MATHEMATICAL STUDIES ON THE EVOLUTIONARY CHANGE OF DNA SEQUENCES

With the aim of understanding the mechanism of molecular evolution, mathematical problems on the evolutionary change of DNA sequences are studied. The problems studied and the results obtained are as follows: (1) Estimation of evolutionary distance between nucleotide sequences. Studying the pattern of nucleotide substitution for the case of unequal substitution rates, a new mathematical formula for estimating the average number of nucleotide substitutions per site between two homologous DNA sequences is developed. It is shown that this formula has a wider applicability than currently available formulae. A statistical method for estimating the number of nucleotide changes due to deletion and insertion is also developed. (2) Biases of the estimates of nucleotide substitutions obtained by the restriction enzyme method. The deviation of the estimate of nucleotide substitutions obtained by the restriction enzyme method from the true value is investigated theoretically. It is shown that the amount of the deviation depends on the nucleotides in the recognition sequence of the restriction enzyme used, unequal rates of substitution among different nucleotides, and nucleotide frequences, but the primary factor is the unequal rates of nucleotide substitution. When many different kinds of enzymes are used, however, the amount of average deviation is generally small. (3) Distribution of restriction fragment lengths. To see the effect of undetectable restriction fragments and fragment differences on the estimate of nucleotide differences, the theoretical distribution of fragment lengths is studied. This distribution depends on the type of restriction enzymes used as well as on the relative frequencies of four nucleotides. It is shown that undetectability of small fragments or fragment differences gives a serious underestimate of nucleotide substitutions when the length-difference method of estimation is used, but the extent of underestimation is small when the site-difference method is used. (4) Evolutionary relationships of DNA sequences in finite populations. A mathematical theory on the expected evolutionary relationships among DNA sequences (nucleons) randomly chosen from the same or different populations is developed under the assumption that the evolutionary change of nucleons is determined solely by mutation and random genetic drift. . . . (Author's abstract exceeds stipulated maximum length. Discontinued here with permission of author). UMI ^

Wet tundra polygon centers and distance between polygon centroids on Samoylov Island, Lena Delta, Siberia, Russia, with links to shape files

Subgrid processes occur in various ecosystems and landscapes but, because of their small scale, they are not represented or poorly parameterized in climate models. These local heterogeneities are often important or even fundamental for energy and carbon balances. This is especially true for northern peatlands and in particular for the polygonal tundra, where methane emissions are strongly influenced by spatial soil heterogeneities. We present a stochastic model for the surface topography of polygonal tundra using Poisson-Voronoi diagrams and we compare the results with available recent field studies. We analyze seasonal dynamics of water table variations and the landscape response under different scenarios of precipitation income. We upscale methane fluxes by using a simple idealized model for methane emission. Hydraulic interconnectivities and large-scale drainage may also be investigated through percolation properties and thresholds in the Voronoi graph. The model captures the main statistical characteristics of the landscape topography, such as polygon area and surface properties as well as the water balance. This approach enables us to statistically relate large-scale properties of the system to the main small-scale processes within the single polygons.

Microsensor studies on Padina from a natural CO2 seep: implications of morphology on acclimation to low pH

Low seawater pH can be harmful to many calcifying marine organisms, but the calcifying macroalgae Padina spp. flourish at natural submarine carbon dioxide seeps where seawater pH is low. We show that the microenvironment created by the rolled thallus margin of Padina australis facilitates supersaturation of CaCO3 and calcifi-cation via photosynthesis-induced elevated pH. Using microsensors to investigate oxygen and pH dynamics in the microenvironment of P. australis at a shallow CO2 seep, we found that, under saturating light, the pH inside the microenvironment (pHME) was higher than the external seawater (pHSW) at all pHSW levels investigated, and the difference (i.e., pHME-pHSW) increased with decreasing pHSW (0.9 units at pHSW 7.0). Gross photosynthesis (Pg) inside the microenvironment increased with decreasing pHSW, but algae from the control site reached a threshold at pH 6.5. Seep algae showed no pH threshold with respect to Pg within the pHSW range investigated. The external carbonic anhydrase (CA) inhibitor, acetazolamide, strongly inhibited Pg of P. australis at pHSW 8.2, but the effect was diminished under low pHSW (6.4-7.5), suggesting a greater dependence on membrane-bound CA for the dehydration of HCO3- ions during dissolved inorganic carbon uptake at the higher pHSW. In comparison, a calcifying green alga, Halimeda cuneata f. digitata, was not inhibited by AZ, suggesting efficient bicarbonate transport. The ability of P. australis to elevate pHME at the site of calcification and its strong dependence on CA may explain why it can thrive at low pHSW.

The Role of Distance in Determining International Transport Costs: Evidence from Philippine Import Data

This paper presents an empirical investigation of the appropriateness of distance as a determinant of international transport costs by using Philippine import data. This study addresses three specific questions. First, does distance really matter in the determination of transport costs? Second, if distance is a significant factor, what is the magnitude of its impact? Third, does the impact of distance on transport costs vary by commodity? Results indicate that while distance is important in determining transport costs, using distance alone as the proxy of international transport costs is insufficient, and such use underestimates the impact of distance on international transport costs. Results also indicate that the impact of distance varies across commodity groups, but it is difficult to precisely determine the direction and the magnitude of this impact.

