On the calculation of the bandgap of periodic solids with MGGA functionals using the total energy

During the last few years, it has become more and more clear that functionals of the meta generalized gradient approximation (MGGA) are more accurate than GGA functionals for the geometry and energetics of electronic systems. However, MGGA functionals are also potentially more interesting for the electronic structure, in particular, when the potential is nonmultiplicative (i.e., when MGGAs are implemented in the generalized Kohn-Sham framework), which may help to get more accurate bandgaps. Here, we show that the calculation of bandgap of solids with MGGA functionals can also be done very accurately in a non-self-consistent manner. This scheme uses only the total energy and can, therefore, be very useful when the self-consistent implementation of a particular MGGA functional is not available. Since self-consistent MGGA calculations may be difficult to converge, the non-self-consistent scheme may also help to speed up the calculations. Furthermore, it can be applied to any other types of functionals, for which the implementation of the corresponding potential is not trivial

In Silico Enhanced Restriction Enzyme Based Methylation Analysis of the Human Glioblastoma Genome Using Agilent 244K CpG Island Microarrays

Genome wide methylation profiling of gliomas is likely to provide important clues to improving treatment outcomes. Restriction enzyme based approaches have been widely utilized for methylation profiling of cancer genomes and will continue to have importance in combination with higher density microarrays. With the availability of the human genome sequence and microarray probe sequences, these approaches can be readily characterized and optimized via in silico modeling. We adapted the previously described HpaII/MspI based Methylation Sensitive Restriction Enzyme (MSRE) assay for use with two-color Agilent 244K CpG island microarrays. In this assay, fragmented genomic DNA is digested in separate reactions with isoschizomeric HpaII (methylation-sensitive) and MspI (methylation-insensitive) restriction enzymes. Using in silico hybridization, we found that genomic fragmentation with BfaI was superior to MseI, providing a maximum effective coverage of 22,362 CpG islands in the human genome. In addition, we confirmed the presence of an internal control group of fragments lacking HpaII/MspI sites which enable separation of methylated and unmethylated fragments. We used this method on genomic DNA isolated from normal brain, U87MG cells, and a glioblastoma patient tumor sample and confirmed selected differentially methylated CpG islands using bisulfite sequencing. Along with additional validation points, we performed a receiver operating characteristics (ROC) analysis to determine the optimal threshold (p ≤ 0.001). Based on this threshold, we identified ∼2,400 CpG islands common to all three samples and 145 CpG islands unique to glioblastoma. These data provide general guidance to individuals seeking to maximize effective coverage using restriction enzyme based methylation profiling approaches

Federated Learning with Nesterov Accelerated Gradient Momentum Method

Federated learning (FL) is a fast-developing technique that allows multiple workers to train a global model based on a distributed dataset. Conventional FL employs gradient descent algorithm, which may not be efficient enough. It is well known that Nesterov Accelerated Gradient (NAG) is more advantageous in centralized training environment, but it is not clear how to quantify the benefits of NAG in FL so far. In this work, we focus on a version of FL based on NAG (FedNAG) and provide a detailed convergence analysis. The result is compared with conventional FL based on gradient descent. One interesting conclusion is that as long as the learning step size is sufficiently small, FedNAG outperforms FedAvg. Extensive experiments based on real-world datasets are conducted, verifying our conclusions and confirming the better convergence performance of FedNAG.Comment: 15 pages, 5 figure

Aktiepris under turbulens - En studie om nyemissioners kortsiktiga aktiekurspåverkan

Syftet med studien är att identifiera och förklara hur aktiekurser vid nyemissioner, när turbulensen ökar, fluktuerar på Stockholmsbörsen och vilka faktorer som påverkar aktiekursutvecklingen. Detta sker genom att undersöka hur olika faktorer kan bidra till att förklara variationen i kursrörelserna vid nyemissioner på kort sikt. Resultatet ämnar hjälpa befintliga och potentiella aktieägare samt övriga intressenter som söker information om nyemissioners påverkan för aktiekursutvecklingen på kort sikt och bidra med ny vetskap på området. Studien görs m.h.a. två eventstudier, tillkännagivandet av nyemissioner och nyemissioners teckningsperiod. Författarna kan då påvisa om det förekommer negativ överavkastning till följd av tillkännagivandet och under teckningsperioden. Överavkastningen beräknas m.h.a. marknadsmodellen. Studien påvisar värdeförstörande i form av negativ överavkastning vid annonseringsbesked av en nyemission. Negativ överavkastning kunde även påvisas under teckningsperioden, dock till en lägre grad än vid annonseringsperioden. Teckningsperioden visade även ett par dagar med positiv överavkastning även om den totala överavkastningen var negativ. Faktorer som premie och bolagsstorlek hade en påverkan på överavkastningen

Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis

Previous models of glycolysis in the sleeping sickness parasite Trypanosoma brucei assumed that the core part of glycolysis in this unicellular parasite is tightly compartimentalized within an organelle, the glycosome, which had previously been shown to contain most of the glycolytic enzymes. The glycosomes were assumed to be largely impermeable, and exchange of metabolites between the cytosol and the glycosome was assumed to be regulated by specific transporters in the glycosomal membrane. This tight compartmentalization was considered to be essential for parasite viability. Recently, size-specific metabolite pores were discovered in the membrane of glycosomes. These channels are proposed to allow smaller metabolites to diffuse across the membrane but not larger ones. In light of this new finding, we re-analyzed the model taking into account uncertainty about the topology of the metabolic system in T. brucei, as well as uncertainty about the values of all parameters of individual enzymatic reactions. Our analysis shows that these newly-discovered nonspecific pores are not necessarily incompatible with our current knowledge of the glycosomal metabolic system, provided that the known cytosolic activities of the glycosomal enzymes play an important role in the regulation of glycolytic fluxes and the concentration of metabolic intermediates of the pathway

G-TRACE: rapid Gal4-based cell lineage analysis in Drosophila.

We combined Gal4-UAS and the FLP recombinase-FRT and fluorescent reporters to generate cell clones that provide spatial, temporal and genetic information about the origins of individual cells in Drosophila melanogaster. We named this combination the Gal4 technique for real-time and clonal expression (G-TRACE). The approach should allow for screening and the identification of real-time and lineage-traced expression patterns on a genomic scale

Retinoblastoma: Past, Present, and Future

The purpose of this research timeline is to synthesize the natural history of retinoblastoma to understand its societal effects and develop a public health message to raise awareness of the disease. We used literature-based research in order to gain an understanding about the discovery of this disease and investigate its most current state of knowledge. Retinoblastoma is an intraocular cancer that manifests early in childhood. It is typically linked to a somatic or germline insertion, deletion, or single-base substitution mutation on both alleles of RB1, a tumor-suppressor gene. Retinoblastoma was first identified in 1809 by James Wardrop, and since then, research has been focused on improved treatment methods to prevent enucleation and has been steady with focus on the RB1 allele. Retinoblastoma is characterized by many assorted phenotypes that vary in severity based on the size of the chromosomal deletion. The most common symptoms include leukocoria, poor vision tracking, swelling and inflammation, all of which can be treated upon early detection. Methods of treatment include enucleation that completely removes the eye with the tumor, leaving the muscles and orbital contents intact, and it is 95% effective. Chemotherapy is also used in severe cases. The discovery of the Rb1 gene has had significant impacts with the advancement of cancer research. Because of this, mutations in the Rb gene are vastly studied due to the association of Rb in other cancers and its molecular action in the cell cycle. It is often taught in foundational biology courses, as a result.https://digitalscholarship.unlv.edu/durep_posters/1004/thumbnail.jp

Combustion-derived nanoparticles: A review of their toxicology following inhalation exposure

This review considers the molecular toxicology of combustion-derived nanoparticles (CDNP) following inhalation exposure. CDNP originate from a number of sources and in this review we consider diesel soot, welding fume, carbon black and coal fly ash. A substantial literature demonstrates that these pose a hazard to the lungs through their potential to cause oxidative stress, inflammation and cancer; they also have the potential to redistribute to other organs following pulmonary deposition. These different CDNP show considerable heterogeneity in composition and solubility, meaning that oxidative stress may originate from different components depending on the particle under consideration. Key CDNP-associated properties of large surface area and the presence of metals and organics all have the potential to produce oxidative stress. CDNP may also exert genotoxic effects, depending on their composition. CDNP and their components also have the potential to translocate to the brain and also the blood, and thereby reach other targets such as the cardiovascular system, spleen and liver. CDNP therefore can be seen as a group of particulate toxins unified by a common mechanism of injury and properties of translocation which have the potential to mediate a range of adverse effects in the lungs and other organs and warrant further research

Plasma carnitine is associated with fatigue in chronic hepatitis C but not in irritable bowel syndrome : Carnitine and fatigue in hepatitis C

International audienceObjectives Fatigue is an important determinant of altered quality of life in patients affected by chronic hepatitis C (CHC) or the irritable bowel syndrome (IBS). In this study, we aimed at determining the contributory role of plasma levels of leptin and carnitine on fatigue in CHC and IBS. Methods We enrolled 70 patients with CHC, 42 with IBS and 44 healthy subjects. Fatigue was evaluated using the Fatigue Impact Scale questionnaire. Body composition was assessed through impedance analysis. Plasma carnitine and leptin were measured. Results Fatigue scores were significantly more elevated in patients with CHC and IBS than in healthy subjects. Patients with CHC, but not with IBS, had significant lower plasma levels of total and free carnitine adjusted for fat mass compared to healthy subjects. In patients with CHC, and not with IBS, fatigue scores were negatively correlated with plasma levels of carnitine. Levels of free carnitine were significantly and independently associated with the severity of fatigue in patients with CHC (OR=2.019, p=0.02, CI 95% [1.01-1.23]).Conclusions In patients with CHC, the severity of fatigue is associated with low level of carnitine, suggesting that an oral supplementation may be effective to relieve fatigue in CHC. The underlying mechanism of fatigue in IBS does not seem to involve carnitine