Three-dimensional tomographic reconstruction of an exceptionally well preserved ichnological assemblage from the Stainmore Foundation, Carboniferous, UK

This Ph.D. thesis addresses current issues with ichnotaxonomic practice, and characterizes an exceptionally well preserved ichnological assemblage from the Carboniferous Stainmore Formation, Northumberland, United Kingdom. Samples were collected from closely localized float representative of various units throughout the succession, which was deposited in a storm-dominated marine shoreface. Three dominant ichnotaxa were selected for three-dimensional morphological analysis due to their complicated morphology and/or unclear taxonomic status: 1) Dactyloidites jordii isp. nov.; 2) Beaconites capronus, and; 3) Neoeione moniliformis comb. nov. Using serial grinding and photography, these ichnotaxa were ground and modelled in true colour. High-resolution models of three taxa produced in this study are the basis of the first complete three-dimensional consideration of the traces, and forms the basis for refined palaeobiological and ethological analysis of these taxa. Dactyloidites jordii isp. nov. is a stellate to palmate burrow composed of numerous long, narrow rays that exhibit three orders of branching arranged into tiered galleries radiating from a central shaft. It is considered to be the feeding structure produced by a vermiform organism. Beaconites capronus is a winding trace with distinctly chevron-shaped, meniscate backfill demonstrated herein to backfill the vertical shafts associated with its burrows in a comparable fashion to the horizontal portion of the burrow. This lack of a surface connection would result in the trace making organism being exposed to low-oxygen porewater. Coping with this porewater dysoxia could be approached by burrowing organisms in a number of ways: 1) revisiting the sediment-water interface; 2) creating periodic shafts; or 3) employing anaerobic metabolism. Neoeione moniliformis was originally introduced as Eione moniliformis, however, the genus Eione Tate, 1859 is a junior homonym of Eione Rafinesque, 1814. This led to the transfer of Eione moniliformis to Parataenidium. Through careful examination and three-dimensional characterization of topotypes, the transfer to Parataenidium moniliformis is demonstrated herein to be problematic, as Parataenidium refers to primarily horizontal burrows with two distinct layers and Eione moniliformis is composed of one distinct level. As such, the new ichnogenus Neoeione is created to accommodate Neoeione moniliformis.

The issue of macroeconomic closure revisited and extended

Léon Walras (1874) already had realized that his neo-classical general equilibrium model could not accommodate autonomous investment. Sen analysed the same issue in a simple, one-sector macroeconomic model of a closed economy. He showed that fixing investment in the model, built strictly on neo-classical assumptions, would make the system overdetermined, thus, one should loosen some neo-classical condition of competitive equilibrium. He analysed three not neo-classical “closure options”, which could make the model well determined in the case of fixed investment. Others later extended his list and it showed that the closure dilemma arises in the more complex computable general equilibrium (CGE) models as well, as does the choice of adjustment mechanism assumed to bring about equilibrium at the macro level. By means of numerical models, it was also illustrated that the adopted closure rule can significantly affect the results of policy simulations based on a CGE model. Despite these warnings, the issue of macro closure is often neglected in policy simulations. It is, therefore, worth revisiting the issue and demonstrating by further examples its importance, as well as pointing out that the closure problem in the CGE models extends well beyond the problem of how to incorporate autonomous investment into a CGE model. Several closure rules are discussed in this paper and their diverse outcomes are illustrated by numerical models calibrated on statistical data. First, the analyses is done in a one-sector model, similar to Sen’s, but extended into a model of an open economy. Next, the same analyses are repeated using a fully-fledged multisectoral CGE model, calibrated on the same statistical data. Comparing the results obtained by the two models it is shown that although, using the same closure option, they generate quite similar results in terms of the direction and – to a somewhat lesser extent – of the magnitude of change in the main macro variables, the predictions of the multi-sectoral CGE model are clearly more realistic and balanced.

The Metrology Enhanced Tooling for Aerospace (META) framework

Aerospace manufacturers typically use monolithic steel fixtures to control the form of assemblies. This tooling is very expensive, has long lead times and has little ability to accommodate product variation and design changes. Since the tool setting and recertification process is manual and time consuming, monolithic structures are required in order to maintain the tooling tolerances for multiple years without recertification. This paper introduces the Metrology Enhanced Tooling for Aerospace (META) Framework which interfaces multiple metrology technologies with the tooling, components, workers and automation. This will allow rapid or even real-time fixture re-certification with improved product verification leading to a reduced risk of product non-conformance and increased fixture utilization while facilitating flexible fixtures.

