Comparing the artificial neural network with parcial least squares for prediction of soil organic carbon and pH at different moisture content levels using visible and near-infrared spectroscopy

Visible and near infrared (vis-NIR) spectroscopy is widely used to detect soil properties. The objective of this study is to evaluate the combined effect of moisture content (MC) and the modeling algorithm on prediction of soil organic carbon (SOC) and pH. Partial least squares (PLS) and the Artificial neural network (ANN) for modeling of SOC and pH at different MC levels were compared in terms of efficiency in prediction of regression. A total of 270 soil samples were used. Before spectral measurement, dry soil samples were weighed to determine the amount of water to be added by weight to achieve the specified gravimetric MC levels of 5, 10, 15, 20, and 25 %. A fiber-optic vis-NIR spectrophotometer (350-2500 nm) was used to measure spectra of soil samples in the diffuse reflectance mode. Spectra preprocessing and PLS regression were carried using Unscrambler® software. Statistica® software was used for ANN modeling. The best prediction result for SOC was obtained using the ANN (RMSEP = 0.82 % and RPD = 4.23) for soil samples with 25 % MC. The best prediction results for pH were obtained with PLS for dry soil samples (RMSEP = 0.65 % and RPD = 1.68) and soil samples with 10 % MC (RMSEP = 0.61 % and RPD = 1.71). Whereas the ANN showed better performance for SOC prediction at all MC levels, PLS showed better predictive accuracy of pH at all MC levels except for 25 % MC. Therefore, based on the data set used in the current study, the ANN is recommended for the analyses of SOC at all MC levels, whereas PLS is recommended for the analysis of pH at MC levels below 20 %.

Pattern selection in a lattice of pulse-coupled oscillators

We study spatio-temporal pattern formation in a ring of N oscillators with inhibitory unidirectional pulselike interactions. The attractors of the dynamics are limit cycles where each oscillator fires once and only once. Since some of these limit cycles lead to the same pattern, we introduce the concept of pattern degeneracy to take it into account. Moreover, we give a qualitative estimation of the volume of the basin of attraction of each pattern by means of some probabilistic arguments and pattern degeneracy, and show how they are modified as we change the value of the coupling strength. In the limit of small coupling, our estimative formula gives a pefect agreement with numerical simulations.

Selection of Salix myrsinifolia clones for biomass forestry in Finland

Summary

Growth decrease in Alpine whitefish: investigating the relative contribution of fishing induced selection and environmental change and its implication for conservation measures

La pression exercée par les activités humaines menace pratiquement tous les écosystèmes aquatiques du globe. Ainsi, sous l'effet de divers facteurs tels que la pollution, le réchauffement climatique ou encore la pêche industrielle, de nombreuses populations de poissons ont vu leurs effectifs chuter et divers changements morphologiques ont été observés. Dans cette étude, nous nous sommes intéressés à une menace particulière: la sélection induite par la pêche sur la croissance des poissons. En effet, la génétique des populations prédit que la soustraction régulière des individus les plus gros peut entraîner des modifications rapides de certains traits physiques comme la croissance individuelle. Cela a par ailleurs été observé dans de nombreuses populations marines ou lacustres, dont les populations de féras, bondelles et autres corégones des lacs suisses. Toutefois, malgré un nombre croissant d'études décrivant ce phénomène, peu de plans de gestion en tiennent compte, car l'importance des effets génétiques liés à la pêche est le plus souvent négligée par rapport à l'impact des changements environnementaux. Le but premier de cette étude a donc été de quantifier l'importance des facteurs génétiques et environnementaux. Dans le premier chapitre, nous avons étudié la population de palée du lac de Joux (Coregonus palaea). Nous avons déterminé les différentiels de sélection dus à la pêche, c'est-à-dire l'intensité de la sélection sur le taux de croissance, ainsi que les changements nets de croissance au cours du temps. Nous avons observé une baisse marquée de croissance et un différentiel de sélection important indiquant qu'au moins 30% de la diminution de croissance observée était due à la pression de sélection induite par la pêche. Dans le deuxième chapitre, nous avons effectué les mêmes analyses sur deux espèces proches du lac de Brienz (C. albellus et C. fatioi) et avons observé des effets similaires dont l'intensité était spécifique à chaque espèce. Dans le troisième chapitre, nous avons analysé deux autres espèces : C. palaea et C. confusus du lac de Bienne, et avons constaté que le lien entre la pression de sélection et la diminution de croissance était influencé par des facteurs environnementaux. Finalement, dans le dernier chapitre, nous avons étudié les effets potentiels de différentes modifications de la taille des mailles des filets utilisés pour la pêche à l'aide de modèles mathématiques. Nous concluons que la pêche a un effet génétique non négligeable (et donc peu réversible) sur la croissance individuelle dans les populations observée, que cet effet est lié à la compétition pour la nourriture et à la qualité de l'environnement, et que certaines modifications simples de la taille des mailles des filets de pêche pourraient nettement diminuer l'effet de sélection et ainsi ralentir, voir même renverser la diminution de croissance observée.

