An Algorithmic Approach to Inferring Cross-Ontology Links while Mapping Anatomical Ontologies

ACM Computing Classification System (1998): J.3.

Mapping and Merging of Anatomical Ontologies

This article presents the principal results of the Ph.D. thesis Intelligent systems in bioinformatics: mapping and merging anatomical ontologies by Peter Petrov, successfully defended at the St. Kliment Ohridski University of Sofia, Faculty of Mathematics and Informatics, Department of Information Technologies, on 26 April 2013.

Az európai vállalkozó karaktere (The characters of the European entrepreneur and the European manager)

Miben különböznek motivációjukat, értékeit, habitusukat tekintve a vállalkozók, illetve a menedzserek a társadalom többi tagjától és egymástól? Egy 29 európai országra kiterjedő reprezentatív lakossági kérdőíves felmérés (European Social Survey) alapján keresik a szerzők a választ e kérdésre. A Schwartz-értéktesztet használják, amelynek segítségével meghatározhatók az általános célok, elvek, amelyek követését egy személy fontosnak tartja az életében. Így felrajzolható a személy karaktere. Hozzájárulásuk az irodalomhoz kettős. Bár készültek európai szinten elemzések a vállalkozók által vallott sajátos értékekről, a Schwartz-teszt átfogóbb, árnyaltabb és megbízhatóbb elemzést tesz lehetővé. Továbbá, az említett elemzések csak az önfoglalkoztatókat vizsgálták, amely kategória magában foglalja ugyan a vállalkozókat, ám tágabb annál. Az alkalmazott menedzserekről pedig tudomásuk szerint egyáltalán nem készült hasonló elemzés. / === / What distinguishes entrepreneurs and managers from the rest of society and from each other in terms of motivation and values? The authors attempt to answer these questions by analysing data from the European Social Survey covering the populations of 29 countries. They use the Schwartz value-test to identify the general goals and principles people choose to follow in their lives. The test enables them to paint the typical personal characters of entrepreneurs and managers. Their contribution to the literature is threefold. First, although the values held by European entrepreneurs have been investigated before, the Schwartz test provides for a more comprehensive and nuanced analysis. Second, prior statistical analyses have focussed on self-employed, which is a much broader category than entrepreneurs. Third, the distinguishing values of employed managers have not been analysed so far in a similar way.

Interaction of the parasitic angiosperm {\it Cassytha filiformis\/} L. (Lauraceae) with the exotic {\it Schinus terebinthifolius\/} Raddi (Anacardiaceae) in southern Florida

Brazilian pepper (Schinus terebinthifolius) is an exotic shrub or small tree that has become well established as an invasive and highly competitive species through much of southern Florida. Love vine (Cassytha filiformis), a native parasitic plant, was noted parasitizing Brazilian pepper, apparently affecting its health. The objective of this study was to investigate the nature of this parasitic interaction in southern Florida. Brazilian pepper populations were studied to determine whether parasitism by love vine may affect growth and reproduction. Anatomical studies of love vine parasitizing Brazilian pepper determined physical aspects of the parasitic interaction at the cell and tissue level. Physiological aspects of this interaction were investigated to help describe love vine resource acquisition as a parasite on host Brazilian pepper plants, and as an autotrophic plant. An investigation of ecological aspects of this parasitic interaction was done to determine whether physical or biological aspects of habitats may contribute to love vine parasitism on Brazilian pepper. These studies indicated that: (1) parasitism by love vine significantly decreased growth and reproduction of Brazilian pepper plants; (2) anatomical and physiological investigations indicated that love vine was primarily a xylem parasite on Brazilian pepper, but that some assimilated carbon nutrients may also be acquired from the host; (3) love vine is autotrophic (i.e., hemiparasitic), but is totally dependent on its host for necessary resources; (4) the occurrence of love vine parasitism on Brazilian pepper is mediated by physical characters of the biological community. ^

Interaction of the parasitic angiosperm cassytha filiformis L. (Lauraceae) with the exotic schinus terebinthifolius RADDI (Anacardiaceae) in southern Florida

