Seasonal contrast: Unsupervised pre-training from uncurated remote sensing data

Remote sensing and automatic earth monitoring are key to solve global-scale challenges such as disaster prevention, land use monitoring, or tackling climate change. Although there exist vast amounts of remote sensing data, most of it remains unlabeled and thus inaccessible for supervised learning algorithms. Transfer learning approaches can reduce the data requirements of deep learning algorithms. However, most of these methods are pre-trained on ImageNet and their generalization to remote sensing imagery is not guaranteed due to the domain gap. In this work, we propose Seasonal Contrast (SeCo), an effective pipeline to leverage unlabeled data for in-domain pre-training of remote sensing representations. The SeCo pipeline is composed of two parts. First, a principled procedure to gather large-scale, unlabeled and uncurated remote sensing datasets containing images from multiple Earth locations at different timestamps. Second, a self-supervised algorithm that takes advantage of time and position invariance to learn transferable representations for remote sensing applications. We empirically show that models trained with SeCo achieve better performance than their ImageNet pre-trained counterparts and state-of-the-art self-supervised learning methods on multiple downstream tasks. The datasets and models in SeCo will be made public to facilitate transfer learning and enable rapid progress in remote sensing applications.Peer ReviewedObjectius de Desenvolupament Sostenible::15 - Vida d'Ecosistemes Terrestres::15.2 - Per a 2020, promoure la gestió sostenible de tots els tipus de boscos, posar fi a la desforestació, recuperar els boscos degradats i incrementar substancialment la repoblació forestal i la reforestació a escala mundialObjectius de Desenvolupament Sostenible::15 - Vida d'Ecosistemes Terrestres::15.3 - Per a 2030, lluitar contra la desertificació, rehabilitar les terres i els sòls degradats, incloses les terres afec­tades per la desertificació, la sequera i les inundacions, i procurar assolir un món neutral quant a la degradació de les terresObjectius de Desenvolupament Sostenible::15 - Vida d'Ecosistemes Terrestres::15.9 - Per a 2020, integrar els valors dels ecosistemes i de la biodiversitat a la planificació nacional i local i als processos de desenvolupament, així com a les estratègies i als informes de reducció de la pobresaObjectius de Desenvolupament Sostenible::15 - Vida d'Ecosistemes TerrestresPostprint (author's final draft

Imported cysticercosis in Spain: A retrospective case series from the +REDIVI Collaborative Network

Neurocysticercosis (NCC) is the most common parasitic neurological disease worldwide and a major cause of epilepsy. Spain is the country reporting the highest number of NCC imported cases in Europe. Retrospective case series of NCC patients registered in the +REDIVI Network from October 1, 2009 to July 2018. A specific questionnaire, including clinical and diagnostic characteristics, was created and sent to the collaborator centers. 46 cases were included in the analysis. 55% were male, mean age of 40 years. 95.6% were migrants. The median duration since migration from an endemic area was 10 years. Predominant nationalities were Ecuadorians (50%) and Bolivians (30.4%). Frequent locations were parenchymal (87%), subarachnoid (26.1%) and intraventricular cysts (10.9%). Serological analysis was performed in 91.3%, being 54.8% positive. Most prevalent clinical manifestations were persistent headache (60.9%), epilepsy (43.5%) and visual changes (13%). Patients were mainly treated with albendazole (76.1%), corticosteroids (67.4%), and anticonvulsionants (52.2%). 82.5% had a favorable clinical outcome. Most NCC cases were long-standing migrants. Few clinical differences were observed depending on the cysticerci location. The treatment was often not according to current recommendations, and no uniform criteria were followed when it came to the therapeutic regimen. NCC case management in Spain (including clinician awareness and laboratory capacity improvements) needs to be strengthened.We would thanks María Jesús Perteguer from the National Center of Microbiology for the information and update on NCC lab techniques currently performed in Spain. The corresponding author’s affiliation centre belongs to the ISCIII-Sub. Gral. Redes- Network Biomedical Research on Tropical Diseases (RICET in Spanish) grant RD16CIII/0003/0001, RD16/0027/0020, RD16CIII/0003/0001 and the European Regional Development Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.S

Nontypable Haemophilus influenzae Displays a Prevalent Surface Structure Molecular Pattern in Clinical Isolates

