Fitting Time Series Models to Fisheries Data to Ascertain Age

The ability of government agencies to assign accurate ages of fish is important to fisheries management. Accurate ageing allows for most reliable age-based models to be used to support sustainability and maximize economic benefit. Assigning age relies on validating putative annual marks by evaluating accretional material laid down in patterns in fish ear bones, typically by marginal increment analysis. These patterns often take the shape of a sawtooth wave with an abrupt drop in accretion yearly to form an annual band and are typically validated qualitatively. Researchers have shown key interest in modeling marginal increments to verify the marks do, in fact, occur yearly. However, it has been challenging in finding the best model to predict this sawtooth wave pattern. We propose three new applications of time series models to validate the existence of the yearly sawtooth wave patterned data: autoregressive integrated moving average (ARIMA), unobserved component, and copula. These methods are expected to enable the identification of yearly patterns in accretion. ARIMA and unobserved components account for the dependence of observations and error, while copula incorporates a variety of marginal distributions and dependence structures. The unobserved component model produced the best results (AIC: -123.7, MSE 0.00626), followed by the time series model (AIC: -117.292, MSE: 0.0081), and then the copula model (AIC: -96.62, Kendall\u27s tau: -0.5503). The unobserved component model performed best due to the completeness of the dataset. In conclusion, all three models are effective tools to validate yearly accretional patterns in fish ear bones despite their differences in constraints and assumptions

Spatial Variation in Otolith Chemistry of Atlantic Croaker Larvae in the Mid-Atlantic Bight

Larval Atlantic croaker Micropogonias undulatus (1 to 7 mm in standard length) were collected on the east coast of the United States from North Carolina to Delaware during 2000. We defined 3 water-mass boundaries for potential groups of spawning Atlantic croaker using temperature and salinity measured at each sampling station. We tested the hypothesis that distinct otolith chemistries existed among 3 groups of larval Atlantic croaker collected from these water masses using solution-based inductively coupled plasma-mass spectrometry. Multivariate analysis of variance indicated that otolith chemistry differed significantly among water masses. Using a quadratic discriminant function, we were able to correctly classify fish from the Mid-Atlantic Bight (MAB) 73 % of the time, South Atlantic Bight (SAB) 53 % of the time, and Chesapeake Bay plume 36 % of the time. The correct reclassification rates observed were significantly better than random. Results from this study indicate that it is possible to obtain measurable elemental concentrations from otoliths much smaller than previously analyzed (weight 0.015 to 1.976 μg). Moreover, contrary to previous studies, our results indicate that it is possible to distinguish natal signatures among larvae on different spawning grounds in the MAB and SAB. Further, this new information could benefit investigations of dispersal from offshore spawning grounds to estuaries or other nursery habitats

Patterns of Larval Atlantic Croaker Ingress into Chesapeake Bay, USA

We compared ingress patterns of Atlantic croaker Micropogonias undulatus larvae into Chesapeake Bay, USA, with published ingress patterns through barrier island inlets, the accepted model for larval fish ingress. This model asserts that larvae ingress on night flood tides at the flooddominated side of the inlet and at all depths. At the Chesapeake Bay mouth and in the adjacent coastal waters, we compared the distribution of abundance, size, age, and growth rates of croaker prior to ingress, In contrast to the barrier island inlet model, croaker larvae were more abundant at depth than closer to the surface regardless of location. However, the response to light was variable, where croaker larvae farther offshore showed no response to light, but croaker larvae in the bay mouth were more abundant at night. Croaker larvae followed an expected pattern of increasing age and length from offshore stations to the bay mouth station. Further, among nearshore coastal stations there was evidence of larger and older croaker larvae at the northern portion of the bay mouth than at middle or southern stations. Patterns in growth were similar at all locations, indicating the likelihood of a single source location or similar environments among transport pathways for croaker larvae. Ingress can occur across the entire mouth of Chesapeake Bay; however, net tidal inflow may result in age and size structuring, which allows more rapid movement into the northern flood-dominated portions of the bay mouth

