Indication strength of coenological similarity patterns based on genus-level taxon lists and prevalence distribution

Several methods and indicators can be used to evaluate the coenological state of a given habitat, the ones which can be created simply, quickly, standardizably and reliably and which can be used to exactly quantify the state of a given habitat in point of numbers can be of outstanding practical importance in ecology. One possible method is the examination of the genera which can be found in a given habitat in great abundance and have little number of species and various ecological characteristics. For this purpose one of the most appropriate groups is that of ground-dwelling oribatid mites (Acari: Oribatida). In our research, joining the bioindication methodological project of the “Adaptation to Climate Change” Research Group of the Hungarian Academy of Sciences, the indication strength of genus-level taxon lists and the effects of the main pattern-generating factors creating similarity patterns were analysed with the help of data series on oribatid mites collected by us and originating from literature. Our aim was to develop a method with the help of which the difference expressed with distance functions between two oribatid mite genus lists originating from any sources can correspond to spatial and temporal scales. Our results prove that these genus lists are able to express the spatial distance of the habitats. With the help of this base of comparison changes in disturbed or transformed habitats can be expressed by means of oribatid mite communities, with spatial and temporal distances.

A földrajzi távolság, a kulturális hasonlóság és a szabadkereskedelem hatása a borkereskedelemre = Effects on the global wine trade of geographical distance, cultural and linguistic similarity, and free trade

A globalizálódó világgazdaságban a vezető bortermelő országok egyre jelentősebb borkereskedelmet bonyolítanak le egymás között. Míg Európában a fogyasztók egyre kevesebb bort vásárolnak, addig Amerikában és Ázsiában a bor iránti kereslet folyamatosan bővül: a borkereskedelem földrajzi átrendeződése zajlik. A kulturális hasonlóság és a földrajzi távolság kereskedelemre gyakorolt hatását gyakran a kereskedelemelméletek gravitációs modelljével elemzik. E tanulmány azt vizsgálja, hogy a fő borexportáló országok közötti földrajzi távolság, kulturális hasonlóság és szabadkereskedelem milyen hatással van a nemzetközi borkereskedelemre, annak költségeire. A regressziós becslés eredményei alátámasztják, hogy a borkereskedelem költségei alacsonyabbak, ha a kereskedelmi partnerek kulturálisan hasonlók, földrajzilag közel helyezkednek el egymáshoz, vagy van tengeri kikötőjük, tagjai a WTO-nak, illetve ha kötöttek egymással regionális kereskedelmi megállapodást. Ezenkívül megállapítható, hogy az angolszász, a latin-amerikai és az európai kulturális klaszterek elsősorban egymással kereskednek. A kutatás számos kulturális változó alkalmazásával és több ökonometriai modell, illetve becslési eljárás nagymintás tesztelésével gazdagítja a szakirodalmat. ____ In a globalizing world, major wine-producing countries export considerable quantities to the global wine market and turn over a notable trade, but in what happens European wine regions differ markedly from the New World. Here major wine producers suffered a remarkable fall in domestic wine consumption in recent decades, while New World wine producers increased their production potential and generated new foreign demand. The changes have been joined by geographical relocation of wine consumption and exports. The gravity equation can be derived from demand-side or supply-side theory-consistent estimation methods that suggest relationships between the size of the economies, geographical distances, cultural similarities, and size of their trade. The paper analyses the effects of cultural and geographical proximity, free trade, and linguistic similarity on bilateral trade in the main wine-producing countries, using a cross-section gravity model for 2012. The results suggest that larger countries export more wine, while transport costs rise in line with geographical distance and are higher for landlocked trading partners. Wine export costs are lower if trading partners are culturally similar, share a dominant religion, or are both WTO members with regional trade agreements. Anglo-Saxon, Germanic, Latin American and Latin European countries mainly trade wines within their groups. The paper looks to extend the number of trading partners, investigate the effect of language clusters, and confirm that the results are robust by different econometric methodologies.

A generalized multidimensional index structure for multimedia data to support content-based similarity searches in a collaborative search environment

Since multimedia data, such as images and videos, are way more expressive and informative than ordinary text-based data, people find it more attractive to communicate and express with them. Additionally, with the rising popularity of social networking tools such as Facebook and Twitter, multimedia information retrieval can no longer be considered a solitary task. Rather, people constantly collaborate with one another while searching and retrieving information. But the very cause of the popularity of multimedia data, the huge and different types of information a single data object can carry, makes their management a challenging task. Multimedia data is commonly represented as multidimensional feature vectors and carry high-level semantic information. These two characteristics make them very different from traditional alpha-numeric data. Thus, to try to manage them with frameworks and rationales designed for primitive alpha-numeric data, will be inefficient. An index structure is the backbone of any database management system. It has been seen that index structures present in existing relational database management frameworks cannot handle multimedia data effectively. Thus, in this dissertation, a generalized multidimensional index structure is proposed which accommodates the atypical multidimensional representation and the semantic information carried by different multimedia data seamlessly from within one single framework. Additionally, the dissertation investigates the evolving relationships among multimedia data in a collaborative environment and how such information can help to customize the design of the proposed index structure, when it is used to manage multimedia data in a shared environment. Extensive experiments were conducted to present the usability and better performance of the proposed framework over current state-of-art approaches.

