Temporal extension of Laplacian Eigenmaps for unsupervised dimensionality reduction of time series

A novel non-linear dimensionality reduction method, called Temporal Laplacian Eigenmaps, is introduced to process efficiently time series data. In this embedded-based approach, temporal information is intrinsic to the objective function, which produces description of low dimensional spaces with time coherence between data points. Since the proposed scheme also includes bidirectional mapping between data and embedded spaces and automatic tuning of key parameters, it offers the same benefits as mapping-based approaches. Experiments on a couple of computer vision applications demonstrate the superiority of the new approach to other dimensionality reduction method in term of accuracy. Moreover, its lower computational cost and generalisation abilities suggest it is scalable to larger datasets. © 2010 IEEE.

A population-based association study of SNPs of GSTP1, MnSOD, GPX2 and Barrett's esophagus and esophageal adenocarcinoma

Oxidative stress appears to be important in the pathogenesis of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). Single-nucleotide polymorphisms (SNPs) of antioxidant enzyme genes may play a part in determining individual susceptibility to these diseases. The Factors Influencing the Barrett's Adenocarcinoma Relationship (FINBAR) study is a population-based, case-control study of BE and EAC in Ireland. DNA from EAC (n = 207), BE (> or =3 cm BE at endoscopy with specialized intestinal metaplasia on biopsy, n = 189) and normal population controls (n = 223) were analyzed. Several SNPs spanning the genes for glutathione S-transferase P1 (GSTP1), manganese superoxide dismutase (MnSOD) and glutathione peroxidase 2 (GPX2) were genotyped using multiplex polymerase chain reaction and SNaPshottrade mark. The chi(2) test was used to compare genotype and allele frequencies between case and control subjects. Linkage disequilibrium between SNPs was quantified using Lewontin's D' value and haplotype frequency estimates obtained using Haploview. Eleven SNPs were genotyped (six for GSTP1, three for MnSOD and two for GPX2); all were in Hardy-Weinberg equilibrium. None was significantly associated with EAC or BE even before Bonferroni correction. Odds ratios for EAC for individual SNPs ranged from 0.68 [95% confidence interval (CI) 0.43-1.08] to 1.25 (95% CI 0.73-2.16), and for BE from 0.84 (95% CI 0.52-1.30) to 1.30 (95% CI 0.85-1.97). SNPs in all three genes were in strong linkage disequilibrium (D' > 0.887) but haplotype analysis did not show any significant association with EAC or BE. SNPs involving the GSTP1, MnSOD and GPX2 genes were not associated with BE or EAC. Further studies aimed at identifying susceptibility genes should focus on different antioxidant genes or different pathways.

Oxidative-nitrosative stress and systemic vascular function in highlanders with and without exaggerated hypoxemia

