Ultrathin TaOx film based photovoltaic device

International Nuclear Information System (INIS)

Tyagi, Pawan

2011-01-01

Application of the economical metal oxide thin-film photovoltaic devices is hindered by the poor energy efficiency. This paper investigates the photovoltaic effect with an ultrathin tantalum oxide (TaOx) tunnel barrier, formed by the plasma oxidation of a pre-deposited tantalum (Ta) film. These ∼ 3 nm TaOx tunnel barriers showed approximately 160 mV open circuit voltage and 3-5% energy efficiency, for varying light intensity. The ultrathin TaOx (∼ 3 nm) could absorb approximately 12% of the incident light radiation in 400-1000 nm wavelength range; this strong light absorbing capability was found to be associated with the dramatically large extinction coefficient. Spectroscopic ellipsometry revealed that the extinction coefficient of 3 nm TaOx was ∼ 0.2, two orders higher than that of tantalum penta oxide (Ta 2 O 5 ). Interestingly, refractive index of this 3 nm thick TaOx was comparable with that of stochiometeric Ta 2 O 5 . However, heating and prolonged high-intensity light exposure deteriorated the photovoltaic effect in TaOx junctions. This study provides the basis to explore the photovoltaic effect in a highly economical and easily processable ultrathin metal oxide tunnel barrier or analogous systems.

Blockade of OX40/OX40 ligand to decrease cytokine messenger RNA expression in acute renal allograft rejection in vitro.

Science.gov (United States)

Wang, Y-L; Li, G; Fu, Y-X; Wang, H; Shen, Z-Y

2013-01-01

The aim of this study was to investigate cytokine messenger RNA (mRNA) expression by peripheral blood mononuclear cells (PBMCs) from renal recipients experiencing acute rejection by blocking OX40-OX40L interactions with recombinant human OX40-Fc fusion protein (rhOX40Fc) in vitro. PBMCs were isolated from 20 recipients experiencing acute rejection episodes (rejection group) and 20 recipients with stable graft function (stable group). Levels of Th1 (interferon [IFN]-γ) and Th2 (interleukin [IL]-4) mRNA expressions by PBMCs were measured using real-time reverse transcriptase-polymerase chain reactions. IFN-γ mRNA expression levels were significantly higher in the rejection than the stable group (P rejection group, rhOX40Fc reduced significantly the expression of IFN-γ and IL-4 mRNA by anti-CD3-monoclonal antibody stimulated PBMCs (P type cytokines. Copyright © 2013 Elsevier Inc. All rights reserved.

A new support measure to quantify the impact of local optima in phylogenetic analyses.

KAUST Repository

Brammer, Grant; Sul, Seung-Jin; Williams, Tiffani L

2011-01-01

Phylogentic analyses are often incorrectly assumed to have stabilized to a single optimum. However, a set of trees from a phylogenetic analysis may contain multiple distinct local optima with each optimum providing different levels of support

The clinical investigation of OX40/OX40L from lymphocytes of patients with Graves' disease after 131I therapy

International Nuclear Information System (INIS)

Shi Bimin; Du Xuan; Wang Qin

2013-01-01

Objective To investigate the clinical value and the expression of OX40/OX40L from lymphocytes of patients with Graves' disease (GD) before and after 131 I therapy.Methods The expression of OX40/OX40L on T,B lymphocytes and the percentage of lymphocyte subsets were analyzed using immunofluorescence staining and flow cytometry in 32 patients with GD before and after 131 I therapy.Twenty-five healthy subjects were considered as the control group.The data between GD patients and controls were compared with two-sample t test.The correlation between the expression of OX40/OX40L and the function of thyroid (FT3,FT4 and TRAb level) was performed with linear correlation analysis.Results Compared with the healthy subjects,the percentage of CD4+ T cells and ratio of CD4+/CD8+ were decreased ((34.36 ±6.73)% vs (45.60-±5.72)%,t=2.634; 1.24±0.26 vs 1.84±0.37,t=2.125,both P<0.05).Whereas the percentage of CD19+ B cells in patients with GD were significantly higher than that in healthy subjects ((21.42 ±3.92)% vs (15.35 ± 3.15)%,t =2.653,P<0.05).The expression of OX40 increased in CD4+ T lymphocytes ((12.92 ± 2.26) %) and OX40L expression was up-regulated in CD19+ B lymphocytes ((15.33 ± 3.75)%) of patients with GD,compared with the healthy subjects ((4.19 ±1.45) % and (8.64 ± 1.73) %,respectively,t =2.112 and 2.467,both P<0.05).The expression of OX40 in CD4+ T lymphocytes ((7.65 ± 1.64) %) and OX40L in CD19+ B lymphocytes ((11.50 ±2.72)%) were increased after 131 I therapy(t =2.795,2.393,both P<0.05).The thyroid functions of 32 GD patients were improved.The levels of FT3,FT4 and TRAb decreased significantly after 131 I treatment (from 20.79 ±6.05 to 4.53 ± 2.54,from 49.65 ± 10.12 to 13.69 ± 4.35,and from 24.78 ± 8.46 to 11.74 ±6.19,respectively; t =2.219,2.441 and 2.293,all P<0.05).The levels of FT3 and FT4 were positively correlated with the percentage of OX40 expression in CD4+ T lymphocytes (r =0.65 and 0.73,both P<0.05).TRAb was positively correlated

Kinetic properties of 'dual' orexin receptor antagonists at OX1R and OX2R orexin receptors.

Directory of Open Access Journals (Sweden)

Gabrielle Elizabeth Callander

2013-12-01

Full Text Available Orexin receptor antagonists represent attractive targets for the development of drugs for the treatment of insomnia. Both efficacy and safety are crucial in clinical settings and thorough investigations of pharmacokinetics and pharmacodynamics can predict contributing factors such as duration of action and undesirable effects. To this end, we studied the interactions between various ‘dual’ orexin receptor antagonists and the orexin receptors, OX1R and OX2R, over time using saturation and competition radioligand binding with [3H]-BBAC ((S-N-([1,1'-biphenyl]-2-yl-1-(2-((1-methyl-1H-benzo[d]imidazol-2-ylthioacetylpyrrolidine-2-carboxamide. In addition, the kinetics of these compounds were investigated in cells expressing human, mouse and rat OX1R and OX2R using FLIPR® assays for calcium accumulation. We demonstrate that almorexant reaches equilibrium very slowly at OX2R, whereas SB-649868, suvorexant and filorexant may take hours to reach steady state at both orexin receptors. By contrast, compounds such as BBAC or the selective OX2R antagonist IPSU ((2-((1H-Indol-3-ylmethyl-9-(4-methoxypyrimidin-2-yl-2,9-diazaspiro[5.5]undecan-1-one bind rapidly and reach equilibrium very quickly in both binding and / or functional assays. Overall, the dual antagonists tested here tend to be rather unselective under non-equilibrium conditions and reach equilibrium very slowly. Once equilibrium is reached, each ligand demonstrates a selectivity profile that is however, distinct from the non-equilibrium condition. The slow kinetics of the dual antagonists tested suggest that in vitro receptor occupancy may be longer lasting than would be predicted. This raises questions as to whether pharmacokinetic studies measuring plasma or brain levels of these antagonists are accurate reflections of receptor occupancy in vivo.

Effect of OX-VIRIN versus phytoplankton; Eficacia de OX.VIRIN frente a fitoplancton

Energy Technology Data Exchange (ETDEWEB)

Sevilla Miguel, E.; Peleato Sanchez, M. L.; Gomez-Moreno Calera, C.; Oros Monje, J.; Vergara Larrayad, Y.

2003-07-01

The effect of the peroxide biocides OX-VIRIN has been tested on the survival of several representative phytoplankton species. Scenedesmus vacuolatus green algae, Anabaena sp. PCC7120 filamentous cyanobacteria and Microcystis aeruginosa PCC7005 unicellular cyanobacteria have been used. The parameters used to control the effectiveness of the biocide have been the chlorophyll determination and re culture. It has been shown that OX-VIRIN at dosages of 0.2, 0.5 and 1% is lethal against Microcystis, Anabaena, and Scenedesmus vacuolatus (formerly called Chlorella fusca), being the first mentioned organisms the most sensible to the biocide. (Author)

The HTLV-I tax protein transcriptionally modulates OX40 antigen expression.

Science.gov (United States)

Pankow, R; Dürkop, H; Latza, U; Krause, H; Kunzendorf, U; Pohl, T; Bulfone-Paus, S

2000-07-01

OX40 is a member of the TNF receptor family, expressed on activated T cells. It is the only costimulatory T cell molecule known to be specifically up-regulated in human T cell leukemia virus type-I (HTLV-I)-producing cells. In a T cell line, OX40 surface expression was shown to be induced by HTLV-I Tax alone. To understand molecular mechanisms of OX40 gene regulation and modulation by HTLV-I Tax, we have cloned the human OX40 gene and analyzed its 5'-flanking region. By reporter gene analysis with progressive 5' deletions from nucleotides -1259 to -64, we have defined a 157-bp DNA fragment as a minimal promoter for constitutive expression. In addition, we show that in the OX40+ cell line, Co, Tax is able to further increase OX40 surface expression. Up-regulation of OX40 promoter activity by Tax requires two upstream NF-kappaB sites, which are not active in the constitutive OX40 expression. Their deletion abrogates Tax responsiveness in reporter gene analysis. The site-directed mutagenesis of each NF-kappaB site demonstrates that cooperative NF-kappaB binding is a prerequisite for Tax-directed activity as neither site alone is sufficient for a full Tax responsiveness of the OX40 promoter. Upon Tax expression, both sites bind p65 and c-Rel. These data provide new insight into the direct regulation of OX40 by Tax and add to our understanding of the possible role of the OX40/OX40 ligand system in the proliferation of HTLV-I+ T cells.

Hydrogenated CoOx nanowire@Ni(OH)2 nanosheet core-shell nanostructures for high-performance asymmetric supercapacitors

Science.gov (United States)

Zhu, Jianxiao; Huang, Lei; Xiao, Yuxiu; Shen, Leo; Chen, Qi; Shi, Wangzhou

2014-05-01

We report a facile strategy to prepare 3D core-shell nanowire heterostructures with microporous hydrogenated CoOx (H-CoOx) nanowires as the conducting scaffold to support Ni(OH)2 nanosheets. Benefiting from the H-CoOx nanowire core to provide the effective pathway for charge transport and the core-shell heterostructures with synergistic effects, the H-CoOx@Ni(OH)2 core-shell nanowire electrode achieved the specific capacitance of 2196 F g-1 (areal capacitance of 5.73 F cm-2), which is approximately a 1.4-fold enhancement compared with the Co3O4@Ni(OH)2 core-shell nanowires. An aqueous asymmetric supercapacitor (ASC) device was fabricated by using H-CoOx@Ni(OH)2 nanowires as the positive electrode and reduced graphene oxide @Fe3O4 nanocomposites as the negative electrode. The ASCs achieved high energy density (~45.3 W h kg-1 at 1010 W kg-1), high power density (~7080 W kg-1 at 23.4 W h kg-1) and high cycling stability. Furthermore, after charging for ~1 min, one such 22 cm2 ASC device demonstrated to be able to drive a small windmill (0.8 V, 0.1 W) for 20 min. Two such ASCs connected in series can power up a seven-color LED (3.2 V) efficiently.We report a facile strategy to prepare 3D core-shell nanowire heterostructures with microporous hydrogenated CoOx (H-CoOx) nanowires as the conducting scaffold to support Ni(OH)2 nanosheets. Benefiting from the H-CoOx nanowire core to provide the effective pathway for charge transport and the core-shell heterostructures with synergistic effects, the H-CoOx@Ni(OH)2 core-shell nanowire electrode achieved the specific capacitance of 2196 F g-1 (areal capacitance of 5.73 F cm-2), which is approximately a 1.4-fold enhancement compared with the Co3O4@Ni(OH)2 core-shell nanowires. An aqueous asymmetric supercapacitor (ASC) device was fabricated by using H-CoOx@Ni(OH)2 nanowires as the positive electrode and reduced graphene oxide @Fe3O4 nanocomposites as the negative electrode. The ASCs achieved high energy density (~45.3 W h kg-1 at

OX62+OX6+OX35+ rat dendritic cells are unable to prime CD4+ T cells for an effective immune response following acute burn injury.

Science.gov (United States)

Fazal, Nadeem

2013-01-01

Co-stimulatory molecules expressed on Dendritic Cells (DCs) function to coordinate an efficient immune response by T cells in the peripheral lymph nodes. We hypothesized that CD4+ T cell-mediated immune suppression following burn injury may be related to dysfunctional DCs residing in gut associated lymphoid tissues (GALT), such as Mesenteric Lymph Nodes (MLN). Therefore, we studied co-stimulatory molecules expressed on burn rat MLN DCs as an index of functional DCs that would mount an effective normal CD4+ T cell immune response. In a rat model of 30% Total Body Surface Area (TBSA) scald burn, OX62+OX6+OX35+ DCs and CD4+ T cells were isolated from MLN of day 3 post-burn and sham control rats. DCs were tested for their expression of co-stimulatory molecules, and prime CD4+ T cell (DC:CD4+T cell co-culture assays) to determine an effector immune response such as CD4+ T cell proliferation. The surface receptor expressions of MLN DCs co-stimulatory molecules, i.e., MHC-II, CD40, CD80 (B7-1), and CD86 (B7-2) were determined by Flow cytometry (quantitatively) and confocal microscopy (qualitatively). Tritiated thymidine and CFDA-SE determined CD4+ T cell proliferation following co-incubation with DCs. Cytokine milieu of MLN (IL-12 and IL-10) was assessed by mRNA determination by RT-PCR. The results showed down-regulated expressions of co-stimulatory markers (CD80, CD86, CD40 and MHC-II) of MLN DCs obtained from burn-injured rats, as well as lack of ability of these burn-induced DCs to stimulate CD4+ T cell proliferation in co-culture assays, as compared to the sham rats. Moreover, anti-CD40 stimulation of affected burn MLN DCs did not reverse this alteration. Furthermore, a marked up-regulation of mRNA IL-10 and down-regulation of mRNA IL-12 in burn MLN as compared to sham animals was also observed. To surmise, the data indicated that dysfunctional OX62+OX6+OX35+ rat MLN DCs may contribute to CD4+ T-cell-mediated immune suppression observed following acute burn injury.

OX62+OX6+OX35+ rat dendritic cells are unable to prime CD4+ T cells for an effective immune response following acute burn injury☆

Science.gov (United States)

Fazal, Nadeem

2013-01-01

Co-stimulatory molecules expressed on Dendritic Cells (DCs) function to coordinate an efficient immune response by T cells in the peripheral lymph nodes. We hypothesized that CD4+ T cell-mediated immune suppression following burn injury may be related to dysfunctional DCs residing in gut associated lymphoid tissues (GALT), such as Mesenteric Lymph Nodes (MLN). Therefore, we studied co-stimulatory molecules expressed on burn rat MLN DCs as an index of functional DCs that would mount an effective normal CD4+ T cell immune response. In a rat model of 30% Total Body Surface Area (TBSA) scald burn, OX62+OX6+OX35+ DCs and CD4+ T cells were isolated from MLN of day 3 post-burn and sham control rats. DCs were tested for their expression of co-stimulatory molecules, and prime CD4+ T cell (DC:CD4+T cell co-culture assays) to determine an effector immune response such as CD4+ T cell proliferation. The surface receptor expressions of MLN DCs co-stimulatory molecules, i.e., MHC-II, CD40, CD80 (B7-1), and CD86 (B7-2) were determined by Flow cytometry (quantitatively) and confocal microscopy (qualitatively). Tritiated thymidine and CFDA-SE determined CD4+ T cell proliferation following co-incubation with DCs. Cytokine milieu of MLN (IL-12 and IL-10) was assessed by mRNA determination by RT-PCR. The results showed down-regulated expressions of co-stimulatory markers (CD80, CD86, CD40 and MHC-II) of MLN DCs obtained from burn-injured rats, as well as lack of ability of these burn-induced DCs to stimulate CD4+ T cell proliferation in co-culture assays, as compared to the sham rats. Moreover, anti-CD40 stimulation of affected burn MLN DCs did not reverse this alteration. Furthermore, a marked up-regulation of mRNA IL-10 and down-regulation of mRNA IL-12 in burn MLN as compared to sham animals was also observed. To surmise, the data indicated that dysfunctional OX62+OX6+OX35+ rat MLN DCs may contribute to CD4+ T-cell-mediated immune suppression observed following acute burn injury

Efficient and rapid microwave-assisted route to synthesize Pt–MnOx hydrogen peroxide sensor

International Nuclear Information System (INIS)

Kivrak, Hilal; Alal, Orhan; Atbas, Dilan

2015-01-01

Highlights: • Carbon supported Pt-MnOx catalyst could be synthesized succesfully by microwave irradiation method. • Carbon supported Pt-MnOx non-enzymatic H 2 O 2 sensor exhibits excellent selectivity, stability, and reproducibility • Carbon supported Pt-MnOx sensor can effectively resist the effect of interferents such as uric acid and ascorbic acid. - Abstract: A novel electrochemical sensor for the detection of hydrogen peroxide (H 2 O 2 ) is proposed based on carbon supported Pt-MnO x and Pt nanoparticles, successfully synthesized via microwave irradiation polyol method. The physicochemical properties of the Pt-MnO x and Pt nanoparticles were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Transmission electron microscopy (TEM). Electrochemical properties of the nanoparticles were investigated by cyclic voltammetry (CV) and chronoamperometry (CA). Electrochemical measurements indicate that the oxidation current of H 2 O 2 is linear (R 2 =0.998) to its concentration from 2 μM to 4.0 mM with a detection limit of 0.7 μM (signal/noise = 3). In addition, Pt-MnO x is not affected by ascorbic acid (AA) and uric acid (UA) which are common interfering species. Meanwhile, this Pt-MnO x non-enzymatic H 2 O 2 sensor exhibits excellent selectivity, stability and reproducibility. Thus, this novel non-enzymatic sensor can be found practical applications in H 2 O 2 detection

Carbon Supported Oxide-Rich Pd-Cu Bimetallic Electrocatalysts for Ethanol Electrooxidation in Alkaline Media Enhanced by Cu/CuOx

Directory of Open Access Journals (Sweden)

Zengfeng Guo

2016-04-01

Full Text Available Different proportions of oxide-rich PdCu/C nanoparticle catalysts were prepared by the NaBH4 reduction method, and their compositions were tuned by the molar ratios of the metal precursors. Among them, oxide-rich Pd0.9Cu0.1/C (Pd:Cu = 9:1, metal atomic ratio exhibits the highest electrocatalytic activity for ethanol oxidation reaction (EOR in alkaline media. X-ray photoelectron spectroscopy (XPS and high resolution transmission electron microscopy (HRTEM confirmed the existence of both Cu and CuOx in the as-prepared Pd0.9Cu0.1/C. About 74% of the Cu atoms are in their oxide form (CuO or Cu2O. Besides the synergistic effect of Cu, CuOx existed in the Pd-Cu bimetallic nanoparticles works as a promoter for the EOR. The decreased Pd 3d electron density disclosed by XPS is ascribed to the formation of CuOx and the spill-over of oxygen-containing species from CuOx to Pd. The low Pd 3d electron density will decrease the adsorption of CH3COads intermediates. As a result, the electrocatalytic activity is enhanced. The onset potential of oxide-rich Pd0.9Cu0.1/C is negative shifted 150 mV compared to Pd/C. The oxide-rich Pd0.9Cu0.1/C also exhibited high stability, which indicated that it is a candidate for the anode of direct ethanol fuel cells (DEFCs.

Distributional patterns of the Neotropical genus Thecomyia Perty (Diptera, Sciomyzidae and phylogenetic support

Directory of Open Access Journals (Sweden)

Amanda Ciprandi Pires

2011-03-01

Full Text Available Distributional patterns of the Neotropical genus Thecomyia Perty (Diptera, Sciomyzidae and phylogenetic support. The distributional pattern of the genus Thecomyia Perty, 1833 was defined using panbiogeographic tools, and analyzed based on the phylogeny of the group. This study sought to establish biogeographical homologies in the Neotropical region between different species of the genus, based on their distribution pattern and later corroboration through its phylogeny. Eight individual tracks and 16 generalized tracks were identified, established along nearly the entire swath of the Neotropics. Individual tracks are the basic units of a panbiogeographic study, and correspond to the hypothesis of minimum distribution of the organisms involved. The generalized tracks, obtained from the spatial congruence between two or more individual tracks, are important in the identification of smaller areas of endemism. Thus, we found evidence from the generalized tracks in support of previous classification for the Neotropical region. The Amazon domain is indicated as an area of outstanding importance in the diversification of the group, by the confluence of generalized tracks and biogeographic nodes in the region. Most of the generalized tracks and biogeographical nodes were congruent with the phylogenetic hypothesis of the genus, indicating support of the primary biogeographical homologies originally defined by the track analysis.

Ultrasmall PdmMn1-mOx binary alloyed nanoparticles on graphene catalysts for ethanol oxidation in alkaline media

Science.gov (United States)

Ahmed, Mohammad Shamsuddin; Park, Dongchul; Jeon, Seungwon

2016-03-01

A rare combination of graphene (G)-supported palladium and manganese in mixed-oxides binary alloyed catalysts (BACs) have been synthesized with the addition of Pd and Mn metals in various ratios (G/PdmMn1-mOx) through a facile wet-chemical method and employed as an efficient anode catalyst for ethanol oxidation reaction (EOR) in alkaline fuel cells. The as prepared G/PdmMn1-mOx BACs have been characterized by several instrumental techniques; the transmission electron microscopy images show that the ultrafine alloyed nanoparticles (NPs) are excellently monodispersed onto the G. The Pd and Mn in G/PdmMn1-mOx BACs have been alloyed homogeneously, and Mn presents in mixed-oxidized form that resulted by X-ray diffraction. The electrochemical performances, kinetics and stability of these catalysts toward EOR have been evaluated using cyclic voltammetry in 1 M KOH electrolyte. Among all G/PdmMn1-mOx BACs, the G/Pd0.5Mn0.5Ox catalyst has shown much superior mass activity and incredible stability than that of pure Pd catalysts (G/Pd1Mn0Ox, Pd/C and Pt/C). The well dispersion, ultrafine size of NPs and higher degree of alloying are the key factor for enhanced and stable EOR electrocatalysis on G/Pd0.5Mn0.5Ox.

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales.

Science.gov (United States)

Purschke, Oliver; Michalski, Stefan G; Bruelheide, Helge; Durka, Walter

2017-12-01

Although spatial and temporal patterns of phylogenetic community structure during succession are inherently interlinked and assembly processes vary with environmental and phylogenetic scales, successional studies of community assembly have yet to integrate spatial and temporal components of community structure, while accounting for scaling issues. To gain insight into the processes that generate biodiversity after disturbance, we combine analyses of spatial and temporal phylogenetic turnover across phylogenetic scales, accounting for covariation with environmental differences. We compared phylogenetic turnover, at the species- and individual-level, within and between five successional stages, representing woody plant communities in a subtropical forest chronosequence. We decomposed turnover at different phylogenetic depths and assessed its covariation with between-plot abiotic differences. Phylogenetic turnover between stages was low relative to species turnover and was not explained by abiotic differences. However, within the late-successional stages, there was high presence-/absence-based turnover (clustering) that occurred deep in the phylogeny and covaried with environmental differentiation. Our results support a deterministic model of community assembly where (i) phylogenetic composition is constrained through successional time, but (ii) toward late succession, species sorting into preferred habitats according to niche traits that are conserved deep in phylogeny, becomes increasingly important.

Assessment of oxLDL, anti-oxLDL antibodies and lipoprotein-associated phospholipase A2 as cardiovascular risk markers in obese adolescents with and without T1DM

Directory of Open Access Journals (Sweden)

Nesreen N. Omar

2017-12-01

Full Text Available Background: Oxidized low density lipoprotein (oxLDL, anti-oxLDL antibodies (oxLDL Ab and lipoprotein-associated phospholipase A2 (Lp-PLA2 are the sequel of lipoprotein oxidation and were not studied contemporarily in obese adolescents with and without type 1 diabetes (T1DM. Subjects and methods: The current study enrolled seventy-five adolescents with T1DM who were selected as having hyperglycemia and seventy-five matched control subjects. Both the diabetic and the control groups were further divided into obese, normal weight and underweight subgroups according to body mass index (BMI. The following tests were performed: fasting plasma glucose (FG glycated hemoglobin (HbA1c, insulin, apolipoprotein AI (apo AI, apolipoprotein B (apo B, oxLDL, oxLDL Ab and Lp-PLA2 mass. The diabetic subgroups were selected as having hyperglycemia. Results: Obese diabetic subgroup had higher insulin level and HOMA value than underweight and normal weight diabetic subgroups. oxLDL, oxLDL Ab and Lp-PLA2 showed higher concentrations in patients with T1DM than in control subjects (118.48 ± 23.7, 1231.8 ± 940 and 401.26 ± 97.2 vs. 58.1 ± 17.9, 424.9 ± 290.0 and 315.7 ± 70; p < 0.001.. In patients with T1DM, direct correlations were found between oxLDL, oxLDL Ab and Lp-PLA2 and cardiometabolic markers represented by apo B/apo AI ratio, FG and BMI. Conclusion: The current data provide evidence that oxLDL, its retroactive enzyme and antibody are present in circulation early in childhood when primed by obesity and hyperglycemia in T1DM and suggests that they could be useful markers for cardiovascular diseases (CVD. Keywords: OxLDL, OxLDL Ab, Lp-PLA2, Cardiometabolic markers, Obese, Diabetes

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum.

Science.gov (United States)

Gatesy, John; Springer, Mark S

2014-11-01

Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree of Life. Currently, two divergent systematic methods are commonly applied to such datasets: the traditional supermatrix approach (= concatenation) and "shortcut" coalescence (= coalescence methods wherein gene trees and the species tree are not co-estimated). When applied to ancient clades, these contrasting frameworks often produce congruent results, but in recent phylogenetic analyses of Placentalia (placental mammals), this is not the case. A recent series of papers has alternatively disputed and defended the utility of shortcut coalescence methods at deep phylogenetic scales. Here, we examine this exchange in the context of published phylogenomic data from Mammalia; in particular we explore two critical issues - the delimitation of data partitions ("genes") in coalescence analysis and hidden support that emerges with the combination of such partitions in phylogenetic studies. Hidden support - increased support for a clade in combined analysis of all data partitions relative to the support evident in separate analyses of the various data partitions, is a hallmark of the supermatrix approach and a primary rationale for concatenating all characters into a single matrix. In the most extreme cases of hidden support, relationships that are contradicted by all gene trees are supported when all of the genes are analyzed together. A valid fear is that shortcut coalescence methods might bypass or distort character support that is hidden in individual loci because small gene fragments are analyzed in isolation. Given the extensive systematic database for Mammalia, the assumptions and applicability of shortcut coalescence methods can be assessed with rigor to complement a small but growing body of simulation work that has directly compared these methods to concatenation. We document several remarkable cases of hidden support in both supermatrix and coalescence paradigms and argue

Properties and practical application of thin CeOx films

Directory of Open Access Journals (Sweden)

Maksimchuk N. V.

2010-10-01

Full Text Available The properties of CeOx films produced by various methods have been investigated. According to the comparative analisys “metallic mirror oxidation” method allows to produce films with significantly better characteristics than the «explosive evaporation» method. Though the latter method yields higher photosensitivity of CeOx films and structures on their base. In the process the optimal value of the substrate temperature was determined. Obtained data expand the CeOx application potential in microelectronic sensor sphere.

CMOS Thermal Ox and Diffusion Furnace: Tystar Tytan 2000

Data.gov (United States)

Federal Laboratory Consortium — Description:CORAL Names: CMOS Wet Ox, CMOS Dry Ox, Boron Doping (P-type), Phos. Doping (N-Type)This four-stack furnace bank is used for the thermal growth of silicon...

Phylogenetic classification of bony fishes.

Science.gov (United States)

Betancur-R, Ricardo; Wiley, Edward O; Arratia, Gloria; Acero, Arturo; Bailly, Nicolas; Miya, Masaki; Lecointre, Guillaume; Ortí, Guillermo

2017-07-06

Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution

Soluble OX40L is associated with presence of autoantibodies in early rheumatoid arthritis

DEFF Research Database (Denmark)

Laustsen, Julie K; Rasmussen, Tue K; Stengaard-Pedersen, Kristian

2014-01-01

) and with methotrexate alone (n = 37). Adalimumab was discontinued after the first year, and patients were followed for additional 12 months. For comparison, sOX40 and sOX40L were measured in patients with chronic RA (cRA, n = 15) and healthy volunteers (HV, n = 34). Membrane-bound OX40 and OX40L expression on T cells......, B cells and monocytes were quantified. RESULTS: Soluble OX40 plasma levels of eRA patients were not different at the time of treatment initiation, but were significantly higher after 12 months of treatment, compared with HV or cRA patients. Soluble OX40L was significantly elevated throughout...... the first 12 months of treatment compared with HVs and patients with cRA. Adalimumab treatment did not influence sOX40 or sOX40L plasma levels. At baseline, sOX40L levels were strongly associated with the presence of anti-citrullinated protein antibodies (ACPA) (P

Ultrafast Approximation for Phylogenetic Bootstrap

NARCIS (Netherlands)

Bui Quang Minh, [No Value; Nguyen, Thi; von Haeseler, Arndt

Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and

Anti-tumour therapeutic efficacy of OX40L in murine tumour model.

Science.gov (United States)

Ali, Selman A; Ahmad, Murrium; Lynam, June; McLean, Cornelia S; Entwisle, Claire; Loudon, Peter; Choolun, Esther; McArdle, Stephanie E B; Li, Geng; Mian, Shahid; Rees, Robert C

2004-09-09

OX40 ligand (OX40L), a member of TNF superfamily, is a co-stimulatory molecule involved in T cell activation. Systemic administration of mOX40L fusion protein significantly inhibited the growth of experimental lung metastasis and subcutaneous (s.c.) established colon (CT26) and breast (4T1) carcinomas. Vaccination with OX40L was significantly enhanced by combination treatment with intra-tumour injection of a disabled infectious single cycle-herpes simplex virus (DISC-HSV) vector encoding murine granulocyte macrophage-colony stimulating factor (mGM-CSF). Tumour rejection in response to OX40L therapy required functional CD4+ and CD8+ T cells and correlated with splenocyte cytotoxic T lymphocytes (CTLs) activity against the AH-1 gp70 peptide of the tumour associated antigen expressed by CT26 cells. These results demonstrate the potential role of the OX40L in cancer immunotherapy.

Evolution of resistive switching mechanism through H2O2 sensing by using TaOx-based material in W/Al2O3/TaOx/TiN structure

Science.gov (United States)

Chakrabarti, Somsubhra; Panja, Rajeswar; Roy, Sourav; Roy, Anisha; Samanta, Subhranu; Dutta, Mrinmoy; Ginnaram, Sreekanth; Maikap, Siddheswar; Cheng, Hsin-Ming; Tsai, Ling-Na; Chang, Ya-Ling; Mahapatra, Rajat; Jana, Debanjan; Qiu, Jian-Tai; Yang, Jer-Ren

2018-03-01

Understanding of resistive switching mechanism through H2O2 sensing and improvement of switching characteristics by using TaOx-based material in W/Al2O3/TaOx/TiN structure have been reported for the first time. Existence of amorphous Al2O3/TaOx layer in the RRAM devices has been confirmed by transmission electron microscopy. By analyzing the oxidation states of Ta2+/Ta5+ for TaOx switching material and W0/W6+ for WOx layer at the W/TaOx interface through X-ray photoelectron spectroscopy and H2O2 sensing, the reduction-oxidation mechanism under Set/Reset occurs only in the TaOx layer for the W/Al2O3/TaOx/TiN structures. This leads to higher Schottky barrier height at the W/Al2O3 interface (0.54 eV vs. 0.46 eV), higher resistance ratio, and long program/erase endurance of >108 cycles with 100 ns pulse width at a low operation current of 30 μA. Stable retention of more than 104 s at 85 °C is also obtained. Using conduction mechanism and reduction-oxidation reaction, current-voltage characteristic has been simulated. Both TaOx and WOx membranes have high pH sensitivity values of 47.65 mV/pH and 49.25 mV/pH, respectively. Those membranes can also sense H2O2 with a low concentration of 1 nM in an electrolyte-insulator-semiconductor structure because of catalytic activity, while the Al2O3 membrane does not show sensing. The TaOx material in W/Al2O3/TaOx/TiN structure does not show only a path towards high dense, small size memory application with understanding of switching mechanism but also can be used for H2O2 sensors.

Energy level alignment at Co/AlOx/pentacene interfaces

NARCIS (Netherlands)

Popinciuc, M.; Jonkman, H. T.; van Wees, B. J.

2007-01-01

X-ray and ultraviolet photoemission spectroscopy (XPS and UPS) experiments were performed in order to study the energy level alignment and electronic structure at Co/AlOx/pentacene interfaces as a function of the aluminum oxide (AlOx) tunnel barrier thickness and the oxidation state of Co. XPS was

Global analysis of gene expression mediated by OX1 orexin receptor signaling in a hypothalamic cell line.

Directory of Open Access Journals (Sweden)

Eric Koesema

Full Text Available The orexins and their cognate G-protein coupled receptors have been widely studied due to their associations with various behaviors and cellular processes. However, the detailed downstream signaling cascades that mediate these effects are not completely understood. We report the generation of a neuronal model cell line that stably expresses the OX1 orexin receptor (OX1 and an RNA-Seq analysis of changes in gene expression seen upon receptor activation. Upon treatment with orexin, several families of related transcription factors are transcriptionally regulated, including the early growth response genes (Egr, the Kruppel-like factors (Klf, and the Nr4a subgroup of nuclear hormone receptors. Furthermore, some of the transcriptional effects observed have also been seen in data from in vivo sleep deprivation microarray studies, supporting the physiological relevance of the data set. Additionally, inhibition of one of the most highly regulated genes, serum and glucocorticoid-regulated kinase 1 (Sgk1, resulted in the diminished orexin-dependent induction of a subset of genes. These results provide new insight into the molecular signaling events that occur during OX1 signaling and support a role for orexin signaling in the stimulation of wakefulness during sleep deprivation studies.

Catalytic decomposition of gaseous 1,2-dichlorobenzene over CuOx/TiO₂ and CuOx/TiO₂-CNTs catalysts: Mechanism and PCDD/Fs formation.

Science.gov (United States)

Wang, Qiu-lin; Huang, Qun-xing; Wu, Hui-fan; Lu, Sheng-yong; Wu, Hai-long; Li, Xiao-dong; Yan, Jian-hua

2016-02-01

Gaseous 1,2-dichlorobenzene (1,2-DCBz) was catalytically decomposed in a fixed-bed catalytic reactor using composite copper-based titanium oxide (CuOx/TiO2) catalysts with different copper ratios. Carbon nanotubes (CNTs) were introduced to produce novel CuOx/TiO2-CNTs catalysts by the sol-gel method. The catalytic performances of CuOx/TiO2 and CuOx/TiO2-CNTs on 1,2-DCBz oxidative destruction under different temperatures (150-350 °C) were experimentally examined and the correlation between catalyst structure and catalytic activity was characterized and the role of oxygen in catalytic reaction was discussed. Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) generation during 1,2-DCBz catalytic oxidation by CuOx/TiO2-CNTs composite catalyst was also examined. Results indicate that the 1,2-DCBz destruction/removal efficiencies of CuOx (4 wt%)/TiO2 catalyst at 150 °C and 350 °C with a GHSV of 3400 h(-1) are 59% and 94% respectively and low-temperature (150 °C) catalytic activity of CuOx/TiO2 on 1,2-DCBz oxidation can be improved from 59 to 77% when CNTs are introduced. Furthermore, oxygen either in catalyst or from reaction atmosphere is indispensible in reaction. The former is offered to activate and oxidize the 1,2-DCBz adsorbed on catalyst, thus can be generally consumed during reaction and the oxygen content in catalyst is observed lost from 39.9 to 35.0 wt% after reacting under inert atmosphere; the latter may replenish the vacancy in catalyst created by the consumed oxygen thus extends the catalyst life and raises the destruction/removal efficiency. The introduction of CNTs also increases the Cu(2+)/Cu(+) ratio, chemisorbed oxygen concentration and surface lattice oxygen binding energy which are closely related with catalytic activity. PCDD/Fs is confirmed to be formed when 1,2-DCBz catalytically oxidized by CuOx/TiO2-CNTs composite catalyst with sufficient oxygen (21%), proper temperature (350 °C) and high concentration of 1,2-DCBz feed (120 ppm

MoOx modified ZnGaO based transparent conducting oxides

Science.gov (United States)

Dutta, Titas; Gupta, P.; Bhosle, V.; Narayan, J.

2009-03-01

We report here the growth of high work function bilayered structures of thin MoOx (2.0MoOx layer, molybdenum exists in Mo4+, Mo5+, and Mo6+ oxidation states, and the ratio of (Mo4++Mo5+) to Mo6+ was determined to be ˜2:1. The bilayer films showed good optical transparency (≥80%) and low resistivity of ˜10-4 Ω cm. Different transport behavior of the MoOx/ZnGa0.05O films grown at different Ts (substrate temperature) was observed in temperature-dependent resistivity measurements. The bilayer film at higher Ts showed metallic conductivity behavior down to 113 K. Moreover, a blueshift of the absorption edge in the transmission spectrum was observed with the increase in Ts, indicating an increase in the carrier concentration. It was observed that the ZnGa0.05O films with ultrathin MoOx (˜1-2 nanometers) overlayer showed a higher work function (varying from 4.7 to 5.1 eV) as compared to the single layer ZnGa0.05O film work function (˜4.4 eV). A correlation between the surface work function and MoOx layer thickness is observed. The higher work function of the MoOx overlayer is envisaged to improve the transport of the carriers across the heterojunction in a solid state device, thus resulting an increase in device efficiency.

Introduction of OX40 ligand into lymphoma cells elicits anti-lymphoma immunity in vivo.

Science.gov (United States)

Kaneko, Hitomi; Hori, Toshiyuki; Yanagita, Soshi; Kadowaki, Norimitsu; Uchiyama, Takashi

2005-03-01

OX40, a member of the TNF receptor superfamily, and its ligand (OX40L) play crucial roles in induction and maintenance of integrated T cell immune response. Engagement of OX40L delivers a costimulatory signal to T cells. In this study, we investigated whether inoculation of OX40L-transfected EL4, a murine T cell lymphoma cell line, could induce anti-lymphoma immunity in mice. Female C57BL/6 mice were inoculated with 1 x 10(5) cells of parental EL4, OX40L-transfected EL4 (EL4-OX40L), or mock control vector-transfected EL4 (EL4-mock), and then the tumor size, overall survival, CTL activity of spleen cells, and the immunohistochemistry were compared. While both parental EL4 and EL4-mock grew rapidly, EL4-OX40L was rejected or grew slower than parental EL4 or EL4-mock. Pretreatment of mice with either anti-CD4 or anti-CD8 mAb accelerated the growth of EL4-OX40L, suggesting that both CD4+ and CD8+ T cells were involved in anti-lymphoma immunity. The immunohistochemical study revealed the infiltration of CD8+ T cells into the tumor of EL4-OX40L. In vitro CTL assay demonstrated that spleen cells of mice that had rejected EL4-OX40L had significant cytotoxic activity against parental EL4. The gene transfer of OX40L into lymphoma cells is an eligible and efficient modality to induce anti-lymphoma immunity.

A nanostructured electrode of IrOx foil on the carbon nanotubes for supercapacitors

Science.gov (United States)

Chen, Yi-Min; Cai, Jhen-Hong; Huang, Ying-Sheng; Lee, Kuei-Yi; Tsai, Dah-Shyang; Tiong, Kwong-Kau

2011-09-01

IrOx nanofoils (IrOxNF) of high surface area are sputtered on multi-wall carbon nanotubes (CNT) in the preparation of a structured electrode on a stainless steel (SUS) substrate for supercapacitor applications. This IrOx/CNT/SUS electrode is featured with intriguing IrOx curved foils of 2-3 nm in thickness and 400-500 nm in height, grown on top of the vertically aligned CNT film with a tube diameter of ~ 40 nm. These nanofoils are moderately oxidized during reactive sputtering and appeared translucent under the electron microscope. Detailed structural analysis shows that they are comprised of contiguous grains of iridium metal, iridium dioxide, and glassy iridium oxide. Considerable Raman line broadening is also evidenced for the attributed nanosized iridium oxides. Two capacitive properties of the electrode are significantly enhanced with addition of the curved IrOx foils. First, IrOxNF reduces the electrode Ohmic resistance, which was measured at 3.5 Ω cm2 for the CNT/SUS and 2.5 Ω cm2 for IrOxNF/CNT/SUS using impedance spectroscopy. Second, IrOxNF raises the electrode capacitance from 17.7 F g - 1 (CNT/SUS) to 317 F g - 1 (IrOx/CNT/SUS), measured with cyclic voltammetry. This notable increase is further confirmed by the galvanostatic charge/discharge experiment, measuring 370 F g - 1 after 2000 uninterrupted cycles between - 1.0 and 0.0 V (versus Ag/AgCl).

From single-site tantalum complexes to nanoparticles of TaxNy and TaOxNy supported on silica: elucidation of synthesis chemistry by dynamic nuclear polarization surface enhanced NMR spectroscopy and X-ray absorption spectroscopy

KAUST Repository

Mohandas, Janet Chakkamadathil; Abou-Hamad, Edy; Callens, Emmanuel; Samantaray, Manoja; Gajan, David; Gurinov, Andrei; Ma, Tao; Ould-Chikh, Samy; Hoffman, Adam S.; Gates, Bruce C.; Basset, Jean-Marie

2017-01-01

Air-stable catalysts consisting of tantalum nitride nanoparticles represented as a mixture of TaxNy and TaOxNy with diameters in the range of 0.5 to 3 nm supported on highly dehydroxylated silica were synthesized from TaMe5 (Me = methyl) and dimeric

Serum ox-LDL Level is Reduced with the Extent of Stenosis in Coronary Arteries

Directory of Open Access Journals (Sweden)

Mohammad Najafi

2013-05-01

Full Text Available Oxidized LDL (ox-LDL lipoproteins are proposed as important modified particles triggering pro-inflammatory events through receptor-mediated pathways. We evaluated the circulating ox-LDL level on the concept that the chronic immune events may affect ox-LDL clearance as the vessel stenosis develops in coronary arteries. One hundred sixty five subjects underwent coronary angiography and then, subdivided into four subgroups controls (n=85; SVD, 2VD and 3VD (n=80. The serum ox-LDL level and other biochemical parameters were measured using ELISA method and routine laboratory techniques, respectively. The serum ox-LDL level in the control group (4.81±1.41 mU/mg was significantly higher than patients (4.28±1.73 mU/mg, P<0.05. The ox-LDL/LDL ratio was conversely reduced with the extent of stenosis as compared with the controls (P<0.05. Furthermore, no difference was observed in the ox-LDL/LDL ratio between the 2VD and 3VD patients. We suggested the atherosclerosis process increases the total clearing capacities of the circulating ox-LDL particles.

Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae), including a reassessment of previous infrageneric classifications.

Science.gov (United States)

Tang, Chin Cheung; Thomas, Daniel C; Saunders, Richard M K

2015-09-01

Data is presented in support of a phylogenetic reconstruction of the species-rich early-divergent angiosperm genus Goniothalamus (Annonaceae) (Tang et al., Mol. Phylogenetic Evol., 2015) [1], inferred using chloroplast DNA (cpDNA) sequences. The data includes a list of primers for amplification and sequencing for nine cpDNA regions: atpB-rbcL, matK, ndhF, psbA-trnH, psbM-trnD, rbcL, trnL-F, trnS-G, and ycf1, the voucher information and molecular data (GenBank accession numbers) of 67 ingroup Goniothalamus accessions and 14 outgroup accessions selected from across the tribe Annoneae, and aligned data matrices for each gene region. We also present our Bayesian phylogenetic reconstructions for Goniothalamus, with information on previous infrageneric classifications superimposed to enable an evaluation of monophyly, together with a taxon-character data matrix (with 15 morphological characters scored for 66 Goniothalamus species and seven other species from the tribe Annoneae that are shown to be phylogenetically correlated).

Molecular and morphological data supporting phylogenetic reconstruction of the genus Goniothalamus (Annonaceae, including a reassessment of previous infrageneric classifications

Directory of Open Access Journals (Sweden)

Chin Cheung Tang

2015-09-01

Full Text Available Data is presented in support of a phylogenetic reconstruction of the species-rich early-divergent angiosperm genus Goniothalamus (Annonaceae (Tang et al., Mol. Phylogenetic Evol., 2015 [1], inferred using chloroplast DNA (cpDNA sequences. The data includes a list of primers for amplification and sequencing for nine cpDNA regions: atpB-rbcL, matK, ndhF, psbA-trnH, psbM-trnD, rbcL, trnL-F, trnS-G, and ycf1, the voucher information and molecular data (GenBank accession numbers of 67 ingroup Goniothalamus accessions and 14 outgroup accessions selected from across the tribe Annoneae, and aligned data matrices for each gene region. We also present our Bayesian phylogenetic reconstructions for Goniothalamus, with information on previous infrageneric classifications superimposed to enable an evaluation of monophyly, together with a taxon-character data matrix (with 15 morphological characters scored for 66 Goniothalamus species and seven other species from the tribe Annoneae that are shown to be phylogenetically correlated.

The Cladistic Basis for the Phylogenetic Diversity (PD Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

Directory of Open Access Journals (Sweden)

Rob Knight

2009-11-01

Full Text Available The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional specieslevel ecological indices to the features level. The “phylogenetic beta diversity” framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework’s success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.

From single-site tantalum complexes to nanoparticles of TaxNy and TaOxNy supported on silica: elucidation of synthesis chemistry by dynamic nuclear polarization surface enhanced NMR spectroscopy and X-ray absorption spectroscopy

KAUST Repository

Mohandas, Janet Chakkamadathil

2017-06-08

Air-stable catalysts consisting of tantalum nitride nanoparticles represented as a mixture of TaxNy and TaOxNy with diameters in the range of 0.5 to 3 nm supported on highly dehydroxylated silica were synthesized from TaMe5 (Me = methyl) and dimeric Ta-2(OMe)(10) with guidance by the principles of surface organometallic chemistry (SOMC). Characterization of the supported precursors and the supported nanoparticles formed from them was carried out by IR, NMR, UV-Vis, extended X-ray absorption fine structure, and X-ray photoelectron spectroscopies complemented with XRD and high-resolution TEM, with dynamic nuclear polarization surface enhanced NMR spectroscopy being especially helpful by providing enhanced intensities of the signals of H-1, C-13, Si-29, and N-15 at their natural abundances. The characterization data provide details of the synthesis chemistry, including evidence of (a) O-2 insertion into Ta-CH3 species on the support and (b) a binuclear to mononuclear transformation of species formed from Ta-2(OMe)(10) on the support. A catalytic test reaction, cyclooctene epoxidation, was used to probe the supported nanoparticles, with 30% H2O2 serving as the oxidant. The catalysts gave selectivities up to 98% for the epoxide at conversions as high as 99% with a 3.4 wt% loading of Ta present as TaxNy/TaOxNy.

Modeling of Oxidized PTH (oxPTH and Non-oxidized PTH (n-oxPTH Receptor Binding and Relationship of Oxidized to Non-Oxidized PTH in Children with Chronic Renal Failure, Adult Patients on Hemodialysis and Kidney Transplant Recipients

Directory of Open Access Journals (Sweden)

Berthold Hocher

2013-07-01

Full Text Available Background: The biological properties of oxidized and non-oxidized PTH are substantially different. Oxidized PTH (oxPTH loses its PTH receptor-stimulating properties, whereas non-oxidized PTH (n-oxPTH is a full agonist of the receptor. This was described in more than 20 well published studies in the 1970s and 80s. However, PTH oxidation has been ignored during the development of PTH assays for clinical use so far. Even the nowadays used third generation assay systems do not consider oxidation of PTH We recently developed an assay to differentiate between oxPTH and n-oxPTH. In the current study we established normal values for this assay system. Furthermore, we compare the ratio of oxPTH to n-oxPTH in different population with chronic renal failure: 620 children with renal failure stage 2-4 of the 4C study, 342 adult patients on dialysis, and 602 kidney transplant recipients. In addition, we performed modeling of the interaction of either oxPTH or n-oxPTH with the PTH receptor using biophysical structure approaches. Results: The children had the highest mean as well as maximum n-oxPTH concentrations as compared to adult patients (both patients on dialysis as well as kidney transplant recipients. The relationship between oxPTH and n-oxPTH of individual patients varied substantially in all three populations with renal impairment. The analysis of n-oxPTH in 89 healthy control subjects revealed that n-oxPTH concentrations in patient with renal failure were higher as compared to healthy adult controls (2.25-fold in children with renal failure, 1.53-fold in adult patients on dialysis, and 1.56-fold in kidney transplant recipients, respectively. Computer assisted biophysical structure modeling demonstrated, however, minor sterical- and/or electrostatic changes in oxPTH and n-oxPTH. This indicated that PTH oxidation may induce refolding of PTH and hence alters PTH-PTH receptor interaction via oxidation induced three-dimensional structure alteration of

Ox : Lunch Menu

OpenAIRE

Ox, Belfast

2015-01-01

In March 2013 two long standing friends, each passionate about their craft, each with a desire to bring something new to the Belfast restaurant scene combined forces and opened OX overlooking the River Lagan. Belfast-born Stephen and Brittany native Alain met while working in L’Arpège, the iconic, world-famous restaurant of radical talent Alain Passard in Paris. Having gone on to work in various other influential and inspirational restaurants they have honed their skills, developed their t...

Ox : Tasting Menu

OpenAIRE

Ox, Belfast

2015-01-01

In March 2013 two long standing friends, each passionate about their craft, each with a desire to bring something new to the Belfast restaurant scene combined forces and opened OX overlooking the River Lagan. Belfast-born Stephen and Brittany native Alain met while working in L’Arpège, the iconic, world-famous restaurant of radical talent Alain Passard in Paris. Having gone on to work in various other influential and inspirational restaurants they have honed their skills, developed their t...

Photosensitive Ox/GaAs heterojunctions: Creation and properties

Energy Technology Data Exchange (ETDEWEB)

Rud' , V. Yu. [St. Petersburg State Polytechnical University (Russian Federation); Rud' , Yu. V., E-mail: yuryrud@mail.ioffe.ru; Terukov, E. I.; Ushakova, T. N. [Russian Academy of Sciences, Ioffe Physical-Technical Institute (Russian Federation)

2012-06-15

A method for the thermal oxidation of GaAs crystals in air is suggested and the first photosensitive Ox/n-GaAs heterojunctions, where Ox is a native oxide, are fabricated. The steady current-voltage characteristics and spectra of relative quantum efficiency of the new structures are studied. The features of the spectra of photoactive absorption of the obtained heterojunctions are discussed. The potential of using vacuumfree thermal oxidation of the GaAs crystals in air to fabricate broadband heterophotoconverters of optical radiation on their basis is established.

Growth and electrical properties of AlOx grown by mist chemical vapor deposition

Directory of Open Access Journals (Sweden)

Toshiyuki Kawaharamura

2013-03-01

Full Text Available Aluminum oxide (AlOx thin films were grown using aluminum acetylacetonate (Al(acac3 as a source solute by mist chemical vapor deposition (mist CVD. The AlOx thin films grown at temperatures above 400°C exhibited a breakdown field (EBD over 6 MV/cm and a dielectric constant (κ over 6. It is suggested that residual OH bonding in the AlOx thin films grown at temperatures below 375°C caused degradation of the breakdown field (EBD. With FC type mist CVD, the reaction proceeded efficiently (Ea = 22–24 kJ/mol because the solvent, especially H2O, worked as a stronger oxygen source. The AlOx film could be grown at 450°C with a high deposition rate (23 nm/min and smooth surface (RMS = 1.5 nm. Moreover, the AlOx thin films grown by mist CVD had excellent practicality as insulators because the gate leakage current (IG of the oxide thin film transistor (TFT with an IGZO/AlOx stack was suppressed below 1 pA at a gate voltage (VG of 20 V.

Phylogenetic system and zoogeography of the Plecoptera.

Science.gov (United States)

Zwick, P

2000-01-01

Information about the phylogenetic relationships of Plecoptera is summarized. The few characters supporting monophyly of the order are outlined. Several characters of possible significance for the search for the closest relatives of the stoneflies are discussed, but the sister-group of the order remains unknown. Numerous characters supporting the presently recognized phylogenetic system of Plecoptera are presented, alternative classifications are discussed, and suggestions for future studies are made. Notes on zoogeography are appended. The order as such is old (Permian fossils), but phylogenetic relationships and global distribution patterns suggest that evolution of the extant suborders started with the breakup of Pangaea. There is evidence of extensive recent speciation in all parts of the world.

Effect of HMB and 2-Ox administered during pregnancy on bone properties in primiparous and multiparous minks (Neivison vison

Directory of Open Access Journals (Sweden)

Tomaszewska Ewa

2015-12-01

Full Text Available The aim of the study was to determine the mechanical and geometric properties as well as bone tissue density of long bones in primiparous and multiparous dams of minks supplemented with β-hydroxy β-methylbutyrate (HMB and/or 2-oxoketoglutarate (2-Ox during gestation. Powdered 2-Ox was given at the daily dosage of 0.4 g/kg b.w. separately or simultaneously with HMB, which was administered at the daily dosage of 0.02 g/kg b.w. The study demonstrates for the first time that administration of 2-Ox and/or HMB to dams markedly influences bone tissue density and the mechanical and geometrical properties of mother`s bones in minks. Moreover, it was demonstrated that the supplementation was more effective in the thoracic limb, which was comprehensively used in contrast to the pelvic limb. The mechanical parameters and bone tissue density significantly increased in the humerus in multiparous minks. Only such diet may provide satisfactory production results in the animals. Nutritional deficiencies occurring during pregnancies may trigger body`s own reserves to cover the bone mass increase in developing foetuses and support milk production. This can prevent regeneration of dams’ organisms, which negatively affects their reproductive performance. 2-Ox or HMB may be regarded as a protective metabolite when administered orally to minks, counteracting the negative influences of pregnancy and lactation periods on bones condition. Both simultaneous treatment with 2-Ox and HMB and their separate administration were equally effective.

Rod-like hierarchical Sn/SnOx@C nanostructures with enhanced lithium storage properties

Science.gov (United States)

Yang, Juan; Chen, Sanmei; Tang, Jingjing; Tian, Hangyu; Bai, Tao; Zhou, Xiangyang

2018-03-01

Rod-like hierarchical Sn/SnOx@C nanostructures have been designed and synthesized via calcining resorcinol-formaldehyde (RF) resin coated Sn-based metal-organic frameworks. The rod-like hierarchical Sn/SnOx@C nanostructures are made of a great number of carbon-wrapped primary Sn/SnOx nanospheres of 100-200 nm in diameter. The as-prepared hierarchical Sn/SnOx@C nanocomposite manifests a high initial reversible capacity of 1177 mAh g-1 and remains 1001 mAh g-1 after 240 cycles at a current density of 200 mA g-1. It delivers outstanding high-rate performance with a reversible capacity of 823 mAh g-1 even at a high current density of 1000 mA g-1. The enhanced electrochemical performances of the Sn/SnOx@C electrode are mainly attributed to the synergistic effect of the unique hierarchical micro/nanostructures and the protective carbon layer.

Facile solution-processed aqueous MoOx for feasible application in organic light-emitting diode

Science.gov (United States)

Zheng, Qinghong; Qu, Disui; Zhang, Yan; Li, Wanshu; Xiong, Jian; Cai, Ping; Xue, Xiaogang; Liu, Liming; Wang, Honghang; Zhang, Xiaowen

2018-05-01

Solution-processed techniques attract increasing attentions in organic electronics for their low-cost and scalable manufacturing. We demonstrate the favorite hole injection material of solution-processed aqueous MoOx (s-MoOx) with facile fabrication process and cast successful application to constructing efficient organic light-emitting diodes (OLEDs). Atomic force microscopy and X-ray photoelectron spectroscopy analysis show that s-MoOx behaves superior film morphology and non-stoichiometry with slight oxygen deficiency. With tris(8-hydroxy-quinolinato)aluminium as emitting layer, s-MoOx based OLED shows maximum luminous efficiency of 7.9 cd/A and power efficiency of 5.9 lm/W, which have been enhanced by 43.6% and 73.5%, respectively, in comparison with the counterpart using conventional vacuum thermal evaporation MoOx. Current-voltage, impedance-voltage, phase-voltage and capacitance-voltage characteristics of hole-only devices indicate that s-MoOx with two processes of "spin-coating/annealing" shows mostly enhanced hole injection capacity and thus promoting device performance. Our experiments provide an alternative approach for constructing efficient OLED with solution process.

SU-F-T-662: Feasibility Study of Fe3O4/TaOx Nano Particles as a Radiosensitizer for Radiation Therapy

Energy Technology Data Exchange (ETDEWEB)

Ahn, S [Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University (Korea, Republic of); Lee, N [School of Advanced Materials Engineering College of Engineering, Kookmin Uiniversity (Japan); Shin, S; Choi, C; Han, Y; Park, H; Choi, D; Lim, D [Samsung Medical Center, Sungkyunkwan University School of Medicine radiation oncology (Korea, Republic of)

2016-06-15

Purpose: To investigate the feasibility of using multifunctional Fe{sub 3}O{sub 4}/TaOx(core / shell) nano particles developed for CT and MRI contrast agent as dose enhancing radiosensitizers. Methods: Firstly, to verify the imaging detectability of Fe{sub 3}O{sub 4}/TaOx nano particles, in-vivo tests were conducted. Approximately 600 mg/kg of 19 nm diameter Fe{sub 3}O{sub 4}/TaOx nano particles dispersed in phosphate buffered saline(PBS) were injected to ten nude Balb/c mice through the tail vein. Difference between pre- and post-injection images was analyzed by computing the pixel histogram and correlation coefficient factor using MATLAB in the user defined ROI. Secondly, to quantify the potential therapeutic enhancement with nano materials, DER (Dose Enhancement Ratio) and number of SER (Secondary Electron Ratio) were computed using TOPAS(ver.2.0 P-03) MC simulation. Results: In CT, MRI imaging, the aorta, the blood vessel, and the liver were clearly visualized after intravenous injection of Fe{sub 3}O{sub 4}/TaOx nano particles. There was large different between pre and post-injection images of Histogram data and Coefficients of correlation factor in CT and MR are 0.006, 0.060, respectively. When 70 MeV protons were irradiated for a Gold, Tantalum, TaOx, Fe{sub 3}O{sub 4}/TaOx, Fe{sub 3}O{sub 4} nano particle, DER was 2.59, 2.41, 1.68, 1.54 and 1.36 respectively. Similarly, SER increment was 2.31, 2.15, 1.56, 1.46, and 1.27 for Gold, Tantalum, TaOx, Fe{sub 3}O{sub 4}/TaOx, Fe{sub 3}O{sub 4} nano particle, respectively. Conclusion: Fe{sub 3}O{sub 4}/TaOx nano particles have potential as a multifunctional agent which enhances the accuracy in cancer detection through visualization of developed tumor lesion and increases the therapeutic effect in proton therapy. The dose enhancement with Fe{sub 3}O{sub 4}/TaOx was estimated as half of the Gold. However, tumor targeting such as combined with magnetic field may overcome the low DER. This research was supported by the

Phylogenetic diversity and biodiversity indices on phylogenetic networks.

