Method for extracting pigment characteristic spectra from the phytoplankton absorption spectrum.

The extraction of pigment characteristic spectra from the phytoplankton absorption spectrum has high application value in phytoplankton identification and classification and in quantitative extraction of pigment concentrations. Derivative analysis, which has been widely used in this field, is easily interfered with by noisy signals and the selection of the derivative step, resulting in the loss and distortion of the pigment characteristic spectra. In this study, a method based on the one-dimensional discrete wavelet transform (DWT) was proposed to extract the pigment characteristic spectra of phytoplankton. DWT and derivative analysis were applied simultaneously to the phytoplankton absorption spectra of 6 phyla (Dinophyta, Bacillariophyta, Haptophyta, Chlorophyta, Cyanophyta, and Prochlorophyta) to verify the effectiveness of DWT in the extraction of pigment characteristic spectra.

Effects of typical marine environmental factors on the bioluminescence intensity of individual Noctiluca scintillans.

Red Noctiluca scintillans (RNS) is one of the major red tide species and dominant bioluminescent plankton in the global offshore. Bioluminescence offers a number of applications for ocean environment assessments such as interval waves study, fish stocks evaluation and underwater target detection making it of significant interest in forecasting bioluminescence occurrence and intensity. RNS is susceptible to changes in marine environmental factors. However, the effects of marine environmental factors on the bioluminescent intensity (BLI, photon s-1) of individual RNS cells (IRNSC) is poorly known. In this study, the effects of temperature, salinity and nutrients on the BLI were studied by field and laboratory culture experiments. In the field experiments, bulk BLI was measured by an underwater bioluminescence assessment tool at various temperature, salinity and nutrient concentrations. To exclude the contribution by other bioluminescent planktons, an identification method of IRNSC was first developed using the features of the bioluminescence flash kinetics (BFK) curve of RNS to identify and extract BLI emitted by an individual RNS cell. To decouple the effects of each environmental factor, laboratory culture experiments were conducted to examine the effects of a single factor on the BLI of IRNSC. The field experiments showed that BLI of IRNSC negatively correlated with temperature (3-27°C) and salinity (30-35‰). The logarithmic BLI can be well fitted using a linear equation with temperature or salinity with Pearson correlation coefficients of -0.95 and -0.80, respectively. The fitting function with salinity was verified by the laboratory culture experiment. On the other hand, no significant correlation was observed between BLI of IRNSC and nutrients. These relationships could be used in the RNS bioluminescence prediction model to improve the prediction accuracy of bioluminescent intensity and spatial distribution.

Construction of circRNA-miRNA-mRNA Network Reveal Functional circRNAs and Key Genes in Acute Myeloid Leukemia.

Introduction: CircRNA is closely correlated with a wide variety of processes of acute myeloid leukemia (AML), whereas the novel circRNAs, their molecular mechanism and the specific function they played in AML should be explored in depth. Methods: The microarray chip data of AML patients and normal samples in the Gene Expression Omnibus (GEO) database were selected to differentially expressed (DE) circRNA, miRNA, and mRNA genes. The miRNA gene was the intersection of the circRNA target gene predicted using CSCD and the miRNA gene screened from AML patients, while the mRNA gene was the intersection of the target gene mRNA of miRNA predicted using miRanda and miRTarBase software and the mRNA gene screened from AML patients. The hub mRNAs related to survival were further screened through Cox proportional hazard regression. CircRNA/miRNA/mRNA interaction network was constructed by using Cytoscape software.10 circRNAs and 6 miRNAs in bone marrow mononuclear cells (BMMNCs) of AML patients (n=43) and healthy controls (n=35) were determined by RT-qPCR. Correlations between them were analyzed by Pearson correlation coefficient. Results: 10 circRNAs, 6 miRNAs, and 33 mRNAs were identified. Subsequently, the network of circRNAs, miRNAs, and hub genes was built using Cystoscope. Four key circRNAs, seven hub genes and their regulatory pathways were identified. The result of RT-qPCRs showed that hsa_circ_0009581 and hsa_circ_0005273 were significantly upregulated in AML patients while hsa_circ_0000497 and hsa_circ_0001947 were significantly downregulated. Hsa-miR-150-5p was significantly downregulated; hsa-miR-454-3p was upregulated in AML patients. Hsa_circ_0009581 and hsa-miR-150-5p; hsa_ circ_0001947 and hsa-miR-454-3p were inversely correlated using Pearson's correlation coefficient. Conclusion: This study suggests that differentially expressed circRNAs take on a critical significance to AML development and may be the effective therapeutic targets. We suppose that hsa_circ_0009581 promotes leukemia development through hsa-miR-150-5p and hsa_circ_0001947 through hsa-miR-454-3p. hsa_circ_0001947 and hsa_circ_0009581 may provide new directions in the pathogenesis of AML.

