High nutrient transport and cycling potential revealed in the microbial metagenome of australian sea lion (neophoca cinerea) faeces

Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production. © 2012 Lavery et al

Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes-organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem. © 2012 Author(s)

Word Embeddings for Entity-annotated Texts

Learned vector representations of words are useful tools for many information retrieval and natural language processing tasks due to their ability to capture lexical semantics. However, while many such tasks involve or even rely on named entities as central components, popular word embedding models have so far failed to include entities as first-class citizens. While it seems intuitive that annotating named entities in the training corpus should result in more intelligent word features for downstream tasks, performance issues arise when popular embedding approaches are naively applied to entity annotated corpora. Not only are the resulting entity embeddings less useful than expected, but one also finds that the performance of the non-entity word embeddings degrades in comparison to those trained on the raw, unannotated corpus. In this paper, we investigate approaches to jointly train word and entity embeddings on a large corpus with automatically annotated and linked entities. We discuss two distinct approaches to the generation of such embeddings, namely the training of state-of-the-art embeddings on raw-text and annotated versions of the corpus, as well as node embeddings of a co-occurrence graph representation of the annotated corpus. We compare the performance of annotated embeddings and classical word embeddings on a variety of word similarity, analogy, and clustering evaluation tasks, and investigate their performance in entity-specific tasks. Our findings show that it takes more than training popular word embedding models on an annotated corpus to create entity embeddings with acceptable performance on common test cases. Based on these results, we discuss how and when node embeddings of the co-occurrence graph representation of the text can restore the performance.Comment: This paper is accepted in 41st European Conference on Information Retrieva

Microbial micropatches within microbial hotspots

© 2018 Dann et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur

The effect of sea temperature and food availability on the spawning success of Cape Anchovy engraulis capensis in the Southern Benguela

Data on the thermal structure, copepod biomass and production, and total number of eggs of the Cape anchovy Engraulis capensis were obtained from monthly surveys during the periods August 1993 – March1994 and September 1994 – March 1995 on the western Agulhas Bank and off the South-Western Cape, South Africa. Previous work suggested that anchovy spawn on the western Agulhas Bank in temperaturesbetween 16 and 19°C, where they feed predominantly on copepods. This study shows that the western Bank is a more suitable spawning area for anchovy, having greater thermal stability, a larger area of 16–19°Cwater and a more consistent food environment than off the South-Western Cape. Also, copepod production on the western Bank was highest in 16–19°C water. To identify factors controlling the area of this watermass, a cluster analysis was used on a suite of hydrographic variables. Three periods were identified: winter (August-September), spring (October-December) and summer (January-March), reflecting changes in theextent of the 16–19°C water and anchovy spawning, both of which peaked during spring. Spring was further characterized by infrequent surface upwelling. During summer, upwelling frequently reached the surface andthe upwelling front migrated offshore, constricting the area of 16–19°C water. It is hypothesized that spawning success in anchovy is dependent upon the extent of suitable spawning habitat, both spatially (16–19°Cwater) and temporally (spring). To put this concept into a predictive framework, the number of anchovy eggs was regressed against the area of 16–19°C water; a significant, positive relationship (p < 0.001, r2 = 0.56, n = 17) was found. An implication of the hypothesis is that the duration of spawning may be important to recruitment

Can people guess what happened to others from their reactions?