Brazilian pepper (Schinus terebinthifolius) is an exotic shrub or small tree that has become well established as an invasive and highly competitive species through much of southern Florida. Love vine (Cassytha filiformis), a native parasitic plant, was noted parasitizing Brazilian pepper, apparently affecting its health. The objective of this study was to investigate the nature of this parasitic interaction in southern Florida. Brazilian pepper populations were studied to determine whether parasitism by love vine may affect growth and reproduction. Anatomical studies of love vine parasitizing Brazilian pepper determined physical aspects of the parasitic interaction at the cell and tissue level. Physiological aspects of this interaction were investigated to help describe love vine resource acquisition as a parasite on host Brazilian pepper plants, and as an autotrophic plant. An investigation of ecological aspects of this parasitic interaction was done to determine whether physical or biological aspects of habitats may contribute to love vine parasitism on Brazilian pepper. These studies indicated that: 1) parasitism by love vine significantly decreased growth and reproduction of Brazilian pepper plants; 2) anatomical and physiological investigations indicated that love vine was primarily a xylem parasite on Brazilian pepper, but that some assimilated carbon nutrients may also be acquired from the host; 3) love vine is autotrophic (i. e., hemiparasitic), but is totally dependent on its host for necessary resources; 4) the occurrence of love vine parasitism on Brazilian pepper is mediated by physical characters of the biological community.

I want out of the labels : how Chuck Palahniuk's characters challenge the dominant discourse

The purpose of this study was to explore postmodern identity in the work of Chuck Palahniuk. The characters within Palahniuk's text Invisible Monsters realize the manner in which identity is a construct, and their response is to oppose and redefine it. In my research, I looked at how postmodern identity is defined by some of the leading critical thinkers in the field, and then I applied their thought to Palahniuk's characters. I showed how these characters come to understand the process by which society defines them, and with that realization, they oppose its totalizing definitions. The characters deconstruct the natural attitudes society has towards identity, and they reveal that it is in some way possible to create a unique identity that is not easily definable by the ruling discourse. I concluded that his attention to identity highlights Palahniuk's concern for the place, identity, and influence of his generation.

Anatomical and morphological responses of papaya, Carica papaya L., to various light conditions

Plants that develop under foliar shade encounter both low photosynthetically active radiation (PAR) and low red to far red ratios (R:FR). Both of these factors are important in determining developmental responses to shade. Papaya (Carica papaya L.) seedlings grown under filtered shade (low PAR and low R:FR) were compared with seedlings grown under neutral shade (low PAR with R:FR similar to that of full sunlight), and high light (moderate PAR with R:FR similar to that of full sunlight). The results indicated that papaya exhibits a light seeking strategy as evidenced by morphological and anatomical differences between treatments. Based on past research the results also indicate shade developmental responses in papaya to be phytochrome mediated.

The evolutionary relationships and age of Homo naledi : an assessment using dated Bayesian phylogenetic methods

Acknowledgements We wish to express our gratitude to the National Geographic Society and the National Research Foundation of South Africa for funding the discovery, recovery, and analysis of the H. naledi material. The study reported here was also made possible by grants from the Social Sciences and Humanities Research Council of Canada, the Canada Foundation for Innovation, the British Columbia Knowledge Development Fund, the Canada Research Chairs Program, Simon Fraser University, the DST/NRF Centre of Excellence in Palaeosciences (COE-Pal), as well as by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada, a Young Scientist Development Grant from the Paleontological Scientific Trust (PAST), a Baldwin Fellowship from the L.S.B. Leakey Foundation, and a Seed Grant and a Cornerstone Faculty Fellowship from the Texas A&M University College of Liberal Arts. We would like to thank the South African Heritage Resource Agency for the permits necessary to work on the Rising Star site; the Jacobs family for granting access; Wilma Lawrence, Bonita De Klerk, Merrill Van der Walt, and Justin Mukanku for their assistance during all phases of the project; Lucas Delezene for valuable discussion on the dental characters of H. naledi. We would also like to thank Peter Schmid for the preparation of the Dinaledi fossil material; Yoel Rak for explaining in detail some of the characters used in previous studies; William Kimbel for drawing our attention to the possibility that there might be a problem with Dembo et al.’s (2015) codes for the two characters related to the articular eminence; Will Stein for helpful discussion about the Bayesian analyses; Mike Lee for his comments on this manuscript; John Hawks for his support in organizing the Rising Star workshop; and the associate editor and three anonymous reviewers for their valuable comments. We are grateful to S. Potze and the Ditsong Museum, B. Billings and the School of Anatomical Sciences at the University of the Witwatersrand, and B. Zipfel and the Evolutionary Studies Institute at the University of the Witwatersrand for providing access to the specimens in their care; the University of the Witwatersrand, the Evolutionary Studies Institute, and the South African National Centre of Excellence in PalaeoSciences for hosting a number of the authors while studying the material; and the Western Canada Research Grid for providing access to the high-performance computing facilities for the Bayesian analyses. Last but definitely not least, we thank the head of the Rising Star project, Lee Berger, for his leadership and support, and for encouraging us to pursue the study reported here.

