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307 results for “Model combination”
Data from: Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional, and separate models for combined molecular phylogenetic analyses of multilocus sequence data
Proportional and separate models able to apply different combination of substitution rate matrix and among-site rate variation model to each locus are frequently used in phylogenetic studies of multilocus data. However, the selection from among nonpartitioned (i.e., a common combination of models is applied to all-loci concatenated sequences), proportional, and separate models is usually based on the researcher's preference rather than on any information criteria. The present study describes two programs, "Kakusan4" (for DNA sequences) and "Aminosan" (for amino-acid sequences), that allow the selection of evolutionary models based on several types of information criteria. The programs can handle both multilocus and single-locus data, in addition to providing an easy-to-use wizard interface and a non-interactive command line interface. In the case of multilocus data, substitution rate matrices and among-site rate variation models are compared at each locus and at all-loci concatenated sequences, after which nonpartitioned, proportional, and separate models are compared based on information criteria. The programs also provide model configuration files for MrBayes, PAUP*, PHYML, RAxML, and Treefinder to support further phylogenetic analysis using a selected model. The best-fit models were found to differ depending on the data set. Furthermore, differences in the information criteria among nonpartitioned, proportional, and separate models were much larger than those among the nonpartitioned models. These findings suggest that selecting from nonpartitioned, proportional, and separate models results in a better phylogenetic tree. Kakusan4 and Aminosan are available at http://www.fifthdimension.jp/. They are licensed under GNU GPL Ver.2, and are able to run on Windows, MacOS X, and Linux.
Data from: Are Bitcoin bubbles predictable? Combining a generalized Metcalfe's law and the LPPLS model
We develop a strong diagnostic for bubbles and crashes in Bitcoin, by analyzing the coincidence (and its absence) of fundamental and technical indicators. Using a generalized Metcalfe's law based on network properties, a fundamental value is quantified and shown to be heavily exceeded, on at least four occasions, by bubbles that grow and burst. In these bubbles, we detect a universal super-exponential unsustainable growth. We model this universal pattern with the Log-Periodic Power Law Singularity (LPPLS) model, which parsimoniously captures diverse positive feedback phenomena, such as herding and imitation. The LPPLS model is shown to provide an ex-ante warning of market instabilities, quantifying a high crash hazard and probabilistic bracket of the crash time consistent with the actual corrections; although, as always, the precise time and trigger (which straw breaks the camel's back) being exogenous and unpredictable. Looking forward, our analysis identifies a substantial but not unprecedented overvaluation in the price of Bitcoin, suggesting many months of volatile sideways Bitcoin prices ahead (from the time of writing, March 2018).
Data from: PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models. These methods allow millions of partitioning schemes to be compared in realistic timeframes, and so permit the objective selection of partitioning schemes even for large multi-locus DNA datasets. We demonstrate that these methods significantly outperform previous approaches, including the ad hoc selection of partitioning schemes (e.g. partitioning by gene or codon position), and a recently proposed hierarchical clustering method. We have implemented these methods in an open-source program, PartitionFinder. This program allows users to select partitioning schemes and substitution models using a range of information-theoretic metrics (e.g. the BIC, AIC, and AICc). We hope that PartitionFinder will encourage the objective selection of partitioning schemes, and thus lead to improvements in phylogenetic analyses. PartitionFinder is written in Python and runs under Mac OSX 10.4 and above. The program, source code, and a detailed manual are freely available from .
Figure 6 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 6 Anti-proliferation effect of EGCG and baicalin in combination treatment against EMT-6/V different doses of EGCG with a fixed dose of baicalin (70 µM).
Figure 17 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 17 Effect of baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), a combination of baicalin and EGCG (75 and 50 mg/kg/day) respectively, vincristine 2 mg/kg/every other day, combination with vincristine (75 and 50 mg/kg/day) for combination and (2 mg/kg/every other day) for vincristine, Positive control (PBS and tween 20%), and healthy group on serum AST average level measured by (IU/L) in EMT-6/P.
Figure 18 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 18 Effect of baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), a combination of baicalin and EGCG (75 and 50 mg/kg/day) respectively, vincristine 2 mg/kg/every other day, combination with vincristine (75 and 50 mg/kg/day) for combination and (2 mg/kg/every other day) for vincristine, Positive control (PBS and tween 20%), and healthy group on serum AST average level measured by (IU/L) in EMT-6/V.
