Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Binocular interaction:Contrast matching and contrast discrimination are predicted by the same model

How do signals from the 2 eyes combine and interact? Our recent work has challenged earlier schemes in which monocular contrast signals are subject to square-law transduction followed by summation across eyes and binocular gain control. Much more successful was a new 'two-stage' model in which the initial transducer was almost linear and contrast gain control occurred both pre- and post-binocular summation. Here we extend that work by: (i) exploring the two-dimensional stimulus space (defined by left- and right-eye contrasts) more thoroughly, and (ii) performing contrast discrimination and contrast matching tasks for the same stimuli. Twenty-five base-stimuli made from 1 c/deg patches of horizontal grating, were defined by the factorial combination of 5 contrasts for the left eye (0.3-32%) with five contrasts for the right eye (0.3-32%). Other than in contrast, the gratings in the two eyes were identical. In a 2IFC discrimination task, the base-stimuli were masks (pedestals), where the contrast increment was presented to one eye only. In a matching task, the base-stimuli were standards to which observers matched the contrast of either a monocular or binocular test grating. In the model, discrimination depends on the local gradient of the observer's internal contrast-response function, while matching equates the magnitude (rather than gradient) of response to the test and standard. With all model parameters fixed by previous work, the two-stage model successfully predicted both the discrimination and the matching data and was much more successful than linear or quadratic binocular summation models. These results show that performance measures and perception (contrast discrimination and contrast matching) can be understood in the same theoretical framework for binocular contrast vision. © 2007 VSP.

Loss of chance and the evaluation of hypothetical's in contractual claims

Analyses how to calculate damages for the loss of an opportunity by reason of a breach of contract, in the light of the House of Lords judgment in Gregg v Scott concerning clinical negligence. Discusses whether different principles apply to contract claims and torts.

Zero weights and non-zero slacks:different solution to the same problem

This paper re-assesses three independently developed approaches that are aimed at solving the problem of zero-weights or non-zero slacks in Data Envelopment Analysis (DEA). The methods are weights restricted, non-radial and extended facet DEA models. Weights restricted DEA models are dual to envelopment DEA models with restrictions on the dual variables (DEA weights) aimed at avoiding zero values for those weights; non-radial DEA models are envelopment models which avoid non-zero slacks in the input-output constraints. Finally, extended facet DEA models recognize that only projections on facets of full dimension correspond to well defined rates of substitution/transformation between all inputs/outputs which in turn correspond to non-zero weights in the multiplier version of the DEA model. We demonstrate how these methods are equivalent, not only in their aim but also in the solutions they yield. In addition, we show that the aforementioned methods modify the production frontier by extending existing facets or creating unobserved facets. Further we propose a new approach that uses weight restrictions to extend existing facets. This approach has some advantages in computational terms, because extended facet models normally make use of mixed integer programming models, which are computationally demanding.

Hearing and vision:the age old problem

Opticians and audiologists tend to see the same people. Many factors that are associated with poorer vision, whether hereditary, pre-natal, or post-natal, are also associated with poorer hearing. The most common factor is simply old age. According to the Royal National Institute for Deaf People (RNID), more than half of all people aged over 60 have some degree of hearing loss and are gradually losing their hearing as part of the ageing process – a process known as presbycusis.

Are we on the same page? Knowledge boundaries and transactive memory system development in cross-functional teams

One of the key challenges that organizations face when trying to integrate knowledge across different functions is the need to overcome knowledge boundaries between team members. In cross-functional teams, these boundaries, associated with different knowledge backgrounds of people from various disciplines, create communication problems, necessitating team members to engage in complex cognitive processes when integrating knowledge toward a joint outcome. This research investigates the impact of syntactic, semantic, and pragmatic knowledge boundaries on a team’s ability to develop a transactive memory system (TMS)—a collective memory system for knowledge coordination in groups. Results from our survey show that syntactic and pragmatic knowledge boundaries negatively affect TMS development. These findings extend TMS theory beyond the information-processing view, which treats knowledge as an object that can be stored and retrieved, to the interpretive and practice-based views of knowledge, which recognize that knowledge (in particular specialized knowledge) is localized, situated, and embedded in practice.

