Find research datasets worth reusing

opencc-by-4.0Mar 2020View details →

Fig. 8 in Reproductive success of Trypoxylon (Trypargilum) lactitarse (Hymenoptera: Crabronidae) in a fragmented landscape

Fig. 8. Results of the Linear Mixed Model (LMM) between the intergular length of each individual and fragment size category. Fragment size was foUnd to have no inflUence on the size of hatched wasps (z = -0.741, p = 0.982).

opencc-by-4.0Dec 2017View details →

Рис. 12. Характер фрагментации и повреЖдений створок спиЗулы сахалинской Spisula sachalinensis иЗ раскопа 1. Fig. 12. Fragmentation and preservation patterns of valves of Spisula sachalinensis from excavation 1. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy

Рис. 12. Характер фрагментации и повреЖдений створок спиЗулы сахалинской Spisula sachalinensis иЗ раскопа 1. Fig. 12. Fragmentation and preservation patterns of valves of Spisula sachalinensis from excavation 1.

opencc-by-4.0Dec 2017View details →

Рис. 11. Характер фрагментации створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 11. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy

Рис. 11. Характер фрагментации створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 11. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1.

opencc-by-4.0Dec 2017View details →

Рис. 10. Характер повреЖдений створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 10. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy

Рис. 10. Характер повреЖдений створок приморского гребешка (Mizuhopecten yessoensis) иЗ раскопа 1. Fig. 10. Fragmentation patterns of valves of the Japanese scallop (Mizuhopecten yessoensis) from excavation 1.

opencc-by-4.0Dec 2024View details →

Detection of detached ice-fragments at polar scarps of Mars

This dataset includes the detections of the detached ice-fragments from 19 polar steep scarps of Mars. The results were detected by a deep learning model, and were saved in shapefile form.

opencc-by-4.0Dec 2020View details →

6MSM_CFTR_MD_EQUILIBRATED_MISSING_R_DOMAIN_FRAGMENT_MODELLED

A protein structure based on PDB ID 6MSM with the unidentified fragment filled in based on results from molecular dynamics investigations and comparisons with alphafold. In addition to the molecular dynamics workflow used to simulate it.

opencc-by-4.0Sep 2021View details →

Research data for "Cluster Fragments in Amorphous Phosphorus and their Evolution under Pressure"

This dataset supports the paper: "Cluster Fragments in Amorphous Phosphorus and their Evolution under Pressure". The paper is online here: https://doi.org/10.1002/adma.202107515.  The following .xyz and .zip files are provided: <ul> <li>"LDA_structure_final.xyz": the atomic structure of the LDA model generated in this work.</li> <li>"slow_melt_quench.zip": the trajectory of the slow melt-quench process in (extended) XYZ format. </li> <li>"compress_decompress.zip": the trajectory of the ambient-pressure compression and the subsequent decompression processes in (extended) XYZ format. </li> <li>"Structure_factor.zip": atomic structures in (extended) XYZ format at different pressures (used to calculate the structure factors). </li> </ul>

opencc-by-4.0Apr 2022View details →

ProtNAff: Protein-bound Nucleic Acid filters and fragment libraries

This archive contains data obtained by running the ProtNAff pipeline (<a href="https://github.com/isaureCdB/ProtNAff">https://github.com/isaureCdB/ProtNAff</a>) and used to perform the analyses described in the original ProtNAff paper. The input list of PDB IDs was obtained in October 2021 by searching all PDB structures that contain protein chains and RNA chains but no DNA, and where the resolution is less than 3 A or where the method is NMR. The ribosomes are removed from this database due to their size. The files provided are: - structures.json : the database containing metadata and parsing data for all the protein-RNA structures from the input list - fragments_clust.json : the list and description of all the trinucleotide fragments extracted from those structures - trinucl_clust1A_allatom: the all-atom coordinates of the trinucleotide fragment library , i.e. the centers of 1A clusters such that each initial fragment has a RMSD of less than 1A from at least one of those centers. - trinucl_clust1A_ATTRACT: the coordinates of the trinucleotide fragment library , but reduced into ATTRACT coarse-grained representation (Setny and Zacharias, NAR 2011).

