Fast, Linear Time Hierarchical Clustering using the Baire Metric

The Baire metric induces an ultrametric on a dataset and is of linear computational complexity, contrasted with the standard quadratic time agglomerative hierarchical clustering algorithm. In this work we evaluate empirically this new approach to hierarchical clustering. We compare hierarchical clustering based on the Baire metric with (i) agglomerative hierarchical clustering, in terms of algorithm properties; (ii) generalized ultrametrics, in terms of definition; and (iii) fast clustering through k-means partititioning, in terms of quality of results. For the latter, we carry out an in depth astronomical study. We apply the Baire distance to spectrometric and photometric redshifts from the Sloan Digital Sky Survey using, in this work, about half a million astronomical objects. We want to know how well the (more costly to determine) spectrometric redshifts can predict the (more easily obtained) photometric redshifts, i.e. we seek to regress the spectrometric on the photometric redshifts, and we use clusterwise regression for this.Comment: 27 pages, 6 tables, 10 figure

Health Aspects of the Pre-Departure Phase of Migration

In the second article in a six-part PLoS Medicine series on Migration & Health, Brian Gushulak and Douglas MacPherson discuss the pre-departure phase of migration and the specific health risks and policy needs associated with this phase

Perturbation of the yeast mitochondrial lipidome and associated membrane proteins following heterologous expression of Artemia-ANT

Heterologous expression is a landmark technique for studying a protein itself or its effect on the expression host, in which membrane-embedded proteins are a common choice. Yet, the impact of inserting a foreign protein to the lipid environment of host membranes, has never been addressed. Here we demonstrated that heterologous expression of the Artemia franciscana adenine nucleotide translocase (ANT) in yeasts altered lipidomic composition of their inner mitochondrial membranes. Along with this, activities of complex II, IV and ATP synthase, all membrane-embedded components, were significantly decreased while their expression levels remained unaffected. Although the results represent an individual case of expressing a crustacean protein in yeast inner mitochondrial membranes, it cannot be excluded that host lipidome alterations is a more widespread epiphenomenon, potentially biasing heterologous expression experiments. Finally, our results raise the possibility that not only lipids modulate protein function, but also membrane-embedded proteins modulate lipid composition, thus revealing a reciprocal mode of regulation for these two biomolecular entities

Impact of voluntary exercise and housing conditions on hippocampal glucocorticoid receptor, miR-124 and anxiety

Background: Lack of physical activity and increased levels of stress contribute to the development of multiple physical and mental disorders. An increasing number of studies relate voluntary exercise with greater resilience to psychological stress, a process that is highly regulated by the hypothalamic-pituitary-adrenal (HPA) axis. However, the molecular mechanisms underlying the beneficial effects of exercise on stress resilience are still poorly understood. Here we have studied the impact of long term exercise and housing conditions on: a) hippocampal expression of glucocorticoid receptor (Nr3c1), b) epigenetic regulation of Nr3c1 (DNA methylation at the Nr3c1-1F promoter and miR-124 expression), c) anxiety (elevated plus maze, EPM), and d) adrenal gland weight and adrenocorticotropic hormone receptor (Mc2r) expression. Results: Exercise increased Nr3c1 and Nr3c1-1F expression and decreased miR-124 levels in the hippocampus in single-housed mice, suggesting enhanced resilience to stress. The opposite was found for pair-housed animals. Bisulfite sequencing showed virtually no DNA methylation in the Nr3c1-1F promoter region. Single-housing increased the time spent on stretch attend postures. Exercise decreased the time spent at the open arms of the EPM, however, the mobility of the exercise groups was significantly lower. Exercise had opposite effects on the adrenal gland weight of single and pair-housed mice, while it had no effect on adrenal Mc2r expression. Conclusions: These results suggest that exercise exerts a positive impact on stress resilience in single-housed mice that could be mediated by decreasing miR-124 and increasing Nr3c1 expression in the hippocampus. However, pair-housing reverses these effects possibly due to stress from dominance disputes between pairs

A diarylamine derived from anthranilic acid inhibits ZIKV replication

Zika virus (ZIKV) is a mosquito-transmitted Flavivirus, originally identified in Uganda in 1947 and recently associated with a large outbreak in South America. Despite extensive efforts there are currently no approved antiviral compounds for treatment of ZIKV infection. Here we describe the antiviral activity of diarylamines derived from anthranilic acid (FAMs) against ZIKV. A synthetic FAM (E3) demonstrated anti-ZIKV potential by reducing viral replication up to 86%. We analyzed the possible mechanisms of action of FAM E3 by evaluating the intercalation of this compound into the viral dsRNA and its interaction with the RNA polymerase of bacteriophage SP6. However, FAM E3 did not act by these mechanisms. In silico results predicted that FAM E3 might bind to the ZIKV NS3 helicase suggesting that this protein could be one possible target of this compound. To test this, the thermal stability and the ATPase activity of the ZIKV NS3 helicase domain (NS3Hel) were investigated in vitro and we demonstrated that FAM E3 could indeed bind to and stabilize NS3Hel

