Semantic Mining based on graph theory and ontologies. Case Study: Cell Signaling Pathways

In this paper we use concepts from graph theory and cellular biology represented as ontologies, to carry out semantic mining tasks on signaling pathway networks. Specifically, the paper describes the semantic enrichment of signaling pathway networks. A cell signaling network describes the basic cellular activities and their interactions. The main contribution of this paper is in the signaling pathway research area, it proposes a new technique to analyze and understand how changes in these networks may affect the transmission and flow of information, which produce diseases such as cancer and diabetes. Our approach is based on three concepts from graph theory (modularity, clustering and centrality) frequently used on social networks analysis. Our approach consists into two phases: the first uses the graph theory concepts to determine the cellular groups in the network, which we will call them communities; the second uses ontologies for the semantic enrichment of the cellular communities. The measures used from the graph theory allow us to determine the set of cells that are close (for example, in a disease), and the main cells in each community. We analyze our approach in two cases: TGF-β and the Alzheimer Disease.

Increased hospital-based physical rehabilitation and information provision after intensive care unit discharge: the RECOVER randomized clinical trial.

Importance: critical illness results in disability and reduced health-related quality of life (HRQOL), but the optimum timing and components of rehabilitation are uncertain. Objective: to evaluate the effect of increasing physical and nutritional rehabilitation plus information delivered during the post–intensive care unit (ICU) acute hospital stay by dedicated rehabilitation assistants on subsequent mobility, HRQOL, and prevalent disabilities. Design, Setting, and Participants: a parallel group, randomized clinical trial with blinded outcome assessment at 2 hospitals in Edinburgh, Scotland, of 240 patients discharged from the ICU between December 1, 2010, and January 31, 2013, who required at least 48 hours of mechanical ventilation. Analysis for the primary outcome and other 3-month outcomes was performed between June and August 2013; for the 6- and 12-month outcomes and the health economic evaluation, between March and April 2014. Interventions: during the post-ICU hospital stay, both groups received physiotherapy and dietetic, occupational, and speech/language therapy, but patients in the intervention group received rehabilitation that typically increased the frequency of mobility and exercise therapies 2- to 3-fold, increased dietetic assessment and treatment, used individualized goal setting, and provided greater illness-specific information. Intervention group therapy was coordinated and delivered by a dedicated rehabilitation practitioner. Main Outcomes and Measures: the Rivermead Mobility Index (RMI) (range 0-15) at 3 months; higher scores indicate greater mobility. Secondary outcomes included HRQOL, psychological outcomes, self-reported symptoms, patient experience, and cost-effectiveness during a 12-month follow-up (completed in February 2014). Results: median RMI at randomization was 3 (interquartile range [IQR], 1-6) and at 3 months was 13 (IQR, 10-14) for the intervention and usual care groups (mean difference, −0.2 [95% CI, −1.3 to 0.9; P = .71]). The HRQOL scores were unchanged by the intervention (mean difference in the Physical Component Summary score, −0.1 [95% CI, −3.3 to 3.1; P = .96]; and in the Mental Component Summary score, 0.2 [95% CI, −3.4 to 3.8; P = .91]). No differences were found for self-reported symptoms of fatigue, pain, appetite, joint stiffness, or breathlessness. Levels of anxiety, depression, and posttraumatic stress were similar, as were hand grip strength and the timed Up & Go test. No differences were found at the 6- or 12-month follow-up for any outcome measures. However, patients in the intervention group reported greater satisfaction with physiotherapy, nutritional support, coordination of care, and information provision. Conclusions and Relevance: post-ICU hospital-based rehabilitation, including increased physical and nutritional therapy plus information provision, did not improve physical recovery or HRQOL, but improved patient satisfaction with many aspects of recovery.