Protein and Drug Design Algorithms Using Improved Biophysical Modeling

This thesis focuses on the development of algorithms that will allow protein design calculations to incorporate more realistic modeling assumptions. Protein design algorithms search large sequence spaces for protein sequences that are biologically and medically useful. Better modeling could improve the chance of success in designs and expand the range of problems to which these algorithms are applied. I have developed algorithms to improve modeling of backbone flexibility (DEEPer) and of more extensive continuous flexibility in general (EPIC and LUTE). I’ve also developed algorithms to perform multistate designs, which account for effects like specificity, with provable guarantees of accuracy (COMETS), and to accommodate a wider range of energy functions in design (EPIC and LUTE).

Examining current provision, practice and experience of initial teacher training providers in Ireland preparing pre service teachers for the inclusion of students with special education needs in physical education classes.

Research from an international perspective in relation to the preparation of pre service teachers in physical education and special educational needs indicates that initial teacher training providers are inconsistent in the amount of time spent addressing the issue and the nature of curricular content (Vickerman, 2007). In Ireland, research of Meegan and MacPhail (2005) and Crawford (2011) indicates that physical education teachers do not feel adequately prepared to accommodate students with Special Educational Needs (SEN) in physical education classes. This study examined initial teacher training provision in Ireland in the training of pre service physical education teachers in SEN. The methodology used was qualitative and included questionnaires and interviews (n=4). Findings indicated that time allocation (semester long modules), working with children with disabilities in mainstream settings (school or leisure centre based), lack of collaboration with other PETE providers (n=4) and a need for continued professional development were themes in need of address. Using a combined approach where the recently designed European Inclusive Physical Education Training (Kudlácěk, Jesina, & Flanagan, 2010) model is infused through the undergraduate degree programme is proposed. Further, the accommodation of hands on experience for undergraduates in mainstream settings and the establishment of inter institutional communities of practice, with a national disability research initiative, is essential to ensure quality adapted physical activity training can be accommodated throughout Ireland.

Bayesian Learning with Dependency Structures via Latent Factors, Mixtures, and Copulas

Bayesian methods offer a flexible and convenient probabilistic learning framework to extract interpretable knowledge from complex and structured data. Such methods can characterize dependencies among multiple levels of hidden variables and share statistical strength across heterogeneous sources. In the first part of this dissertation, we develop two dependent variational inference methods for full posterior approximation in non-conjugate Bayesian models through hierarchical mixture- and copula-based variational proposals, respectively. The proposed methods move beyond the widely used factorized approximation to the posterior and provide generic applicability to a broad class of probabilistic models with minimal model-specific derivations. In the second part of this dissertation, we design probabilistic graphical models to accommodate multimodal data, describe dynamical behaviors and account for task heterogeneity. In particular, the sparse latent factor model is able to reveal common low-dimensional structures from high-dimensional data. We demonstrate the effectiveness of the proposed statistical learning methods on both synthetic and real-world data.

Occurrence and Function of Hoogsteen Base Pairs in Nucleic Acids

Nucleic acids (DNA and RNA) play essential roles in the central dogma of biology for the storage and transfer of genetic information. The unique chemical and conformational structures of nucleic acids – the double helix composed of complementary Watson-Crick base pairs, provide the structural basis to carry out their biological functions. DNA double helix can dynamically accommodate Watson-Crick and Hoogsteen base-pairing, in which the purine base is flipped by ~180° degrees to adopt syn rather than anti conformation as in Watson-Crick base pairs. There is growing evidence that Hoogsteen base pairs play important roles in DNA replication, recognition, damage or mispair accommodation and repair. Here, we constructed a database for existing Hoogsteen base pairs in DNA duplexes by a structure-based survey from the Protein Data Bank, and structural analyses based on the resulted Hoogsteen structures revealed that Hoogsteen base pairs occur in a wide variety of biological contexts and can induce DNA kinking towards the major groove. As there were documented difficulties in modeling Hoogsteen or Watson-Crick by crystallography, we collaborated with the Richardsons’ lab and identified potential Hoogsteen base pairs that were mis-modeled as Watson-Crick base pairs which suggested that Hoogsteen can be more prevalent than it was thought to be. We developed solution NMR method combined with the site-specific isotope labeling to characterize the formation of, or conformational exchange with Hoogsteen base pairs in large DNA-protein complexes under solution conditions, in the absence of the crystal packing force. We showed that there are enhanced chemical exchange, potentially between Watson-Crick and Hoogsteen, at a sharp kink site in the complex formed by DNA and the Integration Host Factor protein. In stark contrast to B-form DNA, we found that Hoogsteen base pairs are strongly disfavored in A-form RNA duplex. Chemical modifications N1-methyl adenosine and N1-methyl guanosine that block Watson-Crick base-pairing, can be absorbed as Hoogsteen base pairs in DNA, but rather potently destabilized A-form RNA and caused helix melting. The intrinsic instability of Hoogsteen base pairs in A-form RNA endows the N1-methylation as a functioning post-transcriptional modification that was known to facilitate RNA folding, translation and potentially play roles in the epitranscriptome. On the other hand, the dynamic property of DNA that can accommodate Hoogsteen base pairs could be critical to maintaining the genome stability.