A method for tracking the Brownian motion to estimate the size distribution of submicron particles in seawater.

Because the diffusivity of particles undergoing the Brownian motion is inversely proportional to their sizes, the size distribution of submicron particles can be estimated by tracking their movement. This particle tracking analysis (PTA) has been applied in various fields, but mainly focused on resolving monodispersed particle populations and is rarely used for measuring oceanic particles that are naturally polydispersed. We demonstrated using Monte Carlo simulation that, in principle, PTA can be used to size natural, oceanic particles. We conducted a series of lab experiments using microbeads of NIST-traceable sizes to evaluate the performance of ViewSizer 3000, a PTA-based commercial instrument, and found two major uncertainties: (1) the sample volume varies with the size of particles and (2) the signal-to-noise ratio for particles of sizes < 200-250 nm was reduced and hence their concentration was underestimated with the presence of larger particles. After applying the volume correction, we found the instrument can resolve oceanic submicron particles of sizes greater than 250 nm with a mean absolute error of 3.9% in size and 38% in concentration.

Deriving the angular response function for backscattering sensors.

We derived the angular response function (WN) for scattering sensors that automatically satisfies the normalization criterion and its corresponding weight (WT). WN's, derived for two commercial sensors, HydroScat-6 (HOBI Labs) and ECO-BB (Sea-Bird Inc.), agrees well with the Monte Carlo simulation and direct measurements. The backscattering measured for microbeads of known sizes agrees better with Mie calculation when the derived WN was applied. We deduced that the reduction of WT with increasing attenuation coefficient is related to path length attenuation and showed that this theoretically derived correction factor performs better than the default methods for the two commercial backscattering sensors. The analysis conducted in this study also leads to an estimate of uncertainty budget for the two sensors. The major uncertainty for ECO-BB is associated with its angular response function because of its wide field of view, whereas the main uncertainty for the HydrScat-6 is due to attenuation correction because of its relatively long path length.

Evaluation of regions suitable for vicarious calibration of ocean color satellite sensors in the South China Sea.

Accurate retrieval of biogeochemical components of the ocean at a global scale from space requires accurately calibrated top-of-atmosphere (TOA) radiance, which is usually achieved by deriving a vicarious gain coefficient (g-factor) through a process called system vicarious calibration (SVC). Currently, only two SVC sites, Marine Optical Buoy (MOBY) and BOUée pour l'acquiSition d'une Série Optique à Long termE (BOUSSOLE), are routinely operated to support the SVC process for all on-orbit ocean color satellite payloads. However, high-quality matchups between satellite observations and in situ measurements are rare because of the strict requirements of the SVC process. Meanwhile, a stable g-factor is usually computed by averaging sufficient gain measurements. Therefore, more SVC sites are required to derive a stable g-factor in a short duration, particularly for the initial calibration of newly launched satellite sensors. In this study, nearly twenty years of well-calibrated ocean color satellite data were used to calculate the mean and standard deviation of physical and optical properties of waters and the atmosphere in the South China Sea (SCS) to evaluate the feasibility of establishing a SVC site. A region was identified that meets all requirements that were used to evaluate the MOBY and BOUSSOLE sites. Two in situ measurements within this region were used to derive a g-factor for MODIS-Terra and MODIS-Aqua and were compared with the g-factor derived using MOBY data. The consistence of the two g-factors indicates that the identified region in the SCS could be a potential area for establishing a long-term moored SVC site.

Shape of particle backscattering in the North Pacific Ocean: the χ factor.

