Characterization and potential functional significance of human-chimpanzee large INDEL variation

<p>Abstract</p> <p>Background</p> <p>Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at protein-coding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species. It has been hypothesized that the genetic basis of the phenotypic differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL) variation between the two species. To test the hypothesis that large INDELs (80 to 12,000 bp) may have contributed significantly to differences in gene regulation between the two species, we categorized human-chimpanzee INDEL variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression.</p> <p>Results</p> <p>Extensive, large INDEL variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them.</p> <p>Conclusions</p> <p>The results presented herein are consistent with the hypothesis that large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.</p

Quantum Algorithm for Dynamic Programming Approach for DAGs. Applications for Zhegalkin Polynomial Evaluation and Some Problems on DAGs

In this paper, we present a quantum algorithm for dynamic programming approach for problems on directed acyclic graphs (DAGs). The running time of the algorithm is $O(\sqrt{\hat{n}m}\log \hat{n})$, and the running time of the best known deterministic algorithm is $O(n+m)$, where $n$ is the number of vertices, $\hat{n}$ is the number of vertices with at least one outgoing edge; $m$ is the number of edges. We show that we can solve problems that use OR, AND, NAND, MAX and MIN functions as the main transition steps. The approach is useful for a couple of problems. One of them is computing a Boolean formula that is represented by Zhegalkin polynomial, a Boolean circuit with shared input and non-constant depth evaluating. Another two are the single source longest paths search for weighted DAGs and the diameter search problem for unweighted DAGs.Comment: UCNC2019 Conference pape

In vitro faecal fermentation of Tritordeum breads and its effect on the human gut health

Spontaneous fermentation of Tritordeum flour enhances the nutritional potential of this hybrid cereal. However, the effect of consumption of Tritordeum sourdough bread (SDB) on gut health remains to be elucidated. This study investigated the effect of in vitro digestion and faecal fermentation of SDB compared to that of traditional baker's yeast (BYB) Tritordeum bread. After 24-h anaerobic faecal fermentation, both SDB and BYB (1% w/v) induced an increase in the relative abundances of Bifidobacterium, Megasphaera, Mitsuokella, and Phascolarctobacterium genera compared to baseline, while concentrations of acetate and butyrate were significantly higher at 24 h for SDB compared to those for BYB. Integrity of intestinal epithelium, as assessed through in vitro trans-epithelial electrical resistance (TEER) assay, was slightly increased after incubation with SDB fermentation supernatants, but not after incubation with BYB fermentation supernatants. The SDB stimulated in vitro mucosal immune response by inducing early secretion of inflammatory cytokines, IL-6 and TNF-α, followed by downregulation of the inflammatory trigger through induction of anti-inflammatory IL-10 expression. Overall, our findings suggest that Tritordeum sourdough can modulate gut microbiota fermentation activity and positively impact the gut health

On Generalizations of Network Design Problems with Degree Bounds

Iterative rounding and relaxation have arguably become the method of choice in dealing with unconstrained and constrained network design problems. In this paper we extend the scope of the iterative relaxation method in two directions: (1) by handling more complex degree constraints in the minimum spanning tree problem (namely, laminar crossing spanning tree), and (2) by incorporating `degree bounds' in other combinatorial optimization problems such as matroid intersection and lattice polyhedra. We give new or improved approximation algorithms, hardness results, and integrality gaps for these problems.Comment: v2, 24 pages, 4 figure

Earthquake networks based on similar activity patterns

Earthquakes are a complex spatiotemporal phenomenon, the underlying mechanism for which is still not fully understood despite decades of research and analysis. We propose and develop a network approach to earthquake events. In this network, a node represents a spatial location while a link between two nodes represents similar activity patterns in the two different locations. The strength of a link is proportional to the strength of the cross-correlation in activities of two nodes joined by the link. We apply our network approach to a Japanese earthquake catalog spanning the 14-year period 1985-1998. We find strong links representing large correlations between patterns in locations separated by more than 1000 km, corroborating prior observations that earthquake interactions have no characteristic length scale. We find network characteristics not attributable to chance alone, including a large number of network links, high node assortativity, and strong stability over time.Comment: 8 pages text, 9 figures. Updated from previous versio

