Acute and chronic toxicity of magnesium to the early life stages of two tropical freshwater mussel species.

Magnesium (Mg) is a common contaminant in mine water discharges. Although Mg is an essential element in biological processes, increased concentrations from anthropogenic sources can stress aquatic ecosystems. Additionally, studies evaluating the effects of Mg on north Australian freshwater species have indicated that in very soft waters there is a high risk to some species. Freshwater mussels are an ecologically and culturally important taxon in many freshwater environments, but knowledge of their sensitivity to Mg is limited. In the present study, the acute and chronic sensitivity of two freshwater mussel species, Velesunio angasi and an undescribed Velesunio species, to Mg was assessed (using MgSO4) on their early life stages, larval glochidia and post-parasitic juveniles. Acute 24-h exposures with glochidia generated a mean median lethal (LC50) toxicity estimate of 284mg/L for the five tests with V. angasi, and a mean LC50 of 300mg/L for the three tests with Velesunio sp. Mean chronic 14-d toxicity estimates resulting in 50% (EC50) and 10% (EC10) growth rate reductions for juveniles were 241 and 88mg/L respectively for the three tests with V. angasi juveniles, and 232 and 87mg/L respectively for the three tests with Velesunio sp. juveniles. The results represent the first acute and chronic Mg toxicity data for tropical freshwater mussels, and indicated that V. angasi and Velesunio sp. exhibited similar sensitivity and were moderately sensitive to Mg when compared to other tropical species. These results are a valuable contribution to the small existing dataset for Mg toxicity to tropical freshwater species, which can be used to inform water management in areas where Mg is a contaminant of concern, and ensure the protection of these taxa.

EBOVAC-Salone: Lessons learned from implementing an Ebola vaccine trial in an Ebola-affected country.

Background/aims During the 2014-2016 West African Ebola epidemic, clinical trials were fast-tracked in order to identify prophylactic vaccines and experimental treatments that might be useful in preventing or treating Ebola. These trials included the ongoing EBOVAC-Salone study, which was established and implemented in Sierra Leone to assess the safety and immunogenicity of the Ad26.ZEBOV/MVA-BN-Filo prime-boost Ebola vaccine regimen. Methods This article describes the experiences of the EBOVAC-Salone research team in setting up and implementing the trial, and provides recommendations for research teams aiming to conduct clinical trials in future outbreak situations. Results Establishing a clinical trial during an outbreak brought some unique challenges, including those related to trial design and the regulatory environment, operational issues, and community engagement. The situation was further complicated by the weak infrastructure and limited experience of clinical trials in Sierra Leone. However, operating in an outbreak context also brought some benefits to the research team, including strong stakeholder support. The EBOVAC-Salone study recruited participants both during and after the outbreak, leading to additional challenges to trial implementation during the post-outbreak transition. Conclusion Many lessons have been learned about setting up and implementing a clinical trial during a devastating Ebola epidemic, and some of the experiences of the EBOVAC-Salone team were mirrored by those of other researchers operating in the region. Common to several of these research groups is a recommendation that research should be more closely incorporated into outbreak response planning, which could expedite the establishment of timely and appropriate research projects. We recommend that the lessons learned by researchers during the West African Ebola epidemic are built into programmes and strategies to improve the responses to future epidemics, wherever they occur.

Genome Modeling System: A Knowledge Management Platform for Genomics.

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

Power, fairness and trust: understanding and engaging with vaccine trial participants and communities in the setting up the EBOVAC-Salone vaccine trial in Sierra Leone.

BACKGROUND: This paper discusses the establishment of a clinical trial of an Ebola vaccine candidate in Kambia District, Northern Sierra Leone during the epidemic, and analyses the role of social science research in ensuring that lessons from the socio-political context, the recent experience of the Ebola outbreak, and learning from previous clinical trials were incorporated in the development of community engagement strategies. The paper aims to provide a case study of an integrated social science and communications system in the start-up phase of the clinical trial. METHODS: The paper is based on qualitative research methods including ethnographic observation, interviews with trial participants and key stakeholder interviews. RESULTS: Through the case study of EBOVAC Salone, the paper suggests ways in which research can be used to inform communication strategies before and during the setting up of the trial. It explores notions of power, fairness and trust emerging from analysis of the Sierra Leonean context and through ethnographic research, to reflect on three situations in which social scientists and community liaison officers worked together to ensure successful community engagement. Firstly, a section on "power" considers the pitfalls of considering communities as homogeneous and shows the importance of understanding intra-community power dynamics when engaging communities. Secondly, a section on "fairness" shows how local understandings of what is fair can help inform the design of volunteer recruitment strategies. Finally, a section on "trust" highlights how historically rooted rumours can be effectively addressed through active dialogue rather than through an approach focused on correcting misinformation. CONCLUSION: The paper firstly emphasises the value of social science in the setting up of clinical trials, in terms of providing an in depth understanding of context and social dynamics. Secondly, the paper suggests the importance of a close collaboration between research and community engagement to effectively confront political and social dynamics, especially in the context of an epidemic.

