Contour methods for long-range Ising models: weakening nearest-neighbor interactions and adding decaying fields

We consider ferromagnetic long-range Ising models which display phase transitions. They are long-range one-dimensional Ising ferromagnets, in which the interaction is given by $J_{x,y} = J(|x-y|)\equiv \frac{1}{|x-y|^{2-\alpha}}$ with $\alpha \in [0, 1)$, in particular, $J(1)=1$. For this class of models one way in which one can prove the phase transition is via a kind of Peierls contour argument, using the adaptation of the Fr\"ohlich-Spencer contours for $\alpha \neq 0$, proposed by Cassandro, Ferrari, Merola and Presutti. As proved by Fr\"ohlich and Spencer for $\alpha=0$ and conjectured by Cassandro et al for the region they could treat, $\alpha \in (0,\alpha_{+})$ for $\alpha_+=\log(3)/\log(2)-1$, although in the literature dealing with contour methods for these models it is generally assumed that $J(1)\gg1$, we can show that this condition can be removed in the contour analysis. In addition, combining our theorem with a recent result of Littin and Picco we prove the persistence of the contour proof of the phase transition for any $\alpha \in [0,1)$. Moreover, we show that when we add a magnetic field decaying to zero, given by $h_x= h_*\cdot(1+|x|)^{-\gamma}$ and $\gamma >\max\{1-\alpha, 1-\alpha^* \}$ where $\alpha^*\approx 0.2714$, the transition still persists.Comment: 13 page

Genomic adaptation of giant viruses in polar oceans

寒冷域と温暖域ではウイルスの遺伝子組成が異なる --巨大ウイルスの環境適応--. 京都大学プレスリリース. 2023-10-13.Despite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phyla Nucleocytoviricota and Mirusviricota are groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

publication en ligne. Article dans revue scientifique avec comité de lecture. nationale.National audienceThe human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

Local limits of spatial Gibbs random graphs

We study the spatial Gibbs random graphs introduced in Mourrat and Valesin (2018) from the point of view of local convergence. These are random graphs embedded in an ambient space consisting of a line segment, defined through a probability measure that favors graphs of small (graph-theoretic) diameter but penalizes the presence of edges whose extremities are distant in the geometry of the ambient space. In Mourrat and Valesin (2018) these graphs were shown to exhibit threshold behavior with respect to the various parameters that define them; this behavior was related to the formation of hierarchical structures of edges organized so as to produce a small diameter. Here we prove that, for certain values of the underlying parameters, the spatial Gibbs graphs may or may not converge locally, in a manner that is compatible with the aforementioned hierarchical structures

Dyson Models Under Renormalization and in Weak Fields

We consider one-dimensional long-range spin models (usually called Dyson models), consisting of Ising ferromagnets with slowly decaying long-range pair potentials of the form $${1}/{| i-j |^\alpha }$$, mainly focusing on the range of slow decays $$1 <\alpha \le 2$$. We describe two recent results, one about renormalization and one about the effect of external fields at low temperature