Density-functional embedding using a plane-wave basis

The constrained electron density method of embedding a Kohn-Sham system in a substrate system (first described by P. Cortona, Phys. Rev. B {\bf 44}, 8454 (1991) and T.A. Wesolowski and A. Warshel, J. Phys. Chem {\bf 97}, 8050 (1993)) is applied with a plane-wave basis and both local and non-local pseudopotentials. This method divides the electron density of the system into substrate and embedded electron densities, the sum of which is the electron density of the system of interest. Coupling between the substrate and embedded systems is achieved via approximate kinetic energy functionals. Bulk aluminium is examined as a test case for which there is a strong interaction between the substrate and embedded systems. A number of approximations to the kinetic-energy functional, both semi-local and non-local, are investigated. It is found that Kohn-Sham results can be well reproduced using a non-local kinetic energy functional, with the total energy accurate to better than 0.1 eV per atom and good agreement between the electron densities.Comment: 11 pages, 4 figure

Precise calculation of parity nonconservation in cesium and test of the standard model

We have calculated the 6s-7s parity nonconserving (PNC) E1 transition amplitude, E_{PNC}, in cesium. We have used an improved all-order technique in the calculation of the correlations and have included all significant contributions to E_{PNC}. Our final value E_{PNC} = 0.904 (1 +/- 0.5 %) \times 10^{-11}iea_{B}(-Q_{W}/N) has half the uncertainty claimed in old calculations used for the interpretation of Cs PNC experiments. The resulting nuclear weak charge Q_{W} for Cs deviates by about 2 standard deviations from the value predicted by the standard model.Comment: 24 pages, 8 figure

Investigation of previously implicated genetic variants in chronic tic disorders: a transmission disequilibrium test approach

Genetic studies in Tourette syndrome (TS) are characterized by scattered and poorly replicated findings. We aimed to replicate findings from candidate gene and genome-wide association studies (GWAS). Our cohort included 465 probands with chronic tic disorder (93% TS) and both parents from 412 families (some probands were siblings). We assessed 75 single nucleotide polymorphisms (SNPs) in 465 parent–child trios; 117 additional SNPs in 211 trios; and 4 additional SNPs in 254 trios. We performed SNP and gene-based transmission disequilibrium tests and compared nominally significant SNP results with those from a large independent case–control cohort. After quality control 71 SNPs were available in 371 trios; 112 SNPs in 179 trios; and 3 SNPs in 192 trios. 17 were candidate SNPs implicated in TS and 2 were implicated in obsessive–compulsive disorder (OCD) or autism spectrum disorder (ASD); 142 were tagging SNPs from eight monoamine neurotransmitter-related genes (including dopamine and serotonin); 10 were top SNPs from TS GWAS; and 13 top SNPs from attention-deficit/hyperactivity disorder, OCD, or ASD GWAS. None of the SNPs or genes reached significance after adjustment for multiple testing. We observed nominal significance for the candidate SNPs rs3744161 (TBCD) and rs4565946 (TPH2) and for five tagging SNPs; none of these showed significance in the independent cohort. Also, SLC1A1 in our gene-based analysis and two TS GWAS SNPs showed nominal significance, rs11603305 (intergenic) and rs621942 (PICALM). We found no convincing support for previously implicated genetic polymorphisms. Targeted re-sequencing should fully appreciate the relevance of candidate genes

Synaptic processes and immune-related pathways implicated in Tourette syndrome.

Tourette syndrome (TS) is a neuropsychiatric disorder of complex genetic architecture involving multiple interacting genes. Here, we sought to elucidate the pathways that underlie the neurobiology of the disorder through genome-wide analysis. We analyzed genome-wide genotypic data of 3581 individuals with TS and 7682 ancestry-matched controls and investigated associations of TS with sets of genes that are expressed in particular cell types and operate in specific neuronal and glial functions. We employed a self-contained, set-based association method (SBA) as well as a competitive gene set method (MAGMA) using individual-level genotype data to perform a comprehensive investigation of the biological background of TS. Our SBA analysis identified three significant gene sets after Bonferroni correction, implicating ligand-gated ion channel signaling, lymphocytic, and cell adhesion and transsynaptic signaling processes. MAGMA analysis further supported the involvement of the cell adhesion and trans-synaptic signaling gene set. The lymphocytic gene set was driven by variants in FLT3, raising an intriguing hypothesis for the involvement of a neuroinflammatory element in TS pathogenesis. The indications of involvement of ligand-gated ion channel signaling reinforce the role of GABA in TS, while the association of cell adhesion and trans-synaptic signaling gene set provides additional support for the role of adhesion molecules in neuropsychiatric disorders. This study reinforces previous findings but also provides new insights into the neurobiology of TS

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

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

EXPERIMENTAL VALIDATION OF NUCLEAR REACTION DATA FOR INVENTORY SIMULATIONS ON MOLYBDENUM

Molybdenum is being considered as a potential material for future nuclear fusion experiments and power plants. It has good thermo-mechanical properties and can be easily fabricated, making it attractive as an alternative first wall material to tungsten, which is the current leading candidate. Unfortunately, according to simulations, fusion-neutron irradiated Mo may become too activated during reactor operation to maintain the objective of fusion of avoiding the generation of long-term, higher-level radioactive waste. However, these simulated predictions rely heavily on having high-quality, accurate nuclear reaction data. For example, reliable simulations of the radiological response of isotopically-tailored Mo would be required by reactor designers and eventually nuclear regulators to assess if it is a viable low-activation fusion solution (in comparison to pure Mo). In recent years, UKAEA has developed benchmarks to test and validate the FISPACT-II inventory code and the input international nuclear data libraries against experimental measurements. This paper presents nuclear code prediction comparisons to new data acquired from γ-spectroscopy measurements of Mo irradiated in the ASP 14 MeV facility at AWE in the UK. Results demonstrate that FISPACT-II predictions for Mo are remarkably accurate; particularly for activity generated from the shorter-lived radionuclides explored by these laboratory experiments, such as 91Mo and 97Nb, etc., and their metastable isomeric states

