An Accurate and Clean Calibration Method for MALDI-MS

A new method for the mass calibration of the matrix-assisted laser desorption/ionization-mass spectrometry spectrum is introduced. This method achieves the same accuracy as that of internal calibration but without its drawbacks. The interference and signal suppression by calibration standard are avoided, and a pure/clean sample spectrum is obtained. No prior knowledge about the sample quantity is required for the calibration. The effectiveness of the method is demonstrated with protein identification data.     

A Simple and Accurate Method for Infra-Red Gas Analyser Calibration

An alternative method for calibrating infra-red gas analysersis described which uses gas mixtures prepared with a gas mixingcircuit constructed from commonly available materials. It isshown that the maximum error in the gas mixture is about 1.5%,and possible improvements to the technique are discussed. Key words: Infra-red gas analyser, Calibration     

数字PCR仪校准方法研究

数字PCR仪是核酸绝对定量的重要仪器,因此确保数字PCR仪检测结果的准确性十分重要。通过对国内市场上数字PCR仪的比较分析,剖析了数字PCR仪的性能指标,对数字PCR仪的校准方法进行了探讨,设定了拷贝数浓度相对示值误差、拷贝数浓度重复性、荧光通道一致性和反应单元个数重复性作为数字PCR仪整机校准的计量技术指标,采用具有溯源性的国家有证标准物质,对方法进行了试验验证。验证结果表明了校准思路和方法的可行性,该方法操作性强,能够满足仪器技术要求以及用户需求, 提高了数字PCR仪检测结果的准确性和可靠性,对进一步拓展和深化数字PCR 技术的应用具有积极的促进作用。     

An Intelligent Ellipsoid Calibration Method Based on the Grey Wolf Algorithm for Magnetic Compass

With the measurement of the Earth's magnetic field,magnetic compass can provide high frequency heading information.However,it suffers from local magnetic interf...     

Site-specific and hydrophilic ADCs through disulfide-bridged linker and branched PEG

Kadcyla® (T-DM1), an antibody–drug conjugates (ADCs) for HER2+ breast cancer treatment, has been approved by the Food and Drug Administration (FDA) in 2013. An ADC of random lysine conjugation, it has difficulties in DAR control and unsatisfactory PK due to uneven DAR distribution. It also gives rise to aggregation during conjugation because of the hydrophobicity nature of the cytotoxin, DM1. The linker-drug in T-DM1, SMCC-DM1 is hydrophobic and requires certain percentage of organic solvent such as DMA in the conjugation solution, limiting the manufacturing process in an organic-solvent-compatible device and adding extra costs. To address these problems, a site-specific conjugation method was developed involving full reduction of antibody and full conjugation with the bridge-like conjugator-drug, based on the work of Caddick and co-workers, to obtain a site-directed antibody-drug conjugate with DAR 4. The bridge-like conjugator was assembled with SMCC-DM1 and different lengths of hydrophilic polyethylene glycol (PEG) moiety. By applying PEG moiety in the side chain of the linker-drug, the organic solvent used in the conjugation can be reduced. When the PEG length is about 26 units, organic solvent is no longer needed in the conjugation. Reducing the amount of organic solvent in conjugation could also diminish the aggregation occurrence during the conjugation. Moreover, the conjugation configuration with the designed conjugator was also discussed in the article. The binding affinity of the resulting ADCs did not show significant decrease and the cell based assay and animal study have shown the comparable results with T-DM1.     

