Xu, Haibo

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    Design and characterization of a passive wireless DNA sensor
    (2014) Xu, Haibo; Jia, Yi; College of Engineering; Toledo Quiñones, Manuel; Sundaram, Paul; Department of Mechanical Engineering; De Jesús, Marco A.
    In order to predict and avoid disasters due to gene mutation, reliable DNA information is necessary to be monitored in real time. Existing DNA sensing technologies offer outstanding performance in terms of the resolution and time response. However, these technologies require either physical connection of signal communication, a battery power supply or expensive equipment for acquiring DNA information. The limitations make existing DNA sensing technologies complex and hard to access. The motivation of the proposed research is to develop an innovative DNA sensing platform which exploits a multidisciplinary area synthesizing the conventional DNA capacitive sensing mechanism and surface-based conformational characterization throughout DNA immobilization and hybridization. Compared with previous work [1], in which the capacitance measurement is fully employed, we develop another method – impedance measurement with expected features of high sensitivity, passively and wirelessly integrated. The sensor is activated by electromagnetic waves and the resonant frequency of the sensor is interrogated remotely with a single loop antenna by monitoring the frequency response of the voltage across it. The feasibility of using electrochemical impedance measurements on the proposed planar circuit to detect DNA behavior directly without chemical labels is demonstrated. The resonant frequency shift caused by the change of capacitance throughout DNA immobilization and hybridization occurring on top of a capacitor is monitored by the means of impedance analyzer, with which it is possible to inspect the graph amplitude on the behavior of signal strength and compute the quality factor of the coupling element represented by bandwidth. In order to get a sensor with the best sensitivity, smallest size, longest detection distance and highest quality factor, the design consideration and method for the sensor together with the interdigital capacitor and the planar inductor are indicated in a posterior section. Experiments for measuring the frequency shift due to interface charge transmission were carried out in order to study its DNA sensing mechanism and possibility of DNA sensing enhancement. Finally, 32 samples were measured throughout the experiment and the average capacitance values which represented a variety of surface charge resulting from DNA molecule behavior were obtained. The capacitance changed from 11.58pF to 114.5pF when specific ssDNA was attached to electrodes and then increased to 218.6pF once complementary strand DNA was involved and hybridized with existing DNA chains. In addition, using impedance analyzer measurements, the resonant frequency decreased from 2.01MHz to 1.97MHz in the presence of ssDNA and further down to 0.95MHz since complementary strand DNA was deposited. Consequently an innovative passive wireless DNA sensor has been successfully demonstrated.
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    Oceanographic pathways and hydrodynamic connectivity between marine protected areas in the US Virgin Islands and eastern Puerto Rico
    (2022-12-12) Xu, Haibo; Canals Silander, Miguel F.; College of Arts and Sciences - Sciences; Esteves Amador, René F.; Mercado, Aurelio; Morell Rodríguez, Julio M.; Department of Marine Sciences; Morales Payán, José P.
    In order to better understand the coastal circulation in Puerto Rico and the US Virgin Islands (PRVI), a high-resolution coastal modeling system using the Finite Volume Community Ocean Model (FVCOM) was implemented by Caribbean Coastal Ocean Observing System (CARICOOS). This model was composed of unstructured triangular elements horizontally to provide a more accurate geometric representation of complex coastlines with a resolution of up to 100 m toward the coasts. The model configuration was improved and used to run a hindcast simulation for 2019 (climatological year). Its boundary was forced by the operational AmSeas forecasting system. CARICOOS 2-km Weather Research and Forecasting Models (WRF) provided meteorological conditions on the surface. Fourteen tidal constituents were derived from the T tide Matlab toolbox with harmonic constants of the TPXO-7.2 module. Daily sea surface temperature and elevation observed by satellite products and hourly surface currents measured by High-Frequency Radars (HFR) along the southern and western coast of Puerto Rico were assimilated into the simulation. Its performance was evaluated statistically using various observational data from field observations. Additionally, the AmSeas model acted as a benchmark in this work, showing the improvement of FVCOM in model skill. The connectivity network of marine protected areas (MPAs) and potential settlement sites with spawning aggregations sites in PRVI were examined through simulated pathways of two fish larvae: red hind and mutton snapper. The analysis was based on an offline particle tracking model (PTM) incorporating hourly surface currents from the validated FVCOM for 2019. The virtual larvae were released in peak spawning seasons (December-February for red hind (Epinephelus guttatus) and April-June for mutton snapper (Lutjanus analis)) at recorded MPAs, then tracked for a time period determined by their own pelagic larval duration (PLD). Ontogenetic behavior after larval flexion was presented by a species-specific vertical distribution probability matrix, which was derived from the fish surveys conducted in PRVI from 2007 to 2010 and used to simulate the vertical migration of larvae for capturing the depth-varied currents. Several connectivity indices such as potential self-recruitment, successful settlement rate, and betweenness centrality were qualitatively and quantitatively analyzed. Our findings suggested that, in general, the spawning aggregations sites of red hind were well connected to the shelf of PRVI, and mutton snapper spawning aggregation areas in the southwest of St. Croix presented a unique connection to the south/southeast of Puerto Rico. A significant self-recruitment pattern was found in Hind Bank. Moreover, sensitivity analysis was conducted to explore the impact of major factors such as settlement sites, release sites, and time on larval connectivity. Our simulated results revealed that the fraction of released larvae that settled on suitable habitats were highly sensitive to those factors. The dispersal and trajectories were similar to previous connectivity studies conducted by other researchers and agreed well with the few observational studies within PRVI. The study contributed to the present understanding of the role of these fish spawning sites and their relative contribution to local vs. far-field recruitment. It could help the Caribbean Fishery Management Council (CFMC) address the evaluation of the marine protected areas as sources and determine the sinks for the eggs and larvae spawned off the US Virgin Islands (USVI).