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13,864 results for “staging”
Staged Separation Logic for Unrestricted Effect Handlers
<p>To support our paper submission: Separation Logic for Unrestricted Effect Handlers. </p> <p>This repository provides the latest version of the implementation (in the code folder) and testing benchmark (in the benchmark folder) here.</p> <p> </p>
FIG. 3 in Few Impacts of Introduced Cutthroat Trout (Oncorhynchus clarki) on Aquatic Stages of Boreal Toads (Anaxyrus boreas boreas)
FIG. 3. Estimated relationships between Cutthroat Trout habitat use and water depth (a), vegetation density (b), and temperature (c) by using the most parsimonious occupancy model, Ψ(size + depth + veg + temp), p(.), during the embryo stage of Boreal Toad development. Relationships with each covariate is plotted using the average values of other covariates. The dashed line designates the relationship for small Cutthroat Trout, and the solid line represents the relationships for large Cutthroat Trout. Shaded areas represent 95% confidence intervals. In (a) and (b), the circles indicate the vegetation density and predicted use at the three egg mass locations. In (c), the squares indicate the average morning temperatures and predicted use at the three egg mass locations. The triangles represent the same for the average evening temperatures.
FIG. 1 in Few Impacts of Introduced Cutthroat Trout (Oncorhynchus clarki) on Aquatic Stages of Boreal Toads (Anaxyrus boreas boreas)
FIG. 1. Map of Rocky Mountain National Park and its major water bodies. The two study sites, Spruce Lake and Fay Lakes, are denoted by black triangles.
FIG. 2 in Few Impacts of Introduced Cutthroat Trout (Oncorhynchus clarki) on Aquatic Stages of Boreal Toads (Anaxyrus boreas boreas)
FIG. 2. Photograph of two caged Boreal Toad egg mass halves at Spruce Lake. The paired exposed egg mass halves are not visible, but located directly adjacent to each cage.
Staged Snakemake Workflow: stage
This is a a snapshot of the outputs of a Snakemake workflow
Supporting information for the RNAct Data Science Wizard (DSW) knowledge model for early-stage researchers.
<p>The two attached Excel sheets contain information about the datasets collected by the Early Stage Researchers (ESRs) in the RNAct MSCA-ITN project (RNAct_datasets.xlsx) and on the questionnaire that was put to the ESRs in relation to the Data Science Wizard (DSW) knowledge model that was developed as part of RNAct. </p> <p>The zip file contains data in relation to the Data Science Wizard template development:</p> <p>- DMP_1stRound_introductory_presentation.pdf: Presentation for the ESRs to prepare them for filling in the first version of the DMP</p> <p>- DMPs_1stRound, DMPs_2ndRound: The filled in DMPs by the ESRs in the first and second round</p> <p>- RNAct-ESRtraining-KM_1.0.3.km: The first version of the knowledge model to create the DMP</p> <p>- RNAct-ESRtraining-KM_1.0.14.km: The second and final version of the knowledge model to create the DMP</p> <p>- TemplateDMP_RNAct-ESRtraining-KM_1.0.14.pdf: A PDF overview of the second and final version of the knowledge model</p>
FIGURE 8. Zoea V in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 8. Zoea V of Lysmata ankeri Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod; L) second pereiopod; M) fifth pereiopod; N) third and fourth pereiopods as buds; and O) uropods and telson. (Scale: A, B = 0.5 mm; C, D, I–K, M, O = 0.2 mm; H, L, N = 0.1 mm; E–G = 0.05 mm).
FIGURE 9 in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 9. Morphological characters of larval shrimp of the genus Lysmata Risso, 1816. Phylogeny adapted from Baeza et al. (2009), Baeza (2010), and Alves et al. (2018). Character 1: present in all zoeae; Characters 2–8: only in zoea I; Characters 9–11: only in zoea II; Characters 12–14: only in zoea III. Legend: Character 1, Pterygostomial spine: ● presence Q absence; Character 2, Pereiopod buds: ● in the 1st Q in the 1st–5th ● in the 1st and 2nd; Character 3, Setae in the outer flagellum of the antenulle: ● two Q one; Character 4, Segments in the antenna exopod: ● six Q five; Character 5, Terminal setae on the exopod of the first maxilliped: ● four Q three; Character 6, Base of the second maxilleped with setae distributed in: ● 1+2 Q 2+2 ● 1+2+3; Character 7, Segments in the endopod of the third maxilliped: ● five Q four; Character 8, A pair of simple seta on the third pleonal somite: ● presence Q absence; Character 9, Antenna endopod: ● small and conical shape Q long plumose seta; Character 10, Setae in the antenna scaphocerite: ● eight Q six ● five; Character 11, Pereiopods 1st and 5th: ● developed and functional Q buds or absence; Character 12, Setae in the inner flagellum of the antenulle: ● two Q one; Character 13, Setae in the inner margem of the antenna: ● ten Q eleven ● ≥ twelve; Character 14, Setae in the uropod exopod: ● ≤ nine Q ten ● ≥ eleven.
