A model-independent Particle Swarm Optimisation software for model calibration

This work presents and illustrates the application of hydroPSO, a novel multi-OS and model-independent R package used for model calibration. hydroPSO allows the modeller to perform a standard modelling work flow including, sensitivity analysis, parameter calibration, and assessment of the calibration results, using a single piece of software. hydroPSO implements several state-of-the-art enhancements and fine-tuning options to the Particle Swarm Optimisation (PSO) algorithm to meet specific user needs. hydroPSO easily interfaces the calibration engine to different model codes through simple ASCII files and/or R wrapper functions for exchanging information on the calibration parameters. Then, optimises a user-defined goodness-of-fit measure until a maximum number of iterations or a convergence criterion are met. Finally, advanced plotting functionalities facilitate the interpretation and assessment of the calibration results. The current hydroPSO version allows easy parallelization and works with single-objective functions, with multi-objective functionalities being the subject of ongoing development. We compare hydroPSO against standard algorithms (SCE_UA, DE, DREAM, SPSO-2011, and GML) using a series of benchmark functions. We further illustrate the application of hydroPSO in two real-world case studies: we calibrate, first, a hydrological model for the Ega River Basin (Spain) and, second, a groundwater flow model for the Pampa del Tamarugal Aquifer (Chile). Results from the comparison exercise indicate that hydroPSO is: i) effective and efficient compared to commonly used optimisation algorithms, ii) “scalable”, i.e. maintains a high performance for increased problem dimensionality, and iii) versatile to adapt to different response surfaces of the objective function. Case study results highlight the functionality and ease of use of hydroPSO to handle several issues that are commonly faced by the modelling community such as: working on different operating systems, single or batch model execution, transient- or steady-state modelling conditions, and the use of alternative goodness-of-fit measures to drive parameter optimisation. Although we limit the application of hydroPSO to hydrological models, flexibility of the package suggests it can be implemented in a wider range of models requiring some form of parameter optimisation.     

Pulsed field,ribotype and integron analysis of multidrug resistant isolates of Salmonella enterica serovar Newport

Twenty-one isolates of Salmonella enterica serovar Newport were evaluated for their antimicrobial resistance, pulsed field gel electrophoresis (PFGE) profiles, ribotype profiles, and their integron profiles. Antimicrobial resistance profiles indicated that 20 of the 21 isolates were resistant to the following antibiotics: amoxicillin–clavulanic acid (AMOX/CA), ampicillin (AMPC), cefoxitin (CFOX), ceftiofur (TIO), cephalothin (CRIN), chloramphenicol (CHL), streptomycin (STR), tetracycline (TET), and sulfamethoxazole (SMX). Five isolates showed resistance to gentamycin (GEN) and kanamycin (KAN). Trimethoprim–sulfamethoxazole (SMX/TMP) resistance was observed in six isolates. Eight of the twenty one isolates showed intermediate resistance to ceftriaxone (CTRX), with one isolate exhibiting complete resistance. PFGE clearly resolved the Salmonella Newport isolates into nine distinct clusters, and a good congruence was observed between PFGE and antibiotic resistance patterns. Automated riboprinting clearly distinguished between antibiotic resistant and sensitive strains of Salmonella Newport, and resolved the isolates into two ribogroups. One group consisted of the multidrug resistant isolates, and the other grouping contained the sensitive isolate. Three different integrons (1.0, 1.2, and 1.8 kb) were observed in many of the isolates, and several isolates contained more than one integron. Restriction fragment length polymorphisms (RFLP) indicated that integrons of the same size were indistinguishable.When integron analysis and ribotype analysis were used in conjunction, four subtypes of multidrug resistant Salmonella Newport isolates were clearly defined. These results demonstrate the possibility of utilizing automated ribotyping and integron analysis to rapidly subtype multidrug resistant Salmonella Newport isolates.     

Characterisation of a new hump-free device structure for smart power and embedded memory technologies

A new device structure suitable for smart power and embedded memory technologies is presented that provides ideal hump-free subthreshold behaviour for shallow trench isolations by locally thickening the gate dielectric. This device structure is compared with an alternative approach to remove the hump effect, an improved process that reduces the oxide recess of the isolating trench. The new device offers a superior subthreshold slope. Emphasis has been placed not only on the hump effect but also on the reliability characterisation. The gate integrity of the new structure is comparable and only a minor degradation of the hot-carrier lifetime is observed. The new device structure provides an easy way to remove the hump without any change in the process and is applicable to every technology that offers more than one gate dielectric.     

