Trapping a Highly Reactive Nonheme Iron Intermediate That Oxygenates Strong C-H Bonds with Stereoretention.

PubMed

Serrano-Plana, Joan; Oloo, Williamson N; Acosta-Rueda, Laura; Meier, Katlyn K; Verdejo, Begoña; García-España, Enrique; Basallote, Manuel G; Münck, Eckard; Que, Lawrence; Company, Anna; Costas, Miquel

2015-12-23

An unprecedentedly reactive iron species (2) has been generated by reaction of excess peracetic acid with a mononuclear iron complex [Fe(II)(CF3SO3)2(PyNMe3)] (1) at cryogenic temperatures, and characterized spectroscopically. Compound 2 is kinetically competent for breaking strong C-H bonds of alkanes (BDE ≈ 100 kcal·mol(-1)) through a hydrogen-atom transfer mechanism, and the transformations proceed with stereoretention and regioselectively, responding to bond strength, as well as to steric and polar effects. Bimolecular reaction rates are at least an order of magnitude faster than those of the most reactive synthetic high-valent nonheme oxoiron species described to date. EPR studies in tandem with kinetic analysis show that the 490 nm chromophore of 2 is associated with two S = 1/2 species in rapid equilibrium. The minor component 2a (∼5% iron) has g-values at 2.20, 2.19, and 1.99 characteristic of a low-spin iron(III) center, and it is assigned as [Fe(III)(OOAc)(PyNMe3)](2+), also by comparison with the EPR parameters of the structurally characterized hydroxamate analogue [Fe(III)(tBuCON(H)O)(PyNMe3)](2+) (4). The major component 2b (∼40% iron, g-values = 2.07, 2.01, 1.95) has unusual EPR parameters, and it is proposed to be [Fe(V)(O)(OAc)(PyNMe3)](2+), where the O-O bond in 2a has been broken. Consistent with this assignment, 2b undergoes exchange of its acetate ligand with CD3CO2D and very rapidly reacts with olefins to produce the corresponding cis-1,2-hydroxoacetate product. Therefore, this work constitutes the first example where a synthetic nonheme iron species responsible for stereospecific and site selective C-H hydroxylation is spectroscopically trapped, and its catalytic reactivity against C-H bonds can be directly interrogated by kinetic methods. The accumulated evidence indicates that 2 consists mainly of an extraordinarily reactive [Fe(V)(O)(OAc)(PyNMe3)](2+) (2b) species capable of hydroxylating unactivated alkyl C-H bonds with stereoretention in a rapid and site-selective manner, and that exists in fast equilibrium with its [Fe(III)(OOAc)(PyNMe3)](2+) precursor.

Cytotoxic and anti-angiogenic paclitaxel solubilized and permeation-enhanced by natural product nanoparticles

PubMed Central

Liu, Zhijun; Zhang, Fang; Koh, Gar Yee; Dong, Xin; Hollingsworth, Javoris; Zhang, Jian; Russo, Paul S.; Yang, Peiying; Stout, Rhett W.

2014-01-01

Paclitaxel (PTX) is one of the most potent intravenous chemotherapeutic agents to date, yet an oral formulation has been problematic due to its low solubility and permeability. Using the recently discovered solubilizing properties of rubusoside (RUB), we investigated this unique PTX-RUB formulation. Paclitaxel was solubilized by RUB in water to levels of 1.6 to 6.3 mg/mL at 10 to 40% weight/volume. These, nanomicellar, PTX-RUB complexes were dried to a powder which was subsequently reconstituted in physiologic solutions. After 2.5 hrs in gastric fluid 85 to 99% of PTX-RUB remained soluble, while 79 to 96% remained soluble in intestinal fluid. The solubilization of PTX was mechanized by the formation of water-soluble spherical nanomicelles between PTX and RUB with an average diameter of 6.6 nm. Compared with Taxol®, PTX-RUB nanoparticles were nearly four times more permeable in Caco-2 cell monocultures. In a side-by-side comparison with DMSO-solubilized PTX, PTX-RUB maintained the same level of cytotoxicity against three human cancer cell lines with IC50 values ranging from 4 nM to 20 nM. Additionally, tubular formation and migration of HUVECs were inhibited at levels as low as 5 nM. These chemical and biological properties demonstrated by the PTX-RUB nanoparticles may improve oral bioavailability and enable further pharmacokinetic, toxicologic, and efficacy investigations. PMID:25243454

An ab initio study of the potential energy surface in the S 1 state of 2-hydroxypyridine

NASA Astrophysics Data System (ADS)

Sobolewski, Andrzej L.; Adamowicz, Ludwik

1996-12-01

The potential energy (PE) surface of the lowest excited singlet state relevant to the photophysics of interconversion of the 2-hydroxypyridine/2 (1H)-pyridinone (2HP/2PY) system is characterized by ab initio calculations. The geometry optimizations in the S 1 state performed at the CIS/6-31G (d,p) level confirm the experimental findings that the 2HP form is planar in this state whereas the 2PY form is significantly out-of-plane distorted. The lowest-energy first-order saddle-points which are relevant to the photophysics of the "mobile" hydrogen atom on the S 1 PE surface lead toward its dissociation from the molecule. There is no saddle-point for a "direct" proton transfer reaction on the S 1 PE surface leading from the 2HP form to the 2PY form. The results confirm the hypothesis that the photo-induced dissociation-association (PIDA) mechanism is probably responsible for the excited-state tautomerization observed in this system.

The coordination chemistry of the neutral tris-2-pyridyl silicon ligand [PhSi(6-Me-2-py)3].

PubMed

Plajer, Alex J; Colebatch, Annie L; Enders, Markus; García-Romero, Álvaro; Bond, Andrew D; García-Rodríguez, Raúl; Wright, Dominic S

2018-05-22

Difficulties in the preparation of neutral ligands of the type [RSi(2-py)3] (where 2-py is an unfunctionalised 2-pyridyl ring unit) have thwarted efforts to expand the coordination chemistry of ligands of this type. However, simply switching the pyridyl substituents to 6-methyl-pyridyl groups (6-Me-2-py) in the current paper has allowed smooth, high-yielding access to the [PhSi(6-Me-2-py)3] ligand (1), and the first exploration of its coordination chemistry with transition metals. The synthesis, single-crystal X-ray structures and solution dynamics of the new complexes [{PhSi(6-Me-2-py)3}CuCH3CN][PF6], [{PhSi(6-Me-2-py)3}CuCH3CN][CuCl2], [{PhSi(6-Me-2-py)3}FeCl2], [{PhSi(6-Me-2-py)3}Mo(CO)3] and [{PhSi(6-Me-2-py)3}CoCl2] are reported. The paramagnetic Fe2+ and Co2+ complexes show strongly shifted NMR resonances for the coordinated pyridyl units due to large Fermi-contact shifts. However, magnetic anisotropy also leads to considerable pseudo-contact shifts so that both contributions have to be included in the paramagnetic NMR analysis.

Reaction landscape of a pentadentate N5-ligated Mn(II) complex with O2˙- and H2O2 includes conversion of a peroxomanganese(III) adduct to a bis(μ-oxo)dimanganese(III,IV) species.

PubMed

Leto, Domenick F; Chattopadhyay, Swarup; Day, Victor W; Jackson, Timothy A

2013-09-28

Herein we describe the chemical reactivity of the mononuclear [Mn(II)(N4py)(OTf)](OTf) (1) complex with hydrogen peroxide and superoxide. Treatment of 1 with one equivalent superoxide at -40 °C in MeCN formed the peroxomanganese(III) adduct, [Mn(III)(O2)(N4py)](+) (2) in ~30% yield. Complex 2 decayed over time and the formation of the bis(μ-oxo)dimanganese(III,IV) complex, [Mn(III)Mn(IV)(μ-O)2(N4py)2](3+) (3) was observed. When 2 was formed in higher yields (~60%) using excess superoxide, the [Mn(III)(O2)(N4py)](+) species thermally decayed to Mn(II) species and 3 was formed in no greater than 10% yield. Treatment of [Mn(III)(O2)(N4py)](+) with 1 resulted in the formation of 3 in ~90% yield, relative to the concentration of [Mn(III)(O2)(N4py)](+). This reaction mimics the observed chemistry of Mn-ribonucleotide reductase, as it features the conversion of two Mn(II) species to an oxo-bridged Mn(III)Mn(IV) compound using O2(-) as oxidant. Complex 3 was independently prepared through treatment of 1 with H2O2 and base at -40 °C. The geometric and electronic structures of 3 were probed using electronic absorption, electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), variable-temperature, variable-field MCD (VTVH-MCD), and X-ray absorption (XAS) spectroscopies. Complex 3 was structurally characterized by X-ray diffraction (XRD), which revealed the N4py ligand bound in an unusual tetradentate fashion.

Stonix, Version 0.x

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-05-13

STONIX is a program for configuring UNIX and Linux computer operating systems. It applies configurations based on the guidance from publicly accessible resources such as: NSA Guides, DISA STIGs, the Center for Internet Security (CIS), USGCB and vendor security documentation. STONIX is written in the Python programming language using the QT4 and PyQT4 libraries to provide a GUI. The code is designed to be easily extensible and customizable.

Influence of a Heterocyclic Nitrogen-Donor Group on the Coordination of Trivalent Actinides and Lanthanides by Aminopolycarboxylate Complexants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grimes, Travis S.; Heathman, Colt R.; Jansone-Popova, Santa

Here, the novel metal chelator N-2-(pyridylmethyl)diethylenetriamine- N,N',N",N"-tetraacetic acid (DTTA-PyM) was designed to replace a single oxygen-donor acetate group of the well-known aminopolycarboxylate complexant diethylenetriamine- N,N,N',N",N"-pentaacetic acid (DTPA) with a nitrogen-donor 2-pyridylmethyl. Potentiometric, spectroscopic, computational, and radioisotope distribution methods show distinct differences for the 4f and 5f coordination environments and enhanced actinide binding due to the nitrogen-bearing heterocyclic moiety. The Am 3+, Cm 3+, and Ln 3+ complexation studies for DTTA-PyM reveal an enhanced preference, relative to DTPA, for trivalent actinide binding. Fluorescence studies indicate no changes to the octadentate coordination of trivalent curium, while evidence of heptadentate complexation of trivalentmore » europium is found in mixtures containing EuHL (aq) complexes at the same aqueous acidity. The denticity change observed for Eu 3+ suggests that complex protonation occurs on the pyridyl nitrogen. Formation of the CmHL (aq) complex is likely due to the protonation of an available carboxylate group because the carbonyl oxygen can maintain octadentate coordination through a rotation. The observed suppressed protonation of the pyridyl nitrogen in the curium complexes may be attributed to stronger trivalent actinide binding by DTTA-PyM. Density functional theory calculations indicate that added stabilization of the actinide complexes with DTTA-PyM may originate from π-back-bonding interactions between singly occupied 5f orbitals of Am 3+ and the pyridyl nitrogen. The differences between the stabilities of trivalent actinide chelates (Am 3+, Cm 3+) and trivalent lanthanide chelates (La 3+–Lu 3+) are observed in liquid–liquid extraction systems, yielding unprecedented 4f/5f differentiation when using DTTA-PyM as an aqueous holdback reagent. In addition, the enhanced nitrogen-donor softness of the new DTTA-PyM chelator was perturbed by adding a fluorine onto the pyridine group. The comparative characterization of N-(3-fluoro-2-pyridylmethyl)diethylenetriamine- N,N',N",N"-tetraacetic acid (DTTA-3-F-PyM) showed subdued 4 f/5 f differentiation due to the presence of this electron-withdrawing group.« less

Spectroscopic, Electrochemical and Computational Characterisation of Ru Species Involved in Catalytic Water Oxidation: Evidence for a [Ru(V) (O)(Py2 (Me) tacn)] Intermediate.

PubMed

Casadevall, Carla; Codolà, Zoel; Costas, Miquel; Lloret-Fillol, Julio

2016-07-11

A new family of ruthenium complexes based on the N-pentadentate ligand Py2 (Me) tacn (N-methyl-N',N''-bis(2-picolyl)-1,4,7-triazacyclononane) has been synthesised and its catalytic activity has been studied in the water-oxidation (WO) reaction. We have used chemical oxidants (ceric ammonium nitrate and NaIO4 ) to generate the WO intermediates [Ru(II) (OH2 )(Py2 (Me) tacn)](2+) , [Ru(III) (OH2 )(Py2 (Me) tacn)](3+) , [Ru(III) (OH)(Py2 (Me) tacn)](2+) and [Ru(IV) (O)(Py2 (Me) tacn)](2+) , which have been characterised spectroscopically. Their relative redox and pH stability in water has been studied by using UV/Vis and NMR spectroscopies, HRMS and spectroelectrochemistry. [Ru(IV) (O)(Py2 (Me) tacn)](2+) has a long half-life (>48 h) in water. The catalytic cycle of WO has been elucidated by using kinetic, spectroscopic, (18) O-labelling and theoretical studies, and the conclusion is that the rate-determining step is a single-site water nucleophilic attack on a metal-oxo species. Moreover, [Ru(IV) (O)(Py2 (Me) tacn)](2+) is proposed to be the resting state under catalytic conditions. By monitoring Ce(IV) consumption, we found that the O2 evolution rate is redox-controlled and independent of the initial concentration of Ce(IV) . Based on these facts, we propose herein that [Ru(IV) (O)(Py2 (Me) tacn)](2+) is oxidised to [Ru(V) (O)(Py2 (Me) tacn)](2+) prior to attack by a water molecule to give [Ru(III) (OOH)(Py2 (Me) tacn)](2+) . Finally, it is shown that the difference in WO reactivity between the homologous iron and ruthenium [M(OH2 )(Py2 (Me) tacn)](2+) (M=Ru, Fe) complexes is due to the difference in the redox stability of the key M(V) (O) intermediate. These results contribute to a better understanding of the WO mechanism and the differences between iron and ruthenium complexes in WO reactions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS.

PubMed

van Erven, Gijs; de Visser, Ries; Merkx, Donny W H; Strolenberg, Willem; de Gijsel, Peter; Gruppen, Harry; Kabel, Mirjam A

2017-10-17

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13 C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12 C and 13 C lignin were isolated from nonlabeled and uniformly 13 C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13 C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12 C lignin analogue and was shown to be extremely accurate (>99.9%, R 2 > 0.999) and precise (RSD < 1.5%). Third, 13 C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS

PubMed Central

2017-01-01

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12C and 13C lignin were isolated from nonlabeled and uniformly 13C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12C lignin analogue and was shown to be extremely accurate (>99.9%, R2 > 0.999) and precise (RSD < 1.5%). Third, 13C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin. PMID:28926698

Conductivity of Langmuir-Blodgett films of a disk-shaped liquid-crystalline molecule-DNA complex studied by current-sensing atomic force microscopy.

PubMed

Nayak, Alpana; Suresh, K A

2008-08-01

We have studied the electrical conductivity in monolayer films of an ionic disk-shaped liquid-crystal molecule, pyridinium tethered with hexaalkoxytriphenylene (PyTp), and its complex with DNA by current-sensing atomic force microscopy (CS-AFM). The pure PyTp and PyTp-DNA complex monolayer films were first formed at the air-water interface and then transferred onto conducting substrates by the Langmuir-Blodgett (LB) technique to study the nanoscale electron transport through these films. The conductive tip of CS-AFM, the LB film, and the metal substrate form a nanoscopic metal-LB film-metal (M-LB-M) junction. We have measured the current-voltage (I-V) characteristics for the M-LB-M junction using CS-AFM and have analyzed the data quantitatively. We find that the I-V curves fit well to the Fowler-Nordheim (FN) model, suggesting electron tunneling to be a possible mechanism for electron transport in our system. Further, analysis of the I-V curves based on the FN model yields the barrier heights of PyTp-DNA complex and pure PyTp films. Electron transport studies of films of ionic disk-shaped liquid-crystal molecules and their complex with DNA are important from the point of view of their applications in organic electronics.

Conductivity of Langmuir-Blodgett films of a disk-shaped liquid-crystalline molecule-DNA complex studied by current-sensing atomic force microscopy

NASA Astrophysics Data System (ADS)

Nayak, Alpana; Suresh, K. A.

2008-08-01

We have studied the electrical conductivity in monolayer films of an ionic disk-shaped liquid-crystal molecule, pyridinium tethered with hexaalkoxytriphenylene (PyTp), and its complex with DNA by current-sensing atomic force microscopy (CS-AFM). The pure PyTp and PyTp-DNA complex monolayer films were first formed at the air-water interface and then transferred onto conducting substrates by the Langmuir-Blodgett (LB) technique to study the nanoscale electron transport through these films. The conductive tip of CS-AFM, the LB film, and the metal substrate form a nanoscopic metal-LB film-metal (M-LB-M) junction. We have measured the current-voltage (I-V) characteristics for the M-LB-M junction using CS-AFM and have analyzed the data quantitatively. We find that the I-V curves fit well to the Fowler-Nordheim (FN) model, suggesting electron tunneling to be a possible mechanism for electron transport in our system. Further, analysis of the I-V curves based on the FN model yields the barrier heights of PyTp-DNA complex and pure PyTp films. Electron transport studies of films of ionic disk-shaped liquid-crystal molecules and their complex with DNA are important from the point of view of their applications in organic electronics.

Preparation, spectroscopic and antibacterial studies on charge-transfer complexes of 2-hydroxypyridine with picric acid and 7,7‧,8,8‧-tetracyano-p-quinodimethane

NASA Astrophysics Data System (ADS)

Gaballa, Akmal S.; Amin, Alaa S.

2015-06-01

The reactions of electron acceptors such as picric acid (HPA) and 7,7‧,8,8‧-tetracyano-p-quinodimethane (TCNQ) with 2-hydroxypyridine (HPyO) have been investigated in EtOH at room temperature. Based on elemental analysis and IR spectra of the solid CT-complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge transfer complexes [(H2PyO)(PA)] and [(PyO)(HTCNQ)], respectively. The infrared and 1H NMR spectroscopic data indicate a charge transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding in [(H2PyO)(PA)] complex. Another charge transfer interaction was observed in [(PyO)(HTCNQ)] complex. The formation constants (KCT) for the CT-complexes are shown to be strongly dependent on the type and structure of the electron acceptors. Factors affecting the CT-processes and the kinetics of thermal decomposition of the complexes have been studied. The CT complexes were screened for their antibacterial activities against selected bacterial strains.

Preparation, spectroscopic and antibacterial studies on charge-transfer complexes of 2-hydroxypyridine with picric acid and 7,7',8,8'-tetracyano-p-quinodimethane.

PubMed

Gaballa, Akmal S; Amin, Alaa S

2015-06-15

The reactions of electron acceptors such as picric acid (HPA) and 7,7',8,8'-tetracyano-p-quinodimethane (TCNQ) with 2-hydroxypyridine (HPyO) have been investigated in EtOH at room temperature. Based on elemental analysis and IR spectra of the solid CT-complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge transfer complexes [(H2PyO)(PA)] and [(PyO)(HTCNQ)], respectively. The infrared and (1)H NMR spectroscopic data indicate a charge transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding in [(H2PyO)(PA)] complex. Another charge transfer interaction was observed in [(PyO)(HTCNQ)] complex. The formation constants (KCT) for the CT-complexes are shown to be strongly dependent on the type and structure of the electron acceptors. Factors affecting the CT-processes and the kinetics of thermal decomposition of the complexes have been studied. The CT complexes were screened for their antibacterial activities against selected bacterial strains. Copyright © 2015 Elsevier B.V. All rights reserved.

A comparative study of magnetization dynamics in dinuclear dysprosium complexes featuring bridging chloride or trifluoromethanesulfonate ligands.

PubMed

Burns, Corey P; Wilkins, Branford O; Dickie, Courtney M; Latendresse, Trevor P; Vernier, Larry; Vignesh, Kuduva R; Bhuvanesh, Nattamai S; Nippe, Michael

2017-07-25

We utilized a rigid ligand platform PyCp 2 2- (PyCp 2 2- = [2,6-(CH 2 C 5 H 3 ) 2 C 5 H 3 N] 2- ) to isolate dinuclear Dy 3+ complexes [(PyCp 2 )Dy-(μ-O 2 SOCF 3 )] 2 (1) and [(PyCp 2 )Dy-(μ-Cl)] 2 (3) as well as the mononuclear complex (PyCp 2 )Dy(OSO 2 CF 3 )(thf) (2). Compounds 1 and 2 are the first examples of organometallic Dy 3+ complexes featuring triflate binding. The isolation of compounds 1 and 3 allows us to comparatively evaluate the effects of the bridging anions on the magnetization dynamics of the dinuclear systems. Our investigations show that although the exchange coupling interactions differ for 1 and 3, the dynamic magnetic properties are dominated by relaxation via the first excited state Kramers doublet of the individual Dy sites. Compounds 1 and 3 exhibit barriers to magnetization reversal (U eff = 49 cm -1 ) that can be favorably compared to those of the previously reported examples of [Cp 2 Dy(μ-Cl)] 2 (U eff = 26 cm -1 ) and [Cp 2 Dy(thf)(μ-Cl)] 2 (U eff = 34 cm -1 ).

Exploiting the Reactivity of Actinide Fluoride Bonds for the Synthesis of a New Class of Bis(azide) Uranium Complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erickson, Karla A.; Lichtscheidl, Alejandro G.; Monreal, Marisa Jennifer

The terminal actinide fluoride bonds in (C 5Me 5) 2ThF 2(py) (py = pyridine) and (C 5Me 5) 2UF 2(O=PR 3) (R = Me, Ph) react with two equivalents of Me 3SiN 3 in toluene to form the polymeric thorium bis(azide), [(C 5Me 5) 2Th(N 3)2] ∞, and a new class of monometallic uranium bis(azide) complexes, (C 5Me 5) 2U(N 3)2(O=PR 3), respectively. Full characterization of the novel complexes (C 5Me 5) 2ThF 2(py) and (C 5Me 5) 2UF 2(O=PR 3) are reported, including the solid-state structures of (C 5Me 5) 2ThF 2(py) and (C 5Me 5) 2U(N 3) 2(O=PPhmore » 3). Lastly, electronic absorption spectral data are also reported for (C 5Me 5) 2AnF 2(py) (An = Th, U) and (C 5Me 5) 2U(N 3) 2(O=PR 3) to confirm metal oxidation state and enable elucidation of the fluoride and azide ligand bonding in these complexes.« less

Exploiting the Reactivity of Actinide Fluoride Bonds for the Synthesis of a New Class of Bis(azide) Uranium Complexes

DOE PAGES

Erickson, Karla A.; Lichtscheidl, Alejandro G.; Monreal, Marisa Jennifer; ...

2017-11-04

The terminal actinide fluoride bonds in (C 5Me 5) 2ThF 2(py) (py = pyridine) and (C 5Me 5) 2UF 2(O=PR 3) (R = Me, Ph) react with two equivalents of Me 3SiN 3 in toluene to form the polymeric thorium bis(azide), [(C 5Me 5) 2Th(N 3)2] ∞, and a new class of monometallic uranium bis(azide) complexes, (C 5Me 5) 2U(N 3)2(O=PR 3), respectively. Full characterization of the novel complexes (C 5Me 5) 2ThF 2(py) and (C 5Me 5) 2UF 2(O=PR 3) are reported, including the solid-state structures of (C 5Me 5) 2ThF 2(py) and (C 5Me 5) 2U(N 3) 2(O=PPhmore » 3). Lastly, electronic absorption spectral data are also reported for (C 5Me 5) 2AnF 2(py) (An = Th, U) and (C 5Me 5) 2U(N 3) 2(O=PR 3) to confirm metal oxidation state and enable elucidation of the fluoride and azide ligand bonding in these complexes.« less

Urinary oxytocin in capuchin monkeys: Validation and the influence of social behavior.

PubMed

Benítez, Marcela E; Sosnowski, Meghan J; Tomeo, Olivia B; Brosnan, Sarah F

2018-05-24

In highly social species, like primates, oxytocin plays an important role in cooperation, and in the formation and maintenance of social relationships. Despite recent interest in the relationship between oxytocin and social behavior in nonhuman primates, relatively little is known about endogenous oxytocin in social New World Monkeys. In this paper, we investigate the relationship between oxytocin and affiliative behaviors in socially-housed captive capuchin monkeys (Sapajus [Cebus] apella) by first validating methods of analysis of urinary oxytocin in this species and, second, examining the effects of grooming and fur-rubbing behavior on oxytocin concentrations and further affiliative behavior. In the validation, we found that intranasal exogenous oxytocin significantly increased urinary oxytocin 15-60 min post-administration. Oxytocin was also implicated in both grooming and fur-rubbing behaviors. We found that oxytocin concentrations increased after subjects engaged in grooming or fur-rubbing. In addition, we found that fur-rubbing influenced affiliative behaviors, both during and after a social fur-rubbing bout. While individuals spent more time in contact and proximity while fur-rubbing, immediately following the fur-rubbing event (15-30 min afterwards) all affiliative behaviors decreased. This supports previous research that oxytocin may, in fact, initially be related to increased social distance in this species. Yet, an increase in all affiliative behaviors 30-45 min after the onset of fur-rubbing suggests that fur-rubbing, like grooming, may ultimately function to strengthen social relationships. Overall, these results support a critical role for oxytocin in affiliative behaviors that maintain and strengthen social relationships in capuchin monkeys, and highlight the complexity of the interactions among oxytocin, affiliative behaviors, and social bonding. © 2018 Wiley Periodicals, Inc.

Mono- and Dinuclear Manganese Carbonyls Supported by 1,8-Disubstituted (L = Py, SMe, SH) Anthracene Ligand Scaffolds.

PubMed

Manes, Taylor A; Rose, Michael J

2016-06-06

Presented herein is a synthetic scheme to generate symmetric and asymmetric ligands based on a 1,8-disubstituted anthracene scaffold. The metal-binding scaffolds were prepared by aryl chloride activation of 1,8-dichloroanthracene using Suzuki-type couplings facilitated by [Pd(dba)2] as a Pd source; the choice of cocatalyst (XPhos or SPhos) yielded symmetrically or asymmetrically substituted scaffolds (respectively): namely, Anth-SMe2 (3), Anth-N2 (4), and Anth-NSMe (6). The ligands exhibit a nonplanar geometry in the solid state (X-ray), owing to steric hindrance between the anthracene scaffold and the coupled aryl units. To determine the flexibility and binding characteristics of the anthracene-based ligands, the symmetric scaffolds were complexed with [Mn(CO)5Br] to afford the mononuclear species [(Anth-SMe2)Mn(CO)3Br] (8) and [(Anth-N2)Mn(CO)3Br] (9), in which the donor moieties chelate the Mn center in a cis fashion. The asymmetric ligand Anth-NSMe (6) binds preferentially through the py moieties, affording the bis-ligated complex [(Anth-NSMe)2Mn(CO)3Br] (10), wherein the thioether-S donors remain unbound. Alternatively, deprotection of the thioether in 6 affords the free thiol ligand Anth-NSH (7), which more readily binds the Mn center. Complexation of 7 ultimately affords the mixed-valence Mn(I)/Mn(II) dimer of formula [(Anth-NS)3Mn2(CO)3] (11), which exhibits a fac-{Mn(CO)3} unit supported by a triad of bridging thiolates, which are in turn ligated to a supporting Mn(II) center (EPR: |D| = 0.053 cm(-1), E/|D| = 0.3, Aiso = -150 MHz). All of the metal complexes have been characterized by single-crystal X-ray diffraction, IR spectroscopy and NMR/EPR measurements-all of which demonstrate that the meta-linked, anthracene-based ligand scaffold is a viable approach for the coordination of metal carbonyls.

Effect of deuteration on hydrogen bonding: A comparative concentration dependent Raman and DFT study of pyridine in CH3OH and CD3OD and pyrimidine in H2O and D2O

NASA Astrophysics Data System (ADS)

Singh, Anurag; Gangopadhyay, Debraj; Popp, Jürgen; Singh, Ranjan K.

2012-12-01

The relative effect of hydrogen bonding of pyrimidine (Pyr) in H2O/D2O and pyridine (Py) in CH3OH/CD3OD has been analyzed using Raman Difference Spectroscopic (RDS) technique and DFT calculations. This study is focused on analyzing the concentration dependent variation of linewidth, peak position and intensity of ring breathing mode of Py and Pyr. The ring breathing mode of Pyr in H2O and D2O has three components; due to free Pyr, lighter complexes of mPyr + nH2O/D2O and heavier complexes of mPyr + nH2O/D2O. The pyridine molecules, however, show only two components in CH3OH and CD3OD. Of these two components, one corresponds to free Py and the other inhomogeneously broadened profile corresponds to all mPy + nCH3OH/CD3OD complexes. The variation of peak position and linewidth establishes the role of dipole moment of complexes and the diffusion in the mixture. In case of CD3OD solution splitting was observed in ˜1030 cm-1 band of Py, where an additional band at ˜1034 cm-1 appears at x(Py) ⩽ 0.4. However, this band remains single at all concentrations in case of CH3OH solvent.

Coordination Chemistry of a Strongly-Donating Hydroxylamine with Early Actinides: An Investigation of Redox Properties and Electronic Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

McSkimming, Alex; Su, Jing; Cheisson, Thibault

Separations of f-block elements are a critical aspect of nuclear waste processing. Redox-based separations offer promise, but challenges remain in stabilizing and differentiating actinides in high oxidation states. The investigation of new ligand types that provide thermodynamic stabilization to high-valent actinides is essential for expanding their fundamental chemistry and to elaborate new separation techniques and storage methods. We report herein the preparation and characterization of Th and U complexes of the pyridyl-hydroxylamine ligand, N-tert-butyl-N-(pyridin-2-yl)hydroxylamine (pyNO–). Electrochemical studies performed on the homoleptic complexes [M(pyNO) 4] (M = Th, U) revealed significant stabilization of the U complex upon one-electron oxidation. The saltmore » [U(pyNO) 4] + was isolated by chemical oxidation of [U(pyNO) 4]; spectroscopic and computational data support assignment as a U V cation.« less

Coordination Chemistry of a Strongly-Donating Hydroxylamine with Early Actinides: An Investigation of Redox Properties and Electronic Structure

DOE PAGES

McSkimming, Alex; Su, Jing; Cheisson, Thibault; ...

2018-03-23

Separations of f-block elements are a critical aspect of nuclear waste processing. Redox-based separations offer promise, but challenges remain in stabilizing and differentiating actinides in high oxidation states. The investigation of new ligand types that provide thermodynamic stabilization to high-valent actinides is essential for expanding their fundamental chemistry and to elaborate new separation techniques and storage methods. We report herein the preparation and characterization of Th and U complexes of the pyridyl-hydroxylamine ligand, N-tert-butyl-N-(pyridin-2-yl)hydroxylamine (pyNO–). Electrochemical studies performed on the homoleptic complexes [M(pyNO) 4] (M = Th, U) revealed significant stabilization of the U complex upon one-electron oxidation. The saltmore » [U(pyNO) 4] + was isolated by chemical oxidation of [U(pyNO) 4]; spectroscopic and computational data support assignment as a U V cation.« less

uPy: a ubiquitous computer graphics Python API with Biological Modeling Applications

PubMed Central

Autin, L.; Johnson, G.; Hake, J.; Olson, A.; Sanner, M.

2015-01-01

In this paper we describe uPy, an extension module for the Python programming language that provides a uniform abstraction of the APIs of several 3D computer graphics programs called hosts, including: Blender, Maya, Cinema4D, and DejaVu. A plugin written with uPy is a unique piece of code that will run in all uPy-supported hosts. We demonstrate the creation of complex plug-ins for molecular/cellular modeling and visualization and discuss how uPy can more generally simplify programming for many types of projects (not solely science applications) intended for multi-host distribution. uPy is available at http://upy.scripps.edu PMID:24806987

On the tradeoffs of programming language choice for numerical modelling in geoscience. A case study comparing modern Fortran, C++/Blitz++ and Python/NumPy.

NASA Astrophysics Data System (ADS)

Jarecka, D.; Arabas, S.; Fijalkowski, M.; Gaynor, A.

2012-04-01

The language of choice for numerical modelling in geoscience has long been Fortran. A choice of a particular language and coding paradigm comes with different set of tradeoffs such as that between performance, ease of use (and ease of abuse), code clarity, maintainability and reusability, availability of open source compilers, debugging tools, adequate external libraries and parallelisation mechanisms. The availability of trained personnel and the scale and activeness of the developer community is of importance as well. We present a short comparison study aimed at identification and quantification of these tradeoffs for a particular example of an object oriented implementation of a parallel 2D-advection-equation solver in Python/NumPy, C++/Blitz++ and modern Fortran. The main angles of comparison will be complexity of implementation, performance of various compilers or interpreters and characterisation of the "added value" gained by a particular choice of the language. The choice of the numerical problem is dictated by the aim to make the comparison useful and meaningful to geoscientists. Python is chosen as a language that traditionally is associated with ease of use, elegant syntax but limited performance. C++ is chosen for its traditional association with high performance but even higher complexity and syntax obscurity. Fortran is included in the comparison for its widespread use in geoscience often attributed to its performance. We confront the validity of these traditional views. We point out how the usability of a particular language in geoscience depends on the characteristics of the language itself and the availability of pre-existing software libraries (e.g. NumPy, SciPy, PyNGL, PyNIO, MPI4Py for Python and Blitz++, Boost.Units, Boost.MPI for C++). Having in mind the limited complexity of the considered numerical problem, we present a tentative comparison of performance of the three implementations with different open source compilers including CPython and PyPy, Clang++ and GNU g++, and GNU gfortran.

Temperature and pressure variations of d-d luminescence band maxima of bis(pyridylalkenolato)palladium(II) complexes with different ligand substituents: opposite-signed trends.

PubMed

Poirier, Stéphanie; Czympiel, Lisa; Bélanger-Desmarais, Nicolas; Mathur, Sanjay; Reber, Christian

2016-04-21

Luminescence spectra of two d(8)-configured bis(pyridylalkenolato)palladium(ii) complexes, [Pd{PyCHC(C3F7)O}2] and [Pd{PyCHC(CH3)O}2], are presented at variable temperature and pressure. Bands are assigned as d-d transitions. The heptafluoropropyl and methyl substituents on the ligands have different steric demands, influencing luminescence spectra. Broad bands with maxima at approximately 12 700 cm(-1) (790 nm) for ligands with heptafluoropropyl substituents and 12,100 cm(-1) (830 nm) for ligands with methyl substituents and widths of approximately 2100 cm(-1) for both complexes are observed at 80 K. Quenching of the luminescence is observed as temperature increases. The maxima of [Pd{PyCHC(C3F7)O}2] show a shift of -0.9 ± 0.1 cm(-1) K(-1) due to broadening of the spectra to lower energy. The luminescence maxima of [Pd{PyCHC(CH3)O}2] shift in the opposite direction by +7.2 ± 0.7 cm(-1) K(-1). Shifts with different signs are also obtained from variable-pressure luminescence spectra, with values of +13 ± 2 cm(-1) kbar(-1) and -15 ± 7 cm(-1) kbar(-1) for [Pd{PyCHC(C3F7)O}2] and [Pd{PyCHC(CH3)O}2], respectively. The pressure-induced decrease is unusual and likely caused by intermolecular interactions involving the palladium(ii) center and a vinylic proton of a neighboring complex.

Self-assembly of five 8-hydroxyquinolinate-based complexes: tunable core, supramolecular structure, and photoluminescence properties.

PubMed

Yuan, Guozan; Shan, Weilong; Qiao, Xuelong; Ma, Li; Huo, Yanping

2014-07-01

Five new Zn(II) complexes, namely [Zn(3)(L)(6)] (1), [Zn(2)(Cl)(2)(L)(2) (py)(2)] (2), [Zn(2)(Br)(2) (L)(2)(py)(2)] (3), [Zn(L)(2)(py)] (4), and [Zn(2)(OAc)(2)(L)(2)(py)(2)] (5), were prepared by the solvothermal reaction of ZnX(2) (X(-) =Cl(-), Br(-), F(-), and OAc(-)) salts with a 8-hydroxyquinolinate ligand (HL) that contained a trifluorophenyl group. All of the complexes were characterized by elemental analysis, IR spectroscopy, and powder and single-crystal X-ray crystallography. The building blocks exhibited unprecedented structural diversification and their self-assembly afforded one mononuclear, three binuclear, and one trinuclear Zn(II) structures in response to different anions and solvent systems. Complexes 1-5 featured four types of supramolecular network controlled by non-covalent interactions, such as π⋅⋅⋅π-stacking, C-H⋅⋅⋅π, hydrogen-bonding, and halogen-related interactions. Investigation of their photoluminescence properties exhibited disparate emission wavelengths, lifetimes, and quantum yields in the solid state. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification and characterization of ten new water gaps in seeds and fruits with physical dormancy and classification of water-gap complexes.

PubMed

Gama-Arachchige, N S; Baskin, J M; Geneve, R L; Baskin, C C

2013-07-01

Physical dormancy (PY) occurs in seeds or fruits of 18 angiosperm families and is caused by a water-impermeable palisade cell layer(s) in seed or fruit coats. Prior to germination, the seed or fruit coat of species with PY must become permeable in order to imbibe water. Breaking of PY involves formation of a small opening(s) (water gap) in a morpho-anatomically specialized area in seeds or fruits known as the water-gap complex. Twelve different water-gap regions in seven families have previously been characterized. However, the water-gap regions had not been characterized in Cucurbitaceae; clade Cladrastis of Fabaceae; subfamilies Bombacoideae, Brownlowioideae and Bythnerioideae of Malvaceae; Nelumbonaceae; subfamily Sapindoideae of Sapindaceae; Rhamnaceae; or Surianaceae. The primary aims of this study were to identify and describe the water gaps of these taxa and to classify all the known water-gap regions based on their morpho-anatomical features. Physical dormancy in 15 species was broken by exposing seeds or fruits to wet or dry heat under laboratory conditions. Water-gap regions of fruits and seeds were identified and characterized by use of microtome sectioning, light microscopy, scanning electron microscopy, dye tracking and blocking experiments. Ten new water-gap regions were identified in seven different families, and two previously hypothesized regions were confirmed. Water-gap complexes consist of (1) an opening that forms after PY is broken; (2) a specialized structure that occludes the gap; and (3) associated specialized tissues. In some species, more than one opening is involved in the initial imbibition of water. Based on morpho-anatomical features, three basic water-gap complexes (Types-I, -II and -III) were identified in species with PY in 16 families. Depending on the number of openings involved in initial imbibition, the water-gap complexes were sub-divided into simple and compound. The proposed classification system enables understanding of the relationships between the water-gap complexes of taxonomically unrelated species with PY.

Oxygen Atom Exchange between H2O and Non-Heme Oxoiron(IV) Complexes: Ligand Dependence and Mechanism.

PubMed

Puri, Mayank; Company, Anna; Sabenya, Gerard; Costas, Miquel; Que, Lawrence

2016-06-20

Detailed studies of oxygen atom exchange (OAE) between H2(18)O and synthetic non-heme oxoiron(IV) complexes supported by tetradentate and pentadentate ligands provide evidence that they proceed by a common mechanism but within two different kinetic regimes, with OAE rates that span 2 orders of magnitude. The first kinetic regime involves initial reversible water association to the Fe(IV) complex, which is evidenced by OAE rates that are linearly dependent on [H2(18)O] and H2O/D2O KIEs of 1.6, while the second kinetic regime involves a subsequent rate determining proton-transfer step between the bound aqua and oxo ligands that is associated with saturation behavior with [H2(18)O] and much larger H2O/D2O KIEs of 5-6. [Fe(IV)(O)(TMC)(MeCN)](2+) (1) and [Fe(IV)(O)(MePy2TACN)](2+) (9) are examples of complexes that exhibit kinetic behavior in the first regime, while [Fe(IV)(O)(N4Py)](2+) (3), [Fe(IV)(O)(BnTPEN)](2+) (4), [Fe(IV)(O)(1Py-BnTPEN)](2+) (5), [Fe(IV)(O)(3Py-BnTPEN)](2+) (6), and [Fe(IV)(O)(Me2Py2TACN)](2+) (8) represent complexes that fall in the second kinetic regime. Interestingly, [Fe(IV)(O)(PyTACN)(MeCN)](2+) (7) exhibits a linear [H2(18)O] dependence below 0.6 M and saturation above 0.6 M. Analysis of the temperature dependence of the OAE rates shows that most of these complexes exhibit large and negative activation entropies, consistent with the proposed mechanism. One exception is complex 9, which has a near-zero activation entropy and is proposed to undergo ligand-arm dissociation during the RDS to accommodate H2(18)O binding. These results show that the observed OAE kinetic behavior is highly dependent on the nature of the supporting ligand and are of relevance to studies of non-heme oxoiron(IV) complexes in water or acetonitrile/water mixtures for applications in photocatalysis and water oxidation chemistry.

Thermodynamic Stability of Heterodimetallic [LnLn'] Complexes: Synthesis and DFT Studies

DOE PAGES

Gonzalez-Fabra, Joan; Bandeira, Nuno A. G.; Velasco, Veronica; ...

2017-03-27

The solid-state and solution configurations of the heterodimetallic complexes (Hpy)[LaEr(HL) 3(NO 3)(py)(H 2O)] (1), (Hpy)[CeEr(HL) 3(NO 3)(py)(H 2O)] (2), (Hpy)[CeGd(HL) 3(NO 3)(py)(H 2O)] (3), (Hpy)[PrSm(HL) 3(NO 3)(py)(H 2O)] (4), and (Hpy) 2[LaYb(HL) 3(NO 3)(H 2O)](NO 3) (5), in which H 3L is 6-(3-oxo-3-(2-hydroxyphenyl)propionyl)pyridine-2-carboxylic acid and py is pyridine, were analyzed experimentally and by using DFT calculations. Complexes 3, 4, and 5 are described here for the first time, and were analyzed by using single-crystal X-ray diffraction and mass spectrometry. The theoretical study was also extended to the [LaCe] and [LaLu] analogues. The results are consistent with a remarkable selectivity ofmore » the metal distribution within the molecule in the solid state, enhanced by the size difference between the different ions. This selectivity was reduced in solution, particularly for ions with the most similar radii. This unique entry into 4f–4f" heterometallic chemistry establishes for the first time the difference between the selectivity in solution and that in the solid state, as a result of changes to the coordination that follow the dissociation of terminal ligands upon dissolution of the complexes.« less

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.

PubMed

Dong, Jie; Yao, Zhi-Jiang; Zhang, Lin; Luo, Feijun; Lin, Qinlu; Lu, Ai-Ping; Chen, Alex F; Cao, Dong-Sheng

2018-03-20

With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important. So far, there are no suitable toolkits that can effectively link the chemical and biological space in view of molecular representation. To further explore these complex data, an integrated toolkit for various molecular representation is urgently needed which could be easily integrated with data mining algorithms to start a full data analysis pipeline. Herein, the python library PyBioMed is presented, which comprises functionalities for online download for various molecular objects by providing different IDs, the pretreatment of molecular structures, the computation of various molecular descriptors for chemicals, proteins, DNAs and their interactions. PyBioMed is a feature-rich and highly customized python library used for the characterization of various complex chemical and biological molecules and interaction samples. The current version of PyBioMed could calculate 775 chemical descriptors and 19 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA descriptors from nucleotide sequences, and interaction descriptors from pairwise samples using three different combining strategies. Several examples and five real-life applications were provided to clearly guide the users how to use PyBioMed as an integral part of data analysis projects. By using PyBioMed, users are able to start a full pipelining from getting molecular data, pretreating molecules, molecular representation to constructing machine learning models conveniently. PyBioMed provides various user-friendly and highly customized APIs to calculate various features of biological molecules and complex interaction samples conveniently, which aims at building integrated analysis pipelines from data acquisition, data checking, and descriptor calculation to modeling. PyBioMed is freely available at http://projects.scbdd.com/pybiomed.html .

Stereochemical and electronic control of M-SO/sub 2/ bonding geometry in d/sup 6/ molybdenum and tungsten SO/sub 2/ complexes: novel n/sup 1/reverse arrown/sup 2/ SO/sub 2/ linkage isomerization in Mo(CO)/sub 2/(PPh/sub 3/)/sub 2/(CNR)(SO/sub 2/) and structures of Mo(CO)/sub 3/(P-i-Pr/sub 3/)/sub 2/(SO/sub 2/) and (Mo(CO)/sub 2/(py)(PPh/sub 3/)(. mu. -SO/sub 2/))/sub 2/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kubas, G.J.; Jarvinen, G.D.; Ryan, R.R.

1983-04-06

New complexes, mer,trans,M(CO)/sub 3/(PR/sub 3/)/sub 2/(SO/sub 2/) (M = Mo,W; R = Ph,Cy,i-Pr) (I), cis,trans-Mo(CO)/sub 2/-(PPh/sub 3/)/sub 2/(SO/sub 2/)(L) (L = NCMe,py,CNCy,CN-t-Bu and CN(p-tolyl))(II), and (Mo(CO)/sub 2/(py)(PPh/sub 3/)(..mu..-SO/sub 2/))/sub 2/, have been prepared and characterized by infrared spectroscopy, /sup 17/O and /sup 31/P NMR spectroscopy, and X-ray crystallography. Syntheses for fac-Mo(CO)/sub 3/(n/sup 2/-SO/sub 2/)(LL) (LL = dppe,bpy,phen,2 py) have also been developed. Depending upon L, II has been found to coordinate SO/sub 2/ either in the S-bonded (n/sup 1/ planar) or O,S-bonded (n/sup 2/) geometries. Remarkably, for L = CNCy or CN-t-Bu, II has been found to contain, in themore » solid state, an apparent equimixture of both coordination types. Isomerization of fac-M(CO)/sub 3/(dppe)(n/sup 2/-SO/sub 2/) (M=Mo,w; dppe = 1,2-bis(diphenylphosphino)ethane) to an n/sup 1/-planar SO/sub 2/ form, mer-M(CO)/sub 3/(dppe)(SO/sub 2/), has also been found to occur. Thus, control of the SO/sub 2/ coordination geometry has been achieved by varying either the electronic properties of the ancillary ligands or their disposition with respect to the SO/sub 2/. The X-ray crystal structure of mer,trans-Mo(CO)/sub 3/(P-i-Pr/sub 3/)/sub 2/(SO/sub 2/) revealed n/sup 1/-planar SO/sub 2/ binding, the first example of this geometry for group 6 metals. The M-S distance, 2.239 (3) angstrom, is the longest such distance for this geometry recorded to date. Crystal data: Pbca, Z=8, a=24.712(8) angstrom, b=16.033(6) angstrom, c=14.058(5) angstrom, R=0.079 for 2934 reflections with Igreater than or equal to2sigma(I). The structure of (Mo(CO)/sub 2/(py)(PPh/sub 3/)(..mu..-SO/sub 2/))/sub 2/ showed a novel SO/sub 2/ bridging geometry in which all three atoms of SO/sub 2/ are metal coordinated. Crystal data: P1, Z=1, a=14.883(4) angstrom, b=9.264(2) angstrom, c=10.808(2) angstrom, R=0.039 for 3282 reflections with Igreater than or equal to2sigma(I).« less

Preparation of anticoagulant PyC biomaterials with super-hydrophobic surface.

PubMed

Ze, Wang; Wen-Sheng, Tan; Ye-Xia; Ming, Zhang; Xiao-Ping, Li; Jian-Guo, Qiu; Xiao-Hong, Yang

2018-01-01

Pyrolytic carbon (PyC) is a kind of biomaterial which is chemically inert and has excellent biocompatibility. In order to obtain a super-hydrophobic PyC surface to improve anticoagulation and inhibit thrombus, this study prepares grating pair structure, microhole array structure, helix structure on PyC surface by nanoseconds laser etching. Rod-like ZnO film and ball-like ZnO film are prepared on the PyC surface by the hydrothermal method; polyvinyl pyrrolidone (PVP) nanofiber film and PVP/TiO 2 complex nanofiber film are prepared on the PyC surface by the electrospinning method; the PyC surface is silanized. Finally, surface microstructure and surface energy are characterized by scanning electron microscopy and contact angle meter (OCA20, German DataPhysics Co.). The periodical microstructures are formed respectively by nanoseconds laser etching. The surface roughness is increased by the hydrothermal and electrospinning method. Through infiltration experiment on rough and smooth PyC surfaces, rough PyC surface with microstructure is super-hydrophobic and has greater than 150° contact angle, which decreases blood flow resistance and inhibits thrombus.

Pyrrolidine dithiocarbamate-zinc(II) and -copper(II) complexes induce apoptosis in tumor cells by inhibiting the proteasomal activity☆

PubMed Central

Milacic, Vesna; Chen, Di; Giovagnini, Lorena; Diez, Alejandro; Fregona, Dolores; Dou, Q. Ping

2013-01-01

Zinc and copper are trace elements essential for proper folding, stabilization and catalytic activity of many metalloenzymes in living organisms. However, disturbed zinc and copper homeostasis is reported in many types of cancer. We have previously demonstrated that copper complexes induced proteasome inhibition and apoptosis in cultured human cancer cells. In the current study we hypothesized that zinc complexes could also inhibit the proteasomal chymotrypsin-like activity responsible for subsequent apoptosis induction. We first showed that zinc(II) chloride was able to inhibit the chymotrypsin-like activity of a purified 20S proteasome with an IC50 value of 13.8 μM, which was less potent than copper(II) chloride (IC50 5.3 μM). We then compared the potencies of a pyrrolidine dithiocarbamate (PyDT)-zinc(II) complex and a PyDT-copper(II) complex to inhibit cellular proteasomal activity, suppress proliferation and induce apoptosis in various human breast and prostate cancer cell lines. Consistently, zinc complex was less potent than copper complex in inhibiting the proteasome and inducing apoptosis. Additionally, zinc and copper complexes appear to use somewhat different mechanisms to kill tumor cells. Zinc complexes were able to activate calpain-, but not caspase-3-dependent pathway, while copper complexes were able to induce activation of both proteases. Furthermore, the potencies of these PyDT-metal complexes depend on the nature of metals and also on the ratio of PyDT to the metal ion within the complex, which probably affects their stability and availability for interacting with and inhibiting the proteasome in tumor cells. PMID:18501397

Copper-containing monooxygenases: enzymatic and biomimetic studies of the O-atom transfer catalysis.

PubMed

Blain, Ingrid; Slama, Patrick; Giorgi, Michel; Tron, Thierry; Réglier, Marius

2002-04-01

This review reports our recent studies or the mechanism of O-atom transfer to a benzylic C-H bond promoted by Dopamine beta-Hydroxylase (DBH) and its biomimetic models. We demonstrate that it is possible to carry out parallel and comparative studies on this enzyme (DBH) and its biomimetic models with the same substrate: 2-aminoindane (3). It was chosen because its two stereogenic centers, both in benzylic positions, make it very powerful for studying the stereochemistry of an O-atom transfer reaction. DBH-catalyzed hydroxylation of 3 produced exclusively 14% of trans-(1S,2S)-2-amino-1-indanol (4) (93% ee). Studies with stereospecifically deuterium-labeled 2-aminoindanes (1R,2S)-3b and (1S,2S)-3a showed that the formation of 4 was the rcsult of an overall process with retention of configuration where an O-atom is stereospecifically inserted in the trans pro-S position of the substrate. With copper(I) and (II) complexes of IndPY2 ligands we studied the reaction with dioxygen and observed an O-atom transfer to a benzylic C-H bond which was performed in the same manner as that of DBH. With the deuterium-labeled cis-2-d-IndPY2 ligand, we demonstrated that the reaction occurs by a stereospecific process with retention of configuration. In both cases (enzymatic vs. biomimetic) the O-atom transfers occur in a two-step process involving radical intermediates.

Ligand effects on the ferro- to antiferromagnetic exchange ratio in bis(o-semiquinonato)copper(II).

PubMed

Ovcharenko, Victor I; Gorelik, Elena V; Fokin, Sergey V; Romanenko, Galina V; Ikorskii, Vladimir N; Krashilina, Anna V; Cherkasov, Vladimir K; Abakumov, Gleb A

2007-08-29

Heterospin complexes [Cu(SQ)2Py].C7H8, Cu(SQ)2DABCO, and [Cu(SQ)2NIT-mPy].C6H6, where Cu(SQ)2 is bis(3,6-di-tert-butyl-o-benzosemiquinonato)copper(II), DABCO is 1,4-diazabicyclo(2,2,2)octane, and NIT-mPy is the nitronyl nitroxide 2-(pyridin-3-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl, have been synthesized. The molecules of these complexes have a specific combination of the intramolecular ferro- and antiferromagnetic exchange interactions between the odd electrons of Cu(II) and SQ ligands, characterized by large exchange coupling parameters |J| approximately 100-300 cm(-1). X-ray and magnetochemical studies of a series of mixed-ligand compounds revealed that an extra ligand (Py, NIT-mPy, or DABCO) coordinated to the metal atom produces a dramatic effect on the magnetic properties of the complex, changing the multiplicity of the ground state. Quantum chemical analysis of magnetostructural correlations showed that the energy of the antiferromagnetic exchange interaction between the odd electrons of the SQ ligands in the Cu(SQ)2 bischelate is extremely sensitive to both the nature of the extra ligand and structural distortions of the coordination unit, arising from extra ligand coordination.

Amino Acids 257 to 288 of Mouse p48 Control the Cooperation of Polyomavirus Large T Antigen, Replication Protein A, and DNA Polymerase α-Primase To Synthesize DNA In Vitro

PubMed Central

Kautz, Armin R.; Weisshart, Klaus; Schneider, Annerose; Grosse, Frank; Nasheuer, Heinz-Peter

2001-01-01

Although p48 is the most conserved subunit of mammalian DNA polymerase α-primase (pol-prim), the polypeptide is the major species-specific factor for mouse polyomavirus (PyV) DNA replication. Human and murine p48 contain two regions (A and B) that show significantly lower homology than the rest of the protein. Chimerical human-murine p48 was prepared and coexpressed with three wild-type subunits of pol-prim, and four subunit protein complexes were purified. All enzyme complexes synthesized DNA on single-stranded (ss) DNA and replicated simian virus 40 DNA. Although the recombinant protein complexes physically interacted with PyV T antigen (Tag), we determined that the murine region A mediates the species specificity of PyV DNA replication in vitro. More precisely, the nonconserved phenylalanine 262 of mouse p48 is crucial for this activity, and pol-prim with mutant p48, h-S262F, supports PyV DNA replication in vitro. DNA synthesis on RPA-bound ssDNA revealed that amino acid (aa) 262, aa 266, and aa 273 to 288 are involved in the functional cooperation of RPA, pol-prim, and PyV Tag. PMID:11507202

Heterobimetallic Nitrido Complexes of Group 8 Metalloporphyrins.

PubMed

Cheung, Wai-Man; Chiu, Wai-Hang; de Vere-Tucker, Matthew; Sung, Herman H-Y; Williams, Ian D; Leung, Wa-Hung

2017-05-15

Heterobimetallic nitrido porphyrin complexes with the [(L)(por)M-N-M'(L OEt )Cl 2 ] formula {por 2- = 5,10,15,20-tetraphenylporphyrin (TPP 2- ) or 5,10,15,20-tetra(p-tolyl)porphyrin (TTP 2- ) dianion; L OEt - = [Co(η 5 -C 5 H 5 ){P(O)(OEt) 2 } 3 ] - ; M = Fe, Ru, or Os; M' = Ru or Os; L = H 2 O or pyridine} have been synthesized, and their electrochemistry has been studied. Treatment of trans-[Fe(TPP)(py) 2 ] (py = pyridine) with Ru(VI) nitride [Ru(L OEt )(N)Cl 2 ] (1) afforded Fe/Ru μ-nitrido complex [(py)(TPP)Fe(μ-N)Ru(L OEt )Cl 2 ] (2). Similarly, Fe/Os analogue [(py)(TPP)Fe(μ-N)Os(L OEt )Cl 2 ] (3) was obtained from trans-[Fe(TPP)(py) 2 ] and [Os(L OEt )(N)Cl 2 ]. However, no reaction was found between trans-[Fe(TPP)(py) 2 ] and [Re(L OEt )(N)Cl(PPh 3 )]. Treatment of trans-[M(TPP)(CO)(EtOH)] with 1 afforded μ-nitrido complexes [(H 2 O)(TPP)M(μ-N)Ru(L OEt )Cl 2 ] [M = Ru (4a) or Os (5)]. TTP analogue [(H 2 O)(TTP)Ru(μ-N)Ru(L OEt )Cl 2 ] (4b) was prepared similarly from trans-[Ru(TTP)(CO)(EtOH)] and 1. Reaction of [(H 2 O)(por)M(μ-N)M(L OEt )Cl 2 ] with pyridine gave adducts [(py)(por)M(μ-N)Ru(L OEt )Cl 2 ] [por = TTP, and M = Ru (6); por = TPP, and M = Os (7)]. The diamagnetism and short (por)M-N(nitride) distances in 2 [Fe-N, 1.683(3) Å] and 4b [Ru-N, 1.743(3) Å] are indicative of the M IV ═N═M' IV bonding description. The cyclic voltammograms of the Fe/Ru (2) and Ru/Ru (4b) complexes in CH 2 Cl 2 displayed oxidation couples at approximately +0.29 and +0.35 V versus Fc +/0 (Fc = ferrocene) that are tentatively ascribed to the oxidation of the {L OEt Ru} and {Ru(TTP)} moieties, respectively, whereas the Fe/Os (3) and Os/Ru (5) complexes exhibited Os-centered oxidation at approximately -0.06 and +0.05 V versus Fc +/0 , respectively. The crystal structures of 2 and 4b have been determined.

Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.

PubMed

Chen, Jia-Liang; Zhao, Yu; Gong, Yan-Jun; Pan, Bin-Bin; Wang, Xiao; Su, Xun-Cheng

2018-02-01

Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.

Crystal structure of fac-tri-carbonyl-chlorido-bis-(4-hy-droxy-pyridine)-rhenium(I)-pyridin-4(1H)-one (1/1).

PubMed

Argibay-Otero, Saray; Carballo, Rosa; Vázquez-López, Ezequiel M

2017-10-01

The asymmetric unit of the title compound, [ReCl(C 5 H 5 NO) 2 (CO) 3 ]·C 5 H 5 NO, contains one mol-ecule of the complex fac -[ReCl(4-pyOH) 2 (CO) 3 ] (where 4-pyOH represents 4-hy-droxy-pyridine) and one mol-ecule of pyridin-4(1 H )-one (4-HpyO). In the mol-ecule of the complex, the Re atom is coordinated to two N atoms of the two 4-pyOH ligands, three carbonyl C atoms, in a facial configuration, and the Cl atom. The resulting geometry is slightly distorted octa-hedral. In the crystal structure, both fragments are associated by hydrogen bonds; two 4-HpyO mol-ecules bridge between two mol-ecules of the complex using the O=C group as acceptor for two different HO- groups of coordinated 4-pyOH from two neighbouring metal complexes. The resulting square arrangements are extented into infinite chains by hydrogen bonds involving the N-H groups of the 4-HpyO mol-ecule and the chloride ligands. The chains are further stabilized by π-stacking inter-actions.

New RuII Complex for Dual Activity: Photoinduced Ligand Release and 1O2 Production

PubMed Central

Loftus, Lauren M.; White, Jessica K.; Albani, Bryan A.; Kohler, Lars; Kodanko, Jeremy J.; Thummel, Randolph P.

2016-01-01

The new complex [Ru(pydppn)(biq)(py)]2+ (1) undergoes both py photodissociation in CH3CN with Φ500=0.0070(4) and 1O2 production with ΦΔ=0.75(7) in CH3OH from a long-lived 3ππ* state centered on the pydppn ligand (pydppn=3-(pyrid-2-yl)benzo[i]dipyrido[3,2-a:2′,3′-c]phenazine; biq = 2,2′-biquinoline; py= pyridine). This represents an order of magnitude decrease in the Φ500 compared to the previously reported model compound [Ru(tpy)(biq)(py)]2+ (3) (tpy=2,2′:6′,2″-terpyridine) that undergoes only ligand exchange. The effect on the quantum yields by the addition of a second deactivation pathway through the low-lying 3ππ* state necessary for dual reactivity was investigated using ultrafast and nanosecond transient absorption spectroscopy, revealing a significantly shorter 3MLCT lifetime in 1 relative to that of the model complex 3. Due to the structural similarities between the two compounds, the lower values of Φ500 and ΦΔ compared to that of [Ru(pydppn)(bpy)(py)]2+ (2) (bpy=2,2′-bipyridine) are attributed to a competitive excited state population between the 3LF states involved in ligand dissociation and the long-lived 3ππ* state in 1. Complex 1 represents a model compound for dual activity that may be applied to photochemotherapy. PMID:26715085

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tondreau, Aaron M.; Scott, Brian L.; Boncella, James M.

We explored ligand-induced reduction of ferrous alkyl complexes via homolytic cleavage of the alkyl fragment with simple chelating diphosphines. The reactivities of the sodium salts of diphenylmethane, phenyl(trimethylsilyl)methane, or diphenyl(trimethylsilyl)methane were explored in their reactivity with (py) 4FeCl 2. Furthermore, we prepared a series of monoalkylated salts of the type (py) 2FeRCl and characterized from the addition of 1 equiv of the corresponding alkyl sodium species. These complexes are isostructural and have similar magnetic properties. The double alkylation of (py) 4FeCl 2 resulted in the formation of tetrahedral high-spin iron complexes with the sodium salts of diphenylmethane and phenyl(trimethylsilyl)methane thatmore » readily decomposed. A bis(cyclohexadienyl) sandwich complex was formed with the addition of 2 equiv of the tertiary alkyl species sodium diphenyl(trimethylsilyl)methane. The addition of chelating phosphines to (py) 2FeRCl resulted in the overall transfer of Fe(I) chloride concurrent with loss of pyridine and alkyl radical. (dmpe) 2FeCl was synthesized via addition of 1 equiv of sodium diphenyl(trimethylsilyl)methane, whereas the addition of 2 equiv of the sodium compound to (dmpe) 2FeCl 2 gave the reduced Fe(0) nitrogen complex (dmpe) 2Fe(N 2). Our results demonstrate that iron–alkyl homolysis can be used to afford clean, low-valent iron complexes without the use of alkali metals.« less

Iridium Cyclooctene Complex That Forms a Hyperpolarization Transfer Catalyst before Converting to a Binuclear C-H Bond Activation Product Responsible for Hydrogen Isotope Exchange.

PubMed

Iali, Wissam; Green, Gary G R; Hart, Sam J; Whitwood, Adrian C; Duckett, Simon B

2016-11-21

[IrCl(COE) 2 ] 2 (1) reacts with pyridine (py) and H 2 to form crystallographically characterized IrCl(H) 2 (COE)(py) 2 (2). 2 undergoes py loss to form 16-electron IrCl(H) 2 (COE)(py) (3), with equivalent hydride ligands. When this reaction is studied with parahydrogen, 1 efficiently achieves hyperpolarization of free py (and nicotinamide, nicotine, 5-aminopyrimidine, and 3,5-lutudine) via signal amplification by reversible exchange (SABRE) and hence reflects a simple and readily available precatayst for this process. 2 reacts further over 48 h at 298 K to form crystallographically characterized (Cl)(H)(py)(μ-Cl)(μ-H)(κ-μ-NC 5 H 4 )Ir(H)(py) 2 (4). This dimer is active in the hydrogen isotope exchange process that is used in radiopharmaceutical preparations. Furthermore, while [Ir(H) 2 (COE)(py) 3 ]PF 6 (6) forms upon the addition of AgPF 6 to 2, its stability precludes its efficient involvement in SABRE.

Crystal Structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2

PubMed Central

Soniat, Michael; Sampathkumar, Parthasarathy; Collett, Garen; Gizzi, Anthony S.; Banu, Radhika N.; Bhosle, Rahul C.; Chamala, Swetha; Chowdhury, Sukanya; Fiser, Andras; Glenn, Alan S.; Hammonds, James; Hillerich, Brandan; Khafizov, Kamil; Love, James D.; Matikainen, Bridget; Seidel, Ronald D.; Toro, Rafael; Kumar, P. Rajesh; Bonanno, Jeffery B.; Chook, Yuh Min; Almo, Steven C.

2013-01-01

Import-Karyopherin or Importin proteins bind nuclear localization signals (NLSs) to mediate the import of proteins into the cell nucleus. Karyopherin β2 or Kapβ2, also known as Transportin, is a member of this transporter family responsible for the import of numerous RNA binding proteins. Kapβ2 recognizes a targeting signal termed the PY-NLS that lies within its cargos to target them through the nuclear pore complex. The recognition of PY-NLS by Kapβ2 is conserved throughout eukaryotes. Kap104, the Kapβ2 homolog in Saccharomyces cerevisiae, recognizes PY-NLSs in cargos Nab2, Hrp1, and Tfg2. We have determined the crystal structure of Kapβ2 bound to the PY-NLS of the mRNA processing protein Nab2 at 3.05-Å resolution. A seven-residue segment of the PY-NLS of Nab2 is observed to bind Kapβ2 in an extended conformation and occupies the same PY-NLS binding site observed in other Kapβ2•PY-NLS structures. PMID:23535894

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.

PubMed

Jiménez-García, Brian; Pons, Carles; Fernández-Recio, Juan

2013-07-01

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculations while keeping the same predictive accuracy. Given the 3D coordinates of two interacting proteins, pyDockWEB returns the best docking orientations as scored mainly by electrostatics and desolvation energy. The server does not require registration by the user and is freely accessible for academics at http://life.bsc.es/servlet/pydock. Supplementary data are available at Bioinformatics online.

Characterization of Thermally Activated Metalloenediyne Cytotoxicity in Human Melanoma Cells.

PubMed

Keller, Eric J; Porter, Meghan; Garrett, Joy E; Varie, Meredith; Wang, Haiyan; Pollok, Karen E; Turchi, John J; Zaleski, Jeffrey M; Dynlacht, Joseph R

2018-05-15

Enediynes are a highly cytotoxic class of compounds. However, metallation of these compounds may modulate their activation, and thus their cytotoxicity. We previously demonstrated that cytotoxicity of two different metalloenediynes, including (Z)-N,N'-bis[1-pyridyl-2-yl-meth-(E)-ylidene]octa-4-ene-2,6-diyne-1,8-diamine] (PyED), is potentiated when the compounds are administered to HeLa cells during hyperthermia treatment at concentrations that are minimally or not cytotoxic at 37°C. In this study, we further characterized the concentration, time and temperature dependence of cytotoxicity of PyED on human U-1 melanoma cells. We also investigated the potential mechanisms by which PyED cytotoxicity is enhanced during hyperthermia treatment. Cell killing with PyED was dependent on concentration, temperature during treatment and time of exposure. Potentiation of cytotoxicity was observed when cells were treated with PyED at temperatures ≥39.5°C, and enhancement of cell killing increased with temperature and with increasing time at a given temperature. All cells treated with PyED were shown to have DNA damage, but substantially more damage was observed in cells treated with PyED during heating. DNA repair was also inhibited in cells treated with the drug during hyperthermia. Thus, potentiation of PyED cytotoxicity by hyperthermia may be due to enhancement of drug-induced DNA lesions, and/or the inhibition of repair of sublethal DNA damage. While the selective thermal activation of PyED supports the potential clinical utility of metalloenediynes as cancer thermochemotherapeutic agents, therapeutic gain could be optimized by identifying compounds that produce minimal toxicity at 37°C but which become activated and show enhancement of cytotoxicity within a tumor subjected to localized hyperthermic or thermal ablative treatment, or which might act as bifunctional agents. We thus also describe the development and initial characterization of a novel cofactor complex of PyED, platinated PyED (Pt-PyED). Pt-PyED binds to DNA-like cisplatin, and much like PyED, cytotoxicity is greatly enhanced after treatment with the drug at elevated temperatures. However, in contrast to PyED, Pt-PyED is only minimally cytotoxic at 37°C, at concentrations at which cytotoxicity is enhanced by hyperthermia. Further development of cisplatin-based enediynes may result in compounds which, when activated, will possess multiple DNA binding modalities similar to cisplatin, but produce less side effects in tissues at normothermic temperatures.

A Tertiary Carbon–Iron Bond as an Fe I Cl Synthon and the Reductive Alkylation of Diphosphine-Supported Iron(II) Chloride Complexes to Low-Valent Iron

DOE PAGES

Tondreau, Aaron M.; Scott, Brian L.; Boncella, James M.

2016-05-23

We explored ligand-induced reduction of ferrous alkyl complexes via homolytic cleavage of the alkyl fragment with simple chelating diphosphines. The reactivities of the sodium salts of diphenylmethane, phenyl(trimethylsilyl)methane, or diphenyl(trimethylsilyl)methane were explored in their reactivity with (py) 4FeCl 2. Furthermore, we prepared a series of monoalkylated salts of the type (py) 2FeRCl and characterized from the addition of 1 equiv of the corresponding alkyl sodium species. These complexes are isostructural and have similar magnetic properties. The double alkylation of (py) 4FeCl 2 resulted in the formation of tetrahedral high-spin iron complexes with the sodium salts of diphenylmethane and phenyl(trimethylsilyl)methane thatmore » readily decomposed. A bis(cyclohexadienyl) sandwich complex was formed with the addition of 2 equiv of the tertiary alkyl species sodium diphenyl(trimethylsilyl)methane. The addition of chelating phosphines to (py) 2FeRCl resulted in the overall transfer of Fe(I) chloride concurrent with loss of pyridine and alkyl radical. (dmpe) 2FeCl was synthesized via addition of 1 equiv of sodium diphenyl(trimethylsilyl)methane, whereas the addition of 2 equiv of the sodium compound to (dmpe) 2FeCl 2 gave the reduced Fe(0) nitrogen complex (dmpe) 2Fe(N 2). Our results demonstrate that iron–alkyl homolysis can be used to afford clean, low-valent iron complexes without the use of alkali metals.« less

High-Permeability Magnetic Polymer Additives for Lightweight Electromagnetic Shielding

DTIC Science & Technology

2015-08-01

organometallic complexes containing Fe2+ cations. [Cp] = cyclopentadiene; [Py] = pyrrole ; [Imid] = imidazole. ΔEmag values calculated with DFT using the...27 Table A-6 Energy difference between high- and low-spin magnetic states in transition metal ion- pyrrole (Py) complexes...2-],52 pyrrole (C4NH5),53 and other heterocyclic ligands.36,54 The cyclopentadienyl ligand, in particular, is ubiquitous in organometallic chemistry

Identification and characterization of ten new water gaps in seeds and fruits with physical dormancy and classification of water-gap complexes

PubMed Central

Gama-Arachchige, N. S.; Baskin, J. M.; Geneve, R. L.; Baskin, C. C.

2013-01-01

Background and Aims Physical dormancy (PY) occurs in seeds or fruits of 18 angiosperm families and is caused by a water-impermeable palisade cell layer(s) in seed or fruit coats. Prior to germination, the seed or fruit coat of species with PY must become permeable in order to imbibe water. Breaking of PY involves formation of a small opening(s) (water gap) in a morpho-anatomically specialized area in seeds or fruits known as the water-gap complex. Twelve different water-gap regions in seven families have previously been characterized. However, the water-gap regions had not been characterized in Cucurbitaceae; clade Cladrastis of Fabaceae; subfamilies Bombacoideae, Brownlowioideae and Bythnerioideae of Malvaceae; Nelumbonaceae; subfamily Sapindoideae of Sapindaceae; Rhamnaceae; or Surianaceae. The primary aims of this study were to identify and describe the water gaps of these taxa and to classify all the known water-gap regions based on their morpho-anatomical features. Methods Physical dormancy in 15 species was broken by exposing seeds or fruits to wet or dry heat under laboratory conditions. Water-gap regions of fruits and seeds were identified and characterized by use of microtome sectioning, light microscopy, scanning electron microscopy, dye tracking and blocking experiments. Key Results Ten new water-gap regions were identified in seven different families, and two previously hypothesized regions were confirmed. Water-gap complexes consist of (1) an opening that forms after PY is broken; (2) a specialized structure that occludes the gap; and (3) associated specialized tissues. In some species, more than one opening is involved in the initial imbibition of water. Conclusions Based on morpho-anatomical features, three basic water-gap complexes (Types-I, -II and -III) were identified in species with PY in 16 families. Depending on the number of openings involved in initial imbibition, the water-gap complexes were sub-divided into simple and compound. The proposed classification system enables understanding of the relationships between the water-gap complexes of taxonomically unrelated species with PY. PMID:23649182

uPy: a ubiquitous CG Python API with biological-modeling applications.

PubMed

Autin, Ludovic; Johnson, Graham; Hake, Johan; Olson, Arthur; Sanner, Michel

2012-01-01

The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. Using uPy, researchers have created complex plug-ins for molecular and cellular modeling and visualization. uPy can simplify programming for many types of projects (not solely science applications) intended for multihost distribution. It's available at http://upy.scripps.edu. The first featured Web extra is a video that shows interactive analysis of a calcium dynamics simulation. YouTube URL: http://youtu.be/wvs-nWE6ypo. The second featured Web extra is a video that shows rotation of the HIV virus. YouTube URL: http://youtu.be/vEOybMaRoKc.

Computational Workbench for Multibody Dynamics

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2007-01-01

PyCraft is a computer program that provides an interactive, workbenchlike computing environment for developing and testing algorithms for multibody dynamics. Examples of multibody dynamic systems amenable to analysis with the help of PyCraft include land vehicles, spacecraft, robots, and molecular models. PyCraft is based on the Spatial-Operator- Algebra (SOA) formulation for multibody dynamics. The SOA operators enable construction of simple and compact representations of complex multibody dynamical equations. Within the Py-Craft computational workbench, users can, essentially, use the high-level SOA operator notation to represent the variety of dynamical quantities and algorithms and to perform computations interactively. PyCraft provides a Python-language interface to underlying C++ code. Working with SOA concepts, a user can create and manipulate Python-level operator classes in order to implement and evaluate new dynamical quantities and algorithms. During use of PyCraft, virtually all SOA-based algorithms are available for computational experiments.

A recessive mutation in the RUB1-conjugating enzyme, RCE1, reveals a requirement for RUB modification for control of ethylene biosynthesis and proper induction of basic chitinase and PDF1.2 in Arabidopsis.

PubMed

Larsen, Paul B; Cancel, Jesse D

2004-05-01

By screening etiolated Arabidopsis seedlings for mutants with aberrant ethylene-related phenotypes, we identified a mutant that displays features of the ethylene-mediated triple response even in the absence of ethylene. Further characterization showed that the phenotype observed for the dark-grown seedlings of this mutant is reversible by prevention of ethylene perception and is dependent on a modest increase in ethylene production correlated with an increase in 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO) activity in the hypocotyl. Molecular characterization of leaves of the mutant revealed severely impaired induction of basic chitinase (chiB) and plant defensin (PDF)1.2 following treatment with jasmonic acid and/or ethylene. Positional cloning of the mutation resulted in identification of a 49-bp deletion in RCE1 (related to ubiquitin 1 (RUB1)-conjugating enzyme), which has been demonstrated to be responsible for covalent attachment of RUB1 to the SCF (Skpl Cdc 53 F-box) ubiquitin ligase complex to modify its activity. Our analyses with rce1-2 demonstrate a previously unknown requirement for RUB1 modification for regulation of ethylene biosynthesis and proper induction of defense-related genes in Arabidopsis.

Acquisition of physical dormancy and ontogeny of the micropyle--water-gap complex in developing seeds of Geranium carolinianum (Geraniaceae).

PubMed

Gama-Arachchige, N S; Baskin, J M; Geneve, R L; Baskin, C C

2011-07-01

The 'hinged valve gap' has been previously identified as the initial site of water entry (i.e. water gap) in physically dormant (PY) seeds of Geranium carolinianum (Geraniaceae). However, neither the ontogeny of the hinged valve gap nor acquisition of PY by seeds of Geraniaceae has been studied previously. The aims of the present study were to investigate the physiological events related to acquisition of PY and the ontogeny of the hinged valve gap and seed coat of G. carolinianum. Seeds of G. carolinianum were studied from the ovule stage until dispersal. The developmental stages of acquisition of germinability, physiological maturity and PY were determined by seed measurement, germination and imbibition experiments using intact seeds and isolated embryos of both fresh and slow-dried seeds. Ontogeny of the seed coat and water gap was studied using light microscopy. Developing seeds achieved germinability, physiological maturity and PY on days 9, 14 and 20 after pollination (DAP), respectively. The critical moisture content of seeds on acquisition of PY was 11 %. Slow-drying caused the stage of acquisition of PY to shift from 20 to 13 DAP. Greater extent of cell division and differentiation at the micropyle, water gap and chalaza than at the rest of the seed coat resulted in particular anatomical features. Palisade and subpalisade cells of varying forms developed in these sites. A clear demarcation between the water gap and micropyle is not evident due to their close proximity. Acquisition of PY in seeds of G. carolinianum occurs after physiological maturity and is triggered by maturation drying. The micropyle and water gap cannot be considered as two separate entities, and thus it is more appropriate to consider them together as a 'micropyle--water-gap complex'.

Turbine Engine Stability/Instability With Rub Forces Axisymmetric Rotor-Support Stiffness

NASA Technical Reports Server (NTRS)

Gallardo, Vicente; Lawrence, Charles

2004-01-01

The stability/instability condition of a turbine rotor with axisymmetric supports is determined in the presence of gyroscopic loads and rub-induced destabilizing forces. A modal representation of the turbine engine is used, with one mode in each of the vertical and horizontal planes. The use of non-spinning rotor modes permits an explicit treatment of gyroscopic effects. The two linearized modal equations of motion of a rotor with axisymmetric supports are reduced to a single equation in a complex variable. The resulting eigenvalues yield explicit expressions at the stability boundary, for the whirl frequency as well as the required damping for stability in the presence of the available rub-induced destabilization. Conversely, the allowable destabilization in the presence of the available damping is also given.

Rhenium(I) polypyridine diamine complexes as intracellular phosphorogenic sensors: synthesis, characterization, emissive behavior, biological properties, and nitric oxide sensing.

PubMed

Choi, Alex Wing-Tat; Yim, Vicki Man-Wai; Liu, Hua-Wei; Lo, Kenneth Kam-Wing

2014-07-28

We report the development of a series of rhenium(I) polypyridine complexes appended with an electron-rich diaminoaromatic moiety as phosphorogenic sensors for nitric oxide (NO). The diamine complexes [Re(N^N)(CO)3 (py-DA)][PF6 ] (py-DA=3-(N-(2-amino-5-methoxyphenyl)aminomethyl)pyridine; N^N=1,10-phenanthroline (phen) (1 a), 3,4,7,8-tetramethyl-1,10-phenanthroline (Me4 -phen) (2 a), 4,7-diphenyl-1,10-phenanthroline (Ph2 -phen) (3 a)) have been synthesized and characterized. In contrast to common rhenium(I) diimines, these diamine complexes were very weakly emissive due to quenching of the triplet metal-to-ligand charge-transfer ((3) MLCT) emission by the diaminoaromatic moiety through photoinduced electron transfer (PET). Upon treatment with NO, the complexes were converted into the triazole derivatives [Re(N^N)(CO)3 (py-triazole)][PF6 ] (py-triazole=3-((6-methoxybenzotriazol-1-yl)methyl)pyridine; N^N=phen (1 b), Me4 -phen (2 b), Ph2 -phen (3 b)), resulting in significant emission enhancement (I/I0 ≈60). The diamine complexes exhibited high reaction selectivity to NO, and their emission intensity was found to be independent on pH. Also, these complexes were effectively internalized by HeLa cells and RAW264.7 macrophages with negligible cytotoxicity. Additionally, the use of complex 3 a as an intracellular phosphorogenic sensor for NO has been demonstrated. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A well-defined terminal vanadium(III) oxo complex.

PubMed

King, Amanda E; Nippe, Michael; Atanasov, Mihail; Chantarojsiri, Teera; Wray, Curtis A; Bill, Eckhard; Neese, Frank; Long, Jeffrey R; Chang, Christopher J

2014-11-03

The ubiquity of vanadium oxo complexes in the V+ and IV+ oxidation states has contributed to a comprehensive understanding of their electronic structure and reactivity. However, despite being predicted to be stable by ligand-field theory, the isolation and characterization of a well-defined terminal mononuclear vanadium(III) oxo complex has remained elusive. We present the synthesis and characterization of a unique terminal mononuclear vanadium(III) oxo species supported by the pentadentate polypyridyl ligand 2,6-bis[1,1-bis(2-pyridyl)ethyl]pyridine (PY5Me2). Exposure of [V(II)(NCCH3)(PY5Me2)](2+) (1) to either dioxygen or selected O-atom-transfer reagents yields [V(IV)(O)(PY5Me2)](2+) (2). The metal-centered one-electron reduction of this vanadium(IV) oxo complex furnishes a stable, diamagnetic [V(III)(O)(PY5Me2)](+) (3) species. The vanadium(III) oxo species is unreactive toward H- and O-atom transfer but readily reacts with protons to form a putative vanadium hydroxo complex. Computational results predict that further one-electron reduction of the vanadium(III) oxo species will result in ligand-based reduction, even though pyridine is generally considered to be a poor π-accepting ligand. These results have implications for future efforts toward low-valent vanadyl chemistry, particularly with regard to the isolation and study of formal vanadium(II) oxo species.

Asymmetric and symmetric triazenido cyclopalladated complexes: Synthesis, structural analysis and DFT calculations

NASA Astrophysics Data System (ADS)

Härter Vaniel, Ana Paula; Mauro, Antonio Eduardo; de Godoy Netto, Adelino Vieira; de Almeida, Eduardo Tonon; Piquini, Paulo Cesar; Zambiazi, Priscilla; Back, Davi Fernando; Hörner, Manfredo

2015-03-01

The reaction of [Pd{dmba}(μ-N3)]2 (dmba = N,N-dimethylbenzylamine) with 1-(2-fluorophenyl)-3-(4-nitrophenyl)triazenido (L1) or 1,3-bis(4-nitrophenyl)triazenido (L2) anions, in methanol, and subsequent treatment with pyridine (py) allows the preparation of the corresponding cyclopalladated compounds [Pd(dmba)(L1)(py)] (1) and [Pd(dmba)(L2)(py)]ṡpy (2). The acentric mononuclear entities of (1) and (2) are connected by weak intermolecular non-classical Csbnd H⋯C hydrogen bonds, which results in 2-D arrangements by translation, along the [1 0 0] and [0 0 1] crystallographic directions, respectively.

Iridium N-Heterocyclic Carbene Complexes as Efficient Catalysts for Magnetization Transfer from para-Hydrogen

PubMed Central

2011-01-01

While the characterization of materials by NMR is hugely important in the physical and biological sciences, it also plays a vital role in medical imaging. This success is all the more impressive because of the inherently low sensitivity of the method. We establish here that [Ir(H)2(IMes)(py)3]Cl undergoes both pyridine (py) loss as well as the reductive elimination of H2. These reversible processes bring para-H2 and py into contact in a magnetically coupled environment, delivering an 8100-fold increase in 1H NMR signal strength relative to non-hyperpolarized py at 3 T. An apparatus that facilitates signal averaging has been built to demonstrate that the efficiency of this process is controlled by the strength of the magnetic field experienced by the complex during the magnetization transfer step. Thermodynamic and kinetic data combined with DFT calculations reveal the involvement of [Ir(H)2(η2-H2)(IMes)(py)2]+, an unlikely yet key intermediate in the reaction. Deuterium labeling yields an additional 60% improvement in signal, an observation that offers insight into strategies for optimizing this approach. PMID:21469642

Iridium N-heterocyclic carbene complexes as efficient catalysts for magnetization transfer from para-hydrogen.

PubMed

Cowley, Michael J; Adams, Ralph W; Atkinson, Kevin D; Cockett, Martin C R; Duckett, Simon B; Green, Gary G R; Lohman, Joost A B; Kerssebaum, Rainer; Kilgour, David; Mewis, Ryan E

2011-04-27

While the characterization of materials by NMR is hugely important in the physical and biological sciences, it also plays a vital role in medical imaging. This success is all the more impressive because of the inherently low sensitivity of the method. We establish here that [Ir(H)(2)(IMes)(py)(3)]Cl undergoes both pyridine (py) loss as well as the reductive elimination of H(2). These reversible processes bring para-H(2) and py into contact in a magnetically coupled environment, delivering an 8100-fold increase in (1)H NMR signal strength relative to non-hyperpolarized py at 3 T. An apparatus that facilitates signal averaging has been built to demonstrate that the efficiency of this process is controlled by the strength of the magnetic field experienced by the complex during the magnetization transfer step. Thermodynamic and kinetic data combined with DFT calculations reveal the involvement of [Ir(H)(2)(η(2)-H(2))(IMes)(py)(2)](+), an unlikely yet key intermediate in the reaction. Deuterium labeling yields an additional 60% improvement in signal, an observation that offers insight into strategies for optimizing this approach.

Spirolactone and spirothiolactone rhodamine-pyrene probes for detection of Hg2 + with different sensing properties and its application in living cells

NASA Astrophysics Data System (ADS)

Rui, Qing-Qing; Zhou, Yi; Fang, Yuan; Yao, Cheng

2016-04-01

Two new rhodamine B-based fluorescent probes PyRbS and PyRbO containing pyrene moiety were designed and synthesized. Both of the probes showed colorimetric and fluorometric sensing abilities for Hg2 + with high selectivity over other metal ions. The binding analysis using Job's plot suggested 1:1 stoichiometry for the complexes formed for Hg2 +. Compared with PyRbO, the PyRbS showed higher selectivity and sensitivity due to the thiophilic property of Hg2 + ion. The PyRbS exhibited the linear fluorescence quenching to Hg2 + in the range of 0.3 to 4.8 μM (λex = 365 nm) and 0.3 to 5.4 μM (λex = 515 nm), and the detection limit was 0.72 μM. Moreover, ratiometric changes of PyRbS with Hg2 + in absorption spectrum were observed, which could not be obtained in the combination of PyRbO with Hg2 +. In addition, the methyl thiazolyl tetrazolium (MTT) assay demonstrated that RbPyS had low cytotoxicity and was successfully used to monitor intracellular Hg2 + levels in living cells.

