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3,225 results for “Case of study”
Figure 11 in Dealing with allometry in linear and geometric morphometrics: a taxonomic case study in the Leporinus cylindriformis group (Characiformes: Anostomidae) with description of a new species from Suriname
Figure 11. Scatterplot of (A) principal components one and two and (B) principal components one and three from geometric morphometrics after allometric correction. Polygons represent convex hulls surrounding nominal species of Leporinus.
Figure 6 in Dealing with allometry in linear and geometric morphometrics: a taxonomic case study in the Leporinus cylindriformis group (Characiformes: Anostomidae) with description of a new species from Suriname
Figure 6. Scatterplot of principal component two (PC2) versus one from traditional linear morphometrics for species of Leporinus discussed in text. PC1 is an allometric vector describing size and shape variation, whereas PC2 is essentially size-free. Polygons indicate convex hulls.
Figure 7 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 7. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific: A–H, ventral, dorsal, lateral, and anterior views of complete specimens, CP 2616, 786–836 m depth; A–D, paratype, IB-2013-2; E–H, holotype, IB-2013-1. I, dorsal view of complete specimen, with very long, thin pedicle, paratype, CP 2616, 786–836 m depth, IB- 2013-3. Scale bars: 5 mm.
Figure 6 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 6. rDNA tree of taxa with modified long loops. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2694 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of 15 in-group and three rhynchonellide out-group taxa. Potentially misaligned and gapped sites (5%) were pruned by GBlocks. Several backbone nodes received very low bootstrap support and the tree has been redrawn by hand to remove them, leaving no effective resolution of relationships between the in-group superfamilies represented in this alignment. The sequence for Argyrotheca (JH97) was used with the permission of Dr J. Hoffman.
Figure 2. Case 2 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 2. Case 2: Cancellothyridoid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2810 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 30 in-group and three rhynchonellide out-group taxa. Gblocks was used to prune potentially misaligned and gap sites (18% were discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Four taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon.
Figure 5 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 5. Laqueoidea rDNA tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2882 nucleotides of aligned sequences from SSU and LSU nuclear-encoded genes of seven laqueoid in-group and six terebratulide out-group taxa. The small number of potentially misaligned and gap sites were not removed. The failure of the two Kingenoids to form a clade may be caused by limited sequence data rather than by misclassification.
Figure 9 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 9. Ebiscothyris bellonensis gen. et sp. nov., cruise EBISCO, Coral Sea, South-West Pacific, SEM micrographs; A, B, ventral valve, station CP 2556, 741–791 m depth, IB-2013-7; A, transverse section of the entire shell showing the primary layer (pri) underlain by the fibrous secondary layer (sec), passing into the prismatic tertiary layer (ter); B, section of the shell showing primary (pri), secondary (sec), and tertiary (ter) layers; a puncta with a radiating brush is also visible; C, D, dorsal valve, CP 2557, 800–923 m depth, IB-2013-5; C, latero-oblique view of internal surface, showing the incurved valve margin built of densely arranged sheets of secondary fibres (left) and prisms of tertiary layer (right); D, internal surface showing discrete units of prisms and very small punctae (arrows). E, F, Kanakythyris pachyrhynchos Laurin, 1997, cruise NORFOLK 2, Norfolk Ridge, station DW 2136, 402–410 m depth; E, transverse section of the entire shell; F, internal surface with discrete units of prisms. Scale bars: A, C, D, E, F, 50 μm, B, 20 μm.
Figure 4. Laqueoidea cox1 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 4. Laqueoidea cox1 tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 1218 nucleotides of aligned sequences of the cox1 mitochondrial gene from 14 laqueoid in-group and six terebratulide out-group taxa. The sequences were aligned with no gaps. Nodes with no bootstrap support value attached are considered to be unsupported (bootstrap <50%) and may be collapsed.
Figure 3. Case 3 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus
Figure 3. Case 3: Dyscolioid and Terebratuloid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 3427 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 19 in-group and three rhynchonellide out-group taxa. Pruned of potentially misaligned and gap sites by hand (7% discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Nine taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon. These results validate the placement of Ebiscothyris, Dallithyris, and Dyscolia, each of which is represented by LSU alone.
