Bulletin of Mathematical Biology - facts, figures and comparisons

The Society for Mathematical Biology (SMB) owns the Bulletin of Mathematical Biology (BMB). This is an international journal devoted to the interface of mathematics and biology. At the 2003 SMB annual meeting in Dundee the Society asked the editor of the BMB to produce an analysis of impact factor, subject matter of papers, submission rates etc. Other members of the society were interested in the handling times of articles and wanted comparisons with other (appropriate) journals. In this article we present a brief history of the journal and report on how the journal impact factor has grown substantially in the last few years. We also present an analysis of subject areas of published papers over the past two years. We finally present data on times from receipt of paper to acceptance, acceptance to print (and to online publication) and compare these data with some other journals

Searches for TeV-scale particles at the LHC using jet shapes

New particles at the TeV scale can decay hadronically with strongly collimated jets, thus the standard reconstruction methods based on invariant-masses of well-separated jets can fail. We discuss how to identify such particles in pp collisions at the LHC using jet shapes which help to reduce the contribution of QCD-induced events. We focus on a rather generic example X to ttbar to hadrons, with X being a heavy particle, but the approach is well suited for reconstruction of other decay channels characterized by a cascade decay of known states.Comment: 14 pages, 6 figure

EffiTest: Efficient Delay Test and Statistical Prediction for Configuring Post-silicon Tunable Buffers

At nanometer manufacturing technology nodes, process variations significantly affect circuit performance. To combat them, post- silicon clock tuning buffers can be deployed to balance timing bud- gets of critical paths for each individual chip after manufacturing. The challenge of this method is that path delays should be mea- sured for each chip to configure the tuning buffers properly. Current methods for this delay measurement rely on path-wise frequency stepping. This strategy, however, requires too much time from ex- pensive testers. In this paper, we propose an efficient delay test framework (EffiTest) to solve the post-silicon testing problem by aligning path delays using the already-existing tuning buffers in the circuit. In addition, we only test representative paths and the delays of other paths are estimated by statistical delay prediction. Exper- imental results demonstrate that the proposed method can reduce the number of frequency stepping iterations by more than 94% with only a slight yield loss.Comment: ACM/IEEE Design Automation Conference (DAC), June 201

Ecological role of herbivory on coral reefs of the Saudi Arabian Gulf coast

This study examined the ecological role of herbivory on coral reefs of the Saudi Arabian Gulf coast. Herbivory is a ubiquitous process and important in regulating benthic marine communities. Three reef sites were studied over a 12-month period; one on an inshore fringing reef (1.5 m depth), and two on the fringing reef surrounding an offshore island (3 m and 11 m depth). The inshore site experienced greatest extremes in temperature, salinity and sedimentation. The ecological role of herbivory was determined from algal settlement plates and their selective exclusion from herbivores. The inshore site was naturally dominated by filamentous algae, while both offshore sites supported a higher proportion of crustose forms. Location (i. e. distance from shore) appeared to be more important than seasonality in determining the structure and composition of the epilithic algal community. At the inshore site herbivorous fish (dominated by Siganus spp. ) imposed a uniform, wide-ranging grazing pressure of intermediate intensity. Herbivorous echinoids (Echinometra mathaei) imposed an intensive but localised grazing pressure. At the shallow offshore site, only herbivorous fish (dominated by Scarus sp. ) appeared responsible for grazing impacts, which were also intensive. At the deep offshore site both herbivorous fish (dominated by Pomacentrus spp. ) and echinoids (Diademo setosum) were responsible for limiting algal growth, although other factors (e. g. light penetration) may also inhibit algal productivity at this site. An experiment assessing the effects of extreme perturbations (i. e. removal of the algal community), showed that seasonal life-history strongly affected generic succession and rate of re-colonisation. Perturbation effects were temporary and did not precipitate permanent alternative stable communities. An important secondary effect of herbivory is bioerosion. The mean erosion rate by E. mathaei was comparable to rates recorded elsewhere. Behavioural studies revealed that burrow defence and fidelity were positively correlated with burrow complexity, and that the frequency of agonistic behaviour was low. Foraging range was negatively correlated with burrow complexity. In addition, the risk of mortality by finfish predators at the inshore site was estimated to be very low. The study has shown that Saudi Arabian Gulf reef communities may be particularly vulnerable to the depletion of herbivores, for example by overfishing. Management plans should therefore safeguard the herbivorous community, in order to maintain natural bioerosion rates and other reef processes

The alternating least-squares algorithm for CDPCA

Clustering and Disjoint Principal Component Analysis (CDP CA) is a constrained principal component analysis recently proposed for clustering of objects and partitioning of variables, simultaneously, which we have implemented in R language. In this paper, we deal in detail with the alternating least-squares algorithm for CDPCA and highlight its algebraic features for constructing both interpretable principal components and clusters of objects. Two applications are given to illustrate the capabilities of this new methodology

