Early warning signals: The charted and uncharted territories

The realization that complex systems such as ecological communities can collapse or shift regimes suddenly and without rapid external forcing poses a serious challenge to our understanding and management of the natural world. The potential to identify early warning signals that would allow researchers and managers to predict such events before they happen has therefore been an invaluable discovery that offers a way forward in spite of such seemingly unpredictable behavior. Research into early warning signals has demonstrated that it is possible to define and detect such early warning signals in advance of a transition in certain contexts. Here we describe the pattern emerging as research continues to explore just how far we can generalize these results. A core of examples emerges that shares three properties: the phenomenon of rapid regime shifts, a pattern of 'critical slowing down' that can be used to detect the approaching shift, and a mechanism of bifurcation driving the sudden change. As research has expanded beyond these core examples, it is becoming clear that not all systems that show regime shifts exhibit critical slowing down, or vice versa. Even when systems exhibit critical slowing down, statistical detection is a challenge. We review the literature that explores these edge cases and highlight the need for (a) new early warning behaviors that can be used in cases where rapid shifts do not exhibit critical slowing down, (b) the development of methods to identify which behavior might be an appropriate signal when encountering a novel system; bearing in mind that a positive indication for some systems is a negative indication in others, and (c) statistical methods that can distinguish between signatures of early warning behaviors and noise

The global distribution of Bacillus anthracis and associated anthrax risk to humans, livestock and wildlife.

Bacillus anthracis is a spore-forming, Gram-positive bacterium responsible for anthrax, an acute infection that most significantly affects grazing livestock and wild ungulates, but also poses a threat to human health. The geographic extent of B. anthracis is poorly understood, despite multi-decade research on anthrax epizootic and epidemic dynamics; many countries have limited or inadequate surveillance systems, even within known endemic regions. Here, we compile a global occurrence dataset of human, livestock and wildlife anthrax outbreaks. With these records, we use boosted regression trees to produce a map of the global distribution of B. anthracis as a proxy for anthrax risk. We estimate that 1.83 billion people (95% credible interval (CI): 0.59-4.16 billion) live within regions of anthrax risk, but most of that population faces little occupational exposure. More informatively, a global total of 63.8 million poor livestock keepers (95% CI: 17.5-168.6 million) and 1.1 billion livestock (95% CI: 0.4-2.3 billion) live within vulnerable regions. Human and livestock vulnerability are both concentrated in rural rainfed systems throughout arid and temperate land across Eurasia, Africa and North America. We conclude by mapping where anthrax risk could disrupt sensitive conservation efforts for wild ungulates that coincide with anthrax-prone landscapes

A Presentation of the Religious Content on the Most Visited Croatian Internet Portals

Kompleksan međuodnos religije i medija predmet je zanimanja brojnih teoretičara. Stavivši u središte svoga interesa religiju u medijima (u smislu pojavljivanja i prezentacije institucionalnih religija u medijima), nastojalo se dobiti uvid u način na koji je ona predstavljana na trima najposjećenijim hrvatskim mrežnim portalima (24sata.hr, Index.hr i Net.hr) prema podacima koje je Gemius iznio za Hrvatsku. Istraživanja su pokazala da hrvatski građani imaju najviše povjerenja u informacije objavljene na mreži, a ako se tomu pridoda da je 63% građana Hrvatske starije od 15 godina 2011. rabilo mrežu (podaci istraživanja GfK centra), jasno je da su hrvatski mrežni portali važan čimbenik u oblikovanju javne sfere i hrvatske društvene stvarnosti. S druge strane, činjenica je i da zbog pritiska radi povećanja posjećenosti, što u konačnici rezultira povećanjem profita, mrežni portali pribjegavaju tabloidizaciji sadržaja, negativizmu, banalnim i šokantnim vijestima. Svrha je ovoga rada utvrditi na koji se način na najposjećenijim hrvatskim portalima predstavlja religijski sadržaj. Cilj je bio analizirati priloge o religiji koji su objavljivani na naslovnoj stranici triju najposjećenijih hrvatskih mrežnih portala. Analizom sadržaja njihovih naslovnica u razdoblju od 20. studenoga do 20. prosinca 2012. godine nastojalo se utvrditi koliko se tabloidni pristup novinarstvu odnosi na religijske sadržaje, odnosno koja su osnovna obilježja priloga s religijskom tematikom.The complex interplay between religion and the media is the subject of interest of many theorists. Thus, by focusing on the topic of religion in the media (in terms of appearance and presentation of institutional religion in the media), we have tried to gain insight into the way in which religion is presented on the three most visited Croatian Internet portals (24sata.hr, Index.hr and Net.hr, according to the GemiusAudience data for Croatia). Studies have shown that Croatian citizens place most of their confidence in the information available on the Internet. Also, 63% of Croatian citizens above the age of 15 availed themselves of the Internet in 2011 according to GfK research. It is clear therefore that Croatian Internet portals are an important factor in shaping the public sphere as well as Croatian social reality. On the other hand, due to the pressure for increased usage, ultimately resulting in increased profits, the fact remains that Internet portals have resorted to the tabloidization of content, negativism and reporting of banal and shocking news. The purpose of this article was to determine the way in which religious content is presented on the three most visited Croatian Internet portals. The aim was to analyze religious articles published on the front page of these portals with regard to the period between November 20 to December 20, 2012, and in so doing to try to determine in how far the tabloid approach to journalism applies to religious content, that is, to determine the main features of articles with religious themes

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages.

