Magnetic field configuration associated with solar gamma ray flares in June, 1991

The vector magnetic field configuration of the solar active region AR 6659 that produced very high levels of flare activity in Jun. 1991 is described. The morphology and evolution of the photospheric fields are described for the period 7-10 Jun., and the flares taking place around these dates and their locations relative to the photospheric fields are indicated. By comparing the observed vector field with the potential field calculated from the observed line-of-sight flux, we identify the nonpotential characteristics of the fields along the magnetic neutral lines where the flares were observed. These results are compared with those from the earlier study of gamma-ray flares

Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer

Tissue-resident memory T (TRM) cells provide immune defense against local infection and can inhibit cancer progression. However, it is unclear to what extent chronic inflammation impacts TRM activation and whether TRM cells existing in tissues before tumor onset influence cancer evolution in humans. We performed deep profiling of healthy lungs and lung cancers in never-smokers (NSs) and ever-smokers (ESs), finding evidence of enhanced immunosurveillance by cells with a TRM-like phenotype in ES lungs. In preclinical models, tumor-specific or bystander TRM-like cells present prior to tumor onset boosted immune cell recruitment, causing tumor immune evasion through loss of MHC class I protein expression and resistance to immune checkpoint inhibitors. In humans, only tumors arising in ES patients underwent clonal immune evasion, unrelated to tobacco-associated mutagenic signatures or oncogenic drivers. These data demonstrate that enhanced TRM-like activity prior to tumor development shapes the evolution of tumor immunogenicity and can impact immunotherapy outcomes

Woody lianas increase in dominance and maintain compositional integrity across an Amazonian dam-induced fragmented landscape

Tropical forest fragmentation creates insular biological communities that undergo species loss and changes in community composition over time, due to area- and edge-effects. Woody lianas thrive in degraded and secondary forests, due to their competitive advantage over trees in these habitats. Lianas compete both directly and indirectly with trees, increasing tree mortality and turnover. Despite our growing understanding of liana-tree dynamics, we lack detailed knowledge of the assemblage-level responses of lianas themselves to fragmentation, particularly in evergreen tropical forests. We examine the responses of both sapling and mature liana communities to landscape-scale forest insularization induced by a mega hydroelectric dam in the Brazilian Amazon. Detailed field inventories were conducted on islands created during reservoir filling, and in nearby mainland continuous forest. We assess the relative importance of variables associated with habitat fragmentation such as area, isolation, surrounding forest cover, fire and wind disturbance, on liana community attributes including abundance, basal area, diversity, and composition. We also explore patterns of liana dominance relative to tree saplings and adults ≥10 cm diameter at breast height. We find that 1) liana community composition remains remarkably similar across mainland continuous forest and islands, regardless of extreme area- and edge- effects and the loss of vertebrate dispersers in the latter; and 2) lianas are increasing in dominance relative to trees in the sapling layer in the most degraded islands, with both the amount of forest cover surrounding islands and fire disturbance history predicting liana dominance. Our data suggest that liana communities persist intact in isolated forests, regardless of extreme area- and edge-effects; while in contrast, tree communities simultaneously show evidence of increased turnover and supressed recruitment. These processes may lead to lianas becoming a dominant component of this dam-induced fragmented landscape in the future, due to their competitive advantage over trees in degraded forest habitats. Additional loss of tree biomass and diversity brought about through competition with lianas, and the concurrent loss of carbon storage, should be accounted for in impact assessments of future dam development

Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets

Mass cytometry (CyTOF) is a technology that has revolutionised single-cell biology. By detecting over 40 proteins on millions of single cells, CyTOF allows the characterisation of cell subpopulations in unprecedented detail. However, most CyTOF studies require the integration of data from multiple CyTOF batches usually acquired on different days and possibly at different sites. To date, the integration of CyTOF datasets remains a challenge due to technical differences arising in multiple batches. To overcome this limitation, we developed an approach called CytofRUV for analysing multiple CyTOF batches, which includes an R-Shiny application with diagnostic plots. CytofRUV can correct for batch effects and integrate data from large numbers of patients and conditions across batches, to confidently compare cellular changes and correlate these with clinically relevant outcomes

Towards a Multidisciplinary Framework to Include Privacy in the Design of Video Surveillance Systems

International audiencePrivacy impacts of video surveillance systems are a major concern. This paper presents our ongoing multidisciplinary approach to integrate privacy concerns in the design of video surveillance systems. The project aims at establishing a reference framework for the collection of privacy concepts and principles, the description of surveillance contexts, surveillance technologies, and accountability capabilities

Transcriptional activation during cell reprogramming correlates with the formation of 3D open chromatin hubs

Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome conformation capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We apply TADdyn on in situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterize the structural rearrangements that take place upon changes in the transcriptional state of 21 genomic loci of diverse expression dynamics. By measuring various structural and dynamical properties, we find that during gene activation, the transcription starting site contacts with open and active regions in 3D chromatin domains. We propose that these 3D hubs of open and active chromatin may constitute a general feature to trigger and maintain gene transcription.This work was partially supported by the European Research Council under the 7th Framework Program FP7/2007-2013 (ERC grant agreement 609989 to M.A.M-R. and T.G.), the European Union’s Horizon 2020 research and innovation programme (grant agreement 676556 to M.A.M-R.) and the Spanish Ministerio de Ciencia e Innovación (BFU2013-47736-P and BFU2017-85926-P to M.A.M-R. as well as IJCI-2015-23352 to I.F.). R.S. is supported by the Netherlands Organization for Scientific Research (VENI 91617114) and an Erasmus MC Fellowship. We also knowledge support from “Centro de Excelencia Severo Ochoa 2013-2017”, SEV-2012-0208 the Spanish ministry of Science and Innovation to the EMBL partnership and the CERCA Programme/Generalitat de Catalunya to the CRG. We also acknowledge support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program to CNA