Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza.

The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor species levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor species level, the upper respiratory tract microbiomes were composed of 13-20 species and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection

Dissecting and reprogramming the folding and assembly of tandem-repeat proteins.

Studying protein folding and protein design in globular proteins presents significant challenges because of the two related features, topological complexity and co-operativity. In contrast, tandem-repeat proteins have regular and modular structures composed of linearly arrayed motifs. This means that the biophysics of even giant repeat proteins is highly amenable to dissection and to rational design. Here we discuss what has been learnt about the folding mechanisms of tandem-repeat proteins. The defining features that have emerged are: (i) accessibility of multiple distinct routes between denatured and native states, both at equilibrium and under kinetic conditions; (ii) different routes are favoured for folding compared with unfolding; (iii) unfolding energy barriers are broad, reflecting stepwise unravelling of an array repeat by repeat; (iv) highly co-operative unfolding at equilibrium and the potential for exceptionally high thermodynamic stabilities by introducing consensus residues; (v) under force, helical-repeat structures are very weak with non-co-operative unfolding leading to elasticity and buffering effects. This level of understanding should enable us to create repeat proteins with made-to-measure folding mechanisms, in which one can dial into the sequence the order of repeat folding, number of pathways taken, step size (co-operativity) and fine-structure of the kinetic energy barriers.We acknowledge funding from the Medical Research Council of the UK (grant G1002329) and the Leverhulme Trust. AP is funded by a BBSRC Doctoral Training Program studentship. LSI acknowledges support of a Fellowship from the Medical Research Foundation.This is the accepted manuscript. The final version is available at http://www.biochemsoctrans.org/content/43/5/881

Fully Quantized Always-on Face Detector Considering Mobile Image Sensors

Despite significant research on lightweight deep neural networks (DNNs) designed for edge devices, the current face detectors do not fully meet the requirements for "intelligent" CMOS image sensors (iCISs) integrated with embedded DNNs. These sensors are essential in various practical applications, such as energy-efficient mobile phones and surveillance systems with always-on capabilities. One noteworthy limitation is the absence of suitable face detectors for the always-on scenario, a crucial aspect of image sensor-level applications. These detectors must operate directly with sensor RAW data before the image signal processor (ISP) takes over. This gap poses a significant challenge in achieving optimal performance in such scenarios. Further research and development are necessary to bridge this gap and fully leverage the potential of iCIS applications. In this study, we aim to bridge the gap by exploring extremely low-bit lightweight face detectors, focusing on the always-on face detection scenario for mobile image sensor applications. To achieve this, our proposed model utilizes sensor-aware synthetic RAW inputs, simulating always-on face detection processed "before" the ISP chain. Our approach employs ternary (-1, 0, 1) weights for potential implementations in image sensors, resulting in a relatively simple network architecture with shallow layers and extremely low-bitwidth. Our method demonstrates reasonable face detection performance and excellent efficiency in simulation studies, offering promising possibilities for practical always-on face detectors in real-world applications.Comment: Accepted to ICCV 2023 Workshop on Low-Bit Quantized Neural Networks (LBQNN), Ora

A colimit decomposition for homotopy algebras in Cat

Badzioch showed that in the category of simplicial sets each homotopy algebra of a Lawvere theory is weakly equivalent to a strict algebra. In seeking to extend this result to other contexts Rosicky observed a key point to be that each homotopy colimit in simplicial sets admits a decomposition into a homotopy sifted colimit of finite coproducts, and asked the author whether a similar decomposition holds in the 2-category of categories Cat. Our purpose in the present paper is to show that this is the case.Comment: Some notation changed; small amount of exposition added in intr

Decision making under uncertainty in environmental projects using mathematical simulation modeling

