Spatial variability of soil carbon in forested and cultivated sites: Implications for change detection

The potential to sequester atmospheric carbon in agricultural and forest soils to offset greenhouse gas emissions has generated interest in measuring changes in soil carbon resulting from changes in land management. However, inherent spatial variability of soil carbon limits the precision of measurement of changes in soil carbon and hence, the ability to detect changes. We analyzed variability of soil carbon by intensively sampling sites under different land management as a step toward developing efficient soil sampling designs. Sites were tilled crop-land and a mixed deciduous forest in Tennessee, and old-growth and second-growth coniferous forest in western Washington, USA. Six soil cores within each of three microplots were taken as an initial sample and an additional six cores were taken to simulate resampling. Soil C variability was greater in Washington than in Tennessee, and greater in less disturbed than in more disturbed sites. Using this protocol, our data suggest that differences on the order of 2.0 Mg C ha(-1) could be detected by collection and analysis of cores from at least five (tilled) or two (forest) microplots in Tennessee. More spatial variability in the forested sites in Washington increased the minimum detectable difference, but these systems, consisting of low C content sandy soil with irregularly distributed pockets of organic C in buried logs, are likely to rank among the most spatially heterogeneous of systems. Our results clearly indicate that consistent intramicroplot differences at all sites will enable detection of much more modest changes if the same microplots are resampled.

Upper-body morbidity following breast cancer treatment is common, may persist longer-term and adversely influences quality of life

Background: Impairments in upper-body function (UBF) are common following breast cancer. However, the relationship between arm morbidity and quality of life (QoL) remains unclear. This investigation uses longitudinal data to describe UBF in a population-based sample of women with breast cancer and examines its relationship with QoL. ---------- Methods: Australian women (n = 287) with unilateral breast cancer were assessed at three-monthly intervals, from six- to 18-months post-surgery (PS). Strength, endurance and flexibility were used to assess objective UBF, while the Disability of the Arm, Shoulder and Hand questionnaire and the Functional Assessment of Cancer Therapy- Breast questionnaire were used to assess self-reported UBF and QoL, respectively. ---------- Results: Although mean UBF improved over time, up to 41% of women revealed declines in UBF between sixand 18-months PS. Older age, lower socioeconomic position, treatment on the dominant side, mastectomy, more extensive lymph node removal and having lymphoedema each increased odds of declines in UBF by at least twofold (p < 0.05). Lower baseline and declines in perceived UBF between six- and 18-months PS were each associated with poorer QoL at 18-months PS (p < 0.05). ---------- Conclusions: Significant upper-body morbidity is experienced by many following breast cancer treatment, persisting longer term, and adversely influencing the QoL of breast cancer survivors.

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.

Mineralized human primary osteoblast matrices as a model system to analyse interactions of prostate cancer cells with the bone microenvironment

Prostate cancer metastasis is reliant on the reciprocal interactions between cancer cells and the bone niche/micro-environment. The production of suitable matrices to study metastasis, carcinogenesis and in particular prostate cancer/bone micro-environment interaction has been limited to specific protein matrices or matrix secreted by immortalised cell lines that may have undergone transformation processes altering signaling pathways and modifying gene or receptor expression. We hypothesize that matrices produced by primary human osteoblasts are a suitable means to develop an in vitro model system for bone metastasis research mimicking in vivo conditions. We have used a decellularized matrix secreted from primary human osteoblasts as a model for prostate cancer function in the bone micro-environment. We show that this collagen I rich matrix is of fibrillar appearance, highly mineralized, and contains proteins, such as osteocalcin, osteonectin and osteopontin, and growth factors characteristic of bone extracellular matrix (ECM). LNCaP and PC3 cells grown on this matrix, adhere strongly, proliferate, and express markers consistent with a loss of epithelial phenotype. Moreover, growth of these cells on the matrix is accompanied by the induction of genes associated with attachment, migration, increased invasive potential, Ca2+ signaling and osteolysis. In summary, we show that growth of prostate cancer cells on matrices produced by primary human osteoblasts mimics key features of prostate cancer bone metastases and thus is a suitable model system to study the tumor/bone micro-environment interaction in this disease.

