Formalising extended finite state machine transition merging

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordModel inference from system traces, e.g. for analysing legacy components or generating security tests for distributed components, is a common problem. Extended Finite State Machine (EFSM) models, managing an internal data state as a set of registers, are particularly well suited for capturing the behaviour of stateful components however existing inference techniques for (E)FSMs lack the ability to infer the internal state and its update functions. In this paper, we present the underpinning formalism for an EFSM inference technique that involves the merging of transitions with updates to the internal data state. Our model is formalised in Isabelle/HOL, allowing for the machine-checked validation of transition merges and system properties

A Formal Model of Extended Finite State Machines

This is the final version. Available from AFP via the link in this recordIn this AFP entry, we provide a formalisation of extended finite state machines (EFSMs) where models are represented as finite sets of transitions between states. EFSMs execute traces to produce observable outputs. We also define various simulation and equality metrics for EFSMs in terms of traces and prove their strengths in relation to each other. Another key contribution is a framework of function definitions such that LTL properties can be phrased over EFSMs. Finally, we provide a simple example case study in the form of a drinks machine

Inference of Extended Finite State Machines

This is the final version. Available from AFP via the link in this recordIn this AFP entry, we provide a formal implementation of a state-merging technique to infer extended finite state machines (EFSMs), complete with output and update functions, from black-box traces. In particular, we define the subsumption in context relation as a means of determining whether one transition is able to account for the behaviour of another. Building on this, we define the direct subsumption relation, which lifts the subsumption in context relation to EFSM level such that we can use it to determine whether it is safe to merge a given pair of transitions. Key proofs include the conditions necessary for subsumption to occur and that subsumption and direct subsumption are preorder relations. We also provide a number of different heuristics which can be used to abstract away concrete values into registers so that more states and transitions can be merged and provide proofs of the various conditions which must hold for these abstractions to subsume their ungeneralised counterparts. A Code Generator setup to create executable Scala code is also defined

Incorporating Data into EFSM Inference

This is the author accepted manuscript. The final version is available from Springer Verlag via the DOI in this record17th International Conference, SEFM 2019 Oslo, Norway, September 18–20, 2019Models are an important way of understanding software systems. If they do not already exist, then we need to infer them from system behaviour. Most current approaches infer classical FSM models that do not consider data, thus limiting applicability. EFSMs provide a way to concisely model systems with an internal state but existing inference techniques either do not infer models which allow outputs to be computed from inputs, or rely heavily on comprehensive white-box traces that reveal the internal program state, which are often unavailable. In this paper, we present an approach for inferring EFSM models, including functions that modify the internal state. Our technique uses black-box traces which only contain information visible to an external observer of the system. We implemented our approach as a prototype

Developmental pathways towards mood disorders in adult life: Is there a role for sleep disturbances?

Introduction: Mood disorders are among the most prevalent and serious mental disorders and rank high among to the leading global burdens of disease. The developmental psychopathology framework can offer a life course perspective on them thus providing a basis for early prevention and intervention. Sleep disturbances, are considered risk factors for mood disorders across childhood, adolescence and adulthood. Assuming that sleep disturbances may play a pivotal role in the pathogenesis of mood disorders from a life course point of view, we reviewed the data on developmental pathways towards mood disorders in adult life in relation to sleep disturbances. Method: From February 2017, a systematic search was conducted in PubMed, PsycINFO and Embase electronic databases for literature on developmental pathways to mood disorders in adult life in relation to sleep disturbances and to 1) pre-natal stress, 2) early brain developmental processes, and 3) temperaments, character and attachment style. Results: Eleven, 54 and 15 articles were respectively selected. Conclusions: Experimental and clinical studies revealed that exposure to prenatal/early life stress results in sleep disturbances such as poor sleep and altered circadian regulation phases and may predict or even precipitate mood disorders in adulthood. Chronic sleep disruption may interfere with neuronal plasticity, connectivity and the developing brain thus contributing to the development of mood disorders. In addition sleep and circadian dysregulations have been shown to be related to those temperaments, character and attachment styles which are considered precursors of mood disorders. Sleep and circadian behaviours may serve as early targets regarding mood disorders

