Orca: A Visualization Toolkit for High-Dimensional Data

Abstract

This article describes constructing interactive and dynamic linked data views using the Java programming language. The data views are designed for data that have a multivariate component. The approach to displaying data comes from earlier research on building statistical graphics based on data pipelines, in which different aspects of data processing and graphical rendering are organized conceptually into segments of a pipeline. The software design takes advantage of the object-oriented nature of the Java language to open up the data pipeline, allowing developers to have greater control over their visualization applications. Importantly, new types of data views coded to adhere to a few simple design requirements can easily be integrated with existing pipe sections. This allows access to sophisticated linking and dynamic interaction across all (new and existing) view types. Pipe segments can be accessed from data analysis packages such as Omegahat or R, providing a tight coupling of visual and numerical methods.     

Structural and Electronic Control of the Bidentate 1-(2-pyridyl)benzotriazole Ligand in Copper Chemistry with Application to Catalysis in the A3 Coupling Reaction

The hybrid bidentate 1-(2-pyridyl)benzotriazole (pyb) ligand was introduced into 3d transition metal catalysis. Specifically, [Cu^II(OTf)₂(pyb)₂] ⋅ 2 CH₃CN ( 1 ) enables the synthesis of a wide range of propargylamines by the A³ coupling reaction at room temperature in the absence of additives. Experimental and high-level theoretical calculations suggest that the bridging N atom of the ligand imposes exclusive trans coordination at Cu and allows ligand rotation, while the N atom of the pyridine group modulates charge distribution and flux, and thus orchestrates structural and electronic precatalyst control permitting alkyne binding with simultaneous activation of the C−H bond via a transient Cu^I species.     

Understanding the Synthesis of Supported Vanadium Oxide Catalysts Using Chemical Grafting

The complexity of variables during incipient wetness impregnation synthesis of supported metal oxides precludes an in-depth understanding of the chemical reactions governing the formation of the dispersed oxide sites. This contribution describes the use of vapor phase deposition chemistry (also known as grafting) as a tool to systematically investigate the influence of isopropanol solvent on VO(OⁱPr)₃ anchoring during synthesis of vanadium oxide on silica. The availability of anchoring sites on silica was found to depend not only on the pretreatment of the silica but also on the solvent present. H-bond donors can reduce the reactivity of isolated silanols whereas disruption of silanol nests by H-bond acceptors can turn unreactive H-bonded silanols into reactive anchoring sites. The model suggested here can inform improved syntheses with increased dispersion of metal oxides on silica.     

Intraventricular thrombus formation in the LVAD-assisted heart studied in a mock circulatory loop

Left ventricular assist devices (LVADs) are mechanical pumps that are surgically attached to the left ventricle and aorta. Clinical studies show that LVADs improve patient health and quality of life, and dramatically reduce the mortality of cardiac failure. During periods of high LVAD support, blood flow occurs entirely through the LVAD, the aortic valve is continuously closed, and the heart operates in series with the pump. Thus the normal fluid dynamics of intraventricular flow are altered and linked to the development of thrombus in both the native heart and LVAD. Our goal in this study was to simulate a patient with a recurring thrombus and quantify the variations in the flow field in the LV as the thrombus developed. Particle image velocimetry measurements of transparent silicone models were performed for a range of LVAD support conditions. Results show that the presence of a small thrombus in the LVOT creates a favorable condition for further growth, especially in the presence of high LVAD support. As the thrombus enlarges, it begins to affect the normal vortex-flow pattern, further reducing flow rate and pulsatility in the LVOT. Evaluation of vortex dynamics and stasis regions in both patients and experimental models of LVAD support yield quantitative metrics that can be used to assess the risk of thrombus and the development of strategies to reduce this risk in LVAD patients.     