Science.gov (United States)

Wicke, Kristina; Fischer, Mareike

2018-04-01

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been developed as a generalization of phylogenetic trees, allowing for the representation of non-treelike evolutionary events, such as hybridization. Here, we extend the concepts of phylogenetic diversity and phylogenetic diversity indices from phylogenetic trees to phylogenetic networks. On the one hand, we consider the treelike content of a phylogenetic network, e.g. the (multi)set of phylogenetic trees displayed by a network and the so-called lowest stable ancestor tree associated with it. On the other hand, we derive the phylogenetic diversity of subsets of taxa and biodiversity indices directly from the internal structure of the network. We consider both approaches that are independent of so-called inheritance probabilities as well as approaches that explicitly incorporate these probabilities. Furthermore, we introduce our software package NetDiversity, which is implemented in Perl and allows for the calculation of all generalized measures of phylogenetic diversity and generalized phylogenetic diversity indices established in this note that are independent of inheritance probabilities. We apply our methods to a phylogenetic network representing the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), a group of species characterized by widespread hybridization. Copyright © 2018 Elsevier Inc. All rights reserved.

A role for VEGFR2 activation in endothelial responses caused by barrier disruptive OxPAPC concentrations.

Directory of Open Access Journals (Sweden)

Anna A Birukova

Full Text Available Oxidation products of 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphatidylcholine (OxPAPC differentially modulate endothelial cell (EC barrier function in a dose-dependent fashion. Vascular endothelial growth factor receptor-2 (VEGFR2 is involved in the OxPAPC-induced EC inflammatory activation. This study examined a role of VEGFR2 in barrier dysfunction caused by high concentrations of OxPAPC and evaluated downstream signaling mechanisms resulting from the effect of OxPAPC in EC from pulmonary and systemic circulation.EC monolayer permeability in human pulmonary artery endothelial cells (HPAEC and human aortic endothelial cells (HAEC was monitored by changes in transendothelial electrical resistance (TER across EC monolayers. Actin cytoskeleton was examined by immunostaining with Texas Red labeled phalloidin. Phosphorylation of myosin light chains (MLC and VE-Cadherin was examined by Western blot and immunofluorescence techniques. The role of VEGFR2 in OxPAPC-induced permeability and cytoskeletal arrangement were determined using siRNA-induced VEGFR2 knockdown.Low OxPAPC concentrations (5-20 µg/ml induced a barrier protective response in both HPAEC and HAEC, while high OxPAPC concentrations (50-100 µg/ml caused a rapid increase in permeability; actin stress fiber formation and increased MLC phosphorylation were observed as early as 30 min after treatment. VEGFR2 knockdown dramatically decreased the amount of MLC phosphorylation and stress fiber formation caused by high OxPAPC concentrations with modest effects on the amount of VE-cadherin phosphorylation at Y(731. We present evidence that activation of Rho is involved in the OxPAPC/VEGFR2 mechanism of EC permeability induced by high OxPAPC concentrations. Knockdown of VEGFR2 did not rescue the early drop in TER but prevented further development of OxPAPC-induced barrier dysfunction.This study shows that VEGFR2 is involved in the delayed phase of EC barrier dysfunction caused by high Ox

Amorphous Ni(Fe)OxHy-coated nanocone arrays self-supported on stainless steel mesh as a promising oxygen-evolving anode for large scale water splitting

Science.gov (United States)

Shen, Junyu; Wang, Mei; Zhao, Liang; Zhang, Peili; Jiang, Jian; Liu, Jinxuan

2018-06-01

The development of highly efficient, robust, and cheap water oxidation electrodes is a major challenge in constructing industrially applicable electrolyzers for large-scale production of hydrogen from water. Herein we report a hierarchical stainless steel mesh electrode which features Ni(Fe)OxHy-coated self-supported nanocone arrays. Through a facile, mild, low-cost and readily scalable two-step fabrication procedure, the electrochemically active area of the optimized electrode is enlarged by a factor of 3.1 and the specific activity is enhanced by a factor of 250 at 265 mV overpotential compared with that of a corresponding pristine stainless steel mesh electrode. Moreover, the charge-transfer resistance is reduced from 4.47 Ω for the stainless steel mesh electrode to 0.13 Ω for the Ni(Fe)OxHy-coated nanocone array stainless steel mesh electrode. As a result, the cheap and easily fabricated electrode displays 280 and 303 mV low overpotentials to achieve high current densities of 500 and 1000 mA cmgeo-2, respectively, for oxygen evolution reaction in 1 M KOH. More importantly, the electrode exhibits a good stability over 340 h of chronopotentiometric test at 50 mA cmgeo-2 and only a slight attenuation (4.2%, ∼15 mV) in catalytic activity over 82 h electrolysis at a constant current density of 500 mA cmgeo-2.

Carbon and graphene double protection strategy to improve the SnOx electrode performance anodes for lithium-ion batteries

Science.gov (United States)

Zhu, Jian; Lei, Danni; Zhang, Guanhua; Li, Qiuhong; Lu, Bingan; Wang, Taihong

2013-05-01

SnOx is a promising high-capacity anode material for lithium-ion batteries (LIBs), but it usually exhibits poor cycling stability because of its huge volume variation during the lithium uptake and release process. In this paper, SnOx carbon nanofibers (SnOx@CNFs) are firstly obtained in the form of a nonwoven mat by electrospinning followed by calcination in a 0.02 Mpa environment at 500 °C. Then we use a simple mixing method for the synthesis of SnOx@CNF@graphene (SnOx@C@G) nanocomposite. By this technique, the SnOx@CNFs can be homogeneously deposited in graphene nanosheets (GNSs). The highly scattered SnOx@C@G composite exhibits enhanced electrochemical performance as anode material for LIBs. The double protection strategy to improve the electrode performance through producing SnOx@C@G composites is versatile. In addition, the double protection strategy can be extended to the fabrication of various types of composites between metal oxides and graphene nanomaterials, possessing promising applications in catalysis, sensing, supercapacitors and fuel cells.SnOx is a promising high-capacity anode material for lithium-ion batteries (LIBs), but it usually exhibits poor cycling stability because of its huge volume variation during the lithium uptake and release process. In this paper, SnOx carbon nanofibers (SnOx@CNFs) are firstly obtained in the form of a nonwoven mat by electrospinning followed by calcination in a 0.02 Mpa environment at 500 °C. Then we use a simple mixing method for the synthesis of SnOx@CNF@graphene (SnOx@C@G) nanocomposite. By this technique, the SnOx@CNFs can be homogeneously deposited in graphene nanosheets (GNSs). The highly scattered SnOx@C@G composite exhibits enhanced electrochemical performance as anode material for LIBs. The double protection strategy to improve the electrode performance through producing SnOx@C@G composites is versatile. In addition, the double protection strategy can be extended to the fabrication of various types of

Plasma-polymerized SiOx deposition on polymer film surfaces for preparation of oxygen gas barrier polymeric films

International Nuclear Information System (INIS)

Inagaki, N.

2003-01-01

SiOx films were deposited on surfaces of three polymeric films, PET, PP, and Nylon; and their oxygen gas barrier properties were evaluated. To mitigate discrepancies between the deposited SiOx and polymer film, surface modification of polymer films was done, and how the surface modification could contribute to was discussed from the viewpoint of apparent activation energy for the permeation process. The SiOx deposition on the polymer film surfaces led to a large decrease in the oxygen permeation rate. Modification of polymer film surfaces by mans of the TMOS or Si-COOH coupling treatment in prior to the SiOx deposition was effective in decreasing the oxygen permeation rate. The cavity model is proposed as an oxygen permeation process through the SiOx-deposited Nylon film. From the proposed model, controlling the interface between the deposited SiOx film and the polymer film is emphasized to be a key factor to prepare SiOx-deposited polymer films with good oxygen gas barrier properties. (author)

Growth, Properties and Applications of Mo Ox Thin-Films Deposited by Reactive Sputtering

DEFF Research Database (Denmark)

Fernandes Cauduro, André Luis

properties of metal-oxide thin films through surface defect engineering is vital to fine-tune their optoelectronic properties, and thus also their integration in novel optoelectronic devices. In this work, MoOx thin-films with various different phases and compositions were prepared by direct-current reactive...... molecules DBP and C70 are also covered in this work. The devices show interesting characteristics for very thin layers of the as-deposited MoOx films, displaying similar device efficiencies as those of in situ prepared MoOx thin-films formed from thermal evaporation. For the annealed MoOx films......Transition metal-oxide (TMOs) thin-films are commonly used in optoelectronic devices such as in photovoltaics and light emitting diodes, using both organic, inorganic and hybrid technologies. In such devices, TMOs typically act as an interfacial layer, where its functionality is to facilitate hole...

Silicon heterojunction solar cell with passivated hole selective MoOx contact

Science.gov (United States)

Battaglia, Corsin; de Nicolás, Silvia Martín; De Wolf, Stefaan; Yin, Xingtian; Zheng, Maxwell; Ballif, Christophe; Javey, Ali

2014-03-01

We explore substoichiometric molybdenum trioxide (MoOx, x MoOx, we observe a substantial gain in photocurrent of 1.9 mA/cm2 in the ultraviolet and visible part of the solar spectrum, when compared to a p-type amorphous silicon emitter of a traditional silicon heterojunction cell. Our results emphasize the strong potential for oxides as carrier selective heterojunction partners to inorganic semiconductors.

A Built-In Self-Test Structure (BIST) for Resistive RAMs characterization: Application to bipolar OxRRAM

Science.gov (United States)

Aziza, H.; Bocquet, M.; Moreau, M.; Portal, J.-M.

2015-01-01

Resistive Random Access Memory (RRAM) is a form of nonvolatile storage that operates by changing the resistance of a specially formulated solid dielectric material [1]. Among RRAMs, oxide-based Resistive RAMs (so-called OxRRAMs) are promising candidates due their compatibility with CMOS processes and high ON/OFF resistance ratio. Common problems with OxRRAM are related to high variability in operating conditions and low yield. OxRRAM variability mainly impact ON/OFF resistance ratio. This ratio is a key parameter to determine the overall performance of an OxRRAM memory. In this context, the presented built-in structure allows collecting statistical data related to the OxRRAM memory array (ON/OFF resistance distributions) for reliability assessment of the technology.

A Forming-Free Bipolar Resistive Switching in HfOx-Based Memory with a Thin Ti Cap

Science.gov (United States)

Pang, Hua; Deng, Ning

2014-10-01

The electroforming process of Ti/HfOx stacked RRAM devices is removed via the combination of low temperature atomic layer deposition and post metal annealing. The Pt/Ti/HfOx/Pt RRAM devices show a forming-free bipolar resistive switching behavior. By x-ray photoelectron emission spectroscopy analysis, it is found that there are many oxygen vacancies and nonlattice oxygen pre-existing in the HfOx layer that play a key role in removing the electroforming process. In addition, when the thickness ratio of the Ti and HfOx layer is 1, the uniformity of the switching parameters of Pt/Ti/HfOx/Pt devices is significantly improved. The OFF/ON window maintains about 100 at the read voltage of 0.1 V.

Polysaccharide from Fuzi protects against Ox-LDL-induced calcification of human vascular smooth muscle cells by increasing autophagic activity

Science.gov (United States)

Liao, Lizhen; Zhuang, Xiaodong; Li, Weidong; Su, Qibiao; Zhao, Jie; Liu, Ying

2018-01-01

Polysaccharide from Fuzi (FPS) is a water-soluble polysaccharide isolated from the traditional Chinese herbal medicine Fuzi. It has been demonstrated to protect hepatocytes against ischemia-reperfusion injury through its potent antioxidant effects, and to attenuate starvation-induced cytotoxicity in H9c2 cells by increasing autophagic activity. In the present study, Alizarin Red S staining was used to detect mineral deposition and reverse transcription-quantitative polymerase chain reaction was used to detect the core binding factor α1 and smooth muscle 22α mRNA expression. To analyze autophagic activity, western blotting was used to detect microtubule-associated protein 1A/1B light chain 3 and nucleoporin P62 expression. In addition, green fluorescent protein-LC3 dots-per-cell was observed by fluorescence microscopy. It was demonstrated that oxidized low-density lipoprotein (Ox-LDL) could increase the calcification of human vascular smooth muscle cells (VSMCs) in a concentration-dependent manner, and that FPS treatment had a significant protective effect against Ox-LDL-induced calcification of human VSMCs. Furthermore, FPS treatment alleviated the Ox-LDL-induced downregulation of autophagic activity, and the protective effect of FPS on Ox-LDL-induced calcification was attenuated by the autophagy inhibitor 3-methyladenine. In conclusion, the present study demonstrated for the first time to the best of the authors' knowledge that FPS can protect against Ox-LDL-induced vascular calcification in human VSMCs, and that this likely occurs via the activation of autophagy. This supports the hypothesis that autophagy may be an endogenous protective mechanism counteracting vascular calcification, and that FPS may be used as a potential therapeutic for vascular calcification. PMID:29393437

Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.

Science.gov (United States)

Jansen, Robert K; Kaittanis, Charalambos; Saski, Christopher; Lee, Seung-Bum; Tomkins, Jeffrey; Alverson, Andrew J; Daniell, Henry

2006-04-09

The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses place

Phylogenetic analyses of Vitis (Vitaceae based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

Directory of Open Access Journals (Sweden)

Alverson Andrew J

2006-04-01

Full Text Available Abstract Background The Vitaceae (grape is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. Results The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade

Influence of MoOx interlayer on the maximum achievable open-circuit voltage in organic photovoltaic cells

Science.gov (United States)

Zou, Yunlong; Holmes, Russell

2013-03-01

Transition metal oxides including molybdenum oxide (MoOx) are characterized by large work functions and deep energy levels relative to the organic semiconductors used in photovoltaic cells (OPVs). These materials have been used in OPVs as interlayers between the indium-tin-oxide anode and the active layers to increase the open-circuit voltage (VOC) and power conversion efficiency. We examine the role of MoOx in determining the maximum achievable VOC in planar heterojunction OPVs based on the donor-acceptor pairing of boron subphthalocyanine chloride (SubPc) and C60. While causing minor changes in VOC at room temperature, the inclusion of MoOx significantly changes the temperature dependence of VOC. Devices containing no interlayer show a maximum VOC\\ of 1.2 V, while devices containing MoOx show no saturation in VOC, reaching a value of >1.4 V at 110 K. We propose that the MoOx-SubPc interface forms a dissociating Schottky junction that provides an additional contribution to VOC at low temperature. Separate measurements of photoluminescence confirm that excitons in SubPc can be quenched by MoOx. Charge transfer at this interface is by hole extraction from SubPc to MoOx, and this mechanism favors donors with a deep highest occupied molecular orbital (HOMO) energy level. Consistent with this expectation, the temperature dependence of VOC for devices constructed using a donor with a shallower HOMO level, e.g. copper phthalocyanine, is independent of the presence of MoOx.

Fabrication and lithium storage performance of sugar apple-shaped SiOx@C nanocomposite spheres

Science.gov (United States)

Li, Mingqi; Zeng, Ying; Ren, Yurong; Zeng, Chunmei; Gu, Jingwei; Feng, Xiaofang; He, Hongyan

2015-08-01

Nonstoichiometric SiOx is a kind of very attractive anode material for high-energy lithium-ion batteries because of a high specific capacity and facile synthesis. However, the poor electrical conductivity and unstable electrode structure of SiOx severely limit its electrochemical performance as anode in lithium-ion batteries. In this work, highly durable sugar apple-shaped SiOx@C nanocomposite spheres are fabricated to achieve significantly improved electrochemical performance. The composite is synthesized by homogenous one-pot synthesis, using ethyltriethoxysilanes (EtSi(OEt)3) and resorcinol/formaldehyde (RF) as starting materials. The morphology, composition and structure of the composite are investigated by scanning electron microscopy (SEM), transmission electron microscopy (TEM), elemental analysis (EA) and X-ray photoelectron spectroscopy (XPS). At a current density of 50 mA g-1, the sugar apple-shaped SiOx@C spheres exhibit a stable discharge capacity of about 630 mAh g-1 calculated on the total mass of both SiOx and C. At a current density of 100 mA g-1, a stable discharge capacity of about 550 mAh g-1 is obtained and the capacity has been kept up to 400 cycles. The excellent cycling performance is attributed to the homogeneous dispersion of SiOx in disordered carbon at the nanometer scale and the unique structure of the composite.

Cobalt doped CuMnOx catalysts for the preferential oxidation of carbon monoxide

Science.gov (United States)

Dey, Subhashish; Dhal, Ganesh Chandra; Mohan, Devendra; Prasad, Ram; Gupta, Rajeev Nayan

2018-05-01

Carbon monoxide (CO) is a poisonous gas, recognized as a silent killer for the 21st century. It is produced from the partial oxidation of carbon containing compounds. The catalytic oxidation of CO receives a huge attention due to its applications in different fields. In the present work, hopcalite (CuMnOx) catalysts were synthesized using a co-precipitation method for CO oxidation purposes. Also, it was doped with the cobalt by varying concentration from 1 to 5wt%. It was observed that the addition of cobalt into the CuMnOx catalyst (by the deposition-precipitation method) improved the catalytic performance for the low-temperature CO oxidation. CuMnOx catalyst doped with 3wt% of cobalt exhibited most active performance and showed the highest activity than other cobalt concentrations. Different analytical tools (i.e. XRD, FTIR, BET, XPS and SEM-EDX) were used to characterize the as-synthesized catalysts. It was expected that the introduction of cobalt will introduce new active sites into the CuMnOx catalyst that are associated with the cobalt nano-particles. The order of calcination strategies based on the activity for cobalt doped CuMnOx catalysts was observed as: Reactive calcinations (RC) > flowing air > stagnant air. Therefore, RC (4.5% CO in air) route can be recommended for the synthesis of highly active catalysts. The catalytic activity of doped CuMnOx catalysts toward CO oxidation shows a correlation among average oxidation number of Mn and the position and the nature of the doped cobalt cation.

Unrealistic phylogenetic trees may improve phylogenetic footprinting.

Science.gov (United States)

Nettling, Martin; Treutler, Hendrik; Cerquides, Jesus; Grosse, Ivo

2017-06-01

The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily. Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting. The proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo. : martin.nettling@informatik.uni-halle.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Electrodeposited ultrafine TaOx/CB catalysts for PEFC cathode application: Their oxygen reduction reaction kinetics

KAUST Repository

Seo, Jeongsuk

2014-12-01

Ultrafine TaOx nanoparticles were electrodeposited on carbon black (CB) powder in a nonaqueous Ta complex solution at room temperature, and the resultant TaOx/CB catalysts were assessed as oxygen reduction reaction (ORR) electrocatalysts for polymer electrolyte fuel cell (PEFC) cathodes. The Ta electrodeposition process was scaled up using a newly designed working electrode containing a CB dense layer, without introducing any binder such as the ionomer Nafion in the electrode for electrodeposition. The electrodeposited TaOx/CB powders were removed from the deposition electrode and subsequent H2 treatment at varying temperatures between 523 and 1073 K was attempted to increase the ORR performance. The TaOx/CB samples were characterized by SEM, STEM, XPS, and EELS measurements. XPS and EELS results indicated the reduced nature of the Ta species caused by the high-temperature treatment in H2, while STEM images clearly revealed that the TaOx particles aggregated as the treatment temperature increased. When the TaOx/CB catalyst, which was treated at 873 K for 2 h, was deposited on a glassy carbon substrate with Nafion ionomer, it resulted in the highest activity among the samples investigated, giving an onset potential of 0.95 VRHE at -2 μA cm-2 in a 0.1 M H2SO4 solution. Moreover, the long-term stability test with 10,000 cycles of the voltammetry only led to a 6% loss in the ORR currents, demonstrating the high stability of the TaOx/CB catalysts. Kinetic analysis by R(R)DE indicated that the four-electron transfer pathway in the ORR process was dominant for this TaOx/CB catalyst, and Tafel plots showed a slope corresponding to a one-electron reaction for the rate-determining step.

Electrodeposited ultrafine TaOx/CB catalysts for PEFC cathode application: Their oxygen reduction reaction kinetics

KAUST Repository

Seo, Jeongsuk; Anjum, Dalaver H.; Takanabe, Kazuhiro; Kubota, Jun; Domen, Kazunari

2014-01-01

Ultrafine TaOx nanoparticles were electrodeposited on carbon black (CB) powder in a nonaqueous Ta complex solution at room temperature, and the resultant TaOx/CB catalysts were assessed as oxygen reduction reaction (ORR) electrocatalysts for polymer electrolyte fuel cell (PEFC) cathodes. The Ta electrodeposition process was scaled up using a newly designed working electrode containing a CB dense layer, without introducing any binder such as the ionomer Nafion in the electrode for electrodeposition. The electrodeposited TaOx/CB powders were removed from the deposition electrode and subsequent H2 treatment at varying temperatures between 523 and 1073 K was attempted to increase the ORR performance. The TaOx/CB samples were characterized by SEM, STEM, XPS, and EELS measurements. XPS and EELS results indicated the reduced nature of the Ta species caused by the high-temperature treatment in H2, while STEM images clearly revealed that the TaOx particles aggregated as the treatment temperature increased. When the TaOx/CB catalyst, which was treated at 873 K for 2 h, was deposited on a glassy carbon substrate with Nafion ionomer, it resulted in the highest activity among the samples investigated, giving an onset potential of 0.95 VRHE at -2 μA cm-2 in a 0.1 M H2SO4 solution. Moreover, the long-term stability test with 10,000 cycles of the voltammetry only led to a 6% loss in the ORR currents, demonstrating the high stability of the TaOx/CB catalysts. Kinetic analysis by R(R)DE indicated that the four-electron transfer pathway in the ORR process was dominant for this TaOx/CB catalyst, and Tafel plots showed a slope corresponding to a one-electron reaction for the rate-determining step.

Modeling of Oxidized PTH (oxPTH) and Non-oxidized PTH (n-oxPTH) Receptor Binding and Relationship of Oxidized to Non-Oxidized PTH in Children with Chronic Renal Failure, Adult Patients on Hemodialysis and Kidney Transplant Recipients

DEFF Research Database (Denmark)

Hocher, Berthold; Oberthür, Dominik; Slowinski, Torsten

2013-01-01

Background: The biological properties of oxidized and non-oxidized PTH are substantially different. Oxidized PTH (oxPTH) loses its PTH receptor-stimulating properties, whereas non-oxidized PTH (n-oxPTH) is a full agonist of the receptor. This was described in more than 20 well published studies i......PTH measures describes most likely oxidative stress in patients with renal failure rather than the PTH hormone status. This, however, needs to be demonstrated in further clinical studies. © 2013 S. Karger AG, Basel......., we performed modeling of the interaction of either oxPTH or n-oxPTH with the PTH receptor using biophysical structure approaches. Results: The children had the highest mean as well as maximum n-oxPTH concentrations as compared to adult patients (both patients on dialysis as well as kidney transplant......-oxPTH. This indicated that PTH oxidation may induce refolding of PTH and hence alters PTH-PTH receptor interaction via oxidation induced three-dimensional structure alteration of PTH. Conclusion: A huge proportion of circulating PTH measured by current state-of-the-art assay systems is oxidized and thus...

Heterogeneous catalytic ozonation of ciprofloxacin in water with carbon nanotube supported manganese oxides as catalyst

Energy Technology Data Exchange (ETDEWEB)

Sui, Minghao, E-mail: suiminghao.sui@gmail.com [State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092 (China); Xing, Sichu; Sheng, Li; Huang, Shuhang; Guo, Hongguang [State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092 (China)

2012-08-15

Highlights: Black-Right-Pointing-Pointer Ciprofloxacin in water was degraded by heterogeneous catalytic ozonation. Black-Right-Pointing-Pointer MnOx were supported on MWCNTs to serve as catalyst for ozonation. Black-Right-Pointing-Pointer MnOx/MWCNT exhibited highly catalytic activity on ozonation of ciprofloxacin in water. Black-Right-Pointing-Pointer MnOx/MWCNT resulted in effective antibacterial activity inhibition on ciprofloxacin. Black-Right-Pointing-Pointer MnOx/MWCNT promoted the generation of hydroxyl radicals. - Abstract: Carbon nanotube-supported manganese oxides (MnOx/MWCNT) were used as catalysts to assist ozone in degrading ciprofloxacin in water. Manganese oxides were successfully loaded on multi-walled carbon nanotube surfaces by simply impregnating the carbon nanotube with permanganate solution. The catalytic activities of MnOx/MWCNT in ciprofloxacin ozonation, including degradation, mineralization effectiveness, and antibacterial activity change, were investigated. The presence of MnOx/MWCNT significantly elevated the degradation and mineralization efficiency of ozone on ciprofloxacin. The microbiological assay with a reference Escherichia coli strain indicated that ozonation with MnOx/MWCNT results in more effective antibacterial activity inhibition of ciprofloxacin than that in ozonation alone. The effects of catalyst dose, initial ciprofloxacin concentration, and initial pH conditions on ciprofloxacin ozonation with MnOx/MWCNT were surveyed. Electron spin resonance trapping was applied to assess the role of MnOx/MWCNT in generating hydroxyl radicals (HO{center_dot}) during ozonation. Stronger 5,5-dimethyl-1-pyrroline-N-oxide-OH signals were observed in the ozonation with MnOx/MWCNT compared with those in ozonation alone, indicating that MnOx/MWCNT promoted the generation of hydroxyl radicals. The degradation of ciprofloxacin was studied in drinking water and wastewater process samples to gauge the potential effects of water background matrix on

Phylogenetic trees

OpenAIRE

Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

2016-01-01

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

A Permselective CeOx Coating Improves the Stability of Oxygen Evolution Electrocatalysts

KAUST Repository

Obata, Keisuke

2017-12-05

Highly active NiFeOx electrocatalysts for the oxygen evolution reaction (OER) suffer gradual deactivation with time due to the loss of Fe species from the active sites into solution during catalysis. Here, we describe the anodic deposition of a CeOx layer that prevents the loss of such Fe species from the OER catalysts, achieving a highly stable performance. The CeOx layer does not affect the OER activity of the catalyst underneath but exhibits unique permselectivity, allowing the permeation of OH- and O2 through while preventing the diffusion of redox ions through the layer to function as a selective O2-evolving electrode. The use of such permselective protective layer provides a new strategy for improving the durability of electrocatalysts.

A Permselective CeOx Coating Improves the Stability of Oxygen Evolution Electrocatalysts

KAUST Repository

Obata, Keisuke; Takanabe, Kazuhiro

2017-01-01

Highly active NiFeOx electrocatalysts for the oxygen evolution reaction (OER) suffer gradual deactivation with time due to the loss of Fe species from the active sites into solution during catalysis. Here, we describe the anodic deposition of a CeOx layer that prevents the loss of such Fe species from the OER catalysts, achieving a highly stable performance. The CeOx layer does not affect the OER activity of the catalyst underneath but exhibits unique permselectivity, allowing the permeation of OH- and O2 through while preventing the diffusion of redox ions through the layer to function as a selective O2-evolving electrode. The use of such permselective protective layer provides a new strategy for improving the durability of electrocatalysts.

Fabrication and current–voltage characteristics of NiOx/ZnO based MIIM tunnel diode

Energy Technology Data Exchange (ETDEWEB)

Singh, Aparajita, E-mail: asing044@fiu.edu [BioMEMS and Microsystems Laboratory, Department of Electrical and Computer Engineering, Florida International University, Miami, Florida 33174, United States of America (United States); Ratnadurai, Rudraskandan [Global Foundaries, Malta, New York 12020 (United States); Kumar, Rajesh [BioMEMS and Microsystems Laboratory, Department of Electrical and Computer Engineering, Florida International University, Miami, Florida 33174 (United States); Department of Physics, Panjab University, Chandigarh 160014 (India); Krishnan, Subramanian [BioMEMS and Microsystems Laboratory, Department of Electrical and Computer Engineering, Florida International University, Miami, Florida 33174 (United States); Emirov, Yusuf [Advanced Materials Engineering Research Institute, Florida International University, Miami, Florida 33174 (United States); Bhansali, Shekhar [BioMEMS and Microsystems Laboratory, Department of Electrical and Computer Engineering, Florida International University, Miami, Florida 33174 (United States)

2015-04-15

Highlights: • Fabrication of single and bilayer tunnel diodes by sputter deposition. • Current–voltage characteristics study. • Enhanced asymmetry and non-linearity. • Study of tunneling mechanism. - Abstract: Enhanced asymmetric and non-linear characteristics of Ni–NiOx based MIM diode has been reported by the addition of a second insulator layer ZnO to form MIIM configuration. These properties are required for applications like energy-harvesting devices, terahertz electronics, macro electronics, etc. In this work, single insulator layer Ni–NiOx–Cr and double insulator Ni–NiOx–ZnO–Cr tunnel diodes were fabricated and their I–V characteristics were studied. A significant increase by one order of magnitude in asymmetry has been observed in case of bilayer NiOx/ZnO dielectric configuration at low voltages. The sensitivity of the NiOx and NiOx/ZnO dielectric configuration in MIM stack was 11 V{sup −1} and 16 V{sup −1}. The improved performance of the bilayer insulator diode is due to the second insulator which enables resonant tunneling or step-tunneling. Resonant tunneling was found to be dominant through trap assisted tunneling in the NiOx/ZnO diode.

SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences.

Science.gov (United States)

Ropiquet, Anne; Li, Blaise; Hassanin, Alexandre

2009-09-01

Supermatrix and supertree are two methods for constructing a phylogenetic tree by using multiple data sets. However, these methods are not a panacea, as conflicting signals between data sets can lead to misinterpret the evolutionary history of taxa. In particular, the supermatrix approach is expected to be misleading if the species-tree signal is not dominant after the combination of the data sets. Moreover, most current supertree methods suffer from two limitations: (i) they ignore or misinterpret secondary (non-dominant) phylogenetic signals of the different data sets; and (ii) the logical basis of node robustness measures is unclear. To overcome these limitations, we propose a new approach, called SuperTRI, which is based on the branch support analyses of the independent data sets, and where the reliability of the nodes is assessed using three measures: the supertree Bootstrap percentage and two other values calculated from the separate analyses: the mean branch support (mean Bootstrap percentage or mean posterior probability) and the reproducibility index. The SuperTRI approach is tested on a data matrix including seven genes for 82 taxa of the family Bovidae (Mammalia, Ruminantia), and the results are compared to those found with the supermatrix approach. The phylogenetic analyses of the supermatrix and independent data sets were done using four methods of tree reconstruction: Bayesian inference, maximum likelihood, and unweighted and weighted maximum parsimony. The results indicate, firstly, that the SuperTRI approach shows less sensitivity to the four phylogenetic methods, secondly, that it is more accurate to interpret the relationships among taxa, and thirdly, that interesting conclusions on introgression and radiation can be drawn from the comparisons between SuperTRI and supermatrix analyses.

Sputter Deposited TiOx Thin-Films as Electron Transport Layers in Organic Solar Cells

DEFF Research Database (Denmark)

Mirsafaei, Mina; Bomholt Jensen, Pia; Lakhotiya, Harish

transparency and favorable energy-level alignment with many commonly used electron-acceptor materials. There are several methods available for fabricating compact TiOx thin-films for use in organic solar cells, including sol-gel solution processing, spray pyrolysis and atomic-layer deposition; however...... of around 7%, by incorporating sputter deposited TiOx thin-films as electron-transport and exciton-blocking layers. In the work, we report on the effect of different TiOx deposition temperatures and thicknesses on the organic-solar-cell device performance. Besides optical characterization, AFM and XRD...... analyses are performed to characterize the morphology and crystal structure of the films, and external quantum efficiency measurements are employed to shed further light on the device performance. Our study presents a novel method for implementation of TiOx thin-films as electron-transport layer in organic...

Increased expression of OX40 is associated with progressive disease in patients with HTLV-1-associated myelopathy/tropical spastic paraparesis.

Science.gov (United States)

Saito, Mineki; Tanaka, Reiko; Arishima, Shiho; Matsuzaki, Toshio; Ishihara, Satoshi; Tokashiki, Takashi; Ohya, Yusuke; Takashima, Hiroshi; Umehara, Fujio; Izumo, Shuji; Tanaka, Yuetsu

2013-05-07

OX40 is a member of the tumor necrosis factor receptor family that is expressed primarily on activated CD4+ T cells and promotes the development of effector and memory T cells. Although OX40 has been reported to be a target gene of human T-cell leukemia virus type-1 (HTLV-1) viral transactivator Tax and is overexpressed in vivo in adult T-cell leukemia (ATL) cells, an association between OX40 and HTLV-1-associated inflammatory disorders, such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), has not yet been established. Moreover, because abrogation of OX40 signals ameliorates chronic inflammation in animal models of autoimmune disease, novel monoclonal antibodies against OX40 may offer a potential treatment for HTLV-1-associated diseases such as ATL and HAM/TSP. In this study, we showed that OX40 was specifically expressed in CD4+ T cells naturally infected with HTLV-1 that have the potential to produce pro-inflammatory cytokines along with Tax expression. We also showed that OX40 was overexpressed in spinal cord infiltrating mononuclear cells in a clinically progressive HAM/TSP patient with a short duration of illness. The levels of the soluble form of OX40 (sOX40) in the cerebrospinal fluid (CSF) from chronic progressive HAM/TSP patients or from patients with other inflammatory neurological diseases (OINDs) were not different. In contrast, sOX40 levels in the CSF of rapidly progressing HAM/TSP patients were higher than those in the CSF from patients with OINDs, and these patients showed higher sOX40 levels in the CSF than in the plasma. When our newly produced monoclonal antibody against OX40 was added to peripheral blood mononuclear cells in culture, HTLV-1-infected T cells were specifically removed by a mechanism that depends on antibody-dependent cellular cytotoxicity. Our study identified OX40 as a key molecule and biomarker for rapid progression of HAM/TSP. Furthermore, blocking OX40 may have potential in therapeutic intervention for

Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life.

Science.gov (United States)

Puigbò, Pere; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

Genome-wide comparison of phylogenetic trees is becoming an increasingly common approach in evolutionary genomics, and a variety of approaches for such comparison have been developed. In this article, we present several methods for comparative analysis of large numbers of phylogenetic trees. To compare phylogenetic trees taking into account the bootstrap support for each internal branch, the Boot-Split Distance (BSD) method is introduced as an extension of the previously developed Split Distance method for tree comparison. The BSD method implements the straightforward idea that comparison of phylogenetic trees can be made more robust by treating tree splits differentially depending on the bootstrap support. Approaches are also introduced for detecting tree-like and net-like evolutionary trends in the phylogenetic Forest of Life (FOL), i.e., the entirety of the phylogenetic trees for conserved genes of prokaryotes. The principal method employed for this purpose includes mapping quartets of species onto trees to calculate the support of each quartet topology and so to quantify the tree and net contributions to the distances between species. We describe the application of these methods to analyze the FOL and the results obtained with these methods. These results support the concept of the Tree of Life (TOL) as a central evolutionary trend in the FOL as opposed to the traditional view of the TOL as a "species tree."

Preparation and characterization of alumina supported nickel-oxalate catalyst for the hydrodeoxygenation of oleic acid into normal and iso-octadecane biofuel

International Nuclear Information System (INIS)

Ayodele, O.B.; Togunwa, Olayinka S.; Abbas, Hazzim F.; Daud, Wan Mohd Ashri Wan

2014-01-01

Highlights: • Preparation of nickel oxalate complex as catalyst precursor. • Incorporation of nickel oxalate complex into alumina support. • Characterization of the alumina supported nickel oxalate catalyst. • Hydrodeoxygenation of oleic acid with nickel oxalate catalyst. • Nickel oxalate catalyst reusability studies. - Abstract: In this study, nickel II oxalate complex (NiOx) was prepared by functionalization of nickel with oxalic acid (OxA) and incorporated into Al 2 O 3 to synthesize alumina supported nickel oxalate (NiOx/Al 2 O 3 ) catalyst for the hydrodeoxygenation (HDO) of oleic acid (OA) into biofuel. The synthesized NiOx/Al 2 O 3 was characterized and the X-ray fluorescence and elemental dispersive X-ray results showed that NiOx was successfully incorporated into the structure of Al 2 O 3 . The X-ray diffraction and Raman spectroscopy results confirmed that highly dispersed Ni species are present in the NiOx/Al 2 O 3 due to the functionalization with OxA. The catalytic activity of the NiOx/Al 2 O 3 on the HDO of OA produced a mixture of 21% iso-C18 and 72% n-C18 at a 360 °C, 20 bar, 30 mg NiOx/Al 2 O 3 loading pressure and gas flow rate of 100 mL/min. The presence of i-C 18 was ascribed to the OxA functionalization which increased the acidity of NiOx/Al 2 O 3 . The NiOx/Al 2 O 3 reusability study showed consistent HDO ability after 5 runs. These results are promising for further research into biofuel production for commercialization

Selective Hydrogenation of m-Dinitrobenzene to m-Nitroaniline over Ru-SnOx/Al2O3 Catalyst

Directory of Open Access Journals (Sweden)

Haiyang Cheng

2014-07-01

Full Text Available Series catalysts of Ru-SnOx/Al2O3 with varying SnOx loading of 0–3 wt% were prepared, and their catalytic activity and selectivity have been discussed and compared for the selective hydrogenation of m-dinitrobenzene (m-DNB to m-nitroaniline (m-NAN. The Ru-SnOx/Al2O3 catalysts were characterized by X-ray powder diffraction (XRD, X-ray photoelectron spectroscopy (XPS, transmission electron microscopy (TEM and hydrogen temperature-programmed reduction (H2-TPR and desorption (H2-TPD. Under the modification of SnOx, the reaction activity increased obviously, and the best selectivity to m-NAN reached above 97% at the complete conversion of m-DNB. With the increasing of the SnOx loading, the amount of active hydrogen adsorption on the surface of the catalyst increased according to the H2-TPD analysis, and the electron transferred from Ru to SnOx species, as determined by XPS, inducing an electron-deficient Ru, which is a benefit for the absorption of the nitro group. Therefore, the reaction rate and product selectivity were greatly enhanced. Moreover, the Ru-SnOx/Al2O3 catalyst presented high stability: it could be recycled four times without any loss in activity and selectivity.

Effect of TiOx compact layer with varied components on the performance of dye-sensitized solar cells

Energy Technology Data Exchange (ETDEWEB)

Fang, Yanling; Ai, Xianglong; Wang, Xiaomeng; Wang, Qi; Huang, Jianguo; Wu, Tao, E-mail: tao_wu@zju.edu.cn

2014-05-01

Graphical abstract: - Highlights: • TiOx compact layers with varied components are deposited by sputtering deposition. • TiOx compact layers suppressed the recombination at the FTO glass/ electrolyte interface effectively. • 20 nm-TiOx compact layer with the lowest x value (named T1) gave the highest charge transfer or transport and reduced recombination most. • Lower value of x in TiOx showed slightly better transmittance. • Lower value of x in TiOx reveals higher conductivity and better charge transfer from the porous TiO{sub 2} to the substrate. - Abstract: In this study, approximately 20 nm thick compact layers of TiOx with varied components are deposited by physical vapor deposition. The performance of these layers in solar cells is investigated. The TiOx compact layers consist of T1 (with Ti{sup 0}, Ti{sup 2+}, Ti{sup 3+}, and Ti{sup 4+}), T2 (with Ti{sup 3+} and Ti{sup 4+}), and T3 (with Ti{sup 4+}). Results show that the optimum compact layer is T1, which exhibits an approximately 61% enhancement in energy conversion efficiency compared with the bare cell. Mott–Schottky plots indicate that the carrier concentration decreases and the flatband becomes less negative with decreasing x, which consequently increases the likelihood of charge transfer from the nanoporous TiO{sub 2} to the TiOx compact layers. Furthermore, a decrease in the x value of TiOx results in lower resistance. Voltage decay and electrical impedance spectrum (EIS) show that the electron-carrier lifetime and charge recombination reduction are improved the most by T1. Consequently, TiOx with smaller x works better as a compact layer. However, a solar cell with T2 shows weak enhancement of photovoltaic performance. Cyclic voltammetry and EIS illustrate that the low recombination blocking and high resistance of T2 may be a result of its large pore size and weak adhesion to fluorine-doped tin oxide glass.

MicroRNAs expression in ox-LDL treated HUVECs: MiR-365 modulates apoptosis and Bcl-2 expression

Energy Technology Data Exchange (ETDEWEB)

Qin, Bing; Xiao, Bo [Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008 (China); Liang, Desheng [State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410078 (China); Xia, Jian; Li, Ye [Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008 (China); Yang, Huan, E-mail: yangh69@yahoo.cn [Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008 (China)

2011-06-24

Highlights: {yields} We evaluated the role of miRNAs in ox-LDL induced apoptosis in ECs. {yields} We found 4 up-regulated and 11 down-regulated miRNAs in apoptotic ECs. {yields} Target genes of the dysregulated miRNAs regulate ECs apoptosis and atherosclerosis. {yields} MiR-365 promotes ECs apoptosis via suppressing Bcl-2 expression. {yields} MiR-365 inhibitor alleviates ECs apoptosis induced by ox-LDL. -- Abstract: Endothelial cells (ECs) apoptosis induced by oxidized low-density lipoprotein (ox-LDL) is thought to play a critical role in atherosclerosis. MicroRNAs (miRNAs) are a class of noncoding RNAs that posttranscriptionally regulate the expression of genes involved in diverse cell functions, including differentiation, growth, proliferation, and apoptosis. However, whether miRNAs are associated with ox-LDL induced apoptosis and their effect on ECs is still unknown. Therefore, this study evaluated potential miRNAs and their involvement in ECs apoptosis in response to ox-LDL stimulation. Microarray and qRT-PCR analysis performed on human umbilical vein endothelial cells (HUVECs) exposed to ox-LDL identified 15 differentially expressed (4 up- and 11 down-regulated) miRNAs. Web-based query tools were utilized to predict the target genes of the differentially expressed miRNAs, and the potential target genes were classified into different function categories with the gene ontology (GO) term and KEGG pathway annotation. In particular, bioinformatics analysis suggested that anti-apoptotic protein B-cell CLL/lymphoma 2 (Bcl-2) is a target gene of miR-365, an apoptomir up-regulated by ox-LDL stimulation in HUVECs. We further showed that transfection of miR-365 inhibitor partly restored Bcl-2 expression at both mRNA and protein levels, leading to a reduction of ox-LDL-mediated apoptosis in HUVECs. Taken together, our findings indicate that miRNAs participate in ox-LDL-mediated apoptosis in HUVECs. MiR-365 potentiates ox-LDL-induced ECs apoptosis by regulating the

Effect of Ti Doping to Maintain Structural Disorder in InOx-Based Thin-Film Transistors Fabricated by RF Magnetron Sputtering

Science.gov (United States)

Aikawa, Shinya

2017-12-01

The effect of Ti doping in an indium oxide (InOx)-based semiconductor is investigated for the thin-film transistor (TFT) property and crystal structure of the film. InOx and Ti-doped InOx (InTiOx) films deposited by RF magnetron sputtering under the same O2 partial pressure conditions were systematically compared. The TFT behavior of the InOx showed higher conductivity than that of the InTiOx and was drastically changed to metallic conduction after annealing at 150 °C. Under the annealing conditions when the electrical transition to the metallic behavior occurred, the InOx film was crystallized. The X-ray diffraction analysis revealed that the shrinkage of the In2O3 unit cell is pronounced in the case of InOx films. Thus, Ti dopants may play the role as a suppressor for shrinkage of the unit cell, i.e. maintaining neighboring In-In distances, in addition to suppression of oxygen vacancies. The In-In distance, which is related to the overlapping of In 5 s orbitals, is considered to be one of the key factor for which InOx-based materials are utilized as conducting films or semiconducting channels.

Charge storage and tunneling mechanism of Ni nanocrystals embedded HfOx film

Science.gov (United States)

Zhu, H. X.; Zhang, T.; Wang, R. X.; Zhang, Y. Y.; Li, L. T.; Qiu, X. Y.

2016-05-01

A nano-floating gate memory structure based on Ni nanocrystals (NCs) embedded HfOx film is deposited by means of radio-frequency magnetron sputtering. Microstructure investigations reveal that self-organized Ni-NCs with diameters of 4-8 nm are well dispersed in amorphous HfOx matrix. Pt/Ni-NCs embedded HfOx/Si/Ag capacitor structures exhibit voltage-dependent capacitance-voltage hysteresis, and a maximum flat-band voltage shift of 1.5 V, corresponding to a charge storage density of 6.0 × 1012 electrons/cm2, is achieved. These capacitor memory cells exhibit good endurance characteristic up to 4 × 104 cycles and excellent retention performance of 105 s, fulfilling the requirements of next generation non-volatile memory devices. Schottky tunneling is proven to be responsible for electrons tunneling in these capacitors.

Gibberellin 20-oxidase gene OsGA20ox3 regulates plant stature and disease development in rice.

Science.gov (United States)

Qin, Xue; Liu, Jun Hua; Zhao, Wen Sheng; Chen, Xu Jun; Guo, Ze Jian; Peng, You Liang

2013-02-01

Gibberellin (GA) 20-oxidase (GA20ox) catalyses consecutive steps of oxidation in the late part of the GA biosynthetic pathway. A T-DNA insertion mutant (17S-14) in rice, with an elongated phenotype, was isolated. Analysis of the flanking sequences of the T-DNA insertion site revealed that an incomplete T-DNA integration resulted in enhanced constitutively expression of downstream OsGA20ox3 in the mutant. The accumulation of bioactive GA(1) and GA(4) were increased in the mutant in comparison with the wild-type plant. Transgenic plants overexpressing OsGA20ox3 showed phenotypes similar to those of the 17S-14 mutant, and the RNA interference (RNAi) lines that had decreased OsGA20ox3 expression exhibited a semidwarf phenotype. Expression of OsGA20ox3 was detected in the leaves and roots of young seedlings, immature panicles, anthers, and pollens, based on β-glucuronidase (GUS) activity staining in transgenic plants expressing the OsGA20ox3 promoter fused to the GUS gene. The OsGA20ox3 RNAi lines showed enhanced resistance against rice pathogens Magnaporthe oryzae (causing rice blast) and Xanthomonas oryzae pv. oryzae (causing bacterial blight) and increased expression of defense-related genes. Conversely, OsGA20ox3-overexpressing plants were more susceptible to these pathogens comparing with the wild-type plants. The susceptibility of wild-type plants to X. oryzae pv. oryzae was increased by exogenous application of GA(3) and decreased by S-3307 treatment. Together, the results provide direct evidence for a critical role of OsGA20ox3 in regulating not only plant stature but also disease resistance in rice.

Mechanism of internal browning of pineapple: The role of gibberellins catabolism gene (AcGA2ox) and GAs

Science.gov (United States)

Zhang, Qin; Rao, Xiuwen; Zhang, Lubin; He, Congcong; Yang, Fang; Zhu, Shijiang

2016-01-01

Internal browning (IB), a physiological disorder (PD) that causes severe losses in harvested pineapple, can be induced by exogenous gibberellins (GAs). Over the years, studies have focused on roles of Gibberellin 2-oxidase (GA2oxs), the major GAs catabolic enzyme in plants, in the regulation of changes in morphology or biomass. However, whether GA2oxs could regulate PD has not been reported. Here, a full-length AcGA2ox cDNA was isolated from pineapple, with the putative protein sharing 23.59% to 72.92% identity with GA2oxs from five other plants. Pineapples stored at 5 °C stayed intact, while those stored at 20 °C showed severe IB. Storage at 5 °C enhanced AcGA2ox expression and decreased levels of a GAs (GA4) ‘compared with storage at 20 °C. However, at 20 °C, exogenous application of abscisic acid (ABA) significantly suppressed IB. ABA simultaneously upregulated AcGA2ox and reduced GA4. Ectopic expression of AcGA2ox in Arabidopsis resulted in reduced GA4, lower seed germination, and shorter hypocotyls and roots, all of which were restored by exogenous GA4/7. Moreover, in pineapple, GA4/7 upregulated polyphenol oxidase, while storage at 5 °C and ABA downregulated it. These results strongly suggest the involvement of AcGA2ox in regulation of GAs levels and a role of AcGA2ox in regulating IB. PMID:27982026

NF-kB activity-dependent P-selectin involved in ox-LDL-induced foam cell formation in U937 cell

International Nuclear Information System (INIS)

Wang, Yi; Wang, Xiang; Sun, Minghui; Zhang, Zhenyu; Cao, Heng; Chen, Xiaoqing

2011-01-01

Highlights: → Ox-LDL induced foam cell formation in the human U937 promonocytic cell line in a dose- and time-dependent manner. → Ox-LDL induced expression of P-selectin through degradation of IkBa and augment of NF-kB activity and protein level during macrophage-derived foam cell formation. → P-selectin and NF-kB may be identified as pivotal regulators of ox-LDL-induced foam cell formation. → Therapy based on the inhibition of P-selectin and NF-kB may complement conventional treatments to prevent atherosclerosis. -- Abstract: Oxidized low-density lipoprotein (ox-LDL) plays a critical role in regulation of atherosclerosis. However, little is known about the role of Nuclear factor kB (NF-kB) activity-dependent P-selectin in ox-LDL-induced foam cell formation during atherosclerosis. In this study, we first investigated ox-LDL induced foam cell formation in the human U937 promonocytic cell line in a dose- and time-dependent manner. Treatment of U937 cells with ox-LDL increased lipid accumulation as well as intracellular cholesterol content. Next, a comparative analysis of gene expression profiling using cDNA microarray and Real-time-PCR indicated that ox-LDL exposure induced, in three treated groups, an extremely marked increase in the mRNA level of P-selectin. Protein levels of P-selectin and its upstream regulators IkBa and NF-kB showed that NF-kB pathway is involved in the ox-LDL-induced foam cell formation. Finally, overexpression of NF-kB significantly accelerated, whereas, inhibition of NF-kB with siRNA remarkably attenuated ox-LDL-induced macrophage-derived foam cell formation. It was concluded that the activity of NF-kB is augmented during macrophage-derived foam cell formation. Activation of NF-kB increased, whereas, inhibition of NF-kB decreased ox-LDL-induced P-selectin expression and lipid accumulation in macrophages, suggesting ox-LDL induced expression of P-selectin through degradation of IkBa and activation of NF-kB in the regulation of foam

NF-kB activity-dependent P-selectin involved in ox-LDL-induced foam cell formation in U937 cell

Energy Technology Data Exchange (ETDEWEB)

Wang, Yi, E-mail: wangyi2004a@126.com [Department of Cardiology, Shanghai First People' s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080 (China); Wang, Xiang; Sun, Minghui; Zhang, Zhenyu; Cao, Heng; Chen, Xiaoqing [Department of Cardiology, Shanghai First People' s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200080 (China)

2011-08-05

Highlights: {yields} Ox-LDL induced foam cell formation in the human U937 promonocytic cell line in a dose- and time-dependent manner. {yields} Ox-LDL induced expression of P-selectin through degradation of IkBa and augment of NF-kB activity and protein level during macrophage-derived foam cell formation. {yields} P-selectin and NF-kB may be identified as pivotal regulators of ox-LDL-induced foam cell formation. {yields} Therapy based on the inhibition of P-selectin and NF-kB may complement conventional treatments to prevent atherosclerosis. -- Abstract: Oxidized low-density lipoprotein (ox-LDL) plays a critical role in regulation of atherosclerosis. However, little is known about the role of Nuclear factor kB (NF-kB) activity-dependent P-selectin in ox-LDL-induced foam cell formation during atherosclerosis. In this study, we first investigated ox-LDL induced foam cell formation in the human U937 promonocytic cell line in a dose- and time-dependent manner. Treatment of U937 cells with ox-LDL increased lipid accumulation as well as intracellular cholesterol content. Next, a comparative analysis of gene expression profiling using cDNA microarray and Real-time-PCR indicated that ox-LDL exposure induced, in three treated groups, an extremely marked increase in the mRNA level of P-selectin. Protein levels of P-selectin and its upstream regulators IkBa and NF-kB showed that NF-kB pathway is involved in the ox-LDL-induced foam cell formation. Finally, overexpression of NF-kB significantly accelerated, whereas, inhibition of NF-kB with siRNA remarkably attenuated ox-LDL-induced macrophage-derived foam cell formation. It was concluded that the activity of NF-kB is augmented during macrophage-derived foam cell formation. Activation of NF-kB increased, whereas, inhibition of NF-kB decreased ox-LDL-induced P-selectin expression and lipid accumulation in macrophages, suggesting ox-LDL induced expression of P-selectin through degradation of IkBa and activation of NF-kB in the

High-performance flexible resistive memory devices based on Al2O3:GeOx composite

Science.gov (United States)

Behera, Bhagaban; Maity, Sarmistha; Katiyar, Ajit K.; Das, Samaresh

2018-05-01

In this study a resistive switching random access memory device using Al2O3:GeOx composite thin films on flexible substrate is presented. A bipolar switching characteristic was observed for the co-sputter deposited Al2O3:GeOx composite thin films. Al/Al2O3:GeOx/ITO/PET memory device shows excellent ON/OFF ratio (∼104) and endurance (>500 cycles). GeOx nanocrystals embedded in the Al2O3 matrix have been found to play a significant role in enhancing the switching characteristics by facilitating oxygen vacancy formation. Mechanical endurance was retained even after several bending. The conduction mechanism of the device was qualitatively discussed by considering Ohmic and SCLC conduction. This flexible device is a potential candidate for next-generation electronics device.

OsGA2ox5, a Gibberellin Metabolism Enzyme, Is Involved in Plant Growth, the Root Gravity Response and Salt Stress

Science.gov (United States)

Cai, Weiming; Shan, Chi

Gibberellin (GA) 2-oxidases play an important role in the GA catabolic pathway through 2b-hydroxylation. There are two classes of GA2oxs, i.e., a larger class of C19-GA2oxs and a smaller class of C20-GA2oxs. In this study, the gene encoding a GA 2-oxidase of rice, Oryza sativa GA 2-oxidase 5 (OsGA2ox5), was cloned and characterized. BLASTP analysis showed that OsGA2ox5 belongs to the C20-GA2oxs subfamily, a subfamily of GA2oxs acting on C20-GAs (GA12, GA53). Subcellular localization of OsGA2ox5-YFP in transiently transformed onion epidermal cells revealed the presence of this protein in both of the nucleus and cytoplasm. Real-time PCR analysis, along with GUS staining, revealed that OsGA2ox5 is expressed in the roots, culms, leaves, sheaths and panicles of rice. Rice plants overexpressing OsGA2ox5 exhibited dominant dwarf and GAdeficient phenotypes, with shorter stems and later development of reproductive organs than the wild type. The dwarfism phenotype was partially rescued by the application of exogenous GA3 at a concentration of 10 mM. Ectopic expression of OsGA2ox5 cDNA in Arabidopsis resulted in a similar phenotype. Real-time PCR assays revealed that both GA synthesis-related genes and GA signaling genes were expressed at higher levels in transgenic rice plants than in wild-type rice; OsGA3ox1, which encodes a key enzyme in the last step of the bioactive GAs synthesis pathway, was highly expressed in transgenic rice. The roots of OsGA2ox5-ox plants exhibited increased starch granule accumulation and gravity responses, revealing a role for GA in root starch granule development and gravity responses. Furthermore, rice and Arabidopsis plants overexpressing OsGA2ox5 were more resistant to high-salinity stress than wild-type plants. These results suggest that OsGA2ox5 plays important roles in GAs homeostasis, development, gravity responses and stress tolerance in rice.

OsGA2ox5, a gibberellin metabolism enzyme, is involved in plant growth, the root gravity response and salt stress.

Directory of Open Access Journals (Sweden)

Chi Shan

Full Text Available Gibberellin (GA 2-oxidases play an important role in the GA catabolic pathway through 2β-hydroxylation. There are two classes of GA2oxs, i.e., a larger class of C₁₉-GA2oxs and a smaller class of C₂₀-GA2oxs. In this study, the gene encoding a GA 2-oxidase of rice, Oryza sativa GA 2-oxidase 5 (OsGA2ox5, was cloned and characterized. BLASTP analysis showed that OsGA2ox5 belongs to the C₂₀-GA2oxs subfamily, a subfamily of GA2oxs acting on C₂₀-GAs (GA₁₂, GA₅₃. Subcellular localization of OsGA2ox5-YFP in transiently transformed onion epidermal cells revealed the presence of this protein in both of the nucleus and cytoplasm. Real-time PCR analysis, along with GUS staining, revealed that OsGA2ox5 is expressed in the roots, culms, leaves, sheaths and panicles of rice. Rice plants overexpressing OsGA2ox5 exhibited dominant dwarf and GA-deficient phenotypes, with shorter stems and later development of reproductive organs than the wild type. The dwarfism phenotype was partially rescued by the application of exogenous GA3 at a concentration of 10 µM. Ectopic expression of OsGA2ox5 cDNA in Arabidopsis resulted in a similar phenotype. Real-time PCR assays revealed that both GA synthesis-related genes and GA signaling genes were expressed at higher levels in transgenic rice plants than in wild-type rice; OsGA3ox1, which encodes a key enzyme in the last step of the bioactive GAs synthesis pathway, was highly expressed in transgenic rice. The roots of OsGA2ox5-ox plants exhibited increased starch granule accumulation and gravity responses, revealing a role for GA in root starch granule development and gravity responses. Furthermore, rice and Arabidopsis plants overexpressing OsGA2ox5 were more resistant to high-salinity stress than wild-type plants. These results suggest that OsGA2ox5 plays important roles in GAs homeostasis, development, gravity responses and stress tolerance in rice.

Gly[14]-humanin inhibits ox-LDL uptake and stimulates cholesterol efflux in macrophage-derived foam cells.