Simultaneous amoebic liver abscess and hepatitis A infection

Continuous ambulatory peritoneal dialysis (CAPD) is associated with various problems, including damage to the CAPD catheter. We encountered catheter rupture around the titanium adaptor in a patient who had been on CAPD for 7 years. The area near the adaptor generally suffers damage secondary to deterioration of the silicon composing the catheter. However, stereoscopic and electron microscopic observation of the surface of the catheter revealed no deterioration. Instead, there were fine scratches around the site of rupture and the broken surface was rough. Since the patient did not protect the catheter with gauze near the titanium adaptor, it was probably damaged by the adaptor and then ruptured by some external force.     

Cholesterol interaction with recombinant human sterol carrier protein-2

The interaction of human recombinant sterol carrier protein-2 (SCP-2) with sterols was examined. Two independent ligand binding methods, Lipidex 1000 binding of [³H]cholesterol and a fluorescent dehydroergosterol binding assay, were used to determine the affinity of SCP-2 for sterols. Binding analysis indicated SCP-2 bound [³H]cholesterol and dehydroergosterol with aK _d of 0.3 and 1.7 μM, respectively, and suggested the presence of a single binding site. Phase fluorometry and circular dichroism were used to characterize the SCP-2 sterol binding site. Alterations in dehydroergosterol lifetime, SCP-2 tryptophan lifetime, and SCP-2 tryptophan quenching by acrylamide upon cholesterol binding demonstrated a shielding of the SCP-2 tryptophan from the aqueous solvent by bound sterol. Differential polarized phase fluorometry revealed decreased SCP-2 tryptophan rotational correlation time upon cholesterol binding. Circular dichroism of SCP-2 indicated that cholesterol elicited a small decrease in SCP-2 alpha helical content. The data suggest that SCP-2 binds sterols with affinity consistent with a lipid transfer protein that may act either as an aqueous carrier or at a membrane surface to enhance sterol desorption.     

Assessing corn water stress using spectral reflectance

Multiple remote-sensing techniques have been developed to identify crop-water stress; however, some methods may be difficult for farmers to apply. If spectral reflectance data can be used to monitor crop-water stress, growers could use this information as a quick low-cost guideline for irrigation management, thus helping save water by preventing over-irrigating and achieving desired crop yields. Data was collected in the 2013 growing season near Greeley, Colorado, where drip irrigation was used to irrigate 12 corn (Zea mays L.) treatments with varying water-deficit levels. Ground-based multispectral data were collected and three different vegetation indices were evaluated. These included the normalized difference vegetation index (NDVI), the optimized soil-adjusted vegetation index (OSAVI), and the Green normalized difference vegetation index (GNDVI). The three vegetation indices were compared to water stress as indicated by the stress coefficient (K_s), and water deficit in the root zone was calculated using a soil water balance. To compare the indices to K_s, vegetation ratios were developed from vegetation indices in the process of normalization. Vegetation ratios are defined as the non-stressed vegetation index divided by the stressed vegetation index. Results showed that vegetation ratios were sensitive to water stress as indicated by the good coefficient of determination (R² > 0.46) values and low root mean square error (RMSE < 0.076) values when compared to K_s. To use spectral reflectance to manage crop-water stress, an example irrigation trigger point of 0.93 for the vegetation ratios was determined for a 10–12% loss in yield. These results were validated using data collected from a different field. The performance of the vegetation ratio approach was better than when applied to the main field giving higher goodness of fit values (R² > 0.63), and lower error values (RMSE < 0.043) between K_s and the vegetation indices.     

Effective Vaccination Policies

We present a framework for modeling the spread of pathogens throughout a population and generating policies that minimize the impact of those pathogens on the population. This framework is used to study the spread of human viruses between cities via airplane travel. It combines agent-based simulation, mathematical analysis, and an Evolutionary Algorithm (EA) optimizer. The goal of this study is to develop tools that determine the optimal distribution of a vaccine supply in the model. Using plausible benchmark vaccine allocation policies of uniform and proportional distribution, we compared their effectiveness to policies found by the EA. We then designed and tested a new, more effective policy which increased the importance of vaccinating smaller cities that are flown to more often. This “importance factor” was validated using US influenza data from the last four years.     

Effects of furfural activated crumb rubber on the properties of rubberized asphalt

The use of furfural (C₅H₄O₂) as an activation agent has been suggested as a method to improve the rheological properties of asphalt binders due to its compatibility with crumb rubber. This study uses five different crude sources and both ambient and cryogenic produced crumb rubber modifiers (CRM). The rheological properties for furfural activated and conventional CRM binders were evaluated using the dynamic shear rheometer (DSR) and the gel permeation chromatography (GPC). The results indicated that furfural activation has variable effects on the properties of the CRM binder. However, the most pronounced effect is shown in the storage stability improvement which will have an effect on the storage of CRM binder. Also, the activation caused a reduction in the ratio of the small molecular size distribution which is considered an improvement in the binder properties.