Solution of the Least Squares Method problem of pairwise comparison matrices

The aim of the paper is to present a new global optimization method for determining all the optima of the Least Squares Method (LSM) problem of pairwise comparison matrices. Such matrices are used, e.g., in the Analytic Hierarchy Process (AHP). Unlike some other distance minimizing methods, LSM is usually hard to solve because of the corresponding nonlinear and non-convex objective function. It is found that the optimization problem can be reduced to solve a system of polynomial equations. Homotopy method is applied which is an efficient technique for solving nonlinear systems. The paper ends by two numerical example having multiple global and local minima.

On Saaty's and Koczkodaj's inconsistencies of pairwise comparison matrices

The aim of the paper is to obtain some theoretical and numerical properties of Saaty’s and Koczkodaj’s inconsistencies of pairwise comparison matrices (PRM). In the case of 3 × 3 PRM, a differentiable one-to-one correspondence is given between Saaty’s inconsistency ratio and Koczkodaj’s inconsistency index based on the elements of PRM. In order to make a comparison of Saaty’s and Koczkodaj’s inconsistencies for 4 × 4 pairwise comparison matrices, the average value of the maximal eigenvalues of randomly generated n × n PRM is formulated, the elements aij (i < j) of which were randomly chosen from the ratio scale ... ... with equal probability 1/(2M − 1) and a ji is defined as 1/a ij . By statistical analysis, the empirical distributions of the maximal eigenvalues of the PRM depending on the dimension number are obtained. As the dimension number increases, the shape of distributions gets similar to that of the normal ones. Finally, the inconsistency of asymmetry is dealt with, showing a different type of inconsistency.

On pairwise comparison matrices that can be made consistent by the modification of a few elements

Pairwise comparison matrices are often used in Multi-attribute Decision Making forweighting the attributes or for the evaluation of the alternatives with respect to a criteria. Matrices provided by the decision makers are rarely consistent and it is important to index the degree of inconsistency. In the paper, the minimal number of matrix elements by the modification of which the pairwise comparison matrix can be made consistent is examined. From practical point of view, the modification of 1, 2, or, for larger matrices, 3 elements seems to be relevant. These cases are characterized by using the graph representation of the matrices. Empirical examples illustrate that pairwise comparison matrices that can be made consistent by the modification of a few elements are present in the applications.

Incomplete pairwise comparison matrices and weighting methods

A special class of preferences, given by a directed acyclic graph, is considered. They are represented by incomplete pairwise comparison matrices as only partial information is available: for some pairs no comparison is given in the graph. A weighting method satisfies the property linear order preservation if it always results in a ranking such that an alternative directly preferred to another does not have a lower rank. We study whether two procedures, the Eigenvector Method and the Logarithmic Least Squares Method meet this axiom. Both weighting methods break linear order preservation, moreover, the ranking according to the Eigenvector Method depends on the incomplete pairwise comparison representation chosen.

The development of direct ultra-fast PCR for forensic genotyping using short channel microfluidic systems with enhanced sieving matrices

There are situations in which it is very important to quickly and positively identify an individual. Examples include suspects detained in the neighborhood of a bombing or terrorist incident, individuals detained attempting to enter or leave the country, and victims of mass disasters. Systems utilized for these purposes must be fast, portable, and easy to maintain. The goal of this project was to develop an ultra fast, direct PCR method for forensic genotyping of oral swabs. The procedure developed eliminates the need for cellular digestion and extraction of the sample by performing those steps in the PCR tube itself. Then, special high-speed polymerases are added which are capable of amplifying a newly developed 7 loci multiplex in under 16 minutes. Following the amplification, a postage stamp sized microfluidic device equipped with specially designed entangled polymer separation matrix, yields a complete genotype in 80 seconds. The entire process is rapid and reliable, reducing the time from sample to genotype from 1-2 days to under 20 minutes. Operation requires minimal equipment and can be easily performed with a small high-speed thermal-cycler, reagents, and a microfluidic device with a laptop. The system was optimized and validated using a number of test parameters and a small test population. The overall precision was better than 0.17 bp and provided a power of discrimination greater than 1 in 106. The small footprint, and ease of use will permit this system to be an effective tool to quickly screen and identify individuals detained at ports of entry, police stations and remote locations. The system is robust, portable and demonstrates to the forensic community a simple solution to the problem of rapid determination of genetic identity.