Science.gov (United States)

Zhu, Wa-Wa; Wang, Shu-Rong; Liu, Zhi-Hua; Cao, Yong-Jun; Wang, Fen; Wang, Jing; Liu, Chun-Feng; Xie, Ying; Xie, Ying; Zhang, Yan-Lin

2017-01-01

Foam cell formation, which is caused by imbalanced cholesterol influx and efflux by macrophages, plays a vital role in the occurrence and development of atherosclerosis. Humanin (HN), a mitochondria-derived peptide, can prevent the production of reactive oxygen species and death of human aortic endothelial cells exposed to oxidized low-density lipoprotein (ox-LDL) and has a protective effect on patients with in early atherosclerosis. However, the effects of HN on the regulation of cholesterol metabolism in RAW 264.7 macrophages are still unknown. This study was designed to investigate the role of [Gly14]-humanin (HNG) in lipid uptake and cholesterol efflux in RAW 264.7 macrophages. Flow cytometry and live cell imaging results showed that HNG reduced Dil-ox-LDL accumulation in the RAW 264.7 macrophages. A similar result was obtained for lipid accumulation by measuring cellular cholesterol content. Western blot analysis showed that ox-LDL treatment upregulated not only the protein expression of CD36 and LOX-1, which mediate ox-LDL endocytosis, but also ATP-binding cassette (ABC) transporter A1 and ABCG1, which mediate ox-LDL exflux. HNG pretreatment inhibited the upregulation of CD36 and LOX-1 levels, prompting the upregulation of ABCA1 and ABCG1 levels induced by ox-LDL. Therefore we concluded that HNG could inhibit ox-LDL-induced macrophage-derived foam cell formation, which occurs because of a decrease in lipid uptake and an increase in cholesterol efflux from macrophage cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

Science.gov (United States)

Davies, T Jonathan; Kraft, Nathan J B; Salamin, Nicolas; Wolkovich, Elizabeth M

2012-02-01

The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

Temperature-Dependent Physical and Memory Characteristics of Atomic-Layer-Deposited RuOx Metal Nanocrystal Capacitors

Directory of Open Access Journals (Sweden)

S. Maikap

2011-01-01

Full Text Available Physical and memory characteristics of the atomic-layer-deposited RuOx metal nanocrystal capacitors in an n-Si/SiO2/HfO2/RuOx/Al2O3/Pt structure with different postdeposition annealing temperatures from 850–1000°C have been investigated. The RuOx metal nanocrystals with an average diameter of 7 nm and a highdensity of 0.7 × 1012/cm2 are observed by high-resolution transmission electron microscopy after a postdeposition annealing temperature at 1000°C. The density of RuOx nanocrystal is decreased (slightly by increasing the annealing temperatures, due to agglomeration of multiple nanocrystals. The RuO3 nanocrystals and Hf-silicate layer at the SiO2/HfO2 interface are confirmed by X-ray photoelectron spectroscopy. For post-deposition annealing temperature of 1000°C, the memory capacitors with a small equivalent oxide thickness of ~9 nm possess a large hysteresis memory window of >5 V at a small sweeping gate voltage of ±5 V. A promising memory window under a small sweeping gate voltage of ~3 V is also observed due to charge trapping in the RuOx metal nanocrystals. The program/erase mechanism is modified Fowler-Nordheim (F-N tunneling of the electrons and holes from Si substrate. The electrons and holes are trapped in the RuOx nanocrystals. Excellent program/erase endurance of 106 cycles and a large memory window of 4.3 V with a small charge loss of ~23% at 85°C are observed after 10 years of data retention time, due to the deep-level traps in the RuOx nanocrystals. The memory structure is very promising for future nanoscale nonvolatile memory applications.

Industrial high-rate (~14 nm/s) deposition of low resistive and transparent ZnOx:Al films on glass

NARCIS (Netherlands)

Illiberi, A.; Kniknie, B.; Deelen, J. van; Steijvers, H.L.A.H.; Habets, D.; Simons, P.J.P.M.; Janssen, A.C.; Beckers, E.H.A.

2011-01-01

Aluminum doped ZnOx (ZnOx:Al) films have been deposited on glass in an in-line industrial-type reactor by a metalorganic chemical vapor deposition process at atmospheric pressure. Tertiary-butanol has been used as oxidant for diethylzinc and trimethylaluminium as dopant gas. ZnOx:Al films can be

Plasma enhanced atomic layer deposited MoOx emitters for silicon heterojunction solar cells

OpenAIRE

Ziegler, J.; Mews, M.; Kaufmann, K.; Schneider, T.; Sprafke, A.N.; Korte, L.; Wehrsporn, R.B

2015-01-01

A method for the deposition of molybdenum oxide MoOx with high growth rates at temperatures below 200 C based on plasma enhanced atomic layer deposition is presented. The stoichiometry of the overstoichiometric MoOx films can be adjusted by the plasma parameters. First results of these layers acting as hole selective contacts in silicon heterojunction solar cells are presented and discussed

1D and 2D Cobalt(II) Coordination Polymers, Co(ox)(en):Synthesis, Structures and Magnetic Properties

International Nuclear Information System (INIS)

Kang, Jae Un; Lee, Yu Mi; Kim, Seung Joo; Yun, Ho Seop; Do, Jung Hwan

2014-01-01

Two ethylenediamine cobalt(II) oxalate complexes Co(ox)(en), 1 and Co(ox)(en)·2H 2 O, 2 have been hydrothermally synthesized and characterized by single crystal X-ray diffraction, IR spectrum, TG analysis, and magnetic measurements. In 1, Co atoms are coordinated by two bis-bidentate oxalate ions in transconfiguration to form Co(ox) chains, which are further bridged by ethylenediamine molecules to produce 2D grid layers, Co(ox)(en). In 2, Co atoms are coordinated by bridging oxalate ions in cis - configuration to form Co(ox) chains, and the additional chelation of ethylenediamine to Co atoms completes 1D zigzag chain, Co(en)(ox). Two lattice water molecules stabilize the chains through hydrogen bonding. Magnetic susceptibility measurements indicate that both complexes exhibit weak antiferromagnetic coupling between cobalt(II) ions with the susceptibility maxima at 23 K for 1 and 20 K for 2, respectively. In 1 and 2, the oxalate ligands afford a much shorter and more effective pathway for the magnetic interaction between cobalt ions compared to the ethylenediamine ligands, so the magnetic behaviors of both complexes could be well described with 1D infinite magnetic chain model

Fabrication of double- and triple-junction solar cells with hydrogenated amorphous silicon oxide (a-SiOx:H) top cell

Czech Academy of Sciences Publication Activity Database

Kim, D.Y.; Guijt, E.; Si, F.T.; Santbergen, R.; Holovský, Jakub; Isabella, O.; van Swaaij, R.A.C.M.M.; Zeman, M.

2015-01-01

Roč. 141, Oct (2015), s. 148-153 ISSN 0927-0248 R&D Projects: GA MŠk 7E12029 EU Projects: European Commission(XE) 283501 - Fast Track Institutional support: RVO:68378271 Keywords : multi-junction solar cel * a-SiOx:H * high voc * current matching Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.732, year: 2015

Upregulation of EMMPRIN (OX47 in Rat Dorsal Root Ganglion Contributes to the Development of Mechanical Allodynia after Nerve Injury

Directory of Open Access Journals (Sweden)

Qun Wang

2015-01-01

Full Text Available Matrix metalloproteinases (MMPs are widely implicated in inflammation and tissue remodeling associated with various neurodegenerative diseases and play an important role in nociception and allodynia. Extracellular Matrix Metalloproteinase Inducer (EMMPRIN plays a key regulatory role for MMP activities. However, the role of EMMPRIN in the development of neuropathic pain is not clear. Western blotting, real-time quantitative RT-PCR (qRT-PCR, and immunofluorescence were performed to determine the changes of messenger RNA and protein of EMMPRIN/OX47 and their cellular localization in the rat dorsal root ganglion (DRG after nerve injury. Paw withdrawal threshold test was examined to evaluate the pain behavior in spinal nerve ligation (SNL model. The lentivirus containing OX47 shRNA was injected into the DRG one day before SNL. The expression level of both mRNA and protein of OX47 was markedly upregulated in ipsilateral DRG after SNL. OX47 was mainly expressed in the extracellular matrix of DRG. Administration of shRNA targeted against OX47 in vivo remarkably attenuated mechanical allodynia induced by SNL. In conclusion, peripheral nerve injury induced upregulation of OX47 in the extracellular matrix of DRG. RNA interference against OX47 significantly suppressed the expression of OX47 mRNA and the development of mechanical allodynia. The altered expression of OX47 may contribute to the development of neuropathic pain after nerve injury.

Effects of Phylogenetic Tree Style on Student Comprehension

Science.gov (United States)

Dees, Jonathan Andrew

Phylogenetic trees are powerful tools of evolutionary biology that have become prominent across the life sciences. Consequently, learning to interpret and reason from phylogenetic trees is now an essential component of biology education. However, students often struggle to understand these diagrams, even after explicit instruction. One factor that has been observed to affect student understanding of phylogenetic trees is style (i.e., diagonal or bracket). The goal of this dissertation research was to systematically explore effects of style on student interpretations and construction of phylogenetic trees in the context of an introductory biology course. Before instruction, students were significantly more accurate with bracket phylogenetic trees for a variety of interpretation and construction tasks. Explicit instruction that balanced the use of diagonal and bracket phylogenetic trees mitigated some, but not all, style effects. After instruction, students were significantly more accurate for interpretation tasks involving taxa relatedness and construction exercises when using the bracket style. Based on this dissertation research and prior studies on style effects, I advocate for introductory biology instructors to use only the bracket style. Future research should examine causes of style effects and variables other than style to inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

MicroRNA-98 rescues proliferation and alleviates ox-LDL-induced apoptosis in HUVECs by targeting LOX-1

Science.gov (United States)

Chen, Zhibo; Wang, Mian; He, Qiong; Li, Zilun; Zhao, Yang; Wang, Wenjian; Ma, Jieyi; Li, Yongxin; Chang, Guangqi

2017-01-01

Oxidized low-density lipoprotein (ox-LDL) is a major and critical mediator of atherosclerosis, and the underlying mechanism is thought to involve the ox-LDL-induced dysfunction of endothelial cells (ECs). MicroRNAs (miRNAs), which are a group of small non-coding RNA molecules that post-transcriptionally regulate the expression of target genes, have been associated with diverse cellular functions and the pathogenesis of various diseases, including atherosclerosis. miRNA-98 (miR-98) has been demonstrated to be involved in the regulation of cellular apoptosis; however, the role of miR-98 in ox-LDL-induced dysfunction of ECs and atherosclerosis has yet to be elucidated. Therefore, the present study aimed to investigate the role of miR-98 in ox-LDL-induced dysfunction of ECs and the underlying mechanism. It was demonstrated that miR-98 expression was markedly downregulated in ox-LDL-treated human umbilical vein ECs (HUVECs) and that miR-98 promoted the proliferation and alleviated apoptosis of HUVECs exposed to ox-LDL. In addition, the results demonstrated that lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1) was a direct target of miR-98 in HUVECs, as indicated by a luciferase assay. The results of the present study suggested that miR-98 may inhibit the uptake of toxic ox-LDL, maintain HUVEC proliferation and protect HUVECs against apoptosis via the suppression of LOX-1. PMID:28565756

Invernaderos: seguimientos de temperatura y oxígeno

OpenAIRE

Sonnenholzner, Stanislaus

2002-01-01

Invernaderos: Seguimientos de Temperatura y Oxígeno Entre diciembre del 2001 y mayo del 2002 se realizaron dos series de experimentos para evaluar el efecto de las temperaturas altas en la supervivencia y el crecimiento del camarón utilizando invernaderos.

Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family.

Science.gov (United States)

Pearce, Stephen; Huttly, Alison K; Prosser, Ian M; Li, Yi-dan; Vaughan, Simon P; Gallova, Barbora; Patil, Archana; Coghill, Jane A; Dubcovsky, Jorge; Hedden, Peter; Phillips, Andrew L

2015-06-05

The gibberellin (GA) pathway plays a central role in the regulation of plant development, with the 2-oxoglutarate-dependent dioxygenases (2-ODDs: GA20ox, GA3ox, GA2ox) that catalyse the later steps in the biosynthetic pathway of particularly importance in regulating bioactive GA levels. Although GA has important impacts on crop yield and quality, our understanding of the regulation of GA biosynthesis during wheat and barley development remains limited. In this study we identified or assembled genes encoding the GA 2-ODDs of wheat, barley and Brachypodium distachyon and characterised the wheat genes by heterologous expression and transcript analysis. The wheat, barley and Brachypodium genomes each contain orthologous copies of the GA20ox, GA3ox and GA2ox genes identified in rice, with the exception of OsGA3ox1 and OsGA2ox5 which are absent in these species. Some additional paralogs of 2-ODD genes were identified: notably, a novel gene in the wheat B genome related to GA3ox2 was shown to encode a GA 1-oxidase, named as TaGA1ox-B1. This enzyme is likely to be responsible for the abundant 1β-hydroxylated GAs present in developing wheat grains. We also identified a related gene in barley, located in a syntenic position to TaGA1ox-B1, that encodes a GA 3,18-dihydroxylase which similarly accounts for the accumulation of unusual GAs in barley grains. Transcript analysis showed that some paralogs of the different classes of 2-ODD were expressed mainly in a single tissue or at specific developmental stages. In particular, TaGA20ox3, TaGA1ox1, TaGA3ox3 and TaGA2ox7 were predominantly expressed in developing grain. More detailed analysis of grain-specific gene expression showed that while the transcripts of biosynthetic genes were most abundant in the endosperm, genes encoding inactivation and signalling components were more highly expressed in the seed coat and pericarp. The comprehensive expression and functional characterisation of the multigene families encoding the 2-ODD

Phylogenetic signal dissection identifies the root of starfishes.

Directory of Open Access Journals (Sweden)

Roberto Feuda

Full Text Available Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.

Light-activated resistance switching in SiOx RRAM devices

Science.gov (United States)

Mehonic, A.; Gerard, T.; Kenyon, A. J.

2017-12-01

We report a study of light-activated resistance switching in silicon oxide (SiOx) resistive random access memory (RRAM) devices. Our devices had an indium tin oxide/SiOx/p-Si Metal/Oxide/Semiconductor structure, with resistance switching taking place in a 35 nm thick SiOx layer. The optical activity of the devices was investigated by characterising them in a range of voltage and light conditions. Devices respond to illumination at wavelengths in the range of 410-650 nm but are unresponsive at 1152 nm, suggesting that photons are absorbed by the bottom p-type silicon electrode and that generation of free carriers underpins optical activity. Applied light causes charging of devices in the high resistance state (HRS), photocurrent in the low resistance state (LRS), and lowering of the set voltage (required to go from the HRS to LRS) and can be used in conjunction with a voltage bias to trigger switching from the HRS to the LRS. We demonstrate negative correlation between set voltage and applied laser power using a 632.8 nm laser source. We propose that, under illumination, increased electron injection and hence a higher rate of creation of Frenkel pairs in the oxide—precursors for the formation of conductive oxygen vacancy filaments—reduce switching voltages. Our results open up the possibility of light-triggered RRAM devices.

One tree to link them all: a phylogenetic dataset for the European tetrapoda.

Science.gov (United States)

Roquet, Cristina; Lavergne, Sébastien; Thuiller, Wilfried

2014-08-08

Since the ever-increasing availability of phylogenetic informative data, the last decade has seen an upsurge of ecological studies incorporating information on evolutionary relationships among species. However, detailed species-level phylogenies are still lacking for many large groups and regions, which are necessary for comprehensive large-scale eco-phylogenetic analyses. Here, we provide a dataset of 100 dated phylogenetic trees for all European tetrapods based on a mixture of supermatrix and supertree approaches. Phylogenetic inference was performed separately for each of the main Tetrapoda groups of Europe except mammals (i.e. amphibians, birds, squamates and turtles) by means of maximum likelihood (ML) analyses of supermatrix applying a tree constraint at the family (amphibians and squamates) or order (birds and turtles) levels based on consensus knowledge. For each group, we inferred 100 ML trees to be able to provide a phylogenetic dataset that accounts for phylogenetic uncertainty, and assessed node support with bootstrap analyses. Each tree was dated using penalized-likelihood and fossil calibration. The trees obtained were well-supported by existing knowledge and previous phylogenetic studies. For mammals, we modified the most complete supertree dataset available on the literature to include a recent update of the Carnivora clade. As a final step, we merged the phylogenetic trees of all groups to obtain a set of 100 phylogenetic trees for all European Tetrapoda species for which data was available (91%). We provide this phylogenetic dataset (100 chronograms) for the purpose of comparative analyses, macro-ecological or community ecology studies aiming to incorporate phylogenetic information while accounting for phylogenetic uncertainty.

Zeolitic imidazolate framework-8-derived N-doped porous carbon coated olive-shaped FeOx nanoparticles for lithium storage

Science.gov (United States)

Gan, Qingmeng; Zhao, Kuangmin; He, Zhen; Liu, Suqin; Li, Aikui

2018-04-01

We propose a new strategy to uniformly coat zeolitic imidazolate framework-8 (ZIF-8) on iron oxides containing no Zn to obtain an α-Fe2O3@ZIF-8 composite. After carbonization, the α-Fe2O3@ZIF-8 transforms into iron oxides@N-doped porous carbon (FeOx@NC). The uniform N-doped porous carbon layer gives rise to a superior electrical conductivity, highly-increased specific BET surface area (179.2 m2 g-1), and abundant mesopores for the FeOx@NC composite. When served as the LIB anode, the FeOx@NC shows a high reversible capacity (of 1064 mA h g-1 at 200 mA g-1), excellent rate performance (of 198.1 mA h g-1 at 10000 mA g-1) as well as brilliant long-term cyclability (with a capacity retention of 93.3% after 800 cycles), which are much better than those of the FeOx@C and pristine FeOx anodes. Specifically, the Li-ion intercalation pseudocapacitive behavior of the FeOx@NC anode is improved by this N-doped porous carbon coating, which is beneficial for rapid Li-ion insertion/extraction processes. The excellent electrochemical performance of FeOx@NC should be ascribed to the increased electrolyte penetration areas, improved electrical conductivity, boosted lithium storage kinetics, and shortened Li-ion transport length.

Employment of fluorine doped zinc tin oxide (ZnSnOx:F) coating layer on stainless steel 316 for a bipolar plate for PEMFC

International Nuclear Information System (INIS)

Park, Ji Hun; Byun, Dongjin; Lee, Joong Kee

2011-01-01

Highlights: → Preparation of fluorine doped tin oxide (SnOx:F) and fluorine doped zinc tin oxide (ZnSnOx:F) coating layer on the surface of stainless steel 316 bipolar plate for PEMFCs (Proton Exchange Membrane Fuel Cells). → Evaluations of the corrosion resistance and the interfacial contact resistance of the bare, SnOx:F and ZnSnOx:F thin film coated stainless steel 316 bipolar plates. → Evaluation of single cell performance such as cell voltage and power density using bare stainless steel, SnOx:F and ZnSnOx:F film coated bipolar plates. - Abstract: The investigation of the electrochemical characteristics of the fluorine doped tin oxide (SnOx:F) and fluorine doped zinc tin oxide (ZnSnOx:F) was carried out in the simulated PEMFC environment and bare stainless steel 316 was used as a reference. The results showed that the ZnSnOx:F coating enhanced both the corrosion resistance and interfacial contact resistance (ICR). The corrosion current for ZnSnOx:F was 1.2 μA cm -2 which was much lower than that of bare stainless steel of 50.16 μA cm -2 . The ZnSnOx:F coated film had the smallest corrosion current due to the formation of a tight surface morphology with very few pin-holes. The ZnSnOx:F coated film exhibited the highest values of the cell voltage and power density due to its having the lowest ICR values.

Nur77 inhibits oxLDL induced apoptosis of macrophages via the p38 MAPK signaling pathway

International Nuclear Information System (INIS)

Shao, Qin; Han, Fei; Peng, Shi; He, Ben

2016-01-01

The interaction between macrophages and oxLDL plays a crucial role in the initiation and progression of atherosclerosis. As a key initiator in a number of plaque promoting processes, oxLDL induces variable effects such as cell apoptosis or proliferation. Orphan nuclear receptor Nur77 is potently induced in macrophages by diverse stimuli, suggesting that it is of importance in vascular inflammation resulting in atherosclerosis, but whether Nur77 induction is detrimental or protective is unclear. In our study, we explore the role of Nur77 in the regulation of oxLDL-induced macrophage apoptosis and the signaling pathways that are involved. We found that oxLDL induced Nur77 expression in a dose and time dependent fashion, and cell viability was decreased in parallel. To determine whether Nur77 induction contributes to the loss of cell viability or is a protective mechanism, the effect of Nur77 overexpression was examined. Importantly, Nur77 overexpression inhibited the oxLDL-induced decrease of cell viability, inhibited the production of apoptotic bodies and restored DNA synthesis following oxLDL exposure. Furthermore, we found that Nur77 induction is mediated through the p38 MAPK signaling pathway. After pretreatment with SB203580, cell viability was decreased, the expression of CyclinA2 and PCNA was attenuated and the percentage of cell apoptosis was enhanced. Likewise, Nur77 overexpression increased the expression of the cell cycle genes PCNA and p21, and attenuated the increase in caspase-3. On the other hand, knockdown of Nur77 expression by specific siRNA resulted in the increased expression of caspase 3. The results demonstrate that Nur77 is induced by oxLDL via the p38 MAPK signaling pathway, which is involved in the regulation of cell survival. Nur77 enhanced cell survival via suppressing apoptosis, without affecting cell proliferation of activated macrophages, which may be beneficial in patients with atherosclerosis. - Highlights: • oxLDL could induce Nur77

Nur77 inhibits oxLDL induced apoptosis of macrophages via the p38 MAPK signaling pathway

Energy Technology Data Exchange (ETDEWEB)

Shao, Qin; Han, Fei; Peng, Shi; He, Ben, E-mail: heben@medmail.com.cn

2016-03-18

The interaction between macrophages and oxLDL plays a crucial role in the initiation and progression of atherosclerosis. As a key initiator in a number of plaque promoting processes, oxLDL induces variable effects such as cell apoptosis or proliferation. Orphan nuclear receptor Nur77 is potently induced in macrophages by diverse stimuli, suggesting that it is of importance in vascular inflammation resulting in atherosclerosis, but whether Nur77 induction is detrimental or protective is unclear. In our study, we explore the role of Nur77 in the regulation of oxLDL-induced macrophage apoptosis and the signaling pathways that are involved. We found that oxLDL induced Nur77 expression in a dose and time dependent fashion, and cell viability was decreased in parallel. To determine whether Nur77 induction contributes to the loss of cell viability or is a protective mechanism, the effect of Nur77 overexpression was examined. Importantly, Nur77 overexpression inhibited the oxLDL-induced decrease of cell viability, inhibited the production of apoptotic bodies and restored DNA synthesis following oxLDL exposure. Furthermore, we found that Nur77 induction is mediated through the p38 MAPK signaling pathway. After pretreatment with SB203580, cell viability was decreased, the expression of CyclinA2 and PCNA was attenuated and the percentage of cell apoptosis was enhanced. Likewise, Nur77 overexpression increased the expression of the cell cycle genes PCNA and p21, and attenuated the increase in caspase-3. On the other hand, knockdown of Nur77 expression by specific siRNA resulted in the increased expression of caspase 3. The results demonstrate that Nur77 is induced by oxLDL via the p38 MAPK signaling pathway, which is involved in the regulation of cell survival. Nur77 enhanced cell survival via suppressing apoptosis, without affecting cell proliferation of activated macrophages, which may be beneficial in patients with atherosclerosis. - Highlights: • oxLDL could induce Nur77

OxCal: versatile tool for developing paleoearthquake chronologies--a primer

Science.gov (United States)

Lienkaemper, J.J.; Ramsey, C.B.

2009-01-01

Ages of paleoearthquakes (events), i.e., evidence of earthquakes inferred from the geologic record, provide a critical constraint on estimation of the seismic hazard posed by an active fault. The radiocarbon calibration program OxCal (4.0.3 and above; Bronk Ramsey 2007, 2001) provides paleoseismologists with a straightforward but rigorous means of estimating these event ages and their uncertainties. Although initially developed for the chronologic modeling of archaeological data from diverse sources (e.g., radiocarbon, historical knowledge, etc.), OxCal is readily adaptable to other disciplines requiring chronological modeling, such as paleoseismology (Fumal et al. 2002; Lindvall et al. 2002; Kelson et al. 2006; Noriega et al. 2006; Lienkaemper and Williams 2007; Yen et al. 2008).

New weighting methods for phylogenetic tree reconstruction using multiple loci.

Science.gov (United States)

Misawa, Kazuharu; Tajima, Fumio

2012-08-01

Efficient determination of evolutionary distances is important for the correct reconstruction of phylogenetic trees. The performance of the pooled distance required for reconstructing a phylogenetic tree can be improved by applying large weights to appropriate distances for reconstructing phylogenetic trees and small weights to inappropriate distances. We developed two weighting methods, the modified Tajima-Takezaki method and the modified least-squares method, for reconstructing phylogenetic trees from multiple loci. By computer simulations, we found that both of the new methods were more efficient in reconstructing correct topologies than the no-weight method. Hence, we reconstructed hominoid phylogenetic trees from mitochondrial DNA using our new methods, and found that the levels of bootstrap support were significantly increased by the modified Tajima-Takezaki and by the modified least-squares method.

Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa.

Science.gov (United States)

Borowiec, Marek L; Lee, Ernest K; Chiu, Joanna C; Plachetzki, David C

2015-11-23

Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans. To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction. Our study further clarifies relationships among early branching metazoan lineages

Humidity dependence of molecular tunnel junctions with an AlOx/COOH- interface

Science.gov (United States)

Zhang, Xiaohang; McGill, Stephen; Xiong, Peng

2006-03-01

We have studied the electron transport in planar tunneling junctions with aluminum oxide and an organic self-assembled monolayer (SAM) as the tunnel barrier. The structure of the junctions is Al/AlOx/SAM/(Au, Pb) with a junction area of ˜ 0.4mm^2. The organic molecules investigated include mercaptohexadecanoic acid (MHA), hexadecanoic acid (HDA), and octadecyltrichlorosilane (OTS); all of which form ordered SAMs on top of aluminum oxide. The use of a superconducting electrode (Al) enables us to determine unambiguously that these are high-quality tunnel junctions. For junctions incorporating MHA, the transport behavior is found to be strongly humidity dependent. The resistance of these junctions drops more than 50% when placed in dry nitrogen and recovers when returned into the ambient. The same drop also occurs when the sample is placed into a vacuum, and backfilling the vacuum with either dry N2 or O2 has negligible effect on the resistance. For comparison, junctions with HDA show the same humidity dependence, while OTS samples do not. Since both MHA and HDA have carboxylic groups and OTS does not, the results suggest that water molecules at the AlOx/COOH- interface play the central role in the observed behavior. Inelastic tunneling spectroscopy (IETS) has also been performed to understand the role of water. This work was supported by a FSU Research Foundation PEG grant.

Trophic phylogenetics: evolutionary influences on body size, feeding, and species associations in grassland arthropods.

Science.gov (United States)

Lind, Eric M; Vincent, John B; Weiblen, George D; Cavender-Bares, Jeannine; Borer, Elizabeth T

2015-04-01

Contemporary animal-plant interactions such as herbivory are widely understood to be shaped by evolutionary history. Yet questions remain about the role of plant phylogenetic diversity in generating and maintaining herbivore diversity, and whether evolutionary relatedness of producers might predict the composition of consumer communities. We tested for evidence of evolutionary associations among arthropods and the plants on which they were found, using phylogenetic analysis of naturally occurring arthropod assemblages sampled from a plant-diversity manipulation experiment. Considering phylogenetic relationships among more than 900 arthropod consumer taxa and 29 plant species in the experiment, we addressed several interrelated questions. First, our results support the hypothesis that arthropod functional traits such as body size and trophic role are phylogenetically conserved in community ecological samples. Second, herbivores tended to cooccur with closer phylogenetic relatives than would be expected at random, whereas predators and parasitoids did not show phylogenetic association patterns. Consumer specialization, as measured by association through time with monocultures of particular host plant species, showed significant phylogenetic signal, although the. strength of this association varied among plant species. Polycultures of phylogenetically dissimilar plant species supported more phylogenetically dissimilar consumer communities than did phylogenetically similar polycultures. Finally, we separated the effects of plant species richness and relatedness in predicting the phylogenetic distribution of the arthropod assemblages in this experiment. The phylogenetic diversity of plant communities predicted the phylogenetic diversity of herbivore communities even after accounting for plant species richness. The phylogenetic diversity of secondary consumers differed by guild, with predator phylogenetic diversity responding to herbivore relatedness, while parasitoid

Simultaneous analysis of five molecular markers provides a well-supported phylogenetic hypothesis for the living bony-tongue fishes (Osteoglossomorpha: Teleostei).

Science.gov (United States)

Lavoué, Sébastien; Sullivan, John P

2004-10-01

Fishes of the Superorder Osteoglossomorpha (the "bonytongues") constitute a morphologically heterogeneous group of basal teleosts, including highly derived subgroups such as African electric fishes, the African butterfly fish, and Old World knifefishes. Lack of consensus among hypotheses of osteoglossomorph relationships advanced during the past 30 years may be due in part to the difficulty of identifying shared derived characters among the morphologically differentiated extant families of this group. In this study, we present a novel phylogenetic hypothesis for this group, based on the analysis of more than 4000 characters from five molecular markers (the mitochondrial cytochrome b, 12S and 16S rRNA genes, and the nuclear genes RAG2 and MLL). Our taxonomic sampling includes one representative of each extant non-mormyrid osteoglossomorph genus, one representative for the monophyletic family Mormyridae, and four outgroup taxa within the basal Teleostei. Maximum parsimony analysis of combined and equally weighted characters from the five molecular markers and Bayesian analysis provide a single, well-supported, hypothesis of osteoglossomorph interrelationships and show the group to be monophyletic. The tree topology is the following: (Hiodon alosoides, (Pantodon buchholzi, (((Osteoglossum bicirrhosum, Scleropages sp.), (Arapaima gigas, Heterotis niloticus)), ((Gymnarchus niloticus, Ivindomyrus opdenboschi), ((Notopterus notopterus, Chitala ornata), (Xenomystus nigri, Papyrocranus afer)))))). We compare our results with previously published phylogenetic hypotheses based on morpho-anatomical data. Additionally, we explore the consequences of the long terminal branch length for the taxon Pantodon buchholzi in our phylogenetic reconstruction and we use the obtained phylogenetic tree to reconstruct the evolutionary history of electroreception in the Notopteroidei.

Transportadores de oxígeno en cirugía cardíaca

OpenAIRE

Molina Méndez,Francisco Javier

2006-01-01

Los transportadores de oxígeno pueden ser agrupados en dos categorías: Soluciones basadas en hemoglobina y emulsiones basadas en perfluoroquímicos. La transfusión de eritrocitos alogénicos representa un recurso limitado y está asociada con eventos adversos como reacciones de transfusión aguda, transmisión de enfermedades infecciosas, inmunosupresión e infecciones postoperatorias. Aunque la "sangre artificial" no es una realidad clínica, algunos "transportadores artificiales de oxígeno" están ...

IrOx-carbon nanotube hybrids: a nanostructured material for electrodes with increased charge capacity in neural systems.

Science.gov (United States)

Carretero, Nina M; Lichtenstein, Mathieu P; Pérez, Estela; Cabana, Laura; Suñol, Cristina; Casañ-Pastor, Nieves

2014-10-01

Nanostructured iridium oxide-carbon nanotube hybrids (IrOx-CNT) deposited as thin films by dynamic electrochemical methods are suggested as novel materials for neural electrodes. Single-walled carbon nanotubes (SWCNT) serve as scaffolds for growing the oxide, yielding a tridimensional structure with improved physical, chemical and electrical properties, in addition to high biocompatibility. In biological environments, SWCNT encapsulation by IrOx makes more resistant electrodes and prevents the nanotube release to the media, preventing cellular toxicity. Chemical, electrochemical, structural and surface characterization of the hybrids has been accomplished. The high performance of the material in electrochemical measurements and the significant increase in cathodal charge storage capacity obtained for the hybrid in comparison with bare IrOx represent a significant advance in electric field application in biosystems, while its cyclability is also an order of magnitude greater than pure IrOx. Moreover, experiments using in vitro neuronal cultures suggest high biocompatibility for IrOx-CNT coatings and full functionality of neurons, validating this material for use in neural electrodes. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Facile Synthesis of Coaxial CNTs/MnOx-Carbon Hybrid Nanofibers and Their Greatly Enhanced Lithium Storage Performance.

Science.gov (United States)

Yang, Zunxian; Lv, Jun; Pang, Haidong; Yan, Wenhuan; Qian, Kun; Guo, Tailiang; Guo, Zaiping

2015-12-01

Carbon nanotubes (CNTs)/MnOx-Carbon hybrid nanofibers have been successfully synthesized by the combination of a liquid chemical redox reaction (LCRR) and a subsequent carbonization heat treatment. The nanostructures exhibit a unique one-dimensional core/shell architecture, with one-dimensional CNTs encapsulated inside and a MnOx-carbon composite nanoparticle layer on the outside. The particular porous characteristics with many meso/micro holes/pores, the highly conductive one-dimensional CNT core, as well as the encapsulating carbon matrix on the outside of the MnOx nanoparticles, lead to excellent electrochemical performance of the electrode. The CNTs/MnOx-Carbon hybrid nanofibers exhibit a high initial reversible capacity of 762.9 mAhg(-1), a high reversible specific capacity of 560.5 mAhg(-1) after 100 cycles, and excellent cycling stability and rate capability, with specific capacity of 396.2 mAhg(-1) when cycled at the current density of 1000 mAg(-1), indicating that the CNTs/MnOx-Carbon hybrid nanofibers are a promising anode candidate for Li-ion batteries.

Phylogenetic comparative methods on phylogenetic networks with reticulations.

Science.gov (United States)

Bastide, Paul; Solís-Lemus, Claudia; Kriebel, Ricardo; Sparks, K William; Ané, Cécile

2018-04-25

The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing.

Science.gov (United States)

Olvera, Alex; Busquets, Núria; Cortey, Marti; de Deus, Nilsa; Ganges, Llilianne; Núñez, José Ignacio; Peralta, Bibiana; Toskano, Jennifer; Dolz, Roser

2010-05-01

Changes in livestock production systems in recent years have altered the presentation of many diseases resulting in the need for more sophisticated control measures. At the same time, new molecular assays have been developed to support the diagnosis of animal viral disease. Nucleotide sequences generated by these diagnostic techniques can be used in phylogenetic analysis to infer phenotypes by sequence homology and to perform molecular epidemiology studies. In this review, some key elements of phylogenetic analysis are highlighted, such as the selection of the appropriate neutral phylogenetic marker, the proper phylogenetic method and different techniques to test the reliability of the resulting tree. Examples are given of current and future applications of phylogenetic reconstructions in viral livestock diseases. Copyright 2009 Elsevier Ltd. All rights reserved.

Molecular phylogenetic analysis supports a Gondwanan origin of the Hyriidae (Mollusca: Bivalvia: Unionida) and the paraphyly of Australasian taxa.

Science.gov (United States)

Graf, Daniel L; Jones, Hugh; Geneva, Anthony J; Pfeiffer, John M; Klunzinger, Michael W

2015-04-01

The freshwater mussel family Hyriidae (Mollusca: Bivalvia: Unionida) has a disjunct trans-Pacific distribution in Australasia and South America. Previous phylogenetic analyses have estimated the evolutionary relationships of the family and the major infra-familial taxa (Velesunioninae and Hyriinae: Hyridellini in Australia; Hyriinae: Hyriini, Castaliini, and Rhipidodontini in South America), but taxon and character sampling have been too incomplete to support a predictive classification or allow testing of biogeographical hypotheses. We sampled 30 freshwater mussel individuals representing the aforementioned hyriid taxa, as well as outgroup species representing the five other freshwater mussel families and their marine sister group (order Trigoniida). Our ingroup included representatives of all Australian genera. Phylogenetic relationships were estimated from three gene fragments (nuclear 28S, COI and 16S mtDNA) using maximum parsimony, maximum likelihood, and Bayesian inference, and we applied a Bayesian relaxed clock model calibrated with fossil dates to estimate node ages. Our analyses found good support for monophyly of the Hyriidae and the subfamilies and tribes, as well as the paraphyly of the Australasian taxa (Velesunioninae, (Hyridellini, (Rhipidodontini, (Castaliini, Hyriini)))). The Hyriidae was recovered as sister to a clade comprised of all other Recent freshwater mussel families. Our molecular date estimation supported Cretaceous origins of the major hyriid clades, pre-dating the Tertiary isolation of South America from Antarctica/Australia. We hypothesize that early diversification of the Hyriidae was driven by terrestrial barriers on Gondwana rather than marine barriers following disintegration of the super-continent. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata).

Science.gov (United States)

Weisrock, David W; Macey, J Robert; Matsui, Masafumi; Mulcahy, Daniel G; Papenfuss, Theodore J

2013-01-01

The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylogenetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S-16S region (the 3' end of 12S rRNA, tRNA(VAI), and the 5' end of 16S rRNA), and a ND2-COI region (ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), the origin for light strand replication--O(L), tRNA(Cys), tRNAT(Tyr), and the 5' end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phylogenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger

Immunomodulatory effects of OX40Ig gene-modified adipose tissue-derived mesenchymal stem cells on rat kidney transplantation

OpenAIRE

Liu, Tao; Zhang, Yue; Shen, Zhongyang; Zou, Xunfeng; Chen, Xiaobo; Chen, Li; Wang, Yuliang

2016-01-01

Recent studies have suggested that adipose tissue-derived mesenchymal stem cell (ADSC) therapy and OX40 costimulation blockade are two immunomodulatory strategies used to suppress the immune response to alloantigens. However, relatively little has been reported regarding the immunomodulatory potential of the abilityof these two strategies to synergize. Thus, in the present study, we aimed to investigate OX40-Ig fusion protein (OX40Ig) expression in ADSCs and to validate their more potent immu...

Influence of a MoOx interlayer on the open-circuit voltage in organic photovoltaic cells

Science.gov (United States)

Zou, Yunlong; Holmes, Russell J.

2013-07-01

Metal-oxides have been used as interlayers at the anode-organic interface in organic photovoltaic cells (OPVs) to increase the open-circuit voltage (VOC). We examine the role of MoOx in determining the maximum VOC in a planar heterojunction OPV and find that the interlayer strongly affects the temperature dependence of VOC. Boron subphthalocyanine chloride (SubPc)-C60 OPVs that contain no interlayer show a maximum VOC of 1.2 V at low temperature, while those with MoOx show no saturation, reaching VOC > 1.4 V. We propose that the MoOx-SubPc interface forms a Schottky junction that provides an additional contribution to VOC at low temperature.

DendroPy: a Python library for phylogenetic computing.

Science.gov (United States)

Sukumaran, Jeet; Holder, Mark T

2010-06-15

DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).

Supramolecular self-assembly of novel thermo-responsive double-hydrophilic and hydrophobic Y-shaped [MPEO-b-PEtOx-b-(PCL)2] terpolymers

Czech Academy of Sciences Publication Activity Database

Petrova, Svetlana; Venturini, Cristina Garcia; Jäger, Alessandro; Jäger, Eliezer; Hrubý, Martin; Pavlova, Ewa; Štěpánek, Petr

2015-01-01

Roč. 5, č. 77 (2015), s. 62844-62854 ISSN 2046-2069 R&D Projects: GA MŠk(CZ) LH14079; GA MŠk(CZ) 7F14009 Institutional support: RVO:61389013 Keywords : Y-shaped [PEO-b-PEtOx-b-(PCL)2] terpolymers * light scattering * nanoparticles Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.289, year: 2015

Novel thermo-responsive double-hydrophilic and hydrophobic MPEO-b-PEtOx-b-PCL triblock terpolymers: synthesis, characterization and self-assembly studies

Czech Academy of Sciences Publication Activity Database

Petrova, Svetlana; Venturini, Cristina Garcia; Jäger, Alessandro; Jäger, Eliezer; Černoch, Peter; Kereiche, S.; Kováčik, L.; Raška, I.; Štěpánek, Petr

2015-01-01

Roč. 59, 24 February (2015), s. 215-225 ISSN 0032-3861 R&D Projects: GA ČR GAP208/10/1600; GA MŠk(CZ) 7F14009 Institutional support: RVO:61389013 Keywords : MPEO-b-PEtOx-b-PCL triblock terpolymers * light-scattering * thermo-responsive nanoparticles Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.586, year: 2015

White OLED with high stability and low driving voltage based on a novel buffer layer MoOx

Energy Technology Data Exchange (ETDEWEB)

Jiang Xueyin [School of Materials Science and Engineering, Shanghai University, Jiading, Shanghai 201800 (China); Zhang Zhilin [School of Materials Science and Engineering, Shanghai University, Jiading, Shanghai 201800 (China); Cao Jin [Key Laboratory of Advanced Display and System Application, Ministry of Education, Shanghai University, Shanghai 200072 (China); Khan, M A [School of Materials Science and Engineering, Shanghai University, Jiading, Shanghai 201800 (China); Khizar-ul-Haq [School of Materials Science and Engineering, Shanghai University, Jiading, Shanghai 201800 (China); Zhu Wenqing [School of Materials Science and Engineering, Shanghai University, Jiading, Shanghai 201800 (China)

2007-09-21

White organic light emitting diodes (WOLEDs) with copper phthalocyanine (CuPc), 4,4',4-prime-tris(N-3-methylphenyl-N-phenyl-amino) triphenylamine (m-MTDATA), tungsten oxide (WO{sub 3}) and molybdenum oxide (MoOx) as buffer layers have been investigated. The MoOx based device shows superior performance with low driving voltage, high power efficiency and much longer lifetime than those with other buffer layers. For the Cell using MoOx as buffer layer and 4,7-diphenyl-1,10-phenanthroline (Bphen) as electron transporting layer (ETL), at the luminance of 1000 cd m{sup -2}, the driving voltage is 4.9 V, which is 4.2 V, 2 V and 0.7 V lower than that of the devices using CuPc (Cell-CuPc), m-MTDATA (Cell-m-MTDATA) and WO{sub 3} (Cell-WO{sub 3}) as buffer layers, respectively. Its power efficiency is 7.67 Lm W{sup -1}, which is 2.37 times higher than that of Cell-CuPc and a little higher than that of Cell-m-MTDATA. The projected half-life under the initial luminance of 100 cd m{sup -2} is 55 260 h, which is more than 4.6 times longer than that of Cell-m-MTDATA and Cell-CuPc. The superior performance of Cell-MoOx is attributed to its high hole injection ability and the stable interface between MoOx and organic material. The work function of MoOx has been measured by the contact potential difference method. The J-V curves of 'hole-only' devices indicate that a small hole injection barrier between MoOx/N,'-bis(naphthalene-1-y1)-N, N'-bis(phenyl)-benzidine (NPB) leads to a strong hole injection, resulting in a low driving voltage and a high stability.

Reversal of lattice, electronic structure, and magnetism in epitaxial SrCoOx thin films

Science.gov (United States)

Jeen, H.; Choi, W. S.; Lee, J. H.; Cooper, V. R.; Lee, H. N.; Seo, S. S. A.; Rabe, K. M.

2014-03-01

SrCoOx (x = 2.5 - 3.0, SCO) is an ideal material to study the role of oxygen content for electronic structure and magnetism, since SCO has two distinct topotactic phases: the antiferromagnetic insulating brownmillerite SrCoO2.5 and the ferromagnetic metallic perovskite SrCoO3. In this presentation, we report direct observation of a reversible lattice and electronic structure evolution in SrCoOx epitaxial thin films as well as different magnetic and electronic ground states between the topotactic phases.[2] By magnetization measurements, optical absorption, and transport measurements drastically different electronic and magnetic ground states are found in the epitaxially grown SrCoO2.5 and SrCoO3 thin films by pulsed laser epitaxy. First-principles calculations confirm substantial, which originate from the modification in the Co valence states and crystallographic structures. By real-time spectroscopic ellipsometry, the two electronically and magnetically different phases can be reversibly changed by changing the ambient pressure at greatly reduced temperatures. Our finding provides an important pathway to understanding the novel oxygen-content-dependent phase transition uniquely found in multivalent transition metal oxides. The work was supported by the U.S. Department of Energy, Basic Energy Sciences, Materials Sciences and Engineering Division.

Highly dispersed TaOx nanoparticles prepared by electrodeposition as oxygen reduction electrocatalysts for polymer electrolyte fuel cells

KAUST Repository

Seo, Jeongsuk; Zhao, Lan; Cha, Dong Kyu; Takanabe, Kazuhiro; Katayama, Masao; Kubota, Jun; Domen, Kazunari

2013-01-01

for the oxygen reduction reaction (ORR) in polymer electrolyte fuel cells (PEFCs). Electrodeposition conditions of Ta complexes and subsequent various heat treatments for the deposited TaOx were examined for the best performance of the ORR. TaOx particles

Susceptibility of CoFeB/AlOx/Co Magnetic Tunnel Junctions to Low-Frequency Alternating Current

Directory of Open Access Journals (Sweden)

Yuan-Tsung Chen

2013-10-01

Full Text Available This investigation studies CoFeB/AlOx/Co magnetic tunneling junction (MTJ in the magnetic field of a low-frequency alternating current, for various thicknesses of the barrier layer AlOx. The low-frequency alternate-current magnetic susceptibility (χac and phase angle (θ of the CoFeB/AlOx/Co MTJ are determined using an cac analyzer. The driving frequency ranges from 10 to 25,000 Hz. These multilayered MTJs are deposited on a silicon substrate using a DC and RF magnetron sputtering system. Barrier layer thicknesses are 22, 26, and 30 Å. The X-ray diffraction patterns (XRD include a main peak at 2θ = 44.7° from hexagonal close-packed (HCP Co with a highly (0002 textured structure, with AlOx and CoFeB as amorphous phases. The full width at half maximum (FWHM of the Co(0002 peak, decreases as the AlOx thickness increases; revealing that the Co layer becomes more crystalline with increasing thickness. χac result demonstrates that the optimal resonance frequency (fres that maximizes the χac value is 500 Hz. As the frequency increases to 1000 Hz, the susceptibility decreases rapidly. However, when the frequency increases over 1000 Hz, the susceptibility sharply declines, and almost closes to zero. The experimental results reveal that the mean optimal susceptibility is 1.87 at an AlOx barrier layer thickness of 30 Å because the Co(0002 texture induces magneto-anisotropy, which improves the indirect CoFeB and Co spin exchange-coupling strength and the χac value. The results concerning magnetism indicate that the magnetic characteristics are related to the crystallinity of Co.

Simple Synthesis and Growth Mechanism of Core/Shell CdSe/SiOx Nanowires

Directory of Open Access Journals (Sweden)

Guozhang Dai

2010-01-01

Full Text Available Core-shell-structured CdSe/SiOx nanowires were synthesized on an equilateral triangle Si (111 substrate through a simple one-step thermal evaporation process. SEM, TEM, and XRD investigations confirmed the core-shell structure; that is, the core zone is single crystalline CdSe and the shell zone is SiOx amorphous layer and CdSe core was grown along (001 direction. Two-stage growth process was present to explain the growth mechanism of the core/shell nanwires. The silicon substrate of designed equilateral triangle providing the silicon source is the key factor to form the core-shell nanowires, which is significant for fabrication of nanowire-core sheathed with a silica system. The PL of the product studied at room temperature showed two emission bands around 715 and 560 nm, which originate from the band-band transition of CdSe cores and the amorphous SiOx shells, respectively.

Genomic repeat abundances contain phylogenetic signal

Czech Academy of Sciences Publication Activity Database

Dodsworth, S.; Chase, M.W.; Kelly, L.J.; Leitch, I.J.; Macas, Jiří; Novák, Petr; Piednoël, M.; Weiß-Schneeweiss, H.; Leitch, A.R.

2015-01-01

Roč. 64, č. 1 (2015), s. 112-126 ISSN 1063-5157 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Repetitive DNA * continuous characters * genomics * next-generation sequencing * phylogenetics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.225, year: 2015

Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships.

Science.gov (United States)

Beloukas, Apostolos; Magiorkinis, Emmanouil; Magiorkinis, Gkikas; Zavitsanou, Asimina; Karamitros, Timokratis; Hatzakis, Angelos; Paraskevis, Dimitrios

2012-06-01

Phylogenetic analysis has been extensively used as a tool for the reconstruction of epidemiological relations for research or for forensic purposes. It was our objective to assess the sensitivity of different phylogenetic methods and various phylogenetic programs to reconstruct epidemiological links among HIV-1 infected patients that is the probability to reveal a true transmission relationship. Multiple datasets (90) were prepared consisting of HIV-1 sequences in protease (PR) and partial reverse transcriptase (RT) sampled from patients with documented epidemiological relationship (target population), and from unrelated individuals (control population) belonging to the same HIV-1 subtype as the target population. Each dataset varied regarding the number, the geographic origin and the transmission risk groups of the sequences among the control population. Phylogenetic trees were inferred by neighbor-joining (NJ), maximum likelihood heuristics (hML) and Bayesian methods. All clusters of sequences belonging to the target population were correctly reconstructed by NJ and Bayesian methods receiving high bootstrap and posterior probability (PP) support, respectively. On the other hand, TreePuzzle failed to reconstruct or provide significant support for several clusters; high puzzling step support was associated with the inclusion of control sequences from the same geographic area as the target population. In contrary, all clusters were correctly reconstructed by hML as implemented in PhyML 3.0 receiving high bootstrap support. We report that under the conditions of our study, hML using PhyML, NJ and Bayesian methods were the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals. Copyright © 2012 Elsevier B.V. All rights reserved.

Effect of the post-annealing temperature on the thermal-decomposed NiOx hole contact layer for perovskite solar cells

Directory of Open Access Journals (Sweden)

Yuxiao Guo

2018-02-01

Full Text Available A hysteresis-less inverted perovskite solar cell (PSC with power conversion efficiency (PCE of 13.57% was successfully achieved based on the thermal-decomposed NiOx hole contact layer, possessing better electron blocking and hole extraction properties for its suitable work function and high-conduction band edge position. Herein, the transparent and high-crystalline NiOx film is prepared by thermal-decomposing of the solution-derived Ni(OH2 film in our study, which is then employed as hole transport layer (HTL of the organic–inorganic hybrid PSCs. Reasonably, the post-annealing treatment, especially for the annealing temperature, could greatly affect the Ni(OH2 decomposition process and the quality of decomposed NiOx nanoparticles. The vital NiOx HTLs with discrepant morphology, crystallinity and transmission certainly lead to a wide range of device performance. As a result, an annealing process of 400∘C/2h significantly promotes the photovoltaic properties of the NiOx layer and the further device performance.

Temperature dependence of interlayer coupling in perpendicular magnetic tunnel junctions with GdOX barriers

Science.gov (United States)

Newhouse-Illige, T.; Xu, Y. H.; Liu, Y. H.; Huang, S.; Kato, H.; Bi, C.; Xu, M.; LeRoy, B. J.; Wang, W. G.

2018-02-01

Perpendicular magnetic tunnel junctions with GdOX tunneling barriers have shown a unique voltage controllable interlayer magnetic coupling effect. Here, we investigate the quality of the GdOX barrier and the coupling mechanism in these junctions by examining the temperature dependence of the tunneling magnetoresistance and the interlayer coupling from room temperature down to 11 K. The barrier is shown to be of good quality with the spin independent conductance only contributing a small portion, 14%, to the total room temperature conductance, similar to AlOX and MgO barriers. The interlayer coupling, however, shows an anomalously strong temperature dependence including sign changes below 80 K. This non-trivial temperature dependence is not described by previous models of interlayer coupling and may be due to the large induced magnetic moment of the Gd ions in the barrier.

Phylogenetic assessment of global Suillus ITS sequences supports morphologically defined species and reveals synonymous and undescribed taxa.

Science.gov (United States)

Nguyen, Nhu H; Vellinga, Else C; Bruns, Thomas D; Kennedy, Peter G

The genus Suillus represents one of the most recognizable groups of mushrooms in conifer forests throughout the Northern Hemisphere. Although for decades the genus has been relatively well defined morphologically, previous molecular phylogenetic assessments have provided important yet preliminary insights into its evolutionary history. We present the first large-scale phylogenetic study of the boundaries of each species in the genus Suillus based on the most current internal transcribed spacer (ITS) barcode sequences available inPUBLIC databases, as well as sequencing of 224 vouchered specimens and cultures, 15 of which were type specimens from North America. We found that species boundaries delimited by morphological data are broadly congruent with those based on ITS sequences. However, some species appear to have been described several times under different names, several species groups cannot be resolved by ITS sequences alone, and undescribed taxa are apparent, especially in Asia. Therefore, we elevated S. tomentosus var. discolor to S. discolor; proposed synonymies of S. neoalbidipes with S. glandulosipes, S. borealis with S. brunnescens, Boletus serotinus and B. solidipes with Suillus elbensis, S. lactifluus with S. granulatus, S. himalayensis with S. americanus; and proposed usage of the names S. clintonianus in the place of the North American S. grevillei, S. weaverae for North American S. granulatus, S. ampliporus in the place of the North American S. cavipes, and S. elbensis in place of the North American S. viscidus. We showed that the majority of Suillus species have strong affinities for particular host genera. Although deep node support was low, geographic differentiation was apparent, with species from North America, Eurasia, and Asia often forming their own clades. Collectively, this comprehensive genus-level phylogenetic integration of currently available Suillus ITS molecular data and metadata will aid future taxonomic and ecological work on an

Interfacial Characteristics of Efficient Bulk Heterojunction Solar Cells Fabricated on MoOx Anode Interlayers.

Science.gov (United States)

Jasieniak, Jacek J; Treat, Neil D; McNeill, Christopher R; de Villers, Bertrand J Tremolet; Della Gaspera, Enrico; Chabinyc, Michael L

2016-05-01

The role of the interface between an MoOx anode interlayer and a polymer:fullerene bulk heterojunction is investigated. Processing differences in the MoOx induce large variations in the vertical stratification of the bulk heterojunction films. These variations are found to be inconsistent in predicting device performance, with a much better gauge being the quantity of polymer chemisorbed to the anode interlayer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

Science.gov (United States)

Vaughan, Timothy G

2017-08-01

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree . Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. tgvaughan@gmail.com. © The Author(s) 2017. Published by Oxford University Press.

Native High Density Lipoproteins (HDL Interfere with Platelet Activation Induced by Oxidized Low Density Lipoproteins (OxLDL

Directory of Open Access Journals (Sweden)

Ivo Volf

2013-05-01

Full Text Available Platelets and lipoproteins play a crucial role in atherogenesis, in part by their ability to modulate inflammation and oxidative stress. While oxidized low density lipoproteins (OxLDL play a central role in the development of this disease, high density lipoproteins (HDL represent an atheroprotective factor of utmost importance. As platelet function is remarkably sensitive to the influence of plasma lipoproteins, it was the aim of this study to clarify if HDL are able to counteract the stimulating effects of OxLDL with special emphasis on aspects of platelet function that are relevant to inflammation. Therefore, HDL were tested for their ability to interfere with pro-thrombotic and pro-inflammatory aspects of platelet function. We are able to show that HDL significantly impaired OxLDL-induced platelet aggregation and adhesion. In gel-filtered platelets, HDL decreased both the formation of reactive oxygen species and CD40L expression. Furthermore, HDL strongly interfered with OxLDL-induced formation of platelet-neutrophil aggregates in whole blood, suggesting that platelets represent a relevant and sensitive target for HDL. The finding that HDL effectively competed with the binding of OxLDL to the platelet surface might contribute to their atheroprotective and antithrombotic properties.

Electrochemical Behavior of TiO(x)C(y) as Catalyst Support for Direct Ethanol Fuel Cells at Intermediate Temperature: From Planar Systems to Powders.

Science.gov (United States)

Calvillo, Laura; García, Gonzalo; Paduano, Andrea; Guillen-Villafuerte, Olmedo; Valero-Vidal, Carlos; Vittadini, Andrea; Bellini, Marco; Lavacchi, Alessandro; Agnoli, Stefano; Martucci, Alessandro; Kunze-Liebhäuser, Julia; Pastor, Elena; Granozzi, Gaetano

2016-01-13

To achieve complete oxidation of ethanol (EOR) to CO2, higher operating temperatures (often called intermediate-T, 150-200 °C) and appropriate catalysts are required. We examine here titanium oxycarbide (hereafter TiOxCy) as a possible alternative to standard carbon-based supports to enhance the stability of the catalyst/support assembly at intermediate-T. To test this material as electrocatalyst support, a systematic study of its behavior under electrochemical conditions was carried out. To have a clear description of the chemical changes of TiOxCy induced by electrochemical polarization of the material, a special setup that allows the combination of X-ray photoelectron spectroscopy and electrochemical measurements was used. Subsequently, an electrochemical study was carried out on TiOxCy powders, both at room temperature and at 150 °C. The present study has revealed that TiOxCy is a sufficiently conductive material whose surface is passivated by a TiO2 film under working conditions, which prevents the full oxidation of the TiOxCy and can thus be considered a stable electrode material for EOR working conditions. This result has also been confirmed through density functional theory (DFT) calculations on a simplified model system. Furthermore, it has been experimentally observed that ethanol molecules adsorb on the TiOxCy surface, inhibiting its oxidation. This result has been confirmed by using in situ Fourier transform infrared spectroscopy (FTIRS). The adsorption of ethanol is expected to favor the EOR in the presence of suitable catalyst nanoparticles supported on TiOxCy.

Silicon Heterojunction Solar Cells Using AlOx and Plasma-Immersion Ion Implantation

Directory of Open Access Journals (Sweden)

Yu-Hsien Lin

2014-06-01

Full Text Available Aluminum oxide (AlOx and plasma immersion ion implantation (PIII were studied in relation to passivated silicon heterojunction solar cells. When aluminum oxide (AlOx was deposited on the surface of a wafer; the electric field near the surface of wafer was enhanced; and the mobility of the carrier was improved; thus reducing carrier traps associated with dangling bonds. Using PIII enabled implanting nitrogen into the device to reduce dangling bonds and achieve the desired passivation effect. Depositing AlOx on the surface of a solar cell increased the short-circuit current density (Jsc; open-circuit voltage (Voc; and conversion efficiency from 27.84 mA/cm2; 0.52 V; and 8.97% to 29.34 mA/cm2; 0.54 V; and 9.68%; respectively. After controlling the depth and concentration of nitrogen by modulating the PIII energy; the ideal PIII condition was determined to be 2 keV and 10 min. As a result; a 15.42% conversion efficiency was thus achieved; and the Jsc; Voc; and fill factor were 37.78 mA/cm2; 0.55 V; and 0.742; respectively.

Highly dispersed TaOx nanoparticles prepared by electrodeposition as oxygen reduction electrocatalysts for polymer electrolyte fuel cells

KAUST Repository

Seo, Jeongsuk

2013-06-06

Based on the chemical stability of group IV and V elements in acidic solutions, TaOx nanoparticles prepared by electrodeposition in an ethanol-based Ta plating bath at room temperature were investigated as novel nonplatinum electrocatalysts for the oxygen reduction reaction (ORR) in polymer electrolyte fuel cells (PEFCs). Electrodeposition conditions of Ta complexes and subsequent various heat treatments for the deposited TaOx were examined for the best performance of the ORR. TaOx particles on carbon black (CB), electrodeposited at a constant potential of -0.5 V Ag/AgCl for 10 s and then heat-treated by pure H2 flow at 523 K for 1 h, showed excellent catalytic activity with an onset potential of 0.93 VRHE (for 2 μA cm-2) for the ORR. Surface characterizations of the catalysts were performed by scanning transmission electron microscopy (STEM), transmission electron microscopy (TEM), and energy dispersive X-ray spectroscopy (EDS). The loading amounts of the electrodeposited material on the CB were determined by inductively coupled plasma atomic emission spectroscopy (ICP-AES). All the physical results suggested that high dispersion of TaOx particles on the CB surface with 2-3 nm size was critical and key for high activity. The chemical identity and modified surface structure for the deposited TaOx catalysts before and after H 2 heat treatment were analyzed by X-ray photoelectron spectroscopy (XPS). The formation of more exposed active sites on the electrode surface and enhanced electroconductivity of the tantalum oxide promoted from the H 2 treatment greatly improved the ORR performance of the electrodeposited TaOx nanoparticles on CB. Finally, the highly retained ORR activity after an accelerated durability test in an acidic solution confirmed and proved the chemical stability of the oxide nanoparticles. The high utilization of the electrodeposited TaOx nanoparticles uniformly dispersed on CB for the ORR was comparable to that of commercial Pt/CB catalysts

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

Science.gov (United States)

Wang, Juan; Guo, Maozu; Xing, Linlin; Che, Kai; Liu, Xiaoyan; Wang, Chunyu

2013-09-15

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/. © 2013 Elsevier B.V. All rights reserved.

