Symmetry of the Atomic Electron Density in Hartree, Hartree-Fock, and Density Functional Theory

The density of an atom in a state of well-defined angular momentum has a specific finite spherical harmonic content, without and with interactions. Approximate single-particle schemes, such as the Hartree, Hartree-Fock, and Local Density Approximations, generally violate this feature. We analyze, by means of perturbation theory, the degree of this violation and show that it is small. The correct symmetry of the density can be assured by a constrained-search formulation without significantly altering the calculated energies. We compare our procedure to the (different) common practice of spherically averaging the self-consistent potential. Kohn-Sham density functional theory with the exact exchange-correlation potential has the correct finite spherical harmonic content in its density; but the corresponding exact single particle potential and wavefunctions contain an infinite number of spherical harmonics.Comment: 11 pages, 6 figures. Expanded discussion of spherical harmonic expansion of Hartree density. Some typos corrected, references adde

Descending Post-commissural Fornix Lesions Produce Impaired Spatial Working Memory in a 12-arm Maze

Memory is supported in the brain by a distributed neural network, comprised of cortical, limbic and brainstem structures and fibre pathways. The descending component of the post-commissural fornix (dPCFx) conveys hippocampal efferents to the mammillary bodies (MB), and so presents as a critical pathway along the hippocampal-MB-anterior thalamic axis, structures all crucial to memory function. However, two previous studies have reported surprisingly mild, if any, effect of selective dPCFx lesions on spatial memory in an 8-arm radial arm maze (RAM). To examine the impact of dPCFx lesions on electrophysiological activity in the anterior thalamus, dorsal hippocampus and prefrontal cortex, and in an effort to substantially increase task difficulty, we trained rats postoperatively in a 12-arm RAM. We found that dPCFx lesions produced a severe RAM impairment, showing that the RAM can elicit spatial working memory deficits after dPCFx lesions when task demands are high and suggesting that the dPCFx may indeed play an important mnemonic role

Anterior thalamic nuclei neurons sustain memory

A hippocampal-diencephalic-cortical network supports memory function. The anterior thalamic nuclei (ATN) form a key anatomical hub within this system. Consistent with this, injury to the mammillary body-ATN axis is associated with examples of clinical amnesia. However, there is only limited and indirect support that the output of ATN neurons actively enhances memory. Here, in rats, we first showed that mammillothalamic tract (MTT) lesions caused a persistent impairment in spatial working memory. MTT lesions also reduced rhythmic electrical activity across the memory system. Next, we introduced 8.5 Hz optogenetic theta-burst stimulation of the ATN glutamatergic neurons. The exogenously-triggered, regular pattern of stimulation produced an acute and substantial improvement of spatial working memory in rats with MTT lesions and enhanced rhythmic electrical activity. Neither behaviour nor rhythmic activity was affected by endogenous stimulation derived from the dorsal hippocampus. Analysis of immediate early gene activity, after the rats foraged for food in an open field, showed that exogenously-triggered ATN stimulation also increased Zif268 expression across memory-related structures. These findings provide clear evidence that increased ATN neuronal activity supports memory. They suggest that ATN-focused gene therapy may be feasible to counter clinical amnesia associated with dysfunction in the mammillary body-ATN axis

Effective action and density functional theory

The effective action for the charge density and the photon field is proposed as a generalization of the density functional. A simple definition is given for the density functional, as the functional Legendre transform of the generator functional of connected Green functions for the density and the photon field, offering systematic approximation schemes. The leading order of the perturbation expansion reproduces the Hartree-Fock equation. A renormalization group motivated method is introduced to turn on the Coulomb interaction gradually and to find corrections to the Hartree-Fock and the Kohn-Sham schemes.Comment: New references and a numerical algorithm added, to appear in Phys. Rev. B. 30 pages, no figure

Thermal Density Functional Theory in Context

This chapter introduces thermal density functional theory, starting from the ground-state theory and assuming a background in quantum mechanics and statistical mechanics. We review the foundations of density functional theory (DFT) by illustrating some of its key reformulations. The basics of DFT for thermal ensembles are explained in this context, as are tools useful for analysis and development of approximations. We close by discussing some key ideas relating thermal DFT and the ground state. This review emphasizes thermal DFT's strengths as a consistent and general framework.Comment: Submitted to Spring Verlag as chapter in "Computational Challenges in Warm Dense Matter", F. Graziani et al. ed

Density functional theories and self-energy approaches

A purpose-designed microarray platform (Stressgenes, Phase 1) was utilised to investigate the changes in gene expression within the liver of rainbow trout during exposure to a prolonged period of confinement. Tissue and blood samples were collected from trout at intervals up to 648 h after transfer to a standardised confinement stressor, together with matched samples from undisturbed control fish. Plasma ACTH, cortisol, glucose and lactate were analysed to confirm that the neuroendocrine response to confinement was consistent with previous findings and to provide a phenotypic context to assist interpretation of gene expression data. Liver samples for suppression subtractive hybridisation (SSH) library construction were selected from within the experimental groups comprising “early” stress (2–48 h) and “late” stress (96–504 h). In order to reduce redundancy within the four SSH libraries and yield a higher number of unique clones an additional subtraction was carried out. After printing of the arrays a series of 55 hybridisations were executed to cover 6 time points. At 2 h, 6 h, 24 h, 168 h and 504 h 5 individual confined fish and 5 individual control fish were used with control fish only at 0 h. A preliminary list of 314 clones considered differentially regulated over the complete time course was generated by a combination of data analysis approaches and the most significant gene expression changes were found to occur during the 24 h to 168 h time period with a general approach to control levels by 504 h. Few changes in expression were apparent over the first 6 h. The list of genes whose expression was significantly altered comprised predominantly genes belonging to the biological process category (response to stimulus) and one cellular component category (extracellular region) and were dominated by so-called acute phase proteins. Analysis of the gene expression profile in liver tissue during confinement revealed a number of significant clusters. The major patterns comprised genes that were up-regulated at 24 h and beyond, the primary examples being haptoglobin, β-fibrinogen and EST10729. Two representative genes from each of the six k-means clusters were validated by qPCR. Correlations between microarray and qPCR expression patterns were significant for most of the genes tested. qPCR analysis revealed that haptoglobin expression was up-regulated approximately 8-fold at 24 h and over 13-fold by 168 h.This project was part funded by the European Commission (Q5RS-2001-02211), Enterprise Ireland and the Natural Environment Research Council of the United Kingdom

The prediction of preference for unfamiliar urban places

Preferences for unfamiliar urban environments were studied as a function of urban categories, viewing time, and four predictor variables: complexity, coherence, identifiability, and mystery. A nonmetric factor analysis of the preference ratings for the longest viewing-time condition yielded five dimensions: Contemporary Life, Alley/Factory, Urban Nature, Unusual Architecture, and Older Buildings. The five categories differed significantly in preference, with Urban Nature by far the most preferred and Alley/Factory distinctly disliked. The combination of low coherence and high complexity characterizes the least liked Alley/Factory category, while the role of mystery in the urban setting is highlighted by the most preferred Urban Nature category. The results point to various ways in which the urban environment could be more responsive to people's preferences.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43513/1/11111_2005_Article_BF01359051.pd

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of SARS-CoV-2 genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three available genomic nomenclature systems for SARS-CoV-2 to all sequence data from the WHO European Region available during the COVID-19 pandemic until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation. We provide a comparison of the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.Peer reviewe