A Simple Method for Estimating Informative Node Age Priors for the Fossil Calibration of Molecular Divergence Time Analyses

Molecular divergence time analyses often rely on the age of fossil lineages to calibrate node age estimates. Most divergence time analyses are now performed in a Bayesian framework, where fossil calibrations are incorporated as parametric prior probabilities on node ages. It is widely accepted that an ideal parameterization of such node age prior probabilities should be based on a comprehensive analysis of the fossil record of the clade of interest, but there is currently no generally applicable approach for calculating such informative priors. We provide here a simple and easily implemented method that employs fossil data to estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade, which can be used to fit an informative parametric prior probability distribution on a node age. Specifically, our method uses the extant diversity and the stratigraphic distribution of fossil lineages confidently assigned to a clade to fit a branching model of lineage diversification. Conditioning this on a simple model of fossil preservation, we estimate the likely amount of missing history prior to the oldest fossil occurrence of a clade. The likelihood surface of missing history can then be translated into a parametric prior probability distribution on the age of the clade of interest. We show that the method performs well with simulated fossil distribution data, but that the likelihood surface of missing history can at times be too complex for the distribution-fitting algorithm employed by our software tool. An empirical example of the application of our method is performed to estimate echinoid node ages. A simulation-based sensitivity analysis using the echinoid data set shows that node age prior distributions estimated under poor preservation rates are significantly less informative than those estimated under high preservation rates.     

A Flexible Calibration Method Using the Planar Target with a Square Pattern for Line Structured Light Vision System

A flexible calibration approach for line structured light vision system is proposed in this paper. Firstly a camera model is established by transforming the points from the 2D image plane to the world coordinate frame, and the intrinsic parameters of camera can be obtained accurately. Then a novel calibration method for structured light projector is presented by moving a planar target with a square pattern randomly, and the method mainly involves three steps: first, a simple linear model is proposed, by which the plane equation of the target at any orientations can be determined based on the square’s geometry information; second, the pixel coordinates of the light stripe center on the target images are extracted as the control points; finally, the points are projected into the camera coordinate frame with the help of the intrinsic parameters and the plane equations of the target, and the structured light plane can be determined by fitting these three-dimensional points. The experimental data show that the method has good repeatability and accuracy.     

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

High-performance next-generation sequencing (NGS) technologies are advancing genomics and molecular biological research. However, the immense amount of sequence data requires computational skills and suitable hardware resources that are a challenge to molecular biologists. The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput annotation of NGS reads. The DDBJ Pipeline offers a user-friendly graphical web interface and processes massive NGS datasets using decentralized processing by NIG supercomputers currently free of charge. The proposed pipeline consists of two analysis components: basic analysis for reference genome mapping and de novo assembly and subsequent high-level analysis of structural and functional annotations. Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis. Moreover, public NGS reads of the DDBJ Sequence Read Archive located on the same supercomputer can be imported into the pipeline through the input of only an accession number. This proposed pipeline will facilitate research by utilizing unified analytical workflows applied to the NGS data. The DDBJ Pipeline is accessible at http://p.ddbj.nig.ac.jp/.     

Cross-Modal Calibration of Vestibular Afference for Human Balance

To determine how the vestibular sense controls balance, we used instantaneous head angular velocity to drive a galvanic vestibular stimulus so that afference would signal that head movement was faster or slower than actual. In effect, this changed vestibular afferent gain. This increased sway 4-fold when subjects (N = 8) stood without vision. However, after a 240 s conditioning period with stable balance achieved through reliable visual or somatosensory cues, sway returned to normal. An equivalent galvanic stimulus unrelated to sway (not driven by head motion) was equally destabilising but in this situation the conditioning period of stable balance did not reduce sway. Reflex muscle responses evoked by an independent, higher bandwidth vestibular stimulus were initially reduced in amplitude by the galvanic stimulus but returned to normal levels after the conditioning period, contrary to predictions that they would decrease after adaptation to increased sensory gain and increase after adaptation to decreased sensory gain. We conclude that an erroneous vestibular signal of head motion during standing has profound effects on balance control. If it is unrelated to current head motion, the CNS has no immediate mechanism of ignoring the vestibular signal to reduce its influence on destabilising balance. This result is inconsistent with sensory reweighting based on disturbances. The increase in sway with increased sensory gain is also inconsistent with a simple feedback model of vestibular reflex action. Thus, we propose that recalibration of a forward sensory model best explains the reinterpretation of an altered reafferent signal of head motion during stable balance.     

