DNA regulatory motif selection based on support vector machine (SVM) and its application in microarray experiment of Kashin-Beck disease

Conserved DNA sequences are essential to investigate the regulation and expression of nearby genes. The conserved regions can interact with certain proteins and can potentially determine the transcription speed and amount of the corresponding mRNA in gene replication process. In this paper, motifs of coexpressed genes of microarray experiments were explored with discovery algorithms. Then a selection algorithm based on support vector machine (SVM) was applied to identify those motifs which mostly influenced gene expression. This method combined the advantages from both matrix based motif finding and functional motif selection. When applied to Kashin-Beck disease (KBD), this method identified 9 motifs, and revealed that some motifs may be related to the immune reactions. In addition, we suggested that the methods used could be applied to other microarray experiments to explore the underlying relationships between motif types and gene functions.Key words: Support vector machine (SVM), microarray, motif discovery, gene regulation, Kashin-Beck disease

Dynamic analysis of sugar metabolism in different harvest seasons of pineapple (Ananas comosus L. (Merr.))

In pineapple fruits, sugar accumulation plays an important role in flavor characteristics, which varies according to the stage of fruit development. Metabolic changes in the contents of fructose, sucrose and glucose and reducing sugar related to the activities of soluble acid invertase (AI), neutral invertase (NI), sucrose synathase (SS) and sucrose-phosphate synthase (SPS) were studied in winter and summer pineapple fruits in this paper. Sucrose was significantly increased in most of the harvesting winter fruits which reached the peak of 64.87 mg·g-1 FW at 130 days after anthesis, while hexose was mainly accumulated at the 90 day of the summer fruits in July. The ratio of hexose to sucrose was 5.92:0.73 from the winter fruit in February. Interestingly, the activities of SPS and SS synthetic direction of the harvested fruits in February were significantly higher than those in July, whereas the invertase activities were exactly opposite. NI activity showed a similar trend to AI, but the amount of NI activity was higher than AI in both months. Therefore, NI appears to be one of the vital enzymes in pineapple fruit development. Conclusively, the enzyme activities related to sugar play key roles in the eating of quality pineapple, which could be improved by cultivation in different seasons. So we can arbitrate different temperature to improve the quality of pineapple fruits according to market demand.Keywords: Pineapple (Ananas comosus), different harvest seasons, sucrose, sucrose phosphate synthase, sucrose synthas

Effects of hydrogen bond and solvent polarity on the C=O strectching of bis(2-thienyl)ketone in solution

The optimized structural parameters, the absorption and the resonance Raman spectra have been investigated for the bis(2-thienyl)ketone in gas phase, in cyclohexane, methanol, and acetonitrile solvents by means of time dependent density functional theory calculations, the solvent electronic polarization effect on the solvation shift is examined and in well accordance with the calculation. The effect of increasing the polarity of the solvent is well represented by the polarizable continuum model, both for the absorption spectra and resonance Raman intensities. The Raman spectra of the C=O stretching mode, which is sensitive to the intermolecular interaction for bis(2-thienyl)ketone dissolved in solvents, were systematically studied. It was found that the hydrogen bond effect plays an important role in reducing the carbonyl stretching wavenumbers. The results of Raman shifts were interpreted through the dilution effect, solvation effects, and hydrogen bond-forming effects. Furthermore, the excitation profiles of several important Raman bands of bis(2-thienyl)ketone molecule in different solvents have been critically analyzed. The solvent effects on structural and symmetry properties of the molecule in S2 electronic state as well as the short-time photo relaxation dynamics have been discussed.published_or_final_versio

Soliton superlattices in twisted hexagonal boron nitride.

Properties of atomic van der Waals heterostructures are profoundly influenced by interlayer coupling, which critically depends on stacking of the proximal layers. Rotational misalignment or lattice mismatch of the layers gives rise to a periodic modulation of the stacking, the moiré superlattice. Provided the superlattice period extends over many unit cells, the coupled layers undergo lattice relaxation, leading to the concentration of strain at line defects - solitons - separating large area commensurate domains. We visualize such long-range periodic superstructures in thin crystals of hexagonal boron nitride using atomic-force microscopy and nano-infrared spectroscopy. The solitons form sub-surface hexagonal networks with periods of a few hundred nanometers. We analyze the topography and infrared contrast of these networks to obtain spatial distribution of local strain and its effect on the infrared-active phonons of hBN

Computational modelling of EEG and fMRI paradigms indicates a consistent loss of pyramidal cell synaptic gain in schizophrenia

