Metaphors are physical and abstract: ERPs to metaphorically modified nouns resemble ERPs to abstract language

Metaphorical expressions very often involve words referring to physical entities and experiences. Yet, figures of speech such as metaphors are not intended to be understood literally, word-by-word. We used event-related brain potentials (ERPs) to determine whether metaphorical expressions are processed more like physical or more like abstract expressions. To this end, novel adjective-noun word pairs were presented visually in three conditions: (1) Physical, easy to experience with the senses (e.g., printed schedule); (2) Abstract, difficult to experience with the senses (e.g., conditional schedule); and (3) novel Metaphorical, expressions with a physical adjective, but a figurative meaning (e.g., thin schedule). We replicated the N400 lexical concreteness effect for concrete versus abstract adjectives. In order to increase the sensitivity of the concreteness manipulation on the expressions, we divided each condition into high and low groups according to rated concreteness. Mirroring the adjective result, we observed a N400 concreteness effect at the noun for physical expressions with high concreteness ratings versus abstract expressions with low concreteness ratings, even though the nouns per se did not differ in lexical concreteness. Paradoxically, the N400 to nouns in the metaphorical expressions was indistinguishable from that to nouns in the literal abstract expressions, but only for the more concrete subgroup of metaphors; the N400 to the less concrete subgroup of metaphors patterned with that to nouns in the literal concrete expressions. In sum, we not only find evidence for conceptual concreteness separable from lexical concreteness but also that the processing of metaphorical expressions is not driven strictly by either lexical or conceptual concreteness

Meeting report : Ocean ‘omics science, technology and cyberinfrastructure : current challenges and future requirements (August 20-23, 2013)

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 1251-1258, doi:10.4056/sigs.5749944.The National Science Foundation’s EarthCube End User Workshop was held at USC’s Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterise the needs and tools available to the community focusing on microbial and physical oceanography research with a particular focus on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analysing the existing data, and on the need for the construction and curation of diverse federated databases, as well as development of shared interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyberinfrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.We gratefully acknowledge support for the Ocean ‘Omics EarthCube end-user workshop by the Geo-sciences Division of the U.S. National Science Foundation

Nonlinear Optical Microscopy of Murine Abdominal Aortic Aneurysm

Abdominal aortic aneurysm (AAA) is a cardiovascular disease characterized by dilation and weakening of the vessel wall. AAA rupture is responsible for approximately 14,000 deaths annually in the United States [1]. Nonlinear optical (NLO) microscopy presents new possibilities for analyzing AAA tissue samples from murine models. Common NLO techniques are two-photon excitation fluorescence (TPEF), which detects the intrinsic autofluorescent properties of elastin, and second-harmonic generation (SHG), which is specific for collagen fibrils. Elastin and collagen, two major extracellular matrix components, help the aortic wall withstand internal pressure. Murine AAAs were created through 1) subcutaneous continuous systemic infusion of angiotensin II (AngII) in hyperlipidemic apolipoprotein E-deficient mice and 2) by intraluminal infusion of elastase (low 0.5 U/ml and high 25 U/ml concentrations) into the infrarenal aorta of rats [2]. We imaged aneurysmal and control tissue using TPEF and SHG and compared the resulting images to sections stained with standard elastin and collagen markers. TPEF images revealed disorganized elastin sheets and SHG images indicated collagen turnover after aneurysm formation. We quantified the relative degree of elastin degradation and collagen content in the aortic media within a user-defined area on sections stained with Verhoeff-van Gieson (VVG) or Masson’s trichrome (MTC), as well as on TPEF and SHG images. Our analysis with VVG-stained sections shows that elastin content in AAA tissue is significantly decreased by 64% in AngII models (P=0.02), by 34% in low concentration elastase models (P=0.07), and by 99% in high concentration elastase models (P=0.03), relative to control aortic tissue

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm ismobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysismethod, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse.Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver inmaterial accumulation within the DWDS

Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System

The relationship between phage and their microbial hosts is difficult to elucidate in complex natural ecosystems. Engineered systems performing enhanced biological phosphorus removal (EBPR), offer stable, lower complexity communities for studying phage-host interactions. Here, metagenomic data from an EBPR reactor dominated by Candidatus Accumulibacter phosphatis (CAP), led to the recovery of three complete and six partial phage genomes. Heat-stable nucleoid structuring (H-NS) protein, a global transcriptional repressor in bacteria, was identified in one of the complete phage genomes (EPV1), and was most similar to a homolog in CAP. We infer that EPV1 is a CAP-specific phage and has the potential to repress up to 6% of host genes based on the presence of putative H-NS binding sites in the CAP genome. These genes include CRISPR associated proteins and a Type III restriction-modification system, which are key host defense mechanisms against phage infection. Further, EPV1 was the only member of the phage community found in an EBPR microbial metagenome collected seven months prior. We propose that EPV1 laterally acquired H-NS from CAP providing it with a means to reduce bacterial defenses, a selective advantage over other phage in the EBPR system. Phage encoded H-NS could constitute a previously unrecognized weapon in the phage-host arms race

DTK Dominance & Similarity Norming

Offline dominance and zeugmatic similarity normings of variably ambiguous word

UDCK2020 An exploratory data analysis of word form prediction during word-by-word reading.

Data, results, and analysis scripts for Urbach, DeLong, Chan, and Kutas (2020). An exploratory data analysis of word form prediction during word-by-word reading. www.pnas.org/cgi/doi/10.1073/pnas.192202811

Dpr10 and Nocte are required for <i>Drosophila</i> motor axon pathfinding

The paths axons travel to reach their targets and the subsequent synaptic connections they form are highly stereotyped. How cell surface proteins (CSPs) mediate these processes is not completely understood. The Drosophila neuromuscular junction (NMJ) is an ideal system to study how pathfinding and target specificity are accomplished, as the axon trajectories and innervation patterns are known and easily visualized. Dpr10 is a CSP required for synaptic partner choice in the neuromuscular and visual circuits and for axon pathfinding in olfactory neuron organization. In this study, we show that Dpr10 is also required for motor axon pathfinding. To uncover how Dpr10 mediates this process, we used immunoprecipitation followed by mass spectrometry to identify Dpr10 associated proteins. One of these, Nocte, is an unstructured, intracellular protein implicated in circadian rhythm entrainment. We mapped nocte expression in larvae and found it widely expressed in neurons, muscles, and glia. Cell-specific knockdown suggests nocte is required presynaptically to mediate motor axon pathfinding. Additionally, we found that nocte and dpr10 genetically interact to control NMJ assembly, suggesting that they function in the same molecular pathway. Overall, these data reveal novel roles for Dpr10 and its newly identified interactor, Nocte, in motor axon pathfinding and provide insight into how CSPs regulate circuit assembly