Aerial surveys to monitor bluefin tuna abundance and track efficiency of management measures

Conservation and management measures for exploited fish species rely on our ability to monitor variations in population abundance. In the case of the eastern stock of Atlantic bluefin tuna (ABFT), recent changes in management policies have strongly affected the reliability of fishery-dependent indicators due to drastic changes in fishing season/area, fisheries selectivity and strategy. However, fishery-independent indices of abundance are rare for large pelagic fish, and obtaining them is often costly and labor intensive. Here, we show that scientific aerial surveys are an appropriate tool for monitoring juvenile bluefin tuna abundance in the Mediterranean. We present an abundance index based on 62 aerial surveys conducted since 2000, using 2 statistical approaches to deal with the sampling strategy: line and strip transects. Both approaches showed a significant increase in juvenile ABFT abundance in recent years, resulting from the recovery plan established in 2007. Nonetheless, the estimates from the line transect method appear to be more robust and stable. This study provides essential information for fisheries management. Expanding the spatial coverage to other nursery grounds would further increase the reliability and representativeness of this index.

A path-based framework for analyzing large markov models

Reliability and dependability modeling can be employed during many stages of analysis of a computing system to gain insights into its critical behaviors. To provide useful results, realistic models of systems are often necessarily large and complex. Numerical analysis of these models presents a formidable challenge because the sizes of their state-space descriptions grow exponentially in proportion to the sizes of the models. On the other hand, simulation of the models requires analysis of many trajectories in order to compute statistically correct solutions. This dissertation presents a novel framework for performing both numerical analysis and simulation. The new numerical approach computes bounds on the solutions of transient measures in large continuous-time Markov chains (CTMCs). It extends existing path-based and uniformization-based methods by identifying sets of paths that are equivalent with respect to a reward measure and related to one another via a simple structural relationship. This relationship makes it possible for the approach to explore multiple paths at the same time,· thus significantly increasing the number of paths that can be explored in a given amount of time. Furthermore, the use of a structured representation for the state space and the direct computation of the desired reward measure (without ever storing the solution vector) allow it to analyze very large models using a very small amount of storage. Often, path-based techniques must compute many paths to obtain tight bounds. In addition to presenting the basic path-based approach, we also present algorithms for computing more paths and tighter bounds quickly. One resulting approach is based on the concept of path composition whereby precomputed subpaths are composed to compute the whole paths efficiently. Another approach is based on selecting important paths (among a set of many paths) for evaluation. Many path-based techniques suffer from having to evaluate many (unimportant) paths. Evaluating the important ones helps to compute tight bounds efficiently and quickly.

THE FEASIBILITY OF USING WEB-BASED TECHNOLOGY FOR THE MANAGEMENT OF DREDGING PROJECTS

The research investigates the feasibility of using web-based project management systems for dredging. To achieve this objective the research assessed both the positive and negative aspects of using web-based technology for the management of dredging projects. Information gained from literature review and prior investigations of dredging projects revealed that project performance, social, political, technical, and business aspects of the organization were important factors in deciding to use web-based systems for the management of dredging projects. These factors were used to develop the research assumptions. An exploratory case study methodology was used to gather the empirical evidence and perform the analysis. An operational prototype of the system was developed to help evaluate developmental and functional requirements, as well as the influence on performance, and on the organization. The evidence gathered from three case study projects, and from a survey of 31 experts, were used to validate the assumptions. Baselines, representing the assumptions, were created as a reference to assess the responses and qualitative measures. The deviation of the responses was used to evaluate for the analysis. Finally, the conclusions were assessed by validating the assumptions with the evidence, derived from the analysis. The research findings are as follows: 1. The system would help improve project performance. 2. Resistance to implementation may be experienced if the system is implemented. Therefore, resistance to implementation needs to be investigated further and more R&D work is needed in order to advance to the final design and implementation. 3. System may be divided into standalone modules in order to simplify the system and facilitate incremental changes. 4. The QA/QC conceptual approach used by this research needs to be redefined during future R&D to satisfy both owners and contractors. Yin (2009) Case Study Research Design and Methods was used to develop the research approach, design, data collection, and analysis. Markus (1983) Resistance Theory was used during the assumptions definition to predict potential problems to the implementation of web-based project management systems for the dredging industry. Keen (1981) incremental changes and facilitative approach tactics were used as basis to classify solutions, and how to overcome resistance to implementation of the web-based project management system. Davis (1989) Technology Acceptance Model (TAM) was used to assess the solutions needed to overcome the resistances to the implementation of web-base management systems for dredging projects.

