Impacts of environmental conditions on fleas in black-tailed prairie dog burrows

Sylvatic plague, caused by the bacterium Yersinia pestis and transmitted by fleas, occurs in prairie dogs of the western United States. Outbreaks can devastate prairie dog communities, often causing nearly 100% mortality. Three competent flea vectors, prairie dog specialists Oropsylla hirsuta and O. tuberculata, and generalist Pulex simulans, are found on prairie dogs and in their burrows. Fleas are affected by climate, which varies across the range of black-tailed prairie dogs (Cynomys ludovicianus), but these effects may be ameliorated somewhat due to the burrowing habits of prairie dogs. Our goal was to assess how temperature and precipitation affect off-host flea abundance and whether relative flea abundance varied across the range of black-tailed prairie dogs. Flea abundance was measured by swabbing 300 prairie dog burrows at six widely distributed sites in early and late summer of 2016 and 2017. Relative abundance of flea species varied among sites and sampling sessions. Flea abundance and prevalence increased with monthly mean high temperature and declined with higher winter precipitation. Predicted climate change in North America will likely influence flea abundance and distribution, thereby impacting plague dynamics in prairie dog colonies

Safety Risk Registers: Challenges and Guidance

A risk database, or risk register, is a central tool for organisations to use to monitor and reduce risks, both those identified during initial safety assessments and those emerging during operations (Whipple and Pitblado, 2010). The risk register should contain all analysed risks and should prioritise the areas that require managerial attention. When populated with information on each risk, including risk ranking, the risk register can be analysed to present the risk profile for different aspects of the organisation (Filippin and Dreher, 2004). When reviewed and updated over time, it can also be analysed to present trends within the risk profile and focus management attention on the highest risk activities or facilities (Whipple and Pitblado, 2010). In order to successfully develop a risk registry that provides an accurate level of risk within a process, there is a requirement for real time data on risk to be input into a risk registry. Despite their place at the heart of safety management, there is relatively little guidance and research on how to construct, maintain and use a risk register. The challenges and ideas in this paper were developed during the initial phase of a case study to develop a single central risk register for an energy generation company. The case study used workshops with key stakeholders from the company to work through the issues faced in developing a single integrated risk register. Challenges faced ranged from ensuring employees contributing to the risk register had a basic understanding of risk concepts, through identification and scope of hazards to be included, to data collection and automatic population of the risk register. The challenges encountered during this project are believed to be those that many companies face, and therefore the resolutions proposed and adopted for this case study will be presented here as guidance for the implementation and management of risk registries in safety management systems

Could blackbird mortality from avicide DRC-1339 contribute to avian botulism outbreaks in North Dakota?

Blackbird (family Icteridae) depredation on sunflower (Helianthus annuus) crops in the prairie states of the United States has motivated the proposed use of an avicide, DRC-1339 (3-chloro-4-methylaniline), to decrease their numbers. The resulting mortality of blackbirds at wetland roosts could increase the potential of avian botulism occurring in affected marshes. To assess this possibility, we seeded (artificially placed) blackbird carcasses in selected wetlands in Stutsman County, North Dakota, during August–September 2000 and July–September 2001 to evaluate their rate of decomposition and role in initiating avian botulism outbreaks. We monitored carcasses to determine their persistence, the frequency and amount of maggots produced, and the presence of type C. botulinum toxin. In 10 of our 12 study wetlands, blackbird carcasses were not rapidly removed by scavengers, thus providing substrate for maggot growth and potential production of Clostridium botulinum toxin. Decomposition of carcasses occurred rapidly, and maggot production averaged 4–5 g per carcass within 9 days. We were unable to detect C. botulinum type C toxin in any of the 377 blackbird carcasses or the 112 samples of maggots we collected in 2000 or 2001. None of the 25 blackbird carcasses we tested contained botulinum spores, the most probable explanation for the absence of botulinum toxin production. Our results indicate that the likelihood of DRC-1339-poisoned blackbirds causing botulism outbreaks would be minimal in North Dakota wetlands during late summer and early autumn

Spatial distribution of vertical carbon fluxes on the Agulhas Bank and its possible implication for the benthic nepheloid layer

Vertical particle fluxes of particulate organic carbon (POC), chlorophyll a (Chl a) and biogenic silica (bSi) were measured on the productive shelf of southern Africa, the Agulhas Bank (AB), in March 2019. Sinking particulate material in the form of aggregates is hypothesized to form the benthic nepheloid layer (BNL) which is a turbid layer found near the seabed. This layer is known to affect the spawning success of squid as it is linked to high turbidity which reduces visibility during mating. To determine the distribution of fluxes and particle composition in the AB, we collected water samples below the surface mixed layer (‘export’) and near the seabed (‘bottom’) using a Marine Snow Catcher. POC export fluxes were significantly higher inshore than offshore (mean ± SD: 944.6 ± 302.0 & 461.1 ± 162.1 mg POC m−2 d−1, respectively). There was no significant difference in the cross-shelf distribution of Chl a and bSi export fluxes, however the inshore fluxes of Chl a and bSi were higher than offshore, suggesting a link between export fluxes and sinking organic matter derived from the more productive inshore surface waters. All bottom fluxes were significantly higher inshore, suggesting the contribution of sinking organic particles and resuspended bottom sediments to inshore fluxes. POC export efficiency (ratio of exported POC flux relative to net primary production (NPP)) was higher on the AB (range: 0.58–9.56) compared to the global shelf seas ratio of 0.18 and not related to NPP, suggesting an export of standing stock of carbon biomass, likely produced before the cruise. Transfer efficiency (i.e., the amount of exported flux that reaches the bottom) was also high (max: 0.99, 1.0 and 33.04 for POC, Chl a and bSi, respectively) but did not show a clear spatial pattern. We observed a significant positive correlation between bottom turbidity (a proxy for BNL presence) and export POC flux, suggesting the possibility that sinking organic matter is contributing to BNL formation on the AB

