Distribution of arsenic and risk assessment of activities on a golf course fertilised with arsenic-containing Ascophyllum nodosum seaweed

The use of seaweed fertilisers in sports green maintenance has become a common practice across the globe due to its image as an “eco-friendly” alternative to chemical fertilisers. The aim of this study was to characterise the risk of human exposure to arsenic (As), via dermal absorption, from golfing activities on a private golf course in the UK, where As contaminated seaweed fertiliser (~ 100 mg/kg d.wt.) is applied. This was fulfilled by, 1) determining As concentrations in shallow soils with GIS geo-statistical analysis, 2) measuring As concentrations from an on-site borehole groundwater well, and (3) developing a risk assessment calculation for golfing activities based on field and questionnaire data. Total As concentrations in shallow soils were less than the UK threshold for domestic soils, however, frequent and sustained dermal contact between site-users and surface soil attributed to a maximum carcinogenic risk value of 2.75 × 10− 4, which is in the upper limit of the acceptable risk range. Arsenic concentrations in underlying groundwater exceeded the WHO's permissible drinking water standard, demonstrating the risk of groundwater contamination following the application of seaweed fertiliser to golf course soils. This is the first risk study on dermal As absorption via the application of a seaweed fertiliser.

Scientific standards for human intervention trials evaluating health benefits of foods, and their application to infants, children and adolescents

Associations between the consumption of particular foods and health outcomes may be indicated by observational studies. However, intervention trials that evaluate the health benefits of foods provide the strongest evidence to support dietary recommendations for health. Thus, it is important that these trials are carried out safely, and to high scientific standards. Accepted standards for the reporting of the health benefits of pharmaceutical and other medical interventions have been provided by the Consolidated Standards of Reporting Trials (CONSORT) statement. However, there are no generally accepted standards for trials to evaluate the health benefits of foods. Trials with foods differ from medical trials in issues related to safety, ethics, research governance and practical implementation. Furthermore, these important issues can deter the conduct of both medical and nutrition trials in infants, children and adolescents. This paper provides standards for the planning, design, conduct, statistical analysis and interpretation of human intervention trials to evaluate the health benefits of foods that are based on the CONSORT guidelines, and outlines the key issues that need to be addressed in trials in participants in the paediatric age range.

Distribution of terminal nerve entry points to the flexor and extensor groups of forearm muscles:An anatomical study

The motor points of the skeletal muscles, mainly of interest to anatomists and physiologists, have recently attracted much attention from researchers in the field of functional electrical stimulation. The muscle motor point has been defined as the entry point of the motor nerve branch into the epimysium of the muscle belly. Anatomists have pointed out that many muscles in the limbs have multiple motor points. Knowledge of the location of nerve branches and terminal nerve entry points facilitates the exact insertion and the suitable selection of the number of electrodes required for each muscle for functional electrical stimulation. The present work therefore aimed to describe the number, location, and distribution of motor points in the human forearm muscles to obtain optimal hand function in many clinical situations. Twenty three adult human cadaveric forearms were dissected. The numbers of primary nerves and motor points for each muscle were tabulated. The mean numbers and the standard deviation were calculated and grouped in tables. Data analyses were performed with the use of a statistical analysis package (SPSS 13.0). The proximal third of the muscle was the usual part of the muscle that received the motor points. Most of the forearm muscles were innervated from the lateral side and deep surface of the muscle. The information in this study may also be usefully applied in selective denervation procedures to balance muscles in spastic upper limbs. Copyright © 2007 Via Medica.

Computational cancer biology: education is a natural key to many locks

Background: Oncology is a field that profits tremendously from the genomic data generated by high-throughput technologies, including next-generation sequencing. However, in order to exploit, integrate, visualize and interpret such high-dimensional data efficiently, non-trivial computational and statistical analysis methods are required that need to be developed in a problem-directed manner.

Discussion: For this reason, computational cancer biology aims to fill this gap. Unfortunately, computational cancer biology is not yet fully recognized as a coequal field in oncology, leading to a delay in its maturation and, as an immediate consequence, an under-exploration of high-throughput data for translational research.

