Simulation of an Optional Strategy in the Prisoner's Dilemma in Spatial and Non-spatial Environments

This paper presents research comparing the effects of different environments on the outcome of an extended Prisoner's Dilemma, in which agents have the option to abstain from playing the game. We consider three different pure strategies: cooperation, defection and abstinence. We adopt an evolutionary game theoretic approach and consider two different environments: the first which imposes no spatial constraints and the second in which agents are placed on a lattice grid. We analyse the performance of the three strategies as we vary the loner's payoff in both structured and unstructured environments. Furthermore we also present the results of simulations which identify scenarios in which cooperative clusters of agents emerge and persist in both environments.Comment: 12 pages, 8 figures. International Conference on the Simulation of Adaptive Behavio

The body in the library: adventures in realism

This essay looks at two aspects of the virtual ‘material world’ of realist fiction: objects encountered by the protagonist and the latter’s body. Taking from Sartre two angles on the realist pact by which readers agree to lend their bodies, feelings, and experiences to the otherwise ‘languishing signs’ of the text, it goes on to examine two sets of first-person fictions published between 1902 and 1956 — first, four modernist texts in which banal objects defy and then gratify the protagonist, who ends up ready and almost able to write; and, second, three novels in which the body of the protagonist is indeterminate in its sex, gender, or sexuality. In each of these cases, how do we as readers make texts work for us as ‘an adventure of the body’

Spatial regularity of InAs-GaAs quantum dots: quantifying the dependence of lateral ordering on growth rate.

The lateral ordering of arrays of self-assembled InAs-GaAs quantum dots (QDs) has been quantified as a function of growth rate, using the Hopkins-Skellam index (HSI). Coherent QD arrays have a spatial distribution which is neither random nor ordered, but intermediate. The lateral ordering improves as the growth rate is increased and can be explained by more spatially regular nucleation as the QD density increases. By contrast, large and irregular 3D islands are distributed randomly on the surface. This is consistent with a random selection of the mature QDs relaxing by dislocation nucleation at a later stage in the growth, independently of each QD's surroundings. In addition we explore the statistical variability of the HSI as a function of the number N of spatial points analysed, and we recommend N > 10(3) to reliably distinguish random from ordered arrays

Benzyne in V4334 Sqr: A Quest for the Ring with SOFIA/EXES

Large aromatic molecules are ubiquitous in both circumstellar and interstellar environments. Detection of small aromatic molecules, such as benzene (C6H6) and benzyne (C6H4), are rare in astrophysical environments. Detection of such species will have major implications for our understanding of the astrochemistry involved in the formation of the molecules necessary for life, including modeling the chemical pathways to the formation of larger hydrocarbon molecules. We conducted a search for the infrared 18 μm spectral signature of benzyne in V4334 Sgr with the Stratospheric Observatory for Infrared Astronomy (SOFIA)/Echelon-Cross-Echelle Spectrograph (EXES) finding no evidence for a feature at the sensitivity of our observations

A model for transition of 5 '-nuclease domain of DNA polymerase I from inert to active modes

Bacteria contain DNA polymerase I (PolI), a single polypeptide chain consisting of similar to 930 residues, possessing DNA-dependent DNA polymerase, 3'-5' proofreading and 5'-3' exonuclease (also known as flap endonuclease) activities. PolI is particularly important in the processing of Okazaki fragments generated during lagging strand replication and must ultimately produce a double-stranded substrate with a nick suitable for DNA ligase to seal. PolI's activities must be highly coordinated both temporally and spatially otherwise uncontrolled 5'-nuclease activity could attack a nick and produce extended gaps leading to potentially lethal double-strand breaks. To investigate the mechanism of how PolI efficiently produces these nicks, we present theoretical studies on the dynamics of two possible scenarios or models. In one the flap DNA substrate can transit from the polymerase active site to the 5'-nuclease active site, with the relative position of the two active sites being kept fixed; while the other is that the 5'-nuclease domain can transit from the inactive mode, with the 5'-nuclease active site distant from the cleavage site on the DNA substrate, to the active mode, where the active site and substrate cleavage site are juxtaposed. The theoretical results based on the former scenario are inconsistent with the available experimental data that indicated that the majority of 5'-nucleolytic processing events are carried out by the same PolI molecule that has just extended the upstream primer terminus. By contrast, the theoretical results on the latter model, which is constructed based on available structural studies, are consistent with the experimental data. We thus conclude that the latter model rather than the former one is reasonable to describe the cooperation of the PolI's polymerase and 5'-3' exonuclease activities. Moreover, predicted results for the latter model are presented

