Laboratory information management software for genotyping workflows: Applications in high throughput crop genotyping

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow Results: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics. Conclusions: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/bt-software-d-lims.htm

Analyzing information flow in brain networks with nonparametric Granger causality

Multielectrode neurophysiological recording and high-resolution neuroimaging generate multivariate data that are the basis for understanding the patterns of neural interactions. How to extract directions of information flow in brain networks from these data remains a key challenge. Research over the last few years has identified Granger causality as a statistically principled technique to furnish this capability. The estimation of Granger causality currently requires autoregressive modeling of neural data. Here, we propose a nonparametric approach based on widely used Fourier and wavelet transforms to estimate both pairwise and conditional measures of Granger causality, eliminating the need of explicit autoregressive data modeling. We demonstrate the effectiveness of this approach by applying it to synthetic data generated by network models with known connectivity and to local field potentials recorded from monkeys performing a sensorimotor task.

Modification of ventricular repolarization in silent long QT syndrome mutation carriers

Congenital long QT syndrome (LQTS) is a familial disorder characterized by ventricular repolarization that makes carriers vulnerable to malignant ventricular tachycardia and sudden cardiac death. The three main subtypes (LQT1, LQT2 and LQT3) constitute 95% of cases. The disorder is characterized by a prolonged QT interval in electrocardiograms (ECG), but a considerable portion are silent carriers presenting normal (QTc < 440 ms) or borderline (QTc < 470 ms) QT interval. Genetic testing is available only for 60-70% of patients. A number of pharmaceutical compounds also affect ventricular repolarization, causing a clinically similar disorder called acquired long QT syndrome. LQTS carriers - who already have impaired ventricular repolarization - are especially vulnerable. In this thesis, asymptomatic genotyped LQTS mutation carriers with non-diagnostic resting ECG were studied. The body surface potential mapping (BSPM) system was utilized for ECG recording, and signals were analyzed with an automated analysis program. QT interval length, and the end part of the T wave, the Tpe interval, was studied during exercise stress testing and an epinephrine bolus test. In the latter, T wave morphology was also analyzed. The effect of cetirizine was studied in LQTS carriers and also with supra- therapeutic dose in healthy volunteers. At rest, LQTS mutation carriers had a slightly longer heart rate adjusted QTc interval than healthy subjects (427 ± 31 ms and 379 ± 26 ms; p<0.001), but significant overlapping existed. LQT2 mutation carriers had a conspicuously long Tpe-interval (113 ± 24 ms; compared to 79 ± 11 ms in LQT1, 81 ± 17 ms in LQT3 and 78 ± 10 ms in controls; p<0.001). In exercise stress tests, LQT1 mutation carriers exhibit a long QT interval at high heart rates and during recovery, whereas LQT2 mutation carriers have a long Tpe interval at the beginning of exercise and at the end of recovery at low heart rates. LQT3 mutation carriers exhibit prominent shortening of both QT and Tpe intervals during exercise. A small epinephrine bolus revealed disturbed repolarization, especially in LQT2 mutation carriers, who developed prolonged Tpe intervals. A higher epinephrine bolus caused abnormal T waves with a different T wave profile in LQTS mutation carriers compared to healthy controls. These effects were seen in LQT3 as well, a group that may easily escape other provocative tests. In the cetirizine test, the QT and Tpe intervals were not prolonged in LQTS mutation carriers or in healthy controls. Subtype-specific findings in exercise test and epinephrine bolus test help to diagnose silent LQTS mutation carriers and to guide subtype-specific treatments. The Tpe interval, which signifies the repolarization process, seems to be a sensitive marker of disturbed repolarization along with the QT interval, which signifies the end of repolarization. This method may be used in studying compounds that are suspected to affect repolarization. Cetirizine did not adversely alter ventricular repolarization and would not be pro-arrhythmic in common LQT1 and LQT2 subtypes when used at its recommended doses.

