TumorML: Concept and requirements of an in silico cancer modelling markup language

This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification

An Empirical Approach to Temporal Reference Resolution

This paper presents the results of an empirical investigation of temporal reference resolution in scheduling dialogs. The algorithm adopted is primarily a linear-recency based approach that does not include a model of global focus. A fully automatic system has been developed and evaluated on unseen test data with good results. This paper presents the results of an intercoder reliability study, a model of temporal reference resolution that supports linear recency and has very good coverage, the results of the system evaluated on unseen test data, and a detailed analysis of the dialogs assessing the viability of the approach.Comment: 13 pages, latex using aclap.st

Object-Oriented Paradigms for Modelling Vascular\ud Tumour Growth: a Case Study

Motivated by a family of related hybrid multiscale models, we have built an object-oriented framework for developing and implementing multiscale models of vascular tumour growth. The models are implemented in our framework as a case study to highlight how object-oriented programming techniques and good object-oriented design may be used effectively to develop hybrid multiscale models of vascular tumour growth. The intention is that this paper will serve as a useful reference for researchers modelling complex biological systems and that these researchers will employ some of the techniques presented herein in their own projects

Control of contagious bovine pleuropneumonia: knowledge, attitudes, perceptions and practices in Narok district of Kenya

CBPP is an important transboundary disease in sub-Saharan Africa whose control is urgent. Participatory data collection involving 52 focus group discussions in 37 village clusters and key informant interviews, a cross-sectional study involving 232 households and a post-vaccination follow up involving 203 households was carried out in 2006–2007 in Narok South district of Kenya. This was to investigate knowledge, attitudes, perceptions and practices (KAPP) associated with control of CBPP as well as the adverse post-vaccination reactions in animals in order to advice the control policy. The community perceived trans-boundary CBPP threat to their cattle. They had traditional disease coping mechanisms and were conversant with CBPP prevention and control with 49.8% (95%CI: 42.8–56.7%) giving priority to CBPP control. However, 12.9% (95%CI: 9.0–18.1%) of pastoralists had no knowledge of any prevention method and 10.0% (95%CI: 6.5–14.7%) would not know what to do or would do nothing in the event of an outbreak. Although 43.5% (95%CI: 37.1–50.2%) of pastoralists were treating CBPP cases with antimicrobials, 62.5% (95%CI: 52.1–71.7%) of them doubted the effectiveness of the treatments. Pastoralists perceived vaccination to be the solution to CBPP but vaccination was irregular due to unavailability of the vaccine. Vaccination was mainly to control outbreaks rather than preventive and exhibited adverse post-vaccination reactions among 70.4% (95%CI: 63.6–76.5%) of herds and 3.8% (95%CI: 3.5–4.2%) of animals. Consequently, nearly 25.2% (95%CI: 18.5–33.2%) of pastoralists may resist subsequent vaccinations against CBPP. Pastoralists preferred CBPP vaccination at certain times of the year and that it is combined with other vaccinations. In conclusion, pastoralists were not fully aware of the preventive measures and interventions and post-vaccination reactions may discourage subsequent CBPP vaccinations. Consequently there is need for monitoring and management of post vaccination reactions and awareness creation on CBPP prevention and interventions and their merits and demerits. CBPP vaccine was largely unavailable to the pastoralists and the preference of the pastoralists was for vaccination at specified times and vaccine combinations which makes it necessary to avail the vaccine in conformity with the pastoralists preferences. In addition, planning vaccinations should involve pastoralists and neighbouring countries. As the results cannot be generalized, further studies on CBPP control methods and their effectiveness are recommended

Nurse titrated analgesia and sedation in intensive care increases the frequency of comfort assessment and reduces midazolam use in paediatric patients following cardiac surgery

BACKGROUND Pain and sedation protocols are suggested to improve the outcomes of patients within paediatric intensive care. However, it is not clear how protocols will influence practice within individual units. OBJECTIVES Evaluate a nurse led pain and sedation protocols impact on pain scoring and analgesic and sedative administration for post-operative cardiac patients within a paediatric intensive care unit. METHODS A retrospective chart review was performed on 100 patients admitted to a tertiary paediatric intensive care unit pre and post introduction of an analgesic and sedative protocol. Stata12 was used to perform Chi-squared or Student's t-test to compare data between the groups. RESULTS Post protocol introduction documentation of pain assessments increased (pre protocol 3/24h vs post protocol 5/24h, p=0.006). Along with a reduction in administration of midazolam (57.6mcg/kg/min pre protocol vs 24.5mcg/kg/min post protocol, p=0.0001). Children's pain scores remained unchanged despite this change, with a trend towards more scores in the optimal range in the post protocol group (5 pre protocol vs 12 post protocol, p=0.06). CONCLUSIONS Introducing a pain and sedation protocol changed bedside nurse practice in pain and sedation management. The protocol has enabled nurses to provide pain and sedation management in a consistent and timely manner and reduced the dose of midazolam required to maintain comfort according to the patients COMFORT B scores. Individual evaluation of practice change is recommended to units who implement nurse led analgesic and sedative protocols to monitor changes in practice

