Leadership Department Newsletter - June 2015

https://digitalcommons.andrews.edu/ldn-2015/1004/thumbnail.jp

Game theory framework for MAC parameter optimization in energy-delay constrained sensor networks

Optimizing energy consumption and end-to-end (e2e) packet delay in energy-constrained, delay-sensitive wireless sensor networks is a conflicting multiobjective optimization problem. We investigate the problem from a game theory perspective, where the two optimization objectives are considered as game players. The cost model of each player is mapped through a generalized optimization framework onto protocol-specific MAC parameters. From the optimization framework, a game is first defined by the Nash bargaining solution (NBS) to assure energy consumption and e2e delay balancing. Secondy, the Kalai-Smorodinsky bargaining solution (KSBS) is used to find an equal proportion of gain between players. Both methods offer a bargaining solution to the duty-cycle MAC protocol under different axioms. As a result, given the two performance requirements (i.e., the maximum latency tolerated by the application and the initial energy budget of nodes), the proposed framework allows to set tunable system parameters to reach a fair equilibrium point that dually minimizes the system latency and energy consumption. For illustration, this formulation is applied to six state-of-the-art wireless sensor network (WSN) MAC protocols: B-MAC, X-MAC, RI-MAC, SMAC, DMAC, and LMAC. The article shows the effectiveness and scalability of such a framework in optimizing protocol parameters that achieve a fair energy-delay performance trade-off under the application requirements

Protein Structure along the Order–Disorder Continuum

Thermal fluctuations cause proteins to adopt an ensemble of conformations wherein the relative stability of the different ensemble members is determined by the topography of the underlying energy landscape. “Folded” proteins have relatively homogeneous ensembles, while “unfolded” proteins have heterogeneous ensembles. Hence, the labels “folded” and “unfolded” represent attempts to provide a qualitative characterization of the extent of structural heterogeneity within the underlying ensemble. In this work, we introduce an information-theoretic order parameter to quantify this conformational heterogeneity. We demonstrate that this order parameter can be estimated in a straightforward manner from an ensemble and is applicable to both unfolded and folded proteins. In addition, a simple formula for approximating the order parameter directly from crystallographic B factors is presented. By applying these metrics to a large sample of proteins, we show that proteins span the full range of the order–disorder axis.National Institutes of Health (U.S.) (NIH Grant 5R21NS063185-02

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Etude comparative de deux écosystèmes forestiers feuillu et résineux des Ardennes primaires françaises II. - Biomasse aérienne d'une plantation équienne d'Epicéa commun (Picea abies Karst.)

International audienc

Community case management in malaria: review and perspectives after four years of operational experience in Saraya district, south-east Senegal.

BACKGROUND: Despite recent advances in malaria diagnosis and treatment, many isolated communities in rural settings continue to lack access to these life-saving tools. Community-case management of malaria (CCMm), consisting of lay health workers (LHWs) using malaria rapid diagnostic tests (RDTs) and artemisinin-based combination therapy (ACT) in their villages, can address this disparity. METHODS: This study examined routine reporting data from a CCMm programme between 2008 and 2011 in Saraya, a rural district in Senegal, and assessed its impact on timely access to rapid diagnostic tests and ACT. RESULTS: There was a seven-fold increase in the number of LHWs providing care and in the number of patients seen. LHW engagement in the CCM programme varied seasonally, 24,3% of all patients prescribed an ACT had a negative RDT or were never administered an RDT, and less than half of patients with absolute indications for referral (severe symptoms, age under two months and pregnancy) were referred. There were few stock-outs. DISCUSSION: This CCMm programme successfully increased the number of patients with access to RDT and ACT, but further investigation is required to identify the cause for over-prescription, and low rates of referrals for patients with absolute indications. In contrast, previous widespread stock-outs in Saraya's CCMm programme have now been resolved. CONCLUSION: This study demonstrates the potential for CCMm programmes to substantially increase access to life-saving malarial diagnostics and treatment, but also highlights important challenges in ensuring quality