Climatic adaptation of Norway spruce (Picea abies (L.) Karsten) in Finland based on male flowering phenology.

Anthesis was studied at the canopy level in 10 Norway spruce stands from 9 localities in Finland from 1963 to 1974. Distributions of pollen catches were compared to the normal Gaussian distribution. The basis for the timing studies was the 50 per cent point of the anthesis-fitted normal distribution. Development up to this point was given in calendar days, in degree days (>5 °C) and in period units. The count of each parameter began on March 19 (included). Male flowering in Norway spruce stands was found to have more annual variation in quantity than in Scots pine stands studied earlier. Anthesis in spruce in northern Finland occurred at a later date than in the south. The heat sums needed for anthesis varied latitudinally less in spruce than in pine. The variation of pollen catches in spruce increased towards north-west as in the case of Scots pine. In the unprocessed data, calendar days were found to be the most accurate forecast of anthesis in Norway spruce both for a single year and for the majority of cases of stand averages over several years. Locally, the period unit could be a more accurate parameter for the stand average. However, on a calendar day basis, when annual deviations between expected and measured heat sums were converted to days, period units were narrowly superior to days. The geographical correlations respect to timing of flowering, calculated against distances measured along simulated post-glacial migration routes, were stronger than purely latitudinal correlations. Effects of the reinvasion of Norway spruce into Finland are thus still visible in spruce populations just as they were in Scots pine populations. The proportion of the average annual heat sum needed for spruce anthesis grew rapidly north of a latitude of ca. 63° and the heat sum needed for anthesis decreased only slighty towards the timberline. In light of flowering phenology, it seems probable that the northwesterly third of Finnish Norway spruce populations are incompletely adapted to the prevailing cold climate. A moderate warming of the climate would therefore be beneficial for Norway spruce. This accords roughly with the adaptive situation in Scots pine.

Statistical-theory of multiphoton excitation of polyatomic-molecules based on the wigner function

This paper is aimed at establishing a statistical theory of rotational and vibrational excitation of polyatomic molecules by an intense IR laser. Starting from the Wigner function of quantum statistical mechanics, we treat the rotational motion in the classical approximation; the vibrational modes are classified into active ones which are coupled directly with the laser and the background modes which are not coupled with the laser. The reduced Wigner function, i.e., the Wigner function integrated over all background coordinates should satisfy an integro-differential equation. We introduce the idea of ``viscous damping'' to handle the interaction between the active modes and the background. The damping coefficient can be calculated with the aid of the well-known Schwartz–Slawsky–Herzfeld theory. The resulting equation is solved by the method of moment equations. There is only one adjustable parameter in our scheme; it is introduced due to the lack of precise knowledge about the molecular potential. The theory developed in this paper explains satisfactorily the recent absorption experiments of SF6 irradiated by a short pulse CO2 laser, which are in sharp contradiction with the prevailing quasi-continuum theory. We also refined the density of energy levels which is responsible for the muliphoton excitation of polyatomic molecules.

Genetic Variability and Geographical Diversity of the Main Chagas' Disease Vector Panstrongylus megistus (Hemiptera: Triatominae) in Brazil Based on Ribosomal DNA Intergenic Sequences

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Inter- and intra-specific diversity of Cuban Pinguicula (Lentibulariaceae) based on morphometric analyses and its relation with geographical distribution

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Reproductive biology and species geographical distribution in the Melastomataceae: a survey based on New World taxa

