bluuebunny/crossref_metadata_2025_split huggingface dataset:
A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land
Authors: Emiliani Giovanni , Fondi Marco , Fani Renato , Gribaldo Simonetta 
Published: February 2009

AbstractBackgroundThe pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified.ResultsWe have performed an extensive analysis of the taxonomic distribution and phylogeny of Phenylalanine Ammonia Lyase (PAL), which catalyses the first and essential step of the general phenylpropanoid pathway, leading from phenylalanine to p-Coumaric acid and p-Coumaroyl-CoA, the entry points of the flavonoids and lignin routes. We obtained robust evidence that the ancestor of land plants acquired a PALviahorizontal gene transfer (HGT) during symbioses with soil bacteria and fungi that are known to have established very early during the first steps of land colonization. This horizontally acquired PAL represented then the basis for further development of the phenylpropanoid pathway and plant radiation on terrestrial environments.ConclusionOur results highlight a possible crucial role of HGT from soil bacteria in the path leading to land colonization by plants and their subsequent evolution. The few functional characterizations of sediment/soil bacterial PAL (production of secondary metabolites with powerful antimicrobial activity or production of pigments) suggest that the initial advantage of this horizontally acquired PAL in the ancestor of land plants might have been either defense against an already developed microbial community and/or protection against UV.ReviewersThis article was reviewed by Purificación López-García, Janet Siefert, and Eugene Koonin.
A comparative genomics study of genetic products potentially encoding ladderane lipid biosynthesis
Authors: Rattray Jayne E , Strous Marc , Op den Camp Huub JM , Schouten Stefan , Jetten Mike SM , Damsté Jaap S Sinninghe 
Published: February 2009

Abstract

Background
The fatty acids of anaerobic ammonium oxidizing (anammox) bacteria contain linearly concatenated cyclobutane moieties, so far unique to biology. These moieties are under high ring strain and are synthesised by a presently unknown biosynthetic pathway.

Results
Gene clusters encoding enzymes of fatty acid biosynthesis in the anammox bacterium Kuenenia stuttgartiensis and 137 other organisms were analysed and compared in silico to gain further insight into the pathway of (ladderane) fatty acid biosynthesis. In K. stuttgartiensis four large gene clusters encode fatty acid biosynthesis. Next to the regular enzyme complex needed for fatty acid biosynthesis (FASII), the presence of four putative S-adenosyl-methionine (SAM) radical enzymes, two enzymes similar to phytoene desaturases and many divergent paralogues of β-ketoacyl-ACP synthase (fabF) were unusual. Surprisingly, extensive synteny was observed with FASII gene clusters in the deltaproteobacterium Desulfotalea psychrophila. No ladderane lipids were detected in lipid extracts of this organism but we did find unusual polyunsaturated hydrocarbons (PUHC), not detected in K. stuttgartiensis.

Conclusion
We suggest that the unusual gene clusters of K. stuttgartiensis and D. psychrophila encode a novel pathway for anaerobic PUFA biosynthesis and that K. stuttgartiensis further processes PUFA into ladderane lipids, in similar fashion to the previously proposed route of ladderane lipid biosynthesis. However, the presence of divergent paralogues of fabF with radically different active site topologies may suggest an alternative pathway where ladderane moieties are synthesised externally and are recruited into the pathway of fatty acid biosynthesis.

Reviewers
This article was reviewed by Dr Michael Galperin (nominated by Prof E. Koonin), Dr Andrei Osterman and Dr Jeremy Selengut.
Knockdown of astrocyte elevated gene-1 inhibits proliferation and enhancing chemo-sensitivity to cisplatin or doxorubicin in neuroblastoma cells
Authors: Liu Haiyan , Song Xianrang , Liu Chunxi , Xie Li , Wei Ling , Sun Ruopeng 
Published: February 2009

Abstract

Background

Astrocyte elevated gene-1 (AEG-1) was originally characterized as a HIV-1-inducible gene in primary human fetal astrocyte. Recent studies highlight a potential role of AEG-1 in promoting tumor progression and metastasis. The aim of this study was to investigate if AEG-1 serves as a potential therapeutic target of human neuroblastoma.

Methods
We employed RNA interference to reduce AEG-1 expression in human neuroblastoma cell lines and analyzed their phenotypic changes.