MuSiC: identifying mutational significance in cancer genomes.

Massively parallel sequencing technology and the associated rapidly decreasing sequencing costs have enabled systemic analyses of somatic mutations in large cohorts of cancer cases. Here we introduce a comprehensive mutational analysis pipeline that uses standardized sequence-based inputs along with multiple types of clinical data to establish correlations among mutation sites, affected genes and pathways, and to ultimately separate the commonly abundant passenger mutations from the truly significant events. In other words, we aim to determine the Mutational Significance in Cancer (MuSiC) for these large data sets. The integration of analytical operations in the MuSiC framework is widely applicable to a broad set of tumor types and offers the benefits of automation as well as standardization. Herein, we describe the computational structure and statistical underpinnings of the MuSiC pipeline and demonstrate its performance using 316 ovarian cancer samples from the TCGA ovarian cancer project. MuSiC correctly confirms many expected results, and identifies several potentially novel avenues for discovery.

Age-related shifts in the density and distribution of genetic marker water quality indicators in cow and calf feces.

Calves make up about 16% of the current bovine population in the United States and can excrete high levels of human pathogens in their feces. We describe the density and distribution of genetic markers from 9 PCR- and real-time quantitative PCR-based assays, including CF128, CF193, CowM2, CowM3, GenBac3, Entero1, EC23S857, CampF2, and ttr-6, commonly used to help assess ambient surface water quality. Each assay was tested against a collection of 381 individual bovine fecal samples representing 31 mother and calf pairings collected over a 10-month time period from time of birth through weaning. Genetic markers reported to be associated with ruminant and/or bovine fecal pollution were virtually undetected in calves for up to 115 days from birth, suggesting that physiological changes in calf ruminant function impact host-associated genetic marker shedding. In addition, general fecal indicator markers for Bacteroidales, Escherichia coli, and Enterococcus spp. exhibited three separate trends across time, indicating that these bacteria respond differently to age-related physiological and dietary changes during calf development. The results of this study suggest that currently available PCR-based water quality indicator technologies can under- or overestimate fecal pollution originating from calves and identify a need for novel calf-associated source identification methods.

pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection.

Background: Neoantigen targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies are underway globally. Accurate identification and prioritization of neoantigens is highly relevant to designing these trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of massively parallel DNA and RNA sequencing technologies, it is now possible to computationally predict neoantigens based on patient-specific variant information. However, numerous factors must be considered when prioritizing neoantigens for use in personalized therapies. Complexities such as alternative transcript annotations, various binding, presentation and immunogenicity prediction algorithms, and variable peptide lengths/registers all potentially impact the neoantigen selection process. There has been a rapid development of computational tools that attempt to account for these complexities. While these tools generate numerous algorithmic predictions for neoantigen characterization, results from these pipelines are difficult to navigate and require extensive knowledge of the underlying tools for accurate interpretation. This often leads to over-simplification of pipeline outputs to make them tractable, for example limiting prediction to a single RNA isoform or only summarizing the top ranked of many possible peptide candidates. In addition to variant detection, gene expression and predicted peptide binding affinities, recent studies have also demonstrated the importance of mutation location, allele-specific anchor locations, and variation of T-cell response to long versus short peptides. Due to the intricate nature and number of salient neoantigen features, presenting all relevant information to facilitate candidate selection for downstream applications is a difficult challenge that current tools fail to address. Results: We have created pVACview, the first interactive tool designed to aid in the prioritization and selection of neoantigen candidates for personalized neoantigen therapies including cancer vaccines. pVACview has a user-friendly and intuitive interface where users can upload, explore, select and export their neoantigen candidates. The tool allows users to visualize candidates across three different levels, including variant, transcript and peptide information. Conclusions: pVACview will allow researchers to analyze and prioritize neoantigen candidates with greater efficiency and accuracy in basic and translational settings The application is available as part of the pVACtools pipeline at pvactools.org and as an online server at pvacview.org.

