Comparison of time constants of single channel patches,quantum bumps,and noise analysis inLimulus ventral photoreceptors

Summary The characteristic time constants derived from three different experimental procedures for measuring light-evoked currents in photoreceptors are compared; these procedures include single-channel patch-clamp measurements, noise analysis, and current relaxation studies. Recent patch-clamp measurements of the mean open times of single light-activated channels in the ventral photoreceptor ofLimulus (Bacigalupo, J., Lisman, J.E. (1983),Nature (London) 304:268–270) yield a disagreement of the measured mean open time with the relaxation time of the falling phase of quantum bumps and with the inverse characteristic frequency of the noise power spectrum, measured by Wong (Wong, F. (1978),Nature (London) 276:76–79). We present new experimental results which show that the relaxation time of the falling phase of bumps is markedly shortened by light-adaptation. Hence the state of light-adaptation has to be taken into account when comparing different experiments. Secondly, we investigate three simple models for the mechanism of channel opening and closing, and conclude that an agreement of the mean open time of single channels, the relaxation time of the falling phase of bumps, and the inverse characteristic frequency of the noise power spectrum cannot be expected.     

Barrier potentials,molecular structure,force filed calculations and quantum chemical studies of some bipyridine di-carboxylic acids using the experimental and theoretical using (DFT,IVP) approach

ABSTRACT

FT-IR and FT-Raman spectra of 2,2′-bipyridine-3,3′-dicarboxylic acid (B3DA), 2,2′-bipyridine-4,4′-dicarboxylic acid (B4DA) and 2,2′-bipyridine-5,5′-dicarboxylic acid (B5DA) were recorded and analysed. The quantum chemical calculations of the title compounds begin with barrier potentials at different rotation angles around the C–C′ and C–Cα bonds in order to arrive conformation of lowest energy using DFT employing B3LYP functional with 6-311++G(d,p) basis set. This confirmation was further optimised to get the global minimum geometry. The vibrational frequencies along with IR, Raman intensities were computed, the rms error between observed and calculated frequencies were 11.2 cm^?1, 10.2 cm^?1 and 12.2 cm^?1 for B3DA, B4DA, and B5DA. An 87-element modified valence force field is derived by solving the inverse vibrational problem using Wilson’s GF matrix method. This force field is refined using 163 observed fundamentals employing in overlay least-squares technique. The average error between computed and experimental frequencies was found as 12.85 cm^?1 using potential energy distribution (PED) and eigenvectors. By using the gauge-independent atomic orbital (GIAO) method calculate the ¹H and ¹³C NMR chemical shifts of the molecules and compared with experimental results. The first-order hyperpolarisability, HOMO and LUMO energies, molecular electrostatic potential (MESP) and natural orbital analysis (NBO) of titled compounds were evaluated using DFT.     

Reconstruction of Natural RNA Sequences from RNA Shape,Thermodynamic Stability,Mutational Robustness,and Linguistic Complexity by Evolutionary Computation

Abstract

The process of designing novel RNA sequences by inverse RNA folding, available in tools such as RNAinverse and InfoRNA, can be thought of as a reconstruction of RNAs from secondary structure. In this reconstruction problem, no physical measures are considered as additional constraints that are independent of structure, aside of the goal to reach the same secondary structure as the input using energy minimization methods. An extension of the reconstruction problem can be formulated since in many cases of natural RNAs, it is desired to analyze the sequence and structure of RNA molecules using various physical quantifiable measures. In prior works that used secondary structure predictions, it has been shown that natural RNAs differ significantly from random RNAs in some of these measures. Thus, we relax the problem of reconstructing RNAs from secondary structure into reconstructing RNAs from shapes, and in turn incorporate physical quantities as constraints. This allows for the design of novel RNA sequences by inverse folding while considering various physical quantities of interest such as thermodynamic stability, mutational robustness, and linguistic complexity. At the expense of altering the number of nucleotides in stems and loops, for example, physical measures can be taken into account. We use evolutionary computation for the new reconstruction problem and illustrate the procedure on various natural RNAs.     

Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps

Background

High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.

Methods

We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.

Results

Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.

Conclusions

Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.

     

Distributed parameter identification for a label-structured cell population dynamics model using CFSE histogram time-series data

In this work we address the problem of the robust identification of unknown parameters of a cell population dynamics model from experimental data on the kinetics of cells labelled with a fluorescence marker defining the division age of the cell. The model is formulated by a first order hyperbolic PDE for the distribution of cells with respect to the structure variable x (or z) being the intensity level (or the log₁₀-transformed intensity level) of the marker. The parameters of the model are the rate functions of cell division, death, label decay and the label dilution factor. We develop a computational approach to the identification of the model parameters with a particular focus on the cell birth rate α(z) as a function of the marker intensity, assuming the other model parameters are scalars to be estimated. To solve the inverse problem numerically, we parameterize α(z) and apply a maximum likelihood approach. The parametrization is based on cubic Hermite splines defined on a coarse mesh with either equally spaced a priori fixed nodes or nodes to be determined in the parameter estimation procedure. Ill-posedness of the inverse problem is indicated by multiple minima. To treat the ill-posed problem, we apply Tikhonov regularization with the regularization parameter determined by the discrepancy principle. We show that the solution of the regularized parameter estimation problem is consistent with the data set with an accuracy within the noise level in the measurements.      

Integral dose based inverse optimization objective function promises lower toxicity in head-and-neck

PurposeThe voxels in a CT data sets contain density information. Besides its use in dose calculation density has no other application in modern radiotherapy treatment planning. This work introduces the use of density information by integral dose minimization in radiotherapy treatment planning for head-and-neck squamous cell carcinoma (HNSCC).Materials and methodsEighteen HNSCC cases were studied. For each case two intensity modulated radiotherapy (IMRT) plans were created: one based on dose-volume (DV) optimization, and one based on integral dose minimization (Energy hereafter) inverse optimization. The target objective functions in both optimization schemes were specified in terms of minimum, maximum, and uniform doses, while the organs at risk (OAR) objectives were specified in terms of DV- and Energy-objectives respectively. Commonly used dosimetric measures were applied to assess the performance of Energy-based optimization. In addition, generalized equivalent uniform doses (gEUDs) were evaluated. Statistical analyses were performed to estimate the performance of this novel inverse optimization paradigm.ResultsEnergy-based inverse optimization resulted in lower OAR doses for equivalent target doses and isodose coverage. The statistical tests showed dose reduction to the OARs with Energy-based optimization ranging from ∼2% to ∼15%.ConclusionsIntegral dose minimization based inverse optimization for HNSCC promises lower doses to nearby OARs. For comparable therapeutic effect the incorporation of density information into the optimization cost function allows reduction in the normal tissue doses and possibly in the risk and the severity of treatment related toxicities.     

Perceived Stress and Coping Strategies in Relation to Body Mass Index: Cross-Sectional Study of 12,045 Japanese Men and Women

BackgroundAccumulated evidence suggests a weak positive relationship between psychosocial stress and body mass index (BMI), but little is known about stress coping strategies and BMI.ObjectiveWe aimed to examine if perceived stress and coping strategies are related to BMI, with any of their mutual interactions on BMI.MethodsThis cross-sectional study included 5,063 men and 6,982 women aged 40-69 years. A self-administered questionnaire ascertained perceived stress and 5 items of coping strategies (emotion expression, emotional support seeking, positive reappraisal, problem solving, and disengagement). Analyses were performed by gender with adjustment for age, socioeconomic status, and lifestyle factors.ResultsNo significant associations were detected between perceived stress and BMI in either men (P_trend = 0.09) or women (P_trend = 0.58). In men, however, ‘disengagement’ showed an inverse association with BMI (P_trend < 0.001), and ‘positive reappraisal’ and ‘problem solving’ revealed a positive association with BMI (P_trend = 0.04 and 0.007, respectively) even after controlling for perceived stress. A possible interaction between perceived stress and ‘disengagement’ on BMI was found in men (P_interaction = 0.027); the inverse association between ‘disengagement’ and BMI was more evident in higher levels of stress (β = −0.13, P_trend = 0.21 in low; β = −0.22, P_trend = 0.01 in medium; and β = −0.24, P_trend = 0.06 in high). In men, ‘disengagement’ was inversely associated with overweight/obesity (odds ratio 0.79, 95% confidential interval 0.67-0.95), and “positive reappraisal” was positively associated with it (1.25, 1.02-1.54).ConclusionsCoping strategies may have an important role in developing overweight/obesity, particularly in men.     