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

PubMed

Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc; Bernardi, Rafael C; Schulten, Klaus; Tajkhorshid, Emad; Rudack, Till

2018-02-06

Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X 3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

White-rot fungal response to fresh and photolytically-weathered pyrogenic organic matter

NASA Astrophysics Data System (ADS)

Gibson, C. D.; Berry, T. D.; Wang, R.; Bird, J. A.; Filley, T. R.

2013-12-01

Pyrogenic organic matter (PyOM or biochar) is the product of the incomplete combustion of biomass. A better understanding of the microbial-mediated degradation of PyOM is critical to assess its role in soil C sequestration and to serve as an agricultural amendment. Recent studies have shown that PyOM additions can prime native soil C but results have been inconsistent, with studies reporting no effect, an increase, or decrease in C mineralization. This study investigated the ability of saprotrophic white-rot fungus, Trametes versicolor, to decompose an unaltered 'fresh' PyOM and a photo-oxidized PyOM. In addition, we measured PyOM-induced priming effects on the mineralization of malt extract agar media (MEA). Enriched (13C) Pinus banksiana-derived PyOM, produced at 450oC under N2, was added fresh and after 4 weeks exposure to 254 nm light to MEA. Vials containing the various types of media were then monitored for CO2 evolution and oxidative enzyme activity. We found that MEA C respired was stimulated (positive priming) by photolyzed PyOM and was inhibited with fresh PyOM addition (negative priming) relative to controls. Vetryl alcohol addition, a laccase production stimulant, resulted in less activity in the presence of PyOM compared with a control, indicating PyOM may disrupt enzyme induction processes. Loss of PyOM-13CO2 was 0.2% (× 0.001) for fresh PyOM and 1.2% (×0.001) for photolyzed PyOM C during 10 weeks averaged across media treatments. While MEA C mineralization decreased after fresh PyOM addition, both oxidative (laccase and manganese peroxidase) and hydrolytic (β glucosidase) enzyme production increased with fresh PyOM in the absence of veratryl alcohol. However, there was a decrease in its presence. These results suggest that the physiological response of this common wood decay fungus to PyOM is complex and responsive to enzymatic triggers but that PyOM itself can act to promote or suppress overall litter or soil decay by fungi.

The Role of Seven-Coordination in Ru-Catalyzed Water Oxidation

DOE PAGES

Matheu, Roc; Ertem, Mehmed Z.; Pipelier, Muriel; ...

2018-01-19

A family of Ru complexes based on the pentadentate ligand t5a 3– ((2,5-bis(6-carboxylatopyridin-2-yl)pyrrol-1-ide) and pyridine (py) that includes {Ru II(Ht5a-κ-N 2O)(py) 3} (1H II(κ-N 2O)), {Ru III(t5a-κ-N 3O 1.5)(py) 2} (2 III(κ-N 3O 1.5)), and {Ru IV(t5a-κ-N 3O 2)(py) 2}+ ({2 IV(κ-N3O 2)}+) has been prepared and thoroughly characterized. Complexes 1HII(κ-N 2O), 2 III(κ-N 3O 1.5), and {2 IV(κ-N 3O 2)}+ have been investigated in solution by spectroscopic methods (NMR, UV–vis) and in the solid state by single-crystal X-ray diffraction analysis and complemented by density functional theory (DFT) calculations. The redox properties of complex 2 III(κ-N 3O 1.5) have beenmore » studied by electrochemical methods (CV and DPV), showing its easy access to high oxidation states, thanks to the trianionic nature of the t5a 3– ligand. Under neutral to basic conditions complex {2 IV(κ-N3O 2)}+ undergoes aquation, generating {Ru IV(OH)(t5a-κ-N 2O)(py) 2} (2 IV(OH)(κ-N 2O)). Further oxidation of the complex forms {Ru V(O)(t5a-κ-N 2O)(py) 2} (2 V(O)(κ-N 2O)), which is a very efficient water oxidation catalyst, reaching a TOF MAX value of 9400 s –1 at pH 7.0, as measured via foot of the wave analysis. The key to fast kinetics for the catalytic oxidation of water to dioxygen by 2 V(O)(κ-N 2O) is due not only to the easy access to high oxidation states but also to the intramolecular hydrogen bonding provided by the noncoordinated dangling carboxylate at the transition state, as corroborated by DFT calculations.« less

The Role of Seven-Coordination in Ru-Catalyzed Water Oxidation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matheu, Roc; Ertem, Mehmed Z.; Pipelier, Muriel

A family of Ru complexes based on the pentadentate ligand t5a 3– ((2,5-bis(6-carboxylatopyridin-2-yl)pyrrol-1-ide) and pyridine (py) that includes {Ru II(Ht5a-κ-N 2O)(py) 3} (1H II(κ-N 2O)), {Ru III(t5a-κ-N 3O 1.5)(py) 2} (2 III(κ-N 3O 1.5)), and {Ru IV(t5a-κ-N 3O 2)(py) 2}+ ({2 IV(κ-N3O 2)}+) has been prepared and thoroughly characterized. Complexes 1HII(κ-N 2O), 2 III(κ-N 3O 1.5), and {2 IV(κ-N 3O 2)}+ have been investigated in solution by spectroscopic methods (NMR, UV–vis) and in the solid state by single-crystal X-ray diffraction analysis and complemented by density functional theory (DFT) calculations. The redox properties of complex 2 III(κ-N 3O 1.5) have beenmore » studied by electrochemical methods (CV and DPV), showing its easy access to high oxidation states, thanks to the trianionic nature of the t5a 3– ligand. Under neutral to basic conditions complex {2 IV(κ-N3O 2)}+ undergoes aquation, generating {Ru IV(OH)(t5a-κ-N 2O)(py) 2} (2 IV(OH)(κ-N 2O)). Further oxidation of the complex forms {Ru V(O)(t5a-κ-N 2O)(py) 2} (2 V(O)(κ-N 2O)), which is a very efficient water oxidation catalyst, reaching a TOF MAX value of 9400 s –1 at pH 7.0, as measured via foot of the wave analysis. The key to fast kinetics for the catalytic oxidation of water to dioxygen by 2 V(O)(κ-N 2O) is due not only to the easy access to high oxidation states but also to the intramolecular hydrogen bonding provided by the noncoordinated dangling carboxylate at the transition state, as corroborated by DFT calculations.« less

The coordination behaviour of ferrocene-based pyridylphosphine ligands towards Zn(II), Cd(II) and Hg(II).

PubMed

Siemeling, Ulrich; Klemann, Thorsten; Bruhn, Clemens; Schulz, Jiří; Štěpnička, Petr

2011-05-07

The reaction of Group 12 metal dihalides MX(2) with the P,N-ligands [Fe(C(5)H(4)-PPh(2))(C(5)H(4)-2-py)] (1) (2-py = pyrid-2-yl), [Fe(C(5)H(4)-PPh(2))(C(5)H(4)-CH(2)-2-py)] (2) and [Fe(C(5)H(4)-PPh(2))(C(5)H(4)-3-py)] (3) (3-py = pyrid-3-yl) was investigated. For a 1 : 1 molar ratio of MX(2) and the respective ligand, three structure types were found in the solid state, viz. chelate, cyclic dimer and chain-like coordination polymer. The M(II) coordination environment is distorted pseudo-tetrahedral in each case. The P-M-N angle is much larger in the chelates (≥119°) than in the ligand-bridged structures (≤109°). 1 prefers the formation of chelates [MX(2)(1-κ(2)N,P)]. 3 forms coordination polymers [MX(2)(μ-3)](n). With the more flexible 2 all three structure types can occur. Dynamic coordination equilibria were observed in solution for the molecular complexes obtained with 1 and 2. NMR data indicate that the N- and P-donor sites interact most strongly with Zn(II) and Hg(II), respectively. While the formation of bis(phosphine)mercury complexes (soft-soft) was easily achieved, no bis(pyridine)zinc complex (borderline-borderline) could be obtained, which is surprising in view of the HSAB principle.

Synthesis, crystal structure and cytotoxic activity of ruthenium(II) piano-stool complex with N,N-chelating ligand

NASA Astrophysics Data System (ADS)

Rogala, Patrycja; Jabłońska-Wawrzycka, Agnieszka; Kazimierczuk, Katarzyna; Borek, Agnieszka; Błażejczyk, Agnieszka; Wietrzyk, Joanna; Barszcz, Barbara

2016-12-01

A mononuclear compound of the general formula [(η6-p-cymene)RuIICl(2,2‧-PyBIm)]PF6 has been synthesized from a bidentate N,N-donor ligand, viz. 2,-(2‧-pyridyl)benzimidazole (2,2‧-PyBIm) and the corresponding chloro-complex [(η6-p-cymene)Ru(μ-Cl)Cl]2 (precursor). The isolated coordination compound was characterized by IR, UV-vis and 1H, 13C NMR spectroscopies. The single crystal X-ray analysis of the complex reveals that the asymmetric part of the unit cell consists of two symmetrically independent, [(η6-p-cymene)RuCl(2,2‧-PyBIm)]+ cationic complexes. Each cation exhibits a pseudo-octahedral three-legged piano-stool geometry, in which three "legs" are occupied by one chloride ion and two nitrogen donor atoms of the chelating ligand 2,2‧-PyBIm. The Hirshfeld surface analysis of obtained complex was determined, too. The ionic nature of the compound is identified by a strong band at around 830 cm-1 due to the νP-F stretching mode of the PF6- counter ion. The electronic spectrum of this monomeric complex displays high intensity bands in the ultraviolet region assignable to π→π*/n→π* transitions, as well as a band attributable to the metal-to-ligand charge transfer (MLCT) dπ(Ru)→π*(L) transition. Additionally, the complex has been screened for its cytotoxicity against three human cancer lines: non-small cell lung carcinoma (A549), colon adenocarcinoma (HT29) and breast adenocarcinoma (MCF-7) as well as normal mice fibroblast cells (BALB/3T3). The complex demonstrated a moderate antiproliferative activity against the cell lines tested.

A Cu2+-selective fluorescent chemosensor based on BODIPY with two pyridine ligands and logic gate

NASA Astrophysics Data System (ADS)

Huang, Liuqian; Zhang, Jing; Yu, Xiaoxiu; Ma, Yifan; Huang, Tianjiao; Shen, Xi; Qiu, Huayu; He, Xingxing; Yin, Shouchun

2015-06-01

A novel near-infrared fluorescent chemosensor based on BODIPY (Py-1) has been synthesized and characterized. Py-1 displays high selectivity and sensitivity for sensing Cu2+ over other metal ions in acetonitrile. Upon addition of Cu2+ ions, the maximum absorption band of Py-1 in CH3CN displays a red shift from 603 to 608 nm, which results in a visual color change from pink to blue. When Py-1 is excited at 600 nm in the presence of Cu2+, the fluorescent emission intensity of Py-1 at 617 nm is quenched over 86%. Notably, the complex of Py-1-Cu2+ can be restored with the introduction of EDTA or S2-. Consequently, an IMPLICATION logic gate at molecular level operating in fluorescence mode with Cu2+ and S2- as chemical inputs can be constructed. Finally, based on the reversible and reproducible system, a nanoscale sequential memory unit displaying "Writing-Reading-Erasing-Reading" functions can be integrated.

Towards the rational design of the Py5-ligand framework for ruthenium-based water oxidation catalysts.

PubMed

Schilling, Mauro; Böhler, Michael; Luber, Sandra

2018-05-21

In order to rationally design water oxidation catalysts (WOCs), an in-depth understanding of the reaction mechanism is essential. In this study we showcase the complexity of catalytic water oxidation, by elucidating how modifications of the pentapyridyl (Py5) ligand-framework influence the thermodynamics and kinetics of the process. In the reaction mechanism the pyridine-water exchange was identified as a key reaction which appears to determine the reactivity of the Py5-WOCs. Exploring the capabilities of in silico design we show which modifications of the ligand framework appear promising when attempting to improve the catalytic performance of WOCs derived from Py5.

Photo-reduction of CO2 Using a Rhenium Complex Covalently Supported on a Graphene/TiO2 Composite.

PubMed

Cui, Shi-Cong; Sun, Xue-Zhong; Liu, Jin-Gang

2016-07-07

One of the promising solutions for decreasing atmospheric CO2 is artificial photosynthesis, in which CO2 can be photoconverted into solar fuels. In this study, a rhenium complex Re(PyBn)(CO)3 Cl (PyBn=1-(2-picolyl)-4-phenyl-1H-1,2,3-triazole) was covalently grafted onto the surface of reduced graphene oxide (rGO). This was further combined with TiO2 to fabricate a novel catalyst composite TiO2 -rGO-Re(PyBn)(CO)3 Cl for CO2 photo-reduction. This hybrid composite demonstrated high selectivity conversion of CO2 into CO under xenon-lamp irradiation. Compared with the unsupported homogeneous catalyst Re(PyBn)(CO)3 Cl, the covalent immobilized catalyst composite TiO2 -rGO-Re(PyBn)(CO)3 Cl enhanced the turnover number six times and significantly improved catalyst stability. During the process of CO2 photo-reduction, intermediate species with lifetimes longer than hundreds of microseconds were observed and the formation of CO products was revealed using timeresolved infrared spectroscopy. A plausible mechanism for CO2 photo-reduction by the TiO2 -rGO-Re(PyBn)(CO)3 Cl catalyst composite has been suggested. The obtained results have implications for the future design of efficient catalyst composites for CO2 photo-conversion. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spirolactone and spirothiolactone rhodamine-pyrene probes for detection of Hg²⁺ with different sensing properties and its application in living cells.

PubMed

Rui, Qing-Qing; Zhou, Yi; Fang, Yuan; Yao, Cheng

2016-04-15

Two new rhodamine B-based fluorescent probes PyRbS and PyRbO containing pyrene moiety were designed and synthesized. Both of the probes showed colorimetric and fluorometric sensing abilities for Hg(2+) with high selectivity over other metal ions. The binding analysis using Job's plot suggested 1:1 stoichiometry for the complexes formed for Hg(2+). Compared with PyRbO, the PyRbS showed higher selectivity and sensitivity due to the thiophilic property of Hg(2+) ion. The PyRbS exhibited the linear fluorescence quenching to Hg(2+) in the range of 0.3 to 4.8 μM (λ(ex)=365 nm) and 0.3 to 5.4 μM (λ(ex)=515 nm), and the detection limit was 0.72 μM. Moreover, ratiometric changes of PyRbS with Hg(2+) in absorption spectrum were observed, which could not be obtained in the combination of PyRbO with Hg(2+). In addition, the methyl thiazolyl tetrazolium (MTT) assay demonstrated that RbPyS had low cytotoxicity and was successfully used to monitor intracellular Hg(2+) levels in living cells. Copyright © 2016 Elsevier B.V. All rights reserved.

BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience.

PubMed

Van Geit, Werner; Gevaert, Michael; Chindemi, Giuseppe; Rössert, Christian; Courcol, Jean-Denis; Muller, Eilif B; Schürmann, Felix; Segev, Idan; Markram, Henry

2016-01-01

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases.

General synthesis of (salen)ruthenium(III) complexes via N...N coupling of (salen)ruthenium(VI) nitrides.

PubMed

Man, Wai-Lun; Kwong, Hoi-Ki; Lam, William W Y; Xiang, Jing; Wong, Tsz-Wing; Lam, Wing-Hong; Wong, Wing-Tak; Peng, Shie-Ming; Lau, Tai-Chu

2008-07-07

Reaction of [Ru (VI)(N)(L (1))(MeOH)] (+) (L (1) = N, N'-bis(salicylidene)- o-cyclohexylenediamine dianion) with excess pyridine in CH 3CN produces [Ru (III)(L (1))(py) 2] (+) and N 2. The proposed mechanism involves initial equilibrium formation of [Ru (VI)(N)(L (1))(py)] (+), which undergoes rapid N...N coupling to produce [(py)(L (1))Ru (III) N N-Ru (III)(L (1))(py)] (2+); this is followed by pyridine substituion to give the final product. This ligand-induced N...N coupling of Ru (VI)N is utilized in the preparation of a series of new ruthenium(III) salen complexes, [Ru (III)(L)(X) 2] (+/-) (L = salen ligand; X = H 2O, 1-MeIm, py, Me 2SO, PhNH 2, ( t )BuNH 2, Cl (-) or CN (-)). The structures of [Ru (III)(L (1))(NH 2Ph) 2](PF 6) ( 6), K[Ru (III)(L (1))(CN) 2] ( 9), [Ru (III)(L (2))(NCCH 3) 2][Au (I)(CN) 2] ( 11) (L (2) = N, N'-bis(salicylidene)- o-phenylenediamine dianion) and [N ( n )Bu 4][Ru (III)(L (3))Cl 2] ( 12) (L (3) = N, N'-bis(salicylidene)ethylenediamine dianion) have been determined by X-ray crystallography.

A Manganese Alternative to Gadolinium for MRI Contrast

PubMed Central

Gale, Eric M.; Atanasova, Iliyana P.; Blasi, Francesco; Ay, Ilknur; Caravan, Peter

2016-01-01

Contrast-enhanced computed tomography (CT) and magnetic resonance imaging (MRI) are routinely used to diagnose soft tissue and vascular abnormalities. However safety concerns limit the use of iodinated and gadolinium- (Gd) based CT and MRI contrast media in renally compromised patients. With an estimated 14% of the US population suffering from chronic kidney disease (CKD), contrast media compatible with renal impairment is sorely needed. We present the new manganese(II) complex [Mn(PyC3A)(H2O)]- as a Gd alternative. [Mn(PyC3A)(H2O)]- is amongst the most stable Mn(II) complexes at pH 7.4 (log KML = 11.40). In the presence of 25 mol equiv. Zn at pH 6.0, 37 °C, [Mn(PyC3A)(H2O)]- is 20-fold more resistant to dissociation than [Gd(DTPA)(H2O)]2-. Relaxivity of [Mn(PyC3A)(H2O)]- in blood plasma is comparable to commercial Gd contrast agents. Biodistribution analysis confirms that [Mn(PyC3A)(H2O)]- clears via a mixed renal/ hepatobiliary pathway with >99% elimination by 24h. [Mn(PyC3A)(H2O)]- was modified to form a bifunctional chelator and 4 chelates were conjugated to a fibrin-specific peptide to give Mn-FBP. Mn-FBP binds the soluble fibrin fragment DD(E) with Kd = 110 nM. Per Mn relaxivity of Mn-FBP is 4-fold greater than [Mn(PyC3A)(H2O)]- and increases 60% in the presence of fibrin, consistent with binding. Mn-FBP provided equivalent thrombus enhancement to the state of the art Gd analog, EP-2104R, in a rat model of arterial thrombosis. Mn metabolite analysis reveals no evidence of dechelation and the probe was >99% eliminated after 24 hr. [Mn(PyC3A)(H2O)]- is a lead development candidate for an imaging probe that is compatible with renally compromised patients. PMID:26588204

A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data.

PubMed

Delussu, Giovanni; Lianas, Luca; Frexia, Francesca; Zanetti, Gianluigi

2016-01-01

This work presents a scalable data access layer, called PyEHR, designed to support the implementation of data management systems for secondary use of structured heterogeneous biomedical and clinical data. PyEHR adopts the openEHR's formalisms to guarantee the decoupling of data descriptions from implementation details and exploits structure indexing to accelerate searches. Data persistence is guaranteed by a driver layer with a common driver interface. Interfaces for two NoSQL Database Management Systems are already implemented: MongoDB and Elasticsearch. We evaluated the scalability of PyEHR experimentally through two types of tests, called "Constant Load" and "Constant Number of Records", with queries of increasing complexity on synthetic datasets of ten million records each, containing very complex openEHR archetype structures, distributed on up to ten computing nodes.

Taxonomic discrimination of higher plants by pyrolysis mass spectrometry.

PubMed

Kim, S W; Ban, S H; Chung, H J; Choi, D W; Choi, P S; Yoo, O J; Liu, J R

2004-02-01

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex material in a vacuum and has been widely applied to the discrimination of closely related microbial strains. Leaf samples of six species and one variety of higher plants (Rosa multiflora, R. multiflora var. platyphylla, Sedum kamtschaticum, S. takesimense, S. sarmentosum, Hepatica insularis, and H. asiatica) were subjected to PyMS for spectral fingerprinting. Principal component analysis of PyMS data was not able to discriminate these plants in discrete clusters. However, canonical variate analysis of PyMS data separated these plants from one another. A hierarchical dendrogram based on canonical variate analysis was in agreement with the known taxonomy of the plants at the variety level. These results indicate that PyMS is able to discriminate higher plants based on taxonomic classification at the family, genus, species, and variety level.

PyMOL mControl: Manipulating molecular visualization with mobile devices.

PubMed

Lam, Wendy W T; Siu, Shirley W I

2017-01-02

Viewing and manipulating three-dimensional (3D) structures in molecular graphics software are essential tasks for researchers and students to understand the functions of molecules. Currently, the way to manipulate a 3D molecular object is mainly based on mouse-and-keyboard control that is usually difficult and tedious to learn. While gesture-based and touch-based interactions are increasingly popular in interactive software systems, their suitability in handling molecular graphics has not yet been sufficiently explored. Here, we designed the gesture-based and touch-based interaction methods to manipulate virtual objects in PyMOL utilizing the motion and touch sensors in a mobile device. Three fundamental viewing controls-zooming, translation and rotation-and frequently used functions were implemented. Results from a pilot user study reveal that task performances on viewing controls using a mobile device are slightly reduced as compared to mouse-and-keyboard method. However, it is considered to be more suitable for oral presentations and equally suitable for education scenarios such as school classes. Overall, PyMOL mControl provides an alternative way to manipulate objects in molecular graphic software with new user experiences. The software is freely available at http://cbbio.cis.umac.mo/mcontrol.html. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):76-83, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Interaction of formic acid with nitrogen: stabilization of the higher-energy conformer.

PubMed

Marushkevich, Kseniya; Räsänen, Markku; Khriachtchev, Leonid

2010-10-07

Conformational change is an important concept in chemistry and physics. In the present work, we study conformations of formic acid (HCOOH, FA) and report the preparation and identification of the complex of the higher-energy conformer cis-FA with N(2) in an argon matrix. The cis-FA···N(2) complex was synthesized by combining annealing and vibrational excitation of the ground-state trans-FA in a FA/N(2)/Ar matrix. The assignment is based on IR spectroscopic measurements and ab initio calculations. The cis-FA···N(2) complex decay in an argon matrix is much slower compared with the cis-FA monomer. In agreement with the experimental observations, the calculations predict a substantial increase in the stabilization barrier for the cis-FA···N(2) complex compared with the uncomplexed cis-FA monomer. A number of solvation effects in an argon matrix are computationally estimated and discussed. The present results on the cis-FA···N(2) complex show that intermolecular interaction can stabilize intrinsically unstable conformers, as previously found for some other cis-FA complexes.

Computational Insight into the Mechanism of Alkane Hydroxylation by Non-heme Fe(PyTACN) Iron Complexes. Effects of the Substrate and Solvent.

PubMed

Postils, Verònica; Company, Anna; Solà, Miquel; Costas, Miquel; Luis, Josep M

2015-09-08

The reaction mechanisms for alkane hydroxylation catalyzed by non-heme Fe(V)O complexes presented in the literature vary from rebound stepwise to concerted highly asynchronous processes. The origin of these important differences is still not completely understood. Herein, in order to clarify this apparent inconsistency, the hydroxylation of a series of alkanes (methane and substrates bearing primary, secondary, and tertiary C-H bonds) through a Fe(V)O species, [Fe(V)(O)(OH)(PyTACN)](2+) (PyTACN = 1-(2'-pyridylmethyl)-4,7-dimethyl-1,4,7-triazacyclononane), has been computationally examined at the gas phase and in acetonitrile solution. The initial breaking of the C-H bond can occur via hydrogen atom transfer (HAT), leading to an intermediate where there is an interaction between the radical substrate and [Fe(IV)(OH)2(PyTACN)](2+), or through hydride transfer to form a cationic substrate interacting with the [Fe(III)(OH)2(PyTACN)](+) species. Our calculations show the following: (i) except for methane in the rest of the alkanes studied, the intermediate formed by R(+) and [Fe(III)(OH)2(PyTACN)](+) is more stable than that involving the alkyl radical and the [Fe(IV)(OH)2(PyTACN)](2+) complex; (ii) in spite of (i), the first step of the reaction mechanism for all substrates is a HAT instead of hydride abstraction; (iii) the HAT is the rate-determining step for all analyzed cases; and (iv) the barrier for the HAT decreases along methane → primary → secondary → tertiary carbon. The second part of the reaction mechanism corresponds to the rebound process. Therefore, the stereospecific hydroxylation of alkane C-H bonds by non-heme Fe(V)(O) species occurs through a rebound stepwise mechanism that resembles that taking place at heme analogues. Finally, our study also shows that, to properly describe alkane hydroxylation processes mediated by Fe(V)O species, it is essential to consider the solvent effects during geometry optimizations. The use of gas-phase geometries explains the variety of mechanisms for the hydroxylation of alkanes reported in the literature.

Isocyanide or nitrosyl complexation to hemes with varying tethered axial base ligand donors: synthesis and characterization.

PubMed

Sharma, Savita K; Kim, Hyun; Rogler, Patrick J; A Siegler, Maxime; Karlin, Kenneth D

2016-09-01

A series of ferrous-heme 2,6-dimethylphenyl isocyanide (DIMPI) and ferrous-heme mononitrosyl complexes have been synthesized and characterized. The heme portion of the complexes studied is varied with respect to the nature of the axial ligand, including complexes, where it is covalently tethered to the porphyrinate periphery. Reduced heme complexes, [(F8)Fe(II)], [(P(Py))Fe(II)], [(P(Im))Fe(II)], and [(P(ImH))Fe(II)], where F8 = tetrakis(2,6-difluorophenyl)-porphyrinate and P(Py), P(Im), and P(ImH) are partially fluorinated tetraaryl porphyrinates with covalently appended axial base pyridyl/imidazolyl or histamine moieties, were employed; P(ImH) is a new construct. Room temperature addition of DIMPI to these iron(II) complexes affords the bis-isocyanide species [(F8)Fe(II)-(DIMPI)2] in the case of [(F8)Fe(II)], while for the other hemes, mono-DIMPI compounds are obtained, [(P(Py))Fe(II)-(DIMPI)] [(2)-DIMPI], [(P(Im))Fe(II)-(DIMPI)] [(3)-DIMPI], and [(P(ImH))Fe(II)-(DIMPI)] [(4)-DIMPI]. The structures of complexes (3)-DIMPI and (4)-DIMPI have been determined by single crystal X-ray crystallography, where interesting H…F(porphryinate aryl group) interactions are observed. (19)F-NMR spectra determined for these complexes suggest that H…F(porphyrinate aryl groups) attractions also occur in solution, the H atom coming either from the DIMPI methyl groups or from a porphyinate axial base imidazole or porphyrinate pyrrole. Similarly, we have used nitrogen monoxide to generate ferrous-nitrosyl complexes, a five-coordinate species for F8, [(F8)Fe(II)-(NO)], or low-spin six-coordinate compounds [(P(Py))Fe(II)-(NO)], [(P(Im))Fe(II)-(NO)], and [(P(ImH))Fe(II)-(NO)]. The DIMPI and mononitrosyl complexes have also been characterized using UV-Vis, IR, (1)H-NMR, and EPR spectroscopies.

Gadolinium-based nanoparticles for highly efficient T1-weighted magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Lim, Eun-Kyung; Kang, Byunghoon; Choi, Yuna; Jang, Eunji; Han, Seungmin; Lee, Kwangyeol; Suh, Jin-Suck; Haam, Seungjoo; Huh, Yong-Min

2014-06-01

We developed Pyrene-Gadolinium (Py-Gd) nanoparticles as pH-sensitive magnetic resonance imaging (MRI) contrast agents capable of showing a high-Mr signal in cancer-specific environments, such as acidic conditions. Py-Gd nanoparticles were prepared by coating Py-Gd, which is a complex of gadolinium with pyrenyl molecules, with pyrenyl polyethyleneglycol PEG using a nano-emulsion method. These particles show better longitudinal relaxation time (T1) MR signals in acidic conditions than they do in neutral conditions. Furthermore, the particles exhibit biocompatibility and MR contrast effects in both in vitro and in vivo studies. From these results, we confirm that Py-Gd nanoparticles have the potential to be applied for accurate cancer diagnosis and therapy.

p63 threonine phosphorylation signals the interaction with the WW domain of the E3 ligase Itch

PubMed Central

Melino, Sonia; Bellomaria, Alessia; Nepravishta, Ridvan; Paci, Maurizio; Melino, Gerry

2014-01-01

Both in epithelial development as well as in epithelial cancers, the p53 family member p63 plays a crucial role acting as a master transcriptional regulator. P63 steady state protein levels are regulated by the E3 ubiquitin ligase Itch, via a physical interaction between the PPxY consensus sequence (PY motif) of p63 and one of the 4 WW domains of Itch; this substrate recognition process leads to protein-ubiquitylation and p63 proteasomal degradation. The interaction of the WW domains, a highly compact protein-protein binding module, with the short proline-rich sequences is therefore a crucial regulatory event that may offer innovative potential therapeutic opportunity. Previous molecular studies on the Itch-p63 recognition have been performed in vitro using the Itch-WW2 domain and the peptide interacting fragment of p63 (pep63), which includes the PY motif. Itch-WW2-pep63 interaction is also stabilized in vitro by the conformational constriction of the S-S cyclization in the p63 peptide. The PY motif of p63, as also for other proteins, is characterized by the nearby presence of a (T/S)P motif, which is a potential recognition site of the WW domain of the IV group present in the prolyl-isomerase Pin1. In this study, we demonstrate, by in silico and spectroscopical studies using both the linear pep63 and its cyclic form, that the threonine phosphorylation of the (T/S)PPPxY motif may represent a crucial regulatory event of the Itch-mediated p63 ubiquitylation, increasing the Itch-WW domains-p63 recognition event and stabilizing in vivo the Itch-WW-p63 complex. Moreover, our studies confirm that the subsequently trans/cis proline isomerization of (T/S)P motif by the Pin1 prolyl-isomerase, could modulate the E3-ligase interaction, and that the (T/S)pPtransPPxY motif represent the best conformer for the ItchWW-(T/S)PPPxY motif recognition. PMID:25485500

p63 threonine phosphorylation signals the interaction with the WW domain of the E3 ligase Itch.

PubMed

Melino, Sonia; Bellomaria, Alessia; Nepravishta, Ridvan; Paci, Maurizio; Melino, Gerry

2014-01-01

Both in epithelial development as well as in epithelial cancers, the p53 family member p63 plays a crucial role acting as a master transcriptional regulator. P63 steady state protein levels are regulated by the E3 ubiquitin ligase Itch, via a physical interaction between the PPxY consensus sequence (PY motif) of p63 and one of the 4 WW domains of Itch; this substrate recognition process leads to protein-ubiquitylation and p63 proteasomal degradation. The interaction of the WW domains, a highly compact protein-protein binding module, with the short proline-rich sequences is therefore a crucial regulatory event that may offer innovative potential therapeutic opportunity. Previous molecular studies on the Itch-p63 recognition have been performed in vitro using the Itch-WW2 domain and the peptide interacting fragment of p63 (pep63), which includes the PY motif. Itch-WW2-pep63 interaction is also stabilized in vitro by the conformational constriction of the S-S cyclization in the p63 peptide. The PY motif of p63, as also for other proteins, is characterized by the nearby presence of a (T/S)P motif, which is a potential recognition site of the WW domain of the IV group present in the prolyl-isomerase Pin1. In this study, we demonstrate, by in silico and spectroscopical studies using both the linear pep63 and its cyclic form, that the threonine phosphorylation of the (T/S)PPPxY motif may represent a crucial regulatory event of the Itch-mediated p63 ubiquitylation, increasing the Itch-WW domains-p63 recognition event and stabilizing in vivo the Itch-WW-p63 complex. Moreover, our studies confirm that the subsequently trans/cis proline isomerization of (T/S)P motif by the Pin1 prolyl-isomerase, could modulate the E3-ligase interaction, and that the (T/S)pPtransPPxY motif represent the best conformer for the ItchWW-(T/S)PPPxY motif recognition.

Geometric and electronic structures of potassium-adsorbed rubrene complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Tsung-Lung, E-mail: quantum@mail.ncyu.edu.tw; Lu, Wen-Cai, E-mail: wencailu@jlu.edu.cn; State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130021

2015-06-28

The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K{sub 1}RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D{sub 2}- and C{sub 2h}-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K{sub 1}RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules,more » the structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D{sub 2}-like complexes show minimum-energy basins, whereas the C{sub 2h}-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D{sub 2}-like complexes is most likely along the backbone in contrast to the C{sub 2h}-like ones. Although the electronic structures of the minimum-energy structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical environments than the other two on the opposite side, which leads to the largely enhanced resemblance of the simulated to the experimental spectra. Fourth, the HOMO and LUMO are mainly the α and β components of the 2p orbitals of the backbone carbons, respectively.« less

Nanoparticle formulation enhanced protective immunity provoked by PYGPI8p-transamidase related protein (PyTAM) DNA vaccine in Plasmodium yoelii malaria model.

PubMed

Cherif, Mahamoud Sama; Shuaibu, Mohammed Nasir; Kodama, Yukinobu; Kurosaki, Tomoaki; Helegbe, Gideon Kofi; Kikuchi, Mihoko; Ichinose, Akitoyo; Yanagi, Tetsuo; Sasaki, Hitoshi; Yui, Katsuyuki; Tien, Nguyen Huy; Karbwang, Juntra; Hirayama, Kenji

2014-04-07

We have previously reported the new formulation of polyethylimine (PEI) with gamma polyglutamic acid (γ-PGA) nanoparticle (NP) to have provided Plasmodium yoelii merozoite surface protein-1 (PyMSP-1) plasmid DNA vaccine with enhanced protective cellular and humoral immunity in the lethal mouse malaria model. PyGPI8p-transamidase-related protein (PyTAM) was selected as a possible candidate vaccine antigen by using DNA vaccination screening from 29 GPI anchor and signal sequence motif positive genes picked up using web-based bioinformatics tools; though the observed protection was not complete. Here, we observed augmented protective effect of PyTAM DNA vaccine by using PEI and γ-PGA complex as delivery system. NP-coated PyTAM plasmid DNA immunized mice showed a significant survival rate from lethal P. yoelii challenge infection compared with naked PyTAM plasmid or with NP-coated empty plasmid DNA group. Antigen-specific IgG1 and IgG2b subclass antibody levels, proportion of CD4 and CD8T cells producing IFN-γ in the splenocytes and IL-4, IFN-γ, IL-12 and TNF-α levels in the sera and in the supernatants from ex vivo splenocytes culture were all enhanced by the NP-coated PyTAM DNA vaccine. These data indicates that NP augments PyTAM protective immune response, and this enhancement was associated with increased DC activation and concomitant IL-12 production. Copyright © 2014 Elsevier Ltd. All rights reserved.

NMR structural and kinetic assignment of fluoro-3H-naphthopyran photomerocyanines.

PubMed

Delbaere, S; Micheau, J C; Teral, Y; Bochu, C; Campredon, M; Vermeersch, G

2001-11-01

The kinetic and structural behavior of a photochromic compound, 3-(2-fluorophenyl)-3-phenyl-3H-naphtho[2,1-b]pyran (F-Py), was investigated using 1H and 19F nuclear magnetic resonance (NMR) spectroscopy. Upon irradiation, the four theoretically predicted photomerocyanines appear along with a fifth form X, whose final structure has not been elucidated. This last form and two of the photomerocyanines are thermally labile, whereas the other two do not show any signs of decay. The system has been analyzed by NMR spectroscopy. This led to the structural assignment of each photomerocyanine. The kinetics of the thermal bleaching were monitored by directly and separately measuring the concentrations of each species at regular time intervals using 19F NMR spectroscopy. We therefore propose a plausible reaction mechanism. On the basis of this mechanism, the mathematical treatment and the study of the effects of temperature led to the determination of the kinetic and thermodynamic parameters (rate coefficients, enthalpy and entropy of activation) of this photochromic system. The leading role of the labile intermediate X on the formation of trans-transoid-cis (TTC) and cis-transoid-cis (CTC) photomerocyanines is pointed out.

A Cu²⁺-selective fluorescent chemosensor based on BODIPY with two pyridine ligands and logic gate.

PubMed

Huang, Liuqian; Zhang, Jing; Yu, Xiaoxiu; Ma, Yifan; Huang, Tianjiao; Shen, Xi; Qiu, Huayu; He, Xingxing; Yin, Shouchun

2015-06-15

A novel near-infrared fluorescent chemosensor based on BODIPY (Py-1) has been synthesized and characterized. Py-1 displays high selectivity and sensitivity for sensing Cu(2+) over other metal ions in acetonitrile. Upon addition of Cu(2+) ions, the maximum absorption band of Py-1 in CH3CN displays a red shift from 603 to 608 nm, which results in a visual color change from pink to blue. When Py-1 is excited at 600 nm in the presence of Cu(2+), the fluorescent emission intensity of Py-1 at 617 nm is quenched over 86%. Notably, the complex of Py-1-Cu(2+) can be restored with the introduction of EDTA or S(2-). Consequently, an IMPLICATION logic gate at molecular level operating in fluorescence mode with Cu(2+) and S(2-) as chemical inputs can be constructed. Finally, based on the reversible and reproducible system, a nanoscale sequential memory unit displaying "Writing-Reading-Erasing-Reading" functions can be integrated. Copyright © 2015 Elsevier B.V. All rights reserved.

A Novel Solubility-Enhanced Rubusoside-Based Micelles for Increased Cancer Therapy

NASA Astrophysics Data System (ADS)

Zhang, Meiying; Dai, Tongcheng; Feng, Nianping

2017-04-01

Many anti-cancer drugs have a common problem of poor solubility. Increasing the solubility of the drugs is very important for its clinical applications. In the present study, we revealed that the solubility of insoluble drugs was significantly enhanced by adding rubusoside (RUB). Further, it was demonstrated that RUB could form micelles, which was well characterized by Langmuir monolayer investigation, transmission electron microscopy, atomic-force microscopy, and cryogenic transmission electron microscopy. The RUB micelles were ellipsoid with the horizontal distance of 25 nm and vertical distance of 1.2 nm. Insoluble synergistic anti-cancer drugs including curcumin and resveratrol were loaded in RUB to form anti-cancer micelles RUB/CUR + RES. MTT assay showed that RUB/CUR + RES micelles had more significant toxicity on MCF-7 cells compared to RUB/CUR micelles + RUB/RES micelles. More importantly, it was confirmed that RUB could load other two insoluble drugs together for remarkably enhanced anti-cancer effect compared to that of RUB/one drug + RUB/another drug. Overall, we concluded that RUB-based micelles could efficiently load insoluble drugs for enhanced anti-cancer effect.

Compressor seal rub energetics study

NASA Technical Reports Server (NTRS)

Laverty, W. F.

1978-01-01

The rub mechanics of compressor abradable blade tip seals at simulated engine conditions were investigated. Twelve statistically planned, instrumented rub tests were conducted with titanium blades and Feltmetal fibermetal rubstrips. The tests were conducted with single stationary blades rubbing against seal material bonded to rotating test disks. The instantaneous rub torque, speed, incursion rate and blade temperatures were continuously measured and recorded. Basic rub parameters (incursion rate, rub depth, abradable density, blade thickness and rub velocity) were varied to determine the effects on rub energy and heat split between the blade, rubstrip surface and rub debris. The test data was reduced, energies were determined and statistical analyses were completed to determine the primary and interactive effects. Wear surface morphology, profile measurements and metallographic analysis were used to determine wear, glazing, melting and material transfer. The rub energies for these tests were most significantly affected by the incursion rate while rub velocity and blade thickness were of secondary importance. The ratios of blade wear to seal wear were representative of those experienced in engine operation of these seal system materials.

Reactivity of a series of isostructural cobalt pincer complexes with CO2, CO, and H(+).

PubMed

Shaffer, David W; Johnson, Samantha I; Rheingold, Arnold L; Ziller, Joseph W; Goddard, William A; Nielsen, Robert J; Yang, Jenny Y

2014-12-15

The preparation and characterization of a series of isostructural cobalt complexes [Co(t-Bu)2P(E)Py(E)P(t-Bu)2(CH3CN)2][BF4]2 (Py = pyridine, E = CH2, NH, O, and X = BF4 (1a-c)) and the corresponding one-electron reduced analogues [Co(t-Bu)2P(E)Py(E)P(t-Bu)2(CH3CN)2][BF4]2 (2a-c) are reported. The reactivity of the reduced cobalt complexes with CO2, CO, and H(+) to generate intermediates in a CO2 to CO and H2O reduction cycle are described. The reduction of 1a-c and subsequent reactivity with CO2 was investigated by cyclic voltammetry, and for 1a also by infrared spectroelectrochemistry. The corresponding CO complexes of (2a-c) were prepared, and the Co-CO bond strengths were characterized by IR spectroscopy. Quantum mechanical methods (B3LYP-d3 with solvation) were used to characterize the competitive reactivity of the reduced cobalt centers with H(+) versus CO2. By investigating a series of isostructural complexes, correlations in reactivity with ligand electron withdrawing effects are made.

Molecular and structural determinants of adamantyl susceptibility to HLA-DRs allelic variants: an in silico approach to understand the mechanism of MLEs

NASA Astrophysics Data System (ADS)

Zaheer-ul-Haq; Khan, Waqasuddin

2011-01-01

Class II major histocompatibility complex (MHC II) molecules as expressed by antigen-presenting cells are heterodimeric cell-surface glycoprotein receptors that are fundamental in initiating and propagating an immune response by presenting tumor-associated antigenic peptides to CD4+/TH cells. The loading efficiency of such peptides can be improved by small organic compounds (MHC Loading Enhancers—MLEs), that convert the non-receptive peptide conformation of MHC II to a peptide-receptive conformation. In a reversible reaction, these compounds open up the binding site of MHC II molecules by specific interactions with a yet undefined pocket. Here, we performed molecular docking and molecular dynamics simulation studies of adamantyl compounds on the predicted cavity around the P1 pocket of 2 allelic variants of HLA-DRs. The purpose was to investigate the suitability of adamantyl compounds as MLEs at the dimorphic β86 position. Docking studies revealed that besides numerous molecular interactions formed by the adamantyl compounds, Asnβ82, Tyrβ83, and Thrβ90 are the crucial amino acid residues that are characterized as the "sensors" of peptide loading. Molecular dynamics simulation studies exposed the dynamical structural changes that HLA-DRs adopted as a response to binding of 3-(1-adamantyl)-5-hydrazidocarbonyl-1H-pyrazole (AdCaPy). The conformations of AdCaPy complexed with the Glyβ86 HLA-DR allelic variant are well correlated with the stabilized form of peptide-loaded HLA-DRs, further confirming the role of AdCaPy as a MLE. Hydrogen bonding interaction analysis clearly demonstrated that after making suitable contacts with AdCaPy, HLA-DR changes its local conformation. However, AdCaPy complexed with HLA-DR having Valβ86 at the dimorphic position did not accommodate AdCaPy as MLE due to steric hindrance caused by the valine.

Systematic Introduction of Aromatic Rings to Diphosphine Ligands for Emission Color Tuning of Dinuclear Copper(I) Iodide Complexes.

PubMed

Okano, Yuka; Ohara, Hiroki; Kobayashi, Atsushi; Yoshida, Masaki; Kato, Masako

2016-06-06

We have newly synthesized two solution-stable luminescent dinuclear copper(I) complexes, [Cu2(μ-I)2(dpppy)2] (Cu-py) and [Cu2(μ-I)2(dpppyz)2] (Cu-pyz), where dpppy = 2,3-bis(diphenylphosphino)pyridine and dpppyz = 2,3-bis(diphenylphosphino)pyrazine, using chelating diphosphine ligands composed of N-heteroaromatic rings. X-ray analysis clearly indicates that the molecular structures of Cu-py and Cu-pyz are almost identical with that of the parent complex, [Cu2(μ-I)2(dppb)2] [Cu-bz; dppb = 2,3-bis(diphenylphosphino)benzene]. Complexes Cu-py and Cu-pyz exhibit luminescence [emission quantum yield (Φem) = 0.48 and 0.02, respectively] in the solid state at 298 K. A wide emission color tuning, from 497 to 638 nm (energy = 0.55 eV, with an emission color ranging from green to reddish-orange), was achieved in the solid state by the introduction of pyridinic N atoms into the bridging phenyl group between the two diphenylphosphine groups. Density functional theory calculations suggest that the emission could originate from the effective combination of the metal-to-ligand charge-transfer excited state with the halide-to-ligand charge-transfer excited state. Thus, the emission color change is due to stabilization of the π* levels of the central aryl group in the diphosphine ligand. Furthermore, these copper(I) complexes exhibit thermally activated delayed fluorescence at 298 K because of the small singlet-triplet energy difference (ΔE = 523 and 564 cm(-1) for Cu-py and Cu-pyz, respectively). The stability of these complexes in chloroform, due to the rigid bonds between the diphosphine ligands and the Cu(I) ions, enables the preparation of emissive poly(methyl methacrylate) films by the solution-doping technique.

A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data

PubMed Central

Lianas, Luca; Frexia, Francesca; Zanetti, Gianluigi

2016-01-01

This work presents a scalable data access layer, called PyEHR, designed to support the implementation of data management systems for secondary use of structured heterogeneous biomedical and clinical data. PyEHR adopts the openEHR’s formalisms to guarantee the decoupling of data descriptions from implementation details and exploits structure indexing to accelerate searches. Data persistence is guaranteed by a driver layer with a common driver interface. Interfaces for two NoSQL Database Management Systems are already implemented: MongoDB and Elasticsearch. We evaluated the scalability of PyEHR experimentally through two types of tests, called “Constant Load” and “Constant Number of Records”, with queries of increasing complexity on synthetic datasets of ten million records each, containing very complex openEHR archetype structures, distributed on up to ten computing nodes. PMID:27936191

Metal complexes of 3-(4-bromophenyl)-1-pyridin-2-ylprop-2-en-1-one thiosemicarbazone: cytotoxic activity and investigation on the mode of action of the gold(III) complex.

PubMed

Sâmia, Luciana B P; Parrilha, Gabrieli L; Da Silva, Jeferson G; Ramos, Jonas P; Souza-Fagundes, Elaine M; Castelli, Silvia; Vutey, Venn; Desideri, Alessandro; Beraldo, Heloisa

2016-06-01

Complexes [Au(PyCT4BrPh)Cl]Cl (1), [Pt(PyCT4BrPh)Cl]0.5KCl (2), and [Pd(PyCT4BrPh)Cl]KCl (3) were obtained with 3-(4-bromophenyl)-1-pyridin-2-ylprop-2-en-1-one thiosemicarbazone (HPyCT4BrPh). Although complexes (2) and (3) did not exhibit potent cytotoxic activity, HPyCT4BrPh and its gold(III) complex (1) proved to be highly cytotoxic against HL-60 (human promyelocytic leukemia) and THP-1 (human monocytic leukemia) cells, and against MDA-MB 231 and MCF-7 (human breast adenocarcinoma) solid tumor cells. Except for HL-60 cells, upon coordination to gold(III) a 2- to 3-fold increase in the cytotoxic effect was observed. An investigation on the possible biological targets of the gold(III) complex was carried out. Complex (1) but not the free thiosemicarbazone inhibits the enzymatic activity of thioredoxin reductase (TrxR). The affinity of 1 for TrxR suggests metal binding to a selenol residue in the active site of the enzyme. While HPyCT4BrPh was inactive, 1 was able to inhibit topoisomerase IB (Topo IB) activity. Hence, inhibition of TrxR and Topo IB could contribute to the mechanism of cytotoxic action of complex (1).

Three-component entanglements consisting of three crescent-shaped bidentate ligands coordinated to an octahedral metal centre.

PubMed

Durola, Fabien; Russo, Luca; Sauvage, Jean-Pierre; Rissanen, Kari; Wenger, Oliver S

2007-01-01

3,3'-biisoquinoline ligands (biiq) L, bearing aromatic substituents on their 8 and 8' positions, have been used to generate interwoven systems consisting of three crescent-shaped ligands disposed around an octahedral metal centre. Mono-ligand complexes of the type [ReL(CO)3py]+ (py: pyridine) have also been prepared, leading to sterically non-hindering complexes in spite of the endotopic nature of the chelate used. The three-component entanglements have been prepared by using either FeII or RuII as gathering metal centre. The synthetic procedure is simple and efficient, affording fully characterised complexes as their PF6 or SbCl6 salts. X-ray crystallography clearly shows that the crescent-shaped ligands do not repel each other in the tris-chelate complexes. In an analogous way, the ReI complexes show open structures with no steric repulsion between the L ligand and the ancillary CO or py groups. The FeL3 or RuL3 compounds are very unusual in the sense that, contrary to all the other tris-bidentate chelate complexes made till now, the three organic components are tangled up, in a situation which will be very favourable to the formation of new non trivial topologies of the catenane type.

Large structural modification with conserved conformation: analysis of delta(3)-fused aryl prolines in model beta-turns.

PubMed

Jeannotte, Guillaume; Lubell, William D

2004-11-10

For the first time, the influence of a fused Delta3-arylproline on peptide conformation has been studied by the synthesis and comparison of the conformations of peptides containing proline and pyrrolo-proline, 3 (PyPro). Pyrrolo-proline was demonstrated to be a conservative replacement for Pro in model beta-turns, 4 and 5, as shown by their similar DMSO titration curves, cis/trans-isomer populations, and NOESY spectral data. Pyrrolo-proline may thus be used for studying the structure activity relationships of Pro-containing peptides with minimal modification of secondary structures.

BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience

PubMed Central

Van Geit, Werner; Gevaert, Michael; Chindemi, Giuseppe; Rössert, Christian; Courcol, Jean-Denis; Muller, Eilif B.; Schürmann, Felix; Segev, Idan; Markram, Henry

2016-01-01

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases. PMID:27375471

GPU-powered model analysis with PySB/cupSODA.

PubMed

Harris, Leonard A; Nobile, Marco S; Pino, James C; Lubbock, Alexander L R; Besozzi, Daniela; Mauri, Giancarlo; Cazzaniga, Paolo; Lopez, Carlos F

2017-11-01

A major barrier to the practical utilization of large, complex models of biochemical systems is the lack of open-source computational tools to evaluate model behaviors over high-dimensional parameter spaces. This is due to the high computational expense of performing thousands to millions of model simulations required for statistical analysis. To address this need, we have implemented a user-friendly interface between cupSODA, a GPU-powered kinetic simulator, and PySB, a Python-based modeling and simulation framework. For three example models of varying size, we show that for large numbers of simulations PySB/cupSODA achieves order-of-magnitude speedups relative to a CPU-based ordinary differential equation integrator. The PySB/cupSODA interface has been integrated into the PySB modeling framework (version 1.4.0), which can be installed from the Python Package Index (PyPI) using a Python package manager such as pip. cupSODA source code and precompiled binaries (Linux, Mac OS/X, Windows) are available at github.com/aresio/cupSODA (requires an Nvidia GPU; developer.nvidia.com/cuda-gpus). Additional information about PySB is available at pysb.org. paolo.cazzaniga@unibg.it or c.lopez@vanderbilt.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Net clinical benefit of warfarin in individuals with atrial fibrillation across stroke risk and across primary and secondary care.

PubMed

Allan, Victoria; Banerjee, Amitava; Shah, Anoop Dinesh; Patel, Riyaz; Denaxas, Spiros; Casas, Juan-Pablo; Hemingway, Harry

2017-02-01

To investigate net clinical benefit (NCB) of warfarin in individuals with atrial fibrillation (AF) across stroke risk and across primary and secondary care. We conducted a linked electronic health record cohort study of 70 206 individuals with initial record of diagnosis of AF in primary (n=29 568) or secondary care (n=40 638) in England (1998-2010). We defined stroke risk according to the CHA 2 DS 2 -VASc score, and followed individuals over a median 2.2 years for 7005 ischaemic strokes (IS) and for 906 haemorrhagic strokes (HS). We calculated incidence rates (IRs) and 95% CIs per 100 person-years (PYs) (IR (95% CI)/100 PY) of IS and HS, with and without use of warfarin, and the NCB (ie, number of IS avoided) per 100 PYs of warfarin use (NCB (95% CI)/100 PY). Compared with individuals with initial record of diagnosis in secondary care, those in primary care had lower scores of IS risk (CHA 2 DS 2 -VASc≤2: 30.8% vs 20.6%), and lower overall incidence of IS (IR (95% CI)/100 PY: 2.3 (2.2 to 2.4) vs 4.3 (4.2 to 4.4), p value=0.00); however among individuals with CHA 2 DS 2 -VASc=0, 1 or 2 there were no differences in IS rate between those with initial record of diagnosis in primary care or secondary care (IR (95% CI)/100 PY: 0.2 (0.1 to 0.3) vs 0.3 (0.2 to 0.5), p value=0.16), (IR (95% CI)/100 PY: 0.6 (0.4 to 0.7) vs 0.7 (0.6 to 0.9), p value=0.08) and (IR (95% CI)/100 PY: 1.1 (1.00 to 1.3) vs 1.4 (1.2 to 1.6), p value=0.05), respectively. For CHA 2 DS 2 -VASc=0, 1 and 2, IRs of IS with versus without warfarin were (IR (95% CI)/100 PY: 0.4 (0.2 to 0.8) vs 0.2 (0.1 to 0.3), p value=0.16), (IR (95% CI)/100 PY: 0.4 (0.3 to 0.7) vs 0.7 (0.6 to 0.8), p value=0.03) and (IR (95% CI)/100 PY: 0.8 (0.7 to 1.0) vs 1.4 (1.3 to 1.6), p value=0.00), respectively. We found a significant positive NCB of warfarin from CHA 2 DS 2 -VASc≥2 in men (NCB (95% CI)/100 PY: 0.5 (0.1 to 0.9)) and from CHA 2 DS 2 -VASc≥3 in women (NCB (95% CI)/100 PY: 1.5 (1.1 to 1.9)). CHA 2 DS 2 -VASc accurately stratifies IS risk in individuals with AF across both primary and secondary care. However, the incidence rate of ischaemic stroke at CHA 2 DS 2 -VASc=1 are lower than previously reported, which may change the decision to start anticoagulation with warfarin in these individuals. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Net clinical benefit of warfarin in individuals with atrial fibrillation across stroke risk and across primary and secondary care

PubMed Central

Banerjee, Amitava; Shah, Anoop Dinesh; Patel, Riyaz; Denaxas, Spiros; Casas, Juan-Pablo; Hemingway, Harry

2017-01-01

Objective To investigate net clinical benefit (NCB) of warfarin in individuals with atrial fibrillation (AF) across stroke risk and across primary and secondary care. Methods We conducted a linked electronic health record cohort study of 70 206 individuals with initial record of diagnosis of AF in primary (n=29 568) or secondary care (n=40 638) in England (1998–2010). We defined stroke risk according to the CHA2DS2-VASc score, and followed individuals over a median 2.2 years for 7005 ischaemic strokes (IS) and for 906 haemorrhagic strokes (HS). We calculated incidence rates (IRs) and 95% CIs per 100 person-years (PYs) (IR (95% CI)/100 PY) of IS and HS, with and without use of warfarin, and the NCB (ie, number of IS avoided) per 100 PYs of warfarin use (NCB (95% CI)/100 PY). Results Compared with individuals with initial record of diagnosis in secondary care, those in primary care had lower scores of IS risk (CHA2DS2-VASc≤2: 30.8% vs 20.6%), and lower overall incidence of IS (IR (95% CI)/100 PY: 2.3 (2.2 to 2.4) vs 4.3 (4.2 to 4.4), p value=0.00); however among individuals with CHA2DS2-VASc=0, 1 or 2 there were no differences in IS rate between those with initial record of diagnosis in primary care or secondary care (IR (95% CI)/100 PY: 0.2 (0.1 to 0.3) vs 0.3 (0.2 to 0.5), p value=0.16), (IR (95% CI)/100 PY: 0.6 (0.4 to 0.7) vs 0.7 (0.6 to 0.9), p value=0.08) and (IR (95% CI)/100 PY: 1.1 (1.00 to 1.3) vs 1.4 (1.2 to 1.6), p value=0.05), respectively. For CHA2DS2-VASc=0, 1 and 2, IRs of IS with versus without warfarin were (IR (95% CI)/100 PY: 0.4 (0.2 to 0.8) vs 0.2 (0.1 to 0.3), p value=0.16), (IR (95% CI)/100 PY: 0.4 (0.3 to 0.7) vs 0.7 (0.6 to 0.8), p value=0.03) and (IR (95% CI)/100 PY: 0.8 (0.7 to 1.0) vs 1.4 (1.3 to 1.6), p value=0.00), respectively. We found a significant positive NCB of warfarin from CHA2DS2-VASc≥2 in men (NCB (95% CI)/100 PY: 0.5 (0.1 to 0.9)) and from CHA2DS2-VASc≥3 in women (NCB (95% CI)/100 PY: 1.5 (1.1 to 1.9)). Conclusions CHA2DS2-VASc accurately stratifies IS risk in individuals with AF across both primary and secondary care. However, the incidence rate of ischaemic stroke at CHA2DS2-VASc=1 are lower than previously reported, which may change the decision to start anticoagulation with warfarin in these individuals. PMID:27580623

Influence of central metalloligand geometry on electronic communication between metals: syntheses, crystal structures, MMCT properties of isomeric cyanido-bridged Fe2Ru complexes, and TDDFT calculations.

PubMed

Ma, Xiao; Lin, Chen-Sheng; Hu, Sheng-Min; Tan, Chun-Hong; Wen, Yue-Hong; Sheng, Tian-Lu; Wu, Xin-Tao

2014-06-02

To investigate how the central metalloligand geometry influences distant or vicinal metal-to-metal charge-transfer (MMCT) properties of polynuclear complexes, cis- and trans-isomeric heterotrimetallic complexes, and their one- and two-electron oxidation products, cis/trans-[Cp(dppe)Fe(II)NCRu(II)(phen)2CN-Fe(II)(dppe)Cp][PF6]2 (cis/trans-1[PF6]2), cis/trans-[Cp(dppe)Fe(II)NCRu(II)(phen)2CNFe(III)-(dppe)Cp][PF6]3 (cis/trans-1[PF6]3) and cis/trans-[Cp(dppe)Fe(III)NCRu(II)(phen)2CN-Fe(III)(dppe)Cp][PF6]4 (cis/trans-1[PF6]4) have been synthesized and characterized. Electrochemical measurements show the presence of electronic interactions between the two external Fe(II) atoms of the cis- and trans-isomeric complexes cis/trans-1[PF6]2. The electronic properties of all these complexes were studied and compared by spectroscopic techniques and TDDFT//DFT calculations. As expected, both mixed valence complexes cis/trans-1[PF6]3 exhibited different strong absorption signals in the NIR region, which should mainly be attributed to a transition from an MO that is delocalized over the Ru(II)-CN-Fe(II) subunit to a Fe(III) d orbital with some contributions from the co-ligands. Moreover, the NIR transition energy in trans-1[PF6]3 is lower than that in cis-1[PF6]3, which is related to the symmetry of their molecular orbitals on the basis of the molecular orbital analysis. Also, the electronic spectra of the two-electron oxidized complexes show that trans-1[PF6]4 possesses lower vicinal Ru(II) → Fe(III) MMCT transition energy than cis-1[PF6]4. Moreover, the assignment of MMCT transition of the oxidized products and the differences of the electronic properties between the cis and trans complexes can be well rationalized using TDDFT//DFT calculations. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PyDREAM: high-dimensional parameter inference for biological models in python.

PubMed

Shockley, Erin M; Vrugt, Jasper A; Lopez, Carlos F; Valencia, Alfonso

2018-02-15

Biological models contain many parameters whose values are difficult to measure directly via experimentation and therefore require calibration against experimental data. Markov chain Monte Carlo (MCMC) methods are suitable to estimate multivariate posterior model parameter distributions, but these methods may exhibit slow or premature convergence in high-dimensional search spaces. Here, we present PyDREAM, a Python implementation of the (Multiple-Try) Differential Evolution Adaptive Metropolis [DREAM(ZS)] algorithm developed by Vrugt and ter Braak (2008) and Laloy and Vrugt (2012). PyDREAM achieves excellent performance for complex, parameter-rich models and takes full advantage of distributed computing resources, facilitating parameter inference and uncertainty estimation of CPU-intensive biological models. PyDREAM is freely available under the GNU GPLv3 license from the Lopez lab GitHub repository at http://github.com/LoLab-VU/PyDREAM. c.lopez@vanderbilt.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Improved assessment of pyrogenic carbon quantity and quality in soils by liquid chromatography

NASA Astrophysics Data System (ADS)

Wiedemeier, Daniel B.; Hilf, Michael D.; Smittenberg, Rienk H.; Schmidt, Michael W. I.

2013-04-01

Fire-derived (pyrogenic) carbon (PyC) is produced by the incomplete combustion of biomass, for example during wildfires. It can persist in the environment for a long time due to its relative resistance against biological and chemical breakdown. Its accurate quantification in soils, sediments and other environmental media is of great interest because the slow turn-over of PyC has implications for the global carbon cycle. It is thus relevant for climate scenarios and mitigation. Moreover, PyC in pedological and sedimentological records can be used to reconstruct wildfire history, which is closely linked to climate history. PyC assessment is also a valuable tool for characterizing biochars and other pyrogenic products. A whole suite of PyC quantification methods exists because PyC is not a defined chemical structure but rather a continuum of thermally altered biomass. The benzene polycarboxylic acids (BPCA) analysis is a molecular marker method that was shown to yield conservative estimates of PyC quantity in soils and environmental samples. In addition, it yields unique qualitative information about the degree of aromaticity and condensation of PyC, which is indicative for the pyrolysis temperature of PyC and its resistance against degradation. The commonly used BPCA method consists in digesting samples with nitric acid that breaks down the PyC into a suite of BPCAs, which are cleaned, derivatized and finally analyzed by gas chromatography-flame ionization detection (GC-FID). Here, we present a modified BPCA quantification method for soils, sediments and other environmental samples that uses a high performance liquid chromatography system coupled to diode array detection (HPLC-DAD). We demonstrate that this method greatly enhances the reproducibility of PyC measurements while significantly reducing analysis time. Moreover, much less sample material is needed for precise PyC assessment and we show that the HPLC-DAD method yields more consistent PyC measurements than the GC-FID method. Additionally, the new method also facilitates δ13C and 14C measurements of the PyC fraction in these complex matrix samples. The isotopic information of PyC further supports the assessment of carbon budgets in soils, sediments or (bio-)chars and the reconstruction of past burning and climate events, as will be shown with examples.

Low-spin manganese(II) and high-spin manganese(III) complexes derived from disalicylaldehyde oxaloyldihydrazone: Synthesis, spectral characterization and electrochemical studies

NASA Astrophysics Data System (ADS)

Syiemlieh, Ibanphylla; Kumar, Arvind; Kurbah, Sunshine D.; De, Arjune K.; Lal, Ram A.

2018-01-01

Low-spin manganese(II) complexes [MnII(H2slox)].H2O (1), [MnII(H2slox)(SL)] (where SL (secondary ligand) = pyridine (py, 2), 2-picoline (2-pic, 3), 3-picoline (3-pic, 4), and 4-picoline (4-pic, 5) and high-spin manganese(III) complex Na(H2O)4[MnIII(slox)(H2O)2].2.5H2O have been synthesized from disalicyaldehyde oxaloyldihydrazone in methanolic - water medium. The composition of complexes has been established by elemental analyses and thermoanalytical data. The structures of the complexes have been discussed on the basis of data obtained from molar conductance, UV visible, 1H NMR, infrared spectra, magnetic moment and electron paramagnetic resonance spectroscopic studies. Conductivity measurements in DMF suggest that the complexes (1-5) are non-electrolyte while the complex (6) is 1:1 electrolyte. The electronic spectral studies and magnetic moment data suggest five - coordinate square pyramidal structure for the complexes (2-5) and square planar geometry for manganese(II) in complex (1). In complex (6), both sodium and manganese(III) have six coordinate octahedral geometry. IR spectral studies reveal that the dihydrazone coordinates to the manganese centre in keto form in complexes (1-5) and in enol form in complex (6). In all complexes, the ligand is present in anti-cis configuration. Magnetic moment and EPR studies indicate manganese in +2 oxidation state in complexes (1-5), with low-spin square planar complex (1) and square pyramidal stereochemistries complexes (2-5) while in +3 oxidation state in high-spin distorted octahedral stereochemistry in complex (6). The complex (1) involves significant metal - metal interaction in the solid state. All of the complexes show only one metal centred electron transfer reaction in DMF solution in cyclic voltammetric studies. The complexes (1-5) involve MnII→MnI redox reaction while the complex (6) involves MnIII→MnII redox reaction, respectively.

First report of charge-transfer induced heat-set hydrogel. Structural insights and remarkable properties

NASA Astrophysics Data System (ADS)

Bhattacharjee, Subham; Maiti, Bappa; Bhattacharya, Santanu

2016-05-01

The remarkable ability of a charge-transfer (CT) complex prepared from a pyrene-based donor (Py-D) and a naphthalenediimide-based acceptor (NDI-A) led to the formation of a deep-violet in color, transparent hydrogel at room temperature (RT-gel). Simultaneously, the RT-gel was diluted beyond its critical gelator concentration (CGC) to obtain a transparent sol. Very interestingly, the resultant sol, on heating above 70 °C, transformed into a heat-set gel instantaneously with a hitherto unknown CGC value. Detailed studies revealed the smaller globular aggregates of the RT-gels fuse to form giant globules upon heating, which, in turn, resulted in heat-set gelation through further aggregation. The thermoresponsive property of Py-D alone and 1 : 1 Py-D : NDI-A CT complex was investigated in detail which revealed the hydrophobic collapse of the oxyethylene chains of the CT complex upon heating was mainly responsible for heat-set gelation. Thixotropy, injectability, as well as stimuli responsiveness of the RT-gels were also addressed. In contrast, heat-set gel did not show thixotropic behavior. The X-ray diffraction (XRD) patterns of the xerogel depicted lamellar packing of the CT stacks in the gel phase. Single crystal XRD studies further evidenced the 1 : 1 mixed CT stack formation in the lamellae and also ruled out orthogonal hydrogen bonding possibilities among the hydrazide unit in the CT gel although such interaction was observed in a single crystal of NDI-A alone. In addition, a Ag+-ion triggered metallogelation of NDI-A and nematic liquid-crystalline property of Py-D were also observed.The remarkable ability of a charge-transfer (CT) complex prepared from a pyrene-based donor (Py-D) and a naphthalenediimide-based acceptor (NDI-A) led to the formation of a deep-violet in color, transparent hydrogel at room temperature (RT-gel). Simultaneously, the RT-gel was diluted beyond its critical gelator concentration (CGC) to obtain a transparent sol. Very interestingly, the resultant sol, on heating above 70 °C, transformed into a heat-set gel instantaneously with a hitherto unknown CGC value. Detailed studies revealed the smaller globular aggregates of the RT-gels fuse to form giant globules upon heating, which, in turn, resulted in heat-set gelation through further aggregation. The thermoresponsive property of Py-D alone and 1 : 1 Py-D : NDI-A CT complex was investigated in detail which revealed the hydrophobic collapse of the oxyethylene chains of the CT complex upon heating was mainly responsible for heat-set gelation. Thixotropy, injectability, as well as stimuli responsiveness of the RT-gels were also addressed. In contrast, heat-set gel did not show thixotropic behavior. The X-ray diffraction (XRD) patterns of the xerogel depicted lamellar packing of the CT stacks in the gel phase. Single crystal XRD studies further evidenced the 1 : 1 mixed CT stack formation in the lamellae and also ruled out orthogonal hydrogen bonding possibilities among the hydrazide unit in the CT gel although such interaction was observed in a single crystal of NDI-A alone. In addition, a Ag+-ion triggered metallogelation of NDI-A and nematic liquid-crystalline property of Py-D were also observed. Electronic supplementary information (ESI) available: General experimental section, synthesis and characterization, single crystal X-ray data including CIF files and additional experimental results. See DOI: 10.1039/c6nr01128d

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aliphatic and chlorinated alkenes and epoxides as inducers of alkene monooxygenase and epoxidase activities in Xanthobacter strain Py2.

PubMed Central

Ensign, S A

1996-01-01

The inducible nature of the alkene oxidation system of Xanthobacter strain Py2 has been investigated. Cultures grown with glucose as the carbon source did not contain detectable levels of alkene monooxygenase or epoxidase, two key enzymes of alkene and epoxide metabolism. Upon addition of propylene to glucose-grown cultures, alkene monooxygenase and epoxidase activities increased and after an 11-h induction period reached levels of specific activity comparable to those in propylene-grown cells. Addition of chloramphenicol or rifampin prevented the increase in the enzyme activities. Comparison of the banding patterns of proteins present in cell extracts revealed that polypeptides with molecular masses of 43, 53, and 57 kDa accumulate in propylene-grown but not glucose-grown cells. Pulse-labeling of glucose-grown cells with [35S]methionine and [35S]cysteine revealed that the 43-, 53-, and 57-kDa proteins, as well as two additional polypeptides with molecular masses of 12 and 21 kDa, were newly synthesized upon exposure of cells to propylene or propylene oxide. The addition to glucose-grown cells of a variety of other aliphatic and chlorinated alkenes and epoxides, including ethylene, vinyl chloride (1-chloroethylene), cis- and trans-1,2-dichloroethylene, 1-chloropropylene, 1,3-dichloropropylene, 1-butylene, trans-2-butylene, isobutylene, ethylene oxide, epichlorohydrin (3-chloro-1,2-epoxypropane), 1,2-epoxybutane, cis- and trans-2,3-epoxybutane, and isobutylene oxide stimulated the synthesis of the five propylene-inducible polypeptides as well as increases in alkene monooxygenase and epoxidase activities. In contrast, acetylene, and a range of aliphatic and chlorinated alkanes, did not stimulate the synthesis of the propylene-inducible polypeptides or the increase in alkene monooxygenase and epoxidase activities. PMID:8572713

The Role of RUB (related to ubiquitin) Family of Proteins in the Hormone Response. Final Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Callis, Judy

2013-03-22

The Rub pathway is a conserved protein modification pathway. RUB (called Rubp1 in budding yeast, Nedd8 in animals and RUB in plants) is a ubiquitin-like 76-amino acid protein. It covalently attaches to protein using an enzymatic machinery analogous to the enzymes that attach ubiquitin to its substrate proteins. However, the nature of the complement of Rub-modified proteins in organisms was not clear. From bioinformatics analyses, one can identify a Rub activating enzymes and Rub conjugating enzymes. However, in many cases, their biochemical properties were not described. In DOE-funded work, we made major advances in our understanding of the Rub pathwaymore » in yeast and plants, work that is applicable to other organisms as well. There is a multi-subunit enzyme called SCF in all eukaryotes. The SCF consists of several subunits that serve as a scaffold (the cullin, SKP and RBX subunits) and one subunit that interacts with the substrate. This cullin protein (called Cdc53p in yeast and CULLIN 1 in plants and animals) was a known Rub target. In this work, we identified additional Rub targets in yeast as the other cullin-like proteins Cul3p and Rtt101p. Additionally we described the conservation of the Rub pathway because plant RUB1 can conjugated to yeast Cdc53p- in yeast. In the model plant Arabidopsis thaliana, we characterized the Rub activating enzymes and showed that they are not biochemically equivalent. We also showed that the Rub pathway is essential in plants and characterized plants with reduced levels of rub proteins. These plants are affected in multiple developmental processes. We discovered that they over-produce ethylene as dark-grown seedlings. We characterized a mutant allele of CULLIN1 in Arabidopsis with impaired interaction with RBX and showed that it is unstable in vivo. We used our knowledge of monitoring protein degradation to map the degradation determinants in a plant transcription factor. Finally, we took a mass spectrometric approach to identify novel Rub targets in plants and identified DDB1a, a subunit of an different ubiquitin ligase as a potential Rub-modified protein. Altogether, these studies have advanced our knowledge of the Rub pathway in all organisms.« less

Recognition and Cleavage of Related to Ubiquitin 1 (Rub1) and Rub1-Ubiquitin Chains by Components of the Ubiquitin-Proteasome System*

PubMed Central

Singh, Rajesh K.; Zerath, Sylvia; Kleifeld, Oded; Scheffner, Martin; Glickman, Michael H.; Fushman, David

2012-01-01

Of all ubiquitin-like proteins, Rub1 (Nedd8 in mammals) is the closest kin of ubiquitin. We show via NMR that structurally, Rub1 and ubiquitin are fundamentally similar as well. Despite these profound similarities, the prevalence of Rub1/Nedd8 and of ubiquitin as modifiers of the proteome is starkly different, and their attachments to specific substrates perform different functions. Recently, some proteins, including p53, p73, EGFR, caspase-7, and Parkin, have been shown to be modified by both Rub1/Nedd8 and ubiquitin within cells. To understand whether and how it might be possible to distinguish among the same target protein modified by Rub1 or ubiquitin or both, we examined whether ubiquitin receptors can differentiate between Rub1 and ubiquitin. Surprisingly, Rub1 interacts with proteasome ubiquitin-shuttle proteins comparably to ubiquitin but binds more weakly to a proteasomal ubiquitin receptor Rpn10. We identified Rub1-ubiquitin heteromers in yeast and Nedd8-Ub heteromers in human cells. We validate that in human cells and in vitro, human Rub1 (Nedd8) forms chains with ubiquitin where it acts as a chain terminator. Interestingly, enzymatically assembled K48-linked Rub1-ubiquitin heterodimers are recognized by various proteasomal ubiquitin shuttles and receptors comparably to K48-linked ubiquitin homodimers. Furthermore, these heterologous chains are cleaved by COP9 signalosome or 26S proteasome. A derubylation function of the proteasome expands the repertoire of its enzymatic activities. In contrast, Rub1 conjugates may be somewhat resilient to the actions of other canonical deubiquitinating enzymes. Taken together, these findings suggest that once Rub1/Nedd8 is channeled into ubiquitin pathways, it is recognized essentially like ubiquitin. PMID:23105008

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eisenhart, Reed J.; Carlson, Rebecca K.; Clouston, Laura J.

Heterobimetallic complexes that pair cobalt and copper were synthesized and characterized by a suite of physical methods, including X-ray diffraction, X-ray anomalous scattering, cyclic voltammetry, magnetometry, electronic absorption spectroscopy, electron paramagnetic resonance, and quantum chemical methods. Both Cu(II) and Cu(I) reagents were independently added to a Co(II) metalloligand to provide (py3tren)CoCuCl (1-Cl) and (py3tren)CoCu(CH3CN) (2-CH3CN), respectively, where py3tren is the triply deprotonated form of N,N,N-tris(2-(2-pyridylamino)ethyl)amine. Complex 2-CH3CN can lose the acetonitrile ligand to generate a coordination polymer consistent with the formula “(py3tren)CoCu” (2). One-electron chemical oxidation of 2-CH3CN with AgOTf generated (py3tren)CoCuOTf (1-OTf). The Cu(II)/Cu(I) redox couple for 1-OTf andmore » 2-CH3CN is reversible at -0.56 and -0.33 V vs Fc+/Fc, respectively. The copper oxidation state impacts the electronic structure of the heterobimetallic core, as well as the nature of the Co–Cu interaction. Quantum chemical calculations showed modest electron delocalization in the (CoCu)+4 state via a Co–Cu σ bond that is weakened by partial population of the Co–Cu σ antibonding orbital. By contrast, no covalent Co–Cu bonding is predicted for the (CoCu)+3 analogue, and the d-electrons are fully localized at individual metals.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eisenhart, Reed J.; Carlson, Rebecca K.; Clouston, Laura J.

Heterobimetallic complexes that pair cobalt and copper were synthesized and characterized by a suite of physical methods, including X-ray diffraction, X-ray anomalous scattering, cyclic voltammetry, magnetometry, electronic absorption spectroscopy, electron paramagnetic resonance, and quantum chemical methods. Both Cu(II) and Cu(I) reagents were independently added to a Co(II) metalloligand to provide (py 3tren)CoCuCl (1-Cl) and (py 3tren)CoCu(CH 3CN) (2-CH 3CN), respectively, where py3tren is the triply deprotonated form of N,N,N-tris(2-(2-pyridylamino)ethyl)amine. Complex 2-CH 3CN can lose the acetonitrile ligand to generate a coordination polymer consistent with the formula “(py3tren)CoCu” (2). One-electron chemical oxidation of 2-CH 3CN with AgOTf generated (py 3tren)CoCuOTf (1-OTf).more » The Cu(II)/Cu(I) redox couple for 1-OTf and 2-CH 3CN is reversible at -0.56 and -0.33 V vs Fc +/Fc, respectively. The copper oxidation state impacts the electronic structure of the heterobimetallic core, as well as the nature of the Co–Cu interaction. Quantum chemical calculations showed modest electron delocalization in the (CoCu) +4 state via a Co–Cu σ bond that is weakened by partial population of the Co–Cu σ antibonding orbital. By contrast, no covalent Co–Cu bonding is predicted for the (CoCu) +3 analogue, and the d-electrons are fully localized at individual metals.« less

Multiple interactions drive adaptor-mediated recruitment of the ubiquitin ligase rsp5 to membrane proteins in vivo and in vitro.

PubMed

Sullivan, James A; Lewis, Michael J; Nikko, Elina; Pelham, Hugh R B

2007-07-01

Recognition of membrane proteins by the Nedd4/Rsp5 ubiquitin ligase family is a critical step in their targeting to the multivesicular body pathway. Some substrates contain "PY" motifs (PPxY), which bind to WW domains in the ligase. Others lack PY motifs and instead rely on adaptors that recruit the ligase to them. To investigate the mechanism of adaptor-mediated ubiquitination, we have characterized the interactions between the adaptor Bsd2, the ubiquitin ligase Rsp5, and the membrane proteins Cps1, Tre1, and Smf1 from Saccharomyces cerevisiae. We have reconstituted adaptor-mediated modification of Cps1 and Tre1 in vitro, and we show that two PY motifs in Bsd2 and two WW domains (WW2 and WW3) in Rsp5 are crucial for this. The binding of a weak noncanonical DMAPSY motif in Bsd2 to WW3 is an absolute requirement for Bsd2 adaptor function. We show that sorting of the manganese transporter Smf1, which requires both Bsd2 and Tre1, depends upon two PY motifs in Bsd2 and one motif in Tre1 but only two WW domains in Rsp5. We suggest that sequential assembly of first a Bsd2/Rsp5 complex, then a Tre1/Bsd2/Rsp5 complex followed by a rearrangement of PY-WW interactions is required for the ubiquitination of Smf1.

Probing the coordination environment of Ti(3+) ions coordinated to nitrogen-containing Lewis bases.

PubMed

Morra, E; Maurelli, S; Chiesa, M; Van Doorslaer, S

2015-08-28

Multi-frequency continuous-wave and pulsed EPR techniques are employed to investigate the coordination of nitrogen-containing ligands to Ti(3+)-chloro complexes. Frozen solutions of TiCl3 and TiCl3(Py)3 dissolved in nitrogen-containing solvents have been investigated together with the TiCl3(Py)3 solid-state complex. For these different systems, the hyperfine and nuclear quadrupole data of Ti(3+)-bound (14)N nuclei are reported and discussed in the light of DFT computations, allowing for a detailed description of the microscopic structure of these systems.

Rhenium(I) polypyridine dibenzocyclooctyne complexes as phosphorescent bioorthogonal probes: Synthesis, characterization, emissive behavior, and biolabeling properties.

PubMed

Choi, Alex Wing-Tat; Liu, Hua-Wei; Lo, Kenneth Kam-Wing

2015-07-01

We report the development of rhenium(I) polypyridine complexes appended with a dibenzocyclooctyne (DIBO) moiety as bioorthogonal probes for azide-modified biomolecules. Three phosphorescent rhenium(I) polypyridine DIBO complexes [Re(N^N)(CO)3(py-C6-DIBO)][CF3SO3] (py-C6-DIBO=3-(N-(6-(3,4:7,8-dibenzocyclooctyne-5-oxycarbonylamino)hexyl)aminocarbonyl)pyridine; N^N=1,10-phenanthroline (phen) (1a), 3,4,7,8-tetramethyl-1,10-phenanthroline (Me4-phen) (2a), 4,7-diphenyl-1,10-phenanthroline (Ph2-phen) (3a)) and their DIBO-free counterparts [Re(N^N)(CO)3(py-C6-BOC)][CF3SO3] (py-C6-BOC=3-(N-(6-(tert-butoxycarbonylamino)hexyl)aminocarbonyl)pyridine; N^N=phen (1b), Me4-phen (2b), Ph2-phen (3b)) were synthesized and characterized. Upon photoexcitation, all the complexes displayed intense and long-lived yellow triplet metal-to-ligand charge-transfer ((3)MLCT) (dπ(Re)→π*(N^N)) emission. The DIBO complexes underwent facile reactions with benzyl azide in methanol at 298 K with second-order rate constants (k2) in the range of 0.077 to 0.091 M(-1) s(-1). As revealed from SDS-PAGE analysis, the DIBO complexes can selectively label azide-modified proteins and the resulting bioconjugates displayed strong phosphorescence upon photoexcitation. Results of inductively coupled plasma mass spectrometry (ICP-MS) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays indicated that the DIBO complexes accumulated in Chinese Hamster Ovary (CHO) cells with considerable cytotoxic activity. Upon incubation of CHO cells with these complexes, relatively weak intracellular emission was observed. In contrast, upon pretreatment of the cells with 1,3,4,6-tetra-O-acetyl-N-azidoacetyl-D-mannosamine (Ac4ManNAz), intense emission was observed from the cell membrane and some internal compartments. The results suggest that the DIBO complexes are promising candidates for imaging azide-labeled biomolecules. Copyright © 2015 Elsevier Inc. All rights reserved.

Combining anti-cancer drugs with artificial sweeteners: synthesis and anti-cancer activity of saccharinate (sac) and thiosaccharinate (tsac) complexes cis-[Pt(sac)2(NH3)2] and cis-[Pt(tsac)2(NH3)2].

PubMed

Al-Jibori, Subhi A; Al-Jibori, Ghassan H; Al-Hayaly, Lamaan J; Wagner, Christoph; Schmidt, Harry; Timur, Suna; Baris Barlas, F; Subasi, Elif; Ghosh, Shishir; Hogarth, Graeme

2014-12-01

The new platinum(II) complexes cis-[Pt(sac)2(NH3)2] (sac=saccharinate) and cis-[Pt(tsac)2(NH3)2] (tsac=thiosaccharinate) have been prepared, the X-ray crystal structure of cis-[Pt(sac)2(NH3)2] x H2O reveals that both saccharinate anions are N-bound in a cis-arrangement being inequivalent in both the solid-state and in solution at room temperature. Preliminary anti-cancer activity has been assessed against A549 human alveolar type-II like cell lines with the thiosaccharinate complex showing good activity. Copyright © 2014 Elsevier Inc. All rights reserved.

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

PubMed

Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

2015-01-01

Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

Chemical probes of the conformation of DNA modified by cis-diamminedichloroplatinum(II)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marrot, L.; Leng, M.

The purpose of this work was to analyze at the nucleotide level the distortions induced by the binding of cis-diamminedichloroplatinum(II) (cis-DDP) to DNA by means of chemical probes. In order to test the chemical probes, experiments were first carried out on two platinated oligonucleotides. It has been verified by circular dichroism and gel electrophoresis that the binding of cis-DDP to an AG or to a GTG site within a double-stranded oligonucleotide distorts the double helix. The reactivity of the oligonucleotide platinated at the GTG site with chloroacetaldehyde, diethyl pyrocarbonate, and osmium tetraoxide, respectively, suggests a local denaturation of the doublemore » helix. The 5'G residue and the T residue within the adduct are no longer paired, while the 3'G residue is paired. The double helix is more distorted (but not denatured) at the 5' side of the adduct than at the 3' side. The reactivities of the chemical probes with six platinated DNA restriction fragments show that even at a relatively high level of platination only a few base pairs are unpaired but the double helix is largely distorted. No local denaturation has been detected at the GG sites separated from the nearest GG or AG sites by at least three base pairs. The AG sites separated from the nearest AG or GG sites by at least three base pairs do not denature the double helix locally when they are in the sequences puAG/pyTC. It is suggested that the distortion within these sequences is induced by adducts located further away along the DNA fragments, these sequences not being the major sites for the binding of cis-DDP.« less

Epidermal growth factor-induced phosphatidylinositol 3-kinase activation and DNA synthesis. Identification of Grb2-associated binder 2 as the major mediator in rat hepatocytes.

PubMed

Kong, M; Mounier, C; Wu, J; Posner, B I

2000-11-17

In previous work we showed that the phosphatidylinositol 3-kinase (PI3-kinase), not the mitogen-activated protein kinase, pathway is necessary and sufficient to account for insulin- and epidermal growth factor (EGF)-induced DNA synthesis in rat hepatocytes. Here, using a dominant-negative p85, we confirmed the key role of EGF-induced PI3-kinase activation and sought to identify the mechanism by which this is effected. Our results show that EGF activates PI3-kinase with a time course similar to that of the association of p85 with three principal phosphotyrosine proteins (i. e. PY180, PY105, and PY52). We demonstrated that each formed a distinct p85-associated complex. PY180 and PY52 each constituted about 10% of EGF-activated PI3-kinase, whereas PY105 was responsible for 80%. PY105 associated with Grb2 and SHP-2, and although it behaved like Gab1, none of the latter was detected in rat liver. We therefore cloned a cDNA from rat liver, which was found to be 95% homologous to the mouse Grb2-associated binder 2 (Gab2) cDNA sequence. Using a specific Gab2 antibody, we demonstrated its expression in and association with p85, SHP-2, and Grb2 upon EGF treatment of rat hepatocytes. Gab2 accounted for most if not all of the PY105 species, since immunoprecipitation of Gab2 with specific antibodies demonstrated parallel immunodepletion of Gab2 and PY105 from the residual supernatants. We also found that the PI3-kinase activity associated with Gab2 was totally abolished by dominant negative p85. Thus, Gab2 appears to be the principal EGF-induced PY protein recruiting and activating PI3-kinase and mitogenesis.

