Models for cluster randomized designs using ranked set sampling.

Cluster randomized designs (CRD) provide a rigorous development for randomization principles for studies where treatments are allocated to cluster units rather than the individual subjects within clusters. It is known that CRDs are less efficient than completely randomized designs since the randomization of treatment allocation is applied to the cluster units. To mitigate this problem, we embed a ranked set sampling design from survey sampling studies into CRD for the selection of both cluster and subsampling units. We show that ranking groups in ranked set sampling act like a covariate, reduce the expected mean squared cluster error, and increase the precision of the sampling design. We provide an optimality result to determine the sample sizes at cluster and sub-sample level. We apply the proposed sampling design to a dental study on human tooth size, and to a longitudinal study from an education intervention program.

HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences.

BACKGROUND: In diploid organisms, whole-genome haplotype assembly relies on the accurate identification and assignment of heterozygous single-nucleotide polymorphism alleles to the correct homologous chromosomes. This appropriate phasing of these alleles ensures that combinations of single-nucleotide polymorphisms on any chromosome, called haplotypes, can then be used in downstream genetic analysis approaches including determining their potential association with important phenotypic traits. A number of statistical algorithms and complementary computational software tools have been developed for whole-genome haplotype construction from genomic sequence data. However, many algorithms lack the ability to phase long haplotype blocks and simultaneously achieve a competitive accuracy. RESULTS: In this research we present HaploMaker, a novel reference-based haplotype assembly algorithm capable of accurately and efficiently phasing long haplotypes using paired-end short reads and longer Pacific Biosciences reads from diploid genomic sequences. To achieve this we frame the problem as a directed acyclic graph with edges weighted on read evidence and use efficient path traversal and minimization techniques to optimally phase haplotypes. We compared the HaploMaker algorithm with 3 other common reference-based haplotype assembly tools using public haplotype data of human individuals from the Platinum Genome project. With short-read sequences, the HaploMaker algorithm maintained a competitively low switch error rate across all haplotype lengths and was superior in phasing longer genomic regions. For longer Pacific Biosciences reads, the phasing accuracy of HaploMaker remained competitive for all block lengths and generated substantially longer block lengths than the competing algorithms. CONCLUSIONS: HaploMaker provides an improved haplotype assembly algorithm for diploid genomic sequences by accurately phasing longer haplotypes. The computationally efficient and portable nature of the Java implementation of the algorithm will ensure that it has maximal impact in reference-sequence-based haplotype assembly applications.

Reduction in circulating bile acid and restricted diffusion across the intestinal epithelium are associated with a decrease in blood cholesterol in the presence of oat ß-glucan.

Although oat (1,3:1,4)-ß-glucan (BG) has been shown to decrease blood cholesterol in intervention trials, the detailed mechanism is not yet defined, but restricted reabsorption of bile acids (BAs) has been hypothesized. Using pigs as a model for humans we demonstrated that, compared to the control, BG added to the diet for 26 d caused decreases of 24% in blood total BAs (TBAs), 34% in total cholesterol (TC), and 57% in LDL cholesterol (LDL-C) (P < 0.01); decreases of 20% TBA in the midjejunum and terminal ileum (P < 0.01); increases of 80% in cecal total neutral sterols (TNSs) including cholesterol (P < 0.01); a 50% reduction in BA active transport across ex vivo ileum after 40 min (P < 0.001); and 32% decrease in jejunal microvillus heights with apparent increased goblet cell activity. The results suggest that BG not only physically hinders the active reabsorption of BAs and uptake of cholesterol, but also changes the BAs profile with lower circulating levels without excess excretion in the feces, thus resulting in reduced blood TC and LDL-C. Fermentation of sterols reaching the colon enhanced production of therapeutic ursodeoxycholic acid, suppressed toxic lithocholic acid, and decreased the possibility of cholesterol absorption by transforming the latter into coprostanol, a nonabsorbable NS.-Gunness, P., Michiels, J., Vanhaecke, L., De Smet, S., Kravchuk, O., Van de Meene, A., Gidley, M. J. Reduction in circulating bile acid and restricted diffusion across the intestinal epithelium are associated with a decrease in blood cholesterol in the presence of oat ß-glucan.

