Voting-Based Cancer Module Identification by Combining Topological and Data-Driven Properties

Recently, computational approaches integrating copy number aberrations (CNAs) and gene expression (GE) have been extensively studied to identify cancer-related genes and pathways. In this work, we integrate these two data sets with protein-protein interaction (PPI) information to find cancer-related functional modules. To integrate CNA and GE data, we first built a gene-gene relationship network from a set of seed genes by enumerating all types of pairwise correlations, e.g. GE-GE, CNA-GE, and CNA-CNA, over multiple patients. Next, we propose a voting-based cancer module identification algorithm by combining topological and data-driven properties (VToD algorithm) by using the gene-gene relationship network as a source of data-driven information, and the PPI data as topological information. We applied the VToD algorithm to 266 glioblastoma multiforme (GBM) and 96 ovarian carcinoma (OVC) samples that have both expression and copy number measurements, and identified 22 GBM modules and 23 OVC modules. Among 22 GBM modules, 15, 12, and 20 modules were significantly enriched with cancer-related KEGG, BioCarta pathways, and GO terms, respectively. Among 23 OVC modules, 19, 18, and 23 modules were significantly enriched with cancer-related KEGG, BioCarta pathways, and GO terms, respectively. Similarly, we also observed that 9 and 2 GBM modules and 15 and 18 OVC modules were enriched with cancer gene census (CGC) and specific cancer driver genes, respectively. Our proposed module-detection algorithm significantly outperformed other existing methods in terms of both functional and cancer gene set enrichments. Most of the cancer-related pathways from both cancer data sets found in our algorithm contained more than two types of gene-gene relationships, showing strong positive correlations between the number of different types of relationship and CGC enrichment -values (0.64 for GBM and 0.49 for OVC). This study suggests that identified modules containing both expression changes and CNAs can explain cancer-related activities with greater insights.     

Probing the Topological Properties of Complex Networks Modeling Short Written Texts

In recent years, graph theory has been widely employed to probe several language properties. More specifically, the so-called word adjacency model has been proven useful for tackling several practical problems, especially those relying on textual stylistic analysis. The most common approach to treat texts as networks has simply considered either large pieces of texts or entire books. This approach has certainly worked well—many informative discoveries have been made this way—but it raises an uncomfortable question: could there be important topological patterns in small pieces of texts? To address this problem, the topological properties of subtexts sampled from entire books was probed. Statistical analyses performed on a dataset comprising 50 novels revealed that most of the traditional topological measurements are stable for short subtexts. When the performance of the authorship recognition task was analyzed, it was found that a proper sampling yields a discriminability similar to the one found with full texts. Surprisingly, the support vector machine classification based on the characterization of short texts outperformed the one performed with entire books. These findings suggest that a local topological analysis of large documents might improve its global characterization. Most importantly, it was verified, as a proof of principle, that short texts can be analyzed with the methods and concepts of complex networks. As a consequence, the techniques described here can be extended in a straightforward fashion to analyze texts as time-varying complex networks.     

New Inhibitor of Phosphodiesterase with Anti-bronchoconstrictor Properties

IN earlier work on the synthesis of isosteres of purine and in particular of theophylline (I), a series of triazolopyrimidines was found which could protect guinea-pigs against histamine bronchospasm. One compound (II) was also found to be active in certain cases of human asthma but it was found to be of no practical value because it had a tendency to cause nausea and vomiting. But because there is at present no adequate treatment for asthma, we undertook to prepare related substances which retain the activity but which are free of the defect: Thus we produced 3-acetamido-6-methyl-8-n-propyl-s-triazolo [4,3a] pyrazine (III; R=CO.Me;I.C.I.58,301 (ref. 3)). This substance is only in the early stages of clinical study in man, but we report here the chemical, biological and biochemical properties that led to its selection.     

New Indices for Predicting Glycaemic Variability

Blood glucose variability is known to be associated with increased risk of long-term complications. Reliable indices for predicting hyperglycaemic and hypoglycaemic fluctuations are therefore needed. Glycaemic standard deviation (SD) obtained by continuous glucose monitoring correlates closely with nine previously described glycaemic variability formulas. Here, new indices predictive of glycaemic variability were developed, which can be calculated from laboratory measures based on a single blood draw. The indices included the glycated albumin (GA) to HbA1c ratio (GA/A1c ratio) and the fasting C-peptide immunoreactivity (FCPR) to fasting plasma glucose (FPG) ratio (FCPR index). Predictive values of these indices were assessed in 100 adults with diabetes. GA/A1c ratio and FCPR index showed close associations with glycaemic SD in addition to the nine existing glucose variability formulas. Subjects with a GA/A1c ratio ≥2.8 and FCPR index <3.0 showed the greatest SD and longest durations of hypoglycaemia, while those with a GA/A1c ratio <2.8 and FCPR index ≥3.0 had smaller SDs and little sign of hypoglycaemia. In adults with diabetes, a high GA/A1c ratio and low FCPR index value reflect higher glycaemic excursions, irrespective of diabetes type. Simultaneous measurements of GA, HbA1c, FPG and FCPR may help to identify a group of patients who warrant closer monitoring in relation to glycaemic variability and hypoglycaemia.     

