The number of segmental duplications and flanking conserved protein-coding genes within each block.

a<p>The number of observed duplicated blocks, containing miRNAs within the same family or within the different family, that have at least two flanking protein-coding gene surrounding miRNAs.</p>b<p>The percentage of observed duplicated blocks in each test species with respect to the total number of duplicated blocks.</p><p>ath: <i>A. thaliana</i>; ptc: <i>P. trichocarpa</i>; osa: <i>O. sativa</i>; sbi: <i>S. Bicolor.</i></p

The distribution and conservation of repeat-related miRNAs in the four test plant species.

<p>(A) The percentage of RrmiRNAs and NRrmiRNAs in the <i>A. thaliana</i>, <i>P. trichocarpa</i>, <i>O. sativa</i> and <i>S. bicolor</i> genomes. (B) The percentage of repetitive element-related miRNAs located in intragenic regions compared to all known miRNAs in the corresponding genome. (C) The percentage of repeat-related miRNAs with differing degrees of conservation.</p

The overall percentage and copy number data for tandemly duplicated miRNAs in the four test plant species.

<p>(A) The percentage of miRNA families and miRNAs arising by tandem duplication with respect to the total number of miRNA families containing at least one miRNA, and the number of members of the corresponding miRNA family, respectively, for each species tested. (B) The average miRNA copy number in tandemly duplicated regions. (C) The percentage distribution of tandemly duplicated miRNAs on the same or opposite strands. (D) The percentage of conserved or species-specific tandemly duplicated miRNAs with respect to the total number of observed tandemly duplicated miRNAs for each species tested.</p

Characterization and variation between RrmiRNAs and NRrmiRNAs.

<p>(A) The distribution of miRNA hairpin precursor sequence lengths in RrmiRNAs and NRrmiRNAs. (B) The G-C content in miRNA hairpin precursor sequences in RrmiRNAs and NRrmiRNAs (C) The MFEs for miRNA hairpin precursors in RrmiRNAs and NRrmiRNAs.</p

The overview for origins and expansion of miRNAs derived from duplicated events in the four test plant species.

<p>ath: <i>A. thaliana</i>; ptc: <i>P. trichocarpa</i>; osa: <i>O. sativa</i>; sbi: <i>S. bicolor</i>.</p

The results of conservation analysis for miRNA duplicated blocks in the four test plant species.

<p>ath: <i>A. thaliana</i>; ptc: <i>P. trichocarpa</i>; osa: <i>O. sativa</i>; sbi: <i>S. bicolor</i>.</p

Alcohol Solvent Effects in the Synthesis of Co₃O₄ Metal-Oxide Nanoparticles: Disproof of a Surface-Ligand Thermodynamic Effect en Route to Alternative Kinetic and Thermodynamic Explanations

The synthesis of Co₃O₄ core nanoparticles from cobalt acetate is explored in alcohol solvents plus limited water using O₂ as oxidant and NH₄OH as the base, all in comparison to controls in water alone employing the otherwise identical synthetic procedure. Syntheses in EtOH or <i>t</i>-BuOH cosolvents with limited water yield phase-pure and size-controlled (3 ± 1 nm) Co₃O₄-core nanoparticles. In marked contrast, the synthesis in water alone yields mixed phases of Co₃O₄ and β-Co­(OH)₂ with a very large particle-size range (14–400 nm). Importantly, acidic reductive digestion of the Co₃O₄ particles followed by ¹H NMR on the resultant solution yields <i>no detectable EtOH</i> in nanoparticles prepared in EtOH, nor any detectable <i>t</i>-BuOH in nanoparticles prepared in <i>t</i>-BuOH (∼5% detection limits for each alcohol), despite the dramatic effect of each alcohol cosolvent on the resultant cobalt-oxide product. Instead, in both cases <i>HOAc</i> is detected and quantified, indicative of OAc^– as a surface ligandand not EtO^– or <i>t</i>-BuO^– as the surface ligand. The resultant ROH cosolvent-derived particles were characterized by powder X-ray diffraction, Fourier transform infrared spectroscopy, high-resolution transmission electron microscopy, plus elemental analysis to arrive at an approximate, average molecular formula in the case of the particles prepared in EtOH, {[Co₃O₄­(C₂H₃O₂)]⁻­[(NH₄⁺)_0.3­(H⁺_0.7)]⁺­·(H₂O)}_∼216. The key finding is that, because EtOH and <i>t</i>-BuOH have a substantial effect on the phase- and size-dispersion of the cobalt-oxide nanoparticle product, yet the intact alcohol does not show up in the final Co₃O₄ nanoparticle product, the effect of these alcohols cannot be a surface-ligand thermodynamic effect on the net nanoparticle formation reaction. A careful search of the literature provided scattered, but consistent, literature in which anions or other additives have large effects on metal-oxide nanoparticle formation reactions, yet also do not show up in the nanoparticle productsthat is, where the observed effects are again not due to binding by that anion or other additive in a surface-ligand thermodynamic effect on the overall reaction. Alternative hypotheses are provided as to the origin of ROH solvent effects on metal-oxide nanoparticles

