Sensitivity of organic matter decomposition to warming varies with its quality

The relationship between organic matter (OM) lability and temperature sensitivity is disputed, with recent observations suggesting that responses of relatively more resistant OM to increased temperature could be greater than, equivalent to, or less than responses of relatively more labile OM. This lack of clear understanding limits the ability to forecast carbon (C) cycle responses to temperature changes. Here, we derive a novel approach (denoted Q(10-q)) that accounts for changes in OM quality during decomposition and use it to analyze data from three independent sources. Results from new laboratory soil incubations (labile Q(10-q)=2.1 +/- 0.2; more resistant Q(10-q)=3.8 +/- 0.3) and reanalysis of data from other soil incubations reported in the literature (labile Q(10-q)=2.3; more resistant Q(10-q)=3.3) demonstrate that temperature sensitivity of soil OM decomposition increases with decreasing soil OM lability. Analysis of data from a cross-site, field litter bag decomposition study (labile Q(10-q)=3.3 +/- 0.2; resistant Q(10-q)=4.9 +/- 0.2) shows that litter OM follows the same pattern, with greater temperature sensitivity for more resistant litter OM. Furthermore, the initial response of cultivated soils, presumably containing less labile soil OM (Q(10-q)=2.4 +/- 0.3) was greater than that for undisturbed grassland soils (Q(10-q)=1.7 +/- 0.1). Soil C losses estimated using this approach will differ from previous estimates as a function of the magnitude of the temperature increase and the proportion of whole soil OM comprised of compounds sensitive to temperature over that temperature range. It is likely that increased temperature has already prompted release of significant amounts of C to the atmosphere as CO2. Our results indicate that future losses of litter and soil C may be even greater than previously supposed.

Prevalence of upper-body symptoms following breast cancer and its relationship with upper-body function and lymphoedema

This investigation describes the prevalence of upper-body symptoms in a population-based sample of women with breast cancer (BC) and examines their relationships with upper-body function (UBF) and lymphoedema, as two clinically important sequelae. Australian women (n=287) with unilateral BC were assessed at three-monthly intervals, from six to 18 months post-surgery (PS). Participants reported the presence and intensity of upper-body symptoms on the treated side. Objective and self-reported UBF and lymphoedema (bioimpedance spectroscopy) were also assessed. Approximately 50% of women reported at least one moderate-to-extreme symptom at 6- and at 18-months PS. There was a significant relationship between symptoms and function (p<0.01), whereby perceived and objective function declined with increasing number of symptoms present. Those with lymphoedema were more likely to report multiple symptoms and presence of symptoms at baseline increased risk of lymphoedema (ORs>1.3, p=0.02). Although, presence of symptoms explained only 5.5% of the variation in the odds of lymphoedema. Upper-body symptoms are common and persistent following breast cancer and are associated with clinical ramifications, including reduced UBF and increased risk of developing lymphoedema. However, using the presence of symptoms as a diagnostic indicator of lymphoedema is limited.

BLAST Atlas : a function based multiple genome browser

BLAST Atlas is a visual analysis system for comparative genomics that supports genome-wide gene characterisation, functional assignment and function-based browsing of one or more chromosomes. Inspired by applications such as the WorldWide Telescope, Bing Maps 3D and Google Earth, BLAST Atlas uses novel three-dimensional gene and function views that provide a highly interactive and intuitive way for scientists to navigate, query and compare gene annotations. The system can be used for gene identification and functional assignment or as a function-based multiple genome comparison tool which complements existing position based comparison and alignment viewers.

Intrinsically photosensitive melanopsin retinal ganglion cell contributions to the pupillary light reflex and circadian rhythm

Recently discovered intrinsically photosensitive melanopsin retinal ganglion cells contribute to the maintenance of pupil diameter, recovery and post-illumination components of the pupillary light reflex and provide the primary environmental light input to the suprachiasmatic nucleus for photoentrainment of the circadian rhythm. This review summarises recent progress in understanding intrinsically photosensitive ganglion cell histology and physiological properties in the context of their contribution to the pupillary and circadian functions and introduces a clinical framework for using the pupillary light reflex to evaluate inner retinal (intrinsically photosensitive melanopsin ganglion cell) and outer retinal (rod and cone photoreceptor) function in the detection of retinal eye disease.

