Tractable Learning of Probability Distributions Using the Contrastive Hebbian Algorithm

In some tasks (e.g., assigning meanings to ambiguous words) humans produce multiple distinct alternatives in response to a particular stimulus, apparently mirroring the environmental probabilities associated with each alternative. For this purpose, a network architecture is needed that can produce a distribution of outcomes, and a learning algorithm is needed that can lead to the discovery of ensembles of connection weights that reproduce the environmentally specified probabilities. Stochastic symmetric networks such as Boltzmann machines and networks that use graded activations perturbed with Gaussian noise can exhibit such distributions at equilibrium, and they can be trained to match environmentally specified probabilities using Contrastive Hebbian Leaning, the generalized form of the Boltzmann Learning algorithm. Learning distributions exacts a considerable computational cost as processing time is used both in settling to equilibrium and in sampling equilibrium statistics. The work presented here examines the extent of this cost and how it may be minimized, and produces speedups of roughly a factor of 5 compared to previously published results

A LOFAR mini-survey for low-frequency radio emission from the nearest brown dwarfs

We have conducted a mini-survey for low-frequency radio emission from some of the closest brown dwarfs to the Sun with rapid rotation rates: SIMP J013656.5 +093347, WISEPC 150649.97+702736.0, and WISEPA J174124.26+255319.5.We have placed robust 3s upper limits on the flux density in the 111 – 169 MHz frequency range for these targets: WISE 1506: < 0:72 mJy; WISE 1741: < 0:87 mJy; SIMP 0136: < 0:66 mJy. At 8 hours of integration per target to achieve these limits, we find that systematic and detailed study of this class of object at LOFAR frequencies will require a substantial dedication of resources

Improving Hippocampal Memory Through the Experience of a Rich Minecraft Environment

It is well known that the brain changes in response to the surrounding environment. The hippocampus has been shown to be particularly susceptible to environmental enrichment, with effects ranging from the generation of new hippocampal neurons and synapses to an increased expression of neurotrophic factors. While many of these changes in the hippocampus are well documented in animals, our understanding of how environmental enrichment can apply to humans is more ambiguous. In animals, spatial exploration has been shown to be a clear way to elicit the effects of environmental enrichment and considering the role of the hippocampus in spatial navigation, which has been shown in both animal models and humans, it suggests a viable avenue for translation of environmental enrichment to humans. Here, we test the hypothesis that the spatial exploration of a virtual video game environment, can impact the hippocampus and lead to an improvement in hippocampal-dependent memory. Using the video game Minecraft, we tested four groups of participants, each playing on custom servers and focusing on different aspects of Minecraft to test the effects of both building and exploration over the course of 2 weeks. We found an improvement in hippocampus-associated memory from pre-test to post-test and that the degree of improvement was tied to both the amount of exploration of the Minecraft world and the complexity of the structures built within Minecraft. Thus, the number of enrichment participants engaged in while playing Minecraft was directly correlated with improvements in hippocampal-dependent memory outside of the game

Dataset of oxygen, carbon, and strontium isotope values from the Imperial Roman site of Velia (ca. 1st-2nd c. CE), Italy

The oxygen (δ18Ocarbonate), strontium (87Sr/86Sr), and previously unpublished carbon (δ13Ccarbonate) isotope data presented herein from the Imperial Roman site of Velia (ca. 1st to 2nd c. CE) were obtained from the dental enamel of human permanent second molars (M2). In total, the permanent M2s of 20 individuals (10 male and 10 female) were sampled at the Museo delle Civiltà in Rome (formerly the Museo Nazionale Preistorico Etnografico "L. Pigorini") and were subsequently processed and analysed at McMaster University. A subsample of teeth (n=5) was initially subjected to Fourier transform infrared spectroscopy (FTIR) analysis to assess for diagenetic alteration through calculation of crystallinity index (CI) values. Subsequently, tooth enamel was analysed for δ13Ccarbonate and δ18Ocarbonate (VPDB) using a VG OPTIMA Isocarb isotope ratio mass spectrometer (IRMS) at McMaster Research for Stable Isotopologues (MRSI), and 87Sr/86Sr was measured by dynamic multi-collection using a thermal ionization mass spectrometer (TIMS) in the School of Geography and Earth Sciences. The dental enamel isotope data presented represent the first δ18O, δ13Ccarbonate, and 87Sr/86Sr values analysed from Imperial Roman Campania to date, providing data of use for comparative analyses of δ18O, δ13C, and 87Sr/86Sr values within the region and for assisting in documenting human mobility in archaeological contexts. Full interpretation of the δ18O and 87Sr/86Sr data presented here is provided in "Imperial Roman mobility and migration at Velia (1st to 2nd c. CE) in southern Italy" [1]

New Concerns for Neurocognitive Function during Deep Space Exposures to Chronic, Low Dose-Rate, Neutron Radiation.

