Correction for the inherent error in optical density readings.

Except at very low levels, uncorrected photometric determination of bacterial cell densities showed a decreasing proportionally to actual cell density or dry weight. A standard curve was prepared to convert photometric readings to truly proportional optical density values. With one dry weight determination, optical density values may be converted to absolute dry weight values.     

DNA化学合成中的错误去除

在DNA的化学合成过程中,由于合成方法本身的限制,不可避免地会引入错误碱基,而在将化学合成的寡核苷酸拼装成长链DNA时,PCR反应等也会引入突变。为了得到高保真的合成DNA,必须对错误和突变进行纠正,本文介绍了能够用于纠正DNA合成过程中错误的内切核酸酶及错误结合蛋白,并介绍了它们进行错误纠正的方法,最后对这两类方法的优缺点进行了分析。     

内陆湖泊水体固有光学特性的典型季节差异

固有光学特性是水体光学性质的重要内容,是水色反演分析模型建立的基础.本研究利用定量滤膜技术（QFT）和后向散射测量仪BB9,对太湖梅梁湾夏、冬季水体的有色可溶性有机物(CDOM)吸收系数、总悬浮物吸收系数和总悬浮物后向散射系数进行了观测.在分别对两季节水体组分吸收系数、后向散射系数光谱特征分析的基础上,阐明其季节差异性,并结合水质参数的变化,揭示导致两季节水体固有光学特性不同的原因,达到通过固有光学量反映水环境状态的目的.初步建立了后向散射系数与悬浮物浓度的关系模型,为分析模型的构建提供了参数保障.     

The spleen colony technique. I. Correction for the overlap effect and sources of error in CFU-s determination

A linear model for the errors of the 'spleen colony' assay for haemopoietic stem cells has been derived. The components emerging from the model are interpreted and practical recommendations given for interpreting measurements made with this assay. The model permits correction for the effect of overlapping colonies and gives average errors for single measurements of the number of CFU-s. More reliable and more precise information can be obtained using this model. The spleen colony technique detects a population of immature precursor cells designated as CFU-s (Till & McCulloch, 1961). The relative error of measurement is often large when compared with the changes in the phenomena studied. Consequently a better knowledge of the errors of this technique is highly desirable. This paper should be regarded as an extension of the previous analysis of Till (1972). The theory for the errors of the spleen colony technique was applied to 905 determinations of the CFU-s numbers performed on random-bred mice. Data from random-bred mice rather than those from inbred mice have been used because the error components can be expected to be larger and, consequently, more easily detectable. The model of errors has also been validated using data published by Till (1972) and has subsequently been applied to data from several inbred mice strains (Znojil & Necas, 1988).     

Census error and the detection of density dependence

1. Studies aiming to identify the prevalence and nature of density dependence in ecological populations have often used statistical analysis of ecological time-series of population counts. Such time-series are also being used increasingly to parameterize models that may be used in population management. 2. If time-series contain measurement errors, tests that rely on detecting a negative relationship between log population change and population size are biased and prone to spuriously detecting density dependence (Type I error). This is because the measurement error in density for a given year appears in the corresponding change in population density, with equal magnitude but opposite sign. 3. This effect introduces bias that may invalidate comparisons of ecological data with density-independent time-series. Unless census error can be accounted for, time-series may appear to show strongly density-dependent dynamics, even though the density-dependent signal may in reality be weak or absent. 4. We distinguish two forms of census error, both of which have serious consequences for detecting density dependence. 5. First, estimates of population density are based rarely on exact counts, but on samples. Hence there exists sampling error, with the level of error depending on the method employed and the number of replicates on which the population estimate is based. 6. Secondly, the group of organisms measured is often not a truly self-contained population, but part of a wider ecological population, defined in terms of location or behaviour. Consequently, the subpopulation studied may effectively be a sample of the population and spurious density dependence may be detected in the dynamics of a single subpopulation. In this case, density dependence is detected erroneously, even if numbers within the subpopulation are censused without sampling error. 7. In order to illustrate how process variation and measurement error may be distinguished we review data sets (counts of numbers of birds by single observers) for which both census error and long-term variance in population density can be estimated. 8. Tests for density dependence need to obviate the problem that measured population sizes are typically estimates rather than exact counts. It is possible that in some cases it may be possible to test for density dependence in the presence of unknown levels of census error, for example by uncovering nonlinearities in the density response. However, it seems likely that these may lack power compared with analyses that are able to explicitly include census error and we review some recently developed methods.     

High-frequency optical measurements in shallow Lake Taihu, China: determining the relationships between hydrodynamic processes and inherent optical properties

In order to determine the effect of wind-induced waves (influenced by wind velocity and direction) on the dynamics of optical properties in shallow lakes, we determined the short-term variability of the inherent optical properties (IOPs) in Meiliang Bay, Lake Taihu, China, by examining high-frequency data collected between 8 and 21 September 2010 from meteorology and optical sensors. The absorption and beam attenuation coefficients under strong winds were significantly higher than those under weak and moderate winds (t test, P < 0.001). Significant correlations were found between absorption, scattering, beam attenuation, and wind speed, showing that the hydrodynamic process was an important factor that influenced the instantaneous IOPs of the water. However, the different wind directions have a different effect degree on the IOPs. Western wind is the most important driven wind direction of this site. In addition, significant correlations were found between b _p(440), c _p+g(440), b _p(677), c _p+g(677), b _p(440), and turbidity under each wind direction (P < 0.001). Exponential and hyperbolic exponent models of the absorption and beam attenuation coefficients were fitted, and linear models between a _p+g(677), c _p+g(677), and turbidity were developed. Thus, in shallow lakes such as Lake Taihu, using real-time high-frequency monitoring of the turbidity to deduce the water IOPs could be an efficient and practical approach. Our study will be helpful in monitoring the IOPs and in improving the accuracy of bio-optical models to estimate water quality parameters in Lake Taihu.     

