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Find video protocols related to scientific articles indexed in Pubmed.
Network models. Comment on "Control profiles of complex networks".
Science
PUBLISHED: 11-01-2014
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Ruths and Ruths (Reports, 21 March 2014, p. 1373) find that existing synthetic random network models fail to generate control profiles that match those found in real network models. Here, we show that a straightforward extension to the Barabási-Albert model allows the control profile to be "tuned" across the control profile space, permitting more meaningful control profile analyses of real networks.
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Canonical correlation analysis for gene-based pleiotropy discovery.
PLoS Comput. Biol.
PUBLISHED: 10-01-2014
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Genome-wide association studies have identified a wealth of genetic variants involved in complex traits and multifactorial diseases. There is now considerable interest in testing variants for association with multiple phenotypes (pleiotropy) and for testing multiple variants for association with a single phenotype (gene-based association tests). Such approaches can increase statistical power by combining evidence for association over multiple phenotypes or genetic variants respectively. Canonical Correlation Analysis (CCA) measures the correlation between two sets of multidimensional variables, and thus offers the potential to combine these two approaches. To apply CCA, we must restrict the number of attributes relative to the number of samples. Hence we consider modules of genetic variation that can comprise a gene, a pathway or another biologically relevant grouping, and/or a set of phenotypes. In order to do this, we use an attribute selection strategy based on a binary genetic algorithm. Applied to a UK-based prospective cohort study of 4286 women (the British Women's Heart and Health Study), we find improved statistical power in the detection of previously reported genetic associations, and identify a number of novel pleiotropic associations between genetic variants and phenotypes. New discoveries include gene-based association of NSF with triglyceride levels and several genes (ACSM3, ERI2, IL18RAP, IL23RAP and NRG1) with left ventricular hypertrophy phenotypes. In multiple-phenotype analyses we find association of NRG1 with left ventricular hypertrophy phenotypes, fibrinogen and urea and pleiotropic relationships of F7 and F10 with Factor VII, Factor IX and cholesterol levels.
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Quantitative measurement of redox potential in hypoxic cells using SERS nanosensors.
Nanoscale
PUBLISHED: 09-08-2014
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Hypoxia is considered to be a reductive disorder of cells that is caused either by a lack of oxygen or by the dysregulation of metabolic pathways and is thought to play a role in the pathology of diseases including stroke and cancer. One aspect of hypoxia that remains poorly investigated is the dysregulation of cellular redox potential and its role in controlling biological pathway activation. Since there is currently no way of quantitatively measuring the intracellular redox potential of hypoxic cells, this provided us with the motivation to develop optical nanosensors whose Surface-Enhanced Raman (SER) spectrum provides a quantitative measure of redox potential in hypoxic cells. Our nanosensors are made from organic reporter molecules that show oxidation-state-dependent changes in the Raman spectrum and are chemically adsorbed onto gold nanoshells. These nanosensors can be taken up by cells, and by collecting the SER spectrum we can calculate the localised intracellular redox potential from single hypoxic cells in a non-invasive, reversible way.
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Mortality in patients with HIV-1 infection starting antiretroviral therapy in South Africa, Europe, or North America: a collaborative analysis of prospective studies.
PLoS Med.
PUBLISHED: 09-01-2014
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High early mortality in patients with HIV-1 starting antiretroviral therapy (ART) in sub-Saharan Africa, compared to Europe and North America, is well documented. Longer-term comparisons between settings have been limited by poor ascertainment of mortality in high burden African settings. This study aimed to compare mortality up to four years on ART between South Africa, Europe, and North America.
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Ratiometric biological nanosensors.
Biochem. Soc. Trans.
PUBLISHED: 08-12-2014
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The measurement of intracellular analytes has been key in understanding cellular processes and function, and the use of biological nanosensors has revealed the spatial and temporal variation in their concentrations. In particular, ratiometric nanosensors allow quantitative measurements of analyte concentrations. The present review focuses on the recent advances in ratiometric intracellular biological nanosensors, with an emphasis on their utility in measuring analytes that are important in cell function.
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Untold nutrition.
Nutr Cancer
PUBLISHED: 07-18-2014
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Nutrition is generally investigated, and findings interpreted, in reference to the activities of individual nutrients. Nutrient composition of foods, food labeling, food fortification, and nutrient recommendations are mostly founded on this assumption, a practice commonly known as reductionism. While such information on specifics is important and occasionally useful in practice, it ignores the coordinated, integrated and virtually symphonic nutrient activity (wholism) that occurs in vivo. With reductionism providing the framework, public confusion abounds and huge monetary and social costs are incurred. Two examples are briefly presented to illustrate, the long time misunderstandings (1) about saturated and total fat as causes of cancer and heart disease and (2) the emergence of the nutrient supplement industry. A new definition of the science of nutrition is urgently needed.