PyXNAT: XNAT in Python.

PubMed

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S; Poline, Jean-Baptiste

2012-01-01

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line.

Copper-containing ceramic precursor synthesis: Solid-state transformations and materials technology

NASA Technical Reports Server (NTRS)

Hepp, Aloysius F.; Eckles, William E.; Duraj, Stan A.; Andras, Maria T.; Fanwick, Phillip E.; Richman, Robert M.; Sabat, Michael L.; Power, Michael B.; Gordon, Edward M.; Barron, Andrew

1994-01-01

Three copper systems with relevance to materials technology are discussed. In the first, a CuS precursor, Cu4S1O (4-methylpyridine)(sub 4)- (4-MePy), was prepared by three routes: reaction of Cu2S, reaction of CuBr-SMe2, and oxidation of copper powder with excess sulfur in 4-methylpyridine by sulfur. In the second, copper powder was found to react with excess thiourea (H2NC(S)NH2) in 4-methylpyridine to produce thiocyanate (NCS(-)) complexes. Three isolated and characterized compounds are: Cu(NCS)(4-MePy)(sub 2), a polymer, (4-MePy-H)(Cu(NCS)(sub 3)(4-MePy)(sub 2)), a salt, and t-Cu(NCS)(sub 2)(4-MePy)(sub 4). Finally, an attempt to produce a mixed-metal sulfide precursor of Cu and Ga in N-methylimidazole (N-MeIm) resulted in the synthesis of a Cu-containing polymer, Cu(SO4)(N-MeIm). The structures are presented; the chemistry will be briefly discussed in the context of preparation and processing of copper-containing materials for aerospace applications.

PyXNAT: XNAT in Python

PubMed Central

Schwartz, Yannick; Barbot, Alexis; Thyreau, Benjamin; Frouin, Vincent; Varoquaux, Gaël; Siram, Aditya; Marcus, Daniel S.; Poline, Jean-Baptiste

2012-01-01

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programmatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low-level interfaces to databases. We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables PyXNAT to expose the XNAT Web Services and unify their features with a higher level and more expressive language. PyXNAT provides XNAT users direct access to all the scientific packages in Python. Finally PyXNAT aims to be efficient and easy to use, both as a back-end library to build XNAT clients and as an alternative front-end from the command line. PMID:22654752

Nitric oxide production by visible light irradiation of aqueous solution of nitrosyl ruthenium complexes.

PubMed

Sauaia, Marília Gama; de Lima, Renata Galvão; Tedesco, Antonio Claudio; da Silva, Roberto Santana

2005-12-26

[Ru(II)L(NH(3))(4)(pz)Ru(II)(bpy)(2)(NO)](PF(6))(5) (L is NH(3), py, or 4-acpy) was prepared with good yields in a straightforward way by mixing an equimolar ratio of cis-[Ru(NO(2))(bpy)(2)(NO)](PF(6))(2), sodium azide (NaN(3)), and trans-[RuL(NH(3))(4)(pz)] (PF(6))(2) in acetone. These binuclear compounds display nu(NO) at ca. 1945 cm(-)(1), indicating that the nitrosyl group exhibits a sufficiently high degree of nitrosonium ion (NO(+)). The electronic spectrum of the [Ru(II)L(NH(3))(4)(pz)Ru(II)(bpy)(2)(NO)](5+) complex in aqueous solution displays the bands in the ultraviolet and visible regions typical of intraligand and metal-to-ligand charge transfers, respectively. Cyclic voltammograms of the binuclear complexes in acetonitrile give evidence of three one-electron redox processes consisting of one oxidation due to the Ru(2+/3+) redox couple and two reductions concerning the nitrosyl ligand. Flash photolysis of the [Ru(II)L(NH(3))(4)(pz)Ru(II)(bpy)(2)(NO)](5+) complex is capable of releasing nitric oxide (NO) upon irradiation at 355 and 532 nm. NO production was detected and quantified by an amperometric technique with a selective electrode (NOmeter). The irradiation at 532 nm leads to NO release as a consequence of a photoinduced electron transfer. All species exhibit similar photochemical behavior, a feature that makes their study extremely important for their future application in the upgrade of photodynamic therapy in living organisms.

Efficient near-infrared emission of π-extended cyclometalated iridium complexes based on pyrene in solution-processed polymer light-emitting diode

NASA Astrophysics Data System (ADS)

Liu, Yu; Hao, Zhaoran; Meng, Fanyuan; Wang, Pu; Yang, Liang; Wang, Yafei; Pei, Yong; Su, Shijian

2018-05-01

A novel iridium complex grafting hole-transporting triphenylamine (TPA) unit onto cyclometalated ligand, namely t-BuPyrPyTPA)2Ir(acac), was successfully synthesized and characterized. The photophysical, electrochemical and DFT/TD-DFT calculation, as well as electroluminescence properties of this iridium complex were fully investigated. Meanwhile, the PLEDs employing (t-BuPyrPyTPA)2Ir(acac) as dopant presented stable NIR emission peaked at 697 nm and a shoulder at 764 nm with a highest external quantum efficiency (EQE) of 0.56% at 4 wt% dopant concentration. These results demonstrate that expanding the conjugation length of the ligand is an effective way to achieve NIR emission.

Iron Pentapyridyl Complexes as Molecular Water Oxidation Catalysts: Strong Influence of a Chloride Ligand and pH in Altering the Mechanism.

PubMed

Das, Biswanath; Orthaber, Andreas; Ott, Sascha; Thapper, Anders

2016-05-23

The development of molecular water oxidation catalysts based on earth-abundant, non-noble metals is essential for artificial photosynthesis research. Iron, which is the most abundant transition metal in the earth's crust, is a prospective candidate for this purpose. Herein, we report two iron complexes based on the polypyridyl ligand Py5OH (Py5OH=pyridine-2,6-diylbis [di(pyridin-2-yl)methanol]) that can catalyse water oxidation to produce O2 in Ru(III) -induced (at pH 8, highest turnover number (TON)=26.5; turnover frequency (TOF)=2.2 s(-1) ), Ce(IV) -induced (at pH≈1.5 highest TON=16; TOF=0.75 s(-1) ) and photo-induced (at pH 8, highest TON=43.5; TOF=0.6 s(-1) ) reactions. A chloride ligand in one of the iron complexes is shown to affect the activity strongly, improve stability and, thereby, the performance at pH 8 but it inhibits oxygen evolution at pH≈1.5. The observations are consistent with a change in mechanism for catalytic water oxidation with the Fe(Py5OH) complexes between acidic (Ce(IV) ) and near-neutral pH (Ru(III) ). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Three-Fold Intramolecular Ring Closing Alkene Metatheses of Square Planar Complexes with cis Phosphorus Donor Ligands P(X(CH2) mCH═CH2)3 (X = -, m = 5-10; X = O, m = 3-5): Syntheses, Structures, and Thermal Properties of Macrocyclic Dibridgehead Diphosphorus Complexes.

PubMed

Joshi, Hemant; Kharel, Sugam; Ehnbom, Andreas; Skopek, Katrin; Hess, Gisela D; Fiedler, Tobias; Hampel, Frank; Bhuvanesh, Nattamai; Gladysz, John A

2018-05-17

Reactions of cis-PtCl 2 (P((CH 2 ) m CH═CH 2 ) 3 ) 2 and Grubbs' first generation catalyst and then hydrogenations afford cis- PtCl 2 (P((CH 2 ) n ) 3 P) ( cis-2; n = 2 m + 2 = 12 (b), 14 (c), 16 (d), 18 (e), 20 (f), 22 (g); 6-40%), derived from 3-fold interligand metatheses. The phosphite complexes cis-PtCl 2 (P(O(CH 2 ) m* CH═CH 2 ) 3 ) 2 are similarly converted to cis- PtCl 2 (P(O(CH 2 ) n* O) 3 P) ( cis-5; n* = 8 (a), 10 (b), 12 (c), 10-20%). The substitution products cis- PtPh 2 (P((CH 2 ) n ) 3 P) ( cis-6c,d) and cis- PtI 2 (P(O(CH 2 ) 10 O) 3 P) are prepared using Ph 2 Zn and NaI, respectively. Crystal structures of cis-2c,d,f, cis-5a,b, and cis-6c show one methylene bridge that roughly lies in the platinum coordination plane and two that are perpendicular. The thermal behavior of the complexes is examined. When the bridges are sufficiently long, they rapidly exchange via an unusual "triple jump rope" motion over the PtX 2 moieties. NMR data establish Δ H ⧧ , Δ S ⧧ , and Δ G 298K ⧧ /Δ G 393K ⧧ values of 7.8 kcal/mol, -27.9 eu, and 16.1/18.8 kcal/mol for cis-2d, and a Δ G 393K ⧧ of ≥19.6 kcal/mol for the shorter bridged cis-2c. While cis-2c,g gradually convert to trans-2c,g at 150-185 °C in haloarenes, trans-2c,g give little reaction under analogous conditions, establishing the stability order trans > cis. Similar metathesis/hydrogenation sequences with octahedral complexes containing two cis phosphine ligands, fac-ReX(CO) 3 (P((CH 2 ) 6 CH═CH 2 ) 3 ) 2 (X = Cl, Br), give fac- ReX(CO) 3 ( P(CH 2 ) 13 CH 2 )((CH 2 ) 14 )( P(CH 2 ) 13 CH 2 ) (19-50%), which are derived from a combination of interligand and intraligand metathesis. The relative stabilities of cis/ trans and other types of isomers are probed by combinations of molecular dynamics and DFT calculations.

pyLIMA: An Open-source Package for Microlensing Modeling. I. Presentation of the Software and Analysis of Single-lens Models

NASA Astrophysics Data System (ADS)

Bachelet, E.; Norbury, M.; Bozza, V.; Street, R.

2017-11-01

Microlensing is a unique tool, capable of detecting the “cold” planets between ˜1 and 10 au from their host stars and even unbound “free-floating” planets. This regime has been poorly sampled to date owing to the limitations of alternative planet-finding methods, but a watershed in discoveries is anticipated in the near future thanks to the planned microlensing surveys of WFIRST-AFTA and Euclid's Extended Mission. Of the many challenges inherent in these missions, the modeling of microlensing events will be of primary importance, yet it is often time-consuming, complex, and perceived as a daunting barrier to participation in the field. The large scale of future survey data products will require thorough but efficient modeling software, but, unlike other areas of exoplanet research, microlensing currently lacks a publicly available, well-documented package to conduct this type of analysis. We present version 1.0 of the python Lightcurve Identification and Microlensing Analysis (pyLIMA). This software is written in Python and uses existing packages as much as possible to make it widely accessible. In this paper, we describe the overall architecture of the software and the core modules for modeling single-lens events. To verify the performance of this software, we use it to model both real data sets from events published in the literature and generated test data produced using pyLIMA's simulation module. The results demonstrate that pyLIMA is an efficient tool for microlensing modeling. We will expand pyLIMA to consider more complex phenomena in the following papers.

Modeling multi-scale resource selection for bear rub trees in northwestern Montana

USGS Publications Warehouse

Morgan Henderson, Matthew J.; Hebblewhite, Mark; Mitchell, Michael S.; Stetz, Jeffrey B.; Kendall, Katherine C.; Carlson, Ross T.

2015-01-01

Both black (Ursus americanus) and grizzly bears (U. arctos) are known to rub on trees and other objects, producing a network of repeatedly used and identifiable rub sites. In 2012, we used a resource selection function to evaluate hypothesized relationships between locations of 887 bear rubs in northwestern Montana, USA, and elevation, slope angle, density of open roads and distance from areas of heightened plant-productivity likely containing forage for bears. Slope and density of open roads were negatively correlated with rub presence. No other covariates were supported as explanatory variables. We also hypothesized that bear rubs would be more strongly associated with closed roads and developed trails than with game trails. The frequencies of bear rubs on 30 paired segments of developed tracks and game trails were not different. Our results suggest bear rubs may be associated with bear travel routes, and support their use as “random” sampling devices for non-invasive spatial capture–recapture population monitoring.

Influence of rubbing on rotor dynamics, part 1

NASA Technical Reports Server (NTRS)

Muszynska, Agnes; Bently, Donald E.; Franklin, Wesley D.; Hayashida, Robert D.; Kingsley, Lori M.; Curry, Arthur E.

1989-01-01

The results of analytical and experimental research on rotor-to-stationary element rubbing in rotating machines are presented. A characterization of physical phenomena associated with rubbing, as well as a literature survey on the subject of rub is given. The experimental results were obtained from two rubbing rotor rigs: one, which dynamically simulates the space shuttle main engine high pressure fuel turbopump (HPFTP), and the second one, much simpler, a two-mode rotor rig, designed for more generic studies on rotor-to-stator rubbing. Two areas were studied: generic rotor-to-stator rub-related dynamic phenomena affecting rotating machine behavior and applications to the space shuttle HPFTP. An outline of application of dynamic stiffness methodology for identification of rotor/bearing system modal parameters is given. The mathematical model of rotor/bearing/seal system under rub condition is given. The computer program was developed to calculate rotor responses. Compared with experimental results the computed results prove an adequacy of the model.

Direct synthesis of cis-dihalido-bis(NHC) complex of nickel(II) and catalytic application in olefin addition polymerization: effect of halogen co-ligands and density functional theory study.

PubMed

Zhang, Dao; Zhou, Sen; Li, Zhiming; Wang, Quanrui; Weng, Linhong

2013-09-07

Two novel amine-containing N-heterocyclic carbene ligand precursors [H(1a-b)]Br have been prepared in good yield and fully characterized. Direct syntheses of cis- and trans-dihalido-bis(NHC) nickel complexes [Ni(NHC)2X2] (X = Cl, Br) are reported. The solid structures of trans-[Ni(1a-b)2Br2] (2a-b) and cis-[Ni(1a)2Cl2] (3) were determined by single-crystal X-ray analysis and 3 was found to be the first example of cis-configuration coordination of monodentate NHC ligands to a metal center for dihalido-bis(NHC) nickel complexes. DFT calculations were conducted to determine the energy difference between cis- and trans-isomers of complexes 2a and 3 bearing bromide and chloride co-ligands. The cis-[Ni(1a)2Cl2] (cis-3) is 1.77-1.55 kcal mol(-1) lower in energy than its trans-isomer in polar solvents including CH2Cl2 and THF, while the trans-[Ni(1a)2Br2] (trans-2a) is more stable than the cis-isomer similarly in the gas phase. The cis nickel complex 3 with two coordinated monodentate NHCs was tested for olefin addition polymerization at standard conditions. It was found that cis-3 was inactive in ethylene polymerization but showed moderate catalytic activities (0.5-3.0 × 10(6) g of PNB (mol of Ni)(-1) h(-1)) in the addition polymerization of norbornene in the presence of methylaluminoxane (MAO) as cocatalyst.

Ferrocenes as potential chemotherapeutic drugs: Synthesis, cytotoxic activity, reactive oxygen species production and micronucleus assay

PubMed Central

Pérez, Wanda I.; Soto, Yarelys; Ortíz, Carmen; Matta, Jaime; Meléndez, Enrique

2014-01-01

Three new ferrocene complexes were synthesized with 4-(1H-pyrrol-1-yl)phenol group appended to one of the Cp ring. These are: 1,1′-4-(1H-pyrrol-1-yl)phenyl ferrocenedicarboxylate, (“Fc-(CO2-Ph-4-Py)2”), 1,4-(1H-pyrrol-1-yl)phenyl, 1′-carboxyl ferrocenecarboxylate (“Fc-(CO2-Ph-4-Py)CO2H”) and 4-(1H-pyrrol-1-yl)phenyl ferroceneacetylate (“Fc-CH2CO2-Ph-4-Py”). The new species were characterized by standard analytical methods. Cyclic voltammetry experiments showed that Fc-CH2CO2-Ph-4-Py has redox potential very similar to the Fc/Fc+ redox couple whereas Fc-(CO2-Ph-4-Py)2 and Fc-(CO2-Ph-4-Py)CO2H have redox potentials of over 400 mV higher than Fc/Fc+ redox couple. The in vitro studies on Fc-(CO2-Ph-4-Py)2 and Fc-(CO2-Ph-4-Py)CO2H revealed that these two compounds have moderate anti-proliferative activity on MCF-7 breast cancer cell line. In contrast Fc-CH2CO2-Ph-4-Py which displayed low anti-proliferative activity. In the HT-29 colon cancer cell line, the new species showed low anti-proliferaive activity. Cytokinesis-block micronucleus assay (CBMN) was performed on these ferrocenes and it was determined they induce micronucleus formation on binucleated cells and moderate genotoxic effects on the MCF-7 breast cancer cell line. There is a correlation between the IC50 values of the ferrocenes and the amount of micronucleus formation activity on binucleated cells and the reactive oxygen species (ROS) production on MCF-7 cell line. PMID:25555734

Computational, electrochemical, and spectroscopic studies of two mononuclear cobaloximes: the influence of an axial pyridine and solvent on the redox behaviour and evidence for pyridine coordination to cobalt(I) and cobalt(II) metal centres†

PubMed Central

Lawrence, Mark A. W.; Celestine, Michael J.; Artis, Edward T.; Joseph, Lorne S.; Esquivel, Deisy L.; Ledbetter, Abram J.; Cropek, Donald M.; Jarrett, William L.; Bayse, Craig A.; Brewer, Matthew I.; Holder, Alvin A.

2018-01-01

[Co(dmgBF2)2(H2O)2] 1 (where dmgBF2 = difluoroboryldimethylglyoximato) was used to synthesize [Co(dmgBF2)2(H2O)(py)]·0.5(CH3)2CO 2 (where py = pyridine) in acetone. The formulation of complex 2 was confirmed by elemental analysis, high resolution MS, and various spectroscopic techniques. The complex [Co(dmgBF2)2(solv)(py)] (where solv = solvent) was readily formed in situ upon the addition of pyridine to complex 1. A spectrophotometric titration involving complex 1 and pyridine proved the formation of such a species, with formation constants, log K = 5.5, 5.1, 5.0, 4.4, and 3.1 in 2-butanone, dichloromethane, acetone, 1,2-difluorobenzene/acetone (4 : 1, v/v), and acetonitrile, respectively, at 20 °C. In strongly coordinating solvents, such as acetonitrile, the lower magnitude of K along with cyclic voltammetry, NMR, and UV-visible spectroscopic measurements indicated extensive dissociation of the axial pyridine. In strongly coordinating solvents, [Co(dmgBF2)2(solv)(py)] can only be distinguished from [Co(dmgBF2)2(solv)2] upon addition of an excess of pyridine, however, in weakly coordinating solvents the distinctions were apparent without the need for excess pyridine. The coordination of pyridine to the cobalt(II) centre diminished the peak current at the Epc value of the CoI/0 redox couple, which was indicative of the relative position of the reaction equilibrium. Herein we report the first experimental and theoretical 59Co NMR spectroscopic data for the formation of Co(I) species of reduced cobaloximes in the presence and absence of py (and its derivatives) in CD3CN. From spectroelectrochemical studies, it was found that pyridine coordination to a cobalt(I) metal centre is more favourable than coordination to a cobalt(II) metal centre as evident by the larger formation constant, log K = 4.6 versus 3.1, respectively, in acetonitrile at 20 °C. The electrosynthesis of hydrogen by complexes 1 and 2 in various solvents demonstrated the dramatic effects of the axial ligand and the solvent on the turnover number of the respective catalyst. PMID:27244471

Ordered defect compounds in CuInSe{sub 2} for photovoltaic solar cell application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sato, K.; Katayama-Yoshida, H.

2014-02-21

Due to the complete compensation, defect complex (2V{sub Cu}+In{sub Cu}), namely two Cu vacancies and In located at Cu site, is stable in CuInSe{sub 2} (CIS). It is known that the series of ordered defect compounds (ODC) are constracted by ordering the defect complex. Based on the total energy calcalation by using the Korringa-Kohn-Rostoker coherent potential approxiamtion (KKR-CPA) method, we discuss phase separation of the CIS with the defect complexes into ODC and CIS. Since the band alignment between ODC and CIS is calculated to be type 2, effective electron-hole separation at the interface between ODC and CIS can bemore » expected. This causes the enhancement of conversion efficiency of CIS-based solar cell materials.« less

Magnetostriction and complex permeability of [Fe62Co19Ga19/Py]5/glass multilayered films

NASA Astrophysics Data System (ADS)

Liu, Chi-Ching; Jen, Shien-Uang; Lin, Yu-Cha; Lai, Chih-Huang; Liao, Sheng-Chieh; Chien, Chia-Hua

2015-07-01

[Fe62Co19Ga19(x)/Py(40-x)]5/glass multilayered films, where x=0, 5, 10, 15, 20 nm, y=x(nm)/40(nm), and 0≤y≤1, were made by the magnetron sputtering method at room temperature. The total number of combined [Fe-Co-Ga/Py] unit-layers was five. The total film thickness (tf) was fixed at 200 nm. We have performed two kinds of experiments on these films: (i) the saturation magnetostriction (λS) measurement, and (ii) the complex permeability (μ=μR-jμI) experiment to find the resonance frequency (fR) as a function of external magnetic field (HE). By definition, the microwave power absorption Pabs at ferromagnetic resonance (FMR) for a metallic conductor is written as Pabs = [(μR2+ μI2)1/2 +μI ]1/2 . We define the half-width of the absorption peak Δf as Δf ≣ ΔfS+ΔfA, where ΔfS and ΔfA are the symmetric and asymmetric parts in Δf. The degree of asymmetry, ΔfA/Δf, of each absorption peak is associated with the structural and/or magnetic inhomogeneity in the film. The main findings from this study are summarized as follows: (A) maximum λS occurs in the y=1 film, and as y increases, λS increases; (B) biasing field for magnetostriction decreases greatly by adding Py layers; (C) the magnetostriction sensitivity remains almost constant in the range 0.4

N-Picolyl Derivatives of Kemp’s Triamine as Potential Antitumor Agents: A Preliminary Investigation

PubMed Central

Regino, Celeste Aida S.; Torti, Suzy V.; Ma, Rong; Yap, Glenn P.A.; Kreisel, Kevin A.; Torti, Frank M.; Planalp, Roy P.; Brechbiel, Martin W.

2008-01-01

Pre-organized tripodal ligands such as the N-picolyl derivatives of cis,cis-1,3,5-triamino-cis,cis-1,3,5-trimethylcyclohexane (Kemp’s triamine) were prepared as analogs to N,N’,N”- tris(2-pyridylmethyl)-cis,cis-1,3,5-triaminocyclohexane (tachpyr) in hopes of enhancing the rate of formation and stability of the metal complexes. A tricyclic bisaminal was formed via the reduction of the Schiff base while the tri(picolyl) derivative was synthesized via reductive amination of pyridine carboxaldehyde. Their cytotoxicities to the HeLa cell line were evaluated and directly compared to tachpyr and N,N’,N”- tris(2-pyridylmethyl)-tris(2-aminoethyl)amine (trenpyr). Results indicate that N,N’,N”-tris(2-pyridylmethyl)-cis,cis-1,3,5-triamino-cis,cis-1,3,5-trimethylcyclohexane (Kemp’s pyr) exhibits cytotoxic activity against the HeLa cancer cell line comparable to tachpyr (IC50 ~ 8.0 µM). Both Kemp’s pyr and tachpyr show higher cytotoxic activity over the aliphatic analogue of trenpyr (IC50 ~ 14 µM) suggesting that the major contributor to the activity is the ligand’s ability to form a stable and tight complex and that the equatorial/axial equilibrium impacting the complex formation for the cyclohexane-based ligands is not significant. PMID:16335923

Spin crossover behaviour in Hofmann-like coordination polymer Fe(py)2[Pd(CN)4] with 57Fe Mössbauer spectra

NASA Astrophysics Data System (ADS)

Kitazawa, Takafumi; Kishida, Takanori; Kawasaki, Takeshi; Takahashi, Masashi

2017-11-01

We have prepared the 2D spin crossover complexes Fe(L)2Pd(CN)4 (L = py : 1a; py-D5 : 1b and py-15N : 1c). 1a has been characterised by 57Fe Mossbauer spectroscopic measurements, single crystal X-ray determination and SQUID measurements. The Mössbauer spectra for 1a indicate that the iron(II) spin states are in high spin states at 298 K and are in low spin states at 77 K. The crystal structures of 1a at 298 K and 90 K also show the high spin state and the low spin state respectively, associated with the Fe(II)-N distances. The spin transition temperature range of 1a is higher than that of Fe(py)2Ni(CN)4 since Pd(II) ions are larger and heavier than Ni(II) ions. SQUID data indicate isotope effects among 1a, 1b and 1c are observed in very small shifts of the transition temperatures probably due to larger and heavier Pd(II) ions. The delicate shifts would be associated with subtle balances between different vibrations around Fe(II) atoms and electronic factors.

Nucleoprotein Complexes Containing Replicating Simian Virus 40 DNA: Comparison with Polyoma Nucleoprotein Complexes

PubMed Central

Hall, Mark R.; Meinke, William; Goldstein, David A.

1973-01-01

Procedures for isolating nucleoprotein complexes containing replicating polyoma DNA from infected mouse cells were used to prepare short-lived nucleoprotein complexes (r-SV40 complexes) containing replicating simian virus 40 (SV40) DNA from infected monkey cells. Like the polyoma complexes, r-SV40 complexes were only partially released from nuclei by cell lysis but could be extracted from nuclei by prolonged treatment with solutions containing Triton X-100. r-SV40 complexes sedimented faster than complexes containing SV40 supercoiled DNA (SV40 complex) in sucrose gradients, and both types of SV40 nucleoprotein complexes sedimented ahead of polyoma complexes containing supercoiled polyoma DNA (py complex). The sedimentation rates of py complex and SV40 complex were 56 and 61S, respectively, based on the sedimentation rate of the mouse large ribosomal subunit as a marker. r-SV40 complexes sedimented as multiple peaks between 56 and 75S. Sedimentation and buoyant density measurements indicated that protein is bound to all forms of SV40 DNA at about the same ratio of protein to DNA (1-2/1) as was reported for polyoma nucleoproteins. PMID:4359958

Rubbing ointments and asthma morbidity in adolescents.

PubMed

Reznik, Marina; Sharif, Iman; Ozuah, Philip O

2004-12-01

To determine the relationship between the use of rubbing ointments and asthma morbidity in adolescents. Cross-sectional study. Inner-city high school in the Bronx, New York. 165 adolescents with asthma. Asthma morbidity, defined as emergency department (ED) use for asthma in the past year and over the lifetime. While 127 (77%) of subjects used albuterol as the first treatment for their last asthma attack, 18 (11%) used rubbing ointments. The rubs and albuterol groups were similar in asthma severity, mean age, gender, and ethnicity. However, subjects in the the rubs group were less likely than subjects in the albuterol group to have made an ED visit over the past 12 months or over their lifetime. Regression analysis revealed that, after controlling for asthma severity, use of rubs independently predicted less lifetime ED use. After controlling for asthma severity, use of rubs by adolescents with asthma was associated with lower asthma morbidity as measured by ED use.

Rhenium and technetium tricarbonyl complexes of 1,4-Substituted pyridyl-1,2,3-triazole bidentate 'click' ligands conjugated to a targeting RGD peptide.

PubMed

Connell, Timothy U; Hayne, David J; Ackermann, Uwe; Tochon-Danguy, Henri J; White, Jonathan M; Donnelly, Paul S

2014-04-01

New 1,4-substituted pyridyl-1,2,3-triazole ligands with pendent phenyl isothiocyanate functional groups linked to the heterocycle through a short methylene or longer polyethylene glycol spacers were prepared and conjugated to a peptide containing the arginine-glycine-aspartic acid peptide motif. Rhenium and technetium carbonyl complexes, [M(CO)3 L(x) (py)](+) (where M = Re(I) or (99m) Tc(I) ; L(x)  = 1,4-substituted pyridyl-1,2,3-triazole ligands and py = pyridine) were prepared. One rhenium complex has been characterized by X-ray crystallography, and the luminescent properties of [M(CO)3 L(x) (py)](+) are reported. Copyright © 2013 John Wiley & Sons, Ltd.

7 CFR 51.1220 - Leaf or limb rub injury.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Leaf or limb rub injury. 51.1220 Section 51.1220 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Leaf or limb rub injury. “Leaf or limb rub injury” means that the scarring is not smooth, not light...

7 CFR 51.1220 - Leaf or limb rub injury.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 2 2013-01-01 2013-01-01 false Leaf or limb rub injury. 51.1220 Section 51.1220 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards... Leaf or limb rub injury. “Leaf or limb rub injury” means that the scarring is not smooth, not light...

A turn-on supramolecular fluorescent probe for sensing benzimidazole fungicides and its application in living cell imaging

NASA Astrophysics Data System (ADS)

Tang, Qing; Zhang, Jing; Sun, Tao; Wang, Cheng-Hui; Huang, Ying; Zhou, Qingdi; Wei, Gang

2018-02-01

A cucurbit[8]uril-based turn-on supramolecular fluorescent probe between cucurbit[8]uril (Q[8]) and pyronine Y (PyY) (designated 2PyY@Q[8]) in acidic aqueous solution showed a remarkable fluorescence 'turn-on' response to benzimidazole fungicides such as thiabendazole, fuberidazole and carbendazim. The 2PyY@Q[8] fluorescent probe can be used to detect benzimidazole fungicides with high sensitivity and selectivity with a detection limit of 10- 8 mol/L. A good linear relationship of emission intensity at 580 nm for benzimidazole fungicides at concentrations of 0.4-5.0 μmol/L was observed. The proposed sensing mechanism was investigated using 1H NMR spectroscopy combined with density functional theory calculations at the B3LYP/6-31G(d) level. The cell imaging study showed that the 2PyY@Q[8] complex could be used to image benzimidazole fungicide in prostate cancer (PC3) cells, which may help to elucidate relevant biological processes at the molecular level.

[Au(pyb-H)(mnt)]: A novel gold(III) 1,2-dithiolene cyclometalated complex with antimicrobial activity (pyb-H=C-deprotonated 2-benzylpyridine; mnt=1,2-dicyanoethene-1,2-dithiolate).

PubMed

Pintus, Anna; Aragoni, M Carla; Cinellu, Maria A; Maiore, Laura; Isaia, Francesco; Lippolis, Vito; Orrù, Germano; Tuveri, Enrica; Zucca, Antonio; Arca, Massimiliano

2017-05-01

The novel heteroleptic cyclometalated complex [Au III (py b -H)(mnt)] (1; py b -H=C-deprotonated 2-benzylpyridine; mnt =1,2-dicyanoethene-1,2-dithiolate) was tested against a panel of ten Gram positive (belonging to the Staphylococcus, Streptococcus spp. and Bacillus clausii), Gram negative (E. coli, K. pneumoniae, P. aeruginosa) bacteria and three yeasts belonging to the Candida spp. Complex 1 showed a remarkable bacteriostatic antimicrobial activity against staphylococci, with Minimum Inhibitory Concentration (MIC) values of 1.56 and 3.13μg/mL for S. haemoliticus and S. aureus, respectively. Spectroscopic and electrochemical measurements, supported by Density Functional Theory (DFT) calculations, were exploited to fully investigate the electronic structure of complex 1 and its relationship with the antimicrobial activity. Copyright © 2017 Elsevier Inc. All rights reserved.

Nanosized silver (II) pyridoxine complex to cause greater inflammatory response and less cytotoxicity to RAW264.7 macrophage cells

NASA Astrophysics Data System (ADS)

Paul, Avijit; Ju, Hee; Rangasamy, Sabarinathan; Shim, Yumi; Song, Joon Myong

2015-03-01

With advancements in nanotechnology, silver has been engineered into a nanometre size and has attracted great research interest for use in the treatment of wounds. Silver nanoparticles (AgNPs) have emerged as a potential alternative to conventional antibiotics because of their potential antimicrobial property. However, AgNPs also induce cytotoxicity, generate reactive oxygen species (ROS), and cause mitochondrial damage to human cells. Pyridoxine possesses antioxidant and cell proliferation activity. Therefore, in the present investigation, a nanosilver-pyridoxine complex (AgPyNP) was synthesized, and its cytotoxicity and immune response was compared with AgNPs in macrophage RAW264.7 cells. Results revealed that AgPyNPs showed less cytotoxicity compared with AgNPs by producing a smaller amount of ROS in RAW264.7 cells. Surprisingly, however, AgPyNPs caused macrophage RAW264.7 cells to secrete a larger amount of interleukin-8 (IL-8) and generate a more active inflammatory response compared to AgNPs. It activated TNF-α, NF-κB p65, and NF-κB p50 to generate a more vigorous immune protection that produces a greater amount of IL-8 compared to AgNPs. Overall findings indicate that AgPyNPs exhibited less cytotoxicity and evoked a greater immune response in macrophage RAW264.7 cells. Thus, it can be used as a better wound-healing agent than AgNPs.

Massive processing of pyro-chromatogram mass spectra (py-GCMS) of soil samples using the PARAFAC2 algorithm

NASA Astrophysics Data System (ADS)

Cécillon, Lauric; Quénéa, Katell; Anquetil, Christelle; Barré, Pierre

2015-04-01

Due to its large heterogeneity at all scales (from soil core to the globe), several measurements are often mandatory to get a meaningful value of a measured soil property. A large number of measurements can therefore be needed to study a soil property whatever the scale of the study. Moreover, several soil investigation techniques produce large and complex datasets, such as pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) which produces complex 3-way data. In this context, straightforward methods designed to speed up data treatments are needed to deal with large datasets. GC-MS pyrolysis (py-GCMS) is a powerful and frequently used tool to characterize soil organic matter (SOM). However, the treatment of the results of a py-GCMS analysis of soil sample is time consuming (number of peaks, co-elution, etc.) and the treatment of large data set of py-GCMS results is rather laborious. Moreover, peak position shifts and baseline drifts between analyses make the automation of GCMS programs data treatment difficult. These problems can be fixed using the Parallel Factor Analysis 2 (PARAFAC 2, Kiers et al., 1999; Bro et al., 1999). This algorithm has been applied frequently on chromatography data but has never been applied to analyses of SOM. We developed a Matlab routine based on existing Matlab packages dedicated to the simultaneous treatment of dozens of pyro-chromatograms mass spectra. We applied this routine on 40 soil samples. The benefits and expected improvements of our method will be discussed in our poster. References Kiers et al. (1999) PARAFAC2 - PartI. A direct fitting algorithm for the PARAFAC2 model. Journal of Chemometrics, 13: 275-294. Bro et al. (1999) PARAFAC2 - PartII. Modeling chromatographic data with retention time shifts. Journal of Chemometrics, 13: 295-309.

Reactivity of cyclopentadienyl transition metal(ii) complexes with borate ligands: structural characterization of the toluene-activated molybdenum complex [Cp*Mo(CO)2(η3-CH2C6H5)].

PubMed

Ramalakshmi, Rongala; Maheswari, K; Sharmila, Dudekula; Paul, Anamika; Roisnel, Thierry; Halet, Jean-François; Ghosh, Sundargopal

2016-10-18

Reactions of cyclopentadienyl transition-metal halide complexes [Cp*Mo(CO) 3 Cl], 1, and [CpFe(CO) 2 I], 2, (Cp = C 5 H 5 ; Cp* = η 5 -C 5 Me 5 ) with borate ligands are reported. Treatment of 1 with [NaBt 2 ] (Bt 2 = dihydrobis(2-mercapto-benzothiazolyl)borate) in toluene yielded [Cp*Mo(CO) 2 (C 7 H 4 S 2 N)], 3, and [Cp*Mo(CO) 2 (η 3 -CH 2 C 6 H 5 )], 4, with a selective binding of toluene through C-H activation followed by orthometallation. Note that compound 4 is a structurally characterized toluene-activated molecule in which the metal is in η 3 -coordination mode. Under similar reaction conditions, [NaPy 2 ] (Py 2 = dihydrobis(2-mercaptopyridyl)borate) produced only the mercaptopyridyl molybdenum complex [Cp*Mo(CO) 2 (C 5 H 4 SN)], 5, in good yield. On the other hand, when compound 2 was treated individually with [NaBt] (Bt = trihydro(2-mercapto-benzothiazolyl)borate) and [NaPy 2 ] in THF, formation of the η 1 -coordinated complexes [CpFe(CO) 2 (C 7 H 4 S 2 N)], 6, and [CpFe(CO) 2 (C 5 H 4 SN)], 7, was observed. The solid-state molecular structures of compounds 3, 4, 6, and 7 have been established by single-crystal X-ray crystallographic analyses.

7 CFR 51.1220 - Leaf or limb rub injury.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Leaf or limb rub injury. 51.1220 Section 51.1220... STANDARDS) United States Standards for Grades of Peaches Definitions § 51.1220 Leaf or limb rub injury. “Leaf or limb rub injury” means that the scarring is not smooth, not light colored, or aggregates more...

7 CFR 51.1220 - Leaf or limb rub injury.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Leaf or limb rub injury. 51.1220 Section 51.1220... STANDARDS) United States Standards for Grades of Peaches Definitions § 51.1220 Leaf or limb rub injury. “Leaf or limb rub injury” means that the scarring is not smooth, not light colored, or aggregates more...

7 CFR 51.1220 - Leaf or limb rub injury.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 2 2012-01-01 2012-01-01 false Leaf or limb rub injury. 51.1220 Section 51.1220... STANDARDS) United States Standards for Grades of Peaches Definitions § 51.1220 Leaf or limb rub injury. “Leaf or limb rub injury” means that the scarring is not smooth, not light colored, or aggregates more...

Ferromagnetic interactions in Ru(III)-nitronyl nitroxide radical complex: a potential 2p4d building block for molecular magnets.

PubMed

Pointillart, Fabrice; Bernot, Kevin; Sorace, Lorenzo; Sessoli, Roberta; Gatteschi, Dante

2007-07-07

The reaction between [Ru(salen)(PPh3)Cl] and the 4-pyridyl-substituted nitronyl nitroxide radical (NITpPy) leads to the [Ru(salen)(PPh3)(NITpPy)](ClO4)(H2O)2 complex while the reaction with the azido anion (N3-) leads to the [Ru(salen)(PPh3)(N3)] complex 2 (where salen2- = N,N'-ethan-1,2-diylbis(salicylidenamine) and PPh3 = triphenylphosphine). Both compounds have been characterized by single crystal X-ray diffraction. The two crystal structures are composed by a [Ru(III)(salen)(PPh3)]+ unit where the Ru(III) ion is coordinated to a salen2- ligand and one PPh3 ligand in axial position. In 1 the Ru(III) ion is coordinated to the 4-pyridyl-substituted nitronyl nitroxide radical whereas in 2 the second axial position is occupied by the azido ligand. In both complexes the Ru(III) ions are in the same environment RuO2N3P, in a tetragonally elongated octhaedral geometry. The crystal packing of 1 reveals pi-stacking in pairs. While antiferromagnetic intermolecular interaction (J2 = 5.0 cm(-1)) dominates at low temperatures, ferromagnetic intramolecular interaction (J1 = -9.0 cm(-1)) have been found between the Ru(III) ion and the coordinated NITpPy.

Generic tags for Mn(ii) and Gd(iii) spin labels for distance measurements in proteins.

PubMed

Yang, Yin; Gong, Yan-Jun; Litvinov, Aleksei; Liu, Hong-Kai; Yang, Feng; Su, Xun-Cheng; Goldfarb, Daniella

2017-10-11

High-affinity chelating tags for Gd(iii) and Mn(ii) ions that provide valuable high-resolution distance restraints for biomolecules were used as spin labels for double electron-electron resonance (DEER) measurements. The availability of a generic tag that can bind both metal ions and provide a narrow and predictable distance distribution for both ions is attractive owing to their different EPR-related characteristics. Herein we introduced two paramagnetic tags, 4PSPyMTA and 4PSPyNPDA, which are conjugated to cysteine residues through a stable thioether bond, forming a short and, depending on the metal ion coordination mode, a rigid tether with the protein. These tags exhibit high affinity for both Mn(ii) and Gd(iii) ions. The DEER performance of the 4PSPyMTA and 4PSPyNPDA tags, in complex with Gd(iii) or Mn(ii), was evaluated for three double cysteine mutants of ubiquitin, and the Gd(iii)-Gd(iii) and Mn(ii)-Mn(ii) distance distributions they generated were compared. All three Gd(iii) complexes of the ubiquitin-PyMTA and ubiquitin-PyNPDA conjugates produced similar and expected distance distributions. In contrast, significant variations in the maxima and widths of the distance distributions were observed for the Mn(ii) analogs. Furthermore, whereas PyNPDA-Gd(iii) and PyNPDA-Mn(ii) delivered similar distance distributions, appreciable differences were observed for two mutants with PyMTA, with the Mn(ii) analog exhibiting a broader distance distribution and shorter distances. ELDOR (electron-electron double resonance)-detected NMR measurements revealed some distribution in the Mn(ii) coordination environment for the protein conjugates of both tags but not for the free tags. The broader distance distributions generated by 4PSPyMTA-Mn(ii), as compared with Gd(iii), were attributed to the distributed location of the Mn(ii) ion within the PyMTA chelate owing to its smaller size and lower coordination number that leave the pyridine nitrogen uncoordinated. Accordingly, in terms of distance resolution, 4PSPyNPDA can serve as an effective generic tag for Gd(iii) and Mn(ii), whereas 4PSPyMTA is efficient for Gd(iii) only. This comparison between Gd(iii) and Mn(ii) suggests that PyMTA model compounds may not predict sufficiently well the performance of PyMTA-Mn(ii) as a tag for high-resolution distance measurements in proteins because the protein environment can influence its coordination mode.

Metal-polypyridyl catalysts for electro- and photochemical reduction of water to hydrogen.

PubMed

Zee, David Z; Chantarojsiri, Teera; Long, Jeffrey R; Chang, Christopher J

2015-07-21

Climate change, rising global energy demand, and energy security concerns motivate research into alternative, sustainable energy sources. In principle, solar energy can meet the world's energy needs, but the intermittent nature of solar illumination means that it is temporally and spatially separated from its consumption. Developing systems that promote solar-to-fuel conversion, such as via reduction of protons to hydrogen, could bridge this production-consumption gap, but this effort requires invention of catalysts that are cheap, robust, and efficient and that use earth-abundant elements. In this context, catalysts that utilize water as both an earth-abundant, environmentally benign substrate and a solvent for proton reduction are highly desirable. This Account summarizes our studies of molecular metal-polypyridyl catalysts for electrochemical and photochemical reduction of protons to hydrogen. Inspired by concept transfer from biological and materials catalysts, these scaffolds are remarkably resistant to decomposition in water, with fast and selective electrocatalytic and photocatalytic conversions that are sustainable for several days. Their modular nature offers a broad range of opportunities for tuning reactivity by molecular design, including altering ancillary ligand electronics, denticity, and/or incorporating redox-active elements. Our first-generation complex, [(PY4)Co(CH3CN)2](2+), catalyzes the reduction of protons from a strong organic acid to hydrogen in 50% water. Subsequent investigations with the pentapyridyl ligand PY5Me2 furnished molybdenum and cobalt complexes capable of catalyzing the reduction of water in fully aqueous electrolyte with 100% Faradaic efficiency. Of particular note, the complex [(PY5Me2)MoO](2+) possesses extremely high activity and durability in neutral water, with turnover frequencies at least 8500 mol of H2 per mole of catalyst per hour and turnover numbers over 600 000 mol of H2 per mole of catalyst over 3 days at an overpotential of 1.0 V, without apparent loss in activity. Replacing the oxo moiety with a disulfide affords [(PY5Me2)MoS2](2+), which bears a molecular MoS2 triangle that structurally and functionally mimics bulk molybdenum disulfide, improving the catalytic activity for water reduction. In water buffered to pH 3, catalysis by [(PY5Me2)MoS2](2+) onsets at 400 mV of overpotential, whereas [(PY5Me2)MoO](2+) requires an additional 300 mV of driving force to operate at the same current density. Metalation of the PY5Me2 ligand with an appropriate Co(ii) source also furnishes electrocatalysts that are active in water. Importantly, the onset of catalysis by the [(PY5Me2)Co(H2O)](2+) series is anodically shifted by introducing electron-withdrawing functional groups on the ligand. With the [(bpy2PYMe)Co(CF3SO3)](1+) system, we showed that introducing a redox-active moiety can facilitate the electro- and photochemical reduction of protons from weak acids such as acetic acid or water. Using a high-throughput photochemical reactor, we examined the structure-reactivity relationship of a series of cobalt(ii) complexes. Taken together, these findings set the stage for the broader application of polypyridyl systems to catalysis under environmentally benign aqueous conditions.

Effect of rubbing on the in vitro skin permeation of diclofenac-diethylamine 1.16% gel.

PubMed

Hasler-Nguyen, Nathalie; Fotopoulos, Grigorios

2012-06-21

Rubbing a topical NSAID (non steroidal anti-inflammatory drug) on the skin may increase local drug permeation, affecting its distribution to the site of pain and inflammation. The present study evaluates this hypothesis, by assessing in vitro the effect on skin permeation of applying diclofenac-dieythylamine 1.16% gel with or without rubbing. A single dose of 5 mg/cm2 diclofenac-diethylamine 1.16% gel was applied on excised human skin mounted in Franz-type diffusion cells without or with rubbing for 45 s. Drug penetration into the skin layers was determined after 1 h using the tape stripping technique. In vitro cutaneous permeation into the receptor fluid of the diffusion chamber was measured up to 24 h. Skin electrical resistance was also recorded. Application of diclofenac-diethylamine 1.16% gel with rubbing resulted to a 5-fold higher flux of diclofenac through the skin than when applied without rubbing at 8 h (P = 0.04). Skin rubbing for 45 s decreased by 2-fold skin electrical resistance when compared to the standard application. Application of diclofenac-diethylamine 1.16% gel with rubbing tended to result in higher accumulation in the stripped skin vs. the superficial skin layers when applied without rubbing (P = 0.2). These results suggest that rubbing may alter the superficial skin layer resulting in a transient faster initial diffusion of topically applied diclofenac through the stratum corneum into the deeper skin layer of the dermis to the tissue target.

Effect of rubbing on the in vitro skin permeation of diclofenac-diethylamine 1.16% gel

PubMed Central

2012-01-01

Background Rubbing a topical NSAID (non steroidal anti-inflammatory drug) on the skin may increase local drug permeation, affecting its distribution to the site of pain and inflammation. The present study evaluates this hypothesis, by assessing in vitro the effect on skin permeation of applying diclofenac-dieythylamine 1.16% gel with or without rubbing. Methods A single dose of 5 mg/cm2 diclofenac-diethylamine 1.16% gel was applied on excised human skin mounted in Franz-type diffusion cells without or with rubbing for 45 s. Drug penetration into the skin layers was determined after 1 h using the tape stripping technique. In vitro cutaneous permeation into the receptor fluid of the diffusion chamber was measured up to 24 h. Skin electrical resistance was also recorded. Results Application of diclofenac-diethylamine 1.16% gel with rubbing resulted to a 5-fold higher flux of diclofenac through the skin than when applied without rubbing at 8 h (P = 0.04). Skin rubbing for 45 s decreased by 2-fold skin electrical resistance when compared to the standard application. Application of diclofenac-diethylamine 1.16% gel with rubbing tended to result in higher accumulation in the stripped skin vs. the superficial skin layers when applied without rubbing (P = 0.2). Conclusion These results suggest that rubbing may alter the superficial skin layer resulting in a transient faster initial diffusion of topically applied diclofenac through the stratum corneum into the deeper skin layer of the dermis to the tissue target. PMID:22720797

Hand hygiene with alcohol hand rub and gloves reduces the incidence of late onset sepsis in preterm neonates.

PubMed

Janota, Jan; Šebková, Sylva; Višňovská, Magda; Kudláčková, Jana; Hamplová, Drahomíra; Zach, Jiří

2014-10-01

To assess the impact of a hand hygiene protocol, using hand washing, alcohol hand rub and gloves when caring for preterm infants born after 31 weeks of gestation, on the incidence of neonatal late onset sepsis (LOS). All babies delivered between 32 + 0 and 36 + 6 weeks gestation and admitted to the neonatal intensive care unit during a 14-month period were included. We followed a hand hygiene protocol with hand washing and alcohol hand rub (hand rub period) for the first 7 months and a protocol of hand washing, alcohol hand rub and gloves (gloves period) for the second 7 months. The hand rub and gloves groups consisted of 111 and 89 patients, respectively. Five patients were diagnosed with a total of six episodes of LOS in the hand rub group, and the incidence of LOS during the hand rub period was 2.99/1000 hospital days and 54.1/1000 admissions. There were no patients diagnosed with LOS during the gloves period (significant decrease, p = 0.028). Using a hand hygiene protocol with hand washing, hand rub and gloves significantly reduced the incidence of LOS in preterm newborns, and the results suggest that it may produce a sustained improvement in the infection rate. ©2014 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

MCPB.py: A Python Based Metal Center Parameter Builder.

PubMed

Li, Pengfei; Merz, Kenneth M

2016-04-25

MCPB.py, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach. It has an optimized code structure, with far fewer required steps than the previous developed MCPB program. It supports various AMBER force fields and more than 80 metal ions. A series of parametrization schemes to derive force constants and charge parameters are available within the program. We give two examples (one metalloprotein example and one organometallic compound example), indicating the program's ability to build reliable force fields for different metal ion containing complexes. The original version was released with AmberTools15. It is provided via the GNU General Public License v3.0 (GNU_GPL_v3) agreement and is free to download and distribute. MCPB.py provides a bridge between quantum mechanical calculations and molecular dynamics simulation software packages thereby enabling the modeling of metal ion centers. It offers an entry into simulating metal ions in a number of situations by providing an efficient way for researchers to handle the vagaries and difficulties associated with metal ion modeling.

The 2:2 complex of pyridine betaine with squaric acid studied by X-ray diffraction, FTIR, NMR and DTG methods

NASA Astrophysics Data System (ADS)

Dega-Szafran, Z.; Dutkiewicz, G.; Kosturkiewicz, Z.

2012-12-01

The 2:2 ionic crystals of pyridine betaine (PyB) with squaric acid (H2SQ) belong to monoclinic space group C2/c. Supramolecular structure of the crystals investigated is formed by the loss of one proton from every two squaric acid molecules. Pyridine betaines form a homoconjugated cation, [(PyB)2H]+, through a short, symmetric COO⋯H⋯OOC hydrogen bond of 2.463(2) Å. The hydrogen squarate anions are linked into a homoconjugated anion, [(HSQ)2H]-, by a short symmetric, non-linear O⋯H⋯O hydrogen bond of 2.453(1) Å, with the H-atom located on the twofold axis. The bis(hydrogen squarate)hydrogen anions are linked into a centrosymmetric cyclic dimer by two identical asymmetric Osbnd H⋯O hydrogen bonds of 2.536(2) Å. The (PyB)2H cation and cyclic dimer of hydrogen squarate anions are placed around two different systems of inversion centers in the unit cell. The FTIR spectrum is consistent with the X-ray results. The 13C chemical shift of the Cdbnd O atom confirms the presence of the hydrogen squarate anion in the complex studied. The complex decomposed in three thermal stages.

Synthesis of Some "Cobaloxime" Derivatives: A Demonstration of "Umpolung" in the Reactivity of an Organometallic Complex

NASA Astrophysics Data System (ADS)

Jameson, Donald L.; Grzybowski, Joseph J.; Hammels, Deb E.; Castellano, Ronald K.; Hoke, Molly E.; Freed, Kimberly; Basquill, Sean; Mendel, Angela; Shoemaker, William J.

1998-04-01

This article describes a four-reaction sequence for the synthesis of two organometallic "cobaloxime" derivatives. The concept of "Umpolung" or reversal of reactivity is demonstrated in the preparation of complexes. The complex Co(dmgH)2(4-t-BuPy)Et is formed by the reaction of a cobalt (I) intermediate (cobalt in the role of nucleophile) with ethyl iodide. The complex Co(dmgH)2(4-t-BuPy)Ph is formed by the reaction of PhMgBr with a cobalt (III) intermediate (cobalt in the role of electrophile). All the products contain cobalt in the diamagnetic +3 oxidation state and are readily characterized by proton and carbon NMR. The four reaction sequence may be completed in two 4-hour lab periods. Cobaloximes are well known as model complexes for Vitamin B-12 and the experiment exposes students to aspects of classical coordination chemistry, organometallic chemistry and bioinorganic chemistry. The experiment also illustrates an important reactivity parallel between organic and organometallic chemistry.

Spectro- and electrochemical studies of some ruthenium and osmium complexes of 2-(2'-pyridyl)benzimidazole; complexes with intra-molecular charge transfer.

PubMed

Khalil, M M; Ali, S A; Ramadan, R M

2001-04-01

Reaction of Ru3(CO)12, with 2-(2'-pyridyl)benzimidazole (HPBI) resulted in the formation of Ru(CO)3(HPBI) (I) complex. In presence of pyridine or dipyridine, the two derivatives [Ru(CO)3(HPBI)].Py (II) and [Ru(CO)3(HPBI)].dpy (III) were isolated. The corresponding reactions of Os3(CO)12 yielded only one single product; Os(CO)2(HPBI)2 (IV). Spectroscopic studies of these complexes revealed intramolecular metal to ligand CT interactions. Reactions of RuCl3 with HPBI gave three distinct products; [Ru(HPBI)2Cl2]Cl (V), [Ru(HPBI)(dipy)Cl2]C1 (VI) and [Ru(PBI)2(py)2]Cl (VII). The UV-vis studies indicated the presence of intramolecular ligand to metal CT interactions. Electrochemical investigation of the complexes showed some irreversible, reversible and quasi-reversible redox reactions due to tautomeric interconversions through electron transfer.

Combined experimental and theoretical approach to understand the reactivity of a mononuclear Cu(II)-hydroperoxo complex in oxygenation reactions.

PubMed

Kamachi, Takashi; Lee, Yong-Min; Nishimi, Tomonori; Cho, Jaeheung; Yoshizawa, Kazunari; Nam, Wonwoo

2008-12-18

A copper(II) complex bearing a pentadentate ligand, [Cu(II)(N4Py)(CF(3)SO(3))(2)] (1) (N4Py = N,N-bis(2-pyridylmethyl)bis(2-pyridyl)methylamine), was synthesized and characterized with various spectroscopic techniques and X-ray crystallography. A mononuclear Cu(II)-hydroperoxo complex, [Cu(II)(N4Py)(OOH)](+) (2), was then generated in the reaction of 1 and H(2)O(2) in the presence of base, and the reactivity of the intermediate was investigated in the oxidation of various substrates at -40 degrees C. In the reactivity studies, 2 showed a low oxidizing power such that 2 reacted only with triethylphosphine but not with other substrates such as thioanisole, benzyl alcohol, 1,4-cyclohexadiene, cyclohexene, and cyclohexane. In theoretical work, we have conducted density functional theory (DFT) calculations on the epoxidation of ethylene by 2 and a [Cu(III)(N4Py)(O)](+) intermediate (3) at the B3LYP level. The activation barrier is calculated to be 39.7 and 26.3 kcal/mol for distal and proximal oxygen attacks by 2, respectively. This result indicates that the direct ethylene epoxidation by 2 is not a plausible pathway, as we have observed in the experimental work. In contrast, the ethylene epoxidation by 3 is a downhill and low-barrier process. We also found that 2 cannot be a precursor to 3, since the homolytic cleavage of the O-O bond of 2 is very endothermic (i.e., 42 kcal/mol). On the basis of the experimental and theoretical results, we conclude that a mononuclear Cu(II)-hydroperoxo species bearing a pentadentate N5 ligand is a sluggish oxidant in oxygenation reactions.

Effect of eye rubbing on signs and symptoms of allergic conjunctivitis in cat-sensitive individuals.

PubMed

Raizman, M B; Rothman, J S; Maroun, F; Rand, W M

2000-12-01

To evaluate the effect of eye rubbing on signs and symptoms of allergic conjunctivitis in cat-sensitive individuals. Two prospective, nonrandomized comparative studies. Thirteen patients in the first study and 20 patients in the second study with a documented history of acute allergic conjunctivitis induced by exposure to cats were enrolled. In the first trial, all patients had one eye rubbed 15 times by the investigator without exposure to airborne allergens. Both eyes were evaluated after 5, 15, 30, and 60 minutes using subject questionnaires and slit-lamp examination. At least 1 week later, each patient was exposed to cat dander for 75 minutes; 15 minutes after entering the cat room, each patient had one eye rubbed 15 times by the examiner. Subjects' eyes were then evaluated using questionnaires and slit-lamp examination. In the second trial, the visits were identical to the first trial, except that the rubbed eye in each visit was rubbed 20 times and with more force, and that patients wore masks during exposure to cat dander. In both studies, the difference between patients' rubbed and nonrubbed eyes with respect to ocular itching, chemosis, and hyperemia was noted 5, 15, 30, and 60 minutes after controlled eye rubbing. Without exposure to the cat room, rubbed eyes exhibited increased itching at 5 minutes in both studies and at 15 minutes in the second study (P < 0.05), increased chemosis at 5 and 15 minutes in the second study (P < 0.05), and increased hyperemia at 5 minutes in the second study (P < 0.05) compared with nonrubbed eyes. During exposure to cat dander, rubbed eyes consistently exhibited increased itching at 5, 15, and 30 minutes in the first and second study as well as at 60 minutes in the second study compared with nonrubbed eyes. Furthermore, during exposure to cat dander, rubbed eyes consistently exhibited increased chemosis at 5 and 15 minutes (P < 0.05) and increased hyperemia at 5, 15, and 30 minutes (P < 0.05) in the second study compared with nonrubbed eyes. Firm eye rubbing causes a mild and transient increase in ocular itching, chemosis, and hyperemia. However, after exposure to cat allergens in cat-sensitive individuals, the effects of eye rubbing are longer and more dramatic. Eye rubbing may play a role in ocular signs and symptoms of allergic conjunctivitis in cat-sensitive individuals, especially after exposure to cat dander.

Lateral cis-1,3,5,7-tetraazadecalin podands and their complexes: synthesis, structure, and strong binding with Pb(II) and other heavy metal ions.

PubMed

Reany, Ofer; Fuchs, Benzion

2013-02-18

The chemistry and complexation behavior of diaminal podands based on cis-1,3,5,7-tetraazadecalin (cis-TAD) were elaborated, reassessed, and extended. The synthesis of 2,6-bis(hydroxymethylene)-cis-TAD (9) and 2,6-bis(α,α'-dimethyl-β- hydroxyethyl)-cis-TAD (10) as well as of suitably substituted 2,6-diaryl-cis-TAD podands is laid out. For the latter, the effect of electron donating or withdrawing substituents on the benzaldehyde reagents was examined while 9 and 10 were probed and showed considerable propensity for heavy metal-ion chelation. The [Cd(II)·(9)] and [Pb(II)·(9)] complexes stood out indeed, and their structure and properties show a particularly interesting 5-amino-1,3-diazane chelation type and strong ligand-ion binding mode, with intramolecular donor exchange in solution, all strongly influenced by the anomeric effect in the ligand.

Induction of DNA-protein cross-links by platinum compounds.

PubMed

Woźniak, K; Walter, Z

2000-01-01

The differences between cis- and trans-diamminedichloroplatinum II (DDP) in forming DNA-protein cross-links in isolated human lymphocytes were investigated. Both cis- and trans-DDP can induce DNA-protein cross-links. We show that cis-DDP forms complexes between DNA and proteins faster than trans-DDP. This results from an increase in the quantity of DNA and platinum together with an increase in drug concentration. Under the same conditions trans-DDP causes a decrease in DNA-forming complexes with proteins. After a 12 h incubation of lymphocytes we observe a similar level of DNA in DNA-protein cross-links induced by DDP isomers, but more platinum appears in complexes induced by trans-DDP. The results obtained demonstrate that the antitumor drug - cis-DDP and the clinically ineffective trans-DDP induce links between DNA and proteins in a different manner. We suggest that the therapeutic activity of cis-DDP can in part arise from rapidly forming DNA-protein complexes which can destroy the most important cellular processes, such as replication and transcription.

Acquisition of physical dormancy and ontogeny of the micropyle–water-gap complex in developing seeds of Geranium carolinianum (Geraniaceae)

PubMed Central

Gama-Arachchige, N. S.; Baskin, J. M.; Geneve, R. L.; Baskin, C. C.

2011-01-01

Background and Aims The ‘hinged valve gap’ has been previously identified as the initial site of water entry (i.e. water gap) in physically dormant (PY) seeds of Geranium carolinianum (Geraniaceae). However, neither the ontogeny of the hinged valve gap nor acquisition of PY by seeds of Geraniaceae has been studied previously. The aims of the present study were to investigate the physiological events related to acquisition of PY and the ontogeny of the hinged valve gap and seed coat of G. carolinianum. Methods Seeds of G. carolinianum were studied from the ovule stage until dispersal. The developmental stages of acquisition of germinability, physiological maturity and PY were determined by seed measurement, germination and imbibition experiments using intact seeds and isolated embryos of both fresh and slow-dried seeds. Ontogeny of the seed coat and water gap was studied using light microscopy. Key Results Developing seeds achieved germinability, physiological maturity and PY on days 9, 14 and 20 after pollination (DAP), respectively. The critical moisture content of seeds on acquisition of PY was 11 %. Slow-drying caused the stage of acquisition of PY to shift from 20 to 13 DAP. Greater extent of cell division and differentiation at the micropyle, water gap and chalaza than at the rest of the seed coat resulted in particular anatomical features. Palisade and subpalisade cells of varying forms developed in these sites. A clear demarcation between the water gap and micropyle is not evident due to their close proximity. Conclusions Acquisition of PY in seeds of G. carolinianum occurs after physiological maturity and is triggered by maturation drying. The micropyle and water gap cannot be considered as two separate entities, and thus it is more appropriate to consider them together as a ‘micropyle–water-gap complex’. PMID:21546433

Insight into substrate binding in Shibasaki's Li3(THF)n(BINOLate)3Ln complexes and implications in catalysis.

PubMed

Wooten, Alfred J; Carroll, Patrick J; Walsh, Patrick J

2008-06-11

Heterobimetallic Lewis acids M 3(THF) n (BINOLate) 3Ln [M = Li, Na, K; Ln = lanthanide(III)] are exceptionally useful asymmetric catalysts that exhibit high levels of enantioselectivity across a wide range of reactions. Despite their prominence, important questions remain regarding the nature of the catalyst-substrate interactions and, therefore, the mechanism of catalyst operation. Reported herein are the isolation and structural characterization of 7- and 8-coordinate heterobimetallic complexes Li 3(THF) 4(BINOLate) 3Ln(THF) [Ln = La, Pr, and Eu], Li 3(py) 5(BINOLate) 3Ln(py) [Ln = Eu and Yb], and Li 3(py) 5(BINOLate) 3La(py) 2 [py = pyridine]. Solution binding studies of cyclohexenone, DMF, and pyridine with Li 3(THF) n (BINOLate) 3Ln [Ln = Eu, Pr, and Yb] and Li 3(DMEDA) 3(BINOLate) 3Ln [Ln = La and Eu; DMEDA = N, N'-dimethylethylene diamine] demonstrate binding of these Lewis basic substrate analogues to the lanthanide center. The paramagnetic europium, ytterbium, and praseodymium complexes Li 3(THF) n (BINOLate) 3Ln induce relatively large lanthanide-induced shifts on substrate analogues that ranged from 0.5 to 4.3 ppm in the (1)H NMR spectrum. X-ray structure analysis and NMR studies of Li 3(DMEDA) 3(BINOLate) 3Ln [Ln = Lu, Eu, La, and the transition metal analogue Y] reveal selective binding of DMEDA to the lithium centers. Upon coordination of DMEDA, six new stereogenic nitrogen centers are formed with perfect diastereoselectivity in the solid state, and only a single diastereomer is observed in solution. The lithium-bound DMEDA ligands are not displaced by cyclohexenone, DMF, or THF on the NMR time scale. Use of the DMEDA adduct Li 3(DMEDA) 3(BINOLate) 3La in three catalytic asymmetric reactions led to enantioselectivities similar to those obtained with Shibasaki's Li 3(THF) n (BINOLate) 3La complex. Also reported is a unique dimeric [Li 6(en) 7(BINOLate) 6Eu 2][mu-eta (1),eta (1)-en] structure [en = ethylenediamine]. On the basis of these studies, it is hypothesized that the lanthanide in Shibasaki's Li 3(THF) n (BINOLate) 3Ln complexes cannot bind bidentate substrates in a chelating fashion. A hypothesis is also presented to explain why the lanthanide catalyst, Li 3(THF) n (BINOLate) 3La, is often the most enantioselective of the Li 3(THF) n (BINOLate) 3Ln derivatives.

Spectroscopic and Computational Investigations of a Mononuclear Manganese(IV)-Oxo Complex Reveal Electronic Structure Contributions to Reactivity

DOE PAGES

Leto, Domenick F.; Massie, Allyssa A.; Rice, Derek B.; ...

2016-11-01

The mononuclear Mn(IV)-oxo complex [Mn IV(O)(N4py)] 2+, where N4py is the pentadentate ligand N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine, we propose to attack C–H bonds by an excited-state reactivity pattern [Cho, K.-B.; Shaik, S.; Nam, W. J. Phys. Chem. Lett. 2012, 3, 2851-2856 (DOI: 10.1021/jz301241z)]. In this model, a 4E excited state is utilized to provide a lower-energy barrier for hydrogen-atom transfer. This proposal is intriguing, as it offers both a rationale for the relatively high hydrogen-atom-transfer reactivity of [Mn IV(O)(N4py)] 2+ and a guideline for creating more reactive complexes through ligand modification. Here we employ a combination of electronic absorption and variable-temperature magnetic circularmore » dichroism (MCD) spectroscopy to experimentally evaluate this excited-state reactivity model. Using these spectroscopic methods, in conjunction with time-dependent density functional theory (TD-DFT) and complete-active space self-consistent-field calculations (CASSCF), we define the ligand-field and charge-transfer excited states of [MnIV(O)(N4py)]2+. Through a graphical analysis of the signs of the experimental C-term MCD signals, we unambiguously assign a low-energy MCD feature of [Mn IV(O)(N4py)] 2+ as the 4E excited state predicted to be involved in hydrogen-atom-transfer reactivity. The CASSCF calculations predict enhanced Mn III-oxyl character on the excited-state 4E surface, consistent with previous DFT calculations. Potential-energy surfaces, developed using the CASSCF methods, are used to determine how the energies and wave functions of the ground and excited states evolved as a function of Mn=O distance. Furthermore, the unique insights into ground- and excited-state electronic structure offered by these spectroscopic and computational studies are harmonized with a thermodynamic model of hydrogen-atom-transfer reactivity, which predicts a correlation between transition-state barriers and driving force« less

Spectroscopic and Computational Investigations of a Mononuclear Manganese(IV)-Oxo Complex Reveal Electronic Structure Contributions to Reactivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leto, Domenick F.; Massie, Allyssa A.; Rice, Derek B.

The mononuclear Mn(IV)-oxo complex [Mn IV(O)(N4py)] 2+, where N4py is the pentadentate ligand N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine, we propose to attack C–H bonds by an excited-state reactivity pattern [Cho, K.-B.; Shaik, S.; Nam, W. J. Phys. Chem. Lett. 2012, 3, 2851-2856 (DOI: 10.1021/jz301241z)]. In this model, a 4E excited state is utilized to provide a lower-energy barrier for hydrogen-atom transfer. This proposal is intriguing, as it offers both a rationale for the relatively high hydrogen-atom-transfer reactivity of [Mn IV(O)(N4py)] 2+ and a guideline for creating more reactive complexes through ligand modification. Here we employ a combination of electronic absorption and variable-temperature magnetic circularmore » dichroism (MCD) spectroscopy to experimentally evaluate this excited-state reactivity model. Using these spectroscopic methods, in conjunction with time-dependent density functional theory (TD-DFT) and complete-active space self-consistent-field calculations (CASSCF), we define the ligand-field and charge-transfer excited states of [MnIV(O)(N4py)]2+. Through a graphical analysis of the signs of the experimental C-term MCD signals, we unambiguously assign a low-energy MCD feature of [Mn IV(O)(N4py)] 2+ as the 4E excited state predicted to be involved in hydrogen-atom-transfer reactivity. The CASSCF calculations predict enhanced Mn III-oxyl character on the excited-state 4E surface, consistent with previous DFT calculations. Potential-energy surfaces, developed using the CASSCF methods, are used to determine how the energies and wave functions of the ground and excited states evolved as a function of Mn=O distance. Furthermore, the unique insights into ground- and excited-state electronic structure offered by these spectroscopic and computational studies are harmonized with a thermodynamic model of hydrogen-atom-transfer reactivity, which predicts a correlation between transition-state barriers and driving force« less

Tetra-2,3-pyrazinoporphyrazines with externally appended pyridine rings. 15. Effects of the pyridyl substituents and fused exocyclic rings on the UV-visible spectroscopic properties of Mg(II)-porphyrazines: a combined experimental and DFT/TDDFT study.

PubMed

Donzello, Maria Pia; De Mori, Giorgia; Viola, Elisa; Ercolani, Claudio; Ricciardi, Giampaolo; Rosa, Angela

2014-08-04

Two new Mg(II) porphyrazine macrocycles, the octakis(2-pyridyl)porphyrazinato-magnesium(II), [Py8PzMg(H2O)], and the tetrakis-[6,7-di(2-pyridyl)quinoxalino]porphyrazinato-magnesium(II), [Py8QxPzMg(H2O)], were prepared by Mg-template macrocyclization processes, and their general physicochemical properties were examined. The previously reported porphyrazine analog, the tetrakis-2,3-[5,6-di(2-pyridyl)-pyrazino]porphyrazinato-magnesium(II), [Py8PyzPzMg(H2O)], has been also considered in the present work. The UV-visible solution spectra in nonaqueous solvents of this triad of externally octapyridinated Mg(II) complexes exhibit the usual profile observed for phthalocyanine and porphyrazine macrocycles, with intense absorptions in the Soret (300-450 nm) and Q band (600-800 nm) regions. It is observed that the Q band maximum sensibly shifts toward the red with peak values at 635 → 658 → 759 nm along the series [Py8PzMg(H2O)], [Py8PyzPzMg(H2O)], and [Py8QxPzMg(H2O)], as the extension of the macrocycle π-system increases. TDDFT calculations of the electronic absorption spectra were performed for the related water-free model compounds [Py8PzMg], [Py8PyzPzMg], and [Py8QxPzMg] to provide an interpretation of the UV-visible spectral changes occurring upon introduction of the pyrazine and quinoxaline rings at the periphery of the Pz macrocycle. To discriminate the electronic effects of the fused exocyclic rings from those of the appended 2-pyridyl rings, the UV-visible spectra of [PzMg] and [PyzPzMg] were also theoretically investigated. The theoretical results prove to agree very well with the experimental data, providing an accurate description of the UV-visible spectra. The observed spectral changes are interpreted on the basis of the electronic structure changes occurring along the series.

Luminescent Copper(I) Halide Butterfly Dimers Coordinated to [Au(CH3imCH2py)2]BF4 and [Au(CH3imCH2quin)2]BF4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Catalano, V.; Moore, A; Shearer, J

2009-01-01

The coordination chemistry of copper(I) halides to the homoleptic, N-heterocyclic carbene Au(I) complexes [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} and [Au(CH{sub 3}imCH{sub 2}py){sub 2}]BF{sub 4} was explored. The reaction of CuX (X = Cl, Br, I) with either [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} or [Au(CH{sub 3}imCH{sub 2}py){sub 2}]BF{sub 4} produces trimetallic complexes containing Cu{sub 2}X{sub 2}-butterfly copper clusters coordinated to the two imine moieties. The triangular arrangement of the metals places the gold(I) center in close proximity ({approx}2.5-2.6 {angstrom}) to the centroid of the Cu-Cu vector. The Cu-Cu separations vary as a function of bridging halide with the shortest Cu-Cu separationsmore » of {approx}2.5 {angstrom} found in the iodo-complexes and the longest separations of 2.9 {angstrom} found in the bridging chloride complexes. In all six complexes the Au-Cu separations range from {approx}2.8 to 3.0 {angstrom}. In the absence of halides, the dimetallic complex [AuCu(CH{sub 3}imCH{sub 2}py){sub 2}(NCCH{sub 3}){sub 2}](BF{sub 4}){sub 2}, containing a long Au-Cu distance of {approx}4.72 {angstrom} is formed. Additionally, as the byproduct of the reaction of CuBr with [Au(CH{sub 3}imCH{sub 2}quin){sub 2}]BF{sub 4} the deep-red, dimetallic compound, AuCuBr{sub 2}(CH{sub 3}imCH{sub 2}quin){sub 2}, was isolated in very low yield. All of these complexes were studied by NMR spectroscopy, mass spectrometry, and the copper containing species were additionally characterized by X-ray crystallography. In solution the copper centers dissociate from the gold complexes, but as shown by XANES and EXAFS spectroscopy, at low temperature the Cu-Cu linkage is broken, and the individual copper(I) halides reposition themselves to opposite sides of the gold complex while remaining coordinated to one imine moiety. In the solid state all of the complexes are photoluminescent, though the nature of the excited state was not determined.« less

Modeling the rubbing contact in honeycomb seals

NASA Astrophysics Data System (ADS)

Fischer, Tim; Welzenbach, Sarah; Meier, Felix; Werner, Ewald; kyzy, Sonun Ulan; Munz, Oliver

2018-03-01

Metallic honeycomb labyrinth seals are commonly used as sealing systems in gas turbine engines. Because of their capability to withstand high thermo-mechanical loads and oxidation, polycrystalline nickel-based superalloys, such as Hastelloy X and Haynes 214, are used as sealing material. In addition, these materials must exhibit a tolerance against rubbing between the rotating part and the stationary seal component. The tolerance of the sealing material against rubbing preserves the integrity of the rotating part. In this article, the rubbing behavior at the rotor-stator interface is considered numerically. A simulation model is incorporated into the commercial finite element code ABAQUS/explicit and is utilized to simulate a simplified rubbing process. A user-defined interaction routine between the contact surfaces accounts for the thermal and mechanical interfacial behavior. Furthermore, an elasto-plastic constitutive material law captures the extreme temperature conditions and the damage behavior of the alloys. To validate the model, representative quantities of the rubbing process are determined and compared with experimental data from the literature. The simulation results correctly reproduce the observations made on a test rig with a reference stainless steel material (AISI 304). A parametric study using the nickel-based superalloys reveals a clear dependency of the rubbing behavior on the sliding and incursion velocity. Compared to each other, the two superalloys studied exhibit a different rubbing behavior.

Turbomachinery Application of Lagrangian Dynamics to the Motion of Continuous Discrete Rotors

NASA Technical Reports Server (NTRS)

2005-01-01

The stability/instability condition of a turbine rotor with axisymmetric supports is determined in the presence of gyroscopic loads and rub-induced destabilizing forces. A modal representation of the turbine engine is used, with one mode in each of the vertical and horizontal planes. The use of non-spinning rotor modes permits an explicit treatment of gyroscopic effects. The two linearized modal equations of motion of a rotor with axisymmetric supports are reduced to a single equation in a complex variable. The resulting eigenvalues yield explicit expressions at the stability boundary, for the whirl frequency as well as the required damping in the presence of the available rub-induced destabilization. Conversely, the allowable destabilization in the presence of the available damping is also given.

Changes in poisonings among adolescents in the UK between 1992 and 2012: a population based cohort study.

PubMed

Tyrrell, Edward G; Orton, Elizabeth; Tata, Laila J

2016-12-01

Poisonings are a common cause of morbidity and mortality among adolescents. Yet surveillance data indicating current incidence rates (IRs) and time trends are lacking, making policy development and service planning difficult. We utilised population based primary care data to estimate adolescent poisoning rates according to intent across the UK. A cohort study of 1 311 021 adolescents aged 10-17 years, between 1992 and 2012, was conducted using routine primary care data from The Health Improvement Network. IRs and adjusted IRRs with 95% CIs were calculated for all poisonings, intentional, unintentional, unknown intent and alcohol related poisonings, by age, sex, calendar time and socioeconomic deprivation. Overall poisoning incidence increased by 27% from the period 1992-1996 to 2007-2012, with the largest increases in intentional poisonings among females aged 16-17 years (IR 391.4/100 000 person years (PY), CI 328.9 to 465.7 for age 17 years in 1992-1996; 767.0/100 000 PY, CI 719.5 to 817.7 in 2007-2012) and alcohol related poisonings in females aged 15-16 years (IR 65.7/100 000 PY, CI 43.3 to 99.8 rising to 130.0/100 000 PY, CI 110.0 to 150.0 for age 15 years). A strong socioeconomic gradient for all poisonings persisted over time, with higher rates among the more deprived (IRR 2.63, CI 2.41 to 2.88 for the most vs least deprived quintile in 2007-2012). Adolescent poisonings, especially intentional poisonings, have increased substantially over time and remain associated with health inequalities. Social and psychological support for adolescents should be targeted at more deprived communities, and child and adolescent mental health and alcohol support service provision should be commissioned to reflect the changing need. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Synthesis, structural characterization and conversion of dinuclear iron-sulfur clusters containing the disulfide ligand: [Cp*Fe(μ-η2:η2-bdt)(cis-μ-η1:η1-S2)FeCp*], [Cp*Fe(μ-S(C6H4S2))(cis-μ-η1:η1-S2)FeCp*], and [{Cp*Fe(bdt)}2(trans-μ-η1:η1-S2)].

PubMed

Ji, Xiaoxiao; Tong, Peng; Yang, Dawei; Wang, Baomin; Zhao, Jinfeng; Li, Yang; Qu, Jingping

2017-03-21

The treatment of [Cp*Fe(μ-η 2 :η 4 -bdt)FeCp*] (1, Cp* = η 5 -C 5 Me 5 , bdt = benzene-1,2-dithiolate) with 1/4 equiv. of elemental sulfur (S 8 ) gave a dinuclear iron-sulfur cluster [Cp*Fe(μ-η 2 :η 2 -bdt)(cis-μ-η 1 :η 1 -S 2 )FeCp*] (2), which contains a cis-1,2-disulfide ligand. When complex 2 further interacted with 1/8 equiv. of S 8 , another sulfur atom inserted into an Fe-S bond to give a rare product [Cp*Fe(μ-S(C 6 H 4 S 2 ))(cis-μ-η 1 :η 1 -S 2 )FeCp*] (3). Unexpectedly, a trans-1,2 disulfide-bridged diiron complex [{Cp*Fe(bdt)} 2 (trans-μ-η 1 :η 1 -S 2 )] (4) was isolated from the reaction of complex 1 with 1/2 equiv. of S 8 , which represents a structural isomer of [2Fe-2S] ferredoxin-type clusters. In addition, cis-1,2-disulfide-bridged complex 3 can slowly convert into trans-1,2-disulfide-bridged complex 4 and the complex [Cp*Fe(μ-η 2 :η 2 -S 2 )(cis-μ-η 1 :η 1 -S 2 )FeCp*] (5) by self-assembly reaction at ambient temperature, which is evidenced by time-dependent 1 H NMR spectroscopy.

Electronic and elastic properties of new semiconducting oP(12)-type RuB(2) and OsB(2).

PubMed

Hao, Xianfeng; Xu, Yuanhui; Gao, Faming

2011-03-30

Using first-principles total energy calculations we investigate the structural, elastic and electronic properties of new hypothetical oP(12)-type phase RuB(2) and OsB(2). The calculations indicate that the oP(12)-type phase RuB(2) and OsB(2) are thermodynamically and mechanically stable. Remarkably, the new phases RuB(2) and OsB(2) are predicted to be semiconductors, and the appearance of band gaps is ascribed to the enhanced B-B covalent hybridization. Compared to metallic oP(6)-type RuB(2) and OsB(2) phases, the new phases possess similar mechanical properties and hardness. The combination of the probability of tunable electronic properties, strong stiffness and high hardness make RuB(2) and OsB(2) attractive and interesting for advanced applications. © 2011 IOP Publishing Ltd

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

Incidence of pneumonia in nursing home residents in Germany: results of a claims data analysis.

PubMed

Fassmer, A M; Spreckelsen, O; Hoffmann, F

2018-04-26

Pneumonia is one of the most common infectious diseases with a high mortality, especially in the elderly population. To date, there have been only a few population-based studies dealing with the incidence of pneumonia in nursing homes (NHs). We conducted a cohort study using data from a large German statutory health insurance fund. Between 2010 and 2014, 127 227 NH residents 65 years and older were analysed. For the calculation of incidences per 100 person-years (PY) and 95% confidence intervals (CIs), we assessed the first diagnosis of pneumonia during the time in NH. We compared the rates between sexes, age groups, care levels, and comorbidities and we performed a multivariate Cox regression analysis. The mean age in the cohort was 84.0 years (74.6% female). A total of 19 183 incident cases led to an overall 5-year-incidence of 11.8 per 100 PY (95% CI 11.7-12.0). The incidence in men was substantially higher than in women. Rates were highest in the first month after NH placement. Our study revealed that the incidence of pneumonia is high in German NH residents and especially in males. Due to demographic changes, pneumonia will likely be increasingly relevant in the health care of the elderly and institutionalised population.

Entry and Exit Mechanisms at the cis-Face of the Golgi Complex

PubMed Central

Lorente-Rodríguez, Andrés; Barlowe, Charles

2011-01-01

Vesicular transport of protein and lipid cargo from the endoplasmic reticulum (ER) to cis-Golgi compartments depends on coat protein complexes, Rab GTPases, tethering factors, and membrane fusion catalysts. ER-derived vesicles deliver cargo to an ER-Golgi intermediate compartment (ERGIC) that then fuses with and/or matures into cis-Golgi compartments. The forward transport pathway to cis-Golgi compartments is balanced by a retrograde directed pathway that recycles transport machinery back to the ER. How trafficking through the ERGIC and cis-Golgi is coordinated to maintain organelle structure and function is poorly understood and highlights central questions regarding trafficking routes and organization of the early secretory pathway. PMID:21482742

Static Electricity-Responsive Supramolecular Assembly.

PubMed

Jintoku, Hirokuni; Ihara, Hirotaka; Matsuzawa, Yoko; Kihara, Hideyuki

2017-12-01

Stimuli-responsive materials can convert between molecular scale and macroscopic scale phenomena. Two macroscopic static electricity-responsive phenomena based on nanoscale supramolecular assemblies of a zinc porphyrin derivative are presented. One example involves the movement of supramolecular assemblies in response to static electricity. The assembly of a pyridine (Py) complex of the above-mentioned derivative in cyclohexane is drawn to a positively charged material, whereas the assembly of a 3,5-dimethylpyridine complex is drawn to a negatively charged material. The second phenomenon involves the movement of a non-polar solvent in response to static electrical stimulation. A cyclohexane solution containing a small quantity of the Py-complexed assembly exhibited a strong movement response towards negatively charged materials. Based on spectroscopic measurements and electron microscope observations, it was revealed that the assembled formation generates the observed response to static electricity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Retrieving the aerosol complex refractive index using PyMieScatt: A Mie computational package with visualization capabilities

NASA Astrophysics Data System (ADS)

Sumlin, Benjamin J.; Heinson, William R.; Chakrabarty, Rajan K.

2018-01-01

The complex refractive index m = n + ik of a particle is an intrinsic property which cannot be directly measured; it must be inferred from its extrinsic properties such as the scattering and absorption cross-sections. Bohren and Huffman called this approach "describing the dragon from its tracks", since the inversion of Lorenz-Mie theory equations is intractable without the use of computers. This article describes PyMieScatt, an open-source module for Python that contains functionality for solving the inverse problem for complex m using extensive optical and physical properties as input, and calculating regions where valid solutions may exist within the error bounds of laboratory measurements. Additionally, the module has comprehensive capabilities for studying homogeneous and coated single spheres, as well as ensembles of homogeneous spheres with user-defined size distributions, making it a complete tool for studying the optical behavior of spherical particles.

Synthesis, structures and urease inhibitory activity of cobalt(III) complexes with Schiff bases.

PubMed

Jing, Changling; Wang, Cunfang; Yan, Kai; Zhao, Kedong; Sheng, Guihua; Qu, Dan; Niu, Fang; Zhu, Hailiang; You, Zhonglu

2016-01-15

A series of new cobalt(III) complexes were prepared. They are [CoL(1)(py)3]·NO3 (1), [CoL(2)(bipy)(N3)]·CH3OH (2), [CoL(3)(HL(3))(N3)]·NO3 (3), and [CoL(4)(MeOH)(N3)] (4), where L(1), L(2), L(3) and L(4) are the deprotonated form of N'-(2-hydroxy-5-methoxybenzylidene)-3-methylbenzohydrazide, N'-(2-hydroxybenzylidene)-3-hydroxylbenzohydrazide, 2-[(2-dimethylaminoethylimino)methyl]-4-methylphenol, and N,N'-bis(5-methylsalicylidene)-o-phenylenediamine, respectively, py is pyridine, and bipy is 2,2'-bipyridine. The complexes were characterized by infrared and UV-Vis spectra, and single crystal X-ray diffraction. The Co atoms in the complexes are in octahedral coordination. Complexes 1 and 4 show effective urease inhibitory activities, with IC50 values of 4.27 and 0.35 μmol L(-1), respectively. Complex 2 has medium activity against urease, with IC50 value of 68.7 μmol L(-1). While complex 3 has no activity against urease. Molecular docking study of the complexes with Helicobacter pylori urease was performed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Behaviour modification in the management of chronic habits of abnormal eye rubbing.