opencc-zeroApr 2022View details →

Virus classification for viral genomic fragments using PhaGCN2

Viruses are the most ubiquitous and diverse entities in the biome. Due to the rapid growth of newly identified viruses, there is an urgent need for accurate and comprehensive virus classification, particularly for novel viruses. Here, we present PhaGCN2, which can rapidly classify the taxonomy of viral sequences at family level and supports the visualization of the associations of all families. We evaluate the performance of PhaGCN2 and compare it with the state-of-the-art virus classification tools, such as vConTACT2, CAT, and VPF-Class, using the widely accepted metrics. The results show that PhaGCN2 largely improves the precision and recall of virus classification, increases the number of classifiable virus sequences in the Global Ocean Virome dataset (v2.0) by 4 times, and classifies more than 90% of the Gut Phage Database. PhaGCN2 makes it possible to conduct high-throughput and automatic expansion of the database of the International Committee on Taxonomy of Viruses.

opencc-zeroMay 2022View details →

Stable species and interactions in plant-pollinator networks deviate from core position in fragmented habitats

Species and their interactions are more dynamic over time and space in fragmented habitats than in continuous habitats. In fragmented habitats, the low nestedness of mutualistic networks may be related to the position change of stable (high persistence over time/space) species and interactions in the networks. Previous studies have shown that stable species and interactions tend to be in the core position of mutualistic networks. However, in fragmented habitats, it remains unknown whether stable species or interactions still tend to be in the core position. To address this gap, here we evaluated the correlation between the position of proximity to the network core and the temporal/spatial stability of species and interactions, using the observation of 42 plant-pollinator networks conducted in a fragmented island landscape over 3 years. We showed that temporally/spatially stable species and interactions deviated from the network core to varying degrees. Temporally stable plants were most likely to deviate from the network core, followed by pollinators and interactions, while only spatially stable pollinators tend to deviate from the network core. When unstable species (present in few time/space points, typically specialists) and interactions occupy the network core, they cannot interact with most species in the network as generalists do, resulting in the decrease of network nestedness. Therefore, from the perspective of position and stability, stable species and interactions deviate from the network core in fragmented habitats, which is an important reason for the decrease of nestedness in mutualistic networks. Our study suggests that protecting plants that occupy the core in large plant-pollinator networks is essential for maintaining the network persistence in fragmented habitats.

opencc-by-4.0Jul 2021View details →

Multi-taxa environmental DNA inventories reveal distinct taxonomic and functional diversity in urban tropical forest fragments

Urban expansion and associated habitat transformation drives shifts in biodiversity, with declines in taxonomic and functional diversity. Forests fragments within urban landscapes offer a number of ecosystem services, and help to maintain biodiversity and ecosystem functions. Here, we focus on a tropical forest environment, and on the soil biota. Using eDNA metabarcoding, we compare forest fragments within the city of Cayenne, French Guiana, with a neighbouring continuous undisturbed forest. We wished to determine if urban forest fragments conserve high levels of alpha and beta diversity as well as similar functional composition for plants, soil animals, fungi and bacteria. We found that alpha diversity is similar across habitats for plants and fungi, lower in urban forests for metazoans and higher for bacteria. We also found that urban forests communities differ from undisturbed forests in their taxonomic composition, with urban forests exhibiting greater turnover between fragments potentially caused by ecological drift and limited dispersal. However, their functional composition exhibited limited differences, with an enrichment of palms, arbuscular mycorrhizal fungi and bacteria and a depletion of climber plants and termites. Thus, although urban forest fragments do shelter soil biodiversity that differs from native forests, the losses of soil functions may be relatively limited. This study demonstrates the strong potential of a multi-taxa eDNA approach for rapid inventories across taxonomic kingdoms, in particular for cryptic soil diversity. It also demonstrates the key role of urban forest fragments in conserving biodiversity and ecosystem function, and points to a need for more systematic monitoring of these areas in urban management plans. For each of the 16 samples per plot, 15 g of soil was used for eDNA analyses. Extracellular DNA was extracted as described previously (Zinger et al., 2016; 2019), where each soil sample is added to 15ml of saturated phosphate buffer (Na2HPO4; 0.12m; pH ≈8) in 50ml Falcon tubes. This is placed in an agitator for 15 minutes, before a 2ml aliquot of the soil/phosphate buffer mixture is pipetted into an Eppendorf tube and centrifuged for five minutes at 13000 rcf. 500μL of the resulting supernatant is then recovered and used for the next extraction steps that are carried out with a commercial kit for soil DNA (NucleoSpin® Soil; Macherey-Nagel, Düren, Germany), skipping the lysis step and following manufacturer’s instructions. The DNA extract was recovered in 100 μL and diluted 10 times before being used as PCR template.  For each plot one DNA extraction negative control was performed adding up 17 extractions per plot. PCR amplifications were then conducted for four DNA molecular markers, with primers targeting either Viridiplantae (subsequently referred to as plants), Eukaryotes, Fungi or Bacteria (Table 1). For each marker, PCR amplification of samples occurred across 12 plates. Each PCR reaction was performed in a total volume of 20 μl and comprised 10 μl of AmpliTaq Gold Master Mix (Life Technologies, Carlsbad, CA, USA), 5.84 μl of Nuclease-Free Ambion Water (Thermo Fisher Scientific, Massachusetts, USA), 0.25 μM of each primer, 3.2 μg of BSA (Roche Diagnostic, Basel, Switzerland), and 2 μl of DNA template that was before 10-fold diluted to reduce the amounts of PCR inhibitors. Thermocycling conditions for each primer pair are indicated in Table 1.  A negative extraction control per site and a negative PCR control per PCR plate were amplified and sequenced in parallel with the regular samples. Positive controls were also included and consisted of mock communities of plants and fungi DNA (no mock communities were built for bacteria or eukaryotes here), which were used to guide choices in our data curation process. Two PCR replicates were performed for each sample and control. Amplification was conducted using a double indexing system strategy (Binladen et al. 2007) using a system of 32 by 36 octamers with at least five differences between them located at the 5’ end of each primer (Coissac 2012). In doing so, each PCR product had a unique combination of tags for both forward and reverse primers, allowing for the retrieval of sequence data for each sample. Ten wells per PCR plate were left empty to act as sequencing controls (non-used tag combinations) for downstream data curation (see below). PCR products were pooled and sequencing libraries were constructed using the Illumina TruSeq NanoPCRFree kit following the supplier’s instructions (Illumina Inc., San Diego, California, USA), except that the ligation product was not PCR amplified to limit tag-jump biases (Taberlet et al 2018). The libraries were then sequenced on different Illumina platforms (San Diego, CA, USA) depending on the marker considered (Table S1), using the paired-end technology. Bioinformatic analyses were performed on the GenoToul bioinformatics platform (Toulouse, France), with the OBITOOLS package (Boyer et al. 2016). First, ‘illuminapairedend’ was used to assemble paired-end reads. This algorithm is based on an exact alignment algorithm that considers the quality scores at all positions during the assembly process. Subsequently, we used the ‘ngsfilter’ command to identify and remove the primers and tags on each read, and assign reads to their respective samples. This program was used with its default parameters tolerating two mismatches for each of the two primers and no mismatch for the tags. Following this, sequencing reads were dereplicated using the ‘obiuniq’ command. Sequences of low quality (containing Ns or with paired-end alignment scores below 50) were excluded using the ‘obigrep’ command. The same command was used to exclude sequences represented by only one read (singletons) as they are more likely to be molecular artefacts (Taberlet et al. 2018). Sequences outside of the preset range were also discarded (Table 1). To remove PCR/sequencing errors as well as intraspecific variability, we built OTUs (Operational Taxonomic Units) using the ‘sumaclust’ clustering algorithm (Mercier et al. 2013), which considers the most abundant sequence of each cluster as the cluster representative.  