| 1. |
- Ching, Yung-Hao, et al.
(författare)
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High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5
- 2010
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Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 11, s. 106-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Forward genetic screens in mice provide an unbiased means to identify genes and other functional genetic elements in the genome. Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a similar to 50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals. Results: We report the high resolution genetic mapping, complementation analyses, and positional cloning of mutations in the target region. The collection of identified alleles include several with known or presumed functions for which no mutant models have been reported (Tbc1d14, Nol14, Tyms, Cad, Fbxl5, Haus3), and mutations in genes we or others previously reported (Tapt1, Rest, Ugdh, Paxip1, Hmx1, Otoe, Nsun7). We also confirmed the causative nature of a homeotic mutation with a targeted allele, mapped a lethal mutation to a large gene desert, and localized a spermiogenesis mutation to a region in which no annotated genes have coding mutations. The mutation in Tbc1d14 provides the first implication of a critical developmental role for RAB-GAP-mediated protein transport in early embryogenesis. Conclusion: This collection of alleles contributes to the goal of assigning biological functions to all known genes, as well as identifying novel functional elements that would be missed by reverse genetic approaches.
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| 2. |
- Li, Li, et al.
(författare)
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Reversible Modification of CdSe-CdS/ZnS Quantum Dot Fluorescence by Surrounding Ca2+ Ions
- 2014
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 118:19, s. 10424-10433
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Tidskriftsartikel (refereegranskat)abstract
- It has been known for a long time that the fluorescence intensity of colloidal quantum dots (QDs) becomes modified when free ions are added to the QD solution. The consequences of removing free ions from the QD solution, however, have not been closely investigated. In this work we studied fluorescence from 3-mercaptopropionic acid (3-MPA) coated CdSe-CdS/ZnS core-multishell QDs when free Ca2+ ions were added to and subsequently removed from the QD solution. It was found that QD fluorescence intensity was reduced when Ca2+ ions were added to the QD solution, while the wavelength of the QD fluorescence peak remained unchanged. QD fluorescence recovered when the concentration of free Ca2+ ions in the QD solution was reduced by adding Ca2+ chelator (ethylene glycol tetraacetic acid, EGTA). It was further observed that the time of single QD fluorescence at on-state and QD fluorescence lifetimes were also reduced after adding Ca2+ and then recovered when EGTA was added. Theoretical study shows that a free Ca2+ ion can attach stably to the system of [QD + surface ligand], attract the photoexcited electron, and repel the photoexcited hole inside the QD core, leading to the reduction of the radiative recombination between the electron and hole, thereafter decreasing the QD fluorescence intensity, on-state time, and fluorescence lifetimes, as observed experimentally. To the best of our knowledge, this is a first study to show that the changes of QD optical properties are reversible under the influence of Ca2+ ions. We further estimated the equilibrium association constant pK(a) of our QDs with Ca2+, which is much larger than QDs with Mg2+, Na+, and K+, indicating the feasibility of developing a QD-based Ca2+ sensor.
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| 3. |
- Li, Xin, et al.
(författare)
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Electronic structure of bismuth telluride quasi-two-dimensional crystal : A first principles study
- 2011
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 98:8, s. 083113-
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structures of atomically thin layers of bismuth telluride (Bi2Ti3) have been studied by using density functional theory. It is found that quintuple layers of Bi2Te3 are semiconductor with localized shallow bands. The weak covalent Bi-Te-2 interaction in quintuple layer allows to further exfoliate it to form bilayer and trilayer sheets. In the latter cases, the valence electrons cannot fully occupy all the valence bands and the sheets become metallic.
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| 4. |
- Li, Xiaofei, et al.
(författare)
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Important structural factors controlling the conductance of DNA pairs in molecular junctions
- 2010
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 114:33, s. 14240-14242
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Tidskriftsartikel (refereegranskat)abstract
- It has been demonstrated experimentally that DNA base pairs and sequences can be identified by measuring their current changes in metal junctions. We report here a first principles study on electron transport properties of DNA base pairs in gold metal junctions. It is found that the experimentally observed electrode-separation-width-dependent current changes of DNA base pairs are not due to the difference in number of hydrogen bonds involved in different base pairs as proposed in earlier experimental studies but caused by the difference in their stacking structures. It reveals that such an electronic read-out technique is not exact, but practically useful since the statistically favorable misaligned junctions do show distinct dependence on the character of the base pair.
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| 5. |
- Luo, Hao
(författare)
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Generation of Non-normalData : A Study ofFleishman’s PowerMethod
- 2011
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Fleishman's power method is one of the traditional methods used for generatingnon-normal random numbers. In this paper, we use Monte Carlo simulationto test the reliability of this method. Specially, we assess the performance of the method under different conditions of skewness, kurtosis and sample sizes.The power of the normality test statistics proposed by D'Agostino (1986) isstudied based on the generated samples. The results suggest that Fleishman'smethod has difficulties on generating non-normal samples with higher levels of skewness and kurtosis. The effect of sample size is found to be significant on the reliability of the data generation. The parabola, which indicates the bottomboundary of the possible combination of skewness and kurtosis calculated by Fleishman (1978), is shown to be incorrect. When it comes to the power study, a considerable impact of sample size is also observed on obtaining a trustworthytest decision based on the generated non-normal samples.
