Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map

This work examines the conformational ensemble involved in β-hairpin folding by means of advanced molecular dynamics simulations and dimensionality reduction. A fully atomistic description of the protein and the surrounding solvent molecules is used, and this complex energy landscape is sampled by means of parallel tempering metadynamics simulations. The ensemble of configurations explored is analyzed using the recently proposed sketch-map algorithm. Further simulations allow us to probe how mutations affect the structures adopted by this protein. We find that many of the configurations adopted by a mutant are the same as those adopted by the wild-type protein. Furthermore, certain mutations destabilize secondary-structure-containing configurations by preventing the formation of hydrogen bonds or by promoting the formation of new intramolecular contacts. Our analysis demonstrates that machine-learning techniques can be used to study the energy landscapes of complex molecules and that the visualizations that are generated in this way provide a natural basis for examining how the stabilities of particular configurations of the molecule are affected by factors such as temperature or structural mutations.

Diagenetic Alterations and Reservoir Quality Evolution of Lower Cretaceous Fluvial Sandstones: Nubian Formation, Sirt Basin, North-Central Libya

Lower Cretaceous meandering and braided fluvial sandstones of the Nubian Formation form some of the most important subsurface reservoir rocks in the Sirt Basin, north-central Libya. Mineralogical, petrographical and geochemical analyses of sandstone samples from well BB6-59, Sarir oilfield, indicate that the meandering fluvial sandstones are fine- to very fine-grained subarkosic arenites (av. Q91F5L4), and that braided fluvial sandstones are medium- to very coarse-grained quartz arenites (av. Q96F3L1). The reservoir qualities of these sandstones were modified during both eodiagenesis (ca. <70oC; <2 km) and mesodiagenesis (ca. >70oC; >2km). Reservoir quality evolution was controlled primarily by the dissolution and kaolinitization of feldspars, micas and mud intraclasts during eodiagenesis, and by the amount and thicknessof grain-coating clays, chemical compaction and quartz overgrowths during mesodiagenesis. However, dissolution and kaolinitization of feldspars, micas and mud intraclasts resulted in the creation of intercrystalline micro- and mouldic macro-porosity and permeability during eodiagenesis, which were more widespread in braided fluvial than in meandering fluvial sandstones. This was because of the greater depositional porosity and permeability in the braided fluvial sandstones which enhanced percolation of meteoric waters. The development of only limited quartz overgrowths in the braided fluvial sandstones, in which quartz grains are coated by thick illite layers, retained high porosity and permeability (12-23 % and 30- 600 mD). By contrast, meandering fluvial sandstones underwent porosity loss as a result of quartz overgrowth development on quartz grains which lack or have thin and incomplete grain-coating illite (2-15 % and 0-0.1mD). Further loss of porosity in the meandering fluvial sandstones occurred as a result of chemical compaction (pressuredissolution) induced by the occurrence of micas along grains contacts. Otherdiagenetic alterations, such as the growth of pyrite, siderite, dolomite/ankerite and albitization, had little impact on reservoir quality. The albitization of feldspars may have had minor positive influence on reservoir quality throughthe creation of intercrystalline micro-porosity between albite crystals.The results of this study show that diagenetic modifications of the braided and meandering fluvial sandstones in the Nubian Formation, and resulting changes in reservoir quality, are closely linked to depositional porosity and permeability. They are also linked to the thickness of grain-coating infiltrated clays, and to variations in detrital composition, particularly the amounts of mud intraclasts, feldspars and mica grains as well as climatic conditions.

Cross-age tutoring in kindergarten and elementary school settings: a systmeatic review and meta-analysis