Nanowires for 3d silicon interconnection – low temperature compliant nanowire-polymer film for z-axis interconnect

Semiconductor chip packaging has evolved from single chip packaging to 3D heterogeneous system integration using multichip stacking in a single module. One of the key challenges in 3D integration is the high density interconnects that need to be formed between the chips with through-silicon-vias (TSVs) and inter-chip interconnects. Anisotropic Conductive Film (ACF) technology is one of the low-temperature, fine-pitch interconnect method, which has been considered as a potential replacement for solder interconnects in line with continuous scaling of the interconnects in the IC industry. However, the conventional ACF materials are facing challenges to accommodate the reduced pad and pitch size due to the micro-size particles and the particle agglomeration issue. A new interconnect material - Nanowire Anisotropic Conductive Film (NW-ACF), composed of high density copper nanowires of ~ 200 nm diameter and 10-30 µm length that are vertically distributed in a polymeric template, is developed in this work to tackle the constrains of the conventional ACFs and serves as an inter-chip interconnect solution for potential three-dimensional (3D) applications.

Effects of tidal range on mooring systems of wave energy converters

Wave energy converters are currently proposed to be deployed near coastal area for the closeness to the infrastructure and for ease of maintenance in order to reduce operational costs. The motivation behind this work is the fact that the deployment depths during the highest and lowest tides will have a significant effect on the mooring system of WECs. In this paper, the issue will be investigated by numerical modelling (using ANSYS AQWA) for both catenary and taut moorings to examine the performance of the mooring system in varying tides. The case study being considered is the ¼- scale wave energy test site in Galway Bay off the west coast of Ireland where some marine renewable energy devices can be tested. In this test site, the tidal range is macro-tidal with a range of approximately 6 m which is a large value relative to the water depth. In the numerical analysis, ANSYS AQWA suite has been used to simulate moored devices under wave excitation at varying tidal ranges. Results show that the highest tide will give rise to larger forces. While at lower depths, slackening of the mooring occurs. Therefore, the mooring lines must be designed to accommodate both situations.

Les droits réels et personnels sur les titres détenus auprès d'un intermédiaire : analyse comparative en droit québécois interne et international privé