As NASA prepares for a mission to Mars, concerns regarding the health risks associated with deep space radiation exposure have emerged. Until now, the impacts of such exposures have only been studied in animals after acute exposures, using dose rates ∼1.5×105 higher than those actually encountered in space. Using a new, low dose-rate neutron irradiation facility, we have uncovered that realistic, low dose-rate exposures produce serious neurocognitive complications associated with impaired neurotransmission. Chronic (6 month) low-dose (18 cGy) and dose rate (1 mGy/d) exposures of mice to a mixed field of neutrons and photons result in diminished hippocampal neuronal excitability and disrupted hippocampal and cortical long-term potentiation. Furthermore, mice displayed severe impairments in learning and memory, and the emergence of distress behaviors. Behavioral analyses showed an alarming increase in risk associated with these realistic simulations, revealing for the first time, some unexpected potential problems associated with deep space travel on all levels of neurological function

The XMM Cluster Survey: X-ray analysis methodology

The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMM-Newton Science Archive. Its main aims are to measure cosmological parameters and trace the evolution of X-ray scaling relations. In this paper we describe the data processing methodology applied to the 5,776 XMM observations used to construct the current XCS source catalogue. A total of 3,675 > 4-sigma cluster candidates with > 50 background-subtracted X-ray counts are extracted from a total non-overlapping area suitable for cluster searching of 410 deg^2. Of these, 993 candidates are detected with > 300 background-subtracted X-ray photon counts, and we demonstrate that robust temperature measurements can be obtained down to this count limit. We describe in detail the automated pipelines used to perform the spectral and surface brightness fitting for these candidates, as well as to estimate redshifts from the X-ray data alone. A total of 587 (122) X-ray temperatures to a typical accuracy of < 40 (< 10) per cent have been measured to date. We also present the methodology adopted for determining the selection function of the survey, and show that the extended source detection algorithm is robust to a range of cluster morphologies by inserting mock clusters derived from hydrodynamical simulations into real XMM images. These tests show that the simple isothermal beta-profiles is sufficient to capture the essential details of the cluster population detected in the archival XMM observations. The redshift follow-up of the XCS cluster sample is presented in a companion paper, together with a first data release of 503 optically-confirmed clusters.Comment: MNRAS accepted, 45 pages, 38 figures. Our companion paper describing our optical analysis methodology and presenting a first set of confirmed clusters has now been submitted to MNRA

Geography, private costs and uptake of screening for abdominal aortic aneurysm in a remote rural area

BACKGROUND: The relationship between geographical location, private costs, health provider costs and uptake of health screening is unclear. This paper examines these relationships in a screening programme for abdominal aortic aneurysm in the Highlands and Western Isles of Scotland, a rural and remote area of over 10,000 square miles. METHODS: Men aged 65–74 (n = 9323) were invited to attend screening at 51 locations in 50 settlements. Effects of geography, deprivation and age on uptake were examined. Among 8,355 attendees, 8,292 completed a questionnaire detailing mode of travel and costs incurred, time travelled, whether accompanied, whether dependants were cared for, and what they would have been doing if not attending screening, thus allowing private costs to be calculated. Health provider (NHS) costs were also determined. Data were analysed by deprivation categories, using the Scottish Indices of Deprivation (2003), and by settlement type ranging from urban to very remote rural. RESULTS: Uptake of screening was high in all settlement types (mean 89.6%, range 87.4 – 92.6%). Non-attendees were more deprived in terms of income, employment, education and health but there was no significant difference between non-attendees and attendees in terms of geographical access to services. Age was similar in both groups. The highest private costs (median £7.29 per man) and NHS screening costs (£18.27 per man invited) were observed in very remote rural areas. Corresponding values for all subjects were: private cost £4.34 and NHS cost £15.72 per man invited. CONCLUSION: Uptake of screening for abdominal aortic aneurysm in this remote and rural setting was high in comparison with previous studies, and this applied across all settlement types. Geographical location did not affect uptake, most likely due to the outreach approach adopted. Private and NHS costs were highest in very remote settings but still compared favourably with other published studies

The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

<p>Abstract</p> <p>Background</p> <p>Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments.</p> <p>Results</p> <p>In this manuscript, we present the <it>Drosophila melanogaster </it>PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal <url>http://www.drosophila-peptideatlas.org</url> allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s) in which it was observed.</p> <p>Conclusion</p> <p>PeptideAtlas is an open access database for the <it>Drosophila </it>community that has several features and applications that support (1) reduction of the complexity inherently associated with performing targeted proteomic studies, (2) designing and accelerating shotgun proteomics experiments, (3) confirming or questioning gene models, and (4) adjusting gene models such that they are in line with observed <it>Drosophila </it>peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.</p