Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster

Field epidemiology and viral sequencing provide a comprehensive characterization of transmission chains and allow a better identification of superspreading events. However, very few examples have been presented to date during the COVID-19 pandemic. We studied the first COVID-19 cluster detected in Portugal (59 individuals involved amongst extended family and work environments), following the return of four related individuals from work trips to Italy. The first patient to introduce the virus would be misidentified following the traditional field inquiry alone, as shown by the viral sequencing in isolates from 23 individuals. The results also pointed out family, and not work environment, as the primary mode of transmission.This work was funded by Portuguese Foundation for Science and Technology (FCT; Research4COVID19 projects 198_596862267, 617_613735895, 186_596855206). FCT also financed the PhD grant to NP (SFRH/BD/136299/2018) and post-doc grant to VF (SFRH/BPD/114927/2016)

Variabilidade temporal do perfil de dunas na Praia do Cassino, RS, com auxílio de videomonitoramento Argus

The dynamics of coastal sand dunes is a complex process that requires examining several processes at different scales. The analysis of three years morphological database of beach profiles at Cassino Beach, located in the south of Rio Grande do Sul state (RS), Brazil, identified an accretional behavior with an average of 14.86 m3 /m per year. Wind data and Oceanic Niño Index (ONI) showed that these components were the main modeling agents during this period. Digital imaging processing techniques related to the Argus system allowed to verify the increase of vegetation density and how some other factors contributed to increase coastal dune sand volume.A dinâmica sedimentar em dunas costeiras é um processo complexo que exige a análise de vários fatores em diferentes escalas temporais. A análise de um banco de dados morfológicos sequenciais de três anos, realizados em um setor de dunas da praia do Cassino, localizada ao sul do Rio Grande do Sul, Brasil (RS), permitiu identificar a evolução espaço-temporal do perfil de dunas, que apresentou um comportamento predominantemente acrescional médio de 14,86 m3 /m por ano. Dados de ventos e Índice de Oscilação Niño (ION) mostram que esses componentes foram os principais agentes modeladores durante esse período. As técnicas de processamento digital de imagens associadas ao sistema Argus permitiram verificar o aumento da densidade vegetacionalna região que juntamente com os fatores físicos observados contribuíram para o aumento de volume de areia dasdunas costeiras

Physical Mapping of the \u3ci\u3eAnopheles\u3c/i\u3e (\u3ci\u3eNyssorhynchus\u3c/i\u3e) \u3ci\u3edarlingi\u3c/i\u3e Genomic Scaffolds

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes

Adaptive evolution of a recombinant lactose-consuming Saccharomyces cerevisiae strain

In previous work, a recombinant S. cerevisiae flocculent strain (NCYC869-A3/T1, or simply T1) with the ability to express both the LAC4 (coding for beta-galactosidase) and LAC12 (lactose permease) genes of Kluyveromyces lactis was constructed (Domingues et al., Appl Microbiol Biotechnol 51:621–626, 1999). The original recombinant obtained (T1) was able to metabolise lactose but slowly. Thus, it was subjected to an adaptation period, where the recombinant yeast was kept in liquid lactose medium, refreshed periodically. Cells collected after the adaptation process presented improved fermentative characteristics compared to the original transformant, namely higher growth rate and higher ethanol productivity. This evolved strain was named T1-E. The fermentative parameters (shake-flask cultivations with buffered lactose defined mineral medium) of strain T1-E are similar to K. lactis wild-type strain CBS2359 (NRRLY1140). We aim at elucidating what happened during the process of adaptation/evolution that the yeast went through. The plasmid used for transformation (pKR1B-Lac4-1), which harbors a 13 kb region of the K. lactis genome including LAC4 and LAC12 genes, remained autonomous in the recombinant strain. Plasmid isolated from T1 (before adaptation) was identical to pKR1B-Lac4-1. However, we found that the plasmid isolated from T1-E carries a 1594 bp deletion (positions -518 to -2111 from the 5' end of LAC4) in the promoter region between LAC4 and LAC12 genes. This deletion may have improved the transcription of one or both of the genes, which may be the cause for the improved lactose consumption phenotype of the evolved strain. In lactose cultivations, the intracellular beta-galactosidase activity of strain T1-E is about 40 times higher when compared to T1. Moreover, the level of beta-galactosidase activity in strain T1-E is comparable to K. lactis CBS2359. Microarray analysis showed increased expression of genes related with transposable elements in T1-E compared to T1, which reflects the selective pressure that the yeast suffered during the adaptation process. The transcriptome (S. cerevisiae) analysis did not revealed other important differences between T1 and T1-E

Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration

A few molecularly proven severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases of symptomatic reinfection are currently known worldwide, with a resolved first infection followed by a second infection after a 48 to 142-day intervening period. We report a multiple-component study of a clinically severe and prolonged viral shedding coronavirus disease 2019 (COVID-19) case in a 17-year-old Portuguese female. She had two hospitalizations, a total of 19 RT-PCR tests, mostly positive, and criteria for releasing from home isolation at the end of 97 days. The viral genome was sequenced in seven serial samples and in the diagnostic sample from her infected mother. A human genome-wide array (>900 K) was screened on the seven samples, and in vitro culture was conducted on isolates from three late samples. The patient had co-infection by two SARS-CoV-2 lineages, which were affiliated in distinct clades and diverging by six variants. The 20A lineage was absolute at the diagnosis (shared with the patient's mother), but nine days later, the 20B lineage had 3% frequency, and two months later, the 20B lineage had 100% frequency. The 900 K profiles confirmed the identity of the patient in the serial samples, and they allowed us to infer that she had polygenic risk scores for hospitalization and severe respiratory disease within the normal distributions for a Portuguese population cohort. The early-on dynamic co-infection may have contributed to the severity of COVID-19 in this otherwise healthy young patient, and to her prolonged SARS-CoV-2 shedding profile.The authors acknowledge the support of the i3S Scientific Platforms BioSciences Screening and Genomics, members of the national infrastructure PPBI-Portuguese Platform of Bioimaging (PPBI-POCI-01-0145-FEDER-022122), PT-OPENSCREEN, GenomePT project (POCI-01-0145-FEDER-022184)

Extração de Características Cicloestacionárias por Correntropia Cíclica em Canais com Desvanecimento / Extraction of Cystationary Characteristics by Cyclic Correntropy in Fading Channels

A Função de Correntropia Cíclica (CCF - Cyclic Correntropy Function) vem sendo aplicada em diferentes problemas na área de processamento de sinais para comunicações, por exemplo, detecção espectral, estimativa de parâmetros de sinais e classificação automática de modulações. Entretanto, os modelos para os canais de comunicações considerados na maioria desses trabalhos incorporam apenas os efeitos do ruído aditivo gaussiano, ou impulsivo. Neste trabalho, investiga-se o desempenho da CCF na extração de características de sinais para fins de classificação automática de modulações em cenários de comunicações nos quais os sinais se propagam por múltiplos percursos, ficando sujeitos aos efeitos do desvanecimento Rayleigh plano. Os resultados demonstram que a CCF também pode levar a bons resultados nesses ambientes de comunicações

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured

Measurement of the production of a W boson in association with a charm quark in pp collisions at √s = 7 TeV with the ATLAS detector

The production of a W boson in association with a single charm quark is studied using 4.6 fb−1 of pp collision data at s√ = 7 TeV collected with the ATLAS detector at the Large Hadron Collider. In events in which a W boson decays to an electron or muon, the charm quark is tagged either by its semileptonic decay to a muon or by the presence of a charmed meson. The integrated and differential cross sections as a function of the pseudorapidity of the lepton from the W-boson decay are measured. Results are compared to the predictions of next-to-leading-order QCD calculations obtained from various parton distribution function parameterisations. The ratio of the strange-to-down sea-quark distributions is determined to be 0.96+0.26−0.30 at Q 2 = 1.9 GeV2, which supports the hypothesis of an SU(3)-symmetric composition of the light-quark sea. Additionally, the cross-section ratio σ(W + +c¯¯)/σ(W − + c) is compared to the predictions obtained using parton distribution function parameterisations with different assumptions about the s−s¯¯¯ quark asymmetry

Measurements of fiducial and differential cross sections for Higgs boson production in the diphoton decay channel at s√=8 TeV with ATLAS

Measurements of fiducial and differential cross sections are presented for Higgs boson production in proton-proton collisions at a centre-of-mass energy of s√=8 TeV. The analysis is performed in the H → γγ decay channel using 20.3 fb−1 of data recorded by the ATLAS experiment at the CERN Large Hadron Collider. The signal is extracted using a fit to the diphoton invariant mass spectrum assuming that the width of the resonance is much smaller than the experimental resolution. The signal yields are corrected for the effects of detector inefficiency and resolution. The pp → H → γγ fiducial cross section is measured to be 43.2 ±9.4(stat.) − 2.9 + 3.2 (syst.) ±1.2(lumi)fb for a Higgs boson of mass 125.4GeV decaying to two isolated photons that have transverse momentum greater than 35% and 25% of the diphoton invariant mass and each with absolute pseudorapidity less than 2.37. Four additional fiducial cross sections and two cross-section limits are presented in phase space regions that test the theoretical modelling of different Higgs boson production mechanisms, or are sensitive to physics beyond the Standard Model. Differential cross sections are also presented, as a function of variables related to the diphoton kinematics and the jet activity produced in the Higgs boson events. The observed spectra are statistically limited but broadly in line with the theoretical expectations

Search for squarks and gluinos with the ATLAS detector in final states with jets and missing transverse momentum using √s=8 TeV proton-proton collision data

A search for squarks and gluinos in final states containing high-p T jets, missing transverse momentum and no electrons or muons is presented. The data were recorded in 2012 by the ATLAS experiment in s√=8 TeV proton-proton collisions at the Large Hadron Collider, with a total integrated luminosity of 20.3 fb−1. Results are interpreted in a variety of simplified and specific supersymmetry-breaking models assuming that R-parity is conserved and that the lightest neutralino is the lightest supersymmetric particle. An exclusion limit at the 95% confidence level on the mass of the gluino is set at 1330 GeV for a simplified model incorporating only a gluino and the lightest neutralino. For a simplified model involving the strong production of first- and second-generation squarks, squark masses below 850 GeV (440 GeV) are excluded for a massless lightest neutralino, assuming mass degenerate (single light-flavour) squarks. In mSUGRA/CMSSM models with tan β = 30, A 0 = −2m 0 and μ > 0, squarks and gluinos of equal mass are excluded for masses below 1700 GeV. Additional limits are set for non-universal Higgs mass models with gaugino mediation and for simplified models involving the pair production of gluinos, each decaying to a top squark and a top quark, with the top squark decaying to a charm quark and a neutralino. These limits extend the region of supersymmetric parameter space excluded by previous searches with the ATLAS detector