Human Adaptation in Asian Palaeolithic:Hominin Dispersal and Behaviour during the Late Quaternary

This book examines the first human colonization of Asia and particularly the tropical environments of Southeast Asia during the Upper Pleistocene. In studyexamining the unique character of the Asian archaeological record, it reassesses long-accepted propositions about the development of human ‘modernity.’ Ryan J. Rabett reveals an evolutionarily relationship between colonization, the challenges encountered during this process – especially in relation to climatic and environmental change – and the forms of behaviour that emerged. This book argues that human ‘modernity’ is not something achieved in the remote past in one part of the world, but rather is a diverse, flexible, responsive, and on-going process of adaptation, one that continues to this day.

The Fasciola hepatica genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution

BACKGROUND: The liver fluke Fasciola hepatica is a major pathogen of livestock worldwide, causing huge economic losses to agriculture, as well as 2.4 million human infections annually.

RESULTS: Here we provide a draft genome for F. hepatica, which we find to be among the largest known pathogen genomes at 1.3 Gb. This size cannot be explained by genome duplication or expansion of a single repeat element, and remains a paradox given the burden it may impose on egg production necessary to transmit infection. Despite the potential for inbreeding by facultative self-fertilisation, substantial levels of polymorphism were found, which highlights the evolutionary potential for rapid adaptation to changes in host availability, climate change or to drug or vaccine interventions. Non-synonymous polymorphisms were elevated in genes shared with parasitic taxa, which may be particularly relevant for the ability of the parasite to adapt to a broad range of definitive mammalian and intermediate molluscan hosts. Large-scale transcriptional changes, particularly within expanded protease and tubulin families, were found as the parasite migrated from the gut, across the peritoneum and through the liver to mature in the bile ducts. We identify novel members of anti-oxidant and detoxification pathways and defined their differential expression through infection, which may explain the stage-specific efficacy of different anthelmintic drugs.

CONCLUSIONS: The genome analysis described here provides new insights into the evolution of this important pathogen, its adaptation to the host environment and external selection pressures. This analysis also provides a platform for research into novel drugs and vaccines.

Nutritional Status of older patients attending Cork University Dental School and Hospital

Objectives: This study aimed to gather data on the nutritional status of older patients attending Cork University Dental School and Hospital for treatment in the Restorative Department. Information was also collected about the medical status of the patients including the prevalence of self-reported xerostomia.
Methods: Data was collected by a self-completion questionnaire followed by a brief clinical examination. Nutritional Status was measured using the short version of the Mini Nutritional Assessment (MNA) which recorded patients’ Body Mass Index (BMI). The MNA consists of 6 parameters (including questions relating to patients’ history and anthropometric data) with a maximum total of 14 points. Scores of 12-14 indicate “normal nutritional status” whilst those between 8 and 11 indicate a patient “at risk of malnutrition”. Scores lower than 8 are an indication a patient who is “malnourished”. All patients attending Cork University Dental School and Hospital aged 65 years and older were invited to participate in the study.

Results: A total of 22 subjects participated in this study. Twelve patients were partially dentate with 10 edentulous. The results from the MNA indicate that 11 patients were of “normal nutritional status” with 11 patients identified as being “at risk of malnutrition”. None of the subjects were “malnourished”. Edentate patients generally recorded lower MNA scores than partially dentate patients. In total, 9 patients reported experiencing xerostomia with 8 indicating that they needed to sip liquids to aid swallowing but only 3 had difficulty swallowing food.

Conclusion: This small study indicates that a number of the older patients attending Cork University Dental School and Hospital for dental care may be “at risk of malnutrition”. These findings suggest that nutritional advice and dental care should both be included in an overall package of care for older patients.