Circulating triglycerides and bile acids are reduced by a soluble wheat arabinoxylan via modulation of bile concentration and lipid digestion rates in a pig model.

SCOPE: Soluble dietary fibres have shown to have lipid reducing properties. However, their mechanisms of action are still unclear. The present study investigated how a soluble wheat arabinoxylan-rich fraction (AXRF) fed to pigs used as a human model reduced blood triglycerides. METHODS AND RESULTS: After 4 weeks on the experimental diets, blood from the jugular (JV) and hepatic portal (HPV) veins, bile from the gall bladder, and digesta samples from four sites of the small intestine (SI) and cecum were collected. The results showed that the AXRF significantly decreased the concentrations of total bile acid (BA) in the HPV (p < 0.01), JV (p < 0.01), bile (p < 0.05) and SI (p < 0.05), but with no effect on ileal BAs excretion flux. Furthermore, blood triglyceride (TAG) levels were also lower with AXRF (p < 0.01) but with no significant effects on LDL-, HDL- or total cholesterol levels. The lower plasma TAG concentration was consistent with the reduced/delayed digestion and absorption of TAG with the AXRF (total fatty acid and MUFA p < 0.01; unsaturated fatty acid p < 0.05). CONCLUSION: The results suggest that AXRF reduced the levels of circulating BAs which slowed down the digestion of TAG and absorption of free fatty acids, with consequent reduction in blood TAG. Reduction in circulating bile acids by arabinoxylan causes reduction in lipids digestion and absorption.

Chemical Changes in Grape Stem and Their Relationship to Stem Color throughout Berry Ripening in Vitis vinifera L. cv Shiraz.

Little attention has been paid to the color change or chemical compositional changes that occur in grape stems and how this correlates with the berry ripening process. Recently we have found that the change in grape peduncle color of Shiraz (Vitis vinifera) from green at veraison to predominantly brown at harvest occurs in parallel with berry ripening and as such may represent a new way of assisting in the prediction of grape maturity and harvest date. We have now investigated further the link between certain key chemical compositional changes that occur in the grape stem (peduncle and rachis) from veraison to harvest and how these attributes correlate with the observed color change in the vineyard. We report that peduncle moisture content has an excellent linear correlation with the color hue value and is negatively correlated in a strong fashion with the chlorophyll and carotenoid pigment ratio (Ca+b/Cx+c) within the peduncles. Significant differences in the moisture content, total chlorophylls (including chlorophyll a and b levels), total carotenoids, total phenolics, and the antioxidant capacity (DPPH) levels between the peduncles and rachises were found as they evolve from veraison to harvest. Finally, we have demonstrated for the first time that peduncle moisture content codevelops with the prototypical berry ripeness parameters (oBrix, pH, TA), which provides for the development of a new approach for viticulturists and winemakers to evaluate grape ripeness through peduncle moisture levels and therefore assist in harvest decision making.

Storage induced changes to high protein powders: influence on surface properties and solubility.

BACKGROUND: MPC 80 is a high-protein (80%) milk powder commonly used in the food industry as a functional ingredient and valued for its nutritional quality. However, its rehydration properties decline during storage, causing more time to be required for rehydration of the powder by the end user. It is thought that changes at the surface of the powder particles contribute to this reduced solubility during storage. RESULTS: Surface composition and structural changes in milk protein concentrate (MPC) were observed during 90 days of storage at temperatures of 25 and 40 °C and relative humidities of 44, 66 and 84%. No significant changes to the surface composition (fat, protein and lactose) of the MPC powder samples occurred during storage; however, some changes in the microstructure of the powders were observed. Scanning electron microscopy analysis of the powder particles during dissolution showed the formation of a crust, consisting of a thin layer of fused casein micelles, on the surface of the stored powders. An increase in the hydrophobicity at the surface of the particles was evident by X-ray photoelectron spectroscopy analysis of the bonding state of the elements at or near the surface and by atomic force microscopy measurements of the adherence of particles to the surface of a material. CONCLUSION: The development of this 'crust' is thought to contribute to the decrease in the solubility of the powder particles during storage. The increase in the hydrophobicity at the surface and the casein micelle interactions resulting in the surface crust formation appear to contribute to the decrease in the solubility of MPC during storage.

