Search

This report investigates the social demography, learning outcomes and educational experiences of students enrolled in two distinct modes of higher education delivery in Australia – university programs delivered through third party arrangements, and higher education courses delivered by non-university higher education institutions (NUHEIs). In short, the research examines equity at and beyond the boundary of Australian universities. University courses delivered through third party arrangements – particularly those that involve sub-contracting and franchising of program delivery – are not provided directly by public universities, and can therefore be considered as residing at the boundary of the public university. Programs delivered by NUHEIs are positioned definitively beyond the boundary of the Australian public university. Our research examines the equity group participation, retention and success rates – as well as the educational experiences – of students within these two domains of delivery. While maintaining a particular focus on students from low socioeconomic status (SES) backgrounds, we analyse and present data on five of the six nationally recognised equity groups within higher education, including Indigenous students, students with a disability, and students from low SES, regional and non-English speaking backgrounds (NESB).

Nibabel talk at the CZI EOSS conference, December 2020. The theme is - democratizing brain imaging through code We want to build a culture in which it is ordinary for scientists to contribute to their tools. If we succeed, we will go a long way to solving the chronic and severe problems of monoculture in open source. To do this, we need to build use and contribution down into the deepest possible foundation in education.

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments. peerReviewed

Giant bullous emphysema with placental transmogrification is an extremely rare entity, with 30 previously reported cases. Of these reported cases, it is typically identified with varied clinical and radiological impressions, presents in young adulthood to elderly, is always unilateral, and usually involves just one lobe. Despite the unknown pathogenesis, this diagnosis carries an excellent prognosis and is curative with complete resection. The pulmonary placental transmogrification is histologically indistinguishable from placental origin. Although not necessary to utilize because of the male predominance and no reported association, immunohistochemical stains can be used to prove lung origin. We report an extremely rare case of 2-lobe involvement of giant bullous emphysema with placental transmogrification in a boy 14 years of age, who is the youngest diagnosed patient with this lung abnormality.

Urothelial carcinoma can exhibit a wide variety of histopathologic phenotypes or variant morphologies, classifications of which have recently been revised in the 2016 World Health Organization Classification of Tumours of the Urinary System and Male Genital Organs. Many of these variants not only present diagnostic challenges, but also have clinical implications that affect patient prognosis and treatment strategies. This review will discuss these variant morphologies and their relationship to current understanding of the underlying biology of urothelial carcinoma and molecular classification paradigms.

Medullary carcinoma has long been recognized as a subtype of colorectal cancer associated with microsatellite instability and Lynch syndrome. Gastric medullary carcinoma is a very rare neoplasm. We report a 67-year-old male who presented with a solitary gastric mass. Total gastrectomy revealed a well-demarcated, poorly differentiated carcinoma with an organoid growth pattern, pushing borders, and abundant peritumoral lymphocytic response. The prior cytology was cellular with immunohistochemical panel consistent with upper gastrointestinal/pancreaticobiliary origin. Overall, the histopathologic findings were consistent with gastric medullary carcinoma. A mismatch repair panel revealed a mismatch repair protein deficient tumor with loss of MLH1 and PMS2 expression. BRAF V600E immunostain (VE1) and BRAF molecular testing were negative, indicating a wild-type gene. Tumor sequencing of MLH1 demonstrated a wild-type gene, while our molecular panel identified TP53 c.817C>T (p.R273C) mutation. These findings were compatible with a sporadic tumor. Given that morphologically identical medullary tumors often occur in Lynch syndrome, it is possible that mismatch repair loss is an early event in sporadic tumors with p53 mutation being a late event. Despite having wild-type BRAF, this tumor is sporadic and unrelated to Lynch syndrome. This case report demonstrates that coordinate ancillary studies are needed to resolve sporadic versus hereditary rare tumors.