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| 6. |
- Luo, Hao, 1984-
(författare)
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Some Aspects on Confirmatory Factor Analysis of Ordinal Variables and Generating Non-normal Data
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis, which consists of five papers, is concerned with various aspects of confirmatory factor analysis (CFA) of ordinal variables and the generation of non-normal data. The first paper studies the performances of different estimation methods used in CFA when ordinal data are encountered. To take ordinality into account the four estimation methods, i.e., maximum likelihood (ML), unweighted least squares, diagonally weighted least squares, and weighted least squares (WLS), are used in combination with polychoric correlations. The effect of model sizes and number of categories on the parameter estimates, their standard errors, and the common chi-square measure of fit when the models are both correct and misspecified are examined. The second paper focuses on the appropriate estimator of the polychoric correlation when fitting a CFA model. A non-parametric polychoric correlation coefficient based on the discrete version of Spearman's rank correlation is proposed to contend with the situation of non-normal underlying distributions. The simulation study shows the benefits of using the non-parametric polychoric correlation under conditions of non-normality. The third paper raises the issue of simultaneous factor analysis. We study the effect of pooling multi-group data on the estimation of factor loadings. Given the same factor loadings but different factor means and correlations, we investigate how much information is lost by pooling the groups together and only estimating the combined data set using the WLS method. The parameter estimates and their standard errors are compared with results obtained by multi-group analysis using ML. The fourth paper uses a Monte Carlo simulation to assess the reliability of the Fleishman's power method under various conditions of skewness, kurtosis, and sample size. Based on the generated non-normal samples, the power of D'Agostino's (1986) normality test is studied. The fifth paper extends the evaluation of algorithms to the generation of multivariate non-normal data. Apart from the requirement of generating reliable skewness and kurtosis, the generated data also need to possess the desired correlation matrices. Four algorithms are investigated in terms of simplicity, generality, and reliability of the technique.
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| 7. |
- Ni, Ming-jiang, et al.
(författare)
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Naphthalene decomposition in a DC corona radical shower discharge
- 2011
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Ingår i: Journal of Zhejiang University: Science A. - 1673-565X. ; 12:1, s. 71-77
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Tidskriftsartikel (refereegranskat)abstract
- The naphthalene decomposition in a corona radical shower discharge (CRS) was investigated, with attention paid to the influences of voltage and initial naphthalene density. The OH emission spectra were investigated so as to know the naphthalene decomposing process. The by-products were analyzed and a decomposing theory in discharge was proposed. The results showed that higher voltage and relative humidity were effective on decomposition. The initial concentration affected the decomposing efficiency of naphthalene. When the initial naphthalene density was 17 mg/m(3), the decomposition rate was found to be 70% under 14 kV. The main by-products were carbon dioxide and water. However, a small amount of carbonic oxide, 1,2-ethanediol and acetaldehyde were found due to the incomplete oxidization.
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| 8. |
- Ren, Hao, 1982-
(författare)
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First principles simulations of electron transport at the molecule-solid interface
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis I concentrate on the description of electron transport properties of microscopic objects, including molecular junctions and nano junctions, in particular, inelastic electron tunneling in surface-adsorbate systems are examined with more contemplations. Boosted by the rapid advance in experimental techniques at the microscopic scale, various electric experiments and measurements sprung up in the last decade. Electric devices, such as transistors, switches, wires, etc. are expected to be integrated into circuit and performing like traditional semiconductor integrated circuit (IC). On the other hand, detailed information about transport properties also provides new physical observable quantities to characterize the systems. For molecular electronics, which is in the state of growing up, its further applications demands more thorough understanding of the underlying mechanism, for instance, the effects of molecular configuration and conformation, inter- or intra-molecular interactions, molecular-substrate interactions, and so on. Inelastic electron tunneling spectroscopy (IETS), which reflects vibration features of the system, is also a finger print property, and can thus be employed to afford the responsibility of single molecular identification with the help of other experimental techniques and theoretical simulations.There are two parts of work presented in this thesis, the first one is devoted to the calculation of electron transport properties of molecular or nano junctions: we have designed a negative differential resistance (NDR) device based on graphene nanoribbons (GNRs), where the latter is a star material in scientific committee since its birth;The transport properties of DNA base-pair junctions are also examined by theoretical calculation, relevant experimental results on DNA sequencing have been explained and detailed issues are suggested.The second part focused on the simulation of scanning tunneling microscope mediated IETS (STM-IETS). We have implemented a numerical scheme to calculate the inelastic tunneling intensity based on Tersoff-Hamann approximation and finite difference method, benchmark results agree well with experimental and previous theoretical ones; Two applications of single molecular chemical identification are also presented following benchmarking.