FIGURE 7. Zoea IV in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 7. Zoea IV of Lysmata ankeri Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod; L) second pereiopod; M) fifth pereiopod; N) third pereiopod as bud; and O) uropods and telson. (Scale: A, B = 0.5 mm; C, D, I–K, M, O = 0.2 mm; H, L = 0.1 mm; E–G, N = 0.05 mm).
FIGURE 6 in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 6. Zoea III of Lysmata ankeri Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod; L) second pereiopod as bud; M) fifth pereiopod as bud; and N) uropods and telson. (Scale: A = 0.5 mm; B–D, I–K, N = 0.2 mm; H, L, M = 0.1 mm)
FIGURE 5. Zoea II in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 5. Zoea II of Lysmata ankeri Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod as bud; L) fifth pereiopod as bud; and M) uropods and telson. (Scale: A–B, I, J, M = 0.2 mm; C, D, H, K, L = 0.1 mm; E–G = 0.05 mm).
FIGURE 4. Zoea I in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 4. Zoea I of Lysmata ankeri Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod as bud; and L) telson. (Scale: A, B, I, J, L = 0.2 mm; C, D, H, K = 0.1 mm; E–G = 0.05 mm).
FIGURE 2. Zoea II in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 2. Zoea II of Lysmata bahia Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod as bud; L) fifth pereiopod as bud; and M) uropods and telson. (Scale: A, B, I, J, M = 0.2 mm; C, D, H = 0.1 mm; E–G, K, L = 0.05 mm).
FIGURE 3 in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 3. Zoea III of Lysmata bahia Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod; L) second pereiopod as bud; M) fifth pereiopod as bud; and N) uropods and telson. (Scale: A = 0.5 mm; B–D, I–K, N = 0.2 mm; H, L, M = 0.01 mm; E–G = 0.05 mm).
FIGURE 1. Zoea I in Morphology of the early larval stages of Lysmata ankeri Rhyne & Lin, 2006 and Lysmata bahia Rhyne & Lin, 2006 (Caridea: Lysmatidae) and a review of the larval morphology of the early Lysmata stages
FIGURE 1. Zoea I of Lysmata bahia Rhyne & Lin, 2006. A) dorsal view; B) lateral view; C) antennule; D) antenna; E) mandibles; F) maxillule; G) maxilla; H) first maxilliped; I) second maxilliped; J) third maxilliped; K) first pereiopod as bud; and L) telson. (Scale: A, B, I, J, L = 0.2 mm; C, D, H = 0.1 mm; E, F, G, K = 0.05 mm).
Dabrafenib plus trametinib versus anti-PD-1 monotherapy as adjuvant therapy in BRAF V600-mutant stage III melanoma after definitive surgery: a prospectively-powered multicenter, retrospective cohort study
<p><strong>Summary </strong></p> <p>Background Both dabrafenib/trametinib (D/T) and anti-PD-1 monotherapy (PD-1) are approved adjuvant therapies for patients with stage III BRAF V600-mutant melanoma. However, there is still a lack of head-to-head comparative data. We aimed to describe efficacy and toxicity outcomes for these two standard therapies across melanoma centers.</p> <p>Methods This prospectively-powered multicenter, retrospective cohort study was conducted in 15 melanoma centers in Australia, China, Germany, Italy, Japan, UK, and US. We included adult patients with resected stage III BRAF V600-mutant melanoma who received either adjuvant D/T or PD-1. The primary endpoint was recurrence-free survival (RFS). Secondary endpoints included overall survival (OS), recurrence pattern and toxicity.</p> <p>Findings We included 598 patients with stage III BRAF V600-mutant melanoma who received either adjuvant D/T (n=393 [66%]) or PD-1 (n=205 [34%]) post definitive surgery between Jul 2015 and Oct 2022. At a median follow-up of 33 months (IQR 21-43), the median RFS was 51∙0 months (95%CI 41∙0-not reached [NR]) in the D/T group, significantly longer than 44∙8 (95%CI 28∙5-NR) in the PD-1 group (univariate: HR 0∙658, 95%CI 0∙498-0∙869, P=0∙003; multivariate: HR 0∙687, 95% CI 0∙512-0∙922, P = 0∙012), with comparable OS with PD-1 (multivariate, HR 1∙011, 95%CI 0∙637-1∙604, P>0∙95). Similar findings were observed using a restricted-mean-survival-time model. D/T survival benefits were consistent in most subgroups, except for older, male patients and those with V600K mutation. Among those who experienced recurrence, the proportion of distant metastases was higher in the D/T cohort. D/T had a higher incidence of treatment modification due to adverse events (AEs) than PD-1, but fewer persistent AEs.</p> <p>Interpretation In patients with stage III BRAF V600-mutant melanoma post definitive surgery, D/T yielded better RFS than PD-1, with higher transient but lower persistent toxicity, and comparable OS. D/T is potentially a superior adjuvant option compared with PD-1. </p>
Transmission of beneficial yeasts accompanies offspring production in Drosophila – an initial evolutionary stage of insect maternal care through manipulation of microbial load?
