Transcriptome Analysis of Systems Biology for Schizophrenia

Transcriptome analysis of postmortem brain samples provides more insights to evaluate biological dysfunctions by analysis of differential expression and genetic interactions in schizophrenia. The growing development of new technologies such as next-generation sequencing (NGS) helps to explore detailed and underlying molecular changes from global perspective of view, not only focus in single SNP variants. It is implicated that schizophrenia genetic and protein interactions may give rise to biological dysfunction not only in dopamine dysfunction but also in immune, energy metabolism, mitochondrial dysfunction and hemostasis. Epigenetic investigation of schizophrenia provides important information on how the environmental factors affect the genetic architecture of the disease. DNA methylation plays a pivotal role in etiology for schizophrenia. The schizophrenia differential methylation genes and differential expression genes were analyzed to find the potential protein complexes related to the etiology of schizophrenia from alteration of DNA methylation. The protein complexes and pathways involved in schizophrenia differential methylation network may be responsible for the etiology and potential treatment targets. It is implicated that the interaction between differential expression candidate genes and differential methylation genes may describe the global view of disease mechanisms and it has important roles in the pathogenesis for schizophrenia

Titanium-capped carbon chains as promising new hydrogen storage media

The capacity of Ti-capped sp carbon atomic chains for use as hydrogen storage media is studied using first-principles density functional theory. The Ti atom is strongly attached at one end of the carbon chains via d-p hybridization, forming stable TiCn complexes. We demonstrate that the number of adsorbed H2 on Ti through Kubas interaction depends upon the chain types. For polyyne (n even) or cumulene (n odd) structures, each Ti atom can hold up to five or six H2 molecules, respectively. Furthermore, the TiC5 chain effectively terminated on a C20 fullerene can store hydrogen with optimal binding of 0.52 eV/H2. Our results reveal a possible way to explore high-capacity hydrogen storage materials in truly one-dimensional carbon structures.Comment: accepted for publication in Physical Chemistry Chemical Physic

Analysis note: two-particle correlation in e+e−e^+e^- collisions at 91-209 GeV with archived ALEPH data

The first measurement of two-particle angular correlations for charged particles produced in $e^+e^-$ annihilation up to $\sqrt{s}$ = 209 GeV is presented. Hadronic $e^+e^-$ data, archived at center-of-mass energies ranging from 91 to 209 GeV, were collected using the ALEPH detector at LEP between 1992 and 2000. The angular correlation functions have been measured across a wide range of pseudorapidities and the full azimuth in bins of charged particle multiplicity. This is the first such measurement using LEP-II data. With LEP-II data at 91 GeV, neither the beam coordinate analysis nor the thrust coordinate analysis reveals significant long-range correlations, consistent with the finding in the previous measurement with the LEP-I sample. Results for $e^+e^-$ data at energies above 91 GeV, which allow for higher event multiplicities reaching approximately 50, are presented for the first time. A long-range near-side excess in the correlation function has been identified in the thrust axis analysis. Moreover, the two-particle correlation functions were decomposed using a Fourier series, and the resulting Fourier coefficients $v_n$ were compared with event generator outputs. In events with high multiplicity, featuring more than 50 particles, the extracted $v_2$ and $v_3$ magnitudes from the data are higher than those from the Monte Carlo reference.Comment: 37 pages, 17 figure

POINeT: protein interactome with sub-network analysis and hub prioritization

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions (PPIs) are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal consideration. Moreover, the reliability of available PPI resources, which consist of low- and high-throughput data, for network construction remains a significant challenge. Even though a number of software tools are available to facilitate PPI network analysis, an integrated tool is crucial to alleviate the burden on querying across multiple web servers and software tools.</p> <p>Results</p> <p>We have constructed an integrated web service, POINeT, to simplify the process of PPI searching, analysis, and visualization. POINeT merges PPI and tissue-specific expression data from multiple resources. The tissue-specific PPIs and the numbers of research papers supporting the PPIs can be filtered with user-adjustable threshold values and are dynamically updated in the viewer. The network constructed in POINeT can be readily analyzed with, for example, the built-in centrality calculation module and an integrated network viewer. Nodes in global networks can also be ranked and filtered using various network analysis formulas, i.e., centralities. To prioritize the sub-network, we developed a ranking filtered method (S3) to uncover potential novel mediators in the midbody network. Several examples are provided to illustrate the functionality of POINeT. The network constructed from four schizophrenia risk markers suggests that EXOC4 might be a novel marker for this disease. Finally, a liver-specific PPI network has been filtered with adult and fetal liver expression profiles.</p> <p>Conclusion</p> <p>The functionalities provided by POINeT are highly improved compared to previous version of POINT. POINeT enables the identification and ranking of potential novel genes involved in a sub-network. Combining with tissue-specific gene expression profiles, PPIs specific to selected tissues can be revealed. The straightforward interface of POINeT makes PPI search and analysis just a few clicks away. The modular design permits further functional enhancement without hampering the simplicity. POINeT is available at <url>http://poinet.bioinformatics.tw/</url>.</p

Measurements of two-particle correlations in e+e−e^+e^- collisions at 91 GeV with ALEPH archived data

Measurements of two-particle angular correlations of charged particles emitted in hadronic $Z$ decays are presented. The archived $e^+e^-$ annihilation data at a center-of-mass energy of 91 GeV were collected with the ALEPH detector at LEP between 1992 and 1995. The correlation functions are measured over a broad range of pseudorapidity and full azimuth as a function of charged particle multiplicity. No significant long-range correlation is observed in either the lab coordinate analysis or the thrust coordinate analysis, where the latter is sensitive to a medium expanding transverse to the color string between the outgoing $q\bar{q}$ pair from $Z$ boson decays. The associated yield distributions in both analyses are in better agreement with the prediction from the PYTHIA v6.1 event generator than from HERWIG v7.1.5. They provide new insights to showering and hadronization modeling. These results serve as an important reference to the observed long-range correlation in proton-proton, proton-nucleus, and nucleus-nucleus collisions.Comment: Replaced with the published version. Added the journal reference and the DO

First measurement of anti-kT_\mathrm{T} jet spectra and jet substructure using the archived ALEPH e+e−e^+e^- data at 91.2 GeV

We present the first anti-k$_{T}$ jet spectrum and substructure measurements using the archived ALEPH $e^+e^-$ data taken in 1994 at a center of mass energy of $\sqrt{s} = 91.2$ GeV. Jets are reconstructed with the anti-k$_{T}$ algorithm with a resolution parameter of 0.4. It is the cleanest test of jets and QCD without the complication of hadronic initial states. The fixed center-of-mass energy also allows the first direct test of pQCD calculation. We present both the inclusive jet energy spectrum and the leading dijet energy spectra, together with a number of substructure observables. They are compared to predictions from PYTHIA6, PYTHIA8, Sherpa, HERWIG, VINCIA, and PYQUEN. None of the models fully reproduce the data. The data are also compared to two perturbative QCD calculations at NLO and with NLL'+R resummation. The results can also serve as reference measurements to compare to results from hadronic colliders. Future directions, including testing jet clustering algorithms designed for future electron-ion collider experiments, will also be discussed