The process of establishing implementing and maintaining a social support infant feeding programme

Objective To describe the process of establishing and implementing a social support infant feeding intervention. Design This paper outlines the initial stages of a randomised controlled trial which assessed the effectiveness of a social support intervention on a range of infant feeding outcomes. Details are presented of the processes involved in recruiting, training and supporting a group of volunteers who provided support to the study sample. Setting Camden and Islington, London, UK. Results Initial networking with local agencies and organisations provided invaluable information and contacts. Employing a dedicated volunteer co-ordinator is vitally important in the recruitment, training and support of volunteers. Providing child care and travel expenses is an essential incentive for volunteers with young children. Advertisements placed in local newspapers were the most successful means of recruiting volunteers. Appropriate training is needed to equip volunteers with the necessary knowledge and skills to provide effective support. Particular emphasis in the training focused upon developing the necessary interpersonal skills and self-confidence. The evaluation of the training programme demonstrated that it improved volunteers’ knowledge and reported confidence. The provision of ongoing support is also essential to maintain volunteers’ interest and enthusiasm. The retention of volunteers is, however, a key challenge. Conclusions The processes outlined in this paper have demonstrated the feasibility of successfully establishing, implementing and maintaining a community-based social support infant feeding programme. The experiences described provide useful insights into the practical issues that need to be addressed in setting up a social support intervention

Boring bivalve traces in modern reef and deeper-water macroid and rhodolith beds

Macroids and rhodoliths, made by encrusting acervulinid foraminifera and coralline algae, are widely recognized as bioengineers providing relatively stable microhabitats and increasing biodiversity for other species. Macroid and rhodolith beds occur in different depositional settings at various localities and bathymetries worldwide. Six case studies of macroid/rhodolith beds from 0 to 117m water depth in the Pacific Ocean (northern Central Ryukyu Islands, French Polynesia), eastern Australia (Fraser Island, One Tree Reef, Lizard Island), and the Mediterranean Sea (southeastern Spain) show that nodules in the beds are perforated by small-sized boring bivalve traces (Gastrochanolites). On average, boring bivalve shells (gastrochaenids and mytilids) are more slender and smaller than those living inside shallow-water rocky substrates. In the Pacific, Gastrochaena cuneiformis, Gastrochaena sp., Leiosolenus malaccanus, L. mucronatus, L. spp., and Lithophaga/Leiosolenus sp., for the first time identified below 20m water depth, occur as juvenile forms along with rare small-sized adults. In deep-water macroids and rhodoliths the boring bivalves are larger than the shallower counterparts in which growth of juveniles is probably restrained by higher overturn rates of host nodules. In general, most boring bivalves are juveniles that grew faster than the acervulinid foraminiferal and coralline red algal hosts and rarely reached the adult stage. As a consequence of phenotypic plasticity, small-sized adults with slow growth rates coexist with juveniles. Below wave base macroids and rhodoliths had the highest amounts of bioerosion, mainly produced by sponges and polychaete worms. These modern observations provide bases for paleobiological inferences in fossil occurrences.Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) 25247083Erasmus+FAR2012-2017FIR2016FIR2018PRIN "Biotic resilience to global change: biomineralization of planktonic and benthic calcifiers in the past, present and future" 2017RX9XXXYBioMed Central-Prepay Membership at the University of FerraraJunta de Andalucía RNM 190Committee on ResearchMuseum of PaleontologyDepartment of Integrative Biology, UC BerkeleyUC Pacific Rim Projec