Non-typable Haemophilus influenzae (NTHi) is a Gram negative pathogen that causes acute respiratory infections and is associated with the progression of chronic respiratory diseases. Previous studies have established the existence of a remarkable genetic variability among NTHi strains. In this study we show that, in spite of a high level of genetic heterogeneity, NTHi clinical isolates display a prevalent molecular feature, which could confer fitness during infectious processes. A total of 111 non-isogenic NTHi strains from an identical number of patients, isolated in two distinct geographical locations in the same period of time, were used to analyse nine genes encoding bacterial surface molecules, and revealed the existence of one highly prevalent molecular pattern (lgtF+, lic2A+, lic1D+, lic3A+, lic3B+, siaA−, lic2C+, ompP5+, oapA+) displayed by 94.6% of isolates. Such a genetic profile was associated with a higher bacterial resistance to serum mediated killing and enhanced adherence to human respiratory epithelial cells

DVINO: A RISC-V vector processor implemented in 65nm technology

This paper describes the design, verification, implementation and fabrication of the Drac Vector IN-Order (DVINO) processor, a RISC-V vector processor capable of booting Linux jointly developed by BSC, CIC-IPN, IMB-CNM (CSIC), and UPC. The DVINO processor includes an internally developed two-lane vector processor unit as well as a Phase Locked Loop (PLL) and an Analog-to-Digital Converter (ADC). The paper summarizes the design from architectural as well as logic synthesis and physical design in CMOS 65nm technology.The DRAC project is co-financed by the European Union Regional Development Fund within the framework of the ERDF Operational Program of Catalonia 2014-2020 with a grant of 50% of total eligible cost. The authors are part of RedRISCV which promotes activities around open hardware. The Lagarto Project is supported by the Research and Graduate Secretary (SIP) of the Instituto Politecnico Nacional (IPN) from Mexico, and by the CONACyT scholarship for Center for Research in Computing (CIC-IPN).Peer ReviewedArticle signat per 43 autors/es: Guillem Cabo∗, Gerard Candón∗, Xavier Carril∗, Max Doblas∗, Marc Domínguez∗, Alberto González∗, Cesar Hernández†, Víctor Jiménez∗, Vatistas Kostalampros∗, Rubén Langarita∗, Neiel Leyva†, Guillem López-Paradís∗, Jonnatan Mendoza∗, Francesco Minervini∗, Julian Pavón∗, Cristobal Ramírez∗, Narcís Rodas∗, Enrico Reggiani∗, Mario Rodríguez∗, Carlos Rojas∗, Abraham Ruiz∗, Víctor Soria∗, Alejandro Suanes‡, Iván Vargas∗, Roger Figueras∗, Pau Fontova∗, Joan Marimon∗, Víctor Montabes∗, Adrián Cristal∗, Carles Hernández∗, Ricardo Martínez‡, Miquel Moretó∗§, Francesc Moll∗§, Oscar Palomar∗§, Marco A. Ramírez†, Antonio Rubio§, Jordi Sacristán‡, Francesc Serra-Graells‡, Nehir Sonmez∗, Lluís Terés‡, Osman Unsal∗, Mateo Valero∗§, Luís Villa† // ∗Barcelona Supercomputing Center (BSC), Barcelona, Spain. Email: [email protected]; †Centro de Investigación en Computación, Instituto Politécnico Nacional (CIC-IPN), Mexico City, Mexico; ‡ Institut de Microelectronica de Barcelona, IMB-CNM (CSIC), Spain. Email: [email protected]; §Universitat Politecnica de Catalunya (UPC), Barcelona, Spain. Email: [email protected] (author's final draft

Genome-wide meta-analysis for Alzheimer's disease cerebrospinal fluid biomarkers

Amyloid-beta 42 (A beta 42) and phosphorylated tau (pTau) levels in cerebrospinal fluid (CSF) reflect core features of the pathogenesis of Alzheimer's disease (AD) more directly than clinical diagnosis. Initiated by the European Alzheimer & Dementia Biobank (EADB), the largest collaborative effort on genetics underlying CSF biomarkers was established, including 31 cohorts with a total of 13,116 individuals (discovery n = 8074; replication n = 5042 individuals). Besides the APOE locus, novel associations with two other well-established AD risk loci were observed; CR1 was shown a locus for A beta 42 and BIN1 for pTau. GMNC and C16orf95 were further identified as loci for pTau, of which the latter is novel. Clustering methods exploring the influence of all known AD risk loci on the CSF protein levels, revealed 4 biological categories suggesting multiple A beta 42 and pTau related biological pathways involved in the etiology of AD. In functional follow-up analyses, GMNC and C16orf95 both associated with lateral ventricular volume, implying an overlap in genetic etiology for tau levels and brain ventricular volume.Peer reviewe