The influence of HLA genotype on the development of metal hypersensitivity following joint replacement

\ua9 2022, The Author(s). Background: Over five million joint replacements are performed across the world each year. Cobalt chrome (CoCr) components are used in most of these procedures. Some patients develop delayed-type hypersensitivity (DTH) responses to CoCr implants, resulting in tissue damage and revision surgery. DTH is unpredictable and genetic links have yet to be definitively established. Methods: At a single site, we carried out an initial investigation to identify HLA alleles associated with development of DTH following metal-on-metal hip arthroplasty. We then recruited patients from other centres to train and validate an algorithm incorporating patient age, gender, HLA genotype, and blood metal concentrations to predict the development of DTH. Accuracy of the modelling was assessed using performance metrics including time-dependent receiver operator curves. Results: Using next-generation sequencing, here we determine the HLA genotypes of 606 patients. 176 of these patients had experienced failure of their prostheses; the remaining 430 remain asymptomatic at a mean follow up of twelve years. We demonstrate that the development of DTH is associated with patient age, gender, the magnitude of metal exposure, and the presence of certain HLA class II alleles. We show that the predictive algorithm developed from this investigation performs to an accuracy suitable for clinical use, with weighted mean survival probability errors of 1.8% and 3.1% for pre-operative and post-operative models respectively. Conclusions: The development of DTH following joint replacement appears to be determined by the interaction between implant wear and a patient’s genotype. The algorithm described in this paper may improve implant selection and help direct patient surveillance following surgery. Further consideration should be given towards understanding patient-specific responses to different biomaterials

Cross-resistance between myclobutanil and tebuconazole and the genetic basis of tebuconazole resistance in Venturia inaequalis

BACKGROUND: Myclobutanil is one of the most widely used demethylation inhibitor (DMI) fungicides for the management of apple scab, caused by Venturia inaequalis. Strains of V. inaequalis resistant to myclobutanil have been reported across the world. Tebuconazole, another DMI fungicide, has been proposed as an alternative to myclobutanil, and the extent of cross-resistance with myclobutanil therefore needs to be evaluated. The sensitivity to tebuconazole and myclobutanil of a total of 40 isolates was determined. Half the isolates came from an isolated orchard which had never been sprayed with fungicides and half from orchards sprayed regularly with myclobutanil, but still with disease control problems. The progeny of a tebuconazole resistant (R) × sensitive (S) V. inaequalis cross were analysed in order to improve understanding of the genetic control of tebuconazole sensitivity. RESULTS: There is cross-resistance between myclobutanil and tebuconazole (r=0.91; P < 0.001). Sensitivity to tebuconazole of the progeny of a R×S cross varied quantitatively in a pattern which implied at least two gene loci differing between the parental strains. In addition, the asymmetric distribution of the sensitivity in the progeny implied possible epistatic effects. CONCLUSION: Resistance to myclobutanil and tebuconazole is strongly correlated. At least two genes are involved in the control of tebuconazole resistance in V. inaequalis

Viability testing of material derived from Mycobacterium tuberculosis prior to removal from a Containment Level-III Laboratory as part of a Laboratory Risk Assessment Program

