Diversidad florística de la región noreste de México, estados de Coahuila, Nuevo León y Tamaulipas

Antecedentes: El noreste de México, estados de Coahuila, Nuevo León y Tamaulipas, constituye una región heterogénea que incluye sierras, planicies continentales y llanuras costeras con una infinidad de ambientes, substratos geológicos y gradientes altitudinales que favorecen la presencia de una rica biodiversidad. No existe una síntesis que documente la diversidad florística de esta región. Preguntas: ¿Cuál es la magnitud de la diversidad de plantas vasculares en el noreste de México?, ¿Cuáles son las familias y géneros con mayor número de especies?, ¿Cómo se distribuye geográficamente esta riqueza florística en toda la región y cuáles son sus elementos más característicos? Especies de estudio: 7,088 especies de plantas vasculares. Sitio de muestreo: estados de Coahuila, Nuevo León y Tamaulipas. Métodos: Se consultó literatura florística-taxonómica sobre la flora de la región y bases de datos de ejemplares para hacer un análisis espacial de la biodiversidad usando celdas de 1° de longitud y latitud. Se calculó la riqueza y el endemismo en la región, los estados y las celdas. Resultados: Para el noreste de México se reportan 7,088 especies de plantas vasculares, de las cuales 1,767 son endémicas de México. Conclusiones: El noreste de México registra una diversidad florística particularmente interesante y compleja, debido a que su territorio se ubica primordialmente fuera del neotrópico y porque constituye el límite boreal para muchos elementos de la flora de México

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Observation of burst activity from SGR1935+2154 associated to first galactic FRB with H.E.S.S.

Fast radio bursts (FRB) are enigmatic powerful single radio pulses with durations of several milliseconds and high brightness temperatures suggesting coherent emission mechanism. For the time being a number of extragalactic FRBs have been detected in the high-frequency radio band including repeating ones. The most plausible explanation for these phenomena is magnetar hyperflares. The first observational evidence of this scenario was obtained in April 2020 when an FRB was detected from the direction of the Galactic magnetar and soft gamma repeater SGR1935+2154. The FRB was preceded with a number of soft gamma-ray bursts observed by Swift-BAT satellite, which triggered the follow-up program of the H.E.S.S. imaging atmospheric Cherenkov telescopes (IACTs). H.E.S.S. has observed SGR1935+2154 over a 2 hour window few hours prior to the FRB detection by STARE2 and CHIME. The observations overlapped with other X-ray bursts from the magnetar detected by INTEGRAL and Swift-BAT, thus providing first observations of a magnetar in a flaring state in the very-high energy domain. We present the analysis of these observations, discuss the obtained results and prospects of the H.E.S.S. follow-up program for soft gamma repeaters and anomalous X-ray pulsars

Deep observations of Kepler's SNR with H.E.S.S.

Kepler’s supernova remnant (SNR) which is produced by the most recent naked-eye supernova in our Galaxy is one of the best studied SNRs, but its gamma-ray detection has eluded us so far. Observations with modern imaging atmospheric Cherenkov telescopes (IACT) have enlarged the knowledge about nearby SNRs with ages younger than 500 years by establishing Cassiopeia A and Tycho’s SNRs as very high energy (VHE) gamma-ray sources and setting a lower limit on the distance to Kepler’s SNR. This SNR is significantly more distant than the other two and expected to be one of the faintest gamma-ray sources within reach of the IACT arrays of this generation. We report strong evidence for a VHE signal from Kepler’s SNR based on deep observations of the High Energy Stereoscopic System (H.E.S.S.) with an exposure of 152 hours, including 122 hours accumulated in 2017-2020. We further discuss implications of this result for cosmic-ray acceleration in young SNRs