Background: Qualified teaching staffs are neither available nor affordable to provide large numbers of children with individual attention. One solution to providing individual tuition has been the development of tutoring programs that are delivered by nonprofessional tutors, such as classmates, older children and community volunteers. Objectives: We have conducted a systematic review of cross-age tutoring interventions delivered by non-professional tutors to children between 5 and 11 years old. Only randomized controlled trials with reliable measures of academic outcomes, and continuing for at least 12 weeks, compared to instruction as usual, were included. Results: Searches of electronic databases and previous reviews, and contacts with researchers yielded 11,564 titles; after screening, 15 studies were included in the analysis. Cross-age tutoring showed small significant effects for tutees on the composite measure of reading (g=0.18, 95% CI: 0.08, 0.27, N=8251), decoding skills (g=0.29, 95% CI: 0.13, 0.44, N=7081), and reading comprehension (g=0.11, 95% CI: 0.01, 0.21, N=6945). No significant effects were detected for other reading sub-skills or for mathematics. The quality of evidence is decreased by study limitations and high heterogeneity of effects. Conclusions: The benefits for tutees of non-professional peer and cross-age tutoring can be given a positive but weak recommendation, considering the low quality of evidence and lack of cost information. Subgroup analyses suggested that highly-structured reading programs may be more useful than loosely-structured programs. Large-scale replication trials using factorial design, process evaluations, reliable outcome measures and logic models are needed to better understand under what conditions, and for whom, cross-age non-professional tutoring may be effective.

Cross-age tutoring in kindergarten and elementary school settings: A systematic review and meta-analysis

This systematic review summarizes effects of peer tutoring delivered to children between 5 and 11 years old by non-professional tutors, such as classmates, older children and adult community peer volunteers. Inclusion criteria for the review included tutoring studies with a randomized controlled trial design, reliable measures of academic outcomes, and duration of at least 12 weeks. Searches of electronic databases, previous reviews, and contacts with researchers yielded 11,564 titles. After screening, 15 studies were included in the analysis. Cross-age tutoring showed small significant effects for tutees on the composite measure of reading (g = 0.18, 95% CI: 0.08, 0.27, N = 8251), decoding skills (g = 0.29, 95% CI: 0.13, 0.44, N = 7081), and reading comprehension (g = 0.11, 95% CI: 0.01, 0.21, N = 6945). No significant effects were detected for other reading sub-skills or for mathematics. The benefits to tutees of non-professional cross-age peer tutoring can be given a positive, but weak recommendation. Effect Sizes were modest and in the range −0.02 to 0.29. Questions regarding study limitations, lack of cost information, heterogeneity of effects, and the relatively small number of studies that have used a randomized controlled trial design means that the evidence base is not as strong as it could be. Subgroup analyses of included studies indicated that highly-structured reading programmes were of more benefit than those that were loosely-structured. Large-scale replication trials using factorial designs, reliable outcome measures, process evaluations and logic models are needed to better understand under what conditions, and for whom, cross-age non-professional peer tutoring may be most effective.

Algunas reflexiones sobre el Bronce Inicial en el Noroeste peninsular: La cuestión del llamado horizonte “Montelavar”

Although considerable effort has gone into the study of the subject, the Early Bronze Age of northwestern Iberia remains one of the more poorly understood phenomena of the Iberian Bronze Age. Most past attempts to systemise the relevant archaeological evidence did suffer from certain conceptual problems, particulary Harrison’s notion of a ‘Montelavar horizon’ or ‘Montelavar group’, formulated thirty years ago. As a consequence, neither this nor any of the other concepts which have been put forward in the past, has ever been embraced by a majority of scholars. In the present article, we are trying to solve at least some of the problems that plagued earlier concepts, by taking a fresh look at the Early Bronze Age funerary record from northwestern Iberia. At the same time, we are looking at the role played by Galicia and northern Portugal in the network of interregional contacts which characterize the Early Bronze Age in Western Europe.

General practitioners perceptions on advance care planning for patients living with dementia

BACKGROUND: Advance care planning (ACP) facilitates communication and understanding of preferences, nevertheless the use of ACPs in primary care is low. The uncertain course of dementia and the inability to communicate with the patient living with dementia are significant challenges for GPs to initiate discussions on goals of care.

METHODS: A cross-sectional survey, using a purposive, cluster sample of GPs across Northern Ireland with registered dementia patients was used. GPs at selected practices received the survey instrument and up to four mail contacts was implemented.

RESULTS: One hundred and thirty-three GPs (40.6%) participated in the survey, representing 60.9% of surveyed practices. While most respondents regarded dementia as a terminal disease (96.2%) only 37.6% felt that palliative care applied equally from the time of diagnosis to severe dementia. While most respondents thought that early discussions would facilitate decision-making during advanced dementia (61%), respondents were divided on whether ACP should be initiated at the time of diagnoses. While most respondents felt that GPs should take the initiative to introduce and encourage ACP, most survey participants acknowledged the need for improved knowledge to involve families in caring for patients with dementia at the end of life and that a standard format for ACP documentation was needed.

