Manganese(I) poly(mercaptoimidazolyl)borate complexes: spectroscopic and structural characterization of Mn...H-B interactions in solution and in the solid state

The manganese(I) tricarbonyl complexes (Bm(R))Mn(CO)3(R = Me, Bz, But, p-Tol) and (PhBmMe)Mn(CO)3, the first bis(mercaptoimidazolyl)borate derivatives for this metal, have been readily prepared and fully characterized. In particular, the presence of three-center-two-electron Mn...H-B interactions in these species, both in solution and in the solid state, has been investigated using a combination of IR and NMR spectroscopies and, in the case of the methyl-, tert-butyl- and para-tolyl-substituted derivatives, by X-ray crystallography. To complement these synthetic and structural studies, the tris(mercaptoimidazolyl)borate complexes (TmMe)Mn(CO)3(R = Me, Bz, But, p-Tol) and (PhTm(Me))Mn(CO)3, as well as the related pyrazolylbis(mercaptoimidazolyl)borate (pzBmMe)Mn(CO)3, have also been synthesized and characterized by a combination of analytical and spectroscopic techniques.     

Pseudo Approximation Algorithms with Applications to Optimal Motion Planning

We introduce a technique for computing approximate solutions to optimization problems. If $X$ is the set of feasible solutions, the standard goal of approximation algorithms is to compute $x\in X$ that is an $\varepsilon$-approximate solution in the following sense: $$d(x) \leq (1+\varepsilon)\, d(x^*),$$ where $x^* \in X$ is an optimal solution, $d\colon\ X\rightarrow {\Bbb R}_{\geq 0}$ is the optimization function to be minimized, and $\varepsilon>0$ is an input parameter. Our approach is first to devise algorithms that compute pseudo $\varepsilon$-approximate solutions satisfying the bound $$d(x) \leq d(x_R^*) + \varepsilon R,$$ where $R>0$ is a new input parameter. Here $x^*_R$ denotes an optimal solution in the space $X_R$ of $R$-constrained feasible solutions. The parameter $R$ provides a stratification of $X$ in the sense that (1) $X_R \subseteq X_{R}$ for $R < R$ and (2) $X_R = X$ for $R$ sufficiently large. We first describe a highly efficient scheme for converting a pseudo $\varepsilon$-approximation algorithm into a true $\varepsilon$-approximation algorithm. This scheme is useful because pseudo approximation algorithms seem to be easier to construct than $\varepsilon$-approximation algorithms. Another benefit is that our algorithm is automatically precision-sensitive. We apply our technique to two problems in robotics: (A) Euclidean Shortest Path (3ESP), namely the shortest path for a point robot amidst polyhedral obstacles in three dimensions, and (B) $d_1$-optimal motion for a rod moving amidst planar obstacles (1ORM). Previously, no polynomial time $\varepsilon$-approximation algorithm for (B) was known. For (A), our new solution is simpler than previous solutions and has an exponentially smaller complexity in terms of the input precision.     

Catalytic construction and reconstruction of guanidines: Ti-mediated guanylation of amines and transamination of guanidines

Bis(guanidinate) titanium imido complexes [{(Me2N)C(NiPr)2}2TiNAr'] (Ar' = 2,6-Me2C6H3 (1a); C6F5 (1b)) are competent catalysts for the guanylation of a variety of arylamines with carbodiimide. The reversible [2 + 2] addition of iPrN=C=NiPr to 1b is demonstrated and is proposed to be part of the catalytic cycle. Compounds 1a and 1b are also effective precatalysts for the transamination of trialkylguanidines with arylamines to yield aryldialkylguanidines.     

Consensus model for identification of novel PI3K inhibitors in large chemical library

Phosphoinositide 3-kinases (PI3Ks) inhibitors have treatment potential for cancer, diabetes, cardiovascular disease, chronic inflammation and asthma. A consensus model consisting of three base classifiers (AODE, kNN, and SVM) trained with 1,283 positive compounds (PI3K inhibitors), 16 negative compounds (PI3K non-inhibitors) and 64,078 generated putative negatives was developed for predicting compounds with PI3K inhibitory activity of IC₅₀ ≤ 10 μM. The consensus model has an estimated false positive rate of 0.75%. Nine novel potential inhibitors were identified using the consensus model and several of these contain structural features that are consistent with those found to be important for PI3K inhibitory activities. An advantage of the current model is that it does not require knowledge of 3D structural information of the various PI3K isoforms, which is not readily available for all isoforms.     

