Development of a confined water sensitive urban design (WSUD) system using engineered soils

Innovative Water Sensitive Urban Design (WSUD) systems are being investigated at three locations to the north and south of Sydney, Australia. These systems contain porous concrete pipes that are designed so that stormwater exfiltrates through the permeable walls of the pipes into the surrounding substrate media material. The porous pipes and media material treat the passing stormwater. The primary aim of the overall project is to develop a model to describe the treatment effectiveness of confined WSUD systems. This paper focuses on the system located at the Weathertex Industrial Site, Heatherbrae. Due to wood processing operations that occur at this site, it is recognised that the surface runoff will carry a heavy organics loading. Granulated Activated Carbon (GAC) is recognised for its ability to reduce the concentration of dissolved organics present in both wastewater and stormwater. GAC was therefore chosen as a filtration medium to be investigated at this site. To maximise the effectiveness of the GAC, extensive laboratory batch studies were undertaken prior to the field system being constructed to determine the optimum GAC/sand ratio. The purpose of the experimental work was to assess the dissolved organic removal potential through sorption of various concentrations of GAC. The aim of this paper is to describe these laboratory experiments and discuss how they related to the field system. Through these experiments it was determined that a sand/GAC ratio of 25:1 was ideal for the media material at the Heatherbrae site.

Refined Association Mapping for a Quantitative Trait: Weight in the H19-IGF2-INS-TH Region

Previous analyses have provided evidence for one or more loci affecting body weight in the H19-IGF2-INS-TH region on chromosome 11p15. To identify the location of a possible causal locus or loci we applied association analysis by composite likelihood to a large cohort under the Malecot model for body weight. A random sample of 2731 men in the UK were typed for eleven single nucleotide polymorphisms (SNPs) in IGF2, two SNPs in H19, one SNP in INS and one microsatellite marker in the TH genes. Using F tests appropriate to small marker sets, the superiority of regression over correlation was confirmed. All the evidence for association came from IGF2, with P= 0.007 for height-adjusted weight and P= 0.019 for weight additionally adjusted for smoking and alcohol drinking. Although the estimated point location for the suspected causal variant was close to IGF2 ApaI, the 95% confidence and support intervals covered most of IGF2 but none of the other loci. Identification of the causal SNP or SNPs within IGF2 will require typing of more variants in this region.

Multiple mechanisms are implicated in the generation of 5q35 microdeletions in Sotos syndrome

BACKGROUND

Sotos syndrome is characterised by learning difficulties, overgrowth, and a typical facial appearance. Microdeletions at 5q35.3, encompassing NSD1, are responsible for approximately 10% of non-Japanese cases of Sotos. In contrast, a recurrent approximately 2 Mb microdeletion has been reported as responsible for approximately 50% of Japanese cases of Sotos.

METHODS

We screened 471 cases for NSD1 mutations and deletions and identified 23 with 5q35 microdeletions. We investigated the deletion size, parent of origin, and mechanism of generation in these and a further 10 cases identified from published reports. We used "in silico" analyses to investigate whether repetitive elements that could generate microdeletions flank NSD1.

RESULTS

Three repetitive elements flanking NSD1, designated REPcen, REPmid, and REPtel, were identified. Up to 18 cases may have the same sized deletion, but at least eight unique deletion sizes were identified, ranging from 0.4 to 5 Mb. In most instances, the microdeletion arose through interchromosomal rearrangements of the paternally inherited chromosome.

CONCLUSIONS

Frequency, size, and mechanism of generation of 5q35 microdeletions differ between Japanese and non-Japanese cases of Sotos. Our microdeletions were identified from a large case series with a broad range of phenotypes, suggesting that sample selection variability is unlikely as a sole explanation for these differences and that variation in genomic architecture might be a contributory factor. Non-allelic homologous recombination between REPcen and REPtel may have generated up to 18 microdeletion cases in our series. However, at least 15 cannot be mediated by these repeats, including at least seven deletions of different sizes, implicating multiple mechanisms in the generation of 5q35 microdeletions.

Vitamin D intake and status in Irish elderly women and adolescent girls

AIM

To assess vitamin D status during summer and winter in Irish girls and elderly women, and to estimate vitamin D intake in these two age-groups.

