Indirect estimates of natural mortality rate for arrowtooth flounder (Atheresthes stomias) and darkblotched rockfish (Sebastes crameri)

Indirect estimates of instantaneous natural mortality rate (M) are widely used in stock assessment and fisheries management. They are essentially a form of meta-analysis, in which prior information on M and key life history parameters from a variety of stocks is used to estimate M for the stock in question.

Strong, low frequency (decadal) environmental fluctuations during the 20th century in the North Pacific Ocean, on the Washington coast, and in Puget Sound

At decadal period (10-20 years), dynamic linkage was evident between atmospheric low pressure systems over the North Pacific Ocean and circulation in a Pacific Northwest fjord (Puget Sound). As the Aleutian low pressure center shifts, storms arriving from the North Pacific Ocean deposit varying amounts of precipitation in the mountains draining into the estuarine system; in turn, the fluctuating addition of fresh water changes the density distribution near the fjord basin entrance sill, thereby constraining the fjord's vertical velocity structure. This linkage was examined using time series of 21 environmental parameters from 1899 to 1987. Covariation in the time series was evident because of the strong decadal cycles compared with long-term averages, interannual variability, and seasonal cycles.

SLP: A zero-contact non-invasive method for pulmonary function testing

Structured Light Plethysmography (SLP) is a novel non-invasive method that uses structured light to perform pulmonary function testing that does not require physical contact with a patient. The technique produces an estimate of chest wall volume changes over time. A patient is observed continuously by two cameras and a known pattern of light (i.e. structured light) is projected onto the chest using an off-the-shelf projector. Corner features from the projected light pattern are extracted, tracked and brought into correspondence for both camera views over successive frames. A novel self calibration algorithm recovers the intrinsic and extrinsic camera parameters from these point correspondences. This information is used to reconstruct a surface approximation of the chest wall and several novel ideas for 'cleaning up' the reconstruction are used. The resulting volume and derived statistics (e.g. FVC, FEV) agree very well with data taken with a spirometer. © 2010. The copyright of this document resides with its authors.

Thermal annealing behaviour of Ni/Au on n-GaN Schottky contacts

The Schottky behaviour of Ni/Au contact on n-GaN was investigated under various annealing conditions by current-voltage (I-V) measurements. A non-linear fitting method was used to extract the contact parameters from the I-V characteristic curves. Experimental results indicate that high quality Schottky contact with a barrier height and ideality factor of 0.86 +/- 0.02 eV and 1.19 +/- 0.02 eV, respectively, can be obtained under 5 min annealing at 600degreesC in N-2 ambience.

A METHOD OF FITTING TO MOSSBAUER SPECTRUM OF EU-151 AND ITS APPLICATION TO EUROPIUM COMPOUNDS

A method of fitting to Mossbauer spectrum of 151Eu has been proposed. The intensities and the positions of all the possible transitions between the sublevels of the ground state and those of the excited state of nucleus with spin I> 3/2 can be considered at one time in fitting to experimental Mossbauer spectra by this method. The method has been used to fit to the experimental Mossbauer spectra of europium orthophosphate crystal and of europium pentaphosphate crystal, and to derive Mossbauer parameters from...

Interactions between the bloom-forming dinoflagellates Prorocentrum donghaiense and Alexandrium tamarense in laboratory cultures

