A simple theoretical approach to the band gaps of conjugated polymers

Engineering the band gap of a conjugated polymer is an effective way to improve the performance of the corresponding photoelectric device. In this study, a repeating unit of a conjugated polymer is reduced to a phenylene, a vinylene/ethynylene or a combination of them according to the characteristics of the atoms and the bonds. And the trends of the band gaps of polyphenylene, polyvinylene/polyethynylene, their substituted derivatives and alternating copolymers are given by using Hückel molecular orbital method with the parameters for the electron-withdrawing powers and the strengths of the bonding interactions of atoms. The approximation for complex structures and the trends of simple structures make it very convenient to analyse and predict the band gap of a conjugated polymer qualitatively.     

In pursuit of negative Fukui functions: molecules with very small band gaps

Journal of Molecular Modeling - A new 3D graphical representation of DNA sequences is introduced. This representation is called 3D-dynamic representation. It is a generalization of the 2D-dynamic...     

Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments

To understand how protein segments are inserted and deleted during divergent evolution, a set of pairwise alignments contained exactly one gap, and therefore arising from the first insertion-deletion (indel) event in the time separating the homologs, was examined. The alignments showed that "structure breaking" amino acids (PGDNS) were preferred within and flanking gapped regions, as are two residues with hydrophilic side-chains (QE) that frequently occur at the surface of protein folds. Conversely, hydrophobic residues (FMILYVW) occur infrequently within and flanking the gapped region. These preferences are modestly different in protein pairs separated by an episode of adaptive evolution, than in pairs diverging under strong functional constraints. Surprisingly, regions near an indel have not evolved more rapidly than the sequence pair overall, showing no evidence that an indel event must be compensated by local amino acid replacement. The gap-lengths are best approximated by a Zipfian distribution, with the probability of a gap of length L decreasing as a function of L(-1.8). These features are largely independent of the length of the gap and the extent of divergence (measured by both silent and non-silent sequence changes) separating the two proteins. Surprisingly, amino acid repeats were discovered in more than a third of the polypeptide segments in and around the gap. These correspond to repeats in the DNA sequence. This suggests that a signature of the mechanism by which indels occur in the DNA sequence remains in the encoded protein sequences. These data suggest specific tools to score gap placement in an alignment. They also suggest tools that distinguish true indels from gaps created by mistaken gene finding, including under-predicted and over-predicted introns. By providing mechanisms to identify errors, the tools will enhance the value of genome sequence databases in support of integrated paleogenomics strategies used to extract functional information in a post-genomic environment.     

A procedure combining molecular docking and semiempirical method PM7 for identification of selective Shp2 inhibitors

Shp2 and Shp1 make up a small family of protein tyrosine phosphatases. Finding selective inhibitors for Shp2 is useful because although its inhibition is advantageous for the treatment of some types of cancer, inhibition of Shp1 may have the opposite effect, since it acts as a suppressor of tumors. We combined molecular docking and semiempirical molecular orbital-based calculations to produce data that were effective for the identification of selective inhibitors for Shp2. After definition of the interaction modes of the inhibitors with Shp2 and Shp1 by molecular docking, the resulting interaction enthalpy values were calculated following refinement of the enzyme/inhibitor complexes' geometries with the PM7 semiempirical molecular orbital method. Despite the complexity of the thermodynamics involved in the enzyme/inhibitor interaction, the selectivity for Shp2 of a series of 76 inhibitors, divided in two groups, could be effectively correlated with the difference in their interaction enthalpy values with both enzymes. For the first group, composed by 52 Shp2-selective indoline inhibitors for which only Shp2 inhibition activity data are available, we demonstrated that the interaction enthalpy can be used as a criterion for identification of selective Shp2 inhibitors, as it is significantly more favorable for Shp2 than Shp1 at a 99% confidence level. For the second group, composed by 24 oxindole derivatives with available Shp2 and Shp1 inhibition activity data, a satisfactory correlation (R = 0.70) could be obtained between the selectivity, based on the IC₅₀ data, and the relative percentage difference of the calculated interaction enthalpies with the two enzymes.     

