COBRA Master Class: Providing deep-sea expedition leadership training to accelerate early career advancement

Leading deep-sea research expeditions requires a breadth of training and experience, and the opportunities for Early Career Researchers (ECRs) to obtain focused mentorship on expedition leadership are scarce. To address the need for leadership training in deep-sea expeditionary science, the Crustal Ocean Biosphere Research Accelerator (COBRA) launched a 14-week virtual Master Class with both synchronous and asynchronous components to empower students with the skills and tools to successfully design, propose, and execute deep-sea oceanographic field research. The Master Class offered customized and distributed training approaches and created an open-access syllabus with resources, including reading material, lectures, and on-line resources freely-available on the Master Class website (cobra.pubpub.org). All students were Early Career Researchers (ECRs, defined here as advanced graduate students, postdoctoral scientists, early career faculty, or individuals with substantial industry, government, or NGO experience) and designated throughout as COBRA Fellows. Fellows engaged in topics related to choosing the appropriate deep-sea research asset for their Capstone “dream cruise” project, learning about funding sources and how to tailor proposals to meet those source requirements, and working through an essential checklist of pre-expedition planning and operations. The Master Class covered leading an expedition at sea, at-sea operations, and ship-board etiquette, and the strengths and challenges of telepresence. It also included post-expedition training on data management strategies and report preparation and outputs. Throughout the Master Class, Fellows also discussed education and outreach, international ocean law and policy, and the importance and challenges of team science. Fellows further learned about how to develop concepts respectfully with regard to geographic and cultural considerations of their intended study sites. An assessment of initial outcomes from the first iteration of the COBRA Master Class reinforces the need for such training and shows great promise with one-quarter of the Fellows having submitted a research proposal to national funding agencies within six months of the end of the class. As deep-sea research continues to accelerate in scope and speed, providing equitable access to expedition training is a top priority to enable the next generation of deep-sea science leadership

The Effects of external beam radiotherapy on the normal urinary bladder - a histopathological review

Introduction: This literature review presents information relevant to medical radiation technologists with respect to new knowledge on the function of the urinary bladder. These new insights are also explored in relation to radiation-induced histopathological effects and the symptoms of bladder dysfunction reported after external beam radiotherapy. Methods and Materials: The peer-reviewed scientific literature was examined using various electronic medical search engines with appropriate keywords and MeSH headings. Inclusion criteria comprised English language articles published between 1999 and January 2010, with full manuscript available. A critical review was then performed, synthesizing the information contained in those multiple sources into the following subject categories: normal urinary bladder function (basic review and new knowledge), and effect of fractionated radiotherapy on normal bladder (histopathological changes and symptoms of dysfunction). Findings: Previously considered an inert vessel for urine storage, the urinary bladder is actually a complex system of morphologically different tissues, which play an interconnected role in its physiological functions. Injury or abnormal repair in any of the bladder cell layers results in a multifaceted display of interrelated manifestations of dysfunction. In this complex environment, not only can a single symptom of dysfunction have multiple histopathological causes, but the presence of one symptom may exacerbate the presentation of another. To date, this new knowledge has had little impact on radiotherapy clinical practice because subjective methods of collecting toxicity data prevent the identification of a link between radiotherapy dose and urinary dysfunction. The new understanding of the histopathological cause of radiation-induced symptoms, however, has led to the preclinical investigation of many promising methods to prevent or reduce radiotherapy toxicity.9 page(s

Delineating the inner bladder surface using uniform contractions from the outer surface under variable bladder filling conditions

Objective: To evaluate the methods to delineate the inner bladder (IB) surface using a uniform contraction from the outer bladder (OB) surface, assuming the bladder wall (BW) is either of constant thickness, constant volume or variable volume. Methods: 14 prostate intensity-modulated radiotherapy patients with 2 planning CTs were identified. For both CTs, OB was delineated using model-based segmentation. IB was delineated manually. Then, using uniform contractions from OB, the position of IB was approximated using a: 2.5-mm contraction, patient-specific contraction, patient-specific constant wall volume method and variable wall volume method. The structures created using those strategies were compared against the manual IB contours using geometric and dosimetric indices. Results: In the presence of variable bladder filling, use of a generic or patient-specific constant contraction resulted in a significant overestimation of IB volume (+12 and +13 cm(3), respectively; p  0.86). Mean differences across 95% of IB surfaces were ≤2 mm for methods using either constant or variable wall volume. Mean dose-volume histogram (DVH) differences were <1 cm(3) across the whole BW DVH when using the method that assumed a variable wall volume. Conclusion: The variable volume BW model provided the best approximation of the IB surface position under varying filling conditions, based on geometric and dosimetric indices. Advances in knowledge: Use of the equation derived in this research provides a quick and accurate method to delineate the hollow BW on serial imaging for the purposes of dose reconstruction.9 page(s