Famílies botàniques de plantes medicinals

Facultat de Farmàcia, Universitat de Barcelona. Ensenyament: Grau de Farmàcia, Assignatura: Botànica Farmacèutica, Curs: 2013-2014, Coordinadors: Joan Simon, Cèsar Blanché i Maria Bosch.Els materials que aquí es presenten són els recull de 175 treballs d’una família botànica d’interès medicinal realitzats de manera individual. Els treballs han estat realitzat per la totalitat dels estudiants dels grups M-2 i M-3 de l’assignatura Botànica Farmacèutica durant els mesos d’abril i maig del curs 2013-14. Tots els treballs s’han dut a terme a través de la plataforma de GoogleDocs i han estat tutoritzats pel professor de l’assignatura i revisats i finalment co-avaluats entre els propis estudiants. L’objectiu principal de l’activitat ha estat fomentar l’aprenentatge autònom i col·laboratiu en Botànica farmacèutica

Overview of JET results for optimising ITER operation

The JET 2019–2020 scientific and technological programme exploited the results of years of concerted scientific and engineering work, including the ITER-like wall (ILW: Be wall and W divertor) installed in 2010, improved diagnostic capabilities now fully available, a major neutral beam injection upgrade providing record power in 2019–2020, and tested the technical and procedural preparation for safe operation with tritium. Research along three complementary axes yielded a wealth of new results. Firstly, the JET plasma programme delivered scenarios suitable for high fusion power and alpha particle (α) physics in the coming D–T campaign (DTE2), with record sustained neutron rates, as well as plasmas for clarifying the impact of isotope mass on plasma core, edge and plasma-wall interactions, and for ITER pre-fusion power operation. The efficacy of the newly installed shattered pellet injector for mitigating disruption forces and runaway electrons was demonstrated. Secondly, research on the consequences of long-term exposure to JET-ILW plasma was completed, with emphasis on wall damage and fuel retention, and with analyses of wall materials and dust particles that will help validate assumptions and codes for design and operation of ITER and DEMO. Thirdly, the nuclear technology programme aiming to deliver maximum technological return from operations in D, T and D–T benefited from the highest D–D neutron yield in years, securing results for validating radiation transport and activation codes, and nuclear data for ITER

Identification of candidate Parkinson disease genes by integrating genome-wide association study, expression, and epigenetic data sets

Importance Substantial genome-wide association study (GWAS) work in Parkinson disease (PD) has led to the discovery of an increasing number of loci shown reliably to be associated with increased risk of disease. Improved understanding of the underlying genes and mechanisms at these loci will be key to understanding the pathogenesis of PD. Objective To investigate what genes and genomic processes underlie the risk of sporadic PD. Design and Setting This genetic association study used the bioinformatic tools Coloc and transcriptome-wide association study (TWAS) to integrate PD case-control GWAS data published in 2017 with expression data (from Braineac, the Genotype-Tissue Expression [GTEx], and CommonMind) and methylation data (derived from UK Parkinson brain samples) to uncover putative gene expression and splicing mechanisms associated with PD GWAS signals. Candidate genes were further characterized using cell-type specificity, weighted gene coexpression networks, and weighted protein-protein interaction networks. Main Outcomes and Measures It was hypothesized a priori that some genes underlying PD loci would alter PD risk through changes to expression, splicing, or methylation. Candidate genes are presented whose change in expression, splicing, or methylation are associated with risk of PD as well as the functional pathways and cell types in which these genes have an important role. Results Gene-level analysis of expression revealed 5 genes (WDR6 [OMIM 606031], CD38 [OMIM 107270], GPNMB [OMIM 604368], RAB29 [OMIM 603949], and TMEM163 [OMIM 618978]) that replicated using both Coloc and TWAS analyses in both the GTEx and Braineac expression data sets. A further 6 genes (ZRANB3 [OMIM 615655], PCGF3 [OMIM 617543], NEK1 [OMIM 604588], NUPL2 [NCBI 11097], GALC [OMIM 606890], and CTSB [OMIM 116810]) showed evidence of disease-associated splicing effects. Cell-type specificity analysis revealed that gene expression was overall more prevalent in glial cell types compared with neurons. The weighted gene coexpression performed on the GTEx data set showed that NUPL2 is a key gene in 3 modules implicated in catabolic processes associated with protein ubiquitination and in the ubiquitin-dependent protein catabolic process in the nucleus accumbens, caudate, and putamen. TMEM163 and ZRANB3 were both important in modules in the frontal cortex and caudate, respectively, indicating regulation of signaling and cell communication. Protein interactor analysis and simulations using random networks demonstrated that the candidate genes interact significantly more with known mendelian PD and parkinsonism proteins than would be expected by chance. Conclusions and Relevance Together, these results suggest that several candidate genes and pathways are associated with the findings observed in PD GWAS studies

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues