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708 results for “Java”
Oracles for the Equivalence of Java Bytecode
<p>Incidents like <em>log4shell</em> and <em>SolarWinds</em> have led to an increased focus on software supply chain security. A particular concern is the detection and prevention of compromised builds. A common approach is to independently re-build projects, and compare the results. This leads to the availability of different binaries built from the same sources, and raises the question of how to compare the respective binaries (to confirm the integrity of builds, to detect compromised builds, etc). It is however not clear how to do this: naive bitwise comparison is often too strict, and establishing the behavioural equivalence of two binaries is undecidable. <br> <br>A pragmatic step towards a solution is to provision a benchmark that can be used to test and train equivalence relations. We present such a benchmark for Java bytecode, consisting of \input{generated/total-oracle-record-count}pairs of binaries (compiled Java classes) labelled as to whether these classes are equivalent or not. We refer to these pairs as equivalence and non-equivalence oracles, respectively. <br> <br>We derive equivalence oracles from building 56 projects and project versions using 32 dockerised build environments (with different compilers, compiler versions and configurations). Non-equivalence oracles are derived from three different sources: (1) proven breaking API changes, (2) semantic code changes synthesised by means of bytecode mutations, and (3) code changes extracted from vulnerability patches.</p> <p> </p> <p>A detailed description of the dataset can be found in: </p> <p><em>Jens Dietrich, Tim White, Mohammad Mahdi Abdollahpou, Elliott Wen and Behnaz Hassanshahi: BenEq -- A Benchmark of Compiled Java Programs to Assess Alternative Builds. Proceedings of the ACM Workshop on Software Supply Chain Offensive Research and Ecosystem Defenses (SCORED '24). </em></p>
Figure 2. - Sicyopus rubicundus. A in A new species of Sicyopus (Gobiidae) from Java and Bali
Figure 2. - Sicyopus rubicundus. A: Male, Bali, Photo P. Keith; B: Above: male, holotype MZB 22123 (BIF 1485); below: female, paratype MNHN 2014-0133 (BIF 1489), Photo N. Hubert.
Figure 1 in A new species of Sicyopus (Gobiidae) from Java and Bali
Figure 1. - Diagrammatic illustration of the head in Sicyopus rubicundus showing head pores and sensory papillae. A: Dorsal view; B: Lateral view. Scale bar = 5 mm.
Java tool for PCR, in silico PCR and genotyping
<p>We performed in silico PCR analysis of several complete plant genomes using a list of primers corresponding to an inverted repeat sequence of Hordeum-Triticum Athos miniature inverted-repeat transposable element (MITE) sequences. MITE nonautonomous members of Class II element families are derived by internal deletion of autonomous elements, and they are short (70-300 bp in length) and have conserved terminal repeats.</p> <p>For example, Athos, one of the MITE families described in grasses. Athos element sequences were collected from the genome of Hordeum vulgare, of which there are about 205 per complete genome. The Athos element sequences are highly truncated, including partial loss of terminal inverted repeats in the barley genome. Sequences of terminal inverted repeats contain multiple point mutations, insertions or deletions, which creates a difficulty for the selection of universal primers that would cover all whole copies of this element. Therefore, we selected all unique sequence variants for terminal inverted repeats and used them as primers to identify and obtain complete MITE elements for genomes of other cereals and as a negative control, we used the genome of human and long-horned nomad bee (Nomada hirtipes). Since the sequences of terminal inverted repeats for Athos element were different and quite degenerate, we used all 46 unique variants simultaneously as Forward primer in the analysis. The same primer will act as Forward and also Reverse. The length of the primers was 15 nucleotides, which localise to the furthest region of the terminal inverted repeat at the Athos element. The size for the amplicon in this case could be 30 to 200 nucleotides, including truncated elements with a central part. We used search conditions with control options: type=primer number3errors=0; minlen=30; maxlen=200. The results of this analysis are represented in Table 2. In the genome of Hordeum vulgare we identified 768 Athos and related elements, which is much more than was detected by blast analysis (205 copies for GCF_904849725.1, Blast: RefSeq Genome Database). This is because we detected not only Athos elements but also related MITE elements with overlapping end repeats. </p> <p>In our analysis, we could only detect whole Athos and related elements that contained both repeats, whereas the central part could vary. For the Hordeum bulbosum genome, we detected a 1620 record number of complete Athos and related elements compared to other species of the Hordeum family. This corresponds to the doubled genome size of this species compared to other species of the Hordeum family. For wheat genomes (Aegilops tauschii, Triticum dicoccoides), being the most similar to species of the Hordeum family, numerous copies of the related Athos and related elements were detected, with this MITE occurring much more frequently in the wheat genome than in the genome of Hordeum vulgare. It is well observed that the copy number of Athos and related elements directly depends on the genome size; the larger the genome, the greater the copy number of this element detected.</p>
Linked collectors and determiners for: Revision of the land snail genus Landouria Godwin-Austen, 1918 (Gastropoda, Camaenidae) from Java.
