A characterization of the sandy beach surf zone fish community and their ecology in Northern California and the effects of marine protected areas

Historically written off as dull and homogenous, the dynamics of the sandy beach surf zone remains under studied world-wide. Northern California has been no exception to this global standard, as the sandy beach surf zone ecosystem in this region has yet to be characterized, and the effect of Marine Protected Areas (MPAs) on the fish and macroinvertebrate community fully ascertained. Considered data-poor by local wildlife officials, commercially, recreationally and culturally important Amphistichus rhodoterus (redtail surfperch) and common Hyperprosopon ellipticum (silver surfperch) utilize the sandy beach surf zone in Northern California. Little is known about the effect of various environmental factors, or the effect of MPAs on these species. While the trophodynamics of redtail surfperch in this region have been researched, the diet of smaller individuals of this species and of silver surfperch have yet to be explored. This thesis sought to enrich global knowledge of the sandy beach surf zone fish and invertebrate community by sampling four MPAs and four matched reference sites between San Francisco Bay and the California/Oregon border during the summers of 2019 and 2020. Data were gathered on the community by deploying baited remote underwater video cameras (BRUVs), seining, and collecting data on water and physical beach variables. To better understand the effect of MPAs on silver and redtail surfperch a hook and line survey was conducted at two MPAs and two reference sites in Humboldt County during the summer of 2020. A diet analysis on silver and redtail surfperch in Humboldt County was also performed to gain information about the trophodynamics of these important species, and to provide further insight into the ecology of the sandy beach surf zone ecosystem. Twenty-four taxa categories were identified on the underwater BRUV (Baited Remote Underwater Video) cameras such as Triakas semifasciata (leopard shark), Amphistichus spp. (surfperch genus) and Cancer spp (crab family), and 23 species from 12 families were identified in the seine sampling including redtail and silver surfperch, and Leptocottus armatus (pacific staghorn sculpin). The difference in community composition, species richness, and abundance between Drake’s and Doran, the southern-most paired-sites and the rest of the beaches was the clearest result. The study found no differences between years, and little effect of MPAs on the sandy beach surf zone fish and invertebrate community in Northern California. Water temperature (+), salinity (+), and total dissolved solids (-) were correlated with species richness and abundance in the BRUV data, while wave height (-) and salinity (+) were correlated with species richness and abundance in the seine data. Twenty-eight invertebrate diet taxa were observed in the stomachs of 51 redtail and 37 silver surfperch. This study found that silver surfperch have a more heterogenous diet than redtail surfperch, which may be influenced by wave height and water temperature. No significant difference in redtail surfperch length or catch per unit of effort (CPUE) between MPAs and reference sites in Humboldt County was found. This study shows that like in other parts of the world, sandy beach surf zones are inhabited by a diverse fish and macroinvertebrate community that feeds on the smaller and diverse invertebrate community. The fish and macroinvertebrate community varied spatially among beaches, with Drake’s and Doran beaches having a significantly different community than the northernmost beaches. The MPAs showed little to no effect on the fish community, or the surfperch abundance and length, potentially because of the age of the MPAs, lack of enforcement, or minimal fishing pressure outside the MPA boundaries. Few studies on the sandy beach surf zone have implemented both seining and baited remote underwater videos. It was found in this study that by employing these two sampling techniques a more complete picture of the sandy beach surf zone was able to be ascertained. Organisms which would not have been enumerated with seining alone due to their size or ability to escape the net, such as leopard sharks and Lontra canadensis (river otter), were able to be “captured” on video footage. Future research in the sandy beach surf zone habitat would benefit from this more robust sampling protocol, although if utilized in more energetic environments, modifications to the equipment are strongly suggested. The purpose of this study was to (1) characterize the fish community in the sandy beach surf zone habitat in Northern California by quantifying the species richness, abundance and composition of species present, and relating these biotic metrics to environmental variables; (2) evaluate the effectiveness of the MPAs that include sandy beach surf zones of northern California by comparing the fish community within and outside MPA boundaries; (3) explore the effect of MPAs on length and CPUE of redtail surfperch in Humboldt County; and (4) analyze the diet composition of silver and redtail surfperch in the Northern California region. The research presented in this thesis can help better inform fisheries management decisions in Northern California by providing insight into how various spatial, temporal, and environmental factors influence the sandy beach surf zone ecosystem and the trophodynamics of two important fish species, which inhabit this environment. A more complete understanding of the sensitivity of the sandy beach surf zone ecosystem to the factors researched in this thesis can promote knowledge surrounding the effect of large-scale shifts in the environment, and help direct management decisions to benefit future fisheries