Sight distance for traffic safety analysis using GIS

Sight distance is of major importance for road safety either when designing new roads or analysing the alignment of existing roads. It is essential that available sight distance in roads is long enough for emergency stops or overtaking manoeuvres. Also, it is vital for engineers/researchers that the tools used for that analysis are both powerful and intuitive. Based on ArcGIS, the application to be presented not only performs an exhaustive sight distance calculation, but allows an accurate analysis of 3D alignment, using all new tools, from a Digital Elevation Model and vehicle trajectory. The software has been successfully utilised to analyse several two-lane rural roads in Spain. In addition, the software produces thematic maps representing sight distance in which supplementary information about crashes, traffic flow, speed or design consistency could be included, allowing traffic safety studies.

Strategies for Minimum Distance in Simulated Evacuation of Transport Airplanes

The present paper describes the preliminary stages of the development of a new, comprehensive model conceived to simulate the evacuation of transport airplanes in certification studies. Two previous steps were devoted to implementing an efficient procedure to define the whole geometry of the cabin, and setting up an algorithm for assigning seats to available exits. Now, to clarify the role of the cabin arrangement in the evacuation process, the paper addresses the influence of several restrictions on the seat-to-exit assignment algorithm, maintaining a purely geometrical approach for consistency. Four situations are considered: first, an assignment method without limitations to search the minimum for the total distance run by all passengers along their escaping paths; second, a protocol that restricts the number of evacuees through each exit according to updated FAR 25 capacity; third, a procedure which tends to the best proportional sharing among exits but obliges to each passenger to egress through the nearest fore or rear exits; and fourth, a scenario which includes both restrictions. The four assignment strategies are applied to turboprops, and narrow body and wide body jets. Seat to exit distance and number of evacuees per exit are the main output variables. The results show the influence of airplane size and the impact of non-symmetries and inappropriate matching between size and longitudinal location of exits.

Spatial analysis of geometric design consistency and road sight distance

Because of the high number of crashes occurring on highways, it is necessary to intensify the search for new tools that help in understanding their causes. This research explores the use of a geographic information system (GIS) for an integrated analysis, taking into account two accident-related factors: design consistency (DC) (based on vehicle speed) and available sight distance (ASD) (based on visibility). Both factors require specific GIS software add-ins, which are explained. Digital terrain models (DTMs), vehicle paths, road centerlines, a speed prediction model, and crash data are integrated in the GIS. The usefulness of this approach has been assessed through a study of more than 500 crashes. From a regularly spaced grid, the terrain (bare ground) has been modeled through a triangulated irregular network (TIN). The length of the roads analyzed is greater than 100 km. Results have shown that DC and ASD could be related to crashes in approximately 4% of cases. In order to illustrate the potential of GIS, two crashes are fully analyzed: a car rollover after running off road on the right side and a rear-end collision of two moving vehicles. Although this procedure uses two software add-ins that are available only for ArcGIS, the study gives a practical demonstration of the suitability of GIS for conducting integrated studies of road safety.

Phylogenetic analysis of “Volvocacae” for comparative genetic studies

Sequence analysis based on multiple isolates representing essentially all genera and species of the classic family Volvocaeae has clarified their phylogenetic relationships. Cloned internal transcribed spacer sequences (ITS-1 and ITS-2, flanking the 5.8S gene of the nuclear ribosomal gene cistrons) were aligned, guided by ITS transcript secondary structural features, and subjected to parsimony and neighbor joining distance analysis. Results confirm the notion of a single common ancestor, and Chlamydomonas reinharditii alone among all sequenced green unicells is most similar. Interbreeding isolates were nearest neighbors on the evolutionary tree in all cases. Some taxa, at whatever level, prove to be clades by sequence comparisons, but others provide striking exceptions. The morphological species Pandorina morum, known to be widespread and diverse in mating pairs, was found to encompass all of the isolates of the four species of Volvulina. Platydorina appears to have originated early and not to fall within the genus Eudorina, with which it can sometimes be confused by morphology. The four species of Pleodorina appear variously associated with Eudorina examples. Although the species of Volvox are each clades, the genus Volvox is not. The conclusions confirm and extend prior, more limited, studies on nuclear SSU and LSU rDNA genes and plastid-encoded rbcL and atpB. The phylogenetic tree suggests which classical taxonomic characters are most misleading and provides a framework for molecular studies of the cell cycle-related and other alterations that have engendered diversity in both vegetative and sexual colony patterns in this classical family.

Studies on locus content mapping.