Spatial perspective taking is an embodied process, but not for everyone in the same way:differences predicted by sex and social skills score

We re-analysed visuo-spatial perspective taking data from Kessler and Thomson (2010) plus a previously unpublished pilot with respect to individual- and sex differences in embodied processing (defined as body-posture congruence effects). We found that so-called 'systemisers' (males/low-social-skills) showed weaker embodiment than so-called 'embodiers' (females/high-social-skills). We conclude that 'systemisers' either have difficulties with embodied processing or, alternatively, they have a strategic advantage in selecting different mechanisms or the appropriate level of embodiment. In contrast, 'embodiers' have an advantageous strategy of "deep" embodied processing reflecting their urge to empathise or, alternatively, less flexibility in fine-tuning the involvement of bodily representations. © 2012 Copyright Taylor and Francis Group, LLC.

Weight loss strategies, stress, and cognitive function:supervised versus unsupervised dieting

The early stages of dieting to lose weight have been associated with neuro-psychological impairments. Previous work has not elucidated whether these impairments are a function solely of unsupported or supported dieting. Raised cortico-steroid levels have been implicated as a possible causal mechanism. Healthy, overweight, pre-menopausal women were randomised to one of three conditions in which they dieted either as part of a commercially available weight loss group, dieted without any group support or acted as non-dieting controls for 8 weeks. Testing occurred at baseline and at 1, 4 and 8 weeks post baseline. During each session, participants completed measures of simple reaction time, motor speed, vigilance, immediate verbal recall, visuo-spatial processing and (at Week 1 only) executive function. Cortisol levels were gathered at the beginning and 30 min into each test session, via saliva samples. Also, food intake was self-recorded prior to each session and fasting body weight and percentage body fat were measured at each session. Participants in the unsupported diet condition displayed poorer vigilance performance (p=0.001) and impaired executive planning function (p=0.013) (along with a marginally significant trend for poorer visual recall (p=0.089)) after 1 week of dieting. No such impairments were observed in the other two groups. In addition, the unsupported dieters experienced a significant rise in salivary cortisol levels after 1 week of dieting (p<0.001). Both dieting groups lost roughly the same amount of body mass (p=0.011) over the course of the 8 weeks of dieting, although only the unsupported dieters experienced a significant drop in percentage body fat over the course of dieting (p=0.016). The precise causal nature of the relationship between stress, cortisol, unsupported dieting and cognitive function is, however, uncertain and should be the focus of further research. © 2005 Elsevier Ltd. All rights reserved.

Perception of global image contrast is predicted by the same spatial integration model of gain control as detection and discrimination

How are the image statistics of global image contrast computed? We answered this by using a contrast-matching task for checkerboard configurations of ‘battenberg’ micro-patterns where the contrasts and spatial spreads of interdigitated pairs of micro-patterns were adjusted independently. Test stimuli were 20 × 20 arrays with various sized cluster widths, matched to standard patterns of uniform contrast. When one of the test patterns contained a pattern with much higher contrast than the other, that determined global pattern contrast, as in a max() operation. Crucially, however, the full matching functions had a curious intermediate region where low contrast additions for one pattern to intermediate contrasts of the other caused a paradoxical reduction in perceived global contrast. None of the following models predicted this: RMS, energy, linear sum, max, Legge and Foley. However, a gain control model incorporating wide-field integration and suppression of nonlinear contrast responses predicted the results with no free parameters. This model was derived from experiments on summation of contrast at threshold, and masking and summation effects in dipper functions. Those experiments were also inconsistent with the failed models above. Thus, we conclude that our contrast gain control model (Meese & Summers, 2007) describes a fundamental operation in human contrast vision.