Antiproliferative Effect of Colonic Fermented Phenolic Compounds from Jaboticaba (Myrciaria trunciflora) Fruit Peel in a 3D Cell Model of Colorectal Cancer

Jaboticaba is a Brazilian native berry described as a rich source of phenolic compounds (PC) with health promoting effects. PC from jaboticaba peel powder (JPP) have low intestinal bio-accessibility and are catabolized by gut microbiota. However, the biological implication of PC-derived metabolites produced during JPP digestion remains unclear. This study aimed to evaluate the antiproliferative effects of colonic fermented JPP (FJPP) in a 3D model of colorectal cancer (CRC) composed by HT29 spheroids. JPP samples fermented with human feces during 0, 2, 8, 24 or 48 h were incubated (10,000 µg mL⁻¹) with spheroids, and cell viability was assessed after 72 h. Chemometric analyses (cluster and principal component analyses) were used to identify the main compounds responsible for the bioactive effect. The antiproliferative effect of FJPP in the CRC 3D model was increased between 8 h and 24 h of incubation, and this effect was associated with HHDP-digalloylglucose isomer and dihydroxyphenyl-γ-valerolactone. At 48 h of fermentation, the antiproliferative effect of FJPP was negligible, indicating that the presence of urolithins did not improve the bioactivity of JPP. These findings provide relevant knowledge on the role of colonic microbiota fermentation to generate active phenolic metabolites from JPP with positive impact on CRC.     

Cryopreservation of spermatozoa of black marlin, Makaira indica (Teleostei: Istiophoridae)

As a first step towards the development of a method for the cryopreservation of black marlin spermatozoa, this study investigated the effect of dimethylsulfoxide (DMSO) concentration and pellet size on post-thaw spermatozoal motility. Spermatozoa were recovered from the spermatic duct of testes retrieved post-mortem from four adult black marlin caught in the Coral Sea spawning grounds of Australia. Undiluted spermatozoa were stored on ice for 4 to 10 hours during transport to shore, then evaluated for motility after activation in seawater (1:10 v:v). Spermatozoa were prepared for cryopreservation in pellets by extension (1:3 v:v) in a defined fish Ringer's solution to give two final DMSO concentrations of 2.5% or 5.0%. Diluted spermatozoa were frozen directly on a dry ice block in pellet sizes of either 0.25 ml or 0.50 ml. Frozen pellets were thawed in a water bath at 40 degrees C for 60 seconds and assessed for post-thaw motility following activation in seawater. Spermatozoa recovered within 50 minutes of death and chilled on ice for 4 to 10 hours showed a mean (+/- SEM) motility immediately following activation of 91.6 +/- 7.9%. 50% of the spermatozoa remained motile for approximately 4 to 5 minutes. Following cryopreservation, mean motility declined significantly across all cryoprotectant and pellet size combinations (P < 0.001) but spermatozoa frozen in 2.5% DMSO showed higher motility than those frozen in 5.0% DMSO (P = 0.014). Pellet size had no effect on post-thaw motility (P = 0.179).     

On planar fermions with quartic interaction at finite temperature and density

We study the breaking of parity symmetry in the 2+1 Gross-Neveu model at finite temperature with chemical potential μ, in the presence of an external magnetic field. We find that the requirement of gauge invariance, which is considered mandatory in the presence of gauge fields, breaks parity at any finite temperature and provides for dynamical mass generation, preventing symmetry restoration for any non-vanishing μ. The dynamical mass becomes negligibly small as temperature is raised. Received 4 April 2002 / Received in final form 12 July 2002 Published online 15 October 2002 RID="a" ID="a"e-mail: cabra@venus.fisica.unlp.edu.ar     

Tunable supramolecular synthons and versatile, water-soluble building blocks for crystal engineering:

It is shown that the water-soluble dicarboxylic cationic acid [(eta5-C5H4COOH)2Co(III)]+ (1) is an extremely versatile building block for the construction of organometallic crystalline edifices. Removal of one proton from 1 leads to formation of the neutral zwitterion [(eta5-C5H4COOH)(eta5-C5H4COO)Co(III)] (2), while further deprotonation leads to formation of the dicarboxylate monoanion [(eta5-C5H4COO)2Co(III)]- (3). Compounds 1. 2 and 3 possess different hydrogen-bonding capacity and participate in a variety of hydrogen-bonding networks. The cationic form 1 has been characterised as its [PF6]- and Cl- salts 1-[PF6] and 1-Cl.H2O, as well as in its co-crystal with urea, 1-Cl.3(NH2)2CO, and with the zwitterionic form 2, [(eta5-CH4COOH)(eta5-C5H4COO)Co(III)][(eta5-C5H4COOH)2Co(III)]+[PF6]-, 2.1-[PF6]. The neutral zwitterion 2 behaves as a supramolecular crown ether: it encapsulates the alkali cations K+, Rb+ and Cs+ as well as the ammonium cation NH4+ in cages sustained by O-H...O and C-H...O hydrogen bonds to form co-crystalline salts of the type 2(2)-M[PF6] (M = K, Rb, Cs) and 2(2)-[NH4][PF6]. The deprotonated acid 3 has been characterised as its Cs+ salt, Cs+-3.3H2O.     