Adenocarcinoma with osteoblastic metastases is classically seen in prostate, breast, and lung primaries. Less common primary sites include thyroid, kidney, and stomach. We present two cases of primary gastrointestinal adenocarcinoma with metastatic osteoblastic activity from two previously unreported sites. The first case represents an esophageal adenocarcinoma arising in a background of intestinal metaplasia that metastasized with osteoblastic activity to the deltoid muscle. The second case demonstrates a Stage IV sigmoid colon adenocarcinoma with osteoblastic metastases to the liver and lymph nodes. The findings indicate that metastases from various gastrointestinal primary adenocarcinomas can have prominent bone formation.

Classical Hodgkin's lymphoma (CHL) presenting with exclusively pulmonary symptoms is very unusual. We report two cases of CHL with atypical clinical presentations mimicking pulmonary infections. The first case represents a stage IV CHL with secondary lung involvement, and the second case demonstrates a very rare case of CHL with isolated lung involvement, also known as primary pulmonary Hodgkin's lymphoma. The second patient was initially misdiagnosed and treated with six months of antibiotics before the correct diagnosis was made by a lung biopsy. Both patients received chemotherapy; one patient achieved complete remission and the other achieved near-complete remission.

Since the 1970s, the magnitude of turtle cold-stun strandings have increased dramatically within the northwestern Atlantic. Here, we examine oceanic, atmospheric, and biological factors that may affect the increasing trend of cold-stunned Kemp's ridleys in Cape Cod Bay, Massachusetts, United States of America. Using machine learning and Bayesian inference modeling techniques, we demonstrate higher cold-stunning years occur when the Gulf of Maine has warmer sea surface temperatures in late October through early November. Surprisingly, hatchling numbers in Mexico, a proxy for population abundance, was not identified as an important factor. Further, using our Bayesian count model and forecasted sea surface temperature projections, we predict more than 2,300 Kemp's ridley turtles may cold-stun annually by 2031 as sea surface temperatures continue to increase within the Gulf of Maine. We suggest warmer sea surface temperatures may have modified the northerly distribution of Kemp's ridleys and act as an ecological bridge between the Gulf Stream and nearshore waters. While cold-stunning may currently account for a minor proportion of juvenile mortality, we recommend continuing efforts to rehabilitate cold-stunned individuals to maintain population resiliency for this critically endangered species in the face of a changing climate and continuing anthropogenic threats.

Adenocarcinoma ex–goblet cell carcinoid is a very rare and histologically unique appendiceal malignancy with dual glandular and neuroendocrine differentiation. There is a high incidence of this tumor among middle-aged women with metastasis to the gynecologic tract with the mode of metastasis following peritoneal spread rather than hematogenous distribution. Adenocarcinoma ex-goblet cell carcinoid can spread to any peritoneal site including ovaries or omentum. We report a 37-year-old healthy woman who initially presented with right lower quadrant abdominal pain and pseudomyxoma peritonei. Histopathology of the appendectomy specimen revealed an adenocarcinoma ex-goblet cell carcinoid, signet ring cell type. Follow-up right hemicolectomy, omentectomy, bilateral salpingo-oophorectomy, and regional peritoneal resections revealed metastatic involvement by adenocarcinoma ex–goblet cell carcinoid, signet ring cell type. In this report, we describe a case of appendiceal adenocarcinoma ex goblet cell carcinoid with metastases to Meckel’s diverticulum and areas of pelvic endometriosis, which have not been previously reported.

Poster Abstrast submitted to OHBM 2004

Ulcerative colitis has long been linked with an increased risk for colonic adenocarcinoma, whereas Crohn’s disease (CD) has recently been reported to pose a similar increased risk. We report a 33-year-old healthy female with no family history who presented with abdominal pain and a colon mass. Histopathology revealed a moderately differentiated adenocarcinoma extending through the muscularis propria with metastatic lymph nodes and intact mismatch repair proteins by immunohistochemical expression and gene sequencing. The nonneoplastic grossly uninvolved background mucosa showed marked crypt distortion, crypt abscesses, CD-like lymphoid hyperplasia, transmural inflammation, and reactive epithelial atypia. Additional patient questioning revealed frequent loose stools since she was a teenager leading to diagnosis of a previously undiagnosed CD without primary sclerosing cholangitis (PSC). The adenocarcinoma is suspected to be related to the underlying CD. Newly diagnosed adenocarcinoma in a young female as the presenting sign for CD in the absence of PSC is extremely rare.

