Fast computing of some generalized linear mixed pseudo-models with temporal autocorrelation

This paper considers ways to increase computational speed in generalized linear mixed pseudo-models for the case of many repeated measurements on subjects. We obtain linearly increasing computing time with number of observations, as opposed to O(n ³) increasing computing time using numerical optimization. We also find a surprising result; that incomplete optimization for covariance parameters within the larger parameter estimation algorithm actually decreases time to convergence. After comparing various computing algorithms and choosing the best one, we fit a generalized linear mixed model to a binary time series data set with over 100 fixed effects, 50 random effects, and approximately 1.5 ×  10⁵ observations.     

Über einen Satz aus der Theorie der ebenen Kollineationen

Ohne Zusammenfassung     

Synthesis of substituted 1-benzazepin-2-ones via ring-closing olefin metathesis

The 1-benzazepin-2-one ring system is an important structural feature of marketed drugs, clinical candidates, and other bioactive molecules. We have developed a new benzazepinone synthesis that employs ring-closing olefin metathesis as a key step. This route provides efficient access to substituted benzazepinones that are difficult to synthesize via existing procedures.     

Design of short pulse laser driven opacity experiments

Hot electrons created by short, intense laser pulses can heat solid density material to temperatures of order 500 eV. Inertial confinement can maintain such hot-dense plasmas for times of order 10 ps. This provides a platform for measurement of basic properties of hot dense matter, such as opacity and equation-of-state. In this paper we describe the role of computational modeling in the design and analysis of such opacity experiments. We describe a method to model the hot electron transport and deposition and the resulting target radiation-hydrodynamics. We present several design concepts to achieve uniform, long-lasting plasmas.     

荧光寿命的快速傅里叶变换拟合方法

介绍了一种利用快速傅里叶变换算法对稀土掺杂物质的荧光寿命进行数据拟合的方法。稀土掺杂物质可用来制备多种光学传感器,用于温度、pH值等多种参量测量领域。本方法利用快速傅里叶变换(FFT)结果作为基础,从非零项的相位角的正切值得出被测的荧光寿命,具有速度快、误差小、不受本底干扰等一系列优点。以掺铒光纤为例,通过数字仿真将本方法与其它几种传统的拟合方法进行了比较。快速傅里叶变换方法的测量偏差不到Prony方法的50％,为对数似合(log-fit)方法测量偏差的1／6。另外,快速傅里叶变换方法由于不受本底噪声影响,可以不必在信号处理时去掉本底噪声,因而可以明显缩短测量时间。     

Proving programs correct: Some techniques and examples

Proving the correctness of computer programs is justified as both advantageous and feasible. The discipline of proof provides a systematic search for errors, and a completed proof gives sufficient reasons why the program must be correct. Feasibility is demonstrated by exhibiting proofs of five pieces of code. Each proof uses one or more of the illustrated proof techniques of case analysis, assertions, mathematical induction, standard prose proof, sectioning and a table of variable value changes. Proofs of other programs, some quite lengthy, are cited to support the claim that the techniques work on programs much larger than the examples of the paper. Hopefully, more programmers will be encouraged to prove programs correct.     

NMR assignment of protein side chains using residue-correlated labeling and NOE spectra

A new approach for the isotopic labeling of proteins is proposed that aims to facilitate side chain resonance assignments. Residue-correlated (RC) labeling is achieved by the expression of a protein on a medium containing a mixture of labeled, e.g., [U-13C,15N]amino acids, and NMR silent, [U-2H]amino acids. De novo synthesis of amino acids was suppressed by feedback inhibition by the amino acids in the growth medium and by the addition of beta-chloro-L-alanine, a transaminase inhibitor. Incorporation of these amino acids into synthesized proteins results in a relative diminution of inter-residue NOE interactions and a relative enhancement of intra-residue NOEs. Comparison of the resulting NOE spectra with those obtained from a uniformly labeled sample allows identification of intra-residue NOE peaks. Thus, this approach provides direct information for sidechain assignments in the NOE spectra, which are subsequently used for structural analysis. We have demonstrated the feasibility of this strategy for the 143 amino acid nuclease inhibitor NuiA, both at 35 degrees C, corresponding to a rotational correlation time of 9.5 ns, and at 5 degrees C, corresponding to a rotational correlation time of 22 ns.     

Nitrogen-15 n.m.r. studies of 13C, 15N labeled arginine

¹⁵N n.m.r. spectra of [¹³C-2, 3-¹⁵N₂-guanidino]arginine and [¹³C, ¹⁵N₂] urea were obtained in D₂O and H₂O at a variety of pH values both with and without proton decoupling. The effects of the proton exchange rate are readily observable in the proton coupled ¹⁵N spectra. When the guanidino group is deprotonated (pK = 12.5), the terminal nitrogens give a single resonance 6.6 ppm downfield of the protonated species, indicating a rapid tautomeric exchange. The observed NH and CN couplings are compared with calculated values, and good agreement is found for ¹J(CN) using a Blizzard–Santry type calculation. The ramifications of the proton exchange on ¹⁵N n.m.r. spectra of amino acids and peptides are discussed.