Downhole logging of the AND-2A borehole, Victoria Land Basin, McMurdo Sound, Antarctica

Under the framework of the ANDRILL Southern McMurdo Sound (SMS) Project successful downhole experiments were conducted in the 1138.54 metre (m)-deep AND-2A borehole. Wireline logs successfully recorded were: magnetic susceptibility, spectral gamma ray, sonic velocity, borehole televiewer, neutron porosity, density, calliper, geochemistry, temperature and dipmeter. A resistivity tool and its backup both failed to operate, thus resistivity data were not collected. Due to hole conditions, logs were collected in several passes from the total depth at ~1138 metres below sea floor (mbsf) to ~230 mbsf, except for some intervals that were either inaccessible due to bridging or were shielded by the drill string. Furthermore, a Vertical Seismic Profile (VSP) was created from ~1000 mbsf up to the sea floor. The first hydraulic fracturing stress measurements in Antarctica were conducted in the interval 1000-1138 mbsf. This extensive data set will allow the SMS Science Team to reach some of the ambitious objectives of the SMS Project. Valuable contributions can be expected for the following topics: cyclicity and climate change, heat flux and fluid flow, seismic stratigraphy in the Victoria Land Basin, and structure and state of the modern crustal stress field.

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.

Fault tolerance logging-based model for deterministic systems

Fault tolerance allows a system to remain operational to some degree when some of its components fail. One of the most common fault tolerance mechanisms consists on logging the system state periodically, and recovering the system to a consistent state in the event of a failure. This paper describes a general fault tolerance logging-based mechanism, which can be layered over deterministic systems. Our proposal describes how a logging mechanism can recover the underlying system to a consistent state, even if an action or set of actions were interrupted mid-way, due to a server crash. We also propose different methods of storing the logging information, and describe how to deploy a fault tolerant master-slave cluster for information replication. We adapt our model to a previously proposed framework, which provided common relational features, like transactions with atomic, consistent, isolated and durable properties, to NoSQL database management systems.

Regeneration in felling gaps after logging in Acre state, Western Amazon.

Regeneration of tree species in felling gaps were studied during the first two years following harvesting in a tropical forest in Acre state, Brazil. Felling gaps averaged 340 m2 in size, while canopy openings averaged 17%. Seedling mortality in adjacent undisturbed forest was 4.6% yr', and 59.6% yr·1 and 100% yr' in the crown and trunk zones respectively, two years after logging. Recruitment of new seedlings inthe undisturbed forest understorey averaged 462 plants ha' yr', two years after gap creation. Inthe crown zones of the gaps, recruitment of seedlings averaged 1350 ha' yr', and in the trunk zones 1392 ha' yr'. The entire seedling community in trunk zones after logging was composed of new recruits. lhere was a tendency for seedling growth rates to increase from the natural forest (0,21cm yr-1) to the crown zone (0.40cm yr'), Before gap creation, species richness and diversity and seedling density were quite similar. After gap creation a sharp decrease could be verified in the gap.zones, however the differences between gap and undisturbed forest decreased rapidly in the second year after gap creation. lhe regeneration of commercial species was not affected by gap creation apart from the increase in growth rates.

Changes in the spatial distribution of tree species in a terra firme rain forest in Brazilian Amazonia after logging.

The objective of this paper was to determine changes in the spatial distribution of tree species in a logged compared to an unlogged forest of the Tapajos National Forest in the municipality of Belterra, State of Para, Brazil, over an eight-year period. The distribution pattern was determined for trees> 5 cm dbh and, also, for trees > 30 cm dbh. The relationship (a quadrate method) discussed by McGinnis was selected to be used in this study. Forty-seven percent of species with trees > 5 cm dbh showed clumped distribution in the studied forests. Geissospermwn sericeunz Benth & Hook., Minquartia guianensis Aubl., Poureria bilocularis (H. Winkler) Bachni, Protium guacayantan Cuatrec, Sclerolobium chrysophyllunz Poepp. et Endl. and the Sapotaceae family (9 species) occurred in clumps of small trees (5 cm 5 dbh < 30 cm) and big trees (dbh > 30 cm) in both the logged and undisturbed forest. Trees in all sizes of these species certainly have aggregation characteristics in different light condition's during the whole growth-cycle. Only Sclerolobium cizzysophylltan out of fourteen species that occurred aggregated in all forest conditions was light demanding. The shade-tolerant Lecythis lurida (Miers) Mori and Manilkara huberi (Ducke) Stand!. showed also aggregated distribution for small and big trees in the unlogged forest. An aggregated distribution is not always directly correlated to abundance, considering that most of the clumped species had less than seven trees per hectare.