Poster submitted to OHBM 2006

Over the past decade there have been remarkable advancements in the understanding of the molecular underpinnings of malignancy, leading to the development of a number of innovative and highly effective treatments. The success of these treatments can largely be attributed to an increased ability to deliver cancer therapies on a more individualized level based on the genetic makeup of patients’ tumours. Methods of testing such as fluorescent in situ hybridization, polymerase chain reaction and direct sequencing , which can identify the genetic architecture of tumours have improved to the point where there is an increased desire to incorporate the genomic information derived from such tests into treatment selection for cancer patients. There is, however, uncertainty with regards to the impact that genomic testing prior to treatment will have on not only health outcomes but also the costs it will incur. There is therefore a need to develop economic evidence to support the implementation of genomic testing and targeted treatment strategies in oncology to ensure the resources allocated to these approaches offer value for money. This thesis primarily investigates the most appropriate approaches to assessing the value of genomic medicine in oncology. First, factors that are important to consider when undertaking economic evaluations of genomic test and treat strategies are identified and a discussion is presented on how existing methods can be adapted to account for the unique aspects of genomic technologies. Second, one of the first model-based economic evaluations of genomic testing and targeted treatment is developed to provide initial evidence of cost-effectiveness in a metastatic lung adenocarcinoma population. Third, efforts to improve the translation of the economic evidence of genomic medicine in oncology are undertaken to ensure appropriate and timely access to these innovative and potentially beneficial technologies. Finally, the thesis addresses another important issue in the economic evaluation of oncology treatments; the estimation of health state utility values for use in cost-utility analyses. To limit bias in future evaluations, existing estimation approaches are compared and the most reliable approach is identified. The findings from this thesis suggest that a number of test-related characteristics are important to consider and can have large impacts on the results of economic evaluations of genomic approaches to treatment. More complex testing approaches are likely to make the application of traditional methods for assessing clinical and economic value more difficult, suggesting the need to adapt existing methods in the future. The results of the modelled economic evaluation highlight the difficulty in assessing the value of genomic testing when results dictate the use of high cost targeted therapies associated with only small improvements in clinical outcomes. Potential future advancements in testing, however, offer the opportunity for improvements in cost-effectiveness. To facilitate this, a greater understanding and flexibility from all stakeholders involved will be required. With respect to estimating health state utility values in oncology, response mapping is shown to result in the most accurate and reliable predictions and should therefore be used in future economic evaluations, where appropriate. To move the science forward, this program of research would suggest an iterative approach to the economic evaluation of genomic test and treat strategies in oncology. This will greatly improve our understanding of their impact on health outcomes and the overall health budget, thus informing evidence-based decision making.

