Cross-taxon surrogacy of biodiversity in the Indian Garhwal Himalaya

Biodiversity surveys were conducted in 13, 10x50 m(2) plots located between 1400 to 3100 in abode mean sea level in a range of habitats in temperate mixed Oak and Coniferous forests through sub-alpine to the alpine grasslands in Chamoli district of Uttaranchal state in the Indian Garhwal Himalaya. Cross-taxon congruence in biodiversity (alpha-diversity and beta-diversity) across macrolichens, mosses, liverworts, woody plants (shrubs and trees) and ants was investigated, so as to examine the extent to which these group, of organisms can function as Surrogates for each other. Although woody plants provided a major substrate for macrolichens and mosses, there was no species-specific association between them. Woody plant species richness was highly positively correlated with mosses (r(2) = 0.63, P < 0.001) but the relationship, as not particularly very strong with lichens and liverworts. While there was a significant correlation in the species turnover (β-diversity) of macrolichens with mosses (r(2) = 0.21 P < 0.005). the relationship was relatively poor with the woody plants. On the other hand. negative correlations emerged in the species richness of ants with those of macrolichens, mosses and woody plants (r(2) = -0.44 P < 0.05). but most of the complementarity (turnover) relationships among them were positive, Since diversity between taxonomic hierarchies within the group was consistently significantly positively correlated in all these taxa, the higher taxonomic categories Such as genus and family may be employed as surrogates for rapid assessment and monitoring of species diversity, Although no single group other than macrolichens has emerged as a good indicator of changes in species richness in all other groups, some concordant relationships between them conform to the hypothesis that species assemblages of certain taxonomic groups could still be used as surrogates for efficient monitoring of species diversity in other groups whose distribution may further predict the importance of conserving overall biodiversity in landscapes such as the Garhwal Himalaya. (C) 2002 Elsevier Science Ltd. All rights reserved.

Design and analysis of novel compression fracture specimen with constant form factor: Edge cracked semicircular disk (ECSD)

Inspired by the Brazilian disk geometry we examine the utility of an edge cracked semicircular disk (ECSD) specimen for rapid assessment of fracture toughness of brittle materials using compressive loading. It is desirable to optimize the geometry towards a constant form factor F for evaluating K-I. In this investigation photoelastic and finite element results for K-I evaluation highlight the effect of loading modeled using a Hertzian. A Hertzian loading subtending 4 degrees at the center leads to a surprisingly constant form factor of 1.36. This special case is further analyzed by applying uniform pressure over a chord for facilitating testing.

Synthesis and application of weight function for edge cracked semicircular disk (ECSD)

We analyze the utility of edge cracked semicircular disk (ECSD) for rapid assessment of fracture toughness using compressive loading. Continuing our earlier work on ECSD, a theoretical examination here leads to a novel way for synthesizing weight functions using two distinct form factors. The efficacy of ECSD mode-I weight function synthesized using displacement and form factor methods is demonstrated by comparing with finite element results. Theory of elasticity in conjunction with finite element method is utilized to analyze crack opening potency of ECSD under eccentric compression to explore newer configurations of ECSD for fracture testing.

PICES Press, Vol. 17, No. 1, January 2009

Major Outcomes from the 2008 PICES Annual Meeting: A Note from the Chairman (pdf, 0.1 Mb) PICES Science – 2008 (pdf, 0.1 Mb) 2008 PICES Awards (pdf, 0.3 Mb) Charles B. Miller – A Selective Biography (pdf, 0.4 Mb) Latest and Upcoming PICES Publications (pdf, 0.1 Mb) 2008 OECOS Workshop in Dalian (pdf, 0.2 Mb) PICES Calendar (pdf, 0.1 Mb) 2008 PICES Workshop on “Climate Scenarios for Ecosystem Modeling (II)” (pdf, 0.1 Mb) PICES/ESSAS Workshop on “Marine Ecosystem Model Inter-Comparisons” (pdf, 0.2 Mb) Highlights of the PICES Seventeenth Annual Meeting (pdf, 0.5 Mb) 2008 PICES Summer School on “Ecosystem-Based Management” (pdf, 0.3 Mb) 4th PICES Workshop on “The Okhotsk Sea and Adjacent Areas” (pdf, 0.2 Mb) PICES WG 21 Rapid Assessment Surveys (pdf, 0.4 Mb) PICES Interns (pdf, 0.3 Mb) PICES @ Oceans in a High CO2 World (pdf, 0.1 Mb) Coping with Global Change in Marine Social–Ecological Systems: An International Symposium (pdf, 0.1 Mb) The State of the Western North Pacific in the First Half of 2008 (pdf, 1.3 Mb) State of the Northeast Pacific through 2008 (pdf, 0.3 Mb) The Bering Sea: Current Status and Recent Events (pdf, 0.2 Mb) An Opinion Born of Years of Observing Timeseries Observations (pdf, 0.1 Mb) New Chairman for the PICES Fishery Science Committee (pdf, 0.1 Mb)

