4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

© 2018 Shrestha et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Chromatin organization is crucial for nuclear functions such as gene regulation, DNA replication and DNA repair. Insulator binding proteins, such as the Drosophila Boundary Element-Associated Factor (BEAF), are involved in chromatin organization. To further understand the role of BEAF, we detected cis-and trans-interaction partners of four BEAF binding regions (viewpoints) using 4C (circular chromosome conformation capture) and analyzed their association with different genomic features. Previous genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, so our viewpoints were selected to reflect this. Our 4C data show the interaction partners of our viewpoints are highly variable and generally enriched for active chromatin marks. The most consistent association was with housekeeping genes, a feature in common with our viewpoints. Fluorescence in situ hybridization indicated that the long-distance interactions occur even in the absence of BEAF. These data are most consistent with a model in which BEAF is redundant with other factors found at active promoters. Our results point to principles of long-distance interactions made by active chromatin, supporting a previously proposed model in which condensed chromatin is sticky and associates into topologically associating domains (TADs) separated by active chromatin. We propose that the highly variable long-distance interactions we detect are driven by redundant factors that open chromatin to promote transcription, combined with active chromatin filling spaces between TADs while packing of TADs relative to each other varies from cell to cell

Learning and climate change

Learning – i.e. the acquisition of new information that leads to changes in our assessment of uncertainty – plays a prominent role in the international climate policy debate. For example, the view that we should postpone actions until we know more continues to be influential. The latest work on learning and climate change includes new theoretical models, better informed simulations of how learning affects the optimal timing of emissions reductions, analyses of how new information could affect the prospects for reaching and maintaining political agreements and for adapting to climate change, and explorations of how learning could lead us astray rather than closer to the truth. Despite the diversity of this new work, a clear consensus on a central point is that the prospect of learning does not support the postponement of emissions reductions today.Learning; Uncertainty; Climate change; Decision analysis

Machine Learning Techniques for Personalized Detection of Epileptic Events in Clinical Video Recordings

Continuous patient monitoring is essential to achieve an effective and optimal patient treatment in the intensive care unit. In the specific case of epilepsy it is the only way to achieve a correct diagnosis and a subsequent optimal medication plan if possible. In addition to automatic vital sign monitoring, epilepsy patients need manual monitoring by trained personnel, a task that is very difficult to be performed continuously for each patient. Moreover, epileptic manifestations are highly personalized even within the same type of epilepsy. In this work we assess two machine learning methods, dictionary learning and an autoencoder based on long short-term memory (LSTM) cells, on the task of personalized epileptic event detection in videos, with a set of features that were specifically developed with an emphasis on high motion sensitivity. According to the strengths of each method we have selected different types of epilepsy, one with convulsive behaviour and one with very subtle motion. The results on five clinical patients show a highly promising ability of both methods to detect the epileptic events as anomalies deviating from the stable/normal patient status

Deep ocean minerals minimize eccentric exercise-induced inflammatory response of rat skeletal muscle.

Background: We have previously shown an accelerated recovery from muscle fatigue in men challenged by prolonged exercise after oral deep ocean minerals (DOM) supplementation. Here, we hypothesized a decrease in eccentric exercise-induced muscle inflammation in rats regularly consuming DOM-containing drinks (hardness 600 mg/L and fructose 11%). Methods: Forty-seven male Sprague Dawley rats were randomized into 4 groups: Control (C, N = 12), Fructose (F, N = 12), Fructose+Exercise (FE, N = 12), and Fructose+Exercise+DOM (FED, N = 11). Since fructose is a commonly used ingredient in beverages, 11% of fructose was added as a vehicle of the study. Soleus muscles of rats were analyzed 24 h after an acute bout of downhill running following 9 weeks of DOM supplementation. Results: Leukocyte infiltration and TNF-a mRNA of muscle in the FE group were 5 times and 4 times greater the F group, respectively, (P eight fold greater than the C group (P < 0.05). The reduced glutathione (GSH) of muscle in the F group was 34% lower than that in the C group (P < 0.05). However, GSH levels were similar for the C and FED groups. Conclusion: Prolonged fructose supplementation modulates inflammatory balance of rat skeletal muscle. The results of the study suggest that DOM can minimize eccentric exercise-induced inflammatory cytokine responses in rat skeletal muscle.This work was supported by grants from Taiwan Yes Corporation, Ministry of Science and Technology (Grant No. 102-2410-H-845-018-MY3), and University of Taipei. The funding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results

Use of specific Green's functions for solving direct problems involving a heterogeneous rigid frame porous medium slab solicited by acoustic waves

A domain integral method employing a specific Green's function (i.e., incorporating some features of the global problem of wave propagation in an inhomogeneous medium) is developed for solving direct and inverse scattering problems relative to slab-like macroscopically inhomogeneous porous obstacles. It is shown how to numerically solve such problems, involving both spatially-varying density and compressibility, by means of an iterative scheme initialized with a Born approximation. A numerical solution is obtained for a canonical problem involving a two-layer slab.Comment: submitted to Math.Meth.Appl.Sc

A Korean Family with the Muenke Syndrome

The Muenke syndrome (MS) is characterized by unicoronal or bicoronal craniosynostosis, midfacial hypoplasia, ocular hypertelorism, and a variety of minor abnormalities associated with a mutation in the fibroblast growth factor receptor 3 (FGFR3) gene. The birth prevalence is approximately one in 10,000 live births, accounting for 8-10% of patients with coronal synostosis. Although MS is a relatively common diagnosis in patients with craniosynostosis syndromes, with autosomal dominant inheritance, there has been no report of MS, in an affected Korean family with typical cephalo-facial morphology that has been confirmed by molecular studies. Here, we report a familial case of MS in a female patient with a Pro250Arg mutation in exon 7 (IgII-IGIII linker domain) of the FGFR3 gene. This patient had mild midfacial hypoplasia, hypertelorism, downslanting palpebral fissures, a beak shaped nose, plagio-brachycephaly, and mild neurodevelopmental delay. The same mutation was confirmed in the patient's mother, two of the mother's sisters and the maternal grandfather. The severity of the cephalo-facial anomalies was variable among these family members

Dimensionality and dynamics in the behavior of C. elegans

A major challenge in analyzing animal behavior is to discover some underlying simplicity in complex motor actions. Here we show that the space of shapes adopted by the nematode C. elegans is surprisingly low dimensional, with just four dimensions accounting for 95% of the shape variance, and we partially reconstruct "equations of motion" for the dynamics in this space. These dynamics have multiple attractors, and we find that the worm visits these in a rapid and almost completely deterministic response to weak thermal stimuli. Stimulus-dependent correlations among the different modes suggest that one can generate more reliable behaviors by synchronizing stimuli to the state of the worm in shape space. We confirm this prediction, effectively "steering" the worm in real time.Comment: 9 pages, 6 figures, minor correction