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FIGURE 3 in A new endemic Impatiens species on Mount Gorongosa (Mozambique) demonstrates the conservation importance of montane areas in Africa
FIGURE 3. Distribution of I. wuerstenii (black asterisks) on Mount Gorongosa. S. Afr.: South Africa; Zimb: Zimbabwe; Mal.: Malawi.
FIGURE 2. Impatiens wuerstenii. A in A new endemic Impatiens species on Mount Gorongosa (Mozambique) demonstrates the conservation importance of montane areas in Africa
FIGURE 2. Impatiens wuerstenii. A. Habit; B. Frontal view of flower; C. Dorsal petal; D. Lateral sepals; E. United lateral petals; F. Lower sepal and spur (Drawn by A. Fernandez from Ballings 1713)
Supplementary material of SECO-RCI evaluation and SECO-RCR demonstration
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Demonstrating Witness Visualization with the Witness Visualizer Tool
<p>We have three datasets that display visualized <a href="https://sv-comp.sosy-lab.org/">SV-COMP</a> witnesses generated with the help of the Witness Visualizer tool. Each dataset comprises two directories: <code>witnesses</code>, which contains the original witnesses provided by SVCOMP tools, and <code>visualization</code>, which contains our visual representations of the respective witnesses in HTML format. The visualization file name contains the prefix <code>error_trace-</code>, for example, <code>error_trace-witness.2ls.html</code> corresponds to a witness named <code>witness.2ls.graphml</code>.</p> <p> </p> <h3>1. Expert Evaluation of Relevant Elements for SV-COMP Properties (<a href="../records/13736385/files/dataset_1.zip?download=1">dataset_1.zip</a>)</h3> <p>This dataset comprises a selected witness for each SV-COMP property (ReachSafety, MemSafety, Termination, NoOverflow, ConcurrencySafety). The witnesses are presented in the following table:</p> <table> <tbody> <tr> <td>Witness</td> <td>SV-COMP Tool</td> <td>Property</td> <td>Mandatory elements</td> <td>Description</td> </tr> <tr> <td>witness.memory.graphml</td> <td>CPA-BAM-SMG</td> <td>MemSafety</td> <td>Assumptions, conditions, function calls</td> <td>There is an invalid pointer being freed in this line. Using function calls to <code>append</code> helps clarify the structure of the list, while assumptions indicate which branch was chosen</td> </tr> <tr> <td>witness.overflow.graphml</td> <td>Graves-CPA</td> <td>NoOverflow</td> <td>Assumptions</td> <td>The witness showcases an explicit (<code>-2147483648</code>, which represents the minimal value for the <code>int</code> type), which has the potential to cause overflow in specific program.</td> </tr> <tr> <td>witness.termination.graphml</td> <td>CPAChecker</td> <td>NoTermination</td> <td>Assumptions, conditions</td> <td>There is a condition leading to an infinite loop.</td> </tr> <tr> <td>witness.unreach.graphml</td> <td>CPAChecker</td> <td>ReachSafety</td> <td>Function calls</td> <td>The error trace suggests that the same <code>mutex</code> was locked twice, which could result in a potential deadlock.</td> </tr> <tr> <td>witness.concurrency.graphml</td> <td>CPAChecker</td> <td>ConcurrencySafety</td> <td>Function calls, thread operations</td> <td>The error trace illustrates the creation of threads and highlights the assignments made within each thread that ultimately resulted in the violation of the property.</td> </tr> </tbody> </table> <div> </div> <p> </p> <h3>2. Overall thoroughness for all SV-COMP tools (<a href="../records/13736385/files/dataset_2.zip?download=1">dataset_2.zip</a>)</h3> <p>This dataset includes a single random witness for each SV-COMP tool, accompanied by its corresponding visualization. The visualizations showcase the various witness elements such as function calls, conditions, assumptions, thread specifics, and other operations. Cells marked with <code>+/-</code> indicate that some elements were present in the error trace, but not all of them. All witnesses are presented in the table below:</p> <table> <tbody> <tr> <td>Witness</td> <td>SV-COMP Tool</td> <td>Function calls</td> <td>Threads</td> <td>Assumptions</td> <td>Conditions</td> <td>Link to sources</td> </tr> <tr> <td>witness.2ls.graphml</td> <td>2LS</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.aprove.graphml</td> <td>AProVE (2022)</td> <td>-</td> <td>-</td> <td>-</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.brick.graphml</td> <td>BRICK</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.bubaak.graphml</td> <td>Bubaak</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.cbmc.graphml</td> <td>CBMC</td> <td>-</td> <td>+</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.cpa-bam-bnb.graphml</td> <td>CPA-BAM-BnB</td> <td>+</td> <td>-</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.cpa-bam-smg.graphml</td> <td>CPA-BAM-SMG</td> <td>+</td> <td>-</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.cpalockator.graphml</td> <td>CPALockator</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.cpachecker.graphml</td> <td>CPAChecker</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.crux.graphml</td> <td>Crux</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.cseq.graphml</td> <td>Cseq</td> <td>+</td> <td>+</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.dartagnan.graphml</td> <td>Dartagnan</td> <td>-</td> <td>+</td> <td>-</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.deagle.graphml</td> <td>Deagle</td> <td>-</td> <td>+</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>-</td> <td>DIVINE</td> <td>empty</td> </tr> <tr> <td>-</td> <td>EBF</td> <td>empty</td> </tr> <tr> <td>witness.esbmc-incr.graphml</td> <td>ESBMC-incr</td> <td>-</td> <td>+</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.esbmc-kind.graphml</td> <td>ESBMC-kind</td> <td>-</td> <td>+</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>-</td> <td>Frama-C-SV</td> <td>empty</td> </tr> <tr> <td>witness.gazer-theta.graphml</td> <td>Gazer-Theta</td> <td>+</td> <td>-</td> <td>+</td> <td>-</td> <td>wrong path</td> </tr> <tr> <td>witness.gdart.graphml</td> <td>Gdart-LLVM</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>-</td> <td>Goblint</td> <td>empty</td> </tr> <tr> <td>witness.graves_cpa.graphml</td> <td>Graves-CPA</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.graves_par.graphml</td> <td>Graves-Par</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>-</td> <td>Infer</td> <td>empty</td> </tr> <tr> <td>witness.korn.graphml</td> <td>Korn</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.lart.graphml</td> <td>LART (2022)</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.lazy-cseq.graphml</td> <td>Lazy-CSeq</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.lfchecker.graphml</td> <td>LF-checker</td> <td>-</td> <td>+</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>-</td> <td>Locksmith</td> <td>empty</td> </tr> <tr> <td>-</td> <td>Mopsa</td> <td>empty</td> </tr> <tr> <td>witness.pesco_cpa.graphml</td> <td>PeSCo-CPA</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.pichecker.graphml</td> <td>PIChecker</td> <td>+</td> <td>-</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.pinaka.graphml</td> <td>Pinaka</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.predator.graphml</td> <td>PredatorHP</td> <td>-</td> <td>-</td> <td>-</td> <td>-</td> <td>+</td> </tr> <tr> <td>-</td> <td>SESL (2022)</td> <td>empty</td> </tr> <tr> <td>witness.smack.graphml</td> <td>SMACK (until 2022)</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.symbiotic.graphml</td> <td>Symbiotic</td> <td>-</td> <td>+</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.theta.graphml</td> <td>Theta</td> <td>different format</td> </tr> <tr> <td>witness.uatomozer.graphml</td> <td>UAutomizer</td> <td>+/-</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.ucutter.graphml</td> <td>UgemCutter</td> <td>+/-</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.ukojak.graphml</td> <td>UKojak</td> <td>+/-</td> <td>-</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.utaipan.graphml</td> <td>UTaipan</td> <td>+/-</td> <td>+</td> <td>+</td> <td>+</td> <td>+</td> </tr> <tr> <td>witness.veriabs.graphml</td> <td>VeriAbs</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>wrong path</td> </tr> <tr> <td>witness.veriabsl.graphml</td> <td>VeriAbsL</td> <td>+</td> <td>-</td> <td>+</td> <td>+</td> <td>wrong path</td> </tr> <tr> <td>witness.verifuzz.graphml</td> <td>VeriFuzz</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> <tr> <td>witness.verioover.graphml</td> <td>VeriOover</td> <td>-</td> <td>-</td> <td>+</td> <td>-</td> <td>+</td> </tr> </tbody> </table> <div> <h3> </h3> <h3>3. A known bug (<a href="../records/13736385/files/dataset_3.zip?download=1">dataset_3.zip</a>)</h3> <p>This dataset contains witnesses for a known bug from SVCOMP (<code>linux-3.14--drivers--usb--misc--adutux.ko.cil.i</code>) involving a data race on <code>dev->udev</code>, where concurrent writes occur without corresponding locks. Only two tools were able to solve the corresponding verification task: ESBMC-kind and CPALockator. The ESBMC error trace (<code>witness.esbmc_2020.graphml</code>) includes only thread specifics and assumptions, while the CPALockator witness (<code>witness.lockator.graphml</code>) comprises all witness elements and is presented in a human-readable format.</p> </div>