Results
We found that the knockdown of AEG-1 expression in human neuroblastoma cells significantly inhibited cell proliferation and apoptosis. The specific downregulation induced cell arrest in the G0/G1 phase of cell cycle. In the present study, we also observed a significant enhancement of chemo-sensitivity to cisplatin and doxorubicin by knockdown of AEG-1.

Conclusion
Our study suggests that overexpressed AEG-1 enhance the tumorogenic properties of neuroblastoma cells. The inhibition of AEG-1 expression could be a new adjuvant therapy for neuroblastoma.
The contribution of CHEK2 to the TP53-negative Li-Fraumeni phenotype
Authors: Ruijs Marielle WG , Broeks Annegien , Menko Fred H , Ausems Margreet GEM , Wagner Anja , Oldenburg Rogier , Meijers-Heijboer Hanne , van't Veer Laura J , Verhoef Senno 
Published: February 2009

AbstractBackgroundCHEK2has previously been excluded as a major cause of Li-Fraumeni syndrome (LFS). One particularCHEK2germline mutation, c.1100delC, has been shown to be associated with elevated breast cancer risk. The prevalence ofCHEK2*1100delC differs between populations and has been found to be relatively high in the Netherlands. The question remains nevertheless whetherCHEK2germline mutations contribute to the Li-Fraumeni phenotype.MethodsWe have screened 65 DutchTP53-negative LFS/LFL candidate patients forCHEK2germline mutations to determine their contribution to the LFS/LFL phenotype.ResultsWe identified six index patients with aCHEK2sequence variant, four with the c.1100delC variant and two sequence variants of unknown significance, p.Phe328Ser and c.1096-?_1629+?del.ConclusionOur data show thatCHEK2is not a major LFS susceptibility gene in the Dutch population. However,CHEK2might be a factor contributing to individual tumour development inTP53-negative cancer-prone families.
Facial emotion recognition in patients with bipolar I and bipolar II disorder
Authors: Derntl Birgit , Seidel Eva‐Maria , Kryspin‐Exner Ilse , Hasmann Alexander , Dobmeier Matthias 
Published: February 2009

Objectives. The ability to recognize facial emotional expressions is a fundamental skill that is necessary for successful social interaction. Previous studies examining this competency in patients with bipolar disorder have generated mixed results. Since bipolar patients show multiple psychosocial difficulties even after remission, this study was aimed at further elucidating emotion recognition deficits in bipolar patients.Methods and design. Sixty‐two stable bipolar out‐patients (37 females; 25 males) and 62 matched healthy controls participated in the study. Explicit facial emotion recognition accuracy was measured with a computerized task.Results. Analysis of emotion recognition performance revealed no gender effect but a significant group effect, indicating significantly worse accuracy in patients with bipolar I. Patients with bipolar II disorder did not differ significantly from healthy controls. These results were not correlated with either residual symptoms or intellectual impairments.Conclusions. Based on our results, patients with bipolar disorder vary not only in diagnosis, but also in social cognitive functions, all of which should be addressed in clinical treatment. Future studies should clarify whether emotion recognition deficits are involved in the development and maintenance of bipolar disorder.
Hall effect in Taylor-phase and decagonal Al3(Mn,Fe) complex intermetallics
Authors: Stanic Denis , Ivkov Jovica , Smontara Ana , Jaglicic Zvonko , Dolinsek Janez , Heggen Marc , Feuerbacher Michael 
Published: February 2009

Abstract
The Hall coefficient (R
H) of Al73Mn27–xFex (x = 0, 2, 4 and 6) complex metallic alloys has been measured in the temperature interval from 90 to 400 K. All the alloys are T (Taylor) phase except Al73Mn21Fe6 that is a decagonal (d) quasicrystal. The Hall coefficients of all the samples are positive and they decrease strongly with the increase of temperature according to the Curie-Weiss [C/(Tθ)] law. Therefore, for the separation of the normal (R
0) and anomalous (RS
) Hall coefficients, the results for the paramagnetic susceptibility (χ) in the corresponding temperature interval have been used. The values deduced from R
H(χ) plots are about –2 × 10–10 m3 C–1 for R
0, and about 5 × 10–7 m3 C–1 for RS
. When the possible dependence of RS
on temperature, that is due to the temperature dependence of the electrical resistivity ρ(T), is taken into account the values are about zero for R
0, and about 3 × 10–7 m3 C–1 for RS
(295 K). No significant composition dependence of R
0 has been detected.
Antiferromagnetism in two-dimensional quasicrystals
Authors: Jagannathan Anuradha , Szallas Attila 
Published: February 2009

