Categorical colormap optimization with visualization case studies

Mapping a set of categorical values to different colors is an elementary technique in data visualization. Users of visualization software routinely rely on the default colormaps provided by a system, or colormaps suggested by software such as ColorBrewer. In practice, users often have to select a set of colors in a semantically meaningful way (e.g., based on conventions, color metaphors, and logological associations), and consequently would like to ensure their perceptual differentiation is optimized. In this paper, we present an algorithmic approach for maximizing the perceptual distances among a set of given colors. We address two technical problems in optimization, i.e., (i) the phenomena of local maxima that halt the optimization too soon, and (ii) the arbitrary reassignment of colors that leads to the loss of the original semantic association. We paid particular attention to different types of constraints that users may wish to impose during the optimization process. To demonstrate the effectiveness of this work, we tested this technique in two case studies. To reach out to a wider range of users, we also developed a web application called Colourmap Hospital

Rational Design of High-Performance Phosphine Sulfonate Nickel Catalysts for Ethylene Polymerization and Copolymerization with Polar Monomers

Use of palladium catalysts in olefin polymerization and copolymerization has evolved rapidly. In contrast, earth-abundant and low-cost nickel catalysts generally suffer from drawbacks that include low thermal stability and generation of low-molecular-weight polymers in the presence of polar monomers. By taking advantage of several design strategies, high-performance phosphine-sulfonate-based nickel catalysts were developed. These nickel catalysts demonstrated high activities and thermal stabilities to afford high-molecular-weight polyethylene. Most importantly, high-molecular-weight copolymers could be generated through the copolymerization of ethylene with a variety of polar monomers

Additional file 5: Table S4. of Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina

miRNAs and primer sequences for qRT-PCR. (XLSX 10 kb

Additional file 2: Table S2. of Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina

Novel miRNAs identified in the three P. szechuanica libraries. (XLSX 110 kb

Additional file 3: Figure S1. of Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina

Precursor sequences and the predicted secondary structures of the 20 novel miRNAs from P. szechuanica (“(”represent base matches, “.” represent base mismatches). (PDF 387 kb

ROS-dependent G2/M cell cycle arrest by DHA and IR respectively.

<p>(A) Dynamical fluorescence images of ROS generation in living cells after DHA treatment. Cells were incubated with 20 µM DCFH-DA, an oxidation-sensitive fluorescent probe, for 30 min in the dark and then treated with DHA. The levels of intracellular ROS were monitored by a confocal microscope. Scale bar: 20 µm. (B) Dynamics of DHA-induced ROS generation corresponding to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059827#pone-0059827-g002" target="_blank">Figure 2</a> (A). (C and D) FCM assay of ROS generation at 30 min (C) and 120 min (D) after IR, DHA and combination treatment, respectively. (E and F) ROS-dependent G₂/M arrest induced by IR (E) and DHA (F) respectively analyzed by FCM. Cells were irradiated with IR or DHA in the presence or absence of NAC, and then stained with 5 µg/ml of PI before being analyzed by FCM. *<i>*P</i><0.01, compared with control; ^##<i>P</i><0.01, compared with DHA treatment alone (E) and ^##<i>P<0.01</i> and ^&&<i>P<0.01</i>, compared with IR treatment alone (F).</p

IR potentiates DHA-induced extrinsic apoptosis pathway.

<p>(A–B): IR did not accelerate the DHA-induced loss of Δψ_m at 24 h (A) and 36 h (B) after treatment assessed by FCM. <i>**P</i><0.01, compared with control. (C) IR did not accelerate DHA-induced caspase-9 activation. <i>**P</i><0.01, compared with control. (D and E) IR accelerated DHA-induced activation of caspase-8 (D) and -3 (E). Cells treated with IR were then cultured with DHA for 36 h. Caspase-8, -9 and -3 activities were measured by the fluorescence substrate Ac-IETD-AFC, Ac-LEHD-AFC and Ac-DEVD-AFC, respectively. <i>**P</i><0.01, compared with control, <i>^##P</i><0.01, compared with treatment with DHA alone.</p

Electrostatic Interactions between OmpG Nanopore and Analyte Protein Surface Can Distinguish between Glycosylated Isoforms

The flexible loops decorating the entrance of OmpG nanopore move dynamically during ionic current recording. The gating caused by these flexible loops changes when a target protein is bound. The gating is characterized by parameters including frequency, duration, and open-pore current, and these features combine to reveal the identity of a specific analyte protein. Here, we show that OmpG nanopore equipped with a biotin ligand can distinguish glycosylated and deglycosylated isoforms of avidin by their differences in surface charge. Our studies demonstrate that the direct interaction between the nanopore and analyte surface, induced by the electrostatic attraction between the two molecules, is essential for protein isoform detection. Our technique is remarkably sensitive to the analyte surface, which may provide a useful tool for glycoprotein profiling