Raw neural codes and binsizes for the paper 'Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus'
<p>Raw optimal spiking codes and binsizes that maximise information theoretic quantities for the figures of the paper 'Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus' (PLoS Comput Biol. 2024 Feb 20;20(2):e1010706) . Additional data will be added in the coming months.</p>
Pilot scale on-site demonstration and seasonality assessment of nitrogen recovery and water reclamation from pig's slurry liquid fraction
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Demonstrator of 3D printed bonded magnets from rare-earth micropowder alloys
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GitHub Pull Request Demonstration by Dhruvil Prajapati
<div> <p>In this demonstration, NLU student Dhruvil Prajapati walks us through pull requests for the TOPS SCHOOL GitHub repository. You can watch the video below or find a link in the 'Additional details' section.</p> </div>
Data from: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators' diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction.
Poker: Visual Instrumentation of Reactive Programs With Programmable Probes (video demonstration)
<p>This video is supplementary material for a paper submitted to the 2021 workshop on reactive and event-based languages and systems (REBLS 2021): https://2021.splashcon.org/home/rebls-2021</p> <p>Music: <a href="https://www.bensound.com/royalty-free-music">https://www.bensound.com/royalty-free-music</a> </p> <p> </p>
Data from: The little fishes that could: smaller fishes demonstrate slow body size evolution but faster speciation in the family Percidae
<p>Body size impacts numerous aspects of organismal biology and many factors have been invoked to explain body size distributions in a macroecological and macroevolutionary context. Body size in the freshwater fish family Percidae is strongly right-skewed (i.e, dominated by small sizes), with small body size potentially being associated with fast water habitats. We constructed a new species-level, multi-locus, time-calibrated phylogeny of Percidae, and used it to test for changes in the rate and pattern of maximum body size evolution. We also tested whether speciation rates varied as a function of body size. We found that Etheostomatinae evolved towards a smaller adaptive optimum in body size compared to the other subfamilies of Percidae, and that this shift was associated with a reduction in the rate of body size evolution. Speciation rates were associated with body size across percids, showing a peak around small to medium body size. Small body size appears to partially, but not fully, explain the diversity of small percids, as many darters fall well below the "optimum" body size. Reinforcement of selection for small body size via selection for novel morphologies or via sexual selection may help to fully explain the remarkable diversity of the darter radiation.</p>
Figure 3 in Dromaeosaurid crania demonstrate the progressive loss of facial pneumaticity in coelurosaurian dinosaurs
Figure 3. Craniofacial pneumaticity of Tsaagan. Skull (cast of IGM 100/1015) in (A, C) lateral and (B, D) medial views. Abbreviations: aofen, antorbital fenestra; aof, antorbital fossa; pneu fen, additional maxillary pneumatic fenestra; mf, maxillary fenestra; mx, maxilla; pmf, promaxillary fenestra; pmx, premaxilla. In (B), green is the additional maxillary pneumatic fenestra, blue is the maxillary fenestra, and yellow is the promaxillary fenestra.
Figure 9 in Dromaeosaurid crania demonstrate the progressive loss of facial pneumaticity in coelurosaurian dinosaurs
Figure 9. Ancestral state reconstruction of the presence of exterior nasal pneumatic foramina in coelurosaurs. Likelihood estimates for nodes represented by pie charts (blue = present, yellow = absent).
