A Composite Likelihood-based Approach for Change-point Detection in Spatio-temporal Process

This paper develops a unified, accurate and computationally efficient method for change-point inference in non-stationary spatio-temporal processes. By modeling a non-stationary spatio-temporal process as a piecewise stationary spatio-temporal process, we consider simultaneous estimation of the number and locations of change-points, and model parameters in each segment. A composite likelihood-based criterion is developed for change-point and parameters estimation. Asymptotic theories including consistency and distribution of the estimators are derived under mild conditions. In contrast to classical results in fixed dimensional time series that the asymptotic error of change-point estimator is $O_{p}(1)$, exact recovery of true change-points is guaranteed in the spatio-temporal setting. More surprisingly, the consistency of change-point estimation can be achieved without any penalty term in the criterion function. A computational efficient pruned dynamic programming algorithm is developed for the challenging criterion optimization problem. Simulation studies and an application to U.S. precipitation data are provided to demonstrate the effectiveness and practicality of the proposed method

Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology

Abstract Background In many protein-protein interaction (PPI) networks, densely connected hub proteins are more likely to be essential proteins. This is referred to as the "centrality-lethality rule", which indicates that the topological placement of a protein in PPI network is connected with its biological essentiality. Though such connections are observed in many PPI networks, the underlying topological properties for these connections are not yet clearly understood. Some suggested putative connections are the involvement of essential proteins in the maintenance of overall network connections, or that they play a role in essential protein clusters. In this work, we have attempted to examine the placement of essential proteins and the network topology from a different perspective by determining the correlation of protein essentiality and reverse nearest neighbor topology (RNN). Results The RNN topology is a weighted directed graph derived from PPI network, and it is a natural representation of the topological dependences between proteins within the PPI network. Similar to the original PPI network, we have observed that essential proteins tend to be hub proteins in RNN topology. Additionally, essential genes are enriched in clusters containing many hub proteins in RNN topology (RNN protein clusters). Based on these two properties of essential genes in RNN topology, we have proposed a new measure; the RNN cluster centrality. Results from a variety of PPI networks demonstrate that RNN cluster centrality outperforms other centrality measures with regard to the proportion of selected proteins that are essential proteins. We also investigated the biological importance of RNN clusters. Conclusions This study reveals that RNN cluster centrality provides the best correlation of protein essentiality and placement of proteins in PPI network. Additionally, merged RNN clusters were found to be topologically important in that essential proteins are significantly enriched in RNN clusters, and biologically important because they play an important role in many Gene Ontology (GO) processes.http://deepblue.lib.umich.edu/bitstream/2027.42/78257/1/1471-2105-11-505.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78257/2/1471-2105-11-505-S1.DOChttp://deepblue.lib.umich.edu/bitstream/2027.42/78257/3/1471-2105-11-505.pdfPeer Reviewe

Analysis of the Relationships among Longest Common Subsequences, Shortest Common Supersequences and Patterns and its application on Pattern Discovery in Biological Sequences

For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons and analysis. Revealing the relationship between the patterns and LCS,SCS might provide us with a deeper view of the patterns of biological sequences, in turn leading to better understanding of them. However, There is no careful examinaton about the relationship between patterns, LCS and SCS. In this paper, we have analyzed their relation, and given some lemmas. Based on their relations, a set of algorithms called the PALS (PAtterns by Lcs and Scs) algorithms are propsoed to discover patterns in a set of biological sequences. These algorithms first generate the results for LCS and SCS of sequences by heuristic, and consequently derive patterns from these results. Experiments show that the PALS algorithms perform well (both in efficiency and in accuracy) on a variety of sequences. The PALS approach also provides us with a solution for transforming between the heuristic results of SCS and LCS.Comment: Extended version of paper presented in IEEE BIBE 2006 submitted to journal for revie

Cardiac Stem Cells for Myocardial Regeneration: They Are Not Alone

Heart failure is the number one killer worldwide with ~50% of patients dying within 5 years of prognosis. The discovery of stem cells, which are capable of repairing the damaged portion of the heart, has created a field of cardiac regenerative medicine, which explores various types of stem cells, either autologous or endogenous, in the hope of finding the “holy grail” stem cell candidate to slow down and reverse the disease progression. However, there are many challenges that need to be overcome in the search of such a cell candidate. The ideal cells have to survive the harsh infarcted environment, retain their phenotype upon administration, and engraft and be activated to initiate repair and regeneration in vivo. Early bench and bedside experiments mostly focused on bone marrow-derived cells; however, heart regeneration requires multiple coordinations and interactions between various cell types and the extracellular matrix to form new cardiomyocytes and vasculature. There is an observed trend that when more than one cell is coadministered and cotransplanted into infarcted animal models the degree of regeneration is enhanced, when compared to single-cell administration. This review focuses on stem cell candidates, which have also been tested in human trials, and summarizes findings that explore the interactions between various stem cells in heart regenerative therapy

Distinct EMT programs control normal mammary stem cells and tumour-initiating cells