The correlation of in vivo burn scar contraction with the level of α-smooth muscle actin expression.

This study describes the direct association of in vivo burn scar contraction with the level of α-smooth muscle actin (α-SMA) in scar tissue, in a porcine burn model. The expression of α-SMA was investigated in 100 biopsies from 44 6-week old burn scars and in 85 biopsies from 16 2-week old burn wounds. Statistical analysis showed that the levels of α-SMA in 6-week old scars were significantly negatively correlated to scar size (r=-0.68) and the higher levels of α-SMA were observed in smaller scars. Moreover, α-SMA was also found to be significantly positively correlated to re-epithelialisation time (r=0.57) and scar thickness (r=0.58) and higher levels of α-SMA were detected in thicker scars with delayed wound closure. Further statistical analysis revealed that scar contraction can be explained best by the level of α-SMA expression and partially by scar thickness. Other variables, such as different dressings and individual pig, may also partly contribute to scar contraction. At week 2 after-burn, the level of α-SMA expression in 16 burn wounds was significantly related to the depth of burns and wound healing outcome. To our knowledge, this is the first study to provide in vivo evidence of the association of α-SMA expression with scar contraction, scar thickness, re-epithelialisation time and the depth of burn in a large animal burn model with scars similar to human hypertrophic scar.

Ultrasound assessed thickness of burn scars in association with laser Doppler imaging determined depth of burns in paediatric patients.

This study describes the ultrasound assessment of burn scars in paediatric patients and the association of these scar thickness with laser Doppler imaging (LDI) determined burn depth. A total of 60 ultrasound scar assessments were conducted on 33 scars from 21 paediatric burn patients at 3, 6 and 9 months after-burn. The mean of peak scar thickness was 0.39±0.032 cm, with the thickest at 6 months (0.40±0.036 cm). There were 17 scald burn scars (0.34±0.045 cm), 4 contact burn scars (0.61±0.092 cm), and 10 flame burn scars (0.42±0.058 cm). Each group of scars followed normal distributions. Twenty-three scars had original burns successfully scanned by LDI and various depths of burns were presented by different colours according to blood perfusion units (PU), with dark blue <125, light blue 125-250, and green 250-440 PU. The thickness of these scars was significantly different between the predominant colours of burns, with the thinnest scars for green coloured burns and the thickest for dark blue coloured burns. Within light blue burns, grafted burns healed with significantly thinner scars than non-grafted burns. This study indicates that LDI can be used for predicting the risk of hypertrophic scarring and for guiding burn care. To our knowledge, this is the first study to correlate the thickness of burns scars by ultrasound scan with burn depth determined by LDI.

A retrospective review of burn dressings on a porcine burn model.

This is a study to compare wound healing among three types of dressings on a porcine model with deep-dermal-partial-thickness burns. The burns in this study were from eight animal trials conducted in the past for other purposes and only burns with a uniform pale appearance that had served as controls in original experiments were selected. In total, there were 57 burns in 33 pigs, using one of following three dressings: Acticoat (Silver) (3 trials), Jelonet (Gauze) (3 trials), and Solosite Gel/Jelonet (Gel/Gauze) (2 trials). The wound healing assessments included wound re-epithelialisation during a 6-week period, clinical and histological scar assessments at week 6 after burn. Of all wound healing/scar assessments, only re-epithelialisation showed statistical difference between dressings. Earlier re-epithelialisation was observed in Gel/Gauze dressings compared to Silver and/or Gauze dressings. However, this study revealed huge variation in wound healing outcome between 3 trials within both Silver and/or Gauze dressings, supported by significant differences on re-epithelialisation, clinical and histological scar measurements. In addition, it was found that larger animals healed better than smaller ones, based on weights from 21 pigs. Of all dressings, Silver delivers the best protection for wound colonization/infection. Wound colonization/infection was found to confine wound healing and lead to thinner RND in scars. From this study, we cannot find enough evidence to suggest the beneficial effect of one dressing(s) over others on burn wound healing outcome on a porcine model with small deep-dermal-partial-thickness burns with a relative small sample size.