Natural history specimen data linked to collectors and determiners held within, "Revision of the land snail genus Landouria Godwin-Austen, 1918 (Gastropoda, Camaenidae) from Java". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/2da65c0a-9c48-43f5-ada3-e088de28dec1">https://bionomia.net/dataset/2da65c0a-9c48-43f5-ada3-e088de28dec1</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/2da65c0a-9c48-43f5-ada3-e088de28dec1">https://gbif.org/dataset/2da65c0a-9c48-43f5-ada3-e088de28dec1</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Hiding in plain sight on Gunung Muria: A new species and first record of rock gecko (Cnemaspis Strauch, 1887; Squamata, Gekkonidae) from Java, Indonesia.
Natural history specimen data linked to collectors and determiners held within, "Hiding in plain sight on Gunung Muria: A new species and first record of rock gecko (Cnemaspis Strauch, 1887; Squamata, Gekkonidae) from Java, Indonesia". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/2c57ccb3-b64d-4005-8a17-5cb6094bf131">https://bionomia.net/dataset/2c57ccb3-b64d-4005-8a17-5cb6094bf131</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/2c57ccb3-b64d-4005-8a17-5cb6094bf131">https://gbif.org/dataset/2c57ccb3-b64d-4005-8a17-5cb6094bf131</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: On the Scaphidiinae (Coleoptera: Staphylinidae) of Java, Indonesia.
Natural history specimen data linked to collectors and determiners held within, "On the Scaphidiinae (Coleoptera: Staphylinidae) of Java, Indonesia". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/482f3dde-6113-4733-945d-ae301578ea12">https://bionomia.net/dataset/482f3dde-6113-4733-945d-ae301578ea12</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/482f3dde-6113-4733-945d-ae301578ea12">https://gbif.org/dataset/482f3dde-6113-4733-945d-ae301578ea12</a>. Formatted as a Frictionless Data package.
Linked collectors and determiners for: Phyllanthus fluitans Benth. ex Müll.Arg. (Phyllanthaceae): A new record for the alien flora of Java, Indonesia.
Natural history specimen data linked to collectors and determiners held within, "Phyllanthus fluitans Benth. ex Müll.Arg. (Phyllanthaceae): A new record for the alien flora of Java, Indonesia". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/89b6c8da-48f5-480a-bc06-5d5074156d76">https://bionomia.net/dataset/89b6c8da-48f5-480a-bc06-5d5074156d76</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/89b6c8da-48f5-480a-bc06-5d5074156d76">https://gbif.org/dataset/89b6c8da-48f5-480a-bc06-5d5074156d76</a>. Formatted as a Frictionless Data package.
Figs 13-19 in Three new Marsh Beetles (Col.: Scirtidae) from New Guinea and Java
Figs 13-19: Mescirtes javanicus, nov.sp., male: (13) head, dorsal view, right scape removed to expose subantennal groove (arrow); (14) ventro-caudal view of head and part of prothorax; (15) base of right antenna, ventral view; (16) T8; 17, T9; 18, S9; 19, penis and tegmen. 13, 14 not to scale, diagrammatic; 16-18 to the same scale.
Figs 10-12 in Three new Marsh Beetles (Col.: Scirtidae) from New Guinea and Java
Figs 10-12: Prionocyphon papuanus nov.sp., male: (10) ventral view of abdominal tip, segments 8 and 9 protracted; (11) S9, half missing; (12) tegmen and penis, superimposed. 10, 11 to same scale. ep, endophallus; pd, parameroid; pe, paramere; st, stylus; te, tegmen; tr, trigonium.
Fig. 1 in Butterfly (Lepidoptera: Rhopalocera) Distribution Along An Altitudinal Gradient On Mount Tangkuban Parahu, West Java, Indonesia
Fig. 1. Number of butterfly species at different altitudes along the track from the peak of MTP at Upas Crater (2,080 m a.s.l.) to Situ Lembang (1,600 m a.s.l.). P1 to P11 = plot of samplings.
Fig. 2 in Butterfly (Lepidoptera: Rhopalocera) Distribution Along An Altitudinal Gradient On Mount Tangkuban Parahu, West Java, Indonesia
Fig. 2. Frequency of butterfly occurrence along the observation track from Upas Crater to Situ Lembang at MTP during October 2002. 1 = Mycalesis sudra; 2 = Ypthima pandocus; 3 = Pyrameis dejeani; 4 = Faunis canens; 5 = Danaus melaneus; 6 = Pantoporia selenophora; 7 = Neptis mahendra; 8 = Celastrina ceyx; 9 = Cynthia cardui; 10 = Papilio memnon; 11 = Symbrenthia hyplesis; 12 = Celastrina camenae; 13 = Potanthus omaha; 14 = Graphium sarpedon; 15 = Eurema andersonii; 16 = Heliophorus moorei; 17 = Zemeros flegyas; 18 = Chilades pandava; 19 = Jamides abdul; 20 = Abisara savitri; 21 = Lampides boeticus; 22 = Leptosia nina malayana; 23 = Kaniska canace perakana
Fig. 9 in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 9. Glyphocrangon serratirostris, new species, holotype ovigerous female (cl 22.0 mm), MZB Cru5055. A, left maxilliped 3, lateral view; B, same, ultimate article, mesial view; C, left pereopod 1, lateral view; D, left pereopod 2, lateral view; E, right pereopod 2, lateral view; F, left pereopod 3, lateral view; G, left pereopod 4, lateral view; H, same, dactylus, extensor view; I, left pereopod 5, lateral view; J, same, dactylus, extensor view.
