Taxonomy of rare congenital metabolic bone disorders

International audience

ENEOLITHIC, YAMNAYA, CATACOMB AND BABYNO CULTURE CEMETERIES, PIDLISIVKA, BARROW 1, YAMPIL REGION, VINNITSA OBLAST: ARCHAEOMETRY, CHRONOMETRY AND TAXONOMY

The paper presents excavation results and analytical studies concerning the taxonomic classification of a funerary site identified with the communities of the early ‘barrow cultures’ settling the north-western Black Sea Coast in the 4th/3rd-2nd millennium BC. The study focuses on the ceremonial centres of the Eneolithic, Yamnaya, Catacomb and Babyno cultures.

ENEOLITHIC, BABYNO AND NOUA CULTURE CEMETERIES, KLEMBIVKA, SITE 1, YAMPIL REGION, VINNITSA OBLAST: ARCHAEOMETRY, TAXONOMY AND TOPOGENETICS

The paper presents excavation results and analytical studies concerning the taxonomic classification of a funerary site identified with the communities of the ‘barrow cultures’ settling the north-western Black Sea Coast in the first half of the 3rd and the middle of the 2nd millennia BC . The study focuses on the ceremonial centres of the Eneolithic communities of the Babyno and Noua cultures .

TAXONOMY, MORPHOLOGY, AND RNA-SEQ TRANSCRIPTOMICS OF THE CUBOZOAN ALATINA ALATA, AN EMERGING MODEL CNIDARIAN

Cnidarians are often considered simple animals, but the more than 13,000 estimated species (e.g., corals, hydroids and jellyfish) of the early diverging phylum exhibit a broad diversity of forms, functions and behaviors, some of which are demonstrably complex. In particular, cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Some cubozoan species possess complex mating behaviors or particularly potent stings, and all possess well-developed light sensation involving image-forming eyes. Like all cnidarians, cubozoans have specialized subcellular structures called nematocysts that are used in prey capture and defense. The objective of this study is to contribute to the development of the box jellyfish Alatina alata as a model cnidarian. This cubozoan species offers numerous advantages for investigating morphological and molecular traits underlying complex processes and coordinated behavior in free-living medusozoans (i.e., jellyfish), and more broadly throughout Metazoa. First, I provide an overview of Cnidaria with an emphasis on the current understanding of genes and proteins implicated in complex biological processes in a few select cnidarians. Second, to further develop resources for A. alata, I provide a formal redescription of this cubozoan and establish a neotype specimen voucher, which serve to stabilize the taxonomy of the species. Third, I generate the first functionally annotated transcriptome of adult and larval A. alata tissue and apply preliminary differential expression analyses to identify candidate genes implicated broadly in biological processes related to prey capture and defense, vision and the phototransduction pathway and sexual reproduction and gametogenesis. Fourth, to better understand venom diversity and mechanisms controlling venom synthesis in A. alata, I use bioinformatics to investigate gene candidates with dual roles in venom and digestion, and review the biology of prey capture and digestion in cubozoans. The morphological and molecular resources presented herein contribute to understanding the evolution of cubozoan characteristics and serve to facilitate further research on this emerging cubozoan model.

Empathy in the field: towards a taxonomy of empathic communication in information gathering interviews with suspected sex offenders

Research suggests that those suspected of sexual offending might be more willing to reveal information about their crimes if interviewers display empathic behaviour. However, the literature concerning investigative empathy is in its infancy, and so as yet is not well understood. This study explores empathy in a sample of real-life interviews conducted by police officers in England with suspected sex offenders. Using qualitative methodology, the presence and type of empathic verbal behaviours displayed was examined. Resulting categories were quantitatively analysed to investigate their occurrence overall, and across interviewer gender. We identified four distinct types of empathy, some of which were used significantly more often than others. Female interviewers displayed more empathic behaviour per se by a considerable margin.

Polyphasic characterisation of Burkholderia cepacia complex species isolated from children with cystic fibrosis

