From pup to predator; generalized hidden Markov models reveal rapid development of movement strategies in a naïve long‐lived vertebrate

Rapid development of a successful foraging strategy is critical for juvenile survival, especially for naïve animals that receive no parental guidance. However, this process is poorly understood for many species. Although observation of early‐life movements is increasingly possible with miniaturisation of animal‐borne telemetry devices, analytical limitations remain. Here, we tracked 29 recently‐weaned, grey seal Halichoerus grypus pups from colonies in two geographically distinct regions of the United Kingdom. We analysed at‐sea movements of pups throughout their initial months of nutritional independence to investigate the ontogeny of behaviour‐specific (foraging and travelling) movement patterns. Using generalized hidden Markov models (HMMs), we extended the conventional HMM framework to account for temporal changes in putative foraging and travelling movement characteristics, and investigate the effects of intrinsic (sex) and extrinsic (environment) factors on this process. Putative foraging behaviour became more tortuous with time, and travelling became faster and more directed, suggesting a reduction in search scale and an increase in travel efficiency as pups shifted from exploration to an adult‐like repeatable foraging strategy. Sex differences in movement characteristics were evident from colony departure, but sex‐specific activity budgets were only detected in one region. We show that sex‐specific behavioural strategies emerge before sexual size dimorphism in grey seals, and suggest that this phenomenon may occur in other long‐lived species. Our results also indicate that environmental variation may affect the emergence of sex‐specific foraging behaviour, highlighting the need to consider interacting intrinsic and extrinsic factors in shaping movement strategies of long‐lived vertebrates. Moreover, comparing the behavioural state estimations to those of a conventional HMM (no variation in state‐specific movement parameters) revealed differences in the amount and location of foraging activity, with implications for spatial conservation management. Overlooking intrinsic and extrinsic variation in movement processes could distort our understanding of foraging ecology, population dynamics, and conservation requirements

Overview of the ShARe/CLEF eHealth evaluation lab 2013

Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations, and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition. This ShARe/CLEFeHealth2013 lab offered student mentoring and shared tasks: identification and normalisation of disorders (1a and 1b) and normalisation of abbreviations and acronyms (2) in clinical reports with respect to terminology standards in healthcare as well as information retrieval (3) to address questions patients may have when reading clinical reports. The focus on patients' information needs as opposed to the specialised information needs of physicians and other healthcare workers was the main feature of the lab distinguishing it from previous shared tasks. De-identied clinical reports for the three tasks were from US intensive care and originated from the MIMIC II database. Other text documents for Task 3 were from the Internet and originated from the Khresmoi project. Task 1 annotations originated from the ShARe annotations. For Tasks 2 and 3, new annotations, queries, and relevance assessments were created. 64, 56, and 55 people registered their interest in Tasks 1, 2, and 3, respectively. 34 unique teams (3 members per team on average) participated with 22, 17, 5, and 9 teams in Tasks 1a, 1b, 2 and 3, respectively. The teams were from Australia, China, France, India, Ireland, Republic of Korea, Spain, UK, and USA. Some teams developed and used additional annotations, but this strategy contributed to the system performance only in Task 2. The best systems had the F1 score of 0.75 in Task 1a; Accuracies of 0.59 and 0.72 in Tasks 1b and 2; and Precision at 10 of 0.52 in Task 3. The results demonstrate the substantial community interest and capabilities of these systems in making clinical reports easier to understand for patients. The organisers have made data and tools available for future research and development

Establishing a marine monitoring programme to assess antibiotic resistance: a case study from the Gulf Cooperation Council (GCC) region

