Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data.

BACKGROUND: Genomic technologies can be subject to significant batch-effects which are known to reduce experimental power and to potentially create false positive results. The Illumina Infinium Methylation BeadChip is a popular technology choice for epigenome-wide association studies (EWAS), but presently, little is known about the nature of batch-effects on these designs. Given the subtlety of biological phenotypes in many EWAS, control for batch-effects should be a consideration. RESULTS: Using the batch-effect removal approaches in the ComBat and Harman software, we examined two in-house datasets and compared results with three large publicly available datasets, (1214 HumanMethylation450 and 1094 MethylationEPIC BeadChips in total), and find that despite various forms of preprocessing, some batch-effects persist. This residual batch-effect is associated with the day of processing, the individual glass slide and the position of the array on the slide. Consistently across all datasets, 4649 probes required high amounts of correction. To understand the impact of this set to EWAS studies, we explored the literature and found three instances where persistently batch-effect prone probes have been reported in abstracts as key sites of differential methylation. As well as batch-effect susceptible probes, we also discover a set of probes which are erroneously corrected. We provide batch-effect workflows for Infinium Methylation data and provide reference matrices of batch-effect prone and erroneously corrected features across the five datasets spanning regionally diverse populations and three commonly collected biosamples (blood, buccal and saliva). CONCLUSIONS: Batch-effects are ever present, even in high-quality data, and a strategy to deal with them should be part of experimental design, particularly for EWAS. Batch-effect removal tools are useful to reduce technical variance in Infinium Methylation data, but they need to be applied with care and make use of post hoc diagnostic measures.

The Checkpoint Program: Collaborative Care to Reduce the Reliance of Frequent Presenters on ED.

INTRODUCTION: Growing pressures upon Emergency Departments [ED] call for new ways of working with frequent presenters who, although small in number, place extensive demands on services, to say nothing of the costs and consequences for the patients themselves. EDs are often poorly equipped to address the multi-dimensional nature of patient need and the complex circumstances surrounding repeated presentation. Employing a model of intensive short-term community-based case management, the Checkpoint program sought to improve care coordination for this patient group, thereby reducing their reliance on ED. METHOD: This study employed a single group interrupted time series design, evaluating patient engagement with the program and year-on-year individual differences in the number of ED visits pre and post enrolment. Associated savings were also estimated. RESULTS: Prior to intervention, there were two dominant modes in the ED presentation trends of patients. One group had a steady pattern with ≥7 presentations in each of the last four years. The other group had an increasing trend in presentations, peaking in the 12 months immediately preceding enrolment. Following the intervention, both groups demonstrated two consecutive year-on-year reductions. By the second year, and from an overall peak of 22.5 presentations per patient per annum, there was a 53% reduction in presentations. This yielded approximate savings of $7100 per patient. DISCUSSION: Efforts to improve care coordination, when combined with proactive case management in the community, can impact positively on ED re-presentation rates, provided they are concerted, sufficiently intensive and embed the principles of integration. CONCLUSION: The Checkpoint program demonstrated sufficient promise to warrant further exploration of its sustainability. However, health services have yet to determine the ideal organisational structures and funding arrangements to support such initiatives.

Lumos: a statewide linkage programme in Australia integrating general practice data to guide system redesign.

Objective: With ageing of the Australian population, more people are living longer and experiencing chronic or complex health conditions. The challenge is to have information that supports the integration of services across the continuum of settings and providers, to deliver person-centred, seamless, efficient and effective healthcare. However, in Australia, data are typically siloed within health settings, precluding a comprehensive view of patient journeys. Here, we describe the establishment of the Lumos programme-the first statewide linked data asset across primary care and other settings in Australia and evaluate its representativeness to the census population. Methods and analysis: Records extracted from general practices throughout New South Wales (NSW), Australia's most populous state, were linked to patient records from acute and other settings. Innovative privacy and security technologies were employed to facilitate ongoing and regular updates. The marginal demographic distributions of the Lumos cohort were compared with the NSW census population by calculating multiple measures of representation to evaluate its generalisability. Results: The first Lumos programme data extraction linked 1.3 million patients' general practice records to other NSW health system data. This represented 16% of the NSW population. The demographic distribution of patients in Lumos was >95% aligned to that of the NSW population in the calculated measures of representativeness. Conclusion: The Lumos programme delivers an enduring, regularly updated data resource, providing unique insights about statewide, cross-setting healthcare utilisation. General practice patients represented in the Lumos data asset are representative of the NSW population overall. Lumos data can reliably be used to identify at-risk regions and groups, to guide the planning and design of health services and to monitor their impact throughout NSW.