Bioengineered 3D platform to explore cell-ECM interactions and drug resistance of epithelial ovarian cancer cells

The behaviour of cells cultured within three-dimensional (3D) structures rather than onto two-dimensional (2D) culture plastic more closely reflects their in vivo responses. Consequently, 3D culture systems are becoming crucial scientific tools in cancer cell research. We used a novel 3D culture concept to assess cell-matrix interactions implicated in carcinogenesis: a synthetic hydrogel matrix equipped with key biomimetic features, namely incorporated cell integrin-binding motifs (e.g. RGD peptides) and the ability of being degraded by cell-secreted proteases (e.g. matrix metalloproteases). As a cell model, we chose epithelial ovarian cancer, an aggressive disease typically diagnosed at an advanced stage when chemoresistance occurs. Both cell lines used (OV-MZ-6, SKOV-3) proliferated similarly in 2D, but not in 3D. Spheroid formation was observed exclusively in 3D when cells were embedded within hydrogels. By exploiting the design flexibility of the hydrogel characteristics, we showed that proliferation in 3D was dependent on cell-integrin engagement and the ability of cells to proteolytically remodel their extracellular microenvironment. Higher survival rates after exposure to the anti-cancer drug paclitaxel were observed in cell spheroids grown in hydrogels (40-60%) compared to cell monolayers in 2D (20%). Thus, 2D evaluation of chemosensitivity may not reflect pathophysiological events seen in patients. Because of the design flexibility of their characteristics and their stability in long-term cultures (28 days), these biomimetic hydrogels represent alternative culture systems for the increasing demand in cancer research for more versatile, physiologically relevant and reproducible 3D matrices.

The QUT-NOISE-TIMIT corpus for the evaluation of voice activity detection algorithms

The QUT-NOISE-TIMIT corpus consists of 600 hours of noisy speech sequences designed to enable a thorough evaluation of voice activity detection (VAD) algorithms across a wide variety of common background noise scenarios. In order to construct the final mixed-speech database, a collection of over 10 hours of background noise was conducted across 10 unique locations covering 5 common noise scenarios, to create the QUT-NOISE corpus. This background noise corpus was then mixed with speech events chosen from the TIMIT clean speech corpus over a wide variety of noise lengths, signal-to-noise ratios (SNRs) and active speech proportions to form the mixed-speech QUT-NOISE-TIMIT corpus. The evaluation of five baseline VAD systems on the QUT-NOISE-TIMIT corpus is conducted to validate the data and show that the variety of noise available will allow for better evaluation of VAD systems than existing approaches in the literature.

A systematic review of the association between physical activity and colorectal cancer risk

This review evaluated the strength of the evidence for a causal relationship between physical activity (PA) and colorectal cancer (CRC). A systematic review of databases through February 2008 was conducted to identify studies that assessed the association between total or recreational PA and incidence or mortality of CRC (including CRC, rectal cancer, colon cancer, and proximal or distal colon cancer). Studies were evaluated for significant associations between PA and risk of CRC endpoints and for evidence of dose–response relationships in the highest quality studies. Twenty cohort studies were evaluated; 11 were high-quality. Fifty percent of all studies and 64%of highest quality studies reported at least one significant association between PA and risk of a CRC endpoint (Po0.05).However, only 28%of all analyses (31% of analyses of highest quality studies) were significant (Po0.05). Only 40% of analyses of highest quality studies resulted in a significant P for trend (Po0.05); however, a non-significant inverse linear association between PA and colon cancer riskwas apparent.Heterogeneity in the evidence from all studies and from the highest quality studies was evident. Evidence from cohort studies is not sufficient to claim a convincing relationship exists between PA and CRC risk.