A universally delivered CBT based intervention in a Scottish secondary school: a pilot feasibility study

Objectives: To evaluate the feasibility of a universally delivered CBT-based programme for pupils within a Scottish secondary school setting. Design: A pre-post, within and between groups design was utilised. Setting: Religious Moral Citizenship and Education (RMCE) classes in a Scottish secondary school. Participants: Four (n = 103) classes of third year secondary school pupils were arbitrarily allocated to two conditions: RMCE-as usual (RMCE-AU) controls, and LLTTF intervention. Intervention: Living Life to the Full (LLTTF) is a series of Cognitive Behavioural Therapy (CBT)-based booklets and accompanying 8 classes to improve coping skills. An adolescent version of LLTTF was recently developed. This was delivered over nine weeks by school teachers trained in the approach. Outcome measures: The Strengths and Difficulties Questionnaire, Rosenberg Self-Esteem scale, General Self-Efficacy Scale, and Locus of Control scale were administered at baseline and 9 week follow-up. To determine acceptability and utility of the materials course feedback was gathered weekly from the intervention group and a focus group (n=5) was conducted at 3 month follow up. Results: Outcome measures showed no significant improvement in overall wellbeing of those in the intervention group compared with that of the control group. Weekly feedback suggested that the majority of pupils found the materials useful and relevant. Focus group feedback suggested that pupils found the intervention useful, had utilised strategies in everyday life and would welcome recurring provision of such interventions within the school setting. Conclusions: Universally delivered CBT intervention is acceptable and feasible within the secondary school environment. However, objective measurement using standardised tools does not adequately corroborate qualitative feedback from pupils. Issues relating to measurement, study design and implementation of future interventions are discussed.

Soft computing based parameter identification in pavements and geomechanical systems

Accurate estimation of road pavement geometry and layer material properties through the use of proper nondestructive testing and sensor technologies is essential for evaluating pavement’s structural condition and determining options for maintenance and rehabilitation. For these purposes, pavement deflection basins produced by the nondestructive Falling Weight Deflectometer (FWD) test data are commonly used. The nondestructive FWD test drops weights on the pavement to simulate traffic loads and measures the created pavement deflection basins. Backcalculation of pavement geometry and layer properties using FWD deflections is a difficult inverse problem, and the solution with conventional mathematical methods is often challenging due to the ill-posed nature of the problem. In this dissertation, a hybrid algorithm was developed to seek robust and fast solutions to this inverse problem. The algorithm is based on soft computing techniques, mainly Artificial Neural Networks (ANNs) and Genetic Algorithms (GAs) as well as the use of numerical analysis techniques to properly simulate the geomechanical system. A widely used pavement layered analysis program ILLI-PAVE was employed in the analyses of flexible pavements of various pavement types; including full-depth asphalt and conventional flexible pavements, were built on either lime stabilized soils or untreated subgrade. Nonlinear properties of the subgrade soil and the base course aggregate as transportation geomaterials were also considered. A computer program, Soft Computing Based System Identifier or SOFTSYS, was developed. In SOFTSYS, ANNs were used as surrogate models to provide faster solutions of the nonlinear finite element program ILLI-PAVE. The deflections obtained from FWD tests in the field were matched with the predictions obtained from the numerical simulations to develop SOFTSYS models. The solution to the inverse problem for multi-layered pavements is computationally hard to achieve and is often not feasible due to field variability and quality of the collected data. The primary difficulty in the analysis arises from the substantial increase in the degree of non-uniqueness of the mapping from the pavement layer parameters to the FWD deflections. The insensitivity of some layer properties lowered SOFTSYS model performances. Still, SOFTSYS models were shown to work effectively with the synthetic data obtained from ILLI-PAVE finite element solutions. In general, SOFTSYS solutions very closely matched the ILLI-PAVE mechanistic pavement analysis results. For SOFTSYS validation, field collected FWD data were successfully used to predict pavement layer thicknesses and layer moduli of in-service flexible pavements. Some of the very promising SOFTSYS results indicated average absolute errors on the order of 2%, 7%, and 4% for the Hot Mix Asphalt (HMA) thickness estimation of full-depth asphalt pavements, full-depth pavements on lime stabilized soils and conventional flexible pavements, respectively. The field validations of SOFTSYS data also produced meaningful results. The thickness data obtained from Ground Penetrating Radar testing matched reasonably well with predictions from SOFTSYS models. The differences observed in the HMA and lime stabilized soil layer thicknesses observed were attributed to deflection data variability from FWD tests. The backcalculated asphalt concrete layer thickness results matched better in the case of full-depth asphalt flexible pavements built on lime stabilized soils compared to conventional flexible pavements. Overall, SOFTSYS was capable of producing reliable thickness estimates despite the variability of field constructed asphalt layer thicknesses.

