A method for determining a rate constant for biexponential processes using data on dynamics of accumulating the end product of a reaction

A new method the rate constant determination of some biexponential processes is suggested. The method is based on the asymptotic solution of transcendental irrational equations, described such processes. This method can be used when kinetics of the final product of reaction is known. The values of the rate constants obtained by suggested method are precise, if the data used for calculation are also precise. In the other case methods of mathematical statistics should be used for evaluation of the slopes of kinetics curves in the semi-logarithmic coordinates.     

A method to measure predictive ability of an injury risk curve using an observation-adjusted area under the receiver operating characteristic curve

Area under the receiver operating characteristic curve (AROC) is commonly used to choose a biomechanical metric from which to construct an injury risk curve (IRC). However, AROC may not handle censored datasets adequately. Survival analysis creates robust estimates of IRCs which accommodate censored data. We present an observation-adjusted ROC (oaROC) which uses the survival-based IRC to estimate the AROC. We verified and evaluated this method using simulated datasets of different censoring statuses and sample sizes. For a dataset with 1000 left and right censored observations, the median AROC closely approached the oaROC_True, or the oaROC calculated using an assumed “true” IRC, differing by a fraction of a percent, 0.1%. Using simulated datasets with various censoring, we found that oaROC converged onto oaROC_True in all cases. For datasets with right and non-censored observations, AROC did not converge onto oaROC_True. oaROC for datasets with only non-censored observations converged the fastest, and for a dataset with 10 observations, the median oaROC differed from oaROC_True by 2.74% while the corresponding median AROC with left and right censored data differed from oaROC_True by 9.74%. We also calculated the AROC and oaROC for a published side impact dataset, and differences between the two methods ranged between −24.08% and 24.55% depending on metric. Overall, when compared with AROC, we found oaROC performs equivalently for doubly censored data, better for non-censored data, and can accommodate more types of data than AROC. While more validation is needed, the results indicate that oaROC is a viable alternative which can be incorporated into the metric selection process for IRCs.     

Dipole moment, enthalpy, and entropy changes of Hodgkin-Huxley type kinetic units.

Dipole moment, enthalpy, and entropy changes were calculated for hypothetical structural units which control the opening and closing of ionic channels in axon membranes. The changes of these thermodynamic functions were calculated both for activation (transition to intermediate complex) and for the structural transformation as a whole. The calculations are based on the experimentally determined Q10 values and the empirical formulae for the rate constants (alpha's and beta's) as functions of membrane potentials in Hodgkin-Huxley type models. From the calculated thermodynamic functions we suggest that the specific structural units of the axon membranes are probably of macromolecular (possible protein-like) dimensions with large dipole moments (hundreds of debyes). The calculated dipole moment changes of a single structural unit indicate that in many cases these dipole moments saturate at strong depolarizations or hyperpolarizations. The transitions in structural units show substantial activation enthalpies and entropies but the net enthalpy and entropy changes are practically negligible for the transition as a whole, i.e. the structural units presumably undergo displacements. While the calculated dipole moment changes associated with structural transformations in Loligo and Myxicola show similar potential dependencies, those for Rana usually show a different behavior. The relevance of the dipole moment changes to gating currents is discussed.     

基于高分遥感影像的滇西北村域景观格局演变——以大理市低丘缓坡山地开发区为例

人类的开发活动是造成土地覆盖和景观格局变化的主要原因.村域尺度上高强度的人类开发活动对土地覆盖及景观格局演变的影响规律研究尚不多见.本研究采用2009年的GeoEye-1数据和2014年的WorldView 3数据,利用ArcGIS和ENVI,基于面向对象和人机交互的方法解译影像,应用土地利用转移矩阵和景观指数定量研究大理市海东镇低丘缓坡山区改造过程中的土地覆盖变化和景观格局演变.结果表明: 2009年主要土地覆盖类型是林地、水田和旱地,占总面积的82.8%,2014年林地、推平未建地和水田占总面积的70.9%;研究期间,土地利用变化主要由林地、水田和旱地向推平未建地、建设用地转移,尤其是2014年推平未建地面积达531.57 hm²,其中,来自林地、旱地和水田的面积分别占42.8%、21.7%和14.2%.景观空间格局演变表现为斑块数量和密度增加,平均斑块面积变小;边缘指数和形状指数增加,斑块形状更加复杂;斑块破碎化,整体构成更加多样化.     

A Fourier method for the analysis of exponential decay curves.