Phylogenetic Inference of HIV Transmission Clusters

Directory of Open Access Journals (Sweden)

Vlad Novitsky

2017-10-01

Full Text Available Better understanding the structure and dynamics of HIV transmission networks is essential for designing the most efficient interventions to prevent new HIV transmissions, and ultimately for gaining control of the HIV epidemic. The inference of phylogenetic relationships and the interpretation of results rely on the definition of the HIV transmission cluster. The definition of the HIV cluster is complex and dependent on multiple factors, including the design of sampling, accuracy of sequencing, precision of sequence alignment, evolutionary models, the phylogenetic method of inference, and specified thresholds for cluster support. While the majority of studies focus on clusters, non-clustered cases could also be highly informative. A new dimension in the analysis of the global and local HIV epidemics is the concept of phylogenetically distinct HIV sub-epidemics. The identification of active HIV sub-epidemics reveals spreading viral lineages and may help in the design of targeted interventions.HIVclustering can also be affected by sampling density. Obtaining a proper sampling density may increase statistical power and reduce sampling bias, so sampling density should be taken into account in study design and in interpretation of phylogenetic results. Finally, recent advances in long-range genotyping may enable more accurate inference of HIV transmission networks. If performed in real time, it could both inform public-health strategies and be clinically relevant (e.g., drug-resistance testing.

OxDBase: a database of oxygenases involved in biodegradation

Directory of Open Access Journals (Sweden)

Raghava Gajendra PS

2009-04-01

Full Text Available Abstract Background Oxygenases belong to the oxidoreductive group of enzymes (E.C. Class 1, which oxidize the substrates by transferring oxygen from molecular oxygen (O2 and utilize FAD/NADH/NADPH as the co-substrate. Oxygenases can further be grouped into two categories i.e. monooxygenases and dioxygenases on the basis of number of oxygen atoms used for oxidation. They play a key role in the metabolism of organic compounds by increasing their reactivity or water solubility or bringing about cleavage of the aromatic ring. Findings We compiled a database of biodegradative oxygenases (OxDBase which provides a compilation of the oxygenase data as sourced from primary literature in the form of web accessible database. There are two separate search engines for searching into the database i.e. mono and dioxygenases database respectively. Each enzyme entry contains its common name and synonym, reaction in which enzyme is involved, family and subfamily, structure and gene link and literature citation. The entries are also linked to several external database including BRENDA, KEGG, ENZYME and UM-BBD providing wide background information. At present the database contains information of over 235 oxygenases including both dioxygenases and monooxygenases. This database is freely available online at http://www.imtech.res.in/raghava/oxdbase/. Conclusion OxDBase is the first database that is dedicated only to oxygenases and provides comprehensive information about them. Due to the importance of the oxygenases in chemical synthesis of drug intermediates and oxidation of xenobiotic compounds, OxDBase database would be very useful tool in the field of synthetic chemistry as well as bioremediation.

Phylogenetic mixtures and linear invariants for equal input models.

Science.gov (United States)

Casanellas, Marta; Steel, Mike

2017-04-01

The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies becoming indistinguishable from the data, even for infinitely long sequences. However, when the underlying Markov process supports linear phylogenetic invariants, then provided these are sufficiently informative, the identifiability of the tree topology can be restored. In this paper, we investigate a class of processes that support linear invariants once the stationary distribution is fixed, the 'equal input model'. This model generalizes the 'Felsenstein 1981' model (and thereby the Jukes-Cantor model) from four states to an arbitrary number of states (finite or infinite), and it can also be described by a 'random cluster' process. We describe the structure and dimension of the vector spaces of phylogenetic mixtures and of linear invariants for any fixed phylogenetic tree (and for all trees-the so called 'model invariants'), on any number n of leaves. We also provide a precise description of the space of mixtures and linear invariants for the special case of [Formula: see text] leaves. By combining techniques from discrete random processes and (multi-) linear algebra, our results build on a classic result that was first established by James Lake (Mol Biol Evol 4:167-191, 1987).

Fabrication and investigation of photosensitive MoOx/n-CdTe heterojunctions

Science.gov (United States)

Solovan, M. M.; Gavaleshko, N. M.; Brus, V. V.; Mostovyi, A. I.; Maryanchuk, P. D.; Tresso, E.

2016-10-01

MoOx/n-CdTe photosensitive heterostructures were prepared by the deposition of molybdenum oxide thin films onto n-type single-crystal CdTe substrates by DC reactive magnetron sputtering. The obtained heterojunctions possessed sharply defined rectifying properties with the rectification ration RR ˜ 106. The temperature dependences of the height of the potential barrier and series resistance of the MoOx/CdTe heterojunctions were investigated. The dominating current transport mechanisms through the heterojunctions were determined at forward and reverse biases. The analysis of capacitance-voltage (C-V) characteristics, measured at different frequencies of the small amplitude AC signal and corrected by the effect of the series resistance, provided evidence of the presence of electrically charged interface states, which significantly affect the measured capacitance.

Structural, thermal and photomagnetic properties of spin crossover [Fe(bpp)2]2+ salts bearing [Cr(L)(ox)2]- anions.

Science.gov (United States)

Clemente-León, Miguel; Coronado, Eugenio; Giménez-López, M Carmen; Romero, Francisco M; Asthana, Saket; Desplanches, Cédric; Létard, Jean-François

2009-10-14

This paper is divided into two parts: in the first part, the influence of solvate molecules on the magnetic properties of spin crossover salts of [Fe(bpp)(2)][Cr(L)(ox)(2)]ClO(4) x nS (bpp = 2,6-bis(pyrazol-3yl)pyridine; L = 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen); ox = oxalate dianion; S = solvent) is analyzed. The second part is devoted to the photomagnetic properties of the previously reported [Fe(bpp)(2)][Cr(L)(ox)(2)](2) family of compounds. The study describes the crystal structure, differential scanning calorimetry (DSC) and magnetic properties of [Fe(bpp)(2)][Cr(bpy)(ox)(2)]ClO(4) x EtOH x 4 H(2)O (1) and [Fe(bpp)(2)][Cr(phen)(ox)(2)]ClO(4) x 1.5 EtOH x 4 H(2)O (2). Both salts are high-spin (HS) compounds. Desolvation of 1 yields a material exhibiting a gradual spin crossover that involves 50% of the Fe(2+) cations. Rehydration of this desolvated salt induces a significant increase in the low-spin (LS) population. Desolvation of 2 affords a material showing a more abrupt spin crossover with thermal hysteresis (T(1/2)(increasing) = 286 K and T(1/2)(decreasing) = 273 K). This material is not very sensitive to rehydration. The anhydrous compounds [Fe(bpp)(2)][Cr(bpy)(ox)(2)](2) (3) and [Fe(bpp)(2)][Cr(phen)(ox)(2)](2) (4) display some quantitative photomagnetic conversion with T(LIESST) values of 41 and 51 K, respectively. Kinetic parameters governing the photo-induced HS-LS relaxation process have been determined and used to reproduce the T(LIESST) curves.

A highly stable (SnOx-Sn)@few layered graphene composite anode of sodium-ion batteries synthesized by oxygen plasma assisted milling

Science.gov (United States)

Cheng, Deliang; Liu, Jiangwen; Li, Xiang; Hu, Renzong; Zeng, Meiqing; Yang, Lichun; Zhu, Min

2017-05-01

The (SnOx-Sn)@few layered graphene ((SnOx-Sn)@FLG) composite has been synthesized by oxygen plasma-assisted milling. Owing to the synergistic effect of rapid plasma heating and ball mill grinding, SnOx (1 ≤ x ≤ 2) nanoparticles generated from the reaction of Sn with oxygen are tightly wrapped by FLG nanosheets which are simultaneously exfoliated from expanded graphite, forming secondary micro granules. Inside the granules, the small size of the SnOx nanoparticles enables the fast kinetics for Na+ transfer. The in-situ formed FLG and residual Sn nanoparticles improve the electrical conductivity of the composite, meanwhile alleviate the aggregation of SnOx nanoparticles and relieve the volume change during the cycling, which is beneficial for the cyclic stability for the Na+ storage. As an anode material for sodium-ion batteries, the (SnOx-Sn)@FLG composite exhibits a high reversible capacity of 448 mAh g-1 at a current density of 100 mA g-1 in the first cycle, with 82.6% capacity retention after 250 cycles. Even when the current density increases to 1000 mA g-1, this composite retains 316.5 mAh g-1 after 250 cycles. With superior Na+ storage stability, the (SnOx-Sn)@FLG composite can be a promising anode material for high performance sodium-ion batteries.

Some limitations of public sequence data for phylogenetic inference (in plants).

Science.gov (United States)

Hinchliff, Cody E; Smith, Stephen Andrew

2014-01-01

The GenBank database contains essentially all of the nucleotide sequence data generated for published molecular systematic studies, but for the majority of taxa these data remain sparse. GenBank has value for phylogenetic methods that leverage data-mining and rapidly improving computational methods, but the limits imposed by the sparse structure of the data are not well understood. Here we present a tree representing 13,093 land plant genera--an estimated 80% of extant plant diversity--to illustrate the potential of public sequence data for broad phylogenetic inference in plants, and we explore the limits to inference imposed by the structure of these data using theoretical foundations from phylogenetic data decisiveness. We find that despite very high levels of missing data (over 96%), the present data retain the potential to inform over 86.3% of all possible phylogenetic relationships. Most of these relationships, however, are informed by small amounts of data--approximately half are informed by fewer than four loci, and more than 99% are informed by fewer than fifteen. We also apply an information theoretic measure of branch support to assess the strength of phylogenetic signal in the data, revealing many poorly supported branches concentrated near the tips of the tree, where data are sparse and the limiting effects of this sparseness are stronger. We argue that limits to phylogenetic inference and signal imposed by low data coverage may pose significant challenges for comprehensive phylogenetic inference at the species level. Computational requirements provide additional limits for large reconstructions, but these may be overcome by methodological advances, whereas insufficient data coverage can only be remedied by additional sampling effort. We conclude that public databases have exceptional value for modern systematics and evolutionary biology, and that a continued emphasis on expanding taxonomic and genomic coverage will play a critical role in developing

Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species.

Science.gov (United States)

Larkin, Daniel J; Jacobi, Sarah K; Hipp, Andrew L; Kramer, Andrea T

2016-01-01

Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the 'PIECES' index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet-based decision support tool for North American angiosperms is provided; this tool can be customized to

Developing SyrinOX total antioxidant capacity assay for measuring antioxidants in humans.

Science.gov (United States)

Prasetyo, Endry N; Knes, Otto; Nyanhongo, Gibson S; Guebitz, Georg M

2013-02-01

Accurate monitoring of the antioxidant status or of oxidative stress in patients is still a big challenge in clinical laboratories. This study investigates the possibility of applying a newly developed total antioxidant capacity assay method based on laccase or peroxidase oxidized syringaldazine [Tetramethoxy azobismethylene quinone (TMAMQ)] which is referred to here as SyrinOX, as a diagnostic tool for monitoring both oxidative stress and antioxidant status in patients. Attempts to adapt the Randox total antioxidant procedure [simultaneous incubation of the radical generating system (metmyoglobin and H(2) O(2) ) and antioxidant sample] for SyrinOX were abandoned after it was discovered that the H(2) O(2) reacted with enzymatically generated TMAMQ and ABTS radicals at a rate of 6.4 × 10(-2) /μM/s and 5.7 × 10(-3) /μM/s respectively. Thus this study for the first time demonstrates the negative effects of H(2) O(2) in the Randox system. This leads to erroneous results because the total antioxidant values obtained are the sum of radicals reduced by antioxidants plus those reacting with the radical generating system. Therefore they should be avoided not only for this particular method but also when using other similar methods. Consequently, SyrinOX is best applied using a three-step approach involving, production of TMAMQ, recovery and purification (free from enzyme and other impurities) and then using TMAMQ for measuring the total antioxidant capacity of samples. Using this approach, the reaction conditions for application of SyrinOX when measuring the total antioxidant capacity of plasma sample were determined to be 50% (v/v) ethanol/50 mM sodium succinate buffer pH 5.5, between 20 and 25 °C for at least 1 h. © 2012 The Authors. International Journal of Experimental Pathology © 2012 International Journal of Experimental Pathology.

Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales

OpenAIRE

Purschke, Oliver; Michalski, Stefan G.; Bruelheide, Helge; Durka, Walter

2017-01-01

Abstract Although spatial and temporal patterns of phylogenetic community structure during succession are inherently interlinked and assembly processes vary with environmental and phylogenetic scales, successional studies of community assembly have yet to integrate spatial and temporal components of community structure, while accounting for scaling issues. To gain insight into the processes that generate biodiversity after disturbance, we combine analyses of spatial and temporal phylogenetic ...

Creation and studies of the photosensitivity of Ox/n-GaP structures

Energy Technology Data Exchange (ETDEWEB)

Rud' , V. Yu., E-mail: yuryrud@mail.ioffe.ru [St. Petersburg State Polytechnical University (Russian Federation); Rud' , Yu. V.; Terukov, E. I.; Ushakova, T. N. [Russian Academy of Sciences, Ioffe Physical-Technical Institute (Russian Federation)

2012-06-15

Photosensitive heterostructures Ox/n-GaP, where Ox is a native oxide, are created for the first time by thermal interaction of a GaP crystal with ambient air. The photovoltaic effect of the heterostructures, which dominates upon illumination of the structure's oxide film, is revealed. First, the spectral dependences of the relative quantum efficiency of photoconversion for the obtained heterostructures are analyzed, the character of the band-to-band transitions is determined, and the GaP band gap is estimated. A conclusion is drawn regarding the potential of using the vacuum-free thermal oxidation of homogeneous n-GaP single crystals in ambient air to fabricate broadband photoconverters of optical radiation.

Tuning the optoelectronic properties of amorphous MoOx films by reactive sputtering

DEFF Research Database (Denmark)

Fernandes Cauduro, André Luis; Fabrim, Zacarias Eduardo; Ahmadpour, Mehrad

2015-01-01

In this letter, we report on the effect of oxygen partial pressure and sputtering power on amorphous DC-sputtered MoOx films. We observe abrupt changes in the optoelectronic properties of the reported films by increasing the oxygen partial pressure from 1.00 ? 10?3 mbar to 1.37 ? 10?3 mbar during...... significantly the microstructure of the studied films. The presence of states within the band gap due to the lack of oxygen is the most probable mechanism for generat- ing a change in electrical conductivity as well as optical absorption in DC-sputtered MoOx. The large tuning range of the optoelectronic...... properties in these films holds strong promise for their implementation in optoelectronic devices....

[Oxidation behavior and kinetics of representative VOCs emitted from petrochemical industry over CuCeOx composite oxides].

Science.gov (United States)

Chen, Chang-Wei; Yu, Yan-Ke; Chen, Jin-Sheng; He, Chi

2013-12-01

CuCeOx composite catalysts were synthesized via coprecipitation (COP-CuCeO,) and incipient impregnation (IMP-CuCeOx) methods, respectively. The physicochemical properties of the samples were characterized by XRD, low-temperature N2 sorption, H2-TPR and O2-TPD. The influences of reactant composition and concentration, reaction space velocity, O2 content, H2O concentration, and catalyst type on the oxidation behaviors of benzene, toluene, and n-hexane emitted from petrochemical industry were systematically investigated. In addition, the related kinetic parameters were model fitted. Compared with IMP-CuCeOx, COP-CuCeOx had well-dispersed active phase, better low-temperature reducibility, and more active surface oxygen species. The increase of reactant concentration was unfavorable for toluene oxidation, while the opposite phenomenon could be observed in n-hexane oxidation. The inlet concentration of benzene was irrelevant to its conversion under high oxidation rate. The introduction of benzene obviously inhibited the oxidation of toluene and n-hexane, while the presence of toluene had a positive effect on beuzene conversion. The presence of n-hexane could promote the oxidation of toluene, while toluene had a negative influence on e-hexane oxidation. Both low space velocity and high oxygen concentration were beneficial for the oxidation process, and the variation of oxygen content had negligible effect on n-hexane and henzene oxidation. The presence of H2O noticeably inhibited the oxidation of toluene, while significantly accelerated the oxidation procedure of henzene and n-hexane. COP-CuCeOx had superior catalytic performance for toluene and benzene oxidation, while IMP-CuCeOx showed higher n-hexane oxidation activity under dry condition. The oxidation behaviors under different conditions could be well fitted and predicted by the pseudo first-order kinetic model.

High-performance and low-power rewritable SiOx 1 kbit one diode-one resistor crossbar memory array.

Science.gov (United States)

Wang, Gunuk; Lauchner, Adam C; Lin, Jian; Natelson, Douglas; Palem, Krishna V; Tour, James M

2013-09-14

An entire 1-kilobit crossbar device based upon SiOx resistive memories with integrated diodes has been made. The SiOx -based one diode-one resistor device system has promise to satisfy the prerequisite conditions for next generation non-volatile memory applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Solution-processable MoOx nanocrystals enable highly efficient reflective and semitransparent polymer solar cells

KAUST Repository

Jagadamma, Lethy Krishnan

2016-09-09

Solution-manufacturing of organic solar cells with best-in-class power conversion efficiency (PCE) will require all layers to be solution-coated without compromising solar cell performance. To date, the hole transporting layer (HTL) deposited on top of the organic bulk heterojunction layer in the inverted architecture is most commonly an ultrathin (<10 nm) metal oxide layer prepared by vacuum-deposition. Here, we show that an alcohol-based nanocrystalline MoOx suspension with carefully controlled nanocrystal (NC) size can yield state of the art reflective and semitransparent solar cells. Using NCs smaller than the target HTL thickness (∼10 nm) can yield compact, pinhole-free films which result in highly efficient polymer:fullerene bulk heterojunction (BHJ) solar cells with PCE=9.5%. The solution processed HTL is shown to achieve performance parity with vacuum-evaporated HTLs for several polymer:fullerene combinations and is even shown to work as hole injection layer in polymer light emitting diodes (PLED). We also demonstrate that larger MoOx NCs (30–50 nm) successfully composite MoOx with Ag nanowires (NW) to form a highly conducting, transparent top anode with exceptional contact properties. This yields state-of-the-art semitransparent polymer: fullerene solar cells with PCE of 6.5% and overall transmission >30%. The remarkable performance of reflective and semitransparent OPVs is due to the uncommonly high fill factors achieved using a carefully designed strategy for implementation of MoOx nanocrystals as HTL materials. © 2016 Elsevier Ltd

Comprehensive behavioral analysis of Ox1r-/- mice showed implication of orexin receptor-1 in mood, anxiety and social behavior

Directory of Open Access Journals (Sweden)

Md Golam Abbas

2015-12-01

Full Text Available Neuropeptides orexin A and orexin B, which are exclusively produced by neurons in the lateral hypothalamic area, play an important role in the regulation of a wide range of behaviors and homeostatic processes, including regulation of sleep/wakefulness states and energy homeostasis. The orexin system has close anatomical and functional relationships with systems that regulate the autonomic nervous system, emotion, mood, the reward system and sleep/wakefulness states. Recent pharmacological studies using selective antagonists have suggested that orexin receptor-1 (OX1R is involved in physiological processes that regulate emotion, the reward system and autonomic nervous system. Here, we examined Ox1r-/- mice with a comprehensive behavioral test battery to screen additional OX1R functions. Ox1r-/- mice showed increased anxiety-like behavior, altered depression-like behavior, slightly decreased spontaneous locomotor activity, reduced social interaction, increased startle response and decreased prepulse inhibition. These results suggest that OX1R plays roles in social behaviour and sensory motor gating in addition to roles in mood and anxiety.

Marine turtle mitogenome phylogenetics and evolution

DEFF Research Database (Denmark)

Duchene, Sebastián; Frey, Amy; Alfaro-Núñez, Luis Alonso

2012-01-01

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae...... distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses...... to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all...

Laser irradiation in water for the novel, scalable synthesis of black TiOx photocatalyst for environmental remediation

Directory of Open Access Journals (Sweden)

Massimo Zimbone

2017-01-01

Full Text Available Since 1970, TiO2 photocatalysis has been considered a possible alternative for sustainable water treatment. This is due to its material stability, abundance, nontoxicity and high activity. Unfortunately, its wide band gap (≈3.2 eV in the UV portion of the spectrum makes it inefficient under solar illumination. Recently, so-called “black TiO2” has been proposed as a candidate to overcome this issue. However, typical synthesis routes require high hydrogen pressure and long annealing treatments. In this work, we present an industrially scalable synthesis of TiO2-based material based on laser irradiation. The resulting black TiOx shows a high activity and adsorbs visible radiation, overcoming the main concerns related to the use of TiO2 under solar irradiation. We employed a commercial high repetition rate green laser in order to synthesize a black TiOx layer and we demonstrate the scalability of the present methodology. The photocatalyst is composed of a nanostructured titanate film (TiOx synthetized on a titanium foil, directly back-contacted to a layer of Pt nanoparticles (PtNps deposited on the rear side of the same foil. The result is a monolithic photochemical diode with a stacked, layered structure (TiOx/Ti/PtNps. The resulting high photo-efficiency is ascribed to both the scavenging of electrons by Pt nanoparticles and the presence of trap surface states for holes in an amorphous hydrogenated TiOx layer.

An Isotope Study of Hydrogenation of poly-Si/SiOx Passivated Contacts for Si Solar Cells: Preprint

Energy Technology Data Exchange (ETDEWEB)

Schnabel, Manuel; Nemeth, William; van de Loo, Bas, W.H.; Macco, Bart; Kessels, Wilhelmus, M.M.; Stradins, Paul; Young, David, L.

2017-06-26

For many years, the record Si solar cell efficiency stood at 25.0%. Only recently have several companies and institutes managed to produce more efficient cells, using passivated contacts of made doped poly-Si or a-Si:H and a passivating intrinsic interlayer in all cases. Common to these designs is the need to passivate the layer stack with hydrogen. In this contribution, we perform a systematic study of passivated contact passivation by hydrogen, using poly-Si/SiOx passivated contacts on n-Cz-Si, and ALD Al2O3 followed by a forming gas anneal (FGA) as the hydrogen source. We study p-type and n-type passivated contacts with implied Voc exceeding 690 and 720 mV, respectively, and perform either the ALD step or the FGA with deuterium instead of hydrogen in order to separate the two processes via SIMS. By examining the deuterium concentration at the SiOx in both types of samples, we demonstrate that the FGA supplies negligible hydrogen species to the SiOx, regardless of whether the FGA is hydrogenated or deuterated. Instead, it supplies the thermal energy needed for hydrogen species in the Al2O3 to diffuse there. Furthermore, the concentration of hydrogen species at the SiOx can saturate while implied Voc continues to increase, showing that the energy from the FGA is also required for hydrogen species already at the SiOx to find recombination-active defects to passivate.

Investigation of OxProduction Rates in the Mexico City Metropolitan Area during MILAGRO

Science.gov (United States)

Dusanter, S.; Molina, L. T.; Stevens, P. S.

2009-12-01

Understanding the oxidative capacity of the atmosphere and the formation of secondary pollutants are important issues in atmospheric chemistry. For instance, the photochemical production of tropospheric ozone (O3) is of particular interest due to its detrimental effects on both human health and agricultural ecosystems. A detailed characterization of tropospheric O3 production rates will help in the development of effective control strategies. The 2006 Mexico City Metropolitan Area field campaign (MCMA-2006) was one of four components of MILAGRO (Megacity Initiative: Local And Global Research Observations) intended to collect information on the impact of megacity emissions on local, regional and global scales. In this presentation, rates of production of Ox (Ox = O3 + NO2) species during MCMA-2006 at the supersite T0 (Instituto Mexicano del Petroleo) will be presented using different approaches based on measured and modeled concentrations of ROx (OH + HO2 + RO2) radicals. In addition, we will examine both the reactivity of OH and the contribution of specific peroxy radicals to the oxidation rate of NO to estimate the contribution of groups of VOCs (alkanes, alkenes, aromatics, oxygenated and biogenic VOCs) to the total production rate of Ox species.

Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant

Science.gov (United States)

Yin, Jie; Mobarec, Juan Carlos; Kolb, Peter; Rosenbaum, Daniel M.

2015-03-01

The orexin (also known as hypocretin) G protein-coupled receptors (GPCRs) respond to orexin neuropeptides in the central nervous system to regulate sleep and other behavioural functions in humans. Defects in orexin signalling are responsible for the human diseases of narcolepsy and cataplexy; inhibition of orexin receptors is an effective therapy for insomnia. The human OX2 receptor (OX2R) belongs to the β branch of the rhodopsin family of GPCRs, and can bind to diverse compounds including the native agonist peptides orexin-A and orexin-B and the potent therapeutic inhibitor suvorexant. Here, using lipid-mediated crystallization and protein engineering with a novel fusion chimaera, we solved the structure of the human OX2R bound to suvorexant at 2.5 Å resolution. The structure reveals how suvorexant adopts a π-stacked horseshoe-like conformation and binds to the receptor deep in the orthosteric pocket, stabilizing a network of extracellular salt bridges and blocking transmembrane helix motions necessary for activation. Computational docking suggests how other classes of synthetic antagonists may interact with the receptor at a similar position in an analogous π-stacked fashion. Elucidation of the molecular architecture of the human OX2R expands our understanding of peptidergic GPCR ligand recognition and will aid further efforts to modulate orexin signalling for therapeutic ends.

Phylogenetic analyses of behavior support existence of culture among wild chimpanzees.

Science.gov (United States)

Lycett, Stephen J; Collard, Mark; McGrew, William C

2007-11-06

Culture has long been considered to be not only unique to humans, but also responsible for making us qualitatively different from all other forms of life. In recent years, however, researchers studying chimpanzees (Pan troglodytes) have challenged this idea. Natural populations of chimpanzees have been found to vary greatly in their behavior. Because many of these interpopulation differences cannot be readily explained by ecological factors, it has been argued that they result from social learning and, therefore, can be regarded as cultural variations. Recent studies showing social transmission in captive chimpanzee populations suggest that this hypothesis is plausible. However, the culture hypothesis has been questioned on the grounds that the behavioral variation may be explained at a proximate level by genetic differences between subspecies. Here we use cladistic analyses of the major cross-site behavioral data set to test the hypothesis that the behavioral differences among the best-documented chimpanzee populations are genetically determined. If behavioral diversity is primarily the product of genetic differences between subspecies, then population data should show less phylogenetic structure when data from a single subspecies (P. t. schweinfurthii) are compared with data from two subspecies (P. t. verus and P. t. schweinfurthii) analyzed together. Our findings are inconsistent with the hypothesis that the observed behavioral patterns of wild chimpanzee populations can be explained primarily by genetic differences between subspecies. Instead, our results support the suggestion that the behavioral patterns are the product of social learning and, therefore, can be considered cultural.

Time-resolved photoluminescence of SiOx encapsulated Si

Science.gov (United States)

Kalem, Seref; Hannas, Amal; Österman, Tomas; Sundström, Villy

Silicon and its oxide SiOx offer a number of exciting electrical and optical properties originating from defects and size reduction enabling engineering new electronic devices including resistive switching memories. Here we present the results of photoluminescence dynamics relevant to defects and quantum confinement effects. Time-resolved luminescence at room temperature exhibits an ultrafast decay component of less than 10 ps at around 480 nm and a slower component of around 60 ps as measured by streak camera. Red shift at the initial stages of the blue luminescence decay confirms the presence of a charge transfer to long lived states. Time-correlated single photon counting measurements revealed a life-time of about 5 ns for these states. The same quantum structures emit in near infrared close to optical communication wavelengths. Nature of the emission is described and modeling is provided for the luminescence dynamics. The electrical characteristics of metal-oxide-semiconductor devices were correlated with the optical and vibrational measurement results in order to have better insight into the switching mechanisms in such resistive devices as possible next generation RAM memory elements. ``This work was supported by ENIAC Joint Undertaking and Laser-Lab Europe''.

Orexins excite ventrolateral geniculate nucleus neurons predominantly via OX2 receptors.

Science.gov (United States)

Chrobok, Lukasz; Palus, Katarzyna; Lewandowski, Marian Henryk

2016-04-01

Orexins/hypocretins are two neuropeptides that influence many behaviours, such as feeding, sleep or arousal. Orexin A/hypocretin-1 (OXA) and orexin B/hypocretin-2 (OXB) bind to two metabotropic receptors, named the OX1 and OX2 receptors. The lateral geniculate complex of the thalamus is one of the many targets of orexinergic fibres derived from the lateral hypothalamus, although the impact of orexins on the ventrolateral geniculate nucleus (VLG) is poorly understood. The VLG, an important relay station of the subcortical visual system, is implicated in visuomotor and/or circadian processes. Therefore, in this study we evaluated the effects of orexins on single VLG neurons using a patch-clamp technique in vitro. Surprisingly, orexins depolarised the majority of the recorded neurons regardless of their localisation in the borders of the VLG. In addition, data presented in this article show that neurons synthesising NO were also affected by OXA. Moreover, immunohistochemical staining of OXB revealed the moderate density of orexinergic fibbers in the VLG. Our study using specific orexin receptor antagonists suggests that the OX2 receptor has a dominant role in the observed effects of OXA. To our knowledge, this article is the first to show orexinergic modulation of the VLG. These findings strengthen the postulated link between orexins and the circadian system, and propose a new role of these neuropeptides in the modulation of visuomotor functions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogeny and phylogenetic classification of the antbirds, ovenbirds, woodcreepers, and allies (Aves: Passeriformes: Infraorder Furnariides)

Science.gov (United States)

Moyle, R.G.; Chesser, R.T.; Brumfield, R.T.; Tello, J.G.; Marchese, D.J.; Cracraft, J.

2009-01-01

The infraorder Furnariides is a diverse group of suboscine passerine birds comprising a substantial component of the Neotropical avifauna. The included species encompass a broad array of morphologies and behaviours, making them appealing for evolutionary studies, but the size of the group (ca. 600 species) has limited well-sampled higher-level phylogenetic studies. Using DNA sequence data from the nuclear RAG-1 and RAG-2 exons, we undertook a phylogenetic analysis of the Furnariides sampling 124 (more than 88%) of the genera. Basal relationships among family-level taxa differed depending on phylogenetic method, but all topologies had little nodal support, mirroring the results from earlier studies in which discerning relationships at the base of the radiation was also difficult. In contrast, branch support for family-rank taxa and for many relationships within those clades was generally high. Our results support the Melanopareidae and Grallariidae as distinct from the Rhinocryptidae and Formicariidae, respectively. Within the Furnariides our data contradict some recent phylogenetic hypotheses and suggest that further study is needed to resolve these discrepancies. Of the few genera represented by multiple species, several were not monophyletic, indicating that additional systematic work remains within furnariine families and must include dense taxon sampling. We use this study as a basis for proposing a new phylogenetic classification for the group and in the process erect new family-group names for clades having high branch support across methods. ?? 2009 The Willi Hennig Society.

Effects of Ion Beam Irradiation on Nanoscale InOx Cooper-Pair Insulators

Directory of Open Access Journals (Sweden)

Srdjan Milosavljević

2013-01-01

Full Text Available This paper examines the effects of irradiating indium oxide films of nanoscale thickness by ion beams, when these films are in the Cooper-pair insulator state. Radiation effects are predicted on the basis of Monte Carlo simulations of ion transport. Results of numerical experiments are interpreted within the theoretical model of a Cooper-pair insulator. The study suggests that radiation-induced changes in InOx films exposed to ion beams could significantly alter their current-voltage characteristics and that a transition to a metallic state is possible, due to radiation-induced perturbation of the fine-tuned granular structure. Furthermore, incident and displaced ions can break up enough Cooper pairs in InOx films to cause dissolution of this specific insulating state.

Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics

Directory of Open Access Journals (Sweden)

Alexander Safatli

2015-06-01

Full Text Available Summary. Pylogeny is a cross-platform library for the Python programming language that provides an object-oriented application programming interface for phylogenetic heuristic searches. Its primary function is to permit both heuristic search and analysis of the phylogenetic tree search space, as well as to enable the design of novel algorithms to search this space. To this end, the framework supports the structural manipulation of phylogenetic trees, in particular using rearrangement operators such as NNI, SPR, and TBR, the scoring of trees using parsimony and likelihood methods, the construction of a tree search space graph, and the programmatic execution of a few existing heuristic programs. The library supports a range of common phylogenetic file formats and can be used for both nucleotide and protein data. Furthermore, it is also capable of supporting GPU likelihood calculation on nucleotide character data through the BEAGLE library.Availability. Existing development and source code is available for contribution and for download by the public from GitHub (http://github.com/AlexSafatli/Pylogeny. A stable release of this framework is available for download through PyPi (Python Package Index at http://pypi.python.org/pypi/pylogeny.

Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction.

Science.gov (United States)

Beiko, Robert G; Ragan, Mark A

2009-01-01

Phylogenomic methods can be used to investigate the tangled evolutionary relationships among genomes. Building 'all the trees of all the genes' can potentially identify common pathways of horizontal gene transfer (HGT) among taxa at varying levels of phylogenetic depth. Phylogenetic affinities can be aggregated and merged with the information about genetic linkage and biochemical function to examine hypotheses of adaptive evolution via HGT. Additionally, the use of many genetic data sets increases the power of statistical tests for phylogenetic artifacts. However, large-scale phylogenetic analyses pose several challenges, including the necessary abandonment of manual validation techniques, the need to translate inferred phylogenetic discordance into inferred HGT events, and the challenges involved in aggregating results from search-based inference methods. In this chapter we describe a tree search procedure to recover the most parsimonious pathways of HGT, and examine some of the assumptions that are made by this method.

Striation Patterns of Ox Muscle in Rigor Mortis

Science.gov (United States)

Locker, Ronald H.

1959-01-01

Ox muscle in rigor mortis offers a selection of myofibrils fixed at varying degrees of contraction from sarcomere lengths of 3.7 to 0.7 µ. A study of this material by phase contrast and electron microscopy has revealed four distinct successive patterns of contraction, including besides the familiar relaxed and contracture patterns, two intermediate types (2.4 to 1.9 µ, 1.8 to 1.5 µ) not previously well described. PMID:14417790

SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees.

Science.gov (United States)

DeBlasio, Dan F; Wisecaver, Jennifer H

2016-01-01

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.

SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees

Directory of Open Access Journals (Sweden)

Dan F. DeBlasio

2016-08-01

Full Text Available We present the phylogeny analysis software SICLE (Sister Clade Extractor, an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.

PMMA-g-OEtOx Graft Copolymers: Influence of Grafting Degree and Side Chain Length on the Conformation in Aqueous Solution

Directory of Open Access Journals (Sweden)

Irina Muljajew

2018-03-01

Full Text Available Depending on the degree of grafting (DG and the side chain degree of polymerization (DP, graft copolymers may feature properties similar to statistical copolymers or to block copolymers. This issue is approached by studying aqueous solutions of PMMA-g-OEtOx graft copolymers comprising a hydrophobic poly(methyl methacrylate (PMMA backbone and hydrophilic oligo(2-ethyl-2-oxazoline (OEtOx side chains. The graft copolymers were synthesized via reversible addition-fragmentation chain transfer (RAFT copolymerization of methyl methacrylate (MMA and OEtOx-methacrylate macromonomers of varying DP. All aqueous solutions of PMMA-g-OEtOx (9% ≤ DG ≤ 34%; 5 ≤ side chain DP ≤ 24 revealed lower critical solution temperature behavior. The graft copolymer architecture significantly influenced the aggregation behavior, the conformation in aqueous solution and the coil to globule transition, as verified by means of turbidimetry, dynamic light scattering, nuclear magnetic resonance spectroscopy, and analytical ultracentrifugation. The aggregation behavior of graft copolymers with a side chain DP of 5 was significantly affected by small variations of the DG, occasionally forming mesoglobules above the cloud point temperature (Tcp, which was around human body temperature. On the other hand, PMMA-g-OEtOx with elongated side chains assembled into well-defined structures below the Tcp (apparent aggregation number (Nagg = 10 that were able to solubilize Disperse Orange 3. The thermoresponsive behavior of aqueous solutions thus resembled that of micelles comprising a poly(2-ethyl-2-oxazoline (PEtOx shell (Tcp > 60 °C.

Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

Science.gov (United States)

Santos, Bráulio A; Arroyo-Rodríguez, Víctor; Moreno, Claudia E; Tabarelli, Marcelo

2010-09-08

Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment of tree assemblages reduce the phylogenetic diversity of the remaining tree assemblages. We detected a significant loss of tree phylogenetic diversity in forest edges, but not in core areas of small (phylogenetic distance between any two randomly chosen individuals from forest edges; an increase of 17% in the average phylogenetic distance to closest non-conspecific relative for each individual in forest edges; and to the potential manifestation of late edge effects in the core areas of small forest remnants. We found no evidence supporting fragmentation-induced phylogenetic clustering or evenness. This could be explained by the low phylogenetic conservatism of key life-history traits corresponding to vulnerable species. Edge effects must be reduced to effectively protect tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

Physical and Chemical Properties of TiOxNy Prepared by Low-Temperature Oxidation of Ultrathin Metal Nitride Directly Deposited on SiO2

Institute of Scientific and Technical Information of China (English)

HAN Yue-Ping; HAN Yan

2009-01-01

Physical and chemical properties of titanium oxynitride (TiOxNy) formed by low-temperature oxidation of titanium nitride (TIN) layer are investigated for advanced metal-oxide--semiconductor (MOS) gate dielectric application.TiOx Ny exhibits polycrystalline properties after the standard thermal process for MOS device fabrication,showing the preferred orientation at [200].Superior electrical properties of TiOxNy can be maintained before and after the annealing,probably due to the nitrogen incorporation in the oxide bulk and at the interface.Naturally formed transition layer between TiOxNy and SiO2 is also confirmed.

The Microstructures and Electrical Resistivity of (Al, Cr, TiFeCoNiOx High-Entropy Alloy Oxide Thin Films

Directory of Open Access Journals (Sweden)

Chun-Huei Tsau

2015-01-01

Full Text Available The (Al, Cr, TiFeCoNi alloy thin films were deposited by PVD and using the equimolar targets with same compositions from the concept of high-entropy alloys. The thin films became metal oxide films after annealing at vacuum furnace for a period; and the resistivity of these thin films decreased sharply. After optimum annealing treatment, the lowest resistivity of the FeCoNiOx, CrFeCoNiOx, AlFeCoNiOx, and TiFeCoNiOx films was 22, 42, 18, and 35 μΩ-cm, respectively. This value is close to that of most of the metallic alloys. This phenomenon was caused by delaminating of the alloy oxide thin films because the oxidation was from the surfaces of the thin films. The low resistivity of these oxide films was contributed to the nonfully oxidized elements in the bottom layers and also vanishing of the defects during annealing.

Alternatives to SiOx for protective scan mirror coatings in remote sensing instruments

Science.gov (United States)

MacDonald, Michael E.

1999-09-01

Mirrors in remote sensing instruments require durable dielectric coatings, both to prevent oxidation of the reflective surface and to protect it during cleaning. IR absorption bands within widely-used SiOx coatings produce scene radiance and instrument background variations as a function of scan mirror angle which motivate the search for possible substitute materials. In this work several candidate coatings are evaluated including CeF3, HfO2, MgF2 SrF2, and Y2O3. This evaluation consists of reflectance, adhesion, and durability measurements of mirrors with an aluminum reflective surface over-coated with these materials. S-polarized and P- polarized reflectance measurements are presented between 2 and 20 micrometers for incidence angles between 40 and 50 degrees. This angular range is sufficient to scan the earth disk from geostationary orbit. Additional measurements at 45 degrees incidence are presented between 2 and 55 micrometers , covering the IR wavelength range of interest for earth radiation budget sensors. Comparisons are drawn with measurements of scan- mirror witness samples from the imaging and sounding instruments used in the Geostationary Operational Environmental Satellite (GOES). These witness samples exhibit reflectance variations arising from IR absorption bands in the SiOx protective coatings used in these mirrors. The spectral characteristics of several of the alternate materials are found to be quite attractive, however durable coatings of some of these materials require elevated deposition temperature which are incompatible with the nickel-coated beryllium scan mirror substrate construction used in GOES. This work present the achievable reflectance and durability of these alternate dielectric protective coatings at the deposition temperature constraints imposed by the scan mirror substrate. The prospects for substituting one of these coatings for SiOx are evaluated, and contrasted with the capability of radiometric calibration techniques to deal

The effect of oxLDL on microvesicle release from platelets, measured by a sensitive flow cytometry method.

Directory of Open Access Journals (Sweden)

Tine Bo Nielsen

2015-11-01

Full Text Available Microvesicles (MVs are submicron vesicles with sizes of 0.1-1.0-µm in diameter, released from various cell types upon activation or apoptosis. Their involvement in a variety of diseases has been intensively investigated. In blood, platelets are potent MV secretors, and oxLDL, a platelet ligand, induce platelet activation and thus potentially MV secretion. This interaction occurs through binding of oxLDL with CD36, located on the platelet membrane. In this study we investigated the effect of in vitro incubation of platelets with oxLDL on MV release. Furthermore, we compared the results obtained when separating MVs larger than 0.5-µm as a measure of results obtained from less sensitive conventional flow cytometers with MVs below the 0.5-µm limit. MV size-distribution was analysed in plasma from 11 healthy volunteers (4 females, 7 males. MVs were identified as < 1-μm and positive for lactadherin binding and cell specific markers. Platelet rich plasma (PRP was incubated without and with oxLDL or LDL (as control to investigate the impact on platelet activation, evident by release of MVs. Size-calibrated fluorescent beads were used to establish the MV gate, and separate small- and large-size vesicles. CD41+ and CD41+CD36+ MVs increased by 6-8 fold in PRP, when left at room temperature, and the presence of cell specific markers increased. Total MV count was unaffected. Incubations with oxLDL did not increase the MV release or affect the distribution of small- and large-size MVs. We found a large inter-individual variation in the fraction of small- and large-size MVs of 73%. In conclusion, we propose that pro-coagulant activity and activation of platelets induced by interaction of platelet CD36 with oxLDL may not involve release of MVs. Furthermore, our results demonstrate great inter-individual variability in size-distribution of platelet derived MVs and thereby stresses the importance for generation of standardized protocols for MV quantification

A Phylogenetic Comparative Study of Bantu Kinship Terminology Finds Limited Support for Its Co-Evolution with Social Organisation.

Directory of Open Access Journals (Sweden)

Myrtille Guillon

Full Text Available The classification of kin into structured groups is a diverse phenomenon which is ubiquitous in human culture. For populations which are organized into large agropastoral groupings of sedentary residence but not governed within the context of a centralised state, such as our study sample of 83 historical Bantu-speaking groups of sub-Saharan Africa, cultural kinship norms guide all aspects of everyday life and social organization. Such rules operate in part through the use of differing terminological referential systems of familial organization. Although the cross-cultural study of kinship terminology was foundational in Anthropology, few modern studies have made use of statistical advances to further our sparse understanding of the structuring and diversification of terminological systems of kinship over time. In this study we use Bayesian Markov Chain Monte Carlo methods of phylogenetic comparison to investigate the evolution of Bantu kinship terminology and reconstruct the ancestral state and diversification of cousin terminology in this family of sub-Saharan ethnolinguistic groups. Using a phylogenetic tree of Bantu languages, we then test the prominent hypothesis that structured variation in systems of cousin terminology has co-evolved alongside adaptive change in patterns of descent organization, as well as rules of residence. We find limited support for this hypothesis, and argue that the shaping of systems of kinship terminology is a multifactorial process, concluding with possible avenues of future research.

Phylogenetic evidence for cladogenetic polyploidization in land plants.

Science.gov (United States)

Zhan, Shing H; Drori, Michal; Goldberg, Emma E; Otto, Sarah P; Mayrose, Itay

2016-07-01

Polyploidization is a common and recurring phenomenon in plants and is often thought to be a mechanism of "instant speciation". Whether polyploidization is associated with the formation of new species (cladogenesis) or simply occurs over time within a lineage (anagenesis), however, has never been assessed systematically. We tested this hypothesis using phylogenetic and karyotypic information from 235 plant genera (mostly angiosperms). We first constructed a large database of combined sequence and chromosome number data sets using an automated procedure. We then applied likelihood models (ClaSSE) that estimate the degree of synchronization between polyploidization and speciation events in maximum likelihood and Bayesian frameworks. Our maximum likelihood analysis indicated that 35 genera supported a model that includes cladogenetic transitions over a model with only anagenetic transitions, whereas three genera supported a model that incorporates anagenetic transitions over one with only cladogenetic transitions. Furthermore, the Bayesian analysis supported a preponderance of cladogenetic change in four genera but did not support a preponderance of anagenetic change in any genus. Overall, these phylogenetic analyses provide the first broad confirmation that polyploidization is temporally associated with speciation events, suggesting that it is indeed a major speciation mechanism in plants, at least in some genera. © 2016 Botanical Society of America.

Kaempferol alleviates ox-LDL-induced apoptosis by up-regulation of autophagy via inhibiting PI3K/Akt/mTOR pathway in human endothelial cells.

Science.gov (United States)

Che, Jianbo; Liang, Bing; Zhang, Yuan; Wang, Yi; Tang, Jianyu; Shi, Gongning

Oxidized low-density lipoprotein (ox-LDL) has been reported to induce apoptosis of endothelial cells (ECs) and contribute to the progression of atherosclerosis. Kaempferol has been shown to possess antiatherosclerotic effect. The aim of the present study was to evaluate the effect of kaempferol on ox-LDL-induced apoptosis of human umbilical vein endothelial cells (HUVECs) and its possible molecular basis. The results showed that kaempferol alleviated ox-LDL-induced apoptosis. Kaempferol increased the ratio of LC3-II/I and beclin-1 level in ox-LDL-induced HUVECs. Moreover, the expression of p-Akt and p-mTOR was down-regulated after treatment with kaempferol in ox-LDL-treated HUVECs, which is similar to the effect of PI3K inhibitor (LY294002) or mTOR inhibitor [rapamycin (RAP)]. Besides, autophagy induced by kaempferol was enhanced by LY294002 or RAP, while kaempferol-induced autophagy was attenuated with insulin treatment, the activator of PI3K/Akt/mTOR pathway. Furthermore, insulin also abated the effect of kaempferol on cell viability and apoptosis in ox-LDL-induced HUVECs. The results indicated that kaempferol alleviated ox-LDL-induced cell apoptosis by up-regulation of autophagy via inhibiting PI3K/Akt/mTOR pathway in human ECs. Copyright © 2017 Elsevier Inc. All rights reserved.

Nonbinary Tree-Based Phylogenetic Networks.

Science.gov (United States)

Jetten, Laura; van Iersel, Leo

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

Socio-economic impact of ox skidding project to the surrounding ...

African Journals Online (AJOL)

The ox skidding project was initiated with the objective of using oxen for transporting logs from the stump sites to the landings. It was supposed to be a participatory research project aimed at integrating scientific knowledge with practical skills and resource base of the local farmers. Specifically the main objective of the ...

Different Molecular/Behavioral Endophenotypes in C57BL/6J Mice Predict the Impact of OX1 Receptor Blockade on Binge-Like Ethanol Intake

Directory of Open Access Journals (Sweden)

Manuel Alcaraz-Iborra

2017-10-01

Full Text Available Ethanol (EtOH research has focused on stages of dependence. It is of paramount importance to more deeply understand the neurobehavioral factors promoting increased risk for EtOH binge drinking during the early stages of the addiction cycle. The first objective of this study was to evaluate whether C57BL/6J mice showing high drinking in the dark (DID exhibit neurobehavioral traits known to contribute to EtOH binge-drinking disorders. Comparing high vs. low drinkers (HD/LD, we evaluated different types of basal anxiety-like responses, EtOH preference and sensitivity to the reinforcing properties of EtOH, and basal mRNA expression of the OX1/OX2 receptors (OX1r/OX2r within the prefrontal cortex (PFC and the nucleus accumbens (NAcc. Additionally, we tested binge drinking by LD/HD in response to a selective OX1r antagonist following intermittent episodes of DID (iDID. We report that DID consistently segregates two neurobehavioral endophenotypes, HD vs. LD, showing differences in neophobia and/or impulsivity/compulsivity traits. Additionally, HD mice show decreased basal OX1r and OX2r mRNA expression within the NAcc and elevated OX1r within the PFC. Exposure to several intermittent episodes of EtOH DID triggered a rapid increase in EtOH intake over time in LD mice matching that observed in HD mice. Despite HD/LD endophenotypes did not show differences in EtOH intake, they still predicted the response to a pharmacological challenge with a selective OX1r antagonist. The present data underscore the relevance of HD/LD endophenotypes stemming from DID procedures for exploring neurobehavioral processes underlying the early stages of the addiction cycle and EtOH binge-drinking disorders.

Click chemistry for the conservation of cellular structures and fluorescent proteins: ClickOx.

Science.gov (United States)

Löschberger, Anna; Niehörster, Thomas; Sauer, Markus

2014-05-01

Reactive oxygen species (ROS), including hydrogen peroxide, are known to cause structural damage not only in living, but also in fixed, cells. Copper-catalyzed azide-alkyne cycloaddition (click chemistry) is known to produce ROS. Therefore, fluorescence imaging of cellular structures, such as the actin cytoskeleton, remains challenging when combined with click chemistry protocols. In addition, the production of ROS substantially weakens the fluorescence signal of fluorescent proteins. This led us to develop ClickOx, which is a new click chemistry protocol for improved conservation of the actin structure and better conservation of the fluorescence signal of green fluorescent protein (GFP)-fusion proteins. Herein we demonstrate that efficient oxygen removal by addition of an enzymatic oxygen scavenger system (ClickOx) considerably reduces ROS-associated damage during labeling of nascent DNA with ATTO 488 azide by Cu(I)-catalyzed click chemistry. Standard confocal and super-resolution fluorescence images of phalloidin-labeled actin filaments and GFP/yellow fluorescent protein-labeled cells verify the conservation of the cytoskeleton microstructure and fluorescence intensity, respectively. Thus, ClickOx can be used advantageously for structure preservation in conventional and most notably in super-resolution microscopy methods. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular phylogenetics of porcini mushrooms (Boletus section Boletus).

Science.gov (United States)

Dentinger, Bryn T M; Ammirati, Joseph F; Both, Ernst E; Desjardin, Dennis E; Halling, Roy E; Henkel, Terry W; Moreau, Pierre-Arthur; Nagasawa, Eiji; Soytong, Kasem; Taylor, Andy F; Watling, Roy; Moncalvo, Jean-Marc; McLaughlin, David J

2010-12-01

Porcini (Boletus section Boletus: Boletaceae: Boletineae: Boletales) are a conspicuous group of wild, edible mushrooms characterized by fleshy fruiting bodies with a poroid hymenophore that is "stuffed" with white hyphae when young. Their reported distribution is with ectomycorrhizal plants throughout the Northern Hemisphere. Little progress has been made on the systematics of this group using modern molecular phylogenetic tools because sampling has been limited primarily to European species and the genes employed were insufficient to resolve the phylogeny. We examined the evolutionary history of porcini by using a global geographic sampling of most known species, new discoveries from little explored areas, and multiple genes. We used 78 sequences from the fast-evolving nuclear internal transcribed spacers and are able to recognize 18 reciprocally monophyletic species. To address whether or not porcini form a monophyletic group, we compiled a broadly sampled dataset of 41 taxa, including other members of the Boletineae, and used separate and combined phylogenetic analysis of sequences from the nuclear large subunit ribosomal DNA, the largest subunit of RNA polymerase II, and the mitochondrial ATPase subunit six gene. Contrary to previous studies, our separate and combined phylogenetic analyses support the monophyly of porcini. We also report the discovery of two taxa that expand the known distribution of porcini to Australia and Thailand and have ancient phylogenetic connections to the rest of the group. A relaxed molecular clock analysis with these new taxa dates the origin of porcini to between 42 and 54 million years ago, coinciding with the initial diversification of angiosperms, during the Eocene epoch when the climate was warm and humid. These results reveal an unexpected diversity, distribution, and ancient origin of a group of commercially valuable mushrooms that may provide an economic incentive for conservation and support the hypothesis of a tropical

Bias in phylogenetic reconstruction of vertebrate rhodopsin sequences.

Science.gov (United States)

Chang, B S; Campbell, D L

2000-08-01

Two spurious nodes were found in phylogenetic analyses of vertebrate rhodopsin sequences in comparison with well-established vertebrate relationships. These spurious reconstructions were well supported in bootstrap analyses and occurred independently of the method of phylogenetic analysis used (parsimony, distance, or likelihood). Use of this data set of vertebrate rhodopsin sequences allowed us to exploit established vertebrate relationships, as well as the considerable amount known about the molecular evolution of this gene, in order to identify important factors contributing to the spurious reconstructions. Simulation studies using parametric bootstrapping indicate that it is unlikely that the spurious nodes in the parsimony analyses are due to long branches or other topological effects. Rather, they appear to be due to base compositional bias at third positions, codon bias, and convergent evolution at nucleotide positions encoding the hydrophobic residues isoleucine, leucine, and valine. LogDet distance methods, as well as maximum-likelihood methods which allow for nonstationary changes in base composition, reduce but do not entirely eliminate support for the spurious resolutions. Inclusion of five additional rhodopsin sequences in the phylogenetic analyses largely corrected one of the spurious reconstructions while leaving the other unaffected. The additional sequences not only were more proximal to the corrected node, but were also found to have intermediate levels of base composition and codon bias as compared with neighboring sequences on the tree. This study shows that the spurious reconstructions can be corrected either by excluding third positions, as well as those encoding the amino acids Ile, Val, and Leu (which may not be ideal, as these sites can contain useful phylogenetic signal for other parts of the tree), or by the addition of sequences that reduce problems associated with convergent evolution.

Overexpression of Jatropha Gibberellin 2-oxidase 6 (JcGA2ox6 Induces Dwarfism and Smaller Leaves, Flowers and Fruits in Arabidopsis and Jatropha

Directory of Open Access Journals (Sweden)

Ying-Xiong Hu

2017-12-01

Full Text Available Gibberellins (GAs are plant hormones that play fundamental roles in plant growth and development. Gibberellin 2-oxidase (GA2ox plays a direct role in determining the levels of bioactive GAs by catalyzing bioactive GAs or their immediate precursors to inactive forms. In this study, a GA2ox gene, designated JcGA2ox6, was isolated from Jatropha curcas. JcGA2ox6 is expressed in all tissues of adult Jatropha, with the highest expression level in male flowers and the lowest expression level in young leaves. Overexpression of JcGA2ox6 in Arabidopsis resulted in a typical dwarf phenotype, along with late flowering, smaller leaves and flowers, shorter siliques and smaller seeds. Similarly, when JcGA2ox6 was overexpressed in Jatropha, the transgenic plants exhibited a dwarf phenotype with dark-green leaves and smaller inflorescences, flowers, fruits and seeds. However, the flowering time of Jatropha was not affected by overexpression of JcGA2ox6, unlike that in the transgenic Arabidopsis. Moreover, the number of flowers per inflorescence, the weight of 10 seeds and the seed oil content were significantly decreased in transgenic Jatropha. The results indicated that overexpression of JcGA2ox6 had a great impact on the vegetative and reproductive growth of transgenic Jatropha. Furthermore, we found that the dwarf phenotype of transgenic Jatropha was caused by a decrease in endogenous bioactive GA4, which was correlated with the degree of dwarfism.

Highly conducting leakage-free electrolyte for SrCoOx-based non-volatile memory device

Science.gov (United States)

Katase, Takayoshi; Suzuki, Yuki; Ohta, Hiromichi

2017-10-01

The electrochemical switching of SrCoOx-based non-volatile memory with a thin-film-transistor structure was examined by using liquid-leakage-free electrolytes with different conductivities (σ) as the gate insulator. We first examined leakage-free water, which is incorporated in the amorphous (a-) 12CaO.7Al2O3 film with a nanoporous structure (Calcium Aluminate with Nanopore), but the electrochemical oxidation/reduction of the SrCoOx layer required the application of a high gate voltage (Vg) up to 20 V for a very long current-flowing-time (t) ˜40 min, primarily due to the low σ [2.0 × 10-8 S cm-1 at room temperature (RT)] of leakage-free water. We then controlled the σ of the leakage-free electrolyte, infiltrated in the a-NaxTaO3 film with a nanopillar array structure, from 8.0 × 10-8 S cm-1 to 2.5 × 10-6 S cm-1 at RT by changing the x = 0.01-1.0. As the result, the t, required for the metallization of the SrCoOx layer under small Vg = -3 V, becomes two orders of magnitude shorter with increase of the σ of the a-NaxTaO3 leakage-free electrolyte. These results indicate that the ion migration in the leakage-free electrolyte is the rate-determining step for the electrochemical switching, compared to the other electrochemical process, and the high σ of the leakage-free electrolyte is the key factor for the development of the non-volatile SrCoOx-based electro-magnetic phase switching device.

Molecular phylogenetics and historical biogeography of Rhinolophus bats.

Science.gov (United States)

Stoffberg, Samantha; Jacobs, David S; Mackie, Iain J; Matthee, Conrad A

2010-01-01

The phylogenetic relationships within the horseshoe bats (genus Rhinolophus) are poorly resolved, particularly at deeper levels within the tree. We present a better-resolved phylogenetic hypothesis for 30 rhinolophid species based on parsimony and Bayesian analyses of the mitochondrial cytochrome b gene and three nuclear introns (TG, THY and PRKC1). Strong support was found for the existence of two geographic clades within the monophyletic Rhinolophidae: an African group and an Oriental assemblage. The relaxed Bayesian clock method indicated that the two rhinolophid clades diverged approximately 35 million years ago and results from Dispersal Vicariance (DIVA) analysis suggest that the horseshoe bats arose in Asia and subsequently dispersed into Europe and Africa.

