Bi-directional and shared epigenomic signatures following proton and 56Fe irradiation.

The brain's response to radiation exposure is an important concern for patients undergoing cancer therapy and astronauts on long missions in deep space. We assessed whether this response is specific and prolonged and is linked to epigenetic mechanisms. We focused on the response of the hippocampus at early (2-weeks) and late (20-week) time points following whole body proton irradiation. We examined two forms of DNA methylation, cytosine methylation (5mC) and hydroxymethylation (5hmC). Impairments in object recognition, spatial memory retention, and network stability following proton irradiation were observed at the two-week time point and correlated with altered gene expression and 5hmC profiles that mapped to specific gene ontology pathways. Significant overlap was observed between DNA methylation changes at the 2 and 20-week time points demonstrating specificity and retention of changes in response to radiation. Moreover, a novel class of DNA methylation change was observed following an environmental challenge (i.e. space irradiation), characterized by both increased and decreased 5hmC levels along the entire gene body. These changes were mapped to genes encoding neuronal functions including postsynaptic gene ontology categories. Thus, the brain's response to proton irradiation is both specific and prolonged and involves novel remodeling of non-random regions of the epigenome

Does the Geometry of Word Embeddings Help Document Classification? A Case Study on Persistent Homology Based Representations

We investigate the pertinence of methods from algebraic topology for text data analysis. These methods enable the development of mathematically-principled isometric-invariant mappings from a set of vectors to a document embedding, which is stable with respect to the geometry of the document in the selected metric space. In this work, we evaluate the utility of these topology-based document representations in traditional NLP tasks, specifically document clustering and sentiment classification. We find that the embeddings do not benefit text analysis. In fact, performance is worse than simple techniques like $\textit{tf-idf}$, indicating that the geometry of the document does not provide enough variability for classification on the basis of topic or sentiment in the chosen datasets.Comment: 5 pages, 3 figures. Rep4NLP workshop at ACL 201

A model structure on GCat

We define a model structure on the category GCat of small categories with an action by a finite group G by lifting the Thomason model structure on Cat. We show there is a Quillen equivalence between GCat with this model structure and GTop with the standard model structure.Comment: 12 pages. Final version. Will appear in Proceedings for WIT (Women in Topology Workshop

Quantum fidelity approach to the ground state properties of the 1D ANNNI model in a transverse field

In this work we analyze the ground-state properties of the $s=1/2$ one-dimensional ANNNI model in a transverse field using the quantum fidelity approach. We numerically determined the fidelity susceptibility as a function of the transverse field $B_x$ and the strength of the next-nearest-neighbor interaction $J_2$, for systems of up to 24 spins. We also examine the ground-state vector with respect to the spatial ordering of the spins. The ground-state phase diagram shows ferromagnetic, paramagnetic, floating, $\Braket{2,2}$ phases, and we predict an infinite number of modulated phases in the thermodynamic limit ($L \rightarrow \infty$). The transition lines separating the modulated phases seem to be of second-order, whereas the line between the floating and the $\Braket{2,2}$ phases is possibly of first-order.Comment: 10 pages, 20 figure

Analysis of the Utilization of Air-Cooled Blast Furnace Slag as Industrial Waste Aggregates in Self-Compacting Concrete

In this work, the effects of replacing the aggregates of self-compacting concrete by air-cooled blast furnace slag have been analysed. Different mixes have been manufactured by substituting the fine and coarse natural aggregates by air-cooled blast furnace slag. The fracture energy and the tensile and compressive strength have been determined for each mix. The self-compacting properties of the mixes, or the absence of them, have been observed. The main goals of this research are the decrease of the price of aggregates, reduction of the industrial waste, and attenuation the rate of consumption of natural resources. The results show that the self-compactability of the concrete is gradually lost as the slag content is increased, thus, when the ratio of replacement is low, the concrete keeps the self-compacting properties. Nevertheless, the loss of self-compaction affects the mechanical properties by increasing its strength. An air-cooled blast furnace slag did not present problems of heavy metals leaching.Ministerio de Economía y Competitividad BIA2016-75431-RUniversidad de Sevilla VI Plan Propio de Investigació

Deformation of continental crust along a transform boundary, Coast Mountains, British Columbia

New structural, paleomagnetic, and apatite (U-Th)/He results from the continental margin inboard of the Queen Charlotte fault (~54°N) delineate patterns of brittle faulting linked to transform development since ~50 Ma. In the core of the orogen, ~250 km from the transform, north striking, dip-slip brittle faults and vertical axis rotation of large crustal domains occurred after ~50 Ma and before intrusion of mafic dikes at 20 Ma. By 20 Ma, dextral faulting was active in the core of the orogen, but extension had migrated toward the transform, continuing there until <9 Ma. Local tilting in the core of the orogen is associated with glacially driven, post-4 Ma exhumation. Integration with previous results shows that post-50 Ma dextral and normal faulting affected a region ~250 km inboard of the transform and ~300 km along strike. Initially widespread, the zone of active extension narrowed and migrated toward the transform ~25 Ma after initiation of the transform, while dextral faulting continued throughout the region. Differential amounts of post-50 Ma extension created oroclines at the southern and northern boundaries of the deformed region. This region approximately corresponds to continental crust that was highly extended just prior to transform initiation. Variation in Neogene crustal tilts weakens interpretations relying on uniform tilting to explain anomalous paleomagnetic inclinations of mid-Cretaceous plutons. Similarities to the Gulf of California suggest that development of a transform in continental crust is aided by previous crustal extension and that initially widespread extension narrows and moves toward the transform as the margin develops

Competition for hydrogen bond formation in the helix-coil transition and protein folding

The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure; and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained.Comment: 21 pages, 3 figures, submitted to Phys Rev