Abstract
Quasiperiodic structures possess long range positional order, but are freed of constraints imposed by translational invariance. For spins interacting via Heisenberg couplings, one may expect therefore to find novel magnetic configurations in such structures. We have studied magnetic properties for simple two dimensional models, as a first step towards understanding experimentally studied magnetic quasicrystals such as the Zn–Mg–R(rare earth) compounds. We analyse properties of the antiferromagnetic groundstate and magnon excitation modes for bipartite tilings such as the octagonal and Penrose tilings. In the absence of frustration, one has an inhomogeneous Neel-ordered ground state, with local quantum fluctuations of the local staggered magnetic order parameter. We study the spin wave spectrum and wavefunctions of such antiferromagnets within the linear spin wave approximation. Some results for spin-spin correlations in these systems are discussed.
Nanocrystallization and structural correlation in quasicrystalline and crystalline phases during mechanical milling
Authors: Tiwari Radhey Shyam , Yadav Thakur Prasad , Mukhopadhyay Nilay K. , Shaz Mohammad Abu , Srivastava Onkar Nath 
Published: February 2009

Abstract
The main objective of the proposed work is to investigate the formation of nanoquasicrystalline and related nanocrystalline phases in Al—Cu—Fe system during mechanical milling at the initial stage of milling. The mechanical milling of a quasicrystalline Al65Cu20Fe15 alloy was performed in a high-energy ball mill (Szegvari attritor) by varying milling time from 2.5 min to 60 min under liquid hexane medium at the speed of 400 rpm with a ball to powder ratio of 40 : 1. X-ray diffraction was carried out for evaluating the lattice strain, lattice parameters and crystallite sizes of the milled sample. It was found that the evolution of monoclinic Al13Fe4 phase from Al65Cu20Fe15 quasicrystalline phase occurred after 2.5 min of milling, which was further confirmed by transmission electron microscopy. After 5 min of ball milling nano size disordered B2 phase (bcc, a = 0.29 nm) was also found. The systematic analysis of the XRD patterns for evolving lattice parameter, sequential strain suggests that the lattice strain during milling has been quite considerable.
Chirality-selective synthesis of carbon nanotubes by catalytic-chemical vapor deposition using quasicrystal alloys as catalysts
Authors: Kajiwara Kazuo , Suzuki Shogo , Sato Hideki , Hata Koicho 
Published: February 2009

Abstract
We study ultrathin quasicrystalline (QC) films as catalysts for the synthesis of carbon nanotubes (CNTs). To optimize the conditions for the synthesis of CNTs with single chirality, it is important to understand the effects of the catalyst on the chirality-selectivity. Among QC alloys found so far, an icosahedral Al–Cu–Fe alloy system with fivefold symmetry was tested for a catalyst in the synthesis of CNTs by alcohol catalytic-chemical vapor deposition (CCVD). Cross-sectional scanning electron microscopic images of the samples revealed that vertically-aligned CNTs were synthesized reproducibly. It implies that QC films have a significant catalytic activity for the synthesis of CNTs. Moreover, preliminary results of chirality-selectivity are obtained by means of resonance Raman scattering. It is suggested that Al–Cu–Fe ultrathin films are useful for the preferential synthesis of armchair-type CNTs, that is, QC nanoclusters play an important role as catalyst in alcohol CCVD.
e/a Determination for the transition metal element TM in Al–Cu–TM–Si (TM = Fe and Ru) approximants and B2-compounds by means of the FLAPW-Fourier method
Authors: Mizutani Uichiro , Asahi Ryoji , Takeuchi Tsunehiro , Sato Hirokazu , Kontsevoi Oleg , Freeman A. J. 
Published: February 2009