Volume scattering functions were measured using two instruments in waters near the Ocean Station Papa (50°N 145°W) and show consistency in estimating the χ factor attributable to particles (χp). While χp in the study area exhibits a limited variability, it could vary significantly when compared with data obtained in various parts of the global oceans. The global comparison also confirms that the minimal variation of χp is at scattering angles near 120°. With an uncertainty of <10%, χp can be assumed as spectrally independent. For backscatter sensors with wide field of view (FOV), the averaging of scattering within the FOV reduces the values of χp needed to compute the backscattering coefficient by up to 20% at angles <130∘.

Chronic myelomonocytic leukemia (CMML)-0 with pleural effusion as first manifestation: A case report.

RATIONALE: Extramedullary invasion of chronic myelomonocytic leukemia (CMML) usually occurs in the liver, spleen, and lymph nodes, while the pleural infiltration of CMML is rare. The presence of pleural effusion is usually associated with uncontrolled leukocytosis and increased monocytes. PATIENT CONCERNS: Here we reported a rare case of CMML-0 with pleural effusion as the first manifestation in a 44-year-old woman. The pleural effusion was caused by blasts infiltration confirmed by the flow cytometer and the pleural biopsy. DIAGNOSES: CMML with pleural invasion. INTERVENTIONS: The patient was treated with azacitidine 75 mg/m d for 2 cycles, followed by daily oral intake of hydroxyurea (500 mg/d). OUTCOMES: Pleural effusion was resolved and chest pain was relieved. LESSONS: The current case indicated that leukemic infiltration into pleura could occur despite mild leukocytes, while demethylation may be an effective therapy.

Variability of relationship between the volume scattering function at 180° and the backscattering coefficient for aquatic particles.

Properly interpreting lidar (light detection and ranging) signal for characterizing particle distribution relies on a key parameter, χp(π), which relates the particulate volume scattering function (VSF) at 180° (ßp(π)) that a lidar measures to the particulate backscattering coefficient (bbp). However, χp(π) has been seldom studied due to challenges in accurately measuring ßp(π) and bbp concurrently in the field. In this study, χp(π), as well as its spectral dependence, was re-examined using the VSFs measured in situ at high angular resolution in a wide range of waters. ßp(π), while not measured directly, was inferred using a physically sound, well-validated VSF-inversion method. The effects of particle shape and internal structure on the inversion were tested using three inversion kernels consisting of phase functions computed for particles that are assumed as homogenous sphere, homogenous asymmetric hexahedra, or coated sphere. The reconstructed VSFs using any of the three kernels agreed well with the measured VSFs with a mean percentage difference <5% at scattering angles <170∘. At angles immediately near or equal to 180°, the reconstructed ßp(π) depends strongly on the inversion kernel. χp(π) derived with the sphere kernels was smaller than those derived with the hexahedra kernel but consistent with χp(π) estimated directly from high-spectral-resolution lidar and in situ backscattering sensor. The possible explanation was that the sphere kernels are able to capture the backscattering enhancement feature near 180° that has been observed for marine particles. χp(π) derived using the coated sphere kernel was generally lower than those derived with the homogenous sphere kernel. Our result suggests that χp(π) is sensitive to the shape and internal structure of particles and significant error could be induced if a fixed value of χp(π) is to be used to interpret lidar signal collected in different waters. On the other hand, χp(π) showed little spectral dependence.

Calibration of the LISST-VSF to derive the volume scattering functions in clear waters.

The recently commercialized LISST-VSF instrument measures the volume scattering function (VSF) from 0.1° to 15° with a traditional laser diffraction unit (LISST) and from 15° to 155° with an eyeball component. Between these two optical components, only the LISST unit is calibrated. The eyeball measurements are scaled using the VSFs at 15° that are measured by both components. As this relative calibration relies on a valid measurement at 15° by the LISST, it might fail in clear oceanic waters, where the forward scattering is relative weak either due to a lack of large particles or an overall low concentration of all particles. In this study, we calibrated the LISST-VSF eyeball component through a series of lab experiments using standard polystyrene beads. Validation with the beads of two different sizes showed a median difference of 11.1% between theoretical and calibrated values. Further evaluations with in situ data collected by the LISST-VSF and an ECO-BB3 meter indicated that the new calibration worked well in both turbid and clear waters, while the relative calibration method tended to overestimate VSFs in clear waters.

