Integrative multi-omics module network inference with Lemon-Tree

Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different individuals, experimental conditions or time points of a dynamic process. We have developed Lemon-Tree, an open-source, platform-independent, modular, extensible software package implementing state-of-the-art ensemble methods for module network inference. We benchmarked Lemon-Tree using large-scale tumor datasets and showed that Lemon-Tree algorithms compare favorably with state-of-the-art module network inference software. We also analyzed a large dataset of somatic copy-number alterations and gene expression levels measured in glioblastoma samples from The Cancer Genome Atlas and found that Lemon-Tree correctly identifies known glioblastoma oncogenes and tumor suppressors as master regulators in the inferred module network. Novel candidate driver genes predicted by Lemon-Tree were validated using tumor pathway and survival analyses. Lemon-Tree is available from http://lemon-tree.googlecode.com under the GNU General Public License version 2.0.Comment: minor revision; 13 pages text + 4 figures + 4 tables + 4 pages supplementary methods; supplementary tables available from the author

Contacts et acculturations en Méditerranée occidentale

La question des contacts entre les différents peuples qui bordent les rives de la Méditerranée nord occidentale est l’un des sujets phares de la recherche archéologique de ces trente dernières années. Que l’on parle d’époque archaïque et classique ou de Protohistoire et d’âge du Fer, les échanges et les processus d’acculturation de ces peuples qui entrèrent alors en contact les uns avec les autres : Grecs, Celtes, Phéniciens, Ibères, Ligures, Étrusques, ont retenu l’attention des chercheurs travaillant sur l’expansion grecque dans ces régions, sur les trafics commerciaux, sur les échanges culturels. L’œuvre de Michel Bats (Directeur de recherche honoraire du CNRS) traverse toutes ces thématiques : la présence des Phocéens et des Étrusques dans le bassin occidental de la Méditerranée, l’acculturation et les identités ethno-culturelles, les recherches sur la céramique et ses usages dans une perspective anthropologique, l’appropriation de l’écriture par les sociétés protohistoriques. Ses collègues et amis, en organisant ce colloque et en participant à ces actes, entendent lui témoigner leur amitié et leur dette intellectuelle. Ce volume réunit des articles des meilleurs spécialistes, actuels de la question - des chercheurs de toute la Méditerranée - autour des quatre grands thèmes que nous venons d’évoquer afin tout à la fois de dresser un bilan et de définir de nouvelles perspectives. Cet ouvrage présente donc aussi bien des synthèses - sur la présence grecque en Espagne, sur l’origine de l’écriture, sur les pratiques funéraires, sur les identités culturelles et ethniques - que des découvertes récentes concernant la thématique des contacts et de l’acculturation en Méditerranée nord occidentale : l’agglomération du Premier âge du Fer de La Cougourlude (Lattes, Hérault) fouillée durant l’été 2010 ; le sanctuaire hellénistique de Cumes et les fouilles récentes de Fratte en Italie ; les ateliers de potiers de Rosas en Espagne ; les dernières découvertes d’Olbia de Provence

Hybrid ZnO Electron Transport Layer by Down Conversion Complexes for Dual Improvements of Photovoltaic and Stable Performances in Polymer Solar Cells

Polymer solar cells (PSCs) have shown excellent photovoltaic performance, however, extending the spectral response range to the ultraviolet (UV) region and enhancing the UV light stability remain two challenges to overcome in the development of PSCs. Lanthanide down-conversion materials can absorb the UV light and re-emit it at the visible region that matches well with the absorption of the active layer material PTB7-Th (poly[[2,6′-4,8-di(5-ethylhexylthienyl)benzo[1,2-b;3,3-b]dithiophene][3-fluoro-2[(2-ethylhexyl)carbony]thieno[3,4-b]thiophenediyl]]) and PBDB-T-2F, thus helping to enhance the photovoltaic performance and UV light stability of PSCs. In this research, a down-conversion material Eu(TTA)3phen (ETP) is introduced into the cathode transport layer (ZnO) in PSCs to manipulate its nanostructure morphology for its application in hyperfine structure of PSCs. The device based on the ZnO/ETP electron transport layer can obtain power conversion efficiencies (PCEs) of 9.22% (PTB7-Th–PC71BM ([6,6]-phenylC71-butyric acid methyl ester) device) and 13.12% (PBDB-T-2F–IT-4F device), respectively. Besides, in the research on PTB7-Th-PC71BM device, the stability of the device based on ZnO/ETP layer is prolonged by 70% compared with the ZnO device. The results suggest that the ZnO/ETP layer plays the role of enhanced photovoltaic performance and prolonged device stability, as well as reducing photo-loss and UV degradation for PSCs

Precise Control of Copper-Localized Surface Plasmon Resonance in the Near Infrared Region for Enhancement of Up-Conversion Luminescence

