📥 Inbound Notifications 669

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2026-04-05 06:53:40 urn:uuid:5f0787d7-5d22-4070-9d57-e720633a2b21 https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "The last paper was A L2-Norm Regularized Pseudo-Code for Change Analysis in Satellite Image Time by Anamaria Radoi and Mihai Datcu."
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2026-04-05 06:53:16 urn:uuid:ebd95358-5293-4890-8f85-b05a6054097f https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "Actuellement, il est plus simple d'obtenir les s\u00e9quences codantes des g\u00e8nes de ces esp\u00e8ces en s\u00e9quen\u00e7ant leurs transcriptomes puis en les assemblant \u00e0 partir de donn\u00e9es RNA-Seq plut\u00f4t que de s\u00e9quencer leur g\u00e9nome puis d'inf\u00e9rer les s\u00e9quences codantes.Il existe des bases de donn\u00e9es publiques contenant des alignements de s\u00e9quences de g\u00e8nes de diff\u00e9rentes esp\u00e8ces mod\u00e8les pour l'ensemble des familles de g\u00e8nes connus (Ensembl Compara (HERRERO et collab., 2016), Orthomam (DOUZERY et collab., 2014), EGNOGG (HUERTA-CEPAS et collab., 2015))."
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2026-04-05 06:53:16 urn:uuid:e464a683-97be-447a-8d6d-3b6848fdeaf8 https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "Ensuite, chacun des clusters est align\u00e9 avec MAFFT                           puis nettoy\u00e9 avec HMMCleaner (FRANCO et collab., 2019) afin d'enlever les r\u00e9gions mal align\u00e9es."
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2026-04-05 06:53:16 urn:uuid:df72d471-27ba-4047-9b03-b15c501fec3d https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "Trinity, Grabherr et al. (2011)].",
            "Par exemple, nous avons choisi comme assembleur de novo Trinity (GRABHERR et collab., 2011).",
            "Les lectures nettoy\u00e9es sont ensuites assembl\u00e9es de novo avec Trinity (GRABHERR et collab., 2011).",
            "First, CAARS performs a de novo assembly using the commonly used program Trinity (Grabherr et al., 2011).",
            "Then, we used Cap3 (Huang and Madan, 1999) (default parameters) to assemble overlapping Trinity contigs.",
            "On data coming from the Ensembl database, it compared favorably to a pipeline combining Trinity and BLAST, and provided more complete sets of orthologs than Ensembl.",
            "On the same hardware, for each target species, we first assembled RNA-Seq reads into transcripts with Trinity                         using default parameters.",
            "In the standard pipeline, used e.g. in Marra et al. (2014); Konczal et al. (2014); Pereira et al. (2016); Thompson and Ort\u0131 \u00b4(2016) and Ishikawa et al. (2016), the assembly is performed de novo by Trinity (Grabherr et al., 2011) and the annotation by RBH using BLAST (Camacho et al., 2009)."
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2026-04-05 06:53:16 urn:uuid:b8c0f285-b82a-4b45-b8c8-d476c2c4f1fd https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "CAARS is written in the Python programing language for all intermediate steps and in the OCaml language for the main program orchestrating all computational steps.",
            "-The multinomial method has been implemented de novo in Python as well as the identical and topological methods which additionally use executables from the bppsuite [30]."
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            "We used the simulator and benchmark tool of the PCOC toolkit to produce the data used in the panels A and B of figures 2 and 3. We extracted the subtree containing mammals only from the Ensembl Compara tree                                          , and used it to position a random number X of convergent events between two and seven."