The role of cardiopulmonary signals in the dynamics of the eye's wavefront aberrations

Abstract—The role of cardiopulmonary signals in the dynamics of wavefront aberrations in the eye has been examined. Synchronous measurement of the eye’s wavefront aberrations, cardiac function, blood pulse, and respiration signals were taken for a group of young, healthy subjects. Two focusing stimuli, three breathing patterns, as well as natural and cycloplegic eye conditions were examined. A set of tools, including time–frequency coherence and its metrics, has been proposed to acquire a detailed picture of the interactions of the cardiopulmonary system with the eye’s wavefront aberrations. The results showed that the coherence of the blood pulse and its harmonics with the eye’s aberrations was, on average, weak (0.4 ± 0.15), while the coherence of the respiration signal with eye’s aberrations was, on average, moderate (0.53 ± 0.14). It was also revealed that there were significant intervals during which high coherence occurred. On average, the coherence was high (>0.75) during 16% of the recorded time, for the blood pulse, and 34% of the time for the respiration signal. A statistically significant decrease in average coherence was noted for the eye’s aberrations with respiration in the case of fast controlled breathing (0.5 Hz). The coherence between the blood pulse and the defocus was significantly larger for the far target than for the near target condition. After cycloplegia, the coherence of defocus with the blood pulse significantly decreased, while this was not the case for the other aberrations. There was also a noticeable, but not statistically significant, increase in the coherence of the comatic term and respiration in that case. By using nonstationary measures of signal coherence, a more detailed picture of interactions between the cardiopulmonary signals and eye’s wavefront aberrations has emerged.

Remaining useful life prediction using elliptical basis function network and Markov Chain

This paper presents a novel method for remaining useful life prediction using the Elliptical Basis Function (EBF) network and a Markov chain. The EBF structure is trained by a modified Expectation-Maximization (EM) algorithm in order to take into account the missing covariate set. No explicit extrapolation is needed for internal covariates while a Markov chain is constructed to represent the evolution of external covariates in the study. The estimated external and the unknown internal covariates constitute an incomplete covariate set which are then used and analyzed by the EBF network to provide survival information of the asset. It is shown in the case study that the method slightly underestimates the remaining useful life of an asset which is a desirable result for early maintenance decision and resource planning.

