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opencc-by-4.0Dec 2023View details →

FIGURE 5 in Differentiating convergent pathologies in turtle shells using computed tomographic scanning of modern and fossil bone

FIGURE 5. Modern Trachemys scripta plastron and partial carapace elements (UTK 1844) with shell disease. Photograph (A) and orthographic model based on µCT data (B) shown in ventral view. Frames on the photograph and model highlight specific areas of shell disease, shown on the right as both direct µCT data (C, E, G) and heatmapped slices illustrating bone density changes (D, F, H). In the heatmapped cross sections, colors range from purple (lowest density), to orange (medium density), to white (highest density). Patches of shell disease are indicated with purple arrows. Scale bars in A and B equal 5 cm. Scale bars in C, E, and G equal 5 mm.

FIGURE 6. A in Distinguishing between three modern Ellobius species (Rodentia, Mammalia) and identification of fossil Ellobius from Kaldar Cave (Iran) using geometric morphometric analyses of the first lower molar

FIGURE 6. A) First two PCs from the Principal component analysis performed on the size and shape including the reference collection and Kaldar Cave material. B) Boxplot of the total length of Ellobius from the extant reference collections and Kaldar Cave.

FIGURE 4. Ellobius right lower m1. A in Distinguishing between three modern Ellobius species (Rodentia, Mammalia) and identification of fossil Ellobius from Kaldar Cave (Iran) using geometric morphometric analyses of the first lower molar

FIGURE 4. Ellobius right lower m1. A) 14 landmarks: Landmarks on the outermost turning point of buccal (2, 4, 6) and lingual (8, 10, 12, 14) salient angles, and on the innermost turning point of buccal (3, 5) and lingual (9, 11, 13) reentrant angle. B) 60 semi-landmarks on the anterior cap.

FIGURE 2. Ellobius lower m1s in Distinguishing between three modern Ellobius species (Rodentia, Mammalia) and identification of fossil Ellobius from Kaldar Cave (Iran) using geometric morphometric analyses of the first lower molar

FIGURE 2. Ellobius lower m1s (all figured as right ones) from the extant reference collections and Kaldar Cave. A) Ellobius fuscocapillus: A.1-Kaldar Cave, 2014/4/SL5II/E6/125-130, right lower m1, number 157. A.2-Kaldar Cave, 2014/4/SL5/E5/109-111, right lower m1, number 520. A.3-Kaldar Cave, 2014/5/SL7II/E7/170-180, right lower m1, number 104. A.4- Kaldar Cave, 2014/5/SL7II/F6/135-145, right lower m1, number 547.A.5-modern, NHM86101513, Afghanistan, right lower m1. A.6-modern, FM111846, Iran, right lower m1. A.7-modern, NHM86101512, Afghanistan, right lower m1; B) Ellobius lutescens: B.1-Kaldar Cave, 2014/5/SL7II/F6/130-140, right lower m1, number 319. B.2- Kaldar Cave, 2014/4/SL5II/F7/115-118, right lower m1, number 90. B.3- Kaldar Cave, 2014/4/SL5II/F7/115-118, right lower m1, number 91. B.4- Kaldar Cave, 2014/5/SL7II/E7/145-150, right lower m1, number 436. B.5-modern, NMH916416, Turkey, right lower m1. B.6-modern, NMH916414, Turkey, right lower m1. B.7-modern, NMH916412, Turkey, right lower m1; C) Ellobius talpinus: C.1-modern, NHM3421126, Russia, right lower m1. C.2-modern, FM103163, Afghanistan, right lower m1. C.3-modern, AMNH59797, Mongolia, right lower m1. Scale 1 mm.

FIGURE 1. A in Distinguishing between three modern Ellobius species (Rodentia, Mammalia) and identification of fossil Ellobius from Kaldar Cave (Iran) using geometric morphometric analyses of the first lower molar

FIGURE 1. A) Occlusal surface of Ellobius right lower m1: triangle (T); buccal re-entrant angle (BRA); lingual reentrant angle (LRA); anterior cap (AC); posterior lobe (PL); B) Lingual view of left lower m1.