Trace Metal Sensors for Coastal Monitoring, Seaside, California, April 11-13, 2005: workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop on Trace Metal Sensors for Coastal Monitoring was convened April 11-13, 2005 at the Embassy Suites in Seaside, California with partnership from Moss Landing Marine Laboratories (MLML) and the Monterey Bay Aquarium Research Institute (MBARI). Trace metals play many important roles in marine ecosystems. Due to their extreme toxicity, the effects of copper, cadmium and certain organo-metallinc compounds (such as tributyltin and methylmercury) have received much attention. Lately, the sublethal effects of metals on phytoplankton biochemistry, and in some cases the expression of neurotoxins (Domoic acid), have been shown to be important environmental forcing functions determining the composition and gene expression in some groups. More recently the role of iron in controlling phytoplankton growth has led to an understanding of trace metal limitation in coastal systems. Although metals play an important role at many different levels, few technologies exist to provide rapid assessment of metal concentrations or metal speciation in the coastal zone where metal-induced toxicity or potential stimulation of harmful algal blooms, can have major economic impacts. This workshop focused on the state of on-site and in situ trace element detection technologies, in terms of what is currently working well and what is needed to effectively inform coastal zone managers, as well as guide adaptive scientific sampling of the coastal zone. Specifically the goals of this workshop were to: 1) summarize current regional requirements and future targets for metal monitoring in freshwater, estuarine and coastal environments; 2) evaluate the current status of metal sensors and possibilities for leveraging emerging technologies for expanding detection limits and target elements; and 3) help identify critical steps needed for and limits to operational deployment of metal sensors as part of routine water quality monitoring efforts. Following a series of breakout group discussions and overview talks on metal monitoring regulatory issues, analytical techniques and market requirements, workshop participants made several recommendations for steps needed to foster development of in situ metal monitoring capacities: 1. Increase scientific and public awareness of metals of environmental and biological concern and their impacts in aquatic environments. Inform scientific and public communities regarding actual levels of trace metals in natural and perturbed systems. 2. Identify multiple use applications (e.g., industrial waste steam and drinking water quality monitoring) to support investments in metal sensor development. (pdf contains 27 pages)

Análise da contaminação das águas do córrego São Lourenço (Nova Friburgo, RJ) por agrotóxicos organofosforados e carbamatos

O córrego de São Lourenço (Nova Friburgo RJ), situado na principal região agrícola do estado, representa um importante manancial hídrico do município de Nova Friburgo que percorre um vale onde se concentram as principais lavouras responsáveis pela produção de olerícolas do Estado. Esta localidade apresenta expressiva relação de consumo de agrotóxicos por trabalhador (56 kg/trabalhador/ano). Assim, este córrego recebe todos os resíduos provenientes das lavouras situadas em suas margens. As águas desse córrego são usadas após tratamento pela população residente na área metropolitana e, são usadas sem tratamento pela população residente em suas margens. Este estudo tem como objetivo avaliar a contaminação das águas desse córrego por agrotóxicos anticolinesterásicos. Amostras de água foram coletadas mensalmente de abril/07 a fevereiro/08, em seis pontos do Córrego São Lourenço e em um ponto do Córrego das Paixões. Foram utilizadas garrafas previamente rinsadas com metanol e enxaguadas várias vezes com água destilada. A avaliação dos níveis de pesticidas se deu por método enzimático descrito por Cunha Bastos et al (1991) e pela etapa de concentração e extração dos pesticidas em coluna de carvão ativado foi adaptada a partir do método descrito por Kaipper et al. (2001), que possui a vantagem de ser um teste rápido de avaliação inicial e de baixo custo. Como controle negativo foi usado águas coletadas no ponto um, situado em área de floresta, sem terras cultivadas ao redor. Foram geradas 72 amostras, onde 33 apresentaram indícios de contaminação, mas apenas uma atingiu o limite de detecção do método, 5 ppb, em maio/07. Estes resultados, principalmente os obtidos nos pontos localizados na parte final do córrego São Lourenço, sugerem, além da utilização recente de agrotóxicos, a importância de fatores climatológicos e do regime do uso de tais compostos possivelmente interferindo na detecção dos resíduos em questão

