Graphs Cannot Be Indexed in Polynomial Time for Sub-quadratic Time String Matching, Unless SETH Fails

The string matching problem on a node-labeled graph G= (V, E) asks whether a given pattern string P has an occurrence in G, in the form of a path whose concatenation of node labels equals P. This is a basic primitive in various problems in bioinformatics, graph databases, or networks, but only recently proven to have a O(|E||P|)-time lower bound, under the Orthogonal Vectors Hypothesis (OVH). We consider here its indexed version, in which we can index the graph in order to support time-efficient string queries. We show that, under OVH, no polynomial-time indexing scheme of the graph can support querying P in time O(| P| + | E| δ| P| β), with either δ< 1 or β< 1. As a side-contribution, we introduce the notion of linear independent-components (lic) reduction, allowing for a simple proof of our result. As another illustration that hardness of indexing follows as a corollary of a lic reduction, we also translate the quadratic conditional lower bound of Backurs and Indyk (STOC 2015) for the problem of matching a query string inside a text, under edit distance. We obtain an analogous tight quadratic lower bound for its indexed version, improving the recent result of Cohen-Addad, Feuilloley and Starikovskaya (SODA 2019), but with a slightly different boundary condition.Peer reviewe

Drivers of grassland loss in Hungary during the post-socialist transformation (1987–1999)

The increase in the speed of land-cover change experienced worldwide is becoming a growing concern. Major socio-economic transitions, such as the breakdown of socialism in Europe, may lead to particularly high rates of landscape transformations. In this paper we examined the loss of semi-natural grasslands in Hungary between 1987 and 1999. We studied the relationship between 9 potential driving forces and the fate of grasslands using logistic GLMs. Grassland loss was found to be very high (1.31 % per year), which is far higher than either before or after this period. The most influential predictors of grassland loss were environmental and landscape characteristics (soil type, area of remnant grassland patches), and the socio-economic context (distance to paved road, and nearest settlement, human population density). Several processes and relationships can only be understood from a historical perspective (e.g. large extent of afforestation, strong decrease of soil water table). Grassland loss during the study period emerged as a consequence of survival strategies of individual farmers seeking adaptation to the changing environmental and socio-economic conditions, and not urbanization and agricultural intensification which are the main underlying drivers for the ongoing landscape transformations in most parts of the developed world. Though globalization increasingly influences local land use decisions , reconstructing and modelling recent landscape changes cannot be done without a proper understanding of local history and culture. Our analysis shows the importance of large-area yet high resolution landscape change research, which may reveal unexpected patterns of land cover change, undetected at coarser scales

第647回千葉医学会例会・第5回千葉大学小児外科教室例会 6.

<p>(A) A schematic describing the experimental process used to test the four cell separation techniques. A single tumor from each PDX line was processed using a gentleMACS^™ Octo Dissociator to obtain a single cell suspension comprising a heterogeneous mixture of human cells (blue) and mouse cells (orange). The suspension was divided in five samples. The pre-sort sample received no further processing. The remaining 4 tubes were processed using each method to obtain separate human and mouse cell populations. Each resulting human fraction and the pre-sort sample were analyzed using ssPAL. (B) ssPAL analysis results for primer pair 5 and 43 were averaged together to obtain the human DNA percentage for each separation method. After performing ssPAL analysis, results indicate that on average, MCD yields the highest sample purity over FACS, EpCAM-M and EpCAM-SC. The starting amount of murine stromal contamination also influences the effectiveness of the kit used, with EpCAM-M and EpCAM-SC performing poorly with higher initial murine content. Error bars represent standard error.</p

Modelling regional land change scenarios to assess land abandonment and reforestation dynamics in the Pyrenees (France)

International audienceOver the last decades and centuries, European mountain landscapes have experienced substantial transformations. Natural and anthropogenic LULC changes (land use and land cover changes), especially agro-pastoral activities, have directed influenced the spatial organization and composition of European mountain landscapes. For the past 60 years, natural reforestation has been occurring due to a decline in both agricultural production activities and rural population. Stakeholders, to better anticipate future changes, need spatially and temporally explicit models to identiy areas at risk of land change and possible abandonment. This paper presents an integrated approach combining forecasting scenarios and a LULC changes simulation model to assess where LULC changes may occur in the Pyrenees Mountains, based on historical LULC trands and a range of future socio-economic drivers. The proposed methodology considers local specificities of Pyrenan valleys, sub-regional climate and topographical properties, and regional economic policies. Results indicate that some regions are projected to face strong abandonment, regardless of scenario conditions. Overall, high rates of change are associated with administrative regions where land productivity is highly dependent on socio-economic drivers and climatic and environmental conditions limit intensive (agricultural and/or pastoral) production and profitability. The combination of the results for the four scenarios allows assessements of where encroachment (e.g. colonization by shrublands) and reforestation are the most probable. This assessment intends to provide insight into the potential future development of the Pyrenees to help identify areas that are the most sensitive to change and to guide decision makers to help their management decisions