Les transactions sur les valeurs mobilières ainsi que leur mise en garantie se font bien au-delà des frontières nationales. Elles impliquent une multitude d’intervenants, tels que l’émetteur, un grand nombre d’intermédiaires disposés en structure pyramidale, un ou des investisseurs et, bien évidemment, les bénéficiaires desdites valeurs mobilières ou garanties. On peut aussi signaler l’existence de nombreux portefeuilles diversifiés contenant des titres émis par plusieurs émetteurs situés dans plusieurs états. Toute la difficulté d’une telle diversité d’acteurs, de composantes financières et juridiques, réside dans l’application de règles divergentes et souvent conflictuelles provenant de systèmes juridiques d’origines diverses (Common Law et civiliste). De nombreux juristes, de toutes nationalités confondues, ont pu constater ces dernières années que les règles de création, d’opposabilité et de réalisation des sûretés, ainsi que les règles de conflit de lois qui aident à déterminer la loi applicable à ces différentes questions, ne répondaient plus adéquatement aux exigences juridiques nationales dans un marché financier global, exponentiel et sans réelles frontières administratives. Afin de résoudre cette situation et accommoder le marché financier, de nombreux textes de loi ont été révisés et adaptés. Notre analyse du droit québécois est effectuée en fonction du droit américain et canadien, principales sources du législateur québécois, mais aussi du droit suisse qui est le plus proche de la tradition civiliste québécoise, le tout à la lueur de la 36e Convention de La Haye du 5 juillet 2006 sur la loi applicable à certains droits sur des titres détenus auprès d'un intermédiaire. Par exemple, les articles 8 et 9 du Uniform Commercial Code (UCC) américain ont proposé des solutions modernes et révolutionnaires qui s’éloignent considérablement des règles traditionnelles connues en matière de bien, de propriété, de sûreté et de conflits de lois. Plusieurs autres projets et instruments juridiques dédiés à ces sujets ont été adoptés, tels que : la Loi uniforme sur le transfert des valeurs mobilières (LUTVM) canadienne, qui a été intégrée au Québec par le biais de la Loi sur le transfert de valeurs mobilières et l’obtention de titres intermédiés, RLRQ, c.T-11.002 (LTVMQ) ; la 36e Convention de La Haye du 5 juillet 2006 sur la loi applicable à certains droits sur des titres détenus auprès d'un intermédiaire; la Loi fédérale sur le droit international privé (LDIP) suisse, ainsi que la Loi fédérale sur les titres intermédiés (LTI) suisse. L’analyse de ces textes de loi nous a permis de proposer une nouvelle version des règles de conflit de lois en matière de sûretés et de transfert des titres intermédiés en droit québécois. Cette étude devrait susciter une réflexion profonde du point de vue d’un juriste civiliste, sur l’efficacité des nouvelles règles québécoises de sûretés et de conflit de lois en matière de titres intermédiés, totalement inspirées des règles américaines de Common Law. Un choix qui semble totalement ignorer un pan du système juridique civiliste et sociétal.

The Response to an ESL Population Boom in the Beaufort County, South Carolina School System: A Case Study

The purpose of this case study was to examine the why the English language learners (ELLs) in the Beaufort County, South Carolina school system have been so successful. This school system has recently experienced a boom in its ESL student population, and this population has performed very well on standardized tests. This study used critical theory as its theoretical framework and examined why the students have been successful rather than marginalized in Beaufort County schools. This phenomenon was investigated using semi-structured interviews with the ESOL Coordinator for Beaufort County, 4 ESL-lead teachers, and 6 mainstream teachers. Data were collected using semi-structured interviews with Sarah Owen, the Beaufort County ESOL, Gifted and Talented, and World Languages coordinator. Based on the results of her interview, 4 themes emerged that were used for the semi-structured interviews with ESOL and mainstream teachers. The interviews centered on the themes of ESL policy, ESL leadership, and teacher training. The ESL and mainstream teacher interviews also revealed several subthemes that included teacher attitude, why Beaufort County has been successful with the ELLs, and the teachers’ recommendations for other schools systems trying to successfully accommodate a large ESL student population in mainstream classrooms. The findings from the teachers’ interviews revealed that additional training for the teachers without ESL experience helped them become comfortable instructing ELLs. This training should be conducted by the ESOL teachers for those without ESOL certification or endorsement. As the teachers had more training, they had better attitudes about teaching ESOL students in their classes. Finally, those who utilized the additional ESOL training and ESOL accommodations saw better student achievement in their classes. Based on the finding of this study, the researcher proposed a model for other school systems to follow in order to replicate the success of Beaufort County’s ELLs. The implications of this study focus on other schools systems and why ELLs are not obtaining the same level of success as those in Beaufort County’s schools. Finally, recommendations for further research are provided.

La basileía "revolucionaria" de Nabis

El rey Nabis de Esparta es caracterizado por las fuentes literarias antiguas como un tirano al haber emprendido una serie de reformas radicales que, particularmente en sus contenidos sociales, atentaban contra el orden establecido y ponían en peligro la supremacía en el Peloponeso de una conservadora liga aquea sostenida en las clases propietarias y respaldada por las imparables legiones romanas. Es el propósito del presente artículo analizar las bases de esa monarquía "revolucionaria" de Nabis, así como el alcance, los objetivos y la fortuna final de sus medidas, que supusieron un intento de acomodarse a la realidad de los estados helenísticos sin renunciar por ello a las señas de identidad y al acervo cultural espartano. La finalidad última era reconquistar parte de su pasado esplendor militar y lograr un lugar digno, si no hegemónico, en el complejo e inestable tablero geopolítico peloponésico, pero la elite aquea no cesó hasta acallar toda reivindicación socioeconómica en la sociedad lacedemonia.