PICES Press, Vol. 18, No. 1, Winter 2010

•Major Outcomes from the 2009 PICES Annual Meeting: A Note from the Chairman (pp. 1-3, 8) •PICES Science – 2009 (pp. 4-8) •2009 PICES Awards (pp. 9-10) •New Chairmen in PICES (pp. 11-15) •PICES Interns (p. 15) •The State of the Western North Pacific in the First Half of 2009 (pp. 16-17, 27) •The State of the Northeast Pacific in 2009 (pp. 18-19) •The Bering Sea: Current Status and Recent Events (pp. 20-21) •2009 PICES Summer School on “Satellite Oceanography for the Earth Environment” (pp. 22-25) •2009 International Conference on “Marine Bioinvasions” (pp. 26-27) •A New PICES Working Group Holds Workshop and Meeting in Jeju Island (pp. 28-29) •The Second Marine Ecosystem Model Inter-comparison Workshop (pp. 30-32) •ICES/PICES/UNCOVER Symposium on “Rebuilding Depleted Fish Stocks – Biology, Ecology, Social Science and Management Strategies” (pp. 33-35) •2009 North Pacific Synthesis Workshop (pp. 36-37) •2009 PICES Rapid Assessment Survey (pp. 38-40)

PICES Press, Vol. 19, No. 1, Winter 2011

•2010 PICES Science: A Note from the Former Science Board Chairman (pp. 1-4) •2010 PICES Awards (pp. 5-7) •The First Year of FUTURE: A Progress Report (pp. 8-13) •New Chairmen in PICES (pp. 14-19) •Pacific Ocean Interior Carbon Data Synthesis, PACIFICA, in Progress (pp. 20-23) •2011 PICES Calendar (p. 23) •Ecosystems 2010: Global Progress on Ecosystem-based Fisheries Management (pp. 24-26) •PICES 2010 Rapid Assessment Survey (pp. 27-29) •PICES Workshop on “An Introduction to Rapid Assessment Survey Methodologies for Application in Developing Countries” (pp. 30-31) •The State of the Western North Pacific in the First Half of 2010 (pp. 32-34) •PICES Interns (p. 34) •The State of the Bering Sea in 2010 (pp. 35-37) •The State of the Northeast Pacific in 2010 (pp. 38-40)

PICES Press, Vol. 20, No. 1, Winter 2012

•2011 PICES Science: A Note from the Science Board Chairman (pp. 1-6) •2011 PICES Awards (pp. 7-9) •Beyond the Terrible Disaster of the Great East Japan Earthquake (pp. 10-12) •A New Era of PICES-ICES Scientific Cooperation (p. 13) •New PICES Jellyfish Working Group Formed (pp. 14-15) •PICES Working Group on North Pacific Climate Variability (pp. 16-18) •Final U.S. GLOBEC Symposium and Celebration (pp. 19-25) •2011 PICES Rapid Assessment Survey (pp. 26-29) •Introduction to Rapid Assessment Survey Methodologies for Detecting Non-indigenous Marine Species (pp. 30-31) •The 7th International Conference on Marine Bioinvasions (pp. 32-33) •NOWPAP/PICES/WESTPAC Training Course on Remote Sensing Data Analysis (pp. 34-36) •PICES-2011 Workshop on “Trends in Marine Contaminants and their Effects in a Changing Ocean” (pp. 37-39) •The State of the Western North Pacific in the First Half of 2011 (pp. 40-42) •Yeosu Symposium theme sessions (p. 42) •The Bering Sea: Current Status and Recent Events (pp. 43-44) •News of the Northeast Pacific Ocean (pp. 45-47) •Recent and Upcoming PICES Publications (p. 47) •New leadership for the PICES Fishery Science Committee (p. 48)