Interactions between Prorocentrum donghaiense and Alexandrium tamarens, two bloom-forming dinoflagellates, were investigated using bi-algal cultures. All R donghaiense died, but A. tamarense was hardly affected by the end of the experiment when the initial cell density was set at 1.0 X 10(4) cells mL(-1) for P. donghaiense and 0.28 x 10(4) cells mL(-1) for A. tamarense. However, significant growth suppression occurred in either species when the initial cell density of P donghaiense increased to I. 0 X 105 Cells mL(-1) in the bi-algal culture, but no out-competement was observed. The simultaneous assay on the culture filtrates showed that P donghaiense filtrate prepared at a lower initial density (1.0 X 10(4) cells mL(-1)) stimulated growth of the co-cultured A. tanzarense (0.28 x 10(4) cells mL(-1)), but filtrate at a higher initial density (1.0 x 10(5) cells mL(-1)) depressed its growth. The filtrate of A. tamarense at a density of 0.28 x 10(4) cells mL(-1) killed all R donghaiense at a lower density (1.0 x 10(4) cells mL(-1)), but only exhibited an inhibitory effect on it at a higher density (1.0 x 10(5) cells mL(-1)). It is likely that these two species of microalgae interfere with each other mainly by releasing allelochemical substance(s) into the culture medium, and a direct cell-to-cell contact was not necessary for their mutual interaction. The allelopathic test further proved that A. tamarense could affect the growth of co-cultured P. donghaiense by producing allelochemical(s); moreover, A. tamarense culture filtrate at the stationary growth phase (SP) had a strongly inhibitory effect on P donghaiense compared to that at the exponential phase (EP). Results also demonstrated a dose-dependent relationship between the microalgal initial cell density and the degree of the allelopathic effect. The growth of R donghaiense and A. tamarense in the bi-algal cultures was simulated using a mathematical model to quantify the interaction. The estimated parameters from the model showed that the inhibition exerted by A. tamarense on P. donghaiense was about 17 and 8 times stronger than the inhibition P. donghaiense exerted on A. tamarense, when the initial cell density was set at 1.0 X 10(4) and 1.0 X 10(5) cells mL(-1) for P donghaiense, respectively. and 0.28 x 10(4) cells mL(-1) for A. tamarense in the bi-algal cultures. A. tamarense seems to have a survival strategy that is superior to that of P. donghaiense in bi-algal cultures under controlled laboratory conditions. (c) 2006 Elsevier B.V. All rights reserved.

基于随机介质理论的多尺度储层非均质性定量描述

Application of long-term exploration for oil and gas shows that the reservoir technology of prediction is one of the most valuable methods. Quantitative analysis of reservoir complexity is also a key technology of reservoir prediction. The current reservoir technologies of prediction are based on the linear assumption of various physical relationships. Therefore, these technologies cannot handle complex reservoirs with thin sands, high heterogeneities in lithological composition and strong varieties in petrophysical properties. Based on the above-mentioned complex reservoir, this paper conducts a series of researches. Both the comprehending and the quantitative analysis of reservoir heterogeneities have been implemented using statistical and non-linear theories of geophysics. At the beginning, the research of random media theories about reservoir heterogeneities was researched in this thesis. One-dimensional (1-D) and two-dimensional (2-D) random medium models were constructed. The autocorrelation lengths of random medium described the mean scale of heterogeneous anomaly in horizontal and deep directions, respectively. The characteristic of random medium models were analyzed. We also studied the corresponding relationship between the reservoir heterogeneities and autocorrelation lengths. Because heterogeneity of reservoir has fractal nature, we described heterogeneity of reservoir by fractal theory based on analyzing of the one-dimensional (1-D) and two-dimensional (2-D) random medium models. We simulated two-dimensional (2-D) random fluctuation medium in different parameters. From the simulated results, we can know that the main features of the two-dimensional (2-D) random medium mode. With autocorrelation lengths becoming larger, scales of heterogeneous geologic bodies in models became bigger. In addition, with the autocorrelation lengths becoming very larger, the layer characteristic of the models is very obvious. It would be difficult to identify sandstone such as gritstone, clay, dense sandstone and gas sandstone and so on in the reservoir with traditional impedance inversion. According to the obvious difference between different lithologic and petrophysical impedance, we studied multi-scale reservoir heterogeneities and developed new technologies. The distribution features of reservoir lithological and petrophysical heterogeneities along vertical and transverse directions were described quantitatively using multi-scale power spectrum and heterogeneity spectrum methods in this paper. Power spectrum (P spectrum) describes the manner of the vertical distribution of reservoir lithologic and petrophysical parameters and the large-scale and small-scale heterogeneities along vertical direction. Heterogeneity spectrum (H spectrum) describes the structure of the reservoir lithologic and petrophysical parameters mainly, that is to say, proportional composition of each lithological and petrophysical heterogeneities are calculated in this formation. The method is more reasonable to describe the degree of transverse multi-scale heterogeneities in reservoir lithological and petrophysical parameters. Using information of sonic logs in Sulige oil field, two spectral methods have been applied to the oil field, and good analytic results have been obtained. In order to contrast the former researches, the last part is the multi-scale character analysis of reservoir based on the transmission character of wave using the wavelet transform. We discussed the method applied to demarcate sequence stratigraphy and also analyzed the reservoir interlayer heterogeneity.

