Concise Review: The Potential Use of Intestinal Stem Cells to Treat Patients With Intestinal Failure.

: Intestinal failure is a rare life-threatening condition that results in the inability to maintain normal growth and hydration status by enteral nutrition alone. Although parenteral nutrition and whole organ allogeneic transplantation have improved the survival of these patients, current therapies are associated with a high risk for morbidity and mortality. Development of methods to propagate adult human intestinal stem cells (ISCs) and pluripotent stem cells raises the possibility of using stem cell-based therapy for patients with monogenic and polygenic forms of intestinal failure. Organoids have demonstrated the capacity to proliferate indefinitely and differentiate into the various cellular lineages of the gut. Genome-editing techniques, including the overexpression of the corrected form of the defective gene, or the use of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 to selectively correct the monogenic disease-causing variant within the stem cell, make autologous ISC transplantation a feasible approach. However, numerous techniques still need to be further optimized, including more robust ex vivo ISC expansion, native ISC ablation, and engraftment protocols. Large-animal models can to be used to develop such techniques and protocols and to establish the safety of autologous ISC transplantation because outcomes in such models can be extrapolated more readily to humans.The field of intestinal stem cell biology has exploded over the past 5 years with discoveries related to in vivo and in vitro stem cell identity and function. The goal of this review article is to highlight the potential use of these cells to treat various epithelial disorders of the gut and discuss the various roadblocks that will be encountered in the coming years

Localized-density-matrix implementation of time-dependent density-functional theory

The localized single-electron density matrix implementation of time-dependent density-functional theory (TDDFT) was discussed. The excited state properties of atoms and molecules were calculated using the TDDFT. In this regard, the calculations of the absorption spectra of polyacetylene oligomers and linear alkanes by using the TDDFT, were also presented.published_or_final_versio

Machine scheduling with deliveries to multiple customer locations

Department of Logistics, Faculty of Business2005-2006 > Academic research: refereed > Publication in refereed journalAccepted ManuscriptPublishe

Dissipative time-dependent quantum transport theory

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Linear-scaling time-dependent density-functional theory

A linear-scaling time-dependent density-functional theory is developed to evaluate the optical response of large molecular systems. The two-electron Coulomb integrals are evaluated with the fast multipole method, and the calculation of exchange-correlation quadratures utilizes the locality of exchange-correlation functional within the adiabatic local density approximation and the integral prescreening technique. Instead of many-body wave function, the equation of motion is solved for the reduced single-electron density matrix in the time domain. Based on its "nearsightedness", the reduced density matrix cutoffs are employed to ensure that the computational time scales linearly with the system size. As an illustration, the resulting time-dependent density-functional theory is used to calculate the absorption spectra of linear alkanes, and the linear scaling of computational time versus the system size is clearly demonstrated.published_or_final_versio

Time-dependent density-functional theory/localized density matrix method for dynamic hyperpolarizability

Time-dependent density-functional theory/localized density matrix method (TDDFT/LDM) was developed to calculate the excited state energy, absorption spectrum and dynamic polarizability. In the present work we generalize it to calculate the dynamic hyperpolarizabilities in both time and frequency domains. We show that in the frequency domain the 2n+1 rule can be derived readily and the dynamic hyperpolarizabilities are thus calculated efficiently. Although the time-domain TDDFT/LDM is time consuming, its implementation is straightforward because the evaluation of the derivatives of exchange-correlation potential with respect to electron density is avoided. Moreover, the time-domain method can be used to simulate higher order response which is very difficult to be calculated with the frequency-domain method. © 2007 American Institute of Physics.published_or_final_versio

Identification of differentially expressed genes in seeds of two Brassica napus mutant lines with different oleic acid content

The regulation of seed oleic acid synthesis in rapeseed is largely unknown. In this study, gene expression pattern during seed development between two Brassica napus mutants was compared. Using immature seeds 27 days after pollination, differentially expressed cDNA clones were identified bysubtractive suppression hybridization (SSH). A total of 480 cDNA clones corresponding to 88 genes were found up-regulated and 18 genes down-regulated in seeds with high oleic acid content. Most ofthe differentially expressed genes are related to metabolism and regulation. The possible role of these genes in seeds was discussed. Further analysis of the function of these genes may provide novel targets for manipulation of fatty acid composition in rapeseed

Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity.

Runs of homozygosity (ROH) are important genomic features that manifest when an individual inherits two haplotypes that are identical by descent. Their length distributions are informative about population history, and their genomic locations are useful for mapping recessive loci contributing to both Mendelian and complex disease risk. We have previously shown that ROH, and especially long ROH that are likely the result of recent parental relatedness, are enriched for homozygous deleterious coding variation in a worldwide sample of outbred individuals. However, the distribution of ROH in admixed populations and their relationship to deleterious homozygous genotypes is understudied. Here we analyze whole-genome sequencing data from 1,441 unrelated individuals from self-identified African American, Puerto Rican, and Mexican American populations. These populations are three-way admixed between European, African, and Native American ancestries and provide an opportunity to study the distribution of deleterious alleles partitioned by local ancestry and ROH. We re-capitulate previous findings that long ROH are enriched for deleterious variation genome-wide. We then partition by local ancestry and show that deleterious homozygotes arise at a higher rate when ROH overlap African ancestry segments than when they overlap European or Native American ancestry segments of the genome. These results suggest that, while ROH on any haplotype background are associated with an inflation of deleterious homozygous variation, African haplotype backgrounds may play a particularly important role in the genetic architecture of complex diseases for admixed individuals, highlighting the need for further study of these populations

Communication: Linear-expansion shooting techniques for accelerating self-consistent field convergence

Based on the corrected Hohenberg-Kohn-Sham total energy density functional [Y. A. Zhang and Y. A. Wang, J. Chem. Phys. 130, 144116 (2009)]10.1063/1. 3104662, we have developed two linear-expansion shooting techniques (LIST)- direct LIST (LISTd) and indirect LIST (LISTi), to accelerate the convergence of self-consistent field (SCF) calculations. Case studies show that overall LISTi is the most robust and efficient algorithm for accelerating SCF convergence, whereas LISTd is advantageous in the early stage of an SCF process. More importantly, LISTi outperforms Pulays direct inversion in the iterative subspace (DIIS) [P. Pulay, J. Comput. Chem. 3, 556 (1982)]10.1002/jcc.540030413 and its two recent improvements, energy-DIIS [K. N. Kudin, G. E. Scuseria, and E. Cancs, J. Chem. Phys. © 2011 American Institute of Physics.published_or_final_versio