METHODS

Ambulatory free-living, elderly Irish women (aged 70-76 years; n = 43) and girls (aged 11-13 years; n = 17) were recruited. Fasting serums were collected during August/ September 2002 and February/March 2003 and analysed for 25 (OH) D by HPLC.

RESULTS

Mean daily intakes of vitamin D were 4.6 microg and 2.1 microg in elderly women and girls, respectively. Serum 25 (OH) D was significantly lower (P<0.001) during winter than summer in both age-groups. Eight (20%) and one (during late summer) and sixteen (37.2%) and eight (47%) (during late winter) of the elderly women and girls, respectively, had inadequate vitamin D status (serum 25 (OH) D <40 nmol/l).

CONCLUSION

Inadequate vitamin D status during winter time is quite common in elderly women and adolescent girls in Ireland.

Prevalence and transmission of honeybee viruses

Transmission mechanisms of six honeybee viruses, including acute bee paralysis virus (ABPV), black queen cell virus (BQCV), chronic bee paralysis virus (CBPV), deformed wing virus (DWV), Kashmir bee virus (KBV), and sacbrood bee virus (SBV), in honey bee colonies were investigated by reverse transcription-PCR (RT-PCR) methods. The virus status of individual queens was evaluated by examining the presence of viruses in the queens' feces and tissues, including hemolymph, gut, ovaries, spermatheca, head, and eviscerated body. Except for head tissue, all five tissues as well as queen feces were found to be positive for virus infections. When queens in bee colonies were identified as positive for BQCV, DWV, CBPV, KBV, and SBV, the same viruses were detected in their offspring, including eggs, larvae, and adult workers. On the other hand, when queens were found positive for only two viruses, BQCV and DWV, only these two viruses were detected in their offspring. The presence of viruses in the tissue of ovaries and the detection of the same viruses in queens' eggs and young larvae suggest vertical transmission of viruses from queens to offspring. To our knowledge, this is the first evidence of vertical transmission of viruses in honeybee colonies.

Assessment of feto-placental well-being in the mare from mid-gestation to term: transrectal and transabdominal ultrasonographic features

Ultrasound assessment of feto-placental well-being has found its application in the equine field, as a valid diagnostic tool. Most reports on equine fetal parameters focus on advanced to late gestation. The aim of the present study was to further validate the technique of ultrasound evaluation of the equine fetal environment, by extending its application to earlier stages of pregnancy. Fetal parameters were collected (on 150 pregnancies) over a 3-year period. Data included in the study were selected according to the clinical behaviour of the mare, the neonate/fetus and fetal membranes at the termination of gestation. Validation of the ultrasound technique was also undertaken on a number of specimens collected at an abbatoir. At the completion of the study, a substantial number of measurements and observations were collected. No fetal parameters associated in previous reports with a negative outcome were observed at any of the examinations during this study. Therefore, data collected during the present study should be of value in feto-placental assessment of well-being, in mid- to late-gestation.

Regression of NMU-induced mammary tumors with the combination of melatonin and 9-cis-retinoic acid

A significant increase in tumor regression was induced in N-nitroso-N-methylurea-induced mammary tumors in rats treated with the combination of melatonin and 9-cis-retinoic acid (9cRA). Treatment groups included: control (ethanolic saline), 9cRA (30 mg/kg chow/day), melatonin 500 microg/day, melatonin 1000 microg/day, melatonin 500 microg/day+9cRA and melatonin 1000 microg/day+9cRA. Rats treated with the lower dose of melatonin 500 microg+9cRA show the greatest degree of tumor regression (78%), with 54% undergoing complete regression and a significant increase in apoptotic cells observed by TUNEL Assay. Furthermore, tumor multiplicity and burden were significantly decreased by the combination of melatonin and 9cRA.

