Microbial burden prediction model for unmanned planetary spacecraft

The technical development of a computer program for predicting microbial burden on unmanned planetary spacecraft is outlined. The discussion includes the derivation of the basic analytical equations, the selection of a method for handling several random variables, the macrologic of the computer programs and the validation and verification of the model. The prediction model was developed to (1) supplement the biological assays of a spacecraft by simulating the microbial accretion during periods when assays are not taken; (2) minimize the necessity for a large number of microbiological assays; and (3) predict the microbial loading on a lander immediately prior to sterilization and other non-lander equipment prior to launch. It is shown that these purposes not only were achieved but also that the prediction results compare favorably to the estimates derived from the direct assays. The computer program can be applied not only as a prediction instrument but also as a management and control tool. The basic logic of the model is shown to have possible applicability to other sequential flow processes, such as food processing

Partial Volume Segmentation of Brain MRI Scans of any Resolution and Contrast

Partial voluming (PV) is arguably the last crucial unsolved problem in Bayesian segmentation of brain MRI with probabilistic atlases. PV occurs when voxels contain multiple tissue classes, giving rise to image intensities that may not be representative of any one of the underlying classes. PV is particularly problematic for segmentation when there is a large resolution gap between the atlas and the test scan, e.g., when segmenting clinical scans with thick slices, or when using a high-resolution atlas. In this work, we present PV-SynthSeg, a convolutional neural network (CNN) that tackles this problem by directly learning a mapping between (possibly multi-modal) low resolution (LR) scans and underlying high resolution (HR) segmentations. PV-SynthSeg simulates LR images from HR label maps with a generative model of PV, and can be trained to segment scans of any desired target contrast and resolution, even for previously unseen modalities where neither images nor segmentations are available at training. PV-SynthSeg does not require any preprocessing, and runs in seconds. We demonstrate the accuracy and flexibility of the method with extensive experiments on three datasets and 2,680 scans. The code is available at https://github.com/BBillot/SynthSeg.Comment: accepted for MICCAI 202

Effect of Mono and Di-rhamnolipids on Biofilms Pre-formed by Bacillus subtilis BBK006.

Different microbial inhibition strategies based on the planktonic bacterial physiology have been known to have limited efficacy on the growth of biofilms communities. This problem can be exacerbated by the emergence of increasingly resistant clinical strains. Biosurfactants have merited renewed interest in both clinical and hygienic sectors due to their potential to disperse microbial biofilms. In this work, we explore the aspects of Bacillus subtilis BBK006 biofilms and examine the contribution of biologically derived surface-active agents (rhamnolipids) to the disruption or inhibition of microbial biofilms produced by Bacillus subtilis BBK006. The ability of mono-rhamnolipids (Rha-C10-C10) produced by Pseudomonas aeruginosa ATCC 9027 and the di-rhamnolipids (Rha-Rha-C14-C14) produced by Burkholderia thailandensis E264, and phosphate-buffered saline to disrupt biofilm of Bacillus subtilis BBK006 was evaluated. The biofilm produced by Bacillus subtilis BBK006 was more sensitive to the di-rhamnolipids (0.4 g/L) produced by Burkholderia thailandensis than the mono-rhamnolipids (0.4 g/L) produced by Pseudomonas aeruginosa ATCC 9027. Rhamnolipids are biologically produced compounds safe for human use. This makes them ideal candidates for use in new generations of bacterial dispersal agents and useful for use as adjuvants for existing microbial suppression or eradication strategies

The impact of ageing reveals distinct roles for human dentate gyrus and CA3 in pattern separation and object recognition memory

© 2017 The Author(s). Both recognition of familiar objects and pattern separation, a process that orthogonalises overlapping events, are critical for effective memory. Evidence is emerging that human pattern separation requires dentate gyrus. Dentate gyrus is intimately connected to CA3 where, in animals, an autoassociative network enables recall of complete memories to underpin object/event recognition. Despite huge motivation to treat age-related human memory disorders, interaction between human CA3 and dentate subfields is difficult to investigate due to small size and proximity. We tested the hypothesis that human dentate gyrus is critical for pattern separation, whereas, CA3 underpins identical object recognition. Using 3 T MR hippocampal subfield volumetry combined with a behavioural pattern separation task, we demonstrate that dentate gyrus volume predicts accuracy and response time during behavioural pattern separation whereas CA3 predicts performance in object recognition memory. Critically, human dentate gyrus volume decreases with age whereas CA3 volume is age-independent. Further, decreased dentate gyrus volume, and no other subfield volume, mediates adverse effects of aging on memory. Thus, we demonstrate distinct roles for CA3 and dentate gyrus in human memory and uncover the variegated effects of human ageing across hippocampal regions. Accurate pinpointing of focal memory-related deficits will allow future targeted treatment for memory loss