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2026-04-05 06:53:16 urn:uuid:9bc43de4-f9fa-4815-b93a-830b36b6b450 https://datalake.inria.fr https://inria.hal.science ["Offer","coar-notify:ReviewAction"]
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            "In addition, RNA-Seq reads are formatted as BLAST databases, one per target species.",
            "The de novo assembled transcripts are dispatched to gene families using BLAST.",
            "Finally, we retained only transcripts associated by RBH with a guide species transcript using BLAST                        with an evalue of 1e \u00c0 6 and using blastn as task option.",
            "On data coming from the Ensembl database, it compared favorably to a pipeline combining Trinity and BLAST, and provided more complete sets of orthologs than Ensembl.",
            "This step is most often treated by Reciprocal Best Hits (RBHs) (Rivera et al., 1998), typically using BLAST (Camacho et al., 2009), which cannot handle species-specific duplications (Altenhoff and Dessimoz, 2009;Tekaia, 2016).",
            "For each gene of the reference transcriptome and each assembly, we retrieved the RBH sequence when available, using BLAST with a stringent e-value threshold (1e \u00c0 10) and otherwise default parameters                       .",
            "To identify these partial and alternative transcripts, we aligned each transcript of each assembly to the reference transcriptome [BLAST (Camacho et al., 2009) with evalue \u00bc 1e \u00c0 10, and otherwise default parameters], and retrieved the Best Hit sequence (BH).",
            "1 2 1 2 1 2 Paired-end RNA-seq data Blast bait sequence on database of reads Retrieve paired reads de novo assembly Bait sequence contigs Filtering of contigs Formating of reads in BLAST database filtered contig Improvement comparing to the previous iteration?",
            "In particular, the Target Restricted Assembly Method (TRAM) by                      , automated in aTRAM                     , reconstructs a gene sequence by an iterative process where reads are collected by sequence similarity to a reference genome using BLAST                        and then assembled.",
            "J'ai ainsi observ\u00e9 que la diff\u00e9rence d'expression entre esp\u00e8ces est moins importante dans un jeu de donn\u00e9es construit avec CAARS, que dans un jeu de donn\u00e9es construit par un pipeline traditionnel (obtenu par assemblage de novo, puis association des contigs par BLAST dans des familles de g\u00e8nes pr\u00e9existantes).",
            "In the standard pipeline, used e.g. in                                                                  ;                           and                       , the assembly is performed de novo by Trinity                         and the annotation by RBH using BLAST                       ."
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            "On the left, the Ensembl Mammalian phylogeny has been represented, and five transitions have been randomly placed on its branches (black boxes).",
            "We downloaded the Ensembl Compara dataset from the Ensembl database [release                          ;                    ].",
            "For instance, in the Ensembl database                                         ) 10% of all Human genes have no one-to-one orthology relationships with mouse genes.",
            "On data coming from the Ensembl database, it compared favorably to a pipeline combining Trinity and BLAST, and provided more complete sets of orthologs than Ensembl.",
            "We obtained their phylogeny from the Ensembl Github repository                                           (Supplementary Fig.   ).",
            "We used the mammalian subtree of the Ensembl Compara phylogeny, but similar results were obtained on other phylogenies (a phylogeny of birds from Jarvis et al., 2014, a phylogeny of Rodents from                    , and a phylogeny of the PEPC gene in sedges; supplementary figs.",
            "Dans ce cas, le transcriptome provenant d'Ensembl est privil\u00e9gi\u00e9.",