<p>Parent-to-offspring transmission of beneficial microorganisms is intimately interwoven with the evolution of social behaviors. Ancestral stages of complex sociality-microbe vectoring interrelationships may be characterized by high costs of intensive parental care and hence only a weak link between the transmission of microbial symbionts and offspring production. We investigate the relationship between yeast symbiont transmission and egg-laying, as well as some general factors thought to drive the 'farming' of microscopic fungi by the fruit fly <em>Drosophila</em> <em>melanogaster</em>, an insect with no obvious parental care but which is highly dependent on dietary microbes during offspring development. The process of transmitting microbes involves flies ingesting microbes from their previous environment, storing and vectoring them, and finally depositing them in a new environment. This study revealed that fecal materials of adult flies play a significant role in this process, as they contain viable yeast cells that support larval development. During single patch visits, egg-laying female flies transmitted more yeast cells than non-egg-laying females, suggesting that dietary symbiont transmission is not random, but linked to offspring production. The crop, an extension of the foregut, was identified as an organ capable of storing viable yeast cells during travel between egg-laying sites. However, the amount of yeast in the crop reduced rapidly during periods of starvation. Although females starved for 24 hours deposited a smaller amount of yeast than those starved for 6 hours, the yeast inoculum produced still promoted the development of larval offspring. The results of these experiments suggest that female <em>Drosophila</em> fruit flies have the ability to store and regulate the transfer of microorganisms beneficial to their offspring via the shedding of fecal material. We argue that our observation may represent an initial evolutionary stage of maternal care through the manipulation of microbial load, from which more specialized feedbacks of sociality and microbe management may evolve.</p>
two-stage DEA data of the NHRD system
<p>A two-stage data envelopment analysis model to evaluate the efficiency of the talent cultivation and talent utilization of NHRD systems in various countries from the perspective of HRD. The research samples mainly included OECD members, but also included BRIC countries such as China, Brazil, and Russia. After eliminating the countries with incomplete data, there were finally 60 countries. Variable data sources included the Government Finance Statistics Yearbook (GFSY) 2013 (IMF, 2014), the OECD Main Science and Technology Indicators (2014) (OECD, 2014), the World Talent Report (WTR), and the World Competitiveness Yearbook (WCY), both issued by the Institute for Management Development IMD (2014–2017) between 2014 and 2017, the WIPO Statistics Database (2016), the Conference Board Total Economy Database (2017), and World Bank Open Data (2016). Considering that there was a delay, there was a time gap of at least one year between the inputs and outputs. The evaluation period was from 2013 to 2017, for a total of five years.</p>
Microscopy-based assessment of H3K27-acetylation at RNA polymerase II clusters during early stages of zebrafish embryo development
<p>This repository contains the data and MatLab analysis scripts of the analysis of histone 3 lysine 27 acetylation (H3K27ac) at RNA polymerase II clusters over the course of zygotic genome activation and gastrulation of zebrafish embryos. Samples were prepared and images were recorded by Marcel Sobucki in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert.</p> <p>To analyse date data, the raw image data are first extracted into MatLab-native files using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/MultiPosition_extraction_nd2.m">MultiPosition_extraction_nd2.m</a> script. The actual analysis is then carried out using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ClusterAnalysis.m">ClusterAnalysis.m</a> script. Example microscopy images were produced using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ExampleImages.m">ExampleImages.m</a> script. The extracted data can be reviewed using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ReviewExtractedStacks.m">ReviewExtractedStacks.m</a> script.</p> <p>Additional data needed to be stored in an extra repository due to size limitations: <a href="https://doi.org/10.5281/zenodo.8028508">https://doi.org/10.5281/zenodo.8028508</a></p>
Scripts & Raw data - developmental staging of zebrafish embryos based on intra-nuclear distances
<p>Scripts & microscopy image data required for the generation of a developmental staging chart for blastula stage zebrafish embryos. The generated staging chart allows using inter-nuclear distances as a marker for developmental progress.</p> <p>This repository contains the script <em>ProcessTimeLapse.m</em> to process the raw <em>.czi</em> files obtained with a Zeiss Lightsheet microscope. The raw data are not contained, due to excessive file size of >700 GB, but can be obtained upon request. The second script <em>NearestNeighborStaging_Calibration.m</em> processes files obtained with the first script so as to provide the nearest-neighbour distances between nuclei over time. The intermediate <em>.mat</em> files are provided in this repository, so that this step of the analysis can be fully reproduced.</p> <p>To carry out the analysis, the Open Microscopy Environments BioFormats plugin <em>bfmatlab</em> must be added to the MatLab path. Additional monitoring of parallel processing progress is provided via the <em>parfor_progress.m</em> function.</p>
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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.