bluuebunny/crossref_metadata_2025_split huggingface dataset:
New genes expressed in human brains: Implications for annotating evolving genomes
Authors: Zhang Yong E. , Landback Patrick , Vibranovski Maria , Long Manyuan 
Published: September 2012

AbstractNew genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage‐specific genes. It was recently reported that an excess of primate‐specific and human‐specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under‐characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination.
Eu2+ luminescence in SrCaP2O7 pyrophosphate phosphor
Authors: Kohale R.L. , Dhoble S.J. 
Published: September 2012

ABSTRACTA series of Eu2+ activated SrCaP2O7 pyrophosphate phosphors were synthesized by the modified solid‐state reaction method. The X‐ray diffraction (XRD) and photoluminescence (PL) properties of these phosphors were investigated at room temperature. The excitation spectra indicate that these phosphors can be effectively excited by Hg‐free excitation. The emission spectra exhibit strong blue performance, which is due to the 4f65d1→4f7 transition of Eu2+. The Fourier transform infrared spectrum at room temperature was investigated and surface morphology has been studied by scanning electron microscope. The prepared phosphor exhibited intense blue emission at the 427 nm owing to Eu2+ ion by Hg‐free excitation at 330 nm, that is, solid‐state lighting excitation. Hence, the availability of such a phosphor will significantly help in the growth of blue‐emitting solid‐state lighting applications. Copyright © 2012 John Wiley & Sons, Ltd.
Heterobinuclear Zn‐Ln (Ln = La, Nd, Eu, Gd, Tb, Er and Yb) complexes based on asymmetric Schiff‐base ligand: synthesis, characterization and photophysical properties
Authors: Zhao Shunsheng , Liu Xiangrong , Lü Xingqiang , Wong Wai‐Kwok 
Published: September 2012

ABSTRACTWith a novel asymmetric Schiff‐base zinc complex ZnL (H2L = N‐(3‐methoxysalicylidene)‐N′‐(5‐bromo‐3‐methoxysalicylidene)phenylene‐1,2‐diamine), obtained from phenylene‐1,2‐diamine, 3‐methoxysalicylaldehyde and 5‐bromo‐3‐methoxysalicylaldehyde, as the precursor, a series of heterobinuclear Zn‐Ln complexes [ZnLnL(NO3)3(CH3CN)] (Ln = La, 1; Ln = Nd, 2; Ln = Eu, 3; Ln = Gd, 4; Ln = Tb, 5; Ln = Er, 6; Ln = Yb, 7) were synthesized by the further reaction with Ln(NO3)3·6H2O, and characterized by Fourier transform‐infrared, fast atom bombardment mass spectroscopy and elemental analysis. Photophysical studies of these complexes show that the strong and characteristic near‐infrared luminescence of Nd3+, Yb3+and Er3+ with emissive lifetimes in the microsecond range has been sensitized from the excited state of the asymmetric Schiff‐base ligand due to effective intramolecular energy transfer; the other complexes do not show characteristic emission due to the energy gap between the chromophore and lanthanide ions. Copyright © 2012 John Wiley & Sons, Ltd.
Multiple β‐sheet molecular dynamics of amyloid formation from two ABl‐SH3 domain peptides
Authors: Lapidus Dmitrijs , Duka Vita , Stonkus Vladislavs , Czaplewski Cezary , Liwo Adam , Ventura Salvador , Liepina Inta 
Published: September 2012

AbstractMolecular dynamics simulations in explicit water were carried out for two stacks, each composed of six 10‐strand antiparallel β‐sheets for two peptides corresponding to the diverging turn of two homologous Abl‐SH3 domains. The first system, referred to as 10×6×MK contained the DLSFMKGE sequence from the Drosophila, while the second one, referred to as 10×6×KK, contained the human DLSFKKGE sequence. It was found that the 10×6×MK β‐sheet stack is stable, but the 10×6×KK β‐sheet stack is not. The stability of the 10×6×MK β‐sheet stack results from the hydrophobic interactions of the methionine and phenylalanine residues and the leucine residues of the neighboring sheets. The Met, Phe, and Leu hydrophobic units make a hydrophobic core for the stack of β‐sheets. During the MD run, the Met, Phe, and Leu residues of the neighboring β‐sheets acted as a conformational switch moving the β‐sheets so that the Phe residue interacted with the Met residue from the neighboring β‐sheet. Replacement of Met by Lys destroys the hydrophobic core, which is the stability factor of the β‐sheet stack. For the 10×6×KK system, individual β‐sheets were preserved during simulations, but the interactions between the β‐sheets were lost. The calculations of a six β‐sheet stack confirm the conclusion drawn from our earlier studies of single β‐sheet systems that the β‐sheets must form stacks to be stabilized. These results suggest that the two conserved basic residues at the diverging turn of SH3 domains could act as gatekeepers to avoid aggregation. © 2012 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 557–566, 2012.
Effects of motivation on reward and attentional networks: an fMRI study
Authors: Ivanov Iliyan , Liu Xun , Clerkin Suzanne , Schulz Kurt , Friston Karl , Newcorn Jeffrey H. , Fan Jin 
Published: September 2012