FIGURE 5 in Distinguishing between three modern Ellobius species (Rodentia, Mammalia) and identification of fossil Ellobius from Kaldar Cave (Iran) using geometric morphometric analyses of the first lower molar

FIGURE 5. Principal component analysis on the normalized landmarks and sliding semilandmarks and shape configuration at the extreme ends of the two first PCs.

FIGURE 7 in Distinguishing between three modern Ellobius species (Rodentia, Mammalia) and identification of fossil Ellobius from Kaldar Cave (Iran) using geometric morphometric analyses of the first lower molar

FIGURE 7. Morphological differences between Ellobius fuscocapillus (left) and Ellobius lutescens (right). Arrows depict the displacements between corresponding landmarks in the reference (dots) and Ellobius lutescens as target specimens.

opencc-by-4.0Dec 2023View details →

Elution profiles and protein interaction data accompanying "Ancient eukaryotic protein interactions illuminate modern genetic disorders"

<div>   <table> <tbody> <tr> <td> <h2>DESCRIPTION</h2> </td> <td> <h2>FILENAME</h2> </td> <td> <h2>LOCATION</h2> </td> </tr> <tr> <td> LECA 10K OG set </td> <td> leca_ogs_annotated.xlsx </td> <td> Paper, Table S1 Zenodo </td> </tr> <tr> <td> Summary of biological resources </td> <td> resource_summary.xlsx </td> <td> Paper, Table S2 Zenodo </td> </tr> <tr> <td> LECA interactome (complexes) </td> <td> leca_ppis_fdr10_clustered_annotated.xlsx </td> <td> Paper, Table S3 Zenodo </td> </tr> <tr> <td> CFMS - ref proteomes </td> <td> cfms_ref_proteomes.xlsx </td> <td> Paper, Table S4 Zenodo </td> </tr> <tr> <td> ML - top algorithms </td> <td> tpot_top_algorithms.xlsx </td> <td> Paper, Table S5 Zenodo </td> </tr> <tr> <td> LECA interactome (pairwise) </td> <td> leca_ppis_fdr10_pairwise.csv </td> <td> Zenodo </td> </tr> <tr> <td> UniProt Subcellular Localization IDs </td> <td> uniprot_localization_codes.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> Dollo parsimony - ref proteomes </td> <td> dollo_parsimony_ref_proteomes.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> Dollo parsimony - input trait matrix </td> <td> dollo_parsimony_count_matrix.tsv </td> <td> Zenodo </td> </tr> <tr> <td> CFMS - raw elution profiles </td> <td> amorphea_raw_elution_vectors.csv excavata_raw_elution_vectors.csv tsar_raw_elution_vectors.csv archaeplastida_raw_elution_vectors.csv </td> <td> Zenodo </td> </tr> <tr> <td> CFMS - normalized elution profiles </td> <td> amorphea_norm_elution_vectors.csv excavata_norm_elution_vectors.csv tsar_norm_elution_vectors.csv archaeplastida_norm_elution_vectors.csv </td> <td> Zenodo </td> </tr> <tr> <td> CFMS/APMS - complete feature matrix </td> <td> feature_matrix.csv </td> <td> Zenodo </td> </tr> <tr> <td> ML - top features </td> <td> linearsvc_top_100_features.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> OMIM disease propagation, statistics </td> <td> omim_disease_propagation_stats.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> OMIM disease propagation, top 20 hits per disease </td> <td> omim_disease_propagation_top20hits_per_disease.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> Curated OMIM gene-disease relationships for LECA OGs </td> <td> omim_disease_network.tsv </td> <td> Zenodo </td> </tr> <tr> <td>Curated OMIM gene-disease relationships for human UniProt IDs</td> <td>omim_disease_groups.csv</td> <td>Zenodo</td> </tr> </tbody> </table> </div>