Exercise and cancer rehabilitation : a systematic review

Introduction: Cancer is increasingly being viewed as a chronic illness requiring long-term management, and there is a growing need for evidence-based rehabilitation interventions for cancer survivors. Previous reviews have evaluated the benefits of exercise interventions for patients undergoing cancer treatment and long-term survivors, but none have investigated the role of exercise during cancer rehabilitation, the period immediately following cancer treatment completion. This systematic review summarises the literature on the health effects of exercise during cancer rehabilitation and evaluates the methodological rigour of studies in this area to date.----------- Methods: Relevant studies were identified through a systematic search of PubMed and Embase to April 2009. Data on study design, recruitment strategy, participants, exercise intervention, adherence rates, and outcomes were extracted. Methodological rigour was assessed using a structured rating system.---------- Results: Ten studies were included. Breast cancer patients were the predominate patient group represented. Most interventions were aerobic or resistance-training exercise programmes, and exercise type, frequency, duration and intensity varied across studies. Improvements in physical functioning, strength, physical activity levels, quality of life, fatigue, immune function, haemoglobin concentrations, potential markers of recurrence, and body composition were reported. However, all studies were limited by incomplete reporting and methodological limitations.---------- Conclusions: Although the methodological limitations of studies in this new field must be acknowledged, initial evidence indicates that exercise is feasible and may provide physiological and psychological benefits for cancer survivors during the rehabilitation period. Future studies with rigorous study designs are now required to advance the field.

Colorectal cancer survivors’ exercise experiences and preferences : qualitative findings from an exercise rehabilitation programme immediately after chemotherapy

Little is known about cancer survivors’ experiences with and preferences for exercise programmes offered during rehabilitation (immediately after cancer treatment). This study documented colorectal cancer survivors’ experiences in an exercise rehabilitation programme and their preferences for programme content and delivery. At the completion of 12-weeks of supervised exercise, 10 participants took part in one-on-one semi-structured interviews. Data from these interviews were coded, and themes were identified using qualitative software. Key findings were that most participants experienced improvements in treatment symptoms, including reduced fatigue and increased energy and confidence to do activities of daily living. They also reported that interactions with the exercise trainer and a flexible programme delivery were important aspects of the intervention. Most participants reported that they preferred having a choice of exercise, starting to exercise within a month after completing treatment, having supervision and maintaining a one-on-one format. Frustrations included scheduling conflicts and a lack of a transition out of the programme. The findings indicate that colorectal cancers experience benefits from exercise offered immediately after treatment and prefer individual attention from exercise staff. They further indicate directions for the implementation of future exercise programmes with this population.

Bottlenecks detection of track allocation schemes at rail stations by Petri nets

Robustness of the track allocation problem is rarely addressed in literatures and the obtained track allocation schemes (TAS) embody some bottlenecks. Therefore, an approach to detect bottlenecks is needed to support local optimization. First a TAS is transformed to an executable model by Petri nets. Then disturbances analysis is performed using the model and the indicators of the total trains' departure delays are collected to detect bottlenecks when each train suffers a disturbance. Finally, the results of the tests based on a rail hub linking six lines and a TAS about thirty minutes show that the minimum buffer time is 21 seconds and there are two bottlenecks where the buffer times are 57 and 44 seconds respectively, and it indicates that the bottlenecks do not certainly locate at the area where there is minimum buffer time. The proposed approach can further support selection of multi schemes and robustness optimization.

Signature analysis on wheel-rail interaction for rail defect detection

Fibre Bragg Grating (FBG) sensors have been installed along an existing line for the purposes of train detection and weight measurement. The results show fair accuracy and high resolution on the vertical force acted on track when the train wheels are rolling upon. While the sensors are already in place and data is available, further applications beyond train detection are explored. This study presents the analysis on the unique signatures from the data collected to characterise wheel-rail interaction for rail defect detection. Focus of this first stage of work is placed on the repeatability of signals from the same wheel-rail interactions while the rail is in healthy state. Discussions on the preliminary results and hence the feasibility of this condition monitoring application, as well as technical issues to be addressed in practice, are given.