Background Diminished synaptic gain – the sensitivity of postsynaptic responses to neural inputs – may be a fundamental synaptic pathology in schizophrenia. Evidence for this is indirect, however. Furthermore, it is unclear whether pyramidal cells or interneurons (or both) are affected, or how these deficits relate to symptoms. Methods Participants with schizophrenia diagnoses (PScz, n=108), their relatives (n=57), and controls (n=107) underwent three electroencephalography (EEG) paradigms – resting, mismatch negativity, and 40 Hz auditory steady-state response – and resting functional magnetic resonance imaging. Dynamic causal modelling was used to quantify synaptic connectivity in cortical microcircuits. Results Classic group differences in EEG features between PScz and controls were replicated, including increased theta and other spectral changes (resting EEG), reduced mismatch negativity, and reduced 40 Hz power. Across all four paradigms, characteristic PScz data features were all best explained by models with greater self-inhibition (decreased synaptic gain), in pyramidal cells. Furthermore, disinhibition in auditory areas predicted abnormal auditory perception (and positive symptoms) in PScz, in three paradigms. Conclusions First, characteristic EEG changes in PScz in three classic paradigms are all attributable to the same underlying parameter change: greater self-inhibition in pyramidal cells. Second, psychotic symptoms in PScz relate to disinhibition in neural circuits. These findings are more commensurate with the hypothesis that in PScz, a primary loss of synaptic gain on pyramidal cells is then compensated by interneuron downregulation (rather than the converse). They further suggest that psychotic symptoms relate to this secondary downregulation

HPRT Mutations in Lymphocytes from 1,3-Butadiene-Exposed Workers in China

BACKGROUND: 1,3-Butadiene (BD) is an important industrial chemical and an environmental and occupational pollutant. The carcinogenicity of BD in rodents has been proved, but its carcinogenic and mutagenic molecular mechanism(s) are not fully elucidated in humans. OBJECTIVES: In the present study, we compared the mutation frequencies and exon deletions of BD-exposed workers with that of control subjects in China to identify the characteristic mutations associated with BD exposure in the human HPRT (hypoxanthine–guanine–phosphoribosyltransferase) gene. METHODS: Seventy-four workers exposed to BD via inhalation and 157 matched controls were evaluated in Nanjing, China. Molecular analysis of HPRT mutant T lymphocytes from BDexposed workers and nonexposed control subjects was conducted to identify changes in the structure of the HPRT gene. A total of 783 HPRT mutants were analyzed by multiplex polymerase chain reaction, in which 368 HPRT mutants were isolated from BD-exposed workers and 415 mutants from control subjects. RESULTS: The BD-exposed workers showed a higher mutation frequency (18.2 ± 9.4 × 10 –6) than the control subjects (12.7 ± 7.3 × 10 –6), but the difference was not significant (p> 0.05). The frequency of exon deletions in BD-exposed workers (27.4%) was significantly higher than that in control subjects (12.5%) (p < 0.05), which mainly included multiplex exon deletions (2–8 exons). CONCLUSIONS: The results of the present study suggest that BD should increase the frequency of large deletions of HPRT gene in human lymphocytes This change confirms and supports the previous findings in BD-exposed workers. KEY WORDS: 1,3-butadiene, BD, exon deletion, HPRT gene, lymphocyte, occupational exposure. Environ Health Perspect 116:203–208 (2008). doi:10.1289/ehp.10353 available vi

Interrogating Institutionalized Establishments: Urban-Rural Inequalities in China’s Higher Education

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Facile solution-phase synthesis of γ-Mn3O4 hierarchical structures

<p>Abstract</p> <p>Background</p> <p>A lot of effort has been focused on the integration of nanorods/nanowire as building blocks into three-dimensional (3D) complex superstructures. But, the development of simple and effective methods for creating novel assemblies of self-supported patterns of hierarchical architectures to designed materials using a suitable chemical method is important to technology and remains an attractive, but elusive goal.</p> <p>Results</p> <p>The hierarchical structure of Mn₃O₄with radiated spherulitic nanorods was prepared via a simple solution-based coordinated route in the presence of macrocycle polyamine, hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene (CT) with the assistance of thiourea as an additive.</p> <p>Conclusion</p> <p>This approach opens a new and facile route for the morphogenesis of Mn₃O₄material and it might be extended as a novel synthetic method for the synthesis of other inorganic semiconducting nanomaterials such as metal chalcogenide semiconductors with novel morphology and complex form, since it has been shown that thiourea can be used as an effective additive and the number of such water-soluble macrocyclic polyamines also makes it possible to provide various kinds of ligands for different metals in homogeneous water system.</p

An unsymmetric 8-node hexahedral element with high distortion tolerance

Among all 3D 8-node hexahedral solid elements in current finite element library, the ‘best’ one can produce good results for bending problems using coarse regular meshes. However, once the mesh is distorted, the accuracy will drop dramatically. And how to solve this problem is still a challenge that remains outstanding. This paper develops an 8-node, 24-DOF (three conventional DOFs per node) hexahedral element based on the virtual work principle, in which two different sets of displacement fields are employed simultaneously to formulate an unsymmetric element stiffness matrix. The first set simply utilizes the formulations of the traditional 8-node trilinear isoparametric element, while the second set mainly employs the analytical trial functions in terms of 3D oblique coordinates (R, S, T). The resulting element, denoted by US-ATFH8, contains no adjustable factor and can be used for both isotropic and anisotropic cases. Numerical examples show it can strictly pass both the first-order (constant stress/strain) patch test and the second-order patch test for pure bending, remove the volume locking, and provide the invariance for coordinate rotation. Especially, it is insensitive to various severe mesh distortions