Emergency remote teaching in linguistics during the early COVID-19 pandemic

In the spring of 2020, the COVID-19 pandemic forced many higher education institutions to transition suddenly to emergency remote teaching. This paper describes the results of a survey that the Linguistic Society of America carried out on the response to this situation among teachers and learners in the linguistics community. We consider what teachers tried, what students found helpful, and what got overlooked

Verifying the Implementation of An Anisotropic Grain Boundary Energy Model in Idaho National Lab’s MARMOT

This work aims to verify the correct implementation of an anisotropic grain boundary (GB) energy model for face-centered cubic (FCC) and fluorite materials in Idaho National Laboratory’s phase field fuel performance code MARMOT. The model was recently implemented in MARMOT with the purpose of enabling higher fidelity simulations of UO2 nuclear fuels. As part of verification, tests were performed to measure the energy dependence on misorientation of high symmetry GBs in an FCC metal (Cu). The energies of the [100], [110], and [111] twist boundaries result as predicted, as do the energies of the [111] symmetric tilt boundaries. However, the energies of the [100] and [110] symmetric tilt boundaries display an unexpected mirror symmetry about half the rotation period. Further investigations are required to determine the cause of this discrepancy. Possible reasons include an error in the MARMOT implementation of the anisotropic GB energy model

Effects of musical ear training on lexical tone perception

The effect of short term musical experience on lexical tone perception was examined by administering four hours of daily musical ear training to non-tone language speakers. After training, participants showed some improvement in a tone labeling task, but not a tone discrimination task; however, this improvement did not differ reliably from controls indicating that short-term musical training is thus far not able to replicate language effects observed among lifelong musicians, but some linguistic differences between musicians and nonmusicians may likely be due to experience, rather than individual differences or other factors

Singular 'they' and novel pronouns: gender-neutral, nonbinary, or both?

Pronouns have recently become a highly visible aspect of the LGBTQ+ movement among the general public and in linguistics. We investigated whether singular, specific 'they’ and the novel singular gender-neutral pronoun ‘ze’ are interpreted as gender-neutral (slient on gender and the gender binary) or referring specifically to referents of non-binary gender. Participants read descriptions of scholarship applicants, and guessed which photo matched the applicant they read about from an array of male, female, and non-binary subjects. Results suggest that ‘they’ is interpreted as gender-neutral, including non-binary/gender-nonconforming referents. 'Ze’ does not appear to be recognized by enough English speakers to determine a definitive interpretation

Two successive calcium-dependent transitions mediate membrane binding and oligomerization of daptomycin and the related antibiotic A54145

The final publication is available at Elsevier via http://doi.org/10.1016/j.bbamem.2016.05.020 © 2016. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Daptomycin and A54145 are homologous lipopeptide antibiotics that permeabilize the cell membranes of Gram-positive bacteria. Membrane permeabilization depends on the presence of both phosphatidylglycerol (PG) and calcium, and it involves the formation of oligomeric transmembrane pores that consist of approximately 6-8 subunits. We here show that each lipopeptide molecule binds two calcium ions in separable, successive steps. The first calcium ion causes the lipopeptide molecule to bind to the target membrane, and likely to form a loosely associated oligomer. Higher calcium concentrations induce binding of a second ion, which produces the more tightly associated and more deeply membrane-inserted final, functional form of the oligomer. Both calcium dependent steps are accompanied by fluorescence signals that indicate transition of specific amino acid residues into less polar environments, suggestive of insertion into the target membrane. Our findings agree with the earlier observation that two of the four acidic amino acid residues in the daptomycin molecule are essential for antibacterial activity. (C) 2016 Elsevier B.V. All rights reserved.This study was supported by operating grants by NSERC to Scott Taylor (155283-2012) and Michael Palmer (250265-2013)

Thiosquaramides: pH switchable anion transporters

The transport of anions across cellular membranes is an important biological function governed by specialised proteins. In recent years, many small molecules have emerged that mimick the anion transport behaviour of these proteins, but only a few of these synthetic molecules also display the gating/switching behaviour seen in biological systems. A small series of thiosquar-amides was synthesised and their pH-dependent chloride binding and anion transport behaviour was investigated using 1H NMR titrations, single crystal X-ray diffraction and a variety of vesicle-based techniques. Spectrophotometric titrations and DFT calculations revealed that the thiosquaramides are significantly more acidic than their oxosquaramide analogues, with pKa values between 4.0 and 9.0. This led to the observation that at pH 7.2 the anion transport ability of the thiosquaramides is fully switched OFF due to deprotonation of the receptor, but is completely switched ON at lower pH

Bacterioplankton dynamics within a large anthropogenically impacted urban estuary

© 2016 Jeffries, Schmitz Fontes, Harrison, Van-Dongen-Vogels, Eyre, Ralph and Seymour. The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and function of microbial communities within a highly urbanized aquatic ecosystem

Charting a dynamic DNA methylation landscape of the human genome

DNA methylation is a defining feature of mammalian cellular identity and essential for normal development1,2. Most cell types, except germ cells and pre-implantation embryos3–5, display relatively stable DNA methylation patterns with 70–80% of all CpGs being methylated6. Despite recent advances we still have a too limited understanding of when, where and how many CpGs participate in genomic regulation. Here we report the in depth analysis of 42 whole genome bisulfite sequencing (WGBS) data sets across 30 diverse human cell and tissue types. We observe dynamic regulation for only 21.8% of autosomal CpGs within a normal developmental context, a majority of which are distal to transcription start sites. These dynamic CpGs co-localize with gene regulatory elements, particularly enhancers and transcription factor binding sites (TFBS), which allow identification of key lineage specific regulators. In addition, differentially methylated regions (DMRs) often harbor SNPs associated with cell type related diseases as determined by GWAS. The results also highlight the general inefficiency of WGBS as 70–80% of the sequencing reads across these data sets provided little or no relevant information regarding CpG methylation. To further demonstrate the utility of our DMR set, we use it to classify unknown samples and identify representative signature regions that recapitulate major DNA methylation dynamics. In summary, although in theory every CpG can change its methylation state, our results suggest that only a fraction does so as part of coordinated regulatory programs. Therefore our selected DMRs can serve as a starting point to help guide novel, more effective reduced representation approaches to capture the most informative fraction of CpGs as well as further pinpoint putative regulatory elements