Probing lead(II) bonding environments in 4-substituted pyridine adducts of (2,6-Me2C6H3S)2Pb: an X-ray structural and solid-state 207Pb NMR study

The effect of subtle changes in the sigma-electron donor ability of 4-substituted pyridine ligands on the lead(II) coordination environment of (2,6-Me(2)C(6)H(3)S)(2)Pb (1) adducts has been examined. The reaction of 1 with a series of 4-substituted pyridines in toluene or dichloromethane results in the formation of 1:1 complexes [(2,6-Me(2)C(6)H(3)S)(2)Pb(pyCOH)](2) (3), [(2,6-Me(2)C(6)H(3)S)(2)Pb(pyOMe)](2) (4), and (2,6-Me(2)C(6)H(3)S)(2)Pb(pyNMe(2)) (5) (pyCOH = 4-pyridinecarboxaldehyde; pyOMe = 4-methoxypyridine; pyNMe2 = 4-dimethylaminopyridine), all of which have been structurally characterized by X-ray crystallography. The structures of 3 and 4 are dimeric and have psi-trigonal bipyramidal S(3)N bonding environments, with the 4-substituted pyridine nitrogen and bridging sulfur atoms in axial positions and two thiolate sulfur atoms in equatorial sites. Conversely, compound 5 is monomeric and exhibits a psi-trigonal pyramidal S(2)N bonding environment at lead(II). The observed structures may be rationalized in terms of a simple valence bond model and the sigma-electron donor ability of the 4-pyridine ligands as derived from the analysis of proton affinity values. Solid-state (207)Pb NMR experiments are applied in combination with density functional theory (DFT) calculations to provide further insight into the nature of bonding in 4, 5, and (2,6-Me(2)C(6)H(3)S)(2)Pb(py)(2) (2). The lead chemical shielding (CS) tensor parameters of 2, 4, and 5 reveal some of the largest chemical shielding anisotropies (CSA) observed in lead coordination complexes to date. DFT calculations using the Amsterdam Density Functional (ADF) program, which take into account relativistic effects using the zeroth-order regular approximation (ZORA), yield lead CS tensor components and orientations. Paramagnetic contributions to the lead CS tensor from individual pairs of occupied and virtual molecular orbitals (MOs) are examined to gain insight into the origin of the large CSA. The CS tensor is primarily influenced by mixing of the occupied MOs localized on the sulfur and lead atoms with virtual MOs largely comprised of lead 6p orbitals.     

Monitoring of heavy metals in topsoils, atmospheric particles and plant leaves to identify possible contamination sources

The research reveals results of metal pollution on urban topsoil in relation to the metal content in leaves of two plant species and atmospheric particles. The content of pollutants (Ba, Cd, Cu, Fe, Mn, Ni, Pb, V and Ti) was determined by ICP-OES. Twenty-two samples of soil were collected over a six-month period from two different urban sites and one from a rural zone. Regarding the pollution level, the studied soils were found to be low. Results for enrichment (EF) and concentration (CF) factors showed that soils were enriched in Pb, Ba, Cu and Ni. However, both species of plants showed a common behavior for all elements acting as excluders. ANOVA and different multivariate statistical analyses confirmed that the main pollution source of soil was traffic and fertilizers. Cd, Fe, Mn, Ti and V elements were attributed to natural sources. Also, it was suggested that N. oleander leaf is useful as a bio-monitors of soil pollution by Cu. Similarly, a direct relationship was found between the content of Cu in soils with the Cu level in PM₁₀ atmospheric particles. The origin was attributed to dry and wet atmospheric deposition processes.