Water sampling in low productive boreholes: how to ensure of the representativeness of sampling?

International audienceGood practices of wellbore purging advice to draw three to five times the volume of the water column prior to sample. An extensive literature in the past 20 years has established the biases that may be linked to this procedure with emphasis on contaminant sampling and the benefit low-flow sampling may have to avoid redistribution of contaminants in boreholes because of the flow-weighted average character of pumping (Einarson, 2006, Handbook Environmental Site Characterization and GroundWater Monitoring). Low-flow sampling may produce flow-biased samples if operated in long-screened boreholes where vertical gradients exist (McMillan et al., 2014, J. Contam. Hydrol. 1699, 50-61) and is better suited for high permeability boreholes (ISO Standards). Water sampling in low permeability aquifers remains challenging especially for boreholes drilled for water table level monitoring (long-screened boreholes; pumps may not be lowered down in the screened interval). Fluid Electrical Conductivity logging prior to pumping and sampling may help in locating the productive levels albeit the information obtained under ambient flow conditions may be of less relevance than the data collected using salt injection (e.g. Lasher and Nel, 2013, Groundwater Division Conference, Durban). Fiber optic Distributed Temperature Sensing may also resolve hydraulic (McMillan, 2015, PhD dissertation) but is not of common use. We refer to investigations performed in two boreholes (Labruguière and Valdurenque) of low permeabilities (10 −6 to 10 −7 m.s −1), located in detritic formations in SW France. These two boreholes, of 170 m and 123 m depth respectively, have long screened sections (128-170 m and 75-123 m respectively). With such geometries, the sub-mersible pump cannot be placed in the screened interval to perform volume purge. This raises the question of how long the pumping has to be done to get water representative of the downhole chemistry. The purge of three times the volume of the water column is unrealistic. For Labruguière borehole, it would take 12 hours cumulated at ≤1 m 3 .h −1 pumping rate, each session cannot last more than 2 hours (dewatering) and 12 hours are needed to recover the water table level. We thus refer to deep sampling to assess the usefulness of such a method. Several levels were determined on the basis of ambient logging (temperature, conductivity, pH, dissolved oxygen, redox potential). In parallel we use pumping to assess the purge process inside the borehole and determine the minimum amount of drawn water needed to get water from the screens. This also highlights that alternative method to judge of representativeness, such as stabilization of physico-chemical parameters, may lead to false positives, i.e. the parameters were stabilized but the water chemistry was not that of the screened section. Three cycles of logging – deep sampling – pumping were done in each borehole. Based on field data and laboratory analyses, it appears that a protocol for deep boreholes characterization may refer to 1) borehole logging (information on ambient structure of the water column), 2) slight solicitation of the borehole by pumping (renewal of water at productive levels), and 3) deep sampling at the depth(s) suggested by borehole logs

Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier’s permissiveness and supports local epidemic potential

Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector’s intrinsic ability to replicate then transmit the pathogen known as vector competence. Vector competence is a complex, time-dependent,quantitative phenotype influenced by biotic and abiotic factors. A combination of experimental andmodelling approaches is required to assess arbovirus intra-vector dynamics and estimate epidemicpotential. In this study, we measured infection, dissemination, and transmission dynamics of chikungunya virus (CHIKV) in a field-derived Aedes albopictus population (Lyon, France) after oral exposureto a range of virus doses spanning human viraemia. Statistical modelling indicates rapid and efficientCHIKV progression in the vector mainly due to an absence of a dissemination barrier, with 100% ofthe infected mosquitoes ultimately exhibiting a disseminated infection, regardless of the virus dose.Transmission rate data revealed a time-dependent, but overall weak, transmission barrier, with individuals transmitting as soon as 2 days post-exposure (dpe) and >50% infectious mosquitoes at 6dpe for the highest dose. Based on these experimental intra-vector dynamics data, epidemiologicalsimulations conducted with an agent-based model showed that even at low mosquito biting rates,CHIKV could trigger outbreaks locally. Together, this reveals the epidemic potential of CHIKV upontransmission by Aedes albopictus in mainland Franc

Remodeling of the actin network associated with the non-structural protein 1 (NS1) of West Nile virus and formation of NS1-containing tunneling nanotubes

The cellular response to the recombinant NS1 protein of West Nile virus (NS1WNV) was studied using three different cell types: Vero E6 simian epithelial cells, SH-SY5Y human neuroblastoma cells, and U-87MG human astrocytoma cells. Cells were exposed to two different forms of NS1WNV: (i) the exogenous secreted form, sNS1WNV, added to the extracellular milieu; and (ii) the endogenous NS1WNV, the intracellular form expressed in plasmid-transfected cells. The cell attachment and uptake of sNS1WNV varied with the cell type and were only detectable in Vero E6 and SH-SY5Y cells. Addition of sNS1WNV to the cell culture medium resulted in significant remodeling of the actin filament network in Vero E6 cells. This effect was not observed in SH-SY5Y and U-87MG cells, implying that the cellular uptake of sNS1WNV and actin network remodeling were dependent on cell type. In the three cell types, NS1WNV-expressing cells formed filamentous projections reminiscent of tunneling nanotubes (TNTs). These TNT-like projections were found to contain actin and NS1WNV proteins. Interestingly, similar actin-rich, TNT-like filaments containing NS1WNV and the viral envelope glycoprotein EWNV were also observed in WNV-infected Vero E6 cells