The Use of Agricultural and Logging Waste as Litter Materials in Broiler Rearing

A research has been conducted to study the use of agricultural and logging waste as litter materials in broiler rearing. Experimental method was used with completely randomized design. The treatments were the use of agricultural and logging waste as litter materials (L) consisting of L1 = rice hulls, L2 = rice straw, L3 = wood draff and L4 = saw dust. Parameters observed were litter moisture, production index and income over feed and litter cost (IOFLC). The experiment used 96 chickens, which were divided, into 24 cages. Statistical analysis showed that the use of agricultural and logging waste significantly (P<0,01) affected the litter moisture, production index and IOFLC. It could be concluded that rice straw, small plane wood and saw dust could be used as litter materials in broiler rearing. (Animal Production 5(1): 42-49 (2003) Key words: Agricultural, Logging, Waste, Litter, Broiler

The Second Life of urban planning? Using neogeography tools for community engagement

The majority of the world’s citizens now live in cities. Although urban planning can thus be thought of as a field with significant ramifications on the human condition, many practitioners feel that it has reached the crossroads in thought leadership between traditional practice and a new, more participatory and open approach. Conventional ways to engage people in participatory planning exercises are limited in reach and scope. At the same time, socio-cultural trends and technology innovation offer opportunities to re-think the status quo in urban planning. Neogeography introduces tools and services that allow non-geographers to use advanced geographical information systems. Similarly, is there potential for the emergence of a neo-planning paradigm in which urban planning is carried out through active civic engagement aided by Web 2.0 and new media technologies thus redefining the role of practicing planners? This paper traces a number of evolving links between urban planning, neogeography and information and communication technology. Two significant trends – participation and visualisation – with direct implications for urban planning are discussed. Combining advanced participation and visualisation features, the popular virtual reality environment Second Life is then introduced as a test bed to explore a planning workshop and an integrated software event framework to assist narrative generation. We discuss an approach to harness and analyse narratives using virtual reality logging to make transparent how users understand and interpret proposed urban designs.

Morphologic and genomic characterisation of the koala Chlamydia pneumoniae strain