Reduced-graphene-oxide supported tantalum-based electrocatalysts: Controlled nitrogen doping and oxygen reduction reaction

Science.gov (United States)

Yang, Xiaoyun; Mo, Qijie; Guo, Yulin; Chen, Nana; Gao, Qingsheng

2018-03-01

Controlled N-doping is feasible to engineer the surface stoichiometry and the electronic configuration of metal-oxide electrocatalysts toward efficient oxygen reduction reactions (ORR). Taking reduced graphene oxide supported tantalum-oxides (TaOx/RGO) for example, this work illustrated the controlled N-doping in both metal-oxides and carbon supports, and the contribution to the improved ORR activity. The active N-doped TaOx/RGO electrocatalysts were fabricated via SiO2-assisted pyrolysis, in which the amount and kind of N-doping were tailored toward efficient electrocatalysis. The optimal nanocomposites showed a quite positive half-wave potential (0.80 V vs. RHE), the excellent long-term stability, and the outstanding tolerance to methanol crossing. The improvement in ORR was reasonably attributed to the synergy between N-doped TaOx and N-doped RGO. Elucidating the importance of controlled N-doping for electrocatalysis, this work will open up new opportunities to explore noble-metal-free materials for renewable energy applications.

The influence of house dust mite sublingual immunotherapy on the TSLP-OX40L signaling pathway in patients with allergic rhinitis.

Science.gov (United States)

Meng, Qingxiang; Liu, Xiaolong; Li, Peng; He, Long; Xie, Jinghua; Gao, Xionghui; Wu, Xiaozhong; Su, Fang; Liang, Yong

2016-08-01

This study aimed to investigate the clinical efficacy of sublingual immunotherapy (SLIT) with house dust mite (HDM) extract and to examine T helper 2 (Th2)-type immune responses mediated by the thymic stromal lymphopoietin (TSLP-OX40L) signaling pathway in patients with moderate to severe allergic rhinitis (AR) after 12-month HDM SLIT. Forty-six cases of HDM-sensitized patients with persistent AR in southern China were enrolled in this study. Clinical efficacy of SLIT was assessed by determining the individual nasal symptom score (INSS) and total nasal symptom score (TNSS) after 12-month HDM SLIT. Moreover, the TSLP-OX40L signaling pathway was investigated through measurements of TSLP by enzyme-labeled immunosorbent assay (ELISA) and OX40L by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and flow cytometry. After 12 months of HDM SLIT, TNSS and INSS were significantly decreased overall compared with baseline values (p < 0.001). By the end of the 12-month HDM SLIT, TNSS had declined by ∼50% compared with baseline, and the corresponding level of TSLP in nasal lavage decreased significantly (p < 0.05). The level of OX40L messenger RNA (mRNA) in blood was markedly decreased significantly after 12-month HDM SLIT compared with baseline (t = 12.300, p < 0.05). Furthermore, significant decreases in OX40L expression on the surface of peripheral blood mononuclear cells (PBMCs) (t = 13.100, p < 0.05) and OX40L expression on the surface of CD11c+CD86+ cells in PBMCs (t = 9.946, p < 0.05) after 12-month HDM SLIT were observed. HDM SLIT downregulated Th2-type immune responses mediated by the TSLP-OX40L signaling pathway in patients with persistent moderate to severe AR. © 2016 ARS-AAOA, LLC.

Transport current anisotropy in oriented grained bulk YBa2Cu3O(x) superconductor

International Nuclear Information System (INIS)

Selvamanickam, V.; Salama, K.

1990-01-01

The anisotropy in transport current density has been studied on bulk YBa2Cu3O(x) superconductor. The transport current density measurements were performed on oriented grained YBa2Cu3O(x) superconductor with the current aligned at different angles to the a-b plane. The angular dependence of Jc shows a rapid drop when the transport current is misaligned from the a-b plane at small angles and then a slow decrease at higher angles. An anisotropy ratio of about 25 is observed at 77 K and zero field between the Jc along a-b plane and that perpendicular to the plane. 15 refs

Field-emission property of self-purification SiC/SiOx coaxial nanowires synthesized via direct microwave irradiation using iron-containing catalyst

Science.gov (United States)

Zhou, Qing; Yu, Yongzhi; Huang, Shan; Meng, Jiang; Wang, Jigang

2017-07-01

SiC/SiOx coaxial nanowires were rapidly synthesized via direct microwave irradiation in low vacuum atmosphere. During the preparation process, only graphite, silicon, silicon dioxide powders were used as raw materials and iron-containing substance was employed as catalyst. Comprehensive characterizations were employed to investigate the microstructure of the products. The results showed that a great quantity of coaxial nanowires with uniform sizes and high aspect ratio had been successfully achieved. The coaxial nanowires consist of a silicon oxide (SiOx) shell and a β-phase silicon carbide (β-SiC) core that exhibited in special tube brush like. In additional, nearly all the products were achieved in the statement of pure SiC/SiOx coaxial nanowires without the existence of metallic catalyst, indicating that the self-removal of iron (Fe) catalyst should be occurred during the synthesis process. Photoluminescence (PL) spectral analysis result indicated that such novel SiC/SiOx coaxial nanowires exhibited significant blue-shift. Besides, the measurement results of field-emission (FE) demonstrated that the SiC/SiOx coaxial nanowires had ultralow turn-on field and threshold field with values of 0.2 and 2.1 V/μm, respectively. The hetero-junction structure formed between SiOx shell and SiC core, lots of emission sites, as well as clear tips of the nanowires were applied to explain the excellent FE properties.[Figure not available: see fulltext.

Phylogenetic paleobiogeography of Late Ordovician Laurentian brachiopods

Directory of Open Access Journals (Sweden)

Jennifer E. Bauer

2014-12-01

Full Text Available Phylogenetic biogeographic analysis of four brachiopod genera was used to uncover large-scale geologic drivers of Late Ordovician biogeographic differentiation in Laurentia. Previously generated phylogenetic hypotheses were converted into area cladograms, ancestral geographic ranges were optimized and speciation events characterized as via dispersal or vicariance, when possible. Area relationships were reconstructed using Lieberman-modified Brooks Parsimony Analysis. The resulting area cladograms indicate tectonic and oceanographic changes were the primary geologic drivers of biogeographic patterns within the focal taxa. The Taconic tectophase contributed to the separation of the Appalachian and Central basins as well as the two midcontinent basins, whereas sea level rise following the Boda Event promoted interbasinal dispersal. Three migration pathways into the Cincinnati Basin were recognized, which supports the multiple pathway hypothesis for the Richmondian Invasion.

Preparation of SrCoOx thin films on LaAlO3 substrate and their reversible redox process at moderate temperatures

Science.gov (United States)

Hao, L.; Zhang, Z. F.; Xie, X. N.; Wang, H. R.; Yu, Q. X.; Zhu, H.

2015-10-01

Using magnetron sputtering and annealing techniques, we have prepared SrCoOx films on LaAlO3 and SrTiO3 substrates. Distinctly different structures of the films have been found on the two substrates. It is suggested that positive lattice mismatch between film and substrate promotes SrCoO2.5 films with an orthorhombic structure grown on SrTiO3 substrate, whereas negative lattice mismatch from LaAlO3 substrate is in favor of increasing the valence state of Co and thus the growth of oxygen-rich SrCoOx with a tetragonal structure. In addition to the structural characterization, magnetic and electrical measurements confirm that the oxygen content x is between 2.75 and 2.88 for the latter. Reversibility of the topotactic phase transformation between SrCoO2.5 and the oxygen-rich SrCoOx films has also been studied by changing the oxygen pressure during annealing process. Even in the presence of a negative lattice mismatch, the results reveal that the tetragonal SrCoOx films on LaAlO3 substrate retain high oxygen mobility identified before in cubic SrCoOx films.

MoOx thin films deposited by magnetron sputtering as an anode for aqueous micro-supercapacitors

Science.gov (United States)

Liu, Can; Li, Zhengcao; Zhang, Zhengjun

2013-12-01

In order to examine the potential application of non-stoichiometric molybdenum oxide as anode materials for aqueous micro-supercapacitors, conductive MoOx films (2 ⩽ x ⩽ 2.3) deposited via RF magnetron sputtering at different temperatures were systematically studied for composition, structure and electrochemical properties in an aqueous solution of Li2SO4. The MoOx (x ≈ 2.3) film deposited at 150 °C exhibited a higher areal capacitance (31 mF cm-2 measured at 5 mV s-1), best rate capability and excellent stability at potentials below -0.1 V versus saturated calomel electrode, compared to the films deposited at room temperature and at higher temperatures. These superior properties were attributed to the multi-valence composition and mixed-phase microstructure, i.e., the coexistence of MoO2 nanocrystals and amorphous MoOx (2.3 < x ⩽ 3). A mechanism combining Mo(IV) oxidation/reduction on the hydrated MoO2 grain surfaces and cation intercalation/extrusion is proposed to illustrate the pseudo-capacitive process.

MoOx thin films deposited by magnetron sputtering as an anode for aqueous micro-supercapacitors

Directory of Open Access Journals (Sweden)

Can Liu

2013-11-01

Full Text Available In order to examine the potential application of non-stoichiometric molybdenum oxide as anode materials for aqueous micro-supercapacitors, conductive MoOx films (2 ≤ x ≤ 2.3 deposited via RF magnetron sputtering at different temperatures were systematically studied for composition, structure and electrochemical properties in an aqueous solution of Li2SO4. The MoOx (x ≈ 2.3 film deposited at 150 °C exhibited a higher areal capacitance (31 mF cm−2 measured at 5 mV s−1, best rate capability and excellent stability at potentials below −0.1 V versus saturated calomel electrode, compared to the films deposited at room temperature and at higher temperatures. These superior properties were attributed to the multi-valence composition and mixed-phase microstructure, i.e., the coexistence of MoO2 nanocrystals and amorphous MoOx (2.3 < x ≤ 3. A mechanism combining Mo(IV oxidation/reduction on the hydrated MoO2 grain surfaces and cation intercalation/extrusion is proposed to illustrate the pseudo-capacitive process.

Comprehensive Behavioral Analysis of Male Ox1r−/− Mice Showed Implication of Orexin Receptor-1 in Mood, Anxiety, and Social Behavior

Science.gov (United States)

Abbas, Md. G.; Shoji, Hirotaka; Soya, Shingo; Hondo, Mari; Miyakawa, Tsuyoshi; Sakurai, Takeshi

2015-01-01

Neuropeptides orexin A and orexin B, which are exclusively produced by neurons in the lateral hypothalamic area, play an important role in the regulation of a wide range of behaviors and homeostatic processes, including regulation of sleep/wakefulness states and energy homeostasis. The orexin system has close anatomical and functional relationships with systems that regulate the autonomic nervous system, emotion, mood, the reward system, and sleep/wakefulness states. Recent pharmacological studies using selective antagonists have suggested that orexin receptor-1 (OX1R) is involved in physiological processes that regulate emotion, the reward system, and autonomic nervous system. Here, we examined Ox1r−/− mice with a comprehensive behavioral test battery to screen additional OX1R functions. Ox1r−/− mice showed increased anxiety-like behavior, altered depression-like behavior, slightly decreased spontaneous locomotor activity, reduced social interaction, increased startle response, and decreased prepulse inhibition. These results suggest that OX1R plays roles in social behavior and sensory motor gating in addition to roles in mood and anxiety. PMID:26696848

Species divergence and phylogenetic variation of ecophysiological traits in lianas and trees.

Science.gov (United States)

Rios, Rodrigo S; Salgado-Luarte, Cristian; Gianoli, Ernesto

2014-01-01

The climbing habit is an evolutionary key innovation in plants because it is associated with enhanced clade diversification. We tested whether patterns of species divergence and variation of three ecophysiological traits that are fundamental for plant adaptation to light environments (maximum photosynthetic rate [A(max)], dark respiration rate [R(d)], and specific leaf area [SLA]) are consistent with this key innovation. Using data reported from four tropical forests and three temperate forests, we compared phylogenetic distance among species as well as the evolutionary rate, phylogenetic distance and phylogenetic signal of those traits in lianas and trees. Estimates of evolutionary rates showed that R(d) evolved faster in lianas, while SLA evolved faster in trees. The mean phylogenetic distance was 1.2 times greater among liana species than among tree species. Likewise, estimates of phylogenetic distance indicated that lianas were less related than by chance alone (phylogenetic evenness across 63 species), and trees were more related than expected by chance (phylogenetic clustering across 71 species). Lianas showed evenness for R(d), while trees showed phylogenetic clustering for this trait. In contrast, for SLA, lianas exhibited phylogenetic clustering and trees showed phylogenetic evenness. Lianas and trees showed patterns of ecophysiological trait variation among species that were independent of phylogenetic relatedness. We found support for the expected pattern of greater species divergence in lianas, but did not find consistent patterns regarding ecophysiological trait evolution and divergence. R(d) followed the species-level pattern, i.e., greater divergence/evolution in lianas compared to trees, while the opposite occurred for SLA and no pattern was detected for A(max). R(d) may have driven lianas' divergence across forest environments, and might contribute to diversification in climber clades.

pH Mapping on Tooth Surfaces for Quantitative Caries Diagnosis Using Micro Ir/IrOx pH Sensor.

Science.gov (United States)

Ratanaporncharoen, Chindanai; Tabata, Miyuki; Kitasako, Yuichi; Ikeda, Masaomi; Goda, Tatsuro; Matsumoto, Akira; Tagami, Junji; Miyahara, Yuji

2018-04-03

A quantitative diagnostic method for dental caries would improve oral health, which directly affects the quality of life. Here we describe the preparation and application of Ir/IrOx pH sensors, which are used to measure the surface pH of dental caries. The pH level is used as an indicator to distinguish between active and arrested caries. After a dentist visually inspected and defined 18 extracted dentinal caries at various positions as active or arrested caries, the surface pH values of sound and caries areas were directly measured with an Ir/IrOx pH sensor with a diameter of 300 μm as a dental explorer. The average pH values of the sound root, the arrested caries, and active caries were 6.85, 6.07, and 5.30, respectively. The pH obtained with an Ir/IrOx sensor was highly correlated with the inspection results by the dentist, indicating that the types of caries were successfully categorized. This caries testing technique using a micro Ir/IrOx pH sensor provides an accurate quantitative caries evaluation and has potential in clinical diagnosis.

Ambipolar SnOx thin-film transistors achieved at high sputtering power

Science.gov (United States)

Li, Yunpeng; Yang, Jia; Qu, Yunxiu; Zhang, Jiawei; Zhou, Li; Yang, Zaixing; Lin, Zhaojun; Wang, Qingpu; Song, Aimin; Xin, Qian

2018-04-01

SnO is the only oxide semiconductor to date that has exhibited ambipolar behavior in thin-film transistors (TFTs). In this work, ambipolar behavior was observed in SnOx TFTs fabricated at a high sputtering power of 200 W and post-annealed at 150-250 °C in ambient air. X-ray-diffraction patterns showed polycrystallisation of SnO and Sn in the annealed SnOx films. Scanning-electron-microscopy images revealed that microgrooves appeared after the films were annealed. Clusters subsequently segregated along the microgrooves, and our experiments suggest that they were most likely Sn clusters. Atomic force microscopy images indicate an abrupt increase in film roughness due to the cluster segregations. An important implication of this work is that excess Sn in the film, which has generally been thought to be detrimental to the film quality, may promote the ambipolar conduction when it is segregated from the film to enhance the stoichiometric balance.

Medición inalámbrica de concentración de oxígeno para productos vitivinícolas

Directory of Open Access Journals (Sweden)

Jorge Mario Garzon Rey

2012-06-01

Full Text Available En este trabajo se presenta un sistema inalambrico que permite medir la con-centracion de ox geno aplicable para el vino embotellado. El sistema esta basado en alimentacion por medio de telemetr a inductiva, a traves de un sen-sor al interior de la botella que mide la concentracion de ox geno y entrega la informacion medida de manera inalambrica. Posibles niveles altos de con-centracion de ox geno determinan fugas en el corcho, lo que representa mala calidad del proceso de embotellamiento y por ende perdida de las propiedades de la calidad del vino. El sistema propuesto fue validado utilizando una im-plementacion de componentes discretos por la facilidad y disponibilidad en el mercado local, pero las topolog as estudiadas buscan a futuro una posible implementacion a nivel de circuito integrado de aplicacion espec ca (ASIC. El sensor utilizado para el montaje del prototipo es un sensor de ox geno comercial referencia O2A2 de Alphasense. La respuesta en condiciones de funcionamiento es lineal con un coe ciente de correlacion de 0.999.

Formation of defect-fluorite structured NdNiOxHy epitaxial thin films via a soft chemical route from NdNiO3 precursors.

Science.gov (United States)

Onozuka, T; Chikamatsu, A; Katayama, T; Fukumura, T; Hasegawa, T

2016-07-26

A new phase of oxyhydride NdNiOxHy with a defect-fluorite structure was obtained by a soft chemical reaction of NdNiO3 epitaxial thin films on a substrate of SrTiO3 (100) with CaH2. The epitaxial relationship of this phase relative to SrTiO3 could be controlled by changing the reaction temperature. At 240 °C, NdNiOxHy grew with a [001] orientation, forming a thin layer of infinite-layer NdNiO2 at the interface between the NdNiOxHy and the substrate. Meanwhile, a high-temperature reaction at 400 °C formed [110]-oriented NdNiOxHy without NdNiO2.

Transforming phylogenetic networks: Moving beyond tree space

OpenAIRE

Huber, Katharina T.; Moulton, Vincent; Wu, Taoyang

2016-01-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transforme...

Molecular phylogenetics of finches and sparrows: consequences of character state removal in cytochrome b sequences.

Science.gov (United States)

Groth, J G

1998-12-01

The complete mitochondrial cytochrome b genes of 53 genera of oscine passerine birds representing the major groups of finches and some allies were compared. Phylogenetic trees resulting from three levels of character partition removal (no data removed, transitions at third positions of codons removed, and all transitions removed [transversion parsimony]) were generally concordant, and all supported several basic statements regarding relationships of finches and finch-like birds, including: (1) larks (Alaudidae) show no close relationship to any finch group; (2) Peucedramus (olive warbler) is phylogenetically far removed from true wood warblers; (3) a clade consisting of fringillids, passerids, motacillids, and emberizids is supported, and this clade is characterized by evolution of a vestigial 10th wing primary; and (4) Hawaiian honeycreepers are derived from within the cardueline finches. Excluding transition substitutions at third positions of codons resulted in phylogenetic trees similar to, but with greater bootstrap nodal support than, trees derived using either all data (equally weighted) or transversion parsimony. Relative to the shortest trees obtained using all data, the topologies obtained after elimination of third-position transitions showed only slight increases in realized treelength and homoplasy. These increases were negligable compared to increases in overall nodal support; therefore, this partition removal scheme may enhance recovery of deep phylogenetic signal in protein-coding DNA datasets. Copyright 1998 Academic Press.

A molecular phylogenetic appraisal of the acanthostomines Acanthostomum and Timoniella and their position within Cryptogonimidae (Trematoda: Opisthorchioidea).

Science.gov (United States)

Martínez-Aquino, Andrés; Vidal-Martínez, Victor M; Aguirre-Macedo, M Leopoldina

2017-01-01

The phylogenetic position of three taxa from two trematode genera, belonging to the subfamily Acanthostominae (Opisthorchioidea: Cryptogonimidae), were analysed using partial 28S ribosomal DNA (Domains 1-2) and internal transcribed spacers (ITS1-5.8S-ITS2). Bayesian inference and Maximum likelihood analyses of combined 28S rDNA and ITS1 + 5.8S + ITS2 sequences indicated the monophyly of the genus Acanthostomum ( A. cf. americanum and A. burminis ) and paraphyly of the Acanthostominae . These phylogenetic relationships were consistent in analyses of 28S alone and concatenated 28S + ITS1 + 5.8S + ITS2 sequences analyses. Based on molecular phylogenetic analyses, the subfamily Acanthostominae is therefore a paraphyletic taxon, in contrast with previous classifications based on morphological data. Phylogenetic patterns of host specificity inferred from adult stages of other cryptogonimid taxa are also well supported. However, analyses using additional genera and species are necessary to support the phylogenetic inferences from this study. Our molecular phylogenetic reconstruction linked two larval stages of A. cf. americanum cercariae and metacercariae. Here, we present the evolutionary and ecological implications of parasitic infections in freshwater and brackish environments.

A molecular phylogenetic appraisal of the acanthostomines Acanthostomum and Timoniella and their position within Cryptogonimidae (Trematoda: Opisthorchioidea

Directory of Open Access Journals (Sweden)

Andrés Martínez-Aquino

2017-12-01

Full Text Available The phylogenetic position of three taxa from two trematode genera, belonging to the subfamily Acanthostominae (Opisthorchioidea: Cryptogonimidae, were analysed using partial 28S ribosomal DNA (Domains 1–2 and internal transcribed spacers (ITS1–5.8S–ITS2. Bayesian inference and Maximum likelihood analyses of combined 28S rDNA and ITS1 + 5.8S + ITS2 sequences indicated the monophyly of the genus Acanthostomum (A. cf. americanum and A. burminis and paraphyly of the Acanthostominae. These phylogenetic relationships were consistent in analyses of 28S alone and concatenated 28S + ITS1 + 5.8S + ITS2 sequences analyses. Based on molecular phylogenetic analyses, the subfamily Acanthostominae is therefore a paraphyletic taxon, in contrast with previous classifications based on morphological data. Phylogenetic patterns of host specificity inferred from adult stages of other cryptogonimid taxa are also well supported. However, analyses using additional genera and species are necessary to support the phylogenetic inferences from this study. Our molecular phylogenetic reconstruction linked two larval stages of A. cf. americanum cercariae and metacercariae. Here, we present the evolutionary and ecological implications of parasitic infections in freshwater and brackish environments.

Efecto del oxígeno y la glucosa en la metanogénesis y mineralización de resinas poliméricas

Directory of Open Access Journals (Sweden)

Ulises Durán Hinojosa

2010-01-01

Full Text Available En el presente trabajo se evaluó el efecto de la concentración de oxígeno disuelto (OD y la presencia de la glucosa en la metanogénesis y mineralización de los compuestos de resinas poliméricas, mediante cultivos en lote. El inóculo utilizado para los cultivos fueron lodos procedentes de un reactor de lecho de lodos con flujo ascendente UASB (por sus siglas en inglés, alimentado con glucosa y aguas residuales de resinas poliméricas, y 1,0 mg L-1 d-1 de oxígeno disuelto en estado estacionario. Todas las pruebas fueron realizadas con 1500 mg L-1 de demanda química de oxígeno, a 30±2° C, con 23,8 g L-1 de sólidos suspendidos volátiles como inóculo y una relación demanda química de oxígeno / sólidos suspendidos volátiles de 1. El efecto de diferentes concentraciones de oxígeno disuelto mostró que, para la glucosa, con bajas concentraciones (0,6 y 1,0 mg L-1 la eficiencia de remoción de la demanda química de oxígeno y la actividad metanogénicas permanecieron constantes, pero la eficiencia de remoción de la demanda química de oxígeno para los compuestos de resinas poliméricas aumentó 58,1±1% y el rendimiento de metano disminuyó, debido a que una mayor fracción del carbono alimentado fue mineralizada a dióxido de carbono, posiblemente por una ruta aerobia. Los resultados con diferentes proporciones de glucosa / compuestos de resinas poliméricas (CRP en presencia de 0,6 mg L-1 de oxígeno disuelto mostraron que la presencia de glucosa no mejoró la eliminación de los compuestos de resinas poliméricas. Sin embargo, la actividad metanogénica disminuyó en un 75% cuando solamente se usó a los compuestos de resinas poliméricas como sustrato, al compararla con la actividad metanogénica con glucosa como única fuente de carbono, sugiriendo que la glucosa no favorece la eliminación de los compuestos de resinas poliméricas, pero proporciona una mejor tolerancia al oxígeno. Se concluye que la presencia de bajas

Electron tunneling and the energy gap in Bi2Sr2CaCu2Ox

Science.gov (United States)

Lee, Mark; Mitzi, D. B.; Kapitulnik, A.; Beasley, M. R.

1989-01-01

Results of electron tunneling on single crystals of the Bi2Sr2CaCu2Ox superconductor are reported. The junctions show a gap structure with Δ~=25 meV, whose temperature dependence exhibits a qualitatively Bardeen-Cooper-Schrieffer-like behavior with a gap-closing Tc~=81-85 K. Comparisons of these tunneling spectra to those obtained on YBa2Cu3O7-x are made. Evidence that 2Δ/kTc~7 for both Ba2Sr2CaCu2Ox and YBa2Cu3O7-x is also discussed.

Atractylenolide I restores HO-1 expression and inhibits Ox-LDL-induced VSMCs proliferation, migration and inflammatory responses in vitro

Energy Technology Data Exchange (ETDEWEB)

Li, Weifeng, E-mail: liwf@mail.xjtu.edu.cn; Zhi, Wenbing; Liu, Fang; He, Zehong; Wang, Xiuei; Niu, Xiaofeng, E-mail: niuxf@mail.xjtu.edu.cn

2017-04-01

Pathogenesis of atherosclerosis is characterized by the proliferation and migration of vascular smooth muscle cells (VSMCs) and inflammatory lesions. The aim of this study is to elucidate the effect of atractylenolide I (AO-I) on smooth muscle cell inflammation, proliferation and migration induced by oxidized modified low density lipoprotein (Ox-LDL). Here, We found that atractylenolide I inhibited Ox-LDL-induced VSMCs proliferation and migration in a dose-dependent manner, and decreased the production of inflammatory cytokines and the expression of monocyte chemoattractant protein-1 (MCP-1) in VSMCs. The study also identified that AO-I prominently inhibited p38-MAPK and NF-κB activation. More importantly, the specific heme oxygenase-1 (HO-1) inhibitor zinc protoporphyrin (ZnPP) IX partially abolished the beneficial effects of atractylenolide I on Ox-LDL-induced VSMCs. Furthermore, atractylenolide I blocked the foam cell formation in macrophages induced by Ox-LDL. In summary, inhibitory roles of AO-I in VSMCs proliferation and migration, lipid peroxidation and subsequent inflammatory responses might contribute to the anti-atherosclerotic property of AO-I. - Highlights: • AO-I inhibited Ox-LDL-induced VSMCs proliferation and migration. • AO-I alleviated inflammatory response via inhibiting TNF-α, IL-6 and NO production. • AO-I restored HO-1 expression and down-regulated PCNA expression. • MCP-1 overexpression is potentially regulated by NF-κB and p38 MAPK pathway. • AO-I possesses strong anti-lipid peroxidation effect.

Protection of p+-n-Si Photoanodes by Sputter-Deposited Ir/IrOxThin Films

DEFF Research Database (Denmark)

Mei, Bastian Timo; Seger, Brian; Pedersen, Thomas

2014-01-01

Sputter deposition of Ir/IrOx on p+-n-Si without interfacial corrosion protection layers yielded photoanodes capable of efficient water oxidation (OER) in acidic media (1 M H2SO4). Stability of at least 18 h was shown by chronoamperomety at 1.23 V versus RHE (reversible hydrogen electrode) under 38...... density of 1 mA/cm2 at 1.05 V vs. RHE. Further improvement by heat treatment resulted in a cathodic shift of 40 mV and enabled a current density of 10 mA/cm2 (requirements for a 10% efficient tandem device) at 1.12 V vs. RHS under irradiation. Thus, the simple IrOx/Ir/p+-n-Si structures not only provide...

FirefOx Design Reference fO2 Sensor for Hot, Deep Atmospheres

Science.gov (United States)

Izenberg, N.; Papadakis, S.; Deglau, D.; Francomacaro, A. S.

2016-12-01

Understanding the composition of the lowest portion of Venus' atmosphere is critical to knowing the stable mineralogy of the rocks there. Oxygen gas is a critical trace component, with fugacity, or partial pressure, estimated in the range of 10-19 to 10-22 from early probe measurements down to 22km altitude (Pioneer Venus, Venera), chemical equilibrium measurements, and other modeling. "FirefOx" is a simple oxygen fugacity sensor with the express purpose of determining the partial pressure of oxygen in the lowest scale heights of the Venus atmosphere, and especially the lowest hundreds of meters; the surface atmosphere interface, where the atmosphere and surface move to thermodynamic equilibrium. Knowledge of the fO2 at the surface atmosphere interface is crucial to determining the stable mineralogy of surface materials (e.g. magnetite vs. hematite) and gas chemistry in the near-surface atmosphere FirefOx is a Metal/Metal Oxide oxygen fugacity sensor intended to be mounted on the outside of a Venus descent probe, with electronics housed inside a thermally controlled environment. The sole sensor capability is the precise, accurate detection of the partial pressure of oxygen gas (fO2) in the near-surface environment of Venus, at up to 95-bar pressure (predominantly CO2. Surface temperatures at mean planetary elevation are near 735 K, thus a required operational temperature range of 710-740 K covers a range of near-surface elevations. FirefOx system requirements are low ( 100-200 grams, mass, milliwatt power, several kilobytes total science data). A design reference sensor, composed of custom, Yittria-ZrO ceramic electrolyte, with an encapsulated Pd/PdO standard and patterned Pt electrodes has demonstrated scientifically useful signal-to-noise millivolt level potential at temperatures as low as 620 K, relatable to fO2 by a Nernst equation E = RT/4F ln(PO2/PrefO2) where E = open circuit potential across the sensor electrolyte, R = universal gas constant, T

Edge-related loss of tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

Directory of Open Access Journals (Sweden)

Bráulio A Santos

Full Text Available Deforestation and forest fragmentation are known major causes of nonrandom extinction, but there is no information about their impact on the phylogenetic diversity of the remaining species assemblages. Using a large vegetation dataset from an old hyper-fragmented landscape in the Brazilian Atlantic rainforest we assess whether the local extirpation of tree species and functional impoverishment of tree assemblages reduce the phylogenetic diversity of the remaining tree assemblages. We detected a significant loss of tree phylogenetic diversity in forest edges, but not in core areas of small (<80 ha forest fragments. This was attributed to a reduction of 11% in the average phylogenetic distance between any two randomly chosen individuals from forest edges; an increase of 17% in the average phylogenetic distance to closest non-conspecific relative for each individual in forest edges; and to the potential manifestation of late edge effects in the core areas of small forest remnants. We found no evidence supporting fragmentation-induced phylogenetic clustering or evenness. This could be explained by the low phylogenetic conservatism of key life-history traits corresponding to vulnerable species. Edge effects must be reduced to effectively protect tree phylogenetic diversity in the severely fragmented Brazilian Atlantic forest.

Oxidation process of AlOx-based magnetic tunnel junctions studied by photoconductance

NARCIS (Netherlands)

Koller, P.H.P.; Vanhelmont, F.W.M.; Boeve, H.; Lumens, P.G.E.; Jonge, de W.J.M.

2003-01-01

The oxidation process of Co/AlOx/Co magnetic tunnel junctions has been investigated by photoconductance, in addition to traditional transport measurements. The shape of the photoconductance curves is explained within the framework of a simple qualitative model, assuming an oxidation time dependent

Effect of immunization against ox-LDL with two different antigens on formation and development of atherosclerosis

Directory of Open Access Journals (Sweden)

Saberi Salb-Ali

2007-11-01

Full Text Available Abstract Background Several studies were pointed to oxidized LDL (ox-LDL as one of the main immunogenes which have important roles in primary lesions of atherosclerosis. In this study, by immunization against ox-LDL with two different antigens in an animal model (rabbit and consideration of its effect on two different dietary regimens; we tried to clear relation between immune system and atherosclerosis. Methods LDL was isolated from hypercholesterolemic rabbits plasma and oxidized with MDA or Cu++. Rabbits were divided to three groups and immunized with MDA-LDL or Cu-LDL or phosphate-buffer (PBS as a control group. Immunization was repeated after 2, 4, 6, and 8 weeks and concentration of antibodies against ox-LDL was measured in each stage. After immunization, rabbits in each group were divided to two subgroups based on the dietary regimen (fed normal or high cholesterol diet. At the beginning and the end of the study, biochemical factors were measured. Also, fatty streaks in aorta and left and right coronary arteries evaluated. Results Immunization with Cu2+-LDL and MDA-LDL induced statistically significant antibodies against ox-LDL. In hypercholesterolemic rabbits immunized with MDA-LDL the level of cholesterol, LDL-cholesterol, triglyceride, fasting blood sugar and fatty streak lesions in aorta and right coronary arteries were significantly decreased as compared with non-immunized high-cholesterol group. Immunization with Cu2+-LDL in hypercholesterolemic rabbits significantly decreased triglyceride, fasting blood sugar, cholesterol and CRP. No significant differences were detected in the fatty streak lesions in this group as compared with non-immunized high-cholesterol diet. In groups under normal diet immunized with MDA-LDL or Cu2+-LDL no significant effect on biochemical factors and atherosclerotic lesions were observed. Conclusion This study indicates that although the effect of produced antibodies in several methods and different dietary

On Nakhleh's metric for reduced phylogenetic networks

OpenAIRE

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente Feruglio, Gabriel Alejandro

2009-01-01

We prove that Nakhleh’s metric for reduced phylogenetic networks is also a metric on the classes of tree-child phylogenetic networks, semibinary tree-sibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. Furthermore, we propose a generalization of that metric that separates arbitrary phyl...

Phylogenetic Analysis Using Protein Mass Spectrometry.

Science.gov (United States)

Ma, Shiyong; Downard, Kevin M; Wong, Jason W H

2017-01-01

Through advances in molecular biology, comparative analysis of DNA sequences is currently the cornerstone in the study of molecular evolution and phylogenetics. Nevertheless, protein mass spectrometry offers some unique opportunities to enable phylogenetic analyses in organisms where DNA may be difficult or costly to obtain. To date, the methods of phylogenetic analysis using protein mass spectrometry can be classified into three categories: (1) de novo protein sequencing followed by classical phylogenetic reconstruction, (2) direct phylogenetic reconstruction using proteolytic peptide mass maps, and (3) mapping of mass spectral data onto classical phylogenetic trees. In this chapter, we provide a brief description of the three methods and the protocol for each method along with relevant tools and algorithms.

Extended molecular phylogenetics and revised systematics of Malagasy scincine lizards.

Science.gov (United States)

Erens, Jesse; Miralles, Aurélien; Glaw, Frank; Chatrou, Lars W; Vences, Miguel

2017-02-01

Among the endemic biota of Madagascar, skinks are a diverse radiation of lizards that exhibit a striking ecomorphological variation, and could provide an interesting system to study body-form evolution in squamate reptiles. We provide a new phylogenetic hypothesis for Malagasy skinks of the subfamily Scincinae based on an extended molecular dataset comprising 8060bp from three mitochondrial and nine nuclear loci. Our analysis also increases taxon sampling of the genus Amphiglossus by including 16 out of 25 nominal species. Additionally, we examined whether the molecular phylogenetic patterns coincide with morphological differentiation in the species currently assigned to this genus. Various methods of inference recover a mostly strongly supported phylogeny with three main clades of Amphiglossus. However, relationships among these three clades and the limb-reduced genera Grandidierina, Voeltzkowia and Pygomeles remain uncertain. Supported by a variety of morphological differences (predominantly related to the degree of body elongation), but considering the remaining phylogenetic uncertainty, we propose a redefinition of Amphiglossus into three different genera (Amphiglossus sensu stricto, Flexiseps new genus, and Brachyseps new genus) to remove the non-monophyly of Amphiglossus sensu lato and to facilitate future studies on this fascinating group of lizards. Copyright © 2016 Elsevier Inc. All rights reserved.

A RAD-based phylogenetics for Orestias fishes from Lake Titicaca.

Science.gov (United States)

Takahashi, Tetsumi; Moreno, Edmundo

2015-12-01

The fish genus Orestias is endemic to the Andes highlands, and Lake Titicaca is the centre of the species diversity of the genus. Previous phylogenetic studies based on a single locus of mitochondrial and nuclear DNA strongly support the monophyly of a group composed of many of species endemic to the Lake Titicaca basin (the Lake Titicaca radiation), but the relationships among the species in the radiation remain unclear. Recently, restriction site-associated DNA (RAD) sequencing, which can produce a vast number of short sequences from various loci of nuclear DNA, has emerged as a useful way to resolve complex phylogenetic problems. To propose a new phylogenetic hypothesis of Orestias fishes of the Lake Titicaca radiation, we conducted a cluster analysis based on morphological similarities among fish samples and a molecular phylogenetic analysis based on RAD sequencing. From a morphological cluster analysis, we recognised four species groups in the radiation, and three of the four groups were resolved as monophyletic groups in maximum-likelihood trees based on RAD sequencing data. The other morphology-based group was not resolved as a monophyletic group in molecular phylogenies, and some members of the group were diverged from its sister group close to the root of the Lake Titicaca radiation. The evolution of these fishes is discussed from the phylogenetic relationships. Copyright © 2015 Elsevier Inc. All rights reserved.

Phylogenetic placement of the Dominican Republic endemic genus Sarcopilea (Urticaceae)

Czech Academy of Sciences Publication Activity Database

Jestrow, B.; Valdés, James J.; Rodríguez, F. J.; Francisco-Ortega, J.

2012-01-01

Roč. 61, č. 3 (2012), s. 592-600 ISSN 0040-0262 Institutional support: RVO:60077344 Keywords : CAM * Caribbean Islands * cystoliths * epistomatic * hyperstomatic * hydathodes * phylogenetics * Pilea * Sarcopilea * succulent * Urticaceae Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.782, year: 2012

Coatings of nanostructured pristine graphene-IrOx hybrids for neural electrodes: Layered stacking and the role of non-oxygenated graphene

Energy Technology Data Exchange (ETDEWEB)

Pérez, E. [Institut Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193, Bellaterra, Barcelona (Spain); Lichtenstein, M.P.; Suñol, C. [Institut d' Investigacions Biomèdiques de Barcelona (IIBB-CSIC), Institut d' Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), c/Rosselló 161, 08036 Barcelona (Spain); Casañ-Pastor, N., E-mail: nieves@icmab.es [Institut Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, E-08193, Bellaterra, Barcelona (Spain)

2015-10-01

The need to enhance charge capacity in neural stimulation-electrodes is promoting the formation of new materials and coatings. Among all the possible types of graphene, pristine graphene prepared by graphite electrochemical exfoliation, is used in this work to form a new nanostructured IrOx–graphene hybrid (IrOx–eG). Graphene is stabilized in suspension by IrOx nanoparticles without surfactants. Anodic electrodeposition results in coatings with much smaller roughness than IrOx–graphene oxide. Exfoliated pristine graphene (eG), does not electrodeposit in absence of iridium, but IrOx-nanoparticle adhesion on graphene flakes drives the process. IrOx–eG has a significantly different electronic state than graphene oxide, and different coordination for carbon. Electron diffraction shows the reflection features expected for graphene. IrOx 1–2 nm cluster/nanoparticles are oxohydroxo-species and adhere to 10 nm graphene platelets. eG induces charge storage capacity values five times larger than in pure IrOx, and if calculated per carbon atom, this enhancement is one order magnitude larger than the induced by graphene oxide. IrOx–eG coatings show optimal in vitro neural cell viability and function as cell culture substrates. The fully straightforward electrochemical exfoliation and electrodeposition constitutes a step towards the application of graphene in biomedical systems, expanding the knowledge of pristine graphene vs. graphene oxide, in bioelectrodes. - Highlights: • Pristine Graphene is incorporated in coatings as nanostructured IrOx–eG hybrid. • IrOx-nanoparticles drive the electrodeposition of graphene. • Hybrid CSC is one order of magnitude the charge capacity of IrOx. • Per carbon atom, the CSC increase is 35 times larger than for graphene oxide. • Neurons are fully functional on the coating.

Preparation and Characteristics of MAPbBr3 Perovskite Quantum Dots on NiOx Film and Application for High Transparent Solar Cells

Directory of Open Access Journals (Sweden)

Lung-Chien Chen

2018-04-01

Full Text Available In this work, a MAPbBr3 quantum dot (QD-MAPbBr3 layer was prepared by a simple and rapid method. Octylammonium bromide (OABr gives the MAPbBr3 better exciton binding energy, good surface morphology, and stability. To form a nanocrystalline thin film on indium tin oxide (ITO glass, the QD-MAPbBr3 film was coated by a spin-coating method in a nitrogen-filled glove box and the NiOx film was used as an adhesive layer and hole transport layer. The highest transmittance of MAPbBr3 on NiOx/ITO glass was around 75% at 700 nm. This study also reported a high transparent and perovskite bulk-free ITO/NiOx/QD-MAPbBr3/C60/Ag solar cell where the NiOx, QD-MAPbBr3, and C60 were used as a hole transport layer, active layer, and electron transport layer, respectively.

A simple red-ox titrimetric method for the evaluation of photo ...

Indian Academy of Sciences (India)

Unknown

tal conditions in a relatively short duration in R&D labora- tories having basic analytical facilities. The method suggested here could also be adopted to study the photo- catalytic activity of other transition metal oxide based catalysts. For establishing this technique, we have moni- tored a simple one-electron transfer red-ox ...

Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae)

DEFF Research Database (Denmark)

Søchting, Ulrik; Lutzoni, François

2003-01-01

A molecular phylogenetic analysis of rDNA was performed for seven Caloplaca, seven Xanthoria, one Fulgensia and five outgroup species. Phylogenetic hypotheses are constructed based on nuclear small and large subunit rDNA, separately and in combination. Three strongly supported major monophyletic ...

Transforming phylogenetic networks: Moving beyond tree space.

Science.gov (United States)

Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

2016-09-07

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Veronica: Chemical characters for the support of phylogenetic relationships based on nuclear ribosomal and plastid DNA sequence data

DEFF Research Database (Denmark)

Albach, Dirk C.; Jensen, Søren Rosendal; Özgökce, Fevzi

2005-01-01

Molecular phylogenetic analyses have revealed many relationships in Veronica (Plantaginaceae) never anticipated before. However, phytochemical characters show good congruence with DNA-based analyses. We have analysed a combined data set of 49 species and subspecies derived from the nuclear...... are monophyletic sister groups with the annual species consecutive sisters to them. All species of Veronica that contain cornoside are found in this subgenus, although some species seem to have secondarily lost the ability to produce this compound. Subgenera Pocilla and Pentasepalae are well supported sister...... species in the genus analysed to date to contain melittoside and globularifolin. Subgenus Pentasepalae appears to be a clade of diverse lineages from southwestern Asia and a single European clade. Species shown to have 6-hydroxyflavones do not form a monophyletic group. Subgenus Pseudolysimachium seems...

Si@SiOx/Graphene nanosheet anode materials for lithium-ion batteries synthesized by ball milling process

Science.gov (United States)

Tie, Xiaoyong; Han, Qianyan; Liang, Chunyan; Li, Bo; Zai, Jiantao; Qian, Xuefeng

2017-12-01

Si@SiOx/Graphene nanosheet (GNS) nanocomposites as high performance anode materials for lithium-ion batteries are synthesized by mechanically blending the mixture of expanded graphite with Si nanoparticles, and characterized by X-ray diffraction, Raman spectrum, field emission scanning electron microscopy and transmission electron microscopy. During the ball milling process, the size of Si nanoparticles will decrease, and the layer of expanded graphite can be peeled off to thin multilayers. Electrochemical performances reveal that the obtained Si@SiOx/GNS nanocomposites exhibit improved cycling stability, high reversible lithium storage capacity and superior rate capability, e.g. the discharge capacity is kept as high as 1055 mAh g-1 within 50 cycles at a current density of 200 mA g-1, retaining 63.6% of the initial value. The high performance of the obtained nanocomposites can be ascribed to GNS prepared through heat-treat and ball-milling methods, the decrease in the size of Si nanoparticles and SiOx layer on Si surface, which enhance the interactions between Si and GNS.

The Structural Changes of the Sn(y)OX Thin Films Under Influence of Heat Treament

Science.gov (United States)

Vong, V.

2001-04-01

Composite oxide Sn(y) Ox made by thermal oxidation of the Sn(y)-bimetal thin films, in which y is the doped-materials as well as Sb, Ag or Pd. The Sn(y)-bimetal thin films have been made by evaporation in high vacuum onto NaCl-monocrystall and optical glass substrates. In the work the tin and the doped material (y) were put on two different boats and then both the boats were simultaniously heated to evaporate. The Sn(y)Ox thin films were annealed at the differential temperatures. The structural changes of its have been investigated by using X-ray diffraction and transmission electron microscope.

Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature.

Science.gov (United States)

Madzia, Daniel; Cau, Andrea

2017-01-01

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the 'weak spots' in the phylogeny of mosasauroids, we revise the nomenclature of the 'traditionally' recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.

Incorporating phylogenetic information for the definition of floristic districts in hyperdiverse Amazon forests: Implications for conservation.

Science.gov (United States)

Guevara Andino, Juan Ernesto; Pitman, Nigel C A; Ter Steege, Hans; Mogollón, Hugo; Ceron, Carlos; Palacios, Walter; Oleas, Nora; Fine, Paul V A

2017-11-01

Using complementary metrics to evaluate phylogenetic diversity can facilitate the delimitation of floristic units and conservation priority areas. In this study, we describe the spatial patterns of phylogenetic alpha and beta diversity, phylogenetic endemism, and evolutionary distinctiveness of the hyperdiverse Ecuador Amazon forests and define priority areas for conservation. We established a network of 62 one-hectare plots in terra firme forests of Ecuadorian Amazon. In these plots, we tagged, collected, and identified every single adult tree with dbh ≥10 cm. These data were combined with a regional community phylogenetic tree to calculate different phylogenetic diversity (PD) metrics in order to create spatial models. We used Loess regression to estimate the spatial variation of taxonomic and phylogenetic beta diversity as well as phylogenetic endemism and evolutionary distinctiveness. We found evidence for the definition of three floristic districts in the Ecuadorian Amazon, supported by both taxonomic and phylogenetic diversity data. Areas with high levels of phylogenetic endemism and evolutionary distinctiveness in Ecuadorian Amazon forests are unprotected. Furthermore, these areas are severely threatened by proposed plans of oil and mining extraction at large scales and should be prioritized in conservation planning for this region.

Calcination effects on CeZrOx geometry and styrene production from ethylbenzene

NARCIS (Netherlands)

Kovacevic, M.; Brunet Espinosa, Roger; Lefferts, Leonardus; Mojet, Barbara

2014-01-01

A series of CeZrOx catalysts was prepared by calcination of hydrothermally obtained metal oxide precipitate at increasing temperatures. The samples were characterized by HRSEM, XRD and Raman spectroscopy, showing a change in morphology and particle size as a function of calcination temperature.

Continental scale patterns and predictors of fern richness and phylogenetic diversity

Directory of Open Access Journals (Sweden)

Nathalie eNagalingum

2015-04-01

Full Text Available Because ferns have a wide range of habitat preferences and are widely distributed, they are an ideal group for understanding how diversity is distributed. Here we examine fern diversity on a broad-scale using standard and corrected richness measures as well as phylogenetic indices; in addition we determine the environmental predictors of each diversity metric. Using the combined records of Australian herbaria, a dataset of over 60,000 records was obtained for 89 genera to infer richness. A phylogenetic tree of all the genera was constructed and combined with the herbarium records to obtain phylogenetic diversity patterns. A hotspot of both taxic and phylogenetic diversity occurs in the Wet Tropics of northeastern Australia. Although considerable diversity is distributed along the eastern coast, some important regions of diversity are identified only after sample-standardization of richness and through the phylogenetic metric. Of all of the metrics, annual precipitation was identified as the most explanatory variable, in part, in agreement with global and regional fern studies. Precipitation was combined with a different variable for each different metric. For corrected richness, precipitation is combined with temperature seasonality, while correlation of phylogenetic diversity to precipitation plus radiation indicates support for the species-energy hypothesis. Significantly high and significantly low phylogenetic diversity were found in geographically separate areas. These areas are correlated with different climatic conditions such as seasonality in precipitation. The use of phylogenetic metrics identifies additional areas of significant diversity, some of which have not been revealed using traditional taxonomic analyses, suggesting that different ecological and evolutionary processes have operated over the continent. Our study demonstrates that it is possible and vital to incorporate evolutionary metrics when inferring biodiversity hotspots

Integrative taxonomy of ciliates: Assessment of molecular phylogenetic content and morphological homology testing.

Science.gov (United States)

Vďačný, Peter

2017-10-01

The very diverse and comparatively complex morphology of ciliates has given rise to numerous taxonomic concepts. However, the information content of the utilized molecular markers has seldom been explored prior to phylogenetic analyses and taxonomic decisions. Likewise, robust testing of morphological homology statements and the apomorphic nature of diagnostic characters of ciliate taxa is rarely carried out. Four phylogenetic techniques that may help address these issues are reviewed. (1) Split spectrum analysis serves to determine the exact number and quality of nucleotide positions supporting individual nodes in phylogenetic trees and to discern long-branch artifacts that cause spurious phylogenies. (2) Network analysis can depict all possible evolutionary trajectories inferable from the dataset and locate and measure the conflict between them. (3) A priori likelihood mapping tests the suitability of data for reconstruction of a well resolved tree, visualizes the tree-likeness of quartets, and assesses the support of an internal branch of a given tree topology. (4) Reconstruction of ancestral morphologies can be applied for analyzing homology and apomorphy statements without circular reasoning. Since these phylogenetic tools are rarely used, their principles and interpretation are introduced and exemplified using various groups of ciliates. Finally, environmental sequencing data are discussed in this light. Copyright © 2017 The Author. Published by Elsevier GmbH.. All rights reserved.

Morphological support for the phylogenetic positioning of Pentastomida and related fossils

Directory of Open Access Journals (Sweden)

Elaine Christine Costa Eloy

2008-09-01

Full Text Available Pentastomida is a group of parasites that infects the respiratory tracts of vertebrates. They have a mixture of annelid and arthropod characteristics. For that reason, the phylogenetic relationships of the pentastomids have been controversial in proposals of metazoan phylogeny. Forty-seven characters were selected for the analyses of the taxa Annelida, Arthropoda, Kinorhyncha, Loricifera, Nematoda, Nematomorpha, Onychophora, Pentastomida, Priapulida and Tardigrada. The analyses with PAUP resulted in a single shortest cladogram (length 89, ci 0.78, ri 0.86. Our results indicate that Pentastomida is a transitional group between the Arthropoda and some of the Nemathelminth groups such as Nematoda and Nematomorpha.

Functional and phylogenetic ecology in R

CERN Document Server

Swenson, Nathan G

2014-01-01

Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a uni...

A format for phylogenetic placements.

Directory of Open Access Journals (Sweden)

Frederick A Matsen

Full Text Available We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g., short reads into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them. The format is lightweight, versatile, extensible, and is based on the JSON format, which can be parsed by most modern programming languages. Our format is already implemented in several tools for computing and post-processing parsimony- and likelihood-based phylogenetic placements and has worked well in practice. We believe that establishing a standard format for analyzing read placements at this early stage will lead to a more efficient development of powerful and portable post-analysis tools for the growing applications of phylogenetic placement.

Room-temperature ferromagnetic Cr-doped Ge/GeOx core–shell nanowires

Science.gov (United States)

Katkar, Amar S.; Gupta, Shobhnath P.; Motin Seikh, Md; Chen, Lih-Juann; Walke, Pravin S.

2018-06-01

The Cr-doped tunable thickness core–shell Ge/GeOx nanowires (NWs) were synthesized and characterized using x-ray diffraction, field-emission scanning electron microscopy, transmission electron microscopy, energy-dispersive x-ray spectroscopy, x-ray photoelectron spectroscopy and magnetization studies. The shell thickness increases with the increase in synthesis temperature. The presence of metallic Cr and Cr3+ in core–shell structure was confirmed from XPS study. The magnetic property is highly sensitive to the core–shell thickness and intriguing room temperature ferromagnetism is realized only in core–shell NWs. The magnetization decreases with an increase in shell thickness and practically ceases to exist when there is no core. These NWs show remarkably high Curie temperature (TC > 300 K) with the dominating values of its magnetic remanence (MR) and coercivity (HC) compared to germanium dilute magnetic semiconductor nanomaterials. We believe that our finding on these Cr-doped Ge/GeOX core–shell NWs has the potential to be used as a hard magnet for future spintronic devices, owing to their higher characteristic values of ferromagnetic ordering.

Hierarchical nanostructured 3D flowerlike BiOX particles with excellent visible-light photocatalytic activity

Energy Technology Data Exchange (ETDEWEB)

Song, Jinling, E-mail: sjl2010004@imust.cn; Wang, Baoying; Guo, Xianjie; Wang, Ruifen; Dong, Zhongping [Inner Mongolia University of Science and Technology, School of Material and Metallurgy (China)

2016-08-15

BiOX (X = Cl, Br, and I) semiconductors were firstly prepared by a facile mixed solvent solvothermal route. Several characterization tools were employed to study the phase structures, morphologies, and optical properties of the samples. The in situ chemically mixed prepared BiOX particles with diameters 3.0–5.0 μm, fabricated by nanoplates in the thickness range of 5–18 nm, exhibited the highest visible-light photocatalytic activity among the as-prepared samples and Degussa P{sub 25} for the degradation of Rhodamine B (RhB). This result can be due to the narrow bandgap, broad sunlight range, high electronic negativity, and efficient separation of photoinduced electron–hole pairs. Finally, a possible photocatalytic mechanism has been proposed.

Phylogenetic inertia and Darwin's higher law.

Science.gov (United States)

Shanahan, Timothy

2011-03-01

The concept of 'phylogenetic inertia' is routinely deployed in evolutionary biology as an alternative to natural selection for explaining the persistence of characteristics that appear sub-optimal from an adaptationist perspective. However, in many of these contexts the precise meaning of 'phylogenetic inertia' and its relationship to selection are far from clear. After tracing the history of the concept of 'inertia' in evolutionary biology, I argue that treating phylogenetic inertia and natural selection as alternative explanations is mistaken because phylogenetic inertia is, from a Darwinian point of view, simply an expected effect of selection. Although Darwin did not discuss 'phylogenetic inertia,' he did assert the explanatory priority of selection over descent. An analysis of 'phylogenetic inertia' provides a perspective from which to assess Darwin's view. Copyright © 2010 Elsevier Ltd. All rights reserved.

Integrated one diode-one resistor architecture in nanopillar SiOx resistive switching memory by nanosphere lithography.

Science.gov (United States)

Ji, Li; Chang, Yao-Feng; Fowler, Burt; Chen, Ying-Chen; Tsai, Tsung-Ming; Chang, Kuan-Chang; Chen, Min-Chen; Chang, Ting-Chang; Sze, Simon M; Yu, Edward T; Lee, Jack C

2014-02-12

We report on a highly compact, one diode-one resistor (1D-1R) nanopillar device architecture for SiOx-based ReRAM fabricated using nanosphere lithography (NSL). The intrinsic SiOx-based resistive switching element and Si diode are self-aligned on an epitaxial silicon wafer using NSL and a deep-Si-etch process without conventional photolithography. AC-pulse response in 50 ns regime, multibit operation, and good reliability are demonstrated. The NSL process provides a fast and economical approach to large-scale patterning of high-density 1D-1R ReRAM with good potential for use in future applications.

The anatomy, affinity, and phylogenetic significance of Markuelia.

Science.gov (United States)

Dong, Xi-Ping; Donoghue, Philip C J; Cunningham, John A; Liu, Jian-Bo; Cheng, Hong

2005-01-01

The fossil record provides a paucity of data on the development of extinct organisms, particularly for their embryology. The recovery of fossilized embryos heralds new insight into the evolution of development but advances are limited by an almost complete absence of phylogenetic constraint. Markuelia is an exception to this, known from cleavage and pre-hatchling stages as a vermiform and profusely annulated direct-developing bilaterian with terminal circumoral and posterior radial arrays of spines. Phylogenetic analyses have hitherto suggested assignment to stem-Scalidophora (phyla Kinorhyncha, Loricifera, Priapulida). We test this assumption with additional data and through the inclusion of additional taxa. The available evidence supports stem-Scalidophora affinity, leading to the conclusion that scalidophorans, cyclonerualians, and ecdysozoans are primitive direct developers, and the likelihood that scalidophorans are primitively metameric.

Early Transcriptomic Response to LDL and oxLDL in Human Vascular Smooth Muscle Cells.

Directory of Open Access Journals (Sweden)

Salvador Damián-Zamacona

Full Text Available Although nowadays it is well known that the human transcriptome can importantly vary according to external or environmental condition, the reflection of this concept when studying oxidative stress and its direct relationship with gene expression profiling during the process of atherogenesis has not been thoroughly achieved.The ability to analyze genome-wide gene expression through transcriptomics has shown that the genome responds dynamically to diverse stimuli. Here, we describe the transcriptome of human vascular smooth muscle cells (hVSMC stimulated by native and oxidized low-density lipoprotein (nLDL and oxLDL respectively, with the aim of assessing the early molecular changes that induce a response in this cell type resulting in a transcriptomic transformation. This expression has been demonstrated in atherosclerotic plaques in vivo and in vitro, particularly in the light of the oxidative modification hypothesis of atherosclerosis.Total RNA was isolated with TRIzol reagent (Life Technologies and quality estimated using an Agilent 2100 bioanalyzer. The transcriptome of hVSMC under different experimental conditions (1,5 and 24 hours for nLDL and oxLDL was obtained using the GeneChip Human Gene 1.0 ST (Affymetrix designed to measure gene expression of 28,869 well-annotated genes. A fixed fold-change cut-off corresponding to ± 2 was used to identify genes exhibiting the most significant variation and statistical significance (P< 0.05, and 8 genes validated by qPCR using Taqman probes.10 molecular processes were significantly affected in hVSMC: Apoptosis and cell cycle, extracellular matrix remodeling, DNA repair, cholesterol efflux, cGMP biosynthesis, endocytic mechanisms, calcium homeostasis, redox balance, membrane trafficking and finally, the immune response to inflammation. The evidence we present supporting the hypothesis for the involvement of oxidative modification of several processes and metabolic pathways in atherosclerosis is

OX40+ T lymphocytes and IFN-γ are associated with American tegumentary leishmaniasis pathogenesis Linfócitos T OX40+ e IFN-γ estão associados com a patogênese da leishmaniose tegumentar americana

Directory of Open Access Journals (Sweden)

Patrícia Luciana Batista Domingos

2012-12-01

Full Text Available BACKGROUND: Leishmaniases are zoonoses considered a public health problem, representing a complex group of diseases with a broad clinical spectrum and epidemiological diversity. Leishmaniasis is caused by several species of protozoa of the genus Leishmania. The evolution of the pathology and the resolution of the leishmaniasis are dependent mainly on the Leishmania species involved, although the cytokine profile plays an important role in the development of the immune response. OBJECTIVES: The purpose of our study was to evaluate the immune response of patients affected by lesions of cutaneous leishmaniasis by immunostaining of the OX40, CD20, IFN-γ and IL-4 proteins. METHODS: The tissue samples were collected from indolent skin ulcers confirmed as cutaneous leishmaniasis of 41 patients aged between six and 90 years. The lesions were submitted to OX40, CD20, INF-γ and IL-4 immunolabeling. RESULTS: We observed a statistically significant higher expression of IFN-γ compared with IL-4 (p=0.009. Besides, OX40 had higher expression when compared with CD20 (pFUNDAMENTOS: As leishmanioses são zoonoses consideradas um problema de saúde pública, representando um grupo de doenças complexas, com uma diversidade de amplo espectro clínico e epidemiológico. A leishmaniose é uma doença causada por várias espécies de protozoários do gênero Leishmania spp. A evolução da patologia e a resolução da leishmaniose são dependentes principalmente da espécie de Leishmania envolvida; embora o perfil das citocinas tenha um importante papel no desenvolvimento da resposta imune. OBJETIVOS: Proporcionar mais conhecimentos sobre os eventos inflamatórios na leishmaniose tegumentar através da avaliação da imunoexpressão de OX40, CD20, IFN-γ e IL-4. MÉTODOS: Foram coletadas amostras de tecido de 41 pacientes, com idade variando entre 6 a 90 anos, com úlceras indolentes na pele confirmados através de exames de diagnóstico como leishmaniose

The transposition distance for phylogenetic trees

OpenAIRE

Rossello, Francesc; Valiente, Gabriel

2006-01-01

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in bioinformatics. The transposition distance for fully resolved phylogenetic trees is a recent addition to the extensive collection of available metrics for comparing phylogenetic trees. In this paper, we generalize the transposition distance from fully resolved to arbi...

