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Fig. 5 in Reclustering the cluster flies (Diptera: Oestroidea, Polleniidae)

Fig. 5. Morinia tsitsikamma sp.n. (A) Right wing in dorsal view, male paratype 05385; (B) Notopleuron in lateral view, holotype 05392 (scale 200 μm); (C) Left metathoracic spiracle, male paratype 05403, male (scale 200 μm); (D) Abdomen in dorsal view, holotype 05392; (E) Epandrial complex in lateral view, male paratype 05390; (F) Epandrial complex in caudal view, male paratype 05390. c, cercus. s, surstylus. [Colour figure can be viewed at wileyonlinelibrary.com].

Fig. 3 in Reclustering the cluster flies (Diptera: Oestroidea, Polleniidae)

Fig. 3. Total evidence phylogeny (CAD + MCS + MAC + morphology) of Oestroidea as inferred from Bayesian analysis using MRBAYES 2.6. Numbers above branches indicate posterior probability values. Asterisks indicate taxa for which molecular data are not available. [Colour figure can be viewed at wileyonlinelibrary.com].

Fig. 4 in Reclustering the cluster flies (Diptera: Oestroidea, Polleniidae)

Fig. 4. Morinia tsitsikamma sp.n. (A) Habitus in lateral view, holotype 05392, male; (B) head in lateral view, holotype 05392, male; (C) head in frontolateral view, male paratype 05403, head; (D) head in frontal view, male paratype 05403; (E) lunule in frontal view, male paratype 05383 (scale 100 μm); (F) head in frontal view, female paratype 05404; (G) lunule in frontal view, female paratype 0540 (scale 100 μm). [Colour figure can be viewed at wileyonlinelibrary.com].

Fig. 2 in Reclustering the cluster flies (Diptera: Oestroidea, Polleniidae)

Fig. 2. Female habitus of Morinia sp. (undescribed species of the carinata-group) (Polleniidae), South Africa, Western Cape Province, West Coast National Park. [Colour figure can be viewed at wileyonlinelibrary.com].

Fig. 1 in Reclustering the cluster flies (Diptera: Oestroidea, Polleniidae)

Fig. 1. Diversity of Oestroidea. (A) Mesembrinella randa (Walker) (Mesembrinellidae), Ecuador: Yasuni National Park; (B) Sarcophaga sp. (Sarcophagidae), Madagascar: Ranomafana National Park; (C) Cuterebra austeni Sabrosky (Oestridae, Cuterebrinae), U.S.A.: New Mexico, Gila National Forest; (D) Adejeania sp. (Tachinidae), Peru: Wayqecha; (E) Chaetodexia sp. (Tachinidae), Madagascar: Andasibe; (F) Pollenia sp. (Polleniidae), Canada: Wellington County, Fergus; (G) Morinia doronici (Scopoli) (Polleniidae), Europe: Finland, Jyväskylä; (H) Cynomya cadaverina (Robineau-Desvoidy) (Calliphoridae, Calliphorinae), Canada: Ontario, Dunks Bay; (I) Chrysomya putoria Wiedemann (Calliphoridae, Chrysomyinae), Tanzania: Magombera; (J) Bengalia sp. (Calliphoridae, Bengaliinae), Tanzania: Iringa; (K) Stomorhina sp. (Rhiniidae), Mauritius; (L) Silbomyia sp. (Calliphoridae, Ameniinae), Vietman: Cat Ba; (M) Bixinia winkleri Cerretti, Lo Giudice & Pape (Rhinophoridae), Australia, Queensland. Photographs by: Steve Marshall (A–F, H–K); Raimo Peltonen (G), PC (M). [Colour figure can be viewed at wileyonlinelibrary.com].

opencc-by-4.0Jul 2019View details →

Data for Morphological analysis of chiral rod clusters from a coarse-grained single-site chiral potential

Data relating to the paper 'Morphological analysis of chiral rod clusters from a coarse-grained single-site chiral potential'. See the README for details.

opencc-by-4.0Nov 2019View details →

Raw and processed data for publication "Quantitative microscopy reveals dynamics and fate of clustered IRE1alpha"