Tumour-initiating cells (TICs) are responsible for metastatic dissemination and clinical relapse in a variety of cancers. Analogies between TICs and normal tissue stem cells have led to the proposal that activation of the normal stem-cell program within a tissue serves as the major mechanism for generating TICs. Supporting this notion, we and others previously established that the Slug epithelial-to-mesenchymal transition-inducing transcription factor (EMT-TF), a member of the Snail family, serves as a master regulator of the gland-reconstituting activity of normal mammary stem cells, and that forced expression of Slug in collaboration with Sox9 in breast cancer cells can efficiently induce entrance into the TIC state. However, these earlier studies focused on xenograft models with cultured cell lines and involved ectopic expression of EMT-TFs, often at non-physiological levels. Using genetically engineered knock-in reporter mouse lines, here we show that normal gland-reconstituting mammary stem cells residing in the basal layer of the mammary epithelium and breast TICs originating in the luminal layer exploit the paralogous EMT-TFs Slug and Snail, respectively, which induce distinct EMT programs. Broadly, our findings suggest that the seemingly similar stem-cell programs operating in TICs and normal stem cells of the corresponding normal tissue are likely to differ significantly in their details.Breast Cancer Research FoundationSamuel Waxman Cancer Research FoundationLudwig Center for Molecular Oncology at MITNational Cancer Institute (U.S.).(Program P01-CA080111)National Cancer Institute (U.S.).(Program R01-CA078461)National Cancer Institute (U.S.).(Program U01-CA184897

A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages

The cell-biological program termed the epithelial-mesenchymal transition (EMT) confers on cancer cells mesenchymal traits and an ability to enter the cancer stem cell (CSC) state. However, the interactions between CSCs and their surrounding microenvironment are poorly understood. Here we show that tumour-associated monocytes and macrophages (TAMs) create a CSC niche through juxtacrine signalling with CSCs. We performed quantitative proteomic profiling and found that the EMT program upregulates the expression of CD90, also known as Thy1, and EphA4, which mediate the physical interactions of CSCs with TAMs by directly binding with their respective counter-receptors on these cells. In response, the EphA4 receptor on the carcinoma cells activates Src and NF-κ B. In turn, NF-κ B in the CSCs induces the secretion of a variety of cytokines that serve to sustain the stem cell state. Indeed, admixed macrophages enhance the CSC activities of carcinoma cells. These findings underscore the significance of TAMs as important components of the CSC niche.National Institutes of Health (U.S.) (Grant R01-CA078461)National Institutes of Health (U.S.) (Grant P01-CA080111)National Institutes of Health (U.S.) (Grant U54-CA163109

Ternary copper(II)-polypyridyl enantiomers: aldol-type condensation, characterization, DNA-binding recognition, BSA-binding and anticancer property

Chiral enantiomers [Cu(phen)(l-threo)(H2O)]NO31 and [Cu(phen)(d-threo)(H2O)]NO32 (threo = threoninate) underwent aldol-type condensation with formaldehyde, with retention of chirality, to yield their respective enantiomeric ternary copper(ii) complexes, viz.l- and d-[Cu(phen)(5MeOCA)(H2O)]NO3·xH 2O (3 and 4; phen = 1,10-phenanthroline; 5MeOCA = 5-methyloxazolidine-4-carboxylate; x = 0-3) respectively. These chiral complexes were characterized by FTIR, elemental analysis, circular dichroism, UV-Visible spectroscopy, fluorescence spectroscopy (FL), molar conductivity measurement, ESI-MS and X-ray crystallography. Analysis of restriction enzyme inhibition by these four complexes revealed modulation of DNA binding selectivity by the type of ligand, ligand modification and chirality. Their interaction with bovine serum albumin was investigated by FL and electronic spectroscopy. With the aid of the crystal structure of BSA, spectroscopic evidence suggested their binding at the cavity containing Trp134 with numerous Tyr residues in subdomain IA. The products were more antiproliferative than cisplatin against cancer cell lines HK-1, MCF-7, HCT116, HSC-2 and C666-1 except HL-60, and were selective towards nasopharyngeal cancer HK-1 cells over normal NP69 cells of the same organ type

Cryopreservation of Neurospheres Derived from Human Glioblastoma Multiforme

Cancer stem cells have been shown to initiate and sustain tumor growth. In many instances, clinical material is limited, compounded by a lack of methods to preserve such cells at convenient time points. Although brain tumor-initiating cells grown in a spheroid manner have been shown to maintain their integrity through serial transplantation in immune-compromised animals, practically, it is not always possible to have access to animals of suitable ages to continuously maintain these cells. We therefore explored vitrification as a cryopreservation technique for brain tumor-initiating cells. Tumor neurospheres were derived from five patients with glioblastoma multiforme (GBM). Cryopreservation in 90% serum and 10% dimethyl sulfoxide yielded greatest viability and could be explored in future studies. Vitrification yielded cells that maintained self-renewal and multipotentiality properties. Karyotypic analyses confirmed the presence of GBM hallmarks. Upon implantation into NOD/SCID mice, our vitrified cells reformed glioma masses that could be serially transplanted. Transcriptome analysis showed that the vitrified and nonvitrified samples in either the stem-like or differentiated states clustered together, providing evidence that vitrification does not change the genotype of frozen cells. Upon induction of differentiation, the transcriptomes of vitrified cells associated with the original primary tumors, indicating that tumor stem-like cells are a genetically distinct population from the differentiated mass, underscoring the importance of working with the relevant tumor-initiating population. Our results demonstrate that vitrification of brain tumor-initiating cells preserves the biological phenotype and genetic profiles of the cells. This should facilitate the establishment of a repository of tumor-initiating cells for subsequent experimental designs