Diagnostic and treatment pathways for men with prostate cancer in Queensland : investigating spatial and demographic inequalities

Background: Patterns of diagnosis and management for men diagnosed with prostate cancer in Queensland, Australia, have not yet been systematically documented and so assumptions of equity are untested. This longitudinal study investigates the association between prostate cancer diagnostic and treatment outcomes and key area-level characteristics and individual-level demographic, clinical and psychosocial factors.---------- Methods/Design: A total of 1064 men diagnosed with prostate cancer between February 2005 and July 2007 were recruited through hospital-based urology outpatient clinics and private practices in the centres of Brisbane, Townsville and Mackay (82% of those referred). Additional clinical and diagnostic information for all 6609 men diagnosed with prostate cancer in Queensland during the study period was obtained via the population-based Queensland Cancer Registry. Respondent data are collected using telephone and self-administered questionnaires at pre-treatment and at 2 months, 6 months, 12 months, 24 months, 36 months, 48 months and 60 months post-treatment. Assessments include demographics, medical history, patterns of care, disease and treatment characteristics together with outcomes associated with prostate cancer, as well as information about quality of life and psychological adjustment. Complementary detailed treatment information is abstracted from participants’ medical records held in hospitals and private treatment facilities and collated with health service utilisation data obtained from Medicare Australia. Information about the characteristics of geographical areas is being obtained from data custodians such as the Australian Bureau of Statistics. Geo-coding and spatial technology will be used to calculate road travel distances from patients’ residences to treatment centres. Analyses will be conducted using standard statistical methods along with multilevel regression models including individual and area-level components.---------- Conclusions: Information about the diagnostic and treatment patterns of men diagnosed with prostate cancer is crucial for rational planning and development of health delivery and supportive care services to ensure equitable access to health services, regardless of geographical location and individual characteristics. This study is a secondary outcome of the randomised controlled trial registered with the Australian New Zealand Clinical Trials Registry (ACTRN12607000233426)

Repeat participation in colorectal cancer screening utilizing fecal occult blood testing : a community-based project in a rural setting

Background and Aim: To investigate participation in a second round of colorectal cancer screening using a fecal occult blood test (FOBT) in an Australian rural community, and to assess the demographic characteristics and individual perspectives associated with repeat screening. ---------- Methods: Potential participants from round 1 (50–74 years of age) were sent an intervention package and asked to return a completed FOBT (n = 3406). Doctors of participants testing positive referred to colonoscopy as appropriate. Following screening, 119 participants completed qualitative telephone interviews. Multivariable logistic regression models evaluated the association between round-2 participation and other variables.---------- Results: Round-2 participation was 34.7%; the strongest predictor was participation in round 1. Repeat participants were more likely to be female; inconsistent screeners were more likely to be younger (aged 50–59 years). The proportion of positive FOBT was 12.7%, that of colonoscopy compliance was 98.6%, and the positive predictive value for cancer or adenoma of advanced pathology was 23.9%. Reasons for participation included testing as a precautionary measure or having family history/friends with colorectal cancer; reasons for non-participation included apathy or doctors’ advice against screening.---------- Conclusion: Participation was relatively low and consistent across rounds. Unless suitable strategies are identified to overcome behavioral trends and/or to screen out ineligible participants, little change in overall participation rates can be expected across rounds.

Migration of breast cancer cells : understanding the roles of volume exclusion and cell-to-cell adhesion

We study MCF-7 breast cancer cell movement in a transwell apparatus. Various experimental conditions lead to a variety of monotone and nonmonotone responses which are difficult to interpret. We anticipate that the experimental results could be caused by cell-to-cell adhesion or volume exclusion. Without any modeling, it is impossible to understand the relative roles played by these two mechanisms. A lattice-based exclusion process random-walk model incorporating agent-to-agent adhesion is applied to the experimental system. Our combined experimental and modeling approach shows that a low value of cell-to-cell adhesion strength provides the best explanation of the experimental data suggesting that volume exclusion plays a more important role than cell-to-cell adhesion. This combined experimental and modeling study gives insight into the cell-level details and design of transwell assays.

Clone Detection in Repositories of Business Process Models

Business process model repositories capture precious knowledge about an organization or a business domain. In many cases, these repositories contain hundreds or even thousands of models and they represent several man-years of effort. Over time, process model repositories tend to accumulate duplicate fragments, as new process models are created by copying and merging fragments from other models. This calls for methods to detect duplicate fragments in process models that can be refactored as separate subprocesses in order to increase readability and maintainability. This paper presents an indexing structure to support the fast detection of clones in large process model repositories. Experiments show that the algorithm scales to repositories with hundreds of models. The experimental results also show that a significant number of non-trivial clones can be found in process model repositories taken from industrial practice.