GPU-friendly neural networks for remote sensing scene classification

Convolutional neural networks (CNNs) have proven to be very efficient for the analysis of remote sensing (RS) images. Due to the inherent complexity of extracting features from these images, along with the increasing amount of data to be processed (and the diversity of applications), there is a clear tendency to develop and employ increasingly deep and complex CNNs. In this regard, graphics processing units (GPUs) are frequently used to optimize their execution, both for the training and inference stages, optimizing the performance of neural models through their many-core architecture. Hence, the efficient use of the GPU resources should be at the core of optimizations. This letter analyzes the possibilities of using a new family of CNNs, denoted as TResNets, to provide an efficient solution to the RS scene classification problem. Moreover, the considered models have been combined with mixed precision to enhance their training performance. Our experimental results, conducted over three publicly available RS data sets, show that the proposed networks achieve better accuracy and more efficient use of GPU resources than other state-of-the-art networks. Source code is available at https://github.com/mhaut/GPUfriendlyRS

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Background: The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes. Methods: This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status. Findings: Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low. Interpretation: This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant. Funding: Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16–20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

Regreso a la Cueva de los Casares (Guadalajara). Un nuevo proyecto de investigación para el yacimiento del Seno A.

Con autorización de la revista para autores CSIC[EN] In this paper we present a new interdisciplinary project focused on the investigation of the Late Pleisto-cene deposits still preserved in the Room A of Los Casares cave (Riba de Saelices, Guadalajara, Spain). We first make a historical reconstruction of the research carried out in the cave, then we present our objectives, working hypotheses and methods, and finally we show some preliminary results after a first fieldwork season in Los Ca-sares. We have collected soil monoliths for micromorphology and high-resolution sedimentology, sediment samples for palynological and phytolith analyses, as well as charcoal, bone and flowstone samples for chrono-metric dating. With these data we will investigate the site formation processes, the chronology of the Mouste-rian occupations, and eventually the adaptations of Los Casares Neandertals to their environment. Our research is framed in a wider project aimed at studying the relations between population dynamics and ecological varia-tions in Central Iberia during the Late Pleistocene[ES] En este artículo presentamos un nuevo proyecto interdisciplinar dirigido a investigar los depósitos del Pleistoceno Superior aún conservados en el Seno A de la Cueva de Los Casares (Riba de Saelices, Guadalajara). Tras una reconstrucción histórica de las investigaciones desarrolladas en la cavidad, sintetizamos los objetivos, hipótesis de trabajo y métodos de nuestro proyecto, para acabar presentando los resultados preliminares obte-nidos en la primera campaña de excavación en Los Casares. A través de la recogida de columnas de sedimento para análisis micromorfológicos y sedimentológicos, muestras de sedimento para análisis polínicos y de fitolitos, o carbones, hueso y espeleotemas para dataciones cronométricas, pretendemos obtener información que per-mita comprender los procesos de formación del depósito arqueológico del Seno A, conocer su cronología, e in-vestigar las adaptaciones al medio de los Neandertales que habitaron en Los Casares. Nuestras investigaciones en esta cavidad se enmarcan en un proyecto más amplio que estudia la relación entre las dinámicas de pobla-miento y los cambios ecológicos ocurridos en la región central de la Península Ibérica durante el Pleistoceno Su-periorLas investigaciones en la Cueva de Los Ca-sares, enmarcadas en el proyecto Testing popula-tion hiatuses in the Late Pleistocene of Central Ibe-ria: a geoarchaeological approach, se encuentran financiadas por una Marie Curie Intra European Fe-llowship del 7th European Commnunity Framework Programme. También se han visto favorecidas por el apoyo económico del CRC 806 “Our Way to Euro-pe”, financiado por la Deutsche Forschungsgemeins-chaft. Los trabajos de campo en la cueva cuentan con la autorización de la Dirección General de Cul-tura de Castilla – La Mancha. Los análisis palinoló-gicos en curso han sido financiados por el Proyecto de Investigación HAR2013-43701-P del Plan Nacio-nal de I+D+i del Ministerio de Economía y Competitividad. Las Dras. Rosa Barroso y Primitiva Bueno han colaborado en el estudio del material cerámico y la discusión de los niveles de la Prehistoria recien-te, lo cual agradecemos sinceramente. Agradece-mos también las facilidades prestadas por la Dra. Carmen Cacho para el estudio del material arqueo-lógico de Los Casares depositado en el Museo Arqueológico Nacional. Igualmente agradecidos que-damos al personal del Museo de Molina, que amablemente nos facilitó nuestro trabajo en la cuev