Figure 6 in Amblypygi parthenogenesis, embryonic and post-embryonic development: a case study with the Amazonian species Charinus guto Giupponi and Miranda, 2016 (Amblypygi: Charinidae)
Figure 6. Graphs showing the correlation between clutch size (number eggs; left) and number of prenymphs (right) against female carapace length for 43 Amblypygi species in four families. Details on the values are listed in Table 3.
Figure 3 in Amblypygi parthenogenesis, embryonic and post-embryonic development: a case study with the Amazonian species Charinus guto Giupponi and Miranda, 2016 (Amblypygi: Charinidae)
Figure 3. Dorsal habitus of Charinus guto Miranda and Giupponi, 2016 (upper); retrolateral view of ovigerous female (bottom). Photos: César Favacho.
Figure 1 in Amblypygi parthenogenesis, embryonic and post-embryonic development: a case study with the Amazonian species Charinus guto Giupponi and Miranda, 2016 (Amblypygi: Charinidae)
Figure 1. Flowchart illustrating the female specimens of Charinus guto Miranda and Giupponi, 2016 used in the study.
Figure 2 in Amblypygi parthenogenesis, embryonic and post-embryonic development: a case study with the Amazonian species Charinus guto Giupponi and Miranda, 2016 (Amblypygi: Charinidae)
Figure 2. Total number of moults per month of Charinus guto Giupponi and Miranda, 2016 in captivity.
Injecting Software Faults in Python Applications: The OpenStack Case Study - Supplemental Material (https://rdcu.be/cAPUh)
<p>Injecting Software Faults in Python Applications: The OpenStack Case Study - Supplemental Material<br> Link to the paper: <a href="https://rdcu.be/cAPUh">https://rdcu.be/cAPUh</a></p>
What is the current extent of our systematic knowledge? A case study in synthesizing phylogenetic data for building large trees to advance phylogenetic research in Orobanchaceae
To date, no comprehensive phylogenetic analyses have been conducted in Orobanchaceae that include both a wide generic sampling and a large sampling of species. Here, we utilize a recently developed set of tools for synthesizing publicly available data, and apply these to assess where the gaps in our phylogenetic knowledge exist in the angiosperm clade Orobanchaceae. We then use the resulting timetree to investigate diversification dynamics in this clade of mostly parasitic plants. We used the PyPHLAWD pipeline and RAxML to assemble a supermatrix of >900 species and construct a comprehensive phylogenetic hypothesis of Orobanchaceae. Divergence times were estimated with penalized likelihood from a 'congruified' set of secondary calibrations, and diversification dynamics were investigated in both trait-independent and trait-dependent (parasitic habit) contexts with BAMM and HiSSE. We sampled 39.8% of described species from 80 of 108 genera, representing all eight primary clades of Orobanchaceae. Relationships and divergence time estimates were similar to previous, clade-specific studies; however, eight genera were recovered as non-monophyletic, and will require focused systematic attention. Ours is first Orobanchaceae wide study to use model based approach to assess diversification dynamics in the parasitic lineage. Our results reveal elevated diversification rates associated with hemiparasitic habit, and holoparasitic habit was revealed to be an absorbing state, meaning that lineages within Orobanchaceae tend towards a reduction in photosynthetic towards hemiparasitism and finally holoparasitism. Using a synthetic phylogenetic hypothesis in conjunction with a unified taxonomic framework, we are able to understand where our taxonomic and phylogenetic knowledge is incomplete or conflicting, and we predict that this approach will aid in identifying where to focus future systematic efforts in any clade of interest. For Orobanchaceae, our phylogeny reflects the most recent taxonomy, and provides a new, comprehensive temporal framework for the clade that can serve as a stepping-stone for future macroevolutionary studies.