Dye-sensitized MIL-101 metal organic frameworks loaded with Ni/NiOx nanoparticles for efficient visible-light-driven hydrogen generation

Directory of Open Access Journals (Sweden)

Xin-Ling Liu

2015-10-01

Full Text Available The Ni/NiOx particles were in situ photodeposited on MIL-101 metal organic frameworks as catalysts for boosting H2 generation from Erythrosin B dye sensitization under visible-light irradiation. The highest H2 production rate of 125 μmol h−1 was achieved from the system containing 5 wt. % Ni-loaded MIL-101 (20 mg and 30 mg Erythrosin B dye. Moreover, the Ni/NiOx catalysts show excellent stability for long-term photocatalytic reaction. The enhancement on H2 generation is attributed to the efficient charge transfer from photoexcited dye to the Ni catalyst via MIL-101. Our results demonstrate that the economical Ni/NiOx particles are durable and active catalysts for photocatalytic H2 generation.

A phylogenetic study of Boletus section Boletus in Europe

NARCIS (Netherlands)

Beugelsdijk, D.C.M.; Linde, van der S.; Zuccarello, G.C.; Bakker, den H.C.

2008-01-01

A phylogenetic study of the species in Boletus sect. Boletus was undertaken using the molecular markers ITS1-5.8S-ITS2 and Gap dh. Four well-supported lineages, one comprising Boletus edulis s.l., the others referring to B. aereus, B. reticulatus and B. pinophilus have been distinguished. The ML and

Phylogenetic Trees From Sequences

Science.gov (United States)

Ryvkin, Paul; Wang, Li-San

In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

The phylogenetic likelihood library.

Science.gov (United States)

Flouri, T; Izquierdo-Carrasco, F; Darriba, D; Aberer, A J; Nguyen, L-T; Minh, B Q; Von Haeseler, A; Stamatakis, A

2015-03-01

We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www.libpll.org under the GNU General Public License (GPL). © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

The ion capturing effect of 5° SiOx alignment films in liquid crystal devices

Science.gov (United States)

Huang, Yi; Bos, Philip J.; Bhowmik, Achintya

2010-09-01

We show that SiOx, deposited at 5° to the interior surface of a liquid crystal cell allows for a surprisingly substantial reduction in the ion concentration of liquid crystal devices. We have investigated this effect and found that this type of film, due to its surface morphology, captures ions from the liquid crystal material. Ion adsorption on 5° SiOx film obeys the Langmuir isotherm. Experimental results shown allow estimation of the ion capturing capacity of these films to be more than an order of 10 000/μm2. These types of materials are useful for new types of very low power liquid crystal devices such as e-books.

Locating a tree in a phylogenetic network

NARCIS (Netherlands)

Iersel, van L.J.J.; Semple, C.; Steel, M.A.

2010-01-01

Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster

Metabolically active CD4+ T cells expressing Glut1 and OX40 preferentially harbor HIV during in vitro infection.

Science.gov (United States)

Palmer, Clovis S; Duette, Gabriel A; Wagner, Marc C E; Henstridge, Darren C; Saleh, Suah; Pereira, Candida; Zhou, Jingling; Simar, David; Lewin, Sharon R; Ostrowski, Matias; McCune, Joseph M; Crowe, Suzanne M

2017-10-01

High glucose transporter 1 (Glut1) surface expression is associated with increased glycolytic activity in activated CD4+ T cells. Phosphatidylinositide 3-kinases (PI3K) activation measured by p-Akt and OX40 is elevated in CD4+Glut1+ T cells from HIV+ subjects. TCR engagement of CD4+Glut1+ T cells from HIV+ subjects demonstrates hyperresponsive PI3K-mammalian target of rapamycin signaling. High basal Glut1 and OX40 on CD4+ T cells from combination antiretroviral therapy (cART)-treated HIV+ patients represent a sufficiently metabolically active state permissive for HIV infection in vitro without external stimuli. The majority of CD4+OX40+ T cells express Glut1, thus OX40 rather than Glut1 itself may facilitate HIV infection. Furthermore, infection of CD4+ T cells is limited by p110γ PI3K inhibition. Modulating glucose metabolism may limit cellular activation and prevent residual HIV replication in 'virologically suppressed' cART-treated HIV+ persons. © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Molecular Phylogenetics: Concepts for a Newcomer.

Science.gov (United States)

Ajawatanawong, Pravech

Molecular phylogenetics is the study of evolutionary relationships among organisms using molecular sequence data. The aim of this review is to introduce the important terminology and general concepts of tree reconstruction to biologists who lack a strong background in the field of molecular evolution. Some modern phylogenetic programs are easy to use because of their user-friendly interfaces, but understanding the phylogenetic algorithms and substitution models, which are based on advanced statistics, is still important for the analysis and interpretation without a guide. Briefly, there are five general steps in carrying out a phylogenetic analysis: (1) sequence data preparation, (2) sequence alignment, (3) choosing a phylogenetic reconstruction method, (4) identification of the best tree, and (5) evaluating the tree. Concepts in this review enable biologists to grasp the basic ideas behind phylogenetic analysis and also help provide a sound basis for discussions with expert phylogeneticists.

The Pharmacological Profile of a Novel Highly Potent Bisphosphonate, OX14 (1-Fluoro-2-(Imidazo-[1,2-α]Pyridin-3-yl)-Ethyl-Bisphosphonate).

Science.gov (United States)

Lawson, Michelle A; Ebetino, Frank H; Mazur, Adam; Chantry, Andrew D; Paton-Hough, Julia; Evans, Holly R; Lath, Darren; Tsoumpra, Maria K; Lundy, Mark W; Dobson, Roy Lm; Quijano, Michael; Kwaasi, Aaron A; Dunford, James E; Duan, Xuchen; Triffitt, James T; Jeans, Gwyn; Russell, R Graham G

2017-09-01

Bisphosphonates are widely used in the treatment of clinical disorders characterized by increased bone resorption, including osteoporosis, Paget's disease, and the skeletal complications of malignancy. The antiresorptive potency of the nitrogen-containing bisphosphonates on bone in vivo is now recognized to depend upon two key properties, namely mineral binding affinity and inhibitory activity on farnesyl pyrophosphate synthase (FPPS), and these properties vary independently of each other in individual bisphosphonates. The better understanding of structure activity relationships among the bisphosphonates has enabled us to design a series of novel bisphosphonates with a range of mineral binding properties and antiresorptive potencies. Among these is a highly potent bisphosphonate, 1-fluoro-2-(imidazo-[1,2 alpha]pyridin-3-yl)-ethyl-bisphosphonate, also known as OX14, which is a strong inhibitor of FPPS, but has lower binding affinity for bone mineral than most of the commonly studied bisphosphonates. The aim of this work was to characterize OX14 pharmacologically in relation to several of the bisphosphonates currently used clinically. When OX14 was compared to zoledronate (ZOL), risedronate (RIS), and minodronate (MIN), it was as potent at inhibiting FPPS in vitro but had significantly lower binding affinity to hydroxyapatite (HAP) columns than ALN, ZOL, RIS, and MIN. When injected i.v. into growing Sprague Dawley rats, OX14 was excreted into the urine to a greater extent than the other bisphosphonates, indicating reduced short-term skeletal uptake and retention. In studies in both Sprague Dawley rats and C57BL/6J mice, OX14 inhibited bone resorption, with an antiresorptive potency equivalent to or greater than the comparator bisphosphonates. In the JJN3-NSG murine model of myeloma-induced bone disease, OX14 significantly prevented the formation of osteolytic lesions (p < 0.05). In summary, OX14 is a new, highly potent bisphosphonate with lower bone binding

Local-scale Partitioning of Functional and Phylogenetic Beta Diversity in a Tropical Tree Assemblage.

Science.gov (United States)

Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang

2015-08-03

The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

Science.gov (United States)

Smits, Samuel A; Ouverney, Cleber C

2010-08-18

Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

Locating a tree in a phylogenetic network

OpenAIRE

van Iersel, Leo; Semple, Charles; Steel, Mike

2010-01-01

Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster Containment problem asks whether the given cluster is a cluster of some phylogenetic tree embedded in the network. Both problems are known to be NP-complete in general. In this article, we consider t...

Nonbinary tree-based phylogenetic networks

OpenAIRE

Jetten, Laura; van Iersel, Leo

2016-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and st...

Encoding phylogenetic trees in terms of weighted quartets.

Science.gov (United States)

Grünewald, Stefan; Huber, Katharina T; Moulton, Vincent; Semple, Charles

2008-04-01

One of the main problems in phylogenetics is to develop systematic methods for constructing evolutionary or phylogenetic trees. For a set of species X, an edge-weighted phylogenetic X-tree or phylogenetic tree is a (graph theoretical) tree with leaf set X and no degree 2 vertices, together with a map assigning a non-negative length to each edge of the tree. Within phylogenetics, several methods have been proposed for constructing such trees that work by trying to piece together quartet trees on X, i.e. phylogenetic trees each having four leaves in X. Hence, it is of interest to characterise when a collection of quartet trees corresponds to a (unique) phylogenetic tree. Recently, Dress and Erdös provided such a characterisation for binary phylogenetic trees, that is, phylogenetic trees all of whose internal vertices have degree 3. Here we provide a new characterisation for arbitrary phylogenetic trees.

Na effect on flexible Cu(In,Ga)Se{sub 2} photovoltaic cell depending on diffusion barriers (SiOx, i-ZnO) on stainless steel

Energy Technology Data Exchange (ETDEWEB)

Lee, Woo-Jung; Cho, Dae-Hyung; Wi, Jae-Hyung; Han, Won Seok [Electronics and Telecommunications Research Institute, Daejeon 305-700 (Korea, Republic of); Kim, Jeha [Insitute of Photovoltaics, Cheongju University, Cheongju 360-764 (Korea, Republic of); Chung, Yong-Duck, E-mail: ydchung@etri.re.kr [Electronics and Telecommunications Research Institute, Daejeon 305-700 (Korea, Republic of); Department of Advanced Device Engineering, Korea University of Science and Technology, Daejeon 305-350 (Korea, Republic of)

2014-10-15

Cu(In,Ga)Se{sub 2} (CIGS) based-photovoltaic (PV) cells with different diffusion barriers of SiOx and i-ZnO were fabricated on stainless steel (STS) substrate and their electrical characteristics were investigated by measuring J–V curves under illuminated and dark conditions. The physical properties of the CIGS film depending on type of diffusion barrier were also analyzed using X-ray diffraction and secondary ion mass spectroscopy. The efficiency of the CIGS-PV cell with i-ZnO barrier was approximately 2% higher than that with the SiOx barrier. Through the analysis of dark J–V curves, we discovered that distinctive defects were formed in the band gap of CIGS based on which diffusion barrier contacted the STS. The diffraction pattern showed a slightly different tendency of the peak intensity ratio of (220/204)/(112) in the PV cell with the i-ZnO barrier, which was slightly higher than that in the PV cell with SiOx barrier. In elemental depth profile, a deficient Ga profile was observed near the surface of the CIGS film with the SiOx barrier, and an abundant Na profile within the CIGS film with the i-ZnO barrier was detected. This is attributed to a difference in thermal conduction through the diffusion barriers during CIGS film growth, originating from the larger thermal conductivity of ZnO compared with SiOx. - Highlights: • We fabricated CIGS-PV cells with diffusion barriers of SiOx and i-ZnO on STS. • The efficiency of CIGS-PV cell with i-ZnO was ∼2% higher than that with SiOx. • Distinctive defects were formed into CIGS absorber depending on diffusion barrier.

Soft-tissue anatomy of the extant hominoids: a review and phylogenetic analysis

Science.gov (United States)

Gibbs, S; Collard, M; Wood, B

2002-01-01

This paper reports the results of a literature search for information about the soft-tissue anatomy of the extant non-human hominoid genera, Pan, Gorilla, Pongo and Hylobates, together with the results of a phylogenetic analysis of these data plus comparable data for Homo. Information on the four extant non-human hominoid genera was located for 240 out of the 1783 soft-tissue structures listed in the Nomina Anatomica. Numerically these data are biased so that information about some systems (e.g. muscles) and some regions (e.g. the forelimb) are over-represented, whereas other systems and regions (e.g. the veins and the lymphatics of the vascular system, the head region) are either under-represented or not represented at all. Screening to ensure that the data were suitable for use in a phylogenetic analysis reduced the number of eligible soft-tissue structures to 171. These data, together with comparable data for modern humans, were converted into discontinuous character states suitable for phylogenetic analysis and then used to construct a taxon-by-character matrix. This matrix was used in two tests of the hypothesis that soft-tissue characters can be relied upon to reconstruct hominoid phylogenetic relationships. In the first, parsimony analysis was used to identify cladograms requiring the smallest number of character state changes. In the second, the phylogenetic bootstrap was used to determine the confidence intervals of the most parsimonious clades. The parsimony analysis yielded a single most parsimonious cladogram that matched the molecular cladogram. Similarly the bootstrap analysis yielded clades that were compatible with the molecular cladogram; a (Homo, Pan) clade was supported by 95% of the replicates, and a (Gorilla, Pan, Homo) clade by 96%. These are the first hominoid morphological data to provide statistically significant support for the clades favoured by the molecular evidence. PMID:11833653

Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate.

Science.gov (United States)

Lin, Jiannan; Chen, Guangfeng; Gu, Liang; Shen, Yuefeng; Zheng, Meizhu; Zheng, Weisheng; Hu, Xinjie; Zhang, Xiaobai; Qiu, Yu; Liu, Xiaoqing; Jiang, Cizhong

2014-02-01

Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly. Copyright © 2013 Elsevier Inc. All rights reserved.

Tuning the Electronic Structure of Titanium Oxide Support to Enhance the Electrochemical Activity of Platinum Nanoparticles

KAUST Repository

Shi, Feifei

2013-09-11

Two times higher activity and three times higher stability in methanol oxidation reaction, a 0.12 V negative shift of the CO oxidation peak potential, and a 0.07 V positive shift of the oxygen reaction potential compared to Pt nanoparticles on pristine TiO2 support were achieved by tuning the electronic structure of the titanium oxide support of Pt nanoparticle catalysts. This was accomplished by adding oxygen vacancies or doping with fluorine. Experimental trends are interpreted in the context of an electronic structure model, showing an improvement in electrochemical activity when the Fermi level of the support material in Pt/TiOx systems is close to the Pt Fermi level and the redox potential of the reaction. The present approach provides guidance for the selection of the support material of Pt/TiOx systems and may be applied to other metal-oxide support materials, thus having direct implications in the design and optimization of fuel cell catalyst supports. © 2013 American Chemical Society.

Global patterns of amphibian phylogenetic diversity

DEFF Research Database (Denmark)

Fritz, Susanne; Rahbek, Carsten

2012-01-01

Aim  Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary...... processes such as diversification and dispersal have left strong signatures on contemporary species richness. Location  Global; equal-area grid cells of approximately 10,000 km2. Methods  We generated an amphibian global supertree (6111 species) and repeated analyses with the largest available molecular...... phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index...

Phylogenetic relationships in Peniocereus (Cactaceae) inferred from plastid DNA sequence data.

Science.gov (United States)

Arias, Salvador; Terrazas, Teresa; Arreola-Nava, Hilda J; Vázquez-Sánchez, Monserrat; Cameron, Kenneth M

2005-10-01

The phylogenetic relationships of Peniocereus (Cactaceae) species were studied using parsimony analyses of DNA sequence data. The plastid rpl16 and trnL-F regions were sequenced for 98 taxa including 17 species of Peniocereus, representatives from all genera of tribe Pachycereeae, four genera of tribe Hylocereeae, as well as from three additional outgroup genera of tribes Calymmantheae, Notocacteae, and Trichocereeae. Phylogenetic analyses support neither the monophyly of Peniocereus as currently circumscribed, nor the monophyly of tribe Pachycereeae since species of Peniocereus subgenus Pseudoacanthocereus are embedded within tribe Hylocereeae. Furthermore, these results show that the eight species of Peniocereus subgenus Peniocereus (Peniocereus sensu stricto) form a well-supported clade within subtribe Pachycereinae; P. serpentinus is also a member of this subtribe, but is sister to Bergerocactus. Moreover, Nyctocereus should be resurrected as a monotypic genus. Species of Peniocereus subgenus Pseudoacanthocereus are positioned among species of Acanthocereus within tribe Hylocereeae, indicating that they may be better classified within that genus. A number of morphological and anatomical characters, especially related to the presence or absence of dimorphic branches, are discussed to support these relationships.

Tree-Based Unrooted Phylogenetic Networks.

Science.gov (United States)

Francis, A; Huber, K T; Moulton, V

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

The phylogenetic significance of leaf anatomical traits of southern African Oxalis

Czech Academy of Sciences Publication Activity Database

Jooste, M.; Dreyer, L. L.; Oberlander, Kenneth

2016-01-01

Roč. 16, č. 1 (2016), s. 1-19, č. článku 225. ISSN 1471-2148 Institutional support: RVO:67985939 Keywords : ancestral state reconstruction * eEpistomaty * leaf anatomy * stomatal position * phylogenetics Subject RIV: EF - Botanics Impact factor: 3.221, year: 2016

Phylogenetics of the Phlebotomine Sand Fly Group Verrucarum (Diptera: Psychodidae: Lutzomyia)

Science.gov (United States)

Cohnstaedt, Lee W.; Beati, Lorenza; Caceres, Abraham G.; Ferro, Cristina; Munstermann, Leonard E.

2011-01-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity—the Lutzomyia longiflocosa–Lutzomyia sauroida pair and the Lutzomyia quasitownsendi–Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution. PMID:21633028

Phylogenetics of the phlebotomine sand fly group Verrucarum (Diptera: Psychodidae: Lutzomyia).

Science.gov (United States)

Cohnstaedt, Lee W; Beati, Lorenza; Caceres, Abraham G; Ferro, Cristina; Munstermann, Leonard E

2011-06-01

Within the sand fly genus Lutzomyia, the Verrucarum species group contains several of the principal vectors of American cutaneous leishmaniasis and human bartonellosis in the Andean region of South America. The group encompasses 40 species for which the taxonomic status, phylogenetic relationships, and role of each species in disease transmission remain unresolved. Mitochondrial cytochrome c oxidase I (COI) phylogenetic analysis of a 667-bp fragment supported the morphological classification of the Verrucarum group into series. Genetic sequences from seven species were grouped in well-supported monophyletic lineages. Four species, however, clustered in two paraphyletic lineages that indicate conspecificity--the Lutzomyia longiflocosa-Lutzomyia sauroida pair and the Lutzomyia quasitownsendi-Lutzomyia torvida pair. COI sequences were also evaluated as a taxonomic tool based on interspecific genetic variability within the Verrucarum group and the intraspecific variability of one of its members, Lutzomyia verrucarum, across its known distribution.

Treelink: data integration, clustering and visualization of phylogenetic trees.

Science.gov (United States)

Allende, Christian; Sohn, Erik; Little, Cedric

2015-12-29

Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www.treelinkapp.com .

Catalytic Hydrothermal Liquefaction of Food Waste Using CeZrOx

Directory of Open Access Journals (Sweden)

Alex R. Maag

2018-03-01

Full Text Available Approximately 15 million dry tons of food waste is produced annually in the United States (USA, and 92% of this waste is disposed of in landfills where it decomposes to produce greenhouse gases and water pollution. Hydrothermal liquefaction (HTL is an attractive technology capable of converting a broad range of organic compounds, especially those with substantial water content, into energy products. The HTL process produces a bio-oil precursor that can be further upgraded to transportation fuels and an aqueous phase containing water-soluble organic impurities. Converting small oxygenated compounds that partition into the water phase into larger, hydrophobic compounds can reduce aqueous phase remediation costs and improve energy yields. HTL was investigated at 300 °C and a reaction time of 1 h for conversion of an institutional food waste to bio-oil, using either homogeneous Na2CO3 or heterogeneous CeZrOx to promote in situ conversion of water-soluble organic compounds into less oxygenated, oil-soluble products. Results with food waste indicate that CeZrOx improves both bio-oil higher heating value (HHV and energy recovery when compared both to non-catalytic and Na2CO3-catalyzed HTL. The aqueous phase obtained using CeZrOx as an HTL catalyst contained approximately half the total organic carbon compared to that obtained using Na2CO3—suggesting reduced water treatment costs using the heterogeneous catalyst. Experiments with model compounds indicated that the primary mechanism of action was condensation of aldehydes, a reaction which simultaneously increases molecular weight and oxygen-to-carbon ratio—consistent with the improvements in bio-oil yield and HHV observed with institutional food waste. The catalyst was stable under hydrothermal conditions (≥16 h at 300 °C and could be reused at least three times for conversion of model aldehydes to water insoluble products. Energy and economic analysis suggested favorable performance for the

Nodal distances for rooted phylogenetic trees.

Science.gov (United States)

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

2010-08-01

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

Ant-Based Phylogenetic Reconstruction (ABPR: A new distance algorithm for phylogenetic estimation based on ant colony optimization

Directory of Open Access Journals (Sweden)

Karla Vittori

2008-12-01

Full Text Available We propose a new distance algorithm for phylogenetic estimation based on Ant Colony Optimization (ACO, named Ant-Based Phylogenetic Reconstruction (ABPR. ABPR joins two taxa iteratively based on evolutionary distance among sequences, while also accounting for the quality of the phylogenetic tree built according to the total length of the tree. Similar to optimization algorithms for phylogenetic estimation, the algorithm allows exploration of a larger set of nearly optimal solutions. We applied the algorithm to four empirical data sets of mitochondrial DNA ranging from 12 to 186 sequences, and from 898 to 16,608 base pairs, and covering taxonomic levels from populations to orders. We show that ABPR performs better than the commonly used Neighbor-Joining algorithm, except when sequences are too closely related (e.g., population-level sequences. The phylogenetic relationships recovered at and above species level by ABPR agree with conventional views. However, like other algorithms of phylogenetic estimation, the proposed algorithm failed to recover expected relationships when distances are too similar or when rates of evolution are very variable, leading to the problem of long-branch attraction. ABPR, as well as other ACO-based algorithms, is emerging as a fast and accurate alternative method of phylogenetic estimation for large data sets.

Batimetría, salinidad, temperatura y oxígeno disuelto en aguas del Parque Nacional Marino Ballena, Pacífico, Costa Rica

Directory of Open Access Journals (Sweden)

Juan José Alvarado

2009-11-01

Full Text Available Se realizó un estudio sobre la batimetría del PNMB y del comportamiento de la temperatura, salinidad, oxígeno disuelto y porcentaje de saturación de oxígeno entre setiembre 2003 y abril 2005. El parque posee una profundidad promedio de 14.97± 9.11m y una profundidad máxima detectada de 37.33m. La sección interna de la bahía es poco profunda, no alcanzando más de 20m de profundidad, mientras que en la parte externa la pendiente es más pronunciada, alcanzando rápidamente los 37 m. A lo largo del estudio, los valores promedio superficiales de salinidad fueron de 29.1±4.3‰, de temperatura 29.7±1.3ºC, de concentración de oxígeno disuelto 6.7±1.3mg/l, y del porcentaje de saturación de oxígeno 115.6±22.1%. Entre las estaciones interna y externa solo se observaron diferencias significativas en cuanto a la salinidad y la temperatura por profundidad, como producto de la época lluviosa. Los valores más bajos de salinidad y temperatura se observaron para la época lluviosa y los más altos en la época seca, mientras que los valores de oxígeno disuelto y porcentaje de saturación de oxígeno presentaron un incremento continuo a través del tiempo. La similitud entre las estaciones y el hecho de haber encontrado diferencias significativas solamente entre la salinidad y la temperatura en cuanto a la profundidad, hacen pensar que a lo largo del tiempo las aguas del parque se comportan de manera muy similar y que es una zona muy dinámica y homogénea con corrientes lo suficientemente fuertes para mezclar la columna de agua del parque. El PNMB es una zona muy productiva debido a los altos valores de saturación de oxígeno observados a lo largo del tiempo (120%. Esto hace pensar que existen condiciones apropiadas para el desarrollo del fitoplancton, zooplancton y otros grupos tróficos.

Phylogenetic utility of ribosomal genes for reconstructing the phylogeny of five Chinese satyrine tribes (Lepidoptera, Nymphalidae

Directory of Open Access Journals (Sweden)

Mingsheng Yang

2015-03-01

Full Text Available Satyrinae is one of twelve subfamilies of the butterfly family Nymphalidae, which currently includes nine tribes. However, phylogenetic relationships among them remain largely unresolved, though different researches have been conducted based on both morphological and molecular data. However, ribosomal genes have never been used in tribe level phylogenetic analyses of Satyrinae. In this study we investigate for the first time the phylogenetic relationships among the tribes Elymniini, Amathusiini, Zetherini and Melanitini which are indicated to be a monophyletic group, and the Satyrini, using two ribosomal genes (28s rDNA and 16s rDNA and four protein-coding genes (EF-1α, COI, COII and Cytb. We mainly aim to assess the phylogenetic informativeness of the ribosomal genes as well as clarify the relationships among different tribes. Our results show the two ribosomal genes generally have the same high phylogenetic informativeness compared with EF-1α; and we infer the 28s rDNA would show better informativeness if the 28s rDNA sequence data for each sampling taxon are obtained in this study. The placement of the monotypic genus Callarge Leech in Zetherini is confirmed for the first time based on molecular evidence. In addition, our maximum likelihood (ML and Bayesian inference (BI trees consistently show that the involved Satyrinae including the Amathusiini is monophyletic with high support values. Although the relationships among the five tribes are identical among ML and BI analyses and are mostly strongly-supported in BI analysis, those in ML analysis are lowly- or moderately- supported. Therefore, the relationships among the related five tribes recovered herein need further verification based on more sampling taxa.

Combined Analysis of CSF Tau, Aβ42, Aβ1–42% and Aβ1–40ox% in Alzheimer's Disease, Dementia with Lewy Bodies and Parkinson's Disease Dementia

Directory of Open Access Journals (Sweden)

Mirko Bibl

2010-01-01

Full Text Available We studied the diagnostic value of CSF Aβ42/tau versus low Aβ1–42% and high Aβ1–40ox% levels for differential diagnosis of Alzheimer's disease (AD and dementia with Lewy bodies (DLB, respectively. CSF of 45 patients with AD, 15 with DLB, 21 with Parkinson's disease dementia (PDD, and 40 nondemented disease controls (NDC was analyzed by Aβ-SDS-PAGE/immunoblot and ELISAs (Aβ42 and tau. Aβ42/tau lacked specificity in discriminating AD from DLB and PDD. Best discriminating biomarkers were Aβ1–42% and Aβ1–40ox% for AD and DLB, respectively. AD and DLB could be differentiated by both Aβ1–42% and Aβ1–40ox% with an accuracy of 80% at minimum. Thus, we consider Aβ1–42% and Aβ1–40ox% to be useful biomarkers for AD and DLB, respectively. We propose further studies on the integration of Aβ1–42% and Aβ1–40ox% into conventional assay formats. Moreover, future studies should investigate the combination of Aβ1–40ox% and CSF alpha-synuclein for the diagnosis of DLB.

SCR activity of conformed CuOx/ZrO2-SO4 catalysts

DEFF Research Database (Denmark)

Rasmussen, Søren Birk; Yates, Malcolm; Due-Hansen, Johannes

2010-01-01

CuOX/ZrO2-SO4 catalysts have been synthesised as conformed materials with the use of sepiolite as agglomerant and the performance in the NH3-SCR reaction with relation to biomass fired boiler units have been studied. The optimal Cu-loading of the catalysts is 3 wt.% CuO, both in terms of activity...

Role of ox-PAPCs in the differentiation of mesenchymal stem cells (MSCs and Runx2 and PPARγ2 expression in MSCs-like of osteoporotic patients.

Directory of Open Access Journals (Sweden)

Maria Teresa Valenti

Full Text Available BACKGROUND: Mesenchymal stem cells (MSCs can differentiate into osteoblasts and adipocytes and conditions causing bone loss may induce a switch from the osteoblast to adipocyte lineage. In addition, the expression of Runx2 and the PPARγ2 transcription factor genes is essential for cellular commitment to an osteogenic and adipogenic differentiation, respectively. Modified lipoproteins derived from the oxidation of arachidonate-containing phospholipids (ox-PAPCs: POVPC, PGPC and PEIPC are considered important factors in atherogenesis. METHODOLOGY: We investigated the effect of ox-PAPCs on osteogenesis and adipogenesis in human mesenchymal stem cells (hMSCs. In particular, we analyzed the transcription factor Runx2 and the PPARγ2 gene expression during osteogenic and adipogenic differentiation in absence and in presence of ox-PAPCs. We also analyzed gene expression level in a panel of osteoblastic and adipogenic differentiation markers. In addition, as circulating blood cells can be used as a "sentinel" that responds to changes in the macro- or micro-environment, we analyzed the Runx2 and the PPARγ2 gene expression in MSCs-like and ox-PAPC levels in serum of osteoporotic patients (OPs. Finally, we examined the effects of sera obtained from OPs in hMSCs comparing the results with age-matched normal donors (NDs. PRINCIPAL FINDINGS: Quantitative RT-PCR demonstrated that ox-PAPCs enhanced PPARγ2 and adipogenic gene expression and reduced Runx2 and osteoblast differentiation marker gene expression in differentiating hMSCs. In OPs, ox-PAPC levels and PPARγ2 expression were higher than in NDs, whereas Runx2 was lower than in ND circulant MSCs-like. CONCLUSIONS: Ox-PAPCs affect the osteogenic differentiation by promoting adipogenic differentiation and this effect may appear involved in bone loss in OPs.

Microfabrication of SrRuO3 thin films on various oxide substrates using LaAlO3/BaOx sacrificial bilayers

Science.gov (United States)

Harada, Takayuki; Tsukazaki, Atsushi

2018-02-01

Oxides provide various fascinating physical properties that could find use in future device applications. However, the physical properties of oxides are often affected by formation of oxygen vacancies during device fabrication processes. In this study, to develop a damage-free patterning process for oxides, we focus on a lift-off process using a sacrificial template layer, by which we can pattern oxide thin films without severe chemical treatment or plasma bombardment. As oxides need high thin-film growth temperature, a sacrificial template needs to be made of thermally stable and easily etchable materials. To meet these requirements, we develop a sacrificial template with a carefully designed bilayer structure. Combining a thermally and chemically stable LaAlO3 and a water-soluble BaOx, we fabricated a LaAlO3/BaOx sacrificial bilayer. The patterned LaAlO3/BaOx sacrificial bilayers were prepared on oxide substrates by room-temperature pulsed laser deposition and standard photolithography process. The structure of the sacrificial bilayer can be maintained even in rather tough conditions needed for oxide thin film growth: several hundred degrees Celsius under high oxygen pressure. Indeed, the LaAlO3/BaOx bilayer is easily removable by sonication in water. We applied the lift-off method using the LaAlO3/BaOx sacrificial bilayer to a representative oxide conductor SrRuO3 and fabricated micron-scale Hall-bar devices. The SrRuO3 channels with the narrowest line width of 5 μm exhibit an almost identical transport property to that of the pristine film, evidencing that the developed process is beneficial for patterning oxides. We show that the LaAlO3/BaOx lift-off process is applicable to various oxide substrates: SrTiO3, MgO, and Al2O3. The new versatile patterning process will expand the range of application of oxide thin films in electronic and photonic devices.

Low-temperature atomic layer deposition of MoOx for silicon heterojunction solar cells

NARCIS (Netherlands)

Macco, B.; Vos, M.; Thissen, N.F.W.; Bol, A.A.; Kessels, W.M.M.

2015-01-01

The preparation of high-quality molybdenum oxide (MoOx) is demonstrated by plasma-enhanced atomic layer deposition (ALD) at substrate temperatures down to 50 °C. The films are amorphous, slightly substoichiometric with respect to MoO3, and free of other elements apart from hydrogen (&11 at%). The

RBS and XPS study of TiOx layers prepared by the PVD technique .

Czech Academy of Sciences Publication Activity Database

Macková, Anna; Peřina, Vratislav; Krumeich, J.; Zemek, J.; Kolouch, A.

2004-01-01

Roč. 36, č. 8 (2004), s. 1171-1173 ISSN 0142-2421 R&D Projects: GA ČR GP102/01/D069 Institutional research plan: CEZ:AV0Z1048901 Keywords : RBS * ERDA * TiOx Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.209, year: 2004

NanOx, a new model to predict cell survival in the context of particle therapy

Science.gov (United States)

Cunha, M.; Monini, C.; Testa, E.; Beuve, M.

2017-02-01

Particle therapy is increasingly attractive for the treatment of tumors and the number of facilities offering it is rising worldwide. Due to the well-known enhanced effectiveness of ions, it is of utmost importance to plan treatments with great care to ensure tumor killing and healthy tissues sparing. Hence, the accurate quantification of the relative biological effectiveness (RBE) of ions, used in the calculation of the biological dose, is critical. Nevertheless, the RBE is a complex function of many parameters and its determination requires modeling. The approaches currently used have allowed particle therapy to thrive, but still show some shortcomings. We present herein a short description of a new theoretical framework, NanOx, to calculate cell survival in the context of particle therapy. It gathers principles from existing approaches, while addressing some of their weaknesses. NanOx is a multiscale model that takes the stochastic nature of radiation at nanometric and micrometric scales fully into account, integrating also the chemical aspects of radiation-matter interaction. The latter are included in the model by means of a chemical specific energy, determined from the production of reactive chemical species induced by irradiation. Such a production represents the accumulation of oxidative stress and sublethal damage in the cell, potentially generating non-local lethal events in NanOx. The complementary local lethal events occur in a very localized region and can, alone, lead to cell death. Both these classes of events contribute to cell death. The comparison between experimental data and model predictions for the V79 cell line show a good agreement. In particular, the dependence of the typical shoulders of cell survival curves on linear energy transfer are well described, but also the effectiveness of different ions, including the overkill effect. These results required the adjustment of a number of parameters compatible with the application of the model in

On Tree-Based Phylogenetic Networks.

Science.gov (United States)

Zhang, Louxin

2016-07-01

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

Effect of iron content on the catalytic activity of Fe-MnOx electrodeposited films in water oxidation

Science.gov (United States)

Selinger, Elizabeth; Ryczko, Kevin; Lopinski, Gregory; Armandi, Marco; Bonelli, Barbara; Tamblyn, Isaac

We report on the experimental and computational optimization and characterization of an MnOx structure containing a small amount of Fe, used as a catalyst for the water oxidation reaction (WOR), the key limiting reaction in water splitting. MnOx materials are earth-abundant and known to be efficient for WOR, and the method of cathodically electrodepositing catalysts allows for quick synthesis and a homogeneous coverage of the substrate. We present an increase in WOR activity due to the presence of Fe in this MnOx catalyst structure. First, we explored the optimal range for Fe(NO3)3 concentration in an KMnO4 solution for electrodeposition and tested for WOR activity. The catalyst structure was then analyzed using FESEM, XPS, and a Kelvin probe. We then developed a computational model of this structure, using density functional theory to obtain adsorption energies, work functions, projected density of states, and Born-Oppenheimer molecular dynamics. In this theoretical framework, we explore how these observables change with respect to concentration of Fe, and compare the theoretical model with experiment. special acknowledgement to the Italian Cultural Centre of Durham scholarship program.

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

Science.gov (United States)

Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

2016-01-01

Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.

A Consistent Phylogenetic Backbone for the Fungi

Science.gov (United States)

Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

2012-01-01

The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

Functional & phylogenetic diversity of copepod communities

Science.gov (United States)

Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

2016-02-01

The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

treespace: Statistical exploration of landscapes of phylogenetic trees.

Science.gov (United States)

Jombart, Thibaut; Kendall, Michelle; Almagro-Garcia, Jacob; Colijn, Caroline

2017-11-01

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace, combines tree metrics and multivariate analysis to provide low-dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group-specific consensus phylogenies. treespace also provides a user-friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results. © 2017 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Phylogenetic diversity and relationships among species of genus ...

African Journals Online (AJOL)

Fifty six Nicotiana species were used to construct phylogenetic trees and to asses the genetic relationships between them. Genetic distances estimated from RAPD analysis was used to construct phylogenetic trees using Phylogenetic Inference Package (PHYLIP). Since phylogenetic relationships estimated for closely ...

Spontaneous nano-clustering of ZrO2 in atomic layer deposited LayZr1-yOx thin films: Part 1 - Material characterization

NARCIS (Netherlands)

Klootwijk, J.H.; Jinesh, K.B.; Wolters, R.A.M.; Roozeboom, F.; Besling, W.

2008-01-01

During atomic layer deposition (ALD) of uniform LayZr1-yOx thin films, spontaneous segregation of ZrO2 nanocrystals takes place that are embedded in an amorphous La2O3 matrix. This occurs if the Zr content in the LayZr1-yOx film is above 30% i.e. if the pulse ratio between the lanthanum precursor

Production of a Novel OX40 Ligand for Clinical Use

Science.gov (United States)

2012-10-01

that mutating the OX40L:Ig sequence would lead to a “safer” profile for FDA screening purposes, it was not clear whether mutating this sequence... green monkey kidney cell line, Vero, fits this description and was used. The indicator cells are maintained by WuXi AppTec’s Cell Production Laboratory...extra-nuclear and typically appears as small round bodies approximately 0.3 fim in diameter. 10.2 Direct Assay Change in color or turbidity of broth

Nonbinary Tree-Based Phylogenetic Networks

NARCIS (Netherlands)

Jetten, L.; van Iersel, L.J.J.

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example

Oxide Structure Dependence of SiO2/SiOx/3C-SiC/n-Type Si Nonvolatile Resistive Memory on Memory Operation Characteristics

Science.gov (United States)

Yamaguchi, Yuichiro; Shouji, Masatsugu; Suda, Yoshiyuki

2012-11-01

We have investigated the dependence of the oxide layer structure of our previously proposed metal/SiO2/SiOx/3C-SiC/n-Si/metal metal-insulator-semiconductor (MIS) resistive memory device on the memory operation characteristics. The current-voltage (I-V) measurement and X-ray photoemission spectroscopy results suggest that SiOx defect states mainly caused by the oxidation of 3C-SiC at temperatures below 1000 °C are related to the hysteresis memory behavior in the I-V curve. By restricting the SiOx interface region, the number of switching cycles and the on/off current ratio are more enhanced. Compared with a memory device formed by one-step or two-step oxidation of 3C-SiC, a memory device formed by one-step oxidation of Si/3C-SiC exhibits a more restrictive SiOx interface with a more definitive SiO2 layer and higher memory performances for both the endurance switching cycle and on/off current ratio.

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

Directory of Open Access Journals (Sweden)

Cronn Richard

2009-12-01

Full Text Available Abstract Background Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? Results We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2, highlighting their unusual evolutionary properties. Conclusion Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling

The prevalence of terraced treescapes in analyses of phylogenetic data sets.

Science.gov (United States)

Dobrin, Barbara H; Zwickl, Derrick J; Sanderson, Michael J

2018-04-04

The pattern of data availability in a phylogenetic data set may lead to the formation of terraces, collections of equally optimal trees. Terraces can arise in tree space if trees are scored with parsimony or with partitioned, edge-unlinked maximum likelihood. Theory predicts that terraces can be large, but their prevalence in contemporary data sets has never been surveyed. We selected 26 data sets and phylogenetic trees reported in recent literature and investigated the terraces to which the trees would belong, under a common set of inference assumptions. We examined terrace size as a function of the sampling properties of the data sets, including taxon coverage density (the proportion of taxon-by-gene positions with any data present) and a measure of gene sampling "sufficiency". We evaluated each data set in relation to the theoretical minimum gene sampling depth needed to reduce terrace size to a single tree, and explored the impact of the terraces found in replicate trees in bootstrap methods. Terraces were identified in nearly all data sets with taxon coverage densities tree. Terraces found during bootstrap resampling reduced overall support. If certain inference assumptions apply, trees estimated from empirical data sets often belong to large terraces of equally optimal trees. Terrace size correlates to data set sampling properties. Data sets seldom include enough genes to reduce terrace size to one tree. When bootstrap replicate trees lie on a terrace, statistical support for phylogenetic hypotheses may be reduced. Although some of the published analyses surveyed were conducted with edge-linked inference models (which do not induce terraces), unlinked models have been used and advocated. The present study describes the potential impact of that inference assumption on phylogenetic inference in the context of the kinds of multigene data sets now widely assembled for large-scale tree construction.

Different relationships between temporal phylogenetic turnover and phylogenetic similarity and in two forests were detected by a new null model.

Science.gov (United States)

Huang, Jian-Xiong; Zhang, Jian; Shen, Yong; Lian, Ju-yu; Cao, Hong-lin; Ye, Wan-hui; Wu, Lin-fang; Bin, Yue

2014-01-01

Ecologists have been monitoring community dynamics with the purpose of understanding the rates and causes of community change. However, there is a lack of monitoring of community dynamics from the perspective of phylogeny. We attempted to understand temporal phylogenetic turnover in a 50 ha tropical forest (Barro Colorado Island, BCI) and a 20 ha subtropical forest (Dinghushan in southern China, DHS). To obtain temporal phylogenetic turnover under random conditions, two null models were used. The first shuffled names of species that are widely used in community phylogenetic analyses. The second simulated demographic processes with careful consideration on the variation in dispersal ability among species and the variations in mortality both among species and among size classes. With the two models, we tested the relationships between temporal phylogenetic turnover and phylogenetic similarity at different spatial scales in the two forests. Results were more consistent with previous findings using the second null model suggesting that the second null model is more appropriate for our purposes. With the second null model, a significantly positive relationship was detected between phylogenetic turnover and phylogenetic similarity in BCI at a 10 m×10 m scale, potentially indicating phylogenetic density dependence. This relationship in DHS was significantly negative at three of five spatial scales. This could indicate abiotic filtering processes for community assembly. Using variation partitioning, we found phylogenetic similarity contributed to variation in temporal phylogenetic turnover in the DHS plot but not in BCI plot. The mechanisms for community assembly in BCI and DHS vary from phylogenetic perspective. Only the second null model detected this difference indicating the importance of choosing a proper null model.

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

DEFF Research Database (Denmark)

Mouatt, Julia Thidamarth Vilstrup; Ho, Simon Y. W.; Foote, Andrew David

2011-01-01

Previous DNA-based phylogenetic studies of the Delphinidae family suggest it has undergone rapid diversification, as characterised by unresolved and poorly supported taxonomic relationships (polytomies) for some of the species within this group. Using an increased amount of sequence data we test ...

Phylogenetic patterns are not proxies of community assemblymechanisms (they are far better)

Czech Academy of Sciences Publication Activity Database

Gerhold, P.; Cahill, J. F. Jr.; Winter, M.; Bartish, Igor V.; Prinzing, A.

2015-01-01

Roč. 29, č. 5 (2015), s. 600-614 ISSN 0269-8463 Grant - others:AV ČR(CZ) Fellowship J. E. Purkyně Institutional support: RVO:67985939 Keywords : macroecological diversification * phylogenetics * functional traits Subject RIV: EF - Botanics Impact factor: 5.210, year: 2015

Undergraduate Students’ Difficulties in Reading and Constructing Phylogenetic Tree

Science.gov (United States)

Sa'adah, S.; Tapilouw, F. S.; Hidayat, T.

2017-02-01

Representation is a very important communication tool to communicate scientific concepts. Biologists produce phylogenetic representation to express their understanding of evolutionary relationships. The phylogenetic tree is visual representation depict a hypothesis about the evolutionary relationship and widely used in the biological sciences. Phylogenetic tree currently growing for many disciplines in biology. Consequently, learning about phylogenetic tree become an important part of biological education and an interesting area for biology education research. However, research showed many students often struggle with interpreting the information that phylogenetic trees depict. The purpose of this study was to investigate undergraduate students’ difficulties in reading and constructing a phylogenetic tree. The method of this study is a descriptive method. In this study, we used questionnaires, interviews, multiple choice and open-ended questions, reflective journals and observations. The findings showed students experiencing difficulties, especially in constructing a phylogenetic tree. The students’ responds indicated that main reasons for difficulties in constructing a phylogenetic tree are difficult to placing taxa in a phylogenetic tree based on the data provided so that the phylogenetic tree constructed does not describe the actual evolutionary relationship (incorrect relatedness). Students also have difficulties in determining the sister group, character synapomorphy, autapomorphy from data provided (character table) and comparing among phylogenetic tree. According to them building the phylogenetic tree is more difficult than reading the phylogenetic tree. Finding this studies provide information to undergraduate instructor and students to overcome learning difficulties of reading and constructing phylogenetic tree.

Phylogenetic structure in tropical hummingbird communities

DEFF Research Database (Denmark)

Graham, Catherine H; Parra, Juan L; Rahbek, Carsten

2009-01-01

How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic...... composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern...... that is consistent with the idea that competition influences the local composition of hummingbirds. At higher elevations communities are phylogenetically clustered (coexistence of close relatives), consistent with the expectation of environmental filtering, which may result from the challenge of sustaining...

Constructing phylogenetic trees using interacting pathways.

Science.gov (United States)

Wan, Peng; Che, Dongsheng

2013-01-01

Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interacting pathways. We have applied hierarchical clustering on two domains of organisms-eukaryotes and prokaryotes. Our preliminary results have shown the effectiveness of using the interacting pathways in revealing evolutionary relationships.

Investigations towards the use of Gd0.7Ca0.3CoOx as membrane in an exhaust gas sensor for NOx

NARCIS (Netherlands)

Romer, E.W.J.; Nigge, Ulrich; Schulte, Thomas; Wiemhöfer, Hans-Dieter; Bouwmeester, Henricus J.M.

2001-01-01

Application of a material with the nominal composition Gd0.7Ca0.3CoOx is considered for use as membrane material in an exhaust gas sensor for NOx. SEM–EDX and XRD measurements revealed that after sintering at 1200°C in air, three co-existing phases are present: (Gd0.6Ca0.4)2CoOx (60 vol.%), GdCoO3

Physical properties of the heterojunction MoOx/n-CdTe as a function of the parameters of CdTe crystals

Science.gov (United States)

Mostovyi, Andrii I.; Solovan, Mykhailo M.; Brus, Viktor V.; Pullerits, Toǧnu; Maryanchuk, Pavlo D.

2018-01-01

MoOx/n-CdTe photosensitive heterostructures were prepared by the deposition of molybdenum oxide thin films onto three different n-type CdTe substrates (ρ1=0.4 Ωṡcm, ρ2=10 Ωṡcm, ρ3=40 Ωṡcm) by DC reactive magnetron sputtering. The height of the potential barrier and series resistance of the MoOx/CdTe heterojunctions were investigated. The dominating current transport mechanisms through the heterojunctions were determined at forward and reverse biases.

Genome-wide identification and expression profiling reveal tissue-specific expression and differentially-regulated genes involved in gibberellin metabolism between Williams banana and its dwarf mutant.

Science.gov (United States)

Chen, Jingjing; Xie, Jianghui; Duan, Yajie; Hu, Huigang; Hu, Yulin; Li, Weiming

2016-05-27

Dwarfism is one of the most valuable traits in banana breeding because semi-dwarf cultivars show good resistance to damage by wind and rain. Moreover, these cultivars present advantages of convenient cultivation, management, and so on. We obtained a dwarf mutant '8818-1' through EMS (ethyl methane sulphonate) mutagenesis of Williams banana 8818 (Musa spp. AAA group). Our research have shown that gibberellins (GAs) content in 8818-1 false stems was significantly lower than that in its parent 8818 and the dwarf type of 8818-1 could be restored by application of exogenous GA3. Although GA exerts important impacts on the 8818-1 dwarf type, our understanding of the regulation of GA metabolism during banana dwarf mutant development remains limited. Genome-wide screening revealed 36 candidate GA metabolism genes were systematically identified for the first time; these genes included 3 MaCPS, 2 MaKS, 1 MaKO, 2 MaKAO, 10 MaGA20ox, 4 MaGA3ox, and 14 MaGA2ox genes. Phylogenetic tree and conserved protein domain analyses showed sequence conservation and divergence. GA metabolism genes exhibited tissue-specific expression patterns. Early GA biosynthesis genes were constitutively expressed but presented differential regulation in different tissues in Williams banana. GA oxidase family genes were mainly transcribed in young fruits, thus suggesting that young fruits were the most active tissue involved in GA metabolism, followed by leaves, bracts, and finally approximately mature fruits. Expression patterns between 8818 and 8818-1 revealed that MaGA20ox4, MaGA20ox5, and MaGA20ox7 of the MaGA20ox gene family and MaGA2ox7, MaGA2ox12, and MaGA2ox14 of the MaGA2ox gene family exhibited significant differential expression and high-expression levels in false stems. These genes are likely to be responsible for the regulation of GAs content in 8818-1 false stems. Overall, phylogenetic evolution, tissue specificity and differential expression analyses of GA metabolism genes can provide a

Inferring Phylogenetic Networks Using PhyloNet.

Science.gov (United States)

Wen, Dingqiao; Yu, Yun; Zhu, Jiafan; Nakhleh, Luay

2018-07-01

PhyloNet was released in 2008 as a software package for representing and analyzing phylogenetic networks. At the time of its release, the main functionalities in PhyloNet consisted of measures for comparing network topologies and a single heuristic for reconciling gene trees with a species tree. Since then, PhyloNet has grown significantly. The software package now includes a wide array of methods for inferring phylogenetic networks from data sets of unlinked loci while accounting for both reticulation (e.g., hybridization) and incomplete lineage sorting. In particular, PhyloNet now allows for maximum parsimony, maximum likelihood, and Bayesian inference of phylogenetic networks from gene tree estimates. Furthermore, Bayesian inference directly from sequence data (sequence alignments or biallelic markers) is implemented. Maximum parsimony is based on an extension of the "minimizing deep coalescences" criterion to phylogenetic networks, whereas maximum likelihood and Bayesian inference are based on the multispecies network coalescent. All methods allow for multiple individuals per species. As computing the likelihood of a phylogenetic network is computationally hard, PhyloNet allows for evaluation and inference of networks using a pseudolikelihood measure. PhyloNet summarizes the results of the various analyzes and generates phylogenetic networks in the extended Newick format that is readily viewable by existing visualization software.

Opposing assembly mechanisms in a neotropical dry forest: implications for phylogenetic and functional community ecology.

Science.gov (United States)

Swenson, Nathan G; Enquist, Brian J

2009-08-01

Species diversity is promoted and maintained by ecological and evolutionary processes operating on species attributes through space and time. The degree to which variability in species function regulates distribution and promotes coexistence of species has been debated. Previous work has attempted to quantify the relative importance of species function by using phylogenetic relatedness as a proxy for functional similarity. The key assumption of this approach is that function is phylogenetically conserved. If this assumption is supported, then the phylogenetic dispersion in a community should mirror the functional dispersion. Here we quantify functional trait dispersion along several key axes of tree life-history variation and on multiple spatial scales in a Neotropical dry-forest community. We next compare these results to previously reported patterns of phylogenetic dispersion in this same forest. We find that, at small spatial scales, coexisting species are typically more functionally clustered than expected, but traits related to adult and regeneration niches are overdispersed. This outcome was repeated when the analyses were stratified by size class. Some of the trait dispersion results stand in contrast to the previously reported phylogenetic dispersion results. In order to address this inconsistency we examined the strength of phylogenetic signal in traits at different depths in the phylogeny. We argue that: (1) while phylogenetic relatedness may be a good general multivariate proxy for ecological similarity, it may have a reduced capacity to depict the functional mechanisms behind species coexistence when coexisting species simultaneously converge and diverge in function; and (2) the previously used metric of phylogenetic signal provided erroneous inferences about trait dispersion when married with patterns of phylogenetic dispersion.

Musk ox (Ovibos moschatus) of the mammoth steppe

DEFF Research Database (Denmark)

Raghavan, Maanasa; Themudo, Goncalo Espregueira Cruz; Smith, Colin

2014-01-01

Stable carbon and nitrogen isotope ratios have been used as markers for palaeoclimatic and palaeoecological reconstructions across various geographical and temporal ranges. Such studies are essential for understanding how a particular species responded to changing environmental conditions...... in precipitation and that these variations were closely associated with events such as the cold and arid Last Glacial Maximum (LGM), Bolling-Allerod interstadial, Younger Dryas stadial and the warmer and humid Holocene. Regional differences in the isotopic composition of the musk ox populations are also noticeable...

High-performance supercapacitors using flexible and freestanding MnOx/carbamide carbon nanofibers

Science.gov (United States)

Samuel, Edmund; Jo, Hong Seok; Joshi, Bhavana; Park, Hyun Goo; Kim, Yong Il; An, Seongpil; Swihart, Mark T.; Yun, Je Moon; Kim, Kwang Ho; Yoon, Sam S.

2017-11-01

We demonstrate the fabrication of a MnOx/carbamide carbon nanofiber (CCNF) composite consisting of MnO particles embedded in CCNFs as a highly flexible and freestanding electrode material for supercapacitors. A sacrificial polymer component, polymethylmethacrylate, included in the precursor solution, pyrolyzes during heating, resulting in pores in the fibers, some of which are filled by the MnO nanocrystals. Carbamide is added to control the size of the MnOx particles as well as to increase the carbon content of the composite and hence its conductivity. The X-ray diffraction and Raman spectra of the composite show that the MnO particles formed have low crystallinity. Transmission electron microscopy confirms that the MnO particles are distributed very uniformly over the CCNFs. Symmetric supercapacitors constructed using electrodes of this composite exhibit specific capacitances of 498 F•g-1 at a scan rate of 10 mV•s-1 and 271 F•g-1 at a current density of 1 A•g-1. They also exhibit excellent long-term cycling performance, retaining 93% of their initial capacity after 5000 cycles of galvanostatic charging/discharging.

Intrinsic Activity of MnOx-CeO2 Catalysts in Ethanol Oxidation

Directory of Open Access Journals (Sweden)

Dimitrios Delimaris

2017-11-01

Full Text Available MnOx-CeO2 mixed oxides are considered efficient oxidation catalysts superior to the corresponding single oxides. Although these oxides have been the subject of numerous studies, their fundamental performance indicators, such as turnover frequency (TOF or specific activity, are scarcely reported. The purpose of the present work is to investigate the effect of catalyst composition on the concentration of active sites and intrinsic activity in ethanol oxidation by the employment of temperature-programmed desorption and oxidation of isotopically-labelled ethanol, 12CH313CH2OH. The transformation pathways of preadsorbed ethanol in the absence of gaseous oxygen refer to dehydrogenation to acetaldehyde followed by its dissociation combined with oxidation by lattice oxygen. In the presence of gaseous oxygen, lattice oxygen is rapidly restored and the main products are acetaldehyde, CO2, and water. CO2 forms less easily on mixed oxides than on pure MnOx. The TOF of ethanol oxidation has been calculated assuming that the amount of adsorbed ethanol and CO2 produced during temperature-programmed oxidation (TPO is a reliable indicator of the concentration of the active sites.

The space of ultrametric phylogenetic trees.

Science.gov (United States)

Gavryushkin, Alex; Drummond, Alexei J

2016-08-21

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

The End of the Lines for OX 169: No Binary Broad-Line Region

Science.gov (United States)

Halpern, J. P.; Eracleous, M.

2000-03-01

We show that unusual Balmer emission-line profiles of the quasar OX 169, frequently described as either self-absorbed or double peaked, are actually neither. The effect is an illusion resulting from two coincidences. First, the forbidden lines are quite strong and broad. Consequently, the [N II] λ6583 line and the associated narrow-line component of Hα present the appearance of twin Hα peaks. Second, the redshift of 0.2110 brings Hβ into coincidence with Na I D at zero redshift, and ISM absorption in Na I D divides the Hβ emission line. In spectra obtained over the past decade, we see no substantial change in the character of the line profiles and no indication of intrinsic double-peaked structure. The Hγ, Mg II, and Lyα emission lines are single peaked, and all of the emission-line redshifts are consistent once they are correctly attributed to their permitted and forbidden-line identifications. A systematic shift of up to 700 km s-1 between broad and narrow lines is seen, but such differences are common and could be due to gravitational and transverse redshift in a low-inclination disk. Stockton & Farnham had called attention to an apparent tidal tail in the host galaxy of OX 169 and speculated that a recent merger had supplied the nucleus with a coalescing pair of black holes that was now revealing its existence in the form of two physically distinct broad-line regions. Although there is no longer any evidence for two broad emission-line regions in OX 169, binary black holes should form frequently in galaxy mergers, and it is still worthwhile to monitor the radial velocities of emission lines that could supply evidence of their existence in certain objects.

Calibration and modelling of the SODART-OXS Bragg spectrometer onboard the SRG satellite

DEFF Research Database (Denmark)

Halm, Ingolf; Wiebicke, Hans-Joachim; Christensen, Finn Erland

1998-01-01

The SODART X-ray telescope includes an Objective Crystal Spectrometer (OXS) providing a high energy resolving power by Bragg reflection upon crystals. To cover a wide energy range, 3 types of natural crystals (LiF, Si, RAP) and a Co/C multilayer structure upon Si are used in the ranges 5-11 keV, ...

phylo-node: A molecular phylogenetic toolkit using Node.js.

Science.gov (United States)

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

phangorn: phylogenetic analysis in R.

Science.gov (United States)

Schliep, Klaus Peter

2011-02-15

phangorn is a package for phylogenetic reconstruction and analysis in the R language. Previously it was only possible to estimate phylogenetic trees with distance methods in R. phangorn, now offers the possibility of reconstructing phylogenies with distance based methods, maximum parsimony or maximum likelihood (ML) and performing Hadamard conjugation. Extending the general ML framework, this package provides the possibility of estimating mixture and partition models. Furthermore, phangorn offers several functions for comparing trees, phylogenetic models or splits, simulating character data and performing congruence analyses. phangorn can be obtained through the CRAN homepage http://cran.r-project.org/web/packages/phangorn/index.html. phangorn is licensed under GPL 2.

Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus.

