Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data

<p>Abstract</p> <p>Background</p> <p>A key stage for all microarray analyses is the extraction of feature-intensities from an image. If this step goes wrong, then subsequent preprocessing and processing stages will stand little chance of rectifying the matter. Illumina employ random construction of their BeadArrays, making feature-intensity extraction even more important for the Illumina platform than for other technologies. In this paper we show that using raw Illumina data it is possible to identify, control, and perhaps correct for a range of spatial-related phenomena that affect feature-intensity extraction.</p> <p>Results</p> <p>We note that feature intensities can be unnaturally high when in the proximity of a number of phenomena relating either to the images themselves or to the layout of the beads on an array. Additionally we note that beads neighbour beads of the same type more often than one might expect, which may cause concern in some models of hybridization. We highlight issues in the identification of a bead's location, and in particular how this both affects and is affected by its intensity. Finally we show that beads can be wrongly identified in the image on either a local or array-wide scale, with obvious implications for data quality.</p> <p>Conclusions</p> <p>The image processing issues identified will often pass unnoticed by an analysis of the standard data returned from an experiment. We detail some simple diagnostics that can be implemented to identify problems of this nature, and outline approaches to correcting for such problems. These approaches require access to the raw data from the arrays, not just the summarized data usually returned, making the acquisition of such raw data highly desirable.</p

Current quark mass dependence of nucleon magnetic moments and radii

A calculation of the current-quark-mass-dependence of nucleon static electromagnetic properties is necessary in order to use observational data as a means to place constraints on the variation of Nature's fundamental parameters. A Poincare' covariant Faddeev equation, which describes baryons as composites of confined-quarks and -nonpointlike-diquarks, is used to calculate this dependence The results indicate that, like observables dependent on the nucleons' magnetic moments, quantities sensitive to their magnetic and charge radii, such as the energy levels and transition frequencies in Hydrogen and Deuterium, might also provide a tool with which to place limits on the allowed variation in Nature's constants.Comment: 23 pages, 2 figures, 4 tables, 4 appendice

Comparison of two normative paediatric gait databases

The availability of age-matched normative data is an essential component of clinical gait analyses. Comparison of normative gait databases is difficult due to the high-dimensionality and temporal nature of the various gait waveforms. The purpose of this study was to provide a method of comparing the sagittal joint angle data between two normative databases. We compared a modern gait database to the historical San Diego database using statistical classifiers developed by Tingley et al. (2002). Gait data were recorded from 60 children aged 1–13 years. A six-camera Vicon 512 motion analysis system and two force plates were utilized to obtain temporal-spatial, kinematic, and kinetic parameters during walking. Differences between the two normative data sets were explored using the classifier index scores, and the mean and covariance structure of the joint angle data from each lab. Significant differences in sagittal angle data between the two databases were identified and attributed to technological advances and data processing techniques (data smoothing, sampling, and joint angle approximations). This work provides a simple method of database comparison using trainable statistical classifiers

Prevalence, predictors and perinatal outcomes of peri-conceptional alcohol exposure - retrospective cohort study in an urban obstetric population in Ireland

<p>Abstract</p> <p>Background</p> <p>Evidence-based advice on alcohol consumption is required for pregnant women and women planning a pregnancy. Our aim was to investigate the prevalence, predictors and perinatal outcomes associated with peri-conceptional alcohol consumption.</p> <p>Methods</p> <p>A cohort study of 61,241 women who booked for antenatal care and delivered in a large urban maternity hospital between 2000 and 2007. Self-reported alcohol consumption at the booking visit was categorised as low (0-5 units per week), moderate (6-20 units per week) and high (>20 units per week).</p> <p>Results</p> <p>Of the 81% of women who reported alcohol consumption during the peri-conceptional period, 71% reported low intake, 9.9% moderate intake and 0.2% high intake. Factors associated with moderate alcohol consumption included being in employment OR 4.47 (95% CI 4.17 to 4.80), Irish nationality OR 16.5 (95% CI 14.9 to 18.3), private health care OR 5.83 (95% CI 5.38 to 6.31) and smoking OR 1.86 (95% CI 1.73 to 2.01). Factors associated with high consumption included maternal age less than 25 years OR 2.70 (95% CI 1.86 to 3.91) and illicit drug use OR 6.46 (95% CI 3.32 to 12.60). High consumption was associated with very preterm birth (<32 weeks gestation) even after controlling for socio-demographic factors, adjusted OR 3.15 (95% CI 1.26-7.88). Only three cases of Fetal Alcohol Syndrome were recorded (0.05 per 1000 total births), one each in the low, moderate and high consumption groups.</p> <p>Conclusions</p> <p>Public Health campaigns need to emphasise the importance of peri-conceptional health and pre-pregnancy planning. Fetal Alcohol Syndrome is likely to be under-reported despite the high prevalence of alcohol consumption in this population.</p