Abstract
By using the FLAPW-Fourier method, we could determine the e/a value for Al–Cu–TM–Si (TM = Fe and Ru) 1/1 – 1/1 – 1/1 approximants and several B2 compounds including CuZn, NiZn, NiAl, MnZn, and AlMg. The NiAl, NiZn and MnZn B2-compounds involving the transition metal element as a partner element are found to be no longer regarded as the 3/2 electron compounds. Moreover, we found that the e/a value is not uniquely assigned to a given transition metal element but depends on its surrounding environments. Hence, it is difficult to use it as a universal parameter in an alloy design.
Thermoelectric properties of Al–Pd–Re quasicrystal sintered by Spark Plasma Sintering (SPS): effect of improvement of microstructure
Authors: Takagiwa Yoshiki , Kamimura Takahiko , Hosoi Sizuka , Okada Junpei Tamura , Kimura Kaoru 
Published: February 2009

Abstract
We report the thermoelectric properties of poly-grain Al–Pd–Re icosahedral quasicrystals and discuss an effect of improvement of their microstructure. The improvement of microstructure by using Spark Plasma Sintering (SPS) method resulted into a large increase of the electrical conductivity but less increase of the thermal conductivity. The relative density dramatically increased up to more than 90% by SPS. On the other hand, the microstructure itself does not have critical influence on the Seebeck coefficient, which is found to be strongly correlated with e/a (sample’s compositions). Consequently, the dimensionless figure of merit (ZT) increased three times from 0.05 to 0.15.
Vibrational properties of MgZn2
Authors: Brommer Peter , Boissieu Marc de , Euchner Holger , Francoual Sonia , Gähler Franz , Johnson Mark , Parlinski Krzysztof , Schmalzl Karin 
Published: February 2009

Abstract
We present here simulation results on the dynamical structure factor of the C14 Laves Phase of MgZn2, the simplest of the Mg–(Al,Zn) Frank-Kasper alloy phases. The dynamical structure factor was determined in two ways. Firstly, the dynamical matrix was obtained in harmonic approximation from ab-initio forces. The dynamical structure factor can then be computed from the eigenvalues of the dynamical matrix. Alternatively, Molecular Dynamics simulations of a larger sample were used to measure the correlation function corresponding to the dynamical structure factor. Both results are compared to data from neutron scattering experiments. This comparison also includes the intensity distribution, which is a very sensitive test. We find that the dynamical structure factor determined with either method agrees reasonably well with the experiment. In particular, the intensity transfer from acoustic to optic phonon modes can be reproduced correctly. This shows that simulation studies can complement phonon dispersion measurements.
Spiky density of states in large complex Al–Mn phases
Authors: Trambly de Laissardiere Guy 
Published: February 2009

Abstract
First-principle electronic structure calculations have been performed in crystalline complex phases μ-Al4.12Mn and λ-Al4.6Mn using the TB-LMTO method. The atomic structures contain about 560 atoms in a large hexagonal unit cell. One of the main characteristic of their density of states is the presence of fine peaks the so-called “spiky structure”. From multiple-scattering calculations in real space, we show that these fine peaks are not artifacts in ab-initio calculations, since they result from a specific localization of electrons by atomic clusters of different length scales.
Thermal conductivity of the Al-based quasicrystals and approximants
Authors: Takeuchi Tsunehiro 
Published: February 2009

Abstract
At high temperatures above 200 K, significant increase in thermal conductivity (κ) was observed for the Al-based icosahedral quasicrystals and their corresponding approximants. By comparing the measured κ of the Al—Re—Si 1/1-cubic approximants with their electronic density of states at the Fermi level (ε
F) determined by the low temperature specific heat measurements, we found that the increase in κ at high temperature was most pronounced when ε
F is located at the bottom of the pseudogap. This fact indicates that the large increase in κ is not brought about by the lattice but by the conduction electrons in associated with the narrow pseudogap at ε
F. It is also found that the behavior of κ at high temperature is well accounted for in terms of the bipolar diffusion effect of conduction electrons that is generally employed to analyze κ of the narrow-gap semiconductors and semimetals.
Compressibility of Al64Pd30.4Fe5.6
Authors: Krauss Günter , Gu Qinfen , Feuerbacher Michael , Steurer Walter 
Published: February 2009

