Automated Image Analysis of Offshore Infrastructure Marine Biofouling

Supplementary Materials: The following are available online at www.mdpi.com/2077-1312/6/1/2/s1 Acknowledgments: This project was funded by the Natural Environmental Research Council (NERC) project No.: NE/N019865/1. The authors would like to thank Melanie Netherway and Don Orr, from our project partner (company requested to remain anonymous) for the provision of survey footage and for supporting the project. In addition, many thanks to Oscar Beijbom, University California Berkley for providing guidance and support to the project. Additional thanks to Calum Reay, Bibby Offshore; George Gair, Subsea 7; and Alan Buchan, Wood Group Kenny for help with footage collection and for allowing us to host workshops with them and their teams, their feedback and insights were very much appreciated.Peer reviewedPublisher PD

Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

Determining both the expression levels of mRNA and the regulation of its translation is important in understanding specialized cell functions. In this study, we describe both the expression profiles of cells within spatiotemporal domains of the Arabidopsis thaliana flower and the post-transcriptional regulation of these mRNAs, at nucleotide resolution. We express a tagged ribosomal protein under the promoters of three master regulators of flower development. By precipitating tagged polysomes, we isolated cell type specific mRNAs that are probably translating, and quantified those mRNAs through deep sequencing. Cell type comparisons identified known cell-specific transcripts and uncovered many new ones, from which we inferred cell type-specific hormone responses, promoter motifs and coexpressed cognate binding factor candidates, and splicing isoforms. By comparing translating mRNAs with steady-state overall transcripts, we found evidence for widespread post-transcriptional regulation at both the intron splicing and translational stages. Sequence analyses identified structural features associated with each step. Finally, we identified a new class of noncoding RNAs associated with polysomes. Findings from our profiling lead to new hypotheses in the understanding of flower development

Interactions between the neuromodulatory systems and the amygdala: exploratory survey using the Allen Mouse Brain Atlas.

Neuromodulatory systems originate in nuclei localized in the subcortical region of the brain and control fundamental behaviors by interacting with many areas of the central nervous system. An exploratory survey of the cholinergic, dopaminergic, noradrenergic, and serotonergic receptor expression energy in the amygdala, and in the neuromodulatory areas themselves was undertaken using the Allen Mouse Brain Atlas. The amygdala was chosen because of its importance in cognitive behavior and its bidirectional interaction with the neuromodulatory systems. The gene expression data of 38 neuromodulatory receptor subtypes were examined across 13 brain regions. The substantia innominata of the basal forebrain and regions of the amygdala had the highest amount of receptor expression energy for all four neuromodulatory systems examined. The ventral tegmental area also displayed high receptor expression of all four neuromodulators. In contrast, the locus coeruleus displayed low receptor expression energy overall. In general, cholinergic receptor expression was an order of magnitude greater than other neuromodulatory receptors. Since the nuclei of these neuromodulatory systems are thought to be the source of specific neurotransmitters, the projections from these nuclei to target regions may be inferred by receptor expression energy. The comprehensive analysis revealed many connectivity relations and receptor localization that had not been previously reported. The methodology presented here may be applied to other neural systems with similar characteristics, and to other animal models as these brain atlases become available

Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Brazelton, W. J., McLean, C., Putman, L. I., Hyer, A., Kubo, M. D. Y., Hoehler, T., Cardace, D., & Schrenk, M. O. . Carbon assimilation strategies in ultrabasic groundwater: clues from the integrated study of a serpentinization-influenced aquifer. mSystems, 5(2), (2020): e00607-00619, doi: 10.1128/mSystems.00607-19.Serpentinization is a low-temperature metamorphic process by which ultramafic rock chemically reacts with water. Such reactions provide energy and materials that may be harnessed by chemosynthetic microbial communities at hydrothermal springs and in the subsurface. However, the biogeochemistry mediated by microbial populations that inhabit these environments is understudied and complicated by overlapping biotic and abiotic processes. We applied metagenomics, metatranscriptomics, and untargeted metabolomics techniques to environmental samples taken from the Coast Range Ophiolite Microbial Observatory (CROMO), a subsurface observatory consisting of 12 wells drilled into the ultramafic and serpentinite mélange of the Coast Range Ophiolite in California. Using a combination of DNA and RNA sequence data and mass spectrometry data, we found evidence for several carbon fixation and assimilation strategies, including the Calvin-Benson-Bassham cycle, the reverse tricarboxylic acid cycle, the reductive acetyl coenzyme A (acetyl-CoA) pathway, and methylotrophy, in the microbial communities inhabiting the serpentinite-hosted aquifer. Our data also suggest that the microbial inhabitants of CROMO use products of the serpentinization process, including methane and formate, as carbon sources in a hyperalkaline environment where dissolved inorganic carbon is unavailable.We thank McLaughlin Reserve, in particular Paul Aigner and Cathy Koehler, for hosting sampling at CROMO and providing access to the wells, A. Daniel Jones and Anthony Schilmiller for their advice regarding metabolite extraction and mass spectrometry, Elizabeth Kujawinski for her guidance in metabolomics data analysis and interpretation, and Julia McGonigle, Christopher Thornton, and Katrina Twing for assistance with metagenomic and computational analyses

Data work: how energy advisors and clients make IoT data accountable

We present fieldwork findings from the deployment of an interactive sensing system that supports the work of energy advisors who give face-to-face advice to low-income households in the UK. We focus on how the system and the data it produced are articulated in the interactions between professional energy advisors and their clients, and how they collaboratively anticipate, rehearse, and perform data work. In addition to documenting how the system was appropriated in advisory work, we elaborate the ‘overhead cost’ of building collaborative action into connected devices and sensing systems, and the commensurate need to support discrete workflows and accountability systems to enable the methodical incorporation of the IoT into collaborative action. We contribute an elaboration of the social, collaborative methods of data work relevant to those who seek to design and study collaborative IoT systems

Extensive horizontal gene transfer in cheese-associated bacteria.