Effects of uranium concentration on microbial community structure and functional potential.

Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg-1 ), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg-1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg-1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience.

Effect of prenatal DHA supplementation on the infant epigenome: results from a randomized controlled trial.

BACKGROUND: Evidence is accumulating that nutritional exposures in utero can influence health outcomes in later life. Animal studies and human epidemiological studies have implicated epigenetic modifications as playing a key role in this process, but there are limited data from large well-controlled human intervention trials. This study utilized a large double-blind randomized placebo-controlled trial to test whether a defined nutritional exposure in utero, in this case docosahexaenoic acid (DHA), could alter the infant epigenome. Pregnant mothers consumed DHA-rich fish oil (800 mg DHA/day) or placebo supplements from 20 weeks' gestation to delivery. Blood spots were collected from the children at birth (n = 991) and blood leukocytes at 5 years (n = 667). Global DNA methylation was measured in all samples, and Illumina HumanMethylation450K BeadChip arrays were used for genome-wide methylation profiling in a subset of 369 children at birth and 65 children at 5 years. RESULTS: There were no differences in global DNA methylation levels between the DHA and control group either at birth or at 5 years, but we identified 21 differentially methylated regions (DMRs) at birth, showing small DNA methylation differences (<5%) between the treatment groups, some of which seemed to persist until 5 years. The number of DMRs at birth was greater in males (127 DMRs) and in females (72 DMRs) separately, indicating a gender-specific effect. CONCLUSION: Maternal DHA supplementation during the second half of pregnancy had small effects on DNA methylation of infants. While the potential functional significance of these changes remains to be determined, these findings further support the role of epigenetic modifications in developmental programming in humans and point the way for future studies. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (ANZCTR), ACTRN12605000569606 and ACTRN12611001127998.

Risk-conscious correction of batch effects: maximising information extraction from high-throughput genomic datasets.

BACKGROUND: Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets. At their most benign, they reduce the power of statistical tests resulting in actual effects going unidentified. At their worst, they constitute confounds and render datasets useless. Attempting to remove batch effects will result in some of the biologically meaningful component of the measurement (i.e. signal) being lost. We present and benchmark a novel technique, called Harman. Harman maximises the removal of batch noise with the constraint that the risk of also losing biologically meaningful component of the measurement is kept to a fraction which is set by the user. RESULTS: Analyses of three independent publically available datasets reveal that Harman removes more batch noise and preserves more signal at the same time, than the current leading technique. Results also show that Harman is able to identify and remove batch effects no matter what their relative size compared to other sources of variation in the dataset. Of particular advantage for meta-analyses and data integration is Harman's superior consistency in achieving comparable noise suppression - signal preservation trade-offs across multiple datasets, with differing number of treatments, replicates and processing batches. CONCLUSION: Harman's ability to better remove batch noise, and better preserve biologically meaningful signal simultaneously within a single study, and maintain the user-set trade-off between batch noise rejection and signal preservation across different studies makes it an effective alternative method to deal with batch effects in high-throughput genomic datasets. Harman is flexible in terms of the data types it can process. It is available publically as an R package ( https://bioconductor.org/packages/release/bioc/html/Harman.html ), as well as a compiled Matlab package ( http://www.bioinformatics.csiro.au/harman/ ) which does not require a Matlab license to run.

Long-term exposure to commercially available sunscreens containing nanoparticles of TiO2 and ZnO revealed no biological impact in a hairless mouse model.

BACKGROUND: The application of sunscreen is a critical component of a sun-safe strategy, however the possibility of unexpected, adverse outcomes resulting from long-term use of sunscreens containing nanoparticles of titanium dioxide (TiO2) and zinc oxide (ZnO) has not yet been examined. Here, immune-competent hairless mice were exposed over a 36-week period to weekly topical applications of sunscreens containing nanoparticles of ZnO or TiO2, or no metal oxide nanoparticles, with or without subsequent exposure to ultraviolet radiation (UVR). Control groups received no sunscreen applications, with or without UVR. RESULTS: Mice exposed to UVR in the absence of sunscreen developed statistically significant incidences of histologically-diagnosed malignant and benign skin neoplasms, whereas no statistically significant adverse biological outcomes were found in mice treated with the sunscreens containing ZnO or TiO2 nanoparticles. Elevated levels of Ti were detected in the livers of mice treated with sunscreen containing TiO2 nanoparticles compared to untreated control, but total Zn concentrations did not significantly alter in any major organs except for the skin of mice treated with ZnO sunscreen. Exposure to UVR did not have a significant impact on examined tissue concentrations of Zn or Ti. Few to no transcriptional changes were found in ZnO or TiO2-treated groups, but mice treated with the sunscreen containing only organic filters showed substantial gene disregulation. CONCLUSIONS: Taken together with previous work, this long-term study provided no basis to avoid the use of sunscreens containing metal oxide nanoparticles.

