The mechanical response of semiflexible networks to localized perturbations

Previous research on semiflexible polymers including cytoskeletal networks in cells has suggested the existence of distinct regimes of elastic response, in which the strain field is either uniform (affine) or non-uniform (non-affine) under external stress. Associated with these regimes, it has been further suggested that a new fundamental length scale emerges, which characterizes the scale for the crossover from non-affine to affine deformations. Here, we extend these studies by probing the response to localized forces and force dipoles. We show that the previously identified nonaffinity length [D.A. Head et al. PRE 68, 061907 (2003).] controls the mesoscopic response to point forces and the crossover to continuum elastic behavior at large distances.Comment: 16 pages, 18 figures; substantial changes to text and figures to clarify the crossover to continuum elasticity and the role of finite-size effect

Unfolding cross-linkers as rheology regulators in F-actin networks

We report on the nonlinear mechanical properties of a statistically homogeneous, isotropic semiflexible network cross-linked by polymers containing numerous small unfolding domains, such as the ubiquitous F-actin cross-linker Filamin. We show that the inclusion of such proteins has a dramatic effect on the large strain behavior of the network. Beyond a strain threshold, which depends on network density, the unfolding of protein domains leads to bulk shear softening. Past this critical strain, the network spontaneously organizes itself so that an appreciable fraction of the Filamin cross-linkers are at the threshold of domain unfolding. We discuss via a simple mean-field model the cause of this network organization and suggest that it may be the source of power-law relaxation observed in in vitro and in intracellular microrheology experiments. We present data which fully justifies our model for a simplified network architecture.Comment: 11 pages, 4 figures. to appear in Physical Review

Coupled dynamics of voltage and calcium in paced cardiac cells

We investigate numerically and analytically the coupled dynamics of transmembrane voltage and intracellular calcium cycling in paced cardiac cells using a detailed physiological model and its reduction to a three-dimensional discrete map. The results provide a theoretical framework to interpret various experimentally observed modes of instability ranging from electromechanically concordant and discordant alternans to quasiperiodic oscillations of voltage and calcium

Indeterminacy of Spatiotemporal Cardiac Alternans

Cardiac alternans, a beat-to-beat alternation in action potential duration (at the cellular level) or in ECG morphology (at the whole heart level), is a marker of ventricular fibrillation, a fatal heart rhythm that kills hundreds of thousands of people in the US each year. Investigating cardiac alternans may lead to a better understanding of the mechanisms of cardiac arrhythmias and eventually better algorithms for the prediction and prevention of such dreadful diseases. In paced cardiac tissue, alternans develops under increasingly shorter pacing period. Existing experimental and theoretical studies adopt the assumption that alternans in homogeneous cardiac tissue is exclusively determined by the pacing period. In contrast, we find that, when calcium-driven alternans develops in cardiac fibers, it may take different spatiotemporal patterns depending on the pacing history. Because there coexist multiple alternans solutions for a given pacing period, the alternans pattern on a fiber becomes unpredictable. Using numerical simulation and theoretical analysis, we show that the coexistence of multiple alternans patterns is induced by the interaction between electrotonic coupling and an instability in calcium cycling.Comment: 20 pages, 10 figures, to be published in Phys. Rev.

Word Embeddings for Entity-annotated Texts

Learned vector representations of words are useful tools for many information retrieval and natural language processing tasks due to their ability to capture lexical semantics. However, while many such tasks involve or even rely on named entities as central components, popular word embedding models have so far failed to include entities as first-class citizens. While it seems intuitive that annotating named entities in the training corpus should result in more intelligent word features for downstream tasks, performance issues arise when popular embedding approaches are naively applied to entity annotated corpora. Not only are the resulting entity embeddings less useful than expected, but one also finds that the performance of the non-entity word embeddings degrades in comparison to those trained on the raw, unannotated corpus. In this paper, we investigate approaches to jointly train word and entity embeddings on a large corpus with automatically annotated and linked entities. We discuss two distinct approaches to the generation of such embeddings, namely the training of state-of-the-art embeddings on raw-text and annotated versions of the corpus, as well as node embeddings of a co-occurrence graph representation of the annotated corpus. We compare the performance of annotated embeddings and classical word embeddings on a variety of word similarity, analogy, and clustering evaluation tasks, and investigate their performance in entity-specific tasks. Our findings show that it takes more than training popular word embedding models on an annotated corpus to create entity embeddings with acceptable performance on common test cases. Based on these results, we discuss how and when node embeddings of the co-occurrence graph representation of the text can restore the performance.Comment: This paper is accepted in 41st European Conference on Information Retrieva