Establishing a quality assurance plan for nucleic acid-based diagnostic laboratories: from planning to implementation

Nucleic acid-based technologies have opened new perspectives in diagnosis, prognosis, and treatment in clinical medicine. To maintain patient confidence in this rapidly expanding field and to provide the highest standard of analysis, strict laboratory quality assurance procedures must be followed. While impressive break-through are taking place in this field, the need for an appropriate and suitable quality assurance (QA) plan for nucleic acid-based diagnostic laboratories must be a top priority. In this study, we developed a systematic QA plan for this kind of diagnostic laboratories that would enable us to assure the highest quality standards of their services. We focus on those labs that would like to start introducing a quality system for the first time and discuss the most appropriate ways to pave the way to implement a QA plan from the beginning. This QA plan is suitable for any nucleic acid-based techniques laboratory regardless of the field or services provided.     

Comparative evaluation of software for retention time alignment of gas chromatography/time-of-flight mass spectrometry-based metabonomic data

In chromatography-based metabonomic research, retention time (RT) alignment of chromatographic peaks poses a challenge for the accurate profiling of biomarkers. Although a number of RT alignment software has been reported, the performance of these software packages have not been comprehensively evaluated. This study aimed to evaluate the RT alignment accuracy of publicly available and commercial RT alignment software. Two gas chromatography/mass spectrometry (GC/MS) datasets acquired from a mixture of standard metabolites and human bladder cancer urine samples, were used to assess three publicly available software packages, MetAlign, MZmine and TagFinder, and two commercial applications comprising the Calibration feature and Statistical Compare of ChromaTOF software. The overall RT alignment accuracies in aligning standard compounds mixture were 93, 92, 74, 73 and 42% for Calibration feature, MZmine, MetAlign, Statistical Compare and TagFinder, respectively. Additionally, unique trends were observed for the individual software with regards to the different experimental conditions related to extent and direction of RT shifts. Conflicting performance was observed for human urine samples suggesting that RT misalignments still occurred despite the use of RT alignment software. While RT alignment remains an inevitable step in data preprocessing, metabonomic researchers are recommended to perform manual check on the RT alignment of important biomarkers as part of their validation process.     

Costly punishment and cooperation in the evolutionary snowdrift game

The role of punishments in promoting cooperation is an important issue. We incorporate costly punishments into the snowdrift game (SG) by introducing a third punishing (P) character, and study the effects. The punishers, who carry basically a cooperative (C) character, are willing to pay a cost α so as to punish a non-cooperative (D) opponent by β. Depending on the initial fractions of the characters, α, β, and the cost-to-benefit ratio r in the SG, the three-character system evolves into a steady state consisting either only of C and P characters or only of C and D characters, in a well-mixed population. The former situation represents an enhancement in cooperation relative to the SG, while the latter is similar to the SG. The dynamics in approaching these different steady states are found to be different. Analytically, the key features in the dynamics and the steady states observed in simulations are captured by a set of differential equations. The sensitivity to the initial distribution of characters is studied by depicting the flow in a phase portrait and analyzing the nature of fixed points. The analysis also shows the role of P-character agents in preventing a system from invasion by D-character agents. Starting from a population consisting only of C and P agents, a D-character agent intended to invade the system cannot survive when the initial fraction of P agents is greater than r/β. Our model, defined intentionally as a simulation algorithm, can be readily generalized to incorporate many interesting effects, such as those in a networked population.     

Nanosecond laser ablation and deposition of silicon

Nanosecond-pulsed KrF (248 nm, 25 ns) and Nd:YAG (1064 nm, 532 nm, 355 nm, 5 ns) lasers were used to ablate a polycrystalline Si target in a background pressure of <10⁻⁴ Pa. Si films were deposited on Si and GaAs substrates at room temperature. The surface morphology of the films was characterized using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Round droplets from 20 nm to 5 μm were detected on the deposited films. Raman Spectroscopy indicated that the micron-sized droplets were crystalline and the films were amorphous. The dependence of the properties of the films on laser wavelengths and fluence is discussed.