AbstractExisting evidence suggests that reward and attentional networks function in concert and that activation in one system influences the other in a reciprocal fashion; however, the nature of these influences remains poorly understood. We therefore developed a three‐component task to assess the interaction effects of reward anticipation and conflict resolution on the behavioral performance and the activation of brain reward and attentional systems. Sixteen healthy adult volunteers aged 21–45 years were scanned with functional magnetic resonance imaging (fMRI) while performing the task. A two‐way repeated measures analysis of variance (ANOVA) with cue (reward vs. non‐reward) and target (congruent vs. incongruent) as within‐subjects factors was used to test for main and interaction effects. Neural responses to anticipation, conflict, and reward outcomes were tested. Behaviorally there were main effects of both reward cue and target congruency on reaction time. Neuroimaging results showed that reward anticipation and expected reward outcomes activated components of the attentional networks, including the inferior parietal and occipital cortices, whereas surprising non‐rewards activated the frontoinsular cortex bilaterally and deactivated the ventral striatum. In turn, conflict activated a broad network associated with cognitive control and motor functions. Interaction effects showed decreased activity in the thalamus, anterior cingulated gyrus, and middle frontal gyrus bilaterally when difficult conflict trials (e.g., incongruent targets) were preceded by reward cues; in contrast, the ventral striatum and orbitofrontal cortex showed greater activation during congruent targets preceded by reward cues. These results suggest that reward anticipation is associated with lower activation in attentional networks, possibly due to increased processing efficiency, whereas more difficult, conflict trials are associated with lower activity in regions of the reward system, possibly because such trials are experienced as less rewarding.
Motivations and Barriers to Corporate Environmental Management
Authors: Ervin David , Wu JunJie , Khanna Madhu , Jones Cody , Wirkkala Teresa 
Published: September 2012

ABSTRACTThis paper integrates two conceptual frameworks, utility maximization and institutional theory, to analyze voluntary corporate environmental management. The utility maximization or economic approach centers on motivations to decrease cost, increase revenue and improve manager utility. Institutional theory emphasizes how external pressures from market and non‐market constituents shape the firm's environmental efforts. We view the two frameworks as complementary and postulate a model that includes both types of influences. Survey data from six major industries consisting of a diverse set of facilities are used to estimate the effects of economic and institutional factors on a facility's use of environmental practices and pollution‐prevention activities. Our results support the hypothesized model, and show that cost barriers, management attitudes toward environmental stewardship, company ownership and external institutional forces, including competitiveness, investor and regulatory pressures, all affect a facility's environmental practices and pollution prevention activities. Findings suggest that a multifaceted policy strategy is needed to advance corporate environmental management across diverse firms. Copyright © 2012 John Wiley & Sons, Ltd and ERP Environment
The Inactivation Mechanism of Human Group IIA Phospholipase A2 by Scalaradial
Authors: Margarucci Luigi , Monti Maria Chiara , Chini Maria Giovanna , Tosco Alessandra , Riccio Raffaele , Bifulco Giuseppe , Casapullo Agostino 
Published: September 2012