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| 9. |
- Ren, Hao, et al.
(författare)
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Identifying configuration and orientation of adsorbed molecules by inelastic electron tunneling spectra
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 133:6, s. 064702-
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Tidskriftsartikel (refereegranskat)abstract
- Scanning tunneling microscopy (STM) topographical images and inelastic electron tunneling spectra (IETS) of a cis-2-butene molecule adsorbed on a Pd(110) surface have been simulated by first-principles calculations. Calculations have eliminated the ambiguity between the STM image and the adsorption orientation caused by the symmetry of the system and local chemical environment. A combination of STM images and IETS spectra has been shown to be particularly useful in determining the configuration of the molecule on the surface. (C) 2010 American Institute of Physics. [doi:10.1063/1.3474807]
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| 10. |
- Sheng, Zheya, et al.
(författare)
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Genetic dissection of growth traits in a Chinese indigenous × commercial broiler chicken cross.
- 2013
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: In China, consumers often prefer indigenous broiler chickens over commercial breeds, as they have characteristic meat qualities requested within traditional culinary customs. However, the growth-rate of these indigenous breeds is slower than that of the commercial broilers, which means they have not yet reached their full economic value. Therefore, combining the valuable meat quality of the native chickens with the efficiency of the commercial broilers is of interest. In this study, we generated an F2 intercross between the slow growing native broiler breed, Huiyang Beard chicken, and the fast growing commercial broiler breed, High Quality chicken Line A, and used it to map loci explaining the difference in growth rate between these breeds.RESULTS: A genome scan to identify main-effect loci affecting 24 growth-related traits revealed nine distinct QTL on six chromosomes. Many QTL were pleiotropic and conformed to the correlation patterns observed between phenotypes. Most of the mapped QTL were found in locations where growth QTL have been reported in other populations, although the effects were greater in this population. A genome scan for pairs of interacting loci identified a number of additional QTL in 10 other genomic regions. The epistatic pairs explained 6-8% of the residual phenotypic variance. Seven of the 10 epistatic QTL mapped in regions containing candidate genes in the ubiquitin mediated proteolysis pathway, suggesting the importance of this pathway in the regulation of growth in this chicken population.CONCLUSIONS: The main-effect QTL detected using a standard one-dimensional genome scan accounted for a significant fraction of the observed phenotypic variance in this population. Furthermore, genes in known pathways present interesting candidates for further exploration. This study has thus located several QTL regions as promising candidates for further study, which will increase our understanding of the genetic mechanisms underlying growth-related traits in chickens.
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| 11. |
- Wang, Yang, et al.
(författare)
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Role of point defects on the reactivity of reconstructed anatase titanium dioxide (001) surface
- 2013
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 4, s. 2214-
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Tidskriftsartikel (refereegranskat)abstract
- The chemical reactivity of different surfaces of titanium dioxide (TiO2) has been the subject of extensive studies in recent decades. The anatase TiO2(001) and its (1 x 4) reconstructed surfaces were theoretically considered to be the most reactive and have been heavily pursued by synthetic chemists. However, the lack of direct experimental verification or determination of the active sites on these surfaces has caused controversy and debate. Here we report a systematic study on an anatase TiO2(001)-(1 x 4) surface by means of microscopic and spectroscopic techniques in combination with first-principles calculations. Two types of intrinsic point defects are identified, among which only the Ti3+ defect site on the reduced surface demonstrates considerable chemical activity. The perfect surface itself can be fully oxidized, but shows no obvious activity. Our findings suggest that the reactivity of the anatase TiO2(001) surface should depend on its reduction status, similar to that of rutile TiO2 surfaces.
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| 12. |
- Yang-Wallentin, Fan, et al.
(författare)
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Confirmatory Factor Analysis of Ordinal Variables With Misspecified Models
- 2010
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Ingår i: Structural Equation Modeling. - : Taylor&Francis Group. - 1070-5511 .- 1532-8007. ; 17:3, s. 392-423
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Tidskriftsartikel (refereegranskat)abstract
- Ordinal variables are common in many empirical investigations in the social and behavioral sciences. Researchers often apply the maximum likelihood method to fit structural equation models to ordinal data. This assumes that the observed measures have normal distributions, which is not the case when the variables are ordinal. A better approach is to use polychoric correlations and fit the models using methods such as unweighted least squares (ULS), maximum likelihood (ML), weighted least squares (WLS), or diagonally weighted least squares (DWLS). In this simulation evaluation we study the behavior of these methods in combination with polychoric correlations when the models are misspecified. We also study the effect of model size and number of categories on the parameter estimates, their standard errors, and the common chi-square measures of fit when the models are both correct and misspecified. When used routinely, these methods give consistent parameter estimates but ULS, ML, and DWLS give incorrect standard errors. Correct standard errors can be obtained for these methods by robustification using an estimate of the asymptotic covariance matrix W of the polychoric correlations. When used in this way the methods are here called RULS, RML, and RDWLS.
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