Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Head roll dependent variability of subjective visual vertical and ocular counterroll

We compared the variability of the subjective visual vertical (SVV) and static ocular counterroll (OCR), and hypothesized a correlation between the measurements because of their shared macular input. SVV and OCR were measured simultaneously in various whole-body roll positions [upright, 45 degrees right-ear down (RED), and 75 degrees RED] in six subjects. Gains of OCR were -0.18 (45 degrees RED) and -0.12 (75 degrees RED), whereas gains of compensation for body roll in the SVV task were -1.11 (45 degrees RED) and -0.96 (75 degrees RED). Normalized SVV and OCR variabilities were not significantly different (P > 0.05), i.e., both increased with increasing roll. Moreover, a significant correlation (R (2) = 0.80, slope = 0.29) between SVV and OCR variabilities was found. Whereas the gain of OCR is different from the gain of SVV, trial-to-trial variability of OCR follows the same roll-dependent modulation observed in SVV variability. We propose that the similarities in variability reflect a common otolith input, which, however, is subject to distinct central processing for determining the gain of SVV and OCR

The Social Dimensions of Biological Invasions in South Africa

Thischapterexaminescurrentknowledgerelatingtothehumanandsocial dimensions of biological invasions in South Africa. We do so by advancing 12 propo- sitions and examining the evidence for or against each using South African literature. The propositions cover four broad issues: how people cause invasions; how they conceptualise them; effects of invasive species on people; and peoples’ responses to them. The propositions we assess include: (1) intentional introductions were and continue to reflect the social ethos of the time; (2) people go to great lengths to ensure that newly introduced species establish themselves; (3) human-mediated modifications help invasive species to establish; (4) how people think about and study invasive species is strongly shaped by social-ecological contexts; (5) knowledge and awareness of invasive species is low amongst the general public; (6) personal values are the primary factor affecting perceptions of invasive alien species and their control; (7) specific social-ecological contexts mediate how invasive species affect people; (8) research on social effects of invasive species primarily focuses on negative impacts; (9) the negative social impacts of invasive species on local livelihoods are of more concern to people than impacts on biodiversity; (10) people are less willing to manage species regarded as ‘charismatic’; (11) social heterogeneity increases conflicts around the management of biological invasions; and (12) engagement with society is key to successful manage- ment. By advancing and questioning propositions, we were able to determine what is known, provide evidence for where gaps lie, and thus identify areas for future research

Piccolo Directs Activity Dependent F-Actin Assembly from Presynaptic Active Zones via Daam1.

The dynamic assembly of filamentous (F) actin plays essential roles in the assembly of presynaptic boutons, the fusion, mobilization and recycling of synaptic vesicles (SVs), and presynaptic forms of plasticity. However, the molecular mechanisms that regulate the temporal and spatial assembly of presynaptic F-actin remain largely unknown. Similar to other F-actin rich membrane specializations, presynaptic boutons contain a set of molecules that respond to cellular cues and trans-synaptic signals to facilitate activity-dependent assembly of F-actin. The presynaptic active zone (AZ) protein Piccolo has recently been identified as a key regulator of neurotransmitter release during SV cycling. It does so by coordinating the activity-dependent assembly of F-Actin and the dynamics of key plasticity molecules including Synapsin1, Profilin and CaMKII. The multidomain structure of Piccolo, its exquisite association with the AZ, and its ability to interact with a number of actin-associated proteins suggest that Piccolo may function as a platform to coordinate the spatial assembly of F-actin. Here we have identified Daam1, a Formin that functions with Profilin to drive F-actin assembly, as a novel Piccolo binding partner. We also found that within cells Daam1 activation promotes Piccolo binding, an interaction that can spatially direct the polymerization of F-Actin. Moreover, similar to Piccolo and Profilin, Daam1 loss of function impairs presynaptic-F-actin assembly in neurons. These data suggest a model in which Piccolo directs the assembly of presynaptic F-Actin from the AZ by scaffolding key actin regulatory proteins including Daam1