Uncertainty in the optical remote estimation of the biomass of Ulva prolifera macroalgae using MODIS imagery in the Yellow Sea.

A laboratory experiment was conducted to obtain a floating algae index (FAI) of the floating macroalgae (Ulva prolifera), corresponding to various values of biomass per unit area (BPA). A piecewise empirical model was used to fit the statistical relationships between BPA and FAI, corresponding to FAI ≤ 0.2 (BPA ≤ 1.81kg/m2) and FAI ˃ 0.2 (BPA ˃ 1.81 kg/m2). Spectral mixing derived results show that a linear relationship between FAI and BPA is maintained when the BPA of endmembers is less than 1.81 kg/m2. However, when the BPA of the endmembers exceeds 1.81 kg/m2, there is substantial uncertainty in the optical remote estimation of biomass. Although the MODIS-derived FAI of Ulva prolifera is often less than 0.2, it is very difficult to determine whether the FAI results from low BPA (≤ 1.81kg/m2) of the endmembers, or from a low area ratio including high BPA (˃ 1.81 kg/m2), due to pixel mixing. If it is assumed that the unit biomass distribution of pure endmembers is a standard Gaussian distribution, then the uncertainty in the biomass estimation of Ulva prolifera from MODIS data can be expressed. This results in the uncertainty of ~36% in total biomass estimation, ~43% of which was contributed by a few pixels (10% of total pixels) with high FAI (˃ 0.05). The uncertainty in BPA caused by high FAI (˃ 0.05) pixels is about 7.2 times that for low FAI (≤ 0.05) pixels. In future research, the spatial distribution characteristics of the FAI of pure endmembers need to be considered in order to improve the accuracy of optical remote estimation of floating Ulva prolifera.

Vertical variations in optical properties of the waters in the Yellow Sea and Bohai Sea at seasonal scales and their influencing mechanisms.

This research used the profile data measured extensively in the Yellow Sea and Bohai Sea (YSBS) to explain the temporal and spatial distribution characteristics of optical properties and systematically analyzed the influencing mechanisms of the seasonal variations of optical properties in the YSBS in conjunction with synchronously measured hydrological and biogeochemical data in vertical profiles. The main conclusions obtained are as follows: the vertical variations in the optical properties in the YSBS are mainly influenced by the stratification effect, vertical mixing function, and phytoplankton growth process; and the variations of optical properties are dominated by the change of particle characteristics. The backscattering ratio can be used to discriminate particle types as a proxy of particulate bulk refractive index. In the YSBS, for waters with a backscattering ratio of less than 0.012, the variations of optical properties are dominated by the phytoplankton particles. For waters with a backscattering ratio greater than 0.012, the variations of optical properties are dominated by inorganic sediment particles. In addition, for the YSBS, the variations in optical properties of upper surface layer waters can be elucidated well by the vertical variations.

Instantaneous influence of dust storms on the optical scattering property of the ocean: a case study in the Yellow Sea, China.

Asian dust storms originating from arid or semi-arid regions of China or her adjacent regions have important impact on the atmosphere and water composition, and ecological environment of the Eastern China Seas. This research used data collected in the middle of the South Yellow Sea, China, during a dust storm event from 23 April to 24 April 2006 to analyze the instantaneous influence of dust storms on optical scattering properties, which are closely related to particle characteristics. The analysis results showed that the dust storm had a remarkable influence on the optical scattering property in the upper mixed layer of water, and dust particles drily deposited from the dust storm with an aerosol optical depth of nearly 2.5 into the water could induce a 0.14 m-1 change in the water optical scattering coefficient at 532 nm at the depth of 4 m. The duration of the instantaneous influence of the dust storm on the water optical scattering properties was short, and this influence disappeared rapidly within approximately 3 hours after the end of the dust storm.

The research on borehole stability in depleted reservoir and caprock: using the geophysics logging data.