Cystic fibrosis (CF) patients with Burkholderia cepacia complex (Bcc) pulmonary infections have high morbidity and mortality. The aim of this study was to compare different methods for identification of Bcc species isolated from paediatric CF patients. Oropharyngeal swabs from children with CF were used to obtain isolates of Bcc samples to evaluate six different tests for strain identification. Conventional (CPT) and automatised (APT) phenotypic tests, polymerase chain reaction (PCR)-recA, restriction fragment length polymorphism-recA, recA sequencing, and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) were applied. Bacterial isolates were also tested for antimicrobial susceptibility. PCR-recA analysis showed that 36 out of the 54 isolates were Bcc. Kappa index data indicated almost perfect agreement between CPT and APT, CPT and PCR-recA, and APT and PCR-recA to identify Bcc, and MALDI-TOF and recA sequencing to identify Bcc species. The recA sequencing data and the MALDI-TOF data agreed in 97.2% of the isolates. Based on recA sequencing, the most common species identified were Burkholderia cenocepacia IIIA (33.4%), Burkholderia vietnamiensis (30.6%), B. cenocepacia IIIB (27.8%), Burkholderia multivorans (5.5%), and B. cepacia (2.7%). MALDI-TOF proved to be a useful tool for identification of Bcc species obtained from CF patients, although it was not able to identify B. cenocepacia subtypes.

The taxonomy, zoogeography and ecology of amphibians and reptiles of Hin Nam No National Protected Area (Laos) in comparison with data from Phong Nha – Ke Bang National Park (Vietnam).

In this thesis the mostly unknown herpetofauna in Hin Nam No National Protected Area Laos in the northern Truong Son Range was for the first time intensively investigated, and its diversity was compared to the bordering, and well-investigated Phong Nha - Ke Bang National Park in Vietnam. Twelve new vertebrate species were described comprising 11 geckonids (Cyrtodactylus bansocensis, C. calamei, C. hinnamnoensis, C. jaegeri, C. rufford, C. sommerladi, C. soudthichaki, Gekko boehmei, G. bonkowskii, G. sengchanthavongi, G. thakhekensis, Lycodon banksi and one colubrid snake (Lycodon banksi). Seven species were discovered for the first time in Laos including three frogs (Gracixalus quyeti, G. supercornutus, Rhacophorus maximus), two geckos (Cyrtodactylus cryptus, C. pseudoquadrivirgatus) and two snakes (Lycodon futsingensis, L. ruhstrati abditus). The main hypothesis that the Truong Son Range acted as a biogeographic barrier for the distribution of amphibians and reptiles could be confirmed at least for karst adapted gekkonids. Compared to other herpetofaunal groups the number of gekkonids in karst formations was particularly high (seven bent-toed geckos, four true geckos). By comparing the relative amounts of shared species in Hin Nam No and Phong Nha - Ke Bang, it is interesting to note that fewer reptile species (38%) than amphibian species (66%) were shared between both regions. This might indicate that the Truong Son Range acts as a stronger biogeographical barrier for reptiles than for amphibians. Two pairs of karst-adapted cryptic gecko species (i.e. species with distinct genetic differences, but a similar phenotype) occurred on both sides of the Truong Son Range. Only in one case these were sibling species (Crytodactylus sommerladi in Laos versus C. roesleri in Vietnam), but not in the other (C. hinnamnoensis in Laos versus C. phongnhakebangensis in Vietnam). On the Laotian side, nine gecko species (Cyrtodactylus bansocensis, C. calamei, C. darevskii, C. hinnamnoensis, C. khammouanensis, C. multiporus, C. sommerladi, G. boehmei, G. sengchanthavongi) currently have to be regarded as endemic to the Hin Nam No region. On the Vietnamese side, seven species including two bent-toed geckos (Cyrtodactylus phongnhakebangensis and C. roesleri), three skinks (Lygosoma boehmei, Sphenomorphus tetradactylus and Tropidophorus noggei), and two snakes (Hebius andreae and Boiga bourreti) are currently only known from Phong Nha - Ke Bang and adjacent regions. These high numbers of potential endemic species together with the cryptic species complex in Cyrtodactylus provide strong evidence that the karst formations in the northern Truong Son Range represent a hot spot of reptile diversity and of speciation in Crytodactylus in particular. Correct species identification is a fundamental requirement for conservation measures. The discovery of cryptic species complexes poses a challenge for alpha taxonomy and species conservation, because the true distribution ranges of the species are in fact much smaller than previously assumed. Species conservation in this area of Laos is facing a number of further problems. New and potentially endemic species were discovered in highly populated and disturbed areas. Conversion of the Ho Chi Minh Trail into a highway provided easy access for farmers and still continues to accelerate the destruction of remote forest areas. Southern Hin Nam No with its high diversity of endemic species was identified as the first priority area for conservation. Also Ban Soc, an area isolated from Hin Nam No, should be among the conservation priorities because this region houses a so far overlooked population of the critically endangered Siamese crocodile. Efforts to establish a legal conservation status for this habitat are in progress.