Simplifying mooring analysis for deepwater systems using truncation

Over recent years academia and industry have engaged with the challenge of model testing deepwater structures at conventional scales. One approach to the limited depth problem has been to truncate the lines. This concept will be introduced, highlighting the need to better understand line dynamic processes. The type of line truncation developed here models the upper sections of each line in detail, capturing wave action and all coupling effects with the vessel, terminating to an approximate analytical model that aims to simulate the remainder of the line. A rationale for this is that in deep water transverse elastic waves of a line are likely to decay before they are reflected at the seabed because of nonlinear hydrodynamic drag forces. The first part of this paper is centered on verification of this rationale. A simplified model of a mooring line that describes the transverse dynamics in wave frequency is used, adopting the equation of motion of an inextensible taut string. The line is submerged in still water, one end fixed at the bottom the other assumed to follow the vessel response, which can be harmonic or random. A dimensional analysis, supported by exact benchmark numerical solutions, has shown that it is possible to produce a universal curve for the decay of transverse vibrations along the line, which is suitable for any kind of line with any top motion. This has a significant engineering benefit, allowing for a rapid assessment of line dynamics - it can be useful in deciding whether a truncated line model is appropriate, and if so, at which point truncation might be applied. This is followed by developing a truncation mechanism, formulating an end approximation that can reproduce the correct impedance, had the line been continuous to full depth. It has been found that below a certain length criterion, which is also universal, the transverse vibrational characteristics for each line are inertia driven. As such the truncated model can assume a linear damper whose coefficient depends on the line properties and frequency of vibration. Copyright © 2011 by the International Society of Offshore and Polar Engineers (ISOPE).

Decay of vibrations along deepwater mooring lines

Model tests for global design verification of deepwater floating structures cannot be made at reasonable scales. An overview of recent research efforts to tackle this challenge is given first, introducing the concept of line truncation techniques. In such a method the upper sections of each line are modelled in detail, capturing the wave action zone and all coupling effects with the vessel. These terminate to an approximate analytical model, that aims to simulate the remainder of the line. The rationale for this is that in deep water the transverse elastic waves of a line are likely to decay before they are reflected at the seabed. The focus of this paper is the verification of this rationale and the ongoing work, which is considering ways to produce a truncation model. Transverse dynamics of a mooring line are modelled using the equations of motion of an inextensible taut string, submerged in still water, one end fixed at the bottom the other assumed to follow the vessel response, which can be harmonic or random. Nonlinear hydrodynamic damping is included; bending and VIV effects are neglected. A dimensional analysis, supported by exact benchmark numerical solutions, has shown that it is possible to produce a universal curve for the decay of transverse vibrations along the line, which is suitable for any kind of line with any top motion. This has a significant engineering benefit, allowing for a rapid assessment of line dynamics - it is very useful in deciding whether a truncated line model is appropriate, and if so, at which point truncation might be applied. Initial efforts in developing a truncated model show that a linearized numerical solution in the frequency domain matches very closely the exact benchmark. Copyright © 2011 by ASME.

