Sparse graphs with bounded induced cycle packing number have logarithmic treewidth

A graph is $O_k$-free if it does not contain $k$ pairwise vertex-disjoint and non-adjacent cycles. We show that Maximum Independent Set and 3-Coloring in $O_k$-free graphs can be solved in quasi-polynomial time. As a main technical result, we establish that "sparse" (here, not containing large complete bipartite graphs as subgraphs) $O_k$-free graphs have treewidth (even, feedback vertex set number) at most logarithmic in the number of vertices. This is proven sharp as there is an infinite family of $O_2$-free graphs without $K_{3,3}$-subgraph and whose treewidth is (at least) logarithmic. Other consequences include that most of the central NP-complete problems (such as Maximum Independent Set, Minimum Vertex Cover, Minimum Dominating Set, Minimum Coloring) can be solved in polynomial time in sparse $O_k$-free graphs, and that deciding the $O_k$-freeness of sparse graphs is polynomial time solvable.Comment: 28 pages, 6 figures. v3: improved complexity result

Serological Evidence of Multiple Zoonotic Viral Infections among Wild Rodents in Barbados

Background: Rodents are reservoirs for several zoonotic pathogens that can cause human infectious diseases, including orthohantaviruses, mammarenaviruses and orthopoxviruses. Evidence exists for these viruses circulating among rodents and causing human infections in the Americas, but much less evidence exists for their presence in wild rodents in the Caribbean. Methods: Here, we conducted serological and molecular investigations of wild rodents in Barbados to determine the prevalence of orthohantavirus, mammarenavirus and orthopoxvirus infections, and the possible role of these rodent species as reservoirs of zoonotic pathogens. Using immunofluorescent assays (IFA), rodent sera were screened for the presence of antibodies to orthohantavirus, mammarenavirus (Lymphocytic choriomeningitis virus—LCMV) and orthopoxvirus (Cowpox virus—CPXV) infections. RT-PCR was then conducted on orthohantavirus and mammarenavirus-seropositive rodent sera and tissues, to detect the presence of viral RNA. Results: We identified antibodies against orthohantavirus, mammarenavirus, and orthopoxvirus among wild mice and rats (3.8%, 2.5% and 7.5% seropositivity rates respectively) in Barbados. No orthohantavirus or mammarenavirus viral RNA was detected from seropositive rodent sera or tissues using RT–PCR. Conclusions: Key findings of this study are the first serological evidence of orthohantavirus infections in Mus musculus and the first serological evidence of mammarenavirus and orthopoxvirus infections in Rattus norvegicus and M. musculus in the English-speaking Caribbean. Rodents may present a potential zoonotic and biosecurity risk for transmission of three human pathogens, namely orthohantaviruses, mammarenaviruses and orthopoxviruses in Barbados

Serological Evidence of Multiple Zoonotic Viral Infections among Wild Rodents in Barbados

Background: Rodents are reservoirs for several zoonotic pathogens that can cause human infectious diseases, including orthohantaviruses, mammarenaviruses and orthopoxviruses. Evidence exists for these viruses circulating among rodents and causing human infections in the Americas, but much less evidence exists for their presence in wild rodents in the Caribbean. Methods: Here, we conducted serological and molecular investigations of wild rodents in Barbados to determine the prevalence of orthohantavirus, mammarenavirus and orthopoxvirus infections, and the possible role of these rodent species as reservoirs of zoonotic pathogens. Using immunofluorescent assays (IFA), rodent sera were screened for the presence of antibodies to orthohantavirus, mammarenavirus (Lymphocytic choriomeningitis virus—LCMV) and orthopoxvirus (Cowpox virus—CPXV) infections. RT-PCR was then conducted on orthohantavirus and mammarenavirus-seropositive rodent sera and tissues, to detect the presence of viral RNA. Results: We identified antibodies against orthohantavirus, mammarenavirus, and orthopoxvirus among wild mice and rats (3.8%, 2.5% and 7.5% seropositivity rates respectively) in Barbados. No orthohantavirus or mammarenavirus viral RNA was detected from seropositive rodent sera or tissues using RT–PCR. Conclusions: Key findings of this study are the first serological evidence of orthohantavirus infections in Mus musculus and the first serological evidence of mammarenavirus and orthopoxvirus infections in Rattus norvegicus and M. musculus in the English-speaking Caribbean. Rodents may present a potential zoonotic and biosecurity risk for transmission of three human pathogens, namely orthohantaviruses, mammarenaviruses and orthopoxviruses in Barbados

The Continuing Use of Problematic Sexual Stereotypes in Judicial Decision-Making

This article examines the continuing use of problematic sexual stereotypes at appellate level in the English and Welsh legal system. Using five cases as illustrations, it argues that, notwithstanding professional training and guidance on sexual equality matters, certain senior judges in this jurisdiction still at least sometimes openly employ crude and problematic sexual stereotypes in their judgments or fail to deal appropriately with the use of these stereotypes by trial judges. The central point is that there is still a significant problem with the open use of crude sexual stereotypes in legal reasoning at a senior level in this jurisdiction, despite the pressure on all members of the legal system to appear to be ‘politically correct’