Proportioning variability in the dispensation of hand-mixed dental cements

Objectives: The purpose of this investigation was to determine for dispensed multiples (1 through 4) of powder (P) and liquid (L) in hand-mixed dental cement whether: (1) the mean (P/L) ratio (m/m) and (2) the maximum difference in (P/L) ratio is dependent on the number of multiples dispensed. The Null hypotheses were: (a) mean (P/L) ratio is independent of the number of multiples dispensed and (b) maximum difference in (P/L) ratio is independent of the number of multiples dispensed.
Methods: The materials investigated are listed in the Table. The masses of dispensed aliquots of powder and liquid were measured by a single operator (n=10, for multiples 1 through 4) on a 4-place analytical balance. All measurements were made independently and all possible (P/L) ratios calculated for each sample. The effect of multiple dispensations on (P/L) ratios and maximum (P/L) differences was by one-way ANOVA and linear regression, respectively, with the Tukey post-hoc correction for multiple comparisons.MULTIPLE DISPENSEDDISPENSED MU(x1)(x2)(x3)(x4)Zinc phosphateHeraeus12.271(0.691)a13.051(1.269)b13.215(0.824)b13.118(1.149)bFuji IXGC4.209(0.373)a4.085(0.275)b4.095(0.226)b4.095(0.217)bIRMDentsply7.933(0.767)a7.430(0.451)b7.977(0.729)a8.186(0.929)aKetac-Cem3M Espe9.6206(0.613)a9.714(0.523)a9.298(0.314)b9.321(0.292)bMean (SD) powder/liquid ratio (m/m). Superscript letters represent significances (α = 0.05) within each material
Results: Mean (SD) (P/L) ratios are presented in the Table. Null hypothesis (a) is rejected: either (x1) or (x2) dispensation yields a different (P/L) ratio to (x3) or (x4) (p < 0.05). Null hypothesis (b) is rejected: a negative correlation is observed in max (P/L) ratio difference with dispensed multiple for Ketac Cem (p = 0.029).
Conclusion: For hand-mixed dental cements: (1) more consistent (P/L) ratios may be observed with multiple dispensations of powder & liquid; (2) maximum differences in (P/L) ratio may be negatively correlated with dispensation multiple in some materials.

The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Understanding the extent, scale and genetic basis of local adaptation is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here we compare the fitness of communally-reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically-based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.

Quality of reporting of dental survival analyses

To explore the quality of reporting (writing and graphics) of articles that used time-to-event analyses to report dental treatment outcomes. A systematic search of the top 50 dental journals in 2008 produced the sample of articles for this analysis. Articles reporting treatment outcomes with (n = 95) and without (n = 91) time-to-event statistics were reviewed. Survival descriptive words used in the two groups were analysed (Pearson's chi-square). The quality of life tables, survival curves and time-to-event statistics were assessed (Kappa analysed agreement) and explored. Words describing dental outcomes 'over time' were more common in time-to-event compared with control articles (77%, 3%, P < 0.001). Non-specific use of 'rate' was common across both groups. Life tables and survival curves were used by 39% and 48% of the time-to-event articles, with at least one used by 82%. Construction quality was poor: 21% of life tables and 28% of survival curves achieved an acceptable standard. Time-to-event statistical reporting was poor: 3% achieved a high and 59% achieved an acceptable standard. The survival statistic, summary figure and standard error were reported in 76%, 95% and 20% of time-to-event articles. Individual statistical terms and graphic aids were common within and unique to time-to-event articles. Unfortunately, important details were regularly omitted from statistical descriptions and survival figures making the overall quality poor. It is likely this will mean such articles will be incorrectly indexed in databases, missed by searchers and unable to be understood completely if identified.

Accuracy of medical subject heading indexing of dental survival analyses

PURPOSE: To assess the Medical Subject Headings (MeSH) indexing of articles that employed time-to-event analyses to report outcomes of dental treatment in patients.

MATERIALS AND METHODS: Articles published in 2008 in 50 dental journals with the highest impact factors were hand searched to identify articles reporting dental treatment outcomes over time in human subjects with time-to-event statistics (included, n = 95), without time-to-event statistics (active controls, n = 91), and all other articles (passive controls, n = 6,769). The search was systematic (kappa 0.92 for screening, 0.86 for eligibility). Outcome-, statistic- and time-related MeSH were identified, and differences in allocation between groups were analyzed with chi-square and Fischer exact statistics.

RESULTS: The most frequently allocated MeSH for included and active control articles were "dental restoration failure" (77% and 52%, respectively) and "treatment outcome" (54% and 48%, respectively). Outcome MeSH was similar between these groups (86% and 77%, respectively) and significantly greater than passive controls (10%, P < .001). Significantly more statistical MeSH were allocated to the included articles than to the active or passive controls (67%, 15%, and 1%, respectively, P < .001). Sixty-nine included articles specifically used Kaplan-Meier or life table analyses, but only 42% (n = 29) were indexed as such. Significantly more time-related MeSH were allocated to the included than the active controls (92% and 79%, respectively, P = .02), or to the passive controls (22%, P < .001).