Functional educational characterisation of the utility of embalming fluids for anatomical education and research

Human cadavers have long been used to teach human anatomy and are increasingly used in other disciplines. Different embalming techniques have been reported in the literature; however there is no clear consensus on the opinion of anatomists on the utility of embalmed cadavers for the teaching of anatomy. To this end, we aimed to survey British and Irish anatomy teachers to report their opinions on different preservation methods for the teaching of anatomy. In this project eight human cadavers were embalmed using formalin, Genelyn, Thiel and Imperial College London- Soft Preserving (ICL-SP) techniques to compare different characteristics of these four techniques. The results of this thesis show that anatomy teachers consider hard-fixed cadavers not to be the most accurate teaching model in comparison to the human body, although it still serves as a useful teaching method (Chapter 2). In addition, our findings confirm that joints of cadavers embalmed using ICL-SP solution faithfully mimics joints of an unembalmed cadaver compared to the other techniques (Chapter 3). Embalming a human body prevents the deterioration in the quality of images and our findings highlight that the influence of the embalming solutions varied with the radiological modality used (Chapter 4). The method developed as part of this thesis enables anatomists and forensic scientists to quantify the decomposition rate of an embalmed human cadaver (Chapter 5). Formalin embalming solution showed the strongest antimicrobial abilities followed by Thiel, Genelyn and finally by ICL-SP (Chapter 6). The overarching viewpoint of this set of studies show that it is inaccurate to state that one embalming technique is ultimately the best. The value of each technique differs based on the requirement of the particular education or research area. Hence we highlight how different embalming techniques may be better suited to certain fields of study.

MIMU sensors for joint kinematic estimation: anatomical landmarking and frame correction

The ability to capture human motion allows researchers to evaluate an individual’s gait. Gait can be measured in different ways, from camera-based systems to Magnetic and Inertial Measurement Units (MIMU). The former uses cameras to track positional information of photo-reflective markers, while the latter uses accelerometers, gyroscopes, and magnetometers to measure segment orientation. Both systems can be used to measure joint kinematics, but the results vary because of their differences in anatomical calibrations. The objective of this thesis was to study potential solutions for reducing joint angle discrepancies between MIMU and camera-based systems. The first study worked to correct the anatomical frame differences between MIMU and camera-based systems via the joint angles of both systems. This study looked at full lower body correction versus correcting a single joint. Single joint correction showed slightly better alignment of both systems, but does not take into account that body segments are generally affected by more than one joint. The second study explores the possibility of anatomical landmarking using a single camera and a pointer apparatus. Results showed anatomical landmark position could be determined using a single camera, as the anatomical landmarks found from this study and a camera-based system showed similar results. This thesis worked on providing a novel way for obtaining anatomical landmarks with a single point-and-shoot camera, as well aligning anatomical frames between MIMUs and camera-based systems using joint angles.

Students' views on the learning of kanji : A study the views and experiences of students at the Swedish universities concerning the teaching and learning of Chinese characters as used in Japanese

Kanji, the Chinese characters adopted to write the Japanese language, is often mentioned as one of the most difficult aspects of mastering said language. This is especially said about people from outside the Sinosphere i.e. PRC, Taiwan, North and South Korea, Japan and Vietnam. In the following thesis 12 students studying the Japanese language at Swedish universities were interviewed about their experiences when it comes to learning and being taught about kanji. A chapter summarizing some of the research that is relevant to this thesis is also included. Topics touched upon in this and the result chapter include the desire for more structured approach to kanji learning based on breaking down the characters into elemental components, spaced repetition (SRS), mnemonics.

Tractographie de la matière blanche orientée par a priori anatomiques et microstructurels = White matter tractography guided by anatomical and microstructural priors