基于6S模型的FY-3A/MERSI可见光到近红外波段大气校正

基于山西省太原市及其周边区域气象台站观测数据,为6S模型提供所需的大气状态参数,对晴空状况下FY-3A/MERSI可见光到近红外波段（250 m分辨率）数据进行大气校正.结果表明：大气校正后,MERSI可见光到近红外波段数据范围加宽、反射率数据普遍增大,波峰高移,各波段反射率的分布更趋平滑;校正后,反映植被状况的归一化植被指数的值域比校正前增大、峰值变高,更接近实际情况;校正后彩色合成图显现出更丰富的地物信息,亮度增大,层次变强,对比度增强,地物信息更接近实际.     

Magnetic resonance thermometry at 7T for real-time monitoring and correction of ultrasound induced mild hyperthermia

While Magnetic Resonance Thermometry (MRT) has been extensively utilized for non-invasive temperature measurement, there is limited data on the use of high field (≥7T) scanners for this purpose. MR-guided Focused Ultrasound (MRgFUS) is a promising non-invasive method for localized hyperthermia and drug delivery. MRT based on the temperature sensitivity of the proton resonance frequency (PRF) has been implemented in both a tissue phantom and in vivo in a mouse Met-1 tumor model, using partial parallel imaging (PPI) to speed acquisition. An MRgFUS system capable of delivering a controlled 3D acoustic dose during real time MRT with proportional, integral, and derivative (PID) feedback control was developed and validated. Real-time MRT was validated in a tofu phantom with fluoroptic temperature measurements, and acoustic heating simulations were in good agreement with MR temperature maps. In an in vivo Met-1 mouse tumor, the real-time PID feedback control is capable of maintaining the desired temperature with high accuracy. We found that real time MR control of hyperthermia is feasible at high field, and k-space based PPI techniques may be implemented for increasing temporal resolution while maintaining temperature accuracy on the order of 1°C.     

Chromosomal localization of a human band 3-like gene to region 7q35----7q36.

Band 3, the major transmembrane protein of erythrocytes, mediates the exchange of anions across the membrane and anchors the erythroid membrane skeleton. Proteins immunologically related to Band 3 have been detected in a variety of nonerythroid cells. We have isolated a human cDNA clone that encodes a protein related to but distinct from the erythroid form of Band 3, based on the comparison of the amino acid sequence for the two proteins. The presence of the gene for the Band 3-like protein in a panel of mouse-human somatic cell hybrids containing subsets of human chromosomes correlated with the presence of human chromosome 7. In situ hybridization analysis using the c-DNA for this nonerythroid Band 3 gene further localized the gene to region 7q35----7q36 of human metaphase chromosomes.     

Empirical Bayes identification [correction of identication] of tumor progression genes from microarray data

The use of microarray data has become quite commonplace in medical and scientific experiments. We focus here on microarray data generated from cancer studies. It is potentially important for the discovery of biomarkers to identify genes whose expression levels correlate with tumor progression. In this article, we propose a simple procedure for the identification of such genes, which we term tumor progression genes. The first stage involves estimation based on the proportional odds model. At the second stage, we calculate two quantities: a q-value, and a shrinkage estimator of the test statistic is constructed to adjust for the multiple testing problem. The relationship between the proposed method with the false discovery rate is studied. The proposed methods are applied to data from a prostate cancer microarray study.     

Models of sequence evolution for DNA sequences containing gaps

Most evolutionary tree estimation methods for DNA sequences ignore or inefficiently use the phylogenetic information contained within shared patterns of gaps. This is largely due to the computational difficulties in implementing models for insertions and deletions. A simple way to incorporate this information is to treat a gap as a fifth character (with the four nucleotides being the other four) and to incorporate it within a Markov model of nucleotide substitution. This idea has been dismissed in the past, since it treats a multiple-site insertion or deletion as a sequence of independent events rather than a single event. While this is true, we have found that under many circumstances it is better to incorporate gap information inadequately than to ignore it, at least for topology estimation. We propose an extension to a class of nucleotide substitution models to incorporate the gap character and show that, for data sets (both real and simulated) with short and medium gaps, these models do lead to effective use of the information contained within insertions and deletions. We also implement an ad hoc method in which the likelihood at columns containing multiple-site gaps is downweighted in order to avoid giving them undue influence. The precision of the estimated tree, assessed using Markov chain Monte Carlo techniques to find the posterior distribution over tree space, improves under these five-state models compared with standard methods which effectively ignore gaps.     

