| 1. |
- Adam, A, et al.
(author)
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Abstracts from Hydrocephalus 2016.
- 2017
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In: Fluids and Barriers of the CNS. - : Springer Science and Business Media LLC. - 2045-8118. ; 14:Suppl 1
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Journal article (peer-reviewed)
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| 2. |
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| 3. |
- Ivanov, Sergey A., et al.
(author)
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Evolution of the structural and multiferroic properties of PbFe2/3W1/3O3 ceramics upon Mn-doping
- 2017
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In: Materials Chemistry and Physics. - : Elsevier BV. - 0254-0584 .- 1879-3312. ; 187, s. 218-232
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Journal article (peer-reviewed)abstract
- The perovskite system Pb(Fe1-xMnx)(2/3)W1/3O3 (0 <= x <= 1, PFMWO) has been prepared by conventional solid-state reaction under different sintering conditions. Structures and phase composition as well as thermal, magnetic and dielectric properties of the compounds have been systematically investigated experimentally and by first-principles density functional calculations. A clean perovskite phase is established at room temperature for compositions 0 <= x <= 0.4. Rietveld refinements of X-ray and neutron powder diffraction patterns demonstrate that the compounds crystallize in space group Pm-3m (0 <= x <= 0.4). The degree of ordering of the Fe and W/Mn cations was found to depend on the concentration of Mn. First-principles calculations suggest that the structural properties of PFMWO are strongly influenced by the Jahn Teller effect. The PFMWO compounds behave as relaxor ferroelectrics at weak Mn-doping with a dielectric constant that rapidly decreases with increasing Mn content. A low temperature antiferromagnetic G-type order with propagation vector k = (1/2,1/2,1/2) is derived from neutron powder diffraction data for the samples with x <= 0.4. However with increasing doping concentration, the magnetic order is perturbed. First principles calculations show that the dominant exchange coupling is antiferromagnetic and occurs between nearest neighbor Fe atoms. When the system is doped with Mn, a relatively weak ferromagnetic (FM) interaction between Fe and Mn atoms emerges. However, due to the presence of this FM interaction, the correlation length of the magnetic order is greatly shortened already at rather low doping levels.
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| 4. |
- Akansel, Serkan, et al.
(author)
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Enhanced Gilbert damping in Re-doped FeCo films : Combined experimental and theoretical study
- 2019
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In: Physical Review B. - 2469-9950 .- 2469-9969. ; 99:17
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Journal article (peer-reviewed)abstract
- The effects of rhenium doping in the range 0-10 at.% on the static and dynamic magnetic properties of Fe65Co35 thin films have been studied experimentally as well as with first-principles electronic structure calculations focusing on the change of the saturation magnetization (M-s) and the Gilbert damping parameter (alpha). Both experimental and theoretical results show that M-s decreases with increasing Re-doping level, while at the same time alpha increases. The experimental low temperature saturation magnetic induction exhibits a 29% decrease, from 2.31 to 1.64 T, in the investigated doping concentration range, which is more than predicted by the theoretical calculations. The room temperature value of the damping parameter obtained from ferromagnetic resonance measurements, correcting for extrinsic contributions to the damping, is for the undoped sample 2.1 x 10(-3), which is close to the theoretically calculated Gilbert damping parameter. With 10 at.% Re doping, the damping parameter increases to 7.8 x 10(-3), which is in good agreement with the theoretical value of 7.3 x 10(-3). The increase in damping parameter with Re doping is explained by the increase in the density of states at the Fermi level, mostly contributed by the spin-up channel of Re. Moreover, both experimental and theoretical values for the damping parameter weakly decrease with decreasing temperature.
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| 5. |
- Ivanov, Sergey A, et al.
(author)
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Polar Order and Frustrated Antiferromagnetism in Perovskite Pb2MnWO6 Single Crystals.