Figure 5 in Dromaeosaurid crania demonstrate the progressive loss of facial pneumaticity in coelurosaurian dinosaurs
Figure 5. Nasal pneumaticity in coelurosaurs. Nasals of (A) Velociraptor, (B) Deinonychus, (C) Tsaagan, (D) Gorgosaurus (cast), (E) Tyrannosaurus (cast of AMNH 5027) and (F) Tyrannosaurus (FMNH PR2081). Abbreviations: nf, neurovascular foramina; rs, rugose surface; nepf, exterior nasal pneumatic foramina. Photo of Deinonychus courtesy of the Division of Vertebrate Paleontology, Peabody Museum of Natural History.
Figure 4 in Dromaeosaurid crania demonstrate the progressive loss of facial pneumaticity in coelurosaurian dinosaurs
Figure 4. Reconstruction of the antorbital sinus in coelurosaurs. The second sentence in the figure caption should read: Skulls of (A) Velociraptor, (B) Tsaagan, (C) Tyrannosaurus, (D) Deinonychus, (E) Saurornithoides, and (F) Khaan. Antorbital sinus in blue, with location of the maxillary fenestra in black and promaxillary fenestra in yellow. Photo of Deinonychus courtesy of the Division of Vertebrate Paleontology, Peabody Museum of Natural History.
Data underlying RSOS-210474: Mitochondrial DNA sequencing of a wet-collection syntype demonstrates the importance of type material as genetic resource for Lantern Shark taxonomy (Chondrichthyes: Etmopteridae)
<p>After initial detection of target archival DNA of a 116 year old syntype specimen of the Smooth Lanternshark, <i>Etmopterus pusillus</i> in a single stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial DNA characteristics and reconstruction of the mitochondrial genome. The archival DNA is highly fragmented. A total of 4,599 mitochondrial reads were available for the genome reconstruction using an iterative mapping approach. The resulting genome sequence has a 12 times coverage and a length of 16,741 basepairs. All 37 vertebrate mitochondrial loci plus the control region were identified and annotated. The mitochondrial NADH2 gene was subsequently used to place the syntype haplotype in a network comprising multiple <i>E. pusillus</i> samples from various distant localities as well as sequences from a morphological similar species, the Shortfin Smooth Lantern Shark <i>Etmopterus joungi</i>. Results confirm the almost global distribution of <i>E. pusillus</i> and suggest <i>E. joungi </i>to be a junior synonym of <i>E. pusillus</i>. As mitochondrial DNA often represents the only available reference information in non-model organisms, this study illustrates the importance of mitochondrial DNA from an aged, wet-collection type specimen for taxonomy.</p>
FIG. 4 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 4. Allele frequencies at the LDH locus in the 25 populations of Potamonautes studied. Refer to Žgure 1 for collection localities.
FIG. 1 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 1. Sampling localities of the 25 populations of Potamonautes studied. Potamonautes granularis (), P. perlatus () and P. sidneyi () were collected from the Western Cape (WC), Eastern Cape (EC), KwaZulu-Natal (KZN), Mpumalanga (MP) and the Northern Province (NP). Localities include: (1) Klawer, (2) Doring River, (3) Clanwilliam, (4) Paarl, (5) Tokai, (6) Liesbeek, (7) Bonnievale, (8) Tradouw Pass, (9) Tsitsikamma, (10) Smitskraal, (11) Hankey, (12) Belmont, (13) Umtata, (14) Pinetown, (15) University of Zululand, (16) Dakaneni, (17) Blood River, (18) Oliviershoek, (19) Mahai, (20) Cathedral Peak, (21) Wakkerstroom, (22) Vaal River, (23) Sterkspruit, (24) Mukhasa and (25) Tchiombedi.
FIG. 2 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 2. UPGMA-dendrogram, reecting genetic similarity amongst the 25 Potamonautes populations studied, as calculated from Nei's (1978) unbiased genetic identities (I) obtained in pair-wise comparisons of populations.
FIG. 5 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 5. Scatterplots of geographic distance (km) over Nei's (1978) unbiased genetic identity (I) for each pair-wise comparison of (a) the eight P. perlatus populations, and (b) the 13 P. sidneyi populations studied. Solid lines represent least-squares regressions and dotted lines represent 95% conŽdence limits.
ScienceDex guides
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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.