Fig. 7 in Sexually dimorphic ornamentation in modern spinicaudatans and the taxonomic implications for fossil clam shrimps

Fig. 7. Ornamentations on the growth bands in extant spinicaudatans species of Cyzicus Audouin, 1837, Ozestheria Schwentner, Just, and Richter, 2015, and Diestheria longinqua Chen in Zhang et al., 1976. A. Carapace of Ozestheria pilosa (Rogers, Thaimuangphol, Saengphan, and Sanoamuang, 2013), from Thailand (after Rogers et al. 2013: fig. 3A). B. Cyzicus gifuensis (Ishikawa, 1895), from Anhui, China, NIPG Cr.121, male; ornamentation in the ventral part of the carapace (B1) and near the ventral margin of carapace (B2); radial lirae along the lower margin of each growth band (B3). in ornamentations might suggest a close affinity between The carapaces of the family Limnadiidae are thin and hermaphroditic Cyzicus and Aquilonoglypta as suggested by lightly mineralized, which commonly resulted in a reticulate Astrop and Hegna (2015). depressiononthecarapacesurface, suchas Eulimnadiatexana The transition pattern from reticulation to lirae in the Packard, 1871 (Astrop 2014). However, the carapace surfaces ventral part of the carapace in the Ozestheria differs from of most species of Eulimnadia are unornamented (smooth the Cyzicus which has the large undeveloped reticulation. surface pattern). This pattern also occurs in Metalimnadia Australian species of Ozestheria had reticulation, granulated serratus Mattox, 1952, Paralimnadia badia (Wolf, 1911) and ornaments, or a combination of punctae and lirae (Timms some Triassic fossil species of Paleolimnadiidae (Table 1). 2018). The ornamentation pattern of O. pilosa was similar The fossil family Palaeolimnadiopsidae is characterized by to species of Diestheriidae, in which transversely enlarged the recurvature of growth lines to form carinate at the posreticulation overlapped on the lirae ornamentation of each terior-dorsal marginal junction of the carapace. This feature growth band of the carapace (Rogers et al. 2013). The larger has also been observed in living species of Limnadopsis. secondary reticulation was likely originated from the in- The ornamentation documented for Palaeolimnadiopsidae tra-cuticular layer rather than the reticulation from procuti- ranged from reticulation to reticulation-lirae combination. cle (Astrop 2014). The ornamentation pattern in Ozestheria However, the ornamentation possessed by Limnadopsis ocsp. (males, Fig. 1A5), including punctae-reticulation-lirae cidentalis Timms, 2009, is nodular (Astrop 2014). Imnadia combination, the transition from reticulation to lirae, and yeyetta Hertzog, 1935, was reported to exhibit punctae ornathe larger undeveloped reticulation, is in line with that of mentation (Astrop 2014). Nevertheless, this pattern was not fossil species Triglypta yabraiensis Wang, 2014 (Wang 2014: mentioned in the original descriptions of the fossil families pl. 2: 2). The close morphological resemblance of ornamen- Paleolimnadiidae, Palaeolimnadiopsidae or Perilimnadiidae. tations and carapace shape suggests that Ozestheria might The phenotypic differentiation of ornamentation pattern is be closely related to Triglypta or Tianzhuestheria. a model to investigate morpho-functional adaptation to some

Fig. 6 in Sexually dimorphic ornamentation in modern spinicaudatans and the taxonomic implications for fossil clam shrimps

Fig. 6. Carapaces and ornamentations of representatives of the extant spinicaudatan family Leptestheriidae. A. Leptestheria kawachiensis Uéno, 1927, from Hubei, China, NIGP Cr. 101, male, lateral view; left valve, oval outline (A1); growth bands in the upper part of carapace with wide radial fringes pattern (A2). B. Eoleptestheria ticinensis (Balsamo-Crivelli, 1859), from Jiangsu, China, NIGP Cr. 61, male, lateral view; right valve, oval outline (B1); growth bands in the ventral part of carapace with shallow fringes pattern, never developing reticulation or punctae between fringes (B2); details of ventral growth bands with shallow fringes pattern separated with smooth surface (B3, B4).

