Element release and reaction-induced porosity alteration during shale-hydraulic fracturing fluid interactions

The use of hydraulic fracturing techniques to extract oil and gas from low permeability shale reservoirs has increased significantly in recent years. During hydraulic fracturing, large volumes of water, often acidic and oxic, are injected into shale formations. This drives fluid-rock interaction that can release metal contaminants (e.g., U, Pb) and alter the permeability of the rock, impacting the transport and recovery of water, hydrocarbons, and contaminants. To identify the key geochemical processes that occur upon exposure of shales to hydraulic fracturing fluid, we investigated the chemical interaction of hydraulic fracturing fluids with a variety of shales of different mineralogical texture and composition. Batch reactor experiments revealed that the dissolution of both pyrite and carbonate minerals occurred rapidly, releasing metal contaminants and generating porosity. Oxidation of pyrite and aqueous Fe drove precipitation of Fe(III)-(oxy)hydroxides that attenuated the release of these contaminants via co-precipitation and/or adsorption. The precipitation of these (oxy)hydroxides appeared to limit the extent of pyrite reaction. Enhanced removal of metals and contaminants in reactors with higher fluid pH was inferred to reflect increased Fe-(oxy)hydroxide precipitation associated with more rapid aqueous Fe(II) oxidation. The precipitation of both Al- and Fe-bearing phases revealed the potential for the occlusion of pores and fracture apertures, whereas the selective dissolution of calcite generated porosity. These pore-scale alterations of shale texture and the cycling of contaminants indicate that chemical interactions between shales and hydraulic fracturing fluids may exert an important control on the efficiency of hydraulic fracturing operations and the quality of water recovered at the surface

An improved method for undertaking limiting dilution assays for in vitro cloning of Plasmodium falciparum parasites

Abstract. Background: Obtaining single parasite clones is required for many techniques in malaria research. Cloning by limiting dilution using microscopy-based assessment for parasite growth is an arduous and labor-intensive process. An alternative method for the detection of parasite growth in limiting dilution assays is using a commercial ELISA histidine-rich protein II (HRP2) detection kit. Methods. Detection of parasite growth was undertaken using HRP2 ELISA and compared to thick film microscopy. An HRP2 protein standard was used to determine the detection threshold of the HRP2 ELISA assay, and a HRP2 release model was used to extrapolate the amount of parasite growth required for a positive result. Results: The HRP2 ELISA was more sensitive than microscopy for detecting parasite growth. The minimum level of HRP2 protein detection of the ELISA was 0.11ng/ml. Modeling of HRP2 release determined that 2,116 parasites are required to complete a full erythrocytic cycle to produce sufficient HRP2 to be detected by the ELISA. Under standard culture conditions this number of parasites is likely to be reached between 8 to 14 days of culture. Conclusions: This method provides an accurate and simple way for the detection of parasite growth in limiting dilution assays, reducing time and resources required in traditional methods. Furthermore the method uses spent culture media instead of the parasite-infected red blood cells, enabling culture to continue

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Rehabilitation versus surgical reconstruction for non-acute anterior cruciate ligament injury (ACL SNNAP): a pragmatic randomised controlled trial