The effects of muscle fatigue on knee function during landing

The human knee acts as a sophisticated shock absorber during landing movements. The ability of the knee to perform this function in the real world is remarkable given that the context of the landing movement may vary widely between performances. For this reason, humans must be capable of rapidly adjusting the mechanical properties of the knee under impact load in order to satisfy many competing demands. However, the processes involved in regulating these properties in response to changing constraints remain poorly understood. In particular, the effects of muscle fatigue on knee function during step landing are yet to be fully explored. Fatigue of the knee muscles is significant for 2 reasons. First, it is thought to have detrimental effects on the ability of the knee to act as a shock absorber and is considered a risk factor for knee injury. Second, fatigue of knee muscles provides a unique opportunity to examine the mechanisms by which healthy individuals alter knee function. A review of the literature revealed that the effect of fatigue on knee function during landing has been assessed by comparing pre and postfatigue measurements, with fatigue induced by a voluntary exercise protocol. The information is limited by inconsistent results with key measures, such as knee stiffness, showing varying results following fatigue, including increased stiffness, decreased stiffness or failure to detect any change in some experiments. Further consideration of the literature questions the validity of the models used to induce and measure fatigue, as well as the pre-post study design, which may explain the lack of consensus in the results. These limitations cast doubt on the usefulness of the available information and identify a need to investigate alternative approaches. Based on the results of this review, the aims of this thesis were to: • evaluate the methodological procedures used in validation of a fatigue model • investigate the adaptation and regulation of post-impact knee mechanics during repeated step landings • use this new information to test the effects of fatigue on knee function during a step-landing task. To address the aims of the thesis, 3 related experiments were conducted that collected kinetic, kinematic and electromyographic data from 3 separate samples of healthy male participants. The methodologies involved optoelectronic motion capture (VICON), isokinetic dynamometry (System3 Pro, BIODEX) and wireless surface electromyography (Zerowire, Aurion, Italy). Fatigue indicators and knee function measures used in each experiment were derived from the data. Study 1 compared the validity and reliability of repetitive stepping and isokinetic contractions with respect to fatigue of the quadriceps and hamstrings. Fifteen participants performed 50 repetitions of each exercise twice in randomised order, over 4 sessions. Sessions were separated by a minimum of 1 week’s rest, to ensure full recovery. Validity and reliability depended on a complex interaction between the exercise protocol, the fatigue indicator, the individual and the muscle of interest. Nevertheless, differences between exercise protocols indicated that stepping was less effective in eliciting valid and reliable changes in peak power and spectral compression, compared with isokinetic exercise. A key finding was that fatigue progressed in a biphasic pattern during both exercises. The point separating the 2 phases, known as the transition point, demonstrated superior between-test reliability during the isokinetic protocol, compared with stepping. However, a correction factor should be used to accurately apply this technique to the study of fatigue during landing. Study 2 examined alterations in knee function during repeated landings, with a different sample (N =12) performing 60 consecutive step landing trials. Each landing trial was separated by 1-minute rest periods. The results provided new information in relation to the pre-post study design in the context of detecting adjustments in knee function during landing. First, participants significantly increased or decreased pre-impact muscle activity or post-impact mechanics despite environmental and task constraints remaining unchanged. This is the 1st study to demonstrate this effect in healthy individuals without external feedback on performance. Second, single-subject analysis was more effective in detecting alterations in knee function compared to group-level analysis. Finally, repeated landing trials did not reduce inter-trial variability of knee function in some participants, contrary to assumptions underpinning previous studies. The results of studies 1 and 2 were used to modify the design of Study 3 relative to previous research. These alterations included a modified isokinetic fatigue protocol, multiple pre-fatigue measurements and singlesubject analysis to detect fatigue-related changes in knee function. The study design incorporated new analytical approaches to investigate fatiguerelated alterations in knee function during landing. Participants (N = 16) were measured during multiple pre-fatigue baseline trial blocks prior to the fatigue model. A final block of landing trials was recorded once the participant met the operational fatigue definition that was identified in Study 1. The analysis revealed that the effects of fatigue in this context are heavily dependent on the compensatory response of the individual. A continuum of responses was observed within the sample for each knee function measure. Overall, preimpact preparation and post-impact mechanics of the knee were altered with highly individualised patterns. Moreover, participants used a range of active or passive pre-impact strategies to adapt post-impact mechanics in response to quadriceps fatigue. The unique patterns identified in the data represented an optimisation of knee function based on priorities of the individual. The findings of these studies explain the lack of consensus within the literature regarding the effects of fatigue on knee function during landing. First, functional fatigue protocols lack validity in inducing fatigue-related changes in mechanical output and spectral compression of surface electromyography (sEMG) signals, compared with isokinetic exercise. Second, fatigue-related changes in knee function during landing are confounded by inter-individual variation, which limits the sensitivity of group-level analysis. By addressing these limitations, the 3rd study demonstrated the efficacies of new experimental and analytical approaches to observe fatigue-related alterations in knee function during landing. Consequently, this thesis provides new perspectives into the effects of fatigue in knee function during landing. In conclusion: • The effects of fatigue on knee function during landing depend on the response of the individual, with considerable variation present between study participants, despite similar physical characteristics. • In healthy males, adaptation of pre-impact muscle activity and postimpact knee mechanics is unique to the individual and reflects their own optimisation of demands such as energy expenditure, joint stability, sensory information and loading of knee structures. • The results of these studies should guide future exploration of adaptations in knee function to fatigue. However, research in this area should continue with reduced emphasis on the directional response of the population and a greater focus on individual adaptations of knee function.

Caveat Anicula! Beware of the Quiet Little Old Ladies : Demographics, Pharmacotherapy, Survival and Readmissions in a 10 Year Cohort of Heart Failure Patients with Preserved Systolic Function