PubMed

McMonnies, Charles W

2009-04-01

To describe how and why many keratoconus patients do not comply with strong advice to control chronic habits of abnormal rubbing. To outline a behaviour modification approach for controlling chronic habits of abnormal rubbing. Common reasons for chronic habits of abnormal rubbing have been reviewed as a basis for specifying a behavioural modification approach to habit reversal. The methods described are organized into the classic behavioural modification structure of: (1) habit awareness, (2) competing responses, (3) development of motivation, and (4) social support. This structure is supported by the application of social influence principles to achieve optimum compliance. The use of take-home written information in the form of an Abnormal Rubbing Guide is the basis for the development of motivation. Family social support is based upon a widening of the responsibility for avoiding eye rubbing to all family members. Some patients will need minimal application of these principles with patient education being sufficient intervention to achieve habit reversal. For patients with strong provocation to rubbing and/or by having a well established rubbing habit, a greater exposure to the habit reversal program described is indicated. Successful habit reversal may slow the rate of ectasia progression. Prophylactic application of the methods described for patients who are at risk for developing keratoconus, or post-laser assisted in situ keratomileusis keratectasia, may show that some forms of keratectasia are preventable.

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides.

PubMed

Buchmueller, Karen L; Staples, Andrew M; Uthe, Peter B; Howard, Cameron M; Pacheco, Kimberly A O; Cox, Kari K; Henry, James A; Bailey, Suzanna L; Horick, Sarah M; Nguyen, Binh; Wilson, W David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, -ImPy- and -PyPy-. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and DeltaT (M) experiments. The f/Py pairing, when placed next to the -ImPy- or -PyPy- central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With -ImPy- central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson-Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the -PyPy- central pairings.

Recognition of Mg²⁺ by a new fluorescent "turn-on" chemosensor based on pyridyl-hydrazono-coumarin.

PubMed

Orrego-Hernández, Jessica; Nuñez-Dallos, Nelson; Portilla, Jaime

2016-05-15

A new fluoroionophore PyHC bearing 2-pyridylhydrazone and 7-hydroxycoumarin moieties for selective detection of Mg(2+) was synthesized and characterized. This chemosensor exhibited "turn-on" fluorescence behavior and was sensitive to Mg(2+) concentrations as low as 105 nmol L(-1) in ethanol-water solution. Detailed spectroscopic studies revealed the binding mode of a 1:1 complex between PyHC and Mg(2+) that leads to a fluorescence enhancement. Copyright © 2016 Elsevier B.V. All rights reserved.

Water-refined solution structure of the human Grb7-SH2 domain in complex with the erbB2 receptor peptide pY1139.

PubMed

Pias, Sally C; Johnson, Dennis L; Smith, David E; Lyons, Barbara A

2012-08-01

We report a refinement in implicit water of the previously published solution structure of the Grb7-SH2 domain bound to the erbB2 receptor peptide pY1139. Structure quality measures indicate substantial improvement, with residues in the most favored regions of the Ramachandran plot increasing by 14 % and with WHAT IF statistics (Vriend, G. J. Mol. Graph., 1990, 8(1), 52-56) falling closer to expected values for well-refined structures.

Synthesis of Sulfonated burdock fructooligosaccharide (BFO)

NASA Astrophysics Data System (ADS)

Zhang, Haiguang; Chen, Kaoshan; Zhang, Pengying; Zhang, Xian; Wang, Zhe; Xue, Jingwen

2017-12-01

Burdock Fructooligosaccharide (BFO) were sulfated using SO3-Py complex. The maximal degree of sulfonation (DSsulf) was 1.56, which were obtained by varying reaction factor such molar ratio of SO3-Py to fructofuranans unit (FU). The FT-IR, 1H NMR and 13C NMR spectra showed the introduction of sulfate group, and the reaction occurred at C-6, C-4 and C-3 in the fructofuranans unit of BFO. The molecular weight estimated by HPGPC were 6104.7-11003.3 g/mol for S-BFO (DS sulf=1.2).

Rubbings deposited by cats elicit defensive behavior in rats.

PubMed

May, Matthew D; Bowen, Michael T; McGregor, Iain S; Timberlake, William

2012-12-05

Laboratory rats display pronounced defensive behaviors when confronted with a range of cat-derived stimuli, including collars worn by a cat, cloths rubbed on a cat, and cat fur. One possible explanation of this phenomenon (the "kairomone hypothesis") is that rats derive a survival advantage by eavesdropping on signals used by cats to communicate with each other. Cats are known to rub their bodies on objects at strategic environmental locations to signal their identity and mating potential to other cats. The current study assessed the sensitivity of laboratory rats to these body rubbings. In Experiment 1, food deprived Sprague-Dawley rats were trained to consume food pellets in one arm of a Y maze. On test day a damp cloth was placed near the food pellets that had been rubbed on a location (wall) where a cat had recently engaged in body rubbing. A control cloth and a collar worn by the cat were also tested. The presence of both the body rubbing residue and the cat collar increased latency to eat and decreased amount of food eaten. The disruption of consummatory behavior in the test environment was still evident 24h later in the absence of odor stimuli. Experiment 2 tested the reaction of naïve Wistar rats to body rubbings using a paradigm in which rats were given the opportunity to hide. Relative to a control condition, rats exposed to a cotton pad wiped on a cat body rubbing location showed increased hiding behavior, decreased exploration and reduced stimulus approach and investigation. These defensive responses persisted for up to 4days following a single stimulus exposure. These results suggest that rats eavesdrop readily on body rubbings cats use for identification purposes, providing further support for a kairomone hypothesis of predator odor avoidance. Copyright © 2012 Elsevier Inc. All rights reserved.

Synthesis and structural characterisation of Pd(II) and Pt(II) complexes with a flexible, ferrocene-based P,S-donor amidophosphine ligand.

PubMed

Tauchman, Jiří; Císařová, Ivana; Stěpnička, Petr

2014-01-28

1'-Diphenylphosphino-1-{[(2-(methylthio)ethyl)amino]carbonyl}ferrocene (1), accessible via amidation of 1'-(diphenylphosphino)ferrocene-1-carboxylic acid (Hdpf) with 2-(methylthio)ethylamine, reacts with [PdCl2(cod)] (cod = cycloocta-1,5-diene) at a 1 : 1 metal-to-ligand ratio to give trans-[PdCl2(1-κ(2)P,S)] (trans-2) as the sole product. A similar reaction with [PtCl2(cod)] affords a mixture of cis- and trans-[PtCl2(1-κ(2)P,S)] (cis- and trans-3), which can be separated by fractional crystallisation. Complexation reactions performed with 2 equiv. of the ligand are less selective, yielding mixtures of the expected bis-phosphine complexes (i.e., trans-[PdCl2(1-κP)2], or a mixture of cis- and trans-[PtCl2(-κP)2]) with the respective monophosphine complexes. The structures of 1, trans-2, cis-3 and trans-3 determined by X-ray diffraction demonstrate the ability of the title ligand to act as a flexible cis- or trans-P,S-chelate donor (the ligand bite angles are 174.03(2)/173.05(2)° for trans-2/3 and 92.86(2)° for cis-3).

Carbon-Based Oxamate Cobalt(III) Complexes as Bioenzyme Mimics for Contaminant Elimination in High Backgrounds of Complicated Constituents.

PubMed

Li, Nan; Zheng, Yun; Jiang, Xuemei; Zhang, Ran; Pei, Kemei; Chen, Wenxing

2017-10-12

Complex wastewater with massive components is now a serious environmental issue facing humanity. Selective removal of low-concentration contaminants in mixed constituents holds great promise for increasing water supplies. Bioenzymes like horseradish peroxidase exhibit oxidizing power and selectivity. Here, we manufactured its mimic through immobilizing non-heme oxamate anionic cobalt(III) complex ([Co III (opba)] - , opba = o-phenylenebis(oxamate)) onto pyridine (Py) modified multiwalled carbon nanotubes ([Co III (opba)] - -Py-MWCNTs, MWCNTs = multiwalled carbon nanotubes), where MWCNTs captured substrates and Py functioned as the fifth ligand. We chose typical azo dye (C.I. Acid Red 1) and antibiotic (ciprofloxacin) as model substrates. Without •OH, this catalyst could detoxify target micropollutants efficiently at pH from 8 to 11. It also remained efficient in repetitive tests, and the final products were non-poisonous OH-containing acids. Combined with radical scavenger tests and electron paramagnetic resonance result, we speculated that high-valent cobalt-oxo active species and oxygen atom transfer reaction dominated in the reaction pathway. According to density functional theory calculations, the electron spin density distribution order showed that electron-withdrawing ligand was beneficial for inward pulling the excess electron and lowering the corresponding energy levels, achieving an electrophilic-attack enhancement of the catalyst. With target removal property and recyclability, this catalyst is prospective in water detoxication.

Influence of rubbing on rotor dynamics, part 2

NASA Technical Reports Server (NTRS)

Muszynska, Agnes; Bently, Donald E.; Franklin, Wesley D.; Hayashida, Robert D.; Kingsley, Lori M.; Curry, Arthur E.

1989-01-01

Rotor dynamic behavior depends considerably on how much the specific physical phenomena accompanying rotor rubbing against the stator is involved. The experimental results of rotor-to-stator rubbing contact are analyzed. The computer code is described for obtaining numerical calculations of rotor-to-stator rubbing system dynamic responses. Computer generated results are provided. The reduced dynamic data from High Pressure Fuel Turbo Pump (HPFTP) hot fire test are given. The results provide some significant conclusions. Information is provided on the electronic instrumentation used in the experimental testing.

Interaction of In(I) and Tl(I) cations with 2,6-diaryl pyridine ligands: cation encapsulation within a very weakly interacting N/arene host environment.

PubMed

Mansaray, Hassanatu B; Tang, Christina Y; Vidovic, Dragoslav; Thompson, Amber L; Aldridge, Simon

2012-12-03

The interaction of 2,6-dimesitylpyridine with Tl(I) and In(I) cations has been investigated with a view to developing tractable molecular M(I) compounds which are soluble in organic media. In stark contrast to isosteric and isoelectronic terphenyl systems, complexes featuring the [(2,6-Mes(2)py)M](+) fragment feature very weak metal-ligand interactions in the solid state, as revealed by M-N distances of the order of 2.45 Å (M = In) and 2.64 Å (M = Tl). While additional weak π interactions are observed with arene solvate molecules in these systems, the related 2:1 complex [(2,6-Mes(2)py)(2)In][BAr(f)(4)] features an In(I) center wholly encapsulated by the bulky Mes(2)py donors, and even longer In-N distances [2.586(6) and 2.662(5) Å]. These contacts are about 0.5 Å greater than the sum of the respective covalent radii (2.13 Å) and provide evidence for an effectively "naked" In(I) cation stabilized to a minor extent by orbital interactions.

Gene expression analysis of enzymes of the carotenoid biosynthesis pathway involved in β-cryptoxanthin accumulation in wild raspberry, Rubus palmatus.

PubMed

Mizuno, Kouichi; Tokiwano, Tetsuo; Yoshizawa, Yuko

2017-03-18

β-cryptoxanthin (β-Cry), a xanthophyll, is unlike other abundant carotenoids, such as α-carotene, β-carotene, lycopene, lutein, and zeaxanthin. It is not found in most fruits or vegetables but is found only in specific fruits, such as hot chili pepper, persimmon, and citrus fruits. Because recent reports suggest that β-Cry intake is beneficial to human health, the xanthophyll requires further investigation. Although β-Cry accumulates in the fruit of wild raspberry, Rubus palmatus, it is not present in cultivated raspberry. In the present study, two wild raspberry species were studied-R. palmatus, which accumulates β-Cry in the fruit, and R. crataegifolius, which does not accumulate β-Cry. Four carotenoid biosynthetic enzymes derived from these two species were analyzed-phytoene synthase (PSY), lycopene β-cyclase (LCYb), β-carotene hydroxylase (HYb), and zeaxanthin epoxidase (ZEP). Expression levels of their genes were also assessed to elucidate mechanism underlying β-Cry accumulation. Partial gene sequences of RubPSY, RubLCYb, RubHYb, and RubZEP, isolated from immature raspberry fruits of R. palmatus, were used as probes for Northern blot analysis. RubZEP expression ceased as the fruits matured, possibly because of reduced production of zeaxanthin. β-Cry is considered to be an intermediate compound that accumulates in the mature fruits of R. palmatus. High expression of RubPSY was detectable in the mature fruits of R. crataegifolius, and the expression of RubLCYb, RubHYb, and RubZEP was detectable during all stages of fruit maturation. In contrast, β-Cry was absent in the mature fruits of R. crataegifolius. Copyright © 2017 Elsevier Inc. All rights reserved.

A comparison of regimen methods for the removal and inactivation of bacteria, fungi and Acanthamoeba from two types of silicone hydrogel lenses.

PubMed

Kilvington, Simon; Lonnen, James

2009-04-01

To compare the antimicrobial efficacy of commercial contact lens solutions when used according to the manufacturers' recommended regimens with two types of silicone hydrogel lenses. Four multipurpose contact lens care solutions were examined, representing manufacturer recommended regimens of "rub & rinse", "no rub, rinse" or "no rub, no rinse". Test organisms were Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Fusarium solani, Candida albicans and Acanthamoeba castellanii (trophozoites and cysts). Organisms, in the presence of organic soil, were inoculated on to Acuvue Oasys or Air Optix lenses and subjected to the solution manufacturer's recommended regimen. The number of surviving organisms on the lenses and in the soak solution was enumerated in accordance with ISO 14729. ISO 14729 dictates that for a given organism the combined average number of surviving microbes from the lenses and disinfectant soaking solution must be

Activity against Mycobacterium tuberculosis with concomitant induction of cellular immune responses by a tetraaza-macrocycle with acetate pendant arms.

PubMed

David, S; Ordway, D; Arroz, M J; Costa, J; Delgado, R

2001-01-01

The novel tetraaza-macrocyclic compound 3,7,11-tris(carboxymethyl)-3,7,11,17-tetraaza-bicyclo[11.3.1]heptadeca-1(17),13,15-triene, abbreviated as ac3py14, was investigated for its activity against Mycobacterium tuberculosis and for induction of protective cellular immune responses. Perspective results show that ac3py14 and its Fe3+ 1:1 complex, [Fe(ac3py14)], inhibited radiometric growth of several strains of M. tuberculosis. Inhibition with 25 microg/mL varied from 99% for H37Rv to 80% and above for multiple drug-resistant clinical isolates. The capacity of ac3py14 to elicit a beneficial immune response without cellular apoptosis was assessed and compared to the effects of virulent M. tuberculosis. The present study produces evidence that after stimulation with ac3py14 there was significant production of interferon gamma (IFN-gamma), whereas the production of interleukin-5 (IL-5) remained low, and there was development of a memory population (CD45RO). The level of binding of Annexin V, a marker of apoptosis, was not sufficient to result in toxic effects toward alphabeta and gammadelta T cells and CD14+ macrophages. This preliminary study is the first report of a compound that simultaneously exerts an inhibitory effect against M. tuberculosis and induces factors associated with protective immune responses.

Mineralogy and trace element geochemistry of the Co- and Cu-bearing sulfides from the Shilu Fe-Co-Cu ore district in Hainan Province of South China

NASA Astrophysics Data System (ADS)

Wang, Zhilin; Xu, Deru; Zhang, Zhaochong; Zou, Fenghui; Wang, Li; Yu, Liangliang; Hu, Mingyue

2015-12-01

Hosted within the metamorphosed, neritic siliciclastic rocks and sedimentary carbonates of the Proterozoic Shilu Group, the Shilu Fe-Co-Cu ore district in Hainan Province of South China comprises the upper Fe- and the lower Co-Cu ore layers. Combined with the field observation, the mineralogical and geochemical studies of sulfides using electron microprobe and laser ablation ICP-MS analyses recognized three types of Co-Cu ores. Type I is represented by massive ores and mainly comprises the first generation of pyrite (PyI) which occurred either as recrystallized, subhedral to euhedral microcrystal aggregates (PyIa) or as elongated, fine-grained euhedral grains (PyIb) with an orientated alignment parallel to S1 foliation. Type II is banded, disseminated and brecciated ores, and composed of the second generation of pyrite (PyII) which displays internal rhythmic growth zoning, the first generations of chalcopyrite (CcpI) and pyrrhotite (PoI), and associated Co-(Ni)-(As)-sulfide minerals. Type III occurring as veins or veinlets mainly consists of the third generation of pyrite (PyIII) and the second generations of chalcopyrite (CcpII) and pyrrhotite (PoII), of which PyIII appears as subhedral to euhedrall grains or as rims of composite pyrite. The moderate Co and As, and high Ni contents as well as the low Co/Ni ratios (∼2-5) in PyI indicate a sedimentary-metamorphic origin for Type I ores. The higher Co, Ni and As concentrations in PyIb relative to PyIa likely was related to an inhomogeneous deformation-metamorphism. The highest Co (av. 51,195 ppm) in PyII and Ni (av. 3374 ppm) in PoI most likely were linked to the preferred incorporation of Co into pyrite and Ni into pyrrhotite. Combined with the high Ag concentrations in CcpI (av. 266 ppm) and PyII (av. 13.32 ppm), the high Co/Ni ratios in PyII (av. 1241) suggest the derivation of Type II ores from a Co-Cu-Ni-Ag-rich hydrothermal fluid. Further, up to 9 wt.% Co concentrations in PyII show a temperature condition of 310-400 °C. In contrast, the depletion of trace elements in CcpII and PyIII, and the lower Co/Ni ratios (av. 46) in PyIII suggest a Co-poor but Cu-bearing hydrothermal fluid for origin of Type III ores. The complex texture and chemical composition of sulfides combined with previous work confirm a four-stage metallogenesis for the Shilu Co-Cu ores. From early to late, these include: (1) the ca. 1075-880 Ma deposition of the primary Co-Cu ore source beds which most likely were derived from submarine, metalliferous hydrothermal fluids, (2) the syn-structural metamorphism which led to Type I ores due to the South China Caledonian Orogeny, (3) the first stage of hydrothermalism which produced Type II ores and most likely was associated with Indosinian magmatism, and (4) the second stage of hydrothermalism which yielded Type III ores and likely was related to Yanshanian magmatism. The first stage of hydrothermalism was considered to be significant for the Co-Cu enrichment. The Shilu Co-Cu ores thus are better attributed to a BIF origin, but greatly reworked and enriched by late structural deformation and hydrothermal activities.

PyXRD v0.6.7: a free and open-source program to quantify disordered phyllosilicates using multi-specimen X-ray diffraction profile fitting

NASA Astrophysics Data System (ADS)

Dumon, M.; Van Ranst, E.

2016-01-01

This paper presents a free and open-source program called PyXRD (short for Python X-ray diffraction) to improve the quantification of complex, poly-phasic mixed-layer phyllosilicate assemblages. The validity of the program was checked by comparing its output with Sybilla v2.2.2, which shares the same mathematical formalism. The novelty of this program is the ab initio incorporation of the multi-specimen method, making it possible to share phases and (a selection of) their parameters across multiple specimens. PyXRD thus allows for modelling multiple specimens side by side, and this approach speeds up the manual refinement process significantly. To check the hypothesis that this multi-specimen set-up - as it effectively reduces the number of parameters and increases the number of observations - can also improve automatic parameter refinements, we calculated X-ray diffraction patterns for four theoretical mineral assemblages. These patterns were then used as input for one refinement employing the multi-specimen set-up and one employing the single-pattern set-ups. For all of the assemblages, PyXRD was able to reproduce or approximate the input parameters with the multi-specimen approach. Diverging solutions only occurred in single-pattern set-ups, which do not contain enough information to discern all minerals present (e.g. patterns of heated samples). Assuming a correct qualitative interpretation was made and a single pattern exists in which all phases are sufficiently discernible, the obtained results indicate a good quantification can often be obtained with just that pattern. However, these results from theoretical experiments cannot automatically be extrapolated to all real-life experiments. In any case, PyXRD has proven to be useful when X-ray diffraction patterns are modelled for complex mineral assemblages containing mixed-layer phyllosilicates with a multi-specimen approach.

Acoustic emissions diagnosis of rotor-stator rubs using the KS statistic

NASA Astrophysics Data System (ADS)

Hall, L. D.; Mba, D.

2004-07-01

Acoustic emission (AE) measurement at the bearings of rotating machinery has become a useful tool for diagnosing incipient fault conditions. In particular, AE can be used to detect unwanted intermittent or partial rubbing between a rotating central shaft and surrounding stationary components. This is a particular problem encountered in turbines used for power generation. For successful fault diagnosis, it is important to adopt AE signal analysis techniques capable of distinguishing between various types of rub mechanisms. It is also useful to develop techniques for inferring information such as the severity of rubbing or the type of seal material making contact on the shaft. It is proposed that modelling the cumulative distribution function of rub-induced AE signals with respect to appropriate theoretical distributions, and quantifying the goodness of fit with the Kolmogorov-Smirnov (KS) statistic, offers a suitable signal feature for diagnosis. This paper demonstrates the successful use of the KS feature for discriminating different classes of shaft-seal rubbing.

Simulated Tip Rub Testing of Low-Density Metal Foam

NASA Technical Reports Server (NTRS)

Bowman, Cheryl L.; Jones, Michael G.

2009-01-01

Preliminary acoustic studies have indicated that low-density, open-cell, metal foams may be suitable acoustic liner material for noise suppression in high by-pass engines. Metal foam response under simulated tip rub conditions was studied to assess whether its durability would be sufficient for the foam to serve both as a rub strip above the rotor as well as an acoustic treatment. Samples represented four metal alloys, nominal cell dimensions ranging from 60 to 120 cells per inch (cpi), and relative densities ranging from 3.4 to 10 percent. The resulting rubbed surfaces were relatively smooth and the open cell structure of the foam was not adversely affected. Sample relative density appeared to have significant influence on the forces induced by the rub event. Acoustic responses of various surface preparations were measured using a normal incidence tube. The results of this study indicate that the foam s open-cell structure was retained after rubbing and that the acoustic absorption spectra variation was minimal.

The Influence of Solvent on the Structural Properties of trans-(NHC)PtI2Py Complex: A Platinum-Based Anticancer Drug

NASA Astrophysics Data System (ADS)

Sadigh Vishkaee, Teherh; Fazaeli, Reza

2018-06-01

Quantum chemical calculations using MPW1PW91 method were applied to analyze the solvent effect on the structural, spectral, and thermochemical parameters for a platinum-based anticancer drug trans-(NHC)PtI2Py complex. The solvent effects were examined by the self-consistent reaction field theory (SCRF) based on Polarizable Continuum Model (PCM). The linear correlations between the solvation energies, HOMO-LUMO gaps, IR-active stretching vibration of Pt-N bonds and N-H of NHC ligand with dielectric constants of solvents were studied. The wave numbers of these IR-active stretching vibrations in different solvents were correlated with the Kirkwood-Bauer-Magat equation (KBM). The thermodynamic activation parameter such free energy of solvation, enthalpy of solvation were also calculated.

Mechanisms of rubbing-related corneal trauma in keratoconus.

PubMed

McMonnies, Charles W

2009-07-01

Corneal scarring in keratoconus, which is observed prior to contact lens wear and in association with a chronic habit of abnormal rubbing, suggests a keratocyte change to a repair phenotype in response to rubbing trauma. This review examines known and putative mechanisms for rubbing-related corneal trauma and cone formation. Responses to eye rubbing (and possible causal links) may include increased corneal temperature, epithelial thinning, increased concentrations of inflammatory mediators in the precorneal tears, abnormal enzyme activity, large intraocular pressure spikes, high hydrostatic tissue pressure, thixotropically reduced ground substance viscosity, temporary displacement of ground substance from the corneal apex, buckling and flexure of fibrils associated with waves of corneal indentation, biomechanically coupled curvature transfer to the cone apex, slippage between collagen fibrils at the cone apex, and changes to keratocytes due to mechanical trauma and/or high hydrostatic pressure, in addition to scar formation. Cone formation appears to depend on a loss of shear strength and may be a consequence of a reduction in ground substance viscosity and glue function, which could allow the cornea to bend and yield to intraocular pressure. For some forms of keratoconus, a reduction in shear strength and cone-forming deformation may be responses to rubbing trauma. Some of the mechanisms for corneal rubbing trauma may be relevant to post-laser-assisted in situ keratomileusis ectasia or complications following other types of corneal surgery. There appear to be indications for the control of chronic habits of abnormal rubbing.

Mechanistic Investigation of Catalyst-Transfer Suzuki-Miyaura Condensation Polymerization of Thiophene-Pyridine Biaryl Monomers with the Aid of Model Reactions.

PubMed

Tokita, Yu; Katoh, Masaru; Ohta, Yoshihiro; Yokozawa, Tsutomu

2016-11-21

We have investigated the requirements for efficient Pd-catalyzed Suzuki-Miyaura catalyst-transfer condensation polymerization (Pd-CTCP) reactions of 2-alkoxypropyl-6-(5-bromothiophen-2-yl)-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (12) as a donor-acceptor (D-A) biaryl monomer. As model reactions, we first carried out the Suzuki-Miyaura coupling reaction of X-Py-Th-X' (Th=thiophene, Py=pyridine, X, X'=Br or I) 1 with phenylboronic acid ester 2 by using tBu 3 PPd 0 as the catalyst. Monosubstitution with a phenyl group at Th-I mainly took place in the reaction of Br-Py-Th-I (1 b) with 2, whereas disubstitution selectively occurred in the reaction of I-Py-Th-Br (1 c) with 2, indicating that the Pd catalyst is intramolecularly transferred from acceptor Py to donor Th. Therefore, we synthesized monomer 12 by introduction of a boronate moiety and bromine into Py and Th, respectively. However, examination of the relationship between monomer conversion and the M n of the obtained polymer, as well as the matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectra, indicated that Suzuki-Miyaura coupling polymerization of 12 with (o-tolyl)tBu 3 PPdBr initiator 13 proceeded in a step-growth polymerization manner through intermolecular transfer of the Pd catalyst. To understand the discrepancy between the model reactions and polymerization reaction, Suzuki-Miyaura coupling reactions of 1 c with thiopheneboronic acid ester instead of 2 were carried out. This resulted in a decrease of the disubstitution product. Therefore, step-growth polymerization appears to be due to intermolecular transfer of the Pd catalyst from Th after reductive elimination of the Th-Pd-Py complex formed by transmetalation of polymer Th-Br with (Pin)B-Py-Th-Br monomer 12 (Pin=pinacol). Catalysts with similar stabilization energies of metal-arene η 2 -coordination for D and A monomers may be needed for CTCP reactions of biaryl D-A monomers. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of a reaction medium on the oxidation of aromatic nitrogen-containing compounds by peroxyacids

NASA Astrophysics Data System (ADS)

Dutka, V. S.; Matsyuk, N. V.; Dutka, Yu. V.

2011-01-01

The influence of different solvents on the oxidation reaction rate of pyridine (Py), quinoline (QN), acridine (AN), α-oxyquinoline (OQN) and α-picolinic acid (APA) by peroxydecanoic acid (PDA) was studied. It was found that the oxidation rate grows in the series Py < QN < AN, and the rate of the oxidation reaction of compounds containing a substituent in the α position from a reactive center is significantly lower than for unsubstituted analogues. The effective energies of activation of the oxidation reaction were found. It was shown that in the first stage, the reaction mechanism includes the rapid formation of an intermediate complex nitrogen-containing compound, peroxyacid, which forms products upon decomposing in the second stage. A kinetic equation that describes the studied process is offered. The constants of equilibrium of the intermediate complex formation ( K eq) and its decomposition constant ( k 2) in acetone and benzene were calculated. It was shown that the nature of the solvent influences the numerical values of both K p and k 2. It was established that introduction of acetic acid (which is able to form compounds with Py) into the reaction medium slows the rate of the oxidation process drastically. Correlation equations linking the polarity, polarizability, electrophilicity, and basicity of solvents with the constant of the PDA oxidation reaction rate for Py were found. It was concluded that the basicity and polarity of the solvent have a decisive influence on the oxidation reaction rate, while the polarizability and electrophilicity of the reaction medium do not influence the oxidation reaction rate.

The Role of Specific Alcohol-Related Problems in Predicting Depressive Experiences in a Cross-Sectional National Household Survey.

PubMed

McBride, Orla; Cheng, Hui G; Slade, Tim; Lynskey, Michael T

2016-11-01

This study examines the type of alcohol-related problems that commonly occur before the onset of depressive experiences to shed light on the mechanisms underlying the alcohol-depression comorbidity relationship. Data were from the 1992 USA National Longitudinal Alcohol Epidemiologic Survey. Analytical sample comprised of drinkers with a prior to past year (PPY) history of alcohol-related problems with or without any experiences of depressed mood in the past year (PY). The prevalence of PPY alcohol-related problems was examined, as well as the ability of specific alcohol problems to predict PY experiences of depressed mood. The type of depressed mood experienced by drinkers with PPY history of alcohol-related problems was compared to those without. All but one alcohol-related problem PPY was more frequently endorsed among drinkers with PY experiences of depressed mood. Controlling for confounders, five alcohol-related problems experienced PPY were significantly predictive of depressed mood PY: tolerance, drinking longer than intended, inability to perform important social and occupational roles/obligations, as well as drinking in physically hazardous situations. Drinkers with alcohol-related problems PPY more frequently experienced difficulties with concentration, energy, and thoughts of death, than those without. Alcohol-related problems are likely associated with depressive experiences through a complex network, whereby experiences of physical dependence and negative consequences increase the likelihood of negative affect. Novel study designs are necessary to fully understand the complex mechanisms underlying this comorbidity. © The Author 2016. Medical Council on Alcohol and Oxford University Press. All rights reserved.

A new method to assess skin treatments for lowering the impedance and noise of individual gelled Ag-AgCl electrodes.

PubMed

Piervirgili, G; Petracca, F; Merletti, R

2014-10-01

A model-based new procedure for measuring the single electrode-gel-skin impedance (ZEGS) is presented. The method is suitable for monitoring the contact impedance of the electrodes of a large array with limited modifications of the hardware and without removing or disconnecting the array from the amplifier. The procedure is based on multiple measurements between electrode pairs and is particularly suitable for electrode arrays. It has been applied to study the effectiveness of three skin treatments, with respect to no treatment, for reducing the electrode-gel-skin impedance (ZEGS) and noise: (i) rubbing with alcohol; (ii) rubbing with abrasive conductive paste; (iii) stripping with adhesive tape. The complex impedances ZEGS of the individual electrodes were measured by applying this procedure to disposable commercial Ag-AgCl gelled electrode arrays (4  ×  1) with a 5 mm(2) contact area. The impedance unbalance ΔZ = ZEGS1 - ZEGS2 and the RMS noise (VRMS) were measured between pairs of electrodes. The tissue impedance ZT was also obtained, as a collateral result. Measurements were repeated at t0 = 0 min and at t30 = 30 min from the electrode application. Mixed linear models and linear regression analysis applied to ZEGS, ΔZ and noise VRMS for the skin treatment factor demonstrated (a) that skin rubbing with abrasive conductive paste is more effective in lowering ZEGS, ΔZ and VRMS (p < 0.01) than the other treatments or no treatment, and (b) a statistically significant decrement (p < 0.01), between t0 and t30, of magnitude and phase of ZEGS.Rubbing with abrasive conductive paste significantly decreased the noise VRMS with respect to other treatments or no treatment.

Quantifying changes in total and pyrogenic carbon stocks across fire severity gradients using active wildfire incidents

NASA Astrophysics Data System (ADS)

Miesel, Jessica; Reiner, Alicia; Ewell, Carol; Maestrini, Bernardo; Dickinson, Matthew

2018-05-01

Positive feedbacks between wildfire emissions and climate are expected to increase in strength in the future; however, fires not only release carbon (C) from terrestrial to atmospheric pools, they also produce pyrogenic C (PyC) which contributes to longer-term C stability. Our objective was to quantify wildfire impacts on total C and PyC stocks in California mixed-conifer forest, and to investigate relationships between C and PyC stocks and changes across gradients of fire severity, using metrics derived from remote sensing and field observations. Our unique study accessed active wildfires to establish and measure plots within days before and after fire, prior to substantial erosion. We measured pre- and post-fire aboveground forest structure and woody fuels to calculate aboveground biomass, C and PyC, and collected forest floor and 0-5 cm mineral soil samples. Tree mortality increased with severity, but overstory C loss was minimal and limited primarily to foliage. Fire released 85% of understory and herbaceous C (comprising <1.0% of total ecosystem C). The greatest C losses occurred from downed wood and forest floor pools (19.3±5.1 Mg ha-1 and 25.9±3.2 Mg ha-1, respectively). Tree bark and downed wood contributed the greatest PyC gains (1.5±0.3 Mg ha-1 and 1.9±0.8 Mg ha-1, respectively), and PyC in tree bark showed non-significant positive trends with increasing severity. Overall PyC losses of 1.9±0.3 Mg ha-1 and 0.5±0.1 Mg ha-1 occurred from forest floor and 0-5 cm mineral soil, with no clear patterns across severity. Fire resulted in a net ecosystem PyC gain (0.96±0.98 Mg ha-1) across aboveground and belowground components of these forests, and there were no differences among severity levels. Carbon emissions represented only 21.6% of total forest C; however, extensive conversion of C from live to dead pools will contribute to large downed wood C pools susceptible to release in a subsequent fire, indicating that there may be a delayed relationship between fire severity and C emissions. This research advances understanding of forest C loss and stabilization as PyC in wildfires; however, poor relationships between C and PyC gains or losses and fire severity highlight the complexity of fire impacts on forest C.

cis-Dioxorhenium(V/VI) Complexes Supported by Neutral Tetradentate N4 Ligands. Synthesis, Characterization, and Spectroscopy.

PubMed

Ng, Vicky Yin-Ming; Tse, Chun-Wai; Guan, Xiangguo; Chang, Xiaoyong; Yang, Chen; Low, Kam-Hung; Lee, Hung Kay; Huang, Jie-Sheng; Che, Chi-Ming

2017-12-18

A series of cis-dioxorhenium(V) complexes containing chiral tetradentate N 4 ligands, including cis-[Re V (O) 2 (pyxn)] + (1; pyxn = N,N'-dimethyl-N,N'-bis(2-pyridylmethyl)cyclohexane-1,2-diamine), cis-[Re V (O) 2 (6-Me 2 pyxn)] + (cis-2), cis-[Re V (O) 2 (R,R-pdp)] + (3; R,R-pdp = 1,1'-bis((R,R)-2-pyridinylmethyl)-2,2'-bipyrrolidine), cis-[Re V (O) 2 (R,R-6-Me 2 pdp)] + (4), and cis-[Re V (O) 2 (bqcn)] + (5; bqcn = N,N'-dimethyl-N,N'-di(quinolin-8-yl)cyclohexane-1,2-diamine), were synthesized. Their structures were established by X-ray crystallography, showing Re-O distances in the range of 1.740(3)-1.769(8) Å and O-Re-O angles of 121.4(2)-124.8(4)°. Their cyclic voltammograms in MeCN (0.1 M [NBu 4 ]PF 6 ) display a reversible Re VI/V couple at E 1/2 = 0.39-0.49 V vs SCE. In aqueous media, three proton-coupled electron transfer reactions corresponding to Re VI/V , Re V/III , and Re III/II couples were observed at pH 1. The Pourbaix diagrams of 1·OTf, 3·OTf, and 5·OTf have been examined. The electronic absorption spectra of the cis-dioxorhenium(V) complexes show three absorption bands at around 800 nm (600-1730 dm 3 mol -1 cm -1 ), 580 nm (1700-5580 dm 3 mol -1 cm -1 ), and 462-523 nm (3170-6000 dm 3 mol -1 cm -1 ). Reaction of 1 with Lewis acids (or protic acids) gave cis-[Re V (O)(OH)(pyxn)] 2+ (1·H + ), in which the Re-O distances are lengthened to 1.788(5) Å. Complex cis-2 resulted from isomerization of trans-2 at elevated temperature. cis-[Re VI (O) 2 (pyxn)](PF 6 ) 2 (1'·(PF 6 ) 2 ) was obtained by constant-potential electrolysis of 1·PF 6 in MeCN (0.1 M [NBu 4 ]PF 6 ) at 0.56 V vs SCE; it displays shorter Re-O distances (1.722(4), 1.726(4) Å) and a smaller O-Re-O angle (114.88(18)°) relative to 1 and shows a d-d transition absorption band at 591 nm (ε = 77 dm 3 mol -1 cm -1 ). With a driving force of ca. 75 kcal mol -1 , 1' oxidizes hydrocarbons with weak C-H bonds (75.5-76.3 kcal mol -1 ) via hydrogen atom abstraction. DFT and TDDFT calculations on the electronic structures and spectroscopic properties of the cis-dioxorhenium(V/VI) complexes were performed.

The Snowball Blizzard Incident: A Reality Rub Life Space Interview.

ERIC Educational Resources Information Center

Long, Nicholas J.; Pinciotti, Dennis

1992-01-01

Focuses on Reality Rub Interview, one type of Life Space Interview (LSI), effective intervention strategy for use during crisis work with troubled students. Presents actual Reality Rub Interview, used with students who have "social blindness, social myopia, and tunnel vision" and who, when upset, misinterpret words and behaviors of…

Rotor-to-stator Partial Rubbing and Its Effects on Rotor Dynamic Response

NASA Technical Reports Server (NTRS)

Muszynska, Agnes; Franklin, Wesley D.; Hayashida, Robert D.

1991-01-01

Results from experimental and analytical studies on rotor to stationary element partial rubbings at several locations and their effects on rotor dynamic responses are presented. The mathematical model of a rubbing rotor is given. The computer program provides numerical results which agree with experimentally obtained rotor responses.

The response of turbine engine rotors to interference rubs

NASA Technical Reports Server (NTRS)

Kascak, A. F.

1980-01-01

A method was developed for the direct integration of a rotor dynamics system experiencing a blade loss induced rotor rub. Both blade loss and rotor rub were simulated on a rotor typical of a small gas turbine. A small change in the coefficient of friction (from 0.1 to 0.2) caused the rotor to change from forward to backward whirl and to theoretically destroy itself in a few rotations. This method provides an analytical capability to study the susceptibility of rotors to rub induced backward whirl problems.

Prevalence of muzzle-rubbing and hand-rubbing behavior in wild chimpanzees in Mahale Mountains National Park, Tanzania.

PubMed

Corp, Nadia; Hayaki, Hitoshige; Matsusaka, Takahisa; Fujita, Shiho; Hosaka, Kazuhiko; Kutsukake, Nobuyuki; Nakamura, Michio; Nakamura, Miho; Nishie, Hitonaru; Shimada, Masaki; Zamma, Koichiro; Wallauer, William; Nishida, Toshisada

2009-04-01

In 1998, four chimpanzees in the Mahale Mountains National Park, Tanzania, were observed wiping their mouths with non-detached leaves or stalks of grass, or rubbing their mouths with a tree trunk or branch, especially while eating lemons. The number of mouth-wiping/rubbing individuals increased to 18 in 1999. By 2005, 29 chimpanzees were documented wiping/rubbing their muzzles in this way. Although it is difficult to determine whether the chimpanzees acquired this behavior as a result of trial and error or social learning, the fact that chimpanzees at other sites perform this behavior with detached leaves or leafy twigs much more often than with intact items suggests the possibility that cleaning with intact plant parts at Mahale spread via social learning.

Evaluating cis-2,6-Dimethylpiperidide (cis-DMP) as a Base Component in Lithium-Mediated Zincation Chemistry

PubMed Central

Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan

2013-01-01

Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N′,N′-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78 % and 48 % following D2O quenching of zincated benzamide intermediates). An 88 % yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis-DMP)tBu2] and the post-metallation complex [(TMEDA)Li(cis-DMP){2-[1-C(=O)N(iPr)2]C6H4}Zn(tBu)], shed valuable light on the structures and mechanisms involved in these alkali-metal-mediated zincation reactions. Aspects of these reactions are also modelled by DFT calculations. PMID:23955639

Synthesis, characterization and cytotoxic properties of platinum(II) complexes containing the nucleosides adenosine and cytidine.

PubMed

Montagner, Diego; Gandin, Valentina; Marzano, Cristina; Longato, Bruno

2011-06-01

Cytidine (cyt) and adenosine (ado) react with cis-[L(2)Pt(μ-OH)](2)(NO(3))(2) (L=PMe(3), PPh(3)) in various solvents to give the nucleoside complexes cis-[L(2)Pt{cyt(-H),N(3)N(4)}](3)(NO(3))(3) (L=PMe(3), 1),cis-[L(2)Pt{cyt(-H),N(4)}(cyt,N(3))]NO(3) (L=PPh(3), 2), cis-[L(2)Pt{ado(-H),N(1)N(6)}](2)(NO(3))(2) (L=PMe(3), 3) and cis-[L(2)Pt{ado(-H),N(6)N(7)}]NO(3) (L=PPh(3), 4). When the condensation reaction is carried out in solution of nitriles (RCN, R=Me, Ph) the amidine derivatives cis-[(PPh(3))(2)PtNH=C(R){cyt(-2H)}]NO(3) (R=Me, 5a; R=Ph, 5b) and cis-[(PPh(3))(2)PtNH=C(R){ado(-2H)}]NO(3) (R=Me, 6a: R=Ph, 6b) are quantitatively formed. The coordination mode of these nucleosides, characterized in solution by multinuclear NMR spectroscopy and mass spectrometry, is similar to that previously observed for the nucleobases 1-methylcytosine (1-MeCy) and 9-methyladenine (9-MeAd). The cytotoxic properties of the new complexes, and those of the nucleobase analogs, cis-[(PPh(3))(2)PtNH=C(R){1-MeCy(-2H)}]NO(3) (R=Me, 7a: R=Ph, 7b), cis-[(PPh(3))(2)PtNH=C(R){9-MeAd(-2H)}]NO(3) (R=Me, 8a: R=Ph, 8b) have been investigated in a wide panel of human cancer cells. Interestingly, whereas the Pt(II) nucleoside complexes (1-4) did not show appreciable cytotoxicity, the corresponding amidine derivatives (7a, 7b, 8a, 8b, 5b, and 6b) exhibited a significant in vitro antitumor activity. Copyright © 2011 Elsevier Inc. All rights reserved.

pySPACE—a signal processing and classification environment in Python

PubMed Central

Krell, Mario M.; Straube, Sirko; Seeland, Anett; Wöhrle, Hendrik; Teiwes, Johannes; Metzen, Jan H.; Kirchner, Elsa A.; Kirchner, Frank

2013-01-01

In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in acquisition techniques and questions addressed. Here, automated signal processing and machine learning tools can help to process the data, e.g., to separate signal and noise. With the presented software pySPACE (http://pyspace.github.io/pyspace), signal processing algorithms can be compared and applied automatically on time series data, either with the aim of finding a suitable preprocessing, or of training supervised algorithms to classify the data. pySPACE originally has been built to process multi-sensor windowed time series data, like event-related potentials from the electroencephalogram (EEG). The software provides automated data handling, distributed processing, modular build-up of signal processing chains and tools for visualization and performance evaluation. Included in the software are various algorithms like temporal and spatial filters, feature generation and selection, classification algorithms, and evaluation schemes. Further, interfaces to other signal processing tools are provided and, since pySPACE is a modular framework, it can be extended with new algorithms according to individual needs. In the presented work, the structural hierarchies are described. It is illustrated how users and developers can interface the software and execute offline and online modes. Configuration of pySPACE is realized with the YAML format, so that programming skills are not mandatory for usage. The concept of pySPACE is to have one comprehensive tool that can be used to perform complete signal processing and classification tasks. It further allows to define own algorithms, or to integrate and use already existing libraries. PMID:24399965

pySPACE-a signal processing and classification environment in Python.

PubMed

Krell, Mario M; Straube, Sirko; Seeland, Anett; Wöhrle, Hendrik; Teiwes, Johannes; Metzen, Jan H; Kirchner, Elsa A; Kirchner, Frank

2013-01-01

In neuroscience large amounts of data are recorded to provide insights into cerebral information processing and function. The successful extraction of the relevant signals becomes more and more challenging due to increasing complexities in acquisition techniques and questions addressed. Here, automated signal processing and machine learning tools can help to process the data, e.g., to separate signal and noise. With the presented software pySPACE (http://pyspace.github.io/pyspace), signal processing algorithms can be compared and applied automatically on time series data, either with the aim of finding a suitable preprocessing, or of training supervised algorithms to classify the data. pySPACE originally has been built to process multi-sensor windowed time series data, like event-related potentials from the electroencephalogram (EEG). The software provides automated data handling, distributed processing, modular build-up of signal processing chains and tools for visualization and performance evaluation. Included in the software are various algorithms like temporal and spatial filters, feature generation and selection, classification algorithms, and evaluation schemes. Further, interfaces to other signal processing tools are provided and, since pySPACE is a modular framework, it can be extended with new algorithms according to individual needs. In the presented work, the structural hierarchies are described. It is illustrated how users and developers can interface the software and execute offline and online modes. Configuration of pySPACE is realized with the YAML format, so that programming skills are not mandatory for usage. The concept of pySPACE is to have one comprehensive tool that can be used to perform complete signal processing and classification tasks. It further allows to define own algorithms, or to integrate and use already existing libraries.

Molecules Designed to Contain Two Weakly Coupled Spins with a Photoswitchable Spacer.

PubMed

Uber, Jorge Salinas; Estrader, Marta; Garcia, Jordi; Lloyd-Williams, Paul; Sadurní, Anna; Dengler, Dominik; van Slageren, Joris; Chilton, Nicholas F; Roubeau, Olivier; Teat, Simon J; Ribas-Ariño, Jordi; Aromí, Guillem

2017-10-04

Controlling the charges and spins of molecules lies at the heart of spintronics. A photoswitchable molecule consisting of two independent spins separated by a photoswitchable moiety was designed in the form of new ligand H 4 L, which features a dithienylethene photochromic unit and two lateral coordinating moieties, and yields molecules with [MM⋅⋅⋅MM] topology. Compounds [M 4 L 2 (py) 6 ] (M=Cu, 1; Co, 2; Ni, 3; Zn, 4) were prepared and studied by single-crystal X-ray diffraction (SCXRD). Different metal centers can be selectively distributed among the two chemically distinct sites of the ligand, and this enables the preparation of many double-spin systems. Heterometallic [MM'⋅⋅⋅M'M] analogues with formulas [Cu 2 Ni 2 L 2 (py) 6 ] (5), [Co 2 Ni 2 L 2 (py) 6 ] (6), [Co 2 Cu 2 L 2 (py) 6 ] (7), [Cu 2 Zn 2 L 2 (py) 6 ] (8), and [Ni 2 Zn 2 L 2 (py) 6 ] (9) were prepared and analyzed by SCXRD. Their composition was established unambiguously. All complexes exhibit two weakly interacting [MM'] moieties, some of which embody two-level quantum systems. Compounds 5 and 8 each exhibit a pair of weakly coupled S=1/2 spins that show quantum coherence in pulsed Q-band EPR spectroscopy, as required for quantum computing, with good phase memory times (T M =3.59 and 6.03 μs at 7 K). Reversible photoswitching of all the molecules was confirmed in solution. DFT calculations on 5 indicate that the interaction between the two spins of the molecule can be switched on and off on photocyclization. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Linking pyrolysis and anaerobic digestion (Py-AD) for the conversion of lignocellulosic biomass.

PubMed

Fabbri, Daniele; Torri, Cristian

2016-04-01

Biogas is a mixture of CO2 and CH4 produced by a consortia of Bacteria and Archeae operating in anaerobic digestion (AD) plants. Biogas can be burnt as such in engines to produce electricity and heat or upgraded into biomethane. Biomethane is a drop-in fuel that can be injected in the natural gas grid or utilised as a transport fuel. While a wide array of biomass feedstock can be degraded into biogas, unconverted lignin, hemicellulose and cellulose end up in the co-product digestate leaving a large portion of chemical energy unutilised. Pyrolysis (Py) transforms in a single step and without chemical reagents the lignocellulose matrix into gaseous (syngas), liquid (bio-oil, pyrolysis oil) and solid (biochar) fractions for the development of renewable fuels and materials. The Py route applied downstream to AD is actively investigated in order to valorise the solid digestate presently destined only for soil applications. Coupling Py upstream to AD is an emerging field of research aimed at expanding the feedstock towards biologically recalcitrant substrates (wood, paper, sludge). The biomethanation potential was demonstrated for gaseous (H2/CO) and water soluble pyrolysis products, while the influence of insoluble pyrolytic lignin remains fairly unexplored. Biochar can promote the production of biomethane by acting as a support for microorganism colonisation, conductor for direct interspecies electron transfer, sorbent for hydrophobic inhibitors, and reactant for in situ biogas upgrading. Enhancing the advantages (carbon source) over the side effects (toxicity) of Py fractions represents the main challenge of Py-AD. This can be addressed by increasing the selectivity of the thermochemical process or improving the ecological flexibility of mixed bacterial consortia towards chemically complex environments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Management of Varicose Veins and Chronic Venous Insufficiency in a Comparative Registry with Nine Venoactive Products in Comparison with Stockings.

PubMed

Belcaro, G; Dugall, M; Luzzi, R; Corsi, M; Ledda, A; Ricci, A; Pellegrini, L; Cesarone, M R; Hosoi, M; Errichi, B M; Cornelli, U; Cotellese, R; Agus, G; Feragalli, B

2017-09-01

The aim of this registry study was to compare products used to control symptoms of CVI. Endpoints of the study were microcirculation, effects on volume changes, and symptoms (analogue scale). Pycnogenol, venoruton, troxerutin, the complex diosmin-hesperidin, Antistax, Mirtoselect (bilberry), escin, and the combination Venoruton-Pycnogenol (VE-PY) were compared with compressions. No safety or tolerability problems were observed. At inclusion, measurements in the groups were comparable: 1,051 patients completed the registry. Best performers : Venoruton, Pycnogenol, and the combination VE-PY produced the best effects on skin flux. These products and the combination VE-PY better improved PO 2 and PCO 2 . The edema score was decreased more effectively with the combination and with Pycnogenol. Venoruton; Antistax also had good results. Considering volumetry, the best performers were the combination PY-VE and the two single products Venoruton and Pycnogenol. Antistax results for edema were also good. The best improvement in symptoms score were obtained with Pycnogenol and compression. A larger decrease in oxidative stress was observed with Pycnogenol, Venoruton, and with the VE-PY combination. Good effects of Antistax were also observed. Parestesias were lower with Pycnogenol and with Antistax. Considering the need for interventions, the best performers were Pycnogenol, VE-PY, and compression. The efficacy of Pycnogenol and the combination are competitive with stockings that do not have the same tolerability in warmer climates. A larger and more prolonged evaluation is suggested to evaluate cost-efficacy (and non-interference with drugs) of these products in the management of CVI. The registry is in progress; other products are in evaluation.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research

PubMed Central

Campagnola, Luke; Kratz, Megan B.; Manis, Paul B.

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org. PMID:24523692

Effects of cytotoxic cis- and trans-diammine monochlorido platinum(II) complexes on selenium-dependent redox enzymes and DNA.

PubMed

Lemmerhirt, Heidi; Behnisch, Steven; Bodtke, Anja; Lillig, Christopher H; Pazderova, Lucia; Kasparkova, Jana; Brabec, Viktor; Bednarski, Patrick J

2018-01-01

Here we present the preparation of 14 pairs of cis- and trans-diammine monochlorido platinum(II) complexes, coordinated to heterocycles (i.e., imidazole, 2-methylimidazole and pyrazole) and linked to various acylhydrazones, which were designed as potential inhibitors of the selenium-dependent enzymes glutathione peroxidase 1 (GPx-1) and thioredoxin reductase 1 (TrxR-1). However, no inhibition of bovine GPx-1 and only weak inhibition of murine TrxR-1 was observed in in vitro assays. Nonetheless, the cis configured diammine monochlorido Pt(II) complexes exhibited cytotoxic and apoptotic properties on various human cancer cell lines, whereas the trans configured complexes generally showed weaker potency with a few exceptions. On the other hand, the trans complexes were generally more likely to lack cross-resistance to cisplatin than the cis analogues. Platinum was found bound to the nuclear DNA of cancer cells treated with representative Pt complexes, suggesting that DNA might be a possible target. Thus, detailed in vitro binding experiments with DNA were conducted. Interactions of the compounds with calf thymus DNA were investigated, including Pt binding kinetics, circular dichroism (CD) spectral changes, changes in DNA melting temperatures, unwinding of supercoiled plasmids and ethidium bromide displacement in DNA. The CD results indicate that the most active cis configured pyrazole-derived complex causes unique structural changes in the DNA compared to the other complexes as well as to those caused by cisplatin, suggesting a denaturation of the DNA structure. This may be important for the antiproliferative activity of this compound in the cancer cells. Copyright © 2017. Published by Elsevier Inc.

Using phosphine ligands with a biological role to modulate reactivity in novel platinum complexes

NASA Astrophysics Data System (ADS)

Echeverri, Marcelo; Alvarez-Valdés, Amparo; Navas, Francisco; Perles, Josefina; Sánchez-Pérez, Isabel; Quiroga, A. G.

2018-02-01

Three platinum complexes with cis and trans configuration cis-[Pt(TCEP)2Cl2], cis-[Pt(tmTCEP)2Cl2] and trans-[Pt(TCEP)2Cl2], where TCEP is tris(2-carboxyethyl)phosphine, have been synthesized and fully characterized by usual techniques including single-crystal X-ray diffraction for trans-[Pt(TCEP)2Cl2] and cis-[Pt(tmTCEP)2Cl2]. Here, we also report on an esterification process of TCEP, which takes place in the presence of alcohols, leading to a platinum complex coordinated to an ester tmTCEP (2-methoxycarbonylethyl phosphine) ligand. The stability in solution of the three compounds and their interaction with biological models such as DNA (pBR322 and calf thymus DNA) and proteins (lysozyme and RNase) have also been studied.

Synthesis and antitumor activity of seleno- and thio-purines complexed with cis-diamminoplatinum (II).

PubMed

Maeda, M; Abiko, N; Sasaki, T

1982-02-01

cis-Diamminoplatinum (II) complexes with selenoguanine, thioguanine, 6-thioxanthine, or 6-mercaptopurine were synthesized by the reaction of stoichiometric amounts of selenopurine or thiopurine with aquated cis-dichlorodimmineplatinum (II) in slightly acidic medium, and their antitumor activity was studied against L1210 cells in mice. These compounds exhibited a medium antitumor activity with very low toxicity. The antitumor activity was dependent on the nature of the purine ligand. These complexes were very stable in various aqueous solvents at 37 degrees C for 10 d but not in the presence of mouse serum. The mechanism of the action effected by the complex is not clear. However, the slow release of an antitumor active purine from the complex, SeG-Pt (NH3)2, was observed.

Theoretical and experimental investigation on the sudden unbalance and rub-impact in rotor system caused by blade off

NASA Astrophysics Data System (ADS)

Wang, Cun; Zhang, Dayi; Ma, Yanhong; Liang, Zhichao; Hong, Jie

2016-08-01

Blade loss from a running turbofan rotor will introduce sudden unbalance into the dynamical system, and as a consequence leads to the rub-impact, the asymmetry of rotor and a series of interesting dynamic characteristics. The paper focuses on the theoretical study on the sudden unbalance and rub-impact caused by blade loss, in particular investigates the response of the rotor on a rotor test rig with sudden unbalance and rub-impact device designed respectively. The results reveal that the sudden unbalance will induce impact effect on the rotor, and critical speed frequency is excited in frequency spectrum. Meantime, the impact effect is more obvious for the rotor operating above critical speed. The influence of rub-impact is considered as additional constraint to the rotor, analyzed by the theory of time-varying system for the first time, and the results are evaluated by experimental tests. The study shows that great attention should be paid to the dynamical design for the overhung rotor system, additional constraint and corresponding analysis method in rub-impact need to be intensively studied.

Analytical and experimental investigation of rubbing interaction in labyrinth seals for a liquid hydrogen fuel pump. [space shuttle main engine

NASA Technical Reports Server (NTRS)

Dolan, F. X.; Kennedy, F. E.; Schulson, E. M.

1984-01-01

Cracking of the titanium knife edges on the labyrinth seals of the liquid hydrogen fuel pump in the Space Shuttle main engine is considered. Finite element analysis of the thermal response of the knife edge in sliding contact with the wear ring surface shows that interfacial temperatures can be quite high and they are significantly influenced by the thermal conductivity of the surfaces in rubbing contact. Thermal shock experiments on a test specimen similar to the knife edge geometry demonstrate that cracking of the titanium alloy is possible in a situation involving repeated thermal cycles over a wide temperature range, as might be realized during a rub in the liquid hydrogen fuel pump. High-speed rub interaction tests were conducted using a representative knife edge and seal geometry over a broad range of interaction rates and alternate materials were experimentally evaluated. Plasma-sprayed aluminum-graphite was found to be significantly better than presently used aluminum alloy seals from the standpoint of rub performance. Ion nitriding the titanium alloy knife-edges also improved rub performance compared to the untreated baseline.

Effects of geometric variables on rub characteristics of Ti-6Al-4V

NASA Technical Reports Server (NTRS)

Bill, R. C.; Wolak, J.; Wisander, D. W.

1981-01-01

Experiments simulating rub interactions between Ti-6Al-4V blade tips and various seal materials were conducted. The number of blade tips and the blade tip geometry were varied to determine their effects on rub forces and on wear phenomena. Contact was found to be quite unsteady for all blade tip geometries except for those incorporating deliberately rounded blade tips. The unsteady contact was characterized by long periods of rubbing contact and increasing blade tip that terminated in sudden rapid metal removal, sometimes accompanied by tearing and disruption of porous seal material under the rub surface. A model describing the blade tip loading is proposed and is based on the propagation of an elastic stress wave through the seal material as the seal material is dynamically compressed by the blade tip leading edge.

Reactivity and biological properties of a series of cytotoxic PtI2(amine)2 complexes, either cis or trans configured.

PubMed

Messori, Luigi; Cubo, Leticia; Gabbiani, Chiara; Álvarez-Valdés, Amparo; Michelucci, Elena; Pieraccini, Giuseppe; Ríos-Luci, Carla; León, Leticia G; Padrón, José M; Navarro-Ranninger, Carmen; Casini, Angela; Quiroga, Adoración G

2012-02-06

Six diiodido-diamine platinum(II) complexes, either cis or trans configured, were prepared, differing only in the nature of the amine ligand (isopropylamine, dimethylamine, or methylamine), and their antiproliferative properties were evaluated against a panel of human tumor cell lines. Both series of complexes manifested pronounced cytotoxic effects, with the trans isomers being, generally, more effective than their cis counterparts. Cell cycle analysis revealed different modes of action for these new Pt(II) complexes with respect to cisplatin. The reactivity of these platinum compounds with a number of biomolecules, including cytochrome c, two sulfur containing modified amino acids, 9-ethylguanine, and a single strand oligonucleotide, was analyzed in depth by mass spectrometry and NMR spectroscopy. Interestingly, significant differences in the reactivity of the investigated compounds toward the various model biomolecules were observed: in particular we observed that trans complexes preferentially release their iodide ligands upon biomolecule binding, while the cis isomers may release the amine ligands with retention of iodides. Such differences in reactivity may have important mechanistic implications and a relevant impact on the respective pharmacological profiles.

Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment

PubMed Central

Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C.

2017-01-01

ABSTRACT Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria, particularly Actinomycetales, was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and contributes to soil biogeochemical cycling. This study identified the bacterial community composition associated with PyOMs on the basis of high-throughput sequencing and demonstrated that both PyOM pyrolysis temperature and the colonization environment determined the bacterial community composition. Our work increases our understanding of the dominant phylogenetic taxa associated with PyOMs, demonstrates mechanisms mediating microbial metabolism and growth in PyOMs, and expands a new research area for pyrogenic organic matter. This study identified the bacterial community composition associated with PyOM, which is widely distributed in the environment. Most bacterial OTUs preferentially thrived on PyOM pyrolyzed at low temperature, while some specific OTUs thrived on PyOM pyrolyzed at high temperature. PMID:28405627

Bacterial Community Composition Associated with Pyrogenic Organic Matter (Biochar) Varies with Pyrolysis Temperature and Colonization Environment.

PubMed

Dai, Zhongmin; Barberán, Albert; Li, Yong; Brookes, Philip C; Xu, Jianming

2017-01-01

Microbes that colonize pyrogenic organic matter (PyOM) (also called biochar) play an important role in PyOM mineralization and crucially affect soil biogeochemical cycling, while the microbial community composition associated with PyOM particles is poorly understood. We generated two manure-based PyOMs with different characteristics (PyOM pyrolyzed at the low temperature of 300°C [i.e., PyOM300] and at the high temperature of 700°C [i.e., PyOM700]) and added them to high-carbon (4.15%) and low-C (0.37%) soil for microbial colonization. 16S rRNA gene sequencing showed that Actinobacteria , particularly Actinomycetales , was the dominant taxon in PyOM, regardless of the PyOM pyrolysis temperature and soil type. Bacterial communities associated with PyOM particles from high-C soils were similar to those in non-PyOM-amended soils. PyOM300 had higher total microbial activity and more differential bacterial communities than PyOM700. More bacterial operational taxonomic units (OTUs) preferentially thrived on the low-pyrolysis-temperature PyOM, while some specific OTUs thrived on high-pyrolysis-temperature PyOM. In particular, Chloroflexi species tended to be more prevalent in high-pyrolysis-temperature PyOM in low-C soils. In conclusion, the differences in colonized bacterial community composition between the different PyOMs were strongly influenced by the pyrolysis temperatures of PyOM, i.e., under conditions of easily mineralizable C or fused aromatic C, and by other properties, e.g., pH, surface area, and nutrient content. IMPORTANCE Pyrogenic organic matter (PyOM) is widely distributed in soil and fluvial ecosystems and plays an important role in biogeochemical cycling. Many studies have reported changes in soil microbial communities stimulated by PyOM, but very little is known about the microbial communities associated with PyOM. The microbes that colonize PyOMs can participate in the mineralization of PyOM, so changing its structure affects the fate of PyOMs and contributes to soil biogeochemical cycling. This study identified the bacterial community composition associated with PyOMs on the basis of high-throughput sequencing and demonstrated that both PyOM pyrolysis temperature and the colonization environment determined the bacterial community composition. Our work increases our understanding of the dominant phylogenetic taxa associated with PyOMs, demonstrates mechanisms mediating microbial metabolism and growth in PyOMs, and expands a new research area for pyrogenic organic matter. This study identified the bacterial community composition associated with PyOM, which is widely distributed in the environment. Most bacterial OTUs preferentially thrived on PyOM pyrolyzed at low temperature, while some specific OTUs thrived on PyOM pyrolyzed at high temperature.

Revisiting the hand wipe versus gel rub debate: is a higher-ethanol content hand wipe more effective than an ethanol gel rub?

PubMed

D'Antonio, Natalie N; Rihs, John D; Stout, Janet E; Yu, Victor L

2010-11-01

The Centers for Disease Control and Prevention's guidelines for hand hygiene state that the use of alcohol-based hand wipes is not an effective substitute for the use of an alcohol-based hand rub or handwashing with an antimicrobial soap and water. The objective of this study was to determine whether a hand wipe with higher ethanol content (65.9%) is as effective as an ethanol hand rub or antimicrobial soap in removing bacteria and spores from hands. In two separate experiments, the hands of 7 subjects were inoculated with a suspension of Serratia marcescens or Geobacillus stearothermophilus. Subjects washed with each of 3 different products: 65.9% ethanol hand wipes (Sani-Hands ALC), 62% ethanol gel rub (Purell), and antimicrobial soap containing 0.75% triclosan (Kindest Kare). A total of 56 observations were analyzed for S marcescens removal and 70 observations were analyzed for G stearothermophilus removal. The rank order of product efficacy for both bacteria and spore removal was antibacterial soap > 65.9% ethanol hand wipes >62% ethanol hand rub. Mean S marcescens log reductions (±SD) for the 65.9% ethanol alcohol wipe, 62% ethanol alcohol rub, and antimicrobial foam soap were 3.44 ± 0.847, 2.32 ± 1.065, and 4.44 ± 1.018, respectively (P < .001). Mean G stearothermophilus log reductions for the 65.9% ethanol wipe, 62% ethanol rub, and antimicrobial foam soap were 0.51 ± 0.26, -0.8 ± 0.32 increase over baseline, and 1.72 ± 0.62, respectively (P < .001). The alcohol-based hand wipe containing 65.9% ethanol was significantly more effective than the 62% ethanol rub in reducing the number of viable bacteria and spores on the hands. Copyright © 2010 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Electron-transfer reactions of cobalt(III) complexes. 1. The kinetic investigation of the reduction of various surfactant cobalt(III) complexes by iron(II) in surface active ionic liquids

NASA Astrophysics Data System (ADS)

Nagaraj, Karuppiah; Senthil Murugan, Krishnan; Thangamuniyandi, Pilavadi; Sakthinathan, Subramanian

2015-05-01

The kinetics of outer sphere electron transfer reaction of surfactant cobalt(III) complex ions, cis-[Co(en)2(C12H25NH2)2]3+ (1), cis-[Co(dp)2(C12H25NH2)2]3+ (2), cis-[Co(trien)(C12H25NH2)2]3+ (3), cis-[Co(bpy)2(C12H25NH2)2]3+ (4) and cis-[Co(phen)2(C12H25NH2)2]3+ (5) (en: ethylenediamine, dp: diaminopropane, trien : triethylenetetramine, bpy: 2,2‧-bipyridyl, phen: 1,10-phenanthroline and C12H25NH2 : dodecylamine) have been interrogated by Fe2+ ion in ionic liquid (1-butyl-3-methylimidazoliumbromide) medium at different temperatures (298, 303, 308, 313, 318 and 323 K) by the spectrophotometry method under pseudo first order conditions using an excess of the reductant. Experimentally the reactions were found to be of second order and the electron transfer as outer sphere. The second order rate constant for the electron transfer reaction in ionic liquids was found to increase with increase in the concentration of all these surfactant cobalt(III) complexes. Among these complexes (from en to phen ligand), complex containing the phenanthroline ligand rate is higher compared to other complexes. By assuming the outer sphere mechanism, the results have been explained based on the presence of aggregated structures containing cobalt(III) complexes at the surface of ionic liquids formed by the surfactant cobalt(III) complexes in the reaction medium. The activation parameters (enthalpy of activation ΔH‡ and entropy of activation ΔS‡) of the reaction have been calculated which substantiate the kinetics of the reaction.

Degraded Chinese rubbing images thresholding based on local first-order statistics

NASA Astrophysics Data System (ADS)

Wang, Fang; Hou, Ling-Ying; Huang, Han

2017-06-01

It is a necessary step for Chinese character segmentation from degraded document images in Optical Character Recognizer (OCR); however, it is challenging due to various kinds of noising in such an image. In this paper, we present three local first-order statistics method that had been adaptive thresholding for segmenting text and non-text of Chinese rubbing image. Both visual inspection and numerically investigate for the segmentation results of rubbing image had been obtained. In experiments, it obtained better results than classical techniques in the binarization of real Chinese rubbing image and PHIBD 2012 datasets.

Synthesis of highly functionalized macrocycles by the peripheral functionalization of macrocyclic diimines.

PubMed

Sierra, Miguel A; Pellico, Daniel; Gómez-Gallego, Mar; Mancheño, María José; Torres, Rosario

2006-11-10

The easily available macrocyclic diimines 4-7 can be stereoselectively transformed to macrocyclic bis-beta-amino acids 13-17, macrocyclic bisazetidines 18-20, and macrocyclic bisamides 21 and 22 by means of the corresponding bis-beta-lactam scaffolds 8-12. These key intermediates are available through standard Staudinger reaction and obtained as the cis-cis diastereomers, exclusively. An interesting relation between the proximity of the reactive C=N bonds and the selectivity in the formation of the bis-beta-lactams 8-12 is observed. Thus, diimine 4 leads to low selectivities, producing a 1:1 mixture of cis-syn-cis and cis-anti-cis diastereomers, while diimines 5-7 having the diimine sites more separated lead almost exclusively to the cis-anti-cis diastereomers. The stereochemistry of all the products was unambiguously assigned by X-ray diffraction analysis of compounds cis-syn-cis 8 and cis-anti-cis 12-Co2CO6 complex.

The malaria parasite RhopH protein complex interacts with erythrocyte calmyrin identified from a comprehensive erythrocyte protein library.

PubMed

Miura, Toyokazu; Takeo, Satoru; Ntege, Edward H; Otsuki, Hitoshi; Sawasaki, Tatsuya; Ishino, Tomoko; Takashima, Eizo; Tsuboi, Takafumi

2018-06-02

Malaria merozoite apical organelles; microneme and rhoptry secreted proteins play functional roles during and following invasion of host erythrocytes. Among numerous proteins, the rhoptries discharge high molecular weight proteins known as RhopH complex. Recent reports suggest that the RhopH complex is essential for growth and survival of the malaria parasite within erythrocytes. However, an in-depth understanding of the host-parasite molecular interactions is indispensable. Here we utilized a comprehensive mouse erythrocyte protein library consisting of 443 proteins produced by a wheat germ cell-free system, combined with AlphaScreen technology to identify mouse erythrocyte calmyrin as an interacting molecule of the rodent malaria parasite Plasmodium yoelii RhopH complex (PyRhopH). The PyRhopH interaction was dependent on the calmyrin N-terminus and divalent cation capacity. The finding unveils a recommendable and invaluable usefulness of our comprehensive mouse erythrocyte protein library together with the AlphaScreen technology in investigating a wide-range of host-parasite molecular interactions. Copyright © 2018 Elsevier Inc. All rights reserved.

Pd(II) and Pt(II) complexes of α-keto stabilized sulfur ylide: Synthesis, structural, theoretical and catalytic activity studies

NASA Astrophysics Data System (ADS)

Sabounchei, Seyyed Javad; Hashemi, Ali; Sedghi, Asieh; Bayat, Mehdi; Akhlaghi Bagherjeri, Fateme; Gable, Robert W.

2017-05-01

Reaction of dimethyl sulfide with 2, 3‧-dibromoacetophenone led to formation of sulfonium salt [Me2SCH2C(O)C6H4-m-Br]Br (1). The resulted sulfonium salt was treated with NaOH and gave the α-keto stabilized sulfur ylide Me2SC(H)C(O)C6H4-m-Br (2). This ligand was reacted with [MCl2(cod)] (M = Pd, Pt; cod = 1,5-cyclooctadiene) to form the new cis- and trans-[MCl2(ylide)2] (M = Pd (cis- and trans-3), Pt (cis- and trans-4)) complexes. Characterization of the obtained compounds was performed by elemental analysis, IR, 1H and 13C NMR. Recrystallization of dichlorobis(ylide) palladium(II) and platinum(II) complexes from DMSO solution yielded the crystalline products, which X-ray diffraction data revealed that the both compounds were crystallized as cis-[MCl2(ylide)(DMSO)] (M = Pd (5), Pt (6)) complexes. Also, a theoretical study on structure and nature of the Msbnd C bonding between the Y ligand (ylide) and [MCl2·DMSO] fragments in [YMCl2·DMSO] (M = Pd, Pt) complexes has been reported via NBO and energy-decomposition analysis (EDA). Furthermore, the palladium catalyzed Suzuki-Miyaura reaction of various aryl chlorides with arylboronic acids was performed. The results showed that the Pd(II) complexes cis- and trans-3 catalyzed efficiently coupling reactions at low catalyst loading and short reaction time.

Molecular recognition of DNA base pairs by the formamido/pyrrole and formamido/imidazole pairings in stacked polyamides

PubMed Central

Buchmueller, Karen L.; Staples, Andrew M.; Uthe, Peter B.; Howard, Cameron M.; Pacheco, Kimberly A. O.; Cox, Kari K.; Henry, James A.; Bailey, Suzanna L.; Horick, Sarah M.; Nguyen, Binh; Wilson, W. David; Lee, Moses

2005-01-01

Polyamides containing an N-terminal formamido (f) group bind to the minor groove of DNA as staggered, antiparallel dimers in a sequence-specific manner. The formamido group increases the affinity and binding site size, and it promotes the molecules to stack in a staggered fashion thereby pairing itself with either a pyrrole (Py) or an imidazole (Im). There has not been a systematic study on the DNA recognition properties of the f/Py and f/Im terminal pairings. These pairings were analyzed here in the context of f-ImPyPy, f-ImPyIm, f-PyPyPy and f-PyPyIm, which contain the central pairing modes, –ImPy– and –PyPy–. The specificity of these triamides towards symmetrical recognition sites allowed for the f/Py and f/Im terminal pairings to be directly compared by SPR, CD and ΔTM experiments. The f/Py pairing, when placed next to the –ImPy– or –PyPy– central pairings, prefers A/T and T/A base pairs to G/C base pairs, suggesting that f/Py has similar DNA recognition specificity to Py/Py. With –ImPy– central pairings, f/Im prefers C/G base pairs (>10 times) to the other Watson–Crick base pairs; therefore, f/Im behaves like the Py/Im pair. However, the f/Im pairing is not selective for the C/G base pair when placed next to the –PyPy– central pairings. PMID:15703305

Effects of eye rubbing on the levels of protease, protease activity and cytokines in tears: relevance in keratoconus.

PubMed

Balasubramanian, Sivaraman A; Pye, David C; Willcox, Mark D P

2013-03-01

Proteases, protease activity and inflammatory molecules in tears have been found to be relevant in the pathogenesis of keratoconus. We sought to determine the influence of eye rubbing on protease expression, protease activity and concentration of inflammatory molecules in tears. Basal tears were collected from normal volunteers before and after 60 seconds of experimental eye rubbing. The total amount of matrix metalloproteinase (MMP)-13 and inflammatory molecules interleukin (IL)-6 and tumour necrosis factor (TNF)-α in the tear samples were measured using specific enzyme-linked immunosorbent assays (ELISA). Tear collagenase activity was investigated using a specific activity assay. The concentrations of MMP-13 (51.9 ± 34.3 versus 63 ± 36.8 pg/ml, p = 0.006), IL-6 (1.24 ± 0.98 versus 2.02 ± 1.52 pg/ml, p = 0.004) and TNF-α (1.16 ± 0.74 versus 1.44 ± 0.66 pg/ml, p = 0.003) were significantly increased in normal subjects after eye rubbing. The experimental eye rub did not alter significantly the collagenase activity (5.02 ± 3 versus 7.50 ± 3.90 fluorescent intensity units, p = 0.14) of tears. Eye rubbing for 60 seconds increased the level of tear MMP-13, IL-6 and TNF-α in normal study subjects. This increase in protease, protease activity and inflammatory mediators in tears after eye rubbing may be exacerbated even further during persistent and forceful eye rubbing seen in people with keratoconus and this in turn may contribute to the progression of the disease. © 2013 The Authors. Clinical and Experimental Optometry © 2013 Optometrists Association Australia.

The effect of prolonged exposure to 750 C air on the tribological performance of PM212

NASA Technical Reports Server (NTRS)

Bemis, Kirk; Bogdanski, Michael S.; Dellacorte, Christopher; Sliney, Harold E.

1994-01-01

The effect of prolonged exposure to 750 C air on the tribological performance and dimensional stability of PM212, a high temperature, self-lubricating composite, is studied. PM212, by weight, contains 70 percent metal-bonded Cr3C2, 15 percent BaF2/CaF2 eutectic, and 15 percent silver. Rub blocks were fabricated from PM212 by cold isostatic pressing followed by sintering. Prior to tribo-testing, the rub blocks were exposed to 750 C air for periods ranging from 100 to 1000 hours. Then, the rub blocks were slid against nickel-based superalloy disks in a double-rub-block tribometer in air under a 66 N load at temperatures from 25 to 750 C with a sliding velocity of 0.36 m/s. Unexposed rub blocks were tested for baseline comparison. Friction coefficients ranged from 0.24 to 0.37 for the unexposed rub blocks and from 0.32 to 0.56 for the exposed ones. Wear for both the composite blocks and superalloy disks was typically in the moderate to low range of 10(exp -5) to 10(exp -6) mm(exp 3)/N-m. Friction and wear data were similar for the rub blocks exposed for 100, 500, and 1000 hours. Prolonged exposure to 750 C air increased friction and wear of the PM212 rub blocks at room temperature, but their triboperformance remained unaffected at higher temperatures, probably due to the formation of lubricious metal oxides. Dimensional stability of the composite was studied by exposing specimens of varying thicknesses for 500 hours in air at 750 C. Block thicknesses were found to increase with increased exposure time until steady state was reached after 100 hours of exposure, probably due to oxidation.

Single-step electrodeposition of CIS thin films with the complexing agent triethanolamine

NASA Astrophysics Data System (ADS)

Chiu, Yu-Shuen; Hsieh, Mu-Tao; Chang, Chih-Min; Chen, Chun-Shuo; Whang, Thou-Jen

2014-04-01

Some difficulties have long been encountered by single-step electrodeposition such as the optimization of electrolyte composition, deposition potentials, deposition time, and pH values. The approach of introducing ternary components into single-step electrodeposition is rather challenging especially due to the different values of the equilibrium potential for each constituent. Complexing agents play an important role in single-step electrodeposition of CuInSe2 (CIS), since the equilibrium potential of every constituent can be brought closer to each other when complexing agents are employed. In this work, single-step electrodeposition of CIS was enhanced by adding triethanolamine (TEA) into deposition bath, the CIS thin films were improved consequently in the form of polycrystalline cauliflower structures through the examination of SEM images and XRD patterns. The optimum composition of the solution for single-step electrodeposition of CIS is found to be 5 mM CuCl2, 22 mM InCl3, and 22 mM SeO2 at pH 1.5 with 0.1 M TEA. The structures, compositions, and morphologies of as-deposited and of annealed films were investigated.

Formation of carbonato and hydroxo complexes in the reaction of platinum anticancer drugs with carbonate.

PubMed

Di Pasqua, Anthony J; Centerwall, Corey R; Kerwood, Deborah J; Dabrowiak, James C

2009-02-02

The second-generation Pt(II) anticancer drug carboplatin is here shown to react with carbonate, which is present in blood, interstitial fluid, cytosol, and culture medium, to produce platinum-carbonato and -hydroxo complexes. Using [(1)H-(15)N] HSQC NMR and (15)N-labeled carboplatin, we observe that cis-[Pt(CBDCA-O)(OH)(NH(3))(2)](-), cis-[Pt(OH)(2)(NH(3))(2)], cis-[Pt(CO(3))(OH)(NH(3))(2)](-), and what may be cis-[Pt(CO(3))(NH(3))(2)] are produced when 1 is allowed to react in 23.8 mM carbonate buffer. When (15)N-labeled carboplatin is allowed to react in 0.5 M carbonate buffer, these platinum species, as well as other hydroxo and carbonato species, some of which may be dinuclear complexes, are produced. Furthermore, we show that the carbonato species cis-[Pt(CO(3))(OH)(NH(3))(2)](-) is also produced when cisplatin is allowed to react in carbonate buffer. The study outlines the conditions under which carboplatin and cisplatin form carbonato and aqua/hydroxo species in carbonate media.

The molecular characteristics of pyrogenic organic materials and their aqueous leachates

NASA Astrophysics Data System (ADS)

Wozniak, A. S.; Hatcher, P.; Mitra, S.; Bostick, K. W.; Zimmerman, A. R.

2016-12-01

Pyrogenic organic matter (Py-OM), or black carbon, is known to impact soil chemistry, pollutant transport, regional and global carbon cycling, and climate. Py-OM is incorporated into soils via atmospheric deposition (e.g., from biomass, fossil fuel combustion) or direct applications by humans (e.g., biochars applied for agricultural production). Due to its presumed refractory and immobile nature, soil Py-OM is thought to be efficiently buried, sequestering atmospheric CO2. However, tracers of dissolved Py-OM (Py-DOM) have been detected in appreciable quantities in riverine, estuarine, and oceanic waters suggesting that Py-OM is more mobile in the environment than expected. The molecular characteristics of Py-OM are likely to be a controlling factor in the quantities and impacts of Py-DOM released to aqueous systems. Yet, little is known about the detailed molecular composition of these materials, let alone how those molecular characteristics vary with combustion conditions or are altered by environmental processes. Here, we examine oak and grass Py-OM (combusted over a range of temperatures), natural Py-OM (chars aged in the environment for variable lengths of time), and their Py-DOM leachates via nuclear magnetic resonance spectroscopy (NMR) and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Multi-CP 13C NMR analyses of Py-OM materials and 1H NMR analyses of corresponding Py-DOM leachates reveal that Py-OM combustion temperature, environmental exposure, and molecular characteristics are reflected in Py-DOM quantities and characteristics. The relative amounts of aromatic C in Py-OM 1) decreases with environmental exposure, the relative oxygen-content in both Py-OM and Py-DOM, and the amount of Py-DOC released per g of Py-OC but 2) is positively correlated with combustion temperature and the relative contributions of acetate and aliphatic hydrogens (CH2) in Py-DOM. Preliminary FTICR-MS analyses show Py-DOM produced from oak at 400 °C to have lost carbohydrate-like compounds found in 250 °C Py-DOM and to contain an abundance of oxygenated aromatic compounds. Oak combusted at 650 °C produces Py-DOM characterized by high H/C, low O/C compounds. The results from this work will improve our understanding of Py-OM transport within and between terrestrial and aqueous systems.

PyMCT: A Very High Level Language Coupling Tool For Climate System Models

NASA Astrophysics Data System (ADS)

Tobis, M.; Pierrehumbert, R. T.; Steder, M.; Jacob, R. L.

2006-12-01

At the Climate Systems Center of the University of Chicago, we have been examining strategies for applying agile programming techniques to complex high-performance modeling experiments. While the "agile" development methodology differs from a conventional requirements process and its associated milestones, the process remain a formal one. It is distinguished by continuous improvement in functionality, large numbers of small releases, extensive and ongoing testing strategies, and a strong reliance on very high level languages (VHLL). Here we report on PyMCT, which we intend as a core element in a model ensemble control superstructure. PyMCT is a set of Python bindings for MCT, the Fortran-90 based Model Coupling Toolkit, which forms the infrastructure for the inter-component communication in the Community Climate System Model (CCSM). MCT provides a scalable model communication infrastructure. In order to take maximum advantage of agile software development methodologies, we exposed MCT functionality to Python, a prominent VHLL. We describe how the scalable architecture of MCT allows us to overcome the relatively weak runtime performance of Python, so that the performance of the combined system is not severely impacted. To demonstrate these advantages, we reimplemented the CCSM coupler in Python. While this alone offers no new functionality, it does provide a rigorous test of PyMCT functionality and performance. We reimplemented the CPL6 library, presenting an interesting case study of the comparison between conventional Fortran-90 programming and the higher abstraction level provided by a VHLL. The powerful abstractions provided by Python will allow much more complex experimental paradigms. In particular, we hope to build on the scriptability of our coupling strategy to enable systematic sensitivity tests. Our most ambitious objective is to combine our efforts with Bayesian inverse modeling techniques toward objective tuning at the highest level, across model architectures.

Anion-assisted trans-cis isomerization of palladium(II) phosphine complexes containing acetanilide functionalities through hydrogen bonding interactions.

PubMed

Lu, Xiao-Xia; Tang, Hau-San; Ko, Chi-Chiu; Wong, Jenny Ka-Yan; Zhu, Nianyong; Yam, Vivian Wing-Wah

2005-03-28

The anion-assisted shift of trans-cis isomerization equilibrium of a palladium(II) complex containing acetanilide functionalities brought about by allosteric hydrogen bonding interactions has been established by UV/Vis, 1H NMR, 31P NMR and ESI-MS studies.

SNPs located at CpG sites modulate genome-epigenome interaction

USDA-ARS?s Scientific Manuscript database

DNA methylation is an important molecular-level phenotype that links genotypes and complex disease traits. Previous studies have found local correlation between genetic variants and DNA methylation levels (cis-meQTLs). However, general mechanisms underlying cis-meQTLs are unclear. We conducted a cis...

Heterometallic and homometallic complexes containing bifunctional ligands and their application in high-temperature oxide superconductor materials

NASA Astrophysics Data System (ADS)

Breeze, Steven R.