AbstractSecretory phospholipases A2 (sPLA2s) are implicated in the pathogenesis of several inflammation diseases, such as rheumatoid arthritis, septic shock, psoriasis, and asthma. Thus, an understanding of their inactivation mechanisms could be useful for the development of new classes of chemical selective inhibitors. In the marine environment, several bioactive terpenoids possess interesting anti‐inflammatory activity, often through covalent and/or noncovalent inactivation of sPLA2. Herein, we report the molecular mechanism of human group IIA phospholipase A2 (sPLA2‐IIA) inactivation by Scalaradial (SLD), a marine 1,4‐dialdehyde terpenoid isolated from the sponge Cacospongia mollior and endowed with a significant anti‐inflammatory profile. Our results have been collected by a combination of biochemical approaches, advanced mass spectrometry, surface plasmon resonance, and molecular modeling. These suggest that SLD acts as a competitive inhibitor. Indeed, the sPLA2‐IIA inactivation process seems to be driven by the noncovalent recognition process of SLD in the enzyme active site and by chelation of the catalytic calcium ion. In contrast, covalent modification of the enzyme by the SLD dialdehyde moiety emerges as only a minor side event in the ligand–enzyme interaction. These results could be helpful for the rational design of new PLA2 inhibitors that would be able to selectively target the enzyme active site.
Mixing Analysis for a Fermentation Broth of the Fungus Beauveria bassiana under Different Hydrodynamic Conditions in a Bioreactor
Authors: Núñez‐Ramírez D. M. , Valencia‐López J. J. , Calderas F. , Solís‐Soto A. , López‐Miranda J. , Medrano‐Roldán H. , Medina‐Torres L. 
Published: September 2012

AbstractThe performances of radial‐axial flow (Rushton‐Maxflo impellers) and axial‐radial flow (Maxflo‐Rushton impellers) mixers in the laminar‐transitional flow regime were experimentally and numerically investigated with Newtonian and non‐Newtonian fluids. The rheological properties for a fermentation broth consisting of the fungus Beauveria bassiana were studied under different hydrodynamic conditions in these systems. The bioreactor was a continuous stirred‐tank reactor (CSTR), set at different stirring velocities. The rheology of the systems exhibited shear‐thinning behavior which was modeled with the power law model. The experimental hydrodynamics and configuration modes were compared and simulated with a model fluid system and by numerical criteria (computational fluid dynamics). The R‐M mode was found to be more efficient than the M‐R rotating mode in terms of energy and homogenization time. The results will help in the optimization of scale‐up production of these fungi.
Poly(9,9′‐diheylfluorene carbazole) Functionalized with Reduced Graphene Oxide: Convenient Synthesis using Nitrogen‐Based Nucleophiles and Potential Applications in Optical Limiting
Authors: Xu Xiujuan , Chen Jun , Luo Xiaoliang , Lu Jingjing , Zhou Haixin , Wu Wenbo , Zhan Hongbing , Dong Yongqiang , Yan Shouke , Qin Jingui , Li Zhen 
Published: September 2012

AbstractCovalently functionalized reduced graphene oxide (RGO) sheet was prepared by treating nitrogen‐centered anions generated from poly(9,9′‐diheylfluorene carbazole) (PCF) with GO. The resultant hybrids with different chemical behavior were separated by centrifugation. The covalent modification was fully characterized by IR spectroscopy, UV/Vis spectroscopy, thermogravimetric analysis (TGA), Raman spectroscopy, TEM, and SEM. It was found that RGO‐PCF‐s, the soluble part, was split into small platelets with a size of about 200 nm, and the hydrophobic polymer PCF became hydrophilic after wrapping by RGO. The content of RGO in RGO‐PCF‐s was about 11.9 %, and the hybrid material showed good dispersion stability in water. Besides, RGO‐PCF‐i, the insoluble part, with larger size, displayed excellent optical‐limiting response, in which both nonlinear absorption and nonlinear scattering play important roles. As nitrogen‐centered anions are an important type of intermediates in chemistry, this one‐step “grafting‐to” strategy could be used to obtain RGO‐based materials with different applications.
A Native‐Chemical‐Ligation‐Mechanism‐Based Ratiometric Fluorescent Probe for Aminothiols
Authors: Yuan Lin , Lin Weiying , Xie Yinan , Zhu Sasa , Zhao Sheng 
Published: September 2012