Spin-Valve-Like Magnetoresistance in Mn2NiGa at Room Temperature

Spin valves have revolutionized the field of magnetic recording and memory devices. Spin valves are generally realized in thin film heterostructures, where two ferromagnetic (FM) layers are separated by a nonmagnetic conducting layer. Here, we demonstrate spin-valve-like magnetoresistance at room temperature in a bulk ferrimagnetic material that exhibits a magnetic shape memory effect. The origin of this unexpected behavior in Mn2NiGa has been investigated by neutron diffraction, magnetization, and ab initio theoretical calculations. The refinement of the neutron diffraction pattern shows the presence of antisite disorder where about 13% of the Ga sites are occupied by Mn atoms. On the basis of the magnetic structure obtained from neutron diffraction and theoretical calculations, we establish that these antisite defects cause the formation of FM nanoclusters with parallel alignment of Mn spin moments in a Mn2NiGa bulk lattice that has antiparallel Mn spin moments. The direction of the Mn moments in the soft FM cluster reverses with the external magnetic field. This causes a rotation or tilt in the antiparallel Mn moments at the cluster-lattice interface resulting in the observed asymmetry in magnetoresistance.

A fisheries management plan for the River Tweed in the Scottish Borders

The River Tweed is, in rod-catch terms, the second most important river in Britain for Atlantic salmon, with an annual rod catch of ca.10,000 fish. This article gives an outline of the second edition of the Tweed Fisheries Management Plan, which is defined as "The co-ordination of data collection and analyses with fundamental research into relevant topics to devise management actions that will beneficially affect the future state of fish stocks". Much of the work set down for the present is concerned with setting up recording and measuring systems for fish catches and exploitation rates, and for the operation of monitoring sites for juvenile densities and adult trout and salmon spawning runs. While surveys show the present state of affairs, the collection of records and regular monitoring of sites will mean that in the future, the past will be better known through a longer series of records. Two case histories are described. The first is concerned with setting aims for managing the brown trout of the Tweed and defining the present state of the fishery. The second is an investigation into the spring salmon of the Tweed.

组合外加电场提高Fe：LiNbO3中90°记录体全息的衍射效率

针对90°全息记录结构的特殊性，在记录和读出阶段分别施加不同极性的外加电场，实现了Fe：LiNbO3晶体中高衍射效率的全息记录和读出。在库赫塔列夫（Kukhtarev）方程基础上引人两维耦合波理论，对组合外加电场提高掺铁铌酸锂晶体光折变特性的机理进行了探讨。实验和理论计算结果都表明这种分别在记录和读出过程施加不同极性组合的外加电场是在Fe：LiNbO3中实现高衍射效率90°记录结构体全息的有效技术方案。

(Ce,Cu)∶LiNbO3晶体非挥发全息记录理论研究与优化

根据双中心带输运模型,对(Ce,Cu)∶LiNbO3晶体双中心非挥发全息记录进行了理论研究与优化。推导了(Ce,Cu)∶LiNbO3晶体的微观参量,采用数值方法通过严格求解模拟双中心带输运方程来模拟全息记录过程。分析了记录过程中,记录与敏化光强、Ce和Cu掺杂浓度以及晶体微观参量对(Ce,Cu)∶LiNbO3晶体双中心全息记录的影响。发现(Ce,Cu)∶LiNbO3晶体非挥发全息记录中实现高衍射效率与固定效率的主导因素是深中心Cu,在记录过程中,深中心Cu建立起了很强的空间电荷场。数值模拟的结果经过实验验

Theoretical investigation of nonvolatile holographic storage in doubly doped lithium niobate crystals

We have studied theoretically the inherent mechanisms of nonvolatile holographic storage in doubly doped LiNbO3 crystals. The photochromic effect of doubly doped LiNbO3 crystals is discussed, and the criterion for this effect is obtained through the photochromism-bleach factor a = S(21)gamma(1)/S(11)gamma(2) that we define. The two-center recording and fixing processes are analytically discussed with extended Kukhtarev equations, and analytical expressions for recorded and fixed steady-state space-charge fields as well as temporal behavior during the fixing process are obtained. The effects of microphysical quantities, the macrophotochromic effect on fixing efficiency, and recorded and fixed steady-state space-charge fields, are discussed analytically and numerically. (C) 2002 Optical Society of America.

Nonvolatile photorefractive holograms in LiNbO3 : Cu : Ce crystals

We report experimental and theoretical studies of nonvolatile photorefractive holographic recording in LiNbO3:Cu:Ce crystals with two illumination schemes: (1) UV light for sensitization and a red interfering pattern for recording and (2) blue light for sensitization and a red pattern for recording. The results show that the oxidized LiNbO3:Cu:Ce crystals can provide high, persistent refractive-index modulation with weak lightinduced scattering. The optimal working conditions and the prescription for doping and oxidation-reduction processing that yields the maximum refractive-index modulation are discussed. (C) 2000 Optical Society of America OCIS codes: 050.7330, 190.5330, 090.2900.

