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

Scaling-Up: A Fifth Year of Restoring Oyster Reefs in Great Bay Estuary, NH 2013 Annual Program Report

The eastern oyster (Crassostrea virginica) in New Hampshire’s Great Bay Estuary has declined in the past decades, with local populations reduced due primarily to disease, excessive siltation, and past over-harvest. The loss of filtering oysters results in diminished ecological benefits for water quality, nitrogen control, and other services that healthy oyster populations provide. In support of management objectives to restore oyster populations, The Nature Conservancy (TNC) and the University of New Hampshire (UNH) have combined for a fifth consecutive year of scaled-up methods to rebuild oyster reefs and populations. Since 2009, we have “planted” seasoned shell, primarily surf-clam and oyster mix, on channel bottom as a hard substrate foundation to recruit spawn from nearby native populations. Constructed areas are amended to supplement recruitment with laboratory-raised and volunteer-grown “spat-on-shell” from remotely set larvae. Following four consecutive years of experience and adaptation, 2013 was a year of unprecedented effort and conservation outcomes. We successfully constructed and seeded five new acres of reef adjacent to native oysters in the Piscataqua River in Dover (1.5 acres) and in the Lamprey River in Newmarket (3.5 acres). Notably, we employed a new shell deployment method to achieve large-scale reef construction. Restoration efforts were greatly enhanced by excellent remote set success and outstanding natural recruitment, resulting in over 2M oysters. In addition, community engagement through the volunteer Oyster Conservationist program reached another all-time high with fifty families producing our largest oyster stock ever for restoration. Over the past five years, our efforts have added over 13 acres and 3M oysters to the ecosystem, increasing native Great Bay Estuary oyster populations by about 10%

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

Down-regulation of Cdc6, a cell cycle regulatory gene, in prostate cancer

CDC6 plays a critical role in regulation of the onset of DNA replication in eukaryotic cells. We have found that Cdc6 expression is down-regulated in prostate cancer as detected by semiquantitative reverse transcriptase-PCR of prostate cell lines and laser-captured microdissected prostate tissues. This result was substantiated by immunohistochemical analysis of paraffin-embedded tissue sections and immunoblot analysis of benign (BPH-1) and adenocarcinomatous prostatic cells. Furthermore, a 100-fold reduction in the transcription efficiency of the Cdc6 promoter-luciferase construct was noted in the metastatic PC3 cells compared with that in BPH-1 cells. Concentration of the E2F and Oct1 transcription factors that have putative binding sites in the Cdc6 promoter was substantially low in PC3 cells compared with BPH cells. Mutagenesis of the two E2F binding sites on the Cdc6 promoter resulted in increased promoter activity in PC3 cells owing to elimination of the negative regulation by pRb-E2F complex but not to the level of that obtained in BPH cells. We conclude that an altered interaction of transcription factors may be responsible for the down-regulation of Cdc6 transcription in PC3 cells. Our study suggests a potential use of the lack of CDC6 expression as an index of prostate cancer development

Down-regulation of Cdc6, a cell cycle regulatory gene, in prostate cancer

CDC6 plays a critical role in regulation of the onset of DNA replication in eukaryotic cells. We have found that Cdc6 expression is down-regulated in prostate cancer as detected by semiquantitative reverse transcriptase-PCR of prostate cell lines and laser-captured microdissected prostate tissues. This result was substantiated by immunohistochemical analysis of paraffin-embedded tissue sections and immunoblot analysis of benign (BPH-1) and adenocarcinomatous prostatic cells. Furthermore, a 100-fold reduction in the transcription efficiency of the Cdc6 promoter-luciferase construct was noted in the metastatic PC3 cells compared with that in BPH-1 cells. Concentration of the E2F and Oct1 transcription factors that have putative binding sites in the Cdc6 promoter was substantially low in PC3 cells compared with BPH cells. Mutagenesis of the two E2F binding sites on the Cdc6 promoter resulted in increased promoter activity in PC3 cells owing to elimination of the negative regulation by pRb-E2F complex but not to the level of that obtained in BPH cells. We conclude that an altered interaction of transcription factors may be responsible for the down-regulation of Cdc6 transcription in PC3 cells. Our study suggests a potential use of the lack of CDC6 expression as an index of prostate cancer development

