Multilevel Optimization for Policy Design with Agent-Based Epidemic Models

Epidemiological models can not only be used to forecast the course of a pandemic like COVID-19, but also to propose and design non-pharmaceutical interventions such as school and work closing. In general, the design of optimal policies leads to nonlinear optimization problems that can be solved by numerical algorithms. Epidemiological models come in different complexities, ranging from systems of simple ordinary differential equations (ODEs) to complex agent-based models (ABMs). The former allow a fast and straightforward optimization, but are limited in accuracy, detail, and parameterization, while the latter can resolve spreading processes in detail, but are extremely expensive to optimize. We consider policy optimization in a prototypical situation modeled as both ODE and ABM, review numerical optimization approaches, and propose a heterogeneous multilevel approach based on combining a fine-resolution ABM and a coarse ODE model. Numerical experiments, in particular with respect to convergence speed, are given for illustrative examples

Impacts of Forest Fire on Understory Species Diversity in Canary Pine Ecosystems on the Island of La Palma

Forest fires are drivers of spatial patterns and temporal dynamics of vegetation and biodiversity. On the Canary Islands, large areas of pine forest exist, dominated by the endemic Canary Island pine, Pinus canariensis C. Sm. These mostly natural forests experience wildfires frequently. P. canariensis is well-adapted to such impacts and has the ability to re-sprout from both stems and branches. In recent decades, however, anthropogenically caused fires have increased, and climate change further enhances the likelihood of large forest fires. Through its dense, long needles, P. canariensis promotes cloud precipitation, which is an important ecosystem service for the freshwater supply of islands such as La Palma. Thus, it is important to understand the regeneration and vegetation dynamics of these ecosystems after fire. Here, we investigated species diversity patterns in the understory vegetation of P. canariensis forests after the large 2016 fire on the southern slopes of La Palma. We analyzed the effect of fire intensity, derived from Sentinel-2 NDVI differences, and of environmental variables, on species richness (alpha diversity) and compositional dissimilarity (beta diversity). We used redundancy analysis (dbRDA), Bray–Curtis dissimilarity, and variance partitioning for this analysis. Fire intensity accounted for a relatively small proportion of variation in alpha and beta diversity, while elevation was the most important predictor. Our results also reveal the important role of the endemic Lotus campylocladus ssp. hillebrandii (Christ) Sandral & D.D.Sokoloff for understory diversity after fire. Its dominance likely reduces the ability of other species to establish by taking up nutrients and water and by shading the ground. The mid-to long-term effects are unclear since Lotus is an important nitrogen fixer in P. canariensis forests and can reduce post-fire soil erosion on steep slopes

Anticipating ubiquitous computing: Logics to forecast technological futures

Visions of the future predict spaces apparently teaming with ever more novel and pervasive technologies. Significant amongst such forecasts is the notion of 'ubiquitous computing' (ubicomp), understood as an affordance or capacity tied (in)to people, places and things. This article stages an encounter between the futurity of ubicomp and recent debates in geography around anticipation. So, first, the future orientation in ubicomp research and development (R&D) is investigated as a mode of anticipation. 'Knowledges', and 'logics' of anticipation are subsequently, and second, discussed as the conceptual apparatus that constructs and perpetuates the 'proximate future' of ubicomp. This analysis connects recent discussion about 'anticipation' in social sciences research with the methods of ubicomp research, which fits with an emergent agenda around futurity in human geography. Third, the conceptual articulation of 'anticipatory logic' is applied to the analysis of empirical investigations of ubicomp R&D to identify the specific logics of anticipation at play. This article accordingly examines the logics of anticipation that both support and destabilise the certainty with which the future is imagined within ubicomp. In conclusion, the multiple ways of anticipating a future world and the ways in which they discipline understandings of futurity are framed as a politics of anticipation. © 2010 Elsevier Ltd

Assessing the potential replacement of laurel forest by a novel ecosystem in the steep terrain of an Oceanic Island

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. T. Biological invasions are a major global threat to biodiversity and often affect ecosystem services negatively. They are particularly problematic on oceanic islands where there are many narrow-ranged endemic species, and the biota may be very susceptible to invasion. Quantifying and mapping invasion processes are important steps for management and control but are challenging with the limited resources typically available and particularly difficult to implement on oceanic islands with very steep terrain. Remote sensing may provide an excellent solution in circumstances where the invading species can be reliably detected from imagery. We here develop a method to map the distribution of the alien chestnut (Castanea sativa Mill.) on the island of La Palma (Canary Islands, Spain), using freely available satellite images. On La Palma, the chestnut invasion threatens the iconic laurel forest, which has survived since the Tertiary period in the favourable climatic conditions of mountainous islands in the trade wind zone. We detect chestnut presence by taking advantage of the distinctive phenology of this alien tree, which retains its deciduousness while the native vegetation is evergreen. Using both Landsat 8 and Sentinel-2 (parallel analyses), we obtained images in two seasons (chestnuts leafless and in-leaf, respectively) and performed image regression to detect pixels changing from leafless to in-leaf chestnuts. We then applied supervised classification using Random Forest to map the present-day occurrence of the chestnut. Finally, we performed species distribution modelling to map the habitat suitability for chestnut on La Palma, to estimate which areas are prone to further invasion. Our results indicate that chestnuts occupy 1.2% of the total area of natural ecosystems on La Palma, with a further 12–17% representing suitable habitat that is not yet occupied. This enables targeted control measures with potential to successfully manage the invasion, given the relatively long generation time of the chestnut. Our method also enables research on the spread of the species since the earliest Landsat images