油气勘探风险评价与决策技术研究

PetroChina and other national petroleum incorporations need rigorous procedures and practical methods in risk evaluation and exploration decision at home and abroad to safeguard their international exploration practice in exploration licence bidding, finding appropriate ratio of risk sharing with partners, as well as avoiding high risk projects and other key exploration activities. However, due to historical reasons, we are only at the beginning of a full study and methodology development in exploration risk evaluation and decision. No rigorous procedure and practical methods are available in our exercises of international exploration. Completely adopting foreign procedure, methods and tools by our national incorporations are not practical because of the differences of the current economic and management systems in China. The objective of this study is to establish a risk evaluation and decision system with independent intellectual property right in oil and gas exploration so that a smooth transition from our current practice into international norm can take place. The system developed in this dissertation includes the following four components: 1. A set of quantitative criteria for risk evaluation is derived on the basis of an anatomy of the parameters from thirty calibration regions national wide as well as the characteristics and the geological factors controlling oil and gas occurrence in the major petroleum-bearing basins in China, which provides the technical support for the risk quantification in oil and gas exploration. 2. Through analysis of existing methodology, procedure and methods of exploration risk evaluation considering spatial information are proposed. The method, utilizing Mahalanobis Distance (MD) and fuzzy logic for data and information integration, provides probabilistic models on the basis of MD and fuzzy logic classification criteria, thus quantifying the exploration risk using Bayesian theory. A projection of the geological risk into spatial domain provides a probability map of oil and gas occurrence in the area under study. The application of this method to the Nanpu Sag shows that this method not only correctly predicted the oil and gas occurrence in the areas where Beibu and Laoyemiao oil fields are found in the northwest of the onshore area, but also predicted Laopu south, Nanpu south and Hatuo potential areas in the offshore part where exploration maturity was very low. The prediction of the potential areas are subsequently confirmed by 17 exploration wells in the offshore area with 81% success, indicating this method is very effective for exploration risk visualization and reduction. 3. On the basis of “Methods and parameters of economic evaluation for petroleum exploration and development projects in China”, a ”pyramid” method for sensitivity analysis was developed, which meets not only the need for exploration target evaluation and exploration decision at home, but also allows a transition from our current practice to international norm in exploration decision. This provides the foundation for the development of a software product “Exploration economic evaluation and decision system of PetroChina” (EDSys). 4. To solve problem in methodology of exploration decision, effort was made on the method of project portfolio management. A drilling decision method was developed employing the concept of geologically risked net present value. This method overcame the dilemma of handling simultaneously both geological risk and portfolio uncertainty, thus casting light into the application of modern portfolio theory to the evaluation of high risk petroleum exploration projects.

三维非均匀各向异性介质中的纵波走时反演研究

Many observations show that seismic anisotropy is very common in the crust and upper mantle of the Earth. Seismic anisotropy can provide some clue about the changing and transporting process inside the earth. in recent years, abundant earthquake travel time data are accumulated, computers become more powerful, and these make the inversion of earthquake travel time data practical. In this thesis we studied the theory of elastic wave in anisotropic media, some formule for travel time inversion were derived. We present an iterative procedure to determine 21 elastic parameters from qP wave travel times. No a priori assumptions about heterogeneity and anisotropy of the model are made. The procedure is suitable for the case when we know nothing about the symmetry of anisotropy of the media, as well as for the case of earthquake travel time inversion which may contain various symmetry of anisotropy. The procedure is tested with a synthetic multiple-source offset VSP experiment. The results proved that the formulae are correct, and the procedure is practical. The results and the related theory indicate that the anisotropic inversion needs more rays than isotropic case. For a 2-D weak anisotropic (WA) medium, we need at least 5 rays in different directions to retrieve the elastic parameters on one grid point, and for a 3-D WA medium we need at least 15 rays in different directions to retrieve the elastic parameters on one grid point. The results also indicate that the starting background velocity has no influence on the final results, at least for the model we specified. Our results also show that insufficient illumination coverage will slow down the convergence rate, and make the results more sensitive to noise. We apply the procedure to a set of field travel time data. The data is from an artificial seismic observation. This observation is for locating micro-seismic events around a tunnel, its purpose is to find out if the digging process and the stress condition around the tunnel can generate micro-cracks. The size of this area is around 100m. The anisotropy derived from qP travel times is the same as the anisotropy showed by apparent velocities, and is also consistent with the anisotropy derived from S-wave splitting phenomena.