Application of polydimethylsiloxane-based optical system for measuring optical density of microbial culture

The performance of recently developed polydimethylsiloxane (PDMS)-based optical system was tested for measuring optical density of microbial culture. The data showed that PDMS-based spectrometer is superior to “one drop” spectrometers in the accuracy, and has an advantage over conventional spectrometers in measuring dense culture without dilution.     

Correction of infra-red gas analyser readings for changes in reference tube CO2 concentration

Abstract The theoretical basis for correcting infra-red gas analyser readings for changes in reference tube CO₂ concentration is developed, but in practice the corrections made are empirical. Analyser gain (G_A) is related to reference tube concentration (A) in hyperbolic manner. The constants in the equation are determined by plotting 1/G_A against A. Calibration and operating procedure for a particular type of analyser are described and a numerical example given.     

Unusual links between inherent and apparent optical properties in shallow lakes,the case of Taihu Lake

The spectral distribution of downwelling solar irradiance is an important factor in the radiative balance, primary productivity and biogeochemistry in most lakes. In the present study, we show the relative importance of different inherent and apparent optical properties in controlling the spectral attenuation of diffuse downwelling irradiance in a large shallow lake in eastern China. Most importantly, we show how elevated concentrations of suspended matter not only increase attenuation, but are linked to a “spectral shift” in major attenuation peaks, with important consequences on biogeochemical processes and remote sensing. The analysis of the lake optical properties in relation to the geographical distribution of submerged macrophytes indicates how heterogenic optical conditions play a role in controlling benthic primary production.     

Influence of optical density on the automated segmentation of rat kidney lysosomes.

After staining for acid phosphatase, video-images were acquired from 0.5-micron sections of rat kidney. Lysosomes in proximal tubules were automatically segmented, using a VICOM digital image processor and measured for area, number and optical density (OD). The purpose of this study is to objectively evaluate the performance of the automated segmentation algorithm at different staining intensities (a) by measuring area after staining with different incubation times, reduced substrate concentration or by adding an inhibitor and (b) by 'simulating' a decrease in OD (reducing grey-values at each point of a digitized image). The results of the experiments showed that: (1) the algorithm will underestimate the size of lysosomes (a) when the OD in close to the local background and (b) when an area is larger than or close to the area of the lowpass square filter; (2) accuracy of the segmentation can be improved by comparing the results of feature extraction after segmentation of the same image at different relative OD levels; (3) lysosomes with very low OD, compared to background are delineated with a large error or not delineated at all and this cannot be corrected. Incorrectly delineated lysosomes can be identified and excluded from further calculations, or their measured area replaced by an estimate of the true area.     

Thickness and density of protein films by optical mixing spectroscopy.

The adsorption of protein films on polystyrene latex spheres was studied by optical mixing spectroscopy. With this technique, we show that both the hydrodynamic thickness of protein films and their optical density can be measured. Thus, we found that films of the glycoproteins isolated from the human erythrocyte membrane were four times as thick as films of either human serum albumin or bovine serum albumin for about the same surface coverage. This result suggests an end-on orientation for the adsorbed glycoprotein molecules, which is consistent with the model proposed by others for the orientation of these molecules at the surface of the red blood cell itself.     

Specific inherent optical quantities of complex turbid inland waters, from the perspective of water classification

For optically complex turbid productive waters, the optical behavior of suspended particles is the keynote of characterizing the unordered variations of inherent optical properties (IOPs). Multiple bio-optical measurements and sampling of optically active substances were performed in Lake Taihu, Lake Chaohu, and Lake Dianchi, and Three Gorges reservoir of China, in 2008, 2009, and 2010. On the basis of obtaining adequate observation data, we developed an improved and robust water classification approach, by which complex water conditions were divided into three types, i.e., Type 1 (Normalized Trough Depth at 675 nm, hereafter NTD675, ≥0.092), Type 2 (0 < NTD675 < 0.092), and Type 3 (NTD675 ≤ 0). Furthermore, the specific inherent optical quantities for suspended particles, including the specific absorption coefficient of non-algal particles (a*(nap)), the specific absorption coefficient of phytoplankton (a*(ph)), and the specific scattering coefficient of the suspended particles (b*(p)), were determined for the three classified types of waters. The validation results showed that our proposed values for these specific inherent optical quantities presented relatively high predictive accuracies, with most mean absolute percentage errors (MAPE) near 30%, and more importantly, performed much better than that of non-classified waters. Additionally, relative contributions of phytoplankton and non-algal particles to the total particulate absorption and scattering, as well as the spectra, were also analyzed, and the differences among the three classified types of waters were clarified. Overall, the results obtained in this study provide us with new knowledge for understanding complex varied inherent optical properties of highly turbid productive waters.