Validation of a model-based inverse kinematics approach based on wearable inertial sensors

Abstract

Wearable inertial measurement units (IMUs) are a promising solution to human motion estimation. Using IMUs 3D orientations, a model-driven inverse kinematics methodology to estimate joint angles is presented. Estimated joint angles were validated against encoder-measured kinematics (robot) and against marker-based kinematics (passive mechanism). Results are promising, with RMS angular errors respectively lower than 3 and 6?deg over a minimum range of motion of 50?deg (robot) and 160?deg (passive mechanism). Moreover, a noise robustness analysis revealed that the model-driven approach reduces the effects of experimental noises, making the proposed technique particularly suitable for application in human motion analysis.     

A Thorough Dynamic Interpretation of Residual Dipolar Couplings in Ubiquitin

The presence of slow motions with large amplitudes, as detected by measurements based on residual dipolar couplings [Peti, W., Meiler, J., Brueschweiler, R. and Griesinger, C. (2002) J. Am. Chem. Soc., 124, 5822–5833], has stirred up much discussion in recent years. Based on ubiquitin NH residual dipolar couplings (rdcs) measured in 31 different alignment conditions, a model-free analysis of structure and dynamics [Meiler, J., Peti, W., Prompers, J., Griesinger, C. and Brueschweiler, R. (2001) J. Am. Chem. Soc., 123, 6098–6107] is presented. Starting from this broad experimental basis, rdc-based order parameters with so far unattained accuracy were determined. These rdc-based order parameters underpin the presence of new modes of motion slower than the inverse overall tumbling correlation time. Amplitudes and anisotropies of the motion were derived. The effect of structural noise on the results was proven to be negligible. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Copper and lipid metabolism: A reciprocal relationship

BackgroundCopper and lipid metabolism are intimately linked, sharing a complex, inverse relationship in the periphery (outside of the central nervous system), which remains to be fully elucidated.ScopeCopper and lipids have independently been implicated in the pathogenesis of diseases involving dyslipidaemia, including obesity, cardiovascular disease and non-alcoholic fatty liver disease and also in Wilson disease, an inherited disorder of copper overload. Here we review the relationship between copper and lipid regulatory pathways, which are potential druggable targets for therapeutic intervention.Major conclusionsWhile the inverse relationship between copper and lipids is apparent, tissue-specific roles for the copper regulatory protein, ATP7B provide further insight into the association between copper and lipid metabolism.General significanceUnderstanding the relationship between copper and lipid metabolism is important for identifying druggable targets for diseases with disrupted copper and/or lipid metabolism; and may reveal similar connections within the brain and in neurological diseases with impaired copper and lipid transport.     

多层生物介质传感器的特性研究（英文）

目的 多层生物介质的生物传感器被广泛应用于各大领域,其检测特性对于传感器优劣的评估尤为重要。本文目的在于量化表征多层生物介质的电学特征。方法 基于生物电阻抗谱技术来探究多层生物介质的电化学阻抗谱特性,并结合保角映射的方法来量化表征多层生物介质,阐明其对阻抗的影响规律,继而为生物传感器的研制与开发提供理论基础。有效提取各生物介质层修饰后电阻抗参数(Z^*),从而量化表征多层生物介质层的电阻抗谱特性。结果 对多层模型进行了理论计算并构建了相关试验测试系统,研究结果表明,随着生物介质层的逐步修饰,检测区域电阻抗参数(Z^*)在f=0.1～50 MHz下持续上升,理论计算结果趋势与试验结果趋势较好吻合,论证了此理论计算方法的正确性。结论 本文证实了可根据生物电阻抗谱和保角映射方法量化表征多层生物介质的电阻抗谱特性,对生物传感器的研制与开发有一定的实用价值。     