Determination of alcohols by high-performance liquid chromatography with fluorimetric detection after pre-column derivatisation with carbazole-9-N-acetic acid and chromatographic behaviour of alcoholic derivatives

Alcohols were derivatised to their carbazole-9-N-acetic acid (CRA) esters with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC . HCl) as the dehydrating agent. Studies on derivatisation conditions indicated that the coupling reaction proceeded rapidly and smoothly in the presence of a base catalyst in acetonitrile to give the corresponding sensitively fluorescent derivatives. The retention behaviour of alcohol derivatives was investigated by varying mobile phase compositions (ACN-water and MeOH-water). The parameters from the equation log k'=A-BX were evaluated by retention data of derivatives using an isocratic elution with different mobile phases. The results indicated that the parameters derived allowed computation of retention factors in good agreement with experiments. At the same time, a general equation was derived that makes possible predictions of partition coefficient in binary mobile phases with different proportions of organic solvent to water based on some simple regression analysis. The LC separation for the derivatised alcohols containing higher carbon alcohols showed good reproducibility on a reversed-phase C-18 column with gradient elution. The detection limits (excitation at 335 nm, emission at 360 nm) for derivatised alcohols (signal-to-noise ratio=3:1) were in the range of 0.1-0.4 pg per injection. (C) 2001 Elsevier Science B.V. All rights reserved.

Automatic Detection of Relevant Head Gestures in American Sign Language Communication

An automated system for detection of head movements is described. The goal is to label relevant head gestures in video of American Sign Language (ASL) communication. In the system, a 3D head tracker recovers head rotation and translation parameters from monocular video. Relevant head gestures are then detected by analyzing the length and frequency of the motion signal's peaks and valleys. Each parameter is analyzed independently, due to the fact that a number of relevant head movements in ASL are associated with major changes around one rotational axis. No explicit training of the system is necessary. Currently, the system can detect "head shakes." In experimental evaluation, classification performance is compared against ground-truth labels obtained from ASL linguists. Initial results are promising, as the system matches the linguists' labels in a significant number of cases.

Knowledge-based IMRT treatment planning for prostate cancer.

PURPOSE: To demonstrate the feasibility of using a knowledge base of prior treatment plans to generate new prostate intensity modulated radiation therapy (IMRT) plans. Each new case would be matched against others in the knowledge base. Once the best match is identified, that clinically approved plan is used to generate the new plan. METHODS: A database of 100 prostate IMRT treatment plans was assembled into an information-theoretic system. An algorithm based on mutual information was implemented to identify similar patient cases by matching 2D beam's eye view projections of contours. Ten randomly selected query cases were each matched with the most similar case from the database of prior clinically approved plans. Treatment parameters from the matched case were used to develop new treatment plans. A comparison of the differences in the dose-volume histograms between the new and the original treatment plans were analyzed. RESULTS: On average, the new knowledge-based plan is capable of achieving very comparable planning target volume coverage as the original plan, to within 2% as evaluated for D98, D95, and D1. Similarly, the dose to the rectum and dose to the bladder are also comparable to the original plan. For the rectum, the mean and standard deviation of the dose percentage differences for D20, D30, and D50 are 1.8% +/- 8.5%, -2.5% +/- 13.9%, and -13.9% +/- 23.6%, respectively. For the bladder, the mean and standard deviation of the dose percentage differences for D20, D30, and D50 are -5.9% +/- 10.8%, -12.2% +/- 14.6%, and -24.9% +/- 21.2%, respectively. A negative percentage difference indicates that the new plan has greater dose sparing as compared to the original plan. CONCLUSIONS: The authors demonstrate a knowledge-based approach of using prior clinically approved treatment plans to generate clinically acceptable treatment plans of high quality. This semiautomated approach has the potential to improve the efficiency of the treatment planning process while ensuring that high quality plans are developed.

Computational Inference of Genome-Wide Protein-DNA Interactions Using High-Throughput Genomic Data

Transcriptional regulation has been studied intensively in recent decades. One important aspect of this regulation is the interaction between regulatory proteins, such as transcription factors (TF) and nucleosomes, and the genome. Different high-throughput techniques have been invented to map these interactions genome-wide, including ChIP-based methods (ChIP-chip, ChIP-seq, etc.), nuclease digestion methods (DNase-seq, MNase-seq, etc.), and others. However, a single experimental technique often only provides partial and noisy information about the whole picture of protein-DNA interactions. Therefore, the overarching goal of this dissertation is to provide computational developments for jointly modeling different experimental datasets to achieve a holistic inference on the protein-DNA interaction landscape.