            "This is demonstrated here with families from the Ensembl Compara database.",
            "We downloaded the Ensembl Compara dataset from the Ensembl database [release                          ;                    ].",
            "Thanks to its high quality output gene trees, CAARS also improves upon Ensembl Compara in terms of the number of orthologs it can recover.",
            "Notably, we found that it could recover more sets of orthologs than the Ensembl Compara pipeline and was better at recovering one-to-many or many-to-many orthologs than the standard pipeline, probably because it relies on gene trees reconstructed with a reconciliation approach.",
            "This is substantially more than the number found by the equivalent request in Ensembl Compara (4505 sets of genes with high confidence one-to-one orthology relationship), a gain attributable to our reconciliation step, which improves gene trees                       .",
            "We compared the set of orthologs obtained without target species to the 'high confidence' orthologs available on the Ensembl Compara database.",
            "We computed the percentage of the reference transcript that aligns with the reconstructed transcript (P reference ) for 11 577 Ensembl CDS with a matched sequence in at least one of the assemblies (Fig. 2C).",
            "On data coming from the Ensembl database, it compared favorably to a pipeline combining Trinity and BLAST, and provided more complete sets of orthologs than Ensembl.",
            "Les donn\u00e9es d'entr\u00e9e de ce pipeline sont les assemblages de novo du pipeline pr\u00e9c\u00e9dent auxquels on ajoute les transcriptomes complets des esp\u00e8ces provenant d'Ensembl.",
            "Le jeu de donn\u00e9es \"s\u00e9quences\" est compos\u00e9 de 30 esp\u00e8ces, 11 pour lesquelles nous avons uniquement des donn\u00e9es RNA-Seq, 10 pour lesquelles on a seulement les transcriptomes complets 4. D\u00e9tection de la convergence dans un jeu de donn\u00e9es r\u00e9elles provenant d'Ensembl (Version 92) et 9 pour lesquelles on a les deux.",
            "As CAARS annotates transcripts using a phylogeny, it is expected to be more effective than the standard pipeline, which used a RBH annotation, to retrieve genes in the target species that have been duplicated since the divergence with the guide species (one-tomany or many-to-many orthologs in Ensembl Compara).",
            "S E Tamias sibiricus 769 141 S Ictidomys tridecemlineatus 601 51 S E Fukomys mechowii 1243 1 S E Fukomys micklemi 808 1 S E 655 10 Heterocephalus glaber S E Fukomys damarensis 455 1 S E Chinchilla lanigera 81 10 S Octodon degus 468 7 S Cavia aperea 1117 147 S E Cavia porcellus 1474 152 S Dipodomys ordii 327 34 S E Dipodomys spectabilis 343 25 S E Chaetodipus baileyi 277 11 S E Heteromys desmarestianus 2223 152 S Cricetulus griseus 338 13 S E Mesocricetus auratus 339 36 S Microtus ochrogaster 869 73 S E Myodes glareolus 638 111 S E Peromyscus eremicus 290 4 19 S E Peromyscus leucopus 934 134 S Peromyscus maniculatus 487 55 S E Meriones unguiculatus 137 3 S E Rattus norvegicus 746 143 S E Mus caroli 1841 46 S E Mus musculus 627 82 S Mus spretus 592 104 S E Mus pahari 2595 42 S E Eospalax fontanierii 527 11 S Nannospalax galili 508 0 S Jaculus jaculus 74 0 0.01 Family: Muridae Octodontidae Caviidae Dipodidae Chinchillidae Sciuridae Cricetidae Bathyergidae Heteromyidae Spalacidae S: Sequences de novo Ensembl E: Expression Bio12: <= 500mm > 500mm > 1500mm Bio14: <= 10mm > 10mm Bio17: <= 40mm > 40mm BIO12 = Annual Precipitation BIO14 = Precipitation of Driest Month BIO17 = Precipitation of Driest Quarter Dataset Ph\u00e9notype convergent Transition vers ph\u00e9notype convergent Ph\u00e9notype ancestral"
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            "System outputs are not always uniquely determined by a single input, a phenomenon known as input redundancy, where different inputs produce the same output.",
            "System \u03a3, according to Definition 2.1, can be described by the following equations for all t \u2265 0:",