A method based on the Fourier convolution theorem is developed for the analysis of data composed of random noise, plus an unknown constant "base line," plus a sum of (or an integral over a continuous spectrum of) exponential decay functions. The Fourier method's usual serious practical limitation of needing high accuracy data over a very wide range is eliminated by the introduction of convergence parameters and a Gaussian taper window. A computer program is described for the analysis of discrete spectra, where the data involves only a sum of exponentials. The program is completely automatic in that the only necessary inputs are the raw data (not necessarily in equal intervals of time); no potentially biased initial guesses concerning either the number or the values of the components are needed. The outputs include the number of components, the amplitudes and time constants together with their estimated errors, and a spectral plot of the solution. The limiting resolving power of the method is studied by analyzing a wide range of simulated two-, three-, and four-component data. The results seem to indicate that the method is applicable over a considerably wider range of conditions than nonlinear least squares or the method of moments.     

黄土塬区不同地形部位和土地利用方式对土壤物理性质的影响

在黄土塬区王东沟流域采集不同地形部位和不同土地利用方式下土壤样品,测定其颗粒组成、容重和饱和导水率,借助变异系数、非参数检验等方法研究了不同地形部位和不同利用方式对土壤物理性质的影响.结果表明：土壤物理性质在水平方向和沿垂直剖面都存在变异,但在同一地形部位或同一土地利用类型内,容重和颗粒组成基本相似.水平方向,饱和导水率属强变异,粘粒和砂粒含量属中等变异,粉粒含量和容重属弱变异;沿垂直剖面,土壤的粒级分布具有连续性,但0～25 cm的土壤容重和饱和导水率与下层土壤差异显著.沿坡面从上向下,土壤趋向粘重,但饱和导水率增大;其中上坡位和中坡位的土壤性质相似,在相关研究中可以进行合并.草地与其他利用方式下的土壤性质差异显著,主要受地形部位的影响;耕地和果园的土壤性质相似且不同于其他利用类型,表明人为干扰对土壤物理性质有重要影响.     

Evaluation of a high resolution genotyping method for Chlamydia trachomatis using routine clinical samples

Background

Genital chlamydia infection is the most commonly diagnosed sexually transmitted infection in the UK. C. trachomatis genital infections are usually caused by strains which fall into two pathovars: lymphogranuloma venereum (LGV) and the genitourinary genotypes D–K. Although these genotypes can be discriminated by outer membrane protein gene (ompA) sequencing or multi-locus sequence typing (MLST), neither protocol affords the high-resolution genotyping required for local epidemiology and accurate contact-tracing.

Principal Findings

We evaluated variable number tandem repeat (VNTR) and ompA sequencing (now called multi-locus VNTR analysis and ompA or “MLVA-ompA”) to study local epidemiology in Southampton over a period of six months. One hundred and fifty seven endocervical swabs that tested positive for C. trachomatis from both the Southampton genitourinary medicine (GUM) clinic and local GP surgeries were tested by COBAS Taqman 48 (Roche) PCR for the presence of C. trachomatis. Samples tested as positive by the commercial NAATs test were genotyped, where possible, by a MLVA-ompA sequencing technique. Attempts were made to isolate C. trachomatis from all 157 samples in cell culture, and 68 (43%) were successfully recovered by repeatable passage in culture. Of the 157 samples, 93 (i.e. 59%) were fully genotyped by MLVA-ompA. Only one mixed infection (E & D) in a single sample was confirmed. There were two distinct D genotypes for the ompA gene. Most frequent ompA genotypes were D, E and F, comprising 20%, 41% and 16% of the type-able samples respectively. Within all genotypes we detected numerous MLVA sub-types.

Conclusions

Amongst the common genotypes, there are a significant number of defined MLVA sub-types, which may reflect particular background demographics including age group, geography, high-risk sexual behavior, and sexual networks.     

Measurement of protein turnover in rat liver. Analysis of the complex curve for decay of label in a mixture of proteins.

The curve for decay of 14C in rat liver protein labelled by injection of NaH14CO3 was analysed to obtain the average turnover rate of mixed liver protein. Three different methods of analysis were used. (1) Unlike decay curves from homogeneous proteins, the curve did not fit a single exponential, but a good fit was obtained with three exponentials. By assuming that the mixture contained three major components with different turnover rates, the calculated value for the average turnover rate (k) was close to 40% per day. (2) k was also calculated from the area under the decay curve, a method which makes no assumptions about the number of proteins in the mixture. This method also gave a value close to 40% per day. (3) It was shown empirically, both by simulation of decay of label in model mixtures of protein and with the decay curve measured in vivo, that k can be calculated from the time taken for the specific radioactivity to fall to 10% of its maximum value. This is an advantage, since the other two methods require the decay curve to be measured over a much longer period of time.     

