Better Integrators for Functional Renormalization Group Calculations

We analyze a variety of integration schemes for the momentum space functional renormalization group calculation with the goal of finding an optimized scheme. Using the square lattice $t-t'$ Hubbard model as a testbed we define and benchmark the quality. Most notably we define an error estimate of the solution for the ordinary differential equation circumventing the issues introduced by the divergences at the end of the FRG flow. Using this measure to control for accuracy we find a threefold reduction in number of required integration steps achievable by choice of integrator. We herewith publish a set of recommended choices for the functional renormalization group, shown to decrease the computational cost for FRG calculations and representing a valuable basis for further investigations.Comment: 13 pages, 5 figure

Data-driven assessment of eQTL mapping methods

<p>Abstract</p> <p>Background</p> <p>The analysis of expression quantitative trait loci (eQTL) is a potentially powerful way to detect transcriptional regulatory relationships at the genomic scale. However, eQTL data sets often go underexploited because legacy QTL methods are used to map the relationship between the expression trait and genotype. Often these methods are inappropriate for complex traits such as gene expression, particularly in the case of epistasis.</p> <p>Results</p> <p>Here we compare legacy QTL mapping methods with several modern multi-locus methods and evaluate their ability to produce eQTL that agree with independent external data in a systematic way. We found that the modern multi-locus methods (Random Forests, sparse partial least squares, lasso, and elastic net) clearly outperformed the legacy QTL methods (Haley-Knott regression and composite interval mapping) in terms of biological relevance of the mapped eQTL. In particular, we found that our new approach, based on Random Forests, showed superior performance among the multi-locus methods.</p> <p>Conclusions</p> <p>Benchmarks based on the recapitulation of experimental findings provide valuable insight when selecting the appropriate eQTL mapping method. Our battery of tests suggests that Random Forests map eQTL that are more likely to be validated by independent data, when compared to competing multi-locus and legacy eQTL mapping methods.</p

Extended van Royen-Weisskopf formalism for lepton-antilepton meson decay widths within non-relativistic quark models

The classical van Royen-Weisskopf formula for the decay width of a meson into a lepton-antilepton pair is modified in order to include non-zero quark momentum contributions within the meson as well as relativistic effects. Besides, a phenomenological electromagnetic density for quarks is introduced. The meson wave functions are obtained from two different models: a chiral constituent quark model and a quark potential model including instanton effects. The modified van Royen-Weisskopf formula is found to improve systematically the results for the widths, giving an overall good description of all known decays.Comment: 22 pages, 3 figures, RevTex, epsfig. To be published in Nucl. Phys.

Rashba spin-orbit coupling in the square lattice Hubbard model: A truncated-unity functional renormalization group study

The Rashba-Hubbard model on the square lattice is the paradigmatic case for studying the effect of spin-orbit coupling, which breaks spin and inversion symmetry, in a correlated electron system. We employ a truncated-unity variant of the functional renormalization group which allows us to analyze magnetic and superconducting instabilities on equal footing. We derive phase diagrams depending on the strengths of Rasbha spin-orbit coupling, real second-neighbor hopping and electron filling. We find commensurate and incommensurate magnetic phases which compete with d-wave superconductivity. Due to the breaking of inversion symmetry, singlet and triplet components mix; we quantify the mixing of d-wave singlet pairing with f-wave triplet pairing.Comment: 9 pages, 7 figure

White Matter Hyperintensities and the Course of Depressive Symptoms in Elderly People with Mild Dementia

