Correlating Bayesian date estimates with climatic events and domestication using a bovine case study

The tribe Bovini contains a number of commercially and culturally important species, such as cattle. Understanding their evolutionary time scale is important for distinguishing between post-glacial and domestication-associated population expansions, but estimates of bovine divergence times have been hindered by a lack of reliable calibration points. We present a Bayesian phylogenetic analysis of 481 mitochondrial D-loop sequences, including 228 radiocarbon-dated ancient DNA sequences, using a multi-demographic coalescent model. By employing the radiocarbon dates as internal calibrations, we co-estimate the bovine phylogeny and divergence times in a relaxed-clock framework. The analysis yields evidence for significant population expansions in both taurine and zebu cattle, European aurochs and yak clades. The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence.

Inbreeding depression and founder diversity among captive and free-living populations of the endangered pink pigeon Columba mayeri

The endemic pink pigeon has recovered from less than 20 birds in the mid-1970s to 355 free-living individuals in 2003. A major concern for the species' recovery has been the potential genetic problem of inbreeding. Captive pink pigeons bred for reintroduction were managed to maximise founder representation and minimise inbreeding. In this paper, we quantify the effect of inbreeding on survival and reproductive parameters in captive and wild populations and quantify DNA sequence variation in the mitochondrial d-loop region for pink pigeon founders. Inbreeding affected egg fertility, squab, juvenile and adult survival, but effects were strongest in highly inbred birds (F≥0.25). Inbreeding depression was more apparent in free-living birds where even moderate levels of inbreeding affected survival, although highly inbred birds were equally compromised in both captive and wild populations. Mitochondrial DNA haplotypic diversity in pink pigeon founders is low, suggesting that background inbreeding is contributing to low fertility and depressed productivity in this species, as well as comparable survival of some groups of non-inbred and nominally inbred birds. Management of wild populations has boosted population growth and may be required long-term to offset the negative effects of inbreeding depression and enhance the species' survival.

The impact of a closed-loop electronic prescribing and administration system on prescribing errors, administration errors and staff time: a before-and-after study

Objectives: To assess the impact of a closed-loop electronic prescribing, automated dispensing, barcode patient identification and electronic medication administration record (EMAR) system on prescribing and administration errors, confirmation of patient identity before administration, and staff time. Design, setting and participants: Before-and-after study in a surgical ward of a teaching hospital, involving patients and staff of that ward. Intervention: Closed-loop electronic prescribing, automated dispensing, barcode patient identification and EMAR system. Main outcome measures: Percentage of new medication orders with a prescribing error, percentage of doses with medication administration errors (MAEs) and percentage given without checking patient identity. Time spent prescribing and providing a ward pharmacy service. Nursing time on medication tasks. Results: Prescribing errors were identified in 3.8% of 2450 medication orders pre-intervention and 2.0% of 2353 orders afterwards (p<0.001; χ2 test). MAEs occurred in 7.0% of 1473 non-intravenous doses pre-intervention and 4.3% of 1139 afterwards (p = 0.005; χ2 test). Patient identity was not checked for 82.6% of 1344 doses pre-intervention and 18.9% of 1291 afterwards (p<0.001; χ2 test). Medical staff required 15 s to prescribe a regular inpatient drug pre-intervention and 39 s afterwards (p = 0.03; t test). Time spent providing a ward pharmacy service increased from 68 min to 98 min each weekday (p = 0.001; t test); 22% of drug charts were unavailable pre-intervention. Time per drug administration round decreased from 50 min to 40 min (p = 0.006; t test); nursing time on medication tasks outside of drug rounds increased from 21.1% to 28.7% (p = 0.006; χ2 test). Conclusions: A closed-loop electronic prescribing, dispensing and barcode patient identification system reduced prescribing errors and MAEs, and increased confirmation of patient identity before administration. Time spent on medication-related tasks increased.

The impact of a closed-loop electronic prescribing and automated dispensing system on the ward pharmacist’s time and activities

Objective To assess the impact of a closed-loop electronic prescribing and automated dispensing system on the time spent providing a ward pharmacy service and the activities carried out. Setting Surgical ward, London teaching hospital. Method All data were collected two months pre- and one year post-intervention. First, the ward pharmacist recorded the time taken each day for four weeks. Second, an observational study was conducted over 10 weekdays, using two-dimensional work sampling, to identify the ward pharmacist's activities. Finally, medication orders were examined to identify pharmacists' endorsements that should have been, and were actually, made. Key findings Mean time to provide a weekday ward pharmacy service increased from 1 h 8 min to 1 h 38 min per day (P = 0.001; unpaired t-test). There were significant increases in time spent prescription monitoring, recommending changes in therapy/monitoring, giving advice or information, and non-productive time. There were decreases for supply, looking for charts and checking patients' own drugs. There was an increase in the amount of time spent with medical and pharmacy staff, and with 'self'. Seventy-eight per cent of patients' medication records could be assessed for endorsements pre- and 100% post-intervention. Endorsements were required for 390 (50%) of 787 medication orders pre-intervention and 190 (21%) of 897 afterwards (P < 0.0001; chi-square test). Endorsements were made for 214 (55%) of endorsement opportunities pre-intervention and 57 (30%) afterwards (P < 0.0001; chi-square test). Conclusion The intervention increased the overall time required to provide a ward pharmacy service and changed the types of activity undertaken. Contact time with medical and pharmacy staff increased. There was no significant change in time spent with patients. Fewer pharmacy endorsements were required post-intervention, but a lower percentage were actually made. The findings have important implications for the design, introduction and use of similar systems.