We have been interested in the development of soluble precursors for the production of YBasb2Cusb3Osb{7-delta} and Bisb2(Ca,Sr)sbn+1CusbnOsb(2n + 4) + delta, superconductor materials. Several heterometallic and homometallic complexes containing the constituent metals of these superconductors and bifunctional ligands such as aminoalcohols, acetates and thioethers have been isolated and structurally characterized. The thermal decomposition properties and magnetic properties of some of these compounds have been investigated. The first ligand system investigated involved 1,3-bis(dimethylamino)-2-propanol (bdmapH). By varying the ratio of bdmapH, Cu(OCHsb3)sb2, and M(Osb2CCFsb3)sb2 (M = Ca, Sr) several heterometallic complexes have been obtained, including Srsb2Cusb2(bdmap)sb4(Osb2CCFsb3)sb4, CaCu(bdmap)sb2(Osb2CCFsb3)sb3(Hsb2O), Srsb2Cusb4(bdmap)sb6-(Osb2CCFsb3)sb4(musb 3-OH)sb2(THF)sb2 and SrCusb2(bdmap)sb3(Osb2CCFsb3)sb3(THF). With the exception of Srsb2Cusb4(bdmap)sb6(Osb2CCFsb3)sb4(musb 3-OH)sb2(THF)sb2, these compounds thermally decompose to form mixtures of fluorides and oxides. An analogous acetate compound SrCusb2(bdmap)sb3(Osb2CCHsb3)sb3(THF) has been produced, which forms the corresponding oxide at high temperature. A bismuth dimer, Bisb2(bdmap)sb2(Osb2CCHsb3)sb4(Hsb2O), has also been obtained. Superconducting powder of the Bisb2Srsb2CaCusb2Osb{8 + delta} and epitaxial superconducting films of the YBasb2Cusb3Osb{7-delta} superconductor have been produced using the bdmap and acetate ligands as cross-linking reagents. The second ligand system investigated involved di-2-pyridylmethanediol. Only homonuclear complexes have been obtained by using this ligand, including the mononuclear compound Cu ((2-py)sb2CO(OH)) sb2(HOsb2CCH sb3)sb2*CHsb2Clsb2, the tetranuclear compound Cusb4 ((2-py)sb2CO(OH)) sb2(Osb2CCHsb 3)sb6(Hsb2O)sb2*CHsb2Clsb2, and the bismuth dimer Bisb2 ((2-py)sb2CO(OH)) sb2(Osb 2CCFsb3)sb4*(THF)sb2. The tetranuclear Cusb4 compound was found to be dominated by ferromagnetic exchanges. The third ligand system examined involved 2,2sp'-thiodiethanol (tdeHsb2). Heterometallic complexes Prsb2Cusb4(tde)sb3(tdeH)sb2(hfacac)sb4(musb6 -O) and Basb2Cusb2(tdeH)sb4(hfacac)sb4 have been obtained using this ligand. The six metal centers in Prsb2Cusb4(tde)sb3(tdeH)sb2(hfacac)sb4(musb6-O) are arranged in a octahedron and are linked by musb6-oxide and 2,2sp'-thiodiethanolato ligands. A metallomacrocyclic Cusb4 compound, Cusb4(tde)sb2(hfacac)sb4 has been produced. Attempts have been made to produce bismuthine complexes with an amino or pyridyl functional group that can coordinate to copper. The reaction of 4-Li-Csb6Hsb4CHsb2N(2-PY)sb2 with BiClsb3 produces the compound BispIII (p-Csb6Hsb4CHsb2N(2-py)sb2rbracksb3. The ability of this compound to coordinate CuClsb2 has been investigated. The complex BispV (p-Csb6Hsb4CHsb2N(2-py)sb2rbracksb3(Osb2CCHsb3)sb2 has also been produced.

Combined MCD/DFT/TDDFT Study of the Electronic Structure of Axially Pyridine Coordinated Metallocorroles.

PubMed

Rhoda, Hannah M; Crandall, Laura A; Geier, G Richard; Ziegler, Christopher J; Nemykin, Victor N

2015-05-18

A series of metallocorroles were investigated by UV-vis and magnetic circular dichroism spectroscopies. The diamagnetic distorted square-pyramidal main-group corrole Ga(tpfc)py (2), the diamagnetic distorted octahedral transition-metal adduct Co(tpfc)(py)2 (3), and paramagnetic distorted octahedral transition-metal complex Fe(tpfc)(py)2 (4) [H3tpfc = tris(perfluorophenyl)corrole] were studied to investigate similarities and differences in the electronic structure and spectroscopy of the closed- and open-shell metallocorroles. Similar to the free-base H3tpfc (1), inspection of the MCD Faraday B-terms for all of the macrocycles presented in this report revealed that a ΔHOMO < ΔLUMO [ΔHOMO is the energy difference between two highest energy corrole-centered π-orbitals and ΔLUMO is the energy difference between two lowest energy corrole-centered π*-orbitals originating from ML ± 4 and ML ± 5 pairs of perimeter] condition is present for each complex, which results in an unusual sign-reversed sequence for π-π* transitions in their MCD spectra. In addition, the MCD spectra of the cobalt and the iron complexes were also complicated by a number of charge-transfer states in the visible region. Iron complex 4 also exhibits a low-energy absorption in the NIR region (1023 nm). DFT and TDDFT calculations were used to elaborate the electronic structures and provide band assignments in UV-vis and MCD spectra of the metallocorroles. DFT and TDDFT calculations predict that the orientation of the axial pyridine ligand(s) has a very minor influence on the calculated electronic structures and absorption spectra in the target systems.

Light and short arc rubs in rotating machines: Experimental tests and modelling

NASA Astrophysics Data System (ADS)

Pennacchi, P.; Bachschmid, N.; Tanzi, E.

2009-10-01

Rotor-to-stator rub is a non-linear phenomenon which has been analyzed many times in rotordynamics literature, but very often these studies are devoted simply to highlight non-linearities, using very simple rotors, rather than to present reliable models. However, rotor-to-stator rub is actually one of the most common faults during the operation of rotating machinery. The frequency of its occurrence is increasing due to the trend of reducing the radial clearance between the seal and the rotor in modern turbine units, pumps and compressors in order to increase efficiency. Often the rub occurs between rotor and seals and the analysis of the phenomenon cannot set aside the consideration of the different relative stiffness. This paper presents some experimental results obtained by means of a test rig in which rub conditions of real machines are reproduced. In particular short arc rubs are considered and the shaft is stiffer than the obstacle. Then a model, suitable to be employed for real rotating machinery, is presented and the simulations obtained are compared with the experimental results. The model is able to reproduce the behaviour of the test rig.

Blade Tip Rubbing Stress Prediction

NASA Technical Reports Server (NTRS)

Davis, Gary A.; Clough, Ray C.

1991-01-01

An analytical model was constructed to predict the magnitude of stresses produced by rubbing a turbine blade against its tip seal. This model used a linearized approach to the problem, after a parametric study, found that the nonlinear effects were of insignificant magnitude. The important input parameters to the model were: the arc through which rubbing occurs, the turbine rotor speed, normal force exerted on the blade, and the rubbing coefficient of friction. Since it is not possible to exactly specify some of these parameters, values were entered into the model which bracket likely values. The form of the forcing function was another variable which was impossible to specify precisely, but the assumption of a half-sine wave with a period equal to the duration of the rub was taken as a realistic assumption. The analytical model predicted resonances between harmonics of the forcing function decomposition and known harmonics of the blade. Thus, it seemed probable that blade tip rubbing could be at least a contributor to the blade-cracking phenomenon. A full-scale, full-speed test conducted on the space shuttle main engine high pressure fuel turbopump Whirligig tester was conducted at speeds between 33,000 and 28,000 RPM to confirm analytical predictions.

Thermodynamic and kinetic data for adduct formation, cis-trans isomerization and redox reactions of ML4 complexes: a case study with rhodium- and iridium-tropp complexes in d8, d9 and d10 valence electron configurations (tropp=dibenzotropylidene phosphanes).

PubMed

Breher, Frank; Rüegger, Heinz; Mlakar, Marina; Rudolph, Manfred; Deblon, Stephan; Schönberg, Hartmut; Boulmaâz, Souad; Thomaier, Jörg; Grützmacher, Hansjörg

2004-02-06

The formation of adducts of the square-planar 16-electron complexes trans-[M(tropp(ph))(2)](+) and cis-[M(tropp(ph))(2)](+) (M=Rh, Ir; tropp(Ph)=5-diphenylphosphanyldibenzo[a,d]cycloheptene) with acetonitrile (acn) and Cl(-), and the redox chemistry of these complexes was investigated by various physical methods (NMR and UV-visible spectroscopy, square-wave voltammetry), in order to obtain some fundamental thermodynamic and kinetic data for these systems. A trans/cis isomerization cannot be detected for [M(tropp(ph))(2)](+) in non-coordinating solvents. However, both isomers are connected through equilibria of the type trans-[M(tropp(ph))(2)](+)+L<==>[ML(tropp(ph))(2)](n)<==>cis-[M(tropp(ph))(2)](+)+L, involving five-coordinate intermediates [ML(tropp(ph))(2)](n) (L=acn, n=+1; L=Cl(-), n=0). Values for K(d) (K(f)), that is, the dissociation (formation) equilibrium constant, and k(d) (k(f)), that is, the dissociation (formation) rate constant, were obtained. The formation reactions are fast, especially with the trans isomers (k(f)>1x10(5) m(-1) s(-1)). The reaction with the sterically more hindered cis isomers is at least one order of magnitude slower. The stability of the five-coordinate complexes [ML(tropp(ph))(2)](n) increases with Ir>Rh and Cl(-)>acn. The dissociation reaction has a pronounced influence on the square-wave (SW) voltammograms of trans/cis-[Ir(tropp(ph))(2)](+). With the help of the thermodynamic and kinetic data independently determined by other physical means, these reactions could be simulated and allowed the setting up of a reaction sequence. Examination of the data obtained showed that the trans/cis isomerization is a process with a low activation barrier for the four-coordinate 17-electron complexes [M(tropp(ph))(2)](0) and especially that a disproportionation reaction 2 trans/cis-[M(tropp(ph))(2)](0)-->[M(tropp(ph))(2)](+)+[M(tropp(ph))(2)](-) may be sufficiently fast to mask the true reactivity of the paramagnetic species, which are probably less reactive than their diamagnetic equilibrium partners.

Synthesis, thermal analyses, characterization and biological evaluation of new enrofloxacin vanadium(V) solvates(L) (L = An, DMF, Py, Et3N and o-Tol)

NASA Astrophysics Data System (ADS)

Zordok, Wael A.; Sadeek, Sadeek A.

2016-09-01

Five metal complexes of antibacterial agent enrofloxacin with vanadium(V) in the presence of aniline, pyridine, orthotolidine and triethylamine as nitrogen donor molecules and dimethylformamide as oxygen donor molecule have been prepared and characterized with physicochemical and diverse spectroscopic techniques (IR, UV-Vis. and 1H NMR spectroscopes) as well as thermal analysis. The deprotonated enrofloxacin complexes of V(V) were isolated as solids with the general formulas; [VO(Enr)2DMF]Cl·5H2O, [VO(Enr)2An]Cl·2H2O, [VO(Enr)2o-Tol]Cl·H2O, [VO(Enr)2Py]Cl·4H2O and [VO(Enr)2Et3N]Cl·6H2O. The prepared complexes are formed with a metal to ligand ratios as 1:2:1 for all complexes. The lowest energy model structure of each complex has been proposed by using the density functional theory (DFT) at the B3LYP/CEP-31G level of theory. The energy barrier for the pyridine complex greater than others complexes while, Et3N complex has lower value. The ligand and their metal complexes were also evaluated for their antibacterial activity against three Gram (+ve) and three Gram (-ve) microorganisms.

Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication.

PubMed

Herod, Morgan R; Ferrer-Orta, Cristina; Loundras, Eleni-Anna; Ward, Joseph C; Verdaguer, Nuria; Rowlands, David J; Stonehouse, Nicola J

2016-08-01

The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a coordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e., via expression from a separate RNA molecule), while others are required in cis (i.e., expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA polymerase (RdRp) 3D are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically active 3D molecules and those that build a replication complex. We report a novel nonenzymatic cis-acting function of 3D that is essential for viral-genome replication. Using an FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans acting. Immunofluorescence studies suggest that both cis- and trans-acting 3D molecules localize to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. This study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further. Foot-and-mouth disease virus (FMDV) is an important animal pathogen responsible for foot-and-mouth disease. The disease is endemic in many parts of the world with outbreaks within livestock resulting in major economic losses. Propagation of the viral genome occurs within replication complexes, and understanding this process can facilitate the development of novel therapeutic strategies. Many of the nonstructural proteins involved in replication possess multiple functions in the viral life cycle, some of which can be supplied to the replication complex from a separate genome (i.e., in trans) while others must originate from the template (i.e., in cis). Here, we present an analysis of cis and trans activities of the RNA-dependent RNA polymerase 3D. We demonstrate a novel cis-acting role of 3D in replication. Our data suggest that this role is distinct from its enzymatic functions and requires interaction with the viral genome. Our data further the understanding of genome replication of this important pathogen. Copyright © 2016 Herod et al.

Both cis and trans Activities of Foot-and-Mouth Disease Virus 3D Polymerase Are Essential for Viral RNA Replication

PubMed Central

Herod, Morgan R.; Ferrer-Orta, Cristina; Loundras, Eleni-Anna; Ward, Joseph C.; Verdaguer, Nuria; Rowlands, David J.

2016-01-01

ABSTRACT The Picornaviridae is a large family of positive-sense RNA viruses that contains numerous human and animal pathogens, including foot-and-mouth disease virus (FMDV). The picornavirus replication complex comprises a coordinated network of protein-protein and protein-RNA interactions involving multiple viral and host-cellular factors. Many of the proteins within the complex possess multiple roles in viral RNA replication, some of which can be provided in trans (i.e., via expression from a separate RNA molecule), while others are required in cis (i.e., expressed from the template RNA molecule). In vitro studies have suggested that multiple copies of the RNA-dependent RNA polymerase (RdRp) 3D are involved in the viral replication complex. However, it is not clear whether all these molecules are catalytically active or what other function(s) they provide. In this study, we aimed to distinguish between catalytically active 3D molecules and those that build a replication complex. We report a novel nonenzymatic cis-acting function of 3D that is essential for viral-genome replication. Using an FMDV replicon in complementation experiments, our data demonstrate that this cis-acting role of 3D is distinct from the catalytic activity, which is predominantly trans acting. Immunofluorescence studies suggest that both cis- and trans-acting 3D molecules localize to the same cellular compartment. However, our genetic and structural data suggest that 3D interacts in cis with RNA stem-loops that are essential for viral RNA replication. This study identifies a previously undescribed aspect of picornavirus replication complex structure-function and an important methodology for probing such interactions further. IMPORTANCE Foot-and-mouth disease virus (FMDV) is an important animal pathogen responsible for foot-and-mouth disease. The disease is endemic in many parts of the world with outbreaks within livestock resulting in major economic losses. Propagation of the viral genome occurs within replication complexes, and understanding this process can facilitate the development of novel therapeutic strategies. Many of the nonstructural proteins involved in replication possess multiple functions in the viral life cycle, some of which can be supplied to the replication complex from a separate genome (i.e., in trans) while others must originate from the template (i.e., in cis). Here, we present an analysis of cis and trans activities of the RNA-dependent RNA polymerase 3D. We demonstrate a novel cis-acting role of 3D in replication. Our data suggest that this role is distinct from its enzymatic functions and requires interaction with the viral genome. Our data further the understanding of genome replication of this important pathogen. PMID:27194768

Production and composition of pyrogenic dissolved organic matter from a logical series of laboratory-generated chars

NASA Astrophysics Data System (ADS)

Bostick, Kyle W.; Zimmerman, Andrew R.; Wozniak, Andrew. S.; Mitra, Siddhartha; Hatcher, Patrick G.

2018-04-01

Though pyrogenic carbon (pyC) has been assumed to be predominantly stable, degradation and transfers of pyC between various pools have been found to influence its cycling and longevity in the environment. Dissolution via leaching may be the main control on loss processes such as microbial or abiotic oxidation, mineral sorption, or export to aquatic systems. Yet, little is known of the controls on pyrogenic dissolved organic matter (pyDOM) generation or composition. Here, the yield and composition of pyDOM generated through batch leaching of a thermal series of oak and grass biochars, as well as several non-pyrogenic reference materials, was compared to that of their parent solids. Over 17 daily leaching cycles, biochars made from oak at 250 to 650° C released decreasing amounts of C on both a weight (16.9 to 0.3%, respectively) and C yield basis (7.4 to 0.2% C, respectively). Aryl-C represented an estimated 32 to 82% of C in the parent solids (identified by 13C-NMR), but only 7 to 38% in the leachates (identified by 1H-NMR), though both increased with pyrolysis temperature. PyC, often operationally defined as condensed aromatic carbon (ConAC), was quantified using the benzenepolycarboxylic acid (BPCA) method. Tri- and tetra-carboxylated BPCAs were formed from non-pyrogenic reference materials, thus, only penta- and hexa-carboxylated BPCAs were used to derive a BPCA-C to ConAC conversion factor of 7.04. ConAC made up 24 to 57% of the pyrogenic solid C (excluding the 250 °C biochar), but only about 9 to 23% of their respective leachates' DOC, though both proportions generally increased with pyrolysis temperature. Weighted BPCA compound distributions, or the BPCA Aromatic Condensation (BACon) Index, indicate that ConAC cluster size increased in pyrogenic solids but not in leachates. Additional evidence presented suggests that both aromatic cluster size and O-containing functional group contents in the pyrogenic solid control pyC solubility. Overall, pyDOM was found to be compositionally dissimilar from its parent chars and contained a complex mixture of organic compound groups. Thus, it is expected that estimates of dissolved pyC production and export, made only by detection of ConAC, are too low by factors of 4 to 11.

Affinity and specificity of interactions between Nedd4 isoforms and the epithelial Na+ channel.

PubMed

Henry, Pauline C; Kanelis, Voula; O'Brien, M Christine; Kim, Brian; Gautschi, Ivan; Forman-Kay, Julie; Schild, Laurent; Rotin, Daniela

2003-05-30

The epithelial Na+ channel (alphabetagammaENaC) regulates salt and fluid homeostasis and blood pressure. Each ENaC subunit contains a PY motif (PPXY) that binds to the WW domains of Nedd4, a Hect family ubiquitin ligase containing 3-4 WW domains and usually a C2 domain. It has been proposed that Nedd4-2, but not Nedd4-1, isoforms can bind to and suppress ENaC activity. Here we challenge this notion and show that, instead, the presence of a unique WW domain (WW3*) in either Nedd4-2 or Nedd4-1 determines high affinity interactions and the ability to suppress ENaC. WW3* from either Nedd4-2 or Nedd4-1 binds ENaC-PY motifs equally well (e.g. Kd approximately 10 microm for alpha- or betaENaC, 3-6-fold higher affinity than WW4), as determined by intrinsic tryptophan fluorescence. Moreover, dNedd4-1, which naturally contains a WW3* instead of WW2, is able to suppress ENaC function equally well as Nedd4-2. Homology models of the WW3*.betaENaC-PY complex revealed that a Pro and Ala conserved in all WW3*, but not other Nedd4-WW domains, help form the binding pocket for PY motif prolines. Extensive contacts are formed between the betaENaC-PY motif and the Pro in WW3*, and the small Ala creates a large pocket to accommodate the peptide. Indeed, mutating the conserved Pro and Ala in WW3* reduces binding affinity 2-3-fold. Additionally, we demonstrate that mutations in PY motif residues that form contacts with the WW domain based on our previously solved structure either abolish or severely reduce binding affinity to the WW domain and that the extent of binding correlates with the level of ENaC suppression. Independently, we show that a peptide encompassing the PY motif of sgk1, previously proposed to bind to Nedd4-2 and alter its ability to regulate ENaC, does not bind (or binds poorly) the WW domains of Nedd4-2. Collectively, these results suggest that high affinity of WW domain-PY-motif interactions rather than affiliation with Nedd4-1/Nedd-2 is critical for ENaC suppression by Nedd4 proteins.

Improved sensitivity for W-band Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements with shaped pulses

NASA Astrophysics Data System (ADS)

Bahrenberg, Thorsten; Rosenski, Yael; Carmieli, Raanan; Zibzener, Koby; Qi, Mian; Frydman, Veronica; Godt, Adelheid; Goldfarb, Daniella; Feintuch, Akiva

2017-10-01

Chirp and shaped pulses have been recently shown to be highly advantageous for improving sensitivity in DEER (double electron-electron resonance, also called PELDOR) measurements due to their large excitation bandwidth. The implementation of such pulses for pulse EPR has become feasible due to the availability of arbitrary waveform generators (AWG) with high sampling rates to support pulse shaping for pulses with tens of nanoseconds duration. Here we present a setup for obtaining chirp pulses on our home-built W-band (95 GHz) spectrometer and demonstrate its performance on Gd(III)-Gd(III) and nitroxide-nitroxide DEER measurements. We carried out an extensive optimization procedure on two model systems, Gd(III)-PyMTA-spacer-Gd(III)-PyMTA (Gd-PyMTA ruler; zero-field splitting parameter (ZFS) D ∼ 1150 MHz) as well as nitroxide-spacer-nitroxide (nitroxide ruler) to evaluate the applicability of shaped pulses to Gd(III) complexes and nitroxides, which are two important classes of spin labels used in modern DEER/EPR experiments. We applied our findings to ubiquitin, doubly labeled with Gd-DOTA-monoamide (D ∼ 550 MHz) as a model for a system with a small ZFS. Our experiments were focused on the questions (i) what are the best conditions for positioning of the detection frequency, (ii) which pump pulse parameters (bandwidth, positioning in the spectrum, length) yield the best signal-to-noise ratio (SNR) improvements when compared to classical DEER, and (iii) how do the sample's spectral parameters influence the experiment. For the nitroxide ruler, we report an improvement of up to 1.9 in total SNR, while for the Gd-PyMTA ruler the improvement was 3.1-3.4 and for Gd-DOTA-monoamide labeled ubiquitin it was a factor of 1.8. Whereas for the Gd-PyMTA ruler the two setups pump on maximum and observe on maximum gave about the same improvement, for Gd-DOTA-monoamide a significant difference was found. In general the choice of the best set of parameters depends on the D parameter of the Gd(III) complex.

Quantitative analysis of detailed lignin monomer composition by pyrolysis-gas chromatography combined with preliminary acetylation of the samples.

PubMed

Sonoda, T; Ona, T; Yokoi, H; Ishida, Y; Ohtani, H; Tsuge, S

2001-11-15

Detailed quantitative analysis of lignin monomer composition comprising p-coumaryl, coniferyl, and sinapyl alcohol and p-coumaraldehyde, coniferaldehyde, and sinapaldehyde in plant has not been studied from every point mainly because of artifact formation during the lignin isolation procedure, partial loss of the lignin components inherent in the chemical degradative methods, and difficulty in the explanation of the complex spectra generally observed for the lignin components. Here we propose a new method to quantify lignin monomer composition in detail by pyrolysis-gas chromatography (Py-GC) using acetylated lignin samples. The lignin acetylation procedure would contribute to prevent secondary formation of cinnamaldehydes from the corresponding alcohol forms during pyrolysis, which are otherwise unavoidable in conventional Py-GC process to some extent. On the basis of the characteristic peaks on the pyrograms of the acetylated sample, lignin monomer compositions in various dehydrogenative polymers (DHP) as lignin model compounds were determined, taking even minor components such as cinnamaldehydes into consideration. The observed compositions by Py-GC were in good agreement with the supplied lignin monomer contents on DHP synthesis. The new Py-GC method combined with sample preacetylation allowed us an accurate quantitative analysis of detailed lignin monomer composition using a microgram order of extractive-free plant samples.

U(IV) chalcogenolates synthesized via oxidation of uranium metal by dichalcogenides.

PubMed

Gaunt, Andrew J; Scott, Brian L; Neu, Mary P

2006-09-04

Treatment of uranium metal with dichalcogenides in the presence of a catalytic amount of iodine in pyridine affords molecular U(IV) chalcogenolates that do not require stabilizing ancillary ligands. Oxidation of U(0) by PhEEPh yields monomeric seven-coordinate U(EPh)4(py)3 (E = S(1), Se(2)). The dimeric eight-coordinate complexes [U(EPh)2(mu2-EPh)2(CH3CN)2]2 (E = S(3), Se(4)) are obtained by crystallization from solutions of 1 and 2 dissolved in acetonitrile. Oxidation of U(0) by pySSpy and crystallization from thf yields nine-coordinate U(Spy)4(thf) (5). Incorporation of elemental selenium into the oxidation of U(0) by PhSeSePh results in the isolation of [U(py)2(SePh)(mu3-Se)(mu2-SePh)]4.4py (6), a tetrameric cluster in which each U(IV) ion is eight-coordinate and the U4Se4 core forms a distorted cube. The compounds were analyzed spectroscopically and the single-crystal X-ray structures of 1 and 3-6 were determined. The isolation of 1-6 represents six new examples of actinide chalcogenolates and allows insight into the nature of "hard" actinide ion-"soft" chalcogen donor interactions.

Spectroscopic, potentiometric and theoretical studies on the binding properties of a novel tripodal polycatechol-imine ligand towards iron(III)

NASA Astrophysics Data System (ADS)

Kanungo, B. K.; Sahoo, Suban K.; Baral, Minati

2008-12-01

A novel multidentate tripodal ligand, cis, cis-1,3,5-tris[(2,3-dihydroxybenzylidene)aminomethyl]cyclohexane (TDBAC, L) containing one catechol unit in each arms of a tripodal amine, cis, cis-1,3,5-tris(aminomethyl)cyclohexane was investigated as a chelator for iron(III) through potentiometric and spectrophotometric methods in an aqueous medium of 0.1N ionic strength and 25 ± 1 °C as well as in ethanol by continuous variation method. From pH metric in water, three protonation constants characterized for the three-hydroxyl groups of the catechol units at ortho were used as input data to evaluate the stability constants of the complexes. Formation of monomeric complexes FeLH 3, FeLH 2, FeLH and FeL were depicted. In ethanol, formation of complexes FeL, Fe 2L and Fe 3L were characterized. Structures of the complexes were explained by using the experimental evidences and predicted through molecular modeling calculations. The ligand showed potential to coordinate iron(III) through three imine nitrogens and three catecholic oxygens at ortho to form a tris(iminocatecholate) type complex.

Field experiences with rub induced instabilities in turbomachinery

NASA Technical Reports Server (NTRS)

Goggin, D. G.

1982-01-01

Rotordynamic instability problems are not uncommon in high speed industrial turbomachinery. One type of the many destabilizing forces that can occur is caused by a rub between the stationary and rotating parts. Descriptions are given of several cases of rub induced instabilities. Included in the descriptions are the conditions at onset, the whirl frequency and direction, and the steps taken to eliminate the problem.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME.

PubMed

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2016-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments.

Reductive transformation of V(iii) precursors into vanadium(ii) oxide nanowires.

PubMed

Ojelere, Olusola; Graf, David; Ludwig, Tim; Vogt, Nicholas; Klein, Axel; Mathur, Sanjay

2018-05-15

Vanadium(ii) oxide nanostructures are promising materials for supercapacitors and electrocatalysis because of their excellent electrochemical properties and high surface area. In this study, new homoleptic vanadium(iii) complexes with bi-dentate O,N-chelating heteroarylalkenol ligands (DmoxCH[double bond, length as m-dash]COCF3, PyCH[double bond, length as m-dash]COCF3 and PyN[double bond, length as m-dash]COCF3) were synthesized and successfully transformed by reductive conversion into VO nanowires. The chemical identity of V(iii) complexes and their redox behaviour were unambiguously established by single crystal X-ray diffraction studies, cyclic voltammetry, spectrometric studies and DFT calculations. Transformation into the metastable VO phase was verified by powder X-ray diffraction and thermo-gravimetry. Transmission electron microscopy and X-ray photoelectron spectroscopy data confirmed the morphology and chemical composition of VO nanostructures, respectively.

Electrochemical behavior of meso-substituted iron porphyrins in alkaline aqueous media

NASA Astrophysics Data System (ADS)

Berezina, N. M.; Bazanov, M. I.; Maksimova, A. A.; Semeikin, A. S.

2017-12-01

The effect meso-substitution in iron porphyrin complexes has on their redox behavior in alkaline aqueous solutions is studied via cyclic voltammetry. The voltammetric features of the reduction of iron pyridylporphyrins suggest that the sites of electron transfer lie at the ligand, the metal ion, and the pyridyl moieties. The electron transfer reactions between the different forms of these compounds, including the oxygen reduction reaction they mediate, are outlined to show the sequence and potential ranges in which they occur in alkaline aqueous media. Under our experimental conditions, the iron porphyrins exist as μ-oxo dimmers whose activity for the electrocatalytic reduction of oxygen displays a considerable dependence on the nature of the substitutents and nitrogen isomerization (for pyridylporphyrins) and grows in the order (Fe( ms-Ph)4P)2O, (Fe[ ms-(Py-3)Ph3]P)2O, (Fe[ ms-(Py-4)4]P)2O, and (Fe[ ms-(Py-3)4]P)2O.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veseli, S.

As the number of sites deploying and adopting EPICS Version 4 grows, so does the need to support PV Access from multiple languages. Especially important are the widely used scripting languages that tend to reduce both software development time and the learning curve for new users. In this paper we describe PvaPy, a Python API for the EPICS PV Access protocol and its accompanying structured data API. Rather than implementing the protocol itself in Python, PvaPy wraps the existing EPICS Version 4 C++ libraries using the Boost.Python framework. This approach allows us to benefit from the existing code base andmore » functionality, and to significantly reduce the Python API development effort. PvaPy objects are based on Python dictionaries and provide users with the ability to access even the most complex of PV Data structures in a relatively straightforward way. Its interfaces are easy to use, and include support for advanced EPICS Version 4 features such as implementation of client and server Remote Procedure Calls (RPC).« less

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs

PubMed Central

Adoue, Veronique; Schiavi, Alicia; Light, Nicholas; Almlöf, Jonas Carlsson; Lundmark, Per; Ge, Bing; Kwan, Tony; Caron, Maxime; Rönnblom, Lars; Wang, Chuan; Chen, Shu-Huang; Goodall, Alison H; Cambien, Francois; Deloukas, Panos; Ouwehand, Willem H; Syvänen, Ann-Christine; Pastinen, Tomi

2014-01-01

Most complex disease-associated genetic variants are located in non-coding regions and are therefore thought to be regulatory in nature. Association mapping of differential allelic expression (AE) is a powerful method to identify SNPs with direct cis-regulatory impact (cis-rSNPs). We used AE mapping to identify cis-rSNPs regulating gene expression in 55 and 63 HapMap lymphoblastoid cell lines from a Caucasian and an African population, respectively, 70 fibroblast cell lines, and 188 purified monocyte samples and found 40–60% of these cis-rSNPs to be shared across cell types. We uncover a new class of cis-rSNPs, which disrupt footprint-derived de novo motifs that are predominantly bound by repressive factors and are implicated in disease susceptibility through overlaps with GWAS SNPs. Finally, we provide the proof-of-principle for a new approach for genome-wide functional validation of transcription factor–SNP interactions. By perturbing NFκB action in lymphoblasts, we identified 489 cis-regulated transcripts with altered AE after NFκB perturbation. Altogether, we perform a comprehensive analysis of cis-variation in four cell populations and provide new tools for the identification of functional variants associated to complex diseases. PMID:25326100

Mononuclear bromide complexes of Sb(V): crystal structures and thermal behaviour

NASA Astrophysics Data System (ADS)

Adonin, Sergey A.; Bondarenko, Mikhail A.; Samsonenko, Denis G.; Semitut, Evgeniy Yu; Sokolov, Maxim N.; Fedin, Vladimir P.

2018-05-01

Reactions of Sb2O3 dissolved in HBr/Br2 and bromides of pyridinium-derived cations result in mononuclear complexes of Sb(V) - (cation)[SbBr6] (cation = 2-chloropyridinium (1), 2-bromopyridinium (2)). Thermal behaviour of 1 and 2, as well as similar previously reported complexes Et4N [SbBr6] (3) and (N-EtPy)[SbBr6] (4), was studied and discussed.

Pyrogenic carbon erosion: implications for stock and persistence of pyrogenic carbon in soil

NASA Astrophysics Data System (ADS)

Abney, Rebecca B.; Berhe, Asmeret Asefaw

2018-03-01

Pyrogenic carbon (PyC) constitutes an important pool of soil organic matter, particularly for its reactivity and because of its assumed long residence times in soil. In the past, research on the dynamics of PyC in the soil system has focused on quantifying stock and mean residence time of PyC in soil, as well as determining both PyC stabilization mechanisms and loss pathways. Much of this research has focused on decomposition as the most important loss pathway for PyC from soil. However, the low density of PyC and its high concentration on the soil surface after fire indicates that a significant proportion of PyC formed or deposited on the soil surface is likely laterally transported away from the site of production by wind and water erosion. Here, we present a synthesis of available data and literature to compare the magnitude of the water-driven erosional PyC flux with other important loss pathways, including leaching and decomposition, of PyC from soil. Furthermore, we use a simple first-order kinetic model of soil PyC dynamics to assess the effect of erosion and deposition on residence time of PyC in eroding landscapes. Current reports of PyC mean residence time (MRT) range from 250 to 660 years. Using a specific example-based model system, we find that ignoring the role of erosion may lead to the under- or over-estimation of PyC MRT on the centennial time scale. Furthermore, we find that, depending on the specific landform positions, timescales considered, and initial concentrations of PyC in soil, ignoring the role of erosion in distributing PyC across a landscape can lead to discrepancies in PyC concentrations on the order of several hundred g PyC m-2. Erosion is an important PyC flux that can act as a significant control on the stock and residence time of PyC in the soil system.

A Subdominant CD8+ Cytotoxic T Lymphocyte (CTL) Epitope from the Plasmodium yoelii Circumsporozoite Protein Induces CTLs That Eliminate Infected Hepatocytes from Culture

PubMed Central

Franke, Eileen D.; Sette, Alessandro; Sacci, John; Southwood, Scott; Corradin, Giampietro; Hoffman, Stephen L.

2000-01-01

Previous studies indicated that the Plasmodium yoelii circumsporozoite protein (PyCSP) 57–70 region elicits T cells capable of eliminating infected hepatocytes in vitro. Herein, we report that the PyCSP58–67 sequence contains an H-2d binding motif, which binds purified Kd molecules in vitro with low affinity (3,267 nM) and encodes an H-2d-restricted cytotoxic T lymphocyte (CTL) epitope. Immunization of BALB/c mice with three doses of a multiple antigen peptide (MAP) construct containing four branches of amino acids 57 to 70 linked to a lysine-glycine core [MAP4(PyCSP57–70)] and Lipofectin as the adjuvant induced both T-cell proliferation and a peptide-specific CTL response that was PyCSP59–67 specific, H-2d restricted, and CD8+ T cell dependent. Immunization with either DNA encoding the PyCSP or irradiated sporozoites demonstrated that this CTL epitope is subdominant since it is not recognized in the context of whole CSP immunization. The biological relevance of this CTL response was underlined by the demonstration that it could mediate genetically restricted, CD8+- and nitric-oxide-dependent elimination of infected hepatocytes in vitro, as well as partial protection of BALB/c mice against sporozoite challenge. These findings indicate that subdominant epitopes with low major histocompatibility complex affinity can be used to engineer epitope-based vaccines and have implications for the selection of epitopes for subunit-based vaccines. PMID:10816491

A series of complexes with a [Mn 8O 8] 8+ saddle-like core: Facile synthesis, crystal structure and magnetic property

NASA Astrophysics Data System (ADS)

Wang, Hui-Sheng; Ma, Cheng-Bing; Wang, Mei; Chen, Chang-Neng; Liu, Qiu-Tian

2008-03-01

Three manganese complexes formulated as [CeMn8IIIO 8(O 2CMe) 12(H 2O) 4]·4H 2O ( 1·4H 2O), [CeMn8IIIO 8(O 2CMe) 12(py) 3(H 2O)]·6.5H 2O ( 2·6.5H 2O), [CeMn8IIIO 8(O 2CMe) 12(bzd) 2(H 2O) 2]·10H 2O( 3·10H 2O) (where py = pyridine, bzd = benzimidazole), have been synthesized and characterized by elemental analysis, IR and single-crystal X-ray diffraction analyses. Complexes 1- 3 all consist of a central Ce 4+ ion surrounded by a nonplanar, saddle-like [Mn 8O 8] 8+ loop via eight μ 3sbnd O 2- ions, and peripheral ligation is provided by twelve acetate groups, four water molecules for complex 1, twelve acetate groups, three pyridines and one water molecule for complex 2, twelve acetate groups, two benzimidazoles and two water molecules for complex 3. Variable-temperature magnetic susceptibility measurements reveal the ground-state spin ( S) values of 8 for complexes 1 and 2, which are half of the analogous complex previously reported. An explanation for this difference is also included in the text.

Analysis on accuracy improvement of rotor-stator rubbing localization based on acoustic emission beamforming method.

PubMed

He, Tian; Xiao, Denghong; Pan, Qiang; Liu, Xiandong; Shan, Yingchun

2014-01-01

This paper attempts to introduce an improved acoustic emission (AE) beamforming method to localize rotor-stator rubbing fault in rotating machinery. To investigate the propagation characteristics of acoustic emission signals in casing shell plate of rotating machinery, the plate wave theory is used in a thin plate. A simulation is conducted and its result shows the localization accuracy of beamforming depends on multi-mode, dispersion, velocity and array dimension. In order to reduce the effect of propagation characteristics on the source localization, an AE signal pre-process method is introduced by combining plate wave theory and wavelet packet transform. And the revised localization velocity to reduce effect of array size is presented. The accuracy of rubbing localization based on beamforming and the improved method of present paper are compared by the rubbing test carried on a test table of rotating machinery. The results indicate that the improved method can localize rub fault effectively. Copyright © 2013 Elsevier B.V. All rights reserved.

Hair of the dog: obtaining samples from coyotes and wolves noninvasively

USGS Publications Warehouse

Ausband, David E.; Young, Julie; Fannin, Barbara; Mitchell, Michael S.; Stenglein, Jennifer L.; Waits, Lisette P.; Shivik, John A.

2011-01-01

Canids can be difficult to detect and their populations difficult to monitor. We tested whether hair samples could be collected from coyotes (Canis latrans) in Texas, USA and gray wolves (C. lupus) in Montana, USA using lure to elicit rubbing behavior at both man-made and natural collection devices. We used mitochondrial and nuclear DNA to determine whether collected hair samples were from coyote, wolf, or nontarget species. Both coyotes and wolves rubbed on man-made barbed surfaces but coyotes in Texas seldom rubbed on hanging barbed surfaces. Wolves in Montana showed a tendency to rub at stations where natural-material collection devices (sticks and debris) were present. Time to detection was relatively short (5 nights and 4 nights for coyotes and wolves, respectively) with nontarget and unknown species comprising approximately 26% of the detections in both locations. Eliciting rubbing behavior from coyotes and wolves using lures has advantages over opportunistic genetic sampling methods (e.g., scat transects) because it elicits a behavior that deposits a hair sample at a fixed sampling location, thereby increasing the efficiency of sampling for these canids. Hair samples from rub stations could be used to provide estimates of abundance, measures of genetic diversity and health, and detection-nondetection data useful for cost-effective population monitoring.

Surgical hand antisepsis in veterinary practice: evaluation of soap scrubs and alcohol based rub techniques.

PubMed

Verwilghen, Denis R; Mainil, Jacques; Mastrocicco, Emilie; Hamaide, Annick; Detilleux, Johann; van Galen, Gaby; Serteyn, Didier; Grulke, Sigrid

2011-12-01

Recent studies have shown that hydro-alcoholic solutions are more efficient than traditional medicated soaps in the pre-surgical hand antisepsis of human surgeons but there is little veterinary literature on the subject. The aim of this study was to compare the efficiency of medicated soaps and a hydro-alcoholic solution prior to surgery using an in-use testing method in a veterinary setting. A preliminary trial was performed that compared the mean log(10) number of bacterial colony forming units (CFU) and the reduction factors (RF) between two 5-min hand-scrubbing sessions using different soaps, namely, povidone iodine (PVP) and chlorhexidine gluconate (CHX), and the 1.5-min application of a hydro-alcoholic rub. A clinical in-use trial was then used to compare the hydro-alcoholic rub and CHX in a surgical setting. Sampling was performed using finger printing on agar plates. The hydro-alcoholic rub and CHX had a similar immediate effect, although the sustained effect was significantly better for the hydro-alcoholic rub, while PVP had a significantly lower immediate and sustained effect. The hydro-alcoholic rub showed good efficiency in the clinical trial and could be considered as a useful alternative method for veterinary surgical hand antisepsis. Copyright © 2010 Elsevier Ltd. All rights reserved.

Rubbing time and bonding performance of one-step adhesives to primary enamel and dentin.

PubMed

Botelho, Maria Paula Jacobucci; Isolan, Cristina Pereira; Schwantz, Júlia Kaster; Lopes, Murilo Baena; Moraes, Rafael Ratto de

2017-01-01

This study investigated whether increasing the concentration of acidic monomers in one-step adhesives would allow reducing their application time without interfering with the bonding ability to primary enamel and dentin. Experimental one-step self-etch adhesives were formulated with 5 wt% (AD5), 20 wt% (AD20), or 35 wt% (AD35) acidic monomer. The adhesives were applied using rubbing motion for 5, 10, or 20 s. Bond strengths to primary enamel and dentin were tested under shear stress. A commercial etch-and-rinse adhesive (Single Bond 2; 3M ESPE) served as reference. Scanning electron microscopy was used to observe the morphology of bonded interfaces. Data were analysed at p<0.05. In enamel, AD35 had higher bond strength when rubbed for at least 10 s, while application for 5 s generated lower bond strength. In dentin, increased acidic monomer improved bonding only for 20 s rubbing time. The etch-and-rinse adhesive yielded higher bond strength to enamel and similar bonding to dentin as compared with the self-etch adhesives. The adhesive layer was thicker and more irregular for the etch-and-rinse material, with no appreciable differences among the self-etch systems. Overall, increasing the acidic monomer concentration only led to an increase in bond strength to enamel when the rubbing time was at least 10 s. In dentin, despite the increase in bond strength with longer rubbing times, the results favoured the experimental adhesives compared to the conventional adhesive. Reduced rubbing time of self-etch adhesives should be avoided in the clinical setup.

Gd(III)-Gd(III) EPR distance measurements--the range of accessible distances and the impact of zero field splitting.

PubMed

Dalaloyan, Arina; Qi, Mian; Ruthstein, Sharon; Vega, Shimon; Godt, Adelheid; Feintuch, Akiva; Goldfarb, Daniella

2015-07-28

Gd(III) complexes have emerged as spin labels for distance determination in biomolecules through double-electron-electron resonance (DEER) measurements at high fields. For data analysis, the standard approach developed for a pair of weakly coupled spins with S = 1/2 was applied, ignoring the actual properties of Gd(III) ions, i.e. S = 7/2 and ZFS (zero field splitting) ≠ 0. The present study reports on a careful investigation on the consequences of this approach, together with the range of distances accessible by DEER with Gd(III) complexes as spin labels. The experiments were performed on a series of specifically designed and synthesized Gd-rulers (Gd-PyMTA-spacer-Gd-PyMTA) covering Gd-Gd distances of 2-8 nm. These were dissolved in D2O-glycerol-d8 (0.03-0.10 mM solutions) which is the solvent used for the corresponding experiments on biomolecules. Q- and W-band DEER measurements, followed by data analysis using the standard data analysis approach, used for S = 1/2 pairs gave the distance-distribution curves, of which the absolute maxima agreed very well with the expected distances. However, in the case of the short distances of 2.1 and 2.9 nm, the distance distributions revealed additional peaks. These are a consequence of neglecting the pseudo-secular term in the dipolar Hamiltonian during the data analysis, as is outlined in a theoretical treatment. At distances of 3.4 nm and above, disregarding the pseudo-secular term leads to a broadening of a maximum of 0.4 nm of the distance-distribution curves at half height. Overall, the distances of up to 8.3 nm were determined, and the long evolution time of 16 μs at 10 K indicates that a distance of up to 9.4 nm can be accessed. A large distribution of the ZFS parameter, D, as is found for most Gd(III) complexes in a frozen solution, is crucial for the application of Gd(III) complexes as spin labels for distance determination via Gd(III)-Gd(III) DEER, especially for short distances. The larger ZFS of Gd-PyMTA, in comparison to that of Gd-DOTA, makes Gd-PyMTA a better label for short distances.

Platinum-group element concentrations in pyrite from the Main Sulfide Zone of the Great Dyke of Zimbabwe

NASA Astrophysics Data System (ADS)

Piña, R.; Gervilla, F.; Barnes, S.-J.; Oberthür, T.; Lunar, R.

2016-10-01

The Main Sulfide Zone (MSZ) of the Great Dyke of Zimbabwe hosts the world's second largest resource of platinum-group elements (PGE) after the Bushveld Complex in South Africa. The sulfide assemblage of the MSZ comprises pyrrhotite, pentlandite, chalcopyrite, and minor pyrite. Recently, several studies have observed in a number of Ni-Cu-PGE ore deposits that pyrite may host significant amounts of PGE, particularly Pt and Rh. In this study, we have determined PGE and other trace element contents in pyrite from the Hartley, Ngezi, Unki, and Mimosa mines of the Great Dyke by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Based on the textures and PGE contents, two types of pyrite can be differentiated. Py1 occurs as individual euhedral or subhedral grains or clusters of crystals mostly within chalcopyrite and pentlandite, in some cases in the form of symplectitic intergrowths, and is PGE rich (up to 99 ppm Pt and 61 ppm Rh; 1.7 to 47.1 ppm Ru, 0.1 to 7.8 ppm Os, and 1.2 to 20.2 ppm Ir). Py2 occurs as small individual euhedral or subhedral crystals within pyrrhotite, pentlandite, and less frequently within chalcopyrite and silicates and has low PGE contents (<0.11 ppm Pt, <0.34 ppm Rh, <2.5 ppm Ru, <0.37 ppm Ir, and <0.40 ppm Os). Py1 contains higher Os, Ir, Ru, Rh, and Pt contents than the associated pyrrhotite, pentlandite, and chalcopyrite, whereas Py2 has similar PGE contents as coexisting pyrrhotite and pentlandite. Based on the textural relationships, two different origins are attributed for each pyrite type. Py1 intergrowth with pentlandite and chalcopyrite is inferred to have formed by late, low temperature (<300 °C) decomposition of residual Ni-rich monosulfide solid solution, whereas Py2 is suggested to have formed by replacement of pyrrhotite and pentlandite caused by late magmatic/hydrothermal fluids.

NIR and Py-mbms coupled with multivariate data analysis as a high-throughput biomass characterization technique: a review

PubMed Central

Xiao, Li; Wei, Hui; Himmel, Michael E.; Jameel, Hasan; Kelley, Stephen S.

2014-01-01

Optimizing the use of lignocellulosic biomass as the feedstock for renewable energy production is currently being developed globally. Biomass is a complex mixture of cellulose, hemicelluloses, lignins, extractives, and proteins; as well as inorganic salts. Cell wall compositional analysis for biomass characterization is laborious and time consuming. In order to characterize biomass fast and efficiently, several high through-put technologies have been successfully developed. Among them, near infrared spectroscopy (NIR) and pyrolysis-molecular beam mass spectrometry (Py-mbms) are complementary tools and capable of evaluating a large number of raw or modified biomass in a short period of time. NIR shows vibrations associated with specific chemical structures whereas Py-mbms depicts the full range of fragments from the decomposition of biomass. Both NIR vibrations and Py-mbms peaks are assigned to possible chemical functional groups and molecular structures. They provide complementary information of chemical insight of biomaterials. However, it is challenging to interpret the informative results because of the large amount of overlapping bands or decomposition fragments contained in the spectra. In order to improve the efficiency of data analysis, multivariate analysis tools have been adapted to define the significant correlations among data variables, so that the large number of bands/peaks could be replaced by a small number of reconstructed variables representing original variation. Reconstructed data variables are used for sample comparison (principal component analysis) and for building regression models (partial least square regression) between biomass chemical structures and properties of interests. In this review, the important biomass chemical structures measured by NIR and Py-mbms are summarized. The advantages and disadvantages of conventional data analysis methods and multivariate data analysis methods are introduced, compared and evaluated. This review aims to serve as a guide for choosing the most effective data analysis methods for NIR and Py-mbms characterization of biomass. PMID:25147552

ObsPy: A Python toolbox for seismology - Sustainability, New Features, and Applications

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; MacCarthy, J.

2016-12-01

ObsPy (https://www.obspy.org) is a community-driven, open-source project dedicated to offer a bridge for seismology into the scientific Python ecosystem. Amongst other things, it provides Read and write support for essentially every commonly used data format in seismology with a unified interface. This includes waveform data as well as station and event meta information. A signal processing toolbox tuned to the specific needs of seismologists. Integrated access to the largest data centers, web services, and databases. Wrappers around third party codes like libmseed and evalresp. Using ObsPy enables users to take advantage of the vast scientific ecosystem that has developed around Python. In contrast to many other programming languages and tools, Python is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often must be translated to stable and production ready environments, especially in the age of big data. ObsPy has seen constant development for more than six years and enjoys a large rate of adoption in the seismological community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. We will present a short overview of the capabilities of ObsPy and point out several representative use cases and more specialized software built around ObsPy. Additionally we will discuss new and upcoming features, as well as the sustainability of open-source scientific software.

Synthesis, Characterization, Cytotoxic Activity, and Interactions with CT-DNA and BSA of Cationic Ruthenium(II) Complexes Containing Dppm and Quinoline Carboxylates

PubMed Central

da Silva, Edinaldo N.; da Silva, Paulo A. B.; Graminha, Angélica E.; de Oliveira, Pollyanna F.; Damasceno, Jaqueline L.; Tavares, Denise C.; Batista, Alzir A.

2017-01-01

The complexes cis-[Ru(quin)(dppm)2]PF6 and cis-[Ru(kynu)(dppm)2]PF6 (quin = quinaldate; kynu = kynurenate; dppm = bis(diphenylphosphino)methane) were prepared and characterized by elemental analysis, electronic, FTIR, 1H, and 31P{1H} NMR spectroscopies. Characterization data were consistent with a cis arrangement for the dppm ligands and a bidentate coordination through carboxylate oxygens of the quin and kynu anions. These complexes were not able to intercalate CT-DNA as shown by circular dichroism spectroscopy. On the other hand, bovine serum albumin (BSA) binding constants and thermodynamic parameters suggest spontaneous interactions with this protein by hydrogen bonds and van der Waals forces. Cytotoxicity assays were carried out on a panel of human cancer cell lines including HepG2, MCF-7, and MO59J and one normal cell line GM07492A. In general, the new ruthenium(II) complexes displayed a moderate to high cytotoxicity in all the assayed cell lines with IC50 ranging from 10.1 to 36 µM and were more cytotoxic than the precursor cis-[RuCl2(dppm)2]. The cis-[Ru(quin)(dppm)2]PF6 were two to three times more active than the reference metallodrug cisplatin in the MCF-7 and MO59J cell lines. PMID:28814948

ATR-FTIR spectroscopic investigation of the cis- and trans-bis-(α-amino acids) copper(II) complexes

NASA Astrophysics Data System (ADS)

Berestova, Tatyana V.; Kuzina, Lyudmila G.; Amineva, Natalya A.; Faizrakhmanov, Ilshat S.; Massalimov, Ismail A.; Mustafin, Akhat G.

2017-06-01

The crystalline phases of the trans-(a) and cis-(b)-isomers of bis-(α-amino acids) copper(II) complexes [Cu(bL)2] 1-5 (bL - bidentate ligand: gly (1), S-ala (2), R,S-val (3), (±)-thr (4), R,S-phe (5)) were studied by ATR-FTIR spectroscopy in the mid region IR spectrum. It was established that asymmetric νas(COO) and symmetric νs(COO) stretching vibrations of carboxylic groups of 1-5 are sensitive to change of the geometric structure and have a different maxima for the trans(a)- and cis(b)-isomers. It found that νas(COO) and νs(COO) stretching vibrations of cis-isomers are broadened and shifted to longer wavelengths (b) as compared with trans-isomers (a). Shown that peculiarities of crystal packing molecules of geometric isomers may affect on carboxylate stretching vibration bis-α-amino acids complexes copper(II) 1-5 a,b.

Terrestrial pyrogenic carbon export to fluvial ecosystems: Lessons learned from the White Nile watershed of East Africa

NASA Astrophysics Data System (ADS)

Güereña, David T.; Lehmann, Johannes; Walter, Todd; Enders, Akio; Neufeldt, Henry; Odiwour, Holiance; Biwott, Henry; Recha, John; Shepherd, Keith; Barrios, Edmundo; Wurster, Chris

2015-11-01

Pyrogenic carbon (PyC) is important because of its role in the global organic C (OC) cycle and in modifying soil properties. However, our understanding of PyC movement from terrestrial to fluvial ecosystems is not robust. This study examined (i) whether erosion or subsurface transport was more important for PyC export from headwaters, (ii) whether PyC was exported preferentially to total OC (TOC), and (iii) whether the movement of PyC from terrestrial to aquatic ecosystems provides an explanation for the coupling of PyC and non-PyC observed in rivers at a global scale. In the Guineo-Congolian highland forest region of western Kenya, duplicate catchments with sizes of 1-12 ha were equipped with stream gauges in primary forest and adjacent mixed agricultural landscapes that were cleared by fire 10, 16, or 62 years before. Stream water samples were taken weekly throughout 1 year and compared with runoff to assess PyC movement. Additional stream samples were taken from all major tributaries of the White Nile watershed of Lake Victoria. PyC was not found to be preferentially eroded relative to TOC or non-PyC, as topsoil (0-0.15 m) PyC concentrations (6.3 ± 0.3% of TOC; means and standard errors) were greater than runoff sediment (1.9 ± 0.4%) and dissolved PyC concentrations (2.0 ± 0.4%, n = 252). In addition, PyC proportions in eroded sediment were lower than and uncorrelated (r2 = 0.04; P = 0.14) with topsoil PyC. An enrichment of PyC was found with depth in the soil, from 6.3 ± 0.3% of TOC in the topsoil (0-0.15 m) to 12.3 ± 0.3% of TOC at 1-2 m. Base flow PyC proportions of TOC correlated well with subsoil PyC (r2 = 0.57; P < 0.05) but not with topsoil PyC (r2 = 0.18; P > 0.05). Similar PyC proportions were found in the studied headwater streams (2.7 ± 0.2%), their downstream inflow into Lake Victoria (3.7%), the other nine major rivers into Lake Victoria (4.9 ± 0.8%), and its outflow into the White Nile (1.1%). A strong positive correlation between dissolved PyC and non-PyC (r2 = 0.91; P < 0.0001) in the headwater streams reflect relationships previously seen for a range of globally important rivers, and contrasts with a negative relationship for suspended sediments (r2 = -0.5; P < 0.0001). The estimated PyC export from the Lake Victoria watershed of 11 Gg yr-1 may therefore originate to a large extent from subsoil pathways in dissolved form that appeared to be an important source of PyC in aquatic environments and may explain the coupling of PyC and non-PyC at a global scale.

Redox Potential and C-H Bond Cleaving Properties of a Nonheme FeIV=O Complex in Aqueous Solution

PubMed Central

Wang, Dong; Zhang, Mo; Bühlmann, Philippe; Que, Lawrence

2010-01-01

High-valent iron-oxo intermediates have been identified as the key oxidants in the catalytic cycles of many nonheme enzymes. Among the large number of synthetic FeIV=O complexes characterized to date, [FeIV(O)(N4Py)]2+ (1) exhibits the unique combination of thermodynamic stability, allowing its structural characterization by X-ray crystallography, and oxidative reactivity sufficient to cleave C-H bonds as strong as those in cyclohexane (DC-H = 99.3 kcal mol-1). However, its redox properties are not yet well understood. In this work, the effect of protons on the redox properties of 1 has been investigated electrochemically in nonaqueous and aqueous solutions. While the cyclic voltammetry of 1 in CH3CN is complicated by coupling of several chemical and redox processes, the FeIV/III couple is reversible in aqueous solution with E1/2 = +0.41 V vs. SCE at pH 4 and involves the transfer of one electron and one proton to give the FeIII-OH species. This is in fact the first example of reversible electrochemistry to be observed for this family of nonheme oxoiron(IV) complexes. C-H bond oxidations by 1 have been studied in H2O and found to have reactions rates that depend on the C-H bond strength but not on the solvent. Furthermore, our electrochemical results have allowed a DO-H value of 78(2) kcal mol-1 to be calculated for the FeIII-OH unit derived from 1. Interestingly, although this DO-H value is 6-11 kcal mol-1 lower than those corresponding to oxidants such as [FeIV(O)(TMP)] (TMP = tetramesitylporphinate), [RuIV(O)(bpy)2(py)]2+ (bpy = bipyridine, py = pyridine) and the tert-butylperoxyl radical, the oxidation of dihydroanthracene by 1 occurs at a rate comparable to those for these other oxidants. This comparison suggests that the nonheme N4Py ligand environment confers a kinetic advantage over the others that enhances the C-H bond cleavage ability of 1. PMID:20476758

Bisected, complex N-glycans and galectins in mouse mammary tumor progression and human breast cancer

PubMed Central

Miwa, Hazuki E; Koba, Wade R; Fine, Eugene J; Giricz, Orsi; Kenny, Paraic A; Stanley, Pamela

2013-01-01

Bisected, complex N-glycans on glycoproteins are generated by the glycosyltransferase MGAT3 and cause reduced cell surface binding of galectins. Previously, we showed that MGAT3 reduces growth factor signaling and retards mammary tumor progression driven by the Polyoma middle T antigen (PyMT) expressed in mammary epithelium under the mouse mammary tumor virus (MMTV) promoter. However, the penetrance of the tumor phenotype became variable in mixed FVB/N and C57BL/6 female mice and we therefore investigated a congenic C57BL/6 Mgat3−/−/MMTV-PyMT model. In the absence of MGAT3, C57BL/6 Mgat3−/−/MMTV-PyMT females exhibited accelerated tumor appearance and increased tumor burden, glucose uptake in tumors and lung metastasis. Nevertheless, activation of extracellular signal-regulated kinase (ERK)1/2 or protein kinase B (AKT) was reduced in ∼20-week C57BL/6 MMTV-PyMT tumors lacking MGAT3. Activation of focal adhesion kinase (FAK), protein tyrosine kinase Src, and p38 mitogen-activated protein kinase were similar to that of controls. All the eight mouse galectin genes were expressed in mammary tumors and tumor epithelial cells (TECs), but galectin-2 and -12 were not detected by western analysis in tumors, and galectin-7 was not detected in 60% of the TEC lines. From microarray data reported for human breast cancers, at least 10 galectin and 7 N-glycan N-acetylglucosaminyl (GlcNAc)-transferase (MGAT) genes are expressed in tumor tissue, and expression often varies significantly between different breast cancer subtypes. Thus, in summary, while MGAT3 and bisected complex N-glycans retard mouse mammary tumor progression, genetic background may modify this effect; identification of key galectins that promote mammary tumor progression in mice is not straightforward because all the eight galectin genes are expressed; and high levels of MGAT3, galectin-4, -8, -10, -13 and -14 transcripts correlate with better relapse-free survival in human breast cancer. PMID:24037315

Identification of a Polyomavirus microRNA Highly Expressed in Tumors

PubMed Central

Chen, Chun Jung; Cox, Jennifer E.; Azarm, Kristopher; Wylie, Karen N.; Woolard, Kevin D.; Pesavento, Patricia A.; Sullivan, Christopher S.

2014-01-01

Polyomaviruses (PyVs) are associated with tumors including Merkel cell carcinoma (MCC). Several PyVs encode microRNAs (miRNAs) but to date no abundant PyV miRNAs have been reported in tumors. To better understand the function of the Merkel cell PyV (MCPyV) miRNA, we examined phylogenetically-related viruses for miRNA expression. We show that two primate PyVs and the more distantly-related raccoon PyV (RacPyV) encode miRNAs that share genomic position and partial sequence identity with MCPyV miRNAs. Unlike MCPyV miRNA in MCC, RacPyV miRNA is highly abundant in raccoon tumors. RacPyV miRNA negatively regulates reporters of early viral (T antigen) transcripts, yet robust viral miRNA expression is tolerated in tumors. We also identify raccoon miRNAs expressed in RacPyV-associated neuroglial brain tumors, including several likely oncogenic miRNAs (oncomiRs). This work describes the first PyV miRNA abundantly expressed in tumors and is consistent with a possible role for both host and viral miRNAs in RacPyV-associated tumors. PMID:25514573

Homoleptic Ce(III) and Ce(IV) Nitroxide Complexes: Significant Stabilization of the 4+ Oxidation State

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bogart, Justin A.; Lewis, Andrew J.; Medling, Scott A.

2014-06-25

Electrochemical experiments performed on the complex Ce-IV[2-((BuNO)-Bu-t)py](4), where [2-((BuNO)-Bu-t)py](-) = N-tert-butyl-N-2-pyridylnitroxide, indicate a 2.51 V stabilization of the 4+ oxidation state of Ce compared to [(Bu4N)-Bu-n](2)[Ce(NO3)(6)] in acetonitrile and a 2.95 V stabilization compared to the standard potential for the ion under aqueous conditions. Density functional theory calculations suggest that this preference for the higher oxidation state is a result of the tetrakis(nitroxide) ligand framework at the Ce cation, which allows for effective electron donation into, and partial covalent overlap with, vacant 4f orbitals with delta symmetry. The results speak to the behavior of CeO2 and related solid solutions inmore » oxygen uptake and transport applications, in particular an inherent local character of bonding that stabilizes the 4+ oxidation state. The results indicate a cerium(IV) complex that has been stabilized to an unprecedented degree through tuning of its ligand-field environment.« less

Mitochondrial imaging in live or fixed tissues using a luminescent iridium complex.

PubMed

Sorvina, Alexandra; Bader, Christie A; Darby, Jack R T; Lock, Mitchell C; Soo, Jia Yin; Johnson, Ian R D; Caporale, Chiara; Voelcker, Nicolas H; Stagni, Stefano; Massi, Massimiliano; Morrison, Janna L; Plush, Sally E; Brooks, Douglas A

2018-05-29

Mitochondrial morphology is important for the function of this critical organelle and, accordingly, altered mitochondrial structure is exhibited in many pathologies. Imaging of mitochondria can therefore provide important information about disease presence and progression. However, mitochondrial imaging is currently limited by the availability of agents that have the capacity to image mitochondrial morphology in both live and fixed samples. This can be particularly problematic in clinical studies or large, multi-centre cohort studies, where tissue archiving by fixation is often more practical. We previously reported the synthesis of an iridium coordination complex [Ir(ppy) 2 (MeTzPyPhCN)] + ; where ppy is a cyclometalated 2-phenylpyridine and TzPyPhCN is the 5-(5-(4-cyanophen-1-yl)pyrid-2-yl)tetrazolate ligand; and showed that this complex (herein referred to as IraZolve-Mito) has a high specificity for mitochondria in live cells. Here we demonstrate that IraZolve-Mito can also effectively stain mitochondria in both live and fixed tissue samples. The staining protocol proposed is versatile, providing a universal procedure for cell biologists and pathologists to visualise mitochondria.

Impact of pyrogenic organic matter decomposition and induced priming effect on soil C budget.

NASA Astrophysics Data System (ADS)

Maestrini, Bernardo; Abiven, Samuel

2014-05-01

Pyrogenic organic matter (PyOM) results from the incomplete combustion of biomass and may contribute to constitute an important fraction of soil C in forest and agricultural soils, in the form of charcoal (produced by wildfires) or biochar (anthropogenic). Although many evidences exist on the long mean residence time of PyOM there is still a large uncertainty on PyOM loss processes and rate and on possible induced priming effect on non-PyOM. Therefore determining PyOM mineralization rate, loss processes and possible induced priming effect on soil organic matter decomposition are key issues to understand the impact of PyOM on the carbon (C) cycle. We investigated the impact of PyOM on soil C budget by combining results from three independent studies: (i) a field study to investigate PyOM mineralization rate and the relative importance of PyOM loss processes, (ii) a PyOM and soil incubation experiment to correlate C and N mineralization rates, (iii) a review of the priming effect induced by PyOM on soil organic C. We employed 13C labelled pinewood-derived PyOM for the field experiment and 13C labelled ryegrass-derived PyOM in the incubation experiment to trace PyOM losses. In the field experiment it was observed that: (i) Pyrolysis process reduced pinewood decomposition by a factor of 60, (ii) leaching and translocation of fresh PyOM along the soil profile were negligible compared to losses as CO2. In the incubation experiment we found that ryegrass induced a two phase priming effect on native soil organic matter, with a positive priming effect followed by a negative priming effect phase, we also found that ryegrass-derived PyOM decomposition was much slower than pinewood one. The different decomposition rate results probably from the different aromaticity of the two PyOM together with the different set-up of the two experiments. Both the incubation experiment and the meta-analysis revealed that PyOM may induce a two-phase priming effect on native soil organic matter decomposition: positive on the short term and negative on the long term. The meta-analysis showed that that positive priming effect is induced mostly on the native soil organic matter on the short term and by PyOM characterised by a low C content. This result was not confirmed on the freshly added organic matter. We believe that the presence of a labile fraction in PyOM may induce positive priming effect on the short term by mean of co-metabolism. We conclude that PyOM chemical composition and feedstock play an important role in predicting PyOM mineralization rate, and that on the short term PyOM may induce a positive priming effect therefore decreasing the abatement potential of PyOM as a C-sink.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

DOE Office of Scientific and Technical Information (OSTI.GOV)

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Characterization of Trinuclear Oxo Bridged Cobalt Complexes in Isolation

NASA Astrophysics Data System (ADS)

Lang, Johannes; Fries, Daniela V.; Niedner-Schatteburg, Gereon

2018-05-01

This study elucidates molecular structures, fragmentation pathways and relative stabilities of isolated trinuclear oxo bridged cobalt complexes of the structural type [Co3O(OAc)6(Py)n]+ (OAc=acetate, Py=pyridine, n=0, 1, 2, 3). We present infrared multiple photon dissociation (IR-MPD) spectra in combination with quantum chemical calculations. They indicate that the coordination of axial pyridine ligands to the [Co3O(OAc)6]+ subunit disturbs the triangular geometry of the Co3O core. [Co3O(OAc)6]+ exhibits a nearly equilateral triangular Co3O core geometry. The coordination of one or two pyridine ligands disturbs this arrangement resulting in isosceles triangular Co3O core geometries (in the cases of n=1 and 2). Coordination of three pyridine ligands (n=3) results in an equilateral triangular Co3O core geometry as in the case of n=0. Collision induced dissociation (CID) studies reveal that the complexes undergo a consecutive elimination of pyridine and acetate ligands with increasing excitation energy. Relative stabilities of the complexes decrease with the number of coordinated pyridine ligands. The presented results help to gain a fundamental insight into the molecular structure of trinuclear oxo bridged cobalt complexes void of any external effects such as crystal packing or solvation.

Energetic basis for selective recognition of T*G mismatched base pairs in DNA by imidazole-rich polyamides.

PubMed

Lacy, Eilyn R; Nguyen, Binh; Le, Minh; Cox, Kari K; OHare, Caroline; Hartley, John A; Lee, Moses; Wilson, W David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T.G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T.G-polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T.G mismatch containing DNA hairpin duplex and a similar DNA with only Watson-Crick base pairs. Large negative binding enthalpies for all of the polyamide-DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T.G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T.G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T.G mismatch sites.

Energetic basis for selective recognition of T·G mismatched base pairs in DNA by imidazole-rich polyamides

PubMed Central

Lacy, Eilyn R.; Nguyen, Binh; Le, Minh; Cox, Kari K.; O'Hare, Caroline; Hartley, John A.; Lee, Moses; Wilson, W. David

2004-01-01

To complement available structure and binding results and to develop a detailed understanding of the basis for selective molecular recognition of T·G mismatches in DNA by imidazole containing polyamides, a full thermodynamic profile for formation of the T·G–polyamide complex has been determined. The amide-linked heterocycles f-ImImIm and f-PyImIm (where f is formamido group, Im is imidazole and Py is pyrrole) were studied by using biosensor-surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) with a T·G mismatch containing DNA hairpin duplex and a similar DNA with only Watson–Crick base pairs. Large negative binding enthalpies for all of the polyamide–DNA complexes indicate that the interactions are enthalpically driven. SPR results show slower complex formation and stronger binding of f-ImImIm to the T·G than to the match site. The thermodynamic analysis indicates that the enhanced binding to the T·G site is the result of better entropic contributions. Negative heat capacity changes for the complex are correlated with calculated solvent accessible surface area changes and indicate hydrophobic contributions to complex formation. DNase I footprinting analysis in a long DNA sequence provided supporting evidence that f-ImImIm binds selectively to T·G mismatch sites. PMID:15064359

Uranium(iii) complexes supported by hydrobis(mercaptoimidazolyl)borates: synthesis and oxidation chemistry.

PubMed

Maria, Leonor; Santos, Isabel C; Santos, Isabel

2018-05-23

The reaction of [UI3(thf)4] with the sodium or lithium salts of hydrobis(2-mercapto-1-methylimidazolyl)borate ligands ([H(R)B(timMe)2]-) in a 1 : 2 ratio, in tetrahydrofuran, gave the U(iii) complexes [UI{κ3-H,S,S'-H(R)B(timMe)2}2(thf)2] (R = H (1), Ph (2)) in good yields. Crystals of [UI{κ3-H,S,S'-H(Ph)B(timMe)2}2(thf)2] (2) were obtained by recrystallization from a tetrahydrofuran/acetonitrile solution, and the ion-separated uranium complex [U{κ3-H,S,S'-H(Ph)B(timMe)2}2(CH3CN)3][I] (3-I) was obtained by dissolution of 2 in acetonitrile followed by recrystallization. One-electron oxidation of 2 with AgBPh4 or I2 resulted in the formation of the cationic U(iv) complexes [U{κ3-H,S,S'-H(Ph)B(timMe)2}3][X] (X = BPh4 (6-BPh4), I (6-I)), due to a ligand redistribution process. These complexes are the first examples of homoleptic poly(azolyl)borate U(iv) complexes. Treatment of complex 2 with azobenzene led to the isolation of crystals of the U(iv) compound [UI{κ3-H(Ph)B(timMe)2}2(κ2-timMe)] (7). Treatment of 2 with pyridine-N oxide (pyNO) led to the formation of the uranyl complex [UO2{κ2-S,S'-H(Ph)B(timMe)2}2] (8) and of complex 6-I, while from the reaction of [U{κ3-H(Ph)B(timMe)2}2(thf)3][BPh4] (5) with pyNO, the oxo-bridged U(iv) complex [{U{κ3-H(Ph)B(timMe)2}2(pyNO)}2(μ-O)][BPh4]2 (9) was also obtained. In the U(iii) and U(iv) complexes, the bis(azolyl)borate ligands bind to the uranium center in a κ3-H,S,S' coordination mode, while in the U(vi) complex the ligands bind to the metal in a κ2-S,S' mode. The presence of UH-B interactions in the solid-state, for the nine-coordinate complexes 1, 2, 3, 6 and 7 and for the eight-coordinate complex 9, was supported by IR spectroscopy and/or X-ray diffraction analysis.

Pyrogenic carbon from tropical savanna burning: production and stable isotope composition

NASA Astrophysics Data System (ADS)

Saiz, G.; Wynn, J. G.; Wurster, C. M.; Goodrick, I.; Nelson, P. N.; Bird, M. I.

2014-10-01

Widespread burning of mixed tree-grass ecosystems represents the major natural locus of pyrogenic carbon (PyC) production. PyC is a significant, pervasive, and yet poorly understood "slow-cycling" form of carbon present in the atmosphere, hydrosphere, soils and sediments. We conducted sixteen experimental burns on a rainfall transect in northern Australian savannas with C4 grasses ranging from 35 to 99% of total biomass. Residues from each fire were partitioned into PyC and further into recalcitrant (HyPyC) components, with each of these also partitioned into proximal (> 125 μm) and distal (< 125 μm) fluxes. The median [range] PyC production across all burns was 16.0 [11.5]% of total carbon exposed (TCE), with HyPyC accounting for 2.5 [4.9]% of TCE. Both PyC and HyPyC were dominantly partitioned into the proximal flux, likely to remain (initially) close to the site of production. Production of HyPyC was strongly related to fire residence time, with shorter duration fires resulting in higher HyPyC yields. The carbon isotope (δ13C) compositions of PyC and HyPyC were generally lower by 1-3‰ relative to the original biomass, with marked depletion up to 7 ‰ for grasslands dominated by C4 biomass. δ13C values of CO2 produced by combustion was computed by mass balance and ranged from ~0.4 to 1.3‰. The depletion of 13C in PyC and HyPyC relative to the original biomass has significant implications for the interpretation of δ13C values of savanna soil organic carbon and of ancient PyC preserved in the geologic record, and for global 13C isotopic disequilibria calculations.

Extending the language of DNA molecular recognition by polyamides: unexpected influence of imidazole and pyrrole arrangement on binding affinity and specificity.

PubMed

Buchmueller, Karen L; Staples, Andrew M; Howard, Cameron M; Horick, Sarah M; Uthe, Peter B; Le, N Minh; Cox, Kari K; Nguyen, Binh; Pacheco, Kimberly A O; Wilson, W David; Lee, Moses

2005-01-19

Pyrrole (Py) and imidazole (Im) polyamides can be designed to target specific DNA sequences. The effect that the pyrrole and imidazole arrangement, plus DNA sequence, have on sequence specificity and binding affinity has been investigated using DNA melting (DeltaT(M)), circular dichroism (CD), and surface plasmon resonance (SPR) studies. SPR results obtained from a complete set of triheterocyclic polyamides show a dramatic difference in the affinity of f-ImPyIm for its cognate DNA (K(eq) = 1.9 x 10(8) M(-1)) and f-PyPyIm for its cognate DNA (K(eq) = 5.9 x 10(5) M(-1)), which could not have been anticipated prior to characterization of these compounds. Moreover, f-ImPyIm has a 10-fold greater affinity for CGCG than distamycin A has for its cognate, AATT. To understand this difference, the triamide dimers are divided into two structural groupings: central and terminal pairings. The four possible central pairings show decreasing selectivity and affinity for their respective cognate sequences: -ImPy > -PyPy- > -PyIm- approximately -ImIm-. These results extend the language of current design motifs for polyamide sequence recognition to include the use of "words" for recognizing two adjacent base pairs, rather than "letters" for binding to single base pairs. Thus, polyamides designed to target Watson-Crick base pairs should utilize the strength of -ImPy- and -PyPy- central pairings. The f/Im and f/Py terminal groups yielded no advantage for their respective C/G or T/A base pairs. The exception is with the -ImPy- central pairing, for which f/Im has a 10-fold greater affinity for C/G than f/Py has for T/A.

Rubbing time and bonding performance of one-step adhesives to primary enamel and dentin

PubMed Central

Botelho, Maria Paula Jacobucci; Isolan, Cristina Pereira; Schwantz, Júlia Kaster; Lopes, Murilo Baena; de Moraes, Rafael Ratto

2017-01-01

Abstract Objectives: This study investigated whether increasing the concentration of acidic monomers in one-step adhesives would allow reducing their application time without interfering with the bonding ability to primary enamel and dentin. Material and methods: Experimental one-step self-etch adhesives were formulated with 5 wt% (AD5), 20 wt% (AD20), or 35 wt% (AD35) acidic monomer. The adhesives were applied using rubbing motion for 5, 10, or 20 s. Bond strengths to primary enamel and dentin were tested under shear stress. A commercial etch-and-rinse adhesive (Single Bond 2; 3M ESPE) served as reference. Scanning electron microscopy was used to observe the morphology of bonded interfaces. Data were analysed at p<0.05. Results: In enamel, AD35 had higher bond strength when rubbed for at least 10 s, while application for 5 s generated lower bond strength. In dentin, increased acidic monomer improved bonding only for 20 s rubbing time. The etch-and-rinse adhesive yielded higher bond strength to enamel and similar bonding to dentin as compared with the self-etch adhesives. The adhesive layer was thicker and more irregular for the etch-and-rinse material, with no appreciable differences among the self-etch systems. Conclusion: Overall, increasing the acidic monomer concentration only led to an increase in bond strength to enamel when the rubbing time was at least 10 s. In dentin, despite the increase in bond strength with longer rubbing times, the results favoured the experimental adhesives compared to the conventional adhesive. Reduced rubbing time of self-etch adhesives should be avoided in the clinical setup. PMID:29069150

Enantioselective oxidative biaryl coupling reactions catalyzed by 1,5-diazadecalin metal complexes.

PubMed

Li, X; Yang, J; Kozlowski, M C

2001-04-19

[reaction: see text]. Chiral 1,5-diaza-cis-decalins have been examined as ligands in the enantioselective oxidative biaryl coupling of substituted 2-naphthol derivatives. Under the optimal conditions employing a 1,5-diaza-cis-decalin copper(I) iodide complex with oxygen as the oxidant, rapid and highly selective couplings could be achieved (90-93% ee, 85% yield).

Severe acute corneal hydrops in a patient with Down syndrome and persistent eye rubbing.

PubMed

Ozcan, Altan A; Ersoz, T Reha

2007-01-01

We report a case of severe acute corneal hydrops in an 11-year-old boy with keratoconus associated with Down syndrome and vigorous eye rubbing. Complete resolution of the corneal edema and a central corneal scar was seen in the 8th week of final follow-up. Eye-rubbing may play a role in the pathogenesis of acute hydrops, and conventional therapy can be successful in its management, even in severe cases.

Single treatment with ethanol hand rub is ineffective against human rhinovirus--hand washing with soap and water removes the virus efficiently.

PubMed

Savolainen-Kopra, Carita; Korpela, Terttu; Simonen-Tikka, Marja-Leena; Amiryousefi, Ali; Ziegler, Thedi; Roivainen, Merja; Hovi, Tapani

2012-03-01

Ethanol-containing hand rubs are used frequently as a substitute for hand washing with water and soap. However, not all viruses are inactivated by a short term rubbing with alcohol. The capacity of a single round of instructed and controlled hand cleaning with water and soap or ethanol-containing hand rub, respectively, was tested for removal of human rhinovirus administered onto the skin of healthy volunteers on the back of the hands. Hand washing with soap and water appeared to be much more efficient for removing rhinoviruses from skin than rubbing hands with an ethanol-containing disinfectant. After washing with soap and water the virus was detected in 3/9 (33.3%) test persons from the left hand and 1/9 (11.1%) cases from the right hand, whereas the virus was detected invariably by real-time RT-PCR from both hands after cleaning with alcohol hand rub (P-value <0.01). Both substances evaluated clinically were also tested in vitro for virucidal efficacy against Human rhinovirus2 (HRV2) using a standardized assay. Both tested substances were poor within the contact time used in the hand-cleaning test. In conclusion, thorough and conventional hand washing with water and soap can clean efficiently hands contaminated with the virus responsible for an extensive share of common cold episodes. Copyright © 2012 Wiley Periodicals, Inc.

Pyrogenic Carbon in soils: a literature-based inventory and a global estimation of its content in soil organic carbon and stocks

NASA Astrophysics Data System (ADS)

Reisser, Moritz; Purves, Ross; Schmidt, Michael W. I.; Abiven, Samuel

2016-08-01

Pyrogenic carbon (PyC) is considered one of the most stable components in soil and can represent more than 30% of total soil organic carbon (SOC). However, few estimates of global PyC stock or distribution exist and thus PyC is not included in any global carbon cycle models, despite its potential major relevance for the soil pool. To obtain a global picture, we reviewed the literature for published PyC content in SOC data. We generated the first PyC database including more than 560 measurements from 55 studies. Despite limitations due to heterogeneous distribution of the studied locations and gaps in the database, we were able to produce a worldwide PyC inventory. We found that global PyC represent on average 13.7% of the SOC and can be even up to 60%, making it one of the largest groups of identifiable compounds in soil, together with polysaccharides. We observed a consistent range of PyC content in SOC, despite the diverse methods of quantification. We tested the PyC content against different environmental explanatory variables: fire and land use (fire characteristics, land use, net primary productivity), climate (temperature, precipitation, climatic zones, altitude) and pedogenic properties (clay content, pH, SOC content). Surprisingly, soil properties explain PyC content the most. Soils with clay content higher than 50% contain significantly more PyC (> 30% of the SOC) than with clay content lower than 5% (< 6% of the SOC). Alkaline soils contain at least 50% more PyC than acidic soils. Furthermore, climatic conditions, represented by climatic zone or mean temperature or precipitation, correlate significantly with the PyC content. By contrast, fire characteristics could only explain PyC content, if site-specific information was available. Datasets derived from remote sensing did not explain the PyC content. To show the potential of this database, we used it in combination with other global datasets to create a global worldwide PyC content and a stock estimation, which resulted in around 200Pg PyC for the uppermost 2 meters. These modelled estimates indicated a clear mismatch between the location of the current PyC studies and the geographical zones where we expect high PyC stocks.

Blisters

MedlinePlus

... get blisters? Blisters often happen when there is friction - rubbing or pressure - on one spot. For example, ... sure that there is no more rubbing or friction on the blister. You should contact your health ...

Optical metabolic imaging measures early drug response in an allograft murine breast cancer model (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sharick, Joe T.; Cook, Rebecca S.; Skala, Melissa C.

2017-02-01

Previous work has shown that cellular-level Optical Metabolic Imaging (OMI) of organoids derived from human breast cancer cell-line xenografts accurately and rapidly predicts in vivo response to therapy. To validate OMI as a predictive measure of treatment response in an immune-competent model, we used the polyomavirus middle-T (PyVmT) transgenic mouse breast cancer model. The PyVmT model includes intra-tumoral heterogeneity and a complex tumor microenvironment that can influence treatment responses. Three-dimensional organoids generated from primary PyVmT tumor tissue were treated with a chemotherapy (paclitaxel) and a PI3K inhibitor (XL147), each alone or in combination. Cellular subpopulations of response were measured using the OMI Index, a composite endpoint of metabolic response comprised of the optical redox ratio (ratio of the fluorescence intensities of metabolic co-enzymes NAD(P)H to FAD) as well as the fluorescence lifetimes of NAD(P)H and FAD. Combination treatment significantly decreased the OMI Index of PyVmT tumor organoids (p<0.0001) and in vivo tumors (p<0.0001) versus controls. Subpopulation analyses revealed a homogeneous response to combined therapy in both cultured organoids and in vivo tumors, while single agent treatment with XL147 alone or paclitaxel alone elicited heterogeneous responses in organoids. Tumor volume decreased with combination treatment through treatment day 30. These results indicate that OMI of organoids generated from PyVmT tumors can accurately reflect drug response in heterogeneous allografts with both innate and adaptive immunity. Thus, this method is promising for use in humans to predict long-term treatment responses accurately and rapidly, and could aid in clinical treatment planning.

PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins.

PubMed

Lowe, Alan R; Perez-Riba, Albert; Itzhaki, Laura S; Main, Ewan R G

2018-02-06

For many years, curve-fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large data sets. One field that is reliant on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we present PyFolding, a free, open-source, and extensible Python framework for graphing, analysis, and simulation of the biophysical properties of proteins. To demonstrate the utility of PyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: 1) multiphase kinetic folding fitted to linked equations, 2) global fitting of multiple data sets, and 3) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate how PyFolding is easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show that PyFolding can be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and among research teams. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The pool of preactivated Lck in the initiation of T-cell signaling: a critical re-evaluation of the Lck standby model.

PubMed

Ballek, Ondřej; Valečka, Jan; Manning, Jasper; Filipp, Dominik

2015-04-01

The initiation of T-cell receptor (TCR) signaling, based on the cobinding of TCR and CD4-Lck heterodimer to a peptide-major histocompatibility complex II on antigen presenting cells, represents a classical model of T-cell signaling. What is less clear however, is the mechanism which translates TCR engagement to the phosphorylation of immunoreceptor tyrosine-based activation motifs on CD3 chains and how this event is coupled to the delivery of Lck function. Recently proposed 'standby model of Lck' posits that resting T-cells contain an abundant pool of constitutively active Lck (pY394(Lck)) required for TCR triggering, and this amount, upon TCR engagement, remains constant. Here, we show that although maintenance of the limited pool of pY394(Lck) is necessary for the generation of TCR proximal signals in a time-restricted fashion, the total amount of this pool, ~2%, is much smaller than previously reported (~40%). We provide evidence that this dramatic discrepancy in the content of pY394(Lck)is likely the consequence of spontaneous phosphorylation of Lck that occurred after cell solubilization. Additional discrepancies can be accounted for by the sensitivity of different pY394(Lck)-specific antibodies and the type of detergents used. These data suggest that reagents and conditions used for the quantification of signaling parameters must be carefully validated and interpreted. Thus, the limited size of pY394(Lck) pool in primary T-cells invites a discussion regarding the adjustment of the quantitative parameters of the standby model of Lck and reevaluation of the mechanism by which this pool contributes to the generation of proximal TCR signaling.

Desensitization of chemical activation by auxiliary subunits: convergence of molecular determinants critical for augmenting KCNQ1 potassium channels.

PubMed

Gao, Zhaobing; Xiong, Qiaojie; Sun, Haiyan; Li, Min

2008-08-15

Chemical openers for KCNQ potassium channels are useful probes both for understanding channel gating and for developing therapeutics. The five KCNQ isoforms (KCNQ1 to KCNQ5, or Kv7.1 to Kv7.5) are differentially localized. Therefore, the molecular specificity of chemical openers is an important subject of investigation. Native KCNQ1 normally exists in complex with auxiliary subunits known as KCNE. In cardiac myocytes, the KCNQ1-KCNE1 (IsK or minK) channel is thought to underlie the I(Ks) current, a component critical for membrane repolarization during cardiac action potential. Hence, the molecular and pharmacological differences between KCNQ1 and KCNQ1-KCNE1 channels have been important topics. Zinc pyrithione (ZnPy) is a newly identified KCNQ channel opener, which potently activates KCNQ2, KCNQ4, and KCNQ5. However, the ZnPy effects on cardiac KCNQ1 potassium channels remain largely unknown. Here we show that ZnPy effectively augments the KCNQ1 current, exhibiting an increase in current amplitude, reduction of inactivation, and slowing of both activation and deactivation. Some of these are reminiscent of effects by KCNE1. In addition, neither the heteromultimeric KCNQ1-KCNE1 channels nor native I(Ks) current displayed any sensitivity to ZnPy, indicating that the static occupancy by a KCNE subunit desensitizes the reversible effects by a chemical opener. Site-directed mutagenesis of KCNQ1 reveals that residues critical for the potentiation effects by either ZnPy or KCNE are clustered together in the S6 region overlapping with the critical gating determinants. Thus, the convergence of potentiation effects and molecular determinants critical for both an auxiliary subunit and a chemical opener argue for a mechanistic overlap in causing potentiation.