Dermal absorption and short-term biological impact in hairless mice from sunscreens containing zinc oxide nano- or larger particles.

Previous studies have shown no, or very limited, skin penetration of metal oxide nanoparticles following topical application of sunscreens, yet concerns remain about their safety compared to larger particles. Here, we assessed the comparative dermal absorption of a traceable form of Zn ((68)Zn) from (68)ZnO nano-sized and larger particles in sunscreens. Sunscreens were applied to the backs of virgin or pregnant hairless mice over four days. Control groups received topical applications of the sunscreen formulation containing no ZnO particles, or no treatment. Major organs were assessed for changes in (68)Zn/(64)Zn ratios, (68)Zn tracer and total Zn concentrations. Short-term biological impact was assessed by measuring levels of serum amyloid A in blood, and by performing whole-genome transcriptional profiling on livers from each group. Increased concentrations of (68)Zn tracer were detected in internal organs of mice receiving topical applications of (68)ZnO (nano-sized and larger particles), as well as in fetal livers from treated dams, compared with controls. Furthermore, concentrations of (68)Zn in organs of virgin mice treated with sunscreen containing (68)ZnO nanoparticles were found to be significantly higher than in mice treated with sunscreen containing larger (68)ZnO particles. However, no ZnO-mediated change in total Zn concentration in any of the major organs was observed. Thus, despite (68)Zn absorption, which may have been in the form of soluble (68)Zn species or (68)ZnO particles (not known), Zn homeostasis was largely maintained, and the presence of ZnO particles in sunscreen did not elicit an adverse biological response in the mice following short-term topical applications.

Surface coatings of ZnO nanoparticles mitigate differentially a host of transcriptional, protein and signalling responses in primary human olfactory cells.

BACKGROUND: Inhaled nanoparticles have been reported in some instances to translocate from the nostril to the olfactory bulb in exposed rats. In close proximity to the olfactory bulb is the olfactory mucosa, within which resides a niche of multipotent cells. Cells isolated from this area may provide a relevant in vitro system to investigate potential effects of workplace exposure to inhaled zinc oxide nanoparticles. METHODS: Four types of commercially-available zinc oxide (ZnO) nanoparticles, two coated and two uncoated, were examined for their effects on primary human cells cultured from the olfactory mucosa. Human olfactory neurosphere-derived (hONS) cells from healthy adult donors were analyzed for modulation of cytokine levels, activation of intracellular signalling pathways, changes in gene-expression patterns across the whole genome, and compromised cellular function over a 24 h period following exposure to the nanoparticles suspended in cell culture medium. RESULTS: ZnO nanoparticle toxicity in hONS cells was mediated through a battery of mechanisms largely related to cell stress, inflammatory response and apoptosis, but not activation of mechanisms that repair damaged DNA. Surface coatings on the ZnO nanoparticles mitigated these cellular responses to varying degrees. CONCLUSIONS: The results indicate that care should be taken in the workplace to minimize generation of, and exposure to, aerosols of uncoated ZnO nanoparticles, given the adverse responses reported here using multipotent cells derived from the olfactory mucosa.

Reanalysis and simulation suggest a phylogenetic microarray does not accurately profile microbial communities.

The second generation (G2) PhyloChip is designed to detect over 8700 bacteria and archaeal and has been used over 50 publications and conference presentations. Many of those publications reveal that the PhyloChip measures of species richness greatly exceed statistical estimates of richness based on other methods. An examination of probes downloaded from Greengenes suggested that the system may have the potential to distort the observed community structure. This may be due to the sharing of probes by taxa; more than 21% of the taxa in that downloaded data have no unique probes. In-silico simulations using these data showed that a population of 64 taxa representing a typical anaerobic subterranean community returned 96 different taxa, including 15 families incorrectly called present and 19 families incorrectly called absent. A study of nasal and oropharyngeal microbial communities by Lemon et al (2010) found some 1325 taxa using the G2 PhyloChip, however, about 950 of these taxa have, in the downloaded data, no unique probes and cannot be definitively called present. Finally, data from Brodie et al (2007), when re-examined, indicate that the abundance of the majority of detected taxa, are highly correlated with one another, suggesting that many probe sets do not act independently. Based on our analyses of downloaded data, we conclude that outputs from the G2 PhyloChip should be treated with some caution, and that the presence of taxa represented solely by non-unique probes be independently verified.