Fig. 4 in Sexually dimorphic ornamentation in modern spinicaudatans and the taxonomic implications for fossil clam shrimps

Fig. 4. Ornamentations on the growth bands in the extant spinicaudatan branchiopod Eulimnadia sp. and the extant laevicaudatan branchiopod Lynceus sp. A, B. Eulimnadia sp., from Jiangxi, China. A. NIGP Cr. 161, male, carapace in lateral view. B. NIGP Cr. 162, female, unornamented area near the ventral margin. C, D. Lynceus sp., from Heilongjiang, China. C. NIGP Cr. 173, male, carapace in lateral view. D. NIGP Cr. 174, female, isogonal reticulate ornamentation in the valve.

Fig. 3 in Sexually dimorphic ornamentation in modern spinicaudatans and the taxonomic implications for fossil clam shrimps

Fig. 3. Ornamentations on the growth bands of carapace of the extant spinicaudatan branchiopod Eocyzicus orientalis Daday, 1913, from Xinjiang, China. A. NIGP Cr. 1, male, ornamentation in the upper to middle parts of the carapace (A1), reticulate ornaments in the ventral part of the carapace (A2), dense pilosity on the growth lines near the edge of the carapace (A3). B. NIGP Cr. 2, female, ornamentation in the upper to middle parts of the carapace (B1), rows of nodular ornaments in the ventral part of the carapace (B2), stout setae on the growth lines near the edge of the carapace (B3).

Fig. 2 in Sexually dimorphic ornamentation in modern spinicaudatans and the taxonomic implications for fossil clam shrimps

Fig. 2. Ornamentation on the growth bands of carapaces of the extant spinicaudatan branchiopod Cyzicus sp., from Jilin, China. A. NIGP Cr. 141, male, ornamentation in the larval valve (A1), in the middle part of the carapace (A2), large reticulation and the radial lirae along the lower margin of the growth band (A3). B. NIGP Cr. 142, female, ornamentation in the larval valve (B1) and in the middle part of the carapace (B2), weakly ornamented area near the ventral margin (B3).

opencc-by-4.0Jun 2024View details →

pXRF analysis of medieval and modern ceramics from Erbray (France)

This dataset contains analyses of 60 ceramic samples from Les Landelles (Erbray, Loire-Atlantique, France). The chemical composition of the samples was obtained by portable X-ray fluorescence spectrometry (pXRF). Method The outer surfaces of all the samples were mechanically removed prior to analysis. The samples were heated to 950°C for one hour after 24h drying at 50°C, weighted for LOI calculation and ground in a tungsten carbide mortar. Measurements were made on pelletized powders. Measurements were carried out on powders placed in sample holders, through a Mylar film. A Vanta VCR C-series portable X-ray fluorescence spectrometer (Olympus) was used on a laboratory bench with a beam diameter of 10 mm. The spectrometer is equipped with a 4W, 40kV max, 200 µA max X-ray tube (Rh anode) and a silicon drift detector (SDD). For each analysis, the instrument was operated alternately at low energy (10 keV) for 90 s to quantify light elements and at high energy (40 keV) for 90 s to quantify heavy elements. No vacuum or helium flow was used. Analytical repeatability, accuracy and precision were checked using an in-house obsidian standard. Using the GeoChem internal calibration, 15 elements were quantified: Al, Si, K, Ca, Ti, Cr, Mn, Fe, Ni, Cu, Zn, Rb, Sr, Zr, Pb. The files beamspectra.csv and chemistry.csv are the export files as produced by the instrument. The file erbray.csv contains all chemical compositions (only chemical elements for which measurements are considered reliable are retained), with the following columns: <ul> <li>sample: sample reference.</li> <li>laboratory: analysis laboratory.</li> <li>date: date of the analysis.</li> <li>group: technical group.</li> <li>material: type of material.</li> <li>stratigraphy: stratigraphic unit.</li> <li>comments: extra information.</li> <li>LOI: loss on ignition (percent).</li> <li>Al, Si, K, Ca, Ti, Cr, Fe, Rb, Sr, Zr, Pb: amounts and corresponding uncertainties (ppm).</li> </ul>