Nucleon-Nucleon Scattering in a Three Dimensional Approach

The nucleon-nucleon (NN) t-matrix is calculated directly as function of two vector momenta for different realistic NN potentials. To facilitate this a formalism is developed for solving the two-nucleon Lippmann-Schwinger equation in momentum space without employing a partial wave decomposition. The total spin is treated in a helicity representation. Two different realistic NN interactions, one defined in momentum space and one in coordinate space, are presented in a form suited for this formulation. The angular and momentum dependence of the full amplitude is studied and displayed. A partial wave decomposition of the full amplitude it carried out to compare the presented results with the well known phase shifts provided by those interactions.Comment: 26 pages plus 10 jpg figure

Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

Objective: This study aimed to identify the oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on mRNA expression of genes in this amplicon. Methods: Segmentation of DNA copy number changes on 20q was performed by array CGH (comparative genomic hybridisation) in 34 non-progressed colorectal adenomas, 41 progressed adenomas (ie, adenomas that present a focus of cancer) and 33 adenocarcinomas. Moreover, a robust analysis of altered expression of genes in these segments was performed by microarray analysis in 37 adenomas and 31 adenocarcinomas. Protein expression was evaluated by immunohistochemistry on tissue microarrays. Results: The genes C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5, mapping at 20q, were significantly overexpressed in carcinomas compared with adenomas as a consequence of copy number gain of 20q. Conclusion: This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specific biomarkers for colorectal cancer with potential clinical applications

Relativistic Mean Field Model with Generalized Derivative Nucleon-Meson Couplings

The quantum hadrodynamics (QHD) model with minimal nucleon-meson couplings is generalized by introducing couplings of mesons to derivatives of the nucleon field in the Lagrangian density. This approach allows an effective description of a state-dependent in-medium interaction in the mean-field approximation. Various parametrizations for the generalized couplings are developed and applied to infinite nuclear matter. In this approach, scalar and vector self-energies depend on both density and momentum similarly as in the Dirac-Brueckner theory. The Schr\"{o}diger-equivalent optical potential is much less repulsive at high nucleon energies as compared to standard relativistic mean field models and thus agrees better with experimental findings. The derivative couplings in the extended model have significant effects on properties of symmetric nuclear matter and neutron matter.Comment: 35 pages, 1 table, 10 figure

Does delay in diagnosing colorectal cancer in symptomatic patients affect tumor stage and survival? A population-based observational study

<p>Abstract</p> <p>Background</p> <p>Diagnosing colorectal cancer (CRC) at an early stage improves survival. To what extent any delay affects outcome once patients are symptomatic is still unclear.</p> <p>Our objectives were to evaluate the association between diagnostic delay and survival in symptomatic patients with early stage CRC and late stage CRC.</p> <p>Methods</p> <p>Prospective population-based observational study evaluating daily clinical practice in Northern Holland. Diagnostic delay was determined through questionnaire-interviews. Dukes' stage was classified into two groups: early stage (Dukes A or B) and late stage (Dukes C or D) cancer. Patients were followed up for 3.5 years after diagnosis.</p> <p>Results</p> <p>In total, 272 patients were available for analysis. Early stage CRC was present in 136 patients while 136 patients had late stage CRC. The mean total diagnostic delay (SE) was 31 (1.5) weeks in all CRC patients. No significant difference was observed in the mean total diagnostic delay in early versus late stage CRC (<it>p </it>= 0.27).</p> <p>In early stage CRC, no difference in survival was observed between patients with total diagnostic delay shorter and longer than the median (Kaplan-Meier, log-rank <it>p </it>= 0.93).</p> <p>In late stage CRC, patients with a diagnostic delay shorter than the median had a shorter survival than patients with a diagnostic delay longer than the median (log-rank <it>p </it>= 0.01). In the multivariate Cox regression model with survival as dependent variable and median delay, age, open access endoscopy, number and type of symptoms as independent variables, the odd's ratio for survival in patients with long delay (>median) versus short delay (≤median) was 1.8 (95% confidence interval (CI) 1.1 to 3.0; <it>p </it>= 0.01). Tumor-site was not associated with patient survival. When separating late stage CRC in Dukes C and Dukes D tumors, a shorter delay was associated with a shorter survival in Dukes D tumors only and not in Dukes C tumors.</p> <p>Conclusion</p> <p>In symptomatic CRC patients, a longer diagnostic and therapeutic delay in routine clinical practice was not associated with an adverse effect on survival. The time to CRC diagnosis and initiation of treatment did not differ between early stage and late stage colorectal cancer.</p