Objectives: To explore the relationship between white matter hyperintensities (WMH) and the prevalence and course of depressive symptoms in mild Alzheimer’s disease (AD) and Lewy body dementia. Design: This is a prospective cohort study conducted in secondary care outpatient clinics in western Norway. Subjects: The study population consisted of 77 elderly people with mild dementia diagnosed according to standardised criteria. Methods: Structured clinical interviews and physical, neurological, psychiatric, and neuropsychological examinations were performed and routine blood tests were taken. Depression was assessed using the depression subitem of the Neuropsychiatric Inventory and the Montgomery-Åsberg Depression Rating Scale (MADRS). A standardised protocol for magnetic resonance imaging scan was used, and the volumes of WMH were quantified using an automated method, followed by manual editing. Results: The volumes of total and frontal deep WMH were significantly and positively correlated with baseline severity of depressive symptoms, and depressed patients had significantly higher volumes of total and frontal deep WMH than non-depressed patients. Higher volumes of WMH were also associated with having a high MADRS score and incident and persistent depression at follow-up. After adjustment for potential confounders, frontal deep WMH, in addition to prior depression and non-AD dementia, were still significantly associated with baseline depressive symptoms (p = 0.015, OR 3.703, 95% CI 1.294–10.593). Similar results emerged for total WMH. Conclusion: In elderly people with mild dementia, volumes of WMH, in particular frontal deep WMH, were positively correlated with baseline severity of depressive symptoms, and seemed to be associated with persistent and incident depression at follow-up. Further studies of the mechanisms that determine the course of depression in mild dementia are needed

Dental artifacts in the head and neck region::implications for Dixon-based attenuation correction in PET/MR

BACKGROUND: In the absence of CT or traditional transmission sources in combined clinical positron emission tomography/magnetic resonance (PET/MR) systems, MR images are used for MR-based attenuation correction (MR-AC). The susceptibility effects due to metal implants challenge MR-AC in the neck region of patients with dental implants. The purpose of this study was to assess the frequency and magnitude of subsequent PET image distortions following MR-AC. METHODS: A total of 148 PET/MR patients with clear visual signal voids on the attenuation map in the dental region were included in this study. Patients were injected with [(18)F]-FDG, [(11)C]-PiB, [(18)F]-FET, or [(64)Cu]-DOTATATE. The PET/MR data were acquired over a single-bed position of 25.8 cm covering the head and neck. MR-AC was based on either standard MR-AC(DIXON) or MR-AC(INPAINTED) where the susceptibility-induced signal voids were substituted with soft tissue information. Our inpainting algorithm delineates the outer contour of signal voids breaching the anatomical volume using the non-attenuation-corrected PET image and classifies the inner air regions based on an aligned template of likely dental artifact areas. The reconstructed PET images were evaluated visually and quantitatively using regions of interests in reference regions. The volume of the artifacts and the computed relative differences in mean and max standardized uptake value (SUV) between the two PET images are reported. RESULTS: The MR-based volume of the susceptibility-induced signal voids on the MR-AC attenuation maps was between 1.6 and 520.8 mL. The corresponding/resulting bias of the reconstructed tracer distribution was localized mainly in the area of the signal void. The mean and maximum SUVs averaged across all patients increased after inpainting by 52% (± 11%) and 28% (± 11%), respectively, in the corrected region. SUV underestimation decreased with the distance to the signal void and correlated with the volume of the susceptibility artifact on the MR-AC attenuation map. CONCLUSIONS: Metallic dental work may cause severe MR signal voids. The resulting PET/MR artifacts may exceed the actual volume of the dental fillings. The subsequent bias in PET is severe in regions in and near the signal voids and may affect the conspicuity of lesions in the mandibular region. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40658-015-0112-5) contains supplementary material, which is available to authorized users

Nucleons or diquarks? Competition between clustering and color superconductivity in quark matter

We study the instabilities of quark matter in the framework of a generalized Nambu--Jona-Lasinio model, in order to explore possible competition between three-quark clustering to form nucleons and diquark formation leading to color superconductivity. Nucleon and $\Delta$ solutions are obtained for the relativistic Faddeev equation at finite density and their binding energies are compared with those for the scalar and axial-vector diquarks found from the Bethe-Salpeter equation. In a model with interactions in both scalar and axial diquark channels, bound nucleons exist up to nuclear matter density. However, except at densities below about a quarter of that of nuclear matter, we find that scalar diquark formation is energetically favored. This raises the question of whether a realistic phase diagram of baryonic matter can be obtained from any model which does not incorporate color confinement.Comment: 23 pages (RevTeX), 5 figures (epsf

Hypotheses for the Origin of the Hypanis Fan-Shaped Deposit at the Edge of the Chryse Escarpment, Mars: Is it a Delta?