胎儿体重预测的一种新方法

利用B型超声对520例胎儿的股骨长、腹围测量数据,经非线性回归分析得出预测胎儿体重的修正Logistic模型,并用所建模型对982例胎儿进行实例验证,其结果大大优于国内外已有文献报道．     

A New Bithiazole Derivative with Intercalative Properties

Abstract

In the course of studies related to new molecules with intercalative properties, we have been led to design and synthesize a bithiazole derivative, namely the 2-phenyl-6- [2′-(4′-(ethoxy-carbony1)thiazoly1)] thiazolo[3,2-b] [1,2,4]triazole (PETT). Its interaction with calf thymus DNA was studied using thermal denaturation and viscometry. Our results set in evidence that PETT acts as an intercalator, giving Δ Tm, elongation and unwinding of DNA comparable to the values obtained for daunorubicin. The discrepancy between the data presented herein and those precedently obtained for bleomycin and bleomycin models provide evidence that these bithiazole derivatives interact differently with DNA.     

Predicting the Size of Silver Nanoparticles from Their Optical Properties

Plasmonics - In this study, localized surface plasmon resonance (LSPR) of the spherical silver nanoparticles (AgNPs) was evaluated based on experimental and theoretical viewpoints. In the...     

Predicting Statistical Properties of Open Reading Frames in Bacterial Genomes

An analytical model based on the statistical properties of Open Reading Frames (ORFs) of eubacterial genomes such as codon composition and sequence length of all reading frames was developed. This new model predicts the average length, maximum length as well as the length distribution of the ORFs of 70 species with GC contents varying between 21% and 74%. Furthermore, the number of annotated genes is predicted with high accordance. However, the ORF length distribution in the five alternative reading frames shows interesting deviations from the predicted distribution. In particular, long ORFs appear more often than expected statistically. The unexpected depletion of stop codons in these alternative open reading frames cannot completely be explained by a biased codon usage in the +1 frame. While it is unknown if the stop codon depletion has a biological function, it could be due to a protein coding capacity of alternative ORFs exerting a selection pressure which prevents the fixation of stop codon mutations. The comparison of the analytical model with bacterial genomes, therefore, leads to a hypothesis suggesting novel gene candidates which can now be investigated in subsequent wet lab experiments.     

Landscape Excitation Profiles and Excess Thermodynamic Properties of Disaccharide Aqueous Solutions

We will consider the use of the bond model in characterizing, by the direct calculation route, the full excitation profile. The present work sets the temperature behaviour of the excessive value of some thermodynamic quantities, such as configurational entropy and heat capacity of two homologous disaccharide aqueous solutions. The findings represent important data for understanding the better lyoprotectant effectiveness of trehalose in comparison with sucrose.     

Construction of Selection Indexes with Restrictions

In this paper the problem of unistage selection with inequality constraints is formulated. If the predictor and criterion variables are all normally distributed, this problem can be written as a convex programming problem, with a linear objective function and with linear constraints and a quadratic constraint. Using the duality theory, for convex nonlinear programming it is proved, that its dual problem can be transformed into a convex minimization problem with non-negativity conditions. Good computational methods are known for solving this problem. By the help of the dual problem sufficient conditions for a solution of the original primal problem are derived and illustrated by an example of practical interest.     

Structural and Thermodynamic Properties of Septin 3 Investigated by Small-Angle X-Ray Scattering