MiR-17-92 cluster is associated with 13q gain and c-myc expression during colorectal adenoma to adenocarcinoma progression

Background:MicroRNAs are small non-coding RNA molecules, which regulate central mechanisms of tumorigenesis. In colorectal tumours, the combination of gain of 8q and 13q is one of the major factors associated with colorectal adenoma to adenocarcinoma progression. Functional studies on the miR-17-92 cluster localised on 13q31 have shown that its transcription is activated by c-myc, located on 8q, and that it has oncogenic activities. We investigated the contribution of the miR-17-92 cluster during colorectal adenoma to adenocarcinoma progression.Methods:Expression levels of the miR-17-92 cluster were determined in 55 colorectal tumours and in 10 controls by real-time RT-PCR. Messenger RNA c-myc expression was also determined by real-time RT-PCR in 48 tumours with array comparative genomic hybridisation (aCGH) data available.Results:From the six members of the miR-17-92 cluster, all except miR-18a, showed significant increased expression in colorectal tumours with miR-17-92 locus gain compared with tumours without miR-17-92 locus gain. Unsupervised cluster analysis clustered the tumours based on the presence of miR-17-92 locus gain. Significant correlation between the expression of c-myc and the six miRNAs was also found.Conclusion:Increased expression of miR-17-92 cluster during colorectal adenoma to adenocarcinoma progression is associated to DNA copy number gain of miR17-92 locus on 13q31 and c-myc expression. © 2009 Cancer Research UK

Endoscopic full-thickness resection of T1 colorectal cancers:a retrospective analysis from a multicenter Dutch eFTR registry

Background Complete endoscopic resection and accurate histological evaluation for T1 colorectal cancer (CRC) are critical in determining subsequent treatment. Endoscopic full-thickness resection (eFTR) is a new treatment option for T1 CRC<2cm. We aimed to report clinical outcomes and short-term results. Methods Consecutive eFTR procedures for T1 CRC, prospectively recorded in our national registry between November 2015 and April 2020, were retrospectively analyzed. Primary outcomes were technical success and R0 resection. Secondary outcomes were histological risk assessment, curative resection, adverse events, and short-term outcomes. Results We included 330 procedures: 132 primary resections and 198 secondary scar resections after incomplete T1 CRC resection. Overall technical success, R0 resection, and curative resection rates were 87.0% (95% confidence interval [CI] 82.7%-90.3%), 85.6% (95%CI 81.2%-89.2%), and 60.3% (95%CI 54.7%-65.7%). Curative resection rate was 23.7% (95%CI 15.9%-33.6%) for primary resection of T1 CRC and 60.8% (95%CI 50.4%-70.4%) after excluding deep submucosal invasion as a risk factor. Risk stratification was possible in 99.3%. The severe adverse event rate was 2.2%. Additional oncological surgery was performed in 49/320 (15.3%), with residual cancer in 11/49 (22.4%). Endoscopic follow-up was available in 200/242 (82.6%), with a median of 4 months and residual cancer in 1 (0.5%) following an incomplete resection. Conclusions eFTR is relatively safe and effective for resection of small T1 CRC, both as primary and secondary treatment. eFTR can expand endoscopic treatment options for T1 CRC and could help to reduce surgical overtreatment. Future studies should focus on long-term outcomes