Neoantigen Landscape Supports Feasibility of Personalized Cancer Vaccine for Follicular Lymphoma.

Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that 'polyvalent' vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole exome sequencing (WES) and RNA sequencing (RNA-Seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-Seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by alignment of B-cell receptor (BCR) CDR3 regions from RNA-Seq data, grouping at the protein level, and comparison to the BCR repertoire from healthy individuals using RNA-Seq data. An average of 52 somatic mutations per patient (range: 2-172) were identified, and two or more (median: 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide (SLP) vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all four patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field.

Seasonal responses of macroinvertebrate assemblages to magnesium in a seasonally flowing stream.

Macroinvertebrates can be highly sensitive to elevated salinity in freshwater environments, and are known to respond to saline discharges. Magnesium (Mg) is a mine-related contaminant and is a potential environmental risk to a seasonally-flowing, receiving water stream in Kakadu National Park, located in the wet-dry tropics of Australia. The macroinvertebrate assemblage in the stream in the was characterised at four hydrographic phases, from early wet season flow to early dry season pools at flow cessation. On each of the four occasions representing the respective phases, individuals from the most abundant macroinvertebrate species present were collected and acutely exposed to a range (up to 19) of Mg concentrations under laboratory conditions. Sensitivity of taxa to Mg ranged between 39 mg/L Mg (Caenidae: Tasmanocoenis spp.) and 4400 mg/L Mg (Dytiscidae: Clypeodytes feryi), based on the 50% Lethal Concentration (LC50). Characterisation of the macroinvertebrate assemblage at each hydrographic phase indicated the seasons when Mg-sensitive species were present. Whilst no statistical differences in measures of seasonal sensitivity were found, the macroinvertebrate assemblages present during the early flow period had higher Mg-sensitivity than the assemblages present during other hydrographic phases. This could be attributed to the greater relative proportions of Mg-sensitive taxa (e.g. Ephemeroptera) present at early flow compared to greater relative proportions of more Mg-tolerant taxa (C. feryi and Hydacarina spp.) present during later hydrograph phases, especially periods of lower, or no, flow.

Safety and immunogenicity of the two-dose heterologous Ad26.ZEBOV and MVA-BN-Filo Ebola vaccine regimen in children in Sierra Leone: a randomised, double-blind, controlled trial.

BACKGROUND: Children account for a substantial proportion of cases and deaths from Ebola virus disease. We aimed to assess the safety and immunogenicity of a two-dose heterologous vaccine regimen, comprising the adenovirus type 26 vector-based vaccine encoding the Ebola virus glycoprotein (Ad26.ZEBOV) and the modified vaccinia Ankara vector-based vaccine, encoding glycoproteins from the Ebola virus, Sudan virus, and Marburg virus, and the nucleoprotein from the Tai Forest virus (MVA-BN-Filo), in a paediatric population in Sierra Leone. METHODS: This randomised, double-blind, controlled trial was done at three clinics in Kambia district, Sierra Leone. Healthy children and adolescents aged 1-17 years were enrolled in three age cohorts (12-17 years, 4-11 years, and 1-3 years) and randomly assigned (3:1), via computer-generated block randomisation (block size of eight), to receive an intramuscular injection of either Ad26.ZEBOV (5 × 1010 viral particles; first dose) followed by MVA-BN-Filo (1 × 108 infectious units; second dose) on day 57 (Ebola vaccine group), or a single dose of meningococcal quadrivalent (serogroups A, C, W135, and Y) conjugate vaccine (MenACWY; first dose) followed by placebo (second dose) on day 57 (control group). Study team personnel (except for those with primary responsibility for study vaccine preparation), participants, and their parents or guardians were masked to study vaccine allocation. The primary outcome was safety, measured as the occurrence of solicited local and systemic adverse symptoms during 7 days after each vaccination, unsolicited systemic adverse events during 28 days after each vaccination, abnormal laboratory results during the study period, and serious adverse events or immediate reportable events throughout the study period. The secondary outcome was immunogenicity (humoral immune response), measured as the concentration of Ebola virus glycoprotein-specific binding antibodies at 21 days after the second dose. The primary outcome was assessed in all participants who had received at least one dose of study vaccine and had available reactogenicity data, and immunogenicity was assessed in all participants who had received both vaccinations within the protocol-defined time window, had at least one evaluable post-vaccination sample, and had no major protocol deviations that could have influenced the immune response. This study is registered at ClinicalTrials.gov, NCT02509494. FINDINGS: From April 4, 2017, to July 5, 2018, 576 eligible children or adolescents (192 in each of the three age cohorts) were enrolled and randomly assigned. The most common solicited local adverse event during the 7 days after the first and second dose was injection-site pain in all age groups, with frequencies ranging from 0% (none of 48) of children aged 1-3 years after placebo injection to 21% (30 of 144) of children aged 4-11 years after Ad26.ZEBOV vaccination. The most frequently observed solicited systemic adverse event during the 7 days was headache in the 12-17 years and 4-11 years age cohorts after the first and second dose, and pyrexia in the 1-3 years age cohort after the first and second dose. The most frequent unsolicited adverse event after the first and second dose vaccinations was malaria in all age cohorts, irrespective of the vaccine types. Following vaccination with MenACWY, severe thrombocytopaenia was observed in one participant aged 3 years. No other clinically significant laboratory abnormalities were observed in other study participants, and no serious adverse events related to the Ebola vaccine regimen were reported. There were no treatment-related deaths. Ebola virus glycoprotein-specific binding antibody responses at 21 days after the second dose of the Ebola virus vaccine regimen were observed in 131 (98%) of 134 children aged 12-17 years (9929 ELISA units [EU]/mL [95% CI 8172-12 064]), in 119 (99%) of 120 aged 4-11 years (10 212 EU/mL [8419-12 388]), and in 118 (98%) of 121 aged 1-3 years (22 568 EU/mL [18 426-27 642]). INTERPRETATION: The Ad26.ZEBOV and MVA-BN-Filo Ebola vaccine regimen was well tolerated with no safety concerns in children aged 1-17 years, and induced robust humoral immune responses, suggesting suitability of this regimen for Ebola virus disease prophylaxis in children. FUNDING: Innovative Medicines Initiative 2 Joint Undertaking and Janssen Vaccines & Prevention BV.