- 2016
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In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 55:6, s. 2791-2805
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Journal article (peer-reviewed)abstract
- Single crystals of the multiferroic double-perovskite Pb2MnWO6 have been synthesized and their structural, thermal, magnetic and dielectric properties studied in detail. Pure perovskite-phase formation and stoichiometric chemical composition of the as-grown crystals are confirmed by X-ray single-crystal and powder diffraction techniques as well as energy-dispersive X-ray and inductively coupled plasma mass spectrometry. Detailed structural analyses reveal that the crystals experience a structural phase transition from the cubic space group (s.g.) Fm3̅m to an orthorhombic structure in s.g. Pn21a at about 460 K. Dielectric data suggest that a ferrielectric phase transition takes place at that same temperature, in contrast to earlier results on polycrystalline samples, which reported a transition to s.g. Pnma and an antiferroelectric low-temperature phase. Magnetic susceptibility measurements indicate that a frustrated antiferromagnetic phase emerges below 8 K. Density functional theory based calculations confirm that the cationic order between Mn and W is favorable. The lowest total energy was found for an antiferromagnetically ordered state. However, analyses of the calculated exchange parameters revealed strongly competing antiferromagnetic interactions. The large distance between the magnetic atoms, together with magnetic frustration, is shown to be the main reason for the low value of the ordering temperature observed experimentally. We discuss the structure-property relationships in Pb2MnWO6 and compare these observations to reported results on related Pb2BWO6 perovskites with different B cations.
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| 6. |
- Lo, Min-Tzu, et al.
(author)
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Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders
- 2017
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 49:1, s. 152-156
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Journal article (peer-reviewed)abstract
- Personality is influenced by genetic and environmental factors(1) and associated with mental health. However, the underlying genetic determinants are largely unknown. We identified six genetic loci, including five novel loci(2,3), significantly associated with personality traits in a meta-analysis of genome-wide association studies (N = 123,132-260,861). Of these genome-wide significant loci, extraversion was associated with variants in WSCD2 and near PCDH15, and neuroticism with variants on chromosome 8p23.1 and in L3MBTL2. We performed a principal component analysis to extract major dimensions underlying genetic variations among five personality traits and six psychiatric disorders (N = 5,422-18,759). The first genetic dimension separated personality traits and psychiatric disorders, except that neuroticism and openness to experience were clustered with the disorders. High genetic correlations were found between extraversion and attention-deficit- hyperactivity disorder (ADHD) and between openness and schizophrenia and bipolar disorder. The second genetic dimension was closely aligned with extraversion-introversion and grouped neuroticism with internalizing psychopathology (e.g., depression or anxiety).
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| 7. |
- Lo, Min-Tzu, et al.
(author)
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Modeling prior information of common genetic variants improves gene discovery for neuroticism
- 2017
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In: Human Molecular Genetics. - : OXFORD UNIV PRESS. - 0964-6906 .- 1460-2083. ; 26:22, s. 4530-4539
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Journal article (peer-reviewed)abstract
- Neuroticism reflects emotional instability, and is related to various mental and physical health issues. However, the majority of genetic variants associated with neuroticism remain unclear. Inconsistent genetic variants identified by different genome-wide association studies (GWAS) may be attributable to low statistical power. We proposed a novel framework to improve the power for gene discovery by incorporating prior information of single nucleotide polymorphisms (SNPs) and combining two relevant existing tools, relative enrichment score (RES) and conditional false discovery rate (FDR). Here, SNP's conditional FDR was estimated given its RES based on SNP prior information including linkage disequilibrium (LD)-weighted genic annotation scores, total LD scores and heterozygosity. A known significant locus in chromosome 8p was excluded before estimating FDR due to long-range LD structure. Only one significant LD-independent SNP was detected by analyses of unconditional FDR and traditional GWAS in the discovery sample (N = 59 225), and notably four additional SNPs by conditional FDR. Three of the five SNPs, all identified by conditional FDR, were replicated (P < 0.05) in an independent sample (N = 170 911). These three SNPs are located in intronic regions of CADM2, LINGO2 and EP300 which have been reported to be associated with autism, Parkinson's disease and schizophrenia, respectively. Our approach using a combination of RES and conditional FDR improved power of traditional GWAS for gene discovery providing a useful framework for the analysis of GWAS summary statistics by utilizing SNP prior information, and helping to elucidate the links between neuroticism and complex diseases from a genetic perspective.