Locus content maps are derived from monosomic or disomic chromosomes broken by radiation, shearing, or other clastogen, the fragments being distributed among clones by dilution or incorporation into the cells of another species and scored for segregation of markers. Locus content maps provide evidence about radiosensitivity of chromosome regions, support for order, and approximate location. Omission of the most aberrant and least informative clones increases efficiency of localization. Correct analysis must allow for preferential retention of certain sequences, monosomy or polysomy of donor chromosomes, and error filtration. Combination of these refinements extracts substantially more information from fewer clones. Because of unmodeled peculiarities in the data, the best analysis does not recover the physical map but roughly localizes markers that may be monomorphic and therefore unsuitable for linkage mapping. As with linkage for polymorphic loci, distance in the composite map should be confirmed by physical methods.

Computer Networks Virtualization with GNS3: Evaluating a solution to optimize resources and achieve a distance learning

Designing educational resources allow students to modify their learning process. In particular, on-line and downloadable educational resources have been successfully used in engineering education the last years [1]. Usually, these resources are free and accessible from web. In addition, they are designed and developed by lecturers and used by their students. But, they are rarely developed by students in order to be used by other students. In this work-in-progress, lecturers and students are working together to implement educational resources, which can be used by students to improve the learning process of computer networks subject in engineering studies. In particular, network topologies to model LAN (Local Area Network) and MAN (Metropolitan Area Network) are virtualized in order to simulate the behavior of the links and nodes when they are interconnected with different physical and logical design.

Validation of a Spanish version of the Distance Education Learning Environments Survey (DELES) in Spain

The aim of this study was to examine the validity of the Spanish version of the Distance Education Learning Environments Survey (Sp-DELES). This instrument assesses students’ perceptions of virtual learning environments using six scales: Instructor Support, Student Interaction and Collaboration, Personal Relevance, Authentic Learning, Active Learning, and Autonomy. Further, the Sp-DELES includes an additional scale that assesses students’ Satisfaction with their classes. The original DELES has been used in at least 27 independent studies with strong reliability and validity. For this study, we sampled 265 students from the University of Alicante enrolled in various hybrid and distance education courses taught by the Department of Health Psychology. We analysed the Sp-DELES for validity using principal component factor analysis with varimax rotation, and for reliability using Cronbach’s alpha. The Sp-DELES exhibited good reliability (Cronbach’s alpha for the scales ranging from 0.86 to 0.97) and the original six-factor structure was replicated and accounted for 72.9 % of the total variance. Overall the results are consistent with those of the original English-language version of the instrument. The Sp-DELES has proven to be a reliable and valid instrument for assessing psychosocial learning environments in tertiary-level hybrid and distance-education settings.

LMX à distance : analyse qualitative et développement d’une échelle de mesure

Notre recherche a pour objectif général de proposer l’adaptation du concept de la relation d’échange superviseur-subordonné (leader-member exchange ou LMX) à la nouvelle réalité du travail à distance. Il s’agit d’étudier la relation d’échange qui se développe entre le superviseur et le subordonné travaillant à distance. Plus précisément, nous visons à définir et à développer une échelle de mesure valide et fiable du concept du LMX à distance. Jusqu’à présent, aucune définition de cette relation d’échange superviseur-subordonné n'a été proposée et aucune échelle de mesure n'a été développée. Dans l’étude que nous proposons, la notion de la distance n’est pas considérée comme un élément contextuel, mais plutôt un élément indissociable du concept lui-même, contrairement à certaines études qui ont examiné la distance comme modérateur de la relation entre le LMX et ses résultantes (Bligh et Riggio, 2012; Brunelle, 2013). À cet effet, cette étude constitue la première sur le sujet. Étant donné l'importance du LMX à distance pour les travailleurs à distance et dont le nombre atteindrait plus de 50 % d’ici 2020 (ITIF, CAS et CoreNet Global), il est primordial de comprendre et d'analyser la relation d’échange superviseur-subordonné à distance afin de mieux comprendre sa nature et son processus de développement, ce qui permettra aux parties de la dyade superviseur-subordonné de mieux s’adapter à cette nouvelle réalité de travail et de développer des relations d’échanges de qualité. Cette recherche aidera les superviseurs travaillant à distance à mieux gérer leur potentiel humain. Pour cerner ce sujet de recherche, nous avons fait une revue approfondie de la littérature traitant du LMX traditionnel et de la notion de distance, et ce, afin de pouvoir proposer une définition du concept du LMX à distance. En outre, nous avons fait appel aux recommandations de la littérature portant sur la psychométrie et nous avons réalisé une étude exploratoire de nature qualitative pour développer son échelle de mesure. Nous avons donc effectué des entrevues individuelles semi-dirigées auprès de trente professeurs d’une université canadienne. Ces entrevues ont été analysées avec le logiciel qualitatif spécialisé Nvivo et ont permis de présenter une première échelle de mesure du LMX à distance composée de sept dimensions et de 27 indicateurs. En somme, nous avons tenu à acquérir une meilleure compréhension de ce phénomène qui est très répandu dans les organisations modernes et à offrir une plateforme théorique et pratique que les chercheurs pourront utiliser pour enrichir leurs connaissances sur le concept du LMX à distance. Enfin, notre étude permettra aux superviseurs et aux subordonnés de comprendre l'importance de développer et de maintenir des relations de qualité conduisant à des résultats organisationnels et personnels positifs.