Constraining the nature of two Lyα emitters detected by ALMA at z = 4.7

We report optical VLT FORS2 spectroscopy of the two Ly-alpha emitters (LAEs) companions to the quasi-stellar object (QSO) - sub-millimetre galaxy (SMG) system BRI1202-0725 at z = 4.7, which have recently been detected in the [CII]158um line by the Atacama Large Millimetre/Sub-millimetre Array (ALMA). We detect Ly-alpha emission from both sources and so confirm that these Ly-alpha emitter candidates are physically associated with the BRI1202- 0725 system. We also report the lack of detection of any high ionisation emission lines (N V, Si IV, C IV and He II) and find that these systems are likely not photoionised by the quasar, leaving in situ star formation as the main powering source of these LAEs. We also find that both LAEs have Ly-alpha emission much broader (1300 km/s) than the [CII] emission and broader than most LAEs. In addition, both LAEs have roughly symmetric Ly-alpha profiles implying that both systems are within the HII sphere produced by the quasar. This is the first time that the proximity zone of a quasar is probed by exploiting nearby Ly-alpha emitters. We discuss the observational properties of these galaxies in the context of recent galaxy formation models.This work was co-funded under the Marie Curie Actions of the European Commission (FP7-COFUND).This is the final published version, which originally appeared in MNRAS and is available at http://mnras.oxfordjournals.org/content/439/2/2096

Lack of Evidence for an Association between Iridovirus and Colony Collapse Disorder

Colony collapse disorder (CCD) is characterized by the unexplained losses of large numbers of adult worker bees (Apis mellifera) from apparently healthy colonies. Although infections, toxins, and other stressors have been associated with the onset of CCD, the pathogenesis of this disorder remains obscure. Recently, a proteomics study implicated a double-stranded DNA virus, invertebrate iridescent virus (Family Iridoviridae) along with a microsporidium (Nosema sp.) as the cause of CCD. We tested the validity of this relationship using two independent methods: (i) we surveyed healthy and CCD colonies from the United States and Israel for the presence of members of the Iridovirus genus and (ii) we reanalyzed metagenomics data previously generated from RNA pools of CCD colonies for the presence of Iridovirus-like sequences. Neither analysis revealed any evidence to suggest the presence of an Iridovirus in healthy or CCD colonies

The application of sediment fingerprinting to floodplain and lake sediment cores: assumptions and uncertainties evaluated through case studies in the Nene Basin, UK

Purpose: Fine sediment has been shown to be a major cause of the degradation of lakes and rivers and, as a result, research has been directed towards the understanding of fine sediment dynamics and the minimisation of sediment inputs. The use of tracers within a sediment fingerprinting framework has become a heavily used technique to investigate the sources of fine sediment pressures. When combined with the use of historically deposited sediment, the technique provides the opportunity to reconstruct past changes to the environment. However, alterations to tracer signatures during sediment transport and storage are a major potential source of uncertainty associated with tracer use. At present, few studies have quantified the uncertainties associated with tracer use. Materials and methods: This paper investigated uncertainty by determining the differences between sediment provenance predictions obtained using lithogenic radionuclide, geochemical and mineral magnetic signatures when fingerprinting lake and floodplain sedimentary deposits. It also investigated the potential causes of the observed differences. Results and discussion: A reservoir core was fingerprinted with the least uncertainty, with tracer group predictions ∼28 % apart and a consistent down-core trend in changing sediment provenance produced. When fingerprinting an on-line lake core and four floodplain cores, differences between tracer group predictions were as large as 100 %; the down-core trends in changing sediment provenance were also different. The differences between tracer group predictions could be attributed to the organic matter content and particle size of the sediment. There was also evidence of the in-growth of bacterially derived magnetite and chemical dissolution affecting the preservation of tracer signatures. Simple data corrections for sediment organic matter content and particle size did not result in significantly greater agreement between the predictions of the different tracer groups. Likewise, the inclusions of weightings for tracer discriminatory efficiency and within-source variability had minimal effects on the fingerprinting results. Conclusions: This paper highlights the importance of tracer selection and the consideration of recognising tracer non-conservatism when using lake and floodplain sediment deposits to reconstruct anthropogenic changes to the environment and changing sediment dynamics. It was recommended that future research focus on the assessment of uncertainty using the artificial mixing of sediment source samples, the limitation of the fingerprinting to narrow particle size fractions and the development of specific particle size and organic matter correction factors for each tracer