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| 8. |
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| 9. |
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| 10. |
- Zhu, Y., et al.
(author)
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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis
- 2017
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In: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 45:5, s. 2629-2643
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Journal article (peer-reviewed)abstract
- Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotation. Through long-read DNA sequencing, we obtained a gap-free genome assembly for M. sympodialis (ATCC 42132), comprising eight nuclear and one mitochondrial chromosome. We also sequenced and assembled four M. sympodialis clinical isolates, and showed their value for understanding Malassezia reproduction by confirming four alternative allele combinations at the two mating-type loci. Importantly, we demonstrated how proteomics data could be readily integrated with transcriptomics data in standard annotation tools. This increased the number of annotated protein-coding genes by 14% (from 3612 to 4113), compared to using transcriptomics evidence alone. Manual curation further increased the number of protein-coding genes by 9% (to 4493). All of these genes have RNA-seq evidence and 87% were confirmed by proteomics. The M. sympodialis genome assembly and annotation presented here is at a quality yet achieved only for a few eukaryotic organisms, and constitutes an important reference for future host-microbe interaction studies.
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| 11. |
- Autieri, Carmine, et al.
(author)
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Recipe for High Moment Materials with Rare-earth and 3d Transition Metal Composites
- 2016
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
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Journal article (peer-reviewed)abstract
- Materials with high volume magnetization are perpetually needed for the generation of sufficiently large magnetic fields by writer pole of magnetic hard disks, especially for achieving increased areal density in storage media. In search of suitable materials combinations for this purpose, we have employed density functional theory to predict the magnetic coupling between iron and gadolinium layers separated by one to several monolayers of 3d transition metals (Sc-Zn). We demonstrate that it is possible to find ferromagnetic coupling for many of them and in particular for the early transition metals giving rise to high moment. Cr and Mn are the only elements able to produce a significant ferromagnetic coupling for thicker spacer layers. We also present experimental results on two trilayer systems Fe/Sc/Gd and Fe/Mn/Gd. From the experiments, we confirm a ferromagnetic coupling between Fe and Gd across a 3 monolayers Sc spacer or a Mn spacer thicker than 1 monolayer. In addition, we observe a peculiar dependence of Fe/Gd magnetic coupling on the Mn spacer thickness.
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| 12. |
- Chen, Chi-Hua, et al.
(author)
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Leveraging genome characteristics to improve gene discovery for putamen subcortical brain structure
- 2017
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In: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 7
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Journal article (peer-reviewed)abstract
- Discovering genetic variants associated with human brain structures is an on-going effort. The ENIGMA consortium conducted genome-wide association studies (GWAS) with standard multi-study analytical methodology and identified several significant single nucleotide polymorphisms (SNPs). Here we employ a novel analytical approach that incorporates functional genome annotations (e.g., exon or 5′UTR), total linkage disequilibrium (LD) scores and heterozygosity to construct enrichment scores for improved identification of relevant SNPs. The method provides increased power to detect associated SNPs by estimating stratum-specific false discovery rate (FDR), where strata are classified according to enrichment scores. Applying this approach to the GWAS summary statistics of putamen volume in the ENIGMA cohort, a total of 15 independent significant SNPs were identified (conditional FDR < 0.05). In contrast, 4 SNPs were found based on standard GWAS analysis (P < 5 × 10−8). These 11 novel loci include GATAD2B, ASCC3, DSCAML1, and HELZ, which are previously implicated in various neural related phenotypes. The current findings demonstrate the boost in power with the annotation-informed FDR method, and provide insight into the genetic architecture of the putamen.
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| 13. |
- Chimata, Raghuveer, et al.