Ethylene Polymerization and Copolymerization by Palladium and Nickel Catalysts Containing Naphthalene-Bridged Phosphine–Sulfonate Ligands

A series of naphthalene-bridged phosphine–sulfonate ligands and the corresponding Pd­(II) complexes [κ²(<i>P</i>,<i>O</i>)-2-(R₂P)-1-naphthalenesulfonato]­Pd­(Me)­(dmso) (<b>1</b>, R = Ph; <b>2</b>, R = <i>o</i>-MeO-C₆H₄; <b>3</b>, R = Cy) and Ni­(II) complexes [κ²(<i>P</i>,<i>O</i>)-2-(R₂P)-1-naphthalenesulfonato]­Ni­(η³-C₃H₅) (<b>Ni-1</b>, R = <i>o</i>-MeO-C₆H₄; <b>Ni-2</b>, R = Cy) have been prepared and characterized. The analogous benzo-bridged phosphine–sulfonate Pd­(II) complex [κ²(<i>P</i>,<i>O</i>)-(R₂P)-benzenesulfonato]­Pd­(Me)­(dmso) (<b>2</b>′, R = <i>o</i>-MeO-C₆H₄) and Ni­(II) complex [κ²(<i>P</i>,<i>O</i>)-(R₂P)-benzenesulfonato]­Ni­(η³-C₃H₅) (<b>Ni-1</b>′, R = <i>o</i>-MeO-C₆H₄) were prepared for comparison. In ethylene polymerization, complex <b>2</b> showed activity of up to 7.5 × 10⁶ g mol^–1 h^–1, which is among the most active palladium catalysts for ethylene homopolymerization. Under the same conditions, complex <b>2</b> showed up to 1 order of magnitude higher catalytic activity than complex <b>2</b>′, generating polyethylene with slightly smaller molecular weight and similar branching density. The Ni­(II) complex <b>Ni-1</b> was also more active than complex <b>Ni-1</b>′, generating polyethylene with up to 1 order of magnitude higher molecular weight. In ethylene–methyl acrylate copolymerization, complex <b>2</b> showed lower activity, affording a copolymer with higher methyl acrylate incorporation and higher copolymer molecular weight in comparison to complex <b>2</b>′

Ethylene Polymerization and Copolymerization by Palladium and Nickel Catalysts Containing Naphthalene-Bridged Phosphine–Sulfonate Ligands

A series of naphthalene-bridged phosphine–sulfonate ligands and the corresponding Pd­(II) complexes [κ²(<i>P</i>,<i>O</i>)-2-(R₂P)-1-naphthalenesulfonato]­Pd­(Me)­(dmso) (<b>1</b>, R = Ph; <b>2</b>, R = <i>o</i>-MeO-C₆H₄; <b>3</b>, R = Cy) and Ni­(II) complexes [κ²(<i>P</i>,<i>O</i>)-2-(R₂P)-1-naphthalenesulfonato]­Ni­(η³-C₃H₅) (<b>Ni-1</b>, R = <i>o</i>-MeO-C₆H₄; <b>Ni-2</b>, R = Cy) have been prepared and characterized. The analogous benzo-bridged phosphine–sulfonate Pd­(II) complex [κ²(<i>P</i>,<i>O</i>)-(R₂P)-benzenesulfonato]­Pd­(Me)­(dmso) (<b>2</b>′, R = <i>o</i>-MeO-C₆H₄) and Ni­(II) complex [κ²(<i>P</i>,<i>O</i>)-(R₂P)-benzenesulfonato]­Ni­(η³-C₃H₅) (<b>Ni-1</b>′, R = <i>o</i>-MeO-C₆H₄) were prepared for comparison. In ethylene polymerization, complex <b>2</b> showed activity of up to 7.5 × 10⁶ g mol^–1 h^–1, which is among the most active palladium catalysts for ethylene homopolymerization. Under the same conditions, complex <b>2</b> showed up to 1 order of magnitude higher catalytic activity than complex <b>2</b>′, generating polyethylene with slightly smaller molecular weight and similar branching density. The Ni­(II) complex <b>Ni-1</b> was also more active than complex <b>Ni-1</b>′, generating polyethylene with up to 1 order of magnitude higher molecular weight. In ethylene–methyl acrylate copolymerization, complex <b>2</b> showed lower activity, affording a copolymer with higher methyl acrylate incorporation and higher copolymer molecular weight in comparison to complex <b>2</b>′