Dynamical Mean-Field Theory within an Augmented Plane-Wave Framework: Assessing Electronic Correlations in the Iron Pnictide LaFeAsO

We present an approach that combines the local density approximation (LDA) and the dynamical mean-field theory (DMFT) in the framework of the full-potential linear augmented plane waves (FLAPW) method. Wannier-like functions for the correlated shell are constructed by projecting local orbitals onto a set of Bloch eigenstates located within a certain energy window. The screened Coulomb interaction and Hund's coupling are calculated from a first-principle constrained RPA scheme. We apply this LDA+DMFT implementation, in conjunction with continuous-time quantum Monte-Carlo, to study the electronic correlations in LaFeAsO. Our findings support the physical picture of a metal with intermediate correlations. The average value of the mass renormalization of the Fe 3d bands is about 1.6, in reasonable agreement with the picture inferred from photoemission experiments. The discrepancies between different LDA+DMFT calculations (all technically correct) which have been reported in the literature are shown to have two causes: i) the specific value of the interaction parameters used in these calculations and ii) the degree of localization of the Wannier orbitals chosen to represent the Fe 3d states, to which many-body terms are applied. The latter is a fundamental issue in the application of many-body calculations, such as DMFT, in a realistic setting. We provide strong evidence that the DMFT approximation is more accurate and more straightforward to implement when well-localized orbitals are constructed from a large energy window encompassing Fe-3d, As-4p and O-2p, and point out several difficulties associated with the use of extended Wannier functions associated with the low-energy iron bands. Some of these issues have important physical consequences, regarding in particular the sensitivity to the Hund's coupling.Comment: 16 pages, 9 figures, published versio

Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay

Learning to read and write the transcriptional regulatory code is of central importance to progress in genetic analysis and engineering. Here we describe a massively parallel reporter assay (MPRA) that facilitates the systematic dissection of transcriptional regulatory elements. In MPRA, microarray-synthesized DNA regulatory elements and unique sequence tags are cloned into plasmids to generate a library of reporter constructs. These constructs are transfected into cells and tag expression is assayed by high-throughput sequencing. We apply MPRA to compare >27,000 variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon-β enhancer. We first show that the resulting data define accurate maps of functional transcription factor binding sites in both enhancers at single-nucleotide resolution. We then use the data to train quantitative sequence-activity models (QSAMs) of the two enhancers. We show that QSAMs from two cellular states can be combined to design enhancer variants that optimize potentially conflicting objectives, such as maximizing induced activity while minimizing basal activity.National Human Genome Research Institute (U.S.) (grant R01HG004037)National Science Foundation (U.S.) ((NSF) grant PHY-0957573)National Science Foundation (U.S.) (NSF grant PHY-1022140)Broad Institut

Hippocampal IGF-1 expression, neurogenesis and slowed aging: clues to longevity from mutant mice

Recent studies point out the important role of IGF and insulin-related signaling pathways in the control of longevity of laboratory animals. The Ames dwarf mouse is a murine model of circulating GH and IGF-1 deficiency that exhibits dwarf phenotype characteristics and significantly extends lifespan. It is interesting to know that Ames dwarf mice do not experience an age-related decline in cognitive function when compared to their young counterparts. In this study, the most recent works on local GH and IGF-1 expression in the hippocampus of Ames mice are briefly reviewed

Analysis of physical pore space characteristics of two pyrolytic biochars and potential as microhabitat

Background and Aims Biochar amendment to soil is a promising practice of enhancing productivity of agricultural systems. The positive effects on crop are often attributed to a promotion of beneficial soil microorganisms while suppressing pathogens e.g. This study aims to determine the influence of biochar feedstock on (i) spontaneous and fungi inoculated microbial colonisation of biochar particles and (ii) physical pore space characteristics of native and fungi colonised biochar particles which impact microbial habitat quality. Methods Pyrolytic biochars from mixed woods and Miscanthus were investigated towards spontaneous colonisation by classical microbiological isolation, phylogenetic identification of bacterial and fungal strains, and microbial respiration analysis. Physical pore space characteristics of biochar particles were determined by X-ray μ-CT. Subsequent 3D image analysis included porosity, surface area, connectivities, and pore size distribution. Results Microorganisms isolated from Wood biochar were more abundant and proliferated faster than those from the Miscanthus biochar. All isolated bacteria belonged to gram-positive bacteria and were feedstock specific. Respiration analysis revealed higher microbial activity for Wood biochar after water and substrate amendment while basal respiration was on the same low level for both biochars. Differences in porosity and physical surface area were detected only in interaction with biochar-specific colonisation. Miscanthus biochar was shown to have higher connectivity values in surface, volume and transmission than Wood biochars as well as larger pores as observed by pore size distribution. Differences in physical properties between colonised and non-colonised particles were larger in Miscanthus biochar than in Wood biochar. Conclusions Vigorous colonisation was found on Wood biochar compared to Miscanthus biochar. This is contrasted by our findings from physical pore space analysis which suggests better habitat quality in Miscanthus biochar than in Wood biochar. We conclude that (i) the selected feedstocks display large differences in microbial habitat quality as well as physical pore space characteristics and (ii) physical description of biochars alone does not suffice for the reliable prediction of microbial habitat quality and recommend that physical and surface chemical data should be linked for this purpose

Executive Functions of Six-Year-Old Boys with Normal Birth Weight and Gestational Age

Impaired fetal development, reflected by low birth weight or prematurity, predicts an increased risk for psychopathology, especially attention deficit hyperactivity disorder (ADHD). Such effects cut across the normal range of birth weight and gestation. Despite the strength of existing epidemiological data, cognitive pathways that link fetal development to mental health are largely unknown. In this study we examined the relation of birth weight (>2500 g) and gestational age (37–41 weeks) within the normal range with specific executive functions in 195 Singaporean six-year-old boys of Chinese ethnicity. Birth weight adjusted for gestational age was used as indicator of fetal growth while gestational age was indicative of fetal maturity. Linear regression revealed that increased fetal growth within the normal range is associated with an improved ability to learn rules during the intra/extra-dimensional shift task and to retain visual information for short period of time during the delayed matching to sample task. Moreover, faster and consistent reaction times during the stop-signal task were observed among boys born at term, but with higher gestational age. Hence, even among boys born at term with normal birth weight, variations in fetal growth and maturity showed distinct effects on specific executive functions

Holomorphic Blocks in Three Dimensions

We decompose sphere partition functions and indices of three-dimensional N=2 gauge theories into a sum of products involving a universal set of "holomorphic blocks". The blocks count BPS states and are in one-to-one correspondence with the theory's massive vacua. We also propose a new, effective technique for calculating the holomorphic blocks, inspired by a reduction to supersymmetric quantum mechanics. The blocks turn out to possess a wealth of surprising properties, such as a Stokes phenomenon that integrates nicely with actions of three-dimensional mirror symmetry. The blocks also have interesting dual interpretations. For theories arising from the compactification of the six-dimensional (2,0) theory on a three-manifold M, the blocks belong to a basis of wavefunctions in analytically continued Chern-Simons theory on M. For theories engineered on branes in Calabi-Yau geometries, the blocks offer a non-perturbative perspective on open topological string partition functions.Comment: 124 pages, 21 figures. v3: Typos correcte