Bulky DNA adduct levels in normal-appearing colon mucosa,and the prevalence of colorectal adenomas

Abstract

Purpose: Examine the association between bulky DNA adduct levels in colon mucosa and colorectal adenoma prevalence, and explore the correlation between adduct levels in leukocytes and colon tissue.

Methods: Bulky DNA adduct levels were measured using ³²P-postlabelling in biopsies of normal-appearing colon tissue and blood donated by 202 patients. Multivariable logistic regression was used to examine associations between DNA adducts, and interactions of DNA adduct-DNA repair polymorphisms, with the prevalence of colorectal adenomas. Correlation between blood and tissue levels of DNA adducts was evaluated using Spearman’s correlation coefficient.

Results: An interaction between bulky DNA adduct levels and XPA rs1800975 on prevalence of colorectal adenoma was observed. Among individuals with lower DNA repair activity, increased DNA adduct levels were associated with increased colorectal adenoma prevalence (OR?=?1.41 per SD increase, 95%CI: 0.92–2.18). Conversely, among individuals with normal DNA activity, an inverse association was observed (OR?=?0.60 per SD increase, 95%CI: 0.34–1.07). Blood and colon DNA adduct levels were inversely correlated (ρ?=??0.20).

Conclusions: Among genetically susceptible individuals, higher bulky DNA adducts in the colon was associated with the prevalence of colorectal adenomas. The inverse correlation between blood and colon tissue measures demonstrates the importance of quantifying biomarkers in target tissues.     

Evaluation of clinical benefits achievable by using different optimization algorithms during real-time prostate brachytherapy

Background and purposeHigh dose rate (HDR) brachytherapy is a clinically used procedure in prostate cancer treatment. The purpose of this study was to present the influence of using different optimization algorithms in 3D-CBRT planning on the treatment plan quality.Materials and methodsTreatment plans were calculated for 15 patients – three plans for each patient using: geometrical optimization (GO), inverse optimization (IO) and blind inverse optimization (BIO). For each patient, PTV and OAR volumes, number of needles and geometry of the implant were set equal. Differences between dose distributions were tracked using: D90, V100, V200, Dmax (for prostate); D10, Dmax (for urethra); D10, V100, Dmax (for rectum).ResultsThe analysis of mean values of D90 and V100 in the prostate showed that inverse algorithms gave the best results (mean D90 was 12.1% for BIO and 9.3% for IO better than for GO, mean V100 was 8.2% for BIO and 6.3% for IO better than for GO). From a clinical point of view, GO diminished the doses in the PTV and urethra in all analyzed parameters. The lowest mean doses in the rectum were achieved for plans optimized with IO and BIO (mean D10: 61.2% for GO, 58.1% for IO, 58.0% for BIO; mean Dmax: 92.8% for GO, 85.1% for IO, 83.6% for BIO).ConclusionsApplication of the blind inverse optimization (BIO) algorithm led to clinically best dose parameters for PTV and the rectum. Use of geometrical optimization (GO) led to smaller doses in the urethra, which was however associated with a certain dose decrease also in PTV.     

On the Green’s function for a one-dimensional random walk

The Green’s function of a random walk on a lattice is defined as the inverse of the operatorK-z1, whereK is the matrix of transition rates and z is an arbitrary complex parameter. The Green’s function for a symmetrical random walk in one dimension is here explicitly given in closed form for reflecting, periodic, and absorbing boundaries, and also for an infinite lattice.     