The optimal duration and delay of first aid treatment for deep partial thickness burn injuries.

Using our porcine model of deep dermal partial thickness burn injury, various durations (10min, 20min, 30min or 1h) and delays (immediate, 10min, 1h, 3h) of 15 degrees C running water first aid were applied to burns and compared to untreated controls. The subdermal temperatures were monitored during the treatment and wounds observed weekly for 6 weeks, for re-epithelialisation, wound surface area and cosmetic appearance. At 6 weeks after the burn, tissue biopsies were taken of the scar for histological analysis. Results showed that immediate application of cold running water for 20min duration is associated with an improvement in re-epithelialisation over the first 2 weeks post-burn and decreased scar tissue at 6 weeks. First aid application of cold water for as little as 10min duration or up to 1h delay still provides benefit.

An audit of first-aid treatment of pediatric burns patients and their clinical outcome.

This study describes the first aid used and clinical outcomes of all patients who presented to the Royal Children's Hospital, Brisbane, Australia in 2005 with an acute burn injury. A retrospective audit was performed with the charts of 459 patients and information concerning burn injury, first-aid treatment, and clinical outcomes was collected. First aid was used on 86.1% of patients, with 8.7% receiving no first aid and unknown treatment in 5.2% of cases. A majority of patients had cold water as first aid (80.2%), however, only 12.1% applied the cold water for the recommended 20 minutes or longer. Recommended first aid (cold water for >or=20 minutes) was associated with significantly reduced reepithelialization time for children with contact injuries (P=.011). Superficial depth burns were significantly more likely to be associated with the use of recommended first aid (P=.03). Suboptimal treatment was more common for children younger than 3.5 years (P<.001) and for children with friction burns. This report is one of the few publications to relate first-aid treatment to clinical outcomes. Some positive clinical outcomes were associated with recommended first-aid use; however, wound outcomes were more strongly associated with burn depth and mechanism of injury. There is also a need for more public awareness of recommended first-aid treatment.

Silver deposits in cutaneous burn scar tissue is a common phenomenon following application of a silver dressing.

BACKGROUND: Silver dressings have been widely and successfully used to prevent cutaneous wounds, including burns, chronic ulcers, dermatitis and other cutaneous conditions, from infection. However, in a few cases, skin discolouration or argyria-like appearances have been reported. This study investigated the level of silver in scar tissue post-burn injury following application of Acticoat, a silver dressing. METHODS: A porcine deep dermal partial thickness burn model was used. Burn wounds were treated with this silver dressing until completion of re-epithelialization, and silver levels were measured in a total of 160 scars and normal tissues. RESULTS: The mean level of silver in scar tissue covered with silver dressings was 136 microg/g, while the silver level in normal skin was less than 0.747 microg/g. A number of wounds had a slate-grey appearance, and dissection of the scars revealed brown-black pigment mostly in the middle and deep dermis within the scar. The level of silver and the severity of the slate-grey discolouration were correlated with the length of time of the silver dressing application. CONCLUSIONS: These results show that silver deposition in cutaneous scar tissue is a common phenomenon, and higher levels of silver deposits and severe skin discolouration are correlated with an increase in the duration of this silver dressing application.

Laser Doppler imaging in a paediatric burns population.