Summary: Here we argue that this imbalance, favoring 'wet lab-based activities', will be naturally rectified over time, if the next generation of scientists receives an academic education that provides a fair and competent introduction to computational biology and its manifold capabilities. Furthermore, we discuss a number of local educational provisions that can be implemented on university level to help in facilitating the process of harmonization.

Evaluating the use of testate amoebae for palaeohydrological reconstruction in permafrost peatlands

The melting of high-latitude permafrost peatlands is a major concern due to a potential positive feedback on global climate change. We examine the ecology of testate amoebae in permafrost peatlands, based on sites in Sweden (~ 200 km north of the Arctic Circle). Multivariate statistical analysis confirms that water-table depth and moisture content are the dominant controls on the distribution of testate amoebae, corroborating the results from studies in mid-latitude peatlands. We present a new testate amoeba-based water table transfer function and thoroughly test it for the effects of spatial autocorrelation, clustered sampling design and uneven sampling gradients. We find that the transfer function has good predictive power; the best-performing model is based on tolerance-downweighted weighted averaging with inverse deshrinking (performance statistics with leave-one-out cross validation: R2 = 0.87, RMSEP = 5.25 cm). The new transfer function was applied to a short core from Stordalen mire, and reveals a major shift in peatland ecohydrology coincident with the onset of the Little Ice Age (c. AD 1400). We also applied the model to an independent contemporary dataset from Stordalen and find that it outperforms predictions based on other published transfer functions. The new transfer function will enable palaeohydrological reconstruction from permafrost peatlands in Northern Europe, thereby permitting greatly improved understanding of the long-term ecohydrological dynamics of these important carbon stores as well as their responses to recent climate change.

Hybrid probabilistic wind power forecasting using temporally local Gaussian process

The demand for sustainable development has resulted in a rapid growth in wind power worldwide. Despite various approaches have been proposed to improve the accuracy and to overcome the uncertainties associated with traditional methods, the stochastic and variable nature of wind still remains the most challenging issue in accurately forecasting wind power. This paper presents a hybrid deterministic-probabilistic method where a temporally local ‘moving window’ technique is used in Gaussian Process to examine estimated forecasting errors. This temporally local Gaussian Process employs less measurement data while faster and better predicts wind power at two wind farms, one in the USA and the other in Ireland. Statistical analysis on the results shows that the method can substantially reduce the forecasting error while more likely generate Gaussian-distributed residuals, particularly for short-term forecast horizons due to its capability to handle the time-varying characteristics of wind power.

On the Multivariate Gamma-Gamma (ΓΓ) Distribution with Arbitrary Correlation and Applications in Wireless Communications

The statistical properties of the multivariate GammaGamma (ΓΓ) distribution with arbitrary correlation have remained unknown. In this paper, we provide analytical expressions for the joint probability density function (PDF), cumulative distribution function (CDF) and moment generation function of the multivariate ΓΓ distribution with arbitrary correlation. Furthermore, we present novel approximating expressions for the PDF and CDF of the su m of ΓΓ random variables with arbitrary correlation. Based on this statistical analysis, we investigate the performance of radio frequency and optical wireless communication systems. It is noteworthy that the presented expressions include several previous results in the literature as special cases.

Which biomarkers are predictive specifically for cardiovascular or for non-cardiovascular mortality in men? Evidence from the Caerphilly Prospective Study (CaPS)

OBJECTIVE: To examine a panel of 28 biomarkers for prediction of cardiovascular disease (CVD) and non-CVD mortality in a population-based cohort of men.

METHODS: Starting in 1979, middle-aged men in Caerphilly underwent detailed medical examination. Subsequently 2171 men were re-examined during 1989-1993, and fasting blood samples obtained from 1911 men (88%). Fibrinogen, viscosity and white cell count (WCC), routine biochemistry tests and lipids were analysed using fresh samples. Stored aliquots were later analysed for novel biomarkers. Statistical analysis of CVD and non-CVD mortality follow-up used competing risk Cox regression models with biomarkers in thirds tested at the 1% significance level after covariate adjustment.