Methods to study splicing from high-throughput RNA Sequencing data

The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data. We group the methods according to the different questions they address: 1) Assignment of the sequencing reads to their likely gene of origin. This is addressed by methods that map reads to the genome and/or to the available gene annotations. 2) Recovering the sequence of splicing events and isoforms. This is addressed by transcript reconstruction and de novo assembly methods. 3) Quantification of events and isoforms. Either after reconstructing transcripts or using an annotation, many methods estimate the expression level or the relative usage of isoforms and/or events. 4) Providing an isoform or event view of differential splicing or expression. These include methods that compare relative event/isoform abundance or isoform expression across two or more conditions. 5) Visualizing splicing regulation. Various tools facilitate the visualization of the RNA-Seq data in the context of alternative splicing. In this review, we do not describe the specific mathematical models behind each method. Our aim is rather to provide an overview that could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.Comment: 31 pages, 1 figure, 9 tables. Small corrections adde

Validación del índice compuesto DAPSA (Disease Activity for Psoriatic Arthritis) en una cohorte de pacientes con artritis psoriásica en Argentina y determinación de sus valores de corte

Objetivos: Validar el índice DAPSA en pacientes con Artritis Psoriásica (APs) en Argentina, comparar su rendimiento con índices compuestos y con la ultrasonografía (US) y establecer valores de corte

Moonraker -- Enceladus Multiple Flyby Mission

Enceladus, an icy moon of Saturn, possesses an internal water ocean and jets expelling ocean material into space. Cassini investigations indicated that the subsurface ocean could be a habitable environment having a complex interaction with the rocky core. Further investigation of the composition of the plume formed by the jets is necessary to fully understand the ocean, its potential habitability, and what it tells us about Enceladus' origin. Moonraker has been proposed as an ESA M-class mission designed to orbit Saturn and perform multiple flybys of Enceladus, focusing on traversals of the plume. The proposed Moonraker mission consists of an ESA-provided platform, with strong heritage from JUICE and Mars Sample Return, and carrying a suite of instruments dedicated to plume and surface analysis. The nominal Moonraker mission has a duration of 13.5 years. It includes a 23-flyby segment with 189 days allocated for the science phase, and can be expanded with additional segments if resources allow. The mission concept consists in investigating: i) the habitability conditions of present-day Enceladus and its internal ocean, ii) the mechanisms at play for the communication between the internal ocean and the surface of the South Polar Terrain, and iii) the formation conditions of the moon. Moonraker, thanks to state-of-the-art instruments representing a significant improvement over Cassini's payload, would quantify the abundance of key species in the plume, isotopic ratios, and physical parameters of the plume and the surface. Such a mission would pave the way for a possible future landed mission.Comment: Accepted for publication in The Planetary Science Journa

Moonraker: Enceladus Multiple Flyby Mission

Enceladus, an icy moon of Saturn, possesses an internal water ocean and jets expelling ocean material into space. Cassini investigations indicated that the subsurface ocean could be a habitable environment having a complex interaction with the rocky core. Further investigation of the composition of the plume formed by the jets is necessary to fully understand the ocean, its potential habitability, and what it tells us about Enceladus’s origin. Moonraker has been proposed as an ESA M-class mission designed to orbit Saturn and perform multiple flybys of Enceladus, focusing on traversals of the plume. The proposed Moonraker mission consists of an ESA-provided platform with strong heritage from JUICE and Mars Sample Return and carrying a suite of instruments dedicated to plume and surface analysis. The nominal Moonraker mission has a duration of ∼13.5 yr. It includes a 23-flyby segment with 189 days allocated for the science phase and can be expanded with additional segments if resources allow. The mission concept consists of investigating (i) the habitability conditions of present-day Enceladus and its internal ocean, (ii) the mechanisms at play for the communication between the internal ocean and the surface of the South Polar Terrain, and (iii) the formation conditions of the moon. Moonraker, thanks to state-of-the-art instruments representing a significant improvement over Cassini's payload, would quantify the abundance of key species in the plume, isotopic ratios, and the physical parameters of the plume and the surface. Such a mission would pave the way for a possible future landed mission