Sample sonication after trichloroacetic acid precipitation increases protein recovery from cultured hippocampal neurons, and improves resolution and reproducibility in two-dimensional gel electrophoresis

Protein precipitation with TCA followed by acetone washing is frequently used to clean samples before 2-DE. However, the difficulty in solubilizing TCA-precipitated proteins causes some variability in 2-D gels and makes it difficult to detect some proteins. In this work we show that sonication of the samples, after TCA precipitation followed by elution in sample buffer, increases total protein recovery, and improves reproducibility and matching ratios between gels when analyzed by specialized software.     

Ab initio calculations of the O1s XPS spectra of ZnO and Zn oxo compounds

O1s core level binding energies of oxygen atoms in bulk ZnO, at different ZnO surfaces, and in some Zn oxo compounds were calculated by means of wave function based quantum chemical ab initio methods. Initial and final state effects were obtained by Koopmans' theorem and at the DeltaSCF level, respectively. After correction for scalar relativistic effects and electron correlation, the calculated XPS peak positions are in excellent agreement with the available experimental data for all systems included in the present study. The O1s core level shifts between an isolated H2O molecule and the Zn oxo compounds or ZnO, as well as between oxygen atoms in bulk ZnO and at various ZnO surfaces, can be understood by means of Madelung potentials and electronic relaxation or screening. XPS spectra were calculated for various cluster models which are designed to describe different possibilities of stabilizing the polar O-terminated ZnO(0001) surface by the adsorption of H atoms. The experimental spectra are only compatible with the theoretical results for the fully hydroxylated H-ZnO(0001) surface exhibiting a (1x1) surface structure.     

Ab initio calculations for the Zn 2s and 2p core level binding energies in Zn oxo compounds and ZnO

The Zn 2s and 2p core level binding energies of ZnO and a few Zn oxo compounds containing Zn in its oxidation state +2 were calculated by means of wave function based quantum chemical ab initio methods. The computations were performed at two levels of approximation. First, Hartree-Fock calculations were carried out for the ground state of the neutral systems yielding the "initial state" effects, i.e. the shifts of the core level binding energies due to the changes in the chemical environment of the Zn atom under consideration (Koopmans' theorem level, KT). In the second step, Hartree-Fock calculations were performed for the core ionized states in order to account for the relaxation effects after ionization, i.e. for the "final state" effects (DeltaSCF level). Scalar relativistic corrections and spin-orbit coupling were included in a "spin-orbit-coupling configuration interaction" (SOC-CI) treatment both at the KT and DeltaSCF levels. In all Zn oxo compounds (Zn(4)O(formate)(6), Zn(4)O(acetate)(6) and several ZnO cubanes) small negative initial state shifts between -1.0 and 0.0 eV (relative to the free Zn atom) were found which are caused by the negative charges at the surrounding O atoms. The relaxation effects vary between -1.0 and -0.5 eV, such that the calculated total shifts are moderately negative (-1.5 to -0.5 eV). Embedded ZnO clusters of increasing size, ranging from Zn(13)O(4) to Zn(69)O(38), were used as models for bulk ZnO, the Zn 2s and 2p core level shifts calculated for these clusters being extrapolated to infinite cluster size. The calculations show that bulk ZnO has a rather large negative initial state shift of -2.1 +/- 0.1 eV, due to the Madelung potential at the Zn atom, and a comparatively small relaxation contribution of -1.0 +/- 0.1 eV. This yields a total shift of -3.1 +/- 0.2 eV (both for 2s and 2p, relative to atomic Zn), which is in very good agreement with experiment, -2.9 +/- 0.2 eV. The surprising experimental observation that the Zn 2s and 2p XPS peak positions are nearly identical in Zn metal and ZnO is explained by the fact that the sum of initial and final state effects is accidentally the same for the two systems though the individual contributions differ quite significantly: the initial and final state shifts amount to +2.4 and -5.1 eV for Zn metal vs.-2.1 and -1.0 eV for ZnO.     

Synthesis of oxadiazoloquinoxaline,oxathiadiazoloquinoxaline and oxadiazolobenzothiazine derivatives

Bis‐amidoxime 1 reacts with phosgene, thiophosgene and thionylchloride to give the corresponding bisfused oxadiazolo‐ and oxathiadiazoloquinoxalines 2, 4, 5 along with the unexpected furazano‐derivative 3 , while monoamidoximes 9, 13 by treatment with ethyl chloroformate affords the oxadiazoloquinoxaline and the oxadiazolobenzothiazine derivatives 14, 15 along with the dicarboxylated product 16 .     

On the representability of totally unimodular matrices on bidirected graphs

We present a polynomial time algorithm to construct a bidirected graph for any totally unimodular matrix B by finding node-edge incidence matrices Q and S such that QB=S. Seymour’s famous decomposition theorem for regular matroids states that any totally unimodular (TU) matrix can be constructed through a series of composition operations called k-sums starting from network matrices and their transposes and two compact representation matrices B₁,B₂ of a certain ten element matroid. Given that B₁,B₂ are binet matrices we examine the k-sums of network and binet matrices. It is shown that thek-sum of a network and a binet matrix is a binet matrix, but binet matrices are not closed under this operation for k=2,3. A new class of matrices is introduced, the so-called tour matrices, which generalise network, binet and totally unimodular matrices. For any such matrix there exists a bidirected graph such that the columns represent a collection of closed tours in the graph. It is shown that tour matrices are closed under k-sums, as well as under pivoting and other elementary operations on their rows and columns. Given the constructive proofs of the above results regarding the k-sum operation and existing recognition algorithms for network and binet matrices, an algorithm is presented which constructs a bidirected graph for any TU matrix.     