CONCLUSION: Optimal timing of ACP discussions should be determined by the readiness of the patient and family carer to face to face end of life. ACP discussions can be enhanced by educational strategies directed towards the patient and family carer that enable shared decision-making with their GP when considering options in future care.

Tooth replacement for partially dentate elders: a randomised controlled trial

Objective: This study aimed to compare two different tooth replacement strategies for partially dentate older patients namely; removable partial dentures (RPDs) and functionally orientated treatment based on the shortened dental arch (SDA) concept. Method: 88 partially dentate older patients (mean age 69.4 years) completed a randomised controlled clinical trial. 43 patients received RPDs and 45 received functionally orientated treatment where resin bonded bridgework was used to provide 10 pairs of occluding contacts. Patients were followed for 1 year after treatment intervention. The impact of treatment on oral health-related quality of life (OHrQOL) and cost effectiveness were used as outcome measures. Each patient completed the short form of the Oral Health Impact Profile (OHIP-14) at baseline, 6 months and 1 year after treatment intervention. All costs involved in providing and maintaining each intervention were recorded including dental laboratory bills, materials and professional time. Result: Both the RPD (p=0.004) and the functionally orientated (p<0.001) treatment groups demonstrated statistically significant improvements in OHrQOL 1 year after treatment intervention. On average 9.4 visits were required to complete and maintain the RPDs over the 1 year period as compared to 5.3 visits for the functionally orientated group. The average laboratory cost for the RPDs was $537.45 per patient versus $367.89 for functionally orientated treatment. The cost of achieving the Minimally Important Difference of 5 scale points in OHIP-14 score with RPDs was $732.17. For the functionally orientated group the cost was $356.88. Therefore, functionally orientated treatment was more than twice as cost effective (1:2.05). Conclusion: For partially dentate older patients, functionally orientated treatment based on the SDA concept resulted in sustained, significant improvements in OHrQOL. Provision of functionally orientated treatment was also more than twice as cost effective compared to conventional treatment using RPDs.

Cost Effectiveness of Tooth Replacement Strategies for Partially Dentate Elders

Objectives: This study aimed to compare the cost effectiveness of conventional treatment using partial dentures with functionally-orientated treatment based on the shortened dental arch concept to replace missing teeth for partially dentate elders.
Methods: 44 partially dentate patients aged 65 years and older were recruited following routine dental assessment at a university dental hospital. Patients consented to and were randomly assigned to the two treatment arms. The conventional treatment group received a removable partial denture to replace all missing natural teeth. The functionally-orientated group were restored to a shortened dental arch of 10 occluding contacts using resin bonded bridgework. The costs associated with each treatment were recorded including laboratory charges, treatment time and opportunity costs. The impact on quality of life (OHRQoL) was measured using the 14-item Oral Health Impact Profile.
Results: Both groups reported improvements in OHRQoL after completion of treatment. For the conventional group, the mean OHIP-14 score decreased from 12.4 pre-operatively to 3.3 post-operatively (p<0.001). In the functionally-orientated group the OHIP-14 score decreased from 11.4 to 1.8 following treatment (p<0.001). On average the conventional treatment group required 8.3 clinic visits as compared to 4.4 visits for the functionally-orientated group. The mean total treatment time was 183 minutes 19 seconds for the conventional group versus 124 minutes 8 seconds for the functionally-orientated group. The conventional treatment group had an average of 6.33 teeth replaced at a laboratory cost of 337.31 Euros. The functionally-orientated group had an average of 2.64 teeth replaced at a laboratory cost of 244.05 Euros.
Conclusions: Restoration to a shortened dental arch using functionally-orientated treatment resulted in a similar improvement in OHRQoL with fewer clinic visits, less operative time and at a lower laboratory cost compared with conventional treatment.