Mindfulness-Based Cognitive Therapy for older people in a community setting: a mixed methods feasibility study

Rationale: In line with complex intervention development, this research takes a systematic approach to examining the feasibility and acceptability of delivering Mindfulness-Based Cognitive Therapy (MBCT) to older people who experience symptoms of depression. Methods: A mixed methods approach was adopted in line with recommendations made by the MRC Complex Intervention Development framework. Quantitative and qualitative methods were combined by administering questionnaires as well as conducting post intervention interviews. A number of trial feasibility factors were examined such as recruitment and attrition rates. Qualitative data was analysed using Braun and Clarke’s thematic analysis framework. Results: Nine participants started the MBCT intervention and six completed the 8-week programme. The results suggest that MBCT for older people is feasible and acceptable. Participants reported improved mindfulness skills. Participants responded positively to being asked to take part in research and appeared to particularly value the group delivery format of the intervention. Conclusions: MBCT is both feasible and acceptable for older people experiencing symptoms of depression. Further research is required with larger sample sizes to allow for more robust statistical exploration of outcome measures, including mechanisms of change.

“Enjoy your baby” Internet-based CBT for mothers with babies: a feasibility randomised control trial

Background: Postnatal depression is a global health problem with lasting effects on the family. Government policy is focussed on early intervention and increasing access to psychological therapies. There is a growing evidence base for the use of computerised CBT packages and this study investigated the feasibility of a CBT-based self-help internet intervention for new mothers. Objective: To assess the ability to recruit mothers, deliver an internet course, obtain follow-up data and evaluate what mothers think of the course. Design: A feasibility randomised control design was used to compare a waiting list control group (delayed access= DA) to the Enjoy Your Baby course (immediate access= IA). Measures were administered at baseline and 8 week follow-up. Methods: Adverts were placed in the Metro freesheet, on charity web pages, on social media, posters were put up in the community, and leaflets were handed out at mother and baby groups. Participants had to be 18 years old or over with a child less than 18 months old. The IA arm was given access to the course straight away. After 8 weeks all participants were asked to recomplete the original measures and those in the IA arm also gave feedback on the course. Participants in the DA arm were given access after recompleting the questionnaires. Due to a lack of follow-up data a small discussion group was conducted. Intervention: The course contains 4 core modules including helping mothers understand why they feel the way they do and helping them build closeness to their babies. Additional modules, worksheets and homework tasks were available. The DA group were given a list of additional support resources and services, and encouraged to seek additional help if required. All participants received weekly automated emails for 12 weeks as they worked through the course. It was not possible to deliver individualised support. 34 Results: Despite using a number of recruitment strategies, recruitment was lower and slower than anticipated, and attrition was high. 41 women, primarily recruited via the internet, were randomised (IA n=21, DA n=20). No significant differences were observed between participants in either arm at baseline and no statistically significant differences were identified when the demographics and baseline measures of participants who logged-on to the course were compared to those who did not, or when participants who completed follow-up measures were compared to those who did not. Pre and post intervention scores on the EPDS approached statistical significance (P=.059, r=.444) favouring the intervention arm. The discussion group suggested strengths of the course and recommended areas for improvement, including making the course more mobile friendly. Conclusion: Internet interventions show promise; however it is difficult to recruit mothers, engagement is low and attrition high. A number of recommendations are made and a further pilot or an internal pilot of a larger substantive study should be conducted to confirm recruitment and retention. Trial ID: ISRCTN90927910.

