📥 Inbound Notifications 669

Time â–¾ Id From To Type Content
2026-04-05 06:50:26 urn:uuid:65892683-4f88-4ef8-b150-cb3be92477f6 https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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2026-04-05 06:50:25 urn:uuid:debd2af7-e5a3-4ac6-b90b-795ca02fc94f https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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2026-04-05 06:50:21 urn:uuid:36bfceea-ab08-4907-9604-0c9ccf94bd67 https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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2026-04-05 06:50:20 urn:uuid:9c981b9a-80ae-46b9-a9cd-00727ba22af9 https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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2026-04-05 06:50:12 urn:uuid:68897c06-32fc-4c96-815a-07b0f00eacba https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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2026-04-05 06:49:57 urn:uuid:33882409-52d4-43f4-97aa-e2f617ff36ec https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "All measurements were conducted using the parameters listed in Table   and under a constant stoichiometric ratio of H2 (1.1) and air (5), with a relative humidity of 15%.    ) and (   ), a PEMFC model was built with the MATLAB/SIMULINK environment."
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2026-04-05 06:49:57 urn:uuid:2e633623-44b3-4a94-afd5-b8d1f9677dee https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "The PEMFC model was implemented in the Matlab/Simulink environment and was designed with voltage input and current output.",
            "To validate the proposed model, simulations are performed using the Matlab/Simulink environment and compared to experimental data, as detailed in Section 5."
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2026-04-05 06:49:46 urn:uuid:a9ba42fc-3a02-4fbb-8a8e-d388cfc8506b https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "MUMmer (NUCmer)    , which can deal with rearranged but slightly divergent genomes, implements a variation of this strategy, i.e. it uses exact matches that are clustered together in order to produce a non-collinear chain, but does not implement the fourth phase ('last chance alignment' phase).",
            "1) MUMmer (NUCmer) produced almost perfect alignments (99.9% of identity for Lactobacillus, 92.3% for Bacillus cereus) of limited length: on average 2.0 Mb for Lactobacillus (mean coverage: 76.6%) and 3.6 Mb for Bacillus cereus (mean coverage: 69.4%).",
            "This phenomenom was not observed in either MUMmer, or in YOC alignments, for which the proportion of gaps remained low, regardless of the divergence rate.",
            "YOC coverages were between those of MAUVE/ProgressiveMAUVE and MUMmer.",
            "Although a similar, simplified, two-phase strategy is already used in MUMmer    , the solution is not entirely satisfactory.",
            "To summarize, unlike classical WGA tools designed for similar genomes (like MGA, MUMmer (NUCmer), MAUVE, LAGAN, ProgressiveMAUVE), YOC focuses on almost collinear, highly divergent pairwise WGA, and simplifies the anchor based strategy by implementing only the first two phases (see Figure  ), without any refinement steps like realignment, filtering, or recursive alignment.",
            "Based on the preliminary results listed in Table  , we decided to compare five genome aligners, MGA, MUMmer (NUCmer), MAUVE, ProgressiveMAUVE and YOC, using the intra-species pairs of genomes from Dataset 2. Given that MUMmer (NUCmer) uses exact matches (unique or not) and that it does not include the 'last chance alignment phase' , the length of its alignment can serve as a lower bound of the number of alignable positions.",
            "For example, the number of aligned segments, a measure of the alignment fragmentation, is not directly comparable between MAUVE, ProgressiveMAUVE and the other genome aligners: for MUMmer (NUCmer), MAUVE and ProgressiveMAUVE it represents the number of Locally Collinear Blocks (LCBs) in the alignments, i.e. roughly the number of inversions and translocations; for MGA and YOC, it is the number of segments that are interrupted by insertions/deletions and local inversions (for YOC only).",
            "Based on the preliminary results listed in Table  , we decided to compare five genome aligners, MGA, MUMmer (NUCmer), MAUVE, ProgressiveMAUVE and YOC, using the intra-species pairs of genomes from Dataset 2. Given that MUMmer (NUCmer) uses exact matches (unique or not) and that it does not include the 'last chance alignment phase' , the length of its alignment can serve as a lower bound of the number of alignable positions.",
            "Figure 3b shows that increasing the level of divergence mainly affected the alignment mean percentage of identity for all four tools (which decreases linearly), but had more drastic effects on MAUVE and ProgressiveMAUVE alignments than on YOC and MUMmer alignments.",
            "Six genome aligners, all based on the anchoring strategy, were compared on the previously described genome datasets; two state-of-the-art aligners, MGA [4] and LAGAN [14], clearly target collinear genomes, three others, MAUVE [5], ProgressiveMAUVE [6] and MUMmer [9] are able to align either rearranged or collinear genomes whatever their type of rearrangements, while our new method, YOC, aligns pairs of collinear genomes (possibly including locally inversed segments but no translocated segments).",
            "Despite many efforts in this field and the availability of numerous genome aligners, some of which were specially designed for bacterial genomes (e.g., MGA    , MAUVE    , ProgressiveMAUVE    , MUGSY    , MAGIC    ) and others that target more complex genomes (e.g., MUMmer    , GRIMM-Synteny     , CHAINNET     , PipMaker     ), none is yet completely satisfactory."
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