Safety and long-term immunogenicity of the two-dose heterologous Ad26.ZEBOV and MVA-BN-Filo Ebola vaccine regimen in adults in Sierra Leone: a combined open-label, non-randomised stage 1, and a randomised, double-blind, controlled stage 2 trial.

BACKGROUND: The Ebola epidemics in west Africa and the Democratic Republic of the Congo highlight an urgent need for safe and effective vaccines to prevent Ebola virus disease. We aimed to assess the safety and long-term immunogenicity of a two-dose heterologous vaccine regimen, comprising the adenovirus type 26 vector-based vaccine encoding the Ebola virus glycoprotein (Ad26.ZEBOV) and the modified vaccinia Ankara vector-based vaccine, encoding glycoproteins from Ebola virus, Sudan virus, and Marburg virus, and the nucleoprotein from the Tai Forest virus (MVA-BN-Filo), in Sierra Leone, a country previously affected by Ebola. METHODS: The trial comprised two stages: an open-label, non-randomised stage 1, and a randomised, double-blind, controlled stage 2. The study was done at three clinics in Kambia district, Sierra Leone. In stage 1, healthy adults (aged ≥18 years) residing in or near Kambia district, received an intramuscular injection of Ad26.ZEBOV (5 × 1010 viral particles) on day 1 (first dose) followed by an intramuscular injection of MVA-BN-Filo (1 × 108 infectious units) on day 57 (second dose). An Ad26.ZEBOV booster vaccination was offered at 2 years after the first dose to stage 1 participants. The eligibility criteria for adult participants in stage 2 were consistent with stage 1 eligibility criteria. Stage 2 participants were randomly assigned (3:1), by computer-generated block randomisation (block size of eight) via an interactive web-response system, to receive either the Ebola vaccine regimen (Ad26.ZEBOV followed by MVA-BN-Filo) or an intramuscular injection of a single dose of meningococcal quadrivalent (serogroups A, C, W135, and Y) conjugate vaccine (MenACWY; first dose) followed by placebo on day 57 (second dose; control group). Study team personnel, except those with primary responsibility for study vaccine preparation, and participants were masked to study vaccine allocation. The primary outcome was the safety of the Ad26.ZEBOV and MVA-BN-Filo vaccine regimen, which was assessed in all participants who had received at least one dose of study vaccine. Safety was assessed as solicited local and systemic adverse events occurring in the first 7 days after each vaccination, unsolicited adverse events occurring in the first 28 days after each vaccination, and serious adverse events or immediate reportable events occurring up to each participant's last study visit. Secondary outcomes were to assess Ebola virus glycoprotein-specific binding antibody responses at 21 days after the second vaccine in a per-protocol set of participants (ie, those who had received both vaccinations within the protocol-defined time window, had at least one evaluable post-vaccination sample, and had no major protocol deviations that could have influenced the immune response) and to assess the safety and tolerability of the Ad26.ZEBOV booster vaccination in stage 1 participants who had received the booster dose. This study is registered at ClinicalTrials.gov, NCT02509494. FINDINGS: Between Sept 30, 2015, and Oct 19, 2016, 443 participants (43 in stage 1 and 400 in stage 2) were enrolled; 341 participants assigned to receive the Ad26.ZEBOV and MVA-BN-Filo regimen and 102 participants assigned to receive the MenACWY and placebo regimen received at least one dose of study vaccine. Both regimens were well tolerated with no safety concerns. In stage 1, solicited local