Elemental analysis of biological matrices by laser ablation high resolution inductively coupled plasma mass spectrometry (LA-HR-ICP-MS) and high resolution inductively coupled plasma mass spectrometry (HR -ICP -MS)

The need for elemental analysis of biological matrices such as bone, teeth, and plant matter for sourcing purposes has emerged within the forensic and geochemical laboratories. Trace elemental analyses for the comparison of materials such as glass by inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS has been shown to offer a high degree of discrimination between different manufacturing sources. Unit resolution ICP-MS instruments may suffer from some polyatomic interferences including 40Ar16O+, 40Ar 16O1H+, and 40Ca 16O+ that affect iron measurement at trace levels. Iron is an important element in the analysis of glass and also of interest for the analysis of several biological matrices. A comparison of the analytical performance of two different ICP-MS systems for iron analysis in glass for determining the method detection limits (MDLs), accuracy, and precision of the measurement is presented. Acid digestion and laser ablation methods are also compared. Iron polyatomic interferences were reduced or resolved by using dynamic reaction cell and high resolution ICP-MS. MDLs as low as 0.03 μg g-1 and 0.14 μg g-1 for laser ablation and solution based analyses respectively were achieved. The use of helium as a carrier gas demonstrated improvement in the detection limits of both iron isotopes (56Fe and 57Fe) in medium resolution for the HR-ICP-MS and with a dynamic reaction cell (DRC) coupled to a quadrupole ICP-MS system. ^ The development and application of robust analytical methods for the quantification of trace elements in biological matrices has lead to a better understanding of the potential utility of these measurements in forensic chemical analyses. Standard reference materials (SRMs) were used in the development of an analytical method using HR-ICP-MS and LA-HR-ICP-MS that was subsequently applied on the analysis of real samples. Bone, teeth and ashed marijuana samples were analyzed with the developed method. ^ Elemental analysis of bone samples from 12 different individuals provided discrimination between individuals, when femur and humerus bones were considered separately. Discrimination of 14 teeth samples based on elemental composition was achieved with the exception of one case where samples from the same individual were not associated with each other. The discrimination of 49 different ashed plant (cannabis) samples was achieved using the developed method. ^

Environmental analysis of polar herbicides in complex organic-rich matrices by high performance liquid chromatography atmospheric pressure ionization mass spectrometry (HPLC-API-MS)

A comprehensive forensic investigation of sensitive ecosystems in the Everglades Area is presented. Assessing the background levels of contamination in these ecosystems represents a vital resource to build up forensic evidence required to enforce future environmental crimes within the studied areas. This investigation presents the development and validation of a fractionation and isolation method for two families of herbicides commonly applied in the vicinity of the study area, including phenoxy acids like 2,4-D, MCPA, and silvex; as well as the most common triazine-based herbicides like atrazine, prometyne, simazine and related metabolites like DIA and DEA. Accelerated solvent extraction (ASE) and solid phase extraction (SPE) were used to isolate the analytes from abiotic matrices containing large amounts of organic material. Atmospheric-pressure ionization (API) with electrospray ionization in negative mode (ESP-), and Chemical Ionization in the positive mode (APCI+) were used to perform the characterization of the herbicides of interest.