AbstractThiol‐containing amino acids (aminothiols) such as cysteine (Cys) and homocysteine (Hcy) play a key role in various biological processes including maintaining the homeostasis of biological thiols. However, abnormal levels of aminothiols are associated with a variety of diseases. The native chemical ligation (NCL) reaction has attracted great attention in the fields of chemistry and biology. NCL of peptide segments involves cascade reactions between a peptide‐α‐thioester and an N‐terminal cysteine peptide. In this work, we employed the NCL reaction mechanism to formulate a Förster resonance energy transfer (FRET) strategy for the design of ratiometric fluorescent probes that were selective toward aminothiols. On the basis of this new strategy, the ratiometric fluorescent probe 1 for aminothiols was judiciously designed. The new probe is highly selective toward aminothiols over other thiols and exhibits a very large variation (up to 160‐fold) in its fluorescence ratio (I458/I603). The new fluorescent probe is capable of ratiometric detection of aminothiols in newborn calf and human serum samples and is also suitable for ratiometric fluorescent imaging of aminothiols in living cells.
Photophysical Analysis of 1,10‐Phenanthroline‐Embedded Porphyrin Analogues and Their Magnesium(II) Complexes
Authors: Ishida Masatoshi , Lim Jong Min , Lee Byung Sun , Tani Fumito , Sessler Jonathan L. , Kim Dongho , Naruta Yoshinori 
Published: September 2012

AbstractThe synthesis, characterization, photophysical properties, and theoretical analysis of a series of tetraaza porphyrin analogues (HPn: n=1–4) containing a dipyrrin subunit and an embedded 1,10‐phenanthroline subunit are described. The meso‐phenyl‐substituted derivative (HP1) interacts with a Mg2+ salt (e.g., MgCl2, MgBr2, MgI2, Mg(ClO4)2, and Mg(OAc)2) in MeCN solution, thereby giving rise to a cation‐dependent red‐shift in both the absorbance‐ and emission maxima. In this system, as well as in the other HPn porphyrin analogues used in this study, the four nitrogen atoms of the ligand interact with the bound magnesium cation to form Mg2+–dipyrrin–phenanthroline complexes of the general structure MgXPn (X=counteranion). Both single‐crystal X‐ray diffraction analysis of the corresponding zinc‐chloride derivative (ZnClP1) and fluorescence spectroscopy of the Mg‐adducts that are formed from various metal salts provide support for the conclusion that, in complexes such as MgClP1, a distorted square‐pyramidal geometry persists about the metal cation wherein a chloride anion acts as an axial counteranion. Several analogues (HPn) that contain electron‐donating and/or electron‐withdrawing dipyrrin moieties were prepared in an effort to understand the structure–property relationships and the photophysical attributes of these Mg–dipyrrin complexes. Analysis of various MgXPn (X=anion) systems revealed significant substitution effects on their chemical, electrochemical, and photophysical properties, as well as on the Mg2+‐cation affinities. The fluorescence properties of MgClPn reflected the effect of donor‐excited photoinduced electron transfer (d‐PET) processes from the dipyrrin subunit (as a donor site) to the 1,10‐phenanthroline acceptor subunit. The proposed d‐PET process was analyzed by electron paramagnetic resonance (EPR) spectroscopy and by femtosecond transient absorption (TA) spectroscopy, as well as by theoretical DFT calculations. Taken together, these studies provide support for the suggestion that a radical species is produced as the result of an intramolecular charge‐transfer process, following photoexcitation. These photophysical effects, combined with a mixed dipyrrin–phenanthroline structure that is capable of effective Mg2+‐cation complexation, lead us to suggest that porphyrin‐inspired systems, such as HPn, have a role to play as magnesium‐cation sensors.
Understanding the Solvent Effect on the Catalytic Oxidation of 1,4‐Butanediol in Methanol over Au/TiO2 Catalyst: NMR Diffusion and Relaxation Studies
Authors: D'Agostino Carmine , Brett Gemma L. , Miedziak Peter J. , Knight David W. , Hutchings Graham J. , Gladden Lynn F. , Mantle Mick D. 
Published: September 2012

AbstractThe effect of water on the catalytic oxidation of 1,4‐butanediol in methanol over Au/TiO2 has been investigated by catalytic reaction studies and NMR diffusion and relaxation studies. The addition of water to the dry catalytic system led to a decrease of both conversion and selectivity towards dimethyl succinate. Pulsed‐field gradient (PFG)‐NMR spectroscopy was used to assess the effect of water addition on the effective self‐diffusivity of the reactant within the catalyst. NMR relaxation studies were also carried out to probe the strength of surface interaction of the reactant in the absence and presence of water. PFG‐NMR studies revealed that the addition of water to the initial system, although increasing the dilution of the system, leads to a significant decrease of effective diffusion rate of the reactant within the catalyst. From T1 and T2 relaxation measurements it was possible to infer the strength of surface interaction of the reactant with the catalyst surface. The addition of water was found to inhibit the adsorption of the reactant over the catalyst surface, with the T1/T2 ratio of 1,4‐butanediol decreasing significantly when water was added. The results overall suggest that both the decrease of diffusion rate and adsorption strength of the reactant within the catalyst, due to water addition, limits the access of reactant molecules to the catalytic sites, which results in a decrease of reaction rate and conversion.
Andhraxylocarpins A–E: Structurally Intriguing Limonoids from the True Mangroves Xylocarpus granatum and Xylocarpus moluccensis
Authors: Li Jun , Li Min‐Yi , Bruhn Torsten , Götz Daniel C. G. , Xiao Qiang , Satyanandamurty Tirumani , Wu Jun , Bringmann Gerhard 
Published: September 2012