The Compton Spectrometer and Imager

The Compton Spectrometer and Imager (COSI) is a NASA Small Explorer (SMEX) satellite mission in development with a planned launch in 2027. COSI is a wide-field gamma-ray telescope designed to survey the entire sky at 0.2-5 MeV. It provides imaging, spectroscopy, and polarimetry of astrophysical sources, and its germanium detectors provide excellent energy resolution for emission line measurements. Science goals for COSI include studies of 0.511 MeV emission from antimatter annihilation in the Galaxy, mapping radioactive elements from nucleosynthesis, determining emission mechanisms and source geometries with polarization measurements, and detecting and localizing multimessenger sources. The instantaneous field of view for the germanium detectors is >25% of the sky, and they are surrounded on the sides and bottom by active shields, providing background rejection as well as allowing for detection of gamma-ray bursts and other gamma-ray flares over most of the sky. In the following, we provide an overview of the COSI mission, including the science, the technical design, and the project status.Comment: 8 page

The cosipy library: COSI's high-level analysis software

The Compton Spectrometer and Imager (COSI) is a selected Small Explorer (SMEX) mission launching in 2027. It consists of a large field-of-view Compton telescope that will probe with increased sensitivity the under-explored MeV gamma-ray sky (0.2-5 MeV). We will present the current status of cosipy, a Python library that will perform spectral and polarization fits, image deconvolution, and all high-level analysis tasks required by COSI's broad science goals: uncovering the origin of the Galactic positrons, mapping the sites of Galactic nucleosynthesis, improving our models of the jet and emission mechanism of gamma-ray bursts (GRBs) and active galactic nuclei (AGNs), and detecting and localizing gravitational wave and neutrino sources. The cosipy library builds on the experience gained during the COSI balloon campaigns and will bring the analysis of data in the Compton regime to a modern open-source likelihood-based code, capable of performing coherent joint fits with other instruments using the Multi-Mission Maximum Likelihood framework (3ML). In this contribution, we will also discuss our plans to receive feedback from the community by having yearly software releases accompanied by publicly-available data challenges

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional(3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedlyduring eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with theabsence of condensin II subunits. Moreover, condensin II depletion converts the architecture of thehuman genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state,centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physicalmodel in which lengthwise compaction of chromosomes by condensin II during mitosis determineschromosome-scale genome architecture, with effects that are retained during the subsequent interphase.This mechanism likely has been conserved since the last common ancestor of all eukaryotes.C.H. is supported by the Boehringer Ingelheim Fonds; C.H., Á.S.C., and B.D.R. are supported by an ERC CoG (772471, “CohesinLooping”); A.M.O.E. and B.D.R. are supported by the Dutch Research Council (NWO-Echo); and J.A.R. and R.H.M. are supported by the Dutch Cancer Society (KWF). T.v.S. and B.v.S. are supported by NIH Common Fund “4D Nucleome” Program grant U54DK107965. H.T. and E.d.W. are supported by an ERC StG (637597, “HAP-PHEN”). J.A.R., T.v.S., H.T., R.H.M., B.v.S., and E.d.W. are part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. Work at the Center for Theoretical Biological Physics is sponsored by the NSF (grants PHY-2019745 and CHE-1614101) and by the Welch Foundation (grant C-1792). V.G.C. is funded by FAPESP (São Paulo State Research Foundation and Higher Education Personnel) grants 2016/13998-8 and 2017/09662-7. J.N.O. is a CPRIT Scholar in Cancer Research. E.L.A. was supported by an NSF Physics Frontiers Center Award (PHY-2019745), the Welch Foundation (Q-1866), a USDA Agriculture and Food Research Initiative grant (2017-05741), the Behavioral Plasticity Research Institute (NSF DBI-2021795), and an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375). Hi-C data for the 24 species were created by the DNA Zoo Consortium (www.dnazoo.org). DNA Zoo is supported by Illumina, Inc.; IBM; and the Pawsey Supercomputing Center. P.K. is supported by the University of Western Australia. L.L.M. was supported by NIH (1R01NS114491) and NSF awards (1557923, 1548121, and 1645219) and the Human Frontiers Science Program (RGP0060/2017). The draft A. californica project was supported by NHGRI. J.L.G.-S. received funding from the ERC (grant agreement no. 740041), the Spanish Ministerio de Economía y Competitividad (grant no. BFU2016-74961-P), and the institutional grant Unidad de Excelencia María de Maeztu (MDM-2016-0687). R.D.K. is supported by NIH grant RO1DK121366. V.H. is supported by NIH grant NIH1P41HD071837. K.M. is supported by a MEXT grant (20H05936). M.C.W. is supported by the NIH grants R01AG045183, R01AT009050, R01AG062257, and DP1DK113644 and by the Welch Foundation. E.F. was supported by NHGR

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Structure de graphes, mineurs et arbres induits