Collective Oscillations of an Imbalanced Fermi Gas: Axial Compression Modes and Polaron Effective Mass

We investigate the low-lying compression modes of a unitary Fermi gas with imbalanced spin populations. For low polarization, the strong coupling between the two spin components leads to a hydrodynamic behavior of the cloud. For large population imbalance we observe a decoupling of the oscillations of the two spin components, giving access to the effective mass of the Fermi polaron, a quasi-particle composed of an impurity dressed by particle-hole pair excitations in a surrounding Fermi sea. We find $m^*/m=1.17(10)$, in agreement with the most recent theoretical predictions.Comment: 4 pages, 4 figures, submitted to PR

Fast and Automated Peak Bagging with DIAMONDS (FAMED)

Stars of low and intermediate mass that exhibit oscillations may show tens of detectable oscillation modes each. Oscillation modes are a powerful to constrain the internal structure and rotational dynamics of the star, hence tool allowing one to obtain an accurate stellar age. The tens of thousands of solar-like oscillators that have been discovered thus far are representative of the large diversity of fundamental stellar properties and evolutionary stages available. Because of the wide range of oscillation features that can be recognized in such stars, it is particularly challenging to properly characterize the oscillation modes in detail, especially in light of large stellar samples. Overcoming this issue requires an automated approach, which has to be fast, reliable, and flexible at the same time. In addition, this approach should not only be capable of extracting the oscillation mode properties of frequency, linewidth, and amplitude from stars in different evolutionary stages, but also able to assign a correct mode identification for each of the modes extracted. Here we present the new freely available pipeline FAMED (Fast and AutoMated pEak bagging with DIAMONDS), which is capable of performing an automated and detailed asteroseismic analysis in stars ranging from the main sequence up to the core-Helium-burning phase of stellar evolution. This, therefore, includes subgiant stars, stars evolving along the red giant branch (RGB), and stars likely evolving toward the early asymptotic giant branch. In this paper, we additionally show how FAMED can detect rotation from dipolar oscillation modes in main sequence, subgiant, low-luminosity RGB, and core-Helium-burning stars. FAMED can be downloaded from its public GitHub repository (https://github.com/EnricoCorsaro/FAMED).Comment: 46 pages, 19 figures, 4 tables. Accepted for publication in A&

Collective effects in the dynamics of driven atoms in a high-Q resonator

We study the quantum dynamics of N coherently driven two-level atoms coupled to an optical resonator. In the strong coupling regime the cavity field generated by atomic scattering interferes destructively with the pump on the atoms. This suppresses atomic excitation and even for strong driving fields prevents atomic saturation, while the stationary intracavity field amplitude is almost independent of the atom number. The magnitude of the interference effect depends on the detuning between laser and cavity field and on the relative atomic positions and is strongest for a wavelength spaced lattice of atoms placed at the antinodes of the cavity mode. In this case three dimensional intensity minima are created in the vicinity of each atom. In this regime spontaneous emission is suppressed and the dominant loss channel is cavity decay. Even for a cavity linewidth larger than the atomic natural width, one regains strong interference through the cooperative action of a sufficiently large number of atoms. These results give a new key to understand recent experiments on collective cavity cooling and may allow to implement fast tailored atom-atom interactions as well as nonperturbative particle detection with very small energy transfer.Comment: 12 pages, 13 figures, significantly extended version, slightly different from the published on

Do not disturb! The impact of wearing red aprons on medication administration in PICU

Introduction and Aims: Medication errors cause significant morbidity and mortality to patients. The reported financial cost to the NHS annually is £1 billion, but could be up to £2.5 billion. Medication errors are one of the most frequently reported incidents on paediatric intensive care (PIC). Evidence of effective interventions that prevent medication errors is currently limited. However, implementing red apron use for medication administration aims to permit uninterrupted, dedicated time for nurses whilst preparing medications. The effectiveness that this intervention has on minimising medication administration errors in PIC is unknown. This project aimed to evaluate PIC medication administration errors after implementation of safe medication policy that included wearing red aprons. Methods: A retrospective review of PIC medication administration incidents reported during a six-month period before (November 2015-April 2016) and after (November 2016-April 2017) the introduction of the red apron intervention and the promotion of safe medication management. Type and frequency of incidents occurring pre and post intervention were compared. Results: Fifteen medication errors were reported before the intervention. This increased to 20 following. Interestingly, three types of errors that were reported before the intervention did not occur after, but five new error types were only reported after the intervention (figure 1). Four error types were reported at similar frequencies before and after the intervention. Discussion and conclusion: This study has provided valuable insight into medication administration error reporting. It appears that this intervention may not reduce errors in the short term, but may have an effect on culture and behaviour of medication error reporting. This includes raising awareness of medication errors amongst staff, and highlighting the importance of and support for safe administration of medications and reporting of errors. Further research will examine benefits of and barriers to implementing interventions aimed at improving medication safety for children in PIC