(author)
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Magnetism and ultrafast magnetization dynamics of Co and CoMn alloys at finite temperature
- 2017
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In: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 95:21
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Journal article (peer-reviewed)abstract
- Temperature-dependent magnetic experiments such as pump-probe measurements generated by a pulsed laser have become a crucial technique for switching the magnetization in the picosecond time scale. Apart from having practical implications on the magnetic storage technology, the research field of ultrafast magnetization poses also fundamental physical questions. To correctly describe the time evolution of the atomic magnetic moments under the influence of a temperature-dependent laser pulse, it remains crucial to know if the magnetic material under investigation has magnetic excitation spectrum that is more or less dependent on the magnetic configuration, e.g., as reflected by the temperature dependence of the exchange interactions. In this paper, we demonstrate from first-principles theory that the magnetic excitation spectra in Co in fcc, bcc, and hcp structures are nearly identical in a wide range of noncollinear magnetic configurations. This is a curious result of a balance between the size of the magnetic moments and the strength of the Heisenberg exchange interactions, that in themselves vary with configuration, but put together in an effective spin Hamiltonian results in a configuration-independent effective model. We have used such a Hamiltonian, together with ab initio calculated damping parameters, to investigate the magnon dispersion relationship as well as ultrafast magnetization dynamics of Co and Co-rich CoMn alloys.
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| 14. |
- Ivanov, Sergey, et al.
(author)
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Cation ordering, ferrimagnetism and ferroelectric relaxor behavior in Pb(Fe1-xScx)(2/3)W1/3O3 solid solutions
- 2019
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In: European Physical Journal B. - : SPRINGER. - 1434-6028 .- 1434-6036. ; 92:8
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Journal article (peer-reviewed)abstract
- Ceramic samples of the multiferroic perovskite Pb(Fe1-xScx)(2/3)W1/3O3 with 0 <= x <= 0.4 have been synthesized using a conventional solid-state reaction method, and investigated experimentally and theoretically using first-principle calculations. Rietveld analyses of joint synchrotron X-ray and neutron diffraction patterns show the formation of a pure crystalline phase with cubic (Fm3(_)m) structure with partial ordering in the B-sites. The replacement of Fe by Sc leads to the increase of the cation order between the B and B '' sites. As the non-magnetic Sc3+ ions replace the magnetic Fe3+ cations, the antiferromagnetic state of PbFe2/3W1/3O3 is turned into a ferrimagnetic state reflecting the different magnitude of the magnetic moments on the B ' and B '' sites. The materials remain ferroelectric relaxors with increasing Sc content. Results from experiments on annealed and quenched samples show that the cooling rate after high temperature annealing controls the degree of cationic order in Pb(Fe1-xScx)(2/3)W1/3O3 and possibly also in the undoped PbFe2/3W1/3O3.
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| 15. |
- Kacar, Betuel, et al.
(author)
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Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein
- 2017
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In: Journal of Molecular Evolution. - : SPRINGER. - 0022-2844 .- 1432-1432. ; 84:2-3, s. 69-84
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Journal article (peer-reviewed)abstract
- The ability to design synthetic genes and engineer biological systems at the genome scale opens new means by which to characterize phenotypic states and the responses of biological systems to perturbations. One emerging method involves inserting artificial genes into bacterial genomes and examining how the genome and its new genes adapt to each other. Here we report the development and implementation of a modified approach to this method, in which phylogenetically inferred genes are inserted into a microbial genome, and laboratory evolution is then used to examine the adaptive potential of the resulting hybrid genome. Specifically, we engineered an approximately 700-million-year-old inferred ancestral variant of tufB, an essential gene encoding elongation factor Tu, and inserted it in a modern Escherichia coli genome in place of the native tufB gene. While the ancient homolog was not lethal to the cell, it did cause a twofold decrease in organismal fitness, mainly due to reduced protein dosage. We subsequently evolved replicate hybrid bacterial populations for 2000 generations in the laboratory and examined the adaptive response via fitness assays, whole genome sequencing, proteomics, and biochemical assays. Hybrid lineages exhibit a general adaptive strategy in which the fitness cost of the ancient gene was ameliorated in part by upregulation of protein production. Our results suggest that an ancient-modern recombinant method may pave the way for the synthesis of organisms that exhibit ancient phenotypes, and that laboratory evolution of these organisms may prove useful in elucidating insights into historical adaptive processes.
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| 16. |
- Kauppi, Karolina, et al.