Microbial biodiversity in a Malaysian oil field and a systematic comparison with oil reservoirs worldwide.

Microbial diversity within formation water and oil from two compartments in Bokor oil reservoir from a Malaysian petroleum oil field was examined. A total of 1,056 16S rRNA gene clones were screened from each location by amplified ribosomal DNA restriction analysis. All samples were dominated by clones affiliated with Marinobacter, some novel Deferribacteraceae genera and various clones allied to the Methanococci. In addition, either Marinobacterium- or Pseudomonas-like operational taxonomic units were detected from either compartment. A systematic comparison with the existing pertinent studies was undertaken by analysing the microbial amplicons detected and the PCR primers used. The analyses demonstrated that bacterial communities were site specific, while Archaea co-occurred more frequently. Amplicons related to Marinobacter, Marinobacterium and Pseudomonas were detected in a number of the studies examined, suggesting they may be ubiquitous members in oil reservoirs. Further analysis of primers used in those studies suggested that most primer pairs had fairly broad but low matches across the bacterial and archaeal domains, while a minority had selective matches to certain taxa or low matches to all the microbial taxa tested. Thus, it indicated that primers may play an important role in determining which taxa would be detected.

Small amounts of zinc from zinc oxide particles in sunscreens applied outdoors are absorbed through human skin.

Metal oxide nanoparticles are commonly used in personal-care formulations as protective agents against exposure to ultraviolet radiation. Although previous research has concluded that nanoparticles do not penetrate healthy skin, it remains contentious whether this conclusion holds under normal conditions of sunscreen use. Humans (n = 20) were exposed to sunscreens containing zinc oxide (ZnO) particles to determine if Zn from the particles was absorbed through skin over five consecutive days under outdoor conditions. Two sunscreens were tested-"nano sunscreen" containing 19-nm nanoparticles and "bulk sunscreen" containing > 100-nm particles. Venous blood and urine samples were collected 8 days before exposure, twice daily during the trial, and 6 days post-exposure. As the first application in nanotechnology studies, stable isotope tracing was used where the ZnO, enriched to > 99% with the stable isotope (68)Zn, allowed dermally absorbed zinc to be distinguished from naturally occurring zinc. The overwhelming majority of applied (68)Zn was not absorbed, although blood and urine samples from all subjects exhibited small increases in levels of tracer (68)Zn. The amount of tracer detected in blood after the 5-day application period was ∼1/1000 th that of total Zn in the blood compartment. Tracer levels in blood continued to increase beyond the 5-day application phase in contrast to those in urine. Levels of (68)Zn in blood and urine from females receiving the nano sunscreen appeared to be higher than males receiving the same treatment and higher than all subjects receiving the bulk sunscreen. It is not known whether (68)Zn has been absorbed as ZnO particles or soluble Zn or both.

A robotic apparatus that dictates torque fields around joints without affecting inherent joint dynamics.

This manuscript describes how motor behaviour researchers who are not at the same time expert roboticists may implement an experimental apparatus, which has the ability to dictate torque fields around a single joint on one limb or single joints on multiple limbs without otherwise interfering with the inherent dynamics of those joints. Such an apparatus expands the exploratory potential of the researcher wherever experimental distinction of factors may necessitate independent control of torque fields around multiple limbs, or the shaping of torque fields of a given joint independently of its plane of motion, or its directional phase within that plane. The apparatus utilizes torque motors. The challenge with torque motors is that they impose added inertia on limbs and thus attenuate joint dynamics. We eliminated this attenuation by establishing an accurate mathematical model of the robotic device using the Box-Jenkins method, and cancelling out its dynamics by employing the inverse of the model as a compensating controller. A direct measure of the remnant inertial torque as experienced by the hand during a 50 s period of wrist oscillations that increased gradually in frequency from 1.0 to 3.8 Hz confirmed that the removal of the inertial effect of the motor was effectively complete.

Artificial gravity reveals that economy of action determines the stability of sensorimotor coordination.

BACKGROUND: When we move along in time with a piece of music, we synchronise the downward phase of our gesture with the beat. While it is easy to demonstrate this tendency, there is considerable debate as to its neural origins. It may have a structural basis, whereby the gravitational field acts as an orientation reference that biases the formulation of motor commands. Alternatively, it may be functional, and related to the economy with which motion assisted by gravity can be generated by the motor system. METHODOLOGY/PRINCIPAL FINDINGS: We used a robotic system to generate a mathematical model of the gravitational forces acting upon the hand, and then to reverse the effect of gravity, and invert the weight of the limb. In these circumstances, patterns of coordination in which the upward phase of rhythmic hand movements coincided with the beat of a metronome were more stable than those in which downward movements were made on the beat. When a normal gravitational force was present, movements made down-on-the-beat were more stable than those made up-on-the-beat. CONCLUSIONS/SIGNIFICANCE: The ubiquitous tendency to make a downward movement on a musical beat arises not from the perception of gravity, but as a result of the economy of action that derives from its exploitation.