The final publication is available at Springer via http://dx.doi.org/10.1007/s12665-016-6135-yIn decision-making processes, reliability and risk aversion play a decisive role. The aim of this study is to perform an uncertainty assessment of the effects of future scenarios of sustainable groundwater pumping strategies on the quantitative and chemical status of an aquifer. The good status of the aquifer is defined according to the terms established by the EU Water Framework Directive (WFD). A decision support systems (DSS) is presented, which makes use of a stochastic inverse model (GC method) and geostatistical approaches to calibrate equally likely realizations of hydraulic conductivity (K) fields for a particular case study. These K fields are conditional to available field data, including hard and soft information. Then, different future scenarios of groundwater pumping strategies are generated, based on historical information and WFD standards, and simulated for each one of the equally likely K fields. The future scenarios lead to different environmental impacts and levels of socioeconomic development of the region and, hence, to a different degree of acceptance among stakeholders. We have identified the different stakeholders implied in the decision-making process, the objectives pursued and the alternative actions that should be considered by stakeholders in a public participation project (PPP). The MonteCarlo simulation provides a highly effective way for uncertainty assessment and allows presenting the results in a simple and understandable way even for non-experts stakeholders. The methodology has been successfully applied to a real case study and lays the foundations to performa PPP and stakeholders' involvement in a decisionmaking process as required by the WFD. The results of the methodology can help the decision-making process to come up with the best policies and regulations for a groundwater system under uncertainty in groundwater parameters and management strategies and involving stakeholders with conflicting interests.Llopis Albert, C.; Palacios Marqués, D.; Merigó -Lindahl, JM. (2016). Decision making under uncertainty in environmental projects using mathematical simulation modeling. Environmental Earth Sciences. 75(19):1-11. doi:10.1007/s12665-016-6135-yS1117519Arhonditsis GB, Perhar G, Zhang W, Massos E, Shi M, Das A (2008) Addressing equifinality and uncertainty in eutrophication models. Water Resour Res 44:W01420. doi: 10.1029/2007WR005862Capilla JE, Llopis-Albert C (2009) Gradual conditioning of non-gaussian transmissivity fields to flow and mass transport data. J Hydrol 371:66–74. doi: 10.1016/j.jhydrol.2009.03.015CHJ (Júcar Water Agency) (2016) Júcar river basin authority. http://www.chj.es/CHS (Segura Water Agency) (2016) Segura river basin authority. http://www.chsegura.es/Custodio E (2002) Aquifer overexploitation: what does it mean? Hydrogeol J 10:254–277EC (2000). Directive 2000/60/EC of the European Parliament and of the Council of October 23 2000, establishing a framework for community action in the field of water policy. Official Journal of the European Communities L327/1eL327/72. 22.12.2000EC (2006) Directive 2006/118/EC of the European Parliament and of the Council of 12 December 2006 on the protection of groundwater against pollution and deteriorationGómez-Hernández JJ, Srivastava RM (1990) ISIM3D: an ANSI-C three dimensional multiple indicator conditional simulation program. Comput Geosci 16(4):395–440Harbaugh AW, Banta ER, Hill MC and McDonald MG (2000) MODFLOW- 2000, The US geological survey modular groundwater model-user guide to modularization concepts and the groundwater flow process. US Geol. Surv. Open-File Rep 00–92, 12Hu LY (2000) Gradual deformation and iterative calibration of Gaussian related stochastic models. Math Geol 32(1):87–108Jagelke J, Barthel R (2005) Conceptualization and implementation of a regional groundwater model for the Neckar catchment in the framework of an integrated regional model. Adv Geosci 5:105–111Llopis-Albert C (2008) Stochastic inverse modeling conditional to flow, mass transport and secondary information. Universitat Politècnica de València, València. ISBN 978-84-691-9796-7Llopis-Albert C, Capilla JE (2009a) Gradual conditioning of non-gaussian transmissivity fields to flow and mass transport data. Demonstration on a synthetic aquifer. J Hydrol 371:53–55. doi: 10.1016/j.jhydrol.2009.03.014Llopis-Albert C, Capilla JE (2009b) Gradual conditioning of non-gaussian transmissivity fields to flow and mass transport data. Application to the macrodispersion experiment (MADE-2) site, on Columbus air force base in Mississippi (USA). J Hydrol 371:75–84. doi: 10.1016/j.jhydrol.2009.03.016Llopis-Albert C, Capilla JE (2010a) Stochastic simulation of non-gaussian 3D conductivity fields in a fractured medium with multiple statistical populations: a case study. J Hydrol Eng 15(7):554–566. doi: 10.1061/(ASCE)HE.1943-5584.0000214Llopis-Albert C, Capilla JE (2010b) Stochastic inverse modeling of hydraulic conductivity fields taking into account independent stochastic structures: a 3D case study. J Hydrol 391:277–288. doi: 10.1016/j.jhydrol.2010.07.028Llopis-Albert C, Pulido-Velazquez D (2014) Discussion about the validity of sharp-interface models to deal with seawater intrusion in coastal aquifers. Hydrol Process 28(10):3642–3654Llopis-Albert C, Pulido-Velazquez D (2015) Using MODFLOW code to approach transient hydraulic head with a sharp-interface solution. Hydrol Process 29(8):2052–2064. doi: 10.1002/hyp.10354Llopis-Albert C, Palacios-Marqués D, Merigó JM (2014) A coupled stochastic inverse-management framework for dealing with nonpoint agriculture pollution under groundwater parameter uncertainty. J Hydrol 511:10–16. doi: 10.1016/j.jhydrol.2014.01.021Llopis-Albert C, Merigó JM, Palacios-Marqués D (2015) Structure adaptation in stochastic inverse methods for integrating information. Water Resour Manage 29(1):95–107. doi: 10.1007/s11269-014-0829-2Llopis-Albert C, Merigó JM, Xu Y (2016) A coupled stochastic inverse/sharp interface seawater intrusion approach for coastal aquifers under groundwater parameter uncertainty. J Hydrol 540:774–783. doi: 10.1016/j.jhydrol.2016.06.065McDonald MG and Harbaugh AW (1988) A modular three-dimensional finite-difference groundwater flow model. US geological survey technical manual of water resources investigation, Book 6, US geological survey, Reston, Virginia, 586Molina JL, Pulido-Velazquez M, Llopis-Albert C, Peña-Haro S (2013) Stochastic hydro-economic model for groundwater quality management using Bayesian networks. Water Sci Technol 67(3):579–586. doi: 10.2166/wst.2012.598Peña-Haro S, Llopis-Albert C, Pulido-Velazquez M (2010) Fertilizer standards for controlling groundwater nitrate pollution from agriculture: El Salobral-Los Llanos case study, Spain. J Hydrol 392:174–187. doi: 10.1016/j.jhydrol.2010.08.006Peña-Haro S, Pulido-Velazquez M, Llopis-Albert C (2011) Stochastic hydro-economic modeling for optimal management of agricultural groundwater nitrate pollution under hydraulic conductivity uncertainty. Environ Model Softw 26(8):999–1008. doi: 10.1016/j.envsoft.2011.02.010Pulido-Velazquez D, Llopis-Albert C, Peña-Haro S, Pulido-Velazquez M (2011) Efficient conceptual model for simulating the effect of aquifer heterogeneity on natural groundwater discharge to rivers. Adv Water Resour 34(11):1377–1389. doi: 10.1016/j.advwatres.2011.07.010Reichert P, Borsuk M, Hostmann M, Schweizer S, Spörri C, Tockner K, Truffer B (2005) Concepts of decision support for river rehabilitation. Environ Model Softw 22:188–201Wright SAL, Fritsch O (2011) Operationalising active involvement in the EU water framework directive: why, when and how? Ecol Econ 70(12):2268–2274Zhou H, Gómez-Hernández JJ, Li L (2014) Inverse methods in hydrogeology: evolution and recent trends. Adv Water Resour 63:22–37. doi: 10.1016/j.advwatres.2013.10.01