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Environmental risk factors in the incidence of Johne's disease.
Crit. Rev. Microbiol.
PUBLISHED: 03-28-2014
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Abstract This review addresses the survival and persistence of Mycobacterium avium subsp. paratuberculosis (MAP), the causative pathogen of Johne's disease (JD), once it has left its ruminant host. JD has significant economic impact on dairy, beef and sheep industries and is difficult to control due to the long-term sub-clinical nature of the infection, intermittent or persistent MAP shedding during and after this period, inadequate test effectiveness, and the potential for MAP to exist for extended periods outside the host. The role that environmental factors play in the persistence and spread of MAP and consequent disease is assessed. Published risk factor analysis, organism survival across various environmental media and conditions, presence and spread in ruminant and non-ruminant wildlife, and the general potential for survival and multiplication of MAP ex-host both on and off-farm are discussed and knowledge gaps highlighted. An inclusive approach to disease management that takes into account the persistence and transport of the causative organism in on-farm soils and waters, land use and management, dispersal by domestic and non-domestic host species, as well as general animal husbandry is required on those farms where more traditional approaches to disease management have failed to reduce disease prevalence.
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Triggers in advanced neurological conditions: prediction and management of the terminal phase.
BMJ Support Palliat Care
PUBLISHED: 03-20-2014
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The challenge to provide a palliative care service for individuals with advanced neurological conditions is compounded by variability in disease trajectories and symptom profiles. The National End of Life Care Programme (2010) recommended seven 'triggers' for a palliative approach to care for patients with advanced neurological conditions.
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The validity and clinical utility of structured diagnoses of antisocial personality disorder with forensic patients.
J. Pers. Disord.
PUBLISHED: 02-10-2014
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Current DSM-based instruments for personality disorders (PDs) limit the investigation of the course and outcome of treatment of these disorders. This study examined the validity of the Shedler-Westen Assessment Procedure-200 (SWAP-200) and the Structured Clinical Interview for DSM-IV Axis II PD (SCID-II) in a sample of forensic PD patients. Results based on 66 participants indicated that the SWAP-200 Q-factors reduced the frequency of diagnostic comorbidity of PD categories by half compared with the SCID-II. Only the SWAP-200's Antisocial PD category showed good convergent and discriminant validity with respect to other instruments describing aspects of PD. The validity of the cutoff score for severe antisocial PD was confirmed, and this category predicted severe incidents in the hospital at 1 year of follow-up. A violence risk scale was constructed, which differentiated violent and nonviolent offenders. The results support the validity of the SWAP-200 and its potential clinical utility with forensic PD patients.
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Stabilization of perturbed Boolean network attractors through compensatory interactions.
BMC Syst Biol
PUBLISHED: 02-07-2014
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Understanding and ameliorating the effects of network damage are of significant interest, due in part to the variety of applications in which network damage is relevant. For example, the effects of genetic mutations can cascade through within-cell signaling and regulatory networks and alter the behavior of cells, possibly leading to a wide variety of diseases. The typical approach to mitigating network perturbations is to consider the compensatory activation or deactivation of system components. Here, we propose a complementary approach wherein interactions are instead modified to alter key regulatory functions and prevent the network damage from triggering a deregulatory cascade.
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Evaluation of an antibody avidity index method for detecting recent human immunodeficiency virus type 1 infection using an automated chemiluminescence immunoassay.
Enferm. Infecc. Microbiol. Clin.
PUBLISHED: 01-29-2014
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Recent infection testing algorithms (RITAs) are used in public health surveillance to estimate the incidence of recently acquired HIV-1 infection.
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Loss of microbial diversity in soils is coincident with reductions in some specialized functions.
Environ. Microbiol.
PUBLISHED: 01-15-2014
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Loss of microbial diversity is considered a major threat because of its importance for ecosystem functions, but there is a lack of conclusive evidence that diversity itself is reduced under anthropogenic stress, and about the consequences of diversity loss. Heavy metals are one of the largest, widespread pollutant types globally, and these represent a significant environmental stressor for terrestrial microbial communities. Using combined metagenomics and functional assays, we show that the compositional and functional response of microbial communities to long-term heavy metal stress results in a significant loss of diversity. Our results indicate that even at a moderate loss of diversity, some key specialized functions (carried out by specific groups) may be compromised. Together with previous work, our data suggest disproportionate impact of contamination on microbes that carry out specialized, but essential, ecosystem functions. Based on these findings, we propose a conceptual framework to explicitly consider diversity of functions and microbial functional groups to test the relationship between biodiversity and soil functions.