Data from: Ontogeny in the steinmanellines (Bivalvia: Trigoniida): an intra- and interspecific appraisal using the Early Cretaceous faunas from the Neuquén Basin as a case study
<p>Despite the paleontological relevance and paleobiological interest of trigoniid bivalves, our knowledge of their ontogeny –an aspect of crucial evolutionary importance– remains limited. Here, we assess the intra- and interspecific ontogenetic variations exhibited by the genus Steinmanella Crickmay (Myophorellidae: Steinmanellinae) during the early Valanginian – late Hauterivian of Argentina, and explore some of their implications. The (ontogenetic) allometric trajectories of seven species recognized for this interval were estimated from longitudinal data using 3D geometric morphometrics, segmented regressions and model selection tools, and then compared using trajectory analysis and allometric spaces. Our results show that within-species shell shape variation describes biphasic ontogenetic trajectories, decoupled from ontogenetic changes shown by sculpture, and with a gradual decay in magnitude as ontogeny progresses. The mode of change characterizing each phase (crescentic growth and anteroposterior elongation, respectively) is conserved across species, thus representing a feature of Steinmanella ontogeny; its evolutionary origin is inferred to be a consequence of the rate modification and allometric repatterning of the ancestral ontogeny. Among species, trajectories are more variable during early ontogenetic stages, becoming increasingly conservative at later stages. Trajectories' general orientation allows recognition of two stratigraphically-consecutive groups of species, hinting at a potentially higher genus-level diversity in the studied interval. In terms of functional morphology, juveniles had a morphology more suited for active burrowing than adults, whose features are associated with a sedentary lifestyle. The characteristic disparity of trigoniids could be related to the existence of an ontogenetic period of greater shell malleability betrayed by the presence of crescentic shape change.</p>
A Case-Controlled Pilot Study on Rhythmic Auditory Stimulation-Assisted Gait Training and Conventional Physiotherapy in Patients With Parkinson's Disease Submitted to Deep Brain Stimulation
<p>Deep brain stimulation (DBS) is indicated when motor disturbances in patients with idiopathic Parkinson's disease (PD) are refractory to current treatment options and significantly impair quality of life. However, post-DBS rehabilitation is essential, with particular regard to gait. Rhythmic auditory stimulation (RAS)-assisted treadmill gait rehabilitation within conventional physiotherapy program plays a major role in gait recovery. We explored the effects of a monthly RAS-assisted treadmill training within a conventional physiotherapy program on gait performance and gait-related EEG dynamics (while walking on the RAS-aided treadmill) in PD patients with (<em>n</em> = 10) and without DBS (<em>n</em> = 10). Patients with DBS achieved superior results than those without DBS concerning gait velocity, overall motor performance, and the timed velocity and self-confidence in balance, sit-to-stand (and vice versa) and walking, whereas both groups improved in dynamic and static balance, overall cognitive performance, and the fear of falling. The difference in motor outcomes between the two groups was paralleled by a stronger remodulation of gait cycle-related beta oscillations in patients with DBS as compared to those without DBS. Our work suggests that RAS-assisted gait training plus conventional physiotherapy is a useful strategy to improve gait performance in PD patients with and without DBS. Interestingly, patients with DBS may benefit more from this approach owing to a more focused and dynamic re-configuration of sensorimotor network beta oscillations related to gait secondary to the association between RAS-treadmill, conventional physiotherapy, and DBS. Actually, the coupling of these approaches may help restoring a residually altered beta-band response profile despite DBS intervention, thus better tailoring the gait rehabilitation of these PD patients.</p>
Case studies of a multi-product and multiple-sources slurry pipeline network scheduling problem in the phosphate industry
<p>The data shared summarises two case studies of a multi-product and multiple-sources slurry pipeline network scheduling problem in the phosphate industry.</p>
Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins - Case Studies
<p>Dataset and scripts accompanying the publication "Fragment Hotspot Mapping to Identify Selectivity-Determining Regions between Related Proteins"</p>
FIGURE 5 in Using an Asteraceae checklist to understand collection history, species density and conservation implications: a case study in the state of Alagoas, Northeastern Brazil
FIGURE 5. Continental Protected Areas in the state of Alagoas. 1. Natural Monument of the São Francisco. 2. Wildlife Refuge of Morros do Craunã and Padre. 3. Ecological Station Curral do Meio. 4. Ecological Park Pedra do Sino. 5. Biological Reserve Pedra Talhada. 6. Environmental Protection Area Marituba do Peixe. 7. Environmental Protection Area of Piaçabuçu. 8. Extractive Reserve Jequiá. 9. Ecological Mangrove Reserve of Lagoa do Roteiro. 10. Ecological Reserve Saco da Pedra. 11. Environmental Protection Area of Santa Rita. 12. Environmental Protection Area of Catolé e Fernão Velho. 13. Municipal Park of Maceió. 14. Environmental Protection Area Patangy. 15. Environmental Protection Area of Murici. 16. Ecological Station of Murici. *RPPN
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.