BackgroundAnterior cruciate ligament (ACL) rupture is a common debilitating injury that can cause instability of the knee. We aimed to investigate the best management strategy between reconstructive surgery and non-surgical treatment for patients with a non-acute ACL injury and persistent symptoms of instability.MethodsWe did a pragmatic, multicentre, superiority, randomised controlled trial in 29 secondary care National Health Service orthopaedic units in the UK. Patients with symptomatic knee problems (instability) consistent with an ACL injury were eligible. We excluded patients with meniscal pathology with characteristics that indicate immediate surgery. Patients were randomly assigned (1:1) by computer to either surgery (reconstruction) or rehabilitation (physiotherapy but with subsequent reconstruction permitted if instability persisted after treatment), stratified by site and baseline Knee Injury and Osteoarthritis Outcome Score—4 domain version (KOOS4). This management design represented normal practice. The primary outcome was KOOS4 at 18 months after randomisation. The principal analyses were intention-to-treat based, with KOOS4 results analysed using linear regression. This trial is registered with ISRCTN, ISRCTN10110685, and ClinicalTrials.gov, NCT02980367.FindingsBetween Feb 1, 2017, and April 12, 2020, we recruited 316 patients. 156 (49%) participants were randomly assigned to the surgical reconstruction group and 160 (51%) to the rehabilitation group. Mean KOOS4 at 18 months was 73·0 (SD 18·3) in the surgical group and 64·6 (21·6) in the rehabilitation group. The adjusted mean difference was 7·9 (95% CI 2·5–13·2; p=0·0053) in favour of surgical management. 65 (41%) of 160 patients allocated to rehabilitation underwent subsequent surgery according to protocol within 18 months. 43 (28%) of 156 patients allocated to surgery did not receive their allocated treatment. We found no differences between groups in the proportion of intervention-related complications.InterpretationSurgical reconstruction as a management strategy for patients with non-acute ACL injury with persistent symptoms of instability was clinically superior and more cost-effective in comparison with rehabilitation management

Interpreting Parameter Interactions using Global Sensitivity Analysis on a Hillslope-scale Reactive Transport Model

International audienceReactive transport models (RTMs) are valuable tools for understanding, interrogating and forecasting subsurface processes, but the complex interplay between intricate flow paths and simultaneous reactions can make them difficult to optimize and interpret. Global sensitivity analysis (GSA) can alleviate these problems in several ways: by identifying the largest sources of uncertainty in model output, by assigning value of information to model input parameters – which, in turn, improves lab and field investigations through targeted data collection – and by clarifying the combined effects of complex parameter interactions. However, GSA is often neglected within the subsurface modeling community due to the high computational costs required to perform many model simulations.Here, we demonstrate multiple applications of GSA to subsurface modeling by using distance-based generalized sensitivity analysis (DGSA1) to interrogate four separate components of a hillslope-scale RTM. DGSA requires fewer simulations than traditional GSA techniques, while cloud and cluster computing allow us to run 100s of model simulations simultaneously. The 2D model simulates the export of reduced species from pockets of fine-grained, organic-rich sediments embedded in a coarse sand aquifer. Stochastic simulations jointly varied 17 key model input parameters across several orders of magnitude, including the spatial variability of each parameter. DGSA on the model results reveal that the amplitude and variability of exported Fe(II) are most sensitive to the interaction between sand permeability and individual reaction rates. By contrast, the propagation of reducing conditions downgradient from the fine-grained lenses depends most heavily on the rate of dissolved organic carbon and sulfate release from the fines.1Fenwick, D.; Scheidt, C.; Caers, J. Quantifying Asymmetric Parameter Interactions in Sensitivity Analysis: Application to Reservoir Modeling. Math Geosci 2014, 46 (4), 493–511

Impact of Mixing on Fluid-solid Reactions

International audienceThe concentration of solutes transported in hydrological systems evolves through mixing and biogeochemical reactions. These two processes are coupled as biogeochemical reactions depend non-linearly on local solute concentrations. Flow is known to affect solid-fluid reactions, such as dissolution, complexation or redox reactions, which play an important role on geochemical weathering, contaminant transport and the cycle of geochemical elements, such as carbon and nitrogen. The complex interactions between flow and reactions have been often quantified by residence time distribution approaches, which focus on the effect of flow on the exposure time of solute to mineral in each flow path, while generally neglecting mixing between different flow paths. Yet, mixing processes can have a significant impact on fluid-mineral reactions, as their kinetics depend non-linearly on local solute concentrations, which depend directly on mixing rates. In this presentation, we combine reactive transport models with solute mixing theories to establish effective solid-mineral kinetics, which are linked to mixing rates.Using reactive transport simulations with CrunchFlow, we demonstrate that mixing affects solid-mineral reactions characterized by a non-linear dependency on local concentrations. For reactions that give more weight to large concentrations, mixing decreases the overall reaction rate. On the opposite, for reactions that give more weight to low concentrations, mixing increases the overall reaction rate. To quantify this effect, we develop a new approach based on Probability Densiy Functions that describe the full concentration distribution and its coupling with non-linear reaction kinetics. These results open new perspectives to understand and model coupled mixing and solid-fluid reactions in heterogeneous media