We investigated the origin of the fan-shaped deposit at the end of Hypanis Valles that has previously been proposed as an ExoMars, Mars 2020, and human mission candidate landing site, and found evidence that the landform is an ancient delta. Previous work suggests that the deposit originated from a time of fluvial activity both distinct from and prior to catastrophic outflow, and crater counting placed the deposit’s age at  ≥ 3.6 Ga. We found over 30 thin sedimentary strata in the proposed delta wall, and from our slope analysis conclude that the fluvial sequence is consistent with a lowering/retreating shoreline. We measured nearly horizontal bedding dip angles ranging from 0° to 2° over long stretches of cliff and bench exposures seen in HiRISE images and HiRISE stereo DTMs. From THEMIS night IR images we determined that the fan-shaped deposit has a low thermal inertia (150-240 Jm-2 K-1 s-1/2) and the surrounding darker-toned units correspond to thermal inertia values as high as 270-390 Jm-2 K-1 s-1/2. We interpret these findings to indicate that the fan-shaped deposit consists mostly of silt-sized and possibly finer grains, and that the extremely low grade and large lateral extent of these beds implies that the depositional environment was calm and relatively long-lived. We interpret the geomorphology and composition as incompatible with an alluvial fan or mudflow hypothesis. From our stratigraphic mapping we interpret the order of events which shaped the region. After the Chryse impact, sediment filled the basin, a confined lake or sea formed allowing a large delta to be deposited near its shoreline, the water level receded to the north, darker sedimentary/volcanic units covered the region and capped the light-toned deposit as hydro-volcanic eruptions shaped the interior of Lederberg crater, freeze/thaw cycles and desiccation induced local fracturing, and finally wrinkle ridges associated with rounded cones warped the landscape following trends in degraded crater rims and existing tectonic features. The ancient deltaic deposit we observe today was largely untouched by subsequent catastrophic outflows, and its surface has been only moderately reshaped by over 3 billion years of aeolian erosion

Agent based modelling helps in understanding the rules by which fibroblasts support keratinocyte colony formation

Background: Autologous keratincoytes are routinely expanded using irradiated mouse fibroblasts and bovine serum for clinical use. With growing concerns about the safety of these xenobiotic materials, it is desirable to culture keratinocytes in media without animal derived products. An improved understanding of epithelial/mesenchymal interactions could assist in this. Methodology/Principal Findings: A keratincyte/fibroblast o-culture model was developed by extending an agent-based keratinocyte colony formation model to include the response of keratinocytes to both fibroblasts and serum. The model was validated by comparison of the in virtuo and in vitro multicellular behaviour of keratinocytes and fibroblasts in single and co-culture in Greens medium. To test the robustness of the model, several properties of the fibroblasts were changed to investigate their influence on the multicellular morphogenesis of keratinocyes and fibroblasts. The model was then used to generate hypotheses to explore the interactions of both proliferative and growth arrested fibroblasts with keratinocytes. The key predictions arising from the model which were confirmed by in vitro experiments were that 1) the ratio of fibroblasts to keratinocytes would critically influence keratinocyte colony expansion, 2) this ratio needed to be optimum at the beginning of the co-culture, 3) proliferative fibroblasts would be more effective than irradiated cells in expanding keratinocytes and 4) in the presence of an adequate number of fibroblasts, keratinocyte expansion would be independent of serum. Conclusions: A closely associated computational and biological approach is a powerful tool for understanding complex biological systems such as the interactions between keratinocytes and fibroblasts. The key outcome of this study is the finding that the early addition of a critical ratio of proliferative fibroblasts can give rapid keratinocyte expansion without the use of irradiated mouse fibroblasts and bovine serum