Initial AtlantOS Requirements Report

Initial description from ongoing work of the societal imperatives for sustained Atlantic Ocean observations, the phenomena to observe, EOVs, and contributing observing network

Assessing the global threat from Zika virus.

First discovered in 1947, Zika virus (ZIKV) infection remained a little-known tropical disease until 2015, when its apparent association with a considerable increase in the incidence of microcephaly in Brazil raised alarms worldwide. There is limited information on the key factors that determine the extent of the global threat from ZIKV infection and resulting complications. Here, we review what is known about the epidemiology, natural history, and public health effects of ZIKV infection, the empirical basis for this knowledge, and the critical knowledge gaps that need to be filled

Efeito de três formulações de Bacillus amyloliquefaciens ICBB200 sobre o crescimento de plantas de alface (Lactuca sativa L.) em cinco condições edafoclimáticas

Conventional vegetable production is based on the use of chemical fertilizers and pesticides, which contribute to increased food production. However, excessive and inappropriate use of these products can cause several problems to health and the environment. The use of bacteria promoting plant growth, such Bacillus amyloliquefaciens ICBB200 is an alternative, since they act directly on the plant growth due to changes in hormonal levels and increased intake of nutrients such as phosphorus and iron, and also act indirectly by suppressing diseases. Field tests with three different formulations of B. amyloliquefaciens ICBB200 were conducted in lettuce growing areas, in five different soils and climatic conditions in the city of Porto Alegre, Rio Grande do Sul State. After 34 days of cultivation, the plants were collected and evaluated for circumference and fresh weight of aerial part. B. amyloliquefaciens ICBB200 promoted shoot growth of lettuce plants in any of their formulations tested, at all the different conditions tested.A produção convencional de hortaliças se baseia no uso de fertilizantes e defensivos químicos, os quais contribuem para o aumento da produção de alimentos. Porém, o uso exagerado e inadequado desses produtos pode causar vários problemas à saúde e ao meio ambiente. O uso de bactérias promotoras de crescimento de plantas, como Bacillus amyloliquefaciens, surge como uma alternativa, já que as mesmas atuam diretamente no crescimento vegetal por alterações nas concentrações hormonais e maior aporte de nutrientes, como nitrogênio, fósforo e ferro, além de também atuar indiretamente pela supressão de doenças. Com isso, este trabalho objetiva avaliar o efeito da bactéria B. amyloliquefaciens ICBB200, apresentada em três diferentes formulações, sobre o crescimento de plantas de alface, em cinco condições edafoclimáticas diferentes. Ensaios em campo com três diferentes formulações de B. amyloliquefaciens ICBB200 foram conduzidos em áreas de cultivo de alface, em cinco condições edafoclimáticas distintas, na cidade de Porto Alegre, RS. Após 34 dias de cultivo, as plantas foram coletadas e avaliadas quanto à circunferência e peso de massa fresca de parte aérea. B. amyloliquefaciens ICBB200 promoveu o crescimento de parte aérea de plantas de alface, em qualquer uma de suas formulações testadas, em todas diferentes condições edafoclimáticas testadas

Effect of three formulations of Bacillus amyloliquefaciens ICBB200 on lettuce growth (Lactuca sativa L.) in five soil and climate conditions

A produção convencional de hortaliças se baseia no uso de fertilizantes e defensivos químicos, os quais contribuem para o aumento da produção de alimentos. Porém, o uso exagerado e inadequado desses produtos pode causar vários problemas à saúde e ao meio ambiente. O uso de bactérias promotoras de crescimento de plantas, como Bacillus amyloliquefaciens, surge como uma alternativa, já que as mesmas atuam diretamente no crescimento vegetal por alterações nas concentrações hormonais e maior aporte de nutrientes, como nitrogênio, fósforo e ferro, além de também atuar indiretamente pela supressão de doenças. Com isso, este trabalho objetiva avaliar o efeito da bactéria B. amyloliquefaciens ICBB200, apresentada em três diferentes formulações, sobre o crescimento de plantas de alface, em cinco condições edafoclimáticas diferentes. Ensaios em campo com três diferentes formulações de B. amyloliquefaciens ICBB200 foram conduzidos em áreas de cultivo de alface, em cinco condições edafoclimáticas distintas, na cidade de Porto Alegre, RS. Após 34 dias de cultivo, as plantas foram coletadas e avaliadas quanto à circunferência e peso de massa fresca de parte aérea. B. amyloliquefaciens ICBB200 promoveu o crescimento de parte aérea de plantas de alface, em qualquer uma de suas formulações testadas, em todas diferentes condições edafoclimáticas testadas.Conventional vegetable production is based on the use of chemical fertilizers and pesticides, which contribute to increased food production. However, excessive and inappropriate use of these products can cause several problems to health and the environment. The use of bacteria promoting plant growth, such Bacillus amyloliquefaciens ICBB200 is an alternative, since they act directly on the plant growth due to changes in hormonal levels and increased intake of nutrients such as phosphorus and iron, and also act indirectly by suppressing diseases. Field tests with three different formulations of B. amyloliquefaciens ICBB200 were conducted in lettuce growing areas, in five different soils and climatic conditions in the city of Porto Alegre, Rio Grande do Sul State. After 34 days of cultivation, the plants were collected and evaluated for circumference and fresh weight of aerial part. B. amyloliquefaciens ICBB200 promoted shoot growth of lettuce plants in any of their formulations tested, at all the different conditions tested

Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies.

SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient's infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient's progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious

Biomarker-based diagnosis of pacemaker and implantable cardioverter defibrillator pocket infections: A prospective, multicentre, case control evaluation

Background: The use of cardiac implantable electronic devices (CIED) has risen steadily, yet the rate of cardiac device infections (CDI) has disproportionately increased. Amongst all cardiac device infections, the pocket infection is the most challenging diagnosis. Therefore, we aimed to improve diagnosis of such pocket infection by identifying relevant biomarkers. Methods: We enrolled 25 consecutive patients with invasively and microbiologically confirmed pocket infection. None of the patients had any confounding conditions. Pre-operative levels of 14 biomarkers were compared in infected and control (n = 50) patients. Our selected biomarkers included white blood cell count (WBC), C-reactive protein (CRP), procalcitonin (PCT), lipopolysaccharide binding protein, high-sensitivity C-reactive protein (HS-CRP), polymorphonuclear-elastase, presepsin, various interleukins, tumor necrosis factor a (TNF-a), and granulocyte macrophage colony-stimulating factor (GM-CSF). Results: Of the 25 patients with isolated pocket infection (70 13years, 76% male, 40% ICDs), none presented with leukocytosis. In contrast, they had higher serum levels of HS-CRP (p = 0.019) and PCT (p = 0.010) than control patients. Median PCT-level was 0.06 ng/mL (IQR 0.03-0.07 ng/mL) in the study group versus 0.03 ng/mL (IQR 0.02-0.04 ng/mL) in controls. An optimized PCT cut-off value of 0.05 ng/mL suggests pocket infection with a sensitivity of 60% and specificity of 82%. In addition TNF-alpha- and GM-CSF-levels were lower in the study group. Other biomarkers did not differ between groups. Conclusion: Diagnosis of isolated pocket infections requires clinical awareness, physical examination, evaluation of blood cultures and echocardiography assessment. Nevertheless, measurement of PCT- and HS-CRP-levels can aid diagnosis. However, no conclusion can be drawn from normal WBC-values

Accelerated SARS-CoV-2 Intrahost Evolution Leading to Distinct Genotypes During Chronic Infection

The chronic infection hypothesis for novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant emergence is increasingly gaining credence following the appearance of Omicron. Here, we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral genome copies. During the infection, we find an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately 2-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution results in the emergence and persistence of at least three genetically distinct genotypes, suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, we track the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, providing an opportunity for the emergence of genetically divergent variants

Lineage Abundance Estimation for SARS-CoV-2 in Wastewater Using Transcriptome Quantification Techniques

Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable

X-Pipeline: An analysis package for autonomous gravitational-wave burst searches

Autonomous gravitational-wave searches -- fully automated analyses of data that run without human intervention or assistance -- are desirable for a number of reasons. They are necessary for the rapid identification of gravitational-wave burst candidates, which in turn will allow for follow-up observations by other observatories and the maximum exploitation of their scientific potential. A fully automated analysis would also circumvent the traditional "by hand" setup and tuning of burst searches that is both labourious and time consuming. We demonstrate a fully automated search with X-Pipeline, a software package for the coherent analysis of data from networks of interferometers for detecting bursts associated with GRBs and other astrophysical triggers. We discuss the methods X-Pipeline uses for automated running, including background estimation, efficiency studies, unbiased optimal tuning of search thresholds, and prediction of upper limits. These are all done automatically via Monte Carlo with multiple independent data samples, and without requiring human intervention. As a demonstration of the power of this approach, we apply X-Pipeline to LIGO data to search for gravitational-wave emission associated with GRB 031108. We find that X-Pipeline is sensitive to signals approximately a factor of 2 weaker in amplitude than those detectable by the cross-correlation technique used in LIGO searches to date. We conclude with the prospects for running X-Pipeline as a fully autonomous, near real-time triggered burst search in the next LSC-Virgo Science Run.Comment: 18 pages, 10 figures. Minor edits and clarifications; added more background on gravitational waves and detectors. To appear in New Journal of Physics

Tracking smell loss to identify healthcare workers with SARS-CoV-2 infection

Introduction Healthcare workers (HCW) treating COVID-19 patients are at high risk for infection and may also spread infection through their contact with vulnerable patients. Smell loss has been associated with SARS-CoV-2 infection, but it is unknown whether monitoring for smell loss can be used to identify asymptomatic infection among high risk individuals. In this study we sought to determine if tracking smell sensitivity and loss using an at-home assessment could identify SARS-CoV-2 infection in HCW. Methods and findings We performed a prospective cohort study tracking 473 HCW across three months to determine if smell loss could predict SARS-CoV-2 infection in this high-risk group. HCW subjects completed a longitudinal, behavioral at-home assessment of olfaction with household items, as well as detailed symptom surveys that included a parosmia screening questionnaire, and real-time quantitative polymerase chain reaction testing to identify SARS-CoV-2 infection. Our main measures were the prevalence of smell loss in SARS-CoV-2-positive HCW versus SARS-CoV- 2-negative HCW, and timing of smell loss relative to SARS-CoV-2 test positivity. SARS-CoV-2 was identified in 17 (3.6%) of 473 HCW. HCW with SARS-CoV-2 infection were more likely to report smell loss than SARS-CoV-2-negative HCW on both the at-home assessment and the screening questionnaire (9/17, 53% vs 105/456, 23%, P < .01). 6/9 (67%) of SARS-CoV-2-positive HCW reporting smell loss reported smell loss prior to having a positive SARS-CoV-2 test, and smell loss was reported a median of two days before testing positive. Neurological symptoms were reported more frequently among SARS-CoV-2-positive HCW who reported smell loss compared to those without smell loss (9/9, 100% vs 3/8, 38%, P < .01). Conclusions In this prospective study of HCW, self-reported changes in smell using two different measures were predictive of SARS-CoV-2 infection. Smell loss frequently preceded a positive test and was associated with neurological symptoms