adverse events (mostly mild or moderate injection-site pain) were reported in 12 (28%) of 43 participants after Ad26.ZEBOV vaccination and in six (14%) participants after MVA-BN-Filo vaccination. In stage 2, solicited local adverse events were reported in 51 (17%) of 298 participants after Ad26.ZEBOV vaccination, in 58 (24%) of 246 after MVA-BN-Filo vaccination, in 17 (17%) of 102 after MenACWY vaccination, and in eight (9%) of 86 after placebo injection. In stage 1, solicited systemic adverse events were reported in 18 (42%) of 43 participants after Ad26.ZEBOV vaccination and in 17 (40%) after MVA-BN-Filo vaccination. In stage 2, solicited systemic adverse events were reported in 161 (54%) of 298 participants after Ad26.ZEBOV vaccination, in 107 (43%) of 246 after MVA-BN-Filo vaccination, in 51 (50%) of 102 after MenACWY vaccination, and in 39 (45%) of 86 after placebo injection. Solicited systemic adverse events in both stage 1 and 2 participants included mostly mild or moderate headache, myalgia, fatigue, and arthralgia. The most frequent unsolicited adverse event after the first dose was headache in stage 1 and malaria in stage 2. Malaria was the most frequent unsolicited adverse event after the second dose in both stage 1 and 2. No serious adverse event was considered related to the study vaccine, and no immediate reportable events were observed. In stage 1, the safety profile after the booster vaccination was not notably different to that observed after the first dose. Vaccine-induced humoral immune responses were observed in 41 (98%) of 42 stage 1 participants (geometric mean binding antibody concentration 4784 ELISA units [EU]/mL [95% CI 3736-6125]) and in 176 (98%) of 179 stage 2 participants (3810 EU/mL [3312-4383]) at 21 days after the second vaccination. INTERPRETATION: The Ad26.ZEBOV and MVA-BN-Filo vaccine regimen was well tolerated and immunogenic, with persistent humoral immune responses. These data support the use of this vaccine regimen for Ebola virus disease prophylaxis in adults. FUNDING: Innovative Medicines Initiative 2 Joint Undertaking and Janssen Vaccines & Prevention BV.

Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution.

Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between human and other animal sources of fecal pollution making it difficult to identify diffuse pollution sources. Human-associated quantitative real-time PCR (qPCR) methods in combination with low-order headwatershed sampling, precipitation information, and high-resolution geographic information system land use data can be useful for identifying diffuse source of human fecal pollution in receiving waters. To test this assertion, this study monitored nine headwatersheds over a two-year period potentially impacted by faulty septic systems and leaky sanitary sewer lines. Human fecal pollution was measured using three different human-associated qPCR methods and a positive significant correlation was seen between abundance of human-associated genetic markers and septic systems following wet weather events. In contrast, a negative correlation was observed with sanitary sewer line densities suggesting septic systems are the predominant diffuse source of human fecal pollution in the study area. These results demonstrate the advantages of combining water sampling, climate information, land-use computer-based modeling, and molecular biology disciplines to better characterize diffuse sources of human fecal pollution in environmental waters.

Development of a Sublethal Chronic Toxicity Test for the Northern Trout Gudgeon, Mogurnda mogurnda, and Application to Uranium, Magnesium, and Manganese.