Long-term oil and gas exploitation in reservoir will lead to pore pressure depletion. The pore pressure depletion will result in changes of horizontal in-situ stresses both in reservoirs and caprock formations. Using the geophysics logging data, the magnitude and orientation changes of horizontal stresses in caprock and reservoir are studied. Furthermore, the borehole stability can be affected by in-situ stresses changes. To address this issue, the dehydration from caprock to reservoir and roof effect of caprock are performed. Based on that, the influence scope and magnitude of horizontal stresses reduction in caprock above the depleted reservoirs are estimated. The effects of development on borehole stability in both reservoir and caprock are studied step by step with the above geomechanical model.

Scattering by solutions of major sea salts.

Increased scattering by seawater relative to that by pure water is primarily due to additional fluctuation of the refractive index contributed by sea salts. Salts with different ionic weight and sizes, while barely affecting the scattering that is due to density fluctuations, have a significant effect on the scattering that is due to concentration fluctuations. And this explains the major differences of their total scattering that would be observed. Scattering by solutions of NaCl, the major sea salt, is consistently about 6.7% and 4% lower than seawater of the same mass concentration and of the same refractive index, respectively. Because of ionic interactions, the molecular scattering does not follow the simple addition rule that applies to bulk inherent optical properties, with the total less than the summation of the parts. The possible values of scattering by waters of, such as, Dead Sea or Orca Basin, which have different salt composition from seawater, are discussed.

Scattering by pure seawater at high salinity.

A new model for seawater scattering was developed, in which Gibbs function was used exclusively to derive the thermodynamic parameters that are associated with density fluctuation. Because Gibbs function was determined empirically from highly accurate measurements of a group of thermodynamic variables and is valid for S(A) up to 120 g kg(-1) (Deep-Sea Research I, 55, 1639, 2008), we expect the model is also valid over the extended range of salinity. The model agrees with the measurements by Morel (Cahiers Oceanographiques, 20, 157, 1968) with an average difference of -0.6% for S = 0 and 2.7% for S = 38.4. The scattering by seawater as predicted increases with salinity in a non-linear fashion, and linear extrapolation of scattering based on Morel's measurements would overestimate by up to 30%. The extrapolation of ZHH09 model (Optics Express, 17, 5698, 2009), which is valid for S(A) up to 40 g kg(-1), however, agrees with the prediction within +/- 2.5% over the entire range of salinity. Even though there are no measurements available for validation, the results suggested that the uncertainty is limited in using the newly developed model in estimating the scattering by seawater of high salinity.

Scattering by pure seawater: effect of salinity.

A theoretical model was developed estimating the scattering by seawater that are due to concentration fluctuation. Combining with the model proposed for density fluctuation (Optics Express, 17, 1671, 2009), we evaluated the overall effect of sea salts on the scattering. The variation of seawater scattering with the salinity is a combination of two factors: decreasing contribution due to density fluctuation and increasing contribution due to concentration fluctuation, with the latter effect dominating. The trend is, however, slightly non-linear and the linear adjustment of scattering with salinity that is frequently used would lead to an underestimate by an average of 2%. The results estimated at S = 38.4 per thousand agree with the measurements by Morel (Cahiers Oceanographiques, 20, 157, 1968) with an average difference of 1%, well within his experimental error of 2%. The spectral signature also varies with salinity, with the power-law slope increasing from -4.286 to -4.306 for salinity from 0 to 40 per thousand.

Estimating scattering of pure water from density fluctuation of the refractive index.

The use of density derivative of the refractive index from the classic Lorentz-Lorenz equation or its variations performed poorly in estimating the scattering by water, leading to the alternative use of pressure derivative instead, which however has been scarcely measured due to its extremely low sensitivity. Recently, density derivative has been deduced directly from theoretical models. Three characterizations of density derivative of the refractive index were evaluated and scattering of water thus calculated converge with each other within 3.5% and agree with the measurement by Morel (Cahiers Oceanographiques, 20, 157, 1968) within 2% (with depolarization ratio = 0.039), all improving over the earlier estimates based on either density or pressure derivatives. Taking into account of uncertainty associated with the depolarization ratio, the prediction based on the model by Proutiere et al. (J. Phy. Chem., 96, 3485, 1992) still agrees with the measurement within the experimental errors (2%).