Engineering of betabellin 15D: Copper(II)-induced folding of a fibrillar β-sandwich protein

Summary The inverse protein-folding problem has been explored by designing de novo the betabellin target structure (a 64-residue β-sandwich protein), synthesizing a 32-residue peptide chain (HSLTAKIpkLTFSIAphTYTCAVpkYTAKVSH, wherep=DPro,k=DLys, andh=DHis) that might fold into this structure, and studying how its disulfide-bridged form (betabellin 15D) folds in 10 mM ammonium acetate with and without Cu²⁺. Circular dichroic spectropolarimetry indicated that at pH 5.8, 6.4, or 6.7 betabellin 15D exhibited β-sheet structure in the presence of Cu²⁺ but not in its absence. Electrospray mass spectrometry demonstrated that at pH 6.3 each molecule of betabellin 15D bound one or two Cu(II) ions. Electron microscopy showed that at pH 6.7 betabellin 15D formed short broad fibrils in the presence of Cu²⁺ but not in its absence. The observed width of the fibrils (7±2 nm) was consistent with the width (6.8nm) of a structural model of a fibril that contained two adjacent rows of betabellin 15D β-sandwiches joined lengthwise by multiple intersheet hydrogen bonds and widthwise by multiple Cu(II)-imidazole bonds. Electron paramagnetic resonance spectrometry revealed that some pairs of Cu(II) ions in a Cu(II)/betabellin 15D complex were magnetically coupled, which is consistent with the structural model of the Cu(II)/betabellin 15D fibril.     

Prospective association between baseline plasma zinc concentration and development of proteinuria in Chinese hypertensive patients

ObjectiveWe aimed to evaluate the association between baseline plasma zinc and the development of proteinuria as well as possible effect modifiers in hypertensive patients.MethodsThis is a subset of the China Stroke Primary Prevention Trial (CSPPT) Renal Sub-Study. In the CSPPT, participants were randomized to receive a daily oral dose of 1 tablet containing 10 mg enalapril and 0.8 mg folic acid or 1 tablet containing 10 mg enalapril only. A total of 783 participants with plasma zinc measurements and without proteinuria at baseline were included in the current study. The study outcome was the development of proteinuria during the follow-up, defined as a urine dipstick reading of trace or ≥1+ at the exit visit.ResultsDuring a median follow-up duration of 4.4 years, the development of proteinuria occurred in 93 (11.9 %) participants. There was an inverse relation of baseline plasma zinc with the development of proteinuria (per SD increment; OR, 0.74, 95 % CI: 0.55−0.99), p for trend of quartiles = 0.005.ConclusionsIn Chinese hypertensive patients, there was a significant inverse association between baseline plasma zinc and the development of proteinuria, although plasma zinc remained in the reference range.     

A Modified Valley Restrained Monte Carlo Method to Efficiently Search the Low Energy Structures of Peptides

Abstract

A new Monte Carlo sampling scheme, namely the Modified Valley Restrained Monte Carlo procedure, is used to obtain the global energy minimum conformations for polypeptides, such as Met-enkephalin and Melittin. For each peptide, we found close agreement with previous results from both theoretical and experimental studies. The simple idea for controlling the step size according to the Valley Function, provides useful suggestions in searching the global energy minimum structures, and furthermore helps solve the multiple minima problem.     

A distance-type measure approach to the analysis of copy number variation in DNA sequencing data

Background

The next generation sequencing technology allows us to obtain a large amount of short DNA sequence (DNA-seq) reads at a genome-wide level. DNA-seq data have been increasingly collected during the recent years. Count-type data analysis is a widely used approach for DNA-seq data. However, the related data pre-processing is based on the moving window method, in which a window size need to be defined in order to obtain count-type data. Furthermore, useful information can be reduced after data pre-processing for count-type data.

