Mapping and Characterizing Subtidal Oyster Reefs Using Acoustic Techniques, Underwater Videography and Quadrat Counts

Populations of the eastern oyster Crassostrea virginica have been in long-term decline in most areas. A major hindrance to effective oyster management has been lack of a methodology for accurately and economically obtaining data on their distribution and abundance patterns. Here, we describe early results from studies aimed at development of a mapping and monitoring protocol involving acoustic techniques, underwater videography, and destructive sampling (excavated quadrats). Two subtidal reefs in Great Bay, New Hampshire, were mapped with side-scan sonar and with videography by systematically imaging multiple sampling cells in a grid covering the same areas. A single deployment was made in each cell, and a 5-10-s recording was made of a 0.25-m2 area; the location of each image was determined using a differential global position system. A still image was produced for each of the cells and all (n = 40 or 44) were combined into a single photomontage overlaid onto a geo-referenced base map for each reef using Arc View geographic information system. Quadrat (0.25 m2 ) samples were excavated from 9 or 10 of the imaged areas on each reef, and all live oysters were counted and measured. Intercomparisons of the acoustic, video, and quadrat data suggest: (1) acoustic techniques and systematic videography can readily delimit the boundaries of oyster reefs; (2) systematic videography can yield quantitative data on shell densities and information on reef structure; and (3) some combination of acoustics, systematic videography, and destructive sampling can provide spatially detailed information on oyster reef characteristics

Hybrid Zero Dynamics of Planar Biped Walkers

Planar, underactuated, biped walkers form an important domain of applications for hybrid dynamical systems. This paper presents the design of exponentially stable walking controllers for general planar bipedal systems that have one degree-of-freedom greater than the number of available actuators. The within-step control action creates an attracting invariant set—a two-dimensional zero dynamics submanifold of the full hybrid model—whose restriction dynamics admits a scalar linear time-invariant return map. Exponentially stable periodic orbits of the zero dynamics correspond to exponentially stabilizable orbits of the full model. A convenient parameterization of the hybrid zero dynamics is imposed through the choice of a class of output functions. Parameter optimization is used to tune the hybrid zero dynamics in order to achieve closed-loop, exponentially stable walking with low energy consumption, while meeting natural kinematic and dynamic constraints. The general theory developed in the paper is illustrated on a five link walker, consisting of a torso and two legs with knees

Plasma Protein Profiles Differ Between Women Diagnosed with Cervical Intraepithelial Neoplasia (CIN) 1 and 3

Early detection of precancerous cells in the cervix and their clinical management is the main purpose of cervical cancer prevention and treatment programs. Cytological findings or testing for high risk (HR)-human papillomavirus (HPV) are inadequately sensitive for use in triage of women at high risk for cervical cancer. The current study is an exploratory study to identify candidate surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) mass spectrometry (MS) protein profiles in plasma that may distinguish cervical intraepithelial neoplasia (CIN 3) from CIN 1 among women infected with HR-HPV. We evaluated the SELDI-TOF-MS plasma protein profiles of HR-HPV positive 32 women with CIN 3 (cases) and 28 women with CIN1 (controls). Case-control status was kept blinded and triplicates of each sample and quality control plasma samples were randomized and after robotic sample preparations were run on WCX2 chips. After alignment of mass/charge (m-z values), an iterative method was used to develop a classifier on a training data set that had 28 cases and 22 controls. The classifier developed was used to classify the subjects in a test data set that has six cases and six controls. The classifier separated the cases from controls in the test set with 100% sensitivity and 100% specificity suggesting the possibility of using plasma SELDI protein profiles to identify women who are likely to have CIN 3 lesions

Prediagnostic serum biomarkers as early detection tools for pancreatic cancer in a large prospective cohort study

Background: The clinical management of pancreatic cancer is severely hampered by the absence of effective screening tools. Methods: Sixty-seven biomarkers were evaluated in prediagnostic sera obtained from cases of pancreatic cancer enrolled in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). Results: The panel of CA 19-9, OPN, and OPG, identified in a prior retrospective study, was not effective. CA 19-9, CEA, NSE, bHCG, CEACAM1 and PRL were significantly altered in sera obtained from cases greater than 1 year prior to diagnosis. Levels of CA 19-9, CA 125, CEA, PRL, and IL-8 were negatively associated with time to diagnosis. A training/validation study using alternate halves of the PLCO set failed to identify a biomarker panel with significantly improved performance over CA 19-9 alone. When the entire PLCO set was used for training at a specificity (SP) of 95%, a panel of CA 19-9, CEA, and Cyfra 21-1 provided significantly elevated sensitivity (SN) levels of 32.4% and 29.7% in samples collected 1 year prior to diagnosis, respectively, compared to SN levels of 25.7% and 17.2% for CA 19-9 alone. Conclusions: Most biomarkers identified in previously conducted case/control studies are ineffective in prediagnostic samples, however several biomarkers were identified as significantly altered up to 35 months prior to diagnosis. Two newly derived biomarker combinations offered advantage over CA 19-9 alone in terms of SN, particularly in samples collected >1 year prior to diagnosis. However, the efficacy of biomarker-based tools remains limited at present. Several biomarkers demonstrated significant velocity related to time to diagnosis, an observation which may offer considerable potential for enhancements in early detection. © 2014 Nolen et al

Recreational boating activity and its impact on the recruitment and survival of the oyster Crassostrea virginica on intertidal reefs in Mosquito Lagoon, Florida

