Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

Our current understanding of how DNA is packed in the nucleus is most accurate at the fine scale of individual nucleosomes and at the large scale of chromosome territories. However, accurate modeling of DNA architecture at the intermediate scale of ∼50 kb-10 Mb is crucial for identifying functional interactions among regulatory elements and their target promoters. We describe a method, Fit-Hi-C, that assigns statistical confidence estimates to mid-range intra-chromosomal contacts by jointly modeling the random polymer looping effect and previously observed technical biases in Hi-C data sets. We demonstrate that our proposed approach computes accurate empirical null models of contact probability without any distribution assumption, corrects for binning artifacts, and provides improved statistical power relative to a previously described method. High-confidence contacts identified by Fit-Hi-C preferentially link expressed gene promoters to active enhancers identified by chromatin signatures in human embryonic stem cells (ESCs), capture 77% ofRNA polymerase II-mediated enhancer-promoter interactions identified using ChIA-PET in mouse ESCs, and confirm previously validated, cell line-specific interactions in mouse cortex cells. We observe that insulators and heterochromatin regions are hubs for high-confidence contacts, while promoters and strong enhancers are involved in fewer contacts. We also observe that binding peaks of master pluripotency factors such as NANOG and POU5F1 are highly enriched in high-confidence contacts for human ESCs. Furthermore, we show that pairs of loci linked by high-confidence contacts exhibit similar replication timing in human and mouse ESCs and preferentially lie within the boundaries of topological domains for human and mouse cell lines

Inverse problem and Bertrand's theorem

The Bertrand's theorem can be formulated as the solution of an inverse problem for a classical unidimensional motion. We show that the solutions of these problems, if restricted to a given class, can be obtained by solving a numerical equation. This permit a particulary compact and elegant proof of Bertrand's theorem.Comment: 11 pages, 3 figure

Prevalence and predictors of poly-victimization of adolescents in England and Wales

This study examined the change in the prevalence of adolescent polyvictimization and individual and area predictors of poly-victimization in England and Wales. The national representative longitudinal Offending, Crime and Justice Survey (2003–2006) was analyzed with data from 2,066 adolescents, aged between 10 and 18 years (mean±SD at Time 1=13.08±2.01), using multilevel multinomial logit models. Findings revealed that the majority of the adolescents (41.6%, 48.5%, 54.6%, 61.6%, respectively) did not experience victimization between 2003 and 2006. However, 28.3%, 25.9%, 19.5%, and 14.5% of the adolescents experienced poly-victimization (experiencing more than or equal to two types of victimizations), with a decrease of 13.8% over the 4-year period. Furthermore, some adolescents were consistent polyvictims, meaning they were poly-victims in all years that they participated in the survey. In particular, 3.57% of the adolescents who participated in the four waves of the survey were poly-victims in all years; 7.41% of the adolescents who participated in three of the four waves of the survey were poly-victims in all years; and 25.79% of the adolescents who participated in two of the four waves of the survey were poly-victims in both years

The genomes of Darwin's primroses reveal chromosome-scale adaptive introgression and differential permeability of species boundaries

Introgression is an important source of genetic variation that can determine species adaptation to environmental conditions. Yet, definitive evidence of the genomic and adaptive implications of introgression in nature remains scarce. The widespread hybrid zones of Darwin's primroses (Primula elatior, Primula veris, and Primula vulgaris) provide a unique natural laboratory for studying introgression in flowering plants and the varying permeability of species boundaries. Through analysis of 650 genomes, we provide evidence of an introgressed genomic region likely to confer adaptive advantage in conditions of soil toxicity. We also document unequivocal evidence of chloroplast introgression, an important precursor to species-wide chloroplast capture. Finally, we provide the first evidence that the S-locus supergene, which controls heterostyly in primroses, does not introgress in this clade. Our results contribute novel insights into the adaptive role of introgression and demonstrate the importance of extensive genomic and geographical sampling for illuminating the complex nature of species boundaries

Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot

Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots

Natural coagulates for wastewater treatment; a review for application and mechanism