Cloning and nucleotide sequence of cDNA encoding human erythrocyte band 7 integral membrane protein

cDNA clones encoding the human erythrocyte band 7 membrane protein were isolated by immunoscreening from bone marrow and HeLa cell lambda gt 11 cDNA libraries, and their nucleotide sequences were determined. HeLa- and bone marrow cell-derived sequences were identical, except for one nucleotide; the deduced sequence of 287 amino acids was confirmed by sequence identity with peptides of the erythroid protein. Structure analysis assigned band 7 protein to the type Ib transmembrane proteins.     

Isolation and partial characterization of the human erythrocyte band 7 integral membrane protein.

Monoclonal antibodies to the Mr 31,000 major integral membrane protein of the human erythrocyte band 7 region were used to identify the corresponding polypeptide chain and epitope-carrying fragments on immunoblots. Analysis of the erythrocyte membrane, membrane fractions, and cytosol revealed that the Mr 31,000 band 7 integral membrane protein is unique and not related to any of the other water-soluble or membrane-bound band 7 components. Cross-reacting proteins were identified in the membranes of other mammalian erythrocytes and in cell lines of epithelial and lymphoid origin. Proteolytic digestion of intact human erythrocytes or erythrocyte membranes demonstrated that the band 7 integral membrane protein has an intracellular domain larger than Mr 12,000; it does not have an extracellular one. One of the monoclonal antibodies was employed for the isolation of band 7 integral membrane protein by immunoaffinity chromatography; subsequent Edman degradation revealed a blocked N-terminus.     

Conditions for electron runaway under leader breakdown of long gaps

An original hydrodynamic model in which inelastic collisions in the equations of motion and energy balance play a decisive role is developed and applied to simulate electron avalanches in strong electric fields. The mean energy and drift velocity of electrons, as well as the ionization coefficient and electric field in a wide range of mean electron energies, are determined for helium and xenon. A criterion is derived for the runaway of the average electron in discharges with ionization multiplication. It is shown that runaway can take place at any value of E/p, provided that the momentum mean free path exceeds the gap length. The voltage corresponding to electron runaway is found for helium, xenon, and air as a function of the electric field, the electron mean energy, and the parameter pd. Conditions for the formation of a precursor in electronegative gases are analyzed. It is shown that the presence of a precursor with a high electric conductance is necessary for the formation of a new leader step. The voltage and time ranges corresponding to efficient electron runaway and X-ray generation during leader breakdown in air are determined.     

Duplication of the terminal band of the long arm of chromosome 7: a new case

We report on a new case of de novo duplication of the terminal band of chromosome 7, 46, XX dup(7) (q36 > qter), defined by fluorescence in situ hybridization (FISH), which cause a recognizable phenotype consisting of macrocephaly, prominent frontal bossing, slight developmental delay.     

Preparation of η-1,3-dienyl, η-1,2-dienyl and η-cyclobutenone complexes via reactions of transition-metal carbonyl containing anions with allenic electrophiles

The preparation and reaction chemistry of 1,3- and 1,2-diene and related complexes derived from metal carbonyl containing anions and allenic electrophiles are addressed. The preparation of some CpFe(CO)₂ η¹-diene complexes and their conversion into CpFe(CO) η³-diene complexes is presented followed by reactions of CpMo(CO)₃⁻, CpW(CO)₃⁻ and CpMo(CO)₂PR₃⁻ anions with allenic electrophiles which produce metal complexed cyclobutenones (via CO and alkene insertions from the initially formed product) and 1,2-diene complexes, respectively. Lastly, the reactions of PPh₃(CO)₃Co⁻ anions with allenic electrophiles are outlined which result in several different coordination geometries depending on the reaction conditions used.