Many international guidance documents for deriving water quality guideline values recommend the use of chronic toxicity data. For the tropical fish northern trout gudgeon, Mogurnda mogurnda, 96-h acute and 28-d chronic toxicity tests have been developed, but both tests have drawbacks. The 96-h toxicity test is acute and has a lethal endpoint; hence it is not a preferred method for guideline value derivation. The 28-d method has a sublethal (growth) endpoint, but is highly resource intensive and is high risk in terms of not meeting quality control criteria. The present study aimed to determine the feasibility of a 7-d larval growth toxicity test as an alternative to the 96-h survival and 28-d growth tests. Once the method was successfully developed, derived toxicity estimates for uranium, magnesium, and manganese were compared with those for other endpoints and tests lengths within the literature. As a final validation of the 7-d method, the sensitivity of the 7-d growth endpoint was compared with those of 14-, 21-, and 28-d exposures. Fish growth rate, based on length, over 7 d was significantly more sensitive compared with existing acute toxicity endpoints for magnesium and manganese, and was similarly sensitive to existing chronic toxicity endpoints for uranium. For uranium, the sensitivity of the growth endpoint over the 4 exposure periods was similar, suggesting that 7 d as an exposure duration is sufficient to provide an indication of longer term chronic growth effects. The sensitivity of the 7-d method, across the 3 metals tested, highlights the benefit of utilizing the highly reliable short-term 7-d chronic toxicity test method in future toxicity testing using M. mogurnda. Environ Toxicol Chem 2021;40:1596-1605. © 2021 Commonwealth of Australia. Environmental Toxicology and Chemistry © 2021 SETAC.

Elevated Magnesium Concentrations Altered Freshwater Assemblage Structures in a Mesocosm Experiment.

Magnesium (Mg) is a mining-related contaminant in the Alligators Rivers Region of tropical northern Australia. A mesocosm experiment was used to assess Mg toxicity to aquatic freshwater assemblages. Twenty-five 2700-L tubs were arranged, stratified randomly, on the bed of Magela Creek, a seasonally flowing, sandy stream channel in the Alligator Rivers Region of northern Australia. The experiment comprised 5 replicates of 4 nominal Mg treatments, 2.5, 7.5, 23, and 68 mg L-1 , and a control. Phytoplankton biomass, and diatom, zooplankton, and macroinvertebrate assemblages present in the treatment tubs were sampled before and after Mg addition. A significant negative relationship between phytoplankton biomass and Mg was observed 4 wk after Mg addition as measured by chlorophyll a concentrations (r2 = 0.97, p = 0.01). This result was supported by reductions in some major phytoplankton groups in response to increasing Mg concentrations, in the same experiment and from independent field studies. There was a significant negative relationship between zooplankton assemblage similarity (to control) and Mg concentrations (r2 = 0.96, p = 0.002). Seven weeks after Mg addition, macroinvertebrate assemblages were dominated by 3 microcrustacean groups (Ostracoda, Cladocera, and Copepoda), each reaching maximum abundance at intermediate Mg concentrations (i.e., unimodal responses). The responses of phytoplankton and zooplankton were used to derive assemblage effect concentrations (Mg concentrations resulting in x% of the assemblage change [ECx]). Magnesium concentrations resulting in assemblage EC01 values were <3 mg L-1 . Together with candidate guideline values from other laboratory- and field-based lines of evidence, the mesocosm EC01 values were incorporated into a weight-of-evidence framework for a robust regulatory approach to environmental protection. Environ Toxicol Chem 2020;39:1973-1987. © 2020 Commonwealth of Australia. Published by Wiley Periodicals LLC on behalf of SETAC.

CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase.

PURPOSE: Precision oncology depends on the matching of tumor variants to relevant knowledge describing the clinical significance of those variants. We recently developed the Clinical Interpretations for Variants in Cancer (CIViC; civicdb.org) crowd-sourced, expert-moderated, and open-access knowledgebase. CIViC provides a structured framework for evaluating genomic variants of various types (eg, fusions, single-nucleotide variants) for their therapeutic, prognostic, predisposing, diagnostic, or functional utility. CIViC has a documented application programming interface for accessing CIViC records: assertions, evidence, variants, and genes. Third-party tools that analyze or access the contents of this knowledgebase programmatically must leverage this application programming interface, often reimplementing redundant functionality in the pursuit of common analysis tasks that are beyond the scope of the CIViC Web application. METHODS: To address this limitation, we developed CIViCpy (civicpy.org), a software development kit for extracting and analyzing the contents of the CIViC knowledgebase. CIViCpy enables users to query CIViC content as dynamic objects in Python. We assess the viability of CIViCpy as a tool for advancing individualized patient care by using it to systematically match CIViC evidence to observed variants in patient cancer samples. RESULTS: We used CIViCpy to evaluate variants from 59,437 sequenced tumors of the American Association for Cancer Research Project GENIE data set. We demonstrate that CIViCpy enables annotation of > 1,200 variants per second, resulting in precise variant matches to CIViC level A (professional guideline) or B (clinical trial) evidence for 38.6% of tumors. CONCLUSION: The clinical interpretation of genomic variants in cancers requires high-throughput tools for interoperability and analysis of variant interpretation knowledge. These needs are met by CIViCpy, a software development kit for downstream applications and rapid analysis. CIViCpy is fully documented, open-source, and available free online.