opencc-by-4.0Dec 2019View details →

Рис. 3. Схема миграций виΑов рыб, участвующих в современной Αинамике ихтиофауны на территории НТТ: 1 — разΛивы; 2 — намывы. Черным цветом обозначены направΛения миграций из реки Туманной; красным — из оз. Хасан и РазΛивов; синим — с мест зимовки в реках южного Приморья; зеΛеным — сезонные миграции из южных морей Fig. 3. Scheme of migration of fish species involved in the modern dynamics of ichthyofauna on the territory of LRT: 1 — spills; 2 — alluvial. Black color indicates the direction of migration from the Tumannaya river; red — from lake Khasan and spills; blue — from wintering places in the rivers of southern Primorye; green — seasonal migration from the south seas in Transboundary Migration And The Local Constraints In The Dynamic Of Fish Fauna In The Lower Reaches Of Tumannaya River

Рис. 3. Схема миграций виΑов рыб, участвующих в современной Αинамике ихтиофауны на территории НТТ: 1 — разΛивы; 2 — намывы. Черным цветом обозначены направΛения миграций из реки Туманной; красным — из оз. Хасан и РазΛивов; синим — с мест зимовки в реках южного Приморья; зеΛеным — сезонные миграции из южных морей Fig. 3. Scheme of migration of fish species involved in the modern dynamics of ichthyofauna on the territory of LRT: 1 — spills; 2 — alluvial. Black color indicates the direction of migration from the Tumannaya river; red — from lake Khasan and spills; blue — from wintering places in the rivers of southern Primorye; green — seasonal migration from the south seas

FIGURE 7 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India

FIGURE 7. Feeding strategies and progressive growth of the Dotilla pellet structures. Note four types of feeding modes: sector (of a circle) feeding mode covering growth (top to bottom) of the pellet structures arranged in four columns (1-4) corresponding to four different types of pellet designs (homogeneous pellet spread, radial, concentric and concentric-radial); radially diverging feeding mode covering growth (top to bottom) of the radial and asteroid pellet designs (column 5); concentric feeding mode covering growth (top to bottom) of the concentric pellet designs (column 6) and combined concentric-radial feeding mode covering growth (top to bottom) of the concentric-radial pellet design (column 7). Note development of different designs under sector (of a circle) feeding mode within feeding sectors having similar shape and size (column 1- 4 top structures). Also note a pellet design may originate in different feeding modes, but with subtle differences. The lower half of the figure incorporates schematic representation of the growth stages (I - Initial, M - Middle, F - Final from top to bottom) of all the above pellet designs with time and progressive feeding activity under different feeding modes (columns 1-7 are extended from upper to lower half of the figure to maintain analogy). Also note for each schematic structure (not to scale) presented, there is a physical (natural) analogue recorded from the field. Also visualize the growth of structural complexities, acquisition of described barrier elements and SI index along each column from top to bottom in both the natural and schematic presentations.

FIGURE 8. A in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India

FIGURE 8. A: Ex situ preservation (aided by wind action) of Dotilla pellets as pellet-filled burrow tubes in the supratidal flat during low tide situation. B: Ex situ preservation of Dotilla pellets (aided by wind action) in ripple troughs during low tide situation. C: Schematic profile section of the studied beach showing positions of the Dotilla pellet spread and burrow zone, spread of Ocypode burrows, mutual dispositions of different geomorphic units (dune, supratidal, upper - middle intertidal flats) relative to land - sea positions and High and Low Tide Levels (HTL and LTL). Note gradual spreading of the Dotilla pellet and burrow zone towards sea with gradual lowering of substrate water levels (WLs) during tidal recession of sea. D-E: Possible stratigraphic development of the coastal sedimentary units (1-3) and contained burrow zones and other associated features in transgressive (E) and regressive (D) situations. Note the possible position of preserved Dotilla pellets and burrows between Unit 1 and 2 under transgressiveregressive sea conditions. Features are schematic and not to scale.