Objective--To determine whether heart failure with preserved systolic function (HFPSF) has different natural history from left ventricular systolic dysfunction (LVSD). Design and setting--A retrospective analysis of 10 years of data (for patients admitted between 1 July 1994 and 30 June 2004, and with a study census date of 30 June 2005) routinely collected as part of clinical practice in a large tertiary referral hospital.Main outcome measures-- Sociodemographic characteristics, diagnostic features, comorbid conditions, pharmacotherapies, readmission rates and survival.Results--Of the 2961 patients admitted with chronic heart failure, 753 had echocardiograms available for this analysis. Of these, 189 (25%) had normal left ventricular size and systolic function. In comparison to patients with LVSD, those with HFPSF were more often female (62.4% v 38.5%; P = 0.001), had less social support, and were more likely to live in nursing homes (17.9% v 7.6%; P < 0.001), and had a greater prevalence of renal impairment (86.7% v 6.2%; P = 0.004), anaemia (34.3% v 6.3%; P = 0.013) and atrial fibrillation (51.3% v 47.1%; P = 0.008), but significantly less ischaemic heart disease (53.4% v 81.2%; P = 0.001). Patients with HFPSF were less likely to be prescribed an angiotensin-converting enzyme inhibitor (61.9% v 72.5%; P = 0.008); carvedilol was used more frequently in LVSD (1.5% v 8.8%; P < 0.001). Readmission rates were higher in the HFPSF group (median, 2 v 1.5 admissions; P = 0.032), particularly for malignancy (4.2% v 1.8%; P < 0.001) and anaemia (3.9% v 2.3%; P < 0.001). Both groups had the same poor survival rate (P = 0.912). Conclusions--Patients with HFPSF were predominantly older women with less social support and higher readmission rates for associated comorbid illnesses. We therefore propose that reduced survival in HFPSF may relate more to comorbid conditions than suboptimal cardiac management.

Simulated cataract and low contrast stimuli impair cognitive performance in older adults : implications for neuropsychological assessment and everyday function

Objective: To investigate how age-related declines in vision (particularly contrast sensitivity), simulated using cataract-goggles and low-contrast stimuli, influence the accuracy and speed of cognitive test performance in older adults. An additional aim was to investigate whether declines in vision differentially affect secondary more than primary memory. Method: Using a fully within-subjects design, 50 older drivers aged 66-87 years completed two tests of cognitive performance - letter matching (perceptual speed) and symbol recall (short-term memory) - under different viewing conditions that degraded visual input (low-contrast stimuli, cataract-goggles, and low-contrast stimuli combined with cataract-goggles, compared with normal viewing). However, presentation time was also manipulated for letter matching. Visual function, as measured using standard charts, was taken into account in statistical analyses. Results: Accuracy and speed for cognitive tasks were significantly impaired when visual input was degraded. Furthermore, cognitive performance was positively associated with contrast sensitivity. Presentation time did not influence cognitive performance, and visual gradation did not differentially influence primary and secondary memory. Conclusion: Age-related declines in visual function can impact on the accuracy and speed of cognitive performance, and therefore the cognitive abilities of older adults may be underestimated in neuropsychological testing. It is thus critical that visual function be assessed prior to testing, and that stimuli be adapted to older adults' sensory capabilities (e.g., by maximising stimuli contrast).

An enriched radial point interpolation method (e-RPIM) for analysis of crack tip fields

In this paper, an enriched radial point interpolation method (e-RPIM) is developed the for the determination of crack tip fields. In e-RPIM, the conventional RBF interpolation is novelly augmented by the suitable trigonometric basis functions to reflect the properties of stresses for the crack tip fields. The performance of the enriched RBF meshfree shape functions is firstly investigated to fit different surfaces. The surface fitting results have proven that, comparing with the conventional RBF shape function, the enriched RBF shape function has: (1) a similar accuracy to fit a polynomial surface; (2) a much better accuracy to fit a trigonometric surface; and (3) a similar interpolation stability without increase of the condition number of the RBF interpolation matrix. Therefore, it has proven that the enriched RBF shape function will not only possess all advantages of the conventional RBF shape function, but also can accurately reflect the properties of stresses for the crack tip fields. The system of equations for the crack analysis is then derived based on the enriched RBF meshfree shape function and the meshfree weak-form. Several problems of linear fracture mechanics are simulated using this newlydeveloped e-RPIM method. It has demonstrated that the present e-RPIM is very accurate and stable, and it has a good potential to develop a practical simulation tool for fracture mechanics problems.