Safe density ratio modeling

An important problem in logistic regression modeling is the existence of the maximum likelihood estimators. In particular, when the sample size is small, the maximum likelihood estimator of the regression parameters does not exist if the data are completely, or quasicompletely separated. Recognizing that this phenomenon has a serious impact on the fitting of the density ratio model–which is a semiparametric model whose profile empirical log-likelihood has the logistic form because of the equivalence between prospective and retrospective sampling–we suggest a linear programming methodology for examining whether the maximum likelihood estimators of the finite dimensional parameter vector of the model exist. It is shown that the methodology can be effectively utilized in the analysis of case–control gene expression data by identifying cases where the density ratio model cannot be applied. It is demonstrated that naive application of the density ratio model yields erroneous conclusions.     

Elimination of motion and pulsation artifacts using BLADE sequences in knee MR imaging

The purpose of this study is to evaluate the ability of proton density (PD)-BLADE sequences in reducing or even eliminating motion and pulsatile flow artifacts in knee magnetic resonance imaging examinations. Eighty consecutive patients, who had been routinely scanned for knee examination, participated in the study. The following pairs of sequences with and without BLADE were compared: (a) PD turbo spin echo (TSE) sagittal (SAG) fat saturation (FS) in 35 patients, (b) PD TSE coronal (COR) FS in 19 patients, (c) T2 TSE axial in 13 patients and (d) PD TSE SAG in 13 patients. Both qualitative and quantitative analyses were performed based on the signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR) and relative contrast (ReCon) measures of normal anatomic structures. The qualitative analysis was performed by experienced radiologists. Also, the presence of image motion and pulsation artifacts was evaluated. Based on the results of the SNR, CRN and ReCon for the different sequences and anatomical structures, the BLADE sequences were significantly superior in 19 cases, whereas the corresponding conventional sequences were significantly superior in only 6 cases. BLADE sequences eliminated motion artifacts in all the cases. However, motion artifacts were shown in (a) six PD TSE SAG FS, (b) three PD TSE COR FS, (c) three PD TSE SAG and (d) two T2 TSE axial conventional sequences. In our results, it was found that, in PD FS sequences (sagittal and coronal), the differences between the BLADE and conventional sequences regarding the elimination of motion and pulsatile flow artifacts were statistically significant. In all the comparisons, the PD FS BLADE sequences (coronal and sagittal) were significantly superior to the corresponding conventional sequences regarding the classification of their image quality. In conclusion, this technique appears to be capable to potentially eliminate motion and pulsatile flow artifacts in MR images.     

A Bayesian Surprise Approach in Designing Cognitive Radar for Autonomous Driving

This article proposes the Bayesian surprise as the main methodology that drives the cognitive radar to estimate a target’s future state (i.e., velocity, distance) from noisy measurements and execute a decision to minimize the estimation error over time. The research aims to demonstrate whether the cognitive radar as an autonomous system can modify its internal model (i.e., waveform parameters) to gain consecutive informative measurements based on the Bayesian surprise. By assuming that the radar measurements are constructed from linear Gaussian state-space models, the paper applies Kalman filtering to perform state estimation for a simple vehicle-following scenario. According to the filter’s estimate, the sensor measures the contribution of prospective waveforms—which are available from the sensor profile library—to state estimation and selects the one that maximizes the expectation of Bayesian surprise. Numerous experiments examine the estimation performance of the proposed cognitive radar for single-target tracking in practical highway and urban driving environments. The robustness of the proposed method is compared to the state-of-the-art for various error measures. Results indicate that the Bayesian surprise outperforms its competitors with respect to the mean square relative error when one-step and multiple-step planning is considered.     

Highly Efficient Production of Nanoporous Block Copolymers with Arbitrary Structural Characteristics for Advanced Membranes

The great significance of boosting the design of percolating nanopore structures in block copolymers (BCPs) for various cases has been widely demonstrated in the past several decades. However, it still remains challenging to prepare the desired porous structures in a rapid, facile, and universal manner. Here we have developed an unconventional and benchtop strategy to rapidly generate the nanoporous polystyrene-based BCPs with arbitrary structural characteristics regardless of the BCP bulk morphology. This universal pore-forming strategy enables the sustainable CO₂-based BCPs to form advanced membranes after 1 s soaking for efficiently rejecting 94.2 % brilliant blue R (826 g mol⁻¹). Meanwhile, the water permeance retains around 1020 L (m² h bar)⁻¹, which is 1–3 orders of magnitude higher than that of other membranes. This strategy may offer an excellent opportunity to introduce percolating pore structures in those newly developed BCPs with which the previously reported pore-forming methods may not deal.