Apomictic plants are less dependent on pollinator services and able to occupy more diverse habitats than sexual species. However, such assumptions are based on temperate species, and comparable evaluation for species-rich Neotropical taxa is lacking. In this context, the Melastomataceae is a predominantly Neotropical angiosperm family with many apomictic species, which is common in the Campos Rupestres, endemism-rich vegetation on rocky outcrops in central Brazil. In this study, the breeding system of some Campo Rupestre Melastomataceae was evaluated, and breeding system studies for New World species were surveyed to test the hypothesis that apomixis is associated with wide distributions, whilst sexual species have more restricted areas. The breeding systems of 20 Campo Rupestre Melastomataceae were studied using hand pollinations and pollen-tube growth analysis. In addition, breeding system information was compiled for 124 New World species of Melastomataceae with either wide (1000 km) or restricted distributions. Most (80 ) of the Campo Rupestre species studied were self-compatible. Self-incompatibility in Microlicia viminalis was associated with pollen-tube arrest in the style, as described for other Melastomataceae, but most self-incompatible species analysed showed pollen-tube growth to the ovary irrespective of pollination treatment. Apomictic species showed lower pollen viability and were less frequent among the Campo Rupestre plants. Among the New World species compiled, 43 were apomictic and 77 sexual (24 self-incompatible and 53 self-compatible). Most apomictic (86 ) and self-incompatible species (71 ) presented wide distributions, whilst restricted distributions predominate only among the self-compatible ones (53 ). Self-compatibility and dependence on biotic pollination were characteristic of Campo Rupestre and narrowly distributed New World Melastomataceae species, whilst apomictics are widely distributed. This is, to a certain extent, similar to the geographical parthenogenesis pattern of temperate apomictics.

Haplotype frequencies based on eight polymorphic sites at the 3' untranslated region of the HLA-G gene in individuals from two different geographical regions of Brazil

The Brazilian population represents an admixture of native Amerindians, Portuguese settlers and Africans who were brought as slaves during the colonization period that began in the 16th century and was followed by waves of immigrations of Europeans and Asians in the 20th century. The contribution of these different ethnic groups to the constitution of Brazilian populations from different geographic regions is variable and, in addition to environmental factors, might act by determining different allele profiles among Brazilian populations from different regions. We studied polymorphic sites at the 3' untranslated region of the HLA-G gene in individuals from a Northeastern Brazilian region and compared them to our previously published data about a Southeastern Brazilian region, located at a distance of 2589 km. Our results showed that most polymorphic sites present a similar distribution in both populations, except for the lower frequency of the +3003C allele in the Northeastern population compared to the Southeastern population. Although differences in genotypic distribution were only significant for the +3003 locus (P = 0.0201), the diversity of haplotypes was distinct for each population. These results are important for casecontrol studies on the association of human leucocyte antigen-G polymorphism with disease and also in terms of the genetic structure of two distinct Brazilian populations.