This dataset contains all raw and processed data for our PNAS paper titled "Quantitative microscopy reveals dynamics and fate of clustered IRE1alpha". Using the associated analysis code (10.5281/zenodo.3544482), all figures in the paper can be reproduced from the data in this upload. Abstract of the paper is included below: "The endoplasmic reticulum (ER) membrane-resident stress sensor IRE1 governs the most evolutionarily conserved branch of the unfolded protein response. Upon sensing an accumulation of unfolded proteins in the ER lumen, IRE1 activates its cytoplasmic kinase and ribonuclease (RNase) domains to transduce the signal. IRE1 activity correlates with its assembly into large clusters, yet the biophysical characteristics of IRE1 clusters remain poorly characterized. We combined super-resolution microscopy, single-particle tracking, fluorescence recovery and photoconversion to examine IRE1 clustering quantitatively in living human and mouse cells. Our results revealed that (1) by contrast to qualitative impressions gleaned from microscopic images, IRE1 clusters comprise only a small fraction (~5%) of the total IRE1 in the cell. (2) IRE1 clusters have complex topologies that display features of higher-order organization. (3) IRE1 clusters contain a diffusionally constrained core, indicating that they are not phase-separated liquid condensates.  (4) IRE1 molecules in clusters remain diffusionally accessible to the free pool of IRE1 molecules in the general ER network. (5) When IRE1 clusters disappear at later timepoints of ER stress as IRE1 signaling attenuates, their constituent molecules are released back into the ER network and not degraded. (6) IRE1 cluster assembly and disassembly are mechanistically distinct. (7) IRE1 clusters’ mobility is nearly independent of cluster size. Taken together, these insights define the clusters as dynamic assemblies with unique properties. The analysis tools developed for this study will be widely applicable to investigations of clustering behaviors in other signaling proteins."

opencc-by-4.0Aug 2024View details →

Properties of intermediate- to high-mass stars in the young cluster M17 Characterizing the (pre-)Zero Age Main Sequence

Data and extra figures of the paper "Properties of intermediate- to high-mass stars in the young cluster M17 -- Characterizing the (pre-)Zero Age Main Sequence" by Frank Backs. Published in Astronomy and Astrophysics. The observed data and the fitted models are included. The fitting algorithm Kiwi-GA is available on Github: https://github.com/sarahbrands/Kiwi-GA Additional figures are available. These figures give an overview of the best fit models for each line like Fig. 1 in the paper.

opencc-by-4.0Aug 2024View details →

Clustering metrics over multiple configuration of the BERTopic pipeline for two datasets.

Open the record for dataset details and reuse information.

opennotspecifiedJan 2022View details →

Fig. 3 in From clustering to overdispersion: a north to south gradient in the patterns of phylogenetic structure in North American hummingbird assemblages

Fig. 3 Boxplots of MPD, MNTD, pMPD, and pMNTD between breeding and winter seasons by biogeographic region

opennotspecifiedJan 2022View details →

Fig. 2 in From clustering to overdispersion: a north to south gradient in the patterns of phylogenetic structure in North American hummingbird assemblages

Fig. 2 Geographic patterns of phylogenetic and phenotypic MPDs and MNTDs across North America according to seasons considered (breeding and winter)

opennotspecifiedJan 2022View details →

Fig. 1 in From clustering to overdispersion: a north to south gradient in the patterns of phylogenetic structure in North American hummingbird assemblages

Fig. 1 Phylogenetic heatmap of the pruned phylogenetic tree (see Methods) based on McGuire et al. (2014) for North American hummingbird species and the matrix of the PC from phylogenetic PCA scores. Colors indicate standard deviation (SD) values for each PC axis by species

opennotspecifiedJan 2017View details →

FIGURE 22. Syagrus deflexa. A. Clustering habit. B. Inflorescence. C. Solitary habit. D. Flowers. First 5 in A revision of the genus Syagrus (Arecaceae)

FIGURE 22. Syagrus deflexa. A. Clustering habit. B. Inflorescence. C. Solitary habit. D. Flowers. First 5 on left are staminate followed by a pistil and an unopen pistillate flower. Flowers on the right are pistillate flower or pistillate flower parts terminating at the bottom with another pistil. E. Whitish waxy bloom on the underside of the leaflets. F. Infructescence spirally branched. G. Leaf with characteristic deflexed leaflets. H. Close of immature fruit. All grids are in centimeters.

opennotspecifiedJan 2017View details →

FIGURE 11. Syagrus cardenasii. A. Cultivated specimen with Luiz Moreno near Santa Cruz, Bolivia. B. Clustering habit. C in A revision of the genus Syagrus (Arecaceae)

FIGURE 11. Syagrus cardenasii. A. Cultivated specimen with Luiz Moreno near Santa Cruz, Bolivia. B. Clustering habit. C. Close of leaf sheath fibers. D. Canopy of a multistemmed specimen. E. Infructescence. F. Inflorescence with open staminate flowers. G. Inflorescence with receptive pistillate flowers. H. Infructescence with hand for scale.

opencc-by-4.0Aug 2024View details →

Transcription factor clusters in fruit fly embryos

These files represent the dataset used in generating plots shown in <a href="https://arxiv.org/abs/2403.02943">[2403.02943] Transcription factor clusters as information transfer agents (arxiv.org)</a> The MATLAB programs to generate the plots using this data can be found in: https://github.com/ancientman/clusters-plots Please refer to the instructions there.