Zwitterion-Modified Nanogel Responding to Temperature and Ionic Strength: A Dissipative Particle Dynamics Simulation

The self-assembly and stimuli-responsive properties of nanogel poly(n-isopropylacrylamide) (p(NIPAm)) and zwitterion-modified nanogel poly(n-isopropylacrylamide-co-sulfobetainemethacrylate) (p(NIPAm-co-SBMA)) were explored by dissipative particle dynamics simulations. Simulation results reveal that for both types of nanogel, it is beneficial to form spherical nanogels at polymer concentrations of 5–10%. When the chain length (L) elongates from 10 to 40, the sizes of the nanogels enlarge. As for the p(NIPAm) nanogel, it shows thermoresponsiveness; when it switches to the hydrophilic state, the nanogel swells, and vice versa. The zwitterion-modified nanogel p(NIPAm-co-SBMA) possesses thermoresponsiveness and ionic strength responsiveness concurrently. At 293 K, both hydrophilic p(NIPAm) and superhydrophilic polysulfobetaine methacrylate (pSBMA) could appear on the outer surface of the nanogel; however, at 318 K, superhydrophilic pSBMA is on the outer surface to cover the hydrophobic p(NIPAm) core. As the temperature rises, the nanogel shrinks and remains antifouling all through. The salt-responsive property can be reflected by the nanogel size; the volumes of the nanogels in saline systems are larger than those in salt-free systems as the ionic condition inhibits the shrinkage of the zwitterionic pSBMA. This work exhibits the temperature-responsive and salt-responsive behavior of zwitterion-modified-pNIPAm nanogels at the molecular level and provides guidance in antifouling nanogel design

Zwitterion-Modified Nanogel Responding to Temperature and Ionic Strength: A Dissipative Particle Dynamics Simulation

The self-assembly and stimuli-responsive properties of nanogel poly(n-isopropylacrylamide) (p(NIPAm)) and zwitterion-modified nanogel poly(n-isopropylacrylamide-co-sulfobetainemethacrylate) (p(NIPAm-co-SBMA)) were explored by dissipative particle dynamics simulations. Simulation results reveal that for both types of nanogel, it is beneficial to form spherical nanogels at polymer concentrations of 5–10%. When the chain length (L) elongates from 10 to 40, the sizes of the nanogels enlarge. As for the p(NIPAm) nanogel, it shows thermoresponsiveness; when it switches to the hydrophilic state, the nanogel swells, and vice versa. The zwitterion-modified nanogel p(NIPAm-co-SBMA) possesses thermoresponsiveness and ionic strength responsiveness concurrently. At 293 K, both hydrophilic p(NIPAm) and superhydrophilic polysulfobetaine methacrylate (pSBMA) could appear on the outer surface of the nanogel; however, at 318 K, superhydrophilic pSBMA is on the outer surface to cover the hydrophobic p(NIPAm) core. As the temperature rises, the nanogel shrinks and remains antifouling all through. The salt-responsive property can be reflected by the nanogel size; the volumes of the nanogels in saline systems are larger than those in salt-free systems as the ionic condition inhibits the shrinkage of the zwitterionic pSBMA. This work exhibits the temperature-responsive and salt-responsive behavior of zwitterion-modified-pNIPAm nanogels at the molecular level and provides guidance in antifouling nanogel design

Additional file 1: of A novel lncRNA-focus expression signature for survival prediction in endometrial carcinoma

lncRNAs significantly associated with overall survival in univariate Cox regression analyses. (DOC 38 kb