The effect of premature extraction of primary teeth on the subsequent need for orthodontic treatment.

AIM: To investigate if premature extraction of primary teeth was associated with orthodontic need in the permanent dentition. STUDY DESIGN: This was a case-control study based on retrospective dental records. METHODS: As part of NHS (UK) Dental Epidemiology Programme a sample of 366, 12-year-old children from Bradford and Airedale were examined. The survey collected data on patient demographics, dental health status including orthodontic need. Data linkage was undertaken for those children participating in the NHS Dental Epidemiology Programme who had previously accessed the local Salaried Dental Service (SDS). For these children, retrospective dental information was collected about premature extraction of primary teeth. RESULTS: From the 366 children who were surveyed, 116 children had received treatment at the local SDS in the past. Significantly more children from ethnic minorities, low socioeconomic backgrounds and high caries rate (p < 0.001) were seen in the SDS. For the 107 children who attended SDS, an increased total number of primary teeth extractions was positively associated with orthodontic need (odds ratio:1.18, CI -1.01 to 1.37). STATISCTICS: Multilevel modelling was undertaken to identify variables associated with orthodontic need. CONCLUSIONS: In the study group, orthodontic need was significantly associated with the number of primary teeth extracted

The feasibility of measuring the activation of the trunk muscles in healthy older adults during trunk stability exercises

<p>Abstract</p> <p>Background</p> <p>As the older adult population increases, the potential functional and clinical burden of trunk muscle dysfunction may be significant. An evaluation of risk factors including the impact of the trunk muscles in terms of their temporal firing patterns, amplitudes of activation, and contribution to spinal stability is required. Therefore, the specific purpose of this study was to assess the feasibility of measuring the activation of trunk muscles in healthy older adults during specific leg exercises with trunk stabilization.</p> <p>Methods</p> <p>12 asymptomatic adults 65 to 75 years of age were included in the study. Participants performed a series of trunk stability exercises, while bilateral activation of abdominal and back extensor muscles was recorded by 24 pairs of Meditrace™ surface electrodes. Maximal voluntary isometric contractions (MVIC) were performed for electromyographic (EMG) normalization purposes. EMG waveforms were generated and amplitude measures as a percentage of MVIC were calculated along with ensemble average profiles. 3D kinematics data were also recorded, using an electromagnetic sensor placed at the left lateral iliac crest. Furthermore, a qualitative assessment was conducted to establish the participant's ability to complete all experimental tasks.</p> <p>Results</p> <p>Excellent quality abdominal muscle activation data were recorded during the tasks. Participants performed the trunk stability exercises with an unsteady, intermittent motion, but were able to keep pelvic motion to less than 10°. The EMG amplitudes showed that during these exercises, on average, the older adults recruited their abdominal muscles from 15–34% of MVIC and back extensors to less than 10% of MVIC. There were similarities among the abdominal muscle profiles. No participants reported pain during the testing session, although 3 (25%) of the participants reported delayed onset muscle soreness during follow up that was not functionally limiting.</p> <p>Conclusion</p> <p>Older adults were able to successfully complete the trunk stability protocol that was developed for younger adults with some minor modifications. The collected EMG amplitudes were higher than those reported in the literature for young healthy adults. The temporal waveforms for the abdominal muscles showed a degree of synchrony among muscles, except for the early activation from the internal oblique prior to lifting the leg off the table.</p