Algorithms for efficient transaction management and consistent queries in client -server semantic object-oriented parallel databases

Large read-only or read-write transactions with a large read set and a small write set constitute an important class of transactions used in such applications as data mining, data warehousing, statistical applications, and report generators. Such transactions are best supported with optimistic concurrency, because locking of large amounts of data for extended periods of time is not an acceptable solution. The abort rate in regular optimistic concurrency algorithms increases exponentially with the size of the transaction. The algorithm proposed in this dissertation solves this problem by using a new transaction scheduling technique that allows a large transaction to commit safely with significantly greater probability that can exceed several orders of magnitude versus regular optimistic concurrency algorithms. A performance simulation study and a formal proof of serializability and external consistency of the proposed algorithm are also presented.^ This dissertation also proposes a new query optimization technique (lazy queries). Lazy Queries is an adaptive query execution scheme which optimizes itself as the query runs. Lazy queries can be used to find an intersection of sub-queries in a very efficient way, which does not require full execution of large sub-queries nor does it require any statistical knowledge about the data.^ An efficient optimistic concurrency control algorithm used in a massively parallel B-tree with variable-length keys is introduced. B-trees with variable-length keys can be effectively used in a variety of database types. In particular, we show how such a B-tree was used in our implementation of a semantic object-oriented DBMS. The concurrency control algorithm uses semantically safe optimistic virtual "locks" that achieve very fine granularity in conflict detection. This algorithm ensures serializability and external consistency by using logical clocks and backward validation of transactional queries. A formal proof of correctness of the proposed algorithm is also presented. ^

Range Queries on an encrypted outsourced database

This project is about retrieving data in range without allowing the server to read it, when the database is stored in the server. Basically, our goal is to build a database that allows the client to maintain the confidentiality of the data stored, despite all the data is stored in a different location from the client's hard disk. This means that all the information written on the hard disk can be easily read by another person who can do anything with it. Given that, we need to encrypt that data from eavesdroppers or other people. This is because they could sell it or log into accounts and use them for stealing money or identities. In order to achieve this, we need to encrypt the data stored in the hard drive, so that only the possessor of the key can easily read the information stored, while all the others are going to read only encrypted data. Obviously, according to that, all the data management must be done by the client, otherwise any malicious person can easily retrieve it and use it for any malicious intention. All the methods analysed here relies on encrypting data in transit. In the end of this project we analyse 2 theoretical and practical methods for the creation of the above databases and then we tests them with 3 datasets and with 10, 100 and 1000 queries. The scope of this work is to retrieve a trend that can be useful for future works based on this project.

Molecular protein function prediction using sequence similarity-based and similarity-free approaches

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Molecular protein function prediction using sequence similarity-based and similarity-free approaches

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

A cloud-based system for measuring radiation treatment plan similarity

PURPOSE: Radiation therapy is used to treat cancer using carefully designed plans that maximize the radiation dose delivered to the target and minimize damage to healthy tissue, with the dose administered over multiple occasions. Creating treatment plans is a laborious process and presents an obstacle to more frequent replanning, which remains an unsolved problem. However, in between new plans being created, the patient's anatomy can change due to multiple factors including reduction in tumor size and loss of weight, which results in poorer patient outcomes. Cloud computing is a newer technology that is slowly being used for medical applications with promising results. The objective of this work was to design and build a system that could analyze a database of previously created treatment plans, which are stored with their associated anatomical information in studies, to find the one with the most similar anatomy to a new patient. The analyses would be performed in parallel on the cloud to decrease the computation time of finding this plan. METHODS: The system used SlicerRT, a radiation therapy toolkit for the open-source platform 3D Slicer, for its tools to perform the similarity analysis algorithm. Amazon Web Services was used for the cloud instances on which the analyses were performed, as well as for storage of the radiation therapy studies and messaging between the instances and a master local computer. A module was built in SlicerRT to provide the user with an interface to direct the system on the cloud, as well as to perform other related tasks. RESULTS: The cloud-based system out-performed previous methods of conducting the similarity analyses in terms of time, as it analyzed 100 studies in approximately 13 minutes, and produced the same similarity values as those methods. It also scaled up to larger numbers of studies to analyze in the database with a small increase in computation time of just over 2 minutes. CONCLUSION: This system successfully analyzes a large database of radiation therapy studies and finds the one that is most similar to a new patient, which represents a potential step forward in achieving feasible adaptive radiation therapy replanning.