Religious diplomacy and socialism. The Romanian Orthodox Church and the Church of England, 1956-1959

This article analyzes the relationship between the Orthodox Church and the communist regime during one of the most intense periods of religious persecution in the Romanian People's Republic from 1956 to 1959. The church hierarchy demonstrated its support for the socialist construction of the country, while, at the same time, the regime began a campaign against religion by arresting clergy and reducing the number of religious people in monasteries; rumours even circulated that in 1958 Patriarch Justinian was under house arrest. Seeking closer contact with Western Europe, the regime allowed the hierarchy to meet foreign clergymen, especially from the Church of England. These diplomatic religious encounters played a double role. The regime realised that it could benefit from international ecclesiastical relations, while the image of Justinian in the West changed from that of "red patriarch" to that of a leader who was genuinely interested in his church's survival.

Effect of a protein and energy dense n-3 fatty acid enriched oral supplement on loss of weight and lean tissue in cancer cachexia:A randomised double blind trial

Aim: N-3 fatty acids, especially eicosapentaenoic acid (EPA), may possess anticachectic properties. This trial compared a protein and energy dense supplement enriched with n-3 fatty acids and antioxidants (experimental: E) with an isocaloric isonitrogenous control supplement (C) for their effects on weight, lean body mass (LBM), dietary intake, and quality of life in cachectic patients with advanced pancreatic cancer. Methods: A total of 200 patients (95 E; 105 C) were randomised to consume two cans/day of the E or C supplement (480 ml, 620 kcal, 32 g protein ± 2.2 g EPA) for eight weeks in a multicentre, randomised, double blind trial. Results: At enrolment, patients' mean rate of weight loss was 3.3 kg/month. Intake of the supplements (E or C) was below the recommended dose (2 cans/day) and averaged 1.4 cans/day. Over eight weeks, patients in both groups stopped losing weight (Δweight E: -0.25 kg/month versus C: -0.37 kg/month; p=0.74) and LBM (ΔLBM E: +0.27 kg/month versus C: +0.12 kg/month; p=0.88) to an equal degree (change from baseline E and C, p<0.001). In view of evident non-compliance in both E and C groups, correlation analyses were undertaken to examine for potential dose-response relationships. E patients demonstrated significant correlations between their supplement intake and weight gain (r=0.50, p<0.001) and increase in LBM (r=0.33, p=0.036). Such correlations were not statistically significant in C patients. The relationship of supplement intake with change in LBM was significantly different between E and C patients (p=0.043). Increased plasma EPA levels in the E group were associated with weight and LBM gain (r=0.50, p<0.001; r=0.51, p=0.001). Weight gain was associated with improved quality of life (p<0.01) only in the E group. Conclusion: Intention to treat group comparisons indicated that at the mean dose taken, enrichment with n-3 fatty acids did not provide a therapeutic advantage and that both supplements were equally effective in arresting weight loss. Post hoc dose-response analysis suggests that if taken in sufficient quantity, only the n-3 fatty acid enriched energy and protein dense supplement results in net gain of weight, lean tissue, and improved quality of life. Further trials are required to examine the potential role of n-3 enriched supplements in the treatment of cancer cachexia.

Pregnancy loss in lesbian and bisexual women: An online survey of experiences

Background: Although pregnancy loss is a distressing health event for many women, research typically equates women’s experiences of pregnancy loss to ‘married heterosexual women’s experiences of pregnancy loss’. The objective of this study was to explore lesbian and bisexual women’s experiences of miscarriage, stillbirth and neonatal death. Methods: This study analysed predominantly qualitative online survey data from 60 non-heterosexual, mostly lesbian, women from the UK, USA, Canada and Australia. All but one of the pregnancies was planned. Most respondents had physically experienced one early miscarriage during their first pregnancy, although a third had experienced multiple losses. Results: The analysis highlights three themes: processes and practices for conception; amplification of loss; and health care and heterosexism. Of the respondents, 84% conceived using donor sperm; most used various resources to plan conception and engaged in preconception health care. The experience of loss was amplified due to contextual factors and the investment respondents reported making in impending motherhood. Most felt that their loss(es) had made a ‘significant’/‘very significant’ impact on their lives. Many respondents experienced health care during their loss. Although the majority rated the overall standard of care as ‘good’/‘very good’/‘outstanding’, a minority reported experiencing heterosexism from health professionals. Conclusions: The implications for policy and practice are outlined. The main limitation was that the inflexibility of the methodology did not allow the specificities of women’s experiences to be probed further. It is suggested that both coupled and single non-heterosexual women should be made more visible in reproductive health and pregnancy loss research.