Grating coupled SPR microarray analysis of proteins and cells in blood from mice with breast cancer.

PubMed

Mendoza, A; Torrisi, D M; Sell, S; Cady, N C; Lawrence, D A

2016-01-21

Biomarker discovery for early disease diagnosis is highly important. Of late, much effort has been made to analyze complex biological fluids in an effort to develop new markers specific for different cancer types. Recent advancements in label-free technologies such as surface plasmon resonance (SPR)-based biosensors have shown promise as a diagnostic tool since there is no need for labeling or separation of cells. Furthermore, SPR can provide rapid, real-time detection of antigens from biological samples since SPR is highly sensitive to changes in surface-associated molecular and cellular interactions. Herein, we report a lab-on-a-chip microarray biosensor that utilizes grating-coupled surface plasmon resonance (GCSPR) and grating-coupled surface plasmon coupled fluorescence (GCSPCF) imaging to detect circulating tumor cells (CTCs) from a mouse model (FVB-MMTV-PyVT). GCSPR and GCSPCF analysis was accomplished by spotting antibodies to surface cell markers, cytokines and stress proteins on a nanofabricated GCSPR microchip and screening blood samples from FVB control mice or FVB-MMTV-PyVT mice with developing mammary carcinomas. A transgenic MMTV-PyVT mouse derived cancer cell line was also analyzed. The analyses indicated that CD24, CD44, CD326, CD133 and CD49b were expressed in both cell lines and in blood from MMTV-PyVT mice. Furthermore, cytokines such as IL-6, IL-10 and TNF-α, along with heat shock proteins HSP60, HSP27, HSc70(HSP73), HSP90 total, HSP70/HSc70, HSP90, HSP70, HSP90 alpha, phosphotyrosine and HSF-1 were overexpressed in MMTV-PyVT mice.

Investigation of dynamic characteristics of a rotor system with surface coatings

NASA Astrophysics Data System (ADS)

Yang, Yang; Cao, Dengqing; Wang, Deyou

2017-02-01

A Jeffcott rotor system with surface coatings capable of describing the mechanical vibration resulting from unbalance and rub-impact is formulated in this article. A contact force model proposed recently to describe the impact force between the disc and casing with coatings is employed to do the dynamic analysis for the rotor system with rubbing fault. Due to the variation of penetration, the contact force model is correspondingly modified. Meanwhile, the Coulomb friction model is applied to simulate the friction characteristics. Then, the case study of rub-impact with surface coatings is simulated by the Runge-Kutta method, in which a linear interpolation method is adopted to predict the rubbing instant. Moreover, the dynamic characteristics of the rotor system with surface coatings are analyzed in terms of bifurcation plot, waveform, whirl orbit, Poincaré map and spectrum plot. And the effects of the hardness of surface coatings on the response are investigated as well. Finally, compared with the classical models, the modified contact force model is shown to be more suitable to solve the rub-impact of aero-engine with surface coatings.

An experimental investigation of rubbing interaction in labyrinth seals at cryogenic temperature

NASA Technical Reports Server (NTRS)

Dolan, F. X.; Kennedy, F. E.; Schulson, E. M.

1985-01-01

An experimental program was carried out to address issues related to the observed cracking of the titanium knife edges on the labyrinth seals of the high pressure fuel pump (HPFP) in the Space Shuttle main engine (SSME). Thermal shock experiments were carried out using a jet specimen with geometry similar to the knife edge geometry. These tests demonstrate that cracking of the titanium alloy is possible in a situation involving repeated thermal cycles over a wide temperature range, as might be realized during a rub in the liquid hydrogen fuel pump. High speed rub interaction tests were conducted using a representative knife edge and seal geometry over a broad range of interaction rates. Alternative materials were also experimentally evaluated. These tests provide information which can be used to design improved labyrinth seals for the HPFP of the SSME. In particular, plasma-sprayed aluminum-graphite was found to be significantly better than aluminum alloy seals used at present from the standpoint of rub performance. Ion nitriding of the titanium alloy knife edges was also found to improve rub performance compared with the untreated baseline knife edge material.

CisMiner: Genome-Wide In-Silico Cis-Regulatory Module Prediction by Fuzzy Itemset Mining

PubMed Central

Navarro, Carmen; Lopez, Francisco J.; Cano, Carlos; Garcia-Alcalde, Fernando; Blanco, Armando

2014-01-01

Eukaryotic gene control regions are known to be spread throughout non-coding DNA sequences which may appear distant from the gene promoter. Transcription factors are proteins that coordinately bind to these regions at transcription factor binding sites to regulate gene expression. Several tools allow to detect significant co-occurrences of closely located binding sites (cis-regulatory modules, CRMs). However, these tools present at least one of the following limitations: 1) scope limited to promoter or conserved regions of the genome; 2) do not allow to identify combinations involving more than two motifs; 3) require prior information about target motifs. In this work we present CisMiner, a novel methodology to detect putative CRMs by means of a fuzzy itemset mining approach able to operate at genome-wide scale. CisMiner allows to perform a blind search of CRMs without any prior information about target CRMs nor limitation in the number of motifs. CisMiner tackles the combinatorial complexity of genome-wide cis-regulatory module extraction using a natural representation of motif combinations as itemsets and applying the Top-Down Fuzzy Frequent- Pattern Tree algorithm to identify significant itemsets. Fuzzy technology allows CisMiner to better handle the imprecision and noise inherent to regulatory processes. Results obtained for a set of well-known binding sites in the S. cerevisiae genome show that our method yields highly reliable predictions. Furthermore, CisMiner was also applied to putative in-silico predicted transcription factor binding sites to identify significant combinations in S. cerevisiae and D. melanogaster, proving that our approach can be further applied genome-wide to more complex genomes. CisMiner is freely accesible at: http://genome2.ugr.es/cisminer. CisMiner can be queried for the results presented in this work and can also perform a customized cis-regulatory module prediction on a query set of transcription factor binding sites provided by the user. PMID:25268582

The abundance of cis-acting loci leading to differential allele expression in F1 mice and their relationship to loci harboring genes affecting complex traits.

PubMed

Yeo, Seungeun; Hodgkinson, Colin A; Zhou, Zhifeng; Jung, Jeesun; Leung, Ming; Yuan, Qiaoping; Goldman, David

2016-08-11

Genome-wide surveys have detected cis-acting quantitative trait loci altering levels of RNA transcripts (RNA-eQTLs) by associating SNV alleles to transcript levels. However, the sensitivity and specificity of detection of cis- expression quantitative trait loci (eQTLs) by genetic approaches, reliant as it is on measurements of transcript levels in recombinant inbred strains or offspring from arranged crosses, is unknown, as is their relationship to QTL's for complex phenotypes. We used transcriptome-wide differential allele expression (DAE) to detect cis-eQTLs in forebrain and kidney from reciprocal crosses between three mouse inbred strains, 129S1/SvlmJ, DBA/2J, and CAST/EiJ and C57BL/6 J. Two of these crosses were previously characterized for cis-eQTLs and QTLs for various complex phenotypes by genetic analysis of recombinant inbred (RI) strains. 5.4 %, 1.9 % and 1.5 % of genes assayed in forebrain of B6/129SF1, B6/DBAF1, and B6/CASTF1 mice, respectively, showed differential allelic expression, indicative of cis-acting alleles at these genes. Moreover, the majority of DAE QTLs were observed to be tissue-specific with only a small fraction showing cis-effects in both tissues. Comparing DAE QTLs in F1 mice to cis-eQTLs previously mapped in RI strains we observed that many of the cis-eQTLs were not confirmed by DAE. Additionally several novel DAE-QTLs not identified as cis-eQTLs were identified suggesting that there are differences in sensitivity and specificity for QTL detection between the two methodologies. Strain specific DAE QTLs in B6/DBAF1 mice were located in excess at candidate genes for alcohol use disorders, seizures, and angiogenesis previously implicated by genetic linkage in C57BL/6J × DBA/2JF2 mice or BXD RI strains. Via a survey for differential allele expression in F1 mice, a substantial proportion of genes were found to have alleles altering expression in cis-acting fashion. Comparing forebrain and kidney, many or most of these alleles were tissue-specific in action. The identification of strain specific DAE QTLs, can assist in assessment of candidate genes located within the large intervals associated with trait QTLs.

Application of the π-accepting ability parameter of N-heterocyclic carbene ligands in iridium complexes for signal amplification by reversible exchange (SABRE).

PubMed

van Weerdenburg, Bram J A; Eshuis, Nan; Tessari, Marco; Rutjes, Floris P J T; Feiters, Martin C

2015-09-21

The new π-accepting ability parameter (PAAP) appears to be the best tool to analyse the electronic properties of NHC ligands in [Ir(H)2(NHC)(Py)3](+) complexes for SABRE. Together with the buried volume, the efficiency of hyperpolarisation transfer in SABRE, depending on the exchange rate of pyridine, can be described.

Ligand reprogramming in dinuclear helicate complexes: a consequence of allosteric or electrostatic effects?

PubMed

Jeffery, John C; Rice, Craig R; Harding, Lindsay P; Baylies, Christian J; Riis-Johannessen, Thomas

2007-01-01

The ditopic ligand 6,6'-bis(4-methylthiazol-2-yl)-3,3'-([18]crown-6)-2,2'-bipyridine (L(1)) contains both a potentially tetradentate pyridyl-thiazole (py-tz) N-donor chain and an additional "external" crown ether binding site which spans the central 2,2'-bipyridine unit. In polar solvents (MeCN, MeNO(2)) this ligand forms complexes with Zn(II), Cd(II), Hg(II) and Cu(I) ions via coordination of the N donors to the metal ion. Reaction with both Hg(II) and Cu(I) ions results in the self-assembly of dinuclear double-stranded helicate complexes. The ligands are partitioned by rotation about the central py--py bond, such that each can coordinate to both metals as a bis-bidentate donor ligand. With Zn(II) ions a single-stranded mononuclear species is formed in which one ligand coordinates the metal ion in a planar tetradentate fashion. Reaction with Cd(II) ions gives rise to an equilibrium between both the dinuclear double-stranded helicate and the mononuclear species. These complexes can further coordinate s-block metal cations via the remote crown ether O-donor domains; a consequence of which are some remarkable changes in the binding modes of the N-donor domains. Reaction of the Hg(II)- or Cd(II)-containing helicate with either Ba(2+) or Sr(2+) ions effectively reprogrammes the ligand to form only the single-stranded heterobinuclear complexes [MM'(L(1))](4+) (M=Hg(II), Cd(II); M'=Ba(2+), Sr(2+)), where the transition and s-block cations reside in the N- and O-donor sites, respectively. In contrast, the same ions have only a minor structural impact on the Zn(II) species, which already exists as a single-stranded mononuclear complex. Similar reactions with the Cd(II) system result in a shift in equilibrium towards the single-stranded species, the extent of which depends on the size and charge of the s-block cation in question. Reaction of the dicopper(I) double-stranded helicate with Ba(2+) shows that the dinuclear structure still remains intact but the pitch length is significantly increased.

A comparative study on the binding of single and double chain surfactant-cobalt(III) complexes with bovine serum albumin

NASA Astrophysics Data System (ADS)

Vignesh, G.; Sugumar, K.; Arunachalam, S.; Vignesh, S.; Arthur James, R.

2013-09-01

The comparative binding effect of single and double aliphatic chain containing surfactant-cobalt(III) complexes cis-[Co(bpy)2(DA)2](ClO4)3ṡ2H2O (1), cis-[Co(bpy)2(DA)Cl](ClO4)2ṡ2H2O (2), cis-[Co(phen)2(CA)2](ClO4)3ṡ2H2O (3), and cis-[Co(phen)2(CA)Cl](ClO4)2ṡ2H2O (4) with bovine serum albumin (BSA) under physiological condition was analyzed by steady state, time resolved fluorescence, synchronous, three-dimensional fluorescence, UV-Visible absorption and circular dichroism spectroscopic techniques. The results show that these complexes cause the fluorescence quenching of BSA through a static mechanism. The binding constants (Kb) and the number of binding sites were calculated and binding constant values are found in the range of 104-105 M-1. The results indicate that compared to single chain complex, double chain surfactant-cobalt(III) complex interacts strongly with BSA. Also the sign of thermodynamic parameters (ΔG°, ΔH°, and ΔS°) indicate that all the complexes interact with BSA through hydrophobic force. The binding distance (r) between complexes and BSA was calculated using Förster non-radiation energy transfer theory and found to be less than 7 nm. The results of synchronous, three dimensional fluorescence and circular dichroism spectroscopic methods indicate that the double chain surfactant-cobalt(III) complexes changed the conformation of the protein considerably than the respective single chain surfactant-cobalt(III) complexes. Antimicrobial studies of the complexes showed good activities against pathogenic microorganisms.

Synthesis and characterization of fac-[M(CO)3(P)(OO)] and cis-trans-[M(CO)2(P)2(OO)] complexes (M = Re, (99m)Tc) with acetylacetone and curcumin as OO donor bidentate ligands.

PubMed

Triantis, Charalampos; Tsotakos, Theodoros; Tsoukalas, Charalampos; Sagnou, Marina; Raptopoulou, Catherine; Terzis, Aris; Psycharis, Vassilis; Pelecanou, Maria; Pirmettis, Ioannis; Papadopoulos, Minas

2013-11-18

The synthesis and characterization of neutral mixed ligand complexes fac-[M(CO)3(P)(OO)] and cis-trans-[M(CO)2(P)2(OO)] (M = Re, (99m)Tc), with deprotonated acetylacetone or curcumin as the OO donor bidentate ligands and a phosphine (triphenylphosphine or methyldiphenylphosphine) as the monodentate P ligand, is described. The complexes were synthesized through the corresponding fac-[M(CO)3(H2O)(OO)] (M = Re, (99m)Tc) intermediate aqua complex. In the presence of phosphine, replacement of the H2O molecule of the intermediate complex at room temperature generates the neutral tricarbonyl monophosphine fac-[Re(CO)3(P)(OO)] complex, while under reflux conditions further replacement of the trans to the phosphine carbonyl generates the new stable dicarbonyl bisphosphine complex cis-trans-[Re(CO)2(P)2(OO)]. The Re complexes were fully characterized by elemental analysis, spectroscopic methods, and X-ray crystallography showing a distorted octahedral geometry around Re. Both the monophosphine and the bisphosphine complexes of curcumin show selective binding to β-amyloid plaques of Alzheimer's disease. At the (99m)Tc tracer level, the same type of complexes, fac-[(99m)Tc(CO)3(P)(OO)] and cis-trans-[(99m)Tc(CO)2(P)2(OO)], are formed introducing new donor combinations for (99m)Tc(I). Overall, β-diketonate and phosphine constitute a versatile ligand combination for Re(I) and (99m)Tc(I), and the successful employment of the multipotent curcumin as β-diketone provides a solid example of the pharmacological potential of this system.

Consistent Estimates of Very Low HIV Incidence Among People Who Inject Drugs: New York City, 2005–2014

PubMed Central

Arasteh, Kamyar; McKnight, Courtney; Feelemyer, Jonathan; Campbell, Aimée N. C.; Tross, Susan; Smith, Lou; Cooper, Hannah L. F.; Hagan, Holly; Perlman, David

2016-01-01

Objectives. To compare methods for estimating low HIV incidence among persons who inject drugs. Methods. We examined 4 methods in New York City, 2005 to 2014: (1) HIV seroconversions among repeat participants, (2) increase of HIV prevalence by additional years of injection among new injectors, (3) the New York State and Centers for Disease Control and Prevention stratified extrapolation algorithm, and (4) newly diagnosed HIV cases reported to the New York City Department of Health and Mental Hygiene. Results. The 4 estimates were consistent: (1) repeat participants: 0.37 per 100 person-years (PY; 95% confidence interval [CI] = 0.05/100 PY, 1.33/100 PY); (2) regression of prevalence by years injecting: 0.61 per 100 PY (95% CI = 0.36/100 PY, 0.87/100 PY); (3) stratified extrapolation algorithm: 0.32 per 100 PY (95% CI = 0.18/100 PY, 0.46/100 PY); and (4) newly diagnosed cases of HIV: 0.14 per 100 PY (95% CI = 0.11/100 PY, 0.16/100 PY). Conclusions. All methods appear to capture the same phenomenon of very low and decreasing HIV transmission among persons who inject drugs. Public Health Implications. If resources are available, the use of multiple methods would provide better information for public health purposes. PMID:26794160

Pyrogenic carbon from tropical savanna burning: production and stable isotope composition

NASA Astrophysics Data System (ADS)

Saiz, G.; Wynn, J. G.; Wurster, C. M.; Goodrick, I.; Nelson, P. N.; Bird, M. I.

2015-03-01

Widespread burning of mixed tree-grass ecosystems represents the major natural locus of pyrogenic carbon (PyC) production. PyC is a significant, pervasive and yet poorly understood "slow-cycling" form of carbon present in the atmosphere, hydrosphere, soils and sediments. We conducted 16 experimental burns on a rainfall transect through northern Australian savannas with C4 grasses ranging from 35 to 99% of total biomass. Residues from each fire were partitioned into PyC and further into recalcitrant (HyPyC) components, with each of these fluxes also partitioned into proximal components (>125 μm), likely to remain close to the site of burning, and distal components (<125 μm), likely to be transported from the site of burning. The median (range) PyC production across all burns was 16.0 (11.5) % of total carbon exposed (TCE), with HyPyC accounting for 2.5 (4.9) % of TCE. Both PyC and HyPyC were dominantly partitioned into the proximal flux. Production of HyPyC was strongly related to fire residence time, with shorter duration fires resulting in higher HyPyC yields. The carbon isotope (δ13C) compositions of PyC and HyPyC were generally lower by 1-3‰ relative to the original biomass, with marked depletion up to 7‰ for grasslands dominated by C4 biomass. δ13C values of CO2 produced by combustion were computed by mass balance and ranged from ~0.4 to 1.3‰. The depletion of 13C in PyC and HyPyC relative to the original biomass has significant implications for the interpretation of δ13C values of savanna soil organic carbon and of ancient PyC preserved in the geologic record, as well as for global 13C isotopic disequilibria calculations.

Chromatographic instrumentation in space: past, present and future developments for exobiological studies

NASA Astrophysics Data System (ADS)

Raulin, F.; Sternberg, R.; Coscia, D.; Vidal-Madjar, C.; Millot, M.-C.; Sébille, B.; Israel, G.

1999-01-01

Several planetary exploration missions have already used chromatographic techniques to search for organic compounds, including complex organics, in extraterrestrial environments. So far, only gas chromatography (GC) has been used. In two cases (Viking and Cassini-Huygens), a Py-GC-MS instrument, coupling GC with a pyrolyzer and a mass spectrometer, has been flown. Powerful miniaturized Py-GC-MS instrumentation, with high resolution multi-GC columns and time-of-flight or Ion Trap mass spectrometers are under development, in the frame of the preparation of the Rosetta mission. There is now a strong need for new chromatographic instrumentation in space, in particular to perform detailed molecular analyses of complex non-volatile organics, including macromolecular compounds. Liquid Chromatography (LC), in particular High Performance Liquid Chromatography (HPLC) Supercritical Fluid Chromatography (SFC) or Chemical-Derivatization Gas Chromatography (CDGC) could provide a very efficient mean of analyzing a wide variety of exobiologically important compounds. LC or CDGC have never been used in space yet, but feasibility studies on their application in planetary mission are needed.

MOLNs: A CLOUD PLATFORM FOR INTERACTIVE, REPRODUCIBLE, AND SCALABLE SPATIAL STOCHASTIC COMPUTATIONAL EXPERIMENTS IN SYSTEMS BIOLOGY USING PyURDME

PubMed Central

Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas

2017-01-01

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools and a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments. PMID:28190948

Modeling of the competition life cycle using the software complex of cellular automata PyCAlab

NASA Astrophysics Data System (ADS)

Berg, D. B.; Beklemishev, K. A.; Medvedev, A. N.; Medvedeva, M. A.

2015-11-01

The aim of the work is to develop a numerical model of the life cycle of competition on the basis of software complex cellular automata PyCAlab. The model is based on the general patterns of growth of various systems in resource-limited settings. At examples it is shown that the period of transition from an unlimited growth of the market agents to the stage of competitive growth takes quite a long time and may be characterized as monotonic. During this period two main strategies of competitive selection coexist: 1) capture of maximum market space with any reasonable costs; 2) saving by reducing costs. The obtained results allow concluding that the competitive strategies of companies must combine two mentioned types of behavior, and this issue needs to be given adequate attention in the academic literature on management. The created numerical model may be used for market research when developing of the strategies for promotion of new goods and services.

Rsp5-Bul1/2 complex is necessary for the HSE-mediated gene expression in budding yeast.

PubMed

Kaida, Daisuke; Toh-e, Akio; Kikuchi, Yoshiko

2003-07-11

Rsp5 is an essential ubiquitin ligase in Saccharomyces cerevisiae and is concerned with many functions such as endocytosis and transcription through ubiquitination of various substrates. Bul1 or its homologue Bul2 binds to Rsp5 through the PY-motif and the bul1 bul2 double mutant is sensitive to various stresses. We demonstrate here that heat shock element (HSE)-mediated gene expression was defective in both rsp5-101 and bul1 bul2 mutants under high temperature condition. The bul1 gene containing mutations in the PY motif region did not recover this defective gene expression of the bul1 bul2 mutant. The protein level and phosphorylation state of the HSE-binding transcription factor, Hsf1, was not affected by these mutations. Thus, the Rsp5-Bul1/2 complex has a new function for the HSE-mediated gene expression and may regulate it through other factors than Hsf1.

Causes of death in a contemporary adult congenital heart disease cohort.

PubMed

Yu, Christopher; Moore, Benjamin M; Kotchetkova, Irina; Cordina, Rachael L; Celermajer, David S

2018-04-17

The life expectancy of patients with congenital heart disease (CHD) has significantly improved with advances in their paediatric medical care. Mortality patterns are changing as a result. Our study aims to describe survival and causes of death in a contemporary cohort of adult patients with CHD. We reviewed 3068 patients in our adult CHD database (age ≥16 years, seen at least once in our centre between 2000 and 2015), and documented the number and causes of death, via Australia's National Death Index. Survival and mortality patterns were analysed by complexity of CHD and by underlying congenital diagnosis. Our cohort comprised 3068 adult patients (53% male). The distribution of patients (per the Bethesda classification) was 47% simple, 34% moderate and 18% complex (1% not classifiable). Over a median follow-up of 6.2 years (IQR 3.5-10.4), 341 patients (11%) died with an incidence of 0.4 deaths/100 patient years (py). Survival was significantly worse with increasing complexity of CHD (p<0.001); mortality rate in the simple group was 0.3 deaths/100 py with a median age of death 70 years, and in the complex group was 1.0 death/100 py with a median age of death 34 years. Overall, non-cardiac causes of death outnumbered cardiac causes, at 54% and 46%, respectively. The leading single cause of death was heart failure (17%), followed by malignancy (13%). Simple adult CHD patients mostly died due to non-cardiac causes such as malignancy. Perioperative mortality only accounted for 5% of deaths. Premature death is common in adults with CHD. Although heart failure remains the most common cause of death, in the contemporary era in a specialist CHD centre, non-cardiac related deaths outnumber cardiac deaths, particularly in those with simple CHD lesions. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Magnetic properties of 1 : 4 complexes of CoCl2 and pyridines carrying carbenes (S(0) = 4/2, 6/2, and 8/2) in diluted frozen solution; influence of carbene multiplicity on heterospin single-molecule magnets.

PubMed

Karasawa, Satoru; Nakano, Kimihiro; Tanokashira, Jun-ichi; Yamamoto, Noriko; Yoshizaki, Takahito; Koga, Noboru

2012-11-28

The microcrystalline sample of a parent complex, [CoCl(2)(py)(4)], showed a single-molecule magnet (SMM) behavior with an effective activation barrier, U(eff)/k(B), of 16 K for reversal of the magnetism in the presence of a dc field of 3 kOe. Pyridine ligands having 2-4 diazo moieties, DYpy; Y = 2, 3l, 3b, and 4, were prepared and confirmed to be quintet, septet, septet, and nonet in the ground state, respectively, after irradiation. The 1 : 4 complexes, CoCl(2)(DYpy)(4); Y = 2, 3l, 3b, and 4 in frozen solutions after irradiation showed the magnetic behaviors of SMMs with total spin multiplicity, S(total) = 17/2, 25/2, 25/2, and 33/2, respectively. Hysteresis loops depending on the temperature were observed and the values of coercive force, H(c), at 1.9 K were 12, 8.4, 11, and 8.1 kOe for CoCl(2)(CYpy)(4); Y = 2, 3l, 3b, and 4, respectively. In dynamic magnetic susceptibility experiments, ac magnetic susceptibility data obeyed the Arrhenius law to give U(eff)/k(B) values of 94, 92, 93, and 87 K for CoCl(2)(CYpy)(4); Y = 2, 3l, 3b, and 4, respectively, while the relaxation times for CoCl(2)(CYpy)(4); Y = 2 and 3l, obtained by dc magnetization decay in the range of 3.5-1.9 K slightly deviated downward from Arrhenius plots on cooling. The dynamic magnetic behaviors for CoCl(2)(CYpy)(4) including [CoCl(2)(py)(4)] and CoCl(2)(C1py)(4) suggested that the generated carbenes interacted with the cobalt ion to increase the relaxation time, τ(q), due to the spin quantum tunneling magnetization, which became larger with increasing S(total) of the complex.

Using ILD or ITD Cues for Sound Source Localization and Speech Understanding in a Complex Listening Environment by Listeners With Bilateral and With Hearing-Preservation Cochlear Implants.

PubMed

Loiselle, Louise H; Dorman, Michael F; Yost, William A; Cook, Sarah J; Gifford, Rene H

2016-08-01

To assess the role of interaural time differences and interaural level differences in (a) sound-source localization, and (b) speech understanding in a cocktail party listening environment for listeners with bilateral cochlear implants (CIs) and for listeners with hearing-preservation CIs. Eleven bilateral listeners with MED-EL (Durham, NC) CIs and 8 listeners with hearing-preservation CIs with symmetrical low frequency, acoustic hearing using the MED-EL or Cochlear device were evaluated using 2 tests designed to task binaural hearing, localization, and a simulated cocktail party. Access to interaural cues for localization was constrained by the use of low-pass, high-pass, and wideband noise stimuli. Sound-source localization accuracy for listeners with bilateral CIs in response to the high-pass noise stimulus and sound-source localization accuracy for the listeners with hearing-preservation CIs in response to the low-pass noise stimulus did not differ significantly. Speech understanding in a cocktail party listening environment improved for all listeners when interaural cues, either interaural time difference or interaural level difference, were available. The findings of the current study indicate that similar degrees of benefit to sound-source localization and speech understanding in complex listening environments are possible with 2 very different rehabilitation strategies: the provision of bilateral CIs and the preservation of hearing.

Rub al Khali, Arabia

NASA Image and Video Library

2008-08-08

NASA Terra spacecraft shows the Rub al Khali, one of the largest sand deserts in the world, encompassing most of the southern third of the Arabian Peninsula; it includes parts of Oman, United Arab Emirates, and Yemen.

Towards a global assessment of pyrogenic carbon from vegetation fires

NASA Astrophysics Data System (ADS)

Dittmar, Thorsten; Santín, Cristina; Doerr, Stefan; Kane, Evan; Masiello, Caroline; Ohlson, Mikael; De La Rosa, Jose Maria; Preston, Caroline

2016-04-01

The production of pyrogenic carbon (PyC; a continuum of organic carbon (C) ranging from partially charred biomass and charcoal to soot) is a widely acknowledged C sink, with the latest estimates indicating that ~50% of the PyC produced by vegetation fires potentially sequesters C over centuries. Nevertheless, the quantitative importance of PyC in the global C balance remains contentious, and therefore, PyC is rarely considered in global C cycle and climate studies. Here we examine the robustness of existing evidence and identify the main research gaps in the production, fluxes and fate of PyC from vegetation fires. Much of the previous work on PyC production has focused on selected components of total PyC generated in vegetation fires, likely leading to underestimates. We suggest that global PyC production could be in the range of 116-385 Tg C per year, that is ~0.2-0.6% of the annual terrestrial net primary production. According to our estimations, atmospheric emissions of soot/black C might be a smaller fraction of total PyC (<2%) than previously reported. Research on the fate of PyC in the environment has mainly focused on its degradation pathways, and its accumulation and resilience either in situ (surface soils) or in ultimate sinks (marine sediments). Off-site transport, transformation and PyC storage in intermediate pools are often overlooked, which could explain the fate of a substantial fraction of the PyC mobilized annually. Rivers carry about 25-28 Tg dissolved PyC per year into the ocean where it accumulates in dissolved form over ten-thousands of year to one of the largest PyC pool on Earth. The riverine flux of suspended (particulate) PyC is largely unconstrained to date. We propose new research directions addressing gaps in the global PyC cycle to fully understand the importance of the products of burning in global C cycle dynamics. This presentation is based largely on a recent review by the same group of authors (Santín et al., 2016, Global Change Biology 22, 76-91, doi: 10.1111/gcb.12985).

Head rubbing and licking reinforce social bonds in a group of captive African lions, Panthera leo.

PubMed

Matoba, Tomoyuki; Kutsukake, Nobuyuki; Hasegawa, Toshikazu

2013-01-01

Many social animals have a species-specific repertoire of affiliative behaviours that characterise individualised relationships within a group. To date, however, quantitative studies on intragroup affiliative behaviours in social carnivores have been limited. Here, we investigated the social functions of the two most commonly observed affiliative behaviours in captive African lions (Panthera leo): head rubbing and licking. We conducted behavioural observations on a captive group of lions composed of 7 males and 14 females, and tested hypotheses regarding three social functions: tension reduction, social bonding, and social status expression. Disproportionately frequent male-male and female-to-male head rubbing was observed, while more than 95% of all licking interactions occurred in female-female dyads. In accordance with the social bond hypothesis, and in disagreement with the social status expression hypothesis, both head rubbing and licking interactions were reciprocal. After controlling for spatial association, the dyadic frequency of head rubbing was negatively correlated with age difference while licking was positively correlated with relatedness. Group reunion after daily separation did not affect the frequencies of the affiliative behaviours, which was in disagreement with the predictions from the tension reduction hypothesis. These results support the social bond hypothesis for the functions of head rubbing and licking. Different patterns of affiliative behaviour between the sexes may reflect differences in the relationship quality in each sex or the differential predisposition to licking due to its original function in offspring care.

Estimating dermal transfer from PCB-contaminated porous surfaces.

PubMed

Slayton, T M; Valberg, P A; Wait, A D

1998-06-01

Health risks posed by dermal contact with PCB-contaminated porous surfaces have not been directly demonstrated and are difficult to estimate indirectly. Surface contamination by organic compounds is commonly assessed by collecting wipe samples with hexane as the solvent. However, for porous surfaces, hexane wipe characterization is of limited direct use when estimating potential human exposure. Particularly for porous surfaces, the relationship between the amount of organic material collected by hexane and the amount actually picked up by, for example, a person's hand touch is unknown. To better mimic PCB pickup by casual hand contact with contaminated concrete surfaces, we used alternate solvents and wipe application methods that more closely mimic casual dermal contact. Our sampling results were compared to PCB pickup using hexane-wetted wipes and the standard rubbing protocol. Dry and oil-wetted samples, applied without rubbing, picked up less than 1% of the PCBs picked up by the standard hexane procedure; with rubbing, they picked up about 2%. Without rubbing, saline-wetted wipes picked up 2.5%; with rubbing, they picked up about 12%. While the nature of dermal contact with a contaminated surface cannot be perfectly reproduced with a wipe sample, our results with alternate wiping solvents and rubbing methods more closely mimic hand contact than the standard hexane wipe protocol. The relative pickup estimates presented in this paper can be used in conjunction with site-specific PCB hexane wipe results to estimate dermal pickup rates at sites with PCB-contaminated concrete.

PyMidas: Interface from Python to Midas

NASA Astrophysics Data System (ADS)

Maisala, Sami; Oittinen, Tero

2014-01-01

PyMidas is an interface between Python and MIDAS, the major ESO legacy general purpose data processing system. PyMidas allows a user to exploit both the rich legacy of MIDAS software and the power of Python scripting in a unified interactive environment. PyMidas also allows the usage of other Python-based astronomical analysis systems such as PyRAF.

Synthesis, structure, and characterization of two Zn(II) complex containing two-dimensional bilayer structure

NASA Astrophysics Data System (ADS)

Zhang, Meili; Ren, Yixia; Chen, Xiaoli

2014-10-01

Two new Zn(II) complexes, [Zn2(L)(H2O)3]ṡH2O (1) and [Zn3(HL)2(bpp)2(Hbpp)2]ṡ10H2Oṡ2ClO4 (2) (H4L = cis,cis,cis,cis-1,2,3,4-cyclopentanetracarboxylic acid, bpp = 1,3-bis(4-pyridyl)propane), have been synthesized and characterized by elemental analysis, IR spectroscopy and single-crystal X-ray diffraction techniques. The structure indicates that the complex 1 crystallizes in triclinic, space group Pī, in which, the four carboxylate groups of L ligand adopt μ2-η1:η0, μ2-η1:η1, μ1-η1:η1 coordination modes, respectively, bridging Zn(II) atoms to generate a (4,6)-connected 2D bilayer network. The structure indicates that the complex 2 crystallizes in monoclinic, space group C2/c, in which, three deprotonated carboxylate groups of L ligand adopt uniform μ1-η1:η0 coordination mode linking Zn(II) atoms to form a 1D polymeric ribbon, the bpp ligands further extend such ribbon giving rised to a (3,4)-connected 2D bilayer network. The most striking feature of 1 and 2 is that both of bilayer networks contain 1D solvent channel, where water molecules are located. In additional, luminescent properties of two complexes have also been studied.

Multiple Interactions Drive Adaptor-Mediated Recruitment of the Ubiquitin Ligase Rsp5 to Membrane Proteins In Vivo and In Vitro

PubMed Central

Sullivan, James A.; Lewis, Michael J.; Nikko, Elina

2007-01-01

Recognition of membrane proteins by the Nedd4/Rsp5 ubiquitin ligase family is a critical step in their targeting to the multivesicular body pathway. Some substrates contain “PY” motifs (PPxY), which bind to WW domains in the ligase. Others lack PY motifs and instead rely on adaptors that recruit the ligase to them. To investigate the mechanism of adaptor-mediated ubiquitination, we have characterized the interactions between the adaptor Bsd2, the ubiquitin ligase Rsp5, and the membrane proteins Cps1, Tre1, and Smf1 from Saccharomyces cerevisiae. We have reconstituted adaptor-mediated modification of Cps1 and Tre1 in vitro, and we show that two PY motifs in Bsd2 and two WW domains (WW2 and WW3) in Rsp5 are crucial for this. The binding of a weak noncanonical DMAPSY motif in Bsd2 to WW3 is an absolute requirement for Bsd2 adaptor function. We show that sorting of the manganese transporter Smf1, which requires both Bsd2 and Tre1, depends upon two PY motifs in Bsd2 and one motif in Tre1 but only two WW domains in Rsp5. We suggest that sequential assembly of first a Bsd2/Rsp5 complex, then a Tre1/Bsd2/Rsp5 complex followed by a rearrangement of PY–WW interactions is required for the ubiquitination of Smf1. PMID:17429078

Structure transition in lipids and nucleic acids of tumor cells under anticancer drugs applications

NASA Astrophysics Data System (ADS)

Dovbeshko, G. I.; Repnytska, O. P.; Tryndiak, V. P.; Todor, I. N.

2003-12-01

Interaction of DNA and phospholipids from Carcinoma Guerina resistant and sensitive cells of Wistar line rats with anti-cancer drugs - cis-platin and doxorubicin (DOX) have been studied in vivo and in vitro experiments. Surface enhanced infrared absorption (SEIRA) spectroscopy was applied for registration of conformational changes in DNA and lipids induced by anti-cancer drugs. It has been shown in vivo experiment that doxorubicin influences less structural disordering of the membrane than cis-platin. Cis-platin creates irreversible complex with memebrane phospholipids, strongly interacting with phosophates and carbohydrate chains. Doxorubicin influences the ordering of carbohydrate chains and does not strongly influence phosphate heads. This change seems to be partially reversible. In contrast, in vivo experiment the doxorubicin strongly influences the DNA structure, leading to DNA stabilization and formation of new H-bonds in DNA-doxorubicin complex. We have not registered the interaction of DNA with cis-platin in vivo experiment. Experiment in vitro for cis-platin incubation with phospholipids from cancer cells during 0.5 hour at 37°C has not shown those drastic structural peculiarities that it was observed in vivo experiments.

PySE: Software for extracting sources from radio images

NASA Astrophysics Data System (ADS)

Carbone, D.; Garsden, H.; Spreeuw, H.; Swinbank, J. D.; van der Horst, A. J.; Rowlinson, A.; Broderick, J. W.; Rol, E.; Law, C.; Molenaar, G.; Wijers, R. A. M. J.

2018-04-01

PySE is a Python software package for finding and measuring sources in radio telescope images. The software was designed to detect sources in the LOFAR telescope images, but can be used with images from other radio telescopes as well. We introduce the LOFAR Telescope, the context within which PySE was developed, the design of PySE, and describe how it is used. Detailed experiments on the validation and testing of PySE are then presented, along with results of performance testing. We discuss some of the current issues with the algorithms implemented in PySE and their interaction with LOFAR images, concluding with the current status of PySE and its future development.

Synthesis of Unsupported d(1)-d(x) Oxido-Bridged Heterobimetallic Complexes Containing V(IV): A New Direction for Metal-to-Metal Charge Transfer.

PubMed

Wu, Xinyuan; Huang, Tao; Lekich, Travis T; Sommer, Roger D; Weare, Walter W

2015-06-01

Heterobimetallic complexes composed only of first-row transition metals [(TMTAA)V(IV)═O→M(II)Py5Me2](OTf)2 (TMTAA = 7,16-dihydro-6,8,15,17-tetramethyldibenzo[b,i][1,4,8,11]tetraazacyclotetradecine; Py5Me2 = 2,6-bis(1,1-bis(2-pyridyl)ethyl)pyridine; M = Mn(II), Fe(II), Co(II), Ni(II), Cu(II); OTf = trifluoromethanesulfonate) have been synthesized through a dative interaction between a terminal oxido and M(II) metal centers. This is the first series of V(IV)═O→M(II) heterobimetallic complexes containing an unsupported oxido bridge. Among these five complexes, only V(IV)═O→Fe(II) (3b) has a clear new absorption band upon formation of the dinuclear species (502 nm, ε = 1700 M(-1) cm(-1)). This feature is assigned to a metal-to-metal charge transfer (MMCT) transition from V(IV) to Fe(II), which forms a V(V)-O-Fe(I) excited state. This assignment is supported by electrochemical data, electronic absorption profiles, and resonance Raman spectroscopy and represents the first report of visible-light induced MMCT in a heterobimetallic oxido-bridged molecule where the electron originates on a d(1) metal center.

Ruthenium indenylidene “1st generation” olefin metathesis catalysts containing triisopropyl phosphite

PubMed Central

Guidone, Stefano; Nahra, Fady; Slawin, Alexandra M Z

2015-01-01

Summary The reaction of triisopropyl phosphite with phosphine-based indenylidene pre-catalysts affords “1st generation” cis-complexes. These have been used in olefin metathesis reactions. The cis-Ru species exhibit noticeable differences with the trans-Ru parent complexes in terms of structure, thermal stability and reactivity. Experimental data underline the importance of synergistic effects between phosphites and L-type ligands. PMID:26425210

Weathering of pyrogenic organic matter induces fungal oxidative enzyme response in single culture inoculation experiments.

PubMed

Gibson, Christy; Berry, Timothy D; Wang, Ruzhen; Spencer, Julie A; Johnston, Cliff T; Jiang, Yong; Bird, Jeffrey A; Filley, Timothy R

2016-02-01

The addition of pyrogenic organic matter (PyOM), the aromatic carbon-rich product of the incomplete combustion of plant biomass or fossil fuels, to soil can influence the rate of microbial metabolism of native soil carbon. The interaction of soil heterotrophs with PyOM may be governed by the surficial chemical and physical properties of PyOM that evolve with environmental exposure. We present results of a 36-day laboratory incubation investigating the interaction of a common white-rot fungus, Trametes versicolor, with three forms of 13 C-enriched (2.08 atom% 13 C) PyOM derived from Pinus ponderosa (450 °C): one freshly produced, and two artificially weathered (254 nm, UV light-water treatment and water-leaching alone). Analysis (FTIR, XPS) of the UV-weathered PyOM showed increased aliphatic C-H content and oxidation of aromatic carbon relative to both the original and water-leached PyOM. The addition of both weathered forms of PyOM stimulated (positively primed) fungal respiration of the growth media, while the unaltered PyOM mildly inhibited (negatively primed) respiration. Artificial weathering resulted in higher oxidative (laccase and peroxidase) enzyme activity than unaltered PyOM, possibly the result of a diminished capacity to bind reactive substrates and extracellular enzymes after weathering. However, and contrary to expectations, simple water-leached weathering resulted in a relatively higher enzyme activity and respiration than that of UV-weathering. The 13 C content of respired CO 2 indicated negligible fungal oxidation of PyOM for all treatments, demonstrating the overall low microbial reactivity of this high temperature PyOM. The increased enzymatic and positive priming response of T. versicolor to weathered PyOM highlights the importance of weathering-induced chemistry in controlling PyOM-microbe-soil carbon interactions.

Discovery of African bat polyomaviruses and infrequent recombination in the large T antigen in the Polyomaviridae.

PubMed

Carr, Michael; Gonzalez, Gabriel; Sasaki, Michihito; Ito, Kimihito; Ishii, Akihiro; Hang'ombe, Bernard M; Mweene, Aaron S; Orba, Yasuko; Sawa, Hirofumi

2017-04-01

Bat species represent natural reservoirs for a number of high-consequence human pathogens. The present study investigated the diversity of polyomaviruses (PyVs) in Zambian insectivorous and fruit bat species. We describe the complete genomes from four newly proposed African bat PyV species employing the recently recommended criteria provided by the Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses. A comprehensive phylogenetic and recombination analysis was performed to determine genetic relationships and the distribution of recombination events in PyV from mammalian and avian species. The novel species of PyV from Zambian bats segregated with members of the genera Alphapolyomavirus and Betapolyomavirus, forming monophyletic clades with bat and non-human primate PyVs. Miniopterus schreibersii polyomavirus 1 and 2 segregated in a clade with South American bat PyV species, Old World monkey and chimpanzee PyVs and Human polyomavirus 13 (New Jersey PyV). Interestingly, the newly described Egyptian fruit bat PyV, tentatively named Rousettus aegyptiacus polyomavirus 1, had the highest nucleotide sequence identity to species of PyV from Indonesian fruit bats, and Rhinolophus hildebrandtii polyomavirus 1 was most closely related to New World monkey PyVs. The distribution of recombination events in PyV genomes was non-random: recombination boundaries existed in the intergene region between VP1 and LTAg and also at the 3' end of VP2/3 in the structural genes, whereas infrequent recombination was present within the LTAg gene. These findings indicate that recombination within the LTAg gene has been negatively selected against during polyomaviral evolution and support the recent proposal for taxonomic classification based on LTAg to define novel PyV species.

Towards a global assessment of pyrogenic carbon from vegetation fires.

PubMed

Santín, Cristina; Doerr, Stefan H; Kane, Evan S; Masiello, Caroline A; Ohlson, Mikael; de la Rosa, Jose Maria; Preston, Caroline M; Dittmar, Thorsten

2016-01-01

The production of pyrogenic carbon (PyC; a continuum of organic carbon (C) ranging from partially charred biomass and charcoal to soot) is a widely acknowledged C sink, with the latest estimates indicating that ~50% of the PyC produced by vegetation fires potentially sequesters C over centuries. Nevertheless, the quantitative importance of PyC in the global C balance remains contentious, and therefore, PyC is rarely considered in global C cycle and climate studies. Here we examine the robustness of existing evidence and identify the main research gaps in the production, fluxes and fate of PyC from vegetation fires. Much of the previous work on PyC production has focused on selected components of total PyC generated in vegetation fires, likely leading to underestimates. We suggest that global PyC production could be in the range of 116-385 Tg C yr(-1) , that is ~0.2-0.6% of the annual terrestrial net primary production. According to our estimations, atmospheric emissions of soot/black C might be a smaller fraction of total PyC (<2%) than previously reported. Research on the fate of PyC in the environment has mainly focused on its degradation pathways, and its accumulation and resilience either in situ (surface soils) or in ultimate sinks (marine sediments). Off-site transport, transformation and PyC storage in intermediate pools are often overlooked, which could explain the fate of a substantial fraction of the PyC mobilized annually. We propose new research directions addressing gaps in the global PyC cycle to fully understand the importance of the products of burning in global C cycle dynamics. © 2015 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

NASA Astrophysics Data System (ADS)

Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H.

2016-09-01

Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides.

Purification and characterization of monoclonal antibodies to alpha-linolenic acid.

PubMed

Buffière, F; Cook-Moreau, J; Gualde, N; Rigaud, M

1989-01-01

The covalently linked antigenic complex, bovine serum albumin-alpha-linolenic acid, was used to immunize Balb/c mice against the hapten. Hybridization between splenocytes and the myeloma cell line, P 3 X63 Ag 8,651, resulted in stable clones synthesizing monoclonal antibodies (Mab) that were subsequently purified and characterized. Four Mab (A, B, C, D) were retained and their specificities studied by ELISA. Antibody D only recognized 18-carbon fatty acids having a cis,cis,-cis-1,4,7 unsaturated system in the omega-3 position: it was specific for alpha-linolenic acid. B recognized all fatty acids containing the structure cis,cis,cis-1,4,7-octatriene. A and C recognized polyunsaturated fatty acids with a degree of unsaturation superior to two double bonds.

Phosphatidic Acid Sequesters Sec18p from cis-SNARE Complexes to Inhibit Priming.

PubMed

Starr, Matthew L; Hurst, Logan R; Fratti, Rutilio A

2016-10-01

Yeast vacuole fusion requires the activation of cis-SNARE complexes through priming carried out by Sec18p/N-ethylmaleimide sensitive factor and Sec17p/α-SNAP. The association of Sec18p with vacuolar cis-SNAREs is regulated in part by phosphatidic acid (PA) phosphatase production of diacylglycerol (DAG). Inhibition of PA phosphatase activity blocks the transfer of membrane-associated Sec18p to SNAREs. Thus, we hypothesized that Sec18p associates with PA-rich membrane microdomains before transferring to cis-SNARE complexes upon PA phosphatase activity. Here, we examined the direct binding of Sec18p to liposomes containing PA or DAG. We found that Sec18p preferentially bound to liposomes containing PA compared with those containing DAG by approximately fivefold. Additionally, using a specific PA-binding domain blocked Sec18p binding to PA-liposomes and displaced endogenous Sec18p from isolated vacuoles. Moreover, the direct addition of excess PA blocked the priming activity of isolated vacuoles in a manner similar to chemically inhibiting PA phosphatase activity. These data suggest that the conversion of PA to DAG facilitates the recruitment of Sec18p to cis-SNAREs. Purified vacuoles from yeast lacking the PA phosphatase Pah1p showed reduced Sec18p association with cis-SNAREs and complementation with plasmid-encoded PAH1 or recombinant Pah1p restored the interaction. Taken together, this demonstrates that regulating PA concentrations by Pah1p activity controls SNARE priming by Sec18p. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Determinants of user satisfaction with a Clinical Information System.

PubMed

Palm, Jean-Marc; Colombet, Isabelle; Sicotte, Claude; Degoulet, Patrice

2006-01-01

Clinical Information Systems (CIS) implementation has faced user resistance. Consequently, we aimed to assess the acceptability of an integrated CIS. We designed an electronic survey instrument from two theoretical models (Delone and McLean, and Technology Acceptance Model). Dimensions hypothesized to be determinant of user satisfaction were: user characteristics, CIS use, quality, usefulness, and service quality. The questionnaire was administered to physicians, nurses and medical secretaries of the Georges Pompidou university Hospital (HEGP) in Paris. Answers were obtained from 324 users (93 physicians, 174 nurses, and 57 secretaries). Cronbach's alpha coefficients showed a correct reliability within each dimension. Secretaries and nurses were more satisfied with the CIS than physicians. Except for CIS use, after adjustment for confounders, female gender, perceived CIS quality, usefulness, and service quality were strongly correlated with user satisfaction. This study reinforces the necessity of several models and dimensions to evaluate the acceptability of a complex CIS, with a specific approach for different user profiles.

Program to develop sprayed, plastically deformable compressor shroud seal materials

NASA Technical Reports Server (NTRS)

Schwab, R. C.

1979-01-01

A study of fundamental rub behavior for ten dense sprayed materials and eight current compressor clearance materials has been conducted. A literature survey of a wide variety of metallurgical and thermophysical properties was conducted and correlated to rub behavior. Based on these results, the most promising dense rub material was Cu-9Al. Additional studies on the effects of porosity, incursion rate, blade solidity and ambient temperature were carried out on aluminum bronze (Cu-9Al-1Fe) with and without a 515B Feltmetal underlayer.

Rotor vibration caused by external excitation and rub

NASA Technical Reports Server (NTRS)

Matsushita, O.; Takagi, M.; Kikuchi, K.; Kaga, M.

1982-01-01

For turbomachinery with low natural frequencies, considerations have been recently required for rotor vibrations caused by external forces except unbalance one, such as foundation motion, seismic wave, rub and so forth. Such a forced vibration is investigated analytically and experimentally in the present paper. Vibrations in a rotor-bearing system under a harmonic excitation are analyzed by the modal technique in the case of a linear system including gyroscopic effect. For a nonlinear system a new and powerful quasi-modal technique is developed and applied to the vibration caused by rub.

Evaluation of nitrogen-rich macrocyclic ligands for the chelation of therapeutic bismuth radioisotopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, Justin J.; Ferrier, Maryline; Radchenko, Valery

The use of α-emitting isotopes for radionuclide therapy is a promising treatment strategy for small micro-metastatic disease. The radioisotope ²¹³Bi is a nuclide that has found substantial use for targeted α-therapy (TAT). The relatively unexplored aqueous chemistry of Bi³⁺, however, hinders the development of bifunctional chelating agents that can successfully deliver these Bi radioisotopes to the tumor cells. Here, a novel series of nitrogen-rich macrocyclic ligands is explored for their potential use as Bi-selective chelating agents. The ligands, 1,4,7,10-tetrakis(pyridin-2-ylmethyl)-1,4,7,10-tetraazacyclododecane (L py), 1,4,7,10-tetrakis(3-pyridazylmethyl)-1,4,7,10-tetraazacyclododecane (L pyd), 1,4,7,10-tetrakis(4-pyrimidylmethyl)-1,4,7,10-tetraazacyclododecane (L pyr), and 1,4,7,10-tetrakis(2-pyrazinylmethyl)-1,4,7,10-tetraazacyclododecane (L pz), were prepared by a previously reported method and investigatedmore » here for their abilities to bind Bi radioisotopes. The commercially available and commonly used ligands 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) and N-[ (R)-2-amino-3-( p-isothiocyanato-phenyl)propyl]- trans-(S,S)- cyclohexane-1,2-diamine- N,N,N',N",N"-pentaacetic acid (CHX-A''-DTPA) were also explored for comparative purposes. Radio-thin-layer chromatography (TLC) was used to measure the binding kinetics and stabilities of the complexes formed. The long-lived isotope, ²⁰⁷Bi (t 1/2 = 32 years), was used for these studies. Density functional theory (DFT) calculations were also employed to probe the ligand interactions with Bi³⁺ and the generator parent ion Ac³⁺.In contrast to DOTA and CHX-A''-DTPA, these nitrogen-rich macrocycles selectively chelate Bi³⁺ in the presence of the parent isotope Ac³⁺. Among the four tested, L py was found to exhibit optimal Bi³⁺-binding kinetics and complex stability. L py complexes Bi³⁺ more rapidly than DOTA, yet the resulting complexes are of similar stability. DFT calculations corroborate the experimentally observed selectivity of these ligands for Bi³⁺ over Ac³⁺. Taken together, these data implicate L py as a valuable chelating agent for the delivery of ²¹³Bi. Its selectivity for Bi³⁺ and rapid and stable labeling properties warrant further investigation and biological studies.« less

Evaluation of nitrogen-rich macrocyclic ligands for the chelation of therapeutic bismuth radioisotopes

DOE PAGES

Wilson, Justin J.; Ferrier, Maryline; Radchenko, Valery; ...

2015-05-01

The use of α-emitting isotopes for radionuclide therapy is a promising treatment strategy for small micro-metastatic disease. The radioisotope ²¹³Bi is a nuclide that has found substantial use for targeted α-therapy (TAT). The relatively unexplored aqueous chemistry of Bi³⁺, however, hinders the development of bifunctional chelating agents that can successfully deliver these Bi radioisotopes to the tumor cells. Here, a novel series of nitrogen-rich macrocyclic ligands is explored for their potential use as Bi-selective chelating agents. The ligands, 1,4,7,10-tetrakis(pyridin-2-ylmethyl)-1,4,7,10-tetraazacyclododecane (L py), 1,4,7,10-tetrakis(3-pyridazylmethyl)-1,4,7,10-tetraazacyclododecane (L pyd), 1,4,7,10-tetrakis(4-pyrimidylmethyl)-1,4,7,10-tetraazacyclododecane (L pyr), and 1,4,7,10-tetrakis(2-pyrazinylmethyl)-1,4,7,10-tetraazacyclododecane (L pz), were prepared by a previously reported method and investigatedmore » here for their abilities to bind Bi radioisotopes. The commercially available and commonly used ligands 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) and N-[ (R)-2-amino-3-( p-isothiocyanato-phenyl)propyl]- trans-(S,S)- cyclohexane-1,2-diamine- N,N,N',N",N"-pentaacetic acid (CHX-A''-DTPA) were also explored for comparative purposes. Radio-thin-layer chromatography (TLC) was used to measure the binding kinetics and stabilities of the complexes formed. The long-lived isotope, ²⁰⁷Bi (t 1/2 = 32 years), was used for these studies. Density functional theory (DFT) calculations were also employed to probe the ligand interactions with Bi³⁺ and the generator parent ion Ac³⁺.In contrast to DOTA and CHX-A''-DTPA, these nitrogen-rich macrocycles selectively chelate Bi³⁺ in the presence of the parent isotope Ac³⁺. Among the four tested, L py was found to exhibit optimal Bi³⁺-binding kinetics and complex stability. L py complexes Bi³⁺ more rapidly than DOTA, yet the resulting complexes are of similar stability. DFT calculations corroborate the experimentally observed selectivity of these ligands for Bi³⁺ over Ac³⁺. Taken together, these data implicate L py as a valuable chelating agent for the delivery of ²¹³Bi. Its selectivity for Bi³⁺ and rapid and stable labeling properties warrant further investigation and biological studies.« less

[Economical effectiveness of vaccination of cohort of children aged 2 years against chickenpox in the Russian Federation].

PubMed

Kostinov, M P; Zverev, V V

2012-01-01

Perform calculation of the economical effectiveness of realization of a program of vaccination of children aged 2 years against chickenpox (CP) in the Russian Federation. Data of Federal service on customers rights protection and human well-being surveillance on evaluation of morbidity and losses caused by CP in the Russian Federation in 2008 - 2010 were used. A cohort of children (1 760 000) aged 2 years subject to vaccination against CP in 2011, evaluation of cost of 1 case of the infection, the amount of losses per vaccination of 1 child were approximately determined; analysis of prevented losses by implementation ofvaccination program by using mathematical modeling methods was performed. Without vaccination program in the Russian Federation the cost of losses per 1 case of CP related to hospitalization and outpatient visits as well as temporary disability of one of the parent in various age groups was: for children aged 1 - 2 years--8 333 RUB (Russian rubles), 3 - 6 years--21 171 RUB, 7 - 14 years--21 295 RUB. The cost of vaccination against CP of 1 child including 2 doses of vaccines with physician examination and vaccination procedure would be 1600 RUB. In the case of realization of vaccination program against CP in 2011 of children aged 2 years its cost would be 2 488.9 million RUB. Cost prevention already exceeds the cost of vaccination in 1 age cohort of children at year 2 and in 5 years the amount of prevented losses would exceed 15 billion RUB per 1 vaccinated cohort and would continue to increase steadily. The performed calculations show that vaccination against CP in the Russian Federation is a highly efficient investment. Self-sufficiency of a program implemented in 2011 may be obtained already at the start of year 2 after the realization and by 2016 the net economical benefit would be around 8 milliards RUB.

OCT-based angiography of human dermal microvascular reactions to local stimuli: Implications for increasing capillary blood collection volumes.

PubMed

Men, Shaojie; Wong, Jennifer Manyu; Welch, Emily J; Xu, Jingjiang; Song, Shaozhen; Deegan, Anthony J; Ravichander, Aarthi; Casavant, Benjamin; Berthier, Erwin; Wang, Ruikang K

2018-05-25

To measure and compare microvascular responses within the skin of the upper arm to local stimuli, such as heating or rubbing, through the use of optical coherence tomography angiography (OCTA), and to investigate its impact on blood volume collection. With the use of heat packs or rubbing, local stimulation was applied to the skin of either the left or right upper arm. Data from the stimulated sites were obtained using OCTA comparing pre- and post-stimulation microvascular parameters, such as vessel density, mean vessel diameter, and mean avascular pore size. Additionally, blood was collected using a newly designed collection device and volume was recorded to evaluate the effect of the skin stimulation. Nineteen subjects were recruited for local stimulation study (including rubbing and heating) and 21 subjects for blood drawn study. Of these subjects, 14 agreed to participate in both studies. OCTA was successful in monitoring and measuring minute changes in the microvasculature of the stimulated skin. Compared to baseline, significant changes after local heating and rubbing were respectively found in vessel density (16% [P = 0.0004] and 33% [P < 0.0001] increase), mean vessel diameter (14% and 11% increase) and mean avascular pore size (5% [P = 0.0068] and 8% [P = 0.0005] decrease) after stimulations. A gradual recovery was recorded for each parameter, with no difference being measured after 30 minutes. Blood collection volumes significantly increased after stimulations of heating (48% increase; P = 0.049) and rubbing (78% increase; P = 0.048). Significant correlations were found between blood volume and microvascular parameters except mean avascular pore size under the heating condition. OCTA can provide important information regarding microvascular adaptations to local stimuli. With that, both heating and rubbing of the skin have positive effects on blood collection capacity, with rubbing having the most significant effect. Lasers Surg. Med. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

76 FR 33367 - Employment and Training Administration Program Year (PY) 2011 Allotments for the Workforce...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-08

... PY 2010 PY 2011 Difference % Diff Total ....... $52,230,420 $52,125,959 ($104,461) -0.2% AL Inter... State Grantee Name Type PY 2010 PY 2011 Difference % Diff Total ....... $13,861,035 $12,388,708 ($1,472,327) -10.60% AL Inter-Tribal Council of Alabama. ....... $5,098.00 $4,556.00 ($542) -10.60% AK...

The global pyrogenic carbon cycle and its impact on the level of atmospheric CO2 over past and future centuries.

PubMed

Landry, Jean-Sébastien; Matthews, H Damon

2017-08-01

The incomplete combustion of vegetation and dead organic matter by landscape fires creates recalcitrant pyrogenic carbon (PyC), which could be consequential for the global carbon budget if changes in fire regime, climate, and atmospheric CO 2 were to substantially affect gains and losses of PyC on land and in oceans. Here, we included global PyC cycling in a coupled climate-carbon model to assess the role of PyC in historical and future simulations, accounting for uncertainties through five sets of parameter estimates. We obtained year-2000 global stocks of (Central estimate, likely uncertainty range in parentheses) 86 (11-154), 47 (2-64), and 1129 (90-5892) Pg C for terrestrial residual PyC (RPyC), marine dissolved PyC, and marine particulate PyC, respectively. PyC cycling decreased atmospheric CO 2 only slightly between 1751 and 2000 (by 0.8 Pg C for the Central estimate) as PyC-related fluxes changed little over the period. For 2000 to 2300, we combined Representative Concentration Pathways (RCPs) 4.5 and 8.5 with stable or continuously increasing future fire frequencies. For the increasing future fire regime, the production of new RPyC generally outpaced the warming-induced accelerated loss of existing RPyC, so that PyC cycling decreased atmospheric CO 2 between 2000 and 2300 for most estimates (by 4-8 Pg C for Central). For the stable fire regime, however, PyC cycling usually increased atmospheric CO 2 (by 1-9 Pg C for Central), and only the most extreme choice of parameters maximizing PyC production and minimizing PyC decomposition led to atmospheric CO 2 decreases under RCPs 4.5 and 8.5 (by 5-8 Pg C). Our results suggest that PyC cycling will likely reduce the future increase in atmospheric CO 2 if landscape fires become much more frequent; however, in the absence of a substantial increase in fire frequency, PyC cycling might contribute to, rather than mitigate, the future increase in atmospheric CO 2 . © 2016 John Wiley & Sons Ltd.

Chiroptical methods in a wide wavelength range for obtaining Ln3+ complexes with circularly polarized luminescence of practical interest.

PubMed

Górecki, Marcin; Carpita, Luca; Arrico, Lorenzo; Zinna, Francesco; Di Bari, Lorenzo

2018-05-29

We studied enantiopure chiral trivalent lanthanide (Ln3+ = La3+, Sm3+, Eu3+, Gd3+, Tm3+, and Yb3+) complexes with two fluorinated achiral tris(β-diketonate) ligands (HFA = hexafluoroacetylacetonate and TTA = 2-thenoyltrifluoroacetonate), incorporating a chiral bis(oxazolinyl)pyridine (PyBox) unit as a neutral ancillary ligand, by the combined use of optical and chiroptical methods, ranging from UV to IR both in absorption and circular dichroism (CD), and including circularly polarized luminescence (CPL). Ultimately, all the spectroscopic information is integrated into a total and a chiroptical super-spectrum, which allows one to characterize a multidimensional chemical space, spanned by the different Ln3+ ions, the acidity and steric demand of the diketone and the chirality of the PyBox ligand. In all cases, the Ln3+ ions endow the systems with peculiar chiroptical properties, either allied to f-f transitions or induced by the metal onto the ligand. In more detail, we found that Sm3+ complexes display interesting CPL features, which partly superimpose and partly integrate the more common Eu3+ properties. Especially, in the context of security tags, the pair Sm/Eu may be a winning choice for chiroptical barcoding.

Status of Seal Development at Technetics

NASA Astrophysics Data System (ADS)

Chappel, Doug

2002-10-01

Technetics has recently reported results for blade tip seal rub characteristics. Expanding on this work, Technetics will share rub characteristics for knife edge abradable seal systems typical of those found at vane inner air seal and shaft seal locations.

Gas Chromatographic Determination of Methyl Salicylate in Rubbing Alcohol: An Experiment Employing Standard Addition.

ERIC Educational Resources Information Center

Van Atta, Robert E.; Van Atta, R. Lewis

1980-01-01

Provides a gas chromatography experiment that exercises the quantitative technique of standard addition to the analysis for a minor component, methyl salicylate, in a commercial product, "wintergreen rubbing alcohol." (CS)

DNA Adduct Formation from Metabolic 5'-Hydroxylation of the Tobacco-Specific Carcinogen N'-Nitrosonornicotine in Human Enzyme Systems and in Rats.

PubMed

Zarth, Adam T; Upadhyaya, Pramod; Yang, Jing; Hecht, Stephen S

2016-03-21

N'-Nitrosonornicotine (NNN) is carcinogenic in multiple animal models and has been evaluated as a human carcinogen. NNN can be metabolized by cytochrome P450s through two activation pathways: 2'-hydroxylation and 5'-hydroxylation. While most previous studies have focused on 2'-hydroxylation in target tissues of rats, available evidence suggests that 5'-hydroxylation is a major activation pathway in human enzyme systems, in nonhuman primates, and in target tissues of some other rodent carcinogenicity models. In the study reported here, we investigated DNA damage resulting from NNN 5'-hydroxylation by quantifying the adduct 2-(2-(3-pyridyl)-N-pyrrolidinyl)-2'-deoxyinosine (py-py-dI). In rats treated with NNN in the drinking water (7-500 ppm), py-py-dI was the major DNA adduct resulting from 5'-hydroxylation of NNN in vivo. Levels of py-py-dI in the lung and nasal cavity were the highest, consistent with the tissue distribution of CYP2A3. In rats treated with (S)-NNN or (R)-NNN, the ratios of formation of (R)-py-py-dI to (S)-py-py-dI were not the expected mirror image, suggesting that there may be a carrier for one of the unstable intermediates formed upon 5'-hydroxylation of NNN. Rat hepatocytes treated with (S)- or (R)-NNN or (2'S)- or (2'R)-5'-acetoxyNNN exhibited a pattern of adduct formation similar to that of live rats. In vitro studies with human liver S9 fraction or human hepatocytes incubated with NNN (2-500 μM) demonstrated that py-py-dI formation was greater than the formation of pyridyloxobutyl-DNA adducts resulting from 2'-hydroxylation of NNN. (S)-NNN formed more total py-py-dI adducts than (R)-NNN in human liver enzyme systems, which is consistent with the critical role of CYP2A6 in the 5'-hydroxylation of NNN in human liver. The results of this study demonstrate that the major DNA adduct resulting from NNN metabolism by human enzymes is py-py-dI and provide potentially important new insights into the metabolic activation of NNN in rodents and humans.

PyGPlates - a GPlates Python library for data analysis through space and deep geological time

NASA Astrophysics Data System (ADS)

Williams, Simon; Cannon, John; Qin, Xiaodong; Müller, Dietmar

2017-04-01

A fundamental consideration for studying the Earth through deep time is that the configurations of the continents, tectonic plates, and plate boundaries are continuously changing. Within a diverse range of fields including geodynamics, paleoclimate, and paleobiology, the importance of considering geodata in their reconstructed context across previous cycles of supercontinent aggregation, dispersal and ocean basin evolution is widely recognised. Open-source software tools such as GPlates provide paleo-geographic information systems for geoscientists to combine a wide variety of geodata and examine them within tectonic reconstructions through time. The availability of such powerful tools also brings new challenges - we want to learn something about the key associations between reconstructed plate motions and the geological record, but the high-dimensional parameter space is difficult for a human being to visually comprehend and quantify these associations. To achieve true spatio-temporal data-mining, new tools are needed. Here, we present a further development of the GPlates ecosystem - a Python-based tool for geotectonic analysis. In contrast to existing GPlates tools that are built around a graphical user interface (GUI) and interactive visualisation, pyGPlates offers a programming interface for the automation of quantitative plate tectonic analysis or arbitrary complexity. The vast array of open-source Python-based tools for data-mining, statistics and machine learning can now be linked to pyGPlates, allowing spatial data to be seamlessly analysed in space and geological "deep time", and with the ability to spread large computations across multiple processors. The presentation will illustrate a range of example applications, both simple and advanced. Basic examples include data querying, filtering, and reconstruction, and file-format conversions. For the innovative study of plate kinematics, pyGPlates has been used to explore the relationships between absolute plate motions, subduction zone kinematics, and mid-ocean ridge migration and orientation through deep time; to investigate the systematics of continental rift velocity evolution during Pangea breakup; and to make connections between kinematics of the Andean subduction zone and ore deposit formation. To support the numerical modelling community, pyGPlates facilitates the connection between tectonic surface boundary conditions contained within plate tectonic reconstructions (plate boundary configurations and plate velocities) and simulations such as thermo-mechanical models of lithospheric deformation and mantle convection. To support the development of web-based applications that can serve the wider geoscience community, we will demonstrate how pyGPlates can be combined with other open-source tools to serve alternative reconstructions together with a diverse array of reconstructed data sets in a self-consistent framework over the internet. PyGPlates is available to the public via the GPlates web site and contains comprehensive documentation covering installation on Windows/Mac/Linux platforms, sample code, tutorials and a detailed reference of pyGPlates functions and classes.

Microbial adherence to cosmetic contact lenses.

PubMed

Chan, Ka Yin; Cho, Pauline; Boost, Maureen

2014-08-01

To investigate whether cosmetic contact lenses (CCL) with surface pigments affect microbial adherence. Fifteen brands of CCL were purchased from optical, non-optical retail outlets, and via the Internet. A standardized rub-off test was performed on each CCL (five lenses per brand) to confirm the location of the pigments. The rub-off test comprised gentle rubbing on the surfaces of each CCL with wetted cotton buds for a maximum of 20 rubs per surface. A new set of CCL (five lenses per brand) were incubated in Pseudomonas aeruginosa overnight. Viable counts of adhered bacteria were determined by the number of colony-forming units (CFU) on agar media on each lens. The adherence of P. aeruginosa as well as Staphylococcus aureus and Serratia marcescens to three brands of CCL (A-C) (five lenses per brand) were also compared to their adherences on their clear counterparts. Only two of the 15 brands of CCL tested (brands B and C) had pigments that did not detach with the rub-off test. The remaining 13 brands of CCL all failed the rub-off test and these lenses showed higher P. aeruginosa adherence (8.7 × 10(5)-1.9 × 10(6) CFU/lens). Brands B and C lenses showed at least six times less bacterial adhesion than the other 13 brands. Compared to their clear counterparts, bacterial adherence to brands B and C lenses did not differ significantly, whereas brand A lenses showed significantly higher adherence. Surface pigments on CCL resulted in significantly higher bacterial adherence. Copyright © 2013 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

Aspen height, stem-girth and survivorship in an area of high ungulate use

USGS Publications Warehouse

Keigley, R.B.; Frisina, M.R.

2008-01-01

An increase in ungulate population size potentially exposes aspen suckers, saplings, and trees to increased use. This study examined how stem height and girth influenced the selection of stems by ungulates for browsing, rubbing, and gnawing, and reconstructed the history of ungulate use for the study area. Transects were run through each of three aspen clones growing in southwestern Montana to determine height, circumference, and the surface area from which bark was totally and partially removed by rubbing and gnawing. Stems 20-250 cm tall were browsed. Stems 2-13 cm diameter were preferentially selected for rubbing and gnawing. The area of totally removed bark on dead saplings was twice the area of removed bark on live stems of similar diameter, suggesting that bark removal played a major role in the death of some stems. Based on an analysis of stem height and age, ungulate browsing was inferred to have increased from a light-to-moderate level to an intense level in 1991. The depth of scars was used to date scarring events. An increase in rubbing and gnawing was determined to have occurred about 1985. We concluded that elk were primarily responsible for the observed impacts. The combined effect of rubbing, gnawing, and browsing affects a broader span of ages compared to the effect of browsing alone. If prescribed fire is used to rejuvenate aspen stands, the resulting young stems should be protected from heavy browsing, rubbing and gnawing until they reach about 13 cm diameter and have grown out of the browse zone.

[Development of alternative to animal experiment in evaluation of skin irritation caused by alcohol-based hand rubs].

PubMed

Yamamoto, Nobuyuki; Miyamoto, Koji; Katoh, Masakazu

2010-08-01

Alcohol-based hand rubs are widely used for infection control in clinical practice. However, it is known that frequent use of the alcohol-based hand rubs may cause skin irritation. To predict the skin irritation in human, animal experiments are quite useful. Especially, the Draize Test using rabbits is suitable for this purpose because their skin is highly sensitive. On the other hand, the development of alternative to animal experiments is important not only from the viewpoint of ethical aspects but also from the efficient research and development. Reconstructed human epidermis (RhE) was developed as a human skin equivalent model in vitro, and has been applied to the evaluation of skin irritation. But the RhE has not been utilized for the evaluation of alcohol-based hand rubs because of the high skin permeability and cytotoxicity of alcohols. The aim of this study was to develop a new method using the RhE in evaluation of skin irritation caused by alcohol-based hand rubs. The authors propose an experimental technique named "Skin model blowing method (SMBM)" consisting of the sequential procedure as follows; applying small amount of testing sample on RhE, blow-dry, post incubation, and cell viability measurement. According to the SMBM, the skin irritation caused by alcohol-based hand rubs could be evaluated under the similar condition of their actual use. It was found that a high correlation existed between the cell viability obtained from SMBM and the skin irritation index in rabbit which had been reported previously.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jonathan Helmus, Scott Collis

The Python-ARM Radar Toolkit (Py-ART) is a collection of radar quality control and retrieval codes which all work on two unifying Python objects: the PyRadar and PyGrid objects. By building ingests to several popular radar formats and then abstracting the interface Py-ART greatly simplifies data processing over several other available utilities. In addition Py-ART makes use of Numpy arrays as its primary storage mechanism enabling use of existing and extensive community software tools.

Regio- and Stereochemical Control in Ocimene Polymerization by Half-Sandwich Rare-Earth Metal Dialkyl Complexes.

PubMed

Peng, Deqian; Du, Gaixia; Zhang, Pengfei; Yao, Bo; Li, Xiaofang; Zhang, Shaowen

2016-06-01

The polymerization of ocimene has been first achieved by half-sandwich rare-earth metal dialkyl complexes in combination with activator and Al(i) Bu3 . The regio- and stereoselectivity in the ocimene polymerization can be controlled by tuning the cyclopentadienyl ligand and the central metal of the complex. The chiral cyclopentadienyl-ligated Sc complex 1 prepares syndiotactic cis-1,4-polyocimene (cis-1,4-selectivity up to 100%, rrrr = 100%), while the corresponding Lu, Y, and Dy complexes 2-4 and the achiral pentamethylcyclopentadienyl Sc, Lu, and Y complexes 5-7 afford isotactic trans-1,2-polyocimenes (trans-1,2-selectivity up to 100%, mm = 100%). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Platinum(IV)-nitroxyl complexes as possible candidates to circumvent cisplatin resistance in RT112 bladder cancer cells.

PubMed

Cetraz, Maria; Sen, Vasily; Schoch, Sarah; Streule, Karolin; Golubev, Valery; Hartwig, Andrea; Köberle, Beate

2017-02-01

The therapeutic efficacy of the anticancer drug cisplatin is limited by the development of resistance. We therefore investigated newly synthesized platinum-nitroxyl complexes (PNCs) for their potential to circumvent cisplatin resistance. The complexes used were PNCs with bivalent cis-Pt II (R · NH 2 )(NH 3 )Cl 2 and cis-Pt II (DAPO)Ox and four-valent platinum cis,trans,cis-Pt IV (R · NH 2 )(NH 3 )(OR) 2 Cl 2 and cis,trans,cis-Pt IV (DAPO)(OR) 2 Ox, where R · are TEMPO or proxyl nitroxyl radicals, DAPO is trans-3,4-diamino-2,2,6,6-tetramethylpiperidine-1-oxyl, and OR and Ox are carboxylato and oxalato ligands, respectively. The complexes were characterized by spectroscopic methods, HPLC, log P ow data and elemental analysis. We studied intracellular platinum accumulation, DNA platination and cytotoxicity upon treatment with the PNCs in a model system of the bladder cancer cell line RT112 and its cisplatin-resistant subline RT112-CP. Platinum accumulation and DNA platination were similar in RT112 and RT112-CP cells for both bivalent and four-valent PNCs, in contrast to cisplatin for which a reduction in intracellular accumulation and DNA platination was observed in the resistant subline. The PNCs were found to platinate DNA in relation to the length of their axial RO-ligands. Furthermore, the PNCs were increasingly toxic in relation to the elongation of their axial RO-ligands, with similar toxicities in RT112 and its cisplatin-resistant subline. Using a cell-free assay, we observed induction of oxidative DNA damage by cisplatin but not PNCs suggesting that cisplatin exerts its toxic action by platination and oxidative DNA damage, while cells treated with PNCs are protected against oxidatively induced lesions. Altogether, our study suggests that PNCs may provide a more effective treatment for tumors which have developed resistance toward cisplatin.

Photoswitching a Molecular Catalyst to Regulate CO 2 Hydrogenation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Priyadarshani, Nilusha; Ginovska-Pangovska, Bojana; Bays, J. Timothy

2015-07-24

Inspired by nature’s ability to regulate catalysis using physiological stimuli, azobenzene was incorporated into Rh(bis)diphosphine CO 2 hydrogenation catalysts to photoinitiate structural changes to modulate the resulting catalytic activity. The rhodium bound diphosphine ligands (P(Ph 2)-CH 2-N(R) CH 2-P(Ph2)) contain the terminal amine of a non-natural amino acid, either β-alanine (β-Ala) or γ-aminobutyric acid (GABA). For both β-ala and GABA containing complexes, the carboxylic acids of the amino acids were coupled to the amines of diaminoazobenzene, creating a rhodium bound trans-spanning tetraphosphine complex. The photo-induced cis-trans isomerization of the azobenzene-containing complexes imposes structural changes on these complexes, as evidenced bymore » 1H NMR. We found that the CO 2 hydrogenation activity for the β-ala bound Rh complex is 40% faster with azobenzene in the cis configuration (16 s -1) than in the trans conformation (11 s -1), while the γ-aminobutyric acid containing Rh complex has the same rate (~17 s -1) in either the cis or the trans configuration at 27 °C. The corresponding complexes without the attached azobenzene were also prepared, characterized, and catalytically tested for comparison, and have rates of 30 s -1. Computational studies were undertaken to evaluate the difference in rate between the cis and trans isomers for the β-Ala bound Rh complex, and revealed major structural changes between all cis and trans structures, but only minor structural changes that would be unique to the β-Ala bound Rh complex. We postulate that the slower rate of the azobenzene-containing β-Ala bound Rh complex is due to subtle changes in the bite angle arising from steric strain due to the trans-spanning azobenzene, altering hydricity and consequently rate. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for the DOE by Battelle. A portion of this research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Imidazopyridine/Pyrrole and hydroxybenzimidazole/pyrrole pairs for DNA minor groove recognition.

PubMed

Renneberg, Dorte; Dervan, Peter B

2003-05-14

The DNA binding properties of fused heterocycles imidazo[4,5-b]pyridine (Ip) and hydroxybenzimidazole (Hz) paired with pyrrole (Py) in eight-ring hairpin polyamides are reported. The recognition profile of Ip/Py and Hz/Py pairs were compared to the five-membered ring pairs Im/Py and Hp/Py on a DNA restriction fragment at four 6-base pair recognition sites which vary at a single position 5'-TGTNTA-3', where N = G, C, T, A. The Ip/Py pair distinguishes G.C from C.G, T.A, and A.T, and the Hz/Py pair distinguishes T.A from A.T, G.C, and C.G, affording a new set of heterocycle pairs to target the four Watson-Crick base pairs in the minor groove of DNA.

4-Pyridone-3-carboxamide-1-β-D-ribonucleoside triphosphate (4PyTP), a novel NAD metabolite accumulating in erythrocytes of uremic children: a biomarker for a toxic NAD analogue in other tissues?

PubMed

Synesiou, Elena; Fairbanks, Lynnette D; Simmonds, H Anne; Slominska, Ewa M; Smolenski, Ryszard T; Carrey, Elizabeth A

2011-06-01

We have identified a novel nucleotide, 4-pyridone 3/5-carboxamide ribonucleoside triphosphate (4PyTP), which accumulates in human erythrocytes during renal failure. Using plasma and erythrocyte extracts obtained from children with chronic renal failure we show that the concentration of 4PyTP is increased, as well as other soluble NAD(+) metabolites (nicotinamide, N(1)-methylnicotinamide and 4Py-riboside) and the major nicotinamide metabolite N(1)-methyl-2-pyridone-5-carboxamide (2PY), with increasing degrees of renal failure. We noted that 2PY concentration was highest in the plasma of haemodialysis patients, while 4PyTP was highest in erythrocytes of children undergoing peritoneal dialysis: its concentration correlated closely with 4Py-riboside, an authentic precursor of 4PyTP, in the plasma. In the dialysis patients, GTP concentration was elevated: similar accumulation was noted previously, as a paradoxical effect in erythrocytes during treatment with immunosuppressants such as ribavirin and mycophenolate mofetil, which deplete GTP through inhibition of IMP dehydrogenase in nucleated cells such as lymphocytes. We predict that 4Py-riboside and 4Py-nucleotides bind to this enzyme and alter its activity. The enzymes that regenerate NAD(+) from nicotinamide riboside also convert the drugs tiazofurin and benzamide riboside into NAD(+) analogues that inhibit IMP dehydrogenase more effectively than the related ribosides: we therefore propose that the accumulation of 4PyTP in erythrocytes during renal failure is a marker for the accumulation of a related toxic NAD(+) analogue that inhibits IMP dehydrogenase in other cells.

Fire severity alters the distribution of pyrogenic carbon stocks across ecosystem pools in a Californian mixed-conifer forest

NASA Astrophysics Data System (ADS)

Maestrini, Bernardo; Alvey, Erin C.; Hurteau, Matthew D.; Safford, Hugh; Miesel, Jessica R.

2017-09-01

Pyrogenic carbon (PyC) is hypothesized to play an important role in the carbon (C) cycle due to its resistance to decomposition; however, much uncertainty still exists regarding the stocks of PyC that persist on-site after the initial erosion in postfire forests. Therefore, understanding how fire characteristics influence PyC stocks is vital, particularly in the context of California forests for which an increase of high-severity fires is predicted over the next decades. We measured forest C and persistent PyC stocks in areas burned by low-to-moderate and high-severity fire, as well as in adjacent unburned areas in a California mixed-conifer forest, 2 to 3 years after wildfire. We measured C and PyC stocks in the following compartments: standing trees, downed wood, forest floor, and mineral soil (0-5 cm), and we identified PyC using the weak nitric acid digestion method. We found that the total stock of PyC did not differ among fire severity classes (overall mean 248 ± 30 g C m-2); however, fire severity influenced the distribution of PyC in the individual compartments. Areas burned by high-severity fire had 2.5 times more PyC stocked in the coarse woody debris (p < 0.05), 3.3 times more PyC stocked in standing trees (p < 0.05), and a lower PyC stock in the forest floor (-22%, p < 0.05) compared to low-to-moderate fire severity areas. These results have important implications for the permanence time of PyC, which is putatively higher in standing trees and coarse woody debris compared to the forest floor, where it is susceptible to rapid losses through erosion.

Landform Position and Combustion Temperature as Controls of Decomposition of Pyrogenic Organic Matter

NASA Astrophysics Data System (ADS)

Abney, R.; Berhe, A. A.

2016-12-01

Pyrogenic organic matter (PyOM) is the material left behind after incomplete combustion, which includes a spectrum of materials ranging from ash to charred biomass. Early research on PyOM assumed that it served as an inert carbon (C) pool within the soil. However, recent research has demonstrated that the decomposition of PyOM occurs on much shorter time scales. Even so, PyOM can serve as a C sink within the soil, and it can alter many soil properties. This study investigates the roles of both combustion temperature and landform position on decomposition of PyOM. Bark from Pinus jeffreyi was charred at three temperatures (200ºC, 350ºC, and 500ºC) to create PyOM, and this PyOM was incorporated into soil from two landform positions (eroding hillslope and deposition). Many recent studies on the decomposition of PyOM have utilized wood or agricultural byproducts as source material for PyOM, however bark experiences much of the effects of combustion, and it has received little to no research attention. Decomposition was measured via CO2 production from the soil and bark PyOM mixtures over an incubation period of six months. Microbial biomass was also measured throughout the incubation. The soil and PyOM mixtures were analyzed for elemental C and nitrogen, along with their stable isotopes, immediately after each gas measurement. We expect that the bark charred at higher temperatures will decompose slower than the bark charred at lower temperatures. We also expect that the bark incorporated into the depositional soil will decompose faster than the bark incorporated into the eroding soil. Several studies have already illustrated that landform position plays a critical role in controlling C storage and organic matter breakdown, however this has yet to be investigated with PyOM. Understanding the controls on PyOM breakdown is critical for better managing soils and the global C cycle.

Automatic Parallelization of Numerical Python Applications using the Global Arrays Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daily, Jeffrey A.; Lewis, Robert R.

2011-11-30

Global Arrays is a software system from Pacific Northwest National Laboratory that enables an efficient, portable, and parallel shared-memory programming interface to manipulate distributed dense arrays. The NumPy module is the de facto standard for numerical calculation in the Python programming language, a language whose use is growing rapidly in the scientific and engineering communities. NumPy provides a powerful N-dimensional array class as well as other scientific computing capabilities. However, like the majority of the core Python modules, NumPy is inherently serial. Using a combination of Global Arrays and NumPy, we have reimplemented NumPy as a distributed drop-in replacement calledmore » Global Arrays in NumPy (GAiN). Serial NumPy applications can become parallel, scalable GAiN applications with only minor source code changes. Scalability studies of several different GAiN applications will be presented showing the utility of developing serial NumPy codes which can later run on more capable clusters or supercomputers.« less

Relativistic effects in iron-, ruthenium-, and osmium porphyrins

NASA Astrophysics Data System (ADS)

Liao, Meng-Sheng; Scheiner, Steve

2002-12-01

Nonrelativistic and relativistic DFT calculations are performed on four-coordinate metal porphyrins MP and their six-coordinate adducts MP(py) 2 and MP(py)(CO) (py=pyridine) with M=Fe, Ru, and Os. The electronic structures of the MPs are investigated by considering all possible low-lying states with different configurations of nd-electrons. FeP and OsP have a 3A2 g ground state, while this state is nearly degenerate with 3Eg for RuP. Without relativistic corrections, the ground states of both RuP and OsP would be 3Eg. For the six-coordinate adducts with py and CO, the strong-field axial ligands raise the energy of the M d z2-orbital, thereby making the M II ion diamagnetic. The calculated redox properties of MP(py) 2 and MP(py)(CO) are in agreement with experiment. The difference between RuP(py)(CO) and OsP(py)(CO), in terms of site of oxidation, is due to relativistic effects.