Guide Specification for Highway Construction Texturing Concrete Pavement for Reduced Tire/Pavement Noise using Artificial Turf Drag, March 1, 2011

This document provides language that can be used by an Owner-Agency to develop materials and construction specifications with the objective of reducing tire/pavement noise. While the practices described herein are largely prescriptive, they have been demonstrated to increase the likelihood of constructing a durable, quieter concrete surface. Guidance is provided herein for texturing the concrete surface since texture geometry has a paramount effect on tire/pavement noise. Guidance for curing is also provided to improve strength and durability of the surface mortar, and thus to improve texture durability.

Adaptive diversity in heterogeneous environments for populations regulated by a mixture of soft and hard selection

The stable co-existence of two haploid genotypes or two species is studied in a spatially heterogeneous environment submitted to a mixture of soft selection (within-patch regulation) and hard selection (outside-patch regulation) and where two kinds of resource are available. This is analysed both at an ecological time-scale (short term) and at an evolutionary time-scale (long term). At an ecological scale, we show that co-existence is very unlikely if the two competitors are symmetrical specialists exploiting different resources. In this case, the most favourable conditions are met when the two resources are equally available, a situation that should favour generalists at an evolutionary scale. Alternatively, low within-patch density dependence (soft selection) enhances the co-existence between two slightly different specialists of the most available resource. This results from the opposing forces that are acting in hard and soft regulation modes. In the case of unbalanced accessibility to the two resources, hard selection favours the most specialized genotype, whereas soft selection strongly favours the less specialized one. Our results suggest that competition for different resources may be difficult to demonstrate in the wild even when it is a key factor in the maintenance of adaptive diversity. At an evolutionary scale, a monomorphic invasive evolutionarily stable strategy (ESS) always exists. When a linear trade-off exists between survival in one habitat versus that in another, this ESS lies between an absolute adjustment of survival to niche size (for mainly soft-regulated populations) and absolute survival (specialization) in a single niche (for mainly hard-regulated populations). This suggests that environments in agreement with the assumptions of such models should lead to an absence of adaptive variation in the long term.

Comparative genomic analysis of the odorant-binding protein family in 12 Drosophila genomes: purifying selection and birth-and-death evolution

Background: Chemoreception is a widespread mechanism that is involved in critical biologic processes, including individual and social behavior. The insect peripheral olfactory system comprises three major multigene families: the olfactory receptor (Or), the gustatory receptor (Gr), and the odorant-binding protein (OBP) families. Members of the latter family establish the first contact with the odorants, and thus constitute the first step in the chemosensory transduction pathway.Results: Comparative analysis of the OBP family in 12 Drosophila genomes allowed the identification of 595 genes that encode putative functional and nonfunctional members in extant species, with 43 gene gains and 28 gene losses (15 deletions and 13 pseudogenization events). The evolution of this family shows tandem gene duplication events, progressive divergence in DNA and amino acid sequence, and prevalence of pseudogenization events in external branches of the phylogenetic tree. We observed that the OBP arrangement in clusters is maintained across the Drosophila species and that purifying selection governs the evolution of the family; nevertheless, OBP genes differ in their functional constraints levels. Finally, we detect that the OBP repertoire evolves more rapidly in the specialist lineages of the Drosophila melanogaster group (D. sechellia and D. erecta) than in their closest generalists.Conclusion: Overall, the evolution of the OBP multigene family is consistent with the birth-and-death model. We also found that members of this family exhibit different functional constraints, which is indicative of some functional divergence, and that they might be involved in some of the specialization processes that occurred through the diversification of the Drosophila genus.