Abstract
The stability of C2-Al64Pd30.4Fe5.6, an approximant phase to the icosahdral Al–Fe–Pd quasicrystal, has been investigated by high-pressure X-ray diffraction using a diamond-anvil cell and synchrotron radiation up to 24.30(1) GPa. The material is structurally stable within the framework of the experiment. The unit cell volume as a function of pressure follows a second-order Birch-Murnaghan equation of state with K
0 = 169.5(2.5) GPa. This value is comparable to that of other quasicrystals and approximant phases containing Al and heavy transition metals.
Structure and properties of quasicrystalline and approximant EBPVD coatings of Al-based systems
Authors: Ustinov Anatolii , Polishchuk Sergey , Scorodzievskii Valerii , Telychko Volodymir 
Published: February 2009

Abstract
This paper considers main features of the formation of Al–Cu–Fe and Al–Cr–Fe coatings with complex crystalline structures using high-rate electron beam physical vapour deposition (EBPVD). It is shown that the deposition of the coatings at substrate temperatures below approximately 570 K leads to the formation of nanostructured quasicrystalline or approximant phases. Mechanical behaviour at static and dynamic loadings of the coatings was investigated. It is established that the decreasing of the grain size in the materials to nanoscale values results in significant enhancement of their damping capacity (a mechanical energy dissipation in the materials) at alternate strains. Possibilities of the use of materials based on quasicrystalline and/or approximant phases as hard and high damping coatings for the prevention of early destruction of gas turbine blades are discussed.
Charge transfer in DNA: effective Hamiltonian approaches
Authors: Macia Enrique 
Published: February 2009

Abstract
Aperiodic order plays a very significant role in biology, as it determines most informative content of genomes. Amongst the various physical, chemical or biological phenomena that might be inferred from sequence correlations, charge transfer properties deserve particular attention. Indeed, the nature of DNA-mediated charge migration has been related to the understanding of damage recognition process, protein binding, or with the task of engineering biological processes (e.g. designing nanoscale sensing of genomic mutations), opening new challenges for emerging nanobiotechnologies. Nevertheless, the solution of Schrödinger´s equation with a potential that is given by a one-dimensional array of the double-stranded DNA remains as a main open theme in solid state physics of biological macromolecules. In this contribution, I will shortly review several approaches introduced during the last few years in order to describe charge transfer migration in DNA in terms of tight-binding effective Hamiltonians.
The relationship of thyroid hormone status with myocardial function in stress cardiomyopathy
Authors: Lee Seong Jin , Kang Jun Goo , Ryu Ohk Hyun , Kim Chul Sik , Ihm Sung-Hee , Choi Moon Gi , Yoo Hyung Joon , Hong Kyung Soon 
Published: February 2009

ObjectiveThis study aimed to investigate thyroid hormone (TH) status and its relationship with myocardial function as well as clinical and biochemical parameters in stress cardiomyopathy (CMP).MethodsForty-five patients with stress CMP (the patient group), 31 patients without stress CMP (the control II group), and 58 healthy subjects (the control I group) were included. Sick euthyroid syndrome (SES) was defined as low total triiodothyronine (T3) with normal TSH levels.ResultsIn the patient group at admission, prevalence of SES was 62.2%. Compared with the control I group, the patient group had a decrease in left ventricular ejection fraction (LVEF) and systolic blood pressure (BP) and an increase in troponin-I, CK-MB, and B-type natriuretic peptide (BNP) levels. Total T3 levels were reduced, and anti-thyroid peroxidase antibody (anti-TPO Ab) positivity, C-reactive protein (CRP) and cortisol levels were elevated. Total T3 levels were associated with acute physiology and chronic health evaluation II (APACHE II) score, LVEF, systolic BP, and cortisol levels in multivariate analysis. In the control II group, total T3 levels were not associated with any variables. In the SES (n=28) and myocardial dysfunction (MDys, n=27) subgroups, increased APACHE II score and BNP levels as well as decreased LVEF and systolic BP were significant. Total T3 levels were reduced, and CRP, cortisol and catecholamines levels were elevated. In the MDys subgroup, anti-TPO Ab positivity and titer were increased.ConclusionThese results suggest that total T3 levels may be associated with myocardial contractility, clinical severity, and cortisol levels. Thyroid autoimmunity may influence myocardial contractility in stress CMP.