Promoter DNA Methylation of Oncostatin M receptor-β as a Novel Diagnostic and Therapeutic Marker in Colon Cancer

In addition to genetic changes, the occurrence of epigenetic alterations is associated with accumulation of both genetic and epigenetic events that promote the development and progression of human cancer. Previously, we reported a set of candidate genes that comprise part of the emerging “cancer methylome”. In the present study, we first tested 23 candidate genes for promoter methylation in a small number of primary colon tumor tissues and controls. Based on these results, we then examined the methylation frequency of Oncostatin M receptor-β (OSMR) in a larger number of tissue and stool DNA samples collected from colon cancer patients and controls. We found that OSMR was frequently methylated in primary colon cancer tissues (80%, 80/100), but not in normal tissues (4%, 4/100). Methylation of OSMR was also detected in stool DNA from colorectal cancer patients (38%, 26/69) (cut-off in TaqMan-MSP, 4). Detection of other methylated markers in stool DNA improved sensitivity with little effect on specificity. Promoter methylation mediated silencing of OSMR in cell lines, and CRC cells with low OSMR expression were resistant to growth inhibition by Oncostatin M. Our data provide a biologic rationale for silencing of OSMR in colon cancer progression and highlight a new therapeutic target in this disease. Moreover, detection and quantification of OSMR promoter methylation in fecal DNA is a highly specific diagnostic biomarker for CRC

Quantification of the Temporal Evolution of Collagen Orientation in Mechanically Conditioned Engineered Cardiovascular Tissues

Load-bearing soft tissues predominantly consist of collagen and exhibit anisotropic, non-linear visco-elastic behavior, coupled to the organization of the collagen fibers. Mimicking native mechanical behavior forms a major goal in cardiovascular tissue engineering. Engineered tissues often lack properly organized collagen and consequently do not meet in vivo mechanical demands. To improve collagen architecture and mechanical properties, mechanical stimulation of the tissue during in vitro tissue growth is crucial. This study describes the evolution of collagen fiber orientation with culture time in engineered tissue constructs in response to mechanical loading. To achieve this, a novel technique for the quantification of collagen fiber orientation is used, based on 3D vital imaging using multiphoton microscopy combined with image analysis. The engineered tissue constructs consisted of cell-seeded biodegradable rectangular scaffolds, which were either constrained or intermittently strained in longitudinal direction. Collagen fiber orientation analyses revealed that mechanical loading induced collagen alignment. The alignment shifted from oblique at the surface of the construct towards parallel to the straining direction in deeper tissue layers. Most importantly, intermittent straining improved and accelerated the alignment of the collagen fibers, as compared to constraining the constructs. Both the method and the results are relevant to create and monitor load-bearing tissues with an organized anisotropic collagen network

Is increased time to diagnosis and treatment in symptomatic cancer associated with poorer outcomes?:Systematic review

background: It is unclear whether more timely cancer diagnosis brings favourable outcomes, with much of the previous evidence, in some cancers, being equivocal. We set out to determine whether there is an association between time to diagnosis, treatment and clinical outcomes, across all cancers for symptomatic presentations. methods: Systematic review of the literature and narrative synthesis. results: We included 177 articles reporting 209 studies. These studies varied in study design, the time intervals assessed and the outcomes reported. Study quality was variable, with a small number of higher-quality studies. Heterogeneity precluded definitive findings. The cancers with more reports of an association between shorter times to diagnosis and more favourable outcomes were breast, colorectal, head and neck, testicular and melanoma. conclusions: This is the first review encompassing many cancer types, and we have demonstrated those cancers in which more evidence of an association between shorter times to diagnosis and more favourable outcomes exists, and where it is lacking. We believe that it is reasonable to assume that efforts to expedite the diagnosis of symptomatic cancer are likely to have benefits for patients in terms of improved survival, earlier-stage diagnosis and improved quality of life, although these benefits vary between cancers