Aspergillus PCR in Bronchoalveolar Lavage Fluid for the Diagnosis and Prognosis of Aspergillosis in Patients With Hematological and Non-hematological Conditions

Objectives: We evaluated the usefulness of an Aspergillus fumigatus quantitative PCR assay performed in bronchoalveolar lavage fluid (BAL) for the diagnosis and prognosis of both invasive and non-invasive aspergillosis.Methods: This 4-year retrospective study involved 613 at-risk patients who had either hematological disorders or other immunosuppressive conditions, notably solid organ transplants. Thirty-five patients had proven/probable aspergillosis and thirteen had chronic non-invasive aspergillosis. We compared PCR, galactomannan index and mycological analysis of BAL.Results: For invasive aspergillosis (IA), PCR performed in BAL yielded 88.6% sensitivity and 95.5% specificity. Comparatively, galactomannan index and mycological examination yielded only 56.3 and 63.6% sensitivity and 97.6 and 94.5% specificity, respectively. Considering the 13 chronic aspergillosis cases, PCR, galactomannan index and mycological examination yielded 76.9, 15.4, and 84.6% sensitivity and 92.2, 94.9, and 93% specificity, respectively. Fungal load in BAL evaluated by PCR was able to discriminate between aspergillosis and contamination, but not between invasive and non-invasive forms. Finally, fungal load was predictive of 90-day mortality, with 23.1% mortality for patients with less than 500 copies/mL versus 68.4% for patients above that cut-off (p < 0.05).Conclusion: Our results indicate that Aspergillus PCR in BAL is of particular interest for both the diagnosis and the prognosis of IA. It is likewise an interesting tool for the diagnosis of non-invasive forms

Surface gas geochemistry above the natural CO2 reservoir of Montmiral (Drôme, France), source tracking and gas exchange between the soil, biosphere and atmosphere

International audienceOne of the options considered to mitigate greenhouse gas concentrations in the atmosphere is underground storage of CO2. There is a strong need for enhancing and developing methods that would help throughout the duration life of such underground storage, to ensure the safety and able to monitor the evolution of the injected CO2 plume. Among these, geochemical methods can play an important role. Here, we describe results acquired under the research programme “Géocarbone-Monitoring”, partially funded by the French National Research Agency, on the Montmiral natural analogue in South-Eastern France. Other results obtained under the same research programme in the French Massif Central are reported elsewhere in this volume.Spot sampling methods allowing a great geographical coverage and continuous measurements on selected points were undertaken in 2006 and 2007, in order to determine soil gas concentrations and fluxes as well as carbon isotope ratio determinations. One important result is that without any evidence of deep CO2 leakage, both CO2 concentrations and fluxes appear to be higher than can be explained only by biological activities. Further investigations are thus needed to understand the gas evolution better throughout the year

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

COVID-19 symptoms at hospital admission vary with age and sex: results from the ISARIC prospective multinational observational study

Background: The ISARIC prospective multinational observational study is the largest cohort of hospitalized patients with COVID-19. We present relationships of age, sex, and nationality to presenting symptoms. Methods: International, prospective observational study of 60 109 hospitalized symptomatic patients with laboratory-confirmed COVID-19 recruited from 43 countries between 30 January and 3 August 2020. Logistic regression was performed to evaluate relationships of age and sex to published COVID-19 case definitions and the most commonly reported symptoms. Results: ‘Typical’ symptoms of fever (69%), cough (68%) and shortness of breath (66%) were the most commonly reported. 92% of patients experienced at least one of these. Prevalence of typical symptoms was greatest in 30- to 60-year-olds (respectively 80, 79, 69%; at least one 95%). They were reported less frequently in children (≤ 18 years: 69, 48, 23; 85%), older adults (≥ 70 years: 61, 62, 65; 90%), and women (66, 66, 64; 90%; vs. men 71, 70, 67; 93%, each P < 0.001). The most common atypical presentations under 60 years of age were nausea and vomiting and abdominal pain, and over 60 years was confusion. Regression models showed significant differences in symptoms with sex, age and country. Interpretation: This international collaboration has allowed us to report reliable symptom data from the largest cohort of patients admitted to hospital with COVID-19. Adults over 60 and children admitted to hospital with COVID-19 are less likely to present with typical symptoms. Nausea and vomiting are common atypical presentations under 30 years. Confusion is a frequent atypical presentation of COVID-19 in adults over 60 years. Women are less likely to experience typical symptoms than men

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570