Septins comprise a family of proteins involved in a variety of cellular processes and related to several human pathologies. They are constituted by three structural domains: the N- and C-terminal domains, highly variable in length and composition, and the central domain, involved in the guanine nucleotide (GTP) binding. Thirteen different human septins are known to form heterogeneous complexes or homofilaments, which are stabilized by specific interactions between the different interfaces present in the domains. In this work, we have investigated by in-solution small-angle x-ray scattering the structural and thermodynamic properties of a human septin 3 construct, SEPT3-GC, which contains both of both interfaces (G and NC) responsible for septin-septin interactions. In order to shed light on the role of these interactions, small-angle x-ray scattering measurements were performed in a wide range of temperatures, from 2 up to 56°C, both with and without a nonhydrolysable form of GTP (GTP_γS). The acquired data show a temperature-dependent coexistence of monomers, dimers, and higher-order aggregates that were analyzed using a global fitting approach, taking into account the crystallographic structure of the recently reported SEPT3 dimer, PDB:3SOP. As a result, the enthalpy, entropy, and heat capacity variations that control the dimer-monomer dissociation equilibrium in solution were derived and GTPγS was detected to increase the enthalpic stability of the dimeric species. Moreover, a temperature increase was observed to induce dissociation of SEPT3-GC dimers into monomers just preceding their reassembling into amyloid aggregates, as revealed by the Thioflavin-T fluorescence assays.     

Thermodynamic and Transport Properties of Beryllium Vapor in the Supercritical Fluid State

The thermal and caloric equations of state, composition, and conductivity of a supercritical beryllium vapor are calculated using the earlier proposed “3+” chemical model, which incorporates atoms, electrons, ions, and electron jellium with allowance for interatomic and intercharge interactions. The introduction of an electron jellium makes it possible to describe the pressure-induced ionization and explain the increase in the conductivity of beryllium vapor under compression. The cohesive bond of atoms caused by the electron jellium compensates for interactions when calculating the composition and reduces the effect of intercharge interactions on the equation of state. The parameters of the beryllium critical point and the applicability domain of the model are discussed.     

Topological Estimation Biases with Covarion Evolution

Covarion processes allow changes in evolutionary rates at sites along the branches of a phylogenetic tree. Covarion-like evolution is increasingly recognized as an important mode of protein evolution. Several recent reports suggest that maximum likelihood estimation employing covarion models may support different optimal topologies than estimation using standard rates-across-sites (RAS) models. However, it remains to be demonstrated that ignoring covarion evolution will generally result in topological misestimation. In this study we performed analytical and theoretical studies of limiting distances under the covarion model and four-taxon tree simulations to investigate the extent to which the covarion process impacts on phylogenetic estimation. In particular, we assessed the limits of an RAS model-based maximum likelihood method to recover the phylogenies when the sequence data were simulated under the covarion processes. We find that, when ignored, covarion processes can induce systematic errors in phylogeny reconstruction. Surprisingly, when sequences are evolved under a covarion process but an RAS model is used for estimation, we find that a long branch repel bias occurs.     

Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks

The diverse, specialized genes present in today’s lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and alterations in one gene may drive reciprocal changes in its proteins’ binding partners. Like many complex networks, these gene regulatory networks (GRNs) are composed of communities, or clusters of genes with relatively high connectivity. A deep understanding of the relationship between the evolutionary history of single genes and the topological properties of the underlying GRN is integral to evolutionary genetics. Here, we show that the topological properties of an acute myeloid leukemia GRN and a general human GRN are strongly coupled with its genes’ evolutionary properties. Slowly evolving (“cold”), old genes tend to interact with each other, as do rapidly evolving (“hot”), young genes. This naturally causes genes to segregate into community structures with relatively homogeneous evolutionary histories. We argue that gene duplication placed old, cold genes and communities at the center of the networks, and young, hot genes and communities at the periphery. We demonstrate this with single-node centrality measures and two new measures of efficiency, the set efficiency and the interset efficiency. We conclude that these methods for studying the relationships between a GRN’s community structures and its genes’ evolutionary properties provide new perspectives for understanding evolutionary genetics.     

Archaeal Flagella as Biotemplates for Nanomaterials with New Properties

At the end of 1980s, regions of the polypeptide chain of bacterial flagella subunits (flagellins) responsible for different properties of these protein polymers were identified by structural studies. It was found that the N-and C-terminal regions are responsible for the polymerization properties of subunits, and the central region is responsible for antigenic properties of the flagellum. Soon after that, it was proposed to use variability of the central flagellin domain for directed modification to impart new properties to the flagellum surface. Such studies of flagella and other polymeric structures of bacterial origin thrived. However bacterial polymers have some shortcomings, mainly their instability to dissociating effects. This shortcoming is absent in archaeal flagella. A limiting factor was the lack of the three-dimensional structure of archaeal flagellins. A method was developed that allowed modifying flagella of the halophilic archaeon Halobacterium salinarum in a peptide that connects positively charged ions. Later, corresponding procedures were used that allowed preparing the anode material for a lithiumion battery whose characteristics 4-5-fold exceeded those of batteries commonly used in industrial production. We describe other advantages of archaeal flagella over bacterial analogs when used in nanotechnology.