Directory of Open Access Journals (Sweden)

Peter G Foster

Full Text Available Specimens of neotropical Anopheles (Nyssorhynchus were collected and identified morphologically. We amplified three genes for phylogenetic analysis-the single copy nuclear white and CAD genes, and the COI barcode region. Since we had multiple specimens for most species we were able to test how well the single or combined genes were able to corroborate morphologically defined species by placing the species into exclusive groups. We found that single genes, including the COI barcode region, were poor at confirming species, but that the three genes combined were able to do so much better. This has implications for species identification, species delimitation, and species discovery, and we caution that single genes are not enough. Higher level groupings were partially resolved with some well-supported groupings, whereas others were found to be either polyphyletic or paraphyletic. There were examples of known groups, such as the Myzorhynchella Section, which were poorly supported with single genes but were well supported with combined genes. From this we can infer that more sequence data will be needed in order to show more higher-level groupings with good support. We got unambiguously good support (0.94-1.0 Bayesian posterior probability from all DNA-based analyses for a grouping of An. dunhami with An. nuneztovari and An. goeldii, and because of this and because of morphological similarities we propose that An. dunhami be included in the Nuneztovari Complex. We obtained phylogenetic corroboration for new species which had been recognised by morphological differences; these will need to be formally described and named.

Synaptic transistor with a reversible and analog conductance modulation using a Pt/HfOx/n-IGZO memcapacitor

Science.gov (United States)

Yang, Paul; Kim, Hyung Jun; Zheng, Hong; Beom, Geon Won; Park, Jong-Sung; Kang, Chi Jung; Yoon, Tae-Sik

2017-06-01

A synaptic transistor emulating the biological synaptic motion is demonstrated using the memcapacitance characteristics in a Pt/HfOx/n-indium-gallium-zinc-oxide (IGZO) memcapacitor. First, the metal-oxide-semiconductor (MOS) capacitor with Pt/HfOx/n-IGZO structure exhibits analog, polarity-dependent, and reversible memcapacitance in capacitance-voltage (C-V), capacitance-time (C-t), and voltage-pulse measurements. When a positive voltage is applied repeatedly to the Pt electrode, the accumulation capacitance increases gradually and sequentially. The depletion capacitance also increases consequently. The capacitances are restored by repeatedly applying a negative voltage, confirming the reversible memcapacitance. The analog and reversible memcapacitance emulates the potentiation and depression synaptic motions. The synaptic thin-film transistor (TFT) with this memcapacitor also shows the synaptic motion with gradually increasing drain current by repeatedly applying the positive gate and drain voltages and reversibly decreasing one by applying the negative voltages, representing synaptic weight modulation. The reversible and analog conductance change in the transistor at both the voltage sweep and pulse operations is obtained through the memcapacitance and threshold voltage shift at the same time. These results demonstrate the synaptic transistor operations with a MOS memcapacitor gate stack consisting of Pt/HfOx/n-IGZO.

High-performance inverted planar heterojunction perovskite solar cells based on a solution-processed CuOx hole transport layer.

Science.gov (United States)

Sun, Weihai; Li, Yunlong; Ye, Senyun; Rao, Haixia; Yan, Weibo; Peng, Haitao; Li, Yu; Liu, Zhiwei; Wang, Shufeng; Chen, Zhijian; Xiao, Lixin; Bian, Zuqiang; Huang, Chunhui

2016-05-19

During the past several years, methylammonium lead halide perovskites have been widely investigated as light absorbers for thin-film photovoltaic cells. Among the various device architectures, the inverted planar heterojunction perovskite solar cells have attracted special attention for their relatively simple fabrication and high efficiencies. Although promising efficiencies have been obtained in the inverted planar geometry based on poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) sulfonic acid ( PSS) as the hole transport material (HTM), the hydrophilicity of the PSS is a critical factor for long-term stability. In this paper, a CuOx hole transport layer from a facile solution-processed method was introduced into the inverted planar heterojunction perovskite solar cells. After the optimization of the devices, a champion PCE of 17.1% was obtained with an open circuit voltage (Voc) of 0.99 V, a short-circuit current (Jsc) of 23.2 mA cm(-2) and a fill factor (FF) of 74.4%. Furthermore, the unencapsulated device cooperating with the CuOx film exhibited superior performance in the stability test, compared to the device involving the PSS layer, indicating that CuOx could be a promising HTM for replacing PSS in inverted planar heterojunction perovskite solar cells.

Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

Science.gov (United States)

Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

2017-04-01

The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

Improved Maximum Parsimony Models for Phylogenetic Networks.

Science.gov (United States)

Van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2018-05-01

Phylogenetic networks are well suited to represent evolutionary histories comprising reticulate evolution. Several methods aiming at reconstructing explicit phylogenetic networks have been developed in the last two decades. In this article, we propose a new definition of maximum parsimony for phylogenetic networks that permits to model biological scenarios that cannot be modeled by the definitions currently present in the literature (namely, the "hardwired" and "softwired" parsimony). Building on this new definition, we provide several algorithmic results that lay the foundations for new parsimony-based methods for phylogenetic network reconstruction.

Effect of metal ions doping (M = Ti4+, Sn4+) on the catalytic performance of MnOx/CeO2 catalyst for low temperature selective catalytic reduction of NO with NH3

Science.gov (United States)

Xiong, Yan; Tang, Changjin; Dong, Lin

2015-04-01

Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China The abatement of nitrogen oxides (NOx) emission from exhaust gases of diesel and stationary sources is a significant challenge for economic and social development. Ceria-based solid solutions were synthesized and used as supports to prepare MnOx/Ce0.8Ti0.2O2 and MnOx/Ce0.8Sn0.2O2 catalysts (Mn/CeTi and Mn/CeSn) for low temperature selective catalytic reduction of NO by NH3 (NH3-SCR). The effects of Ti or Sn doping on the catalytic performance of MnOx/CeO2 catalyst were investigated. Experimental results show that doping of Ti or Sn increases the NO removal efficiency of MnOx/CeO2. The NO conversion of Mn/CeTi catalyst is more than 90 % at temperature window of 175 ~ 300 °C under a gas hour space velocity of 60,000 mL.g-1.h-1. Modified catalysts are also found to exhibit greatly improved resistance to sulfur-poisoning. NH3-TPD results suggest that NH3 desorption on the catalysts is observed over a wide temperature range, due to the variability of adsorbed NH3 species with different thermal stabilities. Doping of Ti and Sn into Mn/CeO2 greatly increased the NH3 adsorption ability of the composites which could promote the SCR reaction. Characterization results also indicate that doping of Ti or Sn brings about catalysts with higher BET surface area, enhanced oxygen storage capacity and increased surface acidity.

Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling

DEFF Research Database (Denmark)

Simonsen, Martin; Maetschke, S.R.; Ragan, M.A.

2012-01-01

Motivation: Phylogenetic profiling methods can achieve good accuracy in predicting protein–protein interactions, especially in prokaryotes. Recent studies have shown that the choice of reference taxa (RT) is critical for accurate prediction, but with more than 2500 fully sequenced taxa publicly......: We present three novel methods for automating the selection of RT, using machine learning based on known protein–protein interaction networks. One of these methods in particular, Tree-Based Search, yields greatly improved prediction accuracies. We further show that different methods for constituting...... phylogenetic profiles often require very different RT sets to support high prediction accuracy....

Performance evaluation and phylogenetic characterization of anaerobic fluidized bed reactors using ground tire and pet as support materials for biohydrogen production.

Science.gov (United States)

Barros, Aruana Rocha; Adorno, Maria Angela Tallarico; Sakamoto, Isabel Kimiko; Maintinguer, Sandra Imaculada; Varesche, Maria Bernadete Amâncio; Silva, Edson Luiz

2011-02-01

This study evaluated two different support materials (ground tire and polyethylene terephthalate [PET]) for biohydrogen production in an anaerobic fluidized bed reactor (AFBR) treating synthetic wastewater containing glucose (4000 mg L(-1)). The AFBR, which contained either ground tire (R1) or PET (R2) as support materials, were inoculated with thermally pretreated anaerobic sludge and operated at a temperature of 30°C. The AFBR were operated with a range of hydraulic retention times (HRT) between 1 and 8h. The reactor R1 operating with a HRT of 2h showed better performance than reactor R2, reaching a maximum hydrogen yield of 2.25 mol H(2)mol(-1) glucose with 1.3mg of biomass (as the total volatile solids) attached to each gram of ground tire. Subsequent 16S rRNA gene sequencing and phylogenetic analysis of particle samples revealed that reactor R1 favored the presence of hydrogen-producing bacteria such as Clostridium, Bacillus, and Enterobacter. Copyright © 2010 Elsevier Ltd. All rights reserved.

TreeCluster: Massively scalable transmission clustering using phylogenetic trees

OpenAIRE

Moshiri, Alexander

2018-01-01

Background: The ability to infer transmission clusters from molecular data is critical to designing and evaluating viral control strategies. Viral sequencing datasets are growing rapidly, but standard methods of transmission cluster inference do not scale well beyond thousands of sequences. Results: I present TreeCluster, a cross-platform tool that performs transmission cluster inference on a given phylogenetic tree orders of magnitude faster than existing inference methods and supports multi...

Reaction kinetics of metal deposition via surface limited red-ox replacement of underpotentially deposited metal monolayers

International Nuclear Information System (INIS)

Gokcen, Dincer; Bae, Sang-Eun; Brankovic, Stanko R.

2011-01-01

The study of the kinetics of metal deposition via surface limited red-ox replacement of underpotentially deposited metal monolayers is presented. The model system was Pt submonolayer deposition on Au(1 1 1) via red-ox replacement of Pb and Cu UPD monolayers on Au(1 1 1). The kinetics of a single replacement reaction was studied using the formalism of the comprehensive analytical model developed to fit the open circuit potential transients from deposition experiments. The practical reaction kinetics parameters like reaction half life, reaction order and reaction rate constant are determined and discussed with their relevance to design and control of deposition experiments. The effects of transport limitation and the role of the anions/electrolyte on deposition kinetics are investigated and their significance to design of effective deposition process is discussed.

Phylogenetic reconstruction prompts taxonomic changes in Sauropus, Synostemon and Breynia (Phyllanthaceae tribe Phyllantheae)

NARCIS (Netherlands)

Welzen, van P.C.; Pruesapan, K.; Telford, I.R.H.; Esser, H.-J.; Bruhl, J.J.

2014-01-01

Previous molecular phylogenetic studies indicated expansion of Breynia with inclusion of Sauropus s.str. (excluding Synostemon). The present study adds qualitative and quantitative morphological characters to molecular data to find more resolution and/or higher support for the subgroups within

A program for verification of phylogenetic network models.

Science.gov (United States)

Gunawan, Andreas D M; Lu, Bingxin; Zhang, Louxin

2016-09-01

Genetic material is transferred in a non-reproductive manner across species more frequently than commonly thought, particularly in the bacteria kingdom. On one hand, extant genomes are thus more properly considered as a fusion product of both reproductive and non-reproductive genetic transfers. This has motivated researchers to adopt phylogenetic networks to study genome evolution. On the other hand, a gene's evolution is usually tree-like and has been studied for over half a century. Accordingly, the relationships between phylogenetic trees and networks are the basis for the reconstruction and verification of phylogenetic networks. One important problem in verifying a network model is determining whether or not certain existing phylogenetic trees are displayed in a phylogenetic network. This problem is formally called the tree containment problem. It is NP-complete even for binary phylogenetic networks. We design an exponential time but efficient method for determining whether or not a phylogenetic tree is displayed in an arbitrary phylogenetic network. It is developed on the basis of the so-called reticulation-visible property of phylogenetic networks. A C-program is available for download on http://www.math.nus.edu.sg/∼matzlx/tcp_package matzlx@nus.edu.sg Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Head capsule characters in the Hymenoptera and their phylogenetic implications

Directory of Open Access Journals (Sweden)

Lars Vilhelmsen

2011-09-01

Full Text Available The head capsule of a taxon sample of three outgroup and 86 ingroup taxa is examined for characters of possible phylogenetic significance within Hymenoptera. 21 morphological characters are illustrated and scored, and their character evolution explored by mapping them onto a phylogeny recently produced from a large morphological data set. Many of the characters are informative and display unambiguous changes. Most of the character support demonstrated is supportive at the superfamily or family level. In contrast, only few characters corroborate deeper nodes in the phylogeny of Hymenoptera.

OX40 and IL-7 play synergistic roles in the homeostatic proliferation of effector memory CD4⁺ T cells.

Science.gov (United States)

Yamaki, Satoshi; Ine, Shouji; Kawabe, Takeshi; Okuyama, Yuko; Suzuki, Nobu; Soroosh, Pejman; Mousavi, Seyed Fazlollah; Nagashima, Hiroyuki; Sun, Shu-lan; So, Takanori; Sasaki, Takeshi; Harigae, Hideo; Sugamura, Kazuo; Kudo, Hironori; Wada, Motoshi; Nio, Masaki; Ishii, Naoto

2014-10-01

T-cell homeostasis preserves the numbers, the diversity and functional competence of different T-cell subsets that are required for adaptive immunity. Naïve CD4(+) T (TN ) cells are maintained in the periphery via the common γ-chain family cytokine IL-7 and weak antigenic signals. However, it is not clear how memory CD4(+) T-cell subsets are maintained in the periphery and which factors are responsible for the maintenance. To examine the homeostatic mechanisms, CFSE-labeled CD4(+) CD44(high) CD62L(low) effector memory T (TEM ) cells were transferred into sublethally-irradiated syngeneic C57BL/6 mice, and the systemic cell proliferative responses, which can be divided distinctively into fast and slow proliferations, were assessed by CFSE dye dilution. We found that the fast homeostatic proliferation of TEM cells was strictly regulated by both antigen and OX40 costimulatory signals and that the slow proliferation was dependent on IL-7. The simultaneous blockade of both OX40 and IL-7 signaling completely inhibited the both fast and slow proliferation. The antigen- and OX40-dependent fast proliferation preferentially expanded IL-17-producing helper T cells (Th17 cells). Thus, OX40 and IL-7 play synergistic, but distinct roles in the homeostatic proliferation of CD4(+) TEM cells. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region.

Science.gov (United States)

GokulRaj, Kathamuthu; Sundaresan, Natesan; Ganeshan, Enthai Jagan; Rajapriya, Pandi; Muthumary, Johnpaul; Sridhar, Jayavel; Pandi, Mohan

2014-01-01

Endophytic fungi are inhabitants of plants, living most part of their lifecycle asymptomatically which mainly confer protection and ecological advantages to the host plant. In this present study, 48 endophytic fungi were isolated from the leaves of three medicinal plants and characterized based on ITS2 sequence - secondary structure analysis. ITS2 secondary structures were elucidated with minimum free energy method (MFOLD version 3.1) and consensus structure of each genus was generated by 4SALE. ProfDistS was used to generate ITS2 sequence structure based phylogenetic tree respectively. Our elucidated isolates were belonging to Ascomycetes family, representing 5 orders and 6 genera. Colletotrichum/Glomerella spp., Diaporthae/Phomopsis spp., and Alternaria spp., were predominantly observed while Cochliobolus sp., Cladosporium sp., and Emericella sp., were represented by singletons. The constructed phylogenetic tree has well resolved monophyletic groups with >50% bootstrap value support. Secondary structures based fungal systematics improves not only the stability; it also increases the precision of phylogenetic inference. Above ITS2 based phylogenetic analysis was performed for our 48 isolates along with sequences of known ex-types taken from GenBank which confirms the efficiency of the proposed method. Further, we propose it as superlative marker for reconstructing phylogenetic relationships at different taxonomic levels due to their lesser length.

Phylogenetic convolutional neural networks in metagenomics.

Science.gov (United States)

Fioravanti, Diego; Giarratano, Ylenia; Maggio, Valerio; Agostinelli, Claudio; Chierici, Marco; Jurman, Giuseppe; Furlanello, Cesare

2018-03-08

Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a novel deep learning architecture for the classification of metagenomics data based on the Convolutional Neural Networks, with the patristic distance defined on the phylogenetic tree being used as the proximity measure. The patristic distance between variables is used together with a sparsified version of MultiDimensional Scaling to embed the phylogenetic tree in a Euclidean space. Ph-CNN is tested with a domain adaptation approach on synthetic data and on a metagenomics collection of gut microbiota of 38 healthy subjects and 222 Inflammatory Bowel Disease patients, divided in 6 subclasses. Classification performance is promising when compared to classical algorithms like Support Vector Machines and Random Forest and a baseline fully connected neural network, e.g. the Multi-Layer Perceptron. Ph-CNN represents a novel deep learning approach for the classification of metagenomics data. Operatively, the algorithm has been implemented as a custom Keras layer taking care of passing to the following convolutional layer not only the data but also the ranked list of neighbourhood of each sample, thus mimicking the case of image data, transparently to the user.

Wilhelm Troll (1897 - 1978): idealistic morphology, physics, and phylogenetics.

Science.gov (United States)

Rieppel, Olivier

2011-01-01

Idealistic morphology as articulated by the botanist Wilhelm Troll, the main target of the critique voiced by the early phylogeneticists, was firmly embedded in its contemporary scientific, cultural, and political context. Troll appealed to theoretical developments in contemporary physics in support of his research program. He understood burgeoning quantum mechanics not only to threaten the unity of physics, but also the validity of the principle of causality. Troll used this insight in support of his claim of a dualism in biology, relegating the causal-analytical approach to physiology, while rejuvenating the Goethean paradigm in comparative morphology. This embedded idealistic morphology in the völkisch tradition that characterized German culture during the Weimar Republic and its aftermath. In contrast, the contemporary phylogeneticists anchored their research program in the rise of logical positivism and in Darwin's principle of natural selection. This, in turn, brought phylogenetic systematists of the late 1930s and early 1940s into the orbit of national-socialist racial theory and eugenics. In conclusion, the early debate between idealistic morphologists and phylogenetic systematists was not only ideologically tainted, but also implied a philosophical impasse that is best characterized as a conflict between the Goethean and Newtonian paradigm of natural science.

Rearrangement moves on rooted phylogenetic networks.

Science.gov (United States)

Gambette, Philippe; van Iersel, Leo; Jones, Mark; Lafond, Manuel; Pardi, Fabio; Scornavacca, Celine

2017-08-01

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for

Rearrangement moves on rooted phylogenetic networks.

Directory of Open Access Journals (Sweden)

Philippe Gambette

2017-08-01

Full Text Available Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide

Forensic application of phylogenetic analyses - Exploration of suspected HIV-1 transmission case.

Science.gov (United States)

Siljic, Marina; Salemovic, Dubravka; Cirkovic, Valentina; Pesic-Pavlovic, Ivana; Ranin, Jovan; Todorovic, Marija; Nikolic, Slobodan; Jevtovic, Djordje; Stanojevic, Maja

2017-03-01

Transmission of human immunodeficiency virus (HIV) between individuals may have important legal implications and therefore may come to require forensic investigation based upon phylogenetic analysis. In criminal trials results of phylogenetic analyses have been used as evidence of responsibility for HIV transmission. In Serbia, as in many countries worldwide, exposure and deliberate transmission of HIV are criminalized. We present the results of applying state of the art phylogenetic analyses, based on pol and env genetic sequences, in exploration of suspected HIV transmission among three subjects: a man and two women, with presumed assumption of transmission direction from one woman to a man. Phylogenetic methods included relevant neighbor-joining (NJ), maximum likelihood (ML) and Bayesian methods of phylogenetic trees reconstruction and hypothesis testing, that has been shown to be the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals. End-point limiting-dilution PCR (EPLD-PCR) assay, generating the minimum of 10 sequences per genetic region per subject, was performed to assess HIV quasispecies distribution and to explore the direction of HIV transmission between three subjects. Phylogenetic analysis revealed that the viral sequences from the three subjects were more genetically related to each other than to other strains circulating in the same area with the similar epidemiological profile, forming strongly supported transmission chain, which could be in favour of a priori hypothesis of one of the women infecting the man. However, in the EPLD based phylogenetic trees for both pol and env genetic region, viral sequences of one subject (man) were paraphyletic to those of two other subjects (women), implying the direction of transmission opposite to the a priori assumption. The dated tree in our analysis confirmed the clustering pattern of query sequences. Still, in the context of unsampled sequences and

Phylogenetic tests of distribution patterns in South Asia: towards

Indian Academy of Sciences (India)

The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we ...

Fourier transform inequalities for phylogenetic trees.

Science.gov (United States)

Matsen, Frederick A

2009-01-01

Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities". In this paper, we first motivate the edge-parameter inequalities by considering a pathological site-pattern frequency vector corresponding to a quartet tree with a negative internal edge. This site-pattern frequency vector nevertheless satisfies all of the constraints described up to now in the literature. We next describe two complete sets of edge-parameter inequalities for the group-based models; these constraints are square-free monomial inequalities in the Fourier transformed coordinates. These inequalities, along with the phylogenetic invariants, form a complete description of the set of site-pattern frequency vectors corresponding to bona fide trees. Said in mathematical language, this paper explicitly presents two finite lists of inequalities in Fourier coordinates of the form "monomial < or = 1", each list characterizing the phylogenetically relevant semialgebraic subsets of the phylogenetic varieties.

Phylogenetic search through partial tree mixing

Science.gov (United States)

2012-01-01

Background Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques. Results When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda Conclusions The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution. PMID:23320449

Controlling exchange bias in Co-CoOx nanoparticles by oxygen content

OpenAIRE

Kovylina, Miroslavna; del Muro, Montserrat Garcia; Konstantinovic, Zorica; Varela, Manuel; Iglesias, Oscar; Labarta, Amilcar; Batlle, Xavier

2009-01-01

We report on the occurrence of exchange bias on laser-ablated granular thin films composed of Co nanoparticles embedded in amorphous zirconia matrix. The deposition method allows controlling the degree of oxidation of the Co particles by tuning the oxygen pressure at the vacuum chamber (from 2x10^{-5} to 10^{-1} mbar). The nature of the nanoparticles embedded in the nonmagnetic matrix is monitored from metallic, ferromagnetic (FM) Co to antiferromagnetic (AFM) CoOx, with a FM/AFM intermediate...

Phylogenetic Signal in AFLP Data Sets

NARCIS (Netherlands)

Koopman, W.J.M.

2005-01-01

AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment

How does cognition evolve? Phylogenetic comparative psychology

Science.gov (United States)

Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

2014-01-01

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

How does cognition evolve? Phylogenetic comparative psychology.

Science.gov (United States)

MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

2012-03-01

Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

Phylogenetic relationships among species of Lutzomyia, subgenus Lutzomyia (Diptera: Psychodidae).

Science.gov (United States)

Pinto, Israel S; Filho, José D Andrade; Santos, Claudiney B; Falqueto, Aloísio; Leite, Yuri L R

2010-01-01

Lutzomyia França is the largest and most diverse sand fly genus in the New World and contains all the species involved in the transmission of American visceral leishmaniasis (AVL). Morphological characters were used to test the monophyly and to infer phylogenetic relationships among members of the Lutzomyia subgenus. Fifty-two morphological characters from male and female adult specimens belonging to 18 species of Lu. (Lutzomyia) were scored and analyzed. The resulting phylogeny confirms the monophyly of this subgenus and reveals four main internal clades. These four clades, however, do not support the classification of the subgenus in two series, longipalpis and cavernicola, because neither is necessarily monophyletic. Knowledge on phylogenetic relationships among these relevant vectors of AVL should be used as a tool for monitoring target taxa and a first step for establishing an early warning system for disease control.

Particle size dependence on oxygen reduction reaction activity of electrodeposited TaOx catalysts in acidic media

KAUST Repository

Seo, J.; Cha, Dong Kyu; Takanabe, Kazuhiro; Kubota, J.; Domen, K.

2013-01-01

The size dependence of the oxygen reduction reaction activity was studied for TaOx nanoparticles electrodeposited on carbon black for application to polymer electrolyte fuel cells (PEFCs). Compared with a commercial Ta2O5 material, the ultrafine

Phylogenetic reconstruction methods: an overview.

Science.gov (United States)

De Bruyn, Alexandre; Martin, Darren P; Lefeuvre, Pierre

2014-01-01

Initially designed to infer evolutionary relationships based on morphological and physiological characters, phylogenetic reconstruction methods have greatly benefited from recent developments in molecular biology and sequencing technologies with a number of powerful methods having been developed specifically to infer phylogenies from macromolecular data. This chapter, while presenting an overview of basic concepts and methods used in phylogenetic reconstruction, is primarily intended as a simplified step-by-step guide to the construction of phylogenetic trees from nucleotide sequences using fairly up-to-date maximum likelihood methods implemented in freely available computer programs. While the analysis of chloroplast sequences from various Vanilla species is used as an illustrative example, the techniques covered here are relevant to the comparative analysis of homologous sequences datasets sampled from any group of organisms.

Tuning silver ion release properties in reactively sputtered Ag/TiOx nanocomposites

Science.gov (United States)

Xiong, J.; Ghori, M. Z.; Henkel, B.; Strunskus, T.; Schürmann, U.; Deng, M.; Kienle, L.; Faupel, F.

2017-07-01

Silver/titania nanocomposites with strong bactericidal effects and good biocompatibility/environmental safety show a high potential for antibacterial applications. Tailoring the silver ion release is thus highly promising to optimize the antibacterial properties of such coatings and to preserve biocompatibility. Reactive sputtering is a fast and versatile method for the preparation of such Ag/TiOx nanocomposites coatings. The present work is concerned with the influence of sputter parameters on the surface morphology and silver ion release properties of reactively sputtered Ag/TiOx nanocomposites coatings showing a silver nanoparticle size distribution in the range from 1 to 20 nm. It is shown that the silver ion release rate strongly depends on the total pressure: the coatings prepared at lower pressure present a lower but long-lasting release behavior. The much denser structure produced under these conditions reduces the transport of water molecules into the coating. In addition, the influence of microstructure and thickness of titanium oxide barriers on the silver ion release were investigated intensively. Moreover, for the coatings prepared at high total pressure, it was demonstrated that stable and long-lasting silver release can be achieved by depositing a barrier with a high rate. Nanocomposites produced under these conditions show well controllable silver ion release properties for applications as antibacterial coatings.

Nuclear and cpDNA sequences combined provide strong inference of higher phylogenetic relationships in the phlox family (Polemoniaceae).

Science.gov (United States)

Johnson, Leigh A; Chan, Lauren M; Weese, Terri L; Busby, Lisa D; McMurry, Samuel

2008-09-01

Members of the phlox family (Polemoniaceae) serve as useful models for studying various evolutionary and biological processes. Despite its biological importance, no family-wide phylogenetic estimate based on multiple DNA regions with complete generic sampling is available. Here, we analyze one nuclear and five chloroplast DNA sequence regions (nuclear ITS, chloroplast matK, trnL intron plus trnL-trnF intergeneric spacer, and the trnS-trnG, trnD-trnT, and psbM-trnD intergenic spacers) using parsimony and Bayesian methods, as well as assessments of congruence and long branch attraction, to explore phylogenetic relationships among 84 ingroup species representing all currently recognized Polemoniaceae genera. Relationships inferred from the ITS and concatenated chloroplast regions are similar overall. A combined analysis provides strong support for the monophyly of Polemoniaceae and subfamilies Acanthogilioideae, Cobaeoideae, and Polemonioideae. Relationships among subfamilies, and thus for the precise root of Polemoniaceae, remain poorly supported. Within the largest subfamily, Polemonioideae, four clades corresponding to tribes Polemonieae, Phlocideae, Gilieae, and Loeselieae receive strong support. The monogeneric Polemonieae appears sister to Phlocideae. Relationships within Polemonieae, Phlocideae, and Gilieae are mostly consistent between analyses and data permutations. Many relationships within Loeselieae remain uncertain. Overall, inferred phylogenetic relationships support a higher-level classification for Polemoniaceae proposed in 2000.

[CoCuMnOx Photocatalyzed Oxidation of Multi-component VOCs and Kinetic Analysis].

Science.gov (United States)

Meng, Hai-long; Bo, Long-li; Liu, Jia-dong; Gao, Bo; Feng, Qi-qi; Tan, Na; Xie, Shuai

2016-05-15

Solar energy absorption coating CoCuMnOx was prepared by co-precipitation method and applied to photodegrade multi- component VOCs including toluene, ethyl acetate and acetone under visible light irradiation. The photocatalytic oxidation performance of toluene, ethyl acetate and acetone was analyzed and reaction kinetics of VOCs were investigated synchronously. The research indicated that removal rates of single-component toluene, ethyl acetate and acetone were 57%, 62% and 58% respectively under conditions of 400 mg · m⁻³ initial concentration, 120 mm illumination distance, 1 g/350 cm² dosage of CoCuMnOx and 6 h of irradiation time by 100 W tungsten halogen lamp. Due to the competition among different VOCs, removal efficiencies in three-component mixture were reduced by 5%-26% as compared with single VOC. Degradation processes of single-component VOC and three-component VOCs both fitted pseudo first order reaction kinetics, and kinetic constants of toluene, ethyl acetate and acetone were 0.002, 0.002 8 and 0.002 33 min⁻¹ respectively under single-component condition. Reaction rates of VOCs in three-component mixture were 0.49-0.88 times of single components.

Porphyromonas gingivalis Differentially Modulates Cell Death Profile in Ox-LDL and TNF-α Pre-Treated Endothelial Cells.

Directory of Open Access Journals (Sweden)

Isaac Maximiliano Bugueno

Full Text Available Clinical studies demonstrated a potential link between atherosclerosis and periodontitis. Porphyromonas gingivalis (Pg, one of the main periodontal pathogen, has been associated to atheromatous plaque worsening. However, synergism between infection and other endothelial stressors such as oxidized-LDL or TNF-α especially on endothelial cell (EC death has not been investigated. This study aims to assess the role of Pg on EC death in an inflammatory context and to determine potential molecular pathways involved.Human umbilical vein ECs (HUVECs were infected with Pg (MOI 100 or stimulated by its lipopolysaccharide (Pg-LPS (1μg/ml for 24 to 48 hours. Cell viability was measured with AlamarBlue test, type of cell death induced was assessed using Annexin V/propidium iodide staining. mRNA expression regarding caspase-1, -3, -9, Bcl-2, Bax-1 and Apaf-1 has been evaluated with RT-qPCR. Caspases enzymatic activity and concentration of APAF-1 protein were evaluated to confirm mRNA results.Pg infection and Pg-LPS stimulation induced EC death. A cumulative effect has been observed in Ox-LDL pre-treated ECs infected or stimulated. This effect was not observed in TNF-α pre-treated cells. Pg infection promotes EC necrosis, however, in infected Ox-LDL pre-treated ECs, apoptosis was promoted. This effect was not observed in TNF-α pre-treated cells highlighting specificity of molecular pathways activated. Regarding mRNA expression, Pg increased expression of pro-apoptotic genes including caspases-1,-3,-9, Bax-1 and decreased expression of anti-apoptotic Bcl-2. In Ox-LDL pre-treated ECs, Pg increased significantly the expression of Apaf-1. These results were confirmed at the protein level.This study contributes to demonstrate that Pg and its Pg-LPS could exacerbate Ox-LDL and TNF-α induced endothelial injury through increase of EC death. Interestingly, molecular pathways are differentially modulated by the infection in function of the pre-stimulation.

Spiking Neural Networks Based on OxRAM Synapses for Real-Time Unsupervised Spike Sorting.

Science.gov (United States)

Werner, Thilo; Vianello, Elisa; Bichler, Olivier; Garbin, Daniele; Cattaert, Daniel; Yvert, Blaise; De Salvo, Barbara; Perniola, Luca

2016-01-01

In this paper, we present an alternative approach to perform spike sorting of complex brain signals based on spiking neural networks (SNN). The proposed architecture is suitable for hardware implementation by using resistive random access memory (RRAM) technology for the implementation of synapses whose low latency (spike sorting. This offers promising advantages to conventional spike sorting techniques for brain-computer interfaces (BCI) and neural prosthesis applications. Moreover, the ultra-low power consumption of the RRAM synapses of the spiking neural network (nW range) may enable the design of autonomous implantable devices for rehabilitation purposes. We demonstrate an original methodology to use Oxide based RRAM (OxRAM) as easy to program and low energy (Spike Timing Dependent Plasticity. Real spiking data have been recorded both intra- and extracellularly from an in-vitro preparation of the Crayfish sensory-motor system and used for validation of the proposed OxRAM based SNN. This artificial SNN is able to identify, learn, recognize and distinguish between different spike shapes in the input signal with a recognition rate about 90% without any supervision.

Nucleotide diversity and phylogenetic relationships among ...

Indian Academy of Sciences (India)

NIRAJ SINGH

for phylogenetic analysis of Gladiolus and related taxa using combined datasets from chloroplast genome. The psbA–trnH ... phylogenetic relationships among cultivars could be useful for hybridization programmes for further improvement of the crop. [Singh N. ... breeding in nature, and exhibited diverse pollination mech-.

Characterization of NOx emission in the suburbs of Tokyo based on simultaneous and real-time observations of atmospheric Ox and NOx

Science.gov (United States)

Matsumoto, J.

2013-12-01

Nitrogen oxides, NOx (NO, NO2), and volatile organic compounds, VOCs, are important as precursors of photochemical oxidants (tropospheric ozone, O3). To predict and control photochemical oxidants, NOx emission should be captured precisely. In addition, the ratio of NO2/NOx in the exhaust gas is also important as the initial balance between NO and NO2 in the atmosphere. Monitoring the NO2/NOx ratio in the exhaust gases is essential. Especially, the influence of the NOx emission on the real atmosphere should be explored. However, conversion reactions among NO, NO2 and O3 are typically in the time scale of minutes. The NO2/NOx ratio can change rapidly just after emission. Real-time observations of these compounds in the second time scale are essential. In view of photochemical oxidant, near emission sources of NO, ozone concentration can be easily perturbed by reaction with locally emitted NO. As an index of oxidant, the sum of O3 and NO2 (Ox = O3 + NO2) is useful. In this study, a simultaneous and real-time analyzer of atmospheric Ox and NOx has been developed utilizing the dual NO2 detectors based on laser-induced fluorescence technique (LIF), and characterization of NOx emission was explored through the observations of Ox and NOx in the suburbs of Tokyo. The dual LIF detectors consisted of one laser head, two LIF cells, and one common vacuum pump. As the Ox monitor, the excess NO was added to the sample and O3 was converted to NO2, and then the sum of O3 and NO2 in the sample was quantified at the 1st LIF cell. As the NOx monitor, the excess O3 was added to the sample and NO was converted to NO2, and then the sum of NO and NO2 in the sample was quantified at the 2nd LIF cell. Both the ';Ox' and ';NOx' channels in the dual LIF analyzer were simultaneously monitoring Ox and NOx in the sample air, respectively. The temporal resolution of observed data was 1 s. Typical conversion efficiencies of O3 and NO to NO2 were more than 0.98. The lower detection limits were 0

Objective Crystal Spectrometer (OXS) for the Spectrum-X-γ satellite

DEFF Research Database (Denmark)

Christensen, Finn Erland; Byrnak, B.P.; Hornstrup, Allan

1990-01-01

The status of the Objective Crystal Spectrometer (OXS) to be flown on the Soviet Spectrum-X-Gamma satellite together with the X-ray investigation of two of the three natural crystals (LiF(220), Ge(111) and RAP(001) which are chosen as the baseline option are presented. An important result...... on the LiF(220) and Ge(111) surfaces is presented. This design allows simultaneous spectroscopy in two energy bands each centered on cosmically interesting line emission regions. X-ray reflectivity measurements demonstrate that the crystal surface can be made sufficiently smooth for the application...

The Pharmacological Profile of a Novel Highly Potent Bisphosphonate, OX14 (1‐Fluoro‐2‐(Imidazo‐[1,2‐α]Pyridin‐3‐yl)‐Ethyl‐Bisphosphonate)

Science.gov (United States)

Ebetino, Frank H; Mazur, Adam; Chantry, Andrew D; Paton‐Hough, Julia; Evans, Holly R; Lath, Darren; Tsoumpra, Maria K; Lundy, Mark W; Dobson, Roy LM; Quijano, Michael; Kwaasi, Aaron A; Dunford, James E; Duan, Xuchen; Triffitt, James T; Jeans, Gwyn; Russell, R Graham G

2017-01-01

ABSTRACT Bisphosphonates are widely used in the treatment of clinical disorders characterized by increased bone resorption, including osteoporosis, Paget's disease, and the skeletal complications of malignancy. The antiresorptive potency of the nitrogen‐containing bisphosphonates on bone in vivo is now recognized to depend upon two key properties, namely mineral binding affinity and inhibitory activity on farnesyl pyrophosphate synthase (FPPS), and these properties vary independently of each other in individual bisphosphonates. The better understanding of structure activity relationships among the bisphosphonates has enabled us to design a series of novel bisphosphonates with a range of mineral binding properties and antiresorptive potencies. Among these is a highly potent bisphosphonate, 1‐fluoro‐2‐(imidazo‐[1,2 alpha]pyridin‐3‐yl)‐ethyl‐bisphosphonate, also known as OX14, which is a strong inhibitor of FPPS, but has lower binding affinity for bone mineral than most of the commonly studied bisphosphonates. The aim of this work was to characterize OX14 pharmacologically in relation to several of the bisphosphonates currently used clinically. When OX14 was compared to zoledronate (ZOL), risedronate (RIS), and minodronate (MIN), it was as potent at inhibiting FPPS in vitro but had significantly lower binding affinity to hydroxyapatite (HAP) columns than ALN, ZOL, RIS, and MIN. When injected i.v. into growing Sprague Dawley rats, OX14 was excreted into the urine to a greater extent than the other bisphosphonates, indicating reduced short‐term skeletal uptake and retention. In studies in both Sprague Dawley rats and C57BL/6J mice, OX14 inhibited bone resorption, with an antiresorptive potency equivalent to or greater than the comparator bisphosphonates. In the JJN3‐NSG murine model of myeloma‐induced bone disease, OX14 significantly prevented the formation of osteolytic lesions (p < 0.05). In summary, OX14 is a new, highly potent

On the need for phylogenetic ‘corrections’ in functional trait-based approaches

Czech Academy of Sciences Publication Activity Database

de Bello, Francesco; Berg, M. P.; Dias, A. T. C.; Diniz-Filho, J. A. F.; Götzenberger, Lars; Hortal, J.; Ladle, L. J.; Lepš, Jan

2015-01-01

Roč. 50, č. 4 (2015), 349-357 ISSN 1211-9520 R&D Projects: GA ČR GAP505/12/1296; GA ČR GB14-36079G Institutional support: RVO:67985939 ; RVO:60077344 Keywords : adaptation * functional and phylogenetic diversity * limiting similarity Subject RIV: EH - Ecology, Behaviour Impact factor: 1.433, year: 2015

Highly dispersed supported ruthenium oxide as an aerobic catalyst for acetic acid synthesis

DEFF Research Database (Denmark)

Laursen, Anders Bo; Gorbanev, Yury; Cavalca, Filippo

2012-01-01

The increasing need for shifting to renewable feedstocks in the chemical industry has driven research toward using green aerobic, selective oxidation reactions to produce bulk chemicals. Here, we report the use of a ruthenium mixed oxide/hydroxide (RuOx) on different support materials for the sel...

Resistance switching in epitaxial SrCoOx thin films

Science.gov (United States)

Tambunan, Octolia T.; Parwanta, Kadek J.; Acharya, Susant K.; Lee, Bo Wha; Jung, Chang Uk; Kim, Yeon Soo; Park, Bae Ho; Jeong, Huiseong; Park, Ji-Yong; Cho, Myung Rae; Park, Yun Daniel; Choi, Woo Seok; Kim, Dong-Wook; Jin, Hyunwoo; Lee, Suyoun; Song, Seul Ji; Kang, Sung-Jin; Kim, Miyoung; Hwang, Cheol Seong

2014-08-01

We observed bipolar switching behavior from an epitaxial strontium cobaltite film grown on a SrTiO3 (001) substrate. The crystal structure of strontium cobaltite has been known to undergo topotactic phase transformation between two distinct phases: insulating brownmillerite (SrCoO2.5) and conducting perovskite (SrCoO3-δ) depending on the oxygen content. The current-voltage characteristics of the strontium cobaltite film showed that it could have a reversible insulator-to-metal transition triggered by electrical bias voltage. We propose that the resistance switching in the SrCoOx thin film could be related to the topotactic phase transformation and the peculiar structure of SrCoO2.5.

Medición telemétrica de la frecuencia cardiaca y el consumo de oxígeno en competición amistosa

Directory of Open Access Journals (Sweden)

Diego Silla Cascales

2006-03-01

Full Text Available El objetivo de este estudio fue medir el consumo de oxígeno directamente por telemetría en situación real de juego calculando el gasto energético correspondiente y comparar dichos valores con los obtenidos mediante la relación entre la frecuencia cardiaca y el consumo de oxígeno establecida en una prueba progresiva en cinta rodante en laboratorio. Participaron en el estudio un total de siete jugadores (n = 7, elegidos por líneas de juego: tres delanteros, dos medios y dos defensas. Los siete jugadores han sido internacionales sub-21 y cuatro de ellos también con la selección nacional absoluta. La media de consumo máximo de oxígeno obtenido en la muestra de jugadores fue de 4,339 L · min-1 (56,9 mL ·  kg-1 · min-1. No se observaron diferencias significativas entre las tres posiciones tácticas. Existe una elevada correlación entre los valores de frecuencia cardiaca y de consumo de oxígeno en las pruebas de esfuerzo progresivo sobre cinta rodante en laboratorio r = 0,97 y r = 0,99. Durante la competición oficial, la frecuencia cardiaca permaneció una media del 50 % del tiempo de juego por debajo del umbral aeróbico ventilatorio y un 43 % del tiempo en la zona de transición aeróbica-anaeróbica. El consumo de oxígeno medio estimado durante las partes de un partido de competición oficial fue de 3,591 L · min-1 correspondiente a un consumo relativo de 48,5 mL · kg-1 · min-1 (70,7 % del VO2max individual. En el análisis del estudio de correlación lineal entre valores reales y estimados de consumo de oxígeno en cada uno de los jugadores, los coeficientes de correlación de Pearson calculados estaban entre los valores de r = 0,721 y r = 0,904. La cuantificación de la sobreestimación arroja valores de 853 mL · min-1 de media (34 % de sobreestimación sobre el VO2 real, siendo el error estándar de la estimación (378 mL · min-1 de un 15 % sobre el VO2 real

Evaluation of atpB nucleotide sequences for phylogenetic studies of ferns and other pteridophytes.

Science.gov (United States)

Wolf, P

1997-10-01

Inferring basal relationships among vascular plants poses a major challenge to plant systematists. The divergence events that describe these relationships occurred long ago and considerable homoplasy has since accrued for both molecular and morphological characters. A potential solution is to examine phylogenetic analyses from multiple data sets. Here I present a new source of phylogenetic data for ferns and other pteridophytes. I sequenced the chloroplast gene atpB from 23 pteridophyte taxa and used maximum parsimony to infer relationships. A 588-bp region of the gene appeared to contain a statistically significant amount of phylogenetic signal and the resulting trees were largely congruent with similar analyses of nucleotide sequences from rbcL. However, a combined analysis of atpB plus rbcL produced a better resolved tree than did either data set alone. In the shortest trees, leptosporangiate ferns formed a monophyletic group. Also, I detected a well-supported clade of Psilotaceae (Psilotum and Tmesipteris) plus Ophioglossaceae (Ophioglossum and Botrychium). The demonstrated utility of atpB suggests that sequences from this gene should play a role in phylogenetic analyses that incorporate data from chloroplast genes, nuclear genes, morphology, and fossil data.

The phylogenetic distribution of extrafloral nectaries in plants.

Science.gov (United States)

Weber, Marjorie G; Keeler, Kathleen H

2013-06-01

Understanding the evolutionary patterns of ecologically relevant traits is a central goal in plant biology. However, for most important traits, we lack the comprehensive understanding of their taxonomic distribution needed to evaluate their evolutionary mode and tempo across the tree of life. Here we evaluate the broad phylogenetic patterns of a common plant-defence trait found across vascular plants: extrafloral nectaries (EFNs), plant glands that secrete nectar and are located outside the flower. EFNs typically defend plants indirectly by attracting invertebrate predators who reduce herbivory. Records of EFNs published over the last 135 years were compiled. After accounting for changes in taxonomy, phylogenetic comparative methods were used to evaluate patterns of EFN evolution, using a phylogeny of over 55 000 species of vascular plants. Using comparisons of parametric and non-parametric models, the true number of species with EFNs likely to exist beyond the current list was estimated. To date, EFNs have been reported in 3941 species representing 745 genera in 108 families, about 1-2 % of vascular plant species and approx. 21 % of families. They are found in 33 of 65 angiosperm orders. Foliar nectaries are known in four of 36 fern families. Extrafloral nectaries are unknown in early angiosperms, magnoliids and gymnosperms. They occur throughout monocotyledons, yet most EFNs are found within eudicots, with the bulk of species with EFNs being rosids. Phylogenetic analyses strongly support the repeated gain and loss of EFNs across plant clades, especially in more derived dicot families, and suggest that EFNs are found in a minimum of 457 independent lineages. However, model selection methods estimate that the number of unreported cases of EFNs may be as high as the number of species already reported. EFNs are widespread and evolutionarily labile traits that have repeatedly evolved a remarkable number of times in vascular plants. Our current understanding of the

Phylogenetic Position of Barbus lacerta Heckel, 1843

Directory of Open Access Journals (Sweden)

Mustafa Korkmaz

2015-11-01

As a result, five clades come out from phylogenetic reconstruction and in phylogenetic tree Barbus lacerta determined to be sister group of Barbus macedonicus, Barbus oligolepis and Barbus plebejus complex.

The phylogenetics of succession can guide restoration

DEFF Research Database (Denmark)

Shooner, Stephanie; Chisholm, Chelsea Lee; Davies, T. Jonathan

2015-01-01

Phylogenetic tools have increasingly been used in community ecology to describe the evolutionary relationships among co-occurring species. In studies of succession, such tools may allow us to identify the evolutionary lineages most suited for particular stages of succession and habitat...... rehabilitation. However, to date, these two applications have been largely separate. Here, we suggest that information on phylogenetic community structure might help to inform community restoration strategies following major disturbance. Our study examined phylogenetic patterns of succession based...... for species sorting along abiotic gradients (slope and aspect) on the mine sites that had been abandoned for the longest. Synthesis and applications. Understanding the trajectory of succession is critical for restoration efforts. Our results suggest that early colonizers represent a phylogenetically random...

Bayesian models for comparative analysis integrating phylogenetic uncertainty

Directory of Open Access Journals (Sweden)

Villemereuil Pierre de

2012-06-01

Full Text Available Abstract Background Uncertainty in comparative analyses can come from at least two sources: a phylogenetic uncertainty in the tree topology or branch lengths, and b uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow and inflated significance in hypothesis testing (e.g. p-values will be too small. Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible

Bayesian models for comparative analysis integrating phylogenetic uncertainty

Science.gov (United States)

2012-01-01

Background Uncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for

Structural evolution of epitaxial SrCoOx films near topotactic phase transition

OpenAIRE

Hyoungjeen Jeen; Ho Nyung Lee

2015-01-01

Control of oxygen stoichiometry in complex oxides via topotactic phase transition is an interesting avenue to not only modifying the physical properties, but utilizing in many energy technologies, such as energy storage and catalysts. However, detailed structural evolution in the close proximity of the topotactic phase transition in multivalent oxides has not been much studied. In this work, we used strontium cobaltites (SrCoOx) epitaxially grown by pulsed laser epitaxy (PLE) as a model syste...

Inhibitory effect of Piper betel leaf extracts on copper-mediated LDL oxidation and oxLDL-induced lipid accumulation via inducing reverse cholesterol transport in macrophages.

Science.gov (United States)

Ma, Gwo-Chin; Wu, Pei-Fang; Tseng, Hsien-Chun; Chyau, Charng-Cherng; Lu, Hsiu-Chin; Chou, Fen-Pi

2013-12-15

Piper betel leaf (PBL) has the biological capabilities of detoxification and can work as an anti-inflammatory agent and an anti-oxidant. In this study, we evaluated the anti-oxidative activity of the extract of Piper betel leaves (PBLs) on the basis of Cu(2+)-mediated oxidation, and its ability to prevent foam cell formation in a model for oxidised low density lipoprotein (oxLDL)-induced lipid accumulation in macrophages. Our data demonstrated that PBLs were able to inhibit LDL oxidation in vitro and are able to reduce the lipid accumulation in macrophages. We showed the underlying mechanisms to be the following: PBLs up-regulated the protein levels of the class A and class B scavenger receptors, the membrane lipid transporter ABCA1, and its upstream regulator Liver X receptor (LXR) in the macrophages exposed to oxLDL. The results suggested that PBLs activated the reverse cholesterol transport mechanism to enhance the metabolism of the oxLDL that could prevent both lipid accumulation and foam cell formation and further minimise the possible damage of vessels caused by the oxLDL. Copyright © 2013 Elsevier Ltd. All rights reserved.

Electric Characteristic Enhancement of an AZO/Si Schottky Barrier Diode with Hydrogen Plasma Surface Treatment and AlxOx Guard Ring Structure

Directory of Open Access Journals (Sweden)

Chien-Yu Li

2018-01-01

Full Text Available In this study, the design and fabrication of AZO/n-Si Schottky barrier diodes (SBDs with hydrogen plasma treatment on silicon surface and AlxOx guard ring were presented. The Si surface exhibited less interface defects after the cleaning process following with 30 w of H2 plasma treatment that improved the switching properties of the following formed SBDs. The rapid thermal annealing experiment also held at 400 °C to enhance the breakdown voltage of SBDs. The edge effect of the SBDs was also suppressed with the AlxOx guard ring structure deposited by the atomic layer deposition (ALD at the side of the SBDs. Experimental results show that the reverse leakage current was reduced and the breakdown voltage increased with an addition of the AlxOx guard ring. The diode and fabrication technology developed in the study were applicable to the realization of SBDs with a high breakdown voltage (>200 V, a low reverse leakage current density (≤72 μA/mm2@100 V, and a Schottky barrier height of 1.074 eV.

Electric Characteristic Enhancement of an AZO/Si Schottky Barrier Diode with Hydrogen Plasma Surface Treatment and AlxOx Guard Ring Structure

Science.gov (United States)

Li, Chien-Yu; Cheng, Min-Yu; Houng, Mau-Phon; Yang, Cheng-Fu; Liu, Jing

2018-01-01

In this study, the design and fabrication of AZO/n-Si Schottky barrier diodes (SBDs) with hydrogen plasma treatment on silicon surface and AlxOx guard ring were presented. The Si surface exhibited less interface defects after the cleaning process following with 30 w of H2 plasma treatment that improved the switching properties of the following formed SBDs. The rapid thermal annealing experiment also held at 400 °C to enhance the breakdown voltage of SBDs. The edge effect of the SBDs was also suppressed with the AlxOx guard ring structure deposited by the atomic layer deposition (ALD) at the side of the SBDs. Experimental results show that the reverse leakage current was reduced and the breakdown voltage increased with an addition of the AlxOx guard ring. The diode and fabrication technology developed in the study were applicable to the realization of SBDs with a high breakdown voltage (>200 V), a low reverse leakage current density (≤72 μA/mm2@100 V), and a Schottky barrier height of 1.074 eV. PMID:29316726

Nucleotide diversity and phylogenetic relationships among ...

Indian Academy of Sciences (India)

Navya

2 attached at the base of tree as the diverging Iridaceae relative's lineage. Present study revealed that psbA-trnH region are useful in addressing questions of phylogenetic relationships among the Gladiolus cultivars, as these intergenic spacers are more variable and have more phylogenetically informative sites than the ...

Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group.

Science.gov (United States)

Ast, Jennifer C; Dunlap, Paul V

2005-10-01

symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.

Point estimates in phylogenetic reconstructions

OpenAIRE

Benner, Philipp; Bacak, Miroslav; Bourguignon, Pierre-Yves

2013-01-01

Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc methods such as the derivation of a consensus tree makeup for the ill-definition of the usual concepts of posterior mean, while bootstrap methods mitigate the absence of a sound concept of variance. Yielding satisfactory results with sufficiently concentrated pos...

Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

Directory of Open Access Journals (Sweden)

Chodon Sass

2016-01-01

Full Text Available The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.

Phylogenetic heritability of geographic range size in haematophagous ectoparasites: time of divergence and variation among continents.

Science.gov (United States)

Krasnov, Boris R; Shenbrot, Georgy I; van der Mescht, Luther; Warburton, Elizabeth M; Khokhlova, Irina S

2018-04-12

To understand existence, patterns and mechanisms behind phylogenetic heritability in the geographic range size (GRS) of parasites, we measured phylogenetic signal (PS) in the sizes of both regional (within a region) and continental (within a continent) geographic ranges of fleas in five regions. We asked whether (a) GRS is phylogenetically heritable and (b) the manifestation of PS varies between regions. We also asked whether geographic variation in PS reflects the effects of the environment's spatiotemporal stability (e.g. glaciation disrupting geographic ranges) or is associated with time since divergence (accumulation differences among species over time). Support for the former hypothesis would be indicated by stronger PS in southern than in northern regions, whereas support for the latter hypothesis would be shown by stronger PS in regions with a large proportion of species belonging to the derived lineages than in regions with a large proportion of species belonging to the basal lineages. We detected significant PS in both regional and continental GRSs of fleas from Canada and in continental GRS of fleas from Mongolia. No PS was found in the GRS of fleas from Australia and Southern Africa. Venezuelan fleas demonstrated significant PS in regional GRS only. Local Indicators of Phylogenetic Association detected significant local positive autocorrelations of GRS in some clades even in regions in which PS has not been detected across the entire phylogeny. This was mainly characteristic of younger taxa.

Radicales libres de oxígeno y distress respiratorio agudo

Directory of Open Access Journals (Sweden)

Aracelis E. Dorado Lambert

2000-09-01

Full Text Available Se realizó una revisión acerca de la formación de radicales libres de oxígeno en el organismo, así como el aumento exagerado de su génesis durante la exposición a altas concentraciones de oxígeno y en el desarrollo de la explosión respiratoria que acompaña la fagocitosis. Se analiza además la formación de estos radicales en el pulmón durante la evolución del distress respiratorio agudo. Se abordó, posteriormente, el uso actual, sobre todo en el ámbito internacional, de los antioxidantes y bloqueadores de la lipoperoxidación para disminuir los efectos adversos de los radicales libres. A pesar de estas nuevas medidas, se corrobora que la disminución experimentada en la mortalidad por esta entidad, obedece a la optimización de los cuidados respiratorios, en especial la ventilación mecánica.The formation of free oxygen radicals in the body and the excessive increase of its genesis during exposure to high concentrations of oxygen and in the development of respiratory burst accompanying phagocytosis were reviewed. Also the formation of these radicals in lung during acute respiratory distress was analyzed. Similarly, the present use at the international level of antioxidants and lipoperoxidation blockers to diminish adverse effects of free radicals are addressed in this paper. In spite of these new measures, it was confirmed that the reduction of mortality rate from this disease was due to the improvement of respiratory care particularly the mechanical ventilation.

The complete chloroplast genome sequence of Ampelopsis: gene organization, comparative analysis and phylogenetic relationships to other angiosperms

Directory of Open Access Journals (Sweden)

Gurusamy eRaman

2016-03-01

Full Text Available Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of

Open Reading Frame Phylogenetic Analysis on the Cloud

Directory of Open Access Journals (Sweden)

Che-Lun Hung

2013-01-01

Full Text Available Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus.

The Development of Three Long Universal Nuclear Protein-Coding Locus Markers and Their Application to Osteichthyan Phylogenetics with Nested PCR

Science.gov (United States)

Zhang, Peng

2012-01-01

Background Universal nuclear protein-coding locus (NPCL) markers that are applicable across diverse taxa and show good phylogenetic discrimination have broad applications in molecular phylogenetic studies. For example, RAG1, a representative NPCL marker, has been successfully used to make phylogenetic inferences within all major osteichthyan groups. However, such markers with broad working range and high phylogenetic performance are still scarce. It is necessary to develop more universal NPCL markers comparable to RAG1 for osteichthyan phylogenetics. Methodology/Principal Findings We developed three long universal NPCL markers (>1.6 kb each) based on single-copy nuclear genes (KIAA1239, SACS and TTN) that possess large exons and exhibit the appropriate evolutionary rates. We then compared their phylogenetic utilities with that of the reference marker RAG1 in 47 jawed vertebrate species. In comparison with RAG1, each of the three long universal markers yielded similar topologies and branch supports, all in congruence with the currently accepted osteichthyan phylogeny. To compare their phylogenetic performance visually, we also estimated the phylogenetic informativeness (PI) profile for each of the four long universal NPCL markers. The PI curves indicated that SACS performed best over the whole timescale, while RAG1, KIAA1239 and TTN exhibited similar phylogenetic performances. In addition, we compared the success of nested PCR and standard PCR when amplifying NPCL marker fragments. The amplification success rate and efficiency of the nested PCR were overwhelmingly higher than those of standard PCR. Conclusions/Significance Our work clearly demonstrates the superiority of nested PCR over the conventional PCR in phylogenetic studies and develops three long universal NPCL markers (KIAA1239, SACS and TTN) with the nested PCR strategy. The three markers exhibit high phylogenetic utilities in osteichthyan phylogenetics and can be widely used as pilot genes for

Characterization of Escherichia coli Phylogenetic Groups ...

African Journals Online (AJOL)

Background: Escherichia coli strains mainly fall into four phylogenetic groups (A, B1, B2, and D) and that virulent extra‑intestinal strains mainly belong to groups B2 and D. Aim: The aim was to determine the association between phylogenetic groups of E. coli causing extraintestinal infections (ExPEC) regarding the site of ...

Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives

Czech Academy of Sciences Publication Activity Database

Kolanowska, Marta; Grochocka, E.; Konowalik, K.

2017-01-01

Roč. 5, may (2017), č. článku e3328. ISSN 2167-8359 R&D Projects: GA ČR GB14-36098G Institutional support: RVO:86652079 Keywords : campylocentrum orchidaceae * molecular phylogenetics * environmental niches * costa-rica * diversity * models * speciation * ecology * pollination * divergence * Angraecinae * Ecological niche modeling * Orchidaceae * Phylogenetic niche conservatism * Angraecum * Campylocentrum * Dendrophylax Subject RIV: EH - Ecology, Behaviour OBOR OECD: Biodiversity conservation Impact factor: 2.177, year: 2016

Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genus Sorghum.