The increase of water demand and wastewater generation is among the global concerns in the world. The less effective management of water sources leads to serious consequences, the direct disposal of untreated wastewater is associated with the environmental pollution, elimination of aquatic life and the spread of deadly epidemics. The flocculation process is one of the most important stages in water and wastewater treatment plants, wherein this phase the plankton, colloidal particles, and pollutants are precipitated and removed. Two major types of coagulants are used in the flocculation process included the chemical and natural coagulants. Many studies have been performed to optimize the flocculation process while most of these studies have confirmed the hazardous effects of chemical coagulants utilization on the ecosystem. This chapter reviews a summary of the coagulation/flocculation processes using natural coagulants as well as reviews one of the most effective natural methods of water and wastewater treatment

BAs and boride III-V alloys

Boron arsenide, the typically-ignored member of the III-V arsenide series BAs-AlAs-GaAs-InAs is found to resemble silicon electronically: its Gamma conduction band minimum is p-like (Gamma_15), not s-like (Gamma_1c), it has an X_1c-like indirect band gap, and its bond charge is distributed almost equally on the two atoms in the unit cell, exhibiting nearly perfect covalency. The reasons for these are tracked down to the anomalously low atomic p orbital energy in the boron and to the unusually strong s-s repulsion in BAs relative to most other III-V compounds. We find unexpected valence band offsets of BAs with respect to GaAs and AlAs. The valence band maximum (VBM) of BAs is significantly higher than that of AlAs, despite the much smaller bond length of BAs, and the VBM of GaAs is only slightly higher than in BAs. These effects result from the unusually strong mixing of the cation and anion states at the VBM. For the BAs-GaAs alloys, we find (i) a relatively small (~3.5 eV) and composition-independent band gap bowing. This means that while addition of small amounts of nitrogen to GaAs lowers the gap, addition of small amounts of boron to GaAs raises the gap (ii) boron ``semi-localized'' states in the conduction band (similar to those in GaN-GaAs alloys), and (iii) bulk mixing enthalpies which are smaller than in GaN-GaAs alloys. The unique features of boride III-V alloys offer new opportunities in band gap engineering.Comment: 18 pages, 14 figures, 6 tables, 61 references. Accepted for publication in Phys. Rev. B. Scheduled to appear Oct. 15 200

Multiband tight-binding theory of disordered ABC semiconductor quantum dots: Application to the optical properties of alloyed CdZnSe nanocrystals

Zero-dimensional nanocrystals, as obtained by chemical synthesis, offer a broad range of applications, as their spectrum and thus their excitation gap can be tailored by variation of their size. Additionally, nanocrystals of the type ABC can be realized by alloying of two pure compound semiconductor materials AC and BC, which allows for a continuous tuning of their absorption and emission spectrum with the concentration x. We use the single-particle energies and wave functions calculated from a multiband sp^3 empirical tight-binding model in combination with the configuration interaction scheme to calculate the optical properties of CdZnSe nanocrystals with a spherical shape. In contrast to common mean-field approaches like the virtual crystal approximation (VCA), we treat the disorder on a microscopic level by taking into account a finite number of realizations for each size and concentration. We then compare the results for the optical properties with recent experimental data and calculate the optical bowing coefficient for further sizes

Symmetry and topology in antiferromagnetic spintronics

Antiferromagnetic spintronics focuses on investigating and using antiferromagnets as active elements in spintronics structures. Last decade advances in relativistic spintronics led to the discovery of the staggered, current-induced field in antiferromagnets. The corresponding N\'{e}el spin-orbit torque allowed for efficient electrical switching of antiferromagnetic moments and, in combination with electrical readout, for the demonstration of experimental antiferromagnetic memory devices. In parallel, the anomalous Hall effect was predicted and subsequently observed in antiferromagnets. A new field of spintronics based on antiferromagnets has emerged. We will focus here on the introduction into the most significant discoveries which shaped the field together with a more recent spin-off focusing on combining antiferromagnetic spintronics with topological effects, such as antiferromagnetic topological semimetals and insulators, and the interplay of antiferromagnetism, topology, and superconductivity in heterostructures.Comment: Book chapte