A map of the human genome in linkage disequilibrium units

Two genetic maps with additive distances contribute information about recombination patterns, recombinogenic sequences, and discovery of genes affecting a particular phenotype. Recombination is measured in morgans (w) over a single generation in a linkage map but may cover thousands of generations in a linkage disequilibrium (LD) map measured in LD units (LDU). We used a subset of single nucleotide polymorphisms from the HapMap Project to create a genome-wide map in LDU. Recombination accounts for 96.8% of the LDU variance in chromosome arms and 92.4% in their deciles. However, deeper analysis shows that LDU/w, an estimate of the effective bottleneck time (t), is significantly variable among chromosome arms because (i) the linkage map is approximated from the Haldane function, then adjusted toward the Kosambi function that is more accurate but still exaggerates w for all chromosomes, especially shorter ones; (ii) the non-pseudoautosomal region of the X chromosome is subject to hemizygous selection; and (iii) at resolution less than approximately 40,000 markers per w, there are indeterminacies (holes) in the LD map reflecting intervals of very high recombination. Selection and stochastic variation in small regions must have effects, which remain to be investigated by comparisons among populations. These considerations suggest an optimal strategy to eliminate holes quickly, greatly enhance the resolution of sex-specific linkage maps, and maximize the gain in association mapping by using LD maps.

Linkage disequilibrium analysis of case-control data: an application to generalized aggressive periodontitis

Several studies have shown a role for the involvement of interleukin (IL)-1 gene cluster polymorphisms in the risk of periodontal diseases. In the present study, we tested polymorphisms, derived from genes of the IL-1 cluster, for association with generalized aggressive periodontitis (GAP) through both allelic association and by constructing a linkage disequilibrium (LD) map of the 2q13-14 disease candidate region. The IL-1RN (VNTR) genotype distribution observed was significantly different in GAP and control subjects (P=0.019). We also observed some evidence for an association between GAP and the IL-1B(+3953) polymorphism (P=0.039). The pattern of association in the region, represented as an LD map, identifies a recombination hot area between the IL-1B(+3953) and IL-1B(-511) polymorphisms. Multilocus modelling of association with disease gives a location for the peak association at the IL-1B(+3953) marker, although support for the peak is not significant. Haplotype analysis identifies a IL-1B(+3953)-IL-1B(-511) haplotype as having the lowest P-value in the region. Recognition of the presence of a recombination hot area between the IL-1B(+3953) and IL-1B(-511) polymorphisms will have an important bearing on future efforts to develop higher resolution SNP analysis in this region for both this and other diseases for which this cluster is implicated.

Vitamin D intake and status in Irish postmenopausal women

OBJECTIVE

The objective of this study was to assess vitamin D status during late-summer and late-winter/early-spring in postmenopausal Irish women, and whether it was influenced by vitamin D-containing supplement use.

DESIGN

A longitudinal observational study.

SETTING

Cork City, Ireland (51 degrees north).

SUBJECTS

A total of 59 apparently healthy, free-living, postmenopausal women aged between 51 and 69 y were sampled during February/March 2002. Of these, 48 and 47 returned during August/September 2002 and February/March 2003, respectively. None of the women were suffering from any medical condition likely to affect vitamin D status. Fasting serums were collected and analysed for 25-hydroxyvitamin D (25 (OH) D) and parathyroid hormone (PTH) by enzyme immunoassays.

RESULTS

Mean daily intake of vitamin D was 3.2 microg from food sources alone and 5.8 microg when vitamin D-containing supplements were included (P<0.01). Serum 25 (OH) D was significantly lower (P<0.001) during February/March 2002 than both August/September 2002 and February/March 2003. Serum 25 (OH) D was also significantly higher (P < or = 0.05) in women who were vitamin D-containing supplement users than nonusers during all three sampling points. Between 17 and 36% of women had inadequate vitamin D status (defined as serum 25 (OH) D <40 nmol/l) during late-winter, but only 4% had inadequate vitamin D status during late-summer. Serum 25 (OH) D was inversely related to serum PTH (r = -0.33; P = 0.028).

CONCLUSION

Suboptimal vitamin D status is common in postmenopausal Irish women during winter. Vitamin D supplementation is associated with improved vitamin D status, even during summertime.