Science.gov (United States)

Hawkins, Jennifer S; Ramachandran, Dhanushya; Henderson, Ashley; Freeman, Jasmine; Carlise, Michael; Harris, Alex; Willison-Headley, Zachary

2015-08-01

Sorghum is an essential grain crop whose evolutionary placement within the Andropogoneae has been the subject of scrutiny for decades. Early studies using cytogenetic and morphological data point to a poly- or paraphyletic origin of the genus; however, acceptance of poly- or paraphyly has been met with resistance. This study aimed to address the species relationships within Sorghum, in addition to the placement of Sorghum within the tribe, using a phylogenetic approach and employing broad taxon sampling. From 16 diverse Sorghum species, eight low-copy nuclear loci were sequenced that are known to play a role in morphological diversity and have been previously used to study evolutionary relationships in grasses. Further, the data for four of these loci were combined with those from 57 members of the Andropogoneae in order to determine the placement of Sorghum within the tribe. Both maximum likelihood and Bayesian analyses were performed on multilocus concatenated data matrices. The Sorghum-specific topology provides strong support for two major lineages, in alignment with earlier studies employing chloroplast and internal transcribed spacer (ITS) markers. Clade I is composed of the Eu-, Chaeto- and Heterosorghum, while clade II contains the Stipo- and Parasorghum. When combined with data from the Andropogoneae, Clade II resolves as sister to a clade containing Miscanthus and Saccharum with high posterior probability and bootstrap support, and to the exclusion of Clade I. The results provide compelling evidence for a two-lineage polyphyletic ancestry of Sorghum within the larger Andropogoneae, i.e. the derivation of the two major Sorghum clades from a unique common ancestor. Rejection of monophyly in previous molecular studies is probably due to limited taxon sampling outside of the genus. The clade consisting of Para- and Stiposorghum resolves as sister to Miscanthus and Saccharum with strong node support. © The Author 2015. Published by Oxford University Press on

Visualizing phylogenetic tree landscapes.

Science.gov (United States)

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks

NARCIS (Netherlands)

K.T. Huber; L.J.J. van Iersel (Leo); S.M. Kelk (Steven); R. Suchecki

2010-01-01

htmlabstractRecently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks - a type of

A practical algorithm for reconstructing level-1 phylogenetic networks

NARCIS (Netherlands)

Huber, K.T.; Iersel, van L.J.J.; Kelk, S.M.; Suchecki, R.

2011-01-01

Recently, much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here, we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks-a type of network

Protective effect of the silkworm protein 30Kc6 on human vascular endothelial cells damaged by oxidized low density lipoprotein (Ox-LDL.

Directory of Open Access Journals (Sweden)

Wei Yu

Full Text Available Although the 30K family proteins are important anti-apoptotic molecules in silkworm hemolymph, the underlying mechanism remains to be investigated. This is especially the case in human vascular endothelial cells (HUVECs. In this study, a 30K protein, 30Kc6, was successfully expressed and purified using the Bac-to-Bac baculovirus expression system in silkworm cells. Furthermore, the 30Kc6 expressed in Escherichia coli was used to generate a polyclonal antibody. Western blot analysis revealed that the antibody could react specifically with the purified 30Kc6 expressed in silkworm cells. The In vitro cell apoptosis model of HUVEC that was induced by oxidized low density lipoprotein (Ox-LDL and in vivo atherosclerosis rabbit model were constructed and were employed to analyze the protective effects of the silkworm protein 30Kc6 on these models. The results demonstrated that the silkworm protein 30Kc6 significantly enhanced the cell viability in HUVEC cells treated with Ox-LDL, decreased the degree of DNA fragmentation and markedly reduced the level of 8-isoprostane. This could be indicative of the silkworm protein 30Kc6 antagonizing the Ox-LDL-induced cell apoptosis by inhibiting the intracellular reactive oxygen species (ROS generation. Furthermore, Ox-LDL activated the cell mitogen activated protein kinases (MAPK, especially JNK and p38. As demonstrated with Western analysis, 30Kc6 inhibited Ox-LDL-induced cell apoptosis in HUVEC cells by preventing the MAPK signaling pathways. In vivo data have demonstrated that oral feeding of the silkworm protein 30Kc6 dramatically improved the conditions of the atherosclerotic rabbits by decreasing serum levels of total triglyceride (TG, high density lipoprotein cholesterol (HDL-C, low density lipoprotein cholesterol (LDL-C and total cholesterol (TC. Furthermore, 30Kc6 alleviated the extent of lesions in aorta and liver in the atherosclerotic rabbits. These data are not only helpful in understanding the anti

Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae.

Science.gov (United States)

Lv, Changda; Li, Qi; Kong, Lingfeng

2018-01-01

Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.

OxMaR: open source free software for online minimization and randomization for clinical trials.

Science.gov (United States)

O'Callaghan, Christopher A

2014-01-01

Minimization is a valuable method for allocating participants between the control and experimental arms of clinical studies. The use of minimization reduces differences that might arise by chance between the study arms in the distribution of patient characteristics such as gender, ethnicity and age. However, unlike randomization, minimization requires real time assessment of each new participant with respect to the preceding distribution of relevant participant characteristics within the different arms of the study. For multi-site studies, this necessitates centralized computational analysis that is shared between all study locations. Unfortunately, there is no suitable freely available open source or free software that can be used for this purpose. OxMaR was developed to enable researchers in any location to use minimization for patient allocation and to access the minimization algorithm using any device that can connect to the internet such as a desktop computer, tablet or mobile phone. The software is complete in itself and requires no special packages or libraries to be installed. It is simple to set up and run over the internet using online facilities which are very low cost or even free to the user. Importantly, it provides real time information on allocation to the study lead or administrator and generates real time distributed backups with each allocation. OxMaR can readily be modified and customised and can also be used for standard randomization. It has been extensively tested and has been used successfully in a low budget multi-centre study. Hitherto, the logistical difficulties involved in minimization have precluded its use in many small studies and this software should allow more widespread use of minimization which should lead to studies with better matched control and experimental arms. OxMaR should be particularly valuable in low resource settings.

OxMaR: open source free software for online minimization and randomization for clinical trials.

Directory of Open Access Journals (Sweden)

Christopher A O'Callaghan

Full Text Available Minimization is a valuable method for allocating participants between the control and experimental arms of clinical studies. The use of minimization reduces differences that might arise by chance between the study arms in the distribution of patient characteristics such as gender, ethnicity and age. However, unlike randomization, minimization requires real time assessment of each new participant with respect to the preceding distribution of relevant participant characteristics within the different arms of the study. For multi-site studies, this necessitates centralized computational analysis that is shared between all study locations. Unfortunately, there is no suitable freely available open source or free software that can be used for this purpose. OxMaR was developed to enable researchers in any location to use minimization for patient allocation and to access the minimization algorithm using any device that can connect to the internet such as a desktop computer, tablet or mobile phone. The software is complete in itself and requires no special packages or libraries to be installed. It is simple to set up and run over the internet using online facilities which are very low cost or even free to the user. Importantly, it provides real time information on allocation to the study lead or administrator and generates real time distributed backups with each allocation. OxMaR can readily be modified and customised and can also be used for standard randomization. It has been extensively tested and has been used successfully in a low budget multi-centre study. Hitherto, the logistical difficulties involved in minimization have precluded its use in many small studies and this software should allow more widespread use of minimization which should lead to studies with better matched control and experimental arms. OxMaR should be particularly valuable in low resource settings.

Electromagnetic Properties of (Gd, Y)Ba2Cu3Ox Superconducting Tapes With High Levels of Zr Addition

Energy Technology Data Exchange (ETDEWEB)

Liu, Y; Yao, Y; Chen, Y; Khatri, ND; Liu, J; Galtsyan, E; Lei, C; Selvamanickam, V

2013-06-01

The dependence of the critical current density (J(c)) on the orientation of applied magnetic fields was studied in Zr-doped (Gd, Y)Ba2Cu3Ox tapes fabricated by metal organic chemical vapor deposition. The in-field performance of J(c) of (Gd, Y)Ba2Cu3Ox tapes with Zr-doping levels of 7.5-30 at.% was investigated up to 5 T over a temperature range of 40-77 K. The highest critical currents (I-c) at H parallel to c and the highest values of minimum Ic in angular dependence measurements were achieved in the tapes with 20% Zr doping over a broad range of temperature and magnetic field conditions measured. The electromagnetic properties have been related to the changes in BaZrO3 content and microstructure.

Folding and unfolding phylogenetic trees and networks.

Science.gov (United States)

Huber, Katharina T; Moulton, Vincent; Steel, Mike; Wu, Taoyang

2016-12-01

Phylogenetic networks are rooted, labelled directed acyclic graphswhich are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network N can be "unfolded" to obtain a MUL-tree U(N) and, conversely, a MUL-tree T can in certain circumstances be "folded" to obtain aphylogenetic network F(T) that exhibits T. In this paper, we study properties of the operations U and F in more detail. In particular, we introduce the class of stable networks, phylogenetic networks N for which F(U(N)) is isomorphic to N, characterise such networks, and show that they are related to the well-known class of tree-sibling networks. We also explore how the concept of displaying a tree in a network N can be related to displaying the tree in the MUL-tree U(N). To do this, we develop aphylogenetic analogue of graph fibrations. This allows us to view U(N) as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in U(N) and reconciling phylogenetic trees with networks.

Phylogenetic relationships of Hemiptera inferred from mitochondrial and nuclear genes.

Science.gov (United States)

Song, Nan; Li, Hu; Cai, Wanzhi; Yan, Fengming; Wang, Jianyun; Song, Fan

2016-11-01

Here, we reconstructed the Hemiptera phylogeny based on the expanded mitochondrial protein-coding genes and the nuclear 18S rRNA gene, separately. The differential rates of change across lineages may associate with long-branch attraction (LBA) effect and result in conflicting estimates of phylogeny from different types of data. To reduce the potential effects of systematic biases on inferences of topology, various data coding schemes, site removal method, and different algorithms were utilized in phylogenetic reconstruction. We show that the outgroups Phthiraptera, Thysanoptera, and the ingroup Sternorrhyncha share similar base composition, and exhibit "long branches" relative to other hemipterans. Thus, the long-branch attraction between these groups is suspected to cause the failure of recovering Hemiptera under the homogeneous model. In contrast, a monophyletic Hemiptera is supported when heterogeneous model is utilized in the analysis. Although higher level phylogenetic relationships within Hemiptera remain to be answered, consensus between analyses is beginning to converge on a stable phylogeny.

Mechanochemically synthesized LiAlOx catalyst for aqueous aldol condensation of furfural with acetone

Directory of Open Access Journals (Sweden)

Stepanova L. N.

2017-10-01

Full Text Available In the present study, the mechanochemical method is proposed for synthesis of LiAl-layered double hydroxides (LDHs. This method is eco-friendly and allows obtaining LiAl-LDH under relatively mild conditions (centripetal acceleration of milling bodies 300 m s-2 and in a short period of time (15 minutes. The structures of as-prepared LiAl-LDH, LiAl-mixed oxide (calcined LDH and “activated” LiAl-LDH obtained after rehydration of the corresponding mixed oxide were confirmed by X-ray diffraction. The basicity of LiAlOx was measured by temperature-programmed desorption of CO2 and double isotherm technique. According to data obtained, LiAl-mixed oxide has a significant higher carbon dioxide adsorption capacity compared to MgAlmixed oxides prepared by conventional co-precipitation method. This indicates a large amount of basic surface sites with different strength (strong, medium and weak for Li-containing systems. The formation of “activated” LiAl-LDH having Bronsted basic sites (OH groups in the interlayer space provides an increased catalytic activity of LiAlOx in the reaction of aqueous-phase aldol condensation between furfural and acetone.

Alien plants invade more phylogenetically clustered community types and cause even stronger clustering

Czech Academy of Sciences Publication Activity Database

Lososová, Z.; de Bello, Francesco; Chytrý, M.; Kühn, I.; Pyšek, Petr; Sádlo, Jiří; Winter, M.; Zelený, D.

2015-01-01

Roč. 24, č. 7 (2015), s. 786-794 ISSN 1466-822X R&D Projects: GA ČR GAP505/12/1296; GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : biological invasions * phylogenetic diversity * vegetation type Subject RIV: EH - Ecology, Behaviour Impact factor: 5.840, year: 2015

Topological variation in single-gene phylogenetic trees

OpenAIRE

Castresana, Jose

2007-01-01

A recent large-scale phylogenomic study has shown the great degree of topological variation that can be found among eukaryotic phylogenetic trees constructed from single genes, highlighting the problems that can be associated with gene sampling in phylogenetic studies.

Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

Directory of Open Access Journals (Sweden)

David Lee Erickson

2014-11-01

Full Text Available Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1,347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK and psbA-trnH and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance metrics that are commonly used to infer assembly processes were estimated for each plot (Phylogenetic Distance [PD], Mean Phylogenetic Distance [MPD], and Mean Nearest Taxon Distance [MNTD]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for

PHYLOGEOrec: A QGIS plugin for spatial phylogeographic reconstruction from phylogenetic tree and geographical information data

Science.gov (United States)

Nashrulloh, Maulana Malik; Kurniawan, Nia; Rahardi, Brian

2017-11-01

The increasing availability of genetic sequence data associated with explicit geographic and environment (including biotic and abiotic components) information offers new opportunities to study the processes that shape biodiversity and its patterns. Developing phylogeography reconstruction, by integrating phylogenetic and biogeographic knowledge, provides richer and deeper visualization and information on diversification events than ever before. Geographical information systems such as QGIS provide an environment for spatial modeling, analysis, and dissemination by which phylogenetic models can be explicitly linked with their associated spatial data, and subsequently, they will be integrated with other related georeferenced datasets describing the biotic and abiotic environment. We are introducing PHYLOGEOrec, a QGIS plugin for building spatial phylogeographic reconstructions constructed from phylogenetic tree and geographical information data based on QGIS2threejs. By using PHYLOGEOrec, researchers can integrate existing phylogeny and geographical information data, resulting in three-dimensional geographic visualizations of phylogenetic trees in the Keyhole Markup Language (KML) format. Such formats can be overlaid on a map using QGIS and finally, spatially viewed in QGIS by means of a QGIS2threejs engine for further analysis. KML can also be viewed in reputable geobrowsers with KML-support (i.e., Google Earth).

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

Science.gov (United States)

Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

2015-07-01

This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sequence comparison and phylogenetic analysis of core gene of ...

African Journals Online (AJOL)

Phylogenetic analysis suggests that our sequences are clustered with sequences reported from Japan. This is the first phylogenetic analysis of HCV core gene from Pakistani population. Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and ...

PhyDesign: an online application for profiling phylogenetic informativeness

Directory of Open Access Journals (Sweden)

Townsend Jeffrey P

2011-05-01

Full Text Available Abstract Background The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007 phylogenetic informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available. Results Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007 phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest. Conclusions By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu.

Electronic structure evolution and energy level alignment at C60/4,4'-cyclohexylidenebis[N,N-bis(4-methylphenyl) benzenamine]/MoOx/indium tin oxide interfaces

Science.gov (United States)

Liu, Xiaoliang; Yi, Shijuan; Wang, Chenggong; Wang, Congcong; Gao, Yongli

2014-04-01

The electronic structure evolution and energy level alignment have been investigated at interfaces comprising fullerene (C60)/4,4'-cyclohexylidenebis[N,N-bis(4-methylphenyl) benzenamine] (TAPC)/ molybdenum oxide (MoOx)/ indium tin oxide with ultraviolet photoemission spectroscopy and inverse photoemission spectroscopy. With deposition of TAPC upon MoOx, a dipole of 1.58 eV was formed at the TAPC/MoOx interface due to electron transfer from TAPC to MoOx. The highest occupied molecular orbital (HOMO) onset of TAPC was pinned closed to the Fermi level, leading to a p-doped region and thus increasing the carrier concentration at the very interface. The downward band bending and the resulting built-in field in TAPC were favorable for the hole transfer toward the TAPC/MoOx interface. The rigid downward shift of energy levels of TAPC indicated no significant interface chemistry at the interface. With subsequent deposition of C60 on TAPC, a dipole of 0.27 eV was observed at the C60/TAPC heterojunction due to the electron transfer from TAPC to C60. This led to a drop of the HOMO of TAPC near the C60/TAPC interface, and hence further enhanced the band bending in TAPC. The band bending behavior was also observed in C60, similarly creating a built-in field in C60 film and improving the electron transfer away from the C60/TAPC interface. It can be deduced from the interface analysis that a promising maximum open circuit voltage of 1.5 eV is achievable in C60/TAPC-based organic photovoltaic cells.

Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers.

Science.gov (United States)

Deragon, Jean-Marc; Zhang, Xiaoyu

2006-12-01

Short interspersed elements (SINEs) are a class of dispersed mobile sequences that use RNA as an intermediate in an amplification process called retroposition. The presence-absence of a SINE at a given locus has been used as a meaningful classification criterion to evaluate phylogenetic relations among species. We review here recent developments in the characterisation of plant SINEs and their use as molecular makers to retrace phylogenetic relations among wild and cultivated Oryza and Brassica species. In Brassicaceae, further use of SINE markers is limited by our partial knowledge of endogenous SINE families (their origin and evolution histories) and by the absence of a clear classification. To solve this problem, phylogenetic relations among all known Brassicaceae SINEs were analyzed and a new classification, grouping SINEs in 15 different families, is proposed. The relative age and size of each Brassicaceae SINE family was evaluated and new phylogenetically supported subfamilies were described. We also present evidence suggesting that new potentially active SINEs recently emerged in Brassica oleracea from the shuffling of preexisting SINE portions. Finally, the comparative evolution history of SINE families present in Arabidopsis thaliana and Brassica oleracea revealed that SINEs were in general more active in the Brassica lineage. The importance of these new data for the use of Brassicaceae SINEs as molecular markers in future applications is discussed.

The Structural Evolution of (Gd, Y)Ba2Cu3Ox Tapes With Zr Addition Made by Metal Organic Chemical Vapor Deposition

Energy Technology Data Exchange (ETDEWEB)

Lei, CH; Galstyan, E; Chen, YM; Shi, T; Liu, YH; Khatri, N; Liu, JF; Xiong, XM; Majkic, G; Selvamanickam, V

2013-06-01

Structural analysis of (Gd, Y) Ba2Cu3Ox tapes with Zr addition made by metal organic chemical vapor deposition has been conducted with transmission electron microscopy and X-ray diffraction. Zr content in the films was varied from 0 to 25% in the precursor. In all Zr-doped films, self-assembled nanocolumnar structures of BaZrO3 (BZO) were observed along the c-axis. The amount of BaZrO3 was found to increase steadily with Zr content. Additionally, planar BZO plates were found on the (001) plane of (Gd, Y) Ba2Cu3Ox film. The size and thickness of BZO plates were seen to increase with Zr doping level. Rare-earth copper oxide phases were observed to begin to emerge in the 20% Zr-doped film. Cross-sectional study of the interface between (Gd, Y)Ba2Cu3Ox and LaMnO3 cap layer revealed a thin discrete BZO layer on the LaMnO3 in the 20% Zr doped film.

Synthesis of Nanocrystalline SnOx (x = 1–2 Thin Film Using a Chemical Bath Deposition Method with Improved Deposition Time, Temperature and pH

Directory of Open Access Journals (Sweden)

Zulkarnain Zainal

2011-09-01

Full Text Available Nanocrystalline SnOx (x = 1–2 thin films were prepared on glass substrates by a simple chemical bath deposition method. Triethanolamine was used as complexing agent to decrease time and temperature of deposition and shift the pH of the solution to the noncorrosive region. The films were characterized for composition, surface morphology, structure and optical properties. X-ray diffraction analysis confirms that SnOx thin films consist of a polycrystalline structure with an average grain size of 36 nm. Atomic force microscopy studies show a uniform grain distribution without pinholes. The elemental composition was evaluated by energy dispersive X-ray spectroscopy. The average O/Sn atomic percentage ratio is 1.72. Band gap energy and optical transition were determined from optical absorbance data. The film was found to exhibit direct and indirect transitions in the visible spectrum with band gap values of about 3.9 and 3.7 eV, respectively. The optical transmittance in the visible region is 82%. The SnOx nanocrystals exhibit an ultraviolet emission band centered at 392 nm in the vicinity of the band edge, which is attributed to the well-known exciton transition in SnOx. Photosensitivity was detected in the positive region under illumination with white light.

When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA.

Science.gov (United States)

Budaeva, Nataliya; Schepetov, Dmitry; Zanol, Joana; Neretina, Tatiana; Willassen, Endre

2016-01-01

Onuphid polychaetes are tubicolous marine worms commonly reported worldwide from intertidal areas to hadal depths. They often dominate in benthic communities and have economic importance in aquaculture and recreational fishing. Here we report the phylogeny of the family Onuphidae based on the combined analyses of nuclear (18S rDNA) and mitochondrial (16S rDNA) genes. Results of Bayesian and Maximum Likelihood analyses supported the monophyly of Onuphidae and its traditional subdivision into two monophyletic subfamilies: Onuphinae and Hyalinoeciinae. Ten of 22 recognized genera were monophyletic with strong node support; four more genera included in this study were either monotypic or represented by a single species. None of the genera appeared para- or polyphyletic and this indicates a strong congruence between the traditional morphology-based systematics of the family and the newly obtained molecular-based phylogenetic reconstructions. Intergeneric relationships within Hyalinoeciinae were not resolved. Two strongly supported monophyletic groups of genera were recovered within Onuphinae: ((Onuphis, Aponuphis), Diopatra, Paradiopatra) and (Hirsutonuphis, (Paxtonia, (Kinbergonuphis, Mooreonuphis))). A previously accepted hypothesis on the subdivision of Onuphinae into the Onuphis group of genera and the Diopatra group of genera was largely rejected. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

[Comparative leaf anatomy and phylogenetic relationships of 11 species of Laeliinae with emphasis on Brassavola (Orchidaceae)].

Science.gov (United States)

Noguera-Savelli, Eliana; Jáuregui, Damelis

2011-09-01

Brassavola inhabits a wide altitude range and habitat types from Northern Mexico to Northern Argentina. Classification schemes in plants have normally used vegetative and floral characters, but when species are very similar, as in this genus, conflicts arise in species delimitation, and alternative methods should be applied. In this study we explored the taxonomic and phylogenetic value of the anatomical structure of leaves in Brassavola; as ingroup, seven species of Brassavola were considered, and as an outgroup Guarianthe skinneri, Laelia anceps, Rhyncholaelia digbyana and Rhyncholaelia glauca were evaluated. Leaf anatomical characters were studied in freehand cross sections of the middle portion with a light microscope. Ten vegetative anatomical characters were selected and coded for the phylogenetic analysis. Phylogenetic reconstruction was carried out under maximum parsimony using the program NONA through WinClada. Overall, Brassavola species reveal a wide variety of anatomical characters, many of them associated with xeromorphic plants: thick cuticle, hypodermis and cells of the mesophyll with spiral thickenings in the secondary wall. Moreover, mesophyll is either homogeneous or heterogeneous, often with extravascular bundles of fibers near the epidermis at both terete and flat leaves. All vascular bundles are collateral, arranged in more than one row in the mesophyll. The phylogenetic analysis did not resolve internal relationships of the genus; we obtained a polytomy, indicating that the anatomical characters by themselves have little phylogenetic value in Brassavola. We concluded that few anatomical characters are phylogenetically important; however, they would provide more support to elucidate the phylogenetic relantionships in the Orchidaceae and other plant groups if they are used in conjunction with morphological and/or molecular characters.

Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly

Czech Academy of Sciences Publication Activity Database

de Bello, Francesco; Šmilauer, P.; Diniz-Filho, J. A. F.; Carmona, C. P.; Lososová, Z.; Herben, Tomáš; Götzenberger, Lars

2017-01-01

Roč. 8, č. 10 (2017), s. 1200-1211 ISSN 2041-210X R&D Projects: GA ČR(CZ) GA16-15012S; GA ČR GB14-36079G EU Projects: European Commission(XE) 267243 Institutional support: RVO:67985939 Keywords : community ecology * phylogenetic diversity * functional diversity Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 5.708, year: 2016

Predicting rates of interspecific interaction from phylogenetic trees.

Science.gov (United States)

Nuismer, Scott L; Harmon, Luke J

2015-01-01

Integrating phylogenetic information can potentially improve our ability to explain species' traits, patterns of community assembly, the network structure of communities, and ecosystem function. In this study, we use mathematical models to explore the ecological and evolutionary factors that modulate the explanatory power of phylogenetic information for communities of species that interact within a single trophic level. We find that phylogenetic relationships among species can influence trait evolution and rates of interaction among species, but only under particular models of species interaction. For example, when interactions within communities are mediated by a mechanism of phenotype matching, phylogenetic trees make specific predictions about trait evolution and rates of interaction. In contrast, if interactions within a community depend on a mechanism of phenotype differences, phylogenetic information has little, if any, predictive power for trait evolution and interaction rate. Together, these results make clear and testable predictions for when and how evolutionary history is expected to influence contemporary rates of species interaction. © 2014 John Wiley & Sons Ltd/CNRS.

Phylogenetic Structure of Foliar Spectral Traits in Tropical Forest Canopies

Directory of Open Access Journals (Sweden)

Kelly M. McManus

2016-02-01

Full Text Available The Spectranomics approach to tropical forest remote sensing has established a link between foliar reflectance spectra and the phylogenetic composition of tropical canopy tree communities vis-à-vis the taxonomic organization of biochemical trait variation. However, a direct relationship between phylogenetic affiliation and foliar reflectance spectra of species has not been established. We sought to develop this relationship by quantifying the extent to which underlying patterns of phylogenetic structure drive interspecific variation among foliar reflectance spectra within three Neotropical canopy tree communities with varying levels of soil fertility. We interpreted the resulting spectral patterns of phylogenetic signal in the context of foliar biochemical traits that may contribute to the spectral-phylogenetic link. We utilized a multi-model ensemble to elucidate trait-spectral relationships, and quantified phylogenetic signal for spectral wavelengths and traits using Pagel’s lambda statistic. Foliar reflectance spectra showed evidence of phylogenetic influence primarily within the visible and shortwave infrared spectral regions. These regions were also selected by the multi-model ensemble as those most important to the quantitative prediction of several foliar biochemical traits. Patterns of phylogenetic organization of spectra and traits varied across sites and with soil fertility, indicative of the complex interactions between the environmental and phylogenetic controls underlying patterns of biodiversity.

Improved efficiency of NiOx-based p-i-n perovskite solar cells by using PTEG-1 as electron transport layer

Science.gov (United States)

Groeneveld, Bart G. H. M.; Najafi, Mehrdad; Steensma, Bauke; Adjokatse, Sampson; Fang, Hong-Hua; Jahani, Fatemeh; Qiu, Li; ten Brink, Gert H.; Hummelen, Jan C.; Loi, Maria Antonietta

2017-07-01

We present efficient p-i-n type perovskite solar cells using NiOx as the hole transport layer and a fulleropyrrolidine with a triethylene glycol monoethyl ether side chain (PTEG-1) as electron transport layer. This electron transport layer leads to higher power conversion efficiencies compared to perovskite solar cells with PCBM (phenyl-C61-butyric acid methyl ester). The improved performance of PTEG-1 devices is attributed to the reduced trap-assisted recombination and improved charge extraction in these solar cells, as determined by light intensity dependence and photoluminescence measurements. Through optimization of the hole and electron transport layers, the power conversion efficiency of the NiOx/perovskite/PTEG-1 solar cells was increased up to 16.1%.

The combination of phylogenetic analysis with epidemiological and serological data to track HIV-1 transmission in a sexual transmission case.

Directory of Open Access Journals (Sweden)

Min Chen

Full Text Available To investigate the linkage of HIV transmission from a man to a woman through unprotected sexual contact without disclosing his HIV-positive status.Combined with epidemiological information and serological tests, phylogenetic analysis was used to test the a priori hypothesis of HIV transmission from the man to the woman. Control subjects, infected with HIV through heterosexual intercourse, from the same location were also sampled. Phylogenetic analyses were performed using the consensus gag, pol and env sequences obtained from blood samples of the man, the woman and the local control subjects. The env quasispecies of the man, the woman, and two controls were also obtained using single genome amplification and sequencing (SGA/S to explore the paraphyletic relationship by phylogenetic analysis.Epidemiological information and serological tests indicated that the man was infected with HIV-1 earlier than the woman. Phylogenetic analyses of the consensus sequences showed a monophyletic cluster for the man and woman in all three genomic regions. Furthermore, gag sequences of the man and woman shared a unique recombination pattern from subtype B and C, which was different from those of CRF07_BC or CRF08_BC observed in the local samples. These indicated that the viral sequences from the two subjects display a high level of similarity. Further, viral quasispecies from the man exhibited a paraphyletic relationship with those from the woman in the Bayesian and maximum-likelihood (ML phylogenetic trees of the env region, which supported the transmission direction from the man to the woman.In the context of epidemiological and serological evidence, the results of phylogenetic analyses support the transmission from the man to the woman.

Maximizing the phylogenetic diversity of seed banks.

Science.gov (United States)

Griffiths, Kate E; Balding, Sharon T; Dickie, John B; Lewis, Gwilym P; Pearce, Tim R; Grenyer, Richard

2015-04-01

Ex situ conservation efforts such as those of zoos, botanical gardens, and seed banks will form a vital complement to in situ conservation actions over the coming decades. It is therefore necessary to pay the same attention to the biological diversity represented in ex situ conservation facilities as is often paid to protected-area networks. Building the phylogenetic diversity of ex situ collections will strengthen our capacity to respond to biodiversity loss. Since 2000, the Millennium Seed Bank Partnership has banked seed from 14% of the world's plant species. We assessed the taxonomic, geographic, and phylogenetic diversity of the Millennium Seed Bank collection of legumes (Leguminosae). We compared the collection with all known legume genera, their known geographic range (at country and regional levels), and a genus-level phylogeny of the legume family constructed for this study. Over half the phylogenetic diversity of legumes at the genus level was represented in the Millennium Seed Bank. However, pragmatic prioritization of species of economic importance and endangerment has led to the banking of a less-than-optimal phylogenetic diversity and prioritization of range-restricted species risks an underdispersed collection. The current state of the phylogenetic diversity of legumes in the Millennium Seed Bank could be substantially improved through the strategic banking of relatively few additional taxa. Our method draws on tools that are widely applied to in situ conservation planning, and it can be used to evaluate and improve the phylogenetic diversity of ex situ collections. © 2014 Society for Conservation Biology.

Reconstructing phylogenetic networks using maximum parsimony.

Science.gov (United States)

Nakhleh, Luay; Jin, Guohua; Zhao, Fengmei; Mellor-Crummey, John

2005-01-01

Phylogenies - the evolutionary histories of groups of organisms - are one of the most widely used tools throughout the life sciences, as well as objects of research within systematics, evolutionary biology, epidemiology, etc. Almost every tool devised to date to reconstruct phylogenies produces trees; yet it is widely understood and accepted that trees oversimplify the evolutionary histories of many groups of organims, most prominently bacteria (because of horizontal gene transfer) and plants (because of hybrid speciation). Various methods and criteria have been introduced for phylogenetic tree reconstruction. Parsimony is one of the most widely used and studied criteria, and various accurate and efficient heuristics for reconstructing trees based on parsimony have been devised. Jotun Hein suggested a straightforward extension of the parsimony criterion to phylogenetic networks. In this paper we formalize this concept, and provide the first experimental study of the quality of parsimony as a criterion for constructing and evaluating phylogenetic networks. Our results show that, when extended to phylogenetic networks, the parsimony criterion produces promising results. In a great majority of the cases in our experiments, the parsimony criterion accurately predicts the numbers and placements of non-tree events.

Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution.

Science.gov (United States)

Kendall, Michelle; Colijn, Caroline

2016-10-01

Evolutionary relationships are frequently described by phylogenetic trees, but a central barrier in many fields is the difficulty of interpreting data containing conflicting phylogenetic signals. We present a metric-based method for comparing trees which extracts distinct alternative evolutionary relationships embedded in data. We demonstrate detection and resolution of phylogenetic uncertainty in a recent study of anole lizards, leading to alternate hypotheses about their evolutionary relationships. We use our approach to compare trees derived from different genes of Ebolavirus and find that the VP30 gene has a distinct phylogenetic signature composed of three alternatives that differ in the deep branching structure. phylogenetics, evolution, tree metrics, genetics, sequencing. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genome-Wide Analysis of the Biosynthesis and Deactivation of Gibberellin-Dioxygenases Gene Family in Camellia sinensis (L. O. Kuntze

Directory of Open Access Journals (Sweden)

Cheng Pan

2017-09-01

Full Text Available Gibberellins (GAs, a class of diterpenoid phytohormones, play a key role in regulating diverse processes throughout the life cycle of plants. Bioactive GA levels are rapidly regulated by Gibberellin-dioxygenases (GAox, which are involved in the biosynthesis and deactivation of gibberellin. In this manuscript, a comprehensive genome-wide analysis was carried out to find all GAox in Camellia sinensis. For the first time in a tea plant, 14 CsGAox genes, containing two domains, DIOX_N (PF14226 and 2OG-FeII_Oxy, were identified (PF03171. These genes all belong to 2-oxoglutarate-dependent dioxygenases (2-ODD, including four CsGA20ox (EC: 1.14.11.12, three CsGA3ox (EC: 1.14.11.15, and seven CsGA2ox (EC: 1.14.11.13. According to the phylogenetic classification as in Arabidopsis, the CsGAox genes spanned five subgroups. Each CsGAox shows tissue-specific expression patterns, although these vary greatly. Some candidate genes, which may play an important role in response to external abiotic stresses, have been identified with regards to patterns, such as CsGA20ox2, CsGA3ox2, CsGA3ox3, CsGA2ox1, CsGA2ox2, and CsGA2ox4. The bioactive GA levels may be closely related to the GA20ox, GA3ox and GA2ox genes. In addition, the candidate genes could be used as marker genes for abiotic stress resistance breeding in tea plants.

9-genes reinforce the phylogeny of holometabola and yield alternate views on the phylogenetic placement of Strepsiptera.

Directory of Open Access Journals (Sweden)

Duane D McKenna

2010-07-01

Full Text Available The extraordinary morphology, reproductive and developmental biology, and behavioral ecology of twisted wing parasites (order Strepsiptera have puzzled biologists for centuries. Even today, the phylogenetic position of these enigmatic "insects from outer space" [1] remains uncertain and contentious. Recent authors have argued for the placement of Strepsiptera within or as a close relative of beetles (order Coleoptera, as sister group of flies (order Diptera, or even outside of Holometabola.Here, we combine data from several recent studies with new data (for a total of 9 nuclear genes and approximately 13 kb of aligned data for 34 taxa, to help clarify the phylogenetic placement of Strepsiptera. Our results unequivocally support the monophyly of Neuropteroidea (=Neuropterida+Coleoptera+Strepsiptera, but recover Strepsiptera either derived from within polyphagan beetles (order Coleoptera, or in a position sister to Neuropterida. All other supra-ordinal- and ordinal-level relationships recovered with strong nodal support were consistent with most other recent studies.These results, coupled with the recent proposed placement of Strepsiptera sister to Coleoptera, suggest that while the phylogenetic neighborhood of Strepsiptera has been identified, unequivocal placement to a specific branch within Neuropteroidea will require additional study.

Molecular Phylogenetics: Mathematical Framework and Unsolved Problems

Science.gov (United States)

Xia, Xuhua

Phylogenetic relationship is essential in dating evolutionary events, reconstructing ancestral genes, predicting sites that are important to natural selection, and, ultimately, understanding genomic evolution. Three categories of phylogenetic methods are currently used: the distance-based, the maximum parsimony, and the maximum likelihood method. Here, I present the mathematical framework of these methods and their rationales, provide computational details for each of them, illustrate analytically and numerically the potential biases inherent in these methods, and outline computational challenges and unresolved problems. This is followed by a brief discussion of the Bayesian approach that has been recently used in molecular phylogenetics.

Protease activity of Per a 10 potentiates Th2 polarization by increasing IL-23 and OX40L.

Science.gov (United States)

Agrawal, Komal; Kale, Sagar L; Arora, Naveen

2015-12-01

Proteases are implicated in exacerbation of allergic diseases. In this study, the role of proteolytic activity of Per a 10 was evaluated on Th2 polarization. Intranasal administration of Per a 10 in mice led to allergic airway inflammation as seen by higher IgE levels, cellular infiltration, IL-17A, and Th2 cytokines, whereas, inactive (Δ)Per a 10 showed attenuated response. There was an increased OX40L expression on lung and lymph node dendritic cells in Per a 10 immunized group and on Per a 10 stimulated BMDCs. Reduction in CD40 expression without any change at transcript level in lungs of Per a 10 immunized mice suggested CD40 cleavage. BMDCs pulsed with Per a 10 showed reduced CD40 expression with lower IL-12p70 secretion as compared to heat inactivated Per a 10. IL-23, TNF-α, and IL-6 levels were significantly higher in Per a 10 stimulated BMDCs supernatant. In DC-T cell coculture studies, Per a 10 pulsed BMDCs showed higher levels of IL-4 and IL-13 that were reduced on blocking of either IL-23 or OX40L. In conclusion, the data suggests a critical role of protease activity of Per a 10 in promoting Th2 polarization by increasing IL-23 secretion and OX40L expression on dendritic cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phylogenetic community structure: temporal variation in fish assemblage

OpenAIRE

Santorelli, Sergio; Magnusson, William; Ferreira, Efrem; Caramaschi, Erica; Zuanon, Jansen; Amadio, Sidnéia

2014-01-01

Hypotheses about phylogenetic relationships among species allow inferences about the mechanisms that affect species coexistence. Nevertheless, most studies assume that phylogenetic patterns identified are stable over time. We used data on monthly samples of fish from a single lake over 10 years to show that the structure in phylogenetic assemblages varies over time and conclusions depend heavily on the time scale investigated. The data set was organized in guild structures and temporal scales...

Compositional and mutational rate heterogeneity in mitochondrial genomes and its effect on the phylogenetic inferences of Cimicomorpha (Hemiptera: Heteroptera).

Science.gov (United States)

Yang, Huanhuan; Li, Teng; Dang, Kai; Bu, Wenjun

2018-04-18

Mitochondrial genome (mt-genome) data can potentially return artefactual relationships in the higher-level phylogenetic inference of insects due to the biases of accelerated substitution rates and compositional heterogeneity. Previous studies based on mt-genome data alone showed a paraphyly of Cimicomorpha (Insecta, Hemiptera) due to the positions of the families Tingidae and Reduviidae rather than the monophyly that was supported based on morphological characters, morphological and molecular combined data and large scale molecular datasets. Various strategies have been proposed to ameliorate the effects of potential mt-genome biases, including dense taxon sampling, removal of third codon positions or purine-pyrimidine coding and the use of site-heterogeneous models. In this study, we sequenced the mt-genomes of five additional Tingidae species and discussed the compositional and mutational rate heterogeneity in mt-genomes and its effect on the phylogenetic inferences of Cimicomorpha by implementing the bias-reduction strategies mentioned above. Heterogeneity in nucleotide composition and mutational biases were found in mt protein-coding genes, and the third codon exhibited high levels of saturation. Dense taxon sampling of Tingidae and Reduviidae and the other common strategies mentioned above were insufficient to recover the monophyly of the well-established group Cimicomorpha. When the sites with weak phylogenetic signals in the dataset were removed, the remaining dataset of mt-genomes can support the monophyly of Cimicomorpha; this support demonstrates that mt-genomes possess strong phylogenetic signals for the inference of higher-level phylogeny of this group. Comparison of the ratio of the removal of amino acids for each PCG showed that ATP8 has the highest ratio while CO1 has the lowest. This pattern is largely congruent with the evolutionary rate of 13 PCGs that ATP8 represents the highest evolutionary rate, whereas CO1 appears to be the lowest. Notably

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

Science.gov (United States)

Willerslev, Eske; Gilbert, M Thomas P; Binladen, Jonas; Ho, Simon YW; Campos, Paula F; Ratan, Aakrosh; Tomsho, Lynn P; da Fonseca, Rute R; Sher, Andrei; Kuznetsova, Tatanya V; Nowak-Kemp, Malgosia; Roth, Terri L; Miller, Webb; Schuster, Stephan C

2009-01-01

Background The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments. Results In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths. Conclusion Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete mitochondrial

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

Directory of Open Access Journals (Sweden)

Nowak-Kemp Malgosia

2009-05-01

Full Text Available Abstract Background The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments. Results In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis, and the threatened Javan (Rhinoceros sondaicus, Sumatran (Dicerorhinus sumatrensis, and black (Diceros bicornis rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum and Indian (Rhinoceros unicornis rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i The black/white, (ii the woolly/Sumatran, and (iii the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths. Conclusion Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, large-scale sequencing of complete

Multilocus sequence typing and phylogenetic analysis of Propionibacterium acnes

DEFF Research Database (Denmark)

Kilian, Mogens; Scholz, Christian F. P.; Lomholt, Hans B.

2012-01-01

Propionibacterium acnes is a commensal of human skin but is also implicated in the pathogenesis of acne vulgaris, in biofilm-associated infections of medical devices and endophthalmitis, and in infections of bone and dental root canals. Recent studies associate P. acnes with prostate cancer...... schemes were compared with reference to a phylogenetic tree based on 78 P. acnes genomes and their gene contents. Further support for a basically clonal population structure of P. acnes and a scenario of the global spread of epidemic clones of P. acnes was obtained. Compared to the Belfast scheme...

Virulence, serotype and phylogenetic groups of diarrhoeagenic ...

African Journals Online (AJOL)

Dr DADIE Thomas

2014-02-17

Feb 17, 2014 ... The virulence, serotype and phylogenetic traits of diarrhoeagenic Escherichia coli were detected in 502 strains isolated during digestive infections. Molecular detection of the target virulence genes, rfb gene of operon O and phylogenetic grouping genes Chua, yjaA and TSPE4.C2 was performed.

Trypanosoma (Megatrypanum) melophagium in the sheep ked Melophagus ovinus from organic farms in Croatia: phylogenetic inferences support restriction to sheep and sheep keds and close relationship with trypanosomes from other ruminant species.

Science.gov (United States)

Martinković, Franjo; Matanović, Krešimir; Rodrigues, Adriana C; Garcia, Herakles A; Teixeira, Marta M G

2012-01-01

Trypanosoma (Megatrypanum) melophagium is a parasite of sheep transmitted by sheep keds, the sheep-restricted ectoparasite Melophagus ovinus (Diptera: Hippoboscidae). Sheep keds were 100% prevalent in sheep from five organic farms in Croatia, Southeastern Europe, whereas trypanosomes morphologically compatible with T. melophagium were 86% prevalent in the guts of the sheep keds. Multilocus phylogenetic analyses using sequences of small subunit rRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase, spliced leader, and internal transcribed spacer 1 of the rDNA distinguished T. melophagium from all allied trypanosomes from other ruminant species and placed the trypanosome in the subgenus Megatrypanum. Trypanosomes from sheep keds from Croatia and Scotland, the only available isolates for comparison, shared identical sequences. All biologic and phylogenetic inferences support the restriction of T. melophagium to sheep and, especially, to the sheep keds. The comparison of trypanosomes from sheep, cattle, and deer from the same country, which was never achieved before this work, strongly supported the host-restricted specificity of trypanosomes of the subgenus Megatrypanum. Our findings indicate that with the expansion of organic farms, both sheep keds and T. melophagium may re-emerge as parasitic infections of sheep. © 2011 The Author(s) Journal of Eukaryotic Microbiology © 2011 International Society of Protistologists.

Phylogenetic relationships of typical antbirds (Thamnophilidae and test of incongruence based on Bayes factors

Directory of Open Access Journals (Sweden)

Nylander Johan AA

2004-07-01

Full Text Available Abstract Background The typical antbirds (Thamnophilidae form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set. Results The phylogenetic analysis supports both novel relationships, as well as traditional groupings. Among the more interesting novel relationship suggested is that the Terenura antwrens, the wing-banded antbird (Myrmornis torquata, the spot-winged antshrike (Pygiptila stellaris and the russet antshrike (Thamnistes anabatinus are sisters to all other typical antbirds. The remaining genera fall into two major clades. The first includes antshrikes, antvireos and the Herpsilochmus antwrens, while the second clade consists of most antwren genera, the Myrmeciza antbirds, the "professional" ant-following antbirds, and allied species. Our results also support previously suggested polyphyly of Myrmotherula antwrens and Myrmeciza antbirds. The tests of phylogenetic incongruence, using Bayes factors, clearly suggests that allowing the gene partitions to have separate topology parameters clearly increased the model likelihood. However, changing a component of the nucleotide substitution model had much higher impact on the model likelihood. Conclusions The phylogenetic results are in broad agreement with traditional classification of the typical antbirds, but some relationships are unexpected based on external morphology. In these cases their true affinities may have been obscured by convergent evolution and

Hierarchical structures constructed by BiOX (X = Cl, I) nanosheets on CNTs/carbon composite fibers for improved photocatalytic degradation of methyl orange

Energy Technology Data Exchange (ETDEWEB)

Weng, Baicheng, E-mail: baichengweng@gmail.com; Xu, Fenghua; Xu, Jianguang [Yancheng Institute of Technology, Materials Engineering Department (China)

2014-12-15

A hierarchical structure (CNTs/CFs-NSs) of BiOX (X = Cl, I) nanosheets (NSs) on carbon fibers (CFs) embedded with aligned carbon nanotubes (CNTs) with improved photocatalytic activities has been developed on a large scale. In the CNTs/CFs obtained by centrifugal spinning, CNTs align along the axis of the CFs, form π–π stacking interactions with CFs and strength the electrical conductivity of CFs, which favors the electron collection and transportation. Cross-flake BiOX NSs were uniformly grown on the surface of CNTs/CFs through a successive ionic layer adsorption and reaction process. The as-prepared BiOX NSs are less than 20 nm in thickness with dominant reactive (001) facets that are almost fully exposed, promoting the photocatalytic properties. The hierarchical CNTs/CFs-NSs show 3- and 2-fold improved photocatalytic activities for degradation of methyl orange for BiOCl and BiOI compared to corresponding neat NSs, respectively, given the synergistic effects of CNTs/CFs and NSs. Moreover, these novel hierarchical structures with stable performance enhance the recycled ability for the photocatalyst.

Hierarchical structures constructed by BiOX (X = Cl, I) nanosheets on CNTs/carbon composite fibers for improved photocatalytic degradation of methyl orange

International Nuclear Information System (INIS)

Weng, Baicheng; Xu, Fenghua; Xu, Jianguang

2014-01-01

A hierarchical structure (CNTs/CFs-NSs) of BiOX (X = Cl, I) nanosheets (NSs) on carbon fibers (CFs) embedded with aligned carbon nanotubes (CNTs) with improved photocatalytic activities has been developed on a large scale. In the CNTs/CFs obtained by centrifugal spinning, CNTs align along the axis of the CFs, form π–π stacking interactions with CFs and strength the electrical conductivity of CFs, which favors the electron collection and transportation. Cross-flake BiOX NSs were uniformly grown on the surface of CNTs/CFs through a successive ionic layer adsorption and reaction process. The as-prepared BiOX NSs are less than 20 nm in thickness with dominant reactive (001) facets that are almost fully exposed, promoting the photocatalytic properties. The hierarchical CNTs/CFs-NSs show 3- and 2-fold improved photocatalytic activities for degradation of methyl orange for BiOCl and BiOI compared to corresponding neat NSs, respectively, given the synergistic effects of CNTs/CFs and NSs. Moreover, these novel hierarchical structures with stable performance enhance the recycled ability for the photocatalyst

["Long-branch Attraction" artifact in phylogenetic reconstruction].

Science.gov (United States)

Li, Yi-Wei; Yu, Li; Zhang, Ya-Ping

2007-06-01

Phylogenetic reconstruction among various organisms not only helps understand their evolutionary history but also reveal several fundamental evolutionary questions. Understanding of the evolutionary relationships among organisms establishes the foundation for the investigations of other biological disciplines. However, almost all the widely used phylogenetic methods have limitations which fail to eliminate systematic errors effectively, preventing the reconstruction of true organismal relationships. "Long-branch Attraction" (LBA) artifact is one of the most disturbing factors in phylogenetic reconstruction. In this review, the conception and analytic method as well as the avoidance strategy of LBA were summarized. In addition, several typical examples were provided. The approach to avoid and resolve LBA artifact has been discussed.

The development of FISH tools for genetic, phylogenetic and breeding studies in tomato (Solanum lycopersicum)

NARCIS (Netherlands)

Szinay, D.

2010-01-01

In this thesis various fluorescence in situ hybridization (FISH) technologies are described to support genome projects, plant breeding and phylogenetic analysis on tomato (Solanum lycopersicum, 2n=24). Its genome is 980 Mb and only 30 % are single copy sequences, which are mostly found in the

Hydrodeoxygenation of vicinal OH groups over heterogeneous rhenium catalyst promoted by palladium and ceria support.

Science.gov (United States)

Ota, Nobuhiko; Tamura, Masazumi; Nakagawa, Yoshinao; Okumura, Kazu; Tomishige, Keiichi

2015-02-02

Heterogeneous ReOx-Pd/CeO2 catalyst showed excellent performance for simultaneous hydrodeoxygenation of vicinal OH groups. High yield (>99%), turnover frequency (300 h(-1)), and turnover number (10,000) are achieved in the reaction of 1,4-anhydroerythritol to tetrahydrofuran. This catalyst can be applied to sugar alcohols, and mono-alcohols and diols are obtained in high yields (≥85%) from substrates with even and odd numbers of OH groups, respectively. The high catalytic performance of ReOx-Pd/CeO2 can be assigned to rhenium species with +4 or +5 valence state, and the formation of this species is promoted by H2/Pd and the ceria support. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Particle size dependence on oxygen reduction reaction activity of electrodeposited TaOx catalysts in acidic media

KAUST Repository

Seo, J.

2013-11-13

The size dependence of the oxygen reduction reaction activity was studied for TaOx nanoparticles electrodeposited on carbon black for application to polymer electrolyte fuel cells (PEFCs). Compared with a commercial Ta2O5 material, the ultrafine oxide nanoparticles exhibited a distinctively high onset potential different from that of the bulky oxide particles.

AlOx Coating of Ultrastable Zeolite Y: A Possible Method for Vanadium Passivation of FCC Catalysts

NARCIS (Netherlands)

Weckhuysen, B.M.; Catana, Gabriela; Grünert, W.; Voort, P. van der; Vansant, E.F.; Schoonheydt, R.A.

2000-01-01

AlOx coating is proposed as a possible method for vanadium passivation of the ultrastable zeolite Y (USY). Two coating methods are discussed: (i) the deposition of the [Al13O4(OH)24(H2O)12]7+ ([Al13]) complex from aqueous solutions and (ii) the anchoring of alumoxane by in situ triisobutylaluminum

Structural, thermal, and magnetic study of solvation processes in spin-crossover [Fe(bpp)(2)][Cr(L)(ox)(2)](2).nH(2)O complexes.

Science.gov (United States)

Clemente-León, Miguel; Coronado, Eugenio; Giménez-López, M Carmen; Romero, Francisco M

2007-12-24

The influence of lattice water in the magnetic properties of spin-crossover [Fe(bpp)2]X2.nH2O salts [bpp = 2,6-bis(pyrazol-3-yl)pyridine] is well-documented. In most cases, it stabilizes the low-spin state compared to the anhydrous compound. In other cases, it is rather the contrary. Unraveling this mystery implies the study of the microscopic changes that accompany the loss of water. This might be difficult from an experimental point of view. Our strategy is to focus on some salts that undergo a nonreversible dehydration-hydration process without loss of crystallinity. By comparison of the structural and magnetic properties of original and rehydrated samples, several rules concerning the role of water at the microscopic level can be deduced. This paper reports on the crystal structure, thermal studies, and magnetic properties of [Fe(bpp)2][Cr(bpy)(ox)2]2.2H2O (1), [Fe(bpp)2][Cr(phen)(ox)2]2.0.5H2O.0.5MeOH (2), and [Fe(bpp)2][Cr(phen)(ox)2]2.5.5H2O.2.5MeOH (3). Salt 1 contains both high-spin (HS) and low-spin (LS) Fe2+ cations in a 1:1 ratio. Dehydration yields the anhydrous spin-crossover compound with T1/2 downward arrow = 353 K and T1/2 upward arrow = 369 K. Rehydration affords the dihydrate [Fe(bpp)2][Cr(bpy)(ox)2]2.2H2O (1r) with 100% HS Fe2+ sites. Salt 2 also contains both HS and LS Fe2+ cations in a 1:1 ratio. Dehydration yields the anhydrous spin-crossover compound with T1/2 downward arrow = 343 K and T1/2 upward arrow = 348 K. Rehydration affords [Fe(bpp)2][Cr(phen)(ox)2]2.0.5H2O (2r) with 72% Fe2+ sites in the LS configuration. The structural, magnetic, and thermal properties of these rehydrated compounds 1r and 2r are also discussed. Finally, 1 has been dehydrated and resolvated with MeOH to give [Fe(bpp)2][Cr(bpy)(ox)2]2.MeOH (1s) with 33% HS Fe2+ sites. The influence of the guest solvent in the Fe2+ spin state can anticipate the future applications of these compounds in solvent sensing.

Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach

Directory of Open Access Journals (Sweden)

Nishida Mutsumi

2007-10-01

Full Text Available Abstract Background Cichlid fishes in Lake Tanganyika exhibit remarkable diversity in their feeding habits. Among them, seven species in the genus Perissodus are known for their unique feeding habit of scale eating with specialized feeding morphology and behaviour. Although the origin of the scale-eating habit has long been questioned, its evolutionary process is still unknown. In the present study, we conducted interspecific phylogenetic analyses for all nine known species in the tribe Perissodini (seven Perissodus and two Haplotaxodon species using amplified fragment length polymorphism (AFLP analyses of the nuclear DNA. On the basis of the resultant phylogenetic frameworks, the evolution of their feeding habits was traced using data from analyses of stomach contents, habitat depths, and observations of oral jaw tooth morphology. Results AFLP analyses resolved the phylogenetic relationships of the Perissodini, strongly supporting monophyly for each species. The character reconstruction of feeding ecology based on the AFLP tree suggested that scale eating evolved from general carnivorous feeding to highly specialized scale eating. Furthermore, scale eating is suggested to have evolved in deepwater habitats in the lake. Oral jaw tooth shape was also estimated to have diverged in step with specialization for scale eating. Conclusion The present evolutionary analyses of feeding ecology and morphology based on the obtained phylogenetic tree demonstrate for the first time the evolutionary process leading from generalised to highly specialized scale eating, with diversification in feeding morphology and behaviour among species.

Phylogenetically Acquired Representations and Evolutionary Algorithms.

OpenAIRE

Wozniak , Adrianna

2006-01-01

First, we explain why Genetic Algorithms (GAs), inspired by the Modern Synthesis, do not accurately model biological evolution, being rather an artificial version of artificial, rather than natural selection. Being focused on optimisation, we propose two improvements of GAs, with the aim to successfully generate adapted, desired behaviour. The first one concerns phylogenetic grounding of meaning, a way to avoid the Symbol Grounding Problem. We give a definition of Phylogenetically Acquired Re...

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis.

Science.gov (United States)

Stoltzfus, Arlin; O'Meara, Brian; Whitacre, Jamie; Mounce, Ross; Gillespie, Emily L; Kumar, Sudhir; Rosauer, Dan F; Vos, Rutger A

2012-10-22

Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use. Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find that the technical infrastructure is available to support rudimentary archiving, but the frequency of archiving is low. Currently, most phylogenetic knowledge is not easily re-used due to a lack of archiving, lack of awareness of best practices, and lack of community-wide standards for formatting data, naming entities, and annotating data. Most attempts at data re-use seem to end in disappointment. Nevertheless, we find many positive examples of data re-use, particularly those that involve customized species trees generated by grafting to, and pruning from, a much larger tree. The technologies and practices that facilitate data re-use can catalyze synthetic and integrative research. However, success will require engagement from various stakeholders including individual scientists who produce or consume shareable data, publishers, policy-makers, technology developers and resource-providers. The critical challenges for facilitating re-use of phylogenetic trees and associated data, we suggest, include: a broader commitment to public archiving; more extensive use of globally meaningful identifiers; development of user-friendly technology for annotating, submitting, searching, and retrieving data and their metadata; and development of a minimum reporting standard (MIAPA) indicating

Photoresponse and photo-induced memory effect in the organic field-effect transistor based on AlOX nanoparticles at the interface of semiconductor/dielectric

Science.gov (United States)

Cheng, Yunfei; Wang, Wu

2017-10-01

In this work, the photoresponse and photo-induced memory effect were demonstrated in an organic field-effect transistor (OFET) with semiconductor pentacene and SiO2 as the active and gate dielectric layers, respectively. By inserting AlOX nanoparticles (NPs) at the interface of pentacene/SiO2, obvious enhancing photoresponse was obtained in the OFET with the maximum responsivity and photosensitivity of about 15 A/W and 100, respectively. Moreover, the stable photoinduced memory effect was achieved in the OFET, attributing to the photogenerated electrons captured by the interface traps of the AlOX NPs/SiO2.

A program to compute the soft Robinson-Foulds distance between phylogenetic networks.

Science.gov (United States)

Lu, Bingxin; Zhang, Louxin; Leong, Hon Wai

2017-03-14

Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks. Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.

Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History

Directory of Open Access Journals (Sweden)

N.L.P Indi Dharmayanti

2011-03-01

Full Text Available Phylogenetic is described as taxonomy classification of an organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1 Maximum parsimony, (2 Distance, and (3 Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data.

[Effect of TiO2-SiO2-SnOx film with different firing temperatures on bond strength of low-fusing dental porcelain to pure titanium].

Science.gov (United States)

Zhang, Zichuan; Zhang, Pei

2015-07-01

To evaluate the influence of TiO(2)-SiO(2)-SnOx nano-coatings with different firing temperatures on the bond strength of low-fusing dental porcelain to pure titanium. The surface of pure titanium was coated uniformly with TiO(2)-SiO(2)-SnOx nano-coatings by solution-gelatin (Sol-Gel) technology and then fired at 300 °C (group A) or 750 °C (group B) for 1 h. The specimens without any coatings were the control group (group C). There were 10 specimens in each group. Dental porcelain was sintered on the surface of titanium specimens. Surface roughness and contact angle of the coatings were also detected. The titanium-porcelain bond strength was investigated according to YY 0621-2008 standards using three-point flexure bond test. The phase composition of the TiO(2)-SiO(2)-SnOx nano-coatings was characterized by X-ray diffraction(XRD). The interface of titanium-porcelain and TiO(2)-SiO(2)-SnOx nano-coatings were observed using scanning electron microscope (SEM). No rutile phase was found in these specimens of group A and group B. The surface roughness of group A, B, C was (0.97 ± 0.06), (0.99 ± 0.03), (0.96 ± 0.07) µm, respectively. No significant difference was found among the three groups. Compared with that of group C (64.37° ± 3.01°), contact angles detected in group A (52.04° ± 3.15°) and group B (85.27° ± 4.17°) were significantly different (P porcelain in group A [(35.66 ± 2.65) MPa] was significantly increased compared with those in group B [(26.18 ± 2.22) MPa] and group C [(31.66 ± 3.52) MPa]. SEM photomicrographs of titanium-porcelain interface morphology of the specimens before porcelain sintering showed that TiO(2)-SiO(2)-SnOx nano-coatings in group A were compact and homogeneous with petty cracks and those in group B was loose and arranged disorderly. TiO(2)-SiO(2)-SnOx nano-coating fired at 300 °C is significantly effective in improving the titanium-porcelain bond strength.

YBYRÁ facilitates comparison of large phylogenetic trees.

Science.gov (United States)

Machado, Denis Jacob

2015-07-01

The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

Disentangling the phylogenetic and ecological components of spider phenotypic variation.

Science.gov (United States)

Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

2014-01-01

An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.