ABSTRACT BACKGROUND: Acute exposure to high-altitude stimulates free radical formation in lowlanders yet whether this persists during chronic exposure in healthy well-adapted and maladapted highlanders suffering from chronic mountain sickness (CMS) remains to be established. METHODS: Oxidative-nitrosative stress [ascorbate radical (A•-), electron paramagnetic resonance spectroscopy and nitrite (NO2-), ozone-based chemiluminescence] was assessed in venous blood of 25 male highlanders living at 3,600 m with (n = 13, CMS+) and without (n = 12, CMS-) CMS. Twelve age and activity-matched healthy male lowlanders were examined at sea-level and during acute hypoxia. We also measured flow-mediated dilatation (FMD), arterial stiffness (AIx-75) and carotid intima-media thickness (IMT). RESULTS: Compared to normoxic lowlanders, oxidative-nitrosative stress was moderately increased in CMS- (P < 0.05) as indicated by elevated A•- (3,191 ± 457 vs. 2,640 ± 445 arbitrary units (AU)] and lower NO2- (206 ± 55 vs. 420 ± 128 nmol/L) whereas vascular function remained preserved. This was comparable to that observed during acute hypoxia in lowlanders in whom vascular dysfunction is typically observed. In contrast, this response was markedly exaggerated in CMS+ (A•-: 3,765 ± 429 AU and NO2- : 148 ± 50 nmol/L) compared to both CMS- and lowlanders (P < 0.05). This was associated with systemic vascular dysfunction as indicated by lower (P < 0.05 vs. CMS-) FMD (4.2 ± 0.7 vs. 7.6 ± 1.7 %) and increased AIx-75 (23 ± 8 vs. 12 ± 7 %) and carotid IMT (714 ± 127 vs. 588 ± 94 µM). CONCLUSIONS: Healthy highlanders display a moderate sustained elevation in oxidative-nitrosative stress that unlike the equivalent increase evoked by acute hypoxia in healthy lowlanders, failed to affect vascular function. Its more marked elevation in patients with CMS may contribute to systemic vascular dysfunction.Clinical Trials Gov Registration # NCT011827921Neurovascular Research Laboratory, Faculty of Health, Science and Sport, University of Glamorgan, Wales, UK;2Sondes Moléculaires en Biologie et Stress Oxydant, Institut de Chimie Radicalaire, CNRS UMR 7273, Aix-Marseille University, France;3Department of Cardiology, University Hospital of Bern, Bern, Switzerland;4Institute of Clinical Physiology, CNR, Pisa, Italy;5Instituto Bolivano de Biologia de Altura, La Paz, Bolivia;6Centre for Clinical and Population Sciences, Queen's University Belfast, Belfast, Northern Ireland,7Botnar Center for Clinical Research, Hirslanden Group, Lausanne, Switzerland;8Facultad de Ciencias, Departamento de Biología, Universidad de Tarapacá, Arica, Chile and9Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland*Drs Bailey, Rimoldi, Scherrer and Sartori contributed equally to this workCorrespondence: Damian Miles Bailey, Neurovascular Research Laboratory, Faculty of Health, Science and Sport, University of Glamorgan, UK CF37 4AT email: dbailey1@glam.ac.uk.

An ecotoxicological approach to assessing the impact of tanning industry effluent on river health

A study was conducted to investigate the sediment health and water quality of the River Sagana, Kenya, as impacted by the local tanning industry. Chemical analysis identified the main chemical pollutants (pentachlorophenols and chromium) while a bioassay addressed pollutant bioavailability. The bioassay, exploiting the luminescence response of a lux marked bacterial biosensor, was coupled to a dehydrogenase and Dapnia magna test to determine toxicity effects on sediments. Results highlighted the toxicity of the tannery effluent to the sediments at the point of discharge (64% of control bioluminescence) with gradual improvement downstream. There was a significant increase in dehydrogenase downstream, with the enzyme activity attaining a peak at 600 m, also indicating a gradual reduction of toxicity. Biological oxygen demand (19.56 mg L(-1)) dissolved oxygen (3.97 mg L(-1)) and high lethal dose value (85%) of D. magna also confirmed an initial stress at the point of discharge and recovery downstream. Optical density of surface water demonstrated an increase in suspended particulates and colour after the discharge point, eventually decreasing beyond 400 m. In conclusion, the study highlighted the importance of understanding the biogeochemistry of river systems impacted by industries discharging effluent into them and the invaluable role of a biosensor-based ecotoxicological approach to address effluent hazards, particularly in relation to river sediments.

Use of a lux-marked rhizobacterium as a biosensor to assess changes in rhizosphere C flow due to pollutant stress

The flow of carbon from plant roots into soil supports a range of microbial processes and is therefore critical to ecosystem function and health. Pollution-induced stress, which influences rhizosphere C flow is of considerable potential importance, and therefore needs to be evaluated. This paper reports on a method, based on reporter gene technology, for quantifying pollutant effects on rhizosphere C flow. The method uses the lux-marked rhizobacterium Pseudomonas fluorescens, where bioluminescence output of this biosensor is directly correlated with the metabolic activity and reports on C flow in root exudate. Plantago lanceolata was treated with paraquat (representing a model pollutant stress) in a simple microcosm system. The lux-biosensor response correlated closely with C concentrations in the exudate and demonstrated that the pollutant stress increased the C flow from the plantago roots, 24 h after application of the herbicide. The lux-reporter system therefore potentially offers a technique for use in assessing the impact of pollutant stress on rhizosphere C flow through the soil microbial biomass.