Results

In this study, we propose to analyze DNA-seq data based on the related distance-type measure. Distances are measured in base pairs (bps) between two adjacent alignments of short reads mapped to a reference genome. Our experimental data based simulation study confirms the advantages of distance-type measure approach in both detection power and detection accuracy. Furthermore, we propose artificial censoring for the distance data so that distances larger than a given value are considered potential outliers. Our purpose is to simplify the pre-processing of DNA-seq data. Statistically, we consider a mixture of right censored geometric distributions to model the distance data. Additionally, to reduce the GC-content bias, we extend the mixture model to a mixture of generalized linear models (GLMs). The estimation of model can be achieved by the Newton-Raphson algorithm as well as the Expectation-Maximization (E-M) algorithm. We have conducted simulations to evaluate the performance of our approach. Based on the rank based inverse normal transformation of distance data, we can obtain the related z-values for a follow-up analysis. For an illustration, an application to the DNA-seq data from a pair of normal and tumor cell lines is presented with a change-point analysis of z-values to detect DNA copy number alterations.

Conclusion

Our distance-type measure approach is novel. It does not require either a fixed or a sliding window procedure for generating count-type data. Its advantages have been demonstrated by our simulation studies and its practical usefulness has been illustrated by an experimental data application.

     

Impaired Health-Related Quality of Life in Elderly Women is Associated With Multimorbidity: Results From the Korean National Health and Nutrition Examination Survey

BackgroundMultimorbidity is a common problem in elderly populations and is significantly associated with functional decline, disability, and mortality. However, the sex-specific characteristics of multimorbidity and its effect on patients' quality of life (QOL) have not been clearly established.MethodsWe analyzed the Korean National Health and Nutrition Examination Survey database. EuroQol 5D (a standardized health outcomes measurement instrument that includes 2 dimensions, the EuroQol 5 Dimension [EQ-5D] index score and the EuroQol visual analogue scale [EQ-VAS]) was used to evaluate QOL. Multimorbidity was evaluated using data on blood pressure measurements, blood chemistry examinations, and anthropometric assessments, as well as a survey that assessed health status.ResultsA total of 1419 patients aged ≥65 years were included in the analysis (age = 72.40 [0.19] years; 39.3% men). Multimorbidity was significantly associated with being a woman; however, it was not associated with age. The EQ-5D index score and EQ-VAS score were significantly lower in patients with multimorbidity, especially among the elderly women. The inverse association between QOL and the number of chronic diseases was maintained without a floor effect. Hypertension was the most common disease; however, QOL was significantly associated with musculoskeletal disease, stroke, and depression, all of which were more common in female patients. There was no significant difference in QOL between men and women with similar levels of comorbidity.ConclusionBoth the amount and pattern of chronic diseases have been associated with QOL in elderly populations. Elderly women have low levels of QOL due to multimorbidity and a higher prevalence of chronic disease, which is related to impaired QOL.     

蛋白质结构确定领域中的几种矩阵填充算法的对比评估

目的 目前,如何从核磁共振(nuclear magnetic resonance,NMR)光谱实验中准确地确定蛋白质的三维结构是生物物理学中的一个热门课题,因为蛋白质是生物体的重要组成成分,了解蛋白质的空间结构对研究其功能至关重要,然而由于实验数据的严重缺乏使其成为一个很大的挑战。方法 在本文中,通过恢复距离矩阵的矩阵填充(matrix completion,MC)算法来解决蛋白质结构确定问题。首先,初始距离矩阵模型被建立,由于实验数据的缺乏,此时的初始距离矩阵为不完整矩阵,随后通过MC算法恢复初始距离矩阵的缺失数据,从而获得整个蛋白质三维结构。为了进一步测试算法的性能,本文选取了4种不同拓扑结构的蛋白质和6种现有的MC算法进行了测试,探究了算法在不同的采样率以及不同程度噪声的情况下算法的恢复效果。结果 通过分析均方根偏差(root-mean-square deviation,RMSD)和计算时间这两个重要指标的平均值及标准差评估了算法的性能,结果显示当采样率和噪声因子控制在一定范围内时,RMSD值和标准差都能达到很小的值。另外本文更加具体地比较了不同算法的特点和优势,在精确采样情况下...