Anchoring energy of photo-sensitive polyimide alignment film containing methoxy cinnamate

NASA Astrophysics Data System (ADS)

Kim, Suyoung; Shin, Sung Eui; Shin, DongMyung

2010-02-01

Photosensitive polyimide containing 2-methoxy cinnamate was synthesized for photo-alignment layer of liquid crystals (LCs). 2-Methoxy cinnamic acid was confirmed photo-sensitive material by linearly polarized UV light. We studied that effect of polarized UV light on rubbed polyimide film. Anchoring energy of liquid crystal with aligning surface was measured. Irradiation of depolarized UV light on rubbed Polyimide film suppressed effective anchoring energy. Linearly polarized UV light on rubbed polyimide film controlled anchoring energy effectively. Polyimide film containing 2-methoxy cinnamate can control the photo-alignment layer easily due to its photo-sensitivity.

New insights into the burden and costs of multiple sclerosis in Europe: Results for Russia.

PubMed

Boyko, Alexey; Kobelt, Gisela; Berg, Jenny; Boyko, Olga; Popova, Ekaterina; Capsa, Daniela; Eriksson, Jennifer

2017-08-01

In order to assess the value of management strategies in multiple sclerosis (MS), outcome data have to be combined with cost data. This, in turn, requires that cost data be regularly updated. This study is part of a cross-sectional retrospective study in 16 countries collecting current data on resource consumption, work capacity and health-related quality of life (HQoL). Descriptive analyses are presented by level of severity; costs are estimated in the societal perspective, in RUB 2015. A total of 208 patients (mean age: 38.5 years) participated in the Russian study; 97% were below retirement age, and of these, 49% were employed. MS was reported to affect productivity at work in 63% of patients. Overall, 87% and 41% of patients felt that fatigue and cognition were a problem. The mean utility and costs were 0.769 and 578,000 RUB at Expanded Disability Status Scale (EDSS) 0-3, 0.509 and 826,000 RUB at EDSS 4-6.5, and 0.071 and 1,013,000 RUB at EDSS 7-9. The average cost of a relapse was 33,000 RUB. This study illustrates the burden of MS on Russian patients and provides current data that are important for developing health policies.

The Interacting controls of pyrolysis temperature and plant taxa on pyrogenic organic matter stability and decomposition in a Northern Michigan forest soil

NASA Astrophysics Data System (ADS)

Gibson, C. D.; Filley, T. R.; Bird, J. A.; Hatton, P. J.; Stark, R. E.; Nadelhoffer, K. J.

2017-12-01

Pyrogenic organic matter (PyOM) produced during forest fires is considered a large sink of stable soil organic matter (SOM) in boreal-temperate forest ecotones, where fire frequency and intensity is growing with changing climate. Understanding how changes in fire regime and predicted shifts in plant taxa will interact to affect PyOM dynamics in soil is imperative to assessing the impact of climate change on SOM maintenance. The stability of PyOM in soil may be co-determined by the physiochemical structure imparted on PyOM during pyrolysis and by its initial taxa-dependent wood chemistry and anatomy. To determine PyOM-C turnover rates in soil, we followed the fate of 13C-enriched wood or PyOM (200, 300, 450, or 600°C) derived from red maple (RM) or jack pine (JP) wood in soil from a recently burned forest in northern Michigan, USA. We found that pyrolysis temperature-controlled physiochemical changes influenced, with threshold dynamics, PyOM stability resulting in mean residence times of 2 (PyOM 200°C) to 450 years for both taxa, confirming that most PyOM (<600°C) turns over on the century, not millennial time scale. Water leachable C, carbohydrate and non-lignin phenol content correlated positively with early PyOM-C mineralization for both JP and RM, but the pyrolysis temperature at which this interaction was strongest differed with taxa reflecting the difference in thermal transition in which carbonization begins (300°C for JP and 450°C for RM). In contrast to previous studies, the addition of sucrose suggests that a co-metabolism mechanism of PyOM decomposition is minor in this soil. Our results show that while the first order control on PyOM stability in this soil is pyrolysis temperature, wood taxa did affect PyOM C MRT, in part due to differences in the amount of water soluble C released by PyOM during the initial decomposition dynamics in soil.

Clinical Information Systems as the Backbone of a Complex Information Logistics Process: Findings from the Clinical Information Systems Perspective for 2016.

PubMed

Hackl, W O; Ganslandt, T

2017-08-01

Objective: To summarize recent research and to propose a selection of best papers published in 2016 in the field of Clinical Information Systems (CIS). Method: The query used to retrieve the articles for the CIS section of the 2016 edition of the IMIA Yearbook of Medical Informatics was reused. It again aimed at identifying relevant publications in the field of CIS from PubMed and Web of Science and comprised search terms from the Medical Subject Headings (MeSH) catalog as well as additional free text search terms. The retrieved articles were categorized in a multi-pass review carried out by the two section editors. The final selection of candidate papers was then peer-reviewed by Yearbook editors and external reviewers. Based on the review results, the best papers were then chosen at the selection meeting with the IMIA Yearbook editorial board. Text mining, term co-occurrence mapping, and topic modelling techniques were used to get an overview on the content of the retrieved articles. Results: The query was carried out in mid-January 2017, yielding a consolidated result set of 2,190 articles published in 921 different journals. Out of them, 14 papers were nominated as candidate best papers and three of them were finally selected as the best papers of the CIS field. The content analysis of the articles revealed the broad spectrum of topics covered by CIS research. Conclusions: The CIS field is multi-dimensional and complex. It is hard to draw a well-defined outline between CIS and other domains or other sections of the IMIA Yearbook. The trends observed in the previous years are progressing. Clinical information systems are more than just sociotechnical systems for data collection, processing, exchange, presentation, and archiving. They are the backbone of a complex, trans-institutional information logistics process. Georg Thieme Verlag KG Stuttgart.

ScrumPy: metabolic modelling with Python.

PubMed

Poolman, M G

2006-09-01

ScrumPy is a software package used for the definition and analysis of metabolic models. It is written using the Python programming language that is also used as a user interface. ScrumPy has features for both kinetic and structural modelling, but the emphasis is on structural modelling and those features of most relevance to analysis of large (genome-scale) models. The aim is at describing ScrumPy's functionality to readers with some knowledge of metabolic modelling, but implementation, programming and other computational details are omitted. ScrumPy is released under the Gnu Public Licence, and available for download from http://mudshark.brookes.ac.uk/ ScrumPy.

The murine polyomavirus microRNA locus is required to promote viruria during the acute phase of infection.

PubMed

Burke, James M; Bass, Clovis R; Kincaid, Rodney P; Ulug, Emin T; Sullivan, Christopher S

2018-06-06

Polyomaviruses (PyVs) can cause serious disease in immunosuppressed hosts. Several pathogenic PyVs encode microRNAs (miRNAs), small RNAs that regulate gene expression via RNA silencing. Despite recent advances in understanding the activities of PyV miRNAs, the biological functions of PyV miRNAs during in vivo infections are mostly unknown. Studies presented here use murine polyomavirus (MuPyV) as a model to assess the roles of the PyV miRNAs in a natural host. This analysis reveals that a MuPyV mutant that is unable to express miRNAs has enhanced viral DNA loads in select tissues at late times after infection. This is consistent with the PyV miRNAs functioning to reduce viral replication during the persistent phase of infection in a natural host. Additionally, the MuPyV miRNA locus promotes viruria during the acute phase of infection as evidenced by a defect in shedding during infection with the miRNA mutant virus. The viruria defect of the miRNA mutant virus could be rescued by infecting Rag2-/- mice. These findings implicate the miRNA locus as functioning in both the persistent and acute phases of infection and suggest a role for MuPyV miRNA in evading the adaptive immune response. IMPORTANCE MicroRNAs are expressed by diverse viruses, but for only a few is there any understanding of their in vivo function. PyVs can cause serious disease in immunocompromised hosts. Therefore, increased knowledge of how these viruses interact with the immune response is of clinical relevance. Here we show a novel activity for a viral miRNA locus in promoting virus shedding. This work indicates that in addition to any role for the PyV miRNA locus in long-term persistence, that it also has biological activity during the acute phase. As this mutant phenotype is alleviated by infection of mice lacking an adaptive immune response, our work also connects the in vivo activity of the PyV miRNA locus to the immune response. Given that PyV-associated disease is associated with alterations in the immune response, our findings help to better understand how the balance between PyVs and the immune response becomes altered in pathogenic states. Copyright © 2018 American Society for Microbiology.

Identification of Two Novel Members of the Tentative Genus Wukipolyomavirus in Wild Rodents

PubMed Central

Nainys, Juozas; Timinskas, Albertas; Schneider, Julia; Ulrich, Rainer G.; Gedvilaite, Alma

2015-01-01

Two novel polyomaviruses (PyVs) were identified in kidney and chest-cavity fluid samples of wild bank voles (Myodes glareolus) and common voles (Microtus arvalis) collected in Germany. All cloned and sequenced genomes had the typical PyV genome organization, including putative open reading frames for early regulatory proteins large T antigen and small T antigen on one strand and for structural late proteins (VP1, VP2 and VP3) on the other strand. Virus-like particles (VLPs) were generated by yeast expression of the VP1 protein of both PyVs. VLP-based ELISA and large T-antigen sequence-targeted polymerase-chain reaction investigations demonstrated signs of infection of these novel PyVs in about 42% of bank voles and 18% of common voles. In most cases only viral DNA, but not VP1-specific antibodies were detected. In additional animals exclusively VP1-specific antibodies, but no viral DNA was detected, indicative for virus clearance. Phylogenetic and clustering analysis including all known PyV genomes placed novel bank vole and common vole PyVs amongst members of the tentative Wukipolymavirus genus. The other known four rodent PyVs, Murine PyV and Hamster PyV, and Murine pneumotropic virus and Mastomys PyV belong to different phylogenetic clades, tentatively named Orthopolyomavirus I and Orthopolyomavirus II, respectively. In conclusion, the finding of novel vole-borne PyVs may suggest an evolutionary origin of ancient wukipolyomaviruses in rodents and may offer the possibility to develop a vole-based animal model for human wukipolyomaviruses. PMID:26474048

Discerning regulation of cis- and trans-presentation of CD8+ T-cell epitopes by EBV-encoded oncogene LMP-1 through self-aggregation.

PubMed

Smith, Corey; Wakisaka, Naohiro; Crough, Tania; Peet, Jesse; Yoshizaki, Tomokazu; Beagley, Leone; Khanna, Rajiv

2009-06-11

Activation of the nuclear factor-kappaB pathway by Epstein-Barr virus-encoded latent membrane protein-1 (LMP-1) leads to an up-regulation of the major histocompatibility complex class I antigen-processing pathway. Paradoxically, LMP-1 itself induces a subdominant CD8+ T-cell response and appears to have evolved to avoid immune recognition. Here we show that, although expression of LMP-1 in human cells dramatically enhanced the trans-presentation of CD8+ T-cell epitopes, cis-presentation of LMP-1-derived epitopes was severely impaired. Testing of a series of LMP-1 mutants revealed that deletion of the first transmembrane domain of LMP-1, which prevented self-aggregation, significantly enhanced cis-presentation of T-cell epitopes from this protein, whereas it lost its ability to up-regulate trans-presentation. Interestingly, we also found that cis-presentation of LMP-1 epitopes was rescued by blocking the proteasome function. Taken together, these results delineate a novel mechanism of immune evasion, which renders a virally encoded oncogene inaccessible to the conventional major histocompatibility complex class I pathway limiting its cis-presentation to effector cells.

A supramolecular miktoarm star polymer based on porphyrin metal complexation in water.

PubMed

Hou, Zhanyao; Dehaen, Wim; Lyskawa, Joël; Woisel, Patrice; Hoogenboom, Richard

2017-07-25

A novel supramolecular miktoarm star polymer was successfully constructed in water from a pyridine end-decorated polymer (Py-PmDEGA) and a metalloporphyrin based star polymer (ZnTPP-(PEG) 4 ) via metal-ligand coordination. The Py-PmDEGA moiety was prepared via a combination of reversible addition-fragmentation chain transfer polymerization (RAFT) and subsequent aminolysis and Michael addition reactions to introduce the pyridine end-group. The ZnTPP(PEG) 4 star-polymer was synthesized by the reaction between tetrakis(p-hydroxyphenyl)porphyrin and toluenesulfonyl-PEG, followed by insertion of a zinc ion into the porphyrin core. The formation of a well-defined supramolecular AB 4 -type miktoarm star polymer was unambiguously demonstrated via UV-Vis spectroscopic titration, isothermal titration calorimetry (ITC) and diffusion ordered NMR spectroscopy (DOSY).

Photoregeneration of bovine rhodopsin from its signaling state.

PubMed

Arnis, S; Hofmann, K P

1995-07-25

In rhodopsin, 11-cis-retinal is bound by a protonated Schiff base and acts as a strong antagonist, which holds the receptor in its inactive ground state conformation. Light induces cis-/trans-retinal isomerization and a sequence of thermal transitions through intermediates. The active conformation that catalyzes GDP/GTP exchange in the G-protein (Gt) is generated from the metarhodopsin II intermediate (MII) and mediated by Schiff base proton translocation and proton uptake from the aqueous phase. In the stable nucleotide-free MII-Gt complex, any thermal transition of MII into other forms of rhodopsin is blocked. We have now studied how Gt affects flash-induced photochemical conversions of MII. Difference spectra from measured absorption changes show that MII photolyzes through two parallel pathways, with fast (1 ms) and slow (50 ms) kinetics (12 degrees C, pH 6). The slow pathway regenerates rhodopsin (9- or 11-cis) via Schiff base reprotonation and proton release. We infer a cis-isomerized early photoproduct (reverted meta, RM) preceding these thermal transitions. When MII is photolyzed in the MII-Gt complex, the slow absorption change is abolished, indicating that Gt blocks the completion of the regeneration process. This is due to the formation of a stable RM-Gt complex, as shown by successive photolysis of MII, RM, and ground state rhodopsin, and the application of GTP gamma S at different stages. The complex dissociates with GTP gamma S, and rhodopsin relaxes to the ground state. The results indicate that cis-retinal and Gt can bind to the receptor at the same time. We discuss the result that the protonations in the meta II state uncouple retinal geometry from Gt interaction.

PyR@TE 2: A Python tool for computing RGEs at two-loop

NASA Astrophysics Data System (ADS)

Lyonnet, F.; Schienbein, I.

2017-04-01

Renormalization group equations are an essential tool for the description of theories across different energy scales. Even though their expressions at two-loop for an arbitrary gauge field theory have been known for more than thirty years, deriving the full set of equations for a given model by hand is very challenging and prone to errors. To tackle this issue, we have introduced in Lyonnet et al. (2014) a Python tool called PyR@TE; Python Renormalization group equations @ Two-loop for Everyone. With PyR@TE, it is easy to implement a given Lagrangian and derive the complete set of two-loop RGEs for all the parameters of the theory. In this paper, we present the new version of this code, PyR@TE 2, which brings many new features and in particular it incorporates kinetic mixing when several U(1) gauge groups are involved. In addition, the group theory part has been greatly improved as we introduced a new Python module dubbed PyLie that deals with all the group theoretical aspects required for the calculation of the RGEs as well as providing very useful model building capabilities. This allows the use of any irreducible representation of the SU(n) , SO(2 n) and SO(2n + 1) groups. Furthermore, it is now possible to implement terms in the Lagrangian involving fields which can be contracted into gauge singlets in more than one way. As a byproduct, results for a popular model (SM + complex triplet) for which, to our knowledge, the complete set of two-loop RGEs has not been calculated before are presented in this paper. Finally, the two-loop RGEs for the anomalous dimension of the scalar and fermion fields have been implemented as well. It is now possible to export the coupled system of beta functions into a numerical C++ function, leading to a consequent speed up in solving them.

17. Jet Lowe, Photographer, June 1978. FIVEROLL RUB DELIVERY ON ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

17. Jet Lowe, Photographer, June 1978. FIVE-ROLL RUB DELIVERY ON A. JENKS & SON FINISHER CARD; THE DELIVERY IS CONSISTENT WITH MANUFACTURE C. 1845-1855; FROM RIGHT FRONT OF OSCILLATING MECHANISM. - Watkins Mill, County Highway MM, Lawson, Ray County, MO

NMR spectroscopic study of the carbon and nitrogen dynamics of grass-derived pyrogenic organic material during 2.3 years of incubation in soil

NASA Astrophysics Data System (ADS)

Hilscher, André; Knicker, Heike

2010-05-01

Incomplete combustion of vegetation results in pyrogenic organic material (PyOM) which occurs ubiquitously in soils and sediments. To understand the C sequestration potential of PyOM in environmental systems knowledge is required about the respective degradation and humification mechanisms and the stability of the different chemical PyOM structures. The present study focuses on the microbial recalcitrance of PyOM on molecular scale. Therefore, microcosms incubation experiments were performed using PyOM produced from highly isotopically enriched 13C and 15N rye grass (Lolium perenne) at 350°C under oxic conditions for one (1M) and four minutes (4M). Solid-state CPMAS 13C and 15N NMR studies were accomplished to obtain insights into the involved humification mechanisms at different stages the PyOM degradation. In total up to 38% of the bulk PyOM C was mineralised during the 28 months of incubation. The O/N-alkyl C and alkyl C residues which survived the charring process were effectively decomposed. At the end of the incubation up to 73% and 57% of the initial O/N-alkyl C and alkyl C amount were mineralised or converted to other C groups, respectively. The total aryl C group recovery of the PyOM decreased significantly during the 28 months of incubation (P ≤ 0.001). After 20 months of incubation between 26% and 40% of the initial aryl C amount was lost. For this group, relative short half time periods in the range of 3.0 and 3.8 years were obtained. The observed loss of aromatic C structures may be attributed to two simultaneous processes, the mineralisation to CO2 and the conversion to other C groups by partial oxidation. The presence of a readily decomposable co-substrate showed no significant changes in the degradation pattern of the different PyOM, possibly because decomposable sources were already available in the starting PyOM. Most of the organic bound N of the fresh PyOM was assignable to heterocyclic aromatic compounds such as pyrrole and indole-like structures with contributions of 62% and 72% for PyOM 1M and PyOM 4M, respectively. The other part of the 15N NMR signal intensity was assignable to amide-like structures. No major alteration of the amide and heterocyclic N contribution was detected for the PyOM 1M incubates. For the more charred PyOM 4M, the relative heterocyclic N contribution decreased. After the 28 months of incubation no significant difference in the chemical N composition of PyOM 4M related to the PyOM 1M treatments could be observed (P=0.472). Further, we detect a continuous degrease of the total amounts for the amide and heterocyclic N compounds. After 20 months, only 49% to 59% of the heterocyclic N compounds were recovered. The respective amide N recoveries were larger with 59% to 87%. It can be concluded, that PyOM may not be as highly refractory as it is commonly assumed. During the efficient degradation not only a considerable PyOM amount is mineralised, but also the chemical structure of the remaining PyOM is strongly modified. This includes the formation of O-containing functional groups and the loss of aromatic C and N containing heterocyclic domains by mineralisation and conversion to other C and N groups.

Involvement of conformational isomerism in the complexity of the crystal network of 1-(4-nitrophenyl)-1H-1,3-benzimidazole derivatives driven by C-H...A (A = NO2, Npy and π) and orthogonal Npy...NO2 and ONO...Csp2 interactions.

PubMed

García-Aranda, Mónica I; Gómez-Castro, Carlos Z; García-Báez, Efrén V; Gómez, Yolanda Gómez Y; Castrejón-Flores, José L; Padilla-Martínez, Itzia I

2018-04-01

A detailed structural analysis of the benzimidazole nitroarenes 1-(4-nitrophenyl)-1H-1,3-benzimidazole, C 13 H 9 N 3 O 2 , (I), 1-(4-nitrophenyl)-2-phenyl-1H-1,3-benzimidazole, C 19 H 13 N 3 O 2 , (II), and 2-(3-methylphenyl)-1-(4-nitrophenyl)-1H-1,3-benzimidazole, C 20 H 15 N 3 O 2 , (III), has been performed. They are nonplanar structures whose crystal arrangement is governed by Csp 2 -H...A (A = NO 2 , N py and π) hydrogen bonding. The inherent complexity of the supramolecular arrangements of compounds (I) (Z' = 2) and (II) (Z' = 4) into tapes, helices and sheets is the result of the additional participation of π-π NO2 and n-π* (n = O and N py ; π* = Csp 2 and N NO2 ) interactions that contribute to the stabilization of the equi-energetic conformations adopted by each of the independent molecules in the asymmetric unit. In contrast, compound (III) (Z' = 1) is self-paired, probably due to the effect of the steric demand of the methyl group on the crystal packing. Theoretical ab initio calculations confirmed that the presence of the arene ring at the benzimidazole 2-position increases the rotational barrier of the nitrobenzene ring and also supports the electrostatic nature of the orthogonal ONO...Csp 2 and N py ...NO 2 interactions.

Incidence, predictors and outcomes of infective endocarditis in a contemporary adult congenital heart disease population.

PubMed

Moore, Benjamin; Cao, Jacob; Kotchetkova, Irina; Celermajer, David S

2017-12-15

The prevalence of congenital heart disease (CHD) in the adult population is steadily increasing. A substrate of prosthetic material and residual lesions, constantly evolving as surgical techniques change over time, predispose these patients to the potentially devastating complication of infective endocarditis (IE). We retrospectively reviewed 2935 patients in our adult CHD database for all cases of endocarditis between 1991 and 2016. Incidence, clinical course and predictors of outcomes were analysed. We document 74 episodes in 62 patients, with an incidence of 0.9 cases/1000 patient years (py). IE was more common in complex CHD (1.4 cases/1000py) and ventricular septal defects (VSDs) (1.9 cases/1000py). Prosthetic material was involved in 47% and left-sided infection predominated (66%). The incidence in bicuspid aortic valves post aortic valve replacement (AVR) was significantly higher than in unoperated valves, being 1.8 and 1.1 cases/1000 patient years respectively. Streptococcus was the most frequently implicated causative organism (37%). Emboli occurred in 34% of cases with a cerebral predilection. 46% of patients required surgery during the admission for IE, most frequently to replace a severely regurgitant bicuspid aortic valve. Early endocarditis-related mortality was 15%, associated with cerebral emboli and acute renal failure. In a contemporary adult CHD cohort, those with complex underlying lesions, VSDs or an AVR were at higher risk for IE. Mortality remains substantial and is more likely in patients with cerebral emboli and/or acute renal failure. Copyright © 2017 Elsevier B.V. All rights reserved.

Neonatal ethanol exposure from ethanol-based hand sanitisers in isolettes.

PubMed

Hsieh, Shizuka; Sapkota, Amir; Wood, Rebecca; Bearer, Cynthia; Kapoor, Shiv

2018-01-01

The aims of this study is to measure the ethanol vapours in the isolette after use of hands cleaned with ethanol-based hand sanitiser (EBHS). Two squirts (1.5 mL) of hand sanitiser were rubbed on hands for 10 or 20 s before inserting the hands in the isolette for 5 min. Ethanol vapours were measured in the isolette with photoionisation detector and alcohol breathalyser for 30 min. Peak ethanol concentration in the isolette was considerably higher with a 10 s hand rub (381±192 ppm) compared with a 20 s hand rub (99±50 ppm), and dissipated to ≤5 ppm within 30 min. Under routine care, EBHS use by care providers exposes neonates in isolettes to 3.7-7.3 or 1.4-2.8 mg/kg ethanol per day with 10 or 20 s hand rubs, respectively. The expected blood level from average single exposure is 0.036 mg/dL with 10 s hand rub and may increase further with multiple exposures in a short period. Preterm neonates in the isolette are at risk of inadvertent exposure to ethanol. The expected blood alcohol level from this exposure is small and below 1 mg/dL level recommended by European Medicines Agency to limit the ethanol exposure in children. The unintended ethanol exposure can be avoided by rubbing hands for at least 20 s after applying EBHS. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The Rubella Virus Nonstructural Protease Requires Divalent Cations for Activity and Functions in trans

PubMed Central

Liu, Xin; Ropp, Susan L.; Jackson, Richard J.; Frey, Teryl K.

1998-01-01

The rubella virus (RUB) nonstructural (NS) protease is a papain-like cysteine protease (PCP) located in the NS-protein open reading frame (NSP-ORF) that cleaves the NSP-ORF translation product at a single site to produce two products, P150 (the N-terminal product) and P90 (the C-terminal product). The RUB NS protease was found not to function following translation in vitro in a standard rabbit reticulocyte lysate system, although all of the other viral PCPs do so. However, in the presence of divalent cations such as Zn2+, Cd2+, and Co2+, the RUB NS protease functioned efficiently, indicating that these cations are required either as direct cofactors in catalytic activity or for correct acquisition of three-dimensional conformation of the protease. Since other viral and cell PCPs do not require cations for activity and the RUB NS protease contains a putative zinc binding motif, the latter possibility is more likely. Previous in vivo expression studies of the RUB NS protease failed to demonstrate trans cleavage activity (J.-P. Chen et al., J. Virol. 70:4707–4713, 1996). To study whether trans cleavage could be detected in vitro, a protease catalytic site mutant and a mutant in which the C-terminal 31 amino acids of P90 were deleted were independently introduced into plasmid constructs that express the complete NSP-ORF. Cotranslation of these mutants in vitro yielded both the native and the mutated forms of P90, indicating that the protease present in the mutated construct cleaved the catalytic-site mutant precursor. Thus, RUB NS protease can function in trans. PMID:9557742

Neutral Guest Capture via Lewis Acid/Base Molecular Square Receptors. X-ray Crystal Structure of {Cyclobis[(cis-(dppp)Pt(4-ethynylpyridyl)(2))(cis- (PEt(3))(2)Pt)]Ag(2)}(+6)(phenazine)- ((-)OSO(2)CF(3))(6).

PubMed

Whiteford, Jeffery A.; Stang, Peter J.; Huang, Songping D.

1998-10-19

Interaction of {cyclobis[(cis-(dppp)Pt(4-ethynylpyridyl)(2))(cis-(L)M)]Ag(2)}(+6)((-)OSO(2)CF(3))(6), where M = Pt(II) or Pd(II) and L = dppp or 2PEt(3), with pyridine, pyrazine, phenazine, or 4,4'-dipyridyl ketone results in coordination Lewis acid/base host-guest assemblies via the "pi-tweezer effect" and mono or bis neutral guest coordination. All host-guest complexes are air stable microcrystalline solids with decomposition points greater than 170 degrees C. The homometallic Pt(II) receptors are more stable than the heteroaromatic Pt(II)-Pd(II) receptors toward heteratom-containing aromatic guests. The X-ray crystal structure of the host-guest complex {cyclobis[(cis-(dppp)Pt(4-ethynylpyridyl)(2))(cis-(PEt(3))(2)Pt)]Ag(2)}(+6)(phenazine)((-)OSO(2)CF(3))(6) is reported. The crystals with the empirical formula C(62)H(68)AgF(9)N(3)O(9)P(4)Pt(2)S(3) are triclinic P&onemacr; with a = 12.3919(8) Å, b = 17.160(1) Å, c = 18.932(1) Å, alpha = 90.892(1) degrees, beta = 97.127(1) degrees, gamma = 89.969(1) degrees, and Z = 2.

Enhanced anti-cancer activities of a gold(III) pyrrolidinedithiocarbamato complex incorporated in a biodegradable metal-organic framework.

PubMed

Sun, Raymond Wai-Yin; Zhang, Ming; Li, Dan; Li, Mian; Wong, Alice Sze-Tsai

2016-10-01

An anti-cancer active gold(III) pyrrolidinedithiocarbamato complex [(PDTC)Au III Cl 2 ] (1) has been synthesized and characterized by means of X-ray crystallography. Compared to the pyrrolidinedithiocarbamate ligand itself, this gold(III) complex displays an up to 33-fold higher anti-cancer potency towards a panel of cancer cell lines including the cisplatin-resistant ovarian carcinoma cell line (A2780cis). As demonstrated by a set of Transwell® assay-based cytotoxicity experiments, incorporating this gold(III) complex in a zinc-based biodegradable metal-organic framework (MOF) displays a significant enhancement in anti-cancer activity towards A2780cis than the gold(III) complex alone. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthesis and characterization of carbazolide-based iridium PNP pincer complexes. Mechanistic and computational investigation of alkene hydrogenation: evidence for an Ir(III)/Ir(V)/Ir(III) catalytic cycle.

PubMed

Cheng, Chen; Kim, Bong Gon; Guironnet, Damien; Brookhart, Maurice; Guan, Changjian; Wang, David Y; Krogh-Jespersen, Karsten; Goldman, Alan S

2014-05-07

New carbazolide-based iridium pincer complexes ((carb)PNP)Ir(C2H4), 3a, and ((carb)PNP)Ir(H)2, 3b, have been prepared and characterized. The dihydride, 3b, reacts with ethylene to yield the cis-dihydride ethylene complex cis-((carb)PNP)Ir(C2H4)(H)2. Under ethylene this complex reacts slowly at 70 °C to yield ethane and the ethylene complex, 3a. Kinetic analysis establishes that the reaction rate is dependent on ethylene concentration and labeling studies show reversible migratory insertion to form an ethyl hydride complex prior to formation of 3a. Exposure of cis-((carb)PNP)Ir(C2H4)(H)2 to hydrogen results in very rapid formation of ethane and dihydride, 3b. DFT analysis suggests that ethane elimination from the ethyl hydride complex is assisted by ethylene through formation of ((carb)PNP)Ir(H)(Et)(C2H4) and by H2 through formation of ((carb)PNP)Ir(H)(Et)(H2). Elimination of ethane from Ir(III) complex ((carb)PNP)Ir(H)(Et)(H2) is calculated to proceed through an Ir(V) complex ((carb)PNP)Ir(H)3(Et) which reductively eliminates ethane with a very low barrier to return to the Ir(III) dihydride, 3b. Under catalytic hydrogenation conditions (C2H4/H2), cis-((carb)PNP)Ir(C2H4)(H)2 is the catalyst resting state, and the catalysis proceeds via an Ir(III)/Ir(V)/Ir(III) cycle. This is in sharp contrast to isoelectronic (PCP)Ir systems in which hydrogenation proceeds through an Ir(III)/Ir(I)/Ir(III) cycle. The basis for this remarkable difference is discussed.

PlasmaPy: beginning a community developed Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas A.; Huang, Yi-Min; PlasmaPy Collaboration

2016-10-01

In recent years, researchers in several disciplines have collaborated on community-developed open source Python packages such as Astropy, SunPy, and SpacePy. These packages provide core functionality, common frameworks for data analysis and visualization, and educational tools. We propose that our community begins the development of PlasmaPy: a new open source core Python package for plasma physics. PlasmaPy could include commonly used functions in plasma physics, easy-to-use plasma simulation codes, Grad-Shafranov solvers, eigenmode solvers, and tools to analyze both simulations and experiments. The development will include modern programming practices such as version control, embedding documentation in the code, unit tests, and avoiding premature optimization. We will describe early code development on PlasmaPy, and discuss plans moving forward. The success of PlasmaPy depends on active community involvement and a welcoming and inclusive environment, so anyone interested in joining this collaboration should contact the authors.

Aircraft Engine Sump Fire Mitigation

NASA Technical Reports Server (NTRS)

Rosenlieb, J. W.

1973-01-01

An investigation was performed of the conditions in which fires can result and be controlled within the bearing sump simulating that of a gas turbine engine; Esso 4040 Turbo Oil, Mobil Jet 2, and Monsanto MCS-2931 lubricants were used. Control variables include the oil inlet temperature, bearing temperature, oil inlet and scavenge rates, hot air inlet temperature and flow rate, and internal sump baffling. In addition to attempting spontaneous combustion, an electric spark and a rub (friction) mechanism were employed to ignite fires. Spontaneous combustion was not obtained; however, fires were readily ignited with the electric spark while using each of the three test lubricants. Fires were also ignited using the rub mechanism with the only test lubricant evaluated, Esso 4040. Major parameters controlling ignitions were: Sump configuration; Bearing and oil temperatures, hot air temperature and flow and bearing speed. Rubbing between stationary parts and rotating parts (eg. labyrinth seal and mating rub strip) is a very potent fire source suggesting that observed accidental fires in gas turbine sumps may well arise from this cause.

Synthesis and spectroscopy of micro-oxo (O(2)(-))-bridged heme/non-heme diiron complexes: models for the active site of nitric oxide reductase.

PubMed

Wasser, Ian M; Martens, Constantinus F; Verani, Claudio N; Rentschler, Eva; Huang, Hong-Wei; Moënne-Loccoz, Pierre; Zakharov, Lev N; Rheingold, Arnold L; Karlin, Kenneth D

2004-01-26

In this paper, we describe the synthesis and study of a series of heme/non-heme Fe-O-Fe' complexes supported by a porphyrin and the tripodal nitrogen ligand TMPA [TMPA = tris(2-pyridylmethyl)amine]. The complete synthesis of [((6)L)Fe-O-Fe(X)](+) (1) (X = OMe(-) or Cl(-), 69:31 ratio), where (6)L is the dianion of 5-(o-O-[(N,N-bis(2-pyridylmethyl)-2-(6-methoxyl)pyridinemethanamine)phenyl]-10,15,20-tris(2,6-difluorophenyl)porphine, is reported. The crystal structure for 1.PF(6) reveals an intramolecular heme/non-heme diferric complex bridged by an Fe-O-Fe' moiety; 90 degree angle (Fe-O-Fe') = 166.7(3) degrees, and d(Fe.Fe') = 3.556 A. Crystal data for C(70)H(57)ClF(12)Fe(2)N(8)O(3)P (1.PF(6)): triclinic, Ponemacr;, a = 13.185(3) A, b = 14.590 (3) A, c = 16.885(4) A, alpha = 104.219(4) degrees, beta = 91.572(4) degrees, gamma = 107.907(4) degrees, V = 2977.3(11) A(3), Z = 2, T = 150(2) K. Complex 1 (where X = Cl(-)) is further characterized by UV-vis (lambda(max) = 328, 416 (Soret), 569 nm), (1)H NMR (delta 27-24 [TMPA -CH(2)-], 16.1 [pyrrole-H], 15.2-10.5 [PY-3H, PY-5H], 7.9-7.2 [m- and p-phenyl-H], 6.9-5.8 [PY-4H] ppm), resonance Raman (nu(as)(Fe-O-Fe') 844 cm(-)(1)), and Mössbauer (delta(Fe) = 0.47, 0.41 mm/s; deltaE(A) = 1.59, 0.55 mm/s; 80 K) spectroscopies, MALDI-TOF mass spectrometry (m/z 1202), and SQUID susceptometry (J = - 114.82 cm(-)(1), S = 0). We have also synthesized a series of 3-, 4-, and 5-methyl-substituted as well as selectively deuterated TMPA(Fe') complexes and condensed these with the hydroxo complex (F(8))FeOH or (F(8)-d(8))FeOH to yield "untethered" Fe-O-Fe' analogues. Along with selective deuteration of the methylene hydrogens in TMPA, complete (1)H NMR spectroscopic assignments for 1 have been accomplished. The magnetic properties of several of the untethered complexes and a comparison to those of 1 are also presented. Complex 1 and related species represent good structural and spectroscopic models for the heme/non-heme diiron active site in the enzyme nitric oxide reductase.

Synthesis and DNA binding properties of 1-(3-aminopropyl)-imidazole-containing triamide f-Im*PyIm: a novel diamino polyamide designed to target 5'-ACGCGT-3'.

PubMed

Satam, Vijay; Babu, Balaji; Porte, Alexander; Savagian, Mia; Lee, Megan; Smeltzer, Thomas; Liu, Yang; Ramos, Joseph; Wilson, W David; Lin, Shicai; Kiakos, Kostantinos; Hartley, John A; Lee, Moses

2012-09-15

A novel diamino/dicationic polyamide f-Im(*)PyIm (5) that contains an orthogonally positioned aminopropyl chain on an imidazole (Im(*)) moiety was designed to target 5'-ACGCGT-3'. The DNA binding properties of the diamino polyamide 5, determined by CD, ΔT(M), DNase I footprinting, SPR, and ITC studies, were compared with those of its monoamino/monocationic counterpart f-ImPyIm (1) and its diamino/dicationic isomer f-ImPy(*)Im (2), which has the aminopropyl group attached to the central pyrrole unit (Py(*)). The results gave evidence for the minor groove binding and selectivity of polyamide 5 for the cognate sequence 5'-ACGCGT-3', and with strong affinity (K(eq)=2.3×10(7) M(-1)). However, the binding affinities varied according to the order: f-ImPy(*)Im (2)>f-ImPyIm (1)≥f-Im(*)PyIm (5) confirming that the second amino group can improve affinity, but its position within the polyamide can affect affinity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Discrimination in Degradability of Soil Pyrogenic Organic Matter Follows a Return-On-Energy-Investment Principle.

PubMed

Harvey, Omar R; Myers-Pigg, Allison N; Kuo, Li-Jung; Singh, Bhupinder Pal; Kuehn, Kevin A; Louchouarn, Patrick

2016-08-16

A fundamental understanding of biodegradability is central to elucidating the role(s) of pyrogenic organic matter (PyOM) in biogeochemical cycles. Since microbial community and ecosystem dynamics are driven by net energy flows, then a quantitative assessment of energy value versus energy requirement for oxidation of PyOM should yield important insights into their biodegradability. We used bomb calorimetry, stepwise isothermal thermogravimetric analysis (isoTGA), and 5-year in situ bidegradation data to develop energy-biodegradability relationships for a suite of plant- and manure-derived PyOM (n = 10). The net energy value (ΔE) for PyOM was between 4.0 and 175 kJ mol(-1); with manure-derived PyOM having the highest ΔE. Thermal-oxidation activation energy (Ea) requirements ranged from 51 to 125 kJ mol(-1), with wood-derived PyOM having the highest Ea requirements. We propose a return-on-investment (ROI) parameter (ΔE/Ea) for differentiating short-to-medium term biodegradability of PyOM and deciphering if biodegradation will most likely proceed via cometabolism (ROI < 1) or direct metabolism (ROI ≥ 1). The ROI-biodegradability relationship was sigmoidal with higher biodegradability associated with PyOM of higher ROI; indicating that microbes exhibit a higher preference for "high investment value" PyOM.

Polyomavirus and Naturally Occuring Neuroglial Tumors in Raccoons (Procyon Lotor).

PubMed

Pesavento, Patricia A; Brostoff, Terza; Church, Molly E; Dela Cruz, Florante N; Woolard, Kevin D

2016-01-01

Polyomavirus (PyV) infections are widespread in human populations and, although generally associated with silent persistence, rarely cause severe disease. Among diseases convincingly associated with natural PyV infections of humans, there are remarkably different tissue tropisms and outcomes, including progressive multifocal leukoencephalopathy, transient or progressive nephropathy, and cancer. The variable character and unpredictable outcomes of infection attest to large gaps in our basic understanding of PyV biology. In particular, the rich history of research demonstrating the oncogenic potential of PyVs in laboratory animals begs the question of why cancer is not more often associated with infection. Raccoon polyomavirus (RacPyV), discovered in 2010, is consistently identified in neuroglial tumors in free-ranging raccoons in the western United States. Exposure to RacPyV is widespread, and RacPyV is detected in tissues of raccoons without tumors. Studying the relationship of RacPyV with its natural host is a unique opportunity to uncover cogent cellular targets and protein interactions between the virus and its host. Our hypothesis is that RacPyV, as an intact episome, alters cellular pathways within neural progenitor cells and drives oncogenesis. © The Author 2016. Published by Oxford University Press on behalf of the Institute for Laboratory Animal Research. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Intramolecular Oxidative O-Demethylation of an Oxoferryl Porphyrin Complexed with a Per-O-methylated β-Cyclodextrin Dimer.

PubMed

Kitagishi, Hiroaki; Kurosawa, Shun; Kano, Koji

2016-11-22

The intramolecular oxidation of ROCH 3 to ROCH 2 OH, where the latter compound spontaneously decomposed to ROH and HCHO, was observed during the reaction of the supramolecular complex (met-hemoCD3) with cumene hydroperoxide in aqueous solution. Met-hemoCD3 is composed of meso-tetrakis(4-sulfonatophenyl)porphinatoiron(III) (Fe III TPPS) and a per-O-methylated β-cyclodextrin dimer having an -OCH 2 PyCH 2 O- linker (Py=pyridine-3,5-diyl). The O=Fe IV TPPS complex was formed by the reaction of met-hemoCD3 with cumene hydroperoxide, and isolated by gel-filtration chromatography. Although the isolated O=Fe IV TPPS complex in the cyclodextrin cage was stable in aqueous solution at 25 °C, it was gradually converted to Fe II TPPS (t 1/2 =7.6 h). This conversion was accompanied by oxidative O-demethylation of an OCH 3 group in the cyclodextrin dimer. The results indicated that hydrogen abstraction by O=Fe IV TPPS from ROCH 3 yields HO-Fe III TPPS and ROCH 2 . . This was followed by radical coupling to afford Fe II TPPS and ROCH 2 OH. The hemiacetal (ROCH 2 OH) immediately decomposed to ROH and HCHO. This study revealed the ability of oxoferryl porphyrin to induce two-electron oxidation. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Waterless Hand Rub Versus Traditional Hand Scrub Methods for Preventing the Surgical Site Infection in Orthopedic Surgery.

PubMed

Iwakiri, Kentaro; Kobayashi, Akio; Seki, Masahiko; Ando, Yoshiyuki; Tsujio, Tadao; Hoshino, Masatoshi; Nakamura, Hiroaki

2017-11-15

MINI: Fourteen hundred consecutive patients were investigated for evaluating the utility of waterless hand rub before orthopaedic surgery. The risk in the surgical site infection incidence was the same, but costs of liquids used for hand hygiene were cheaper and the hand hygiene time was shorter for waterless protocol, compared with traditional hand scrub. A retrospective cohort study with prospectively collected data. The aim of this study was to compare SSI incidences, the cost of hand hygiene agents, and hand hygiene time between the traditional hand scrub and the waterless hand rub protocols before orthopedic surgery. Surgical site infections (SSI) prolong hospitalization and are a leading nosocomial cause of morbidity and a source of excess cost. Recently, a waterless hand rub protocol comprising alcohol based chlorhexidine gluconate for use before surgery was developed, but no studies have yet examined its utility in orthopedic surgery. Fourteen hundred consecutive patients who underwent orthopedic surgery (spine, joint replacement, hand, and trauma surgeries) in our hospital since April 1, 2012 were included. A total of 712 cases underwent following traditional hand scrub between April 1, 2012 and April 30, 2013 and 688 cases underwent following waterless hand rub between June 1, 2013 and April 30, 2014. We compared SSI incidences within all and each subcategory between two hand hygiene protocols. All patients were screened for SSI within 1 year after surgery. We compared the cost of hand hygiene agents and hand hygiene time between two groups. The SSI incidences were 1.3% (9 of 712) following the traditional protocol (2 deep and 7 superficial infections) and 1.1% (8 of 688) following the waterless protocol (all superficial infections). There were no significant differences between the two groups. The costs of liquids used for one hand hygiene were about $2 for traditional hand scrub and less than $1 for waterless hand rub. The mean hand hygiene time was 264 seconds with the traditional protocol and 160 seconds with the waterless protocol. Waterless hand rub with an alcohol based chlorhexidine gluconate solution can be a safe, quick, and cost-effective alternative to traditional hand scrub. 3.

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter.

PubMed

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; Koechli, Chantal; Campbell, Ashley; Buckley, Daniel H; Lehmann, Johannes

2016-12-01

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.

Pyrazine as a building block for molecular architectures with PtII.

PubMed

Willermann, Michael; Mulcahy, Clodagh; Sigel, Roland K O; Cerdà, Marta Morell; Freisinger, Eva; Sanz Miguel, Pablo J; Roitzsch, Michael; Lippert, Bernhard

2006-03-06

A series of pyrazine (pz) complexes containing cis-(NH(3))(2)Pt(II), (tmeda)Pt(II) (tmeda = N,N,N',N'-tetramethylethylenediamine), and trans-(NH(3))(2)Pt(II) entities have been prepared and characterized by X-ray crystallography and/or 1H NMR spectroscopy. In these compounds, the pz ligands act as monodentate (1-3) or bidentate bridging ligands (4-7). Three variants of the latter case are described: a dinuclear complex [Pt(II)]2 (4b), a cyclic tetranuclear [Pt(II)](4) complex (5), and a trinuclear mixed-metal complex [Pt2Ag] (7). Mono- and bidentate binding modes are readily differentiated by 1H NMR spectroscopy, and the assignment of pz protons in the case of monodentate coordination is aided by the observation of (195)Pt satellites. Formation of the open molecular box cis-[{(NH3)2Pt(pz)}4](NO3)8.3.67H2O (5) from cis-(NH3)2Pt(II) and pz follows expectations of the "molecular library approach" for the generation of a cyclic tetramer.

Novel Rhenium(III, IV, and V) Tetradentate N2O2 Schiff Base Mononuclear and Dinuclear Complexes

PubMed Central

Rotsch, David A.; Reinig, Kimberly M.; Weis, Eric M.; Taylor, Anna B.; Barnes, Charles L.

2013-01-01

Reaction of (Bu4N)[ReOCl4] with the tetradentate Schiff base ligand α, α’-[(1,1-dimethylethylene)dinitrilo]di-o-cresol (sal2ibnH2) yields cis-[ReVOCl(sal2ibn)], which quickly forms trans-[μ-O(ReVO(sal2ibn))2] in solution. The dinuclear complex can also be isolated by the addition of base (Et3N) to the reaction mixture. Conversely, the mononuclear complex can be trapped as cis-[ReVO(NCS)(sal2ibn)] by addition of (Bu4N)SCN to the reaction mixture. Reduction of cis-[ReVO(NCS)sal2ibn] with triphenylphosphine gives the unique trans-[ReIII(NCS)(PPh3)(sal2ibn)] and rare μ-oxo Re(IV) dimer trans-[μ-O(ReIV(NCS)(sal2ibn))2]. All of the complexes were characterized by 1H and 13C NMR, FT-IR spectroscopy, electrospray ionization mass spectrometry (ESI-MS), cyclic voltammetry and single crystal X-ray diffraction. PMID:23824208

Non-cytomegalovirus ocular opportunistic infections in patients with acquired immunodeficiency syndrome.

PubMed

Gangaputra, Sapna; Drye, Lea; Vaidya, Vijay; Thorne, Jennifer E; Jabs, Douglas A; Lyon, Alice T

2013-02-01

To report the incidence and clinical outcomes of non-cytomegalovirus (non-CMV) ocular opportunistic infections in patients with acquired immunodeficiency syndrome (AIDS) in the era of highly active antiretroviral therapy. Multicenter, prospective, observational study of patients with AIDS. Medical history, ophthalmologic examination, and laboratory tests were performed at enrollment and every 6 months subsequently. Once an ocular opportunistic infection was diagnosed, patients were seen every 3 months for outcomes. At enrollment, 37 non-CMV ocular opportunistic infections were diagnosed: 16 patients, herpetic retinitis; 11 patients, toxoplasmic retinitis; and 10 patients, choroiditis. During the follow-up period, the estimated incidences (and 95% confidence intervals [CI]) of these were: herpetic retinitis, 0.007/100 person-years (PY) (95% CI 0.0004, 0.039); toxoplasmic retinitis, 0.007/100 PY (95% CI 0.004, 0.039); and choroiditis, 0.014/ 100 PY (95% CI 0.0025, 0.050). The mortality rates appeared higher among those patients with newly diagnosed or incident herpetic retinitis and choroiditis (rates = 21.7 deaths/100 PY [P = .02] and 12.8 deaths/100 PY [P = .04]), respectively, than those for patients with AIDS without an ocular opportunistic infection (4.1 deaths/100 PY); toxoplasmic retinitis did not appear to be associated with greater mortality (6.4/100 PY, P = .47). Eyes with newly diagnosed herpetic retinitis appeared to have a poor visual prognosis, with high rates of visual impairment (37.9/100 PY) and blindness (17.5/100 PY), whereas those outcomes in eyes with choroiditis appeared to be lower (2.3/100 PY and 0/100 PY, respectively). Although uncommon, non-CMV ocular opportunistic infections may be associated with high rates of visual loss and/or mortality. Copyright © 2013 Elsevier Inc. All rights reserved.

G protein-coupled estrogen receptor (GPER) regulates mammary tumorigenesis and metastasis

PubMed Central

Marjon, Nicole A.; Hu, Chelin

2014-01-01

The role of 17β-estradiol (E2) in breast cancer development and tumor growth has traditionally been attributed exclusively to the activation of ERα. Although targeted inhibition of ERα is a successful approach for patients with ERα+ breast cancer, many patients fail to respond or become resistant to anti-estrogen therapy. The discovery of the G protein-coupled estrogen receptor (GPER1) suggested an additional mechanism through which E2 could exert its effects in breast cancer. Studies have demonstrated clinical correlations between GPER expression in human breast tumor specimens and increased tumor size, distant metastasis, and recurrence, as well as established a proliferative role for GPER in vitro; however, direct in vivo evidence has been lacking. To this end, a GPER null mutation [GPER knockout (KO)] was introduced, through interbreeding, into a widely used transgenic mouse model of mammary tumorigenesis [MMTV-PyMT (PyMT)]. Early tumor development, assessed by the extent of hyperplasia and proliferation, was not different between GPER wild-type/PyMT (WT/PyMT) and those mice harboring the GPER null mutation (KO/PyMT). However, by 12-13 weeks of age, tumors from KO/PyMT mice were smaller with decreased proliferation compared to those from WT/PyMT mice. Furthermore, tumors from the KO/PyMT mice were of histologically lower grade compared to tumors from their WT counterparts, suggesting less aggressive tumors in the KO/PyMT mice. Finally, KO/PyMT mice displayed dramatically fewer lung metastases compared to WT/PyMT mice. Combined, these data provide the first in vivo evidence that GPER plays a critical role in breast tumor growth and distant metastasis. PMID:25030371

Solvent extraction of thorium(IV), uranium(VI), and europium(III) with lipophilic alkyl-substituted pyridinium salts. Final report for subcontract 9-XZ2-1123E-1, June 1, 1992--December 1, 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ensor, D.D.

1997-01-01

In the treatment of high level nuclear wastes, aromatic pyridinium salts which are radiation-resistant are desired for the extraction of actinides and lanthanides. The solvent extraction of Th{sup +4}, UO{sub 2}{sup +2}, and Eu{sup +3} by three aromatic extractants, 3,5-didodecylpyridinium nitrate (35PY), 2,6-didodecylpyridinium nitrate (26PY), and 1-methyl-3,5-didodecyl-pyridinium iodide (1M35PY) has been studied in nitric acid media. The general order of extractability of the three extractants in toluene was 1M35PY>> 26PY > 35PY. The overall extraction efficiency of the metal ions was Th{sup +4} >UO{sub 2}{sup +2} > Eu{sup +3}. The extraction of HNO{sub 3}, which was competitive with the extractionmore » of metal ions, was quantitatively investigated by NaOH titration and UV spectrometry. The loading capacity suggested that the extracted species in the organic phase for thorium was (R{sub 4}N{sup +}){sub 2}Th(NO{sub 3}{sup -}){sub 6}, where R{sub 4}N{sup +} denotes 1M35PY. A comparison of 1M35PY to the well-characterized extractant, Aliquat-336, an aliphatic ammonium salt was made. At the same extractant concentration, 1M35PY extracted thorium more efficiently than Aliquat-336 at high acidity. Thorium could be readily stripped with dilute nitric acid from 1M35PY. After irradiation of 0.1M 1M35PY with {sup 60}Co at 40R/min for 48 hours, no change in the extraction efficiency of thorium was observed.« less

Non-cytomegalovirus ocular opportunistic infections in patients with AIDS

PubMed Central

Gangaputra, Sapna; Drye, Lea; Vaidya, Vijay; Thorne, Jennifer E.; Jabs, Douglas A; Lyon, Alice T.

2014-01-01

Purpose To report the incidence and clinical outcomes of non-cytomegalovirus (non-CMV) ocular opportunistic infections in patients with AIDS in the era of highly active antiretroviral therapy (HAART). Design Multicenter, prospective, observational study of patients with AIDS Methods Medical history, ophthalmologic examination, and laboratory tests were performed at enrollment and every 6 months subsequently. Once an ocular opportunistic infection was diagnosed, patients were seen every 3 months for outcomes. Results At enrollment, 37 non-CMV ocular opportunistic infections were diagnosed: 16 patients, herpetic retinitis; 11 patients, toxoplasmic retinitis; and 10 patients, choroiditis. During the follow-up period, the estimated incidences (and 95% confidence intervals [CI]) of these were: herpetic retinitis, 0.007/100 person-years (PY) (95% CI 0.0004, 0.039); toxoplasmic retinitis, 0.007/100 PY (95% CI 0.004, 0.039); and choroiditis 0.014/100 PY (95% CI 0.0025, 0.050). The mortality rates appeared higher among those patients with newly diagnosed or incident herpetic retinitis and choroiditis (rates=21.7 deaths/100 PY [P=0.02] and 12.8 deaths/100 PY [P=0.04]) respectively, than that for patients with AIDS without an ocular opportunistic infection (4.1 deaths/100 PY); Toxoplasmic retinitis did not appear to be associated with greater mortality (6.4/100 PY, P=0.47). Eyes with newly-diagnosed herpetic retinitis appeared to have a poor visual prognosis with high rates of visual impairment (37.9/100 PY) and blindness (17.5/100 PY), whereas those outcomes in eyes with choroiditis appeared to be lower (2.3/100 PY and 0/100 PY, respectively). Conclusions Although uncommon, non-CMV ocular opportunistic infections may be associated with high rates of visual loss and/or mortality. PMID:23068916

PyNeb: a new tool for analyzing emission lines. I. Code description and validation of results

NASA Astrophysics Data System (ADS)

Luridiana, V.; Morisset, C.; Shaw, R. A.

2015-01-01

Analysis of emission lines in gaseous nebulae yields direct measures of physical conditions and chemical abundances and is the cornerstone of nebular astrophysics. Although the physical problem is conceptually simple, its practical complexity can be overwhelming since the amount of data to be analyzed steadily increases; furthermore, results depend crucially on the input atomic data, whose determination also improves each year. To address these challenges we created PyNeb, an innovative code for analyzing emission lines. PyNeb computes physical conditions and ionic and elemental abundances and produces both theoretical and observational diagnostic plots. It is designed to be portable, modular, and largely customizable in aspects such as the atomic data used, the format of the observational data to be analyzed, and the graphical output. It gives full access to the intermediate quantities of the calculation, making it possible to write scripts tailored to the specific type of analysis one wants to carry out. In the case of collisionally excited lines, PyNeb works by solving the equilibrium equations for an n-level atom; in the case of recombination lines, it works by interpolation in emissivity tables. The code offers a choice of extinction laws and ionization correction factors, which can be complemented by user-provided recipes. It is entirely written in the python programming language and uses standard python libraries. It is fully vectorized, making it apt for analyzing huge amounts of data. The code is stable and has been benchmarked against IRAF/NEBULAR. It is public, fully documented, and has already been satisfactorily used in a number of published papers.

Identification of potentially cytotoxic lesions induced by UVA photoactivation of DNA 4-thiothymidine in human cells

PubMed Central

Reelfs, Olivier; Macpherson, Peter; Ren, Xiaolin; Xu, Yao-Zhong; Karran, Peter; Young, Antony R.

2011-01-01

Photochemotherapy—in which a photosensitizing drug is combined with ultraviolet or visible radiation—has proven therapeutic effectiveness. Existing approaches have drawbacks, however, and there is a clinical need to develop alternatives offering improved target cell selectivity. DNA substitution by 4-thiothymidine (S4TdR) sensitizes cells to killing by ultraviolet A (UVA) radiation. Here, we demonstrate that UVA photoactivation of DNA S4TdR does not generate reactive oxygen or cause direct DNA breakage and is only minimally mutagenic. In an organotypic human skin model, UVA penetration is sufficiently robust to kill S4TdR-photosensitized epidermal cells. We have investigated the DNA lesions responsible for toxicity. Although thymidine is the predominant UVA photoproduct of S4TdR in dilute solution, more complex lesions are formed when S4TdR-containing oligonucleotides are irradiated. One of these, a thietane/S5-(6-4)T:T, is structurally related to the (6-4) pyrimidine:pyrimidone [(6-4) Py:Py] photoproducts induced by UVB/C radiation. These lesions are detectable in DNA from S4TdR/UVA-treated cells and are excised from DNA more efficiently by keratinocytes than by leukaemia cells. UVA irradiation also induces DNA interstrand crosslinking of S4TdR-containing duplex oligonucleotides. Cells defective in repairing (6-4) Py:Py DNA adducts or processing DNA crosslinks are extremely sensitive to S4TdR/UVA indicating that these lesions contribute significantly to S4TdR/UVA cytotoxicity. PMID:21890905

Responses of soil carbon turnover rates to pyrogenic carbon additions to a forest soil of Sierra Nevada, California: effects of pyrolysis temperature and soil depth

NASA Astrophysics Data System (ADS)

Santos, F.; Bird, J. A.; Berhe, A. A.

2017-12-01

Pyrogenic organic carbon (PyC) is a heterogenous mixture of thermally altered residues, ranging from slightly charred plant biomass to soot. Despite its apparent stability in soils, PyC has been reported to either increase or decrease (priming effect, PE), or have no effect on the mineralization rates of native soil organic matter (SOM), highlighting our limited knowledge on the mechanisms driving PyC-induced PE. Little is known about how PyC's pyrolysis temperature, and soil depth (surface versus subsurface) affect the direction of PE. To address this gap knowledge, we conducted from a 1-year laboratory incubation study aimed to investigate the interactive effects of pyrolysis temperature and soil depth on the mineralization rates of native SOM in fine-loamy, temperate forest soil that received additions of dual-labeled 13C and 15N jack pine pyrogenic organic matter produced at 300oC (PyC300) and 450oC (PyC450). Soil and PyC mixture were incubated in surface (0-10 cm) and subsurface (50-70 cm) forest soils in the dark at 55% soil field capacity and 25oC. Losses of native SOM as 13CO2 were measured periodically from the 13C-labeled PyC, and native (unlabeled) SOM during the incubation study using a Thermo Scientific GasBench interfaced to a Delta V Plus isotope ratio mass spectrometer. In surface soils, the addition of PyC300 decreased the turnover rates of native C relative to control treatments, whereas PyC400 had no effect on native C turnover rates. In subsurface soils, neither PyC300 nor PyC400 additions affected native C turnover rates. Our preliminary findings suggest that pyrolysis temperature is an important factor driving the persistence of soil C in Sierra Nevada forest soils.

The autumn effect: timing of physical dormancy break in seeds of two winter annual species of Geraniaceae by a stepwise process

PubMed Central

Gama-Arachchige, N. S.; Baskin, J. M.; Geneve, R. L.; Baskin, C. C.

2012-01-01

Background and Aims The involvement of two steps in the physical dormancy (PY)-breaking process previously has been demonstrated in seeds of Fabaceae and Convolvulaceae. Even though there is a claim for a moisture-controlled stepwise PY-breaking in some species of Geraniaceae, no study has evaluated the role of temperature in the PY-breaking process in this family. The aim of this study was to determine whether a temperature-controlled stepwise PY-breaking process occurs in seeds of the winter annuals Geranium carolinianum and G. dissectum. Methods Seeds of G. carolinianum and G. dissectum were stored under different temperature regimes to test the effect of storage temperature on PY-break. The role of temperature and moisture regimes in regulating PY-break was investigated by treatments simulating natural conditions. Greenhouse (non-heated) experiments on seed germination and burial experiments (outdoors) were carried out to determine the PY-breaking behaviour in the natural habitat. Key Results Irrespective of moisture conditions, sensitivity to the PY-breaking step in seeds of G. carolinianum was induced at temperatures ≥20 °C, and exposure to temperatures ≤20 °C made the sensitive seeds permeable. Sensitivity of seeds increased with time. In G. dissectum, PY-break occurred at temperatures ≥20 °C in a single step under constant wet or dry conditions and in two steps under alternate wet–dry conditions if seeds were initially kept wet. Conclusions Timing of seed germination with the onset of autumn can be explained by PY-breaking processes involving (a) two temperature-dependent steps in G. carolinianum and (b) one or two moisture-dependent step(s) along with the inability to germinate under high temperatures in G. dissectum. Geraniaceae is the third of 18 families with PY in which a two-step PY-breaking process has been demonstrated. PMID:22684684

Soil pyrogenic carbon lacks long-term persistence

NASA Astrophysics Data System (ADS)

Lutfalla, Suzanne; Abiven, Samuel; Barré, Pierre; Wiedemeier, Daniel; Christensen, Bent; Houot, Sabine; Kätterer, Thomas; Macdonald, Andy; van Oort, Fok; Chenu, Claire

2015-04-01

In the context of climate change, one mitigation technique currently investigated is the use of pyrogenic organic carbon (PyOC) -which is biomass turned into charcoal- to sequester carbon in soils with the hypothesis that PyOC is persistent and will not be biodegraded (or mineralized). In this study, we use the unique opportunity offered by five long term bare fallow (LTBF) experiments across Europe (Askov in Denmark, Grignon and Versailles in France, Ultuna in Sweden and Rothamsted in the United Kingdom) to compare the dynamics of PyOC and soil organic carbon (SOC) in the same plots at the decadal time scale (from 25 to 80 years of bare fallow depending on the site). Bare fallow plots were regularly sampled throughout the bare fallow duration and these samples were carefully archived. In bare fallow plots, with negligible external carbon input and with continuing biodegradation, SOC is depleting. Using the Benzene Polycarboxylic Acid (BPCA) technique to estimate the PyOC quantity and quality in the soils at different sampling dates, we investigated if PyOC content was also decreasing and compared the rates of depletion of PyOC and SOC. We found that PyOC contents decreased rapidly in soils at all sites. The loss of PyOC between the first and the last soil sampling ranged from 19.8 to 57.3% of the initial PyOC content. Furthermore, PyOC quality exhibited a similar evolution at all sites, becoming more enriched in condensed material with time. We applied a one pool model with mono-exponential decay to our data and found an average mean residence time of native PyOC of 116 years across the different sites, with a standard deviation of 15 years, just 1.6 times longer than that of SOC. Our results show that, though having a longer residence time than total SOC, PyOC content can decrease rapidly in soils suggesting that the potential for long-term C storage in soil by PyOC amendments is less than currently anticipated. Our results therefore question the concept of biochar production as a climate change mitigation strategy.

Changes in biogeochemistry of pyrogenic carbon in soil after one year

NASA Astrophysics Data System (ADS)

Singh, N.; Abiven, S.; Maestrini, B.; Bird, J. A.; Eoin, E. L.; Torn, M. S.; Schmidt, M. W. I.

2012-04-01

Pyrogenic carbon (PyC), incomplete combustion product of biomass and fossil fuel, is ubiquitous in the environment and widely assumed to remain stable in soil (1). The stability of PyC has been challenged by a series of recent laboratory and field experiments (2-4), which show that it is mineralized slowly to CO2 in soil. We are carrying out a long-term PyC degradation study within an experimental field setup located at Laegeren forest (Wettingen, Switzerland). We have installed cylindrical mesocosms (20 cm long and 10 cm diameter) in a randomized block design with 3 plots, 3 treatments (wood, PyC, and control) and 2 levels of nitrogen (N) input (+N = +60 kg ha-1 y-1 and -N = ambient N deposition). Wood (Pinus ponderosa) and PyC were highly labelled (13C 800‰ and 15N 4.2 atom%) and were added at a rate of 1.5 g-C kg-1 soil and 2.8 g-C kg-1 soil, respectively. We observed that PyC decomposed at a rate of 0.64 % year-1. We extracted the mesocosms after ca. 10 months in situ and sampled soil at different column depths (0-5, 5-10, 10-15 cm). We carried out δ13C and δ15N analysis to estimate the total recovery of the added substrate and its transport within the soil profile inside the mesocosms. The benzenepolycarboxylic acid (BPCA) molecular marker method was employed to quantify and characterize the PyC before and after its addition into the soil. Density fractionation was applied to identify organo-mineral interactions and understand the dynamics of PyC degradation in soil. We analysed soil sub-samples for microbial biomass using fumigation -extraction. We further study the effect of PyC on soil enzyme to determine if PyC could modify soil biological properties. We observed that after 10 months in the soil, 1) the quality of PyC, estimated by relative contribution of individual BPCA molecular markers, remained unchanged; 2) PyC showed negligible vertical movement within the soil profile; 3) most PyC was in free and occluded particulate fractions (22% PyC in occluded fraction); 4) Enzyme activity increased significantly (p <0.05) with increased nitrogen input and showed no significant difference in activity due to different substrate. We conclude that some degree of physical stabilization, for example in aggregates, might occur in the initial stages of PyC decomposition.

Microsolvation of the pyrrole cation (Py+) with nonpolar and polar ligands: infrared spectra of Py+-Ln with L = Ar, N2, and H2O (n ≤ 3).

PubMed

Schütz, Markus; Matsumoto, Yoshiteru; Bouchet, Aude; Öztürk, Murat; Dopfer, Otto

2017-02-01

The solvation of aromatic (bio-)molecular building blocks has a strong impact on the intermolecular interactions and function of supramolecular assemblies, proteins, and DNA. Herein we characterize the initial microsolvation process of the heterocyclic aromatic pyrrole cation (Py + ) in its 2 A 2 ground electronic state with nonpolar, quadrupolar, and dipolar ligands (L = Ar, N 2 , and H 2 O) by infrared photodissociation (IRPD) spectroscopy of cold mass-selected Py + -L n (n ≤ 3) clusters in a molecular beam and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Size- and isomer-specific shifts in the NH stretch frequency (Δν NH ) unravel the competition between various ligand binding sites, the strength of the respective intermolecular bonds, and the cluster growth. In Py + -Ar, linear H-bonding of Ar to the acidic NH group (NHAr) is competitive with π-stacking to the aromatic ring, and both Py + -Ar(H) and Py + -Ar(π) are observed. For L = N 2 and H 2 O, the linear NHL H-bond is much more stable than any other binding site and the only observed binding motif. For the Py + -Ar 2 and Py + -(N 2 ) 2 trimers, the H/π isomer with one H-bonded and one π-bonded ligand strongly competes with a 2H isomer with two bifurcated nonlinear NHL bonds. The latter are equivalent for Ar but nonequivalent for N 2 . Py + -H 2 O exhibits a strong and linear NHO H-bond with charge-dipole configuration and C 2v symmetry. IRPD spectra of cold Py + -H 2 O-L clusters with L = Ar and N 2 reveal that Ar prefers π-stacking to the Py + ring, while N 2 forms an OHN 2 H-bond to the H 2 O ligand. The Δν NH frequency shifts in Py + -L n are correlated with the strength of the NHL H-bond and the proton affinity (PA) of L, and a monotonic correlation between Δν NH of the Py + -L(H) dimers and PA is established. Comparison with neutral Py-L dimers reveals the strong impact of the positive charge on the acidity of the NH group, the strength of the NHL H-bond, and the preferred ligand binding motif.

Analysis of Fluctuating Friction Version in Sheet Metallic Designing

NASA Astrophysics Data System (ADS)

Ambarayil Joy, Jithin; Jung, Dong Won

2018-02-01

Conservative Coulomb method indicates steady constant of rub in thin metal panel making that appears or feels close to the real thing. It contributes to describing attainable future event too high shear pressure in making ahead in the position of high R-value steel (AHRS). The study is conducted by pretend the making and spring back of a specific panel to understand the characteristic of the stamping procedure. Corresponding of the describe probable future results with (i) physical force-dependent changeable rub method, (ii) perpetual rub method, and the conclusion of exploratory facts point out a significant upgrading of spring back forecast with the prospective method.

Chromosome-Encoded Broad-Spectrum Ambler Class A β-Lactamase RUB-1 from Serratia rubidaea

PubMed Central

Didi, Jennifer; Ergani, Ayla; Lima, Sandra

2016-01-01

ABSTRACT Whole-genome sequencing of Serratia rubidaea CIP 103234T revealed a chromosomally located Ambler class A β-lactamase gene. The gene was cloned, and the β-lactamase, RUB-1, was characterized. RUB-1 displayed 74% and 73% amino acid sequence identity with the GIL-1 and TEM-1 penicillinases, respectively, and its substrate profile was similar to that of the latter β-lactamases. Analysis by 5′ rapid amplification of cDNA ends revealed promoter sequences highly divergent from the Escherichia coli σ70 consensus sequence. This work further illustrates the heterogeneity of β-lactamases among Serratia spp. PMID:27956418

Chromosome-Encoded Broad-Spectrum Ambler Class A β-Lactamase RUB-1 from Serratia rubidaea.

PubMed

Bonnin, Rémy A; Didi, Jennifer; Ergani, Ayla; Lima, Sandra; Naas, Thierry

2017-02-01

Whole-genome sequencing of Serratia rubidaea CIP 103234 T revealed a chromosomally located Ambler class A β-lactamase gene. The gene was cloned, and the β-lactamase, RUB-1, was characterized. RUB-1 displayed 74% and 73% amino acid sequence identity with the GIL-1 and TEM-1 penicillinases, respectively, and its substrate profile was similar to that of the latter β-lactamases. Analysis by 5' rapid amplification of cDNA ends revealed promoter sequences highly divergent from the Escherichia coli σ 70 consensus sequence. This work further illustrates the heterogeneity of β-lactamases among Serratia spp. Copyright © 2017 American Society for Microbiology.

Tuning metal-to-metal charge transfer of mixed-valence complexes containing ferrocenylpyridine and rutheniumammines via solvent donicity and substituent effects.

PubMed

Chen, Y J; Kao, C H; Lin, S J; Tai, C C; Kwan, K S

2000-01-24

A homogeneous series of heterobimetallic complexes of [R-Fc(4-py)Ru(NH3)5](PF6)2 (R = H, Et, Br, acetyl; Fc(4-py) = 4-ferrocenylpyridine) have been prepared and characterized. The mixed-valence species generated in situ using ferrocenium hexafluorophosphate as the oxidant show class II behavior, and the oxidized sites are ruthenium centered. deltaE(1/2), E(1/2)(Fe(III)/Fe(II)) - E(1/2)(Ru(III)/Ru(II)), an upper limit for deltaGo that is an energetic difference between the donor and acceptor sites, changes sharply and linearly with Gutmann solvent donor number (DN) and Hammett substituent constants (sigma). The solvent-dependent and substituent-dependent intervalence transfer bands were found to vary almost exclusively with deltaE(1/2). The activation energy for the optical electron transfer versus deltaE(1/2) plot yields a common nuclear reorganization energy (lambda) of 0.74 +/- 0.04 eV for this series. The equation that allows one to incorporate the effect of both solvent donicity and substituents on optical electron transfer is Eop = lambda + deltaGo, where deltaGo = (deltaGo)intrinsic + (deltaGo)solvent donicity + (deltaGo)substituent effect (deltaGo )intinnsic with a numerical value of 0.083 +/- 0.045 eV was obtained from the intercept of the deltaE(1/2) of [H-Fc(4-py)Ru(NH3)5]2+,3+,4+ versus DN plot. (deltaGo)solvent donicity was obtained from the average slopes of the deltaE(1/2) of [R-Fc-(4-py)Ru(NH3)5]2+,3+,4+ versus DN plot, and (deltaGo)substituent effect was obtained from the average slopes of the corresponding deltaE(1/2) versus sigma plot. The empirical equation allows one to finely tune Eop of this series to Eop = 0.82 + 0.019(DN) + 0.44sigma eV at 298 K, and the discrepancy between the calculated and experimental data is less than 6%.

Strongly Circularly Polarized Emission from Water-Soluble Eu(III)- and Tb(III)-Based Complexes: A Structural and Spectroscopic Study.

PubMed

Leonzio, Marco; Melchior, Andrea; Faura, Georgina; Tolazzi, Marilena; Zinna, Francesco; Di Bari, Lorenzo; Piccinelli, Fabio

2017-04-17

Water-soluble Eu(III) and Tb(III) complexes with N,N'-bis(2-pyridylmethyl)-trans-1,2-diaminocyclohexane-N,N'-diacetic acid (H 2 bpcd) have been synthesized and characterized in their racemic and enantiopure forms. The ligand has been designed to bind Ln(III) ions, providing a dissymmetric environment able to solicit strong chiroptical features while at the same time leaving a few coordination sites available for engaging further ancillary ligands. Potentiometric studies show that Ln(III) complexes have a relatively good stability and that at pH 7 the [Ln(bpcd)] + species is largely dominant. DFT calculations carried out on the (S,S)-[Y(bpcd)(H 2 O) 5 ] + complexes (the closed-shell equivalents of [Eu(bpcd)(H 2 O) 5 ] + and [Tb(bpcd)(H 2 O) 5 ] + ) indicate that the two trans-O,O and trans-N py ,N py configurations are equally stable in solution and present two coordinated water molecules. This is in agreement with the hydration number ∼2.6 determined by luminescence lifetime measurements on Tb(III) and Eu(III) complexes. A detailed optical and chiroptical spectroscopic characterization has been carried out and reveals that the complexes display an efficient luminescence in the visible spectral range accompanied by a strong CPL activity. A value for g lum (around 0.1 on the top of the 546 nm band) for the Tb-based complex has been found. This is one of the highest g lum values measured up to now for chiral Tb complexes. These results suggest that in principle Tb(bpcd)Cl is suitable to be employed as a CPL bioprobe for relevant analytes in aqueous media.

Adequate Hand Washing and Glove Use Are Necessary To Reduce Cross-Contamination from Hands with High Bacterial Loads.

PubMed

Robinson, Andrew L; Lee, Hyun Jung; Kwon, Junehee; Todd, Ewen; Rodriguez, Fernando Perez; Ryu, Dojin

2016-02-01

Hand washing and glove use are the main methods for reducing bacterial cross-contamination from hands to ready-to-eat food in a food service setting. However, bacterial transfer from hands to gloves is poorly understood, as is the effect of different durations of soap rubbing on bacterial reduction. To assess bacterial transfer from hands to gloves and to compare bacterial transfer rates to food after different soap washing times and glove use, participants' hands were artificially contaminated with Enterobacter aerogenes B199A at ∼9 log CFU. Different soap rubbing times (0, 3, and 20 s), glove use, and tomato dicing activities followed. The bacterial counts in diced tomatoes and on participants' hands and gloves were then analyzed. Different soap rubbing times did not significantly change the amount of bacteria recovered from participants' hands. Dicing tomatoes with bare hands after 20 s of soap rubbing transferred significantly less bacteria (P < 0.01) to tomatoes than did dicing with bare hands after 0 s of soap rubbing. Wearing gloves while dicing greatly reduced the incidence of contaminated tomato samples compared with dicing with bare hands. Increasing soap washing time decreased the incidence of bacteria recovered from outside glove surfaces (P < 0.05). These results highlight that both glove use and adequate hand washing are necessary to reduce bacterial cross-contamination in food service environments.

Synthesis, X-ray structure and electrochemical oxidation of palladium(II) complexes of ferrocenyldiphenylphosphine.

PubMed

Bennett, Martin A; Bhargava, Suresh K; Bond, Alan M; Burgar, Iko M; Guo, Si-Xuan; Kar, Gopa; Privér, Steven H; Wagler, Jörg; Willis, Anthony C; Torriero, Angel A J

2010-10-14

Four new complexes, [PdX(κ(2)-2-C(6)R(4)PPh(2))(PPh(2)Fc)] [X = Br, R = H (1), R = F (2); X = I, R = H (3), R = F (4)], containing ferrocenyldiphenylphosphine (PPh(2)Fc) have been prepared and fully characterised. The X-ray structures of complexes trans-1, cis-2 and cis-4, and that of a decomposition product of 4, [Pd(κ(2)-2-C(6)F(4)PPh(2))(μ-I)(μ-2-C(6)F(4)PPh(2))PdI(PPh(2)Fc)] (5), have been determined. These complexes show a distorted square planar geometry about the metal atom, the bite angles of the chelate ligands being about 69°, as expected. The cis/trans ratio of 1-4 in solution is strongly dependent on solvent. The new complexes and the uncoordinated PPh(2)Fc ligand were electrochemically characterised by cyclic and rotating disk voltammetry, UV-visible spectroelectrochemistry, and bulk electrolysis in dichloromethane and acetonitrile. In both cases, oxidation occurs at both the ferrocene and phosphine centres, but the complexes oxidise at more positive potentials than uncoordinated PPh(2)Fc; subsequently, the metal-phosphorus bond is cleaved, leading to free PPh(2)Fc(+), which undergoes further chemical and electrochemical reactions.

Comprehensive analysis of mycolic acid subclass and molecular species composition of Mycobacterium bovis BCG Tokyo 172 cell wall skeleton (SMP-105).

PubMed

Uenishi, Yuko; Fujita, Yukiko; Kusunose, Naoto; Yano, Ikuya; Sunagawa, Makoto

2008-02-01

The mycobacterial cell envelope consists of a characteristic cell wall skeleton (CWS), a mycoloyl arabinogalactan peptidoglycan complex, and related hydrophobic components that contribute to the cell surface properties. Since mycolic acids have recently been reported to play crucial roles in host immune response, detailed molecular characterization of mycolic acid subclasses and sub-subclasses of CWS from Mycobacterium bovis BCG Tokyo 172 (SMP-105) was performed. Mycolic acids were liberated by alkali hydrolysis from SMP-105, and their methyl esters were separated by silica gel TLC into three subclasses: alpha-, methoxy-, and keto-mycolates. Each mycolate subclass was further separated by silver nitrate (AgNO(3))-coated silica gel TLC into sub-subclasses. Molecular weights of individual mycolic acid were determined by MALDI-TOF mass spectrometry. alpha-Mycolates were sub-grouped into cis, cis-dicyclopropanoic (alpha1), and cis-monocyclopropanoic-cis-monoenoic (alpha2) series; methoxy-mycolates were sub-grouped into cis-monocyclopropanoic (m1), trans-monocyclopropanoic (m2), trans-monoenoic (m3), cis-monocyclopropanoic-trans-monoenoic (m4), cis-monoenoic (m5), and cis-monocyclopropanoic-cis-monoenoic (m6) series; and keto-mycolates were sub-grouped into cis-monocyclopropanoic (k1), trans-monocyclopropanoic (k2), trans-monoenoic (k3), cis-monoenoic (k4), and cis-monocyclopropanoic-cis-monoenoic (k5) series. The position of each functional group, including cyclopropane rings and methoxy and keto groups, was determined by analysis of the meromycolates with fast atom bombardment (FAB) mass spectrometry and FAB mass-mass spectrometry, and the cis/trans ratio of cyclopropane rings and double bonds were determined by NMR analysis of methyl mycolates. Mycolic acid subclass and molecular species composition of SMP-105 showed characteristic features including newly-identified cis-monocyclopropanoic-trans-monoenoic mycolic acid (m4).

Nickel(II) complexes of tripodal 4N ligands as catalysts for alkane oxidation using m-CPBA as oxidant: ligand stereoelectronic effects on catalysis.

PubMed

Balamurugan, Mani; Mayilmurugan, Ramasamy; Suresh, Eringathodi; Palaniandavar, Mallayan

2011-10-07

Several mononuclear Ni(II) complexes of the type [Ni(L)(CH(3)CN)(2)](BPh(4))(2) 1-7, where L is a tetradentate tripodal 4N ligand such as N,N-dimethyl-N',N'-bis(pyrid-2-ylmethyl)ethane-1,2-diamine (L1), N,N-diethyl-N',N'-bis(pyrid-2-ylmethyl)ethane-1,2-diamine (L2), N,N-dimethyl-N'-(1-methyl-1H-imidazol-2-ylmethyl)-N'-(pyrid-2-ylmethyl)ethane-1,2-diamine (L3), N,N-dimethyl-N',N'-bis(1-methyl-1H-imidazol-2-ylmethyl)ethane-1,2-diamine (L4), N,N-dimethyl-N',N'-bis(quinolin-2-ylmethyl)ethane-1,2-diamine (L5), tris(benzimidazol-2-ylmethyl)amine (L6) and tris(pyrid-2-ylmethyl)amine (L7), have been isolated and characterized using CHN analysis, UV-Visible spectroscopy and mass spectrometry. The single-crystal X-ray structures of the complexes [Ni(L1)(CH(3)CN)(H(2)O)](ClO(4))(2) 1a, [Ni(L2)(CH(3)CN)(2)](BPh(4))(2) 2, [Ni(L3)(CH(3)CN)(2)](BPh(4))(2) 3 and [Ni(L4)(CH(3)CN)(2)](BPh(4))(2) 4 have been determined. All these complexes possess a distorted octahedral coordination geometry in which Ni(II) is coordinated to four nitrogen atoms of the tetradentate ligands and two CH(3)CN (2, 3, 4) or one H(2)O and one CH(3)CN (1a) are located in cis positions. The Ni-N(py) bond distances (2.054(2)-2.078(3) Å) in 1a, 2 and 3 are shorter than the Ni-N(amine) bonds (2.127(2)-2.196(3) Å) because of sp(2) and sp(3) hybridizations of the pyridyl and tertiary amine nitrogens respectively. In 3 the Ni-N(im) bond (2.040(5) Å) is shorter than the Ni-N(py) bond (2.074(4) Å) due to the stronger coordination of imidazole compared with the pyridine donor. In dichloromethane/acetonitrile solvent mixture, all the Ni(ii) complexes possess an octahedral coordination geometry, as revealed by the characteristic ligand field bands in the visible region. They efficiently catalyze the hydroxylation of alkanes when m-CPBA is used as oxidant with turnover number (TON) in the range of 340-620 and good alcohol selectivity for cyclohexane (A/K, 5-9). By replacing one of the pyridyl donors in TPA by a weakly coordinating -NMe(2) or -NEt(2) donor nitrogen atom the catalytic activity decreases slightly with no change in the selectivity. In contrast, upon replacing the pyridyl nitrogen donor by the strongly σ-bonding imidazolyl or sterically demanding quinolyl/benzimidazolyl nitrogen donor, both the catalytic activity and selectivity decrease, possibly due to destabilization of the intermediate [(4N)(CH(3)CN)Ni-O˙](+) radical species. Adamantane is selectively (3°/2°, 12-17) oxidized to 1-adamantanol, 2-adamantanol and 2-adamantanone while cumene is selectively oxidized to 2-phenyl-2-propanol. In contrast to cyclohexane oxidation, the incorporation of sterically hindering quinolyl/benzimidazolyl donors around Ni(ii) leads to a high 3°/2° bond selectivity for adamantane oxidation. A linear correlation between the metal-ligand covalency parameter (β) and the turnover number has been observed.

Effects of protonation and metal coordination on intramolecular charge transfer of tetrathiafulvalene compound.

PubMed

Zhu, Qin-Yu; Liu, Yu; Lu, Wen; Zhang, Yong; Bian, Guo-Qing; Niu, Gai-Yan; Dai, Jie

2007-11-26

A protonated bifunctional pyridine-based tetrathiafulvalene (TTF) derivative (DMT-TTF-pyH)NO3 and a copper(II) complex Cu(acac)2(DMT-TTF-py)2 have been obtained and studied. Electronic spectra of the protonated compound show a large ICT (intramolecular charge transfer) band shift (Deltalambda=136 nm) compared with that of the neutral compound. Cyclic voltammetry also shows a large shift of the redox potentials (DeltaE1/2(1)=77 mV). Theoretical calculation suggests that the pyridium substituent is a strong pi-electron acceptor. Crystal structures of the protonated compound and the metal complex have been obtained. The dihedral angle between least-squares planes of the pyridyl group and the dithiole ring might reflect the intensity of the ICT effect between the TTF moiety and the pyridyl group. It is also noteworthy that the TTF moiety could be oxidized to TTF2+ dication by Fe(ClO4)(3).6H2O when forming a metal complex, while the protonated TTF derivative can only be oxidized to the TTF*+ radical cation by Fe(ClO4)(3).6H2O even with an excess amount of the Fe(III) salt, which can be used to control the oxidation process to obtain neutral TTF, TTF*+ radical cation, or TTF2+ dication.

A theoretical study of the hydrogen bonding between the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride

NASA Astrophysics Data System (ADS)

Rusu, Victor H.; da Silva, João Bosco P.; Ramos, Mozart N.

2009-04-01

MP2/6-31++G(d,p) and B3LYP/6-31++G(d,p) theoretical calculations have been employed to investigate the hydrogen bonding formation involving the vic-, cis- and trans-C 2H 2F 2 isomers and hydrogen fluoride. Our calculations have revealed for each isomer the preferential existence of two possible hydrogen-bonded complexes: a non-cyclic complex and a cyclic complex. For all the three isomers the binding energies for the non-cyclic and cyclic hydrogen complexes are essentially equal using both the MP2 and B3LYP calculations, being that the cyclic structure is slightly more stable. For instance, the binding energies including BSSE and ZPE corrections for the non-cyclic and cyclic structures of cis-C 2H 2F···HF are 8.7 and 9.0 kJ mol -1, respectively, using B3LYP calculations. The cyclic complex formation reduces the polarity, in contrast to what occurs with the non-cyclic complex. This result is more accentuated in vic-C 2H 2F 2···HF. In this latter, Δ μ(cyclic) is -3.07 D, whereas Δ μ(non-cyclic) is +1.92 D using B3LYP calculations. Their corresponding MP2 values are +0.44 D and -1.89 D, respectively. As expected, the complexation produces an H sbnd F stretching frequency downward shift, whereas its IR intensity is enhanced. On the other hand, the vibrational modes of the vic-, cis- and trans-C 2H 2F 2 isomers are little affected by complexation. The new vibrational modes due to hydrogen bonding formation show several interesting features, in particular the HF bending modes which are pure rotations in the free molecule.

27 CFR 20.118 - Rubbing alcohol general-use formula.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Rubbing alcohol general-use formula. 20.118 Section 20.118 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTRIBUTION AND USE OF DENATURED ALCOHOL AND RUM...