Impacts of the Wenchuan Earthquake on the Giant Panda Nature Reserves in China

Ministry of Science and Technology of China [2008BAK47B02, 2008BAC44B04, 2008BAK50B06, 2008BAC43B01, 2006BAC08B06]

Surface Insulation Resistance Degradation and Electrochemical Migration on Printed Circuit Boards

Widespread adoption of lead-free materials and processing for printed circuit board (PCB) assembly has raised reliability concerns regarding surface insulation resistance (SIR) degradation and electrochemical migration (ECM). As PCB conductor spacings decrease, electronic products become more susceptible to these failures mechanisms, especially in the presence of surface contamination and flux residues which might remain after no-clean processing. Moreover, the probability of failure due to SIR degradation and ECM is affected by the interaction between physical factors (such as temperature, relative humidity, electric field) and chemical factors (such as solder alloy, substrate material, no-clean processing). Current industry standards for assessing SIR reliability are designed to serve as short-term qualification tests, typically lasting 72 to 168 hours, and do not provide a prediction of reliability in long-term applications. The risk of electrochemical migration with lead-free assemblies has not been adequately investigated. Furthermore, the mechanism of electrochemical migration is not completely understood. For example, the role of path formation has not been discussed in previous studies. Another issue is that there are very few studies on development of rapid assessment methodologies for characterizing materials such as solder flux with respect to their potential for promoting ECM. In this dissertation, the following research accomplishments are described: 1). Long-term temp-humidity-bias (THB) testing over 8,000 hours assessing the reliability of printed circuit boards processed with a variety of lead-free solder pastes, solder pad finishes, and substrates. 2). Identification of silver migration from Sn3.5Ag and Sn3.0Ag0.5Cu lead-free solder, which is a completely new finding compared with previous research. 3). Established the role of path formation as a step in the ECM process, and provided clarification of the sequence of individual steps in the mechanism of ECM: path formation, electrodeposition, ion transport, electrodeposition, and filament formation. 4). Developed appropriate accelerated testing conditions for assessing the no-clean processed PCBs' susceptibility to ECM: a). Conductor spacings in test structures should be reduced in order to reflect the trend of higher density electronics and the effect of path formation, independent of electric field, on the time-to-failure. b). THB testing temperatures should be modified according to the material present on the PCB, since testing at 85oC can cause the evaporation of weak organic acids (WOAs) in the flux residues, leading one to underestimate the risk of ECM. 5). Correlated temp-humidity-bias testing with ion chromatography analysis and potentiostat measurement to develop an efficient and effective assessment methodology to characterize the effect of no-clean processing on ECM.

Micro-Anatomical Quantitative Imaging Towards Enabling Automated Diagnosis of Thick Tissues at the Point of Care

Histopathology is the clinical standard for tissue diagnosis. However, histopathology has several limitations including that it requires tissue processing, which can take 30 minutes or more, and requires a highly trained pathologist to diagnose the tissue. Additionally, the diagnosis is qualitative, and the lack of quantitation leads to possible observer-specific diagnosis. Taken together, it is difficult to diagnose tissue at the point of care using histopathology.

Several clinical situations could benefit from more rapid and automated histological processing, which could reduce the time and the number of steps required between obtaining a fresh tissue specimen and rendering a diagnosis. For example, there is need for rapid detection of residual cancer on the surface of tumor resection specimens during excisional surgeries, which is known as intraoperative tumor margin assessment. Additionally, rapid assessment of biopsy specimens at the point-of-care could enable clinicians to confirm that a suspicious lesion is successfully sampled, thus preventing an unnecessary repeat biopsy procedure. Rapid and low cost histological processing could also be potentially useful in settings lacking the human resources and equipment necessary to perform standard histologic assessment. Lastly, automated interpretation of tissue samples could potentially reduce inter-observer error, particularly in the diagnosis of borderline lesions.

To address these needs, high quality microscopic images of the tissue must be obtained in rapid timeframes, in order for a pathologic assessment to be useful for guiding the intervention. Optical microscopy is a powerful technique to obtain high-resolution images of tissue morphology in real-time at the point of care, without the need for tissue processing. In particular, a number of groups have combined fluorescence microscopy with vital fluorescent stains to visualize micro-anatomical features of thick (i.e. unsectioned or unprocessed) tissue. However, robust methods for segmentation and quantitative analysis of heterogeneous images are essential to enable automated diagnosis. Thus, the goal of this work was to obtain high resolution imaging of tissue morphology through employing fluorescence microscopy and vital fluorescent stains and to develop a quantitative strategy to segment and quantify tissue features in heterogeneous images, such as nuclei and the surrounding stroma, which will enable automated diagnosis of thick tissues.

