Shallow soil effects for contrasting PGAs at nearby strong-motion stations during the 2017, Mj 5.2, southern Akita Prefecture earthquake

On September 8, 2017, an earthquake of Mj 5.2 occurred with the epicenter in southern Akita Prefecture, Japan, at 22:23 local time. According to the Japan Meteorological Agency (JMA), the focal depth was 9 km. Many strong-motion stations of K-NET and KiK-net recorded ground motions from the earthquake. The maximum horizontal vector peak ground acceleration (PGA) of approximately 136 cm/s2 was recorded at one of the KiK-net stations at an epicentral distance of about 8 km. However, despite being 37 km and 53 km far from the epicenter, two stations recorded PGAs of approximately 126 and 113 cm/s2, respectively, similar to that near the epicenter. Even though these PGAs are not rare, we found that the PGAs at the two sites strongly deviated from the median values suggested by a ground motion prediction equation (GMPE), while the nearby sites generally followed the GMPE. Available velocity models showed that shallow shear wave velocities, especially in the top 5 m, were lower (i.e., the soils were softer) at the two sites compared to those at their nearest neighboring sites. We compared the ratios of the PGAs and peak ground velocities (PGVs) at the two sites with respect to their neighboring sites for many earthquakes covering a wide range of magnitudes and azimuths. We found that the PGAs and PGVs at the two sites were systematically larger than those at the adjacent sites. Linear theoretical site amplifications using the available soil models gave peak frequencies around 6-8 Hz at the larger PGA sites. Bandpass-filtered records showed significantly larger PGAs around these frequencies at the larger PGA sites. The above results showed that local site condition is one of the major contributing factors to induce large PGAs. Furthermore, softer sites experience more substantial nonlinear site amplification than the stiffer sites when input motions exceed some threshold PGAs. This latter effect means that the softer sites can produce a variety of ground motion spectra. Nevertheless, the degree of damage to built structures depends on several factors, including the design and quality of construction. We expect that this study contributes to developing improved microzonation maps for earthquake disaster mitigation.

Thesaurus: quantifying phosphoprotein positional isomers

Proteins can be phosphorylated at neighboring sites resulting in different functional states, and studying the regulation of these sites has been challenging. Here we present Thesaurus, a search engine that detects new positional isomers using site-specific fragment ions from parallel reaction monitoring and data independent acquisition mass spectrometry experiments. We apply Thesaurus to analyze phosphorylation events in the PI3K/AKT signaling pathway and show neighboring sites with distinct quantitative profiles, indicating regulation by different kinases.

Big data analysis of mitochondrial DNA substitution models: A regression approach elucidating the effects of codon position and neighboring nucleotides

We build on the up-to-date version of Phylotree, a comprehensive and continuously updating phylogeny of global human mtDNA variations (van Oven and Kayser 2009), to better understand the substitution mechanism of the mitochondrial DNA (mtDNA) and its most influential factors. We do so by composing Poisson and negative-binomial regression models relating the rate of occurrence of mtDNA substitutions to various factors. Important factors we identify include the identity of the codon at each position, confirming previous findings about the biological significance of different codons for the same amino acid. Importantly, we also identify a significant effect of neighboring sites. This effect cannot be attributed solely to CpG pairs. A similar effect of neighboring sites was recently described for autosomal DNA substitutions, and we speculate it is related to the basic mutational mechanism itself. Once codon composition and context are taken into account, there is no significant difference in substitution rate between different genes in mtDNA.

Radiocarbon Dating Khirbet Qeiyafa and the Iron I–IIA Phases in the Shephelah: Methodological Comments and a Bayesian Model

This article discusses methodological issues related to the radiocarbon dating of Khirbet Qeiyafa, mainly the question of whether the site should be dated solely according to samples retrieved there or dated as part of a regional sequence of stratigraphically based ceramic typology phases. For the latter, we deploy the large number of 14C determinations now available for several sites in the Shephelah, which are located in close proximity to each other, in order to establish a Bayesian model for the absolute chronology of the Iron I–IIA phases in the region. We argue that the information assembled from six neighboring sites in the Shephelah pushes forward the date of Qeiyafa to the 10th century, a date later than the one the excavators estimated based on the more limited 14C information from the site alone.