Assessing probe-specific dye and slide biases in two-color microarray data

A primary reason for using two-color microarrays is that the use of two samples labeled with different dyes on the same slide, that bind to probes on the same spot, is supposed to adjust for many factors that introduce noise and errors into the analysis. Most users assume that any differences between the dyes can be adjusted out by standard methods of normalization, so that measures such as log ratios on the same slide are reliable measures of comparative expression. However, even after the normalization, there are still probe specific dye and slide variation among the data. We define a method to quantify the amount of the dye-by-probe and slide-by-probe interaction. This serves as a diagnostic, both visual and numeric, of the existence of probe-specific dye bias. We show how this improved the performance of two-color array analysis for arrays for genomic analysis of biological samples ranging from rice to human tissue.We develop a procedure for quantifying the extent of probe-specific dye and slide bias in two-color microarrays. The primary output is a graphical diagnostic of the extent of the bias which called ECDF (Empirical Cumulative Distribution Function), though numerical results are also obtained.We show that the dye and slide biases were high for human and rice genomic arrays in two gene expression facilities, even after the standard intensity-based normalization, and describe how this diagnostic allowed the problems causing the probe-specific bias to be addressed, and resulted in important improvements in performance. The R package LMGene which contains the method described in this paper has been available to download from Bioconductor

Bridging the gap between systems biology and medicine

Systems biology has matured considerably as a discipline over the last decade, yet some of the key challenges separating current research efforts in systems biology and clinically useful results are only now becoming apparent. As these gaps are better defined, the new discipline of systems medicine is emerging as a translational extension of systems biology. How is systems medicine defined? What are relevant ontologies for systems medicine? What are the key theoretic and methodologic challenges facing computational disease modeling? How are inaccurate and incomplete data, and uncertain biologic knowledge best synthesized in useful computational models? Does network analysis provide clinically useful insight? We discuss the outstanding difficulties in translating a rapidly growing body of data into knowledge usable at the bedside. Although core-specific challenges are best met by specialized groups, it appears fundamental that such efforts should be guided by a roadmap for systems medicine drafted by a coalition of scientists from the clinical, experimental, computational, and theoretic domains

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Detection of gene pathways with predictive power for breast cancer prognosis

<p>Abstract</p> <p>Background</p> <p>Prognosis is of critical interest in breast cancer research. Biomedical studies suggest that genomic measurements may have independent predictive power for prognosis. Gene profiling studies have been conducted to search for predictive genomic measurements. Genes have the inherent pathway structure, where pathways are composed of multiple genes with coordinated functions. The goal of this study is to identify gene pathways with predictive power for breast cancer prognosis. Since our goal is fundamentally different from that of existing studies, a new pathway analysis method is proposed.</p> <p>Results</p> <p>The new method advances beyond existing alternatives along the following aspects. First, it can assess the predictive power of gene pathways, whereas existing methods tend to focus on model fitting accuracy only. Second, it can account for the joint effects of multiple genes in a pathway, whereas existing methods tend to focus on the marginal effects of genes. Third, it can accommodate multiple heterogeneous datasets, whereas existing methods analyze a single dataset only. We analyze four breast cancer prognosis studies and identify 97 pathways with significant predictive power for prognosis. Important pathways missed by alternative methods are identified.</p> <p>Conclusions</p> <p>The proposed method provides a useful alternative to existing pathway analysis methods. Identified pathways can provide further insights into breast cancer prognosis.</p

Transmission Shifts Underlie Variability in Population Responses to Yersinia pestis Infection

Host populations for the plague bacterium, Yersinia pestis, are highly variable in their response to plague ranging from near deterministic extinction (i.e., epizootic dynamics) to a low probability of extinction despite persistent infection (i.e., enzootic dynamics). Much of the work to understand this variability has focused on specific host characteristics, such as population size and resistance, and their role in determining plague dynamics. Here, however, we advance the idea that the relative importance of alternative transmission routes may vary causing shifts from epizootic to enzootic dynamics. We present a model that incorporates host and flea ecology with multiple transmission hypotheses to study how transmission shifts determine population responses to plague. Our results suggest enzootic persistence relies on infection of an off-host flea reservoir and epizootics rely on transiently maintained flea infection loads through repeated infectious feeds by fleas. In either case, early-phase transmission by fleas (i.e., transmission immediately following an infected blood meal) has been observed in laboratory studies, and we show that it is capable of driving plague dynamics at the population level. Sensitivity analysis of model parameters revealed that host characteristics (e.g., population size and resistance) vary in importance depending on transmission dynamics, suggesting that host ecology may scale differently through different transmission routes enabling prediction of population responses in a more robust way than using either host characteristics or transmission shifts alone

matscipy : materials science at the atomic scale with Python

Behaviour of materials is governed by physical phenomena that occur at an extreme range of length and time scales. Computational modelling requires multiscale approaches. Simulation techniques operating on the atomic scale serve as a foundation for such approaches, providing necessary parameters for upper-scale models. The physical models employed for atomic simulations can vary from electronic structure calculations to empirical force fields. However, construction, manipulation and analysis of atomic systems are independent of the given physical model but dependent on the specific application. matscipy implements such tools for applications in materials science, including fracture, plasticity, tribology and electrochemistry