CONCLUSIONS: MeSH allocation within MEDLINE to time-to-event dental articles was inaccurate and inconsistent. Statistical MeSH were omitted from 30% of the included articles and incorrectly allocated to 15% of active controls. Such errors adversely impact search accuracy.

Will your article be found? Authors choose a confusing variety of words to describe dental survival analyses

OBJECTIVES: Identify the words and phrases that authors used to describe time-to-event outcomes of dental treatments in patients.

MATERIALS AND METHODS: A systematic handsearch of 50 dental journals with the highest Citation Index for 2008 identified articles reporting dental treatment with time-to-event statistics (included "case" articles, n = 95), without time-to-event statistics (active "control" articles, n = 91), and all other articles (passive "control" articles n = 6796). The included and active controls were read, identifying 43 English words across the title, aim and abstract, indicating that outcomes were studied over time. Once identified, these words were sought within the 6796 passive controls. Words were divided into six groups. Differences in use of words were analyzed with Pearson's chi-square across these six groups, and the three locations (title, aim, and abstract).

RESULTS: In the abstracts, included articles used group 1 (statistical technique) and group 2 (statistical terms) more frequently than the active and passive controls (group 1: 35%, 2%, 0.37%, P < 0.001 and group 2: 31%, 1%, 0.06%, P < 0.001). The included and active controls used group 3 (quasi-statistical) equally, but significantly more often than the passive controls (82%, 78%, 3.21%, P < 0.001). In the aims, use of target words was similar for included and active controls, but less frequent for groups 1-4 in the passive controls (P < 0.001). In the title, group 2 (statistical techniques) and groups 3-5 (outcomes) were similar for included and active controls, but groups 2 and 3 were less frequent in the passive controls (P < 0.001). Significantly more included articles used group 6 words (stating the study duration) (54%, 30%, P = 0.001).

CONCLUSION: All included articles used time-to-event analyses, but two-thirds did not include words to highlight this in the abstract. There is great variation in the words authors used to describe dental time-to-event outcomes. Electronic identification of such articles would be inconsistent, with low sensitivity and specificity. Authors should improve the reporting quality. Journals should allow sufficient space in abstracts to summarize research, and not impose unrealistic word limits. Readers should be mindful of these problems when searching for relevant articles. Additional research is required in this field.

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.

Pre-Radiotherapy Dental Assessment of Head and Neck Oncology Patients: An Audit.

Objectives: Approximately 300 people are diagnosed with Head and Neck cancer annually in Northern Ireland. The management may include treatment by surgery or by chemotherapy and radiotherapy,
or a combination of modalities. Patients whose oral cavity, teeth, salivary glands and jaws that
will be affected by treatment, particularly radiotherapy should have a pre-treatment assessment. This should be done as early as possible to maximise the time available for dental management. However, this can be challenging owing to the complexities of cancer diagnosis, treatment planning and multidisciplinary management. At the Belfast Dental Hospital, a number of patients were referred post- radiotherapy with complications after not having received a pre-treatment assessment. The referrals for pre- treatment dental assessment were also late in patients’ multidisciplinary journey, limiting the time period
for dental input. The purpose of this audit was to examine the time period between dental assessment and commencement of radiotherapy and whether this was an adequate time frame for dental management. This audit will also examine the dental diseases present and the treatments required pre-radiotherapy. Methods: Data for this audit was collected over 4 months in 2012
by analysing the dental charts and referrals of new patients who were referred to and attended the dental head and neck oncology clinic. A standardised referral pro-forma was introduced from September 2013 to improve the referral process.
A re-audit was conducted over 4 months in 2014. Data was collected similarly as previous. The time period between dental assessment and commencement of radiotherapy was examined. The presence of dental disease and subsequent treatments required were also noted.
Results: 63 new patients were examined in the dental head and neck oncology clinic over 4 months in 2012. 48 (76.2%) were examined pre-radiotherapy. The average length of time between dental assessment and radiotherapy commencement was 11 days. A new standardised referral pro-forma was introduced in 2013. In the re-audit, 65 new patients were seen over 4 months in 2014.
60 (92.3%) patients were examined pre-radiotherapy. The average length of time between dental assessment and radiotherapy commencement was 18 days.
Conclusion: Given the high prevalence of pre-existing dental disease amongst head and neck cancer patients, prompt dental assessment and treatment is vital. Efforts aimed at improving the care pathway are on-going through the implementation of a mandatory referral pro-forma and a dedicated assessment clinic.