(Table 2, page 10) Bulk spectroscopic, X-ray fluorescence and colorimetric analyses of samples from the San Pablo ferro-manganese pavement

The Bedford Institute of Oceanography provided ship time on the C.S.S. Hudson during the B.I.0. 1967 Metrology and IODAL Cruise for surveying two separate bottom features in the North Atlantic; the Flemish Cap and the San Pablo Seamount one of the Kelvin Seamounts (also known as the New England Seamounts) about 400 miles SSE of Halifax, Nova Scotia. Underwater photography, dredging, and drilling showed San Pablo seamount to have a very considerable covering of manganese deposit, which may be recoverable by mining. San Pablo Seamount was surveyed and sampled; good hauls were made both on the top and on the slopes, at various depths from 500-1000 fathoms; in all cases samples of an unusual stratified manganese-iron ore were recovered. In the hope of gaining additional information in the immediate sample area, one of the dredges had been previously modified to accommodate underwater photographic equipment. X-ray chemical analyses indicate that the ore contains 20 to 25 per cent MnO2, with similar amounts of Fe2O3. Since bottom photographs indicate that these deposits form a continuous cover 1 foot to 3 feet thick over most of the seamount, it is estimated that there are ore reserves in the order of 10 to 30 M tons above 1,000 fathoms.

Annotated record of the detailed examination of Mn deposits from C.S.S. Hudson Cruise 19 (1967) stations

The Bedford Institute of Oceanography provided ship time on the C.S.S. Hudson during the B.I.0. 1967 Metrology and IODAL Cruise for surveying two separate bottom features in the North Atlantic; the Flemish Cap and the San Pablo Seamount one of the Kelvin Seamounts (also known as the New England Seamounts) about 400 miles SSE of Halifax, Nova Scotia. Underwater photography, dredging, and drilling showed San Pablo seamount to have a very considerable covering of manganese deposit, which may be recoverable by mining. San Pablo Seamount was surveyed and sampled; good hauls were made both on the top and on the slopes, at various depths from 500-1000 fathoms; in all cases samples of an unusual stratified manganese-iron ore were recovered. In the hope of gaining additional information in the immediate sample area, one of the dredges had been previously modified to accommodate underwater photographic equipment. X-ray chemical analyses indicate that the ore contains 20 to 25 per cent MnO2, with similar amounts of Fe2O3. Since bottom photographs indicate that these deposits form a continuous cover 1 foot to 3 feet thick over most of the seamount, it is estimated that there are ore reserves in the order of 10 to 30 M tons above 1,000 fathoms.

An Exploration of the challenges associated with software logging in large systems

Over the past few years, logging has evolved from from simple printf statements to more complex and widely used logging libraries. Today logging information is used to support various development activities such as fixing bugs, analyzing the results of load tests, monitoring performance and transferring knowledge. Recent research has examined how to improve logging practices by informing developers what to log and where to log. Furthermore, the strong dependence on logging has led to the development of logging libraries that have reduced the intricacies of logging, which has resulted in an abundance of log information. Two recent challenges have emerged as modern software systems start to treat logging as a core aspect of their software. In particular, 1) infrastructural challenges have emerged due to the plethora of logging libraries available today and 2) processing challenges have emerged due to the large number of log processing tools that ingest logs and produce useful information from them. In this thesis, we explore these two challenges. We first explore the infrastructural challenges that arise due to the plethora of logging libraries available today. As systems evolve, their logging infrastructure has to evolve (commonly this is done by migrating to new logging libraries). We explore logging library migrations within Apache Software Foundation (ASF) projects. We i find that close to 14% of the pro jects within the ASF migrate their logging libraries at least once. For processing challenges, we explore the different factors which can affect the likelihood of a logging statement changing in the future in four open source systems namely ActiveMQ, Camel, Cloudstack and Liferay. Such changes are likely to negatively impact the log processing tools that must be updated to accommodate such changes. We find that 20%-45% of the logging statements within the four systems are changed at least once. We construct random forest classifiers and Cox models to determine the likelihood of both just-introduced and long-lived logging statements changing in the future. We find that file ownership, developer experience, log density and SLOC are important factors in determining the stability of logging statements.