Relationships between Oral Health and Nutritional Status of Older Adults

Objectives: The World Health Organisation has highlighted the paucity of research into the oral health needs of older adults. In particular, the relationships between oral health and nutritional status require further investigation and analysis. This study aimed to describe some of the relationships between the number of remaining occluding tooth contacts, oral health related quality of life and nutritional status of partially dentate older adults.

Methods: 45 partially dentate patients aged 65 years and older were recruited to the study after visiting a university dental hospital. An initial dental examination charted the remaining teeth including the number of occluding contacts. Oral health related quality of life was recorded using the 14 item Oral Health Impact Profile. Nutritional status was measured using the Mini Nutritional Assessment (MNA) in addition to biochemical analysis of a haematological sample. Correlation between data values was measured using a Pearson's correlation coefficient (r).

Results: The patient sample was made up of 44% males and 56% females with a mean age of 72.4 years (range 65-84 years). With increasing age the patients' oral health related quality of life scores improved. (r=-0.25) Within the sample the number of occluding tooth contacts ranged from 6 to 11. It was found that as the number of occluding contacts increased, better oral health related quality of life scores were recorded. (r=-0.30) Generally mini nutritional assessment scores improved with increasing numbers of tooth contacts. (r=0.14) In addition, as the number of occluding teeth contacts increased total lymphocyte count (r=0.35), vitamin B12 (r=0.22) and serum folate (r=0.06) all increased.

Conclusions: In older patients increased numbers of tooth contacts are associated with better oral health related quality of life. Increasing numbers of occluding contacts are also associated with better MNA scores and some haematological indicators of nutritional status.

A systematic review and meta-analysis of the survival of non-feldspathic porcelain veneers over 5 and 10 years

PURPOSE: This systematic review aimed to report and explore the survival of dental veneers constructed from non-feldspathic porcelain over 5 and 10 years.

MATERIALS AND METHODS: A total of 4,294 articles were identified through a systematic search involving all databases in the Cochrane Library, MEDLINE (OVID), EMBASE, Web of Knowledge, specific journals (hand-search), conference proceedings, clinical trials registers, and collegiate contacts. Articles, abstracts, and gray literature were sought by two independent researchers. There were no language limitations. One hundred sixteen studies were identified for full-text assessment, with 10 included in the analysis (5 qualitative, 5 quantitative). Study characteristics and survival (Kaplan-Meier estimated cumulative survival and 95% confidence interval [CI]) were extracted or recalculated. A failed veneer was one which required an intervention that disrupted the original marginal integrity, had been partially or completely lost, or had lost retention more than twice. A meta-analysis and sensitivity analysis of Empress veneers was completed, with an assessment of statistical heterogeneity and publication bias. Clinical heterogeneity was explored for results of all veneering materials from included studies.

RESULTS: Within the 10 studies, veneers were fabricated with IPS Empress, IPS Empress 2, Cerinate, and Cerec computer-aided design/computer-assisted manufacture (CAD/CAM) materials VITA Mark I, VITA Mark II, Ivoclar ProCad. The meta-analysis showed the pooled estimate for Empress veneers to be 92.4% (95% CI: 89.8% to 95.0%) for 5-year survival and 66% to 94% (95% CI: 55% to 99%) for 10 years. Data regarding other non-feldspathic porcelain materials were lacking, with only a single study each reporting outcomes for Empress 2, Cerinate, and various Cerec porcelains over 5 years. The sensitivity analysis showed data from one study had an influencing and stabilizing effect on the 5-year pooled estimate.

CONCLUSION: The long-term outcome (> 5 years) of non-feldspathic porcelain veneers is sparsely reported in the literature. This systematic review indicates that the 5-year cumulative estimated survival for etchable non-feldspathic porcelain veneers is over 90%. Outcomes may prove clinically acceptable with time, but evidence remains lacking and the use of these materials for veneers remains experimental.

Free fatty acid receptors:structural models and elucidation of ligand binding interactions

BACKGROUND: The free fatty acid receptors (FFAs), including FFA1 (orphan name: GPR40), FFA2 (GPR43) and FFA3 (GPR41) are G protein-coupled receptors (GPCRs) involved in energy and metabolic homeostasis. Understanding the structural basis of ligand binding at FFAs is an essential step toward designing potent and selective small molecule modulators.

