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Comprehensive 16s rRNA sequencing and metabolomics to investigate the effect of anticancer bioactive peptides combined with oxaliplatin on gastric cancer
<p>背景: 胃癌的发生、发展与肠道菌群密切相关。既往研究发现抗癌生物活性肽(ACBP)与奥沙利铂(OXA)联合对胃癌有显着的治疗作用,但ACBP-OXA对肠道菌群的影响仍不清楚。</p><p><strong>Methods:</strong> We established a nude mouse model of ACBP-OXA combined therapy for gastric cancer, the diversity of gut microbiota and fecal metabolomics were studied, and the correlation between gut microbiota and metabolites was analyzed.</p><p><strong>Results: </strong>ACBP-OXA联合疗法对肠道菌群具有很强的调节作用。16s rRNA研究发现,在门中,ACBP-OXA处理后,厚壁菌门和拟杆菌门的相对丰度发生显着变化,厚壁菌门的相对丰度下降,拟杆菌门的相对丰度增加。属内,ACBP-OXA组中毛螺菌科NK4AB6组的相对丰度降低,odpribacter和拟杆菌属的相对丰度增加。ACBP组乳酸菌相对丰度增加,ACBP-OXA和OXA组葡萄球菌相对丰度下降。GO和KEGG研究发现联合治疗机制与代谢和免疫有关。通过代谢组学研究,本研究发现差异代谢物与Benzenoids、Ligans、neoligans、其中脂质和脂类大多参与酪氨酸代谢、不饱和脂肪酸生物合成、苯丙氨酸代谢α-生物过程。将代谢组学与16s rRNA长寿素相结合,发现氨基酸相关代谢物与Jetgalilicus、Staphylococcus、Proteiniphilum等细菌属相关。</p><p>结论: ACBP与ACBP-OXA联合治疗可能通过改变肠道菌群的分布多样性和菌群结构来改善和恢复胃癌裸鼠的肠道菌群,这可能是抑制胃癌发生、发展的关键。该研究为进一步研究ACBP-OXA在胃癌治疗中的应用提供了新的方向。</p>
Raw sequencing data for studying the colonization of soil communities after glacier retreat
<p>Glaciers show a pattern of retreat at the global scale. Deglaciated areas are exposed and colonized by multiple organisms, but lack of global studies hampers a complete understanding of the future of these ecosystems. Until now, the complete reconstruction of soil communities was hampered by the complex identification of organisms, thus analyses at broad geographical and taxonomic scale have been so far impossible. The dataset used for this study represents the assemblages of Bacteria, Mycota, Eukaryota, Collembola (springtails), Oligochaeta (Earth worms), Insecta, Arthropoda and Vascular Plants obtained using environmental DNA (eDNA) metabarcoding. eDNA was extracted from soil samples collected from multiple glacier forelands representative of some of the main mountain chains of Europe, Asia, the Americas and Oceania. We investigated chronosequences of glacier retreat (i.e., the chronological sequence of specific geomorphological features along deglaciated areas for which the date of glacier retreat is known) ranging from recent years to the Little Ice Age (~1850). We used this newly assembled global DNA metabarcoding dataset to obtain a complete reconstruction of community changes in novel ecosystems after glacier retreat. Information on assemblages can be then combined with analyses of soil, landscape and climate to identify the drivers of community changes.</p>
Data Set for the Journal Article "Automated Preparation of Nanoscopic Structures: Graph-Based Sequence Analysis, Mismatch Detection, and pH-Consistent Protonation with Uncertainty Estimates"
<p>This repository containes the data generated by ASAP and discussed in the journal article [Csizi, K.-S. and Reiher, M., 2023, arXiv:2307.16344], including Cartesian coordinates of training and test set molecules, and MD trajectories. </p>
Fig. 17 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 17. Retouched artefacts from the Holocene levels of Puritjarra rock shelter. All are from units 1a and 1b except M10/11-1 (unit 1c). Steep-edged scrapers: N11/9-2, N6/5-3, N10/5-3. Notched implements: N9/4-3, QR9/1-9, N10/4-8. Endscraper: M10/11-1.
Fig. 18. Group 2 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 18. Group 2 retouched artefacts from the Holocene levels of Puritjarra rock shelter. All are from units 1a and 1b. Geometric microliths: top row (1–8). Thumbnail scrapers: QR9/3-4, N10/3-1, Z10/2-1, N9/3-11, M9/2-14. Tula adze slugs: M10/1-4, M9/2-3, N5/4-1. (M10/1-4 is the largest tula in this assemblage). Burren adze slug: Z9/9-2. Endscrapers: N6/3-2, Z9/5-2. (Z9/5-2 has usepolish and rounding on the distal end, and fine overhang removal scars along the platform edge).
Fig. 16 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 16. Large flake implements from late Pleistocene levels of Puritjarra rock shelter. All are from unit 2a, except N13/20-1 (unit 2b). Steep-edged scrapers: N11/19-1, N11/22-2, QR9/8-11, N12/14-3. Amorphous retouched artefacts: N5/15-12, M11/18-1, N11/19-3. Notched implements: N13/20-1, N11/21-2. Saws: N10/9-1, N5/19-1.
Fig. 15 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 15. Large flake implements from late Pleistocene levels of Puritjarra rock shelter. All are from unit 2a. Steep-edged scrapers: QR9/8-2, N5/15-11. Amorphous retouched implement: M10/22-2. QR9/8-1 is a large formal implement with extensive shallow invasive flaking and a thin convex working edge.