The optimal measure of linkage disequilibrium reduces error in association mapping of affection status

We have developed a simple yet powerful approach for disease gene association mapping by linkage disequilibrium (LD). This method is unique because it applies a model with evolutionary theory that incorporates a parameter for the location of the causal polymorphism. The method exploits LD maps, which assign a location in LD units (LDU) for each marker. This approach is based on single marker tests within a composite likelihood framework, which avoids the heavy Bonferroni correction through multiple testing. As a proof of principle, we tested an 890 kb region flanking the CYP2D6 gene associated with poor drug-metabolizing activity in order to refine the localization of a causal mutation. Previous LD mapping studies using single markers and haplotypes have identified a 390 kb significant region associated with the poor drug-metabolizing phenotype on chromosome 22. None of the 27 Single nucleotide polymorphisms was within the gene. Using a metric LDU map, the commonest functional polymorphism within the gene was located at 14.9 kb from its true location, surrounded within a 95% confidence interval of 172 kb. The kb map had a relative efficiency of 33% compared with the LDU map. Our findings indicate that the support interval and location error are smaller than any published results. Despite the low resolution and the strong LD in the region, our results provide evidence of the substantial utility of LDU maps for disease gene association mapping. These tests are robust to large numbers of markers and are applicable to haplotypes, diplotypes, whole-genome association or candidate region studies.

Folate levels determine effect of antioxidant supplementation on micronuclei in subjects with cardiovascular risk

We have investigated the effect of modest supplementation with alpha-tocopherol (100 mg/day), beta-carotene (6 mg/day), vitamin C (100 mg/day) and selenium (50 microg/day) on oxidative stress and chromosomal damage, and the influence of methylenetetrahydrofolate reductase (MTHFR) genotype on these end-points. Subjects were two groups of middle-aged men differing in cardiovascular risk; 46 survivors of myocardial infarction before age 50 and 60 healthy controls. They were randomly divided into equal groups to receive antioxidants or placebo for 12 weeks. Twenty-eight patients and 58 controls completed the intervention. Micronucleus levels in peripheral lymphocytes and changes seen after intervention were studied in relation to the MTHFR C677T genotype, basal homocysteine and plasma folate levels. Ferric reducing ability of plasma and concentration of malondialdehyde were measured to assess the antioxidant effect of supplementation. There was no association of micronuclei with folate, homocysteine or malondialdehyde levels before supplementation. Micronucleus frequencies and plasma folate levels did not vary significantly with MTHFR genotype. Homocysteine levels in subjects with the TT variant genotype were significantly higher compared with CT or CC (P = 0.001), especially in subjects with low folate (P = 0.012). In the placebo control group an increase in micronuclei (P = 0.04) was detected at the end of the intervention period. This effect was not seen in the supplemented group. In antioxidant-supplemented myocardial infarction survivors we found an increase in the ferric reducing ability of plasma (P < 0.001) and a decrease in malondialdehyde (P = 0.001). Micronucleus frequency showed a decrease, strongest in subjects with normal folate levels (P = 0.015). In subjects with low folate levels, a high correlation was found between micronuclei after supplementation and homocysteine, both before (r = 0.979, P = 0.002) and after supplementation (r = 0.922, P = 0.009). Thus, folate deficiency may amplify the effect of other risk factors such as elevated homocysteine levels or variant MTHFR genotype, as well as influencing the ability of antioxidant supplementation to protect against genetic damage.

Ecological momentary assessment of temptation and lapse in dieting

Although some research attention has been given to the factors associated with temptation and lapse in dieting, the majority of research has focused on individuals in weight loss clinical trials and relied heavily on retrospective self-report data. The present study sought to overcome these limitations by using ecological momentary assessment (EMA) techniques to examine situations of dietary temptation, lapse, and minimal dietary consequence with a sample of overweight dieters (N=30) attempting to lose weight on their own. Results support and extend previous research findings on dietary temptation and lapse. In general, results indicate that recent consumptive activity, location, mood state, type of activity, and abstinence violation effects were related to moments of temptation and/or lapse. Education on the factors associated with dietary temptation and lapse and strategies for addressing these factors is imperative for both dieters in formal programs and those attempting to lose or maintain weight on their own.