We first present a computational framework that can incorporate the protein binding information in MNase-seq data into a thermodynamic model of protein-DNA interaction. We use a correlation-based objective function to model the MNase-seq data and a Markov chain Monte Carlo method to maximize the function. Our results show that the inferred protein-DNA interaction landscape is concordant with the MNase-seq data and provides a mechanistic explanation for the experimentally collected MNase-seq fragments. Our framework is flexible and can easily incorporate other data sources. To demonstrate this flexibility, we use prior distributions to integrate experimentally measured protein concentrations.

We also study the ability of DNase-seq data to position nucleosomes. Traditionally, DNase-seq has only been widely used to identify DNase hypersensitive sites, which tend to be open chromatin regulatory regions devoid of nucleosomes. We reveal for the first time that DNase-seq datasets also contain substantial information about nucleosome translational positioning, and that existing DNase-seq data can be used to infer nucleosome positions with high accuracy. We develop a Bayes-factor-based nucleosome scoring method to position nucleosomes using DNase-seq data. Our approach utilizes several effective strategies to extract nucleosome positioning signals from the noisy DNase-seq data, including jointly modeling data points across the nucleosome body and explicitly modeling the quadratic and oscillatory DNase I digestion pattern on nucleosomes. We show that our DNase-seq-based nucleosome map is highly consistent with previous high-resolution maps. We also show that the oscillatory DNase I digestion pattern is useful in revealing the nucleosome rotational context around TF binding sites.

Finally, we present a state-space model (SSM) for jointly modeling different kinds of genomic data to provide an accurate view of the protein-DNA interaction landscape. We also provide an efficient expectation-maximization algorithm to learn model parameters from data. We first show in simulation studies that the SSM can effectively recover underlying true protein binding configurations. We then apply the SSM to model real genomic data (both DNase-seq and MNase-seq data). Through incrementally increasing the types of genomic data in the SSM, we show that different data types can contribute complementary information for the inference of protein binding landscape and that the most accurate inference comes from modeling all available datasets.

This dissertation provides a foundation for future research by taking a step toward the genome-wide inference of protein-DNA interaction landscape through data integration.

Disponibilidad del recurso hídrico en la microcuenca del río Bermúdez. Región central de Costa Rica.

La microcuenca del río Bermúdez es parte de la principal zona de explotación hídrica en la región Central de Costa Rica, razón por la cual se realiza un diagnóstico de la disponibilidad del recurso hídrico en esta microcuenca donde se identifican las áreas con mayor problemática de disponibilidad de este recurso. Para ello se calculó un balance hídrico mensual, según uso del suelo, unidad geomorfológica y zona climática. Con base en este balance se determinó y clasificó la disponibilidad del recurso, identificando en la microcuenca solamente tres categorías: alta, media y moderada. No existen áreas de baja disponibilidad de recurso hídrico lo que demuestra que la oferta es suficiente, sin embargo, existe una presión importante sobre el recurso hídrico pues más de la mitad del área de la microcuenca se encuentra con una disponibilidad moderada.

Channelled Waves in Anisotropic Mesh Metamaterials

Channelled waves in 2-D periodic anisotropic L-C mesh metamaterials have been investigated. Circuit simulation and the newly developed analytical model of a unit cell have demonstrated full qualitative agreement for both lossless and lossy cases. Isofrequencies for a lattice unit cell and the circuit simulations of finite meshes have shown that propagating waves are channelled from a point source as pencil beams which can travel only along specific trajectories. The beam direction varies with frequency, and at the resonance frequency, the phase and group velocities of the travelling wave are orthogonal. The effect of losses was explored, and it was shown that losses cause qualitative changes of the channelled wave type. It was proven that the channelled waves do not follow the laws of geometrical optics (Snell's law, specular reflection, etc.) at the interfaces of L-C meshes but are governed by the conditions of phase synchronism and impedance matching. Only in the special case of dual L-C and C-L meshes with the interface parallel to the axis of rectangular grid excited at the resonance frequency (X=1) do the channels follow the trajectories of optical rays. A planar mesh test cell has been designed and used for retrieving the unit cell L-C parameters from the S-parameter measurements.