Combined MFA-LCA for Analysis of Wastewater Pipeline Networks

Oslo's wastewater pipeline network has an aging stock of concrete, steel, and polyvinyl chloride (PVC) pipelines, which calls for a good portion of expenditures to be directed toward maintenance and investments in rehabilitation. The stock, as it is in 2008, is a direct consequence of the influx of pipelines of different sizes, lengths, and materials of construction into the system over the years. A material flow analysis (MFA) facilitates an analysis of the environmental impacts associated with the manufacture, installation, operation, maintenance, rehabilitation, and retirement of the pipelines. The forecast of the future flows of materials—which, again, is highly interlinked with the historic flows—provides insight into the likely future environmental impacts. This will enable decision makers keen on alleviating such impacts to think along the lines of eco-friendlier processes and technologies or simply different ways of doing business. Needless to say, the operation and maintenance phase accounts for the major bulk of emissions and calls for energy-efficient approaches to this phase of the life cycle, even as manufacturers strive to make their processes energy-efficient and attempt to include captive renewable energy in their total energy consumption. This article focuses on the life cycle greenhouse gas emissions associated with the wastewater pipeline network in the city of Oslo.     

Visual vs Fully Automatic Histogram-Based Assessment of Idiopathic Pulmonary Fibrosis (IPF) Progression Using Sequential Multidetector Computed Tomography (MDCT)

Objectives

To describe changes over time in extent of idiopathic pulmonary fibrosis (IPF) at multidetector computed tomography (MDCT) assessed by semi-quantitative visual scores (VSs) and fully automatic histogram-based quantitative evaluation and to test the relationship between these two methods of quantification.

Methods

Forty IPF patients (median age: 70 y, interquartile: 62-75 years; M:F, 33:7) that underwent 2 MDCT at different time points with a median interval of 13 months (interquartile: 10-17 months) were retrospectively evaluated. In-house software YACTA quantified automatically lung density histogram (10^th-90^th percentile in 5^th percentile steps). Longitudinal changes in VSs and in the percentiles of attenuation histogram were obtained in 20 untreated patients and 20 patients treated with pirfenidone. Pearson correlation analysis was used to test the relationship between VSs and selected percentiles.

Results

In follow-up MDCT, visual overall extent of parenchymal abnormalities (OE) increased in median by 5 %/year (interquartile: 0 %/y; +11 %/y). Substantial difference was found between treated and untreated patients in HU changes of the 40th and of the 80th percentiles of density histogram. Correlation analysis between VSs and selected percentiles showed higher correlation between the changes (Δ) in OE and Δ 40^th percentile (r=0.69; p<0.001) as compared to Δ 80^th percentile (r=0.58; p<0.001); closer correlation was found between Δ ground-glass extent and Δ 40^th percentile (r=0.66, p<0.001) as compared to Δ 80^th percentile (r=0.47, p=0.002), while the Δ reticulations correlated better with the Δ 80^th percentile (r=0.56, p<0.001) in comparison to Δ 40^th percentile (r=0.43, p=0.003).

Conclusions

There is a relevant and fully automatically measurable difference at MDCT in VSs and in histogram analysis at one year follow-up of IPF patients, whether treated or untreated: Δ 40^th percentile might reflect the change in overall extent of lung abnormalities, notably of ground-glass pattern; furthermore Δ 80^th percentile might reveal the course of reticular opacities.     

Preparation of Mixtures for the Calibration of Gas Analysers

Differential gas analysers for use in photosynthesis experimentscan be calibrated with the same accuracy as that specified forthe single standard gas mixture that is required. With the useof only one gas mixing pump, the composition of a mixture canbe specified to better than ±1 per cent, compared with±5 per cent usually offered by commercial gas suppliers.