Response of the Native Springtail Parisotoma insularis to Diesel Fuel-Contaminated Soils Under Field-Realistic Exposure Conditions at Subantarctic Macquarie Island.

A number of sites contaminated by petroleum hydrocarbons from past fuel spills are currently undergoing remediation on subantarctic Macquarie Island (under the jurisdiction of Tasmania, Australia). To assess the environmental risks these spills pose, and to establish remediation targets and guideline values, toxicity data for a range of native biota are required. The availability of data for local biota is limited, especially for soil invertebrates, which are critical to soil health. To examine the response of naturally occurring soil invertebrate communities to fuel contamination, intact soil cores from a range of soil types were collected along an organic carbon (OC) gradient. Organic carbon was factored into the toxicity assessment due to its toxicity-modifying potential. Soil cores were spiked with Special Antarctic Blend diesel, to mimic a fresh fuel spill at the soil surface. Springtails were the most abundant taxa, with the community heavily dominated by the native species Parisotoma insularis. This species was sensitive to fuel contamination (EC20 48 mg/kg, CI 5-188), irrespective of soil organic content. This study is the first to derive critical effect concentrations (CECs) for a subantarctic springtail species and provides important data that will be incorporated into future derivation of site-specific soil quality guideline values for fuels for Macquarie Island soils and the broader subantarctic region. Integr Environ Assess Manag 2019;15:565-574. © 2019 SETAC.

Integrating laboratory and field studies to assess impacts of discharge from a uranium mine and validate a water quality guideline value for magnesium.

Magnesium (Mg) is a primary contaminant in mine water discharges from the Ranger Uranium Mine (north Australia). Site-specific water quality guideline values (WQGVs) for Mg have been derived from laboratory and field studies. Contaminated groundwater with elevated electrical conductivity and metals (Mg, Mn, U, SO4 , and Ca) was detected flowing from the mine site into adjacent surface waters. This provided an opportunity to investigate the protectiveness of the Mg WQGV by conducting an integrated laboratory and field study. A direct toxicity assessment (DTA) of the groundwater was conducted with local tropical freshwater species: duckweed (Lemna aequinoctialis), green hydra (Hydra viridissima), and the aquatic snail Amerianna cumingi. An in situ toxicity assessment was carried out in the creek receiving diluted groundwater by use of the same species of snail, to aid interpretation of laboratory-derived data. The toxicity of the contaminated groundwater was higher than Mg-only toxicity testing for H. viridissima, with other elevated metals and major ions contributing to toxicity. However, for duckweed and snail, the contaminated groundwater was less toxic than the Mg-only testing. In situ snail monitoring supported laboratory exposures, showing no effect on reproduction of A. cumingi exposed to an average of approximately 5 mg/L Mg; however, a very small effect was noted closer to the groundwater source, probably associated with other contaminants. The minimal toxicity observed for L. aequinoctialis and A. cumingi, despite the elevated Mg, can be explained by the high calcium (Ca) concentration of the water and the potential amelioration of metal toxicity. The extent of Ca amelioration of Mg toxicity was organism dependent. This study affirms the proposed environmental rehabilitation standard of 3 mg/L Mg for surface waters with a Ca concentration typical of water from this mine site. Integr Environ Assess Manag 2019;15:64-76. © 2018 SETAC.

Health care worker vaccination against Ebola: Vaccine acceptance and employment duration in Sierra Leone.

Health care workers (HCW) are at high risk of Ebola virus disease (EVD) infection during epidemics and may contribute to onward transmission, and therefore HCW-targeted prophylactic vaccination strategies are being considered as interventions. To assess the feasibility of preventive HCW vaccination, we conducted a pilot survey on staff turnover and vaccine acceptance amongst 305 HCW in Freetown and Kambia districts of Sierra Leone. Multivariable logistic regression demonstrated which demographic and behavioural factors were associated with acceptance of a hypothetical new vaccine. We quantified the duration of employment of HCW, and used multivariable gamma regression to detect associations with duration of employment in current or any health care position. Finally, we simulated populations of HCW, to determine the likely future immunisation coverage amongst HCW based on our estimates of vaccine acceptance and employment duration. Most HCW we surveyed had a positive opinion of EVD vaccination (76.3%). We found that being a volunteer HCW (vs being on the government payroll) was associated with increased vaccine acceptance. We found that HCW have stable employment, with a mean duration of employment in the health sector of 10.9 years (median 8.0 years). Older age and being on the government payroll (vs volunteer HCW) were associated with a longer duration of employment in the health sector. Assuming a single vaccine campaign, with 76.3% vaccine acceptance, 100% vaccine efficacy and no waning of vaccine-induced protection, immunisation coverage was sustained over 50% until 6 years after a vaccination campaign. If vaccine-induced immunity wanes at 10% per year, then the immunisation coverage among HCW would fall below 50% after 3 years. Vaccinating HCW against EVD could be feasible as employment appeared stable and vaccine acceptance high. However, even with high vaccine efficacy and long-lasting immunity, repeated campaigns or vaccination at employment start may be necessary to maintain high coverage.