OBJECTIVE: Laser Doppler imaging (LDI) was compared to wound outcomes in children's burns, to determine if the technology could be used to predict these outcomes. METHODS: Forty-eight patients with a total of 85 burns were included in the study. Patient median age was 4 years 10 months and scans were taken 0-186 h post-burn using the fast, low-resolution setting on the Moor LDI2 laser Doppler imager. Wounds were managed by standard practice, without taking into account the scan results. Time until complete re-epithelialisation and whether or not grafting and scar management were required were recorded for each wound. If wounds were treated with Silvazine or Acticoat prior to the scan, this was also recorded. RESULTS: The predominant colour of the scan was found to be significantly related to the re-epithelialisation, grafting and scar management outcomes and could be used to predict those outcomes. The prior use of Acticoat did not affect the scan relationship to outcomes, however, the use of Silvazine did complicate the relationship for light blue and green scanned partial thickness wounds. Scans taken within the 24-h window after-burn also appeared to be accurate predictors of wound outcome. CONCLUSION: Laser Doppler imaging is accurate and effective in a paediatric population with a low-resolution fast-scan.

The evaluation of a clinical scar scale for porcine burn scars.

This study describes the evaluation of a clinical scar scale for our porcine burn scars, which includes scar cosmetic outcome, colour, height and hair, supplemented with reference porcine scar photographs representing each scar outcome and scar colour scores. A total of 72 porcine burn scars at week 6 after burn were rated in vivo and/or on photographs. Good agreements were achieved for both intra-rater reliability (correlation is 0.86-0.98) and inter-rater reliability (ICC=80-85%). The results showed statistically significant correlations for each pair in this clinical scar scale (p<0.01), with the best correlation found between scar cosmetic outcome and scar colour. A multivariate principle components analysis revealed that this clinical scar assessment was highly correlated with scar histology, wound size, and re-epithelialisation data (p<0.001). More severe scars are clinically characterised by darker purple colouration, more elevation, no presence of hair, histologically by thicker scar tissue, thinner remaining normal dermis, are more likely to have worse contraction, and slower re-epithelialisation. This study demonstrates that our clinical scar scale is a reliable, independent and valuable tool for assessing porcine burn outcome and truthfully reflects scar appearance and function. To our knowledge, this is the first study demonstrating a high correlation between clinical scar assessment and scar histology, wound contraction and re-epithelialisation data on porcine burn scars. We believe that the successful use of porcine scar scales is invaluable for assessing potential human burn treatments.

Silver absorption on burns after the application of Acticoat: data from pediatric patients and a porcine burn model.

Silver dressings have been widely used to successfully prevent burn wound infection and sepsis. However, a few case studies have reported the functional abnormality and failure of vital organs, possibly caused by silver deposits. The aim of this study was to investigate the serum silver level in the pediatric burn population and also in several internal organs in a porcine burn model after the application of Acticoat. A total of 125 blood samples were collected from 46 pediatric burn patients. Thirty-six patients with a mean of 13.4% TBSA burns had a mean peak serum silver level of 114 microg/L, whereas 10 patients with a mean of 1.85% TBSA burns had an undetectable level of silver (<5.4 microg/L). Overall, serum silver levels were closely related to burn sizes. However, the highest serum silver was 735 microg/L in a 15-month-old toddler with 10% TBSA burns and the second highest was 367 microg/L in a 3-year old with 28% TBSA burns. In a porcine model with 2% TBSA burns, the mean peak silver level was 38 microg/L at 2 to 3 weeks after application of Acticoat and was then significantly reduced to an almost undetectable level at 6 weeks. Of a total of four pigs, silver was detected in all four livers (1.413 microg/g) and all four hearts (0.342 microg/g), three of four kidneys (1.113 microg/g), and two of four brains (0.402 microg/g). This result demonstrated that although variable, the level of serum silver was positively associated with the size of burns, and significant amounts of silver were deposited in internal organs in pigs with only 2% TBSA burns, after application of Acticoat.

Burn healing is dependent on burn site: a quantitative analysis from a porcine burn model.

This retrospective review examines healing in different sites on a porcine burn model; 24 pairs of burns on 18 pigs from other animal trials were selected for analysis. Each pair of burns was located on the either the cranial or the caudal part of the thoracic ribs region, on the same side of the animal. The burns were 40-50 cm(2) in size and of uniform deep-dermal partial thickness. Caudal burns healed significantly better than cranial burns, demonstrated by earlier closure of wounds, less scar formation and better cosmesis. To our knowledge, this is the first detailed study reporting that burn healing is affected by location on a porcine burn model. We recommend that similar symmetrical burns should be used for future comparative assessments of burn healing.