RESULTS: During an average of 15.4years follow-up, troponin (subhazard ratio per third 1.71, 95% CI 1.46-1.99) and B-natriuretic peptide (BNP) (subhazard ratio per third 1.54, 95% CI 1.34-1.78) showed strong trends with CVD death but not with non-CVD death. WCC and fibrinogen showed similar weaker findings. Plasma viscosity, growth differentiation factor 15 (GDF-15) and interleukin-6 (IL-6) were associated positively with both CVD death and non-CVD death while total cholesterol was associated positively with CVD death but negatively with non-CVD death. C-reactive protein (C-RP), alkaline phosphatase, gamma-glutamyltransferase (GGT), retinol binding protein 4 (RBP-4) and vitamin B6 were significantly associated only with non-CVD death, the last two negatively. Troponin, BNP and IL-6 showed evidence of diminishing associations with CVD mortality through follow-up.

CONCLUSION: Biomarkers for cardiac necrosis were strong, specific predictors of CVD mortality while many inflammatory markers were equally predictive of non-CVD mortality.

Civilianizing Civil Conflict: Civilian Defense Militias and the Logic of Violence in Intra-State Conflict

This article examines how civilian defense militias shape violence during civil war. We define civilian defense forces as a sedentary and defensive form of pro-government militia that incumbents often use to harness the participation of civilians during a counterinsurgency campaign. We argue that civilian defense forces reduce the problem of insurgent identification. This leads to a reduction in state violence against civilians. However, we also claim that these actors undermine civilian support for insurgents, which leads to an increase in rebel violence against civilians and overall intensification of conflict. A statistical analysis of government and rebel violence against civilians from 1981 to 2005, and a qualitative assessment of a civilian defense force operating in Iraq from 2005 to 2009, offer strong support for our theoretical claims. These findings provide further insight into pro-government militias and their effects on violence. They also have wider ethical implications for the use of civilian collaborators during civil war.

The mitochondrial and autosomal mutation landscapes of prostate cancer

BACKGROUND: Prostate cancer (PCa) is the most common cancer in men. PCa is strongly age associated; low death rates in surveillance cohorts call into question the widespread use of surgery, which leads to overtreatment and a reduction in quality of life. There is a great need to increase the understanding of tumor characteristics in the context of disease progression.

OBJECTIVE: To perform the first multigenome investigation of PCa through analysis of both autosomal and mitochondrial DNA, and to integrate exome sequencing data, and RNA sequencing and copy-number alteration (CNA) data to investigate how various different tumor characteristics, commonly analyzed separately, are interconnected.

DESIGN, SETTING, AND PARTICIPANTS: Exome sequencing was applied to 64 tumor samples from 55 PCa patients with varying stage and grade. Integrated analysis was performed on a core set of 50 tumors from which exome sequencing, CNA, and RNA sequencing data were available.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Genes, mutated at a significantly higher rate relative to a genomic background, were identified. In addition, mitochondrial and autosomal mutation rates were correlated to CNAs and proliferation, assessed as a cell cycle gene expression signature.

RESULTS AND LIMITATIONS: Genes not previously reported to be significantly mutated in PCa, such as cell division cycle 27 homolog (Saccharomyces cerevisiae) (CDC27), myeloid/lymphoid or mixed-lineage leukemia 3 (MLL3), lysine (K)-specific demethylase 6A (KDM6A), and kinesin family member 5A (KIF5A) were identified. The mutation rate in the mitochondrial genome was 55 times higher than that of the autosomes. Multilevel analysis demonstrated a tight correlation between high reactive-oxygen exposure, chromosomal damage, high proliferation, and in parallel, a transition from multiclonal indolent primary PCa to monoclonal aggressive disease. As we only performed targeted sequence analysis; copy-number neutral rearrangements recently described for PCa were not accounted for.

CONCLUSIONS: The mitochondrial genome displays an elevated mutation rate compared to the autosomal chromosomes. By integrated analysis, we demonstrated that different tumor characteristics are interconnected, providing an increased understanding of PCa etiology.

Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins

BACKGROUND: Prostate cancer (PCa) is a clinically and pathologically heterogeneous disease. The rapid development of sequencing technology has the potential to deliver new biomarkers with emphasis on aggressive disease and to revolutionise personalised cancer treatment. However, a prostate harbouring cancer commonly contains multiple separate tumour foci, with the potential to aggravate tumour sampling. The level of intraprostatic tumour heterogeneity remains to be determined.

OBJECTIVE: To determine the level of intraprostatic tumour heterogeneity through genome-wide, high-resolution profiling of multiple tumour samples from the same individual.

DESIGN, SETTINGS, AND PARTICIPANTS: Multiple tumour samples were obtained from four individuals following radical prostatectomy. One individual (SWE-1) contained >70% cancer cells in all tumour samples, whereas the other three (SWE-2 to SWE-4) required the use of laser capture microdissection for tumour cell enrichment. Subsequently, DNA was extracted from all tissue samples, and exome sequencing was performed. All tumour foci of SWE-1 were also profiled using a high-resolution array for the identification of copy number alterations (CNA).

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Shared somatic high-frequency single nucleotide variants (SNV) and CNAs were used to infer the level of intraprostatic tumour heterogeneity.

RESULTS AND LIMITATIONS: No high-frequency mutations, common for the three tumour samples of SWE-1, were identified. Ten randomly chosen positions were validated with Sanger sequencing in all foci, which verified the exome data. The high level of intraprostatic heterogeneity was consistent in all individuals. In total, three out of four individuals harboured tumours without an apparent common somatic denominator. Although we cannot exclude the presence of common structural rearrangements, a high-density array was used for the detection of deletions and amplifications in SWE-1, which agreed with the exome data.

CONCLUSIONS: We present evidence for the presence of somatically independent tumours within the same prostate. This finding will have implications for personalised cancer treatment and biomarker discovery.

Comparison of Composite Placement Techniques by Recently Qualified Dental Practitioners.

Objectives: To evaluate the placement of composite materials by new graduates using three alternative placement techniques.Methods: A cohort of 34 recently qualified graduates were asked to restore class II interproximal cavities in plastic teeth using three different techniques.

(i) A conventional incremental filling technique (Herculite XRV) using increments no larger than 2-mm with an initial layer on the cervical floor of the box of 1-mm.
(ii) Flowable bulk fill technique (Dentsply SDR) bulk fill placement in a 3-mm layer followed by an incremental fill of a microhybrid resin
(iii) Bulk fill (Kerr Sonicfill) which involved restorations placed in a 5-mm layer.

The operators were instructed in each technique, didactically and with a hands-on demonstration, prior to restoration placement.
All restorations were cured according to manufacturer’s recommendations. Each participant restored 3 teeth, 1 tooth per treatment technique.
The restorations were evaluated using modified USPHS criteria to assess both the marginal adaptation and the surface texture of the restorations. Blind evaluations were carried out independently by two examiners with the aid of magnification (loupes X2.5). Examiners were standardized prior to evaluation.
Results: Gaps between the tooth margins and the restoration or between the layers of the restoration were found in 13 of Group (i), 3 of Group (ii), and 4 of Group (iii)
Statistical analysis revealed a significant difference between the incrementally filled group (i) and the flowable bulk-fill group (ii) (p=0.0043) and between the incrementally filled (i) and the bulk fill groups (iii) (p=0.012) and no statistical difference (p=0.69) between the bulk filled groups Conclusions: Bulk fill techniques may result in a more satisfactory seal of the cavity margins when restoring with composite.

The prevalence of CALR mutations in a cohort of patients with myeloproliferative neoplasms

INTRODUCTION: To investigate the prevalence of calreticulin (CALR) mutations in JAK2- and MPL-non-mutated patients with suspected myeloproliferative neoplasm (MPN) from a large MPN clinic and confirm a diagnosis of MPN.

METHODS: JAK2/MPL-non-mutated patients from the Belfast City Hospital (BCH) with either of the MPNs - ET or MF - and diagnosed between 1988 and 2014 were selected for CALR screen. All cases were validated according to the WHO 2008 classification for MPNs. Statistical analysis was performed with Minitab 16 Statistical Software package. Exon 9 of CALR was amplified by PCR using genomic DNA, and mutations were detected by fragment analysis.