Effective Kinetics of Chemical Gradient Reactors

International audienceSubsurface environments are biogeochemical reactors characterized by a range of chemical gradients, such as: gradients of dissolved oxygen in the unsaturated zone, gradients of electron donors and acceptors in the hyporheic zone, gradients of chemical compounds in contaminated sites, gradients of groundwater age and dissolved species in catchments. Yet, effective reaction kinetics are generally estimated from batch reactors, i.e. zero gradient conditions. Here we investigate the effect of chemical gradients on the effective kinetics of fluid-mineral reactions (dissolution/precipitation). We focus on non-linear reactions, where the reaction rate is a non-linear function of local concentrations and the exponent is related to the reaction stoichiometry. In this common situation, the effect of chemical gradients on reaction kinetics is expected to be particularly important. We combine reactive transport models with solute mixing theories to establish effective fluid-mineral kinetics, and relate them to mixing rates. We compare the resulting kinetics of chemical gradients to homogeneous systems for a range of Damköhler numbers in order to investigate the respective roles of reaction and mixing processes.We perform Crunchflow simulations of a diffusing pulse of reactant, which create spatially and temporally variable chemical gradients. Numerical results show that effective kinetics of chemical gradient reactors significantly differ from those of batch reactors. For kinetic power law exponents larger than one, chemical gradients in a diffusive pulse are found to increase the overall reaction rate in comparison to batch kinetics. On the opposite, for kinetic power law exponents lower than one, the effective kinetics of chemical gradient reactors are slower than those of batch reactors. We identify two different regimes where local concentration evolution is primarily diffusion-controlled and reaction-controlled. This allows deriving approximate analytical solutions for the evolution of concentration distribution in time and space due to diffusion and reaction. We thus link the effective reaction kinetics to the Damköhler number and the non-linear reaction exponent. These results open new perspectives to understand and model coupled mixing and fluid-mineral reactions in heterogeneous media

A Coupled Sr/U isotopic method for measuring rates of silicate dissolution and infiltration rates at the Hanford Site, Wa.

Long-term vadose zone infiltration rates at the Hanford Site, Washington, are critical for assessing the transport of radionuclides to the groundwater and eventually the Columbia River. Sr isotopes (87Sr/86Sr) in the unsaturated zone pore water are controlled by the ratio of the dissolution rate of the solids to the infiltration flux, and therefore provide either a long-term estimate of the infiltration flux if the weathering rate is constrained, or vise versa. The 234U/238U of the pore water responds to chemical weathering, infiltration, and the a-recoil flux of 234Th to the pore fluid. Previous estimates of the ratio of the dissolution rate to the infiltration flux from Sr isotopes for a 70 meter vadose zone core are combined with a model describing the evolution of 234U/238U values in the pore water and solids to constrain the infiltration flux and dissolution rate. The weathering rates calculated from the two isotopes systems behave differently in response to the assumed value for the infiltration rate weathering rates from the Sr method increase as a function of increasing infiltration, whereas U rates decrease as a function of increasing infiltration. This opposing behavior is due to the difference between the isotopic composition of the solids relative to the fluid at the top of the profile. The coupled model for both the 234U/238U and the 87Sr/86Sr data converges on a long-term infiltration flux of 3-5 mm/yr, and bulk silicate dissolution rates between 10-15.7 and 10-16.8 mol/m2/sec. This suggests that the coupled application of U and Sr isotopes in natural systems may be useful for constraining two widely important variables, fluid flow and reaction rates. In addition, methods to accurately determine the a-recoil loss fraction in heterogeneous sediments are also compared, including geometric arguments and measurements of the 234U/238U in fine-grained size fractions and strong acid leaches. In general, strong acid leaches provide a means of quantifying both the a-recoil loss fraction, and the isotopic composition of the dissolving solids. The U-series isotopic method may be especially useful in determining solid-fluid reaction rates where precise age constraints for the system are not available because the process of a-recoil loss, when accurately quantified, provides a chronometer for the dissolution rate