Organic residues in archaeology - the highs and lows of recent research

YesThe analysis of organic residues from archaeological materials has become increasingly important to our understanding of ancient diet, trade and technology. Residues from diverse contexts have been retrieved and analysed from the remains of food, medicine and cosmetics to hafting material on stone arrowheads, pitch and tar from shipwrecks, and ancient manure from soils. Research has brought many advances in our understanding of archaeological, organic residues over the past two decades. Some have enabled very specific and detailed interpretations of materials preserved in the archaeological record. However there are still areas where we know very little, like the mechanisms at work during the formation and preservation of residues, and areas where each advance produces more questions rather than answers, as in the identification of degraded fats. This chapter will discuss some of the significant achievements in the field over the past decade and the ongoing challenges for research in this area.Full text was made available in the Repository on 15th Oct 2015, at the end of the publisher's embargo period

Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme

Biomolecular function is realized by recognition, and increasing evidence shows that recognition is determined not only by structure but also by flexibility and dynamics. We explored a biomolecular recognition process that involves a major conformational change – protein folding. In particular, we explore the binding-induced folding of IA3, an intrinsically disordered protein that blocks the active site cleft of the yeast aspartic proteinase saccharopepsin (YPrA) by folding its own N-terminal residues into an amphipathic alpha helix. We developed a multi-scaled approach that explores the underlying mechanism by combining structure-based molecular dynamics simulations at the residue level with a stochastic path method at the atomic level. Both the free energy profile and the associated kinetic paths reveal a common scheme whereby IA3 binds to its target enzyme prior to folding itself into a helix. This theoretical result is consistent with recent time-resolved experiments. Furthermore, exploration of the detailed trajectories reveals the important roles of non-native interactions in the initial binding that occurs prior to IA3 folding. In contrast to the common view that non-native interactions contribute only to the roughness of landscapes and impede binding, the non-native interactions here facilitate binding by reducing significantly the entropic search space in the landscape. The information gained from multi-scaled simulations of the folding of this intrinsically disordered protein in the presence of its binding target may prove useful in the design of novel inhibitors of aspartic proteinases

Integrated Multi-Parameter Exploration Footprints of the Canadian Malartic Disseminated Au, McArthur River-Millennium Unconformity U, and Highland Valley Porphyry Cu Deposits: Preliminary Results from the NSERC-CMIC Mineral Exploration Footprints Research Network

Mineral exploration in Canada is increasingly focused on concealed and deeply buried targets, requiring more effective tools to detect large-scale ore-forming systems and to vector from their most distal margins to their high grade cores. A new generation of ore system models is required to achieve this. The Mineral Exploration Footprints Research Network is a consortium of 70 faculty, research associates, and students from 20 Canadian universities working with 30 mining, mineral exploration, and mining service providers to develop new approaches to ore system modelling based on more effective integration and visualization of multi-parameter geological-structural-mineralogical-lithogeochemical-petrophysical-geophysical exploration data. The Network is developing the next generation ore system models and exploration strategies at three sites based on integrated data visualization using self-consistent 3D Common Earth Models and geostatistical/machine learning technologies. Thus far over 60 footprint components and vectors have been identified at the Canadian Malartic stockwork-disseminated Au deposit, 20–30 at the McArthur-Millennium unconformity U deposits, and over 20 in the Highland Valley porphyry Cu system. For the first time, these are being assembled into comprehensive models that will serve as landmark case studies for data integration and analysis in the today’s challenging exploration environment

Robust imaging of hippocampal inner structure at 7T: in vivo acquisition protocol and methodological choices

International audienceOBJECTIVE:Motion-robust multi-slab imaging of hippocampal inner structure in vivo at 7T.MATERIALS AND METHODS:Motion is a crucial issue for ultra-high resolution imaging, such as can be achieved with 7T MRI. An acquisition protocol was designed for imaging hippocampal inner structure at 7T. It relies on a compromise between anatomical details visibility and robustness to motion. In order to reduce acquisition time and motion artifacts, the full slab covering the hippocampus was split into separate slabs with lower acquisition time. A robust registration approach was implemented to combine the acquired slabs within a final 3D-consistent high-resolution slab covering the whole hippocampus. Evaluation was performed on 50 subjects overall, made of three groups of subjects acquired using three acquisition settings; it focused on three issues: visibility of hippocampal inner structure, robustness to motion artifacts and registration procedure performance.RESULTS:Overall, T2-weighted acquisitions with interleaved slabs proved robust. Multi-slab registration yielded high quality datasets in 96 % of the subjects, thus compatible with further analyses of hippocampal inner structure.CONCLUSION:Multi-slab acquisition and registration setting is efficient for reducing acquisition time and consequently motion artifacts for ultra-high resolution imaging of the inner structure of the hippocampus

Cortical localisation of the visual and auditory word form areas: a reconsideration of the evidence.

In this paper we examine the evidence for human brain areas dedicated to visual or auditory word form processing by comparing cortical activation for auditory word repetition, reading, picture naming, and environmental sound naming. Both reading and auditory word repetition activated left lateralised regions in the frontal operculum (Broc