RESULTS: We analyse earlier homology models of FFAs in light of the newly published FFA1 crystal structure co-crystallized with TAK-875, an ago-allosteric ligand, focusing on the architecture of the extracellular binding cavity and agonist-receptor interactions. The previous low-resolution homology models of FFAs were helpful in highlighting the location of the ligand binding site and the key residues for ligand anchoring. However, homology models were not accurate in establishing the nature of all ligand-receptor contacts and the precise ligand-binding mode. From analysis of structural models and mutagenesis, it appears that the position of helices 3, 4 and 5 is crucial in ligand docking. The FFA1-based homology models of FFA2 and FFA3 were constructed and used to compare the FFA subtypes. From docking studies we propose an alternative binding mode for orthosteric agonists at FFA1 and FFA2, involving the interhelical space between helices 4 and 5. This binding mode can explain mutagenesis results for residues at positions 4.56 and 5.42. The novel FFAs structural models highlight higher aromaticity of the FFA2 binding cavity and higher hydrophilicity of the FFA3 binding cavity. The role of the residues at the second extracellular loop used in mutagenesis is reanalysed. The third positively-charged residue in the binding cavity of FFAs, located in helix 2, is identified and predicted to coordinate allosteric modulators.

CONCLUSIONS: The novel structural models of FFAs provide information on specific modes of ligand binding at FFA subtypes and new suggestions for mutagenesis and ligand modification, guiding the development of novel orthosteric and allosteric chemical probes to validate the importance of FFAs in metabolic and inflammatory conditions. Using our FFA homology modelling experience, a strategy to model a GPCR, which is phylogenetically distant from GPCRs with the available crystal structures, is discussed.

Symposium - Organisational transformation in policing: Leadership and change in extreme contexts

Nearly 4000 people died in Northern Ireland’s long running conflict, 314 of them police officers (Brewer and Magee 1991, Brewer 1996, Hennessey 1999, Guelke and Milton-Edwards 2000). The republican and loyalist ceasefires of 1994 were the first significant signal that NI society was moving beyond the ‘troubles’ and towards a normalised political environment. The Belfast (Good Friday) Agreement of 1998 cemented that movement (Hennessey 1999). Policing was a key and seemingly unresolvable element of the conflict, seen as unrepresentative and partisan. Its reform or ‘recasting’ in a new dispensation was an integral part of the conflict transformation endeavour(Ellison 2010). As one of the most controversial elements of the conflicted past, it had remained outside the Agreement and was subject to a specific commission of interest (1999), generally known as the Patten Commission. The Commission’s far reaching proposals included a change of name, badge and uniform, the introduction of 50/50 recruitment (50% Roman Catholic and 50% other), a new focus on human rights, a new district command and headquarter structure, a review of ‘Special Branch’ and covert techniques, a concern for ‘policing with the community’ and a significant voluntary severance process to make room for new recruits, unconnected with the past history of the organisation(Murphy 2013).

This paper reflects upon the first data collection phase of a long term processual study of organisational change within the Royal Ulster Constabulary / Police Service of Northern Ireland. This phase (1996-2002) covers early organisational change initiation (including the pre-change period) and implementation including the instigation of symbolic changes (name, badge, and crest) and structural changes (new HQ structure and District Command structure). It utilises internal documentation including messages from the organisations leaders, interviews with forty key informants (identified through a combination of snow-balling from referrals by initial contacts, and key interviews with significant individuals), as well as external documentation and commentary on public perceptions of the change. Using a processual lens (Langley, Smallman et al. 2013) it seeks to understand this initial change phase and its relative success in a highly politicised environment.

By engaging key individuals internally and externally, setting up a dedicated change team, adopting a non normative, non urgent, calming approach to dissent, communicating in orthodox and unorthodox ways with members, acknowledging the huge emotional strain of letting go of the organisation’s name and all it embodied, and re-emphasising the role of officers as ‘police first’, rather than ‘RUC first’, the organisations leadership remained in control of a volatile and unhappy organisational body and succeeded in moving it on through this initial phase, even while much of the political establishment lambasted them externally. Three years into this change process the organisation had a new name, a new crest, new structures, procedures and was deeply engaged in embedding the joint principles of human rights and community policing within its re-woven fabric. While significant problems remained, the new Police Service of Northern Ireland had successfully begun a long journey to full community acceptance in a post conflict context.