UC-15 Malware Analysis Using Reverse Engineering

The motivation for this project is driven by evaluation of the different tools on the market that allow for breaking down executables or binary files, and understanding what the malware is doing. By reverse-engineering the malware, we can understand its impact and how to protect against it. Our focus is to understand where different tools are stronger than others, as well as understand the evolving landscape of malware and security overall. For this capstone project, we utilized two different tools and many sample malware files. The methods used to debug the malware are detailed in our milestone two report and will be expanded upon in our final presentation. At this point, we\u27ve found the tool WinDbg to be the most versatile for binary and executable debugging. We also evaluated IDA Pro, and understand the many ways in which its graphical display of data and relationships, equips a researcher with the necessary tools and information to walk through an executable. Our focus in milestone 3 is to expand our documentation and guide on malware debugging to the point that it provides a user the full breadth of information and steps needed to start from scratch and end with a broken apart piece of malware. We provided much of this as part of the milestone 2 presentation and report, but we will continue to build on it so it\u27s a useful how-to guide for anyone trying to debug a piece of malicious code.Advisors(s): Dr. Ying Xie [email protected](s): SecurityIT 498

Near-Infrared Spectroscopy of Low Mass X-ray Binaries : Accretion Disk Contamination and Compact Object Mass Determination in V404 Cyg and Cen X-4

We present near-infrared (NIR) broadband (0.80--2.42 $\mu$m) spectroscopy of two low mass X-ray binaries: V404 Cyg and Cen X-4. One important parameter required in the determination of the mass of the compact objects in these systems is the binary inclination. We can determine the inclination by modeling the ellipsoidal modulations of the Roche-lobe filling donor star, but the contamination of the donor star light from other components of the binary, particularly the accretion disk, must be taken into account. To this end, we determined the donor star contribution to the infrared flux by comparing the spectra of V404 Cyg and Cen X-4 to those of various field K-stars of known spectral type. For V404 Cyg, we determined that the donor star has a spectral type of K3 III. We determined the fractional donor contribution to the NIR flux in the H- and K-bands as $0.98 \pm .05$ and $0.97 \pm .09$, respectively. We remodeled the H-band light curve from \citet{sanwal1996} after correcting for the donor star contribution to obtain a new value for the binary inclination. From this, we determined the mass of the black hole in V404 Cyg to be $M_{BH}= 9.0^{+.2}_{-.6}M_{\odot}$. We performed the same spectral analysis for Cen X-4 and found the spectral type of the donor star to be in the range K5 -- M1V. The donor star contribution in Cen X-4 is $0.94\pm.14$ in the H-band while in the K-band, the accretion disk can contribute up to 10% of the infrared flux. We remodeled the H-band light curve from \citet{shahbaz1993}, again correcting for the fractional contribution of the donor star to obtain the inclination. From this, we determined the mass of the neutron star as $M_{NS}= 1.5^{+.1}_{-.4}M_{\odot}$. However, the masses obtained for both systems should be viewed with some caution since contemporaneous light curve and spectral data are required to obtain definitive masses

Cisplatin +/− rucaparib after preoperative chemotherapy in patients with triple-negative or BRCA mutated breast cancer