LIM kinase 1 is essential for the invasive growth of prostate epithelial cells - Implications in prostate cancer

Mammalian LIM kinase 1 (LIMK1) is involved in reorganization of actin cytoskeleton through inactivating phosphorylation of the ADF family protein cofilin, which depolymerizes actin filaments. Maintenance of the actin dynamics in an ordered fashion is essential for stabilization of cell shape or promotion of cell motility depending on the cell type. These are the two key phenomena that may become altered during acquisition of the metastatic phenotype by cancer cells. Here we show that LIMK1 is overexpressed in prostate tumors and in prostate cancer cell lines, that the concentration of phosphorylated cofilin is higher in metastatic prostate cancer cells, and that a partial reduction of LIMK1 altered cell proliferation by arresting cells at G(2)/ M, changed cell shape, and abolished the invasiveness of metastatic prostate cancer cells. We also show that the ectopic expression of LIMK1 promotes acquisition of invasive phenotype by the benign prostate epithelial cells. Our data provide evidence of a novel role of LIMK1 in regulating cell division and invasive property of prostate cancer cells and indicate that the effect is not mediated by phosphorylation of cofilin. Our study correlates with the recent observations showing a metastasis-associated chromosomal gain on 7q11.2 in prostate cancer, suggesting a possible gain in LIMK1 DNA (7q11.23)

Virtual Constraints and Hybrid Zero Dynamics for Realizing Underactuated Bipedal Locomotion

Underactuation is ubiquitous in human locomotion and should be ubiquitous in bipedal robotic locomotion as well. This chapter presents a coherent theory for the design of feedback controllers that achieve stable walking gaits in underactuated bipedal robots. Two fundamental tools are introduced, virtual constraints and hybrid zero dynamics. Virtual constraints are relations on the state variables of a mechanical model that are imposed through a time-invariant feedback controller. One of their roles is to synchronize the robot's joints to an internal gait phasing variable. A second role is to induce a low dimensional system, the zero dynamics, that captures the underactuated aspects of a robot's model, without any approximations. To enhance intuition, the relation between physical constraints and virtual constraints is first established. From here, the hybrid zero dynamics of an underactuated bipedal model is developed, and its fundamental role in the design of asymptotically stable walking motions is established. The chapter includes numerous references to robots on which the highlighted techniques have been implemented.Comment: 17 pages, 4 figures, bookchapte

PCCR: Pancreatic Cancer Collaborative Registry

The Pancreatic Cancer Collaborative Registry (PCCR) is a multi-institutional web-based system aimed to collect a variety of data on pancreatic cancer patients and high-risk subjects in a standard and efficient way. The PCCR was initiated by a group of experts in medical oncology, gastroenterology, genetics, pathology, epidemiology, nutrition, and computer science with the goal of facilitating rapid and uniform collection of critical information and biological samples to be used in developing diagnostic, prevention and treatment strategies against pancreatic cancer. The PCCR is a multi-tier web application that utilizes Java/JSP technology and has Oracle 10 g database as a back-end. The PCCR uses a “confederation model” that encourages participation of any interested center, irrespective of its size or location. The PCCR utilizes a standardized approach to data collection and reporting, and uses extensive validation procedures to prevent entering erroneous data. The PCCR controlled vocabulary is harmonized with the NCI Thesaurus (NCIt) or Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT). The PCCR questionnaire has accommodated standards accepted in cancer research and healthcare. Currently, seven cancer centers in the USA, as well as one center in Italy are participating in the PCCR. At present, the PCCR database contains data on more than 2,700 subjects (PC patients and individuals at high risk of getting this disease). The PCCR has been certified by the NCI Center for Biomedical Informatics and Information Technology as a cancer Biomedical Informatics Grid (caBIG®) Bronze Compatible product. The PCCR provides a foundation for collaborative PC research. It has all the necessary prerequisites for subsequent evolution of the developed infrastructure from simply gathering PC-related data into a biomedical computing platform vital for successful PC studies, care and treatment. Studies utilizing data collected in the PCCR may engender new approaches to disease prognosis, risk factor assessment, and therapeutic interventions