            "System \u03a3 HEV does not belong to the class of over-actuated systems when considering the B matrix in Equation (2.6).",
            "System \u03a3 \u03b8 is said to be Adaptively Input Redundant (a-IR) if there exist an initial condition, a parameter trajectory, and two distinct input trajectories such that the resulting output trajectories are identical, i.e.:",
            "System \u03a3 \u03b8 is said to be a-IR, uniformly in \u03b8 if, for all parameter trajectories, there exist an initial condition and two distinct input trajectories such that the resulting output trajectories are identical, i.e.:",
            "System \u03a3 \u03b8 is said to be Robustly Input Redundant (r-IR) if there exist an initial condition and two distinct input trajectories such that, for all parameter trajectories, the resulting output trajectories are identical, i.e.:",
            "System \u03a3 \u03c3 is assumed to not be subject to continuous input u, and to be linear in the state x.",
            "System \u03a3 \u03c3 can be represented for all t \u2265 0, as follows:",
            "System (2.9) is called right-invertible if for any arbitrarily assigned impulsive-smooth output y, there exists an impulsive-smooth input u yielding that output with zero initial condition, i.e. y = y0,u [70, Def.",
            "System (4.14) is always \u03c3-IR and never \u03c3-IR of kind 2.",
            "). System \u03a3 is said to be Input Redundant (IR) if there exists an initial condition and two distinct input trajectories such that the resulting output trajectories are identical, i.e.:",
            "(i) System (2.9) is IR.",
            "and System (4.1) is not c-IR independently of \u03c3.",
            "(S2) System (2.9) is IR.",
            "From System \u03a3 \u03b8 given by Equation (3.5), the expressions at a given time t of the dynamics can be obtained by composing the matrix functions A, B, C, D depending on an indeterminate \u03be with the time-dependent signal t \u2192 \u03b8(t), as illustrated in Equation (3.6) for the matrix function A.",
            "Consider System (3.5) and let V GA \u2282 R n .",
            "Consider System \u03a3 \u03b8 in the homogeneous polynomial representation (3.16) and let V GA \u2282 R n and n F \u2208 N. Consider",
            "Assume that System (2.9) is IR.",
            "Suppose that System (2.9) is not IR.",
            "Consider an IR System (2.9).",
            "\u2022 X IR\u0338 = \u0338 = \u2205 \u21d4 System (4.14) is \u03c3-IR of kind 3.",
            "\u2022 XIR /X IR= = \u2205 \u21d4 System (4.14) is \u03c3-IR of kind 1.",
            "\u2022 XIR /X IR= \u0338 = \u2205 \u21d4 System (4.14) is \u03c3-IR of kind 3.",
            "Under Assumption 3.5, System (3.5) is a-IR (resp.",
            "\u2022 X IR /X IR= \u0338 = \u2205 \u21d2 System (4.14) is \u03c3-IR of kind 3.",
            "(S2)\u21d2(S1): Suppose that System (2.9) is IR.",
            "Under these assumptions, System \u03a3 \u03b8 can be represented, for all t \u2265 0, as follows:",
            "Under these assumptions, System \u03a3 \u03c3 can be represented for all time t \u2265 0, as follows:",
            "Second property: Assume that System (4.14) is \u03c3-IR of kind 3 and x 0 \u2208 X IR\u0338 = .",
            "By virtue of Proposition 4.2, we know that System (4.14) is either \u03c3-IR of kind 1 or 3. Let us proceed point by point.",
            "The weakly unobservable input subspace N of System (2.9) is defined as the set of input directions 4 that produce a zero output when the state is confined to the weakly unobservable subspace V \u22c6 .",
            "[70, Section 7.3] The weakly unobservable subspace V \u22c6 of System (2.9) is defined as the set of points x 0 \u2208 R n for which there exists an input u such that the corresponding output y x 0 ,u is identically zero.",
            "G \u2282 R n be the generalized weakly unobservable subspace of System (3.5) and let N GA n F =0 denote its generalized adaptively weakly unobservable input application.",