FIGURE 4 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India

FIGURE 4. Concentric - radial pellet design (Figures 3 A, C, E, G, I, K, M, O, Q, S, U and W) produced by the crab Dotilla in the upper intertidal flat of the Bakkhali beach, Bay of Bengal coast, Eastern India. Figures 3 B, D, F, H, J, L, N, P, R, T, V and Xl represent the corresponding line tracings made for measurement of Attack Index (AI) and Safety Index (SI). Figures Q and W represent conjugate concentric - radial structures made by several individuals and possesses shared concentric rows of pellets (Scrp) and very high Combined Safety index (CSI) of 97.23% and 98.33% respectively. Note the majority of the structures are made by young and adults and rarely by juveniles (example Figure 4 E, G). Also note that pellet design at the earlier stage of development has lower safety index (SI) than those in the advanced or final stage of development (SI 70.57% for Figure C vs. 100% for Figure 4 O and S). Note that structures with closed burrow opening have SI value 100% (Figure 4 G and M). Compare size of the feeding territories between A, M, O (larger for the adults) vs E (smaller for the juvenile). Scale bar equals 1 cm.

FIGURE 6 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India

FIGURE 6. Other pellet structures produced by the crab Dotilla on the upper intertidal flat of the Bakkhali beach, Bay of Bengal coast of Eastern India. (A) Petaloid pellet design produced by petal shaped radial rows of pellets and conjugate petals formed around burrow opening. (B) The line tracing corresponding to A shows SI value 100% as the burrow mouth is closed. (C) Leaf-shaped pellet design and (D) its corresponding line tracing shows very poor SI value (13.89%). (E) Asteroid pellet design contains several radiating runways that are well enclosed within the pellet spread areas and (F) its corresponding line tracing shows 100% SI value. (G, J and K) Different stages of formation of pellet mat design in pellet – microzone 1 wherein entire surface is covered by dense population of pellets leaving no space for the predators to sneak into burrow opening (SI = 100%). Note high population density and small size of the pellet designs. (H) Mossy pellet design formed by the crab community. Several burrow openings and corresponding runways are partially to fully covered by pellet spread zones. (I) Line tracing shows variable SI values of the individual structures (marked here by red, yellow and green circles having SI values <70%, 70% - 90% and> 90% respectively) averaged at 85% for the community structure. Arrows indicate possible entry routes of predators into the burrows. (L and M) Concentric radial and concentric pellet structures formed on rippled surface. (N) At times, pellets are formed selectively along the ripple troughs. (O) Beach profile showing extends of lower, middle and upper intertidal flats, besides mudground, supratidal flat and coastal dunes. Note smaller size of the structures (G, H, J, K) due to increased population density and predation pressure.

FIGURE 2 in Ethological interpretation of making the pellet designs by the bubbler crab Dotilla on the modern intertidal beaches: A study from the Bay of Bengal coast, Eastern India

FIGURE 2. Radial pellet structures (A, C, E, G, I and K) produced by the crab Dotilla in the upper intertidal beach of Bakkhali, Eastern India. Corresponding line tracings (B, D, F, H, J and L) are made to calculate Safety Index (SI) and Attack Index (AI). Structures represented by figures I and K suggest early stage of development of radial pellet design and possess lower Safety Index (SI = 61.53% and 46.41%, respectively) compared to other structures (A, C, E and G) that represent later stage of development of radial design and possess very high Safety Index (SI ranging from 100% to 94.74%). Figure GLeft represents a juvenile structure and the rest are produced by young and adult Dotilla. Note larger size of feeding areas made by adults (A, E, K) compared to that of juvenile (GLeft). A represents a more advanced feeding stage (over larger area) than I (over smaller area). Scale bar equals 1 cm.