Action Anthropology and Pedagogy: University-Community Collaborations in Setting Policy

This article describes a student-led, community-participatory project focused on reducing the burden of childhood lead poisoning in rental housing. A multidisciplinary group of students and faculty worked with community members. We compiled the social, public health, economic, and policy information on the human and fiscal costs of childhood lead poisoning. This analysis was done for community advocates to use to persuade policymakers to enact a local law strengthening the prevention of childhood lead poisoning in rental property. In conducting this work, the students gained experience in qualitative research methods, quantitative data analysis, the health consequences of lead exposure, health policy, urban health, science writing, and public presentation

Are superflares on solar analogues caused by extra-solar planets?

Stellar flares with ${10^2-10^7}$ times more energy than the largest solar flare have been detected from 9 normal F and G main sequence stars (Schaefer, King & Deliyannis 1999). These superflares have durations of hours to days and are visible from at least x-ray to optical frequencies. The absence of world-spanning aurorae in historical records and of anomalous extinctions in the geological record indicate that our Sun likely does not suffer superflares. In seeking to explain this new phenomenon, we are struck by its similarity to large stellar flares on RS Canum Venaticorum binary systems, which are caused by magnetic reconnection events associated with the tangling of magnetic fields between the two stars. The superflare stars are certainly not of this class, although we propose a similar flare mechanism. That is, superflares are caused by magnetic reconnection between fields of the primary star and a close-in Jovian planet. Thus, by only invoking known planetary properties and reconnection scenarios, we can explain the energies, durations, and spectra of superflares, as well as explain why our Sun does not have such events.Comment: 13 pages, Accepted for publication in Ap

Many human accelerated regions are developmental enhancers

The genetic changes underlying the dramatic differences in form and function between humans and other primates are largely unknown, although it is clear that gene regulatory changes play an important role. To identify regulatory sequences with potentially human-specific functions, we and others used comparative genomics to find non-coding regions conserved across mammals that have acquired many sequence changes in humans since divergence from chimpanzees. These regions are good candidates for performing human-specific regulatory functions. Here, we analysed the DNA sequence, evolutionary history, histone modifications, chromatin state and transcription factor (TF) binding sites of a combined set of 2649 non-coding human accelerated regions (ncHARs) and predicted that at least 30% of them function as developmental enhancers. We prioritized the predicted ncHAR enhancers using analysis of TF binding site gain and loss, along with the functional annotations and expression patterns of nearby genes. We then tested both the human and chimpanzee sequence for 29 ncHARs in transgenic mice, and found 24 novel developmental enhancers active in both species, 17 of which had very consistent patterns of activity in specific embryonic tissues. Of these ncHAR enhancers, five drove expression patterns suggestive of different activity for the human and chimpanzee sequence at embryonic day 11.5. The changes to human non-coding DNA in these ncHAR enhancers may modify the complex patterns of gene expression necessary for proper development in a human-specific manner and are thus promising candidates for understanding the genetic basis of human-specific biology

Dimensionality dependent electronic structure of the exfoliated van der Waals antiferromagnet NiPS3_3

Resonant Inelastic X-ray Scattering (RIXS) was used to measure the local electronic structure in few-layer exfoliated flakes of the van der Waals antiferromagnet NiPS$_3$. The resulting spectra show a systematic softening and broadening of $NiS_6$ multiplet excitations with decreasing layer count from the bulk to three atomic layers (3L). These trends are driven by a decrease in the transition metal-ligand and ligand-ligand hopping integrals, and in the charge-transfer energy: $\Delta$ = 0.60 eV in the bulk and 0.22 eV in 3L NiPS$_3$. Relevant intralayer magnetic exchange integrals computed from the electronic parameters exhibit a systematic decrease in the average interaction strength with thickness and place 2D NiPS$_3$ close to the phase boundary between stripy and spiral antiferromagnetic order, which may explain the apparent vanishing of long-range order in the 2D limit. This study explicitly demonstrates the influence of $inter$layer electronic interactions on $intra$layer ones in insulating magnets. As a consequence, the magnetic Hamiltonian in few-layer insulating magnets can be significantly different from that in the bulk.Comment: 5 pages, 4 figures; additional 9 pages and 13 figures of supplementary informatio