The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies.N.B. acknowledges funding for this work by the Office of Naval Research through the Naval Research Laboratory's basic research program, and computer time at the AFRL DoD Supercomputing Resource Center through the DoD High Performance Computing Modernization Program (subproject NRLDC04253428). B.L. was supported by EPSRC (grant no. EP/G036136/1) and the Scottish Funding Council. G.C. and B.L. acknowledge support form EPSRC under grant no. EP/J01298X/1. R.C.W. and A.W.G. acknowledge financial support by the National Institutes of Health (R01 GM100934), A.W.G. acknowledges financial support by the Department of Energy (DE-AC36-99GO-10337). This work was partially supported by National Science Foundation (grant no. OCI-1148358) and used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant no. ACI-1053575. Computer time was provided by the San Diego Supercomputer Center through XSEDE award TG-CHE130010.This is the author accepted version of the article. The final published version is available from Wiley at http://onlinelibrary.wiley.com/doi/10.1002/jcc.23839/full

Viral maintenance and excretion dynamics of coronaviruses within an Egyptian rousette fruit bat maternal colony : considerations for spillover

DATA AVAILABILITY : All data generated during this study are included in this published article (and its Supplementary Information files). All model code as well as diagnostic reports are available in the GitHub project code repository (https://github.com/ecohealthalliance/sabrenet-rousettus-dynamics/, with a version on Zenodo https://zenodo. org/record/7709716).Novel coronavirus species of public health and veterinary importance have emerged in the first two decades of the twenty-first century, with bats identified as natural hosts for progenitors of many coronaviruses. Targeted wildlife surveillance is needed to identify the factors involved in viral perpetuation within natural host populations, and drivers of interspecies transmission. We monitored a natural colony of Egyptian rousette bats at monthly intervals across two years to identify circulating coronaviruses, and to investigate shedding dynamics and viral maintenance within the colony. Three distinct lineages were detected, with different seasonal temporal excretion dynamics. For two lineages, the highest periods of coronavirus shedding were at the start of the year, when large numbers of bats were found in the colony. Highest peaks for a third lineage were observed towards the middle of the year. Among individual bat-level factors (age, sex, reproductive status, and forearm mass index), only reproductive status showed significant effects on excretion probability, with reproductive adults having lower rates of detection, though factors were highly interdependent. Analysis of recaptured bats suggests that viral clearance may occur within one month. These findings may be implemented in the development of risk reduction strategies for potential zoonotic coronavirus transmission.The National Research Foundation (NRF) of South Africa, the Poliomyelitis Research Foundation, the Department of the Defense, Defense Threat Reduction Agency and the University of Pretoria’s postdoctoral funding program.https://www.nature.com/srepam2024Medical VirologyNon

Farm-level risk factors of increased abortion and mortality in domestic ruminants during the 2010 Rift Valley fever outbreak in central South Africa

(1) Background: Rift Valley fever (RVF) outbreaks in domestic ruminants have severe socio-economic impacts. Climate-based continental predictions providing early warnings to regions at risk for RVF outbreaks are not of a high enough resolution for ruminant owners to assess their individual risk. (2) Methods: We analyzed risk factors for RVF occurrence and severity at the farm level using the number of domestic ruminant deaths and abortions reported by farmers in central South Africa during the 2010 RVF outbreaks using a Bayesian multinomial hurdle framework. (3) Results: We found strong support that the proportion of days with precipitation, the number of water sources, and the proportion of goats in the herd were positively associated with increased severity of RVF (the numbers of deaths and abortions). We did not find an association between any risk factors and whether RVF was reported on farms. (4) Conclusions: At the farm level we identified risk factors of RVF severity; however, there was little support for risk factors of RVF occurrence. The identification of farm-level risk factors for Rift Valley fever virus (RVFV) occurrence would support and potentially improve current prediction methods and would provide animal owners with critical information needed in order to assess their herd’s risk of RVFV infection

The rockerverse : packages and applications for containerisation with R

The Rocker Project provides widely used Docker images for R across different application scenarios. This article surveys downstream projects that build upon the Rocker Project images and presents the current state of R packages for managing Docker images and controlling containers. These use cases cover diverse topics such as package development, reproducible research, collaborative work, cloud-based data processing, and production deployment of services. The variety of applications demonstrates the power of the Rocker Project specifically and containerisation in general. Across the diverse ways to use containers, we identified common themes: reproducible environments, scalability and efficiency, and portability across clouds. We conclude that the current growth and diversification of use cases is likely to continue its positive impact, but see the need for consolidating the Rockerverse ecosystem of packages, developing common practices for applications, and exploring alternative containerisation software