Toward a Taxonomy of Harmin Knowledge Organization Systems

A starting point for contributing to the greater good is to examine and interrogate existing knowledge organization practices that do harm, whether that harm is intentional or accidental, or an inherent and unavoidable evil. As part of the transition movement, the authors propose to inventory the manifestations and implications of the production of suffering by knowledge organization systems through constructing a taxonomy of harm. Theoretical underpinnings guide ontological commitment, as well as the recognition of the problem of harm in knowledge organization systems. The taxonomy of harm will be organized around three main questions: what hap- pens?, who participates?, and who is affected and how? The aim is to heighten awareness of the violence that classifications and naming practices carry, to unearth some of the social conditions and motivations that contribute to and are reinforced by knowledge organization systems, and to advocate for intentional and ethical knowledge organization practices to achieve a minimal level of harm.

Search engine content analysis

Search engines have forever changed the way people access and discover knowledge, allowing information about almost any subject to be quickly and easily retrieved within seconds. As increasingly more material becomes available electronically the influence of search engines on our lives will continue to grow. This presents the problem of how to find what information is contained in each search engine, what bias a search engine may have, and how to select the best search engine for a particular information need. This research introduces a new method, search engine content analysis, in order to solve the above problem. Search engine content analysis is a new development of traditional information retrieval field called collection selection, which deals with general information repositories. Current research in collection selection relies on full access to the collection or estimations of the size of the collections. Also collection descriptions are often represented as term occurrence statistics. An automatic ontology learning method is developed for the search engine content analysis, which trains an ontology with world knowledge of hundreds of different subjects in a multilevel taxonomy. This ontology is then mined to find important classification rules, and these rules are used to perform an extensive analysis of the content of the largest general purpose Internet search engines in use today. Instead of representing collections as a set of terms, which commonly occurs in collection selection, they are represented as a set of subjects, leading to a more robust representation of information and a decrease of synonymy. The ontology based method was compared with ReDDE (Relevant Document Distribution Estimation method for resource selection) using the standard R-value metric, with encouraging results. ReDDE is the current state of the art collection selection method which relies on collection size estimation. The method was also used to analyse the content of the most popular search engines in use today, including Google and Yahoo. In addition several specialist search engines such as Pubmed and the U.S. Department of Agriculture were analysed. In conclusion, this research shows that the ontology based method mitigates the need for collection size estimation.

Protocol engineering for protection against denial-of-service attacks

Denial-of-service attacks (DoS) and distributed denial-of-service attacks (DDoS) attempt to temporarily disrupt users or computer resources to cause service un- availability to legitimate users in the internetworking system. The most common type of DoS attack occurs when adversaries °ood a large amount of bogus data to interfere or disrupt the service on the server. The attack can be either a single-source attack, which originates at only one host, or a multi-source attack, in which multiple hosts coordinate to °ood a large number of packets to the server. Cryptographic mechanisms in authentication schemes are an example ap- proach to help the server to validate malicious tra±c. Since authentication in key establishment protocols requires the veri¯er to spend some resources before successfully detecting the bogus messages, adversaries might be able to exploit this °aw to mount an attack to overwhelm the server resources. The attacker is able to perform this kind of attack because many key establishment protocols incorporate strong authentication at the beginning phase before they can iden- tify the attacks. This is an example of DoS threats in most key establishment protocols because they have been implemented to support con¯dentiality and data integrity, but do not carefully consider other security objectives, such as availability. The main objective of this research is to design denial-of-service resistant mechanisms in key establishment protocols. In particular, we focus on the design of cryptographic protocols related to key establishment protocols that implement client puzzles to protect the server against resource exhaustion attacks. Another objective is to extend formal analysis techniques to include DoS- resistance. Basically, the formal analysis approach is used not only to analyse and verify the security of a cryptographic scheme carefully but also to help in the design stage of new protocols with a high level of security guarantee. In this research, we focus on an analysis technique of Meadows' cost-based framework, and we implement DoS-resistant model using Coloured Petri Nets. Meadows' cost-based framework is directly proposed to assess denial-of-service vulnerabil- ities in the cryptographic protocols using mathematical proof, while Coloured Petri Nets is used to model and verify the communication protocols using inter- active simulations. In addition, Coloured Petri Nets are able to help the protocol designer to clarify and reduce some inconsistency of the protocol speci¯cation. Therefore, the second objective of this research is to explore vulnerabilities in existing DoS-resistant protocols, as well as extend a formal analysis approach to our new framework for improving DoS-resistance and evaluating the performance of the new proposed mechanism. In summary, the speci¯c outcomes of this research include following results; 1. A taxonomy of denial-of-service resistant strategies and techniques used in key establishment protocols; 2. A critical analysis of existing DoS-resistant key exchange and key estab- lishment protocols; 3. An implementation of Meadows's cost-based framework using Coloured Petri Nets for modelling and evaluating DoS-resistant protocols; and 4. A development of new e±cient and practical DoS-resistant mechanisms to improve the resistance to denial-of-service attacks in key establishment protocols.