Toward a full characterization of native starch: separation and detection by size-exclusion chromatography.

The structure of starch molecules is relevant to nutrition and industrial applications. Size-exclusion chromatography (SEC, also known as GPC) of native starch generally suffers non-satisfactory repeatability and reproducibility of the dissolution and separation. This work combines two polar organic solvents: dimethylsulfoxide for complete dissolution and dimethylacetamide to limit shear degradation. The separation is as repeatable as that of polystyrene standards performing dissolution and separation at 80 degrees C. Successful covalent-labeling on the glucose unit is claimed to be published here for the first time in non-degradative conditions and allows the use of UV detector with significantly higher sensitivity than with a refractometer.

The efficacy of Aloe vera, tea tree oil and saliva as first aid treatment for partial thickness burn injuries.

Many alternative therapies are used as first aid treatment for burns, despite limited evidence supporting their use. In this study, Aloe vera, saliva and a tea tree oil impregnated dressing (Burnaid) were applied as first aid to a porcine deep dermal contact burn, compared to a control of nothing. After burn creation, the treatments were applied for 20 min and the wounds observed at weekly dressing changes for 6 weeks. Results showed that the alternative treatments did significantly decrease subdermal temperature within the skin during the treatment period. However, they did not decrease the microflora or improve re-epithelialisation, scar strength, scar depth or cosmetic appearance of the scar and cannot be recommended for the first aid treatment of partial thickness burns.

Vitronectin: growth factor complexes hold potential as a wound therapy approach.

Topical administration of growth factors has displayed some potential in wound healing, but variable efficacy, high doses, and costs have hampered their implementation. Moreover, this approach ignores the fact that wound repair is driven by interactions between multiple growth factors and extracellular matrix (ECM) proteins. We report herein that complexes comprising IGF and IGF-binding proteins bound to the ECM protein vitronectin (VN) significantly enhance cellular functions relevant to wound repair in human skin keratinocytes in two- and three-dimensional in vitro cell models and are active, even in the presence of wound fluid. Moreover, these responses require activation of both the IGF receptor and the VN-binding alpha(v) integrins. Further, we assessed the complexes as a topical agent in the treatment of deep dermal partial thickness burns in a porcine model. This pilot study revealed that the complexes may hold promise as a wound healing therapy. Critically, the significant responses observed in vitro and the encouraging preliminary data in vivo were obtained with nanogram doses of growth factors. This suggests that coupling delivery of growth factors to ECM proteins such as VN may ultimately prove to be a more effective strategy for developing a wound healing therapy.

Conservative surgical debridement as a burn treatment: supporting evidence from a porcine burn model.

In thermal deep-dermal burns, surgical debridement is normally used in conjunction with skin grafting or skin substitutes and debridement alone as a burn treatment is not usually practiced. The current study addresses whether or not debridement alone would enhance burn wound healing on small deep-dermal-partial thickness burns. This was a prospective and blinded experimental trial using a porcine deep-dermal-partial thickness burn model. Four burns, approximately 50 cm(2) in size, were created on each of eight pigs. Two burns from each pig were immediately surgically debrided and the other two were not debrided as the internal control. Hydrate gel together with paraffin gauze were used to cover the burns for four pigs and silver dressings for the other four. Clinical assessment of wound healing was conducted over a 6-week period. Skin samples were collected at the end of the experiment and histopathological evaluation was performed. The results show thinner scar formation and lower scar height in the debrided compared with nondebrided wounds in the hydrate gel/paraffin gauze groups. There were no statistically significant differences in wound healing assessment between the debrided and nondebrided wounds dressed with silver dressings. This study provides supporting evidence that immediate debridement with an appropriate dressing and without skin grafting may promote wound healing, suggesting its potential benefit for clinical patients.