The surface plasmon resonance of copper in the near infrared region provides a novel method for enhancement of up-conversion luminescence compared to using gold and silver, as the former grants significant cost savings. In this study, we made a flat Cu film covered TiO2 to enhance the up-conversion fluorescence intensity. The results show that the deposition of copper/TiO2 dioxide nanocomposite film prepared via spin-coating has no effect on the structure of NaGdF4:Er3+, Yb3+. The absorption wavelength of the copper film moved from the original visible wavelength (~600 nm) range to the infrared wavelength after covering TiO2, and most obviously, the copper film covered two layers of TiO2 by about 16 nm; the peak of the absorption appeared at 835 nm due to the enhanced excitation field. The behavior of the nanocomposite film with NaGdF4:Er3+ and Yb3+ under 980 nm excitation was investigated; it provides a novel way for studying mental-enhanced fluorescence. Besides, the peaks of the fluorescence spectrum show different emissions at 542 nm and 660 nm, respectively. The copper nanoparticles-covered TiO2 layer can obviously enhance the fluorescence intensity, and the maximum enhancement factors of emission of NaGdF4:Er3+ and Yb3+ nanoparticles are 3.1 and 1.9 on the nanocomposite film, respectively

Polysaccharide-based hydrogels for the immobilization and controlled release of bovine serum albumin

Arabic gum-based and chitosan-based hydrogels were synthesized through chemical crosslinking for the immobilization and controlled release of bovine serum albumin (BSA) and characterized by Fourier-transform infrared spectrometry, scanning electron microscopy and swelling assays. The degrees of swelling of the Arabic gum-based hydrogel were 13.22 and 22.95 g water per g dried hydrogel at pH 4.5 and 7.0, respectively, whereas the degrees of swelling of the chitosan-based hydrogel were 15.32 and 36.10 g water per g dried hydrogel, respectively. The water absorption mechanism in both hydrogels was non-Fickian, which involves diffusion through pores and macromolecular relaxation of the hydrophilic three-dimensional polymer network. BSA immobilization capacities of the Arabic gum-based and chitosan-based hydrogels after 240 min at pH 4.5 were 71.0 and 175.6 mg protein per g dried hydrogel, respectively. BSA immobilization capacities after 240 min at pH 7.0 were 62.5 and 154.2 mg protein per g dried hydrogel, respectively. The controlled release of BSA from the Arabic gum-based hydrogel was slightly more efficient than that of the chitosan-based hydrogel due to its more porous structure and weaker physiochemical interactions between the polymer network and protein molecule. Both hydrogels could be employed as carriers of proteins and as capsules for food supplements120A522528CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA E INOVAÇÃO DO ESTADO DE SANTA CATARINA - FAPESC312356/2015-3sem informaçãosem informaçã

Tb3+/Eu3+ Complex-Doped Rigid Nanoparticles in Transparent Nanofibrous Membranes Exhibit High Quantum Yield Fluorescence

In this study, transparent membranes containing luminescent Tb3+ and Eu3+ complex-doped silica nanoparticles were prepared via electrospinning. We prepared the electrospun fibrous membranes containing Tb(acac)3phen- (acac = acetylacetone, phen = 1,10-phenanthroline) and/or Eu(tta)3phen- (tta = 2-thenoyltrifluoroacetone) doped silica (M-Si-Tb3+ and M-Si-Eu3+) and studied their photoluminescence properties. The fibrous membranes containing the rare earth complexes were prepared by electrospinning. The surface morphology and thermal properties of the fibrous membrane were studied by atomic force microscopy (AFM), thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC), respectively. Fluorescence spectroscopy was used to characterize the fluorescence properties of the membranes. During the electrospinning process, the PVDF transitions from the α phase to the β phase, which exhibits a more rigid structure. The introduction of rigid materials, like PVDF and silica, can improve the fluorescence properties of the hybrid materials by reducing the rate of nonradiative decay. So the emission spectra at 548 nm (Tb) and 612 nm (Eu) were enhanced, as compared to the emission from the pure complex. Furthermore, the fluorescence lifetimes ranged from 0.6 to 1.5 ms and the quantum yields ranged from 32% to 61%. The luminescent fibrous membranes have potential applications in the fields of display panels, innovative electronic and optoelectronic devices

Histidine polypeptide-hybridized nanoscale metal–organic framework to sense drug loading/release

Histidine Polypeptide-Hybridized Nanoscale Metal–Organic Framework (fH12/ZIF-8) can be produced effectively in water at room temperature without using any additives. The fluorescein label also provides a useful method to quantify the extent to which the anti-cancer drug doxorubicin (DOX) is loaded into or released from the resulting MOFs. In vitro studies have shown that fH12/ZIF-8 has the useful property of dissolving and controlled rates at low pH. It ruptured fastest in PBS buffer solution with pH 6.3, and the release rate reached 50% at 4 h. Furthermore, it showed that the addition of histidine polypeptides increases uptake by HepG-2 cells. This study integrates drug loading and detecting aspects into a single theranostic platform by a simple and efficient strategy, opening a new route for the construction of advanced drug delivery systems