Microbial Community in Black Rust Exposed to Hot Ridge Flank Crustal Fluids

During Integrated Ocean Drilling Program Expedition 301, we obtained a sample of black rust from a circulation obviation retrofit kit (CORK) observatory at a borehole on the eastern flank of Juan de Fuca Ridge. Due to overpressure, the CORK had failed to seal the borehole. Hot fluids from oceanic crust had discharged to the overlying bottom seawater and resulted in the formation of black rust analogous to a hydrothermal chimney deposit. Both culture-dependent and culture-independent analyses indicated that the black-rust-associated community differed from communities reported from other microbial habitats, including hydrothermal vents at seafloor spreading centers, while it shared phylotypes with communities previously detected in crustal fluids from the same borehole. The most frequently retrieved sequences of bacterial and archaeal 16S rRNA genes were related to the genera Ammonifex and Methanothermococcus, respectively. Most phylotypes, including phylotypes previously detected in crustal fluids, were isolated in pure culture, and their metabolic traits were determined. Quantification of the dissimilatory sulfite reductase (dsrAB) genes, together with stable sulfur isotopic and electron microscopic analyses, strongly suggested the prevalence of sulfate reduction, potentially by the Ammonifex group of bacteria. Stable carbon isotopic analyses suggested that the bulk of the microbial community was trophically reliant upon photosynthesis-derived organic matter. This report provides important insights into the phylogenetic, physiological, and trophic characteristics of subseafloor microbial ecosystems in warm ridge flank crusts

Temperature and redox effect on mineral colonization in Juan de Fuca Ridge flank subsurface crustal fluids

To examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for one year at the seafloor wellhead of a crustal borehole observatory (IODP Hole U1301A, Juan de Fuca Ridge flank) as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby IODP Hole U1301B). In comparison to previous studies at these same sites, this approach allowed assessment of the effects of temperature, fluid chemistry, and/or mineralogy on colonization patterns of different mineral substrates, and an opportunity to verify the approach of deploying colonization experiments at an observatory wellhead at the seafloor instead of within the borehole. The Hole U1301B deployment did not have biofilm growth, based on microscopy and DNA extraction, thereby confirming the integrity of the colonization design against bottom seawater intrusion. In contrast, the Hole U1301A deployment supported biofilms dominated by Epsilonproteobacteria (43.5% of 370 16S rRNA gene clone sequences) and Gammaproteobacteria (29.3%). Sequence analysis revealed overlap in microbial communities between different minerals incubated at the Hole U1301A wellhead, indicating that mineralogy did not separate biofilm structure within the one-year colonization experiment. Differences in the Hole U1301A wellhead biofilm community composition relative to previous studies from within the borehole using similar mineral substrates suggest that temperature and the diffusion of dissolved oxygen through plastic components influenced the mineral colonization experiments positioned at the wellhead. This highlights the capacity of low abundance crustal fluid taxa to rapidly establish communities on diverse mineral substrates under changing environmental conditions such as from temperature and oxygen

The Effect of delineation method and observer variability on bladder dose-volume histograms for prostate intensity modulated radiotherapy

Purpose: To quantify the effect of delineation method on bladder DVH, observer variability (OV) and contouring time for prostate IMRT plans. Materials and methods: Planning CT scans and IMRT plans of 30 prostate cancer patients were anonymized. For 20 patients, 1 observer delineated the bladder using 9 methods. The effect of delineation method on the DVH curve, discrete dose levels and delineation time was quantified. For the 10 remaining CTs, 6 observers delineated bladder wall using 4 methods. Observer-based volume variation and intraclass correlation coefficient (ICC) were used to describe the dosimetric effects of OV. Results: Manual delineation of the bladder wall (BW-m) was significantly slower than any other method (mean: 20 min vs. ≤13 min) and the dosimetric effect of OV was significantly larger (V70 Gy ICC: 0.78 vs. 0.98). Only volumes created using a 2.5 mm contraction from the outer surface, and a method providing a consistent wall volume, showed no notable dosimetric differences from BW-m in both absolute and relative volume. Conclusions: Automatic contractions from the outer surface provide quicker, more reproducible and reasonably accurate substitutes for BW-m. The widespread use of automatic contractions to create a bladder wall volume would assist in the consistent application of IMRT dose constraints and the interpretation of reported dose.7 page(s

Assessing marine microbial induced corrosion at Santa Catalina Island, California

High iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial-induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, California, USA, for periods of two and six months. Substrates consisted of mild steel – a major constituent of maritime infrastructure – and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting high-flux conditions; a stagnant condition; an active flow-through condition with seawater slowly pumped over the substrates; and an enrichment condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the two-month high flux incubations document coating of substrates with twisted stalks, resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria. Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all six month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that i) high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of marine neutrophilic Fe-oxidizing bacteria and ii) long-term nutrient stimulation results in substrate corrosion and biofilms with different bacterial community composition and structure relative to stagnant and non-nutritionally enhanced incubations. Similar microbial succession scenarios, involving increases in nutritional input leading to the proliferation of anaerobic iron and sulfur-cycling guilds, may occur at the nearby Port of Los Angeles and cause potential damage to maritime port infrastructure