Volume reduction of the corpus callosum and its relationship with deficits in interhemispheric transfer of information in recent-onset psychosis

The present study aimed to investigate the presence of corpus callosum (CC) volume deficits in a population-based recent-onset psychosis (ROP) sample, and whether CC volume relates to interhemispheric communication deficits. For this purpose, we used voxel-based morphometry comparisons of magnetic resonance imaging data between ROP (n = 122) and healthy control (n = 94) subjects. Subgroups (38 ROP and 39 controls) were investigated for correlations between CC volumes and performance on the Crossed Finger Localization Test (CFLT). Significant CC volume reductions in ROP subjects versus controls emerged after excluding substance misuse and non-right-handedness. CC reductions retained significance in the schizophrenia subgroup but not in affective psychoses subjects. There were significant positive correlations between CC volumes and CFLT scores in ROP subjects, specifically in subtasks involving interhemispheric communication. From these results, we can conclude that CC volume reductions are present in association with ROP. The relationship between such deficits and CFLT performance suggests that interhemispheric communication impairments are directly linked to CC abnormalities in ROP. (C) 2010 Elsevier Ireland Ltd. All rights reserved.

A comparison of stress intensity factors through crack closure integral and other approaches using eXtended element-free Galerkin method

In this paper, a new approach for extracting stress intensity factors (SIFs) by the extended element-free Galerkin method, through a crack closure integral (CCI) scheme, is proposed. The CCI calculation is used in conjunction with a local smoothing technique to improve the accuracy of the computed SIFs in a number of case studies of linear elastic fracture mechanics. The cases involve problems of mixed-mode, curved crack and thermo-mechanical loading. The SIFs by CCI, displacement and stress methods are compared with those based on the M-integral technique reported in the literature. The proposed CCI method involves very simple relations, and still gives good accuracy. The convergence of the results is also examined.

Income, deprivation and economic stress in the enlarged European Union

At risk of poverty indicators based on relative income measures suggest that within the enlarged EU societies located at quite different points on a continuum of affluence have similar levels of poverty. Substantial differences in levels of income between societies do not in themselves invalidate this approach. However, the relative income approach fails to capture the fact that, if countries are grouped in terms of level of GDP, between economic cluster differences in life-style deprivation are sharper at lower income levels. Support for the argument relating to restricted reference groups is found in relation to the contrast between the twelve most affluent EU countries and all others. The limitations of relative income poverty lines have little to do with the process of enlargement as such. Instead the major problem involves the weak association between income and deprivation in the more affluent countries. However, as a consequence of such difficulties, such indicators do not provide entirely meaningful comparisons of levels of disadvantage across economic clusters. The current analysis, rather than supporting the alternative of a focus on absolute income or an EU wide poverty line, suggests that we should take the argument for adopting a multidimensional approach to the measurement of poverty more seriously.

Intralaminar toughness characterisation of unbalanced hybrid plain weave laminates

A numerical and experimental investigation on the mode-I intralaminar toughness of a hybrid plain weave composite laminate manufactured using resin infusion under flexible tooling (RIFT) process is presented in this paper. The pre-cracked geometries consisted of overheight compact tension (OCT), double edge notch (DEN) and centrally cracked four-point-bending (4PBT) test specimens. The position as well as the strain field ahead of the crack tip during the loading stage was determined using a digital speckle photogrammetry system. The limitation on the applicability of the standard data reduction schemes for the determination of intralaminar toughness of composite materials is presented and discussed. A methodology based on the numerical evaluation of the strain energy release rate using the J-integral method is proposed to derive new geometric correction functions for the determination of the stress intensity factor for composites. The method accounts for material anisotropy and finite specimen dimension effects regardless of the geometry. The approach has been validated for alternative non-standard specimen geometries. A comparison between different methods currently available for computing the intralaminar fracture toughness in composite laminates is presented and a good agreement between numerical and experimental results using the proposed methodology was obtained. 