OTUs were set at a sequence similarity threshold of 97% for eukaryotes, fungi and bacteria following the standards in microbial ecology, but this was lowered to 95% for plants since the eDNA target region is shorter (typically around 50 base pairs), where one mismatch inherently results in a lower percentage of similarity. To assign a taxon to plant and fungal OTUs, we built two reference sequence databases, one global, using the ecoPCR programme (Ficetola et al. 2010) and the plant / fungi specific markers on the European Molecular Biology Laboratory (EMBL; release 141), a second local, generated from specimens of fungi (Jaouen et al. 2019) and plants (see Zinger et al. 2019) collected in French Guiana. OTUs were then assigned a taxonomy, using OBITOOL’s ecotag programme (Boyer et al. 2016), which performs a global alignment of each OTU sequence (the query) against each reference. The reference taxon assigned to each OTU corresponds to the Last Common Ancestor of all the best-match sequences for the query. For taxonomic assignment of bacteria and eukaryote OTUs, the SILVA taxonomic database was used (version 1.3; Quast et al., 2012). Classification was performed by a local nucleotide BLAST search against the non-redundant version of the SILVA SSU Ref dataset (release 132; http://www.arb-silva.de) using blastn (version 2.2.30+; http://blast.ncbi.nlm.nih.gov/Blast.cgi) with standard settings (Camacho et al., 2009).  Eukaryote derived metazoan OTUs were then further assigned a taxonomy for Phyla identified at the Arthropoda, Annelida and Nematoda level using reference sequence databases built as above for these groups using the ecoPCR programme on EMBL release 141. Datasets were subsequently filtered to remove contaminants as well as artefacts such as PCR chimeras and remaining sequencing errors, following Zinger et al. (2019) and using routines now implemented in the metabaR R package (Zinger et al 2020b), in R version 3.6.1 (R Development Core Team, 2013). The filtering process consisted of four steps: (i) a negative control-based filtering. OTUs whose maximum abundance was found in extraction/PCR negative controls were removed from the dataset, as they were likely to be reagent/aerosol contaminants, better amplified in the absence of competing DNA fragments as it is the case in biological samples. (ii) a reference-based filtering. OTUs which are too dissimilar from sequences available in reference databases are potential chimeras generated during sequencing and amplification. In this study, we chose to set similarity thresholds at 95% for plants, 80% for bacteria and eukaryotes and due to the marker being more polymorphic, 65% for fungi. For plants and fungi, the remaining assignment was then verified with the local database, to confirm if assigned taxa also occurred in the local dataset, with preference given to local assignment. In addition, we removed all taxa that are not targeted by the primer used. (iii) an abundance-based filtering. This procedure targets incorrect assignment of a few numbers of sequences corresponding to true OTUs occurring to the wrong sample, a phenomenon called “tag-switching” (Esling et al. 2015), “tag jumps” (Schnell et al. 2015) or “cross-talk” (Edgar 2018). It consists in setting OTUs abundances to 0 in samples where their abundance represents < 0.03% of the total OTU abundance in the entire dataset. (iv) Finally, we conducted a PCR-based filtering by considering any PCR reaction that yielded less than 100 reads for plants, 1000 reads for fungi, bacteria and eukaryotes as non-functional, and removed them from the dataset. Data provided consists of 4 x OTU tables for each of the markers used to target different components of the soil biota, with rows representing each OTU, and columns the features of the OTU within the dataset, namely their id code, the number of read counts in the analysed dataset, their similarity score against the taxonomic dataset used to identify them, and when possible, a functional group assignment used in the manuscript. Details of these can be found above and in the manuscript and supplementary information. For each of the four datasets, we also provide a .rds file, corresponding to the processed dataset used in manuscript preparation. This is in the format of a metabaR list which includes PCR, Sample, Read count and the seperately provided OTU datasets. To facilitate interpretation, please refer to Zinger, L., Lionnet, C., Benoiston, A.S., Donald, J., Mercier, C. and Boyer, F., 2021. metabaR: an R package for the evaluation and improvement of DNA metabarcoding data quality. Methods in Ecology and Evolution, 12(4), pp.586-592. For the fungal (ITS) data, we also provide :  - the R1/R2 raw fastq files of the samples used in the paper + experimental controls - a tsv file containing the tag combinations corresponding to the samples/PCR replicates, to enable demultiplexing of data. - a csv file containing the description of each sample.