A conserved basic loop in hepatitis C virus p7 protein is required for amantadine-sensitive ion channel activity in mammalian cells but is dispensable for localization to mitochondria

We previously identified the function of the hepatitis C virus (HCV) p7 protein as an ion channel in artificial lipid bilayers and demonstrated that this in vitro activity is inhibited by amantadine. Here we show that the ion channel activity of HCV p7 expressed in mammalian cells can substitute for that of influenza virus M2 in a cell-based assay. This was also the case for the p7 from the related virus, bovine viral diarrhoea virus (BVDV). Moreover, amantadine was shown to abrogate HCV p7 function in this assay at a concentration that specifically inhibits M2. Mutation of a conserved basic loop located between the two predicted trans-membrane alpha helices rendered HCV p7 non-functional as an ion channel. The intracellular localization of p7 was unaffected by this mutation and was found to overlap significantly with membranes associated with mitochondria. Demonstration of p7 ion channel activity in cellular membranes and its inhibition by amantadine affirm the protein as a target for future anti-viral chemotherapy.

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Angstrom. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.

Evolving features-algorithms knowledge map to support NIDS data intelligence and learning loop architecting – a generalised approach to NIDS pattern feature space knowledge processing

This paper describes a proposed new approach to the Computer Network Security Intrusion Detection Systems (NIDS) application domain knowledge processing focused on a topic map technology-enabled representation of features of the threat pattern space as well as the knowledge of situated efficacy of alternative candidate algorithms for pattern recognition within the NIDS domain. Thus an integrative knowledge representation framework for virtualisation, data intelligence and learning loop architecting in the NIDS domain is described together with specific aspects of its deployment.

M-estimator, and D-optimality model construction using orthogonal forward regression

This correspondence introduces a new orthogonal forward regression (OFR) model identification algorithm using D-optimality for model structure selection and is based on an M-estimators of parameter estimates. M-estimator is a classical robust parameter estimation technique to tackle bad data conditions such as outliers. Computationally, The M-estimator can be derived using an iterative reweighted least squares (IRLS) algorithm. D-optimality is a model structure robustness criterion in experimental design to tackle ill-conditioning in model Structure. The orthogonal forward regression (OFR), often based on the modified Gram-Schmidt procedure, is an efficient method incorporating structure selection and parameter estimation simultaneously. The basic idea of the proposed approach is to incorporate an IRLS inner loop into the modified Gram-Schmidt procedure. In this manner, the OFR algorithm for parsimonious model structure determination is extended to bad data conditions with improved performance via the derivation of parameter M-estimators with inherent robustness to outliers. Numerical examples are included to demonstrate the effectiveness of the proposed algorithm.

Synthesis and incorporation into cyclic peptides of tolan amino acids and their hydrogenated congeners: construction of an array of A–B-loop mimetics of the Cε3 domain of human IgE

The disruption of the human immunolobulin E–high affinity receptor I (IgE–FcεRI) protein–protein interaction (PPI) is a validated strategy for the development of anti asthma therapeutics. Here, we describe the synthesis of an array of conformationally constrained cyclic peptides based on an epitope of the A–B loop within the Cε3 domain of IgE. The peptides contain various tolan (i.e., 1,2-biarylethyne) amino acids and their fully and partially hydrogenated congeners as conformational constraints. Modest antagonist activity (IC50 660 μM) is displayed by the peptide containing a 2,2′-tolan, which is the one predicted by molecular modeling to best mimic the conformation of the native A–B loop epitope in IgE.

Closed loop design for a simple nonlinear aircraft model using eigenstructure assignment

Aircraft systems are highly nonlinear and time varying. High-performance aircraft at high angles of incidence experience undesired coupling of the lateral and longitudinal variables, resulting in departure from normal controlled flight. The aim of this work is to construct a robust closed-loop control that optimally extends the stable and decoupled flight envelope. For the study of these systems nonlinear analysis methods are needed. Previously, bifurcation techniques have been used mainly to analyze open-loop nonlinear aircraft models and investigate control effects on dynamic behavior. In this work linear feedback control designs calculated by eigenstructure assignment methods are investigated for a simple aircraft model at a fixed flight condition. Bifurcation analysis in conjunction with linear control design methods is shown to aid control law design for the nonlinear system.

Investigating music tempo as a feedback mechanism for closed-loop BCI control

The feedback mechanism used in a brain-computer interface (BCI) forms an integral part of the closed-loop learning process required for successful operation of a BCI. However, ultimate success of the BCI may be dependent upon the modality of the feedback used. This study explores the use of music tempo as a feedback mechanism in BCI and compares it to the more commonly used visual feedback mechanism. Three different feedback modalities are compared for a kinaesthetic motor imagery BCI: visual, auditory via music tempo, and a combined visual and auditory feedback modality. Visual feedback is provided via the position, on the y-axis, of a moving ball. In the music feedback condition, the tempo of a piece of continuously generated music is dynamically adjusted via a novel music-generation method. All the feedback mechanisms allowed users to learn to control the BCI. However, users were not able to maintain as stable control with the music tempo feedback condition as they could in the visual feedback and combined conditions. Additionally, the combined condition exhibited significantly less inter-user variability, suggesting that multi-modal feedback may lead to more robust results. Finally, common spatial patterns are used to identify participant-specific spatial filters for each of the feedback modalities. The mean optimal spatial filter obtained for the music feedback condition is observed to be more diffuse and weaker than the mean spatial filters obtained for the visual and combined feedback conditions.