Home based exercise programme for knee pain and knee osteoarthritis: randomised controlled trial

Objectives To determine whether a home based exercise programme can improve outcomes in patients with knee pain. Design Pragmatic, factorial randomised controlled trial of two years' duration. Setting Two general practices in Nottingham. Participants 786 men and women aged >45 years with self reported knee pain. Interventions Participants were randomised to four groups to receive exercise therapy, monthly telephone contact, exercise therapy plus telephone contact, or no intervention. Patients in the no intervention and combined exercise and telephone groups were randomised to receive or not receive a placebo health food tablet. Main outcome measures Primary outcome was self reported score for knee pain on the Western Ontario and McMaster universities (WOMAC) osteoarthritis index at two years. Secondary outcomes included knee specific physical function and stiffness (scored on WOMAC index), general physical function (scored on SF­36 questionnaire), psychological outlook (scored on hospital anxiety and depression scale), and isometric muscle strength. Results 600 (76.3%) participants completed the study. At 24 months, highly significant reductions in knee pain were apparent for the pooled exercise groups compared with the non­exercise groups (mean difference –0.82, 95% confidence interval –1.3 to –0.3). Similar improvements were observed at 6, 12, and 18 months. Regular telephone contact alone did not reduce pain. The reduction in pain was greater the closer patients adhered to the exercise plan. Conclusions A simple home based exercise programme can significantly reduce knee pain. The lack of improvement in patients who received only telephone contact suggests that improvements are not just due to psychosocial effects because of contact with the therapist.

Quality of implementation in an evidence-based family prevention program: the Family Competence Program

Family prevention programs need to be evidence-based in order to guarantee the success of their implementation. The Family Competence Program (FCP), a Spanish cultural adaptation of the Strengthening Families Program (SFP), has developed different measures and processes to gauge the quality of the implementation. This article is dedicated specifically to two of these measures: the evaluation of the facilitators and the assessment of the family engagement techniques. For evaluating the facilitators, a Delphi technique with experts and professionals is undertaken. For assessing the family techniques, both self-evaluation of trainers and evaluation by families are used. Finding underpin that, in the case of facilitators, is important that, after to skills and experience, they need to understand the theory of change of the program. In the case of family engagement techniques, more detailed, comprehensive talks, discussions and group activities lead to better family engagement outcomes.

Results of a mindfulness-based social-emotional learning program on portuguese elementary students and teachers: a quasi-experimental study

Recently, mindfulness-based social-emotional learning (SEL) approaches have been taught to children in some schools. Due to deficient methodological consistency observed in most studies, their results should be interpreted with caution. Moreover, research on how mindfulness-based SEL approaches benefit teachers is scarce, and the majority of these studies have been conducted in English-speaking countries; therefore, it is uncertain whether these approaches are suited to other cultural backgrounds. The aim of the present study was to evaluate the efficacy of the MindUp curriculum, an SEL program through mindfulness practice for Portuguese students and teachers. Participants included 454 3rd and 4th grade students and 20 teachers from state schools. A quasiexperimental (pre- and post-test) study compared outcomes for an experimental group with a waitlist control group. Data were collected from teachers and children through self-report measures. Results showed that over 50 % of the children who participated in the MindUp program scored above the control group mean in their ability to regulate emotions, to experience more positive affect, and to be more self-compassionate, and over 50 % scored lower in negative affect. In the group of teachers, over 80 % scored above the control group mean in observing, in personal accomplishment, and in self-kindness. Our results contribute to the recent research on the potential added value of mindfulness practices to a SEL program and strengthen the importance for teachers and students of adding to the academic curriculum a SEL program through mindfulness practices.