Fig. 13 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 13. Artefacts from the palaeosurface at c. 32,000 B.P. N13/24-1 is a large sandstone flake typical of the larger component of the flake assemblage. N13/25-3 shows a sandstone flake detached from a rotated core. Bottom two rows show small finely-made silcrete flakes. N12/26-1, M11/ 27-5 and M11/27-6 are made on exotic silcrete. M11/27-2 (2) is a chalcedony flake with a short length of retouch or edge damage. M11/27-4 (4) is a trimming flake detached from the retouched edge of a chalcedony implement.
Fig. 2 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 2. Plan of Puritjarra rock shelter showing layout of excavation trenches. Also shown are spot heights (m below
Fig. 9 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 9. Flake size and shape by analytical unit. Data are length/ breadth measurements for a representative sample of 769 complete flakes. (A) Comparison of units 1a–b (solid grey circles), and unit 2a (open squares). Late Holocene flakes are smaller and less variable in size than early Holocene/terminal Pleistocene flakes, but have similar proportions. (B) Comparison of units 2b–d (solid grey circles) and unit 2a (open squares). Late Pleistocene flakes are smaller than those in the early Holocene/terminal Pleistocene, but have similar variability and proportions.
Fig. 7 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 7. Large flakes from late Pleistocene levels of Puritjarra rock shelter. All are from unit 2a except M11/26-1 (unit 2b). M10/16-2 is an ironstone flake struck from a horsehoof core, and has fine overhang-removal flaking along the platform edge. M10/20-3 is chert flake with evidence of a prior platform, showing that the core was rotated before this flake was detached.
Fig. 6 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 6. Small flakes from late Pleistocene levels of Puritjarra rock shelter. From unit 2c: N10/11-1. From unit 2b: N12/21-8, N12/21-15, N12/23-1, N18/13-1, M11/25-2. Remainder are from unit 2a. N12/21-8 and N12/17-4 each have a series of fine flakes scars along the platform edge, showing trimming of an overhang prior to detachment of the flake. N12/19- 5 exhibits a facetted platform. N11/22-5 is a sandstone flake struck from a bifacial core.
Fig. 1 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 1. The western part of central Australia showing the location of Puritjarra rock shelter and regional topography
Fig. 12 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 12. Cores and redirecting flakes from the Holocene levels of Puritjarra rock shelter or from nearby Murantji rock hole. From unit 1a: QR9/1-3. From unit 1b: M11/8-6, N5/6-2. From unit 1c: M10/12-19. Unassigned 1b–c: ST5/3-4, ST5/4-4. M10/12-19 and M11/8- 6 are sandstone redirecting flakes. N5/6-2 is a single platform core split during knapping. QR9/1-3 is a small horsehoof core, with a base (shown) reduced as a bifacial core. The large platform core from Murantji (3) is on a flake of yellow-grey chert.
Fig. 10 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 10. Multivariate analysis of flake attributes, using the Canonical variates program in the MVARCH package. Data are for flakes where the full set of platform and flake attributes can be measured (N = 635). Scatter-plot shows the centroids for groups of flakes from each unit plots these against flake variables—raw material grain-size, flake weight, percentage cortex, length, breadth, thickness, platform breadth, platform thickness, platform angle, platform preparation, overhang removal, evidence of core rotation, and the number of flake scars on the dorsal surface.
Fig. 5 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 5. Graph showing increasing use of chert and chalcedony over time. Data are number of chert and chalcedony artefacts per spit (excavation unit), expressed as percentage of total number of artefacts in each spit. The plot shows data for the Main Trench only (excluding the following: spits without lithics; spits in 2d with only doubtful artefacts, features intrusive from higher levels).
Fig. 11 in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 11. Cores from terminal Pleistocene levels of Puritjarra rock shelter. All are from unit 2a. N5/22-1 is a bifacial core on sandstone. Remainder of artefacts are single platform cores. N9/9-2 is a small finely-made silcrete core with a flaked platform and fine overhang removal scars. N9/9-3 is a horsehoof core made on a cobble of exotic silcrete.
Fig. 4. Schematic diagram showing stratigraphic correlations between trenches. Layers I in Characterizing Late Pleistocene and Holocene Stone Artefact Assemblages from Puritjarra Rock Shelter: A Long Sequence from the Australian Desert
Fig. 4. Schematic diagram showing stratigraphic correlations between trenches. Layers I–III are labelled in bold. Identifiable cultural horizons (units 1a, 2a and 2c) are shown (stippled), as well as dated hearths (plano-convex features), 14C determinations (hatched rectangles), luminescence dates (open rectangles) and the maximum depth of late Holocene artefacts in each trench (T tula adzes; B backed artefacts/geometric microliths). Grid lines show depth (cm) below site datum. Horizontal stippled lines at 120 cm depth in N5/ N6 and in the Main Trench show the position of a silty band identified in grain-size analyses.
Fig. 2 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences
Fig. 2. The neighbour-joining (A) and Bayesian (B) trees for Suncus inferred from 1140 base-pairs of cytochrome b gene sequence. Bootstrap and posterior probability values are given above branches.
Fig. 1 in Phylogenetic Relationships Of Malayan And Malagasy Pygmy Shrews Of The Genus Suncus (Soricomorpha: Soricidae) Inferred From Mitochondrial Cytochrome B Gene Sequences
Fig. 1. Male Malayan pygmy shrew (Suncus malayanus) captured in the Cameron Highlands, Pahang, Peninsular Malaysia, in a pitfall trap set on the forest floor. Notice the characteristic large ears and dark fine pelage.
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.