System supporting public transport based on geolocation

El propósito de este proyecto de fin de Grado es el estudio y desarrollo de una aplicación basada en Android que proporcionará soporte y atención a los servicios de transporte público existentes en Cracovia, Polonia. La principal funcionalidad del sistema será consultar la posición de un determinado autobús o tranvía y mostrar su ubicación con exactitud. Para lograr esto, necesitaremos tres fases de desarrollo. En primer lugar, deberemos implementar un sistema que obtenga las coordenadas geográficas de los vehículos de transporte público en cada instante. A continuación, tendremos que registrar todos estos datos y almacenarlos en una base de datos en un servidor web. Por último, desarrollaremos un sistema cliente que realice consultas a tiempo real sobre estos datos almacenados, obteniendo la posición para una línea determinada y mostrando su ubicación con un marcador en el mapa. Para hacer el seguimiento de los vehículos, sería necesario tener acceso a una API pública que nos proporcionase la posición registrada por los GPS que integran cada uno de ellos. Como esta API no existe actualmente para los servicios de autobús, y para los tranvías es de uso meramente privado, desarrollaremos una segunda aplicación en Android que hará las funciones del lado servidor. En ella podremos elegir mediante una simple interfaz el número de línea y un código específico que identificará a cada vehículo en particular (e.g. podemos tener 6 tranvías recorriendo la red al mismo tiempo para la línea 24). Esta aplicación obtendrá las coordenadas geográficas del teléfono móvil, lo cual incluye latitud, longitud y orientación a través del proveedor GPS. De este modo, podremos realizar una simulación de como el sistema funcionará a tiempo real utilizando la aplicación servidora desde dentro de un tranvía o autobús y, al mismo tiempo, utilizando la aplicación cliente haciendo peticiones para mostrar la información de dicho tranvía. El cliente, además, podrá consultar la ruta de cualquier línea sin necesidad de tener acceso a Internet. Almacenaremos las rutas y paradas de cada línea en la memoria del teléfono móvil utilizando ficheros XML debido al poco espacio que ocupan y a lo útil que resulta poder consultar un trayecto en cualquier momento, independientemente del acceso a la red. El usuario también podrá consultar las tablas de horarios oficiales para cada línea. Aunque en este caso si será necesaria una conexión a Internet debido a que se realizará a través de la web oficial de MPK. Para almacenar todas las coordenadas de cada vehículo en cada instante necesitaremos crear una base de datos en un servidor. Esto se resolverá mediante el uso de MYSQL y PHP. Se enviarán peticiones de tipo GET y POST a los servicios PHP que se encargarán de traducir y realizar la consulta correspondiente a la base de datos MYSQL. Por último, gracias a todos los datos recogidos relativos a la posición de los vehículos de transporte público, podremos realizar algunas tareas de análisis. Comparando la hora exacta a la que los vehículos pasaron por cada parada y la hora a la que deberían haber pasado según los horarios oficiales, podremos descubrir fallos en estos. Seremos capaces de determinar si es un error puntual debido a factores externos (atascos, averías,…) o si por el contrario, es algo que ocurre muy a menudo y se debería corregir el horario oficial. ABSTRACT The aim of this final Project (for University) is to develop an Android application thatwill provide support and feedback to the public transport services in Krakow. The main functionality of the system will be to track the position of a desired bus or tram line, and display its position on the map. To achieve this, we will need 3 stages: the first one will be to implement a system that sends the geographical position of the public transport vehicles, the second one will be to collect this data in a web server, and the last one will be to get the last location registered for the desired line and display it on the map. For tracking the vehicles, we would need to have access to a public API that should be connected with each bus/tram GPS. As this doesn’t exist in Krakow or at least is not available for public use, we will develop a second android application that will do the server side job. We will be able to choose in a simple interface the line number and a code letter to identify each vehicle (e.g. we can have 6 trams that belong to the line number 24 working at the same time). It will take the current mobile geolocation; this includes getting latitude, longitude and bearing from the GPS provider. Thus, we will be able to make a simulation of how the system works in real time by using the server app inside a tram and at the same time, using the client app and making requests to display the information of that tram. The client will also be able to check the path of the desired line without internet access. We will store the path and stops for each line locally in the phone memory using xml files due to the few requirements of available space it needs and the usefulness of checking a path when needed. This app will also offer the functionality of checking the timetable for the line, but in this case, it will link to the official Mpk website, so Internet access will be required. For storing all the coordinates for each vehicle at every moment we will need to create a database on a server. We have decided that the easiest way is to use Mysql and PHP for the deployment of the service. We will send GET and POST requests to the php files and those files will make the according queries to our database. Finally, based on all the collected data, we will be able to get some information about errors in the system of public transport timetables. We will check at what time a line was in each specific stop and compare it with the official timetable to find mistakes of time. We will determine if it is something that happens occasionally and related to external factors (e.g. traffic jams, breakdowns…) or if on the other hand, it is something that happens very often and the public transport timetables should be looked over and corrected.