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities

Situation inference and context recognition for intelligent mobile sensing applications

The usage of smart devices is an integral element in our daily life. With the richness of data streaming from sensors embedded in these smart devices, the applications of ubiquitous computing are limitless for future intelligent systems. Situation inference is a non-trivial issue in the domain of ubiquitous computing research due to the challenges of mobile sensing in unrestricted environments. There are various advantages to having robust and intelligent situation inference from data streamed by mobile sensors. For instance, we would be able to gain a deeper understanding of human behaviours in certain situations via a mobile sensing paradigm. It can then be used to recommend resources or actions for enhanced cognitive augmentation, such as improved productivity and better human decision making. Sensor data can be streamed continuously from heterogeneous sources with different frequencies in a pervasive sensing environment (e.g., smart home). It is difficult and time-consuming to build a model that is capable of recognising multiple activities. These activities can be performed simultaneously with different granularities. We investigate the separability aspect of multiple activities in time-series data and develop OPTWIN as a technique to determine the optimal time window size to be used in a segmentation process. As a result, this novel technique reduces need for sensitivity analysis, which is an inherently time consuming task. To achieve an effective outcome, OPTWIN leverages multi-objective optimisation by minimising the impurity (the number of overlapped windows of human activity labels on one label space over time series data) while maximising class separability. The next issue is to effectively model and recognise multiple activities based on the user's contexts. Hence, an intelligent system should address the problem of multi-activity and context recognition prior to the situation inference process in mobile sensing applications. The performance of simultaneous recognition of human activities and contexts can be easily affected by the choices of modelling approaches to build an intelligent model. We investigate the associations of these activities and contexts at multiple levels of mobile sensing perspectives to reveal the dependency property in multi-context recognition problem. We design a Mobile Context Recognition System, which incorporates a Context-based Activity Recognition (CBAR) modelling approach to produce effective outcome from both multi-stage and multi-target inference processes to recognise human activities and their contexts simultaneously. Upon our empirical evaluation on real-world datasets, the CBAR modelling approach has significantly improved the overall accuracy of simultaneous inference on transportation mode and human activity of mobile users. The accuracy of activity and context recognition can also be influenced progressively by how reliable user annotations are. Essentially, reliable user annotation is required for activity and context recognition. These annotations are usually acquired during data capture in the world. We research the needs of reducing user burden effectively during mobile sensor data collection, through experience sampling of these annotations in-the-wild. To this end, we design CoAct-nnotate --- a technique that aims to improve the sampling of human activities and contexts by providing accurate annotation prediction and facilitates interactive user feedback acquisition for ubiquitous sensing. CoAct-nnotate incorporates a novel multi-view multi-instance learning mechanism to perform more accurate annotation prediction. It also includes a progressive learning process (i.e., model retraining based on co-training and active learning) to improve its predictive performance over time. Moving beyond context recognition of mobile users, human activities can be related to essential tasks that the users perform in daily life. Conversely, the boundaries between the types of tasks are inherently difficult to establish, as they can be defined differently from the individuals' perspectives. Consequently, we investigate the implication of contextual signals for user tasks in mobile sensing applications. To define the boundary of tasks and hence recognise them, we incorporate such situation inference process (i.e., task recognition) into the proposed Intelligent Task Recognition (ITR) framework to learn users' Cyber-Physical-Social activities from their mobile sensing data. By recognising the engaged tasks accurately at a given time via mobile sensing, an intelligent system can then offer proactive supports to its user to progress and complete their tasks. Finally, for robust and effective learning of mobile sensing data from heterogeneous sources (e.g., Internet-of-Things in a mobile crowdsensing scenario), we investigate the utility of sensor data in provisioning their storage and design QDaS --- an application agnostic framework for quality-driven data summarisation. This allows an effective data summarisation by performing density-based clustering on multivariate time series data from a selected source (i.e., data provider). Thus, the source selection process is determined by the measure of data quality. Nevertheless, this framework allows intelligent systems to retain comparable predictive results by its effective learning on the compact representations of mobile sensing data, while having a higher space saving ratio. This thesis contains novel contributions in terms of the techniques that can be employed for mobile situation inference and context recognition, especially in the domain of ubiquitous computing and intelligent assistive technologies. This research implements and extends the capabilities of machine learning techniques to solve real-world problems on multi-context recognition, mobile data summarisation and situation inference from mobile sensing. We firmly believe that the contributions in this research will help the future study to move forward in building more intelligent systems and applications