Sea organisms as a source of collagen-derived polymers for skin tissue engineering applications

Advanced therapies combating acute and chronic skin wounds are likely to be brought about using our knowledge of regenerative medicine coupled with appropriately tissue engineered skin substitutes. At the present time, there are no models of an artificial skin that completely replicate normal uninjured skin and they are usually accompanied by fibrotic reactions that result in the production of a scar. Natural biopolymers such as collagen have been a lot investigated as potential source of biomaterial for skin replacement in Tissue Engineering. Collagens are the most abundant high molecular weight proteins in both invertebrate and vertebrate organisms, including mammals, and possess mainly a structural role in connective tissues. From this, they have been elected as one of the key biological materials in tissue regeneration approaches, as skin tissue engineering. In addition, industry is constantly searching for new natural sources of collagen and upgraded methodologies for their production. The most common sources are skin and bone from bovine and porcine origin. However, these last carry high risk of bovine spongiform encephalopathy or transmissible spongiform encephalopathy and immunogenic responses. On the other hand, the increase of jellyfish has led us to consider this marine organism as potential collagen source for tissue engineering applications. In the present study, novel form of acid and pepsin soluble collagen were extracted from dried Rhopilema hispidum jellyfish species in an effort to obtain an alternative and safer collagen. We studied different methods of collagen purification (tissues and experimental procedures). The best collagen yield was obtained using pepsin extraction method (34.16 mg collagen/g of tissue). The isolated collagen was characterized by SDS-polyacrylamide gel electrophoresis and circular dichroism spectroscopy.

Optimización de la factorización de matrices no negativas en Bioinformática

En los últimos años se ha incrementado el interés de la comunidad científica en la Factorización de matrices no negativas (Non-negative Matrix Factorization, NMF). Este método permite transformar un conjunto de datos de grandes dimensiones en una pequeña colección de elementos que poseen semántica propia en el contexto del análisis. En el caso de Bioinformática, NMF suele emplearse como base de algunos métodos de agrupamiento de datos, que emplean un modelo estadístico para determinar el número de clases más favorable. Este modelo requiere de una gran cantidad de ejecuciones de NMF con distintos parámetros de entrada, lo que representa una enorme carga de trabajo a nivel computacional. La mayoría de las implementaciones de NMF han ido quedando obsoletas ante el constante crecimiento de los datos que la comunidad científica busca analizar, bien sea porque los tiempos de cómputo llegan a alargarse hasta convertirse en inviables, o porque el tamaño de esos datos desborda los recursos del sistema. Por ello, esta tesis doctoral se centra en la optimización y paralelización de la factorización NMF, pero no solo a nivel teórico, sino con el objetivo de proporcionarle a la comunidad científica una nueva herramienta para el análisis de datos de origen biológico. NMF expone un alto grado de paralelismo a nivel de datos, de granularidad variable; mientras que los métodos de agrupamiento mencionados anteriormente presentan un paralelismo a nivel de cómputo, ya que las diversas instancias de NMF que se ejecutan son independientes. Por tanto, desde un punto de vista global, se plantea un modelo de optimización por capas donde se emplean diferentes tecnologías de alto rendimiento...

Stabilisation of dehydrated nanoemulsions using sugar - protein matrices

There are numerous review papers discussing liquid nanoemulsions and how they compare to other emulsion systems. Little research is available on dried nanoemulsions. The objectives of this research were to (i) study the effect of varying the continuous phase of nanoemulsions with different carbohydrate/protein ratios on subsequent emulsion stability, and (ii) compare the physicochemical properties, lactose crystallisation properties, microstructure, and lipid oxidation of spray dried nanoemulsions compared to spray dried conventional emulsions having different water and sugar contents. Nanoemulsions containing sunflower oil (10% w/w), β-casein (2.5–10% w/w) and lactose or trehalose (10–17.5%) were produced following optimisation of the continuous phase by maximising and minimising viscosity and glass transition temperature (Tg’) using mixture design software. Increasing levels of β-casein from caused a significant increase in viscosity, particle size, and nanoemulsion stability, while resulting in a decrease in Tg’. Powders were made from spray drying emulsions/nanoemulsions consisting of lactose or a 70:30 mixture of lactose:sucrose (23.9%), sodium caseinate (5.1%) and sunflower oil (11.5%) in water. Nanoemulsions, produced by microfluidisation (100 MPa), had higher stability and lower viscosity than control emulsions (homogenization at 17 MPa) with lower solvent extractable free fat in the resulting powder. Partial replacement of lactose with sucrose decreased Tg and delayed Tcr. DVS and PLM showed that in powdered nanoemulsions, lactose crystallises faster than in powdered conventional emulsions. Microstructure of both powders (CLSM and cryo-SEM) showed different FGS in powders and different structure post lactose crystallisation. Powdered nanoemulsions had lower pentanal and hexanal (indicators of lipid oxidation) after 24 months storage due to their lower free fat and porosity, measured using a validated GC HS-SPME method, This research has shown the effect of altering the continuous phase of nanoemulsions on microstructure of spray dried nanoemulsions, which affects physical properties, sugar crystallisation, and lipid oxidation.