Application of polarization ellipse technique for analysis of ULF magnetic fields from two distant stations in Koyna-Warna seismoactive region, West India

A new approach is developed to find the source azimuth of the ultra low frequency (ULF) electromagnetic (EM) signals believed to be emanating from well defined seismic zone. The method is test applied on magnetic data procured from the seismoactive region of Koyna-Warna, known for prolonged reservoir triggered seismicity. Extremely low-noise, high-sensitivity LEMI-30 search coil magnetometers were used to measure simultaneously the vector magnetic field in the frequency range 0.001–32 Hz at two stations, the one located within and another ~100 km away from the seismic active zone. During the observation campaign extending from 15 March to 30 June 2006 two earthquakes (EQs) of magnitude (M&lt;sub&gt;&lt;I&gt;L&lt;/I&gt;&lt;/sub&gt;&amp;gt;4) occurred, which are searched for the presence of precursory EM signals. &lt;br&gt;&lt;br&gt; Comparison of polarization ellipses (PE) parameters formed by the magnetic field components at the measurement stations, in select frequency bands, allows discrimination of seismo-EM signals from the natural background ULF signals of magnetospheric/ionospheric origin. The magnetic field components corresponding to spectral bands dominated by seismo-EM fields define the PE plane which at any instant contains the source of the EM fields. Intersection lines of such defined PE planes for distant observation stations clutter in to the source region. Approximating the magnetic-dipole configuration for the source, the magnetic field components along the intersection lines suggest that azimuth of the EM source align in the NNW-SSE direction. This direction well coincides with the orientation of nodal plane of normal fault plane mechanism for the two largest EQs recorded during the campaign. More significantly the correspondence of this direction with the tectonic controlled trend in local seismicity, it has been surmised that high pressure fluid flow along the fault that facilitate EQs in the region may also be the source mechanism for EM fields by electrokinetic effect

Parallelizing Deadlock Resolution in Symbolic Synthesis of Distributed Programs

Previous work has shown that there are two major complexity barriers in the synthesis of fault-tolerant distributed programs: (1) generation of fault-span, the set of states reachable in the presence of faults, and (2) resolving deadlock states, from where the program has no outgoing transitions. Of these, the former closely resembles with model checking and, hence, techniques for efficient verification are directly applicable to it. Hence, we focus on expediting the latter with the use of multi-core technology. We present two approaches for parallelization by considering different design choices. The first approach is based on the computation of equivalence classes of program transitions (called group computation) that are needed due to the issue of distribution (i.e., inability of processes to atomically read and write all program variables). We show that in most cases the speedup of this approach is close to the ideal speedup and in some cases it is superlinear. The second approach uses traditional technique of partitioning deadlock states among multiple threads. However, our experiments show that the speedup for this approach is small. Consequently, our analysis demonstrates that a simple approach of parallelizing the group computation is likely to be the effective method for using multi-core computing in the context of deadlock resolution

Colored Non-Crossing Euclidean Steiner Forest

Given a set of $k$-colored points in the plane, we consider the problem of finding $k$ trees such that each tree connects all points of one color class, no two trees cross, and the total edge length of the trees is minimized. For $k=1$, this is the well-known Euclidean Steiner tree problem. For general $k$, a $k\rho$-approximation algorithm is known, where $\rho \le 1.21$ is the Steiner ratio. We present a PTAS for $k=2$, a $(5/3+\varepsilon)$-approximation algorithm for $k=3$, and two approximation algorithms for general~$k$, with ratios $O(\sqrt n \log k)$ and $k+\varepsilon$