AbstractFive new limonoids, including andhraxylocarpins A and B (1 and 2) which contain a 9‐oxa‐tricyclo[3.3.2.17, 10]undecane‐2‐ene motif, andhraxylocarpins C and D (3 and 4), which contain a (Z)‐bicyclo[5.2.1]dec‐3‐en‐8‐one substructure, and andhraxylocarpin E (5), which contains a tricyclo[3.3.1.13, 6]decane‐9‐one scaffold, were isolated from the seeds of two true mangroves, Xylocarpus granatum and Xylocarpus moluccensis, that were collected in the estuaries of Andhra Pradesh, India. The absolute configurations of these compounds were determined by extensive NMR investigations, single‐crystal X‐ray diffraction analysis, and by circular dichroism and optical rotatory dispersion spectroscopy, in combination with quantum‐chemical calculations. The pronounced structural diversity of limonoids from these mangroves might originate from environmental factors.
Analysis of the Electronic Circular Dichroism Spectrum of (−)–[9](2,5)Pyridinophane
Authors: Padula Daniele , Di Bari Lorenzo , Santoro Fabrizio , Gerlach Hans , Rizzo Antonio 
Published: September 2012

ABSTRACTThe results of a combined experimental and theoretical study of the electronic circular dichroism spectrum of (−)–[9] (2,5)Pyridinophane are presented. The features observed in the measured spectrum in the 180–350 nm wavelength region are reproduced by a series of calculations carried out within a density functional time‐dependent approach, coupled with a vibronic analysis allowing rationalizing unambiguously the chiral response of the molecule. Chirality 24:994–1004, 2012. © 2012 Wiley Periodicals, Inc.
Efficient Calculation of ROA Tensors with Analytical Gradients and Fragmentation
Authors: Thorvaldsen Andreas J. , Gao Bin , Ruud Kenneth , Fedorovsky Maxim , Zuber Gérard , Hug Werner 
Published: September 2012

ABSTRACTWe present the results of calculations of Raman optical activity spectra of sizable systems from optical tensors of the fragments, the tensors calculated by an analytic approach at the time‐dependent Hartree–Fock level of theory. The analytic approach permits large basis sets which, together with the limited geometrical extent of the fragments, obviates the need for the use of London‐type orbitals. The implementation of the analytical gradient approach is formulated in the atomic orbital basis by using the elements of the density matrix as variational parameters. This makes the approach directly applicable to linear scaling methods. We do not solve the response equations for the geometrical distortions of the nuclei but determine instead the second‐order perturbed densities with respect to the electromagnetic field perturbations. The number of perturbed density matrices that needs to be determined is thus independent of the number of nuclei, making the approach applicable to fragments with many nuclei and with good quality basis sets. Compared to numerical differentiation schemes, the analytical approach is about 10 times faster even for moderately sized molecules. Chirality 24:1018–1030, 2012. © 2012 Wiley Periodicals, Inc.
The Fokker‐Planck Equation – A Way to Describe Axial Transport and Mixing Processes in a Tube Reactor
Authors: Sommer Karl , Schlosser Eva , Dauth Heinz 
Published: September 2012

AbstractDie Fokker‐Planck‐Gleichung wird zur Beschreibung von kontinuierlichen Prozessen verwendet. In dieser Arbeit werden damit die axialen Transportvorgänge in einem Rohrreaktor beschrieben. Hierfür werden unterschiedliche Produkte und unterschiedliche Maschinenparameter verwendet. Somit wird der Einfluss der Drehzahl und der Partikelgröße untersucht. Mit den entstandenen Ergebnissen soll die Korrelation zwischen den Koeffizienten und den Parametern hergestellt werden.