Freshwater chronic ammonia toxicity: A tropical-to-temperate comparison.

The chronic toxicity of ammonia to tropical freshwater species is understudied, and thus data on temperate species have been used to derive water quality guideline values for tropical regions. Such practices may lead to underprotective guideline values due to differences in toxicities observed between tropical and temperate species. In addition, the presence of ammonia in low-ionic-strength waters may also result in higher toxicity, and studies on this factor are limited. The present study assessed the toxicity of ammonia to 6 tropical freshwater species in low-ionic-strength waters. Because ammonia toxicity varies depending on the pH and temperature, test water pH concentrations were maintained at approximately pH 6.0 ± 0.3 at temperatures between 27.5 and 30 °C. Low-effect chronic inhibition concentrations were derived for the following species: Chlorella sp. 66 mg L-1 ; Lemna aequinoctialis 22 mg L-1 ; Hydra viridissima 1.8 mg L-1 ; Moinodaphnia macleayi 27 mg L-1 ; Amerianna cumingi 17 mg L-1 ; and Mogurnda mogurnda 5.4 mg L-1 total ammonia nitrogen. Two of the species tested (a cnidarian and a fish species) were among the most sensitive reported anywhere within their taxonomic group. Chronic ammonia datasets representing toxicity estimates for temperate and tropical species were plotted and compared using species sensitivity distributions. The results indicate that the differences in chronic toxicity observed between tropical and temperate species were likely due to the low ionic strength of the waters to which tropical species were exposed, rather than any inherent physiological differences between species from tropical and temperate regions. This finding suggests that tropical waters of low ionic strength may be at a higher risk from ammonia compared with other freshwater ecosystems. Environ Toxicol Chem 2019;38:177-189. © 2018 Commonwealth of Australia. Published by Wiley Periodicals, Inc. on behalf of SETAC.

Chronic ammonia toxicity to juveniles of 2 tropical Australian freshwater mussels (Velesunio spp.): Toxicity test optimization and implications for water quality guideline values.

Freshwater mussels play key roles in aquatic ecosystems, but are experiencing a global decline. Although studies have reported high acute sensitivity of mussels to some contaminants, chronic toxicity data are lacking for deriving high-reliability water quality guideline values. Ammonia is a contaminant of potential concern in some catchments of tropical northern Australia, where freshwater mussels are important ecological and cultural components. The extremely soft waters (hardness < 5 mg/L) of these environments can result in increased toxicity of many contaminants including ammonia, and regionally relevant tropical guideline values are needed to adequately protect these unique ecosystems. An optimized 14-d toxicity test protocol was used to assess the chronic toxicity of ammonia for 2 species, the lotic Velesunio sp. and the lentic Velesunio angasi. Ammonia exposures were conducted at pH 6.0 and 27 ± 0.5 °C to represent local environmental conditions, using shell length growth rate as the endpoint. Chronic toxicity estimates indicated high sensitivity to ammonia, with mean median effect concentrations (in total ammonia nitrogen) being 7.0 mg/L for V. angasi from the semi-urbanized Lake Bennett, 9.2 mg/L for V. angasi from Sandy Billabong, and 11.3 mg/L for Velesunio sp. from Gulungul Creek. When the 10% effect concentration values were compared with other chronic ammonia data (normalized to pH 7.0 and 20 °C), Velesunio spp. were found to be more sensitive than 8 of 16 other temperate and 7 of 9 tropical invertebrate and fish species. These chronic toxicity estimates will be used to further inform regionally relevant and site-specific guideline values. Environ Toxicol Chem 2019;38:841-851. © 2019 Commonwealth of Australia. Published by Wiley Periodicals Inc. on behalf of SETAC.