(author)
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Revisiting Antipsychotic Drug Actions Through Gene Networks Associated With Schizophrenia
- 2018
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In: American Journal of Psychiatry. - : AMER PSYCHIATRIC PUBLISHING, INC. - 0002-953X .- 1535-7228. ; 175:7, s. 674-682
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Journal article (peer-reviewed)abstract
- Objective: Antipsychotic drugs were incidentally discovered in the 1950s, but their mechanisms of action are still not understood. Better understanding of schizophrenia pathogenesis could shed light on actions of current drugs and reveal novel "druggable" pathways for unmet therapeutic needs. Recent genome-wide association studies offer unprecedented opportunities to characterize disease gene networks and uncover drug-disease relationships. Polygenic overlap between schizophrenia risk genes and antipsychotic drug targets has been demonstrated, but specific genes and pathways constituting this overlap are undetermined. Risk genes of polygenic disorders do not operate in isolation but in combination with other genes through protein-protein interactions among gene product.Method: The protein interactome was used to map antipsychotic drug targets (N=88) to networks of schizophrenia risk genes (N=328).Results: Schizophrenia risk genes were significantly localized in the interactome, forming a distinct disease module. Core genes of the module were enriched for genes involved in developmental biology and cognition, which may have a central role in schizophrenia etiology. Antipsychotic drug targets overlapped with the core disease module and comprised multiple pathways beyond dopamine. Some important risk genes like CHRN, PCDH, and HCN families were not connected to existing antipsychotics but may be suitable targets for novel drugs or drug repurposing opportunities to treat other aspects of schizophrenia, such as cognitive or negative symptoms.Conclusions: The network medicine approach provides a platform to collate information of disease genetics and drug-gene interactions to shift focus from development of antipsychotics to multitarget antischizophrenia drugs. This approach is transferable to other diseases.
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| 17. |
- Lindström, A., et al.
(author)
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High resistivity in undoped CdTe : carrier compensation of Te antisites and Cd vacancies
- 2016
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In: Journal of Physics D. - : IOP Publishing. - 0022-3727 .- 1361-6463. ; 49:3
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Journal article (peer-reviewed)abstract
- In this paper, we focus on the high resistivity of intentionally undoped CdTe, where the most prevalent defects are Cd vacancies and Te antisites. Our calculated formation energies lead to the conclusion that the Fermi energy of undoped CdTe is at midgap due to carrier compensation of Te antisites and Cd vacancies, which explains the experimentally observed high resistivity. We use density functional theory with the hybrid functional of Heyd, Scuseria and Ernzerhof (HSE06) and show that the proper description of the native defects in general fails using the local density approximation (LDA) instead of HSE06. We conclude that LDA is insufficient to understand the high resistivity of undoped CdTe. We calculate the neutral and double acceptor state of the Te antisite to be intrinsic DX-centers.
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| 18. |
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| 19. |
- Peters, L., et al.
(author)
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Valence and spectral properties of rare-earth clusters
- 2015
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In: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 92:3
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Journal article (peer-reviewed)abstract
- The rare earths are known to have intriguing changes of the valence, depending on the chemical surrounding or geometry. Here, we aim at predicting the transition of valence when passing from the atomic divalent limit to the bulk trivalent limit. This transition is analyzed by addressing clusters of various size for selected rare-earth elements, i.e., Sm, Tb, and Tm, via a theoretical treatment that combines density functional theory with atomic multiplet theory. Our results show that Tm clusters change from pure divalent to pure trivalent at a size of six atoms, while Tb clusters are already divalent for two atoms and stay so until eight atoms and the bulk limit. Instead, Sm clusters are respectively purely divalent up to eight atoms. For larger Sm clusters, a transition to a trivalent configuration is expected and likely accompanied by a regime of mixed valence. The valence of all rare-earth clusters, as a function of size, is predicted from the interpolation of our calculated results. These predictions are argued to be best investigated by spectroscopic measurements. To ease experimental analysis, we provide theoretical spectra, based on dynamical mean-field theory in the Hubbard I approximation.
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| 20. |
- Qiang, Xiaoling, et al.