Service Evaluation of 'Living Well with the Impact of Cancer' Courses

The aim of the Penny Brohn Cancer Care Living Well Service Evaluation was to measure the level of benefit that participants were receiving from the Penny Brohn Cancer Care(PBCC)Living Well course and to inform current and future service provision at PBCC. The Penny Brohn Whole Person Approach model(PB-WPA model), which underpins the Living Well course, was designed to support the ‘whole person’ and the course was intended to meet the needs of people with cancer, as identified by the National Cancer Survivorship Initiative (NCSI). The combined qualitative and quantitative results of the Living Well Service Evaluation have demonstrated, very clearly at times, that participants were highly satisfied with the course. The immediate benefit of attending was measurable, in terms of improved health related quality of life (HRQoL) and improved MYCaW (Measure yourself Concerns and Wellbeing) concerns and wellbeing. The evaluation results show that the Living Well course experience enabled the majority of participants to regain control over many aspects of their life, and to start taking responsibility for their health. The following aspects of the course were identified as the most helpful: -Specific units of ‘education and explanation’ about cancer and why healthy lifestyle changes to areas such as diet, exercise and relaxation are beneficial -Advice and education from medical doctors -The opportunity to share experiences with other participants For some, this empowerment led to long-term changes in exercise, food consumption,use of self-help techniques and the ability to communicate more freely and openly with family, friends and medical professionals. These improvements were reflected in the 12 month outcome data, where a sustained improvement in HRQoL and MYCaW concerns was reported by many clients. Such patient reported outcome measures (PROMs) are limited in what they can measure, thus qualitative data were also collected to ensure that participants were able to share their experiences (positive or negative) of the Living Well course, and their subsequent experiences of applying the education and techniques learnt on the course. A picture emerged that identified difficulties in sustaining lifestyle changes at around the 3-6 month follow-up. Participants who returned to PBCC within the 12 month follow-up period, however, were more likely to benefit by reporting a greater improvement in HRQoL and MYCaW scores, plus an improved understanding of how to make and maintain healthy lifestyle changes to suit their individual circumstances. In regards to the current NCSI priorities, it is hoped that the data reported in this evaluation go some way to informing the following: -Information and support from the point of diagnosis -Managing the consequences of treatment -Promoting recovery -Sustaining recovery -Supporting people with active and advanced disease -Improving survivorship intelligence Finally, this report demonstrates how a patient-centred model of support can be effectively evaluated to provide relevant, practical and evidence-based information to commissioners. Participant satisfaction: Participants were very satisfied with the course content, course delivery and resources provided which often exceeded their needs and expectations. Participant outcomes: The PB-WPA model successfully encompassed and supported all the types of concerns participants arrived with. The most frequently reported participant concerns were psychological and emotional,about their wellbeing and about their physical health. On average, participants experienced statistically and clinically significant improvements in their MYCaW concern and wellbeing scores, and total HRQoL scores,which remained improved over the 12 month follow-up. The aspects of HRQoL that were most likely to improve after attending the Living Well course were spiritual, emotional and functional wellbeing. Supporters had their own profile of concerns, namely psychological and emotional,supporter specific concerns and practical concerns. Concerns were as severely rated as those from participants with a diagnosis of cancer and also showed statistically significant average improvements throughout the 12 month follow-up. The small group of participants with metastatic disease reported significant improvements in their MYCaW concern scores, in line with the whole evaluation group,and a significantly greater improvement in HRQoL over 12 months compared to participants with primary cancer.Participants who returned for more support from PBCC were in more need of support than those who did not return. They were more likely to have poorer HRQoL at baseline and rate their concerns more severely. Participants who returned to PBCC experienced more improvement in HRQoL that was likely to be clinically significant. These participants also had a greater degree of improvement in their MYCaW concerns, compared to non-returners. Over half of the participants experienced new concerns over the 12 month follow-up period. Concerns were most frequently associated with psychological and emotional and physical issues. Furthermore, at 12 months, participants were still experiencing arange of health issues

The Responsiveness, Content Validity, and Convergent Validity of the Measure Yourself Concerns and Wellbeing (MYCaW) Patient-Reported Outcome Measure