Fig. 6 in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 6. Glyphocrangon serratirostris, new species, holotype ovigerous female (cl 22.0 mm), MZB Cru5055, habitus in lateral view, showing living colouration.
Fig. 2. Glyphocrangon juxtaculeata Chace, 1984 in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 2. Glyphocrangon juxtaculeata Chace, 1984, female (cl 17.2 mm), ZRC 2020.0296, habitus in lateral view, showing living colouration.
Fig. 5. Glyphocrangon juxtaculeata Chace, 1984 in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 5. Glyphocrangon juxtaculeata Chace, 1984, female (cl 17.2 mm), ZRC 2020.0296. A, left maxilliped 3, lateral view; B, same, ultimate article, mesial view; C, left pereopod 1, lateral view; D, left pereopod 2, lateral view; E, right pereopod 2, lateral view; F, left pereopod 3, lateral view; G, left pereopod 4, lateral view; H, same, dactylus, extensor view; I, left pereopod 5, lateral view; J, same, dactylus, extensor view.
Fig. 4. Glyphocrangon juxtaculeata Chace, 1984 in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 4. Glyphocrangon juxtaculeata Chace, 1984, female (cl 17.2 mm), ZRC 2020.0296. A, outline of carapace first carina, lateral view; B, upper part of brachial region, including posterior second and third carinae, dorsal view; C, upper part of hepatic region, including anterior fourth carina, lateral view; D, ventrolateral part of carapace; E, dorsal part of pleomere 6 and dorsoproximal part of telson, lateral view; F, right antennal scaphocerite, dorsal view (setae omitted). Abbreviations: A5C, anterior fifth (sublateral) carina; P3C, posterior third (antennal) carina; P4C, posterior fourth (lateral) carina; P5C, posterior fifth (sublateral) carina; 6C, sixth (submarginal) carina.
Fig. 1 in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 1. Habitus in lateral view, showing living colouration. A, Glyphocrangon hakuhoae Takeda & Hanamura, 1994, male (cl 12.4 mm), ZRC 2020.0295; B, G. indonesiensis Komai, 2004b, ovigerous female (cl 28.1 mm), ZRC 2020.0301; C, G. proxima Komai, 2004b, male (cl 12.3 mm), ZRC 2020.0297; D, G. serratirostris, new species, male paratype (cl 20.0 mm), ZRC 2020.0299; E, G. sibogae de Man, 1918, ovigerous female (cl 33.4 mm), ZRC 2020.0310; F, G. sibogae de Man, 1918, juvenile (cl 11.1 mm), ZRC 2020.0309.
Fig. 8 in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 8. Glyphocrangon serratirostris, new species, holotype ovigerous female (cl 22.0 mm), MZB Cru5055. A, outline of carapace first carina, lateral view; B, upper part of brachial region, including posterior second and third carinae, dorsal view; C, upper part of hepatic region, including anterior fourth carina; D, ventrolateral part of carapace; E, pleura of pleomeres 2 and 3, lateral view; F, dorsal part of pleomere 6 and dorsoproximal part of telson, lateral view; G, left antennal scaphocerite, dorsal view. Abbreviations: A5C, anterior fifth (sublateral) carina; P3C, posterior third (antennal) carina; P4C, posterior fourth (lateral) carina; P5C, posterior fifth (sublateral) carina; 6C, sixth (submarginal) carina; 7C, seventh (marginal) carina.
Fig. 10. Glyphocrangon serratirostris, new species. A in Deep-sea shrimps of the genus Glyphocrangon A. Milne-Edwards, 1881 (Decapoda: Caridea: Glyphocrangonidae) collected by the SJADES 2018 expedition off Java, Indonesia, with description of one new species
Fig. 10. Glyphocrangon serratirostris, new species. A, paratype ovigerous female (cl 20.0 mm), ZRC 2020.0298; B–E, paratype male (cl 20.0 mm), ZRC 2020.0306. A, rostrum, dorsal view; B, upper part of branchial region, including posterior second and third carina, dorsal view; C, outline of ventral margins of pleura 2–5, lateral view; D, endopod of left male pleopod 1, ventral view; E, appendices interna and masculina of left male pleopod 2, dorsomesial view.
ScienceDex guides
Understand access before you commit
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.