BACKGROUND: In the field of clinical mycobacteriology, Mycobacterium tuberculosis (MTB) can be a difficult organism to manipulate due to the restrictive environment of a containment level 3 (CL3) laboratory. Tests for rapid diagnostic work involving smears and molecular methods do not require CL3 practices after the organism has been rendered non-viable. While it has been assumed that after organism deactivation these techniques can be performed outside of a CL3, no conclusive study has consistently confirmed that the organisms are noninfectious after the theoretical 'deactivation' steps. Previous studies have shown that initial steps (such as heating /chemical fixation) may not consistently kill MTB organisms. METHODS: An inclusive viability study (n = 226) was undertaken to determine at which point handling of culture extraction materials does not necessitate a CL3 environment. Four different laboratory protocols tested for viability included: standard DNA extractions for IS6110 fingerprinting, crude DNA preparations for PCR by boiling and mechanical lysis, protein extractions, and smear preparations. For each protocol, laboratory staff planted a proportion of the resulting material to Bactec 12B medium that was observed for growth for 8 weeks. RESULTS: Of the 208 isolates initially tested, 21 samples grew within the 8-week period. Sixteen (7.7%) of these yielded positive results for MTB that included samples of: deactivated culture resuspensions exposed to 80°C for 20 minutes, smear preparations and protein extractions. Test procedures were consequently modified and tested again (n = 18), resulting in 0% viability. CONCLUSIONS: This study demonstrates that it cannot be assumed that conventional practices (i.e. smear preparation) or extraction techniques render the organism non-viable. All methodologies, new and existing, should be examined by individual laboratories to validate the safe removal of material derived from MTB to the outside of a CL3 laboratory. This process is vital to establish in house biosafety-validated practices with the aim of protecting laboratory workers conducting these procedures

Team Objective Structured Bedside Assessment (TOSBA) as formative assessment in undergraduate Obstetrics and Gynaecology: a cohort study.

BACKGROUND: Team Objective Structured Bedside Assessment (TOSBA) is a learning approach in which a team of medical students undertake a set of structured clinical tasks with real patients in order to reach a diagnosis and formulate a management plan and receive immediate feedback on their performance from a facilitator. TOSBA was introduced as formative assessment to an 8-week undergraduate teaching programme in Obstetrics and Gynaecology (O\u26G) in 2013/14. Each student completed 5 TOSBA sessions during the rotation. The aim of the study was to evaluate TOSBA as a teaching method to provide formative assessment for medical students during their clinical rotation. The research questions were: Does TOSBA improve clinical, communication and/or reasoning skills? Does TOSBA provide quality feedback? METHODS: A prospective cohort study was conducted over a full academic year (2013/14). The study used 2 methods to evaluate TOSBA as a teaching method to provide formative assessment: (1) an online survey of TOSBA at the end of the rotation and (2) a comparison of the student performance in TOSBA with their performance in the final summative examination. RESULTS: During the 2013/14 academic year, 157 students completed the O\u26G programme and the final summative examination . Each student completed the required 5 TOSBA tasks. The response rate to the student survey was 68 % (n = 107/157). Students reported that TOSBA was a beneficial learning experience with a positive impact on clinical, communication and reasoning skills. Students rated the quality of feedback provided by TOSBA as high. Students identified the observation of the performance and feedback of other students within their TOSBA team as key features. High achieving students performed well in both TOSBA and summative assessments. The majority of students who performed poorly in TOSBA subsequently passed the summative assessments (n = 20/21, 95 %). Conversely, the majority of students who failed the summative assessments had satisfactory scores in TOSBA (n = 6/7, 86 %). CONCLUSIONS: TOSBA has a positive impact on the clinical, communication and reasoning skills of medical students through the provision of high-quality feedback. The use of structured pre-defined tasks, the observation of the performance and feedback of other students and the use of real patients are key elements of TOSBA. Avoiding student complacency and providing accurate feedback from TOSBA are on-going challenges