Are we able to infer what happened to a person from a brief sample of his/her behaviour? It has been proposed that mentalising skills can be used to retrodict as well as predict behaviour, that is, to determine what mental states of a target have already occurred. The current study aimed to develop a paradigm to explore these processes, which takes into account the intricacies of real-life situations in which reasoning about mental states, as embodied in behaviour, may be utilised. A novel task was devised which involved observing subtle and naturalistic reactions of others in order to determine the event that had previously taken place. Thirty-five participants viewed videos of real individuals reacting to the researcher behaving in one of four possible ways, and were asked to judge which of the four ‘scenarios’ they thought the individual was responding to. Their eye movements were recorded to establish the visual strategies used. Participants were able to deduce successfully from a small sample of behaviour which scenario had previously occurred. Surprisingly, looking at the eye region was associated with poorer identification of the scenarios, and eye movement strategy varied depending on the event experienced by the person in the video. This suggests people flexibly deploy their attention using a retrodictive mindreading process to infer events

Comparative study of the Martian suprathermal electron depletions based on Mars Global Surveyor, Mars Express and Mars Atmosphere and Volatile EvolutioN missions observations

Nightside suprathermal electron depletions have been observed at Mars by three spacecraft to date: Mars Global Surveyor, Mars Express, and the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission. This spatial and temporal diversity of measurements allows us to propose here a comprehensive view of the Martian electron depletions through the first multispacecraft study of the phenomenon. We have analyzed data recorded by the three spacecraft from 1999 to 2015 in order to better understand the distribution of the electron depletions and their creation mechanisms. Three simple criteria adapted to each mission have been implemented to identify more than 134,500 electron depletions observed between 125 and 900 km altitude. The geographical distribution maps of the electron depletions detected by the three spacecraft confirm the strong link existing between electron depletions and crustal magnetic field at altitudes greater than ~170 km. At these altitudes, the distribution of electron depletions is strongly different in the two hemispheres, with a far greater chance to observe an electron depletion in the Southern Hemisphere, where the strongest crustal magnetic sources are located. However, the unique MAVEN observations reveal that below a transition region near 160–170 km altitude the distribution of electron depletions is the same in both hemispheres, with no particular dependence on crustal magnetic fields. This result supports the suggestion made by previous studies that these low-altitudes events are produced through electron absorption by atmospheric CO2

Super-resolving phase measurements with a multi-photon entangled state

Using a linear optical elements and post-selection, we construct an entangled polarization state of three photons in the same spatial mode. This state is analogous to a ``photon-number path entangled state'' and can be used for super-resolving interferometry. Measuring a birefringent phase shift, we demonstrate two- and three-fold improvements in phase resolution.Comment: 4 pages, 3 figure

Entanglement-free Heisenberg-limited phase estimation

Measurement underpins all quantitative science. A key example is the measurement of optical phase, used in length metrology and many other applications. Advances in precision measurement have consistently led to important scientific discoveries. At the fundamental level, measurement precision is limited by the number N of quantum resources (such as photons) that are used. Standard measurement schemes, using each resource independently, lead to a phase uncertainty that scales as 1/sqrt(N) - known as the standard quantum limit. However, it has long been conjectured that it should be possible to achieve a precision limited only by the Heisenberg uncertainty principle, dramatically improving the scaling to 1/N. It is commonly thought that achieving this improvement requires the use of exotic quantum entangled states, such as the NOON state. These states are extremely difficult to generate. Measurement schemes with counted photons or ions have been performed with N <= 6, but few have surpassed the standard quantum limit and none have shown Heisenberg-limited scaling. Here we demonstrate experimentally a Heisenberg-limited phase estimation procedure. We replace entangled input states with multiple applications of the phase shift on unentangled single-photon states. We generalize Kitaev's phase estimation algorithm using adaptive measurement theory to achieve a standard deviation scaling at the Heisenberg limit. For the largest number of resources used (N = 378), we estimate an unknown phase with a variance more than 10 dB below the standard quantum limit; achieving this variance would require more than 4,000 resources using standard interferometry. Our results represent a drastic reduction in the complexity of achieving quantum-enhanced measurement precision.Comment: Published in Nature. This is the final versio

Quantum states made to measure

Recent progress in manipulating quantum states of light and matter brings quantum-enhanced measurements closer to prospective applications. The current challenge is to make quantum metrologic strategies robust against imperfections.Comment: 4 pages, 3 figures, Commentary for Nature Photonic