The World Health Organization considers antimicrobial resistance as one of the most pressing global issues which poses a fundamental threat to human health, development, and security. Due to demographic and environmental factors, the marine environment of the Gulf Cooperation Council (GCC) region may be particularly susceptible to the threat of antimicrobial resistance. However, there is currently little information on the presence of AMR in the GCC marine environment to inform the design of appropriate targeted surveillance activities. The objective of this study was to develop, implement and conduct a rapid regional baseline monitoring survey of the presence of AMR in the GCC marine environment, through the analysis of seawater collected from high-risk areas across four GCC states: (Bahrain, Oman, Kuwait, and the United Arab Emirates). 560 Escherichia coli strains were analysed as part of this monitoring programme between December 2018 and May 2019. Multi-drug resistance (resistance to three or more structural classes of antimicrobials) was observed in 32.5% of tested isolates. High levels of reduced susceptibility to ampicillin (29.6%), nalidixic acid (27.9%), tetracycline (27.5%), sulfamethoxazole (22.5%) and trimethoprim (22.5%) were observed. Reduced susceptibility to the high priority critically important antimicrobials: azithromycin (9.3%), ceftazidime (12.7%), cefotaxime (12.7%), ciprofloxacin (44.6%), gentamicin (2.7%) and tigecycline (0.5%), was also noted. A subset of 173 isolates was whole genome sequenced, and high carriage rates of qnrS1 (60/173) and bla CTX-M-15 (45/173) were observed, correlating with reduced susceptibility to the fluoroquinolones and third generation cephalosporins, respectively. This study is important because of the resistance patterns observed, the demonstrated utility in applying genomic-based approaches to routine microbiological monitoring, and the overall establishment of a transnational AMR surveillance framework focussed on coastal and marine environments

Principles to enable comprehensive national marine ecosystem status assessments from disparate data: The state of the marine environment in Kuwait

This paper presents an approach for preparing a comprehensive national marine ecosystem assessment and its application to the marine and coastal areas of the State of Kuwait. The approach is based on a set of principles to enable diverse data sources, of differing data quality and salience, to be combined into a single coordinated national assessment of marine ecosystem status to support the implementation of ecosystem-based management. The approach enables state assessments for multiple components of the marine ecosystem to be undertaken in a coordinated manner, using differing methods varying from quantitative to qualitative assessments depending on data and indicator availability. The marine ecosystem assessment is structured according to 6 major themes: i) Biodiversity, ii) Commercial Fisheries, iii) Food and Water Quality for Human Health, iv) Environmental Pollution, v) Eutrophication and Harmful Algal Blooms, and vi) Coastal Process and Oceanography. Comprehensive ecosystem assessments are an essential part of implementing the ecosystem approach, however detailed data directly related to clear, specified numerical management targets covering all aspects of a marine ecosystem are rarely available. The development of a State of the Marine Environment Report (SOMER) for Kuwait demonstrate that a coordinated comprehensive ecosystem assessment can be conducted using disparate data, and in relation to partially specified regulatory management objectives. The Kuwait SOMER highlighted the issues of coastal pollution, particularly sewage for human health and the environment. It shows that the rapid urbanization of Kuwait has led to significant changes in the ecology, with clear impacts on coral reef health, the availability of nesting locations for turtles and habitats for migratory birds. Long-term changes in nutrient input, via waste water and modified freshwater inputs is resulting in demonstrable impacts on a range of marine species and habitats within Kuwait marine waters. It also supports the move towards a regional approach required due to transboundary properties of many of the ecosystem components, drivers and pressures

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter

Measurement of the inclusive isolated prompt photon cross-section in pp collisions at sqrt(s)= 7 TeV using 35 pb-1 of ATLAS data

A measurement of the differential cross-section for the inclusive production of isolated prompt photons in pp collisions at a center-of-mass energy sqrt(s) = 7 TeV is presented. The measurement covers the pseudorapidity ranges |eta|<1.37 and 1.52<=|eta|<2.37 in the transverse energy range 45<=E_T<400GeV. The results are based on an integrated luminosity of 35 pb-1, collected with the ATLAS detector at the LHC. The yields of the signal photons are measured using a data-driven technique, based on the observed distribution of the hadronic energy in a narrow cone around the photon candidate and the photon selection criteria. The results are compared with next-to-leading order perturbative QCD calculations and found to be in good agreement over four orders of magnitude in cross-section.Comment: 7 pages plus author list (18 pages total), 2 figures, 4 tables, final version published in Physics Letters

Reducing heterotic M-theory to five dimensional supergravity on a manifold with boundary

This paper constructs the reduction of heterotic $M$-theory in eleven dimensions to a supergravity model on a manifold with boundary in five dimensions using a Calabi-Yau three-fold. New results are presented for the boundary terms in the action and for the boundary conditions on the bulk fields. Some general features of dualisation on a manifold with boundary are used to explain the origin of some topological terms in the action. The effect of gaugino condensation on the fermion boundary conditions leads to a `twist' in the chirality of the gravitino which can provide an uplifting mechanism in the vacuum energy to cancel the cosmological constant after moduli stabilisation.Comment: 16 pages, RevTe