The stress process in palliative cancer care:A qualitative study on informal caregiving and its implication for the delivery of care

Objective: The primary objective of this study was to examine how the comprehensive nature of the Stress Process Model could elucidate on the stressors associated with caring for a palliative cancer patient. Method: A qualitative research strategy involving home-based face-to-face interviews with 12 bereaved family caregivers was used to examine the caregiving experience. Results: The primary stressors associated with caring for the palliative cancer care patients stemmed from care recipient symptoms and personal care needs. The absence of adequate support from the formal health care delivery system was a consistent message from all participants. There was evidence of financial stress primarily associated with the purchase of private home care to supplement formal care. In contrast, the resources that family caregivers relied on to moderate the stressful effects of caregiving included extended family, friends, and neighbors. While the stress of direct caregiving was high, the study revealed that formal care was also a significant source of stress for family caregivers. Conclusion: It was concluded that an appropriately financed, integrated system of care that followed a person-centered philosophy of care would best meet the needs of the patient and his or her family. © The Author(s) 2010.

Field observation of sequestration of uranium in iron-rich sediments under sequential reduction-oxidation conditions at the DOE Oak Ridge IFRC

At the U.S. DOE Oak Ridge Integrated Field Research Challenge (ORIFRC) site, the iron content of shallow subsurface materials (i.e. weathered saprolite) is relatively high (up to 5-6% as w/w), and therefore, the forms of the iron species present plays a critical role in the long-term sequestration of uranium. A long term pilot-scale study of the bioreduction and reoxidation of uranium conducted at the ORIFRC area 3 site, adjacent to the former S-3 disposal ponds (source zone), has provided us with the opportunity to study the impact of iron species on the sequestration of U(VI). The aqueous U(VI) concentrations at the site were decreased to below the EPA MCL through the intermittent injection of ethanol as the electron donor. Previous field tests indicated that both oxygen and nitrate could oxidize the bioreduced U(IV) and cause a short-term rebound of aqueous phase uranium concentration after the oxidative agents were delivered directly to the bioreduced zone.

A field test has been conducted to examine the long-term effect of exposure of bioreduced sediments to nitrate in contaminated groundwater for more than 1,380 days at the Area 3 site. Contaminated groundwater was allowed to invade the previously bioreduced zone via the natural groundwater gradient after an extended period in which reducing conditions were maintained and the bioreduced zone was protected from the influx of upgradient contaminated groundwater. The geochemical response to the invasion of contaminated groundwater was dependent on whether the monitoring location is in the middle or the fringe of the previously bioreduced zone. In general, the nitrate concentrations in the previously bioreduced area, increased gradually from near zero to ~50-300 mM within 200 days and then stabilized. The pH declined from bioreduced levels of 6.2-6.7 to below 5.0. Uranium concentrations rebounded in all monitoring wells but at different rates. At most locations U concentrations rebounded, declined and then rebounded again. Methane gas disappeared while a significant level (20,000 to 44,000 ppmv) N2O was found in the groundwater of monitoring wells after three years of reoxidization.

The U(IV) in sediments was mainly reoxidized to U(VI) species. Based on XANES analysis, the predominate uranium in all samples after re-oxidation was similar to a uranyl nitrate form. But the U content in the sediment remained as high as that determined after bioreduction activates were completed, indicating that much of the U is still sequestrated in situ. SEM observations of surged fine sediments revealed that clusters of colloidal-sized (200-500nm) U-containing precipitates appeared to have formed in situ, regardless from sample of FW106 in non-bioactivity control area or of pre-bioreduced FW101-2 and FW102-3. Additionally, SEM-EDS and microprobe analysis, showed that the U-containing precipitates (~1% U) in FW106 are notably higher in Fe, compared to the precipitates (~1-2.5% U) from FW101-2 and FW102-3. However, XRF analysis indicated that the U content was remained as high as 2180 and 1810 mg/kg with U/Fe ratio at 0.077 and 0.055 vs 0.037 g/g, respectively in pre-bioreduced FW101-2 and FW102-3, suggesting more U sequestrated by Fe in pre-bioreduced sediments.