This thesis deals with structural graph theory questions that stem from algorithmic motivations. Indeed, NP-complete graph problems are typically easier on restricted graph classes. On trees, which are connected graphs without cycles, dynamic programming often yields a linear algorithm. Not every graph is a tree, but we can measure how much more complex the graph is. A standard tool is the treewidth which is deeply connected to minor theory, as discussed in the first chapter. Another strategy is to obtain a much simpler structure by deleting as few vertices as possible, as discussed in the second chapter. The first chapter concerns the idea of minor-universality. A graph is minoruniversal for a family of graphs if it contains as a minor every graph in the family. A celebrated result of Robertson, Seymour, and Thomas in 1994 shows that the 2n × 2n-grid is minor-universal for the family of n-vertex planar graphs. One direction to refine this result is to find some subclasses of n-vertex planar graphs that admit a smaller minor-universal grid. A poly-line grid drawing of a planar graph G is a planar embedding of G such that its vertices are mapped on the vertices of the grid and its edges are curves made up of line segments connecting on vertices of the grid. The size of such drawing is the order of the grid. The idea is to establish a relation between the size of a poly-line grid drawing of a graph H and the order of the smallest grid that admits H as a minor. Another direction is to extend the result from planarity to bounded genus. More precisely, we show that there is a graph of genus g minor-universal for the n-vertex graphs of genus g, and whose order is polynomial in n and g. The second chapter focuses on finding a large induced forest in a graph. An interesting case is when the forest is required to be a single path. In 2017, Esperet, Lemoine, and Maffray conjectured that every k-degenerate graph with an n-path admits an induced log nΩk(1)-path. We prove that this holds for several degenerate classes, including the class of topological-minor-free graphs. In the case of a forest, the Erdős-Pósa theorem states that if a graph does not have k vertex-disjoint cycles, then it admits a set of O(k log k) vertices whose removal yields a forest, called the feedback vertex set. We obtain a similar property for the graphs with no Kt,t-subgraph and no k independent cycles (vertex-disjoint and no edge between them). The trade-off for this generalization is a feedback vertex set whose size depends in the logarithm of the order, and this is sharp.Cette thèse traite des questions structurelles de la théorie des graphes qui découlent de motivations algorithmiques.En effet, les problèmes de graphes NP-complets sont typiquement plus faciles dès lors qu'on restreint la classe de graphes.Sur les arbres, qui sont des graphes connexes sans cycles, la programmation dynamique donne souvent un algorithme linéaire. Tous les graphes ne sont pas des arbres, mais il est possible de quantifier à quel point un graphe est plus complexe qu'un arbre.Un outil standard pour cela est la largeur arborescente, qui est profondément liée à la théorie des mineurs, comme nous allons voir dans le premier chapitre. Une autre stratégie consiste à obtenir une structure arborescente en supprimant le moins de sommets possible, comme nous le verrons dans le deuxième chapitre.Le premier chapitre porte sur l'idée de graphes universels pour la relation de mineur.Un graphe est mineur-universel pour une famille de graphes s'il contient comme mineur chaque graphe de la famille. Un résultat célèbre de Robertson, Seymour et Thomas en 1994 montre que la grille 2n times 2n est mineur-universelle pour la famille des graphes planaires à n sommets. Une façon d'affiner ce résultat est de trouver des sous-classes de graphes planaires à n sommets qui admettent une grille mineure-universelle plus petite. On dit que qu'un graphe planaire G admet un dessin sur une grille s'il existe un plongement de G sur une grille, tel que les sommets de G sont des sommets de la grille, et ses arêtes sont des suites de segments dont les jonctions sont placées sur des sommets des la grille. La taille d'un tel dessin est le nombre de sommets de la grille. L'idée est d'établir une relation entre la taille d'un dessin sur une grille d'un graphe H, et la taille de la plus petite grille qui admet H comme mineur.Plutôt que d'affiner le résultat, un autre direction consiste à le généraliser à une classe plus grande.On s'intéresse ici aux graphes de genre borné, le genre d'un graphe étant un paramètre entier qui généralise la notion de planarité.Plus précisément, nous montrons qu'il existe un graphe de genre g mineur-universel pour les graphes à n sommets de genre g, et dont la taille est polynomiale en n et g. Le deuxième chapitre se concentre sur la recherche d'une grande forêt (union de plusieurs arbres) induite dans un graphe. Un cas intéressant est celui où la forêt en question un unique chemin. En 2017, Esperet, Lemoine et Maffray ont conjecturé que tout graphe k-dégénéré avec un chemin à n sommets admet un chemin induit à log n ^{Omega_k(1)} sommets. Nous prouvons que c'est le cas pour plusieurs classes de graphes dégénérés, y compris la classe des graphes excluant un graphe comme mineur topologique. Dans le cas d'une forêt, le théorème d'ErdH{o}s-P'osa stipule que si un graphe n'a pas k cycles disjoints, alors il admet un ensemble de O(klog k) sommets dont l'élimination produit une forêt, appelé textit{feedback vertex set}. Nous obtenons une propriété similaire pour les graphes sans sous-graphe K_{t,t} et sans k cycles indépendants (disjoints et sans arête entre eux). La contrepartie de cette généralisation est un textit{feedback vertex set} dont la taille est logarithmique en la taille du graphe, et cette borne peut être atteinte