opencc-by-4.0Sep 2024View details →

Bacillus subtilis prophages_clustered to vOTUs

This dataset comprises genomic sequences of predicted prophage elements from Bacillus subtilis genomes, organized into separate FASTA files based on clustering results. A total of 64 FASTA files are provided. Within each file, individual prophage sequences are listed, each preceded by a header in the following format: >AP011541.2_Phage_7_Pos_3240205-3266407. This format denotes the host genome ID, phage identifier, and the prophage coordinates within the host genome. Each FASTA file is uniquely numbered to correspond with a viral Operational Taxonomic Unit (vOTU), representing the prophage group to which the sequences belong. The prophage elements were sourced from both complete B. subtilis genome sequences available in NCBI's database (191 genomes; last accessed March 2023) and from 40 local soil microscale isolates (PS strains; PRJNA437002). Prophage coordinates within the bacterial genomes were identified using the PHASTER web tool. Functional categories assigned by PHASTER (complete, questionable, incomplete) were disregarded, and all predicted prophage elements were included. These prophage elements were then clustered using the vContact2 tool. Briefly, prophage genes were predicted using Prodigal, translated into proteins, and subjected to reference-free phylogenetic clustering via vContact2. This tool constructs a network based on the number of shared proteins between phages. The ClusterOne algorithm was then applied to this network to infer groups of related phages, which were used to define vOTUs for further analysis. In addition to the vOTU-based clusters, two artificial clusters were created: Outliers and Singletons. Outliers share some proteins with different vOTUs but fall below the 20% similarity threshold, while Singletons represent prophage elements with no similarity to other clusters. Dataset is described in publication: doi: https://doi.org/10.1101/2024.07.03.601884

FIGURE 1 in Pinanga gruezoi (Arecaceae), a new slender clustering palm from the Philippines with notes on an amended description of P. samarana

FIGURE 1. Pinanga gruezoi Adorador & Fernando. Clustering habit showing variations in density of stems and length of petiole and rachis (A‒C). Leaf disposition and different leaflet costulation: erect (D) or slightly arching with few multi-costulate leaflets (E) or with a number of typically 2-costulate leaflets (F). Infructescence architecture showing variations in rachillae number (G‒I). Localities: Mt. Huraw, San Jose de Buan, Samar (A,D,G = the holotype Adorador 004), Barangay Vigan, Gen.Macarthur, Eastern Samar (B = Adorador 092), Barangay Tenani, Paranas, Samar (C,F,I = from Adorador 053), Sitio Arizona, Barangay Cansolabao, Hinabangan, Samar (E,H = Adorador 008). Scale bar: A = 30 cm, B = 1 m, C = 50 cm, D & E = 15 cm, F = 20 cm, G & H = 6 cm, I = 2 cm. Photos A‒I (Jiro T. Adorador).

FIGURE 2 in Pinanga gruezoi (Arecaceae), a new slender clustering palm from the Philippines with notes on an amended description of P. samarana

FIGURE 2. Pinanga gruezoi Adorador & Fernando. Clustering habit (A), stem with dried infructescence axes (B), basal portion of leaf (adaxial side) including leaf sheath and petiole (C), distal portion of leaf, abaxial side (D), infructescence (E), fruit (F), longitudinal section of fruit showing ruminated endosperm (G), and staminate flower with two petals removed showing some stamens (H). Scale bar: B‒E = 8 cm, F‒G 2 cm, H = 4 mm. All drawn from the holotype (J.T. Adorador 004). Drawn by C.A.T. Rodelas.

FIGURE 4 in Pinanga gruezoi (Arecaceae), a new slender clustering palm from the Philippines with notes on an amended description of P. samarana

FIGURE 4. Pinanga samarana Beccari from Samar Island. Leaflet variations: linear 1-costulate (A), subfalcate 2-costulate (B), and 3- costulate (C). Infructescence and rachillae architecture: drooping (D) or reflexed (E). Fruit arrangement along rachillae and fruit forms: the typical distichously-arranged ovoid-ellipsoid (F) or obovoid fruits (G), or distal portions of rachillae turning spiral with short-ovoid (H) or globose (I) fruits. Localities: Barangay Tenani, Paranas, Samar (A,E,G = from Adorador 003), Sitio Arizona, Barangay Cansolabao, Hinabangan, Samar (D,F = Adorador 025, I = Adorador 018 & Rambacod), Barangay San Isidro, Paranas, Samar (H = Adorador 027). Scale bar: A = 30 cm, B = 40 cm, C = 60 cm, D & E = 15 cm, F = 10 cm, G‒I = 2 cm. Photos A‒I (Jiro T. Adorador).

FIGURE 5 in Pinanga gruezoi (Arecaceae), a new slender clustering palm from the Philippines with notes on an amended description of P. samarana

FIGURE 5. The distribution map of Pinanga samarana Beccari and closely related species based on herbarium records. The gray-shaded area approximates the c. 150 meters below sea level bathymetry line which shows several Pleistocene Aggregated Island Complexes (PAIC) (Heaney 1986).