opencc-zeroJun 2022View details →

Small mammals reduce distance-dependence and increase seed predation risk in tropical rainforest fragments

Seed predation and reduced predation risk with distance from conspecific trees are important influences on tree regeneration in tropical forests. Shifts in animal communities, such as an increase in rodents and other small mammals due to forest fragmentation, could alter patterns of seed predation and affect tree regeneration and community dynamics in forest fragments. We performed a field experiment on four native rainforest tree species in the Western Ghats, India, to test whether fragmentation increases seed predation by mammals and alters the distance-dependence of seed predation. We monitored seed predation within open and mammal-exclosure plots, near and far from the canopies of conspecific trees, in contiguous and fragmented forests. Seed predation of Cullenia exarillata, Ormosia travancorica, and Syzygium rubicundum was markedly higher in forest fragments, and more so within open plots than exclosures, while the predominantly insect-predated Acronychia pedunculata experienced similar predation in contiguous forests and fragments. Seed predation of C. exarillata and S. rubicundum was unrelated to distance from conspecific trees in open plots in both contiguous forests and fragments, in contrast to exclosures that showed marked near versus far differences in seed predation. Our findings suggest that by increasing overall seed predation risk and imposing similar seed predation risk near and far from adults variably across the tree species, small mammals could alter processes that shape tree diversity and species composition in fragmented tropical rainforests.

opencc-zeroSep 2022View details →

Source code and data from: Foraging personalities modify effects of habitat fragmentation on biodiversity

Habitat loss undeniably poses a substantial threat to biodiversity, but whether fragmentation per se drives the loss of species is still widely debated. While negative consequences from fragmentation are often anticipated, many empirical studies report positive effects. However, the intrinsic mechanisms governing species' persistence in fragmented landscapes are not yet understood. In this study, we investigated consistent personality-dependent differences in foraging behavior among individuals as a possible mechanism underlying the discrepancy of reported fragmentation effects. We devised a mechanistic individual-based model simulating the home range behavior of a competitive small mammal community based on the availability of a shared resource. Thereby, an individual's risk-taking behavior dictates its foraging decisions at risky habitat edges, an inherent property of fragmentation per se. Our simulations show that differences in risk-taking while foraging are potentially a further mechanism contributing to reconciling the fragmentation debate. The first scenario considering risk-seeking communities showed a neutral response towards fragmentation, while the second scenario featuring risk-avoiding communities confirmed the negative effects of fragmentation. Notably, the third scenario, simulating behaviorally diverse communities including risk-avoiding and risk-seeking individuals, demonstrated a positive influence of fragmentation on biodiversity. Intraspecific differences in behavior could also enhance the temporal species coexistence (coviability) of communities threatened by an ongoing habitat loss. Our study highlights the importance of recognizing the behavioral composition of populations and communities for estimating fragmentation effects, because differences in risk-taking can influence the coping abilities of animal communities in light of fragmentation.

Text-fig. 5. Scanning electron micrographs (a, b, d–f) and X-ray microtomographic orthoslices (c) of capsular fruits composed of three carpels fruits and fragment of a capsular fruit from Zliv-Řídká Blana locality. a–c: Taxon 12, a – capsules of broadly elliptical shape, no. NM-F3302, b – tricarpellate capsules in apical view, no. NM-F 3302, c – tricarpellate capsules with pentamerous calyx, no. NM-F3302; d, e: Taxon 13, d – tricarpellate capsules of broadly elliptical shape, no. NM-F 4501, e – tricarpellate capsules in apical view, no. NM-F 4501; f: Taxon 11, fragment of a capsular fruit, no. NM-F 4622. in Plant Mesofossils From The Late Cretaceous Klikov Formation, The Czech Republic

Text-fig. 5. Scanning electron micrographs (a, b, d–f) and X-ray microtomographic orthoslices (c) of capsular fruits composed of three carpels fruits and fragment of a capsular fruit from Zliv-Řídká Blana locality. a–c: Taxon 12, a – capsules of broadly elliptical shape, no. NM-F3302, b – tricarpellate capsules in apical view, no. NM-F 3302, c – tricarpellate capsules with pentamerous calyx, no. NM-F3302; d, e: Taxon 13, d – tricarpellate capsules of broadly elliptical shape, no. NM-F 4501, e – tricarpellate capsules in apical view, no. NM-F 4501; f: Taxon 11, fragment of a capsular fruit, no. NM-F 4622.