To select or to weigh: a comparative study of linear combination schemes for superparent-one-dependence estimators

We conduct a large-scale comparative study on linearly combining superparent-one-dependence estimators (SPODEs), a popular family of seminaive Bayesian classifiers. Altogether, 16 model selection and weighing schemes, 58 benchmark data sets, and various statistical tests are employed. This paper's main contributions are threefold. First, it formally presents each scheme's definition, rationale, and time complexity and hence can serve as a comprehensive reference for researchers interested in ensemble learning. Second, it offers bias-variance analysis for each scheme's classification error performance. Third, it identifies effective schemes that meet various needs in practice. This leads to accurate and fast classification algorithms which have an immediate and significant impact on real-world applications. Another important feature of our study is using a variety of statistical tests to evaluate multiple learning methods across multiple data sets.

Evaluating the Effectiveness of Red Light Running Camera Enforcement in Cedar Rapids and Developing Guidelines for Selection and Use of Red Light Running Countermeasures Final Report, November 2011

Red light running (RLR) is a problem in the US that has resulted in 165,000 injuries and 907 fatalities annually. In Iowa, RLR-related crashes make up 24.5 percent of all crashes and account for 31.7 percent of fatal and major injury crashes at signalized intersections. RLR crashes are a safety concern due to the increased likelihood of injury compared to other types of crashes. One tool used to combat red light running is automated enforcement in the form of RLR cameras. Automated enforcement, while effective, is often controversial. Cedar Rapids, Iowa installed RLR and speeding cameras at seven intersections across the city. The intersections were chosen based on crash rates and whether cameras could feasibly be placed at the intersection approaches. The cameras were placed starting in February 2010 with the last one becoming operational in December 2010. An analysis of the effect of the cameras on safety at these intersections was determined prudent in helping to justify the installation and effectiveness of the cameras. The objective of this research was to assess the safety effectiveness of the RLR program that has been implemented in Cedar Rapids. This was accomplished by analyzing data to determine changes in the following metrics:  Reductions in red light violation rates based on overall changes, time of day changes, and changes by lane  Effectiveness of the cameras over time  Time in which those running the red light enter the intersection  Changes in the average headway between vehicles entering the intersection

Artificial-Intelligence-Based Optimization of the Management of Snow Removal Assets and Resources Final Report, October 2002

Geographic information systems (GIS) and artificial intelligence (AI) techniques were used to develop an intelligent snow removal asset management system (SRAMS). The system has been evaluated through a case study examining snow removal from the roads in Black Hawk County, Iowa, for which the Iowa Department of Transportation (Iowa DOT) is responsible. The SRAMS is comprised of an expert system that contains the logical rules and expertise of the Iowa DOT’s snow removal experts in Black Hawk County, and a geographic information system to access and manage road data. The system is implemented on a mid-range PC by integrating MapObjects 2.1 (a GIS package), Visual Rule Studio 2.2 (an AI shell), and Visual Basic 6.0 (a programming tool). The system could efficiently be used to generate prioritized snowplowing routes in visual format, to optimize the allocation of assets for plowing, and to track materials (e.g., salt and sand). A test of the system reveals an improvement in snowplowing time by 1.9 percent for moderate snowfall and 9.7 percent for snowstorm conditions over the current manual system.

Low Water Stream Crossing: Design and Construction Recommendations; A Selection and Design Guide, February 2003

Most Iowa counties maintain low volume roads with at least one bridge or culvert that is structurally deficient or obsolete. In some counties the percentage of deficient drainage structures may be as high as 62%. Replacement with structures of similar size would require large capital expenditures that many counties cannot afford. Low water stream crossings (LWSCs) may be an acceptable lowcost alternative in some cases.

The Effect of Inoculum Size on Selection of In Vitro Resistance to Vancomycin, Daptomycin, and Linezolid in Methicillin-Resistant Staphylococcus aureus.