Chlamydia pneumoniae is a common human and animal pathogen associated with a wide range of upper and lower respiratory tract infections. In more recent years there has been increasing evidence to suggest a link between C. pneumoniae and chronic diseases in humans, including atherosclerosis, stroke and Alzheimer’s disease. C. pneumoniae human strains show little genetic variation, indicating that the human-derived strain originated from a common ancestor in the recent past. Despite extensive information on the genetics and morphology processes of the human strain, knowledge concerning many other hosts (including marsupials, amphibians, reptiles and equines) remains virtually unexplored. The koala (Phascolarctos cinereus) is a native Australian marsupial under threat due to habitat loss, predation and disease. Koalas are very susceptible to chlamydial infections, most commonly affecting the conjunctiva, urogenital tract and/or respiratory tract. To address this gap in the literature, the present study (i) provides a detailed description of the morphologic and genomic architecture of the C. pneumoniae koala (and human) strain, and shows that the koala strain is microscopically, developmentally and genetically distinct from the C. pneumoniae human strain, and (ii) examines the genetic relationship of geographically diverse C. pneumoniae isolates from human, marsupial, amphibian, reptilian and equine hosts, and identifies two distinct lineages that have arisen from animal-to-human cross species transmissions. Chapter One of this thesis explores the scientific problem and aims of this study, while Chapter Two provides a detailed literature review of the background in this field of work. Chapter Three, the first results chapter, describes the morphology and developmental stages of C. pneumoniae koala isolate LPCoLN, as revealed by fluorescence and transmission electron microscopy. The profile of this isolate, when cultured in HEp-2 human epithelial cells, was quite different to the human AR39 isolate. Koala LPCoLN inclusions were larger; the elementary bodies did not have the characteristic pear-shaped appearance, and the developmental cycle was completed within a shorter period of time (as confirmed by quantitative real-time PCR). These in vitro findings might reflect biological differences between koala LPCoLN and human AR39 in vivo. Chapter Four describes the complete genome sequence of the koala respiratory pathogen, C. pneumoniae LPCoLN. This is the first animal isolate of C. pneumoniae to be fully-sequenced. The genome sequence provides new insights into genomic ‘plasticity’ (organisation), evolution and biology of koala LPCoLN, relative to four complete C. pneumoniae human genomes (AR39, CWL029, J138 and TW183). Koala LPCoLN contains a plasmid that is not shared with any of the human isolates, there is evidence of gene loss in nucleotide salvage pathways, and there are 10 hot spot genomic regions of variation that were previously not identified in the C. pneumoniae human genomes. Sequence (partial-length) from a second, independent, wild koala isolate (EBB) at several gene loci confirmed that the koala LPCoLN isolate was representative of a koala C. pneumoniae strain. The combined sequence data provides evidence that the C. pneumoniae animal (koala LPCoLN) genome is ancestral to the C. pneumoniae human genomes and that human infections may have originated from zoonotic infections. Chapter Five examines key genome components of the five C. pneumoniae genomes in more detail. This analysis reveals genomic features that are shared by and/or contribute to the broad ecological adaptability and evolution of C. pneumoniae. This analysis resulted in the identification of 65 gene sequences for further analysis of intraspecific variation, and revealed some interesting differences, including fragmentation, truncation and gene decay (loss of redundant ancestral traits). This study provides valuable insights into metabolic diversity, adaptation and evolution of C. pneumoniae. Chapter Six utilises a subset of 23 target genes identified from the previous genomic comparisons and makes a significant contribution to our understanding of genetic variability among C. pneumoniae human (11) and animal (6 amphibian, 5 reptilian, 1 equine and 7 marsupial hosts) isolates. It has been shown that the animal isolates are genetically diverse, unlike the human isolates that are virtually clonal. More convincing evidence that C. pneumoniae originated in animals and recently (in the last few hundred thousand years) crossed host species to infect humans is provided in this study. It is proposed that two animal-to-human cross species events have occurred in the context of the results, one evident by the nearly clonal human genotype circulating in the world today, and the other by a more animal-like genotype apparent in Indigenous Australians. Taken together, these data indicate that the C. pneumoniae koala LPCoLN isolate has morphologic and genomic characteristics that are distinct from the human isolates. These differences may affect the survival and activity of the C. pneumoniae koala pathogen in its natural host, in vivo. This study, by utilising the genetic diversity of C. pneumoniae, identified new genetic markers for distinguishing human and animal isolates. However, not all C. pneumoniae isolates were genetically diverse; in fact, several isolates were highly conserved, if not identical in sequence (i.e. Australian marsupials) emphasising that at some stage in the evolution of this pathogen, there has been an adaptation/s to a particular host, providing some stability in the genome. The outcomes of this study by experimental and bioinformatic approaches have significantly enhanced our knowledge of the biology of this pathogen and will advance opportunities for the investigation of novel vaccine targets, antimicrobial therapy, or blocking of pathogenic pathways.

Performance analysis of unified enterprise application security framework

Unified Enterprise application security is a new emerging approach for providing protection against application level attacks. Conventional application security approach that consists of embedding security into each critical application leads towards scattered security mechanism that is not only difficult to manage but also creates security loopholes. According to the CSIIFBI computer crime survey report, almost 80% of the security breaches come from authorized users. In this paper, we have worked on the concept of unified security model, which manages all security aspect from a single security window. The basic idea is to keep business functionality separate from security components of the application. Our main focus was on the designing of frame work for unified layer which supports single point of policy control, centralize logging mechanism, granular, context aware access control, and independent from any underlying authentication technology and authorization policy.

Poster : Understanding interactions between autonomous animal control and temperament when cattle are subjected to virtual fencing applications

Virtual fencing has the potential to control grazing livestock. Understanding and refi ning the cues that can alter behaviour is an integral part of autonomous animal control. A series of tests have been completed to explore the relationship between temperament and control. Prior to exposure to virtual fencing control the animals were scored for temperament using fl ight speed and a sociability index using contact logging devices. The behavioural response of 30, Belmont Red steers were observed for behavioural changes when presented with cues prior to receiving an electrical stimulation. A control and four treatments designed to interrupt the animal’s movement down an alley were tested. The treatments consisted of sound plus electrical stimulation, vibration plus electrical stimulation, a visual cue plus electrical stimulation and electrical stimulation by itself. The treatments were randomly applied to each animal over fi ve consecutive trials. A control treatment in which no cues were applied was used to establish a basal behavioural pattern. A trial was considered completed after each animal had been retained behind the cue barrier for at least 60 sec. All cues and electrical stimulation were manually applied from a laptop located on a portable 3.5 m tower located immediately outside the alley. The electric stimulation consisted of 1.0 Kv of electricity. Electric stimulation, sound and vibration along with the Global Position System (GPS) hardware to autonomously record the animal’s path within the alley were recorded every second.