MicroWalk: A Framework for Finding Side Channels in Binaries

Microarchitectural side channels expose unprotected software to information leakage attacks where a software adversary is able to track runtime behavior of a benign process and steal secrets such as cryptographic keys. As suggested by incremental software patches for the RSA algorithm against variants of side-channel attacks within different versions of cryptographic libraries, protecting security-critical algorithms against side channels is an intricate task. Software protections avoid leakages by operating in constant time with a uniform resource usage pattern independent of the processed secret. In this respect, automated testing and verification of software binaries for leakage-free behavior is of importance, particularly when the source code is not available. In this work, we propose a novel technique based on Dynamic Binary Instrumentation and Mutual Information Analysis to efficiently locate and quantify memory based and control-flow based microarchitectural leakages. We develop a software framework named \tool~for side-channel analysis of binaries which can be extended to support new classes of leakage. For the first time, by utilizing \tool, we perform rigorous leakage analysis of two widely-used closed-source cryptographic libraries: \emph{Intel IPP} and \emph{Microsoft CNG}. We analyze $15$ different cryptographic implementations consisting of $112$ million instructions in about $105$ minutes of CPU time. By locating previously unknown leakages in hardened implementations, our results suggest that \tool~can efficiently find microarchitectural leakages in software binaries

14 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathon

Chemistry and materials science are complex. Recently, there have been great successes in addressing this complexity using data-driven or computational techniques. Yet, the necessity of input structured in very specific forms and the fact that there is an ever-growing number of tools creates usability and accessibility challenges. Coupled with the reality that much data in these disciplines is unstructured, the effectiveness of these tools is limited. Motivated by recent works that indicated that large language models (LLMs) might help address some of these issues, we organized a hackathon event on the applications of LLMs in chemistry, materials science, and beyond. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines

Patient Retention and Adherence to Antiretrovirals in a Large Antiretroviral Therapy Program in Nigeria: A Longitudinal Analysis for Risk Factors

Substantial resources and patient commitment are required to successfully scale-up antiretroviral therapy (ART) and provide appropriate HIV management in resource-limited settings. We used pharmacy refill records to evaluate risk factors for loss to follow-up (LTFU) and non-adherence to ART in a large treatment cohort in Nigeria.We reviewed clinic records of adult patients initiating ART between March 2005 and July 2006 at five health facilities. Patients were classified as LTFU if they did not return >60 days from their expected visit. Pharmacy refill rates were calculated and used to assess non-adherence. We identified risk factors associated with LTFU and non-adherence using Cox and Generalized Estimating Equation (GEE) regressions, respectively. Of 5,760 patients initiating ART, 26% were LTFU. Female gender (p < 0.001), post-secondary education (p = 0.03), and initiating treatment with zidovudine-containing (p = 0.004) or tenofovir-containing (p = 0.05) regimens were associated with decreased risk of LTFU, while patients with only primary education (p = 0.02) and those with baseline CD4 counts (cell/ml(3)) >350 and <100 were at a higher risk of LTFU compared to patients with baseline CD4 counts of 100-200. The adjusted GEE analysis showed that patients aged <35 years (p = 0.005), who traveled for >2 hours to the clinic (p = 0.03), had total ART duration of >6 months (p<0.001), and CD4 counts >200 at ART initiation were at a higher risk of non-adherence. Patients who disclosed their HIV status to spouse/family (p = 0.01) and were treated with tenofovir-containing regimens (p < or = 0.001) were more likely to be adherent.These findings formed the basis for implementing multiple pre-treatment visit preparation that promote disclosure and active community outreaching to support retention and adherence. Expansion of treatment access points of care to communities to diminish travel time may have a positive impact on adherence

The Pneumococcal Serine-Rich Repeat Protein Is an Intra-Species Bacterial Adhesin That Promotes Bacterial Aggregation In Vivo and in Biofilms

The Pneumococcal serine-rich repeat protein (PsrP) is a pathogenicity island encoded adhesin that has been positively correlated with the ability of Streptococcus pneumoniae to cause invasive disease. Previous studies have shown that PsrP mediates bacterial attachment to Keratin 10 (K10) on the surface of lung cells through amino acids 273–341 located in the Basic Region (BR) domain. In this study we determined that the BR domain of PsrP also mediates an intra-species interaction that promotes the formation of large bacterial aggregates in the nasopharynx and lungs of infected mice as well as in continuous flow-through models of mature biofilms. Using numerous methods, including complementation of mutants with BR domain deficient constructs, fluorescent microscopy with Cy3-labeled recombinant (r)BR, Far Western blotting of bacterial lysates, co-immunoprecipitation with rBR, and growth of biofilms in the presence of antibodies and competitive peptides, we determined that the BR domain, in particular amino acids 122–166 of PsrP, promoted bacterial aggregation and that antibodies against the BR domain were neutralizing. Using similar methodologies, we also determined that SraP and GspB, the Serine-rich repeat proteins (SRRPs) of Staphylococcus aureus and Streptococcus gordonii, respectively, also promoted bacterial aggregation and that their Non-repeat domains bound to their respective SRRPs. This is the first report to show the presence of biofilm-like structures in the lungs of animals infected with S. pneumoniae and show that SRRPs have dual roles as host and bacterial adhesins. These studies suggest that recombinant Non-repeat domains of SRRPs (i.e. BR for S. pneumoniae) may be useful as vaccine antigens to protect against Gram-positive bacteria that cause infection