Three-dimensional coupled wave study for finite-sized anisotropic volume holographic gratings under ultrashort pulsed beam readout

The three-dimensional coupled wave theory is extended to systematically investigate the diffraction properties of finite-sized anisotropic volume holographic gratings (VHGs) under ultrashort pulsed beam (UPB) readout. The effects of the grating geometrical size and the polarizations of the recording and readout beams on the diffraction properties are presented, in particular under the influence of grating material dispersion. The wavelength selectivity of the finite-sized VHG is analyzed. The wavelength selectivity determines the intensity distributions of the transmitted and diffracted pulsed beams along the output face of the VHG. The distortion and widening of the diffracted pulsed beams are different for different points on the output face, as is numerically shown for a VHG recorded in a LiNbO3 crystal. The beam quality is analyzed, and the variations of the total diffraction efficiency are shown in relation to the geometrical size of the grating and the temporal width of the readout UPB. In addition, the diffraction properties of the finite-sized and one-dimensional VHG for pulsed and continuous-wave readout are compared. The study shows the potential application of VHGs in controlling spatial and temporal features of UPBs simultaneously. (C) 2007 Optical Society of America

双中心全息记录的矢量分析与记录方向优化

对描述双掺杂晶体非挥发性全息记录动力学过程的Kukhtarev方程进行了矢量分析, 分析中考虑了体光生伏特效应和外加电场的作用。在小信号近似的基础上给出了双中心全息记录中记录与固定阶段空间电荷场的矢量解析解。在综合考虑空间电荷场的各向异性以及晶体有效电光系数的各向异性后, 给出了双中心全息记录的优化记录方向。结果表明, 对(Fe, Mn):LiNbO3晶体633 nm寻常光记录, 优化记录方向主要由有效电光系数决定, 光栅波矢与光轴夹角为22°, 方位角为30°;对(Fe, Mn):LiNbO3晶体633

Wideband two-port beam splitter of a binary fused-silica phase grating

The usual beam splitter of multilayer-coated film with a wideband spectrum is not easy to achieve. We describe the realization of a wideband transmission two-port beam splitter based on a binary fused-silica phase grating. To achieve high efficiency and equality in the diffracted 0th and -1st orders, the grating profile parameters are optimized using rigorous coupled-wave analysis at a wavelength of 1550 nm. Holographic recording and the inductively coupled plasma dry etching technique are used to fabricate the fused-silica beam splitter grating. The measured efficiency of (45% x 2) = 90% diffracted into the both orders can be obtained with the fabricated grating under Littrow mounting. The physical mechanism of such a wideband two-port beam splitter grating can be well explained by the modal method based on two-beam interference of the modes excited by the incident wave. With the high damage threshold, low coefficient of thermal expansion, and wideband high efficiency, the presented beam splitter etched in fused silica should be a useful optical element for a variety of practical applications. (C) 2008 Optical Society of America.

超分辨近场功能薄膜的膜层结构及其机理研究进展

超分辨近场结构光盘是最有希望达到100 GB以上的存储容量方式之一,而其记录和读出机理是研究中的重点,在近年文献研究的基础上,阐述了超分辨近场功能薄膜的膜层结构及其机理的研究进展。

A feasible approach to optical-electrical hybrid data storage using phase change material

We present our experimental results supporting optical-electrical hybrid data storage by optical recording and electrical reading using Ge2Sb2Te5as recording medium. The sheet resistance of laser- irradiated Ge2Sb2Te5. lms exhibits an abrupt change of four orders of magnitude ( from 10 7 to 10 3./ sq) with increasing laser power, current- voltage curves of the amorphous area and the laser- crystallized dots, measured by a conductive atomic force microscope ( C- AFM), show that their resistivities are 2.725 and 3.375 x 10- 3., respectively, the surface current distribution in the. lms also shows high and low resistance states. All these results suggest that the laser- recorded bit can be read electrically by measuring the change of electrical resistivity, thus making optical electrical hybrid data storage possible.