Résumé : L'imagerie par résonance magnétique pondérée en diffusion est une modalité unique sensible aux mouvements microscopiques des molécules d'eau dans les tissus biologiques. Il est possible d'utiliser les caractéristiques de ce mouvement pour inférer la structure macroscopique des faisceaux de la matière blanche du cerveau. La technique, appelée tractographie, est devenue l'outil de choix pour étudier cette structure de façon non invasive. Par exemple, la tractographie est utilisée en planification neurochirurgicale et pour le suivi du développement de maladies neurodégénératives. Dans cette thèse, nous exposons certains des biais introduits lors de reconstructions par tractographie, et des méthodes sont proposées pour les réduire. D'abord, nous utilisons des connaissances anatomiques a priori pour orienter la reconstruction. Ainsi, nous montrons que l'information anatomique sur la nature des tissus permet d'estimer des faisceaux anatomiquement plausibles et de réduire les biais dans l'estimation de structures complexes de la matière blanche. Ensuite, nous utilisons des connaissances microstructurelles a priori dans la reconstruction, afin de permettre à la tractographie de suivre le mouvement des molécules d'eau non seulement le long des faisceaux, mais aussi dans des milieux microstructurels spécifiques. La tractographie peut ainsi distinguer différents faisceaux, réduire les erreurs de reconstruction et permettre l'étude de la microstructure le long de la matière blanche. Somme toute, nous montrons que l'utilisation de connaissances anatomiques et microstructurelles a priori, en tractographie, augmente l'exactitude des reconstructions de la matière blanche du cerveau.

Anatomy in the Library: Anatomical Models on Course Reserves

In Fall 2015, the Engineering and Physical Science Library (EPSL) began lending anatomical models as part of its course reserves program. EPSL received a partial skeleton and two muscle model figures from instructors of BSCI105. These models circulate for 4 hours at a time and are generally used by small, collaborative groups of students in the library. This poster will look at the challenges and rewards for adding these items to EPSL’s course reserves.

Development of a simple and fast “DNA extraction kit” for sea food identification and marine species

Seafood products fraud, the misrepresentation of them, have been discovered all around the world in different forms as false labeling, species substitution, short-weighting or over glazing in order to hide the correct identity, origin or weight of the seafood products. Due to the value of seafood products such as canned tuna, swordfish or grouper, these species are the subject of the commercial fraud is mainly there placement of valuable species with other little or no value species. A similar situation occurs with the shelled shrimp or shellfish that are reduced into pieces for the commercialization. Food fraud by species substitution is an emerging risk given the increasingly global food supply chain and the potential food safety issues. Economic food fraud is committed when food is deliberately placed on the market, for financial gain deceiving consumers (Woolfe, M. & Primrose, S. 2004). As a result of the increased demand and the globalization of the seafood supply, more fish species are encountered in the market. In this scenary, it becomes essential to unequivocally identify the species. The traditional taxonomy, based primarily on identification keys of species, has shown a number of limitations in the use of the distinctive features in many animal taxa, amplified when fish, crustacean or shellfish are commercially transformed. Many fish species show a similar texture, thus the certification of fish products is particularly important when fishes have undergone procedures which affect the overall anatomical structure, such as heading, slicing or filleting (Marko et al., 2004). The absence of morphological traits, a main characteristic usually used to identify animal species, represents a challenge and molecular identification methods are required. Among them, DNA-based methods are more frequently employed for food authentication (Lockley & Bardsley, 2000). In addition to food authentication and traceability, studies of taxonomy, population and conservation genetics as well as analysis of dietary habits and prey selection, also rely on genetic analyses including the DNA barcoding technology (Arroyave & Stiassny, 2014; Galimberti et al., 2013; Mafra, Ferreira, & Oliveira, 2008; Nicolé et al., 2012; Rasmussen & Morrissey, 2008), consisting in PCR amplification and sequencing of a COI mitochondrial gene specific region. The system proposed by P. Hebert et al. (2003) locates inside the mitochondrial COI gene (cytochrome oxidase subunit I) the bioidentification system useful in taxonomic identification of species (Lo Brutto et al., 2007). The COI region, used for genetic identification - DNA barcode - is short enough to allow, with the current technology, to decode sequence (the pairs of nucleotide bases) in a single step. Despite, this region only represents a tiny fraction of the mitochondrial DNA content in each cell, the COI region has sufficient variability to distinguish the majority of species among them (Biondo et al. 2016). This technique has been already employed to address the demand of assessing the actual identity and/or provenance of marketed products, as well as to unmask mislabelling and fraudulent substitutions, difficult to detect especially in manufactured seafood (Barbuto et al., 2010; Galimberti et al., 2013; Filonzi, Chiesa, Vaghi, & Nonnis Marzano, 2010). Nowadays,the research concerns the use of genetic markers to identify not only the species and/or varieties of fish, but also to identify molecular characters able to trace the origin and to provide an effective control tool forproducers and consumers as a supply chain in agreementwith local regulations.

Great characters of the New Testament /

"Reprinted June 1925"--T.p. verso.