Analyse simultanée des hormones stéroïdiennes et leurs formes chimiques dans les matrices d'eau et d'urine par SPE-LC-MS/MS en ligne.

Dans les dernières années, les perturbateurs endocriniens ont été observés dans les rivières qui reçoivent des entrées importantes d’eaux usées. Parmi les perturbateurs endocriniens, les hormones stéroïdiennes naturelles et synthétiques sont des composés dont le potentiel d'imiter ou d'interférer avec les fonctions hormonales normales (développement, croissance et reproduction), est reconnu même au niveau ultra-traces (ng L-1). Bien que les hormones conjuguées soient moins actives que les hormones libres, elles peuvent être clivées et redevenir libres une fois exposées aux processus microbiens avant ou pendant le traitement des eaux usées. En raison de la nécessité d'identifier et de quantifier ces composés dans l'eau, une nouvelle méthode, entièrement automatisée, a été développée pour la détermination simultanée des deux formes de plusieurs hormones stéroïdiennes (conjuguées et libres) dans les matrices d'eau et dans l’urine des femmes. La méthode est basée sur l'extraction en phase solide couplée en ligne à la chromatographie liquide et la spectrométrie de masse en tandem (SPE-LC-MS/MS). Plusieurs paramètres ont été évalués dans le but d'optimiser l'efficacité de la méthode, tels que le type et le débit de la phase mobile, des différentes colonnes de SPE et de chromatographie, ainsi que différentes sources et modes d'ionisation des échantillons pour la MS. La méthode démontre une bonne linéarité (R2 > 0.993), ainsi qu'une précision avec un coefficient de variance inférieure à 10%. Les limites de quantification varient d’un minimum de 3 à 15 ng L-1 pour un volume d'injection entre 1 mL et 5 mL et le recouvrement des composés varie de 72 % à 117 %.

Elemental Analysis of Biological Matrices by Laser Ablation High Resolution Inductively Coupled Plasma Mass Spectrometry (LA-HR-ICP-MS) and High Resolution Inductively Coupled Plasma Mass Spectrometry (HR-ICP-MS)

The need for elemental analysis of biological matrices such as bone, teeth, and plant matter for sourcing purposes has emerged within the forensic and geochemical laboratories. Trace elemental analyses for the comparison of aterials such as glass by inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS has been shown to offer a high degree of discrimination between different manufacturing sources. Unit resolution ICP-MS instruments may suffer from some polyatomic interferences including 40Ar16O+, 40Ar16O1H+, and 40Ca16O+ that affect iron measurement at trace levels. Iron is an important element in the analysis of glass and also of interest for the analysis of several biological matrices. A comparison of the nalytical performance of two different ICP-MS systems for iron analysis in glass for determining the method detection limits (MDLs), accuracy, and precision of the measurement is presented. Acid digestion and laser ablation methods are also compared. Iron polyatomic interferences were reduced or resolved by using dynamic reaction cell and high resolution ICP-MS. MDLs as low as 0.03 ìg g-1 and 0.14 ìg g-1 for laser ablation and solution based analyses respectively were achieved. The use of helium as a carrier gas demonstrated improvement in the detection limits of both iron isotopes (56Fe and 57Fe) in medium resolution for the HR-ICP-MS and with a dynamic reaction cell (DRC) coupled to a quadrupole ICP-MS system. The development and application of robust analytical methods for the quantification of trace elements in biological matrices has lead to a better understanding of the potential utility of these measurements in forensic chemical analyses. Standard reference materials (SRMs) were used in the development of an analytical method using HR-ICP-MS and LA-HR-ICP-MS that was subsequently applied on the analysis of real samples. Bone, teeth and ashed marijuana samples were analyzed with the developed method. Elemental analysis of bone samples from 12 different individuals provided discrimination between individuals, when femur and humerus bones were considered separately. Discrimination of 14 teeth samples based on elemental composition was achieved with the exception of one case where samples from the same individual were not associated with each other. The discrimination of 49 different ashed plant (cannabis)samples was achieved using the developed method.