            "Let V \u22c6 GAn F \u2282 R n be the n F -generalized adaptively weakly unobservable subspace of System (4.5) and N GAn F its n F -generalized adaptively weakly unobservable input application.",
            "(i) \u21d2 (ii) Let V G be a generalized controlled invariant and output invisible subspace of System (3.5).",
            "Finally, note the one-to-one correspondence between the modes (A i , B i , C i , D i ) of System (4.3) and the polynomial representation (4.5): for any switching signal \u03c3 \u2208 S, (A(\u03c3(t)), B(\u03c3(t)), C(\u03c3(t)), D(\u03c3(t))) = (A \u03c3(t) , B \u03c3(t) , C \u03c3(t) , D \u03c3(t) ) \u2200t \u2265 0.",
            "A subspace V G \u2282 R n is called a generalized controlled invariant and output invisible subspace for System (3.5) if for any x 0 \u2208 V G , there exists an input function u \u2208 PC(R + , R m ) such that, for all parameter trajectories \u03b8 \u2208 PC(R + , \u0398),",
            "The next lemma shows how to construct a matrix-valued polynomial that interpolates the matrices A i of System (4.3).",
            "[70, Theorem 7.11] Let V \u22c6 and N be the weakly unobservable subspace and weakly unobservable input subspace of System (2.9), respectively.",
            "A subspace V GA \u2282 R n is called a generalized adaptively controlled invariant and output invisible subspace for System (3.5) if for all x 0 \u2208 V GA and all parameter trajectory \u03b8 \u2208 PC(R + , \u0398), there exists an input function u \u2208 PC(R + , R m ) such that",
            ",  ,  ,  ) : \u0398 \u2192 (R n\u00d7n , R n\u00d7m , R p\u00d7n , R p\u00d7m ) be a quadruple of polynomial matrix-valued functions, associated with System (3.5).",
            "Before providing tractable characterizations of the sets V G and V GA , we first need to obtain a homogeneous polynomial representation of System (3.5), which underpins our subsequent results.",
            "By virtue of Theorem 2.1, this is equivalent to dim(N ) = 0 where we recall that N = B -1 V \u22c6 \u2229 ker {D} and V \u22c6 is the weakly unobservable subspace of System (2.9).",
            "The remainder of this section is therefore devoted to developing tractable characterizations of these sets, enabling a systematic procedure to decide whether System (4.14) is \u03c3-IR of kind 1 or kind 3.",
            "Taking \u03b8 : t \u2192 \u03b8(t) = \u03be such that dim(Im {L(\u03be)}) > 0, thus we can take w such that L(\u03b8(t))w(t) \u0338 = 0 for t in some non-zero measure interval, so that u a \u0338 = u b and System (3.5) is a-IR.",
            "for all \u03be \u2208 \u0398, then these subspaces do not have a zero dimension either, and conditions (3.48) and ( 3 with N GA n F =0 the n F = 0-generalized adaptively weakly input application of System (3.5).",
            "The strategy presented in this chapter is a generalized framework dealing both with polynomial systems considering polynomial or constant friends and with the cases already covered in the literature, that are presented now. 1. System (3.16) with linear dependence and with constant friends [48]: The system matrices present a linear dependence on the parameter, then n A = n B = n C = n D = 1 and",
            "Parameter Value Unit Fueling delay (t d ) 90 ms Combustion lag (\u03c4 ) 140 ms Motor armature resistance (R a ) 1 \u2126 (Ohm) Motor armature inductance (L a ) 0.3 H (Henry) Motor back EMF constant (K) 0.25 Vsrad -foot_0 Effective hybrid rotational inertia (J) 0.6 kgm 2 s -2 Effective hybrid rotational damping (b) 0.125 Nms Coefficient related to the torque loss (m) 0.12 -Radius of the wheel (r) 0.3 m Table 2.1: System Parameters and Values."
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            "type": "SoftwareSourceCode",
            "name": "PyMOL",
            "codeRepository": null,
            "referencePublication": null
        },
        "mentionType": "software",
        "mentionContext": [
            "Trajectories of 7l s were obtained and further analyzed with the Gromacs tools and visualized in PyMOL, which served to create the illustrations (Schrodinger, 2015)."
        ]
    }
}