Figure 13 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 13 The volume change (mm3) for treatment groups in vivo for EMT-6/P and EMT-6/V. Only statistically significant associations are shown. Positive control (PBS and tween 20%), baicalin 75 mg/kg/day, EGCG: 50 mg/kg/day, baicalin and EGCG combination 75 and 50 mg/kg/day respectively, vincristine 2mg/kg/every other day, and same doses were used in the triple therapy.
Figure 22 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 22 Effect of baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), a combination of baicalin and EGCG (75 and 50 mg/kg/day) respectively, vincristine 2 mg/kg/every other day, combination with vincristine (75 and 50 mg/kg/day) for combination and (2 mg/kg/every other day) for vincristine, positive control (PBS and tween 20%), and healthy group on average creatinine measured by (mg/dl) in EMT-6/V.
Figure 7 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 7 Caspase concentrations in (ng/ml) for each treatment group in EMT-6/V. Concentrations used were: baicalin 175 µM, EGCG 125 µM, baicalin and EGCG 140 and 100 µM respectively, vincristine 643 µg/ml, and positive control treated with MEM.
Figure 10 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 10 A plot of change in average tumor size (mm³) vs. time in (days) of treatment in the EMT-6/P cell line.
Figure 16 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 16 Effect of baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), a combination of baicalin and EGCG (75 and 50 mg/kg/day) respectively, vincristine 2 mg/kg/every other day, combination with vincristine (75 and 50 mg/kg/day) for combination and (2 mg/kg/every other day) for vincristine, positive control (PBS and tween 20%), and healthy group on serum ALT level measured by (IU/L) in EMT-6/V.
Figure 15 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 15 Effect of baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), a combination of baicalin and EGCG (75 and 50 mg/kg/day) respectively, vincristine 2 mg/kg/every other day, combination with vincristine (75 and 50 mg/kg/day) for combination and (2 mg/kg/every other day) for vincristine, positive control (PBS and tween 20%), and healthy group on serum ALT level measured by (IU/L) in EMT-6/P.
Figure 11 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 11 Tumor sizes in EMT-6/V after dissection at day 10 in all groups compared to each other, n = 7.
Figure 1 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 1 In vivo experiment: groups of EMT-6/P and EMT-6/V inoculated mice, Treatment approaches were: baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), and vincristine (2 mg/kg/every other day). The same concentrations were used in the combination treatment and triple therapy.
Figure 19 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 19 ALT serum level (U/L) in different treatment groups. Concentrations used baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), a combination of baicalin and EGCG (75 and 50 mg/kg/day) respectively, vincristine 2 mg/kg/every other day, combination with vincristine (75 and 50 mg/kg/day) for combination and (2 mg/kg/every other day) for vincristine, positive control (PBS and tween 20%), and healthy group in EMT-6/P and EMT-6/V. Including the statistical correlations between groups.
Figure 14 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 14 The volume change (mm3) for treatment groups in vivo for EMT-6/P and EMT-6/V. Only statistically significant associations are shown. Positive control (PBS and tween 20%), baicalin 75 mg/kg/day, EGCG: 50 mg/kg/day, baicalin and EGCG combination 75 and 50 mg/kg/day respectively, vincristine 2mg/kg/every other day, and same doses were used in the triple therapy.
Figure 9 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 9 Tumor sizes of EMT-6/P after dissection at day 10 in all groups compared to each other, n = 7 except for the last two groups n = 6.
Figure 8 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 8 Folds increase in caspase-3 activity and apoptosis induction, concentrations used were: baicalin 175 µM, EGCG 125 µM, baicalin, and EGCG 140 and 100 µM respectively, vincristine 643 µg/ml and positive control treated with MEM in EMT-6/V.
Figure 3 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 3 Anti-proliferative effect of EGCG in single treatment against EMT-6/P and EMT-6/V cell lines.
Figure 23 from: Awajan D, Abu-Humaidan AHA, Talib WH (2024) Study of the antitumor activity of the combination baicalin and epigallocatechin gallate in a murine model of vincristine-resistant breast cancer. Pharmacia 71: 1-20. https://doi.org/10.3897/pharmacia.71.e113446
Figure 23 Creatinine serum levels (mg/dl) in different treatment groups. Concentrations used baicalin (75 mg/kg/day), EGCG (50 mg/kg/day), a combination of baicalin and EGCG (75 and 50 mg/kg/day) respectively, vincristine 2 mg/kg/every other day, combination with vincristine (75 and 50 mg/kg/day) for combination and (2 mg/kg/every other day) for vincristine, positive control (PBS and tween 20%), and healthy group in EMT-6/P and EMT-6/V. Including the statistical correlations between groups.
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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.