Status, sources and contamination levels of organochlorine pesticide residues in urban and agricultural areas: a preliminary review in central–southern Italian soils

Organochlorine pesticides (OCPs) are synthetic chemicals commonly used in agricultural activities to kill pests and are persistent organic pollutants (POPs). They can be detected in different environmental media, but soil is considered an important reservoir due to its retention capacity. Many different types of OCPs exist, which can have different origins and pathways in the environment. It is therefore important to study their distribution and behaviour in the environment, starting to build a picture of the potential human health risk in different contexts. This study aimed at investigating the regional distribution, possible sources and contamination levels of 24 OCP compounds in urban and rural soils from central and southern Italy. One hundred and forty-eight topsoil samples (0–20 cm top layer) from 78 urban and 70 rural areas in 11 administrative regions were collected and analysed by gas chromatography–electron capture detector (GC–ECD). Total OCP residues in soils ranged from nd (no detected) to 1043 ng/g with a mean of 29.91 ng/g and from nd to 1914 ng/g with a mean of 60.16 ng/g in urban and rural area, respectively. Endosulfan was the prevailing OCP in urban areas, followed by DDTs, Drins, Methoxychlor, HCHs, Chlordane-related compounds and HCB. In rural areas, the order of concentrations was Drins > DDTs > Methoxychlor > Endosulfans > HCHs > Chlordanes > HCB. Diagnostic ratios and robust multivariate analyses revealed that DDT in soils could be related to historical application, whilst (illegal) use of technical DDT or dicofol may still occur in some urban areas. HCH residues could be related to both historical use and recent application, whilst there was evidence that modest (yet significant) application of commercial technical HCH may still be happening in urban areas. Drins and Chlordane compounds appeared to be mostly related to historical application, whilst Endosulfan presented a complex mix of results, indicating mainly historical origin in rural areas as well as potential recent applications on urban areas. Contamination levels were quantified by Soil Quality Index (SoQI), identifying high levels in rural areas of Campania and Apulia, possibly due to the intensive nature of some agricultural practices in those regions (e.g., vineyards and olive plantations). The results from this study (which is in progress in the remaining regions of Italy) will provide an invaluable baseline for OCP distribution in Italy and a powerful argument for follow-up studies in contaminated areas. It is also hoped that similar studies will eventually constitute enough evidence to push towards an institutional response for more adequate regulation as well as a full ratification of the Stockholm Convention

The COGs (context, object, and goals) in multisensory processing

Our understanding of how perception operates in real-world environments has been substantially advanced by studying both multisensory processes and “top-down” control processes influencing sensory processing via activity from higher-order brain areas, such as attention, memory, and expectations. As the two topics have been traditionally studied separately, the mechanisms orchestrating real-world multisensory processing remain unclear. Past work has revealed that the observer’s goals gate the influence of many multisensory processes on brain and behavioural responses, whereas some other multisensory processes might occur independently of these goals. Consequently, other forms of top-down control beyond goal dependence are necessary to explain the full range of multisensory effects currently reported at the brain and the cognitive level. These forms of control include sensitivity to stimulus context as well as the detection of matches (or lack thereof) between a multisensory stimulus and categorical attributes of naturalistic objects (e.g. tools, animals). In this review we discuss and integrate the existing findings that demonstrate the importance of such goal-, object- and context-based top-down control over multisensory processing. We then put forward a few principles emerging from this literature review with respect to the mechanisms underlying multisensory processing and discuss their possible broader implications

Sole coloration as an unusual aposematic signal in a Neotropical toad

Many animals have evolved remarkable strategies to avoid predation. In diurnal, toxic harlequin toads (Atelopus) from the Amazon basin, we find a unique colour signal. Some Atelopus populations have striking red soles of the hands and feet, visible only when walking. When stationary, the toads are hard to detect despite their yellow-black dorsal coloration. Consequently, they switch between high and low conspicuousness. Interestingly, some populations lack the extra colour display of the soles. We found comprehensive support that the red coloration can act as an aposematic signal directed towards potential predators: red soles are significantly more conspicuous than soles lacking red coloration to avian predators and the presence of the red signal significantly increases detection. Further, toads with red soles show bolder behaviour by using higher sites in the vegetation than those lacking this signal. Field experiments hint at a lower attack risk for clay models with red soles than for those lacking the signal, in a population where the red soles naturally occur. We suggest that the absence of the signal may be explained by a higher overall attack risk or potential differences of predator community structure between populations. © 2019, The Author(s)