RESULTS: Of the 62 JAK2/MPL-non-mutated MPN patients screened, 57 had ET and 5 had MF; 34 patients (53.1%) carried CALR mutations. Three of 5 MF patients were CALR positive. Thirty-one ET patients (54.3%) harboured CALR mutation, whereas 26 (45.7%) were classified as 'triple negatives'.

CONCLUSION: Detection of CALR mutations in a cohort of JAK2/MPL-non-mutated patients with suspected MPN confirmed the diagnosis of MPN in around 53% of cases. This is lower than initially reported, but similar to subsequent studies. However, a sizable cohort of patients remains lacking a specific molecular marker.

Single nucleotide polymorphisms in the APCS gene influence geographic atrophy secondary to VEGF inhibition therapy in neovascular macular degeneration.

Introduction: Age-related macular degeneration (AMD) is a leading cause of vision loss in the elderly mostly due to the development of neovascular AMD (nAMD) or geographic atrophy (GA). Intravitreal injections of anti-vascular endothelial growth factor (VEGF) agents are an effective therapeutic option for nAMD. Following anti-VEGF treatments, increased atrophy of the retinal pigment epithelium (RPE) and choriocapillaries that resembles GA has been reported. We sought to evaluate the underlying genetic influences that may contribute to this process. Methods: We selected 68 single nucleotide polymorphisms (SNPs) from genes previously identified as susceptibility factors in AMD, along with 43 SNPs from genes encoding the VEGF protein and its cognate receptors as this pathway is targeted by treatment. We enrolled 467 consecutive patients (Feb 2009 to October 2011) with nAMD who received anti-VEGF therapy. The acutely presenting eye was designated as the study eye and retinal tomograms graded for macular atrophy at study exit. Statistical analysis was performed using PLINK to identify SNPs with a P value < 0.01. Logistic regression models with macular atrophy as dependent variable were fitted with age, gender, smoking status, common genetic risk factors and the identified SNPs as explanatory variables. Results: Grading for macular atrophy was available in 304 study eyes and 70% (214) were classified as showing macular atrophy. In the unadjusted analysis we observed significant associations between macular atrophy and two independent SNPs in the APCS gene: rs6695377: odds ratio (OR) = 1.98; 95% confidence intervals (CI): 1.23, 3.19; P = 0.004; rs1446965: OR = 2.49, CI: 1.29, 4.82; P = 0.006 and these associations remained significant after adjustment for covariates. Conclusions: VEGF is a mitogen and growth factor for choroidal blood vessels and the RPE and its inhibition could lead to atrophy of these key tissues. Anti-VEGF treatment can interfere with ocular vascular maintenance and may be associated with RPE and choroidal atrophy. As such, these medications, which block the effects of VEGF, may influence the development of GA. The top associated SNPs are found in the APCS gene, a highly conserved glycoprotein that encodes Serum amyloid P (SAP) which opsonizes apoptotic cells. SAP can bind to and activate complement components via binding to C1q, a mechanism by which SAP may remove cellular debris, affecting regulation of the three complement pathways.

Coronal properties of planet-bearing stars

Context. Do extrasolar planets affect the activity of their host stars? Indications for chromospheric activity enhancement have been found for a handful of targets, but in the X-ray regime, conclusive observational evidence is still missing. Aims: We want to establish a sound observational basis to confirm or reject major effects of Star-Planet Interactions (SPI) in stellar X-ray emissions. Methods: We therefore conduct a statistical analysis of stellar X-ray activity of all known planet-bearing stars within 30 pc distance for dependencies on planetary parameters such as mass and semimajor axis. Results: In our sample, there are no significant correlations of X-ray luminosity or the activity indicator L_X/L_bol with planetary parameters which cannot be explained by selection effects. Conclusions: Coronal SPI seems to be a phenomenon which might only manifest itself as a strong effect for a few individual targets, but not to have a major effect on planet-bearing stars in general.