Text-fig. 10. Paramblypterus cf. rohani. a: the skull roof in dorsal view, locality Otovice "Chmelnice", P 64665, scale bar 5 mm; b: bones of the skull roof in dorsal view, locality Otovice "Chmelnice", NM-M 4920, scale bar 5 mm; c: right frontal in dorsal view, locality Otovice "Chmelnice", NM-M 4923, scale bar 5 mm; d: right dermopterotic in dorsal view, locality Otovice "Chmelnice", P 30943, scale bar 2 mm; e: right supracleithrum in lateral view, locality Otovice "Chmelnice", P 30944, scale bar 5 mm; f: fragment of not deformed body in lateral view, locality Otovice "Chmelnice", NM-M 4916, scale bar 10 mm; g: right maxilla in lateral view, locality Otovice "Chmelnice", P 64661, scale bar 5 mm; h: right maxilla in lateral view, locality Otovice "Chmelnice", NM-M 4922, scale bar 5 mm. Abbreviations: Dpt – dermopterotic, Dsph – dermosphenotic, Fr – frontal, Pa – parietal. in Actinopterygians Of The Broumov Formation (Permian) In The Czech Part Of The Intra-Sudetic Basin (The Czech Republic)

Text-fig. 10. Paramblypterus cf. rohani. a: the skull roof in dorsal view, locality Otovice "Chmelnice", P 64665, scale bar 5 mm; b: bones of the skull roof in dorsal view, locality Otovice "Chmelnice", NM-M 4920, scale bar 5 mm; c: right frontal in dorsal view, locality Otovice "Chmelnice", NM-M 4923, scale bar 5 mm; d: right dermopterotic in dorsal view, locality Otovice "Chmelnice", P 30943, scale bar 2 mm; e: right supracleithrum in lateral view, locality Otovice "Chmelnice", P 30944, scale bar 5 mm; f: fragment of not deformed body in lateral view, locality Otovice "Chmelnice", NM-M 4916, scale bar 10 mm; g: right maxilla in lateral view, locality Otovice "Chmelnice", P 64661, scale bar 5 mm; h: right maxilla in lateral view, locality Otovice "Chmelnice", NM-M 4922, scale bar 5 mm. Abbreviations: Dpt – dermopterotic, Dsph – dermosphenotic, Fr – frontal, Pa – parietal.

Text-fig. 7. Dehmicyon n. gen. schlosseri (DEHM, 1950), from Wintershof-West, Germany. a: BSP 13562, mandible (holotype), a1 – right hemimandible in buccal view, a2 – occlusal view, a3 – left p4–m2 in occlusal view; b: BSP 12365, left maxilla fragment with M1 in occlusal view; c: BSP 13562, left maxilla fragment with P3 broken, P4–M2 and M3 alveolus (holotype) in occlusal view; d: BSP 12343 left maxilla fragment with P4, alveolus for M1, M2 and M3 alveolus in occlusal view. in The Amphicyoninae (Amphicyonidae, Carnivora, Mammalia) Of The Early Miocene From Tuchořice, The Czech Republic

Text-fig. 7. Dehmicyon n. gen. schlosseri (DEHM, 1950), from Wintershof-West, Germany. a: BSP 13562, mandible (holotype), a1 – right hemimandible in buccal view, a2 – occlusal view, a3 – left p4–m2 in occlusal view; b: BSP 12365, left maxilla fragment with M1 in occlusal view; c: BSP 13562, left maxilla fragment with P3 broken, P4–M2 and M3 alveolus (holotype) in occlusal view; d: BSP 12343 left maxilla fragment with P4, alveolus for M1, M2 and M3 alveolus in occlusal view.

Text-fig. 11. CGM 94-138, right mandible fragment containing p/4–m/3 of Libycochoerus massai from Moghara, Egypt. a: lingual view; b: stereo occlusal view; c: buccal view. in New Suoid Fossils (Mammalia, Artiodactyla) From The Miocene Of Moghara, Egypt, And Gebel Zelten, Libya: Biochronological Implications

Text-fig. 11. CGM 94-138, right mandible fragment containing p/4–m/3 of Libycochoerus massai from Moghara, Egypt. a: lingual view; b: stereo occlusal view; c: buccal view.