27 CFR 20.118 - Rubbing alcohol general-use formula.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Rubbing alcohol general-use formula. 20.118 Section 20.118 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS DISTRIBUTION AND USE OF DENATURED ALCOHOL AND RUM...

A Reality Rub Crisis Intervention: "I Wish There Was a Law against Belts."

ERIC Educational Resources Information Center

Long, Nicholas J.; Techet, Bonnie

1994-01-01

Presents Life Space Interview (LSI) or Life Space Crisis Intervention (LSCI) with second-grade student from threatening home environment. Uses Reality Rub Intervention Interview, focusing on five variations: distorted perceptions, tunnel vision, faulty thinking, avoidance, and alibi. Describes incident that led to intervention, interview itself,…

Recommendations and requirements for soap and hand rub dispensers in healthcare facilities.

PubMed

Assadian, Ojan; Kramer, Axel; Christiansen, Bärbel; Exner, Martin; Martiny, Heike; Sorger, Arno; Suchomel, Miranda

2012-01-01

Hand hygiene is one of the most important measures to prevent transmission of infectious agents and plays a major role in prevention of infection in any type of healthcare setting. While requirements for the efficacy of hand disinfectants are defined in European testing norms such as the EN 1500 for hygienic hand disinfection or EN 12791 for surgical hand preparation, no specific recommendations for hand rub dispensers and liquid soap dispensers have been given yet. Therefore, the intention of the present recommendation on soap and hand rub dispensers in healthcare facilities is to close this gap and to enhance future improvement of dispenser functionality and design. Regardless of manufacture and design of a hand rub or liquid soap dispensers the following requirements shall be met in healthcare facilities:Triggering the dispenser must be possible without using hands. Sensor- or elbow-operated dispensers both fulfill this requirement. Dispensers must be only refillable in a modality where the content, be it a hand rub or liquid soap, cannot be contaminated. This is achieved best by using replaceable cartridge systems. Refilling through "top-up" must not be possible. The disperser should allow usage of different types of cartridges made by different manufacturers. Dispensers must be operated and maintained such that a microbial contamination of the pump nozzle may easily be avoided. It must be possible to identify the products used in a dispenser easily and without any manipulation. Identifying the type of product, be it a hand rub or a liquid soap, as well as reading the product's name and critical manufacturers' warnings must be possible at any time. The disperser must allow identification of the level of the used product without any further manipulation at any time. The design of the dispenser must allow easy cleaning and disinfection the outside and inside of the dispenser. The manufacturer of the dispenser must provide the user with information on applicable chemicals and cleaning products. It must be possible to reprocess the dispenser and all of its permanent parts by applying machine based thermal disinfection at an A(0)-value of minimum 60 (e.g. 80°C/1 minute). Automatically portioning dispensers shall not fail during 200 hubs. The maximal allowed failure rate shall not exceed 1% (2 out of 200 consecutive hubs). A dispenser used for alcohol based hand rubs must allow keeping the alcohol concentration constant over a time period of 3 months. The maximum acceptable decrease in the concentration of the alcohol shall not exceed 5%. Liquid soap and hand rub dispensers with single-use pumps, ideally already mounted on the cartridge and to be discharged with the empty cartridge, are preferable. If pumps are used on the next consecutive cartridge, the manufacturer must provide the user with a detailed introduction for cleansing and reprocessing before further use. Because of forensic reasons it is recommended to place a good readable sign on the dispenser indicating e.g. "Apply alcohol based hand rubs only on the hand! Do not drink, avoid spraying into the eye or application on mucous membranes". It is regarded as an additional benefit, if the dispenser is able to document the consumption of hand rub or the frequency of hubs either mechanically or electronically.

PyHLA: tests for the association between HLA alleles and diseases.

PubMed

Fan, Yanhui; Song, You-Qiang

2017-02-06

Recently, several tools have been designed for human leukocyte antigen (HLA) typing using single nucleotide polymorphism (SNP) array and next-generation sequencing (NGS) data. These tools provide high-throughput and cost-effective approaches for identifying HLA types. Therefore, tools for downstream association analysis are highly desirable. Although several tools have been designed for multi-allelic marker association analysis, they were designed only for microsatellite markers and do not scale well with increasing data volumes, or they were designed for large-scale data but provided a limited number of tests. We have developed a Python package called PyHLA, which implements several methods for HLA association analysis, to fill the gap. PyHLA is a tailor-made, easy to use, and flexible tool designed specifically for the association analysis of the HLA types imputed from genome-wide genotyping and NGS data. PyHLA provides functions for association analysis, zygosity tests, and interaction tests between HLA alleles and diseases. Monte Carlo permutation and several methods for multiple testing corrections have also been implemented. PyHLA provides a convenient and powerful tool for HLA analysis. Existing methods have been integrated and desired methods have been added in PyHLA. Furthermore, PyHLA is applicable to small and large sample sizes and can finish the analysis in a timely manner on a personal computer with different platforms. PyHLA is implemented in Python. PyHLA is a free, open source software distributed under the GPLv2 license. The source code, tutorial, and examples are available at https://github.com/felixfan/PyHLA.

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

DOE PAGES

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; ...

2016-04-29

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterialmore » community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. As a result, we identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.« less

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

PubMed Central

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; Koechli, Chantal; Campbell, Ashley; Buckley, Daniel H; Lehmann, Johannes

2016-01-01

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil. PMID:27128990

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterialmore » community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. As a result, we identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.« less

Discrimination in Degradability of Soil Pyrogenic Organic Matter Follows a Return-On-Energy-Investment Principle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, Omar R.; Myers-Pigg, Allison N.; Kuo, Li-Jung

A fundamental understanding of biodegradability is central to elucidating the role(s) of pyrogenic organic matter (PyOM) in biogeochemical cycles. Since microbial community and ecosystem dynamics are driven by net energy flows, then a quantitative assessment of energy value versus energy requirement for oxidation of PyOM should yield important insights into their biodegradability. We used bomb calorimetry, step-wise isothermal thermogravimetric analysis (isoTGA) and 5-year in-situ bidegradation data, to develop energy-biodegradability relationships for a suite of plant- and manure-derived PyOM (n = 10). The net energy value (ΔE) for PyOM was between 4.0 and 175 kJ mol-1; with manure-derived PyOM having themore » highest ΔE. Thermal-oxidation activation energy (Ea) requirements ranged from 51 to 125 kJ mol-1, with wood-derived PyOM having the highest Ea requirements. We propose a return-on-investment (ROI) parameter (ΔE/Ea) for differentiating short-to-medium term biodegradability of PyOM and deciphering if biodegradation will most likely proceed via co-metabolism (ROI < 1) or direct metabolism (ROI ≥ 1). The ROI-biodegradability relationship was sigmoidal with higher biodegradability associated with PyOM of higher ROI; indicating that microbes exhibit a higher preference for “high investment value” PyOM.« less

Structural and energetic basis of ALS-causing mutations in the atypical proline-tyrosine nuclear localization signal of the Fused in Sarcoma protein (FUS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Zi Chao; Chook, Yuh Min

Mutations in the proline/tyrosine–nuclear localization signal (PY-NLS) of the Fused in Sarcoma protein (FUS) cause amyotrophic lateral sclerosis (ALS). Here we report the crystal structure of the FUS PY-NLS bound to its nuclear import receptor Karyopherinβ2 (Kapβ2; also known as Transportin). The FUS PY-NLS occupies the structurally invariant C-terminal arch of Kapβ2, tracing a path similar to that of other characterized PY-NLSs. Unlike other PY-NLSs, which generally bind Kapβ2 in fully extended conformations, the FUS peptide is atypical as its central portion forms a 2.5-turn α-helix. The Kapβ2-binding epitopes of the FUS PY-NLS consist of an N-terminal PGKM hydrophobic motif,more » a central arginine-rich α-helix, and a C-terminal PY motif. ALS mutations are found almost exclusively within these epitopes. Each ALS mutation site makes multiple contacts with Kapβ2 and mutations of these residues decrease binding affinities for Kapβ2 (K D for wild-type FUS PY-NLS is 9.5 nM) up to ninefold. Thermodynamic analyses of ALS mutations in the FUS PY-NLS show that the weakening of FUS-Kapβ2 binding affinity, the degree of cytoplasmic mislocalization, and ALS disease severity are correlated.« less

Homogeneous reduction of CO2 by photogenerated pyridinyl radicals.

PubMed

Riboni, Francesca; Selli, Elena; Hoffmann, M R; Colussi, A J

2015-05-14

We report that 1-hydropyridinyl radicals (1-PyH(•)) photogenerated in solution react with dissolved CO2 en route to its 2e(-) reduction into carboxylic acids. The 254 nm excitation of pyridine (Py) in deaerated 2-PrOH/H2O mixtures saturated with 1 atm of CO2 yields a suite of products, among which we identified Na(HCOO)2(-) (m/z(-) = 113), C5H6NCOO(-) (m/z(-) = 124), and C5H10O2NCOO(-) (m/z(-) = 160) species by electrospray ionization mass spectrometry. These products demonstrably contain carboxylate functionalities that split CO2 neutrals via collisionally induced dissociation. We infer that 1-PyH(•) [from (1) (3)Py* + 2-PrOH → 1-PyH(•) + (•)PrOH] adds to CO2, in competition with radical-radical reactions, leading to intermediates that are in turn reduced by (•)PrOH into the observed species. The formation of carboxylates in this system, which is shown to require CO2, Py, 2-PrOH, and actinic radiation, amounts to the homogeneous 2e(-) reduction of CO2 by 2-PrOH initiated by Py*. We evaluate a rate constant (2) k2(1-PyH(•) + CO2 → (•)Py-1-COOH) ≈ O (10) M(-1) s(-1) and an activation energy E2 ≥ 9 kcal mol(-1) that are compatible with thermochemical estimates for this reaction.

Twistacene contained molecule for optical nonlinearity: Excited-state based negative refraction and optical limiting

NASA Astrophysics Data System (ADS)

Wu, Xingzhi; Xiao, Jinchong; Sun, Ru; Jia, Jidong; Yang, Junyi; Ao, Guanghong; Shi, Guang; Wang, Yuxiao; Zhang, Xueru; Song, Yinglin

2018-06-01

Spindle-type molecules containing twisted acenes (PyBTA-1 &PyBTA-2) are designed, synthesized characterized. Picosecond Z-scan experiments under 532 nm show reverse saturable absorption and negative nonlinear refraction, indicating large third-order optical nonlinearity in PyBTA-1. The mechanism of the optical nonlinearity is investigated and the results show that the nonlinear absorption and refraction in PyBTA-1 originates from a charge transfer (CT) state. Furthermore, relatively long lifetime and absorptive cross section of the CT state are measured. Based on the excited state absorption in PyBTA-1, strong optical limiting with ∼0.3 J/cm2 thresholds are obtained when excited by picoseconds and nanoseconds pulses. The findings on nonlinear optics suggest PyBTA-1 a promising material of all optical modulation and laser protection, which enrich the potential applications of these spindle-type molecules. Comparing to the previously reported spindle-type molecules with analogous structures, the introduction of ICT in PyBTA-1 &PyBTA-2 dramatically decreases the two-photon absorption while enhances the nonlinear refraction. The results could be used to selectively tailor the optical nonlinearity in such kind of compounds.

Neutral and cationic phosphoramide adducts of silicon tetrachloride: synthesis and characterization of their solution and solid-state structures.

PubMed

Denmark, Scott E; Eklov, Brian M

2008-01-01

The solution and solid-state structures of hexamethylphosphoramide (HMPA) adducts of tetrachlorosilane (SiCl4) are discussed. In solution, the meridional and facial isomers of the hexa-coordinate cationic complex 3 HMPASiCl3 + Cl(-) (2) predominate at all HMPA concentrations, and are in equilibrium with the hexa-coordinate neutral trans- and cis-2 HMPASiCl4 complexes (1), as well as the penta-coordinate cationic cis-2 HMPASiCl3 + Cl(-) (3). Single crystal X-ray analyses are reported for the ionized mer-3 HMPASiCl3 + HCl2 (-) and the neutral trans-2 HMPASiCl4 complexes.

Effect of oxygen and hydrogen on microstructure of pyrolytic carbon deposited from thermal decomposition of methane and ethanol

NASA Astrophysics Data System (ADS)

Ren, Biyun; Zhang, Shouyang; He, LiQun; Gu, Shengyue

2018-05-01

Chemical vapor infiltration (CVI) is the most extensive industrial preparation of carbon/carbon (C/C) composites. Precursor affects the CVI process considerably. In the present study, using carbon fiber bundles as preforms, methane and ethanol as precursors, the C/C composites were densified by decomposition of various gases in CVI. The thickness and texture of deposited pyrolytic carbon (PyC) were characterized by polarized light microscopy (PLM). The microstructure of PyC was analyzed by Raman spectroscopy. The morphologies of PyC were characterized by scanning electron microscopy (SEM). The composition of PyC was detected by X-ray photoelectron spectroscopy (XPS). Adding hydrogen in methane precursor resulted in a sharp decrease in the deposition rate and texture of PyC. Mixture of methane and ethanol as the precursor improved the deposition rate and texture remarkably. Besides, O element in ethanol was not remained as a constitution of PyC, and it was removed before the formation of PyC.

Intramolecular Tsuji-Trost-type Allylation of Carboxylic Acids: Asymmetric Synthesis of Highly π-Allyl Donative Lactones.

PubMed

Suzuki, Yusuke; Seki, Tomoaki; Tanaka, Shinji; Kitamura, Masato

2015-08-05

Tsuji-Trost-type asymmetric allylation of carboxylic acids has been realized by using a cationic CpRu complex with an axially chiral picolinic acid-type ligand (Cl-Naph-PyCOOH: naph = naphthyl, py = pyridine). The carboxylic acid and allylic alcohol intramolecularly condense by the liberation of water without stoichiometric activation of either nucleophile or electrophile part, thereby attaining high atom- and step-economy, and low E factor. This success can be ascribed to the higher reactivity of allylic alcohols as compared with the allyl ester products in soft Ru/hard Brønstead acid combined catalysis, which can function under slightly acidic conditions unlike the traditional Pd-catalyzed system. Detailed analysis of the stereochemical outcome of the reaction using an enantiomerically enriched D-labeled substrate provides an intriguing view of enantioselection.

Structural Diversities in Heterometallic Mn-Ca Cluster Chemistry from the Use of Salicylhydroxamic Acid: {MnIII4Ca2}, {MnII/III6Ca2}, {MnIII/IV8Ca}, and {MnIII8Ca2} Complexes with Relevance to Both High- and Low-Valent States of the Oxygen-Evolving Complex.

PubMed

Alaimo, Alysha A; Koumousi, Evangelia S; Cunha-Silva, Luís; McCormick, Laura J; Teat, Simon J; Psycharis, Vassilis; Raptopoulou, Catherine P; Mukherjee, Shreya; Li, Chaoran; Gupta, Sayak Das; Escuer, Albert; Christou, George; Stamatatos, Theocharis C

2017-09-05

One-pot reactions between the [Mn 3 O(O 2 CPh) 6 (py) x ] +/0 triangular precursors and either CaBr 2 ·xH 2 O or CaCl 2 ·6H 2 O, in the presence of salicylhydroxamic acid (shaH 2 ), have afforded the heterometallic complexes [Mn III 4 Ca 2 (O 2 CPh) 4 (shi) 4 (H 2 O) 3 (Me 2 CO)] (1) and (pyH)[Mn II 2 Mn III 4 Ca 2 Cl 2 (O 2 CPh) 7 (shi) 4 (py) 4 ] (2), respectively, in good yields. Further reactions but using a more flexible synthetic scheme comprising the Mn(NO 3 ) 2 ·4H 2 O/Ca(NO 3 ) 2 ·4H 2 O and Mn(O 2 CPh) 2 ·2H 2 O/Ca(ClO 4 ) 2 ·4H 2 O "metal blends" and shaH 2 , in the presence of external base NEt 3 , led to the new complexes (NHEt 3 ) 2 [Mn III 4 Mn IV 4 Ca(OEt) 2 (shi) 10 (EtOH) 2 ] (3) and (NHEt 3 ) 4 [Mn III 8 Ca 2 (CO 3 ) 4 (shi) 8 ] (4), respectively. In all reported compounds, the anion of the tetradentate (N,O,O,O)-chelating/bridging ligand salicylhydroxime (shi 3- ), resulting from the in situ metal-ion-assisted amide-iminol tautomerism of shaH 2 , was found to bridge both Mn and Ca atoms. Complexes 1-4 exhibit a variety of different structures, metal stoichiometries, and Mn oxidation-state descriptions; 1 possesses an overall octahedral metal arrangement, 2 can be described as a Mn 4 Ca 2 octahedron bound to an additional Mn 2 unit, 3 consists of a Mn 8 "ring" surrounding a Ca II atom, and 4 adopts a rectangular cuboidal motif of eight Mn atoms accommodating two Ca II atoms. Solid-state direct-current magnetic susceptibility studies revealed the presence of predominant antiferromagnetic exchange interactions between the Mn centers, leading to S = 0 spin ground-state values for all complexes. From a bioinorganic chemistry perspective, the reported compounds may demonstrate some relevance to both high-valent scheme (3) and lower-oxidation-level species (1, 2, and 4) of the catalytic cycle of the oxygen-evolving complex.

EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing.

PubMed

Picardi, Ernesto; Quagliariello, Carla

2006-02-01

EdiPy is an online resource appropriately designed to simulate the evolution of plant mitochondrial genes in a biologically realistic fashion. EdiPy takes into account the presence of sites subjected to RNA editing and provides multiple artificial alignments corresponding to both genomic and cDNA sequences. Each artificial data set can successively be submitted to main and widespread evolutionary and phylogenetic software packages such as PAUP, Phyml, PAML and Phylip. As an online bioinformatic resource, EdiPy is available at the following web page: http://biologia.unical.it/py_script/index.html.

Global Distribution of Pyrogenic Carbon

NASA Astrophysics Data System (ADS)

Reisser, Moritz; Abiven, Samuel; Schmidt, Michael W. I.

2016-04-01

Pyrogenic Carbon (PyC) is ubiquitous in the environment and represents presumably one of the most stable compounds of the total organic carbon. Due to its persistence in the soil, it might play an important role in the global carbon cycle. In order to model future CO2 emissions from soils it is thus crucial to know where and how much of PyC exists on a global scale. Yet, only rough estimates for global PyC stocks in soils could be made, and even less is known about the distribution across ecosystems. Therefore we propose here literature analysis of data on PyC concentrations and stocks worldwide. We extracted PyC values in soils from the literature (n = 600) and analysed the percentage of PyC in the soil organic carbon (SOC) as a function of climate (temperature, precipitation), soil parameters (pH, clay content), fire characteristics (fire frequency and fire regime) and land use. Overall, the average contribution of PyC to SOC was 13 %, ranging from 0.1 % up to 60 %. We observed that the PyC content was significantly higher with high clay content, higher pH, and in cultivated land as compared to forest and grassland. We did not observe any relationships between fire activity, frequency or intensity and PyC % at a global scale. When the fire regime was monitored on site (only 12 % of the data we collected), we observed higher PyC concentrations with higher fire frequencies. We hypothesise that the resolution of global fire datasets is neither temporally nor spatially high enough to explain the very local fire history of the soil samples. Data points were not homogeneously distributed on the globe, but rather aggregated in places like Central Europe, the Russian Steppe or North America. Therefore, a global interpolation is not directly possible. We modelled PyC concentrations, based on the five most significant parameters, which were clay content, pH, mean annual temperature and precipitation as well as land use. We then predicted worldwide PyC using global datasets existing for these five variables. We present a global map of PyC concentrations as well as it stocks. In arid ecosystems, where SOC is generally low, stocks of PyC are also low, even though concentrations can be very high. On the other hand, stocks are mostly very large in temperate and boreal ecosystems, even if concentrations are rather low, because total SOC stocks are very high there. Integrating our modelled data, we result in a total global stock of about 230 Pg PyC, corresponding to about 10 % of the total soil organic carbon stock. This value lies well in range with current rule-of-thump estimates of previous studies.

Photochemistry of Iron and Ruthenium Carbonyl Complexes: Evidence for Light-Induced Loss of Carbon Monoxide and Reductive Elimination of Triethylsilane from cis-mer-HM(SiEt3)(CO)3(PPh3).

DTIC Science & Technology

1983-05-21

JEOL FX9OQ Fourier transform or Bruker 250 or 270 MHz Fourier transform spectrometer. Irradiations. Photochemical reactions were carried out using a...Ph 3 ) 3nd -t-Etin V,- a 313 nm quantum yield of -0.6. The process is photochemically everse if the cis-mer-HM(SiPh 3 )(CO) 3 (PPh 3) is irradiated...process is photochemically reversed if the cis-mer-HM(SiPh 3 )(CO)3 (PPh 3 ) is irradiated in t.e presence of excess Et3SiH. Irradiation of cis-mer-HM

PyClone: statistical inference of clonal population structure in cancer.

PubMed

Roth, Andrew; Khattra, Jaswinder; Yap, Damian; Wan, Adrian; Laks, Emma; Biele, Justina; Ha, Gavin; Aparicio, Samuel; Bouchard-Côté, Alexandre; Shah, Sohrab P

2014-04-01

We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination. Single-cell sequencing validation demonstrates PyClone's accuracy.

Redistribution of pyrogenic carbon from hillslopes to stream corridors following a large montane wildfire

Treesearch

M. Francesca Cotrufo; Claudia M. Boot; Stephanie Kampf; Peter A. Nelson; Daniel J. Brogan; Tim Covino; Michelle L. Haddix; Lee H. MacDonald; Sarah Rathburn; Sandra Ryan-Burkett; Sarah Schmeer; Ed Hall

2016-01-01

Pyrogenic carbon (PyC) constitutes a significant fraction of organic carbon in most soils. However, PyC soil stocks are generally smaller than what is expected from estimates of PyC produced from fire and decomposition losses, implying that other processes cause PyC loss from soils. Surface erosion has been previously suggested as one such process. To address this,...

Structure-Property Study on Two New D-A Type Materials Comprising Pyridazine Moiety and the OLED Application as Host.

PubMed

Liu, Shaojie; Zhang, Xunlu; Ou, Changjin; Wang, Shulei; Yang, Xinli; Zhou, Xinhui; Mi, Baoxiu; Cao, Dapeng; Gao, Zhiqiang

2017-08-09

In this paper, two new pyridazine based donor-acceptor type materials, i.e., 3CzPyaPy: 9,9'-(3-(6-(9H-carbazol-9-yl)pyridazin-3-yl)pyridine-2,6-diyl)bis(9H-carbazole) and 4CzPyPyaPy: 3,6-bis(2,6-di(9H-carbazol-9-yl)pyridin-3-yl)pyridazine, were synthesized with high yields. These two materials exhibited strong absorption/emission with high molar extinction coefficients and moderate photoluminescence quantum yield. The glass transition temperature of 3CzPyaPy was detected to be as high as 131 °C, showing its high thermal stability. Although the absorption energies and oxidation/reduction behaviors of the two materials were similar, the emission from 4CzPyPyaPy with longer effective-conjugation length presented hypsochromic shift both in films and in dilute solutions, contradicting to the common sense. The single crystal structure study disclosed their different space stretching and packing: 3CzPyaPy was twisted in larger angles and adopted dimerlike packing, while 4CzPyPyaPy showed smaller torsion angles and exhibited slipped herringbone packing. The dimerlike packing in 3CzPyaPy is responsible for its bathochromic shift of emission in solid state, while its unsymmetrical molecular structure accounts for that in solution. We believe that the unsymmetrical molecular structure of 3CzPyaPy is partially responsible for its high thermal-stability and also responsible for its HOMO dispersion which renders it slightly more difficult to oxidize. 3CzPyaPy was proved to be a bipolar-transport material and when served as a phosphor host, a green phosphorescent device achieved maximum efficiencies of 54.0 cd A -1 , 42.4 lm W -1 , and 17.7%, which are among the best with nonoptimized device structure, demonstrating its great potential for optoelectronic application. Furthermore, the new synthesized pyridazine derivatives and the corresponding structural and molecular-packing influences on material properties give a new insight into molecule tailoring.

Pyrogenic Carbon as a Nonlinear Driver in the Carbon and Nitrogen Cycles

NASA Astrophysics Data System (ADS)

Masiello, C. A.; Silberg, J. J.; Cheng, H. Y.; Gao, X.; Del Valle, I.

2016-12-01

Our first conceptual models of pyrogenic carbon's effects on the carbon cycle treated this material as a form of organic matter whose environmental residence time was long enough to render it inert, and PyC was modeled as an unreactive mass that moved through C cycle reservoirs essentially unmodified. This concept saw modifications with the recognition that some fractions of PyC were labile. For example, the reactive sugars and lignin monomers cleaved off the lignocellulose matrix by heating have lifetimes on the order of hours to weeks. However, the now-common multiple component model of PyC does not satisfactorily explain many nonlinearities that have been observed when it is added to soils. These nonlinearities include the positive and negative "priming" effects sometimes triggered, where the presence of PyC in some matrices can trigger shifts in the overall microbial community metabolism, as well as alteration of microbial community structure, shifts in the behavior of belowground and aboveground plant parasites, and shifted rates of greenhouse gas emissions that are not well-correlated to shifts in soil hydrologic processes. To understand the effects of PyC on the global C and N cycles, we will need a better understanding of the mechanisms behind PyC-driven C and N cycle nonlinearities. This talk will examine potential mechanisms driving the nonlinearities observed in soil systems following the introduction of PyC. Potential mechanisms discussed will include PyC effects on soil microbial communication and PyC effects on microbial electron transfer. Cell-cell communication through the secretion and detection of small molecules is used by soil microbes to manage many biogeochemically relevant processes including production of biofilms, production of extracellular enzymes, and management of methanogenesis and denitrification. PyC disrupts microbial cell-cell communication differentially, altering some species' ability to communicate more than others. Electron transfer between microbes is a central part of many environmental syntrophies, including those responsible for methanogenesis, and has been shown to be altered by the presence of PyC. Both these processes may underlie observed ecosystem-scale shifts following PyC amendment to soils.

Capping Layer (CL) Induced Antidamping in CL/Py/β-W System (CL: Al, β-Ta, Cu, β-W).

PubMed

Behera, Nilamani; Guha, Puspendu; Pandya, Dinesh K; Chaudhary, Sujeet

2017-09-13

For achieving ultrafast switching speed and minimizing dissipation losses, the spin-based data storage device requires a control on effective damping (α eff ) of nanomagnetic bits. Incorporation of interfacial antidamping spin orbit torque (SOT) in spintronic devices therefore has high prospects for enhancing their performance efficiency. Clear evidence of such an interfacial antidamping is found in Al capped Py(15 nm)/β-W(t W )/Si (Py = Ni 81 Fe 19 and t W = thickness of β-W), which is in contrast to the increase of α eff (i.e., damping) usually associated with spin pumping as seen in Py(15 nm)/β-W(t W )/Si system. Because of spin pumping, the interfacial spin mixing conductance (g ↑↓ ) at Py/β-W interface and spin diffusion length (λ SD ) of β-W are found to be 1.63(±0.02) × 10 18 m -2 (1.44(±0.02) × 10 18 m -2 ) and 1.42(±0.19) nm (1.00(±0.10) nm) for Py(15 nm)/β-W(t W )/Si (β-W(t W )/Py(15 nm)/Si) bilayer systems. Other different nonmagnetic capping layers (CL), namely, β-W(2 nm), Cu(2 nm), and β-Ta(2,3,4 nm) were also grown over the same Py(15 nm)/β-W(t W ). However, antidamping is seen only in β-Ta(2,3 nm)/Py(15 nm)/β-W(t W )/Si. This decrease in α eff is attributed to the interfacial Rashba like SOT generated by nonequilibrium spin accumulation subsequent to the spin pumping. Contrary to this, when interlayer positions of Py(15 nm) and β-W(t W ) is interchanged irrespective of the fixed top nonmagnetic layer, an increase of α eff is observed, which is ascribed to spin pumping from Py to β-W layer.

Synthesis, physical properties and self-assembly behavior of azole-fused pyrene derivatives

NASA Astrophysics Data System (ADS)

Xiao, Jinchong; Xiao, Xuyu; Zhao, Yanlei; Wu, Bo; Liu, Zhenying; Zhang, Xuemin; Wang, Sujuan; Zhao, Xiaohui; Liu, Lei; Jiang, Li

2013-05-01

A novel selenadiazole-fused pyrene derivative PySe was successfully synthesized and characterized. Its single structure is almost planar and adopts a sandwich-herringbone packing model. The self-assembly behaviors based on compound PySe and its analogue thiadiazole-fused pyrene derivative PyS were studied in detail and the as-formed nanostructures were fully characterized by means of UV-vis absorption, emission spectra, X-ray diffraction, field emission SEM and TEM. We attribute the bathochromic shift absorption and emission spectra of PyS and PySe in aqueous solution to the formation of J-type aggregation. In addition, our investigation demonstrated that the shape and size of the as-prepared nanostructures could be tuned by different chalcogen analogues and the volume ratio of water to organic solvent.A novel selenadiazole-fused pyrene derivative PySe was successfully synthesized and characterized. Its single structure is almost planar and adopts a sandwich-herringbone packing model. The self-assembly behaviors based on compound PySe and its analogue thiadiazole-fused pyrene derivative PyS were studied in detail and the as-formed nanostructures were fully characterized by means of UV-vis absorption, emission spectra, X-ray diffraction, field emission SEM and TEM. We attribute the bathochromic shift absorption and emission spectra of PyS and PySe in aqueous solution to the formation of J-type aggregation. In addition, our investigation demonstrated that the shape and size of the as-prepared nanostructures could be tuned by different chalcogen analogues and the volume ratio of water to organic solvent. Electronic supplementary information (ESI) available: TGA analysis, spectra characterization data for compound 1, 2, 3 and X-ray crystallographic data for compound PySe (2, CIF). CCDC 917821. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c3nr00523b

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

PubMed Central

Yang, Fan; Wang, Jiebiao; Pierce, Brandon L.; Chen, Lin S.

2017-01-01

The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is “mediation” by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are “cis-mediators” of trans-eQTLs, including those “cis-hubs” involved in regulation of many trans-genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans-eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis-mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis-hubs and trans-eQTL regulation across tissue types. PMID:29021290

Mechanistic analysis of water oxidation catalyst cis-[Ru(bpy) 2(H 2O) 2] 2+: Effect of dimerization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erdman, Darren; Pineda-Galvan, Yuliana; Pushkar, Yulia

While the catalytic activity of some Ru-based polypyridine complexes in water oxidation is well established, the relationship between their chemical structure and activity is less known. In this work, the single site Ru complex [Ru(bpy) 2(H 2O) 2] 2+ (bpy = 2,20-bipyridine)—which can exist as either a cis isomer or a trans isomer—is investigated. While a difference in the catalytic activity of these two isomers is well established, with cis-[Ru(bpy) 2(H 2O) 2] 2+ being much more active, no mechanistic explanation of this fact has been presented. The oxygen evolving capability of both isomers at multiple concentrations has been investigated,more » with cis-[Ru(bpy) 2(H 2O) 2] 2+ showing a second-order dependence of O2 evolution activity with increased catalyst concentration. Measurement of the electron paramagnetic resonance (EPR) spectrum of cis-[Ru(bpy) 2(H 2O) 2] 2+, shortly after oxidation with CeIV, showed the presence of a signal matching that of cis,cis-[Ru III(bpy) 2(H 2O)ORu IV(bpy) 2(OH)] 4+, also known as “blue dimer”. The formation of dimers is a concentration-dependent process, which could serve to explain the greater than first order increase in catalytic activity. The trans isomer showed a first-order dependence of O 2 evolution on catalyst concentration. As a result, behavior of [Ru(bpy) 2(H 2O) 2] 2+ isomers is compared with other Ru-based catalysts, in particular [Ru(tpy)(bpy)(H 2O)] 2+ (tpy = 2,20;6,20 0-terpyridine).« less

Mechanistic analysis of water oxidation catalyst cis-[Ru(bpy) 2(H 2O) 2] 2+: Effect of dimerization

DOE PAGES

Erdman, Darren; Pineda-Galvan, Yuliana; Pushkar, Yulia

2017-01-25

While the catalytic activity of some Ru-based polypyridine complexes in water oxidation is well established, the relationship between their chemical structure and activity is less known. In this work, the single site Ru complex [Ru(bpy) 2(H 2O) 2] 2+ (bpy = 2,20-bipyridine)—which can exist as either a cis isomer or a trans isomer—is investigated. While a difference in the catalytic activity of these two isomers is well established, with cis-[Ru(bpy) 2(H 2O) 2] 2+ being much more active, no mechanistic explanation of this fact has been presented. The oxygen evolving capability of both isomers at multiple concentrations has been investigated,more » with cis-[Ru(bpy) 2(H 2O) 2] 2+ showing a second-order dependence of O2 evolution activity with increased catalyst concentration. Measurement of the electron paramagnetic resonance (EPR) spectrum of cis-[Ru(bpy) 2(H 2O) 2] 2+, shortly after oxidation with CeIV, showed the presence of a signal matching that of cis,cis-[Ru III(bpy) 2(H 2O)ORu IV(bpy) 2(OH)] 4+, also known as “blue dimer”. The formation of dimers is a concentration-dependent process, which could serve to explain the greater than first order increase in catalytic activity. The trans isomer showed a first-order dependence of O 2 evolution on catalyst concentration. As a result, behavior of [Ru(bpy) 2(H 2O) 2] 2+ isomers is compared with other Ru-based catalysts, in particular [Ru(tpy)(bpy)(H 2O)] 2+ (tpy = 2,20;6,20 0-terpyridine).« less

Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.

PubMed

Yang, Fan; Wang, Jiebiao; Pierce, Brandon L; Chen, Lin S

2017-11-01

The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes ( cis -eQTLs). More research is needed to identify effects of genetic variation on distant genes ( trans -eQTLs) and understand their biological mechanisms. One common trans -eQTLs mechanism is "mediation" by a local ( cis ) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are " cis -mediators" of trans -eQTLs, including those " cis -hubs" involved in regulation of many trans -genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans -eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis -mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis -hubs and trans -eQTL regulation across tissue types. © 2017 Yang et al.; Published by Cold Spring Harbor Laboratory Press.

Molecular mechanism of 9-cis-retinoic acid inhibition of adipogenesis in 3T3-L1 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sagara, Chiaki; Takahashi, Katsuhiko; Kagechika, Hiroyuki

2013-03-29

Highlights: ► We examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1. ► 9-cis-RA inhibited lipid accumulation in adipogenetically-induced 3T3-L1 cells. ► A RXR pan-antagonist suppressed the inhibitory effects of 9-cis-RA on adipogenesis. ► This antagonist had no effects on RXRα and PPARγ levels in 9-cis-RA-treated cells. ► 9-cis-RA-induced decrease in both RXRα and PPARγ was independent of RXR activation. -- Abstract: Retinoic acid (RA) signaling is mediated by specific nuclear hormone receptors. Here we examined the effects of 9-cis-RA on adipogenesis in mouse preadipocyte 3T3-L1 cells. 9-cis-RA inhibits the lipid accumulation of adipogenetically induced 3T3-L1 cells. Themore » complex of retinoid X receptor α (RXRα) with peroxisome proliferator-activated receptor γ (PPARγ) is a major transcription factor in the process of adipogenesis, and the levels of these molecules were decreased by 9-cis-RA treatment. A RXR pan-antagonist suppressed 9-cis-RA’s inhibitory effects on adipogenesis, but not on the intracellular levels of both RXRα and PPARγ. These results suggest that 9-cis-RA could inhibit adipogenesis by activating RXR, and decrease both RXR and PPARγs levels in a RXR activation-independent manner.« less

Platinum phosphinothiolato hydride complexes: synthesis, structure and evaluation as tin-free hydroformylation catalysts.

PubMed

Real, Julio; Prat-Gil, Esther; Pagès-Barenys, Montserrat; Polo, Alfonso; Piniella, Joan F; Álvarez-Larena, Ángel

2016-03-07

Ligand 2-diphenylphosphinothiophenol (Hsarp) reacted with Pt(PPh3)4 to yield trans-[PtH(sarp)(PPh3)], which undergoes fast exchange with free PPh3 on the NMR time scale and very slowly and reversibly formed some cis-[PtH(sarp)(PPh3)] over time in solution (11%, 24 h). Reaction of trans-[PtH(sarp)(PPh3)] with Hsarp in boiling toluene gave cis- and trans-[Pt(sarp)2]; the cis isomer being more stable. These complexes were characterized by (1)H and (31)P NMR and also analyzed by XRD in the case of trans-[PtH(sarp)(PPh3)], trans-[Pt(sarp)2], and cis-[Pt(sarp)2]. trans-[PtH(sarp)(PPh3)] was evaluated as a preformed, tin-free hydroformylation catalyst on styrene and found active at 100 °C, at pressures over 75 bar, yielding phenylpropanal (regioselectivities up to 83% in 2-phenylpropanal), with total conversions to aldehydes up to 100% at styrene/platinum ratios from 400/1 to 1000/1 and minimal hydrogenation products.

Comparison between Rinse and Crush-and-Rub Sampling for Aerobic Bacteria Recovery from Hatching Eggs after Sanitization

USDA-ARS?s Scientific Manuscript database

This study compared surface and deep eggshell aerobic bacteria recovered by rinse and crush-and-rub sampling methods for commercial hatching eggs after treatments with sanitizers. Eggs were arranged into 5 treatments consisting of three sanitizers, Water, and No-treatment. Sanitizers were Hydrogen...

Comparison between rinse and crush-and-rub sampling for aerobic bacteria recovery from broiler hatching eggs after sanitization

USDA-ARS?s Scientific Manuscript database

This study compared surface and deep eggshell aerobic bacteria recovered by rinse and crush-and-rub sampling methods for commercial hatching eggs after treatment with sanitizers. Eggs were arranged into 5 treatments consisting of No-treatment, Water, and three sanitizers. Sanitizers were Hydrogen ...

27 CFR 20.118 - Rubbing alcohol general-use formula.

Code of Federal Regulations, 2012 CFR

2012-04-01

... (2) made in accordance with one of the two formulas prescribed in paragraph (b) of this section, and...-use formula. 20.118 Section 20.118 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND... Formulas and Statements of Process General-Use Formulas § 20.118 Rubbing alcohol general-use formula. (a...

27 CFR 20.118 - Rubbing alcohol general-use formula.

Code of Federal Regulations, 2014 CFR

2014-04-01

... (2) made in accordance with one of the two formulas prescribed in paragraph (b) of this section, and...-use formula. 20.118 Section 20.118 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND... Formulas and Statements of Process General-Use Formulas § 20.118 Rubbing alcohol general-use formula. (a...

27 CFR 20.118 - Rubbing alcohol general-use formula.

Code of Federal Regulations, 2013 CFR

2013-04-01

... (2) made in accordance with one of the two formulas prescribed in paragraph (b) of this section, and...-use formula. 20.118 Section 20.118 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND... Formulas and Statements of Process General-Use Formulas § 20.118 Rubbing alcohol general-use formula. (a...

An Australian Response to Michael Bérubé

ERIC Educational Resources Information Center

Frances, Raelene

2016-01-01

This article supports Bérubé's conclusion regarding the intellectual health of humanities scholarship. However, it argues that the case of "contingent faculty"--or academics with short-term or casual contracts--is in many respects different in Australia to the situation he outlines for the US. Whilst a variety of funding pressures have…

Friction and wear of several compressor gas-path seal movements

NASA Technical Reports Server (NTRS)

Bill, R. C.; Wisander, D. W.

1978-01-01

Rub interaction experiments were conducted on a series of sintered and plasma sprayed compressor gas path seal materials in contact with Ti-6Al-4V blade tip and knife edge rotors. The most rub tolerant materials investigated were sintered Nichrome and plasma sprayed nickel 25 percent graphite. The effectiveness of providing a compliant substrate for dense seal material coatings was also demonstrated. In general, it was observed that rotor wear and high frictional energy generation rates accompanied smearing or surface densification of the materials investigated. The onset of smearing was sensitive to rub interaction parameters and seal geometry. Two complementary models were proposed to account for the smearing trends. One is based on thermal effects, the other on particulate escape effects. They were shown to be consistent with the experimental evidence at hand, and together they predict that smearing, with the onset of high energy rub conditions, is favored when incursion rates (radial motion) are low, incursion depths are high, the seal geometry is of a knife-edge character, and the seal particle size is small.

Pressure Actuated Leaf Seals for Improved Turbine Shaft Sealing

NASA Technical Reports Server (NTRS)

Grondahl, Clayton

2006-01-01

This presentation introduces a shaft seal in which leaf seal elements are constructed from slotted shim material formed and layered into a frusto-conical assembly. Limited elastic deflection of seal leaves with increasing system pressure close large startup clearance to a small, non-contacting, steady state running clearance. At shutdown seal elements resiliently retract as differential seal pressure diminishes. Large seal clearance during startup and shutdown provides a mechanism for rub avoidance. Minimum operating clearance improves performance and non-contacting operation promises long seal life. Design features of this seal, sample calculations at differential pressures up to 2400 psid and benefit comparison with brush and labyrinth seals is documented in paper, AIAA 2005 3985, presented at the Advanced Seal Technology session of the Joint Propulsion Conference in Tucson this past July. In this presentation use of bimetallic leaf material will be discussed. Frictional heating of bimetallic leaf seals during a seal rub can relieve the rub condition to some extent with a change in seal shape. Improved leaf seal rub tolerance is expected with bimetallic material.

Synthesis and first use of pyridine-2,6-diylbis(pyrazine-2-ylmethanone) in metal cluster chemistry: a {Mn(III)3Na2} complex with an ideal trigonal bipyramidal geometry.

PubMed

Giannopoulos, Dimosthenis P; Wilson-Konderka, Cody; Gagnon, Kevin J; Teat, Simon J; Escuer, Albert; Metallinos, Costa; Stamatatos, Theocharis C

2015-03-07

The successful organic synthesis of a new dipyrazole/pyridine-dicarbonyl organic molecule, namely pyridine-2,6-diylbis(pyrazine-2-ylmethanone) [(pz)CO(py)CO(pz)], followed by its employment in Mn coordination chemistry has yielded the neutral cluster compound [Mn3Na2O(N3)3(L)3] (1), where L(2-) is the (pz)C(CH2COCH3)(O(-))(py)C(CH2COCH3)(O(-))(pz) dianion. The latter group was formed in situ, presumably by the nucleophilic attack of the carbanion (-)CH2COCH3 to the carbonyl carbon atoms of (pz)CO(py)CO(pz), in the presence of Mn(n+) ions under basic conditions and in solvent Me2CO. Complex 1 possesses an almost ideal trigonal bipyramidal topology, with the two Na(I) ions occupying the apical positions and the three Mn(III) ions residing in the equatorial trigonal plane. The bridging ligation about the metal ions is provided by a μ3-O(2-) ion and six μ-OR(-) groups from the L(2-) ligand, while peripheral ligation is completed by three terminal azido groups and the pyridine N and carbonyl O atoms of L(2-). Magnetic susceptibility studies revealed the presence of predominant antiferromagnetic exchange interactions between the paramagnetic Mn(III) centres; the use of an anisotropic, equilateral Mn(III)3 triangle model allowed us to fit the magnetic data and obtain the best-fit parameters: J = -10.8 cm(-1), D = -5.3 cm(-1), and g = 1.99. The combined results demonstrate the rich chemical reactivity of carbonyl groups and the ability of poly-ketone ligands to stabilize cluster compounds with unprecedented structural motifs and interesting architectures.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danilina, L.I.; Iretskii, A.V.; Kukushkin, Yu.N.

The phosphoniodithiocarboxylato complexes (RhCOA(PPh/sub 3/)(S/sub 2/CPPh/sub 3/))/sup +/ have been obtained by reacting (RhCOA(PPh/sub 3/)/sub 2/)Y (Y = ClO/sub 4//sup -/, NO/sub 3//sup -/) and (Rh(CO)/sub 2/ACl) with CS/sub 2/ in the presence of PPh/sub 3/. In solution they readily eliminate CS/sub 2/ and are converted into (RhCOA(PPh/sub 3/)/sub 2/)/sup +/ (A = py, ..gamma..-pic). Analogous reactions also take place in the case of the bridged complexes with A = 4,4'bipy, the bridged structure of the complexes formed being maintained.

Iridium and Ruthenium Complexes of N-Heterocyclic Carbene- and Pyridinol-Derived Chelates as Catalysts for Aqueous Carbon Dioxide Hydrogenation and Formic Acid Dehydrogenation: The Role of the Alkali Metal

PubMed Central

2017-01-01

Hydrogenation reactions can be used to store energy in chemical bonds, and if these reactions are reversible, that energy can be released on demand. Some of the most effective transition metal catalysts for CO2 hydrogenation have featured pyridin-2-ol-based ligands (e.g., 6,6′-dihydroxybipyridine (6,6′-dhbp)) for both their proton-responsive features and for metal–ligand bifunctional catalysis. We aimed to compare bidentate pyridin-2-ol based ligands with a new scaffold featuring an N-heterocyclic carbene (NHC) bound to pyridin-2-ol. Toward this aim, we have synthesized a series of [Cp*Ir(NHC-pyOR)Cl]OTf complexes where R = tBu (1), H (2), or Me (3). For comparison, we tested analogous bipy-derived iridium complexes as catalysts, specifically [Cp*Ir(6,6′-dxbp)Cl]OTf, where x = hydroxy (4Ir) or methoxy (5Ir); 4Ir was reported previously, but 5Ir is new. The analogous ruthenium complexes were also tested using [(η6-cymene)Ru(6,6′-dxbp)Cl]OTf, where x = hydroxy (4Ru) or methoxy (5Ru); 4Ru and 5Ru were both reported previously. All new complexes were fully characterized by spectroscopic and analytical methods and by single-crystal X-ray diffraction for 1, 2, 3, 5Ir, and for two [Ag(NHC-pyOR)2]OTf complexes 6 (R = tBu) and 7 (R = Me). The aqueous catalytic studies of both CO2 hydrogenation and formic acid dehydrogenation were performed with catalysts 1–5. In general, NHC-pyOR complexes 1–3 were modest precatalysts for both reactions. NHC complexes 1–3 all underwent transformations under basic CO2 hydrogenation conditions, and for 3, we trapped a product of its transformation, 3SP, which we characterized crystallographically. For CO2 hydrogenation with base and dxbp-based catalysts, we observed that x = hydroxy (4Ir) is 5–8 times more active than x = methoxy (5Ir). Notably, ruthenium complex 4Ru showed 95% of the activity of 4Ir. For formic acid dehydrogenation, the trends were quite different with catalytic activity showing 4Ir ≫ 4Ru and 4Ir ≈ 5Ir. Secondary coordination sphere effects are important under basic hydrogenation conditions where the OH groups of 6,6′-dhbp are deprotonated and alkali metals can bind and help to activate CO2. Computational DFT studies have confirmed these trends and have been used to study the mechanisms of both CO2 hydrogenation and formic acid dehydrogenation. PMID:29540958

Iridium and Ruthenium Complexes of N-Heterocyclic Carbene- and Pyridinol-Derived Chelates as Catalysts for Aqueous Carbon Dioxide Hydrogenation and Formic Acid Dehydrogenation: The Role of the Alkali Metal.

PubMed

Siek, Sopheavy; Burks, Dalton B; Gerlach, Deidra L; Liang, Guangchao; Tesh, Jamie M; Thompson, Courtney R; Qu, Fengrui; Shankwitz, Jennifer E; Vasquez, Robert M; Chambers, Nicole; Szulczewski, Gregory J; Grotjahn, Douglas B; Webster, Charles Edwin; Papish, Elizabeth T

2017-03-27

Hydrogenation reactions can be used to store energy in chemical bonds, and if these reactions are reversible, that energy can be released on demand. Some of the most effective transition metal catalysts for CO 2 hydrogenation have featured pyridin-2-ol-based ligands (e.g., 6,6'-dihydroxybipyridine (6,6'-dhbp)) for both their proton-responsive features and for metal-ligand bifunctional catalysis. We aimed to compare bidentate pyridin-2-ol based ligands with a new scaffold featuring an N -heterocyclic carbene (NHC) bound to pyridin-2-ol. Toward this aim, we have synthesized a series of [Cp*Ir(NHC-py OR )Cl]OTf complexes where R = t Bu ( 1 ), H ( 2 ), or Me ( 3 ). For comparison, we tested analogous bipy-derived iridium complexes as catalysts, specifically [Cp*Ir(6,6'-dxbp)Cl]OTf, where x = hydroxy ( 4 Ir ) or methoxy ( 5 Ir ); 4 Ir was reported previously, but 5 Ir is new. The analogous ruthenium complexes were also tested using [(η 6 -cymene)Ru(6,6'-dxbp)Cl]OTf, where x = hydroxy ( 4 Ru ) or methoxy ( 5 Ru ); 4 Ru and 5 Ru were both reported previously. All new complexes were fully characterized by spectroscopic and analytical methods and by single-crystal X-ray diffraction for 1 , 2 , 3 , 5 Ir , and for two [Ag(NHC-py OR ) 2 ]OTf complexes 6 (R = t Bu) and 7 (R = Me). The aqueous catalytic studies of both CO 2 hydrogenation and formic acid dehydrogenation were performed with catalysts 1 - 5 . In general, NHC-py OR complexes 1 - 3 were modest precatalysts for both reactions. NHC complexes 1 - 3 all underwent transformations under basic CO 2 hydrogenation conditions, and for 3 , we trapped a product of its transformation, 3 SP , which we characterized crystallographically. For CO 2 hydrogenation with base and dxbp-based catalysts, we observed that x = hydroxy ( 4 Ir ) is 5-8 times more active than x = methoxy ( 5 Ir ). Notably, ruthenium complex 4 Ru showed 95% of the activity of 4 Ir . For formic acid dehydrogenation, the trends were quite different with catalytic activity showing 4 Ir ≫ 4 Ru and 4 Ir ≈ 5 Ir . Secondary coordination sphere effects are important under basic hydrogenation conditions where the OH groups of 6,6'-dhbp are deprotonated and alkali metals can bind and help to activate CO 2 . Computational DFT studies have confirmed these trends and have been used to study the mechanisms of both CO 2 hydrogenation and formic acid dehydrogenation.

Negative regulation of early polyomavirus expression in mouse embryonal carcinoma cells.

PubMed Central

Cremisi, C; Babinet, C

1986-01-01

Embryonal carcinoma cells are resistant to infection by polyomavirus (Py). We showed that this block was partially removed by inhibiting protein synthesis temporarily. The block was also partially removed when Py was coinfected with simian virus 40. Cycloheximide treatment of cells infected with Py mutants able to grow on PCC4 embryonal carcinoma cells led to 3- to 10-fold increases in the production of T-antigen-positive cells. At 31 degrees C, Py T-antigen expression was enhanced when the cells were treated with cycloheximide. We suggest that a negative labile regulatory protein(s) is synthesized in PCC4 cells, preventing the initiation of early Py transcription by binding to the noncoding sequence, especially the enhancer element B and perhaps also element A, and that the Py mutants retained a binding site(s). PMID:3016339

The Organic Matter Molecular Characteristics of Pyrogenic Solids and Their Aqueous Leachable Fractions

NASA Astrophysics Data System (ADS)

Wozniak, A. S.; Hatcher, P.; Mitra, S.; Bostick, K. W.; Zimmerman, A. R.

2016-02-01

Pyrogenic organic matter (Py-OM), or black carbon (BC), derives from the incomplete combustion of fossil fuels and biomass and is recognized for its impacts on soil chemistry, pollutant transport, climate, and regional and global carbon cycling. In fact, Py-OM is commonly applied to agricultural plots, in the form of "biochars," with the intention of enhancing agricultural production and the expectation of a carbon sequestration side benefit due to Py-OM's refractory and immobile nature. However, several studies of riverine, estuarine, and oceanic waters have detected tracers of dissolved Py-OM in appreciable quantities suggesting that it is more mobile in the environment than previously expected. The quantities and impacts of Py-OM released to aqueous systems are likely dependent on Py-OM molecular characteristics which in turn likely depend on initial combustion conditions and environmental processing. Yet, very little is known about the detailed molecular composition of these materials, let alone their relationships with combustion and environmental processing. Here, pyrophosphate extractable and water leachable components of a range of Py-OM materials (natural charcoals aged in the environment for variable lengths of time, oak and grass combusted over a range of temperatures) are examined by Fourier transform ion cyclotron resonance mass spectrometry. The molecular characteristics of the dissolved and pyrophosphate extractable Py-OM is then compared in the context of production conditions. Results of this study will greatly improve our understanding of Py-OM cycling between watersheds and the oceans.

PyCoTools: A Python Toolbox for COPASI.

PubMed

Welsh, Ciaran M; Fullard, Nicola; Proctor, Carole J; Martinez-Guimera, Alvaro; Isfort, Robert J; Bascom, Charles C; Tasseff, Ryan; Przyborski, Stefan A; Shanley, Daryl P

2018-05-22

COPASI is an open source software package for constructing, simulating and analysing dynamic models of biochemical networks. COPASI is primarily intended to be used with a graphical user interface but often it is desirable to be able to access COPASI features programmatically, with a high level interface. PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. PyCoTools enables the construction of COPASI models and the execution of a subset of COPASI tasks including time courses, parameter scans and parameter estimations. Additional 'composite' tasks which use COPASI tasks as building blocks are available for increasing parameter estimation throughput, performing identifiability analysis and performing model selection. PyCoTools supports exploratory data analysis on parameter estimation data to assist with troubleshooting model calibrations. We demonstrate PyCoTools by posing a model selection problem designed to show case PyCoTools within a realistic scenario. The aim of the model selection problem is to test the feasibility of three alternative hypotheses in explaining experimental data derived from neonatal dermal fibroblasts in response to TGF-β over time. PyCoTools is used to critically analyse the parameter estimations and propose strategies for model improvement. PyCoTools can be downloaded from the Python Package Index (PyPI) using the command 'pip install pycotools' or directly from GitHub (https://github.com/CiaranWelsh/pycotools). Documentation at http://pycotools.readthedocs.io. Supplementary data are available at Bioinformatics.

Steric and Electronic Effects of Bidentate Phosphine Ligands on Ruthenium(II)-Catalyzed Hydrogenation of Carbon Dioxide.

PubMed

Zhang, Pan; Ni, Shao-Fei; Dang, Li

2016-09-20

The reactivity difference between the hydrogenation of CO2 catalyzed by various ruthenium bidentate phosphine complexes was explored by DFT. In addition to the ligand dmpe (Me2 PCH2 CH2 PMe2 ), which was studied experimentally previously, a more bulky diphosphine ligand, dmpp (Me2 PCH2 CH2 CH2 PMe2 ), together with a more electron-withdrawing diphosphine ligand, PN(Me) P (Me2 PCH2 N(Me) CH2 PMe2 ), have been studied theoretically to analyze the steric and electronic effects on these catalyzed reactions. Results show that all of the most favorable pathways for the hydrogenation of CO2 catalyzed by bidentate phosphine ruthenium dihydride complexes undergo three major steps: cis-trans isomerization of ruthenium dihydride complex, CO2 insertion into the Ru-H bond, and H2 insertion into the ruthenium formate ion. Of these steps, CO2 insertion into the Ru-H bond has the lowest barrier compared with the other two steps in each preferred pathway. For the hydrogenation of CO2 catalyzed by ruthenium complexes of dmpe and dmpp, cis-trans isomerization of ruthenium dihydride complex has a similar barrier to that of H2 insertion into the ruthenium formate ion. However, in the reaction catalyzed by the PN(Me) PRu complex, cis-trans isomerization of the ruthenium dihydride complex has a lower barrier than H2 insertion into the ruthenium formate ion. These results suggest that the steric effect caused by the change of the outer sphere of the diphosphine ligand on the reaction is not clear, although the electronic effect is significant to cis-trans isomerization and H2 insertion. This finding refreshes understanding of the mechanism and provides necessary insights for ligand design in transition-metal-catalyzed CO2 transformation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simultaneous Binding of Two Peptidyl Ligands by a Src Homology 2 Domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yanyan; Zhang, Jinjin; Yuan, Chunhua

Src homology 2 (SH2) domains mediate protein-protein interactions by recognizing phosphotyrosine (pY)-containing sequences of target proteins. In all of the SH2 domain-pY peptide interactions described to date, the SH2 domain binds to a single pY peptide. Here, determination of the cocrystal structure of the N-terminal SH2 domain of phosphatase SHP-2 bound to a class IV peptide (VIpYFVP) revealed a noncanonical 1:2 (protein-peptide) complex. The first peptide binds in a canonical manner with its pY side chain inserted in the usual binding pocket, while the second pairs up with the first to form two antiparallel {beta}-strands that extend the central {beta}-sheetmore » of the SH2 domain. This unprecedented binding mode was confirmed in the solution phase by NMR experiments and shown to be adopted by pY peptides derived from cellular proteins. Site-directed mutagenesis and surface plasmon resonance studies revealed that the binding of the first peptide is pY-dependent, but phosphorylation is not required for the second peptide. Our findings suggest a potential new function for the SH2 domain as a molecular clamp to promote dimerization of signaling proteins.« less

Substituent effect in spin-crossover behavior of iron(II)-Ar-pybox complexes (Ar-pybox = 4-aryl-2,6-bis(oxazolin-2-yl)pyridine)

NASA Astrophysics Data System (ADS)

Kimura, Akifumi; Ishida, Takayuki

2018-01-01

Spin-crossover (SCO) is a reversible transition between low-spin (LS) and high-spin (HS) states by external stimuli like heat. The SCO behavior of [Fe(Ar-pybox)2](ClO4)2 was investigated, where Ar-pybox stands for 4-aryl-2,6-bis(oxazolin-2-yl)pyridine with Ar = 4-pyridyl (4Py), 3-thienyl (3Th), and phenyl (Ph). They were characterized by means of single-crystal X-ray diffraction study, being consistent with the results of the magnetic measurements. The SCO temperatures (T1/2) in the polycrystalline state were determined to be 360 and 230 K for Ar = 4Py and Ph, respectively. The 3Th derivative possessed a HS state in all the temperature range. The solution susceptometry was also performed to purge intermolecular interaction and rigid crystal lattice effects, affording T1/2 = 310, 240, and 240 K for Ar = 4Py, 3Th, and Ph, respectively, in acetone. The substituent effect analysis using the Hammett substituent constant (σp) clarified that electron-withdrawing groups raise T1/2. A plausible model describing the substituent effect on T1/2 is proposed based on d-π interaction. The present result is regarded as a successful example of crystal field engineering.

Selective synthesis of cis- and trans-[(NHC(Me))2PtCl2] and [NHC(Me)Pt(cod)Cl][NHC(Me)PtCl3] using NHC(Me)SiCl4.

PubMed

Lewis-Alleyne, Lesley C; Bassil, Bassem S; Böttcher, Tobias; Röschenthaler, Gerd-Volker

2014-11-14

NHC(Me)SiCl4 (NHC(Me) = 1,3-dimethylimidazolidin-2-ylidene) was used to synthesise novel NHC(Me)-Pt(ii) complexes. An atypical trans-cis isomerisation process was also achieved for [(NHC(Me))2PtCl2], while the synthesis of the unique double-complex salt [(NHC(Me))Pt(cod)Cl] [(NHC(Me))PtCl3] (cod = 1,5-cyclooctadiene) revealed the first-ever N-heterocyclic carbene analogue of the Cossa's salt anion.

Molecular detection and in vitro antioxidant activity of S-allyl-L-cysteine (SAC) extracted from Allium sativum.

PubMed

Sun, Y-E; Wang, W-D

2016-06-30

It is well known that Allium sativum has potential applications to clinical treatment of various cancers due to its remarkable ability in eliminating free radicals and increasing metabolism. An allyl-substituted cysteine derivative - S-allyl-L-cysteine (SAC) was separated and identified from Allium sativum. The extracted SAC was reacted with 1-pyrenemethanol to obtain pyrene-labelled SAC (Py-SAC) to give SAC fluorescence properties. Molecular detection of Py-SAC was conducted by steady-state fluorescence spectroscopy and time-resolved fluorescence method to quantitatively measure concentrations of Py-SAC solutions. The ability of removing 1,1-diphenyl-2-picrylhydrazyl (DPPH) and hydroxyl radical using Py-SAC was determined through oxygen radical absorbance capacity (ORAC). Results showed the activity of Py-SAC and Vitamin C (VC) with ORAC as index, the concentrations of Py-SAC and VC were 58.43 mg/L and 5.72 mg/L respectively to scavenge DPPH, and 8.16 mg/L and 1.67 mg/L to scavenge •OH respectively. Compared with VC, the clearance rates of Py-SAC to scavenge DPPH were much higher, Py-SAC could inhibit hydroxyl radical. The ability of removing radical showed a dose-dependent relationship within the scope of the drug concentration.

Continued Transmission of HIV Among Young Adults Who Inject Drugs in San Francisco: Still Room for Improvement.

PubMed

Mirzazadeh, Ali; Evans, Jennifer L; Hahn, Judith A; Jain, Jennifer; Briceno, Alya; Shiboski, Stephen; Lum, Paula J; Bentsen, Christopher; Davis, Geoff; Shriver, Kathy; Dimapasoc, Melanie; Stone, Mars; Busch, Michael P; Page, Kimberly

2018-04-01

We measured HIV incidence rate, trend and risk factors in 564 HIV-negative young people (< 30 years) who inject drugs (PWID) in San Francisco between 2000 and 2014. HIV incidence was 0.93/100 person-years (PY; 95% CI 0.50, 1.73). Incidence varied between 0.62/100 PY in 2000-2002 and 1.06/100 PY in 2012-2014 (P for trend = 1.0). HIV incidence varied significantly (P < 0.01) by race/ethnicity: among Hispanics it was 8.19/100 PY (95% CI 3.41, 19.68), African-Americans 4.59/100 PY (95% CI 1.15, 18.37), and Whites 0.26/100 PY (95% CI 0.06, 1.03). Male participants who reported sex with men (MSM) had higher HIV incidence (2.63/100 PY; 95% CI 1.31, 5.25) compared to males who did not report MSM (0.50/100 PY; 95% CI 0.12, 1.99) (P = 0.01). Despite an overall stable HIV incidence trend, incidence was elevated among African-American and Hispanic PWID, and men who have sex with men. Addressing prevention needs in these key populations is critical for the goal of eliminating HIV transmission.

Pyrolysis-combustion 14C dating of soil organic matter

USGS Publications Warehouse

Wang, Hongfang; Hackley, Keith C.; Panno, S.V.; Coleman, D.D.; Liu, J.C.-L.; Brown, J.

2003-01-01

Radiocarbon (14C) dating of total soil organic matter (SOM) often yields results inconsistent with the stratigraphic sequence. The onerous chemical extractions for SOM fractions do not always produce satisfactory 14C dates. In an effort to develop an alternative method, the pyrolysis-combustion technique was investigated to partition SOM into pyrolysis volatile (Py-V) and pyrolysis residue (Py-R) fractions. The Py-V fractions obtained from a thick glacigenic loess succession in Illinois yielded 14C dates much younger but more reasonable than the counterpart Py-R fractions for the soil residence time. Carbon isotopic composition (??13C) was heavier in the Py-V fractions, suggesting a greater abundance of carbohydrate- and protein-related constituents, and ??13C was lighter in the Py-R fractions, suggesting more lignin- and lipid-related constituents. The combination of 14C dates and ??13C values indicates that the Py-V fractions are less biodegradation resistant and the Py-R fractions are more biodegradation resistant. The pyrolysis-combustion method provides a less cumbersome approach for 14C dating of SOM fractions. With further study, this method may become a useful tool for analyzing unlithified terrestrial sediments when macrofossils are absent. ?? 2003 University of Washington. Published by Elsevier Inc. All rights reserved.

Near-Road Exposure and Impact of Air Pollution on Allergic Diseases in Elementary School Children: A Cross-Sectional Study

PubMed Central

Kim, Ho Hyun; Lee, Chung Soo; Yu, Seung Do; Lee, Jung Sub; Chang, Jun Young; Jeon, Jun Min; Son, Hye Rim; Park, Chan Jung; Shin, Dong Chun

2016-01-01

Purpose The study aims to classify schools based on traffic pollutants and their complex sources, to assess the environment, to determine the state of allergic diseases among students using the International Study of Asthma and Allergies in children (ISAAC) questionnaire, and to assess their connection to air pollutants. Materials and Methods A total of seven schools were divided into three categories according to the characteristics of their surrounding environments: three schools in traffic-related zones, two schools in complex source zones I (urban), and two schools in complex source zones II (industrial complex). ISAAC questionnaires were administered and the 4404 completed questionnaires were analyzed. Results The frequency of asthma treatment during the past 12 months showed a significant increase (p<0.05) with exposure to NO2 [1.67, 95% confidence intervals (CIs) 1.03–2.71] in the complex source zones. The frequency of allergic rhinitis treatment during the past 12 months increased significantly with exposure to Black Carbon (1.60, 95% CIs 1.36–1.90) (p<0.001), SO2 (1.09, 95% CIs 1.01–1.17) (p<0.05), NO2 (1.18, 95% CIs 1.07–1.30) (p<0.01) for all subjects. Conclusion In terms of supporting children's health, care, and prevention related to major spaces for children, such as school zones, spaces used in coming to and leaving school, playgrounds, and classrooms are essential to ensuring not only the safety of children from traffic accidents but also their protection from local traffic pollutants and various hazardous environmental factors. PMID:26996571

Synthesis and structural studies of two pyridine-armed reinforced cyclen chelators and their transition metal complexes.

PubMed

Wilson, Kevin R; Cannon-Smith, Desiray J; Burke, Benjamin P; Birdsong, Orry C; Archibald, Stephen J; Hubin, Timothy J

2016-08-16

Two novel pyridine pendant-armed macrocycles structurally reinforced by an ethyl bridge, either between adjacent nitrogens (for side-bridged) or non-adjacent nitrogens (for cross-bridged), have been synthesized and complexed with a range of transition metal ions (Co 2+ , Ni 2+ , Cu 2+ and Zn 2+ ). X-ray crystal structures of selected cross-bridged complexes were obtained which showed the characteristic cis-V configuration with potential labile cis binding sites. The complexes have been characterized by their electronic spectra and magnetic moments, which show the expected high spin divalent metal complex in most cases. Exceptions are the nickel side-bridged complex, which shows a mixture of high-spin and low spin, and the cobalt cross-bridged complex which has oxidized to cobalt(III). Cyclic voltammetry in acetonitrile was carried out to assess the potential future use of these complexes in oxidation catalysis. Selected complexes offer significant catalytic potential enhanced by the addition of the pyridyl arm to a reinforced cyclen backbone.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Lecocq, Thomas; Megies, Tobias; Krischer, Lion; Sales de Andrade, Elliott; Barsch, Robert; Beyreuther, Moritz

2016-04-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides * read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, * a comprehensive signal processing toolbox tuned to the needs of seismologists, * integrated access to all large data centers, web services and databases, and * convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software. ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it. This contribution will give a short introduction and overview of ObsPy and highlight a number of use cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

ObsPy: A Python toolbox for seismology - Current state, applications, and ecosystem around it

NASA Astrophysics Data System (ADS)

Krischer, L.; Megies, T.; Sales de Andrade, E.; Barsch, R.; Beyreuther, M.

2015-12-01

ObsPy (http://www.obspy.org) is a community-driven, open-source project offering a bridge for seismology into the scientific Python ecosystem. It provides read and write support for essentially all commonly used waveform, station, and event metadata formats with a unified interface, a comprehensive signal processing toolbox tuned to the needs of seismologists, integrated access to all large data centers, web services and databases, and convenient wrappers to third party codes like libmseed and evalresp. Python, in contrast to many other languages and tools, is simple enough to enable an exploratory and interactive coding style desired by many scientists. At the same time it is a full-fledged programming language usable by software engineers to build complex and large programs. This combination makes it very suitable for use in seismology where research code often has to be translated to stable and production ready environments. It furthermore offers many freely available high quality scientific modules covering most needs in developing scientific software.ObsPy has been in constant development for more than 5 years and nowadays enjoys a large rate of adoption in the community with thousands of users. Successful applications include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. Additionally it sparked the development of several more specialized packages slowly building a modern seismological ecosystem around it.This contribution will give a short introduction and overview of ObsPy and highlight a number of us cases and software built around it. We will furthermore discuss the issue of sustainability of scientific software.

On the utility of GPU accelerated high-order methods for unsteady flow simulations: A comparison with industry-standard tools

NASA Astrophysics Data System (ADS)

Vermeire, B. C.; Witherden, F. D.; Vincent, P. E.

2017-04-01

First- and second-order accurate numerical methods, implemented for CPUs, underpin the majority of industrial CFD solvers. Whilst this technology has proven very successful at solving steady-state problems via a Reynolds Averaged Navier-Stokes approach, its utility for undertaking scale-resolving simulations of unsteady flows is less clear. High-order methods for unstructured grids and GPU accelerators have been proposed as an enabling technology for unsteady scale-resolving simulations of flow over complex geometries. In this study we systematically compare accuracy and cost of the high-order Flux Reconstruction solver PyFR running on GPUs and the industry-standard solver STAR-CCM+ running on CPUs when applied to a range of unsteady flow problems. Specifically, we perform comparisons of accuracy and cost for isentropic vortex advection (EV), decay of the Taylor-Green vortex (TGV), turbulent flow over a circular cylinder, and turbulent flow over an SD7003 aerofoil. We consider two configurations of STAR-CCM+: a second-order configuration, and a third-order configuration, where the latter was recommended by CD-adapco for more effective computation of unsteady flow problems. Results from both PyFR and STAR-CCM+ demonstrate that third-order schemes can be more accurate than second-order schemes for a given cost e.g. going from second- to third-order, the PyFR simulations of the EV and TGV achieve 75× and 3× error reduction respectively for the same or reduced cost, and STAR-CCM+ simulations of the cylinder recovered wake statistics significantly more accurately for only twice the cost. Moreover, advancing to higher-order schemes on GPUs with PyFR was found to offer even further accuracy vs. cost benefits relative to industry-standard tools.

On the utility of GPU accelerated high-order methods for unsteady flow simulations: A comparison with industry-standard tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vermeire, B.C., E-mail: brian.vermeire@concordia.ca; Witherden, F.D.; Vincent, P.E.

First- and second-order accurate numerical methods, implemented for CPUs, underpin the majority of industrial CFD solvers. Whilst this technology has proven very successful at solving steady-state problems via a Reynolds Averaged Navier–Stokes approach, its utility for undertaking scale-resolving simulations of unsteady flows is less clear. High-order methods for unstructured grids and GPU accelerators have been proposed as an enabling technology for unsteady scale-resolving simulations of flow over complex geometries. In this study we systematically compare accuracy and cost of the high-order Flux Reconstruction solver PyFR running on GPUs and the industry-standard solver STAR-CCM+ running on CPUs when applied to amore » range of unsteady flow problems. Specifically, we perform comparisons of accuracy and cost for isentropic vortex advection (EV), decay of the Taylor–Green vortex (TGV), turbulent flow over a circular cylinder, and turbulent flow over an SD7003 aerofoil. We consider two configurations of STAR-CCM+: a second-order configuration, and a third-order configuration, where the latter was recommended by CD-adapco for more effective computation of unsteady flow problems. Results from both PyFR and STAR-CCM+ demonstrate that third-order schemes can be more accurate than second-order schemes for a given cost e.g. going from second- to third-order, the PyFR simulations of the EV and TGV achieve 75× and 3× error reduction respectively for the same or reduced cost, and STAR-CCM+ simulations of the cylinder recovered wake statistics significantly more accurately for only twice the cost. Moreover, advancing to higher-order schemes on GPUs with PyFR was found to offer even further accuracy vs. cost benefits relative to industry-standard tools.« less

Practice of skin protection and skin care among German surgeons and influence on the efficacy of surgical hand disinfection and surgical glove perforation

PubMed Central

2014-01-01

Background Surgical hand rub and healthy skin are basic requirements to prevent surgical site infections. Nevertheless, there is little knowledge about the current practice of skin protection and/or skin care products (SP/SC) using among surgeons as well as a lack of data pertaining to the influence of SP/SC on the antimicrobial efficacy of surgical hand rub. Methods A 10 weeks-survey among German surgeons as well as an experimental crossover study involving 26 participants were conducted. The immediate and sustainable efficacy (IE/SE) of surgical hand rub and participants’ hand moisture were measured after an 8-day usage of SP/SC, as well as the influence on micro-perforations on surgical gloves. Results The questionnaire was available to 16,000 German surgeons. Thereof, 1,771 surgeons accessed the questionnaire, representing a total participation rate of 11%. As 19% (n = 338) of questionnaires were incomplete, a total of 1,433 completed questionnaires were available for further analysis. More than 75% of the participants stated not to use any SP/SC, yet, almost 50% suffered from skin irritation or discomfort. Only 5% used SP/SC at the beginning of their shift. 10% refused to use SP/SC because of concerns that SP/SC may reduce the antimicrobial efficacy of surgical hand rub. After usage of SP/SC over 8-days, skin moisture was significantly higher (P < 0.001), whereas no significant influence on the antimicrobial efficacy of surgical hand rub was observed (IE: P = 0.135; SP: P = 0.681). Micro-perforations were detected in 8/52 surgical gloves (15%), with no statistical significant difference between SP/SC users (n = 2/26; 8%) and non-users (n = 6/26; 23%; P = 0.249). Conclusions Following the results of this largest questionnaire base survey among German surgeons on skin care, there is a need to educate and inform surgeons on the correct application and the concept of SP/SC strategies. In the present study, the combination of selected SP/SC products and one alcohol-based hand rub formulation did not show a negative interaction with surgical hand rub or surgical glove perforation. However, it is advisable to ascertain the compatibility of SP/SC products with the used hand disinfectant prior to purchase. PMID:24912541

Structural Basis for Interactions Between Contactin Family Members and Protein-tyrosine Phosphatase Receptor Type G in Neural Tissues

DOE PAGES

Nikolaienko, Roman M.; Hammel, Michal; Dubreuil, Véronique; ...

2016-08-18

Protein-tyrosine phosphatase receptor type G (RPTPγ/PTPRG) interacts in vitro with contactin-3-6 (CNTN3-6), a group of glycophosphatidylinositol-anchored cell adhesion molecules involved in the wiring of the nervous system. In addition to PTPRG, CNTNs associate with multiple transmembrane proteins and signal inside the cell via cis-binding partners to alleviate the absence of an intracellular region. Here, we use comprehensive biochemical and structural analyses to demonstrate that PTPRG·CNTN3-6 complexes share similar binding affinities and a conserved arrangement. Furthermore, as a first step to identifying PTPRG·CNTN complexes in vivo, we found that PTPRG and CNTN3 associate in the outer segments of mouse rod photoreceptormore » cells. In particular, PTPRG and CNTN3 form cis-complexes at the surface of photoreceptors yet interact in trans when expressed on the surfaces of apposing cells. Further structural analyses suggest that all CNTN ectodomains adopt a bent conformation and might lie parallel to the cell surface to accommodate these cis and trans binding modes. Taken together, these studies identify a PTPRG·CNTN complex in vivo and provide novel insights into PTPRG- and CNTN-mediated signaling.« less

PlasmaPy: initial development of a Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas; Leonard, Andrew J.; Stańczak, Dominik; Haggerty, Colby C.; Parashar, Tulasi N.; Huang, Yu-Min; PlasmaPy Community

2017-10-01

We report on initial development of PlasmaPy: an open source community-driven Python package for plasma physics. PlasmaPy seeks to provide core functionality that is needed for the formation of a fully open source Python ecosystem for plasma physics. PlasmaPy prioritizes code readability, consistency, and maintainability while using best practices for scientific computing such as version control, continuous integration testing, embedding documentation in code, and code review. We discuss our current and planned capabilities, including features presently under development. The development roadmap includes features such as fluid and particle simulation capabilities, a Grad-Shafranov solver, a dispersion relation solver, atomic data retrieval methods, and tools to analyze simulations and experiments. We describe several ways to contribute to PlasmaPy. PlasmaPy has a code of conduct and is being developed under a BSD license, with a version 0.1 release planned for 2018. The success of PlasmaPy depends on active community involvement, so anyone interested in contributing to this project should contact the authors. This work was partially supported by the U.S. Department of Energy.

Nonlocal electrical detection of spin accumulation generated by anomalous Hall effect in mesoscopic N i81F e19 films

NASA Astrophysics Data System (ADS)

Qin, Chuan; Chen, Shuhan; Cai, Yunjiao; Kandaz, Fatih; Ji, Yi

2017-10-01

Spin accumulation generated by the anomalous Hall effect (AHE) in mesoscopic ferromagnetic N i81F e19 (permalloy, Py) films is detected electrically by a nonlocal method. The reciprocal phenomenon, the inverse spin Hall effect (ISHE), can also be generated and detected all electrically in the same structure. For accurate quantitative analysis, a series of nonlocal AHE/ISHE structures and supplementary structures are fabricated on each sample substrate to account for statistical variations and to accurately determine all essential physical parameters in situ. By exploring Py thicknesses of 4, 8, and 12 nm, the Py spin diffusion length λPy is found to be much shorter than the film thicknesses. The product of λPy and the Py spin Hall angle αSH is determined to be independent of thickness and resistivity: αSHλPy=(0.066 ±0.009 ) nm at 5 K and (0.041 ±0.010 )nm at 295 K. These values are comparable to those obtained from mesoscopic Pt films.

Is fire a long term sink or source of atmospheric carbon? A comprehensive evaluation of a boreal forest fire

NASA Astrophysics Data System (ADS)

Santin, C.; Doerr, S. H.; Preston, C.; Bryant, R.

2012-12-01

Fires lead to a rapid release of carbon (C) from forest and other fire-prone ecosystems, emitting important quantities of C to the atmosphere. Every year 300-600 Mill. ha burn around the globe, generating CO2 emissions equivalent to half of the current annual global from fossil fuel combustion. Over the longer-term vegetation fires are widely considered as 'net zero Carbon (C) emission events', because C emissions from fires, excluding those associated with deforestation, are balanced by C uptake by regenerating vegetation. This 'zero C emission' scenario, however, may be flawed, as it does not consider the role of pyrogenic C (PyC). During fire, some of the fuel is transformed into PyC (i.e. charcoal, black C, soot), which is characterized by an enhanced recalcitrance and a longer mean residence time in the environment than its 'fresh' precursors. Therefore, after complete regeneration of the vegetation, the PyC generated represents an additional longer-term C pool and, hence, recurring fire-regrowth cycles could be considered as a 'net sink of atmospheric C'. To test the validity of this hypothesis, and to estimate how quantitatively important this PyC pool might be, accurate data on PyC production with respect to the fuel combusted are needed. Unfortunately, detailed quantification of fuel prior to fire is normally only available for prescribed and experimental fires, which are usually of low-intensity and therefore not representative of higher-intensity wildfires. Furthermore, what little data is available is usually based on only a specific fraction of the PyC present following burning rather than the whole range of PyC products and stores (i.e. PyC in soil, ash, downed wood and standing vegetation). The FireSmart project (Ft. Providence, NWT, Canada, June 2012) provided the ideal framework to address this research gap. This experimental fire reproduced wildfire conditions in boreal forest, i.e. stand-replacing crown fire and, at the same time, allowed i) pre-fire fuel assessment, ii) fire behaviour monitoring and iii) immediate post-fire fuel and PyC inventory. Before the fire, fuel characteristics were established and the site was instrumented with auto-logging thermocouples to provide temperature-duration profiles during burning. Also, different types of PyC were placed on the ground to determine PyC loss during the fire. Immediately after fire, the various post-burn PyC products and stores were sampled. Total PyC was quantified and the chemical recalcitrance of the different PyC forms found was determined. The results obtained will be discussed in the context of PyC production, and its different forms and quantities, with respect to (i) fire characteristics and fuel consumed, and (ii) the long term carbon balance in this boreal forest environment for recurring fire-regrowth cycles under current and predicted future climatic conditions.

Synthesis and photocatalytic studies of ZnS nanoparticles from heteroleptic complex of Zn(II) 1-cyano-1-carboethoxy-2,-2-ethylenedithiolato diisopropylthiourea and its adducts with N-donor ligands

NASA Astrophysics Data System (ADS)

Osuntokun, Jejenija; Ajibade, Peter A.; Onwudiwe, Damian C.

2016-12-01

Zinc complexes of the type [Zn(diptu)2(ced)] (1), [Zn(diptu)2(ced)py] (2), [Zn(diptu)2(ced)bpy] (3), and [Zn(diptu)2(ced)phen] (4), (where (diptu)2(ced) = 1-cyano-1-carboethoxyethylene-2,2-dithiolato-κS,S‧-bis(N,N-diisopropyllthiourea), py = pyridine, bpy = 2, 2‧ bipyridine and phen = 1, 10 phenanthroline have been synthesized and characterized by elemental analyses, Fourier transform infra-red (FTIR) and Nuclear magnetic resonance (NMR) spectroscopies. The parent complex (1) was formulated as four coordinate species, which gave rise to 5 coordinate complex in (2) and six coordinate compounds in (3) and (4), with the dithiolate acting as bidentate chelating ligand. The complexes were used as single-source precursors for the synthesis of HDA-capped ZnS nanoparticles. The nanoparticles gave different morphologies with sizes in the range of 1.92-4.72 nm as observed from the TEM analysis and supported by XRD. The UV-vis spectroscopy showed that all the ZnS nanoparticles are blue shifted, with respect to the bulk, which confirmed quantum confinement. The photoluminescence spectra showed narrow and broad emission peaks around 290 and 360 nm which are ascribed to spontaneous emission peaks from band to band transition and surface states respectively. Photocatalytic activities of all the nanoparticles were investigated with methylene blue (MB) acting as the organic dye, and the UV-vis spectral revealed a gradual decrease in absorption peak that confirmed the degradation of the MB.

Molecular complexes of some anthraquinone anti-cancer drugs: experimental and computational study

NASA Astrophysics Data System (ADS)

El-Gogary, Tarek M.

2003-03-01

It is known that anti-cancer drugs target DNA in the cell. The mechanism of interaction of anti-cancer drugs with DNA is not fully understood. It is thought that the forces of interaction have some contribution from charge-transfer (CT) binding. The ability of some anthraquinones (AQs) anti-cancer drugs to form CT complexes with well-known electron donor molecules was investigated by NMR. The NMR spectroscopy has indicated the formation of CT complexes between 1,4-bis{[2-(dimethylamino) ethyl]amino}-5,8-dihydroxyanthracene-9,10-dione, (AQ4), and its des-hydroxylated equivalent 1,4-bis{[2-(dimethylamino) ethyl]amino}anthracene-9,10-dione, (AQ4H), as electron acceptors and pyrene (PY) and hexamethylbenzene (HMB) as electron donors. Association constants of the formed CT complexes were determined from the NMR data. AQ4 showed weaker electron accepting power than AQ4H, which could be easily explained on the basis of the electron donating nature of the two-hydroxyl groups. AQ4 and AQ4H have higher stability constant with PY than with HMB. This reflects the weaker interaction of the AQs with the latter, which is a direct effect of the six bulky methyl groups. Electronic absorption spectroscopy of the studied system was performed in chloroform and showed the absence of new absorption bands. The extent of interaction between AQs and donors has been computed using molecular mechanics and quantum mechanics. The computed values were compared with the experimental results of association constants.

DendroPy: a Python library for phylogenetic computing.

PubMed

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).

Reaction Kinetics of Phenolic Antioxidants toward Photoinduced Pyranine Free Radicals in Biological Models.

PubMed

Aspée, Alexis; Aliaga, Christian; Maretti, Luca; Zúñiga-Núñez, Daniel; Godoy, Jessica; Pino, Eduardo; Cárdenas-Jirón, Gloria; Lopez-Alarcon, Camilo; Scaiano, Juan C; Alarcon, Emilio I

2017-07-06

8-Hydroxy-1,3,6-pyrenetrisulfonic acid (pyranine, PyOH) free radicals were induced by laser excitation at visible wavelengths (470 nm). The photochemical process involves photoelectron ejection from PyO- to produce PyO• and PyO•- with maxima absorption at 450 and 510 nm, respectively. The kinetic rate constants for phenolic antioxidants with PyO•, determined by nanosecond time-resolved spectroscopy, were largely reliant on the ionic strength depending on the antioxidant phenol/phenolate dissociation constant. Further, the apparent rate constant measured in the presence of Triton X100 micelles was influenced by the antioxidant partition between the micelle and the dispersant aqueous media but limited by its exit rates from the micelle. Similarly, the rate reaction between ascorbic acid and PyO• was markedly affected by the presence of human serum albumin responding to the dynamic of the ascorbic acid binding to the protein.

PyKE3: data analysis tools for NASA's Kepler, K2, and TESS missions

NASA Astrophysics Data System (ADS)

Hedges, Christina L.; Cardoso, Jose Vinicius De Miranda; Barentsen, Geert; Gully-Santiago, Michael A.; Cody, Ann Marie; Barclay, Thomas; Still, Martin; BAY AREA ENVIRONMENTAL RESEARCH IN

2018-01-01

The PyKE package is a set of easy to use tools for working with Kepler/K2 data. This includes tools to correct light curves for cotrending basis vectors, turn the raw Target Pixel File data into motion corrected light curves, check for exoplanet false positives and run new PSF photometry. We are now releasing PyKE 3, which is compatible with Python 3, is pip installable and no longer depends on PyRAF. Tools are available both as Python routines and from the command line. New tutorials are available and under construction for users to learn about Kepler and K2 data and how to best use it for their science goals. PyKE is open source and welcomes contributions from the community. Routines and more information are available on the PyKE repository on GitHub.