What do clients learn from counseling?

Thirty-five clients who received counseling participated in this exploratory study by completing a letter to a friend that described in as much detail as possible what they had learned from counseling. The participants’ written responses were analyzed using a content analysis approach. The analysis indicated that the data were best categorized in terms of three broad areas of learnings (Self, Relations with Others, and the Process of Learning and Change). The Self taxonomy was found to consist of six hierarchical levels. The Relations with Others taxonomy consisted of five hierarchical levels, while the Process of Learning and Change taxonomy consisted of five hierarchical levels. The results suggested that these three taxonomies offer a promising and exciting way to view the impact of counseling within a learning framework. If these taxonomies are found to be stable in future research and clients are easily classified using the taxonomies then this approach may have implications for counseling. It may well be that to maximise the learnings counselors could use specific strategies and techniques to enhance their clients’ learning in the three areas.

Location constraints in digital rights management

Digital rights management allows information owners to control the use and dissemination of electronic documents via a machine-readable licence. This paper describes the design and implementation of a system for creating and enforcing licences containing location constraints that can be used to restrict access to sensitive documents to a defined area. Documents can be loaded onto a portable device and used in the approved areas, but cannot be used if the device moves to another area. Our contribution includes a taxonomy for access control in the presence of requests to perform non-instantaneous controlled actions.

A study of entrepreneurship : Taiwanese digital content companies in China

China’s accession to the World Trade Organisation (WTO) has greatly enhanced global interest in investment in the Chinese media market, where demand for digital content is growing rapidly. The East Asian region is positioned as a growth area in many forms of digital content and digital service industries. China is attempting to catch up and take its place as a production centre to offset challenges from neighbouring countries. Meanwhile, Taiwan is seeking to use China both as an export market and as a production site for its digital content. This research investigates entry strategies of Taiwanese digital content firms into the Chinese market. By examining the strategies of a sample of Taiwan-based companies, this study also explores the evolution of their market strategies. However, the focus is on how distinctive business practices such as guanxi are important to Taiwanese business and to relations with Mainland China. This research examines how entrepreneurs manage the characteristics of digital content products and in turn how digital content entrepreneurs adapt to changing market circumstances. This project selected five Taiwan-based digital content companies that have business operations in China: Wang Film, Artkey, CnYES, Somode and iPartment. The study involved a field trip, undertaken between November 2006 and March 2007 to Shanghai and Taiwan to conduct interviews and to gather documentation and archival reports. Six senior managers and nine experts were interviewed. Data were analysed according to Miller’s firm-level entrepreneurship theory, foreign direct investment theory, Life Cycle Model and guanxi philosophy. Most studies of SMEs have focused on free market (capitalist) environments. In contrast, this thesis examines how Taiwanese digital content firms’ strategies apply in the Chinese market. I identified three main types of business strategy: cost-reduction, innovation and quality-enhancement; and four categories of functional strategies: product, marketing, resource acquisition and organizational restructuring. In this study, I introduce the concept of ‘entrepreneurial guanxi’, special relationships that imply mutual obligation, assurance and understanding to secure and exchange favors in entrepreneurial activities. While guanxi is a feature of many studies of business in Pan-Chinese society, it plays an important mediating role in digital content industries. In this thesis, I integrate the ‘Life Cycle Model’ with the dynamic concept of strategy. I outline the significant differences in the evolution of strategy between two types of digital content companies: off-line firms (Wang Film and Artkey) and web-based firms (CnYES, Somode and iPartment). Off-line digital content firms tended to adopt ‘resource acquisition strategies’ in their initial stages and ‘marketing strategies’ in second and subsequent stages. In contrast, web-based digital content companies mainly adopted product and marketing strategies in the early stages, and would adopt innovative approaches towards product and marketing strategies in the whole process of their business development. Some web-based digital content companies also adopted organizational restructuring strategies in the final stage. Finally, I propose the ‘Taxonomy Matrix of Entrepreneurial Strategies’ to emphasise the two dimensions of this matrix: innovation, and the firm’s resource acquisition for entrepreneurial strategy. This matrix is divided into four cells: Effective, Bounded, Conservative, and Impoverished.