OBJECTIVES: The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) at high bacterial densities. The effect of three inoculum sizes on the selection of resistance to vancomycin, daptomycin, and linezolid was investigated in methicillin-resistant Staphylococcus aureus (MRSA). METHODS: Low (10(4) CFU/ml), medium (10(6) CFU/ml), and high (10(8) CFU/ml) inocula of MRSA were exposed to twofold increasing concentrations of either drug during 15 days of cycling. MICs for low (MICL), medium (MICM), and high (MICH) inocula were determined daily. Conventional MICs were measured at days 1, 5, 10, and 15. Experiments were performed in triplicate. RESULTS: At the beginning of the experiment a small IE was observed for vancomycin (MICL=1 μg/ml, MICM=1-2 μg/ml, and MICH=2 μg/ml) and a significant IE for daptomycin (MICL=0.25 μg/ml, MICM=0.25-0.5 μg/ml, and MICH=2 μg/ml). Linezolid exhibited no IE at low and medium inocula (MICL=1 μg/ml and MICM=1-2 μg/ml), but with the high inoculum, concentrations up to 2,048 μg/ml did not fully inhibit visual growth. During cycling, increase of MIC was observed for all antibiotics. At day 15, MICL, MICM, and MICH of vancomycin were 2-4, 4-8, and 4-16 μg/ml and of daptomycin were 0.5-2, 8-128, and 64-256 μg/ml, respectively. MICL and MICM of linezolid were 1 and 2-4 μg/ml, respectively. Conventional MICs showed vancomycin and daptomycin selection of resistance since day 5 depending on the inocula. No selection of linezolid resistance was observed. CONCLUSIONS: Our results showed the importance of the inoculum size in the development of resistance. Measures aimed at lowering the inoculum at the site of infection should be used whenever possible in parallel to antimicrobial therapy.

Autoreactive T cells bypass negative selection and respond to self-antigen stimulation during infection.

Central and peripheral tolerance prevent autoimmunity by deleting the most aggressive CD8(+) T cells but they spare cells that react weakly to tissue-restricted antigen (TRA). To reveal the functional characteristics of these spared cells, we generated a transgenic mouse expressing the TCR of a TRA-specific T cell that had escaped negative selection. Interestingly, the isolated TCR matches the affinity/avidity threshold for negatively selecting T cells, and when developing transgenic cells are exposed to their TRA in the thymus, only a fraction of them are eliminated but significant numbers enter the periphery. In contrast to high avidity cells, low avidity T cells persist in the antigen-positive periphery with no signs of anergy, unresponsiveness, or prior activation. Upon activation during an infection they cause autoimmunity and form memory cells. Unexpectedly, peptide ligands that are weaker in stimulating the transgenic T cells than the thymic threshold ligand also induce profound activation in the periphery. Thus, the peripheral T cell activation threshold during an infection is below that of negative selection for TRA. These results demonstrate the existence of a level of self-reactivity to TRA to which the thymus confers no protection and illustrate that organ damage can occur without genetic predisposition to autoimmunity.

Artificial muscle: the human chimera is the future.

Severe heart failure and cerebral stroke are broadly associated with the impairment of muscular function that conventional treatments struggle to restore. New technologies enable the construction of "smart" materials that could be of great help in treating diseases where the main problem is muscle weakness. These materials "behave" similarly to biological systems, because the material directly converts energy, for example electrical energy into movement. The extension and contraction occur silently like in natural muscles. The real challenge is to transfer this amazing technology into devices that restore or replace the mechanical function of failing muscle. Cardiac assist devices based on artificial muscle technology could envelope a weak heart and temporarily improve its systolic function, or, if placed on top of the atrium, restore the atrial kick in chronic atrial fibrillation. Artificial sphincters could be used to treat urinary incontinence after prostatectomy or faecal incontinence associated with stomas. Artificial muscles can restore the ability of patients with facial paralysis due to stroke or nerve injury to blink. Smart materials could be used to construct an artificial oesophagus including peristaltic movement and lower oesophageal sphincter function to replace the diseased oesophagus thereby avoiding the need for laparotomy to mobilise stomach or intestine. In conclusion, in the near future, smart devices will integrate with the human body to fill functional gaps due to organ failure, and so create a human chimera.

Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.