, but animals at Ankarana are also referable to this form). G. e. occidentalis Albignac, 1971 — CW Madagascar (limestone regions of Bemaraha, Namoroka & Kelifely). in Eupleridae

Subspecies and distribution. G. e. elegans Geoffroy Saint-Hilaire, 1837 — E Madagascar (from the region surrounding the Andapa Basin S to Tolagnaro). G. e. dambrensis Tate & Rand, 1941 — N Madagascar (originally described from Montagne d'Ambre, but animals at Ankarana are also referable to this form). G. e. occidentalis Albignac, 1971 — CW Madagascar (limestone regions of Bemaraha, Namoroka & Kelifely).

opencc-by-4.0Nov 2021View details →

Structural features and according references on the asperities of large earthquakes with the magnitude larger than 6.0

Reviews of Geophysics and Planetary Physics Supporting Information for Structure-controlled asperity on the generation of large earthquakes

FIGURE 2. A in Taxonomy and nomenclature of the southern Malagasy Kalanchoe peltigera, with reference to K. rosei var. seyrigii (Crassulaceae subfam. Kalanchooideae)

FIGURE 2. A. Flower (insert) and leaves and habit of horticultural material of Kalanchoe daigremontiana; cultivated in South Africa (insert) and in Israel. B. A "shield"-like leaf of K. peltigera bearing bulbils; a clone of the material deposited as the holotype, in cultivation in Japan, and a flower (insert), from the same clone, cultivated in Israel. C. General morphology of K. rosei var. rosei with trilobate leaves; cultivated in South Africa. D. Flowers and leaves of simple-, non-peltate-leafed Kalanchoe material such as this is often attributed to K. rosei var. rosei; cultivated in Israel. Photograph credits: A (insert). Gideon F. Smith; B. Jun Ikeda; C. Maddy Ogden; A, B (insert), D. Ronen Shtein. Elements are not to scale.

FIGURE 1. A. A in Taxonomy and nomenclature of the southern Malagasy Kalanchoe peltigera, with reference to K. rosei var. seyrigii (Crassulaceae subfam. Kalanchooideae)

FIGURE 1. A. A specimen on which the original description of K. rosei var. seyrigii was based, but here is attributed to K. peltigera, Seyrig 819 (P P00374207). B–E. Living material of R. Shtein 795, a clone of the holotype of Kalanchoe peltigera in the collection of one of us (RS), cultivated in Israel: B. Inflorescence. C. Typical "shield"-like leaf shape. D, E. Lobed, more oblong leaves. Photograph credits: all Ronen Shtein, except A. Herb. P.

FIGURE 3 in Taxonomy and nomenclature of the southern Malagasy Kalanchoe peltigera, with reference to K. rosei var. seyrigii (Crassulaceae subfam. Kalanchooideae)

FIGURE 3. Comparison of leaves and flowers of living material historically associated with Kalanchoe rosei, to scale. A. K. ×richaudii. B. Two forms of what has been informally referred to as "K. Rauhii". C. K. rosei var. variifolia. D. Three forms of K. rosei var. seyrigii (D2 illustrates material erroneously referred to as "K. rosei cv. Seyrigi"). E. Material variously referred to K. rosei var. variifolia and K. rosei var. rosei. F. Two forms of simple-, non-peltate-leaved Kalanchoe often attributed to K. rosei var. rosei. G. Clone of the holotype of K. peltigera (R. Shtein 795). Photograph credits: Ronen Shtein.

FIGURE 5 in Taxonomy and nomenclature of the southern Malagasy Kalanchoe peltigera, with reference to K. rosei var. seyrigii (Crassulaceae subfam. Kalanchooideae)

FIGURE 5. Comparison of leaves and flowers (inserts) of selected specimens of Kalanchoe rosei and K. peltigera, all elements to scale. A–B. Two specimens of K. rosei from the Onilahy region: A. P-P00444008 and B. P-P00444018. C–D. Two unusual specimens of K. peltigera from the Tsivory region: C. P-P00444011 and D. P-P00444012. E. Seyrig 819 (P-P00374207), a specimen of K. peltigera. F–G. Two specimens of K. rosei from between Tsivory and Behara: F. P-P00444006 and G. P-P00444003. H. Type of K. bouvieri, an abnormal form of K. rosei. I. Isotype of K. rosei (US00603536). Photographs of material held in the Vascular plants collection, Muséum National d'Histoire Naturelle, Paris (P) (A–H); and United States National Herbarium, Smithsonian Institution (US) (I).

opennotspecifiedMay 2011View details →

FIGURES 8–11 in Phylogenetic relationships of Elateridae inferred from adult morphology, with special reference to the position of Cardiophorinae

FIGURES 8–11. Dorsal view of scutellum of Cardiophorinae (scale bar = 0.5 mm). 8, Esthesopus castaneus; 9 Blaiseus bedeli; 10, Cardiophorus gramineus; 11, Negastrius americanus. Figure 12. Latero-ventral view of mesepimeron and mesepisternum of Cardiophorus fenestratus (LeConte) showing measurement of angle (a) of anterolateral corner of mesepisternum (scale bar = 0.5 mm). MST = mesepisternum; MRN = mesepimeron.

opennotspecifiedMay 2011View details →

FIGURES. 5–6 in Phylogenetic relationships of Elateridae inferred from adult morphology, with special reference to the position of Cardiophorinae

FIGURES. 5–6. Latero-ventral view of hypomeron of Cardiophorinae (scale bar = 1 mm). 5, Cardiophorus gagates Erichson; 6, Cardiophorus propinquus Lanchester. Ant = anterior.