Patients with triple-negative breast cancer (TNBC) who have residual disease after neoadjuvant therapy have a high risk of recurrence. We tested the impact of DNA-damaging chemotherapy alone or with PARP inhibition in this high-risk population. Patients with TNBC or deleterious BRCA mutation (TNBC/BRCAmut) who had >2 cm of invasive disease in the breast or persistent lymph node (LN) involvement after neoadjuvant therapy were assigned 1:1 to cisplatin alone or with rucaparib. Germline mutations were identified with BROCA analysis. The primary endpoint was 2-year disease-free survival (DFS) with 80% power to detect an HR 0.5. From Feb 2010 to May 2013, 128 patients were enrolled. Median tumor size at surgery was 1.9 cm (0-11.5 cm) with 1 (0-38) involved LN; median Residual Cancer Burden (RCB) score was 2.6. Six patients had known deleterious BRCA1 or BRCA2 mutations at study entry, but BROCA identified deleterious mutations in 22% of patients with available samples. Toxicity was similar in both arms. Despite frequent dose reductions (21% of patients) and delays (43.8% of patients), 73% of patients completed planned cisplatin. Rucaparib exposure was limited with median concentration 275 (82-4694) ng/mL post-infusion on day 3. The addition of rucaparib to cisplatin did not increase 2-year DFS (54.2% cisplatin vs. 64.1% cisplatin + rucaparib; P = 0.29). In the high-risk post preoperative TNBC/BRCAmut setting, the addition of low-dose rucaparib did not improve 2-year DFS or increase the toxicity of cisplatin. Genetic testing was underutilized in this high-risk population

Alterations of immune response of non-small lung cancer with azacytidine

Innovative therapies are needed for advanced Non-Small Cell Lung Cancer (NSCLC). We have undertaken a genomics based, hypothesis driving, approach to query an emerging potential that epigenetic therapy may sensitize to immune checkpoint therapy targeting PD-L1/PD-1 interaction. NSCLC cell lines were treated with the DNA hypomethylating agent azacytidine (AZA - Vidaza) and genes and pathways altered were mapped by genome-wide expression and DNA methylation analyses. AZA-induced pathways were analyzed in The Cancer Genome Atlas (TCGA) project by mapping the derived gene signatures in hundreds of lung adeno (LUAD) and squamous cell carcinoma (LUSC) samples. AZA up-regulates genes and pathways related to both innate and adaptive immunity and genes related to immune evasion in a several NSCLC lines. DNA hypermethylation and low expression of IRF7, an interferon transcription factor, tracks with this signature particularly in LUSC. In concert with these events, AZA up-regulates PD-L1 transcripts and protein, a key ligand-mediator of immune tolerance. Analysis of TCGA samples demonstrates that a significant proportion of primary NSCLC have low expression of AZA-induced immune genes, including PD-L1. We hypothesize that epigenetic therapy combined with blockade of immune checkpoints - in particular the PD-1/PD-L1 pathway - may augment response of NSCLC by shifting the balance between immune activation and immune inhibition, particularly in a subset of NSCLC with low expression of these pathways. Our studies define a biomarker strategy for response in a recently initiated trial to examine the potential of epigenetic therapy to sensitize patients with NSCLC to PD-1 immune checkpoint blockade

Non-work-related services at the workplace : an exploratory study

In an era of diminishing public funds, the profession of social work is looking more and more toward the private sector as an arena for social work practice. Social work has had a long-standing interest in the impact of work and the workplace on the individual. This study was developed in response to the lack of documentation of non-work-related services in Oregon\u27s businesses and industries. The research team set out to discover what non-work-related services are available to employees at or through the workplace in the TriCounty area (Multnomah, Clackamas, and Washington Counties) of Oregon. This study was exploratory, similar to one done by Hans Spiegel and colleagues in 1974, through Hunter College in New York City

A cryogenic rotation stage with a large clear aperture for the half-wave plates in the Spider instrument

We describe the cryogenic half-wave plate rotation mechanisms built for and used in Spider, a polarization-sensitive balloon-borne telescope array that observed the Cosmic Microwave Background at 95 GHz and 150 GHz during a stratospheric balloon flight from Antarctica in January 2015. The mechanisms operate at liquid helium temperature in flight. A three-point contact design keeps the mechanical bearings relatively small but allows for a large (305 mm) diameter clear aperture. A worm gear driven by a cryogenic stepper motor allows for precise positioning and prevents undesired rotation when the motors are depowered. A custom-built optical encoder system monitors the bearing angle to an absolute accuracy of +/- 0.1 degrees. The system performed well in Spider during its successful 16 day flight.Comment: 11 pages, 7 figures, Published in Review of Scientific Instruments. v2 includes reviewer changes and longer literature revie