Lipid peroxidation in men after dietary supplementation with a mixture of antioxidant nutrients

Antioxidants and antioxidant enzymes protect living organisms against the attack of reactive oxygen species. An adequate daily intake of the individual antioxidants is therefore important to prevent the cells against oxidative damage. We investigated the effect of a modest dietary supplementation with a mixture of antioxidant nutrients (100 mg vitamin E, 100 mg vitamin C,6 mg beta-carotene and 50 microg of selenium per day) for 3 months on the plasma antioxidant capacity and indices of oxidative stress. Two groups of middle-age men were selected: group 1 with survivors of myocardial infarction (MI), and group 2 with clinically normal controls. The values of total antioxidant capacity of plasma (FRAP) significantly increased after supplementation with antioxidants in the both groups. Markers of in vivo lipid peroxidation, plasma malondialdehyde (MDA) and conjugated diene (CD) levels significantly decreased in the both supplemented groups. MDA and CD values were significantly higher at baseline in the group of survivors of myocardial infarction when compared with the group of healthy men. The results demonstrate that short-term and modest supplementation with a mixture of antioxidant nutrients improves antioxidative capacity and reduces products of lipid peroxidation in plasma. Since a more pronounced effect was observed within the group of survivors of myocardial infarction, a recommendation of antioxidant supplements seems appropriate for patients with a history of cardiovascular disease. (Fig. 1, Ref. 19.)

A Metric Linkage Disequilibrium Map of a Human Chromosome

We used LDMAP (Maniatis et al. 2002) to analyse SNP data spanning chromosome 22 (Dawson et al. 2002), to obtain a whole-chromosome metric LD map. The LD map, with map distances analogous to the centiMorgan scale of linkage maps, identifies regions of high LD as plateaus ('blocks') and characterises steps which define the relationship between these regions. From this map we estimate that block regions comprise between 32% and 55% of the euchromatic portion of chromosome 22 and that increasing marker density within steps may increase block coverage. Steps are regions of low LD which correspond to areas of variable recombination intensity. The intensity of recombination is related to the height of the step and thus intense recombination hot-spots can be distinguished from more randomly distributed historical events. The LD maps are more closely related to the high-resolution linkage map (Kong et al. 2002) than average measures of rho with recombination accounting for between 34% and 52% of the variance in patterns of LD (r=0.58 - 0.71, p=0.0001). Step regions are closely correlated with a range of sequence motifs including GT/CA repeats. The LD map identifies holes in which greater marker density is required and defines the optimal SNP spacing for positional cloning, which suggests that some multiple of around 50,000 SNPs will be required to efficiently screen Caucasian genomes. Further analyses which investigate selection of informative SNPs and the effect of SNP allele frequency and marker density will refine this estimate.

Patterns of emotional responses to pregnancy, experience of pregnancy and attitudes to parenthood among IVF couples: a longitudinal study

The aim of this longitudinal study was to compare couples who had conceived by in-vitro fertilization (IVF) with couples who had conceived naturally, regarding patterns of emotional response to different stages of pregnancy and to compare their expectations of and attitudes to pregnancy, parenthood and children. Fifty-seven IVF women and 55 of their male partners, and a control group of 43 pregnant women and 39 of their male partners participated. They completed scales measuring emotional responses to pregnancy, attitudes to pregnancy, parenthood and children. The IVF couples were interviewed about their experience of pregnancy. The overall anxiety about losing the pregnancy was higher among the IVF couples from early to late pregnancy. The IVF women experienced the pregnancy in a more positive way and they were less concerned about the child's gender and loss of freedom in their future lives as parents compared to controls. The IVF men were more anxious about the baby being injured during birth. The interviews with the IVF couples confirmed the self-ratings. In conclusion, the results suggest that it is important for healthcare providers to pay attention to an elevated anxiety among IVF couples and to give them extra time to discuss emotions during pregnancy and their future life as parents.

A corneal model for slit-scanning elevation topography

Computerised videokeratography is increasing in sophistication and accuracy. The Orbscan II Videokeratographer combines the advantages of Placido derived and slit-scanning derived topography, to acquire shape information on the posterior surface of the cornea. The purpose of this paper is to construct a model of slit-scanning elevation topography and highlight potential sources of variation in this methodology. Ray tracing calculations were performed on a defined, theoretical, spherical model to obtain a pachymetric measurement. These calculations were tested by comparing the pachymetry measurement derived from the model, over a refractive index shift from 1.376 to 1.400 with the pachymetry measurement obtained by Orbscan II, of a human eye, with an identical alteration in refractive index. The two methods of measurement differed by only 0.157 microm, suggesting that the model is a good representation of slit-scanning elevation topography, and that refractive index variations have only a minimal effect on Orbscan II pachymetry measurement.