In-vitro evaluation of the quality of Paracetamol and Co-trimoxazole tablets used in Malawi based on pharmacopoeial standards

Objectives This study was an in-vitro evaluation of different brands of paracetamol and cotrimoxazole tablets, used or found in Malawi, based on Pharmacopoeia standards, in order to ascertain the existence and extent of substandard medicines in Malawi and to give an overview of their distribution in the public and private sectors. Methodology A cross-sectional analytical study was conducted using 11 samples each of paracetamol and cotrimoxazole tablets. Stratified random sampling was used to collect samples. Samples were analyzed using HPLC and Spectrophometric methods as outlined in the BP-2007 and USP-32 at the National Drug Quality Control Laboratory (NDQCL)-Lilongwe (under Pharmacy Medicines and Poisons Board-PMPB) and Orient Pharma Co. Ltd of Taiwan. The results were analyzed using Epi Info. Results and discussion Fifty percent of samples (n=22) were not registered in the country by the PMPB as required by the PMP Act with the majority of those coming from public health facilities. All paracetamol and cotrimoxazole samples complied with identification tests using spectrophotometric and HPLC method. Overall, 27.3% of samples failed to meet the BP-2007 standards for Active Ingredient content, while 22.7% of the samples failed the Friability test. The results from Malawi are similar in magnitude to those within surrounding countries in Africa. Conclusion This pilot study provides objective evidence to show that substandard and unregistered paracetamol and cotrimoxazole are present and being used in Malawi, and thus posing a considerable hazard to public health in Malawi. PMPB, together with the Ministry of Health, must continue to develop a quality assurance system to ensure that medicines are randomly and routinely checked.

Evaluation of antibiotic prescription for upper respiratory tract infections in the community pharmacy setting

This is an Open access article distributed under the terms of Creative Commons Attribution 4.0 International License. http://creativecommons.org/licenses/by/4.0/

Development of hydroxyapatite-based nanomaterials to enhance biological response of osteoblast cells for clinical application

Purpose: To develop a novel chitosan/gelatin-hydroxyapatite (CGHaP) microspheres for evaluating the biological response of pre-osteoblast cells. Methods: The microsphere was prepared by water-in-oil emulsion method. Cell proliferation was studied using AlamarBlue colorimetric assay and DAPI staining while alkaline phosphatase assay was carried out by colorimetric assay method. Chitosan microspheres as well as chitosan-hydroxyapatite microspheres was prepared and tested for biological response from MC3T3-E1 cell line. Results: The results showed that CGHaP promotes MC3T3-E1 cell proliferation and spread on the surface of microspheres. The cells were clustered with more actin filaments and well-linked with neighbouring cells or adjacent cells when cultured in CGHaP microspheres whereas fewer cells were spread on chitosan (CH) microspheres. CGHaP microspheres significantly (p < 0.05) promoted cell attachment, proliferation and extracellular matrix mineralization. CGHaP microspheres presented significantly (p < 0.02) higher calcium deposition (0.5 ng) than CH microspheres (0.28 ng). Specifically, CGHaP microspheres exhibited high ALP activity (8 units; 2-fold) compared to CH with 3 units, after 7 days of incubation. The results suggest that CGHaP possesses a great ability to facilitate bone ingrowth formation and possibility of good osteointegration in vivo. Conclusion: The nanomaterial enhances the proliferation of pre-osteoblast cells in tissue engineering microspheres. The outcome of this study may have a major impact on the development of novel nanomaterials for bone tissue engineering.