Endobronchial ultrasound-guided fine needle aspiration (EBUS-FNA) is a safe and minimally invasive bronchoscopic technique that allows both visualization and cytologic sampling with a high diagnostic yield in a patient with mediastinal lymphadenopathy. Besides the most common indication of staging for a patient with a primary lung carcinoma, EBUS-FNA can be used to identify benign infectious and noninfectious processes as well as lymphoma and malignancy of unknown primary. Triaging of procured specimen for diagnostic, prognostic, and therapeutic ancillary studies requires appropriate clinical information at the time of rapid on site evaluation (ROSE) of smears. This case report demonstrates a young, previously healthy nonsmoker presenting clinically with cough, hemoptysis, and a 1.7 cm enlarged subcarinal lymph node by imaging. EBUS-FNA obtained smears from the lymph node revealed a pleomorphic population of smaller cells with a low nuclear to cytoplasmic ratio and prominent nucleoli, and larger cells had nuclei with bizarre shapes, mitoses, multinucleation, enlarged nucleoli, and pigmentation in a background of lymphocytes. The cytomorphologic and immunohistochemical workup of this case confirmed the unexpected diagnosis of metastatic melanoma. This result was a complete surprise to the clinical team managing the patient and prompted a thorough clinical workup. Subcarinal lymphadenopathy with metastatic malignant melanoma as the cause is rare. This case report highlights how ROSE and appropriate triaging of specimen were crucial in appropriately working up this case. We also survey the literature to review the reported unusual presentations of metastatic melanoma.

It was with great excitement that we planned the combined meetings of Northeast Aquaculture Conference and Exposition (NACE) and the International Conference on Shellfish Restoration (ICSR) with the 33rd Milford Aquaculture Seminar (MAS). Bringing these different but complementary audiences together resulted in a meeting that combined many different aspects of fisheries restoration and aquaculture under one umbrella.Four hundred attendees including government representatives, research scientists, industry, and academia at both the university and vocational high school levels attended this event. The meeting commenced on Wednesday December 12th 2012, with over eighty people attending seven field trips to area aquaculture farms and research facilities. The formal program began on Thursday, December 13th with a plenary session including invited speakers Eric Schwabb, Acting Assistant Secretary for Conservation and Management at NOAA; Sebastian Belle, Executive Director of the Maine Aquaculture Association and Boze Hancock from the Nature Conservancy, who discussed the role of aquaculture in fisheries restoration. John Bullard, the Northeast Regional Administrator of NOAA Fisheries Service, addressed the group during the luncheon the following day. The technical papers and workshops presented were divided into 35 sessions over three days of the meeting and included topics such as the history of aquaculture, aquaculture hatchery innovations, siting and planning issues, risk management, aquaculture business management, ocean acidification, climate change, as well as aquaculture disease issues and potential remedies. Having persons present who have experienced problems and successes, along with those in manufacturing and government responsible for addressing concerns and sharing best practices, was invaluable. Discussions among this cross-section of persons who represent different aspects of aquaculture were as important as the well-presented and interesting formal papers and poster sessions. These discussions were facilitated by the many opportunities presented during the large trade show, reception, breaks, lunches, banquet and lobster bake held throughout the meeting.The importance of and need for aquaculture were made evident by all who were in attendance. We are grateful to the twenty four meeting sponsors and to all those who participated and made this such an important and memorable meeting.While oyster restoration efforts have been under way in the Chesapeake Bay for more than two decades, until recently, varying reporting methods and success criteria made it difficult to determine how much progress had been made. A goal to “Restore native oyster habitat and populations in 20 out of 35 to 40 candidate tributaries by 2025” was set in the 2010 strategy to implement the Chesapeake Bay Protection and Restoration Executive Order (signed by President Obama in 2009). This goal made it a priority for state and federal fishery managers, academics, and scientists working on oyster restoration to collaboratively define a “restored tributary” and a “restored reef” to enable them to track progress. A team of these people, led by NOAA staff, agreed on “oyster metrics” in 2011 (http//preview.tinyurl.com/8kmbdpm) that specify key metrics and target ranges for them, including tributary size, how to determine how much restorable bottom a tributary contains, how much of that restorable bottom needs to be restored, and the minimum oyster density and biomass in that restored bottom to count a tributary as restored. These new metrics enable experts to clearly see how oyster restoration efforts are working and use adaptive management to improve these efforts. These metrics serve as a tool to plan and evaluate oyster restoration consistently across the Chesapeake Bay, and the consensus-based framework used to develop them may have broader application to other restoration activities.In the past, oyster restoration in Maryland was performed primarily