Predator-Induced Vertical Behavior of a Ctenophore

Although many studies have focused on Mnemiopsis leidyi predation, little is known about the role of this ctenophore as prey when abundant in native and invaded pelagic systems. We examined the response of the ctenophore M. leidyi to the predatory ctenophore Beroe ovata in an experiment in which the two species could potentially sense each other while being physically separated. On average, M. leidyi responded to the predator’s presence by increasing variability in swimming speeds and by lowering their vertical distribution. Such behavior may help explain field records of vertical migration, as well as stratified and near-bottom distributions of M. leidyi

A cost effectiveness and capacity analysis for the introduction of universal rotavirus vaccination in Kenya : comparison between Rotarix and RotaTeq vaccines

Background Diarrhoea is an important cause of death in the developing world, and rotavirus is the single most important cause of diarrhoea associated mortality. Two vaccines (Rotarix and RotaTeq) are available to prevent rotavirus disease. This analysis was undertaken to aid the decision in Kenya as to which vaccine to choose when introducing rotavirus vaccination. Methods Cost-effectiveness modelling, using national and sentinel surveillance data, and an impact assessment on the cold chain. Results The median estimated incidence of rotavirus disease in Kenya was 3015 outpatient visits, 279 hospitalisations and 65 deaths per 100,000 children under five years of age per year. Cumulated over the first five years of life vaccination was predicted to prevent 34% of the outpatient visits, 31% of the hospitalizations and 42% of the deaths. The estimated prevented costs accumulated over five years totalled US$1,782,761 (direct and indirect costs) with an associated 48,585 DALYs. From a societal perspective Rotarix had a cost-effectiveness ratio of US$142 per DALY (US$5 for the full course of two doses) and RotaTeq US$288 per DALY ($10.5 for the full course of three doses). RotaTeq will have a bigger impact on the cold chain compared to Rotarix. Conclusion Vaccination against rotavirus disease is cost-effective for Kenya irrespective of the vaccine. Of the two vaccines Rotarix was the preferred choice due to a better cost-effectiveness ratio, the presence of a vaccine vial monitor, the requirement of fewer doses and less storage space, and proven thermo-stability

Effect of correlations on network controllability

A dynamical system is controllable if by imposing appropriate external signals on a subset of its nodes, it can be driven from any initial state to any desired state in finite time. Here we study the impact of various network characteristics on the minimal number of driver nodes required to control a network. We find that clustering and modularity have no discernible impact, but the symmetries of the underlying matching problem can produce linear, quadratic or no dependence on degree correlation coefficients, depending on the nature of the underlying correlations. The results are supported by numerical simulations and help narrow the observed gap between the predicted and the observed number of driver nodes in real networks

Branding the nation: Towards a better understanding

This paper aims to clarify some misunderstanding about nation branding. It examines the origins and interpretations of the concept, and draws a comparison between nation branding and commercial branding. A new definition is offered that emphasises the need to shift from “branding” the nation to nation image management