Targeting EGFR Induced Oxidative Stress by PARP1 Inhibition in Glioblastoma Therapy

Despite the critical role of Epidermal Growth Factor Receptor (EGFR) in glioblastoma pathogenesis [1,2], EGFR targeted therapies have achieved limited clinical efficacy [3]. Here we propose an alternate therapeutic strategy based on the conceptual framework of non-oncogene addiction [4,5]. A directed RNAi screen revealed that glioblastoma cells overexpressing EGFRvIII [6], an oncogenic variant of EGFR, become hyper-dependent on a variety of DNA repair genes. Among these, there was an enrichment of Base Excision Repair (BER) genes required for the repair of Reactive Oxygen Species (ROS)-induced DNA damage, including poly-ADP ribose polymerase 1 (PARP1). Subsequent studies revealed that EGFRvIII overexpression in glioblastoma cells caused increased levels of ROS, DNA strand break accumulation, and genome instability. In a panel of primary glioblastoma lines, sensitivity to PARP1 inhibition correlated with the levels of EGFR activation and oxidative stress. Gene expression analysis indicated that reduced expression of BER genes in glioblastomas with high EGFR expression correlated with improved patient survival. These observations suggest that oxidative stress secondary to EGFR hyperactivation necessitates increased cellular reliance on PARP1 mediated BER, and offer critical insights into clinical trial design.

Reducing the psychological distress of family caregivers of home-based palliative care patients: short-term effects from a randomised controlled trial

BACKGROUND: Palliative care is expected to incorporate comprehensive support for family caregivers given that many caregivers suffer psychological morbidity. However, systematically implemented evidence-based psychological support initiatives are lacking.
AIM: The objective of this study was to prepare caregivers for the role of supporting a patient with advanced cancer receiving home-based palliative care by offering a one-to-one psycho-educational intervention. We hypothesised that primary family caregivers who participated in the intervention would report decreased psychological distress (primary outcome), fewer unmet needs and increased levels of perceived preparedness, competence and positive emotions.
METHODS: A three-arm randomised controlled trial was conducted comparing two versions of the intervention (one face-to-face visit versus two visits) plus standard care to a control group (standard care) across four sites in Australia.
RESULTS: A total of 298 participants were recruited; 148 were in the Control condition, 57 in Intervention 1 (one visit) and 93 in Intervention 2 (two visits). Relative to participants in the control group; the psychological well-being of participants in the intervention condition was improved by a small amount but non-significantly. No significant reduction in unmet needs or improvements in positive aspects of caregiving amongst the intervention group were identified. However, the intervention demonstrated significant improvements in participants' levels of preparedness and competence for Intervention 2.
CONCLUSION/IMPLICATIONS: This research adds to accumulating body of evidence demonstrating that relatively short psycho-educational interventions can enable family caregivers to feel more prepared and competent in the role of supporting a dying relative. Further investigation is required to determine the longer term outcomes of such interventions. 

Behavioural and cognitive-behavioural group-based parenting programmes for early-onset conduct problems in children aged 3 to 12 years.