Neuromuscular and biomechanical factors codetermine the solution to motor redundancy in rhythmic multijoint arm movement.

How the CNS deals with the issue of motor redundancy remains a central question for motor control research. Here we investigate the means by which neuromuscular and biomechanical factors interact to resolve motor redundancy in rhythmic multijoint arm movements. We used a two-df motorized robot arm to manipulate the dynamics of rhythmic flexion-extension (FE) and supination-pronation (SP) movements at the elbow-joint complex. Participants were required to produce rhythmic FE and SP movements, either in isolation, or in combination (at the phase relationship of their choice), while we recorded the activity of key bi-functional muscles. When performed in combination, most participants spontaneously produced an in-phase pattern of coordination in which flexion is synchronised with supination. The activity of the Biceps Brachii (BB), the strongest arm muscle which also has the largest moment arms in both flexion and supination was significantly higher for FE and SP performed in combination than in isolation, suggesting optimal exploitation of the mechanical advantage of this muscle. In a separate condition, participants were required to produce a rhythmic SP movement while a rhythmic FE movement was imposed by the motorized robot. Simulations based upon a musculoskeletal model of the arm demonstrated that in this context, the most efficient use of the force-velocity relationship of BB requires that an anti-phase pattern of coordination (flexion synchronized with pronation) be produced. In practice, the participants maintained the in-phase behavior, and BB activity was higher than for SP performed in isolation. This finding suggests that the neural organisation underlying the exploitation of bifunctional muscle properties, in the natural context, constrains the system to maintain the "natural" coordination pattern in an altered dynamic environment, even at the cost of reduced biomechanical efficiency. We suggest an important role for afference from the imposed movement in promoting the "natural" pattern. Practical implications for the emerging field of robot-assisted therapy and rehabilitation are briefly mentioned.

Postural context alters the stability of bimanual coordination by modulating the crossed excitability of corticospinal pathways.

The tendency for movements of the upper limbs to be drawn systematically toward one another and to follow similar spatiotemporal trajectories is well known. Although suppression of this tendency is integral to tasks of daily living, its exploitation may prove to be critical in the rehabilitation of acquired hemiplegias. In general, however, the task-related factors that determine the degree of coupling between the upper limbs and the mechanisms that mediate bilateral interactions between neural pathways projecting to the muscles of the arm and hand are not yet well understood. We present evidence that the postural context in which human participants perform upper limb movements determines the relative stability of patterns of bimanual coordination. Manipulation of the axes of rotation of forearm movements reversed the relative stability of simultaneous and alternating patterns of bimanual coordination. Transcranial magnetic stimulation of motor cortex revealed that these manipulations of postural context altered the crossed modulation of excitability in corticospinal pathways that arises from movement of the opposite limb. Furthermore, modulation of responses to electrical stimulation of the cervicomedullary junction indicated that crossed modulation was also expressed at the level of the spinal motoneurons. Our data support the view that crossed modulation of excitability in corticospinal pathways mediates the stability of bimanual coordination. Furthermore, task-related factors that are sufficient to give rise to changes in the stability of bimanual coordination are accompanied by crossed modulation of excitability at multiple levels of the neuraxis, indicative of a failure of inhibitory control.

Degrees of freedom and motor planning in purposive movement.

This paper presents empirical evidence suggesting that healthy humans can perform a two degree of freedom visuo-motor pursuit tracking task with the same response time delay as a one degree of freedom task. In contrast, the time delay of the response is influenced markedly by the nature of the motor synergy required to produce it. We suggest a conceptual account of this evidence based on adaptive model theory, which combines theories of intermittency from psychology and adaptive optimal control from engineering. The intermittent response planning stage has a fixed period. It possesses multiple optimal trajectory generators such that multiple degrees of freedom can be planned concurrently, without requiring an increase in the planning period. In tasks which require unfamiliar motor synergies, or are deemed to be incompatible, internal adaptive models representing movement dynamics are inaccurate. This means that the actual response which is produced will deviate from the one which is planned. For a given target-response discrepancy, corrective response trajectories of longer duration are planned, consistent with the principle of speed-accuracy trade-off. Compared to familiar or compatible tasks, this results in a longer response time delay and reduced accuracy. From the standpoint of the intermittency approach, the findings of this study help make possible a more integral and predictive account of purposive action.