An easy method for the determination of initial rates.

When the Michaelis-Menten equation is obeyed, the rate near the beginning of an enzyme-catalyzed reaction (or of an experiment on transport) can be found accurately from the slope of a chord joining two points on the progress curve. This slope gives the rate at an intermediate concentration. Exact values of this intermediate concentration are easily calculated from equations in the text, and a number of values have also been tabulated. Methods of using two chords to find the initial rate are given. A mid-point formula for numerical differentiation is advocated when the Michaelis-Menten equation does not hold.     

Automated,accurate, and three-dimensional method for calculating sagittal slope of the tibial plateau

Increased posterior-inferior directed slope of the subchondral bone of the lateral tibial plateau is a risk factor for noncontact rupture of the anterior cruciate ligament (ACL). Previous measures of lateral tibial slope, however, vary from study to study and often lack documentation of their accuracy. These factors impede identifying the magnitude of lateral tibial slope that increases risk of noncontact ACL rupture. Therefore, we developed and evaluated a new method that (1) requires minimal user input; (2) employs 3D renderings of the tibia that are referenced to a 3D anatomic coordinate system; and (3) is precise, reliable, and accurate. The user first isolated the proximal tibia from computed tomography (CT) scans. Then, the algorithm placed the proximal tibia in an automatically generated tibial coordinate system. Next, it identified points along the rim of subchondral bone around the lateral tibial plateau, iteratively fit a plane to this rim of points, and, finally, referenced the plane to the tibial coordinate system. Precision and reliability of the lateral slope measurements were respectively assessed via standard deviation and intra- and inter-class correlation coefficients using CT scans of three cadaveric tibia. Accuracy was quantified by comparing changes in lateral tibial slope calculated by our algorithm to predefined in silico changes in slope. Precision, reliability, and accuracy were ≤0.18°, ≥0.998, and ≤0.13°, respectively. We will use our novel method to better understand the relationship between lateral tibial slope and knee biomechanics towards preventing ACL rupture and improving its treatment.     

Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures.

Recently, new methods for determining time-evolving structures using infrared analogs of NMR spectroscopy have been introduced that have outstanding potential in structural biology. Already, within the past two years, structures of dipeptides, tripeptides and pentapeptides have been determined on much faster timescales than the conformational dynamics. Also, two-dimensional infrared correlation spectra of some proteins and isotopically edited alanine-rich helices have been examined.     

Application of multivariate curve resolution alternating least squares method for determination of caffeic acid in the presence of catechin interference

In the current article, preparation and application of a graphene oxide nanosheets-based sensor for electrochemical determination of caffeic acid (CA) in the presence of catechin is described. This measurement was performed using the differential pulse voltammetry (DPV) technique and chemometric methods such as multivariate curve resolution–alternating least squares (MCR–ALS). The modified sensor was characterized by various techniques such as Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, ultraviolet–visible, X-ray diffraction (XRD), and scanning electron microscopy (SEM). Operating conditions and influencing variables (involving several chemical and instrumental variables) were optimized with central composite rotatable design and response surface methodology. The second-order electrochemical data were generated by changing the pulse height in DPV, and after potential shift correction MCR–ALS was applied. Under the optimized conditions, the dynamic range for CA was from 0.5 to 100.0 μM and the detection limit was found to be 1.1 × 10^–9 M. The results revealed that the modified electrode shows an improvement in anodic oxidation activity of CA due to a marked enhancement in the current response compared with the bare carbon paste electrode. The modified electrode demonstrated good sensitivity, selectivity, and stability. The proposed method was successfully applied in determination of caffeic acid in the presence of unexpected electroactive interferences with a very high degree of overlapping such as catechin in real samples.     

Multivariate curve resolution: a possible tool in the detection of intermediate structures in protein folding.

Different multivariate data analysis techniques based on factor analysis and multivariate curve resolution are shown for the study of biochemical evolutionary processes like conformational changes and protein folding. Several simulated CD spectral data sets describing different hypothetical protein folding pathways are analyzed and discussed in relation to the feasibility of factor analysis techniques to detect and resolve the number of components needed to explain the evolution of the CD spectra corresponding to the process (i.e., to detect the presence of intermediate forms). When more than two components (the native and unordered forms) are needed to explain the evolution of the spectra, an iterative multivariate curve resolution procedure based on an alternating least squares algorithm is proposed to estimate the CD spectrum corresponding to the intermediate form.