Extracellular matrix sub-types and mechanical stretch impact human cardiac fibroblast responses to transforming growth factor beta

Understanding the impact of extracellular matrix sub-types and mechanical stretch on cardiac fibroblast activity is required to help unravel the pathophysiology of myocardial fibrotic diseases. Therefore, the purpose of this study was to investigate pro-fibrotic responses of primary human cardiac fibroblast cells exposed to different extracellular matrix components, including collagen sub-types I, III, IV, VI and laminin. The impact of mechanical cyclical stretch and treatment with transforming growth factor beta 1 (TGFβ1) on collagen 1, collagen 3 and alpha smooth muscle actin mRNA expression on different matrices was assessed using quantitative real-time PCR. Our results revealed that all of the matrices studied not only affected the expression of pro-fibrotic genes in primary human cardiac fibroblast cells at rest but also affected their response to TGFβ1. In addition, differential cellular responses to mechanical cyclical stretch were observed depending on the type of matrix the cells were adhered to. These findings may give insight into the impact of selective pathological deposition of extracellular matrix proteins within different disease states and how these could impact the fibrotic environment.

Long-term statin therapy in patients with systolic heart failure and normal cholesterol:effects on elevated serum markers of collagen turnover, inflammation, and B-type natriuretic peptide

BACKGROUND: The role of statin therapy in heart failure (HF) is unclear. The amino-terminal propeptide of procollagen type III (PIIINP) predicts outcome in HF, and yet there are conflicting reports of statin therapy effects on PIIINP.

OBJECTIVES: This study determined whether there was an increase in serum markers of inflammation, fibrosis (including PIIINP), and B-type natriuretic peptide (BNP) in patients with systolic HF and normal total cholesterol and determined the effects of long-term treatment with atorvastatin on these markers.

METHODS: Fifty-six white patients with systolic HF and normal cholesterol levels (age 72 [13] years; 68% male; body mass index 27.0 [7.3] kg/m(2); ejection fraction 35 [13]%; 46% with history of smoking) were randomly allocated to atorvastatin treatment for 6 months, titrated to 40 mg/d (A group) or not (C group). Age- and/or sex-matched subjects without HF (N group) were also recruited. Biomarkers were measured at baseline (all groups) and 6 months (A and C groups).

RESULTS: Serum markers of collagen turnover, inflammation, and BNP were significantly elevated in HF patients compared with normal participants (all P < 0.05). There were correlations between these markers in HF patients but not in normal subjects. Atorvastatin treatment for 6 months caused a significant reduction in the following biomarkers compared with baseline: BNP, from median (interquartile range) 268 (190-441) pg/mL to 185 (144-344) pg/mL; high-sensitivity C-reactive protein (hs-CRP), from 5.26 (1.95 -9.29) mg/L to 3.70 (2.34-6.81) mg/L; and PIIINP, from 4.65 (1.86) to 4.09 (1.25) pg/mL (all P < 0.05 baseline vs 6 months). Between-group differences were significant for PIIINP only (P = 0.027). There was a positive interaction between atorvastatin effects and baseline hs-CRP and PIIINP (P < 0.01).

CONCLUSIONS: Long-term statin therapy reduced PIIINP in this small, selected HF population with elevated baseline levels. Further evaluation of statin therapy in the management of HF patients with elevated PIIINP is warranted.