To achieve these goals, three specific aims were proposed. The first aim was to develop an image processing method that can differentiate nuclei from background tissue heterogeneity and enable automated diagnosis of thick tissue at the point of care. A computational technique called sparse component analysis (SCA) was adapted to isolate features of interest, such as nuclei, from the background. SCA has been used previously in the image processing community for image compression, enhancement, and restoration, but has never been applied to separate distinct tissue types in a heterogeneous image. In combination with a high resolution fluorescence microendoscope (HRME) and a contrast agent acriflavine, the utility of this technique was demonstrated through imaging preclinical sarcoma tumor margins. Acriflavine localizes to the nuclei of cells where it reversibly associates with RNA and DNA. Additionally, acriflavine shows some affinity for collagen and muscle. SCA was adapted to isolate acriflavine positive features or APFs (which correspond to RNA and DNA) from background tissue heterogeneity. The circle transform (CT) was applied to the SCA output to quantify the size and density of overlapping APFs. The sensitivity of the SCA+CT approach to variations in APF size, density and background heterogeneity was demonstrated through simulations. Specifically, SCA+CT achieved the lowest errors for higher contrast ratios and larger APF sizes. When applied to tissue images of excised sarcoma margins, SCA+CT correctly isolated APFs and showed consistently increased density in tumor and tumor + muscle images compared to images containing muscle. Next, variables were quantified from images of resected primary sarcomas and used to optimize a multivariate model. The sensitivity and specificity for differentiating positive from negative ex vivo resected tumor margins was 82% and 75%. The utility of this approach was further tested by imaging the in vivo tumor cavities from 34 mice after resection of a sarcoma with local recurrence as a bench mark. When applied prospectively to images from the tumor cavity, the sensitivity and specificity for differentiating local recurrence was 78% and 82%. The results indicate that SCA+CT can accurately delineate APFs in heterogeneous tissue, which is essential to enable automated and rapid surveillance of tissue pathology.

Two primary challenges were identified in the work in aim 1. First, while SCA can be used to isolate features, such as APFs, from heterogeneous images, its performance is limited by the contrast between APFs and the background. Second, while it is feasible to create mosaics by scanning a sarcoma tumor bed in a mouse, which is on the order of 3-7 mm in any one dimension, it is not feasible to evaluate an entire human surgical margin. Thus, improvements to the microscopic imaging system were made to (1) improve image contrast through rejecting out-of-focus background fluorescence and to (2) increase the field of view (FOV) while maintaining the sub-cellular resolution needed for delineation of nuclei. To address these challenges, a technique called structured illumination microscopy (SIM) was employed in which the entire FOV is illuminated with a defined spatial pattern rather than scanning a focal spot, such as in confocal microscopy.

Thus, the second aim was to improve image contrast and increase the FOV through employing wide-field, non-contact structured illumination microscopy and optimize the segmentation algorithm for new imaging modality. Both image contrast and FOV were increased through the development of a wide-field fluorescence SIM system. Clear improvement in image contrast was seen in structured illumination images compared to uniform illumination images. Additionally, the FOV is over 13X larger than the fluorescence microendoscope used in aim 1. Initial segmentation results of SIM images revealed that SCA is unable to segment large numbers of APFs in the tumor images. Because the FOV of the SIM system is over 13X larger than the FOV of the fluorescence microendoscope, dense collections of APFs commonly seen in tumor images could no longer be sparsely represented, and the fundamental sparsity assumption associated with SCA was no longer met. Thus, an algorithm called maximally stable extremal regions (MSER) was investigated as an alternative approach for APF segmentation in SIM images. MSER was able to accurately segment large numbers of APFs in SIM images of tumor tissue. In addition to optimizing MSER for SIM image segmentation, an optimal frequency of the illumination pattern used in SIM was carefully selected because the image signal to noise ratio (SNR) is dependent on the grid frequency. A grid frequency of 31.7 mm-1 led to the highest SNR and lowest percent error associated with MSER segmentation.