Objective Measure Yourself Concerns and Wellbeing (MYCaW) is a patient-centred questionnaire that allows cancer patients to identify and quantify the severity of their ‘Concerns’ and Wellbeing, as opposed to using a pre-determined list. MYCaW administration is brief and aids in prioritising treatment approaches. Our goal was to assess the convergent validity and responsiveness of MYCaW scores over time, the generalisability of the existing qualitative coding framework in different complementary and integrative healthcare settings and content validity. Methods Baseline and 6-week follow-up data (n=82) from MYCaW and FACIT-SpEx questionnaires were collected for a service evaluation of the ‘Living Well With The Impact of Cancer’ course at Penny Brohn Cancer Care. MYCaW construct validity was determined using Spearman's Rank Correlation test, and responsiveness indices assessed score changes over time. The existing qualitative coding framework was reviewed using a new dataset (n=158) and coverage of concern categories compared to items of existing outcome measures. Results Good correlation between MYCaW and FACIT-SpEx score changes were achieved (r= -0.57, p≥0.01). MYCaW Profile and Concern scores were highly responsive to change: SRM=1.02 and 1.08; effect size=1.26 and 1.22. MYCaW change scores showed the anticipated gradient of change according to clinically relevant degrees of change. Categories including ‘Spirituality’, ‘weight change’ and ‘practical concerns’ were added to the coding framework to improve generalisability. Conclusions MYCaW scores were highly responsive to change, allowing personalized patient outcomes to be quantified; the qualitative coding framework is generalisable across different oncology settings and has broader coverage of patient-identified concerns compared with existing cancer-related patient-reported outcome measures

Using a whole person approach to support people with cancer: a longitudinal, mixed methods service evaluation

Introduction: Improved models of care are needed to meet all the support needs of people with cancer, which encompass psychological, emotional, physical, spiritual, sexual, occupational, social and existential needs. The aim of this paper is to (1) evaluate short and long-term impacts of using a whole person approach to support people with cancer on the Living Well with the Impact of Cancer Course (LWC); (2) use these data to inform strategic decisions about future service provision at Penny Brohn UK. Methods: Longitudinal mixed-methods service evaluation (n=135). Data collected included health related quality of life (HRQoL) (FACIT-SpEx); Concerns (types and severity - MYCaW); lifestyle behaviour (bespoke questionnaire) and participants’ experiences over 12 months post course. Results: Statistically and clinically significant improvements from baseline - 12 months in severity of MYCaW Concerns (n=64; p<0.000) and mean total HRQoL (n=66; p<0.000). The majority of MYCaW concerns were ‘psychological and emotional’ and about participants’ wellbeing. Spiritual, emotional and functional wellbeing contributed most to HRQoL improvements at 12 months. Barriers to maintaining healthy lifestyle changes included lack of support from family and friends, time constraints, and returning to work. 3-6 months post-course was identified as the time when more support was most likely to be needed. Conclusions: Using a whole person approach for the LWC enabled the needs of participants to be met, and statistically and clinically significant improvements in HRQoL and MYCaW Concerns were reported. Qualitative data analysis explored how experiencing whole person support enabled participants to make and sustain healthy lifestyle changes associated with improved survivorship. Barriers experienced to making health behaviour change were also identified. These data then informed wider and more person-centred clinical provision to increase the maintenance of positive long-term behaviour changes. Comparison of whole person approaches to cancer treatment and support and standard care are now urgently needed

Elastodynamics of radially inhomogeneous spherically anisotropic elastic materials in the Stroh formalism

A method is presented for solving elastodynamic problems in radially inhomogeneous elastic materials with spherical anisotropy, i.e.\ materials such that $c_{ijkl}= c_{ijkl}(r)$ in a spherical coordinate system ${r,\theta,\phi}$. The time harmonic displacement field $\mathbf{u}(r,\theta ,\phi)$ is expanded in a separation of variables form with dependence on $\theta,\phi$ described by vector spherical harmonics with $r$-dependent amplitudes. It is proved that such separation of variables solution is generally possible only if the spherical anisotropy is restricted to transverse isotropy with the principal axis in the radial direction, in which case the amplitudes are determined by a first-order ordinary differential system. Restricted forms of the displacement field, such as $\mathbf{u}(r,\theta)$, admit this type of separation of variables solutions for certain lower material symmetries. These results extend the Stroh formalism of elastodynamics in rectangular and cylindrical systems to spherical coordinates.Comment: 15 page

High-Dimensional Inference with the generalized Hopfield Model: Principal Component Analysis and Corrections

We consider the problem of inferring the interactions between a set of N binary variables from the knowledge of their frequencies and pairwise correlations. The inference framework is based on the Hopfield model, a special case of the Ising model where the interaction matrix is defined through a set of patterns in the variable space, and is of rank much smaller than N. We show that Maximum Lik elihood inference is deeply related to Principal Component Analysis when the amp litude of the pattern components, xi, is negligible compared to N^1/2. Using techniques from statistical mechanics, we calculate the corrections to the patterns to the first order in xi/N^1/2. We stress that it is important to generalize the Hopfield model and include both attractive and repulsive patterns, to correctly infer networks with sparse and strong interactions. We present a simple geometrical criterion to decide how many attractive and repulsive patterns should be considered as a function of the sampling noise. We moreover discuss how many sampled configurations are required for a good inference, as a function of the system size, N and of the amplitude, xi. The inference approach is illustrated on synthetic and biological data.Comment: Physical Review E: Statistical, Nonlinear, and Soft Matter Physics (2011) to appea