Text-fig. 9. CUWM 360, right mandible fragment and associated m/3 of Diamantohyus africanus from Moghara, Egypt. a: stereo occlusal views; b: buccal view; c: lingual view. in New Suoid Fossils (Mammalia, Artiodactyla) From The Miocene Of Moghara, Egypt, And Gebel Zelten, Libya: Biochronological Implications

Text-fig. 9. CUWM 360, right mandible fragment and associated m/3 of Diamantohyus africanus from Moghara, Egypt. a: stereo occlusal views; b: buccal view; c: lingual view.

Text-fig. 4. a: Conglomeratic to massive sandstone facies 1, facies A are composed of Andesit (AF), Clay (CF) and Sandstone (SF) fragments lain on medium-sandstone. b: Conglomeratic to massive sandstone facies, outcropping of massive sandstone facies comprises of fine to medium grain size of grey to yellowish sandstone. c: Heterolithic sandstone-mudstone facies, intercalation of fine sand with silt and shale as type form of heterolithic sandstone mudstone as indicated by a high sand/shale ratio. d: Example outcrops of heterolithic sandstone-mudstone 2 indicated by low sand/shale ratio. e: Heterolithic fine sand and mudstone and mudstone facies, intercalation of thin sandstone and shale. f: Representative of slump deposits outcrops belong to conglomeratic to massive sandstone facies, which is indicated by the intercalation of sandstone and shale and some disturbed beds or layers as seen in slump deposits. The facies type is normally deposited within the basin floor, channel margin or as a product of the overbank deposits. In this figure the slump deposit is shown as internal bedding, some occurred on the bedding-plane. Trend slope measurement of the fold-axis revealed values N 135°E and N 108°E. in Lithofacies And Ichnofacies Of Turbidite Deposits, West Java, Indonesia

Text-fig. 4. a: Conglomeratic to massive sandstone facies 1, facies A are composed of Andesit (AF), Clay (CF) and Sandstone (SF) fragments lain on medium-sandstone. b: Conglomeratic to massive sandstone facies, outcropping of massive sandstone facies comprises of fine to medium grain size of grey to yellowish sandstone. c: Heterolithic sandstone-mudstone facies, intercalation of fine sand with silt and shale as type form of heterolithic sandstone mudstone as indicated by a high sand/shale ratio. d: Example outcrops of heterolithic sandstone-mudstone 2 indicated by low sand/shale ratio. e: Heterolithic fine sand and mudstone and mudstone facies, intercalation of thin sandstone and shale. f: Representative of slump deposits outcrops belong to conglomeratic to massive sandstone facies, which is indicated by the intercalation of sandstone and shale and some disturbed beds or layers as seen in slump deposits. The facies type is normally deposited within the basin floor, channel margin or as a product of the overbank deposits. In this figure the slump deposit is shown as internal bedding, some occurred on the bedding-plane. Trend slope measurement of the fold-axis revealed values N 135°E and N 108°E.

Text-fig. 8. a, b: Bifungites isp. with fragments of vertical shafts, a – concave hyporelief BK 20, Layer No. 26, b – full relief BK 33, Layer No. 23; c–e: Palaeophycus sulcatus (MILLER et DYER, 1878), c – BK 29, Layer No. 22, d – BK 18, Layer No. 16, e – BK 31, Layer No. 6; f: Palaeophycus cf. tubularis HALL, 1847, BK 25, Layer No. 22; g: Megagrapton isp., concave hyporelief, BK 32, Layer No. 16; h: Teichichnus isp. (bottom) crossing Zoophycos isp. (centre to right bottom), BK 16, Layer No. 22. Scale bar = 1 cm. in Early Complex Tiering Pattern: Upper Ordovician, Barrandian Area, The Czech Republic

Text-fig. 8. a, b: Bifungites isp. with fragments of vertical shafts, a – concave hyporelief BK 20, Layer No. 26, b – full relief BK 33, Layer No. 23; c–e: Palaeophycus sulcatus (MILLER et DYER, 1878), c – BK 29, Layer No. 22, d – BK 18, Layer No. 16, e – BK 31, Layer No. 6; f: Palaeophycus cf. tubularis HALL, 1847, BK 25, Layer No. 22; g: Megagrapton isp., concave hyporelief, BK 32, Layer No. 16; h: Teichichnus isp. (bottom) crossing Zoophycos isp. (centre to right bottom), BK 16, Layer No. 22. Scale bar = 1 cm.