(author)
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New melanocortin-like peptide of E. coli can suppress inflammation via the mammalian melanocortin-1 receptor (MC1R) : possible endocrine-like function for microbes of the gut.
- 2017
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In: npj Biofilms and Microbiomes. - : Springer Science and Business Media LLC. - 2055-5008. ; 3
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Journal article (peer-reviewed)abstract
- E. coli releases a 33 amino acid peptide melanocortin-like peptide of E. coli (MECO-1) that is identical to the C-terminus of the E. coli elongation factor-G (EF-G) and has interesting similarities to two prominent mammalian melanocortin hormones, alpha-melanocyte-stimulating hormone (alpha-MSH) and adrenocorticotropin (ACTH). Note that MECO-1 lacks HFRW, the common pharmacophore of the known mammalian melanocortin peptides. MECO-1 and the two hormones were equally effective in severely blunting release of cytokines (HMGB1 and TNF) from macrophage-like cells in response to (i) endotoxin (lipopolysaccharide) or (ii) pro-inflammatory cytokine HMGB-1. The in vitro anti-inflammatoty effects of MECO-1 and of alpha-MSH were abrogated by (i) antibody against melanocortin-1 receptor (MC1R) and by (ii) agouti, an endogenous inverse agonist of MC1R. In vivo MECO-1 was even more potent than alpha-MSH in rescuing mice from death due to (i) lethal doses of LPS endotoxin or (ii) cecal ligation and puncture, models of sterile and infectious sepsis, respectively.
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| 21. |
- Sanyal, Nilotpal, et al.
(author)
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GWASinlps : non-local prior based iterative SNP selection tool for genome-wide association studies
- 2019
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In: Bioinformatics. - : Oxford University Press. - 1367-4803 .- 1367-4811. ; 35:1, s. 1-11
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Journal article (peer-reviewed)abstract
- Motivation: Multiple marker analysis of the genome-wide association study (GWAS) data has gained ample attention in recent years. However, because of the ultra high-dimensionality of GWAS data, such analysis is challenging. Frequently used penalized regression methods often lead to large number of false positives, whereas Bayesian methods are computationally very expensive. Motivated to ameliorate these issues simultaneously, we consider the novel approach of using non-local priors in an iterative variable selection framework.Results: We develop a variable selection method, named, iterative non-local prior based selection for GWAS, or GWASinlps, that combines, in an iterative variable selection framework, the computational efficiency of the screen-and-select approach based on some association learning and the parsimonious uncertainty quantification provided by the use of non-local priors. The hallmark of our method is the introduction of 'structured screen-and-select' strategy, that considers hierarchical screening, which is not only based on response-predictor associations, but also based on response-response associations and concatenates variable selection within that hierarchy. Extensive simulation studies with single nucleotide polymorphisms having realistic linkage disequilibrium structures demonstrate the advantages of our computationally efficient method compared to several frequentist and Bayesian variable selection methods, in terms of true positive rate, false discovery rate, mean squared error and effect size estimation error. Further, we provide empirical power analysis useful for study design. Finally, a real GWAS data application was considered with human height as phenotype.
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| 22. |
- Xu, D. B., et al.
(author)
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Large enhancement of magnetic moment in L1(0) ordered FePt thin films by Nd substitutional doping
- 2015
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In: Journal of Physics D. - : IOP Publishing. - 0022-3727 .- 1361-6463. ; 48:25
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Journal article (peer-reviewed)abstract
- We studied L1(0) ordered Fe50Pt50-xNdx alloy films, which showed a large enhancement (similar to 18.4% at room temperature and similar to 11.7% at 10 K) of magnetic moment with 6 atomic % of Nd. Analysis of the x-ray magnetic circular dichroism spectra at the Fe L-3,L-2 edges and Nd M-5,M-4 edges in Fe50Pt44Nd6 films indicated a significant contribution of the Nd orbital moment. The origin of the large enhancement of magnetic moment was attributed to the effect of ferromagnetic coupling of the total magnetic moments between Fe and Nd. Density functional theory based first principles calculations supported the experimental observations of increasing moment due to Nd substitution of Pt.
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