Executive function effects and numerical development in children : behavioural and ERP evidence from a numerical Stroop paradigm

Most research on numerical development in children is behavioural, focusing on accuracy and response time in different problem formats. However, Temple and Posner (1998) used ERPs and the numerical distance task with 5-year-olds to show that the development of numerical representations is difficult to disentangle from the development of the executive components of response organization and execution. Here we use the numerical Stroop paradigm (NSP) and ERPs to study possible executive interference in numerical processing tasks in 6–8-year-old children. In the NSP, the numerical magnitude of the digits is task-relevant and the physical size of the digits is task-irrelevant. We show that younger children are highly susceptible to interference from irrelevant physical information such as digit size, but that access to the numerical representation is almost as fast in young children as in adults. We argue that the developmental trajectories for executive function and numerical processing may act together to determine numerical development in young children.

An enriched radial point interpolation method (e-RPIM) for analysis of crack tip fields

In this paper, an enriched radial point interpolation method (e-RPIM) is developed the for the determination of crack tip fields. In e-RPIM, the conventional RBF interpolation is novelly augmented by the suitable trigonometric basis functions to reflect the properties of stresses for the crack tip fields. The performance of the enriched RBF meshfree shape functions is firstly investigated to fit different surfaces. The surface fitting results have proven that, comparing with the conventional RBF shape function, the enriched RBF shape function has: (1) a similar accuracy to fit a polynomial surface; (2) a much better accuracy to fit a trigonometric surface; and (3) a similar interpolation stability without increase of the condition number of the RBF interpolation matrix. Therefore, it has proven that the enriched RBF shape function will not only possess all advantages of the conventional RBF shape function, but also can accurately reflect the properties of stresses for the crack tip fields. The system of equations for the crack analysis is then derived based on the enriched RBF meshfree shape function and the meshfree weak-form. Several problems of linear fracture mechanics are simulated using this newlydeveloped e-RPIM method. It has demonstrated that the present e-RPIM is very accurate and stable, and it has a good potential to develop a practical simulation tool for fracture mechanics problems.

Chlamydial infection of immune cells : altered function and implications for disease

Chlamydia trachomatis is an obligate intracellular bacterial pathogen that infects the genital and ocular mucosa of humans, causing infections that can lead to pelvic inflammatory disease, infertility, and blinding trachoma. C. pneumoniae is a respiratory pathogen that is the cause of 12–15% of community-acquired pneumonia. Both chlamydial species were believed to be restricted to the epithelia of the genital, ocular, and respiratory mucosa; however, increasing evidence suggests that both these pathogens can be isolated from peripheral blood of both healthy individuals and patients with inflammatory conditions such as coronary artery disease and asthma. Chlamydia can also be isolated from brain tissues of patients with degenerative neurological disorders such as Alzheimer’s disease and multiple sclerosis, and also from certain lymphomas. An increasing number of in vitro studies suggest that some chlamydial species can infect immune cells, at least at low levels. These infections may alter immune cell function in a way that promotes chlamydial persistence in the host and contributes to the progression of several chronic inflammatory diseases. In this paper, we review the evidence for the growth of Chlamydia in immune cells, particularly monocytes/macrophages and dendritic cells, and describe how infection may affect the function of these cells.

Spatiotemporal investigations of DNA damage repair using microbeams

Cellular response to radiation damage is made by a complex network of pathways and feedback loops whose spatiotemporal organisation is still unclear despite its decisive role in determining the fate of the damaged cell. Revealing the dynamic sequence of the repair proteins is therefore critical in understanding how the DNA repair mechanisms work. There are also still open questions regarding the possible movement of damaged chromatin domains and its role as trigger for lesion recognition and signalling in the DNA repair context. The single-cell approach and the high spatial resolution offered by microbeams provide the perfect tool to study and quantify the dynamic processes associated with the induction and repair of DNA damage. We have followed the development of radiation-induced foci for three DNA damage markers (i.e. γ-H2AX, 53BP1 and hSSB1) using normal fibroblasts (AG01522), human breast adenocarcinoma cells (MCF7) and human fibrosarcoma cells (HT1080) stably transfected with yellow fluorescent protein fusion proteins following irradiation with the QUB X-ray microbeam (carbon X-rays <2 µm spot). The size and intensity of the foci has been analysed as a function of dose and time post-irradiation to investigate the dynamics of the above-mentioned DNA repair processes and monitor the remodelling of chromatin structure that the cell undergoes to deal with DNA damage.

Multiple human single-stranded DNA binding proteins function in genome maintenance : structural, biochemical and functional analysis

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two singlestranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein–protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.