Early-onset child conduct problems are common and costly. A large number of studies and some previous reviews have focused on behavioural and cognitive-behavioural group-based parenting interventions, but methodological limitations are commonplace and evidence for the effectiveness and cost-effectiveness of these programmes has been unclear. To assess the effectiveness and cost-effectiveness of behavioural and cognitive-behavioural group-based parenting programmes for improving child conduct problems, parental mental health and parenting skills. We searched the following databases between 23 and 31 January 2011: CENTRAL (2011, Issue 1), MEDLINE (1950 to current), EMBASE (1980 to current), CINAHL (1982 to current), PsycINFO (1872 to current), Social Science Citation Index (1956 to current), ASSIA (1987 to current), ERIC (1966 to current), Sociological Abstracts (1963 to current), Academic Search Premier (1970 to current), Econlit (1969 to current), PEDE (1980 to current), Dissertations and Theses Abstracts (1980 to present), NHS EED (searched 31 January 2011), HEED (searched 31 January 2011), DARE (searched 31 January 2011), HTA (searched 31 January 2011), mRCT (searched 29 January 2011). We searched the following parent training websites on 31 January 2011: Triple P Library, Incredible Years Library and Parent Management Training. We also searched the reference lists of studies and reviews. We included studies if: (1) they involved randomised controlled trials (RCTs) or quasi-randomised controlled trials of behavioural and cognitive-behavioural group-based parenting interventions for parents of children aged 3 to 12 years with conduct problems, and (2) incorporated an intervention group versus a waiting list, no treatment or standard treatment control group. We only included studies that used at least one standardised instrument to measure child conduct problems. Two authors independently assessed the risk of bias in the trials and the methodological quality of health economic studies. Two authors also independently extracted data. We contacted study authors for additional information. This review includes 13 trials (10 RCTs and three quasi-randomised trials), as well as two economic evaluations based on two of the trials. Overall, there were 1078 participants (646 in the intervention group; 432 in the control group). The results indicate that parent training produced a statistically significant reduction in child conduct problems, whether assessed by parents (standardised mean difference (SMD) -0.53; 95% confidence interval (CI) -0.72 to -0.34) or independently assessed (SMD -0.44; 95% CI -0.77 to -0.11). The intervention led to statistically significant improvements in parental mental health (SMD -0.36; 95% CI -0.52 to -0.20) and positive parenting skills, based on both parent reports (SMD -0.53; 95% CI -0.90 to -0.16) and independent reports (SMD -0.47; 95% CI -0.65 to -0.29). Parent training also produced a statistically significant reduction in negative or harsh parenting practices according to both parent reports (SMD -0.77; 95% CI -0.96 to -0.59) and independent assessments (SMD -0.42; 95% CI -0.67 to -0.16). Moreover, the intervention demonstrated evidence of cost-effectiveness. When compared to a waiting list control group, there was a cost of approximately $2500 (GBP 1712; EUR 2217) per family to bring the average child with clinical levels of conduct problems into the non-clinical range. These costs of programme delivery are modest when compared with the long-term health, social, educational and legal costs associated with childhood conduct problems. Behavioural and cognitive-behavioural group-based parenting interventions are effective and cost-effective for improving child conduct problems, parental mental health and parenting skills in the short term. The cost of programme delivery was modest when compared with the long-term health, social, educational and legal costs associated with childhood conduct problems. Further research is needed on the long-term assessment of outcomes.

Fatigue Life Assessment and Static Testing of Structural GFRP Tubes Based on Coupon Tests

Fiber-reinforced polymer (FRP) hollow tubes are used in structural applications, such as utility poles and pipelines. Concrete-filled FRP tubes (CFFTs) are also used as piles and bridge piers. Applications such as poles and marine piles are typically governed by cyclic bending. In this paper, the fatigue behavior of glass-FRP filament-wound tubes is studied using coupons cut from the tubes. Several coupon configurations were first examined in 24 tension and five compression monotonic loading tests. Fatigue tests were then conducted on 81 coupons to examine several parameters; namely, loading frequency as well as maximum-to-ultimate (max ult) and minimum-to-maximum (min max) stress ratios, including tension tension and tension compression, to simulate reversed bending. The study demonstrated the sensitivity of test results and failure mode to coupon configuration. The presence of compression loads reduced fatigue life, while increasing load frequency increased fatigue life. Stiffness degradation behavior was also established. To achieve at least one million cycles, it is recommended to limit (max ult) to 0.25. Models were used to simulate stiffness degradation and fatigue life curve of the tube. Fatigue life predictions of large CFFT beams showed good correlation with experimental results. © 2008 ASCE.