Once MSER was optimized for SIM image segmentation and the optimal grid frequency was selected, a quantitative model was developed to diagnose mouse sarcoma tumor margins that were imaged ex vivo with SIM. Tumor margins were stained with acridine orange (AO) in aim 2 because AO was found to stain the sarcoma tissue more brightly than acriflavine. Both acriflavine and AO are intravital dyes, which have been shown to stain nuclei, skeletal muscle, and collagenous stroma. A tissue-type classification model was developed to differentiate localized regions (75x75 µm) of tumor from skeletal muscle and adipose tissue based on the MSER segmentation output. Specifically, a logistic regression model was used to classify each localized region. The logistic regression model yielded an output in terms of probability (0-100%) that tumor was located within each 75x75 µm region. The model performance was tested using a receiver operator characteristic (ROC) curve analysis that revealed 77% sensitivity and 81% specificity. For margin classification, the whole margin image was divided into localized regions and this tissue-type classification model was applied. In a subset of 6 margins (3 negative, 3 positive), it was shown that with a tumor probability threshold of 50%, 8% of all regions from negative margins exceeded this threshold, while over 17% of all regions exceeded the threshold in the positive margins. Thus, 8% of regions in negative margins were considered false positives. These false positive regions are likely due to the high density of APFs present in normal tissues, which clearly demonstrates a challenge in implementing this automatic algorithm based on AO staining alone.

Thus, the third aim was to improve the specificity of the diagnostic model through leveraging other sources of contrast. Modifications were made to the SIM system to enable fluorescence imaging at a variety of wavelengths. Specifically, the SIM system was modified to enabling imaging of red fluorescent protein (RFP) expressing sarcomas, which were used to delineate the location of tumor cells within each image. Initial analysis of AO stained panels confirmed that there was room for improvement in tumor detection, particularly in regards to false positive regions that were negative for RFP. One approach for improving the specificity of the diagnostic model was to investigate using a fluorophore that was more specific to staining tumor. Specifically, tetracycline was selected because it appeared to specifically stain freshly excised tumor tissue in a matter of minutes, and was non-toxic and stable in solution. Results indicated that tetracycline staining has promise for increasing the specificity of tumor detection in SIM images of a preclinical sarcoma model and further investigation is warranted.

In conclusion, this work presents the development of a combination of tools that is capable of automated segmentation and quantification of micro-anatomical images of thick tissue. When compared to the fluorescence microendoscope, wide-field multispectral fluorescence SIM imaging provided improved image contrast, a larger FOV with comparable resolution, and the ability to image a variety of fluorophores. MSER was an appropriate and rapid approach to segment dense collections of APFs from wide-field SIM images. Variables that reflect the morphology of the tissue, such as the density, size, and shape of nuclei and nucleoli, can be used to automatically diagnose SIM images. The clinical utility of SIM imaging and MSER segmentation to detect microscopic residual disease has been demonstrated by imaging excised preclinical sarcoma margins. Ultimately, this work demonstrates that fluorescence imaging of tissue micro-anatomy combined with a specialized algorithm for delineation and quantification of features is a means for rapid, non-destructive and automated detection of microscopic disease, which could improve cancer management in a variety of clinical scenarios.

A systematic methodology to assess the impact of human factors in ship design

Evaluating ship layout for human factors (HF) issues using simulation software such as maritimeEXODUS can be a long and complex process. The analysis requires the identification of relevant evaluation scenarios; encompassing evacuation and normal operations; the development of appropriate measures which can be used to gauge the performance of crew and vessel and finally; the interpretation of considerable simulation data. Currently, the only agreed guidelines for evaluating HFs performance of ship design relate to evacuation and so conclusions drawn concerning the overall suitability of a ship design by one naval architect can be quite different from those of another. The complexity of the task grows as the size and complexity of the vessel increases and as the number and type of evaluation scenarios considered increases. Equally, it can be extremely difficult for fleet operators to set HFs design objectives for new vessel concepts. The challenge for naval architects is to develop a procedure that allows both accurate and rapid assessment of HFs issues associated with vessel layout and crew operating procedures. In this paper we present a systematic and transparent methodology for assessing the HF performance of ship design which is both discriminating and diagnostic. The methodology is demonstrated using two variants of a hypothetical naval ship.