This case illustrates the significant challenges of leading change under political pressure, with external oversight and no space for failure(Hannah, Uhl-Bien et al. 2009). It empirically reflects the reality of change implementation as messy, disruptive and unpredictable and highlights the significance of political skill and contextual understanding to success in the early stages(Buchanan and Boddy 1992). The implications of this for change theory and the practice of change implementation are explored (Eisenhardt and Graebner 2007) and some conclusions drawn about what such an extreme case tells us about change generally and change implementation under pressure.

Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled 'reservoir' host, as for bovine tuberculosis (bTB) in British and Irish cattle and badgers. BTB is caused by Mycobacterium bovis, a member of the M. tuberculosis complex that also includes the aetiological agent for human TB. In this study, we identified a spatio-temporally linked group of 26 cattle and 4 badgers infected with the same Variable Number Tandem Repeat (VNTR) type of M. bovis. Single-nucleotide polymorphisms (SNPs) between sequences identified differences that were consistent with bacterial lineages being persistent on or near farms for several years, despite multiple clear whole herd tests in the interim. Comparing WGS data to mathematical models showed good correlations between genetic divergence and spatial distance, but poor correspondence to the network of cattle movements or within-herd contacts. Badger isolates showed between zero and four SNP differences from the nearest cattle isolate, providing evidence for recent transmissions between the two hosts. This is the first direct genetic evidence of M. bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. However, despite unprecedented resolution, directionality of transmission cannot be inferred at this stage. Despite the often notoriously long timescales between time of infection and time of sampling for TB, our results suggest that WGS data alone can provide insights into TB epidemiology even where detailed contact data are not available, and that more extensive sampling and analysis will allow for quantification of the extent and direction of transmission between cattle and badgers. © 2012 Biek et al.

Local conductance: A means to extract polarization and depolarizing fields near domain walls in ferroelectrics

Conducting atomic force microscopy images of bulk semiconducting BaTiO3 surfaces show clear stripe domain contrast. High local conductance correlates with strong out-of-plane polarization (mapped independently using piezoresponse force microscopy), and current- voltage characteristics are consistent with dipole-induced alterations in Schottky barriers at the metallic tip-ferroelectric interface. Indeed, analyzing current-voltage data in terms of established Schottky barrier models allows relative variations in the surface polarization, and hence the local domain structure, to be determined. Fitting also reveals the signature of surface-related depolarizing fields concentrated near domain walls. Domain information obtained from mapping local conductance appears to be more surface-sensitive than that from piezoresponse force microscopy. In the right materials systems, local current mapping could therefore represent a useful complementary technique for evaluating polarization and local electric fields with nanoscale resolution.

Interventions to increase physical activity in patients with COPD: A comprehensive review

It is unknown how interventions aimed at increasing physical activity (PA), other than traditional pulmonary rehabilitation, are structured and whether they are effective in increasing PA in chronic obstructive pulmonary disease (COPD). The primary aim of this review was to outline the typical components of PA interventions in patients with COPD. This review followed the PRISMA guidelines. A structured literature search of relevant electronic databases from inception to April 2014 was undertaken to outline typical components and examine outcome variables of PA interventions in patients with COPD. Over 12000 articles were screened and 20 relevant studies involving 31 PA interventions were included. Data extracted included patient demographics, components of the PA intervention, PA outcome measures and effects of the intervention. Quality was assessed using the PEDro and CASP scales. There were 13 randomised controlled trials and three randomised trials (PEDro score 5-7/10) and four cohort studies (CASP score 5/10). Interventions varied in duration, number of participant/researcher contacts and mode of delivery. The most common behaviour change techniques included information on when and where (n = 26/31) and how (n = 22/31) to perform PA behaviour and self-monitoring (n = 18/31). Significant between-group differences post-intervention in favour of the PA intervention, compared to a control group or to other PA interventions, in one or more PA assessments were found in 7/16 studies. All seven studies used walking as the main type of PA/exercise. In conclusion, although the components of PA interventions were variable, there is some evidence that PA interventions have the potential to increase PA in patients with COPD