Numerical evaluation of pollutant dispersion at a toll plaza based on system dynamics and Computational Fluid Dynamics models

The health of tollbooth workers is seriously threatened by long-term exposure to polluted air from vehicle exhausts. Using traffic data collected at a toll plaza, vehicle movements were simulated by a system dynamics model with different traffic volumes and toll collection procedures. This allowed the average travel time of vehicles to be calculated. A three-dimension Computational Fluid Dynamics (CFD) model was used with a k–ε turbulence model to simulate pollutant dispersion at the toll plaza for different traffic volumes and toll collection procedures. It was shown that pollutant concentration around tollbooths increases as traffic volume increases. Whether traffic volume is low or high (1500 vehicles/h or 2500 vehicles/h), pollutant concentration decreases if electronic toll collection (ETC) is adopted. In addition, pollutant concentration around tollbooths decreases as the proportion of ETC-equipped vehicles increases. However, if the proportion of ETC-equipped vehicles is very low and the traffic volume is not heavy, then pollutant concentration increases as the number of ETC lanes increases.

Development and validation of novel methods for microbial source tracking based on Escherichia coli as an indicator of water quality

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

Tooth fracture risk analysis based on a new finite element dental structure models using micro-CT data

The finite element (FE) analysis is an effective method to study the strength and predict the fracture risk of endodontically-treated teeth. This paper presents a rapid method developed to generate a comprehensive tooth FE model using data retrieved from micro-computed tomography (μCT). With this method, the inhomogeneity of material properties of teeth was included into the model without dividing the tooth model into different regions. The material properties of the tooth were assumed to be related to the mineral density. The fracture risk at different tooth portions was assessed for root canal treatments. The micro-CT images of a tooth were processed by a Matlab software programme and the CT numbers were retrieved. The tooth contours were obtained with thresholding segmentation using Amira. The inner and outer surfaces of the tooth were imported into Solidworks and a three-dimensional (3D) tooth model was constructed. An assembly of the tooth model with the periodontal ligament (PDL) layer and surrounding bone was imported into ABAQUS. The material properties of the tooth were calculated from the retrieved CT numbers via ABAQUS user's subroutines. Three root canal geometries (original and two enlargements) were investigated. The proposed method in this study can generate detailed 3D finite element models of a tooth with different root canal enlargements and filling materials, and would be very useful for the assessment of the fracture risk at different tooth portions after root canal treatments.

Preliminary validation of a novel high-resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes

The major limitation of current typing methods for Streptococcus pyogenes, such as emm sequence typing and T typing, is that these are based on regions subject to considerable selective pressure. Multilocus sequence typing (MLST) is a better indicator of the genetic backbone of a strain but is not widely used due to high costs. The objective of this study was to develop a robust and cost-effective alternative to S. pyogenes MLST. A 10-member single nucleotide polymorphism (SNP) set that provides a Simpson’s Index of Diversity (D) of 0.99 with respect to the S. pyogenes MLST database was derived. A typing format involving high-resolution melting (HRM) analysis of small fragments nucleated by each of the resolution-optimized SNPs was developed. The fragments were 59–119 bp in size and, based on differences in G+C content, were predicted to generate three to six resolvable HRM curves. The combination of curves across each of the 10 fragments can be used to generate a melt type (MelT) for each sequence type (ST). The 525 STs currently in the S. pyogenes MLST database are predicted to resolve into 298 distinct MelTs and the method is calculated to provide a D of 0.996 against the MLST database. The MelTs are concordant with the S. pyogenes population structure. To validate the method we examined clinical isolates of S. pyogenes of 70 STs. Curves were generated as predicted by G+C content discriminating the 70 STs into 65 distinct MelTs.

Investigation into the noise map based on traffic flow prediction in the citywide road network

As one of the measures for decreasing road traffic noise in a city, the control of the traffic flow and the physical distribution is considered. To conduct the measure effectively, the model for predicting the traffic flow in the citywide road network is necessary. In this study, the existing model named AVENUE was used as a traffic flow prediction model. The traffic flow model was integrated with the road vehicles' sound power model and the sound propagation model, and the new road traffic noise prediction model was established. As a case study, the prediction model was applied to the road network of Tsukuba city in Japan and the noise map of the city was made. To examine the calculation accuracy of the noise map, the calculated values of the noise at the main roads were compared with the measured values. As a result, it was found that there was a possibility that the high accuracy noise map of the city could be made by using the noise prediction model developed in this study.