Along the east coast of central Florida in the Indian River Lagoon system, intense recreational boating activity occurs year-round, and intertidal reefs of the eastern oyster Crassostrea virginica (Gmelin) with dead margins (mounds of disarticulated shells) on their seaward edges are commonly found adjacent to major boating channels. These dead margins are caused, at least in part, by boat wakes and extend significantly higher above the high water line than reefs lacking dead margins (pristine reefs). To determine if these impacted oyster reefs alter recruitment and subsequent survival of C. virginica, three 8-wk field trials were run between May 2001 and April 2002 in Mosquito Lagoon. During each trial, data were also collected on total sediment loads, silt/clay fractions and relative water motion. Although recruitment did not differ between impacted and pristine reef\u27s, juvenile survival was significantly reduced on impacted reefs. Additionally, larval recruitment and subsequent mortality were greatest during our summer trial. Total sediment loads, percent silt/clay, and relative water motion were significantly higher on impacted reefs. For these three variables, the largest values were consistently found at the bases of exposed (seaward) regions of impacted reefs. By documenting a positive relationship between reduced success of C. virginica and dead margins, and knowing that boat wakes contribute to the development of dead margins. we have provided the first cause and effect mechanism between intense recreational boating activity and increased oyster morality

Availability and quality of paraffin blocks identified in pathology archives: A multi-institutional study by the Shared Pathology Informatics Network (SPIN)

BACKGROUND: Shared Pathology Informatics Network (SPIN) is a tissue resource initiative that utilizes clinical reports of the vast amount of paraffin-embedded tissues routinely stored by medical centers. SPIN has an informatics component (sending tissue-related queries to multiple institutions via the internet) and a service component (providing histopathologically annotated tissue specimens for medical research). This paper examines if tissue blocks, identified by localized computer searches at participating institutions, can be retrieved in adequate quantity and quality to support medical researchers. METHODS: Four centers evaluated pathology reports (1990–2005) for common and rare tumors to determine the percentage of cases where suitable tissue blocks with tumor were available. Each site generated a list of 100 common tumor cases (25 cases each of breast adenocarcinoma, colonic adenocarcinoma, lung squamous carcinoma, and prostate adenocarcinoma) and 100 rare tumor cases (25 cases each of adrenal cortical carcinoma, gastro-intestinal stromal tumor [GIST], adenoid cystic carcinoma, and mycosis fungoides) using a combination of Tumor Registry, laboratory information system (LIS) and/or SPIN-related tools. Pathologists identified the slides/blocks with tumor and noted first 3 slides with largest tumor and availability of the corresponding block. RESULTS: Common tumors cases (n = 400), the institutional retrieval rates (all blocks) were 83% (A), 95% (B), 80% (C), and 98% (D). Retrieval rate (tumor blocks) from all centers for common tumors was 73% with mean largest tumor size of 1.49 cm; retrieval (tumor blocks) was highest-lung (84%) and lowest-prostate (54%). Rare tumors cases (n = 400), each institution's retrieval rates (all blocks) were 78% (A), 73% (B), 67% (C), and 84% (D). Retrieval rate (tumor blocks) from all centers for rare tumors was 66% with mean largest tumor size of 1.56 cm; retrieval (tumor blocks) was highest for GIST (72%) and lowest for adenoid cystic carcinoma (58%). CONCLUSION: Assessment shows availability and quality of archival tissue blocks that are retrievable and associated electronic data that can be of value for researchers. This study serves to compliment the data from which uniform use of the SPIN query tools by all four centers will be measured to assure and highlight the usefulness of archival material for obtaining tumor tissues for research

Estimating preferences for a dermatology consultation using Best-Worst Scaling: Comparison of various methods of analysis

Background: Additional insights into patient preferences can be gained by supplementing discrete choice experiments with best-worst choice tasks. However, there are no empirical studies illustrating the relative advantages of the various methods of analysis within a random utility framework. Methods: Multinomial and weighted least squares regression models were estimated for a discrete choice experiment. The discrete choice experiment incorporated a best-worst study and was conducted in a UK NHS dermatology context. Waiting time, expertise of doctor, convenience of attending and perceived thoroughness of care were varied across 16 hypothetical appointments. Sample level preferences were estimated for all models and differences between patient subgroups were investigated using ovariateadjusted multinomial logistic regression. Results: A high level of agreement was observed between results from the paired model (which is theoretically consistent with the 'maxdiff' choice model) and the marginal model (which is only an approximation to it). Adjusting for covariates showed that patients who felt particularly affected by their skin condition during the previous week displayed extreme preference for short/no waiting time and were less concerned about other aspects of the appointment. Higher levels of educational attainment were associated with larger differences in utility between the levels of all attributes, although the attributes per use had the same impact upon choices as those with lower levels of attainment. The study also demonstrated the high levels of agreement between summary analyses using weighted least squares and estimates from multinomial models. Conclusion: Robust policy-relevant information on preferences can be obtained from discrete choice experiments incorporating best-worst questions with relatively small sample sizes. The separation of the effects due to attribute impact from the position of levels on the latent utility scale is not possible using traditional discrete choice experiments. This separation is important because health policies to change the levels of attributes in health care may be very different from those aiming to change the attribute impact per se. The good approximation of summary analyses to the multinomial model is a useful finding, because weighted least squares choice totals give better insights into the choice model and promote greater familiarity with the preference data