EXPERIMENTAL VALIDATION OF NUCLEAR REACTION DATA FOR INVENTORY SIMULATIONS ON MOLYBDENUM

Molybdenum is being considered as a potential material for future nuclear fusion experiments and power plants. It has good thermo-mechanical properties and can be easily fabricated, making it attractive as an alternative first wall material to tungsten, which is the current leading candidate. Unfortunately, according to simulations, fusion-neutron irradiated Mo may become too activated during reactor operation to maintain the objective of fusion of avoiding the generation of long-term, higher-level radioactive waste. However, these simulated predictions rely heavily on having high-quality, accurate nuclear reaction data. For example, reliable simulations of the radiological response of isotopically-tailored Mo would be required by reactor designers and eventually nuclear regulators to assess if it is a viable low-activation fusion solution (in comparison to pure Mo). In recent years, UKAEA has developed benchmarks to test and validate the FISPACT-II inventory code and the input international nuclear data libraries against experimental measurements. This paper presents nuclear code prediction comparisons to new data acquired from γ-spectroscopy measurements of Mo irradiated in the ASP 14 MeV facility at AWE in the UK. Results demonstrate that FISPACT-II predictions for Mo are remarkably accurate; particularly for activity generated from the shorter-lived radionuclides explored by these laboratory experiments, such as 91Mo and 97Nb, etc., and their metastable isomeric states

Oviposition Behavior And Development Of Pseudacteon Flies (diptera: Phoridae), Parasitoids Of Solenopsis Fire Ants (hymenoptera: Formicidae)

We studied the opposition behavior and larval development of Pseudacteon phorid flies, which are parasitoids of Solenopsis fire ants. Four South American Pseudacteon spp., P. litoralis Borgmeier, P. tricuspis Borgmeier, P. wasmanni (Schmitz) and P. curvatus Borgmeier (which attack S. invicta Buren), and 2 North American Pseudacteon spp., P. browni Disney and P. crawfordi Coquillett (which attack S. geminata [F.]), were evaluated. In laboratory tests, larger Pseudacteon spp. attacked larger Solenopsis workers. The mean worker size preferred was significantly larger than the colony mean worker size for all but the smallest phorid species, P. curvatus, which preferred workers significantly smaller than the colony mean. Within Pseudacteon spp., larger females preferred larger workers, but this relationship was significant only for the 2 North American species. Natural parasitism rates of Solenopsis workers by the 2 North American Pseudacteon spp. in the field were low (0-2.42% per colony), but >90% of the overall size range of worker ants showed evidence of parasitism. Between 11.8 and 31.0% of apparent oviposition attempts resulted in successful parasitism. Mean larval development times ranged from 13.0 to 18.4 d at 30°C and were shorter for North American species. Larval stages required 24.8-36.5% longer to develop at 25°C than at 30°C. Mean pupal development times ranged from 15.6 to 18.7 d at 30°C. In general, larger Pseudacteon spp. had longer larval and pupal development times. Overall, North and South American Pseudacteon spp. were similar in terms of oviposition behavior and development.263716724Buren, W.F., Revisionary studies on the taxonomy of the imported fire ants (1972) J. Ga. Entomol. 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Sociobiol., 16, pp. 323-336Porter, S.D., Pesquero, M.A., Campiolo, S., Fowler, H.G., Growth and development of Pseudacteon phorid fly maggots (Diptera: Phoridae) in the heads of Solenopsis fire ant workers (Hymenoptera: Formicidae) (1995) Environ. Entomol., 24, pp. 475-479Porter, S.D., Vander Meer, R.K., Pesquero, M.A., Campiolo, S., Fowler, H.G., Solenopsis fire ant reactions to attacks of Pseudacteon flies in southeastern Brazil (Hymenoptera: FormicidaeDiptera: Phoridae) (1995) Ann. Entomol. Soc. Am., 88, pp. 570-575Porter, S.D., Fowler, H.G., Campiolo, S., Pesquero, M.A., Host specificity of several Pseudacteon parasites of fire ants in South America (Diptera: PhoridaeHymenoptera: Formicidae) (1995) Fla. Entomol., 78, pp. 70-75Porter, S.D., Williams, D.F., Patterson, R.S., Rearing the decapitating fly Pseudacteon tricuspis (Diptera: Phoridae) in imported fire ants (Hymenoptera: Formicidae) from the United States (1997) J. Econ. Entomol., , in pressPorter, S.D., Williams, D.F., Patterson, R.S., Fowler, H.G., Intercontinental differences in the abundance of Solenopsis fire ants (Hymenoptera: Formicidae): an escape from natural enemies? (1997) Environ. Entomol., , in pressRice, W.R., Analyzing tables of statistical tests (1989) Evolution, 43, pp. 223-225Tschinkel, W.R., Colony growth and the ontogeny of worker polymorphism in the fire ant, Solenopsis invicta (1988) Behav. Ecol. Sociobiol., 22, pp. 103-115Williams, D.F., Banks, W.A., Pseudacteon obtusus (Diptera: Phoridae) attacking Solenopsis invicta (Hymenoptera: Formicidae) in Brazil (1987) Psyche, 94, pp. 9-13Williams, R.N., Panaia, J.R., Gallo, D., Whitcomb, W.H., Fire ants attacked by phorid flies (1973) Fla. Entomol., 56, pp. 259-26