Similarity between the in vitro activity and toxicity of two different fungizone™ / lipofundin™ admixtures

Amphotericin B (AmB), an antifungal agent that presents a broad spectrum of activity, remains the gold standard in the antifungal therapy. However, sometimes the high level of toxicity forbids its clinical use. The aim of this work was to evaluate and compare the efficacy and toxicity in vitro of Fungizon™ (AmB-D) and two new different AmB formulations. Methods: three products were studied: Fungizon™, and two Fungizon™ /Lipofundin™ admixtures, which were diluted through two methods: in the first one, Fungizon™ was previously diluted with water for injection and then, in Lipofundin™ (AmB-DAL); the second method consisted of a primary dilution of AmB-D as a powder in the referred emulsion (AmB-DL). For the in vitro assay, two cell models were used: Red Blood Cells (RBC) from human donors and Candida tropicallis (Ct). The in vitro evaluation (K+ leakage, hemoglobin leakage and cell survival rate-CSR) was performed at four AmB concentrations (from 50 to 0.05mg.L-1). Results: The results showed that the action of AmB was not only concentration dependent, but also cellular type and vehicle kind dependent. At AmB concentrations of 50 mg.L-1, although the hemoglobin leakage for AmB-D was almost complete (99.51), for AmB-DAL and AmB-DL this value tended to zero. The p = 0.000 showed that AmB-D was significantly more hemolytic. Conclusion: The Fungizon™- Lipofundin™ admixtures seem to be the more valuable AmB carrier systems due to their best therapeutic index presented

On the effect of word frequency on distributional similarity

The dependency of word similarity in vector space models on the frequency of words has been noted in a few studies, but has received very little attention. We study the influence of word frequency in a set of 10 000 randomly selected word pairs for a number of different combinations of feature weighting schemes and similarity measures. We find that the similarity of word pairs for all methods, except for the one using singular value decomposition to reduce the dimensionality of the feature space, is determined to a large extent by the frequency of the words. In a binary classification task of pairs of synonyms and unrelated words we find that for all similarity measures the results can be improved when we correct for the frequency bias.

A Study of Privacy Preserving Queries with Bloom Filters

This thesis focuses on the private membership test (PMT) problem and presents three single server protocols to resolve this problem. In the presented solutions, a client can perform an inclusion test for some record x in a server's database, without revealing his record. Moreover after executing the protocols, the contents of server's database remain secret. In each of these solutions, a different cryptographic protocol is utilized to construct a privacy preserving variant of Bloom filter. The three suggested solutions are slightly different from each other, from privacy perspective and also from complexity point of view. Therefore, their use cases are different and it is impossible to choose one that is clearly the best between all three. We present the software developments of the three protocols by utilizing various pseudocodes. The performance of our implementation is measured based on a real case scenario. This thesis is a spin-off from the Academy of Finland research project "Cloud Security Services".

fuzzySim: Fuzzy similarity in species distributions

fuzzySim is an R package for calculating fuzzy similarity in species occurrence patterns. It includes functions for data preparation, such as converting species lists (long format) to presence-absence tables (wide format), obtaining unique abbreviations of species names, or transposing (parts of) complex data frames; and sample data sets for providing practical examples. It can convert binary presence-absence to fuzzy occurrence data, using e.g. trend surface analysis, inverse distance interpolation or prevalence-independent environmental favourability modelling, for multiple species simultaneously. It then calculates fuzzy similarity among (fuzzy) species distributions and/or among (fuzzy) regional species compositions. Currently available similarity indices are Jaccard, Sørensen, Simpson, and Baroni-Urbani & Buser.

Analysing Similarity in Exam Timetabling

In this paper we carry out an investigation of some of the major features of exam timetabling problems with a view to developing a similarity measure. This similarity measure will be used within a case-based reasoning (CBR) system to match a new problem with one from a case-based of previously solved problems. The case base will also store the heuristic for meta-heuristic techniques applied most successfully to each problem stored. The technique(s) stored with the matched case will be retrieved and applied to the new case. The CBR assumption in our system is that similar problems can be solved equally well by the same technique.

Similarity Measures for Exam Timetabling Problems

A large number of heuristic algorithms have been developed over the years which have been aimed at solving examination timetabling problems. However, many of these algorithms have been developed specifically to solve one particular problem instance or a small subset of instances related to a given real-life problem. Our aim is to develop a more general system which, when given any exam timetabling problem, will produce results which are comparative to those of a specially designed heuristic for that problem. We are investigating a Case based reasoning (CBR) technique to select from a set of algorithms which have been applied successfully to similar problem instances in the past. The assumption in CBR is that similar problems have similar solutions. For our system, the assumption is that an algorithm used to find a good solution to one problem will also produce a good result for a similar problem. The key to the success of the system will be our definition of similarity between two exam timetabling problems. The study will be carried out by running a series of tests using a simple Simulated Annealing Algorithm on a range of problems with differing levels of similarity and examining the data sets in detail. In this paper an initial investigation of the key factors which will be involved in this measure is presented with a discussion of how the definition of good impacts on this.

Analysing Similarity in Exam Timetabling

In this paper we carry out an investigation of some of the major features of exam timetabling problems with a view to developing a similarity measure. This similarity measure will be used within a case-based reasoning (CBR) system to match a new problem with one from a case-based of previously solved problems. The case base will also store the heuristic for meta-heuristic techniques applied most successfully to each problem stored. The technique(s) stored with the matched case will be retrieved and applied to the new case. The CBR assumption in our system is that similar problems can be solved equally well by the same technique.