A common contrast pooling rule for suppression within and between the eyes

Recent work has revealed multiple pathways for cross-orientation suppression in cat and human vision. In particular, ipsiocular and interocular pathways appear to assert their influence before binocular summation in human but have different (1) spatial tuning, (2) temporal dependencies, and (3) adaptation after-effects. Here we use mask components that fall outside the excitatory passband of the detecting mechanism to investigate the rules for pooling multiple mask components within these pathways. We measured psychophysical contrast masking functions for vertical 1 cycle/deg sine-wave gratings in the presence of left or right oblique (645 deg) 3 cycles/deg mask gratings with contrast C%, or a plaid made from their sum, where each component (i) had contrast 0.5Ci%. Masks and targets were presented to two eyes (binocular), one eye (monoptic), or different eyes (dichoptic). Binocular-masking functions superimposed when plotted against C, but in the monoptic and dichoptic conditions, the grating produced slightly more suppression than the plaid when Ci $ 16%. We tested contrast gain control models involving two types of contrast combination on the denominator: (1) spatial pooling of the mask after a local nonlinearity (to calculate either root mean square contrast or energy) and (2) "linear suppression" (Holmes & Meese, 2004, Journal of Vision 4, 1080–1089), involving the linear sum of the mask component contrasts. Monoptic and dichoptic masking were typically better fit by the spatial pooling models, but binocular masking was not: it demanded strict linear summation of the Michelson contrast across mask orientation. Another scheme, in which suppressive pooling followed compressive contrast responses to the mask components (e.g., oriented cortical cells), was ruled out by all of our data. We conclude that the different processes that underlie monoptic and dichoptic masking use the same type of contrast pooling within their respective suppressive fields, but the effects do not sum to predict the binocular case.

Evaluating and improving the performance of video content distribution in lossy networks

The contributions in this research are split in to three distinct, but related, areas. The focus of the work is based on improving the efficiency of video content distribution in the networks that are liable to packet loss, such as the Internet. Initially, the benefits and limitations of content distribution using Forward Error Correction (FEC) in conjunction with the Transmission Control Protocol (TCP) is presented. Since added FEC can be used to reduce the number of retransmissions, the requirement for TCP to deal with any losses is greatly reduced. When real-time applications are needed, delay must be kept to a minimum, and retransmissions not desirable. A balance, therefore, between additional bandwidth and delays due to retransmissions must be struck. This is followed by the proposal of a hybrid transport, specifically for H.264 encoded video, as a compromise between the delay-prone TCP and the loss-prone UDP. It is argued that the playback quality at the receiver often need not be 100% perfect, providing a certain level is assured. Reliable TCP is used to transmit and guarantee delivery of the most important packets. The delay associated with the proposal is measured, and the potential for use as an alternative to the conventional methods of transporting video by either TCP or UDP alone is demonstrated. Finally, a new objective measurement is investigated for assessing the playback quality of video transported using TCP. A new metric is defined to characterise the quality of playback in terms of its continuity. Using packet traces generated from real TCP connections in a lossy environment, simulating the playback of a video is possible, whilst monitoring buffer behaviour to calculate pause intensity values. Subjective tests are conducted to verify the effectiveness of the metric introduced and show that the results of objective and subjective scores made are closely correlated.