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Healthy animals, healthy people: zoonosis risk from animal contact in pet shops, a systematic review of the literature.
PLoS ONE
PUBLISHED: 01-01-2014
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Around 67 million pets are owned by households in the United Kingdom, and an increasing number of these are exotic animals. Approximately a third of pets are purchased through retail outlets or direct from breeders. A wide range of infections can be associated with companion animals.
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A pathway-based data integration framework for prediction of disease progression.
Bioinformatics
PUBLISHED: 10-24-2013
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Within medical research there is an increasing trend toward deriving multiple types of data from the same individual. The most effective prognostic prediction methods should use all available data, as this maximizes the amount of information used. In this article, we consider a variety of learning strategies to boost prediction performance based on the use of all available data.Implementation: We consider data integration via the use of multiple kernel learning supervised learning methods. We propose a scheme in which feature selection by statistical score is performed separately per data type and by pathway membership. We further consider the introduction of a confidence measure for the class assignment, both to remove some ambiguously labeled datapoints from the training data and to implement a cautious classifier that only makes predictions when the associated confidence is high.
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Capillary HPLC-accurate mass MS/MS quantitation of N7-(2,3,4-trihydroxybut-1-yl)-guanine adducts of 1,3-butadiene in human leukocyte DNA.
Chem. Res. Toxicol.
PUBLISHED: 09-12-2013
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1,3-Butadiene (BD) is a high volume industrial chemical commonly used in polymer and rubber production. It is also present in cigarette smoke, automobile exhaust, and urban air, leading to widespread exposure of human populations. Upon entering the body, BD is metabolized to electrophilic epoxides, 3,4-epoxy-1-butene (EB), diepoxybutane (DEB), and 3,4-epoxy-1,2-diol (EBD), which can alkylate DNA nucleobases. The most abundant BD epoxide, EBD, modifies the N7-guanine positions in DNA to form N7-(2, 3, 4-trihydroxybut-1-yl) guanine (N7-THBG) adducts, which can be useful as biomarkers of BD exposure and metabolic activation to DNA-reactive epoxides. In the present work, a capillary HPLC-high resolution ESI?-MS/MS (HPLC-ESI?-HRMS/MS) methodology was developed for accurate, sensitive, and reproducible quantification of N7-THBG in cell culture and in human white blood cells. In our approach, DNA is subjected to neutral thermal hydrolysis to release N7-guanine adducts from the DNA backbone, followed by ultrafiltration, solid-phase extraction, and isotope dilution HPLC-ESI?-HRMS/MS analysis on an Orbitrap Velos mass spectrometer. Following method validation, N7-THBG was quantified in human fibrosarcoma (HT1080) cells treated with micromolar concentrations of DEB and in DNA isolated from blood of smokers, nonsmokers, individuals participating in a smoking cessation program, and occupationally exposed workers. N7-THBG concentrations increased linearly from 31.4 ± 4.84 to 966.55 ± 128.05 adducts per 10? nucleotides in HT1080 cells treated with 1-100 ?M DEB. N7-THBG amounts in leukocyte DNA of nonsmokers, smokers, and occupationally exposed workers were 7.08 ± 5.29, 8.20 ± 5.12, and 9.72 ± 3.80 adducts per 10? nucleotides, respectively, suggesting the presence of an endogenous or environmental source for this adduct. The availability of sensitive HPLC-ESI?-HRMS/MS methodology for BD-induced DNA adducts in humans will enable future population studies of interindividual and ethnic differences in BD bioactivation to DNA-reactive epoxides.
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Minimal oxidation and inflammogenicity of pristine graphene with residence in the lung.
Nanotoxicology
PUBLISHED: 09-05-2013
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Abstract Two-dimensional graphitic carbon, graphene, is a new form of nanomaterial with great potential in a wide variety of applications. It is therefore crucial to investigate the behaviour of graphene in biological systems to assess potential adverse effects that might follow from inhalation exposure. In this study we focussed on medium-term effects of graphene in lung tissue by investigating the pulmonary inflammation 6 weeks after pharyngeal aspiration of unoxidised multilayered graphene platelets (GPs) in mice and assessed their biopersistence in the lung tissue using Raman spectroscopy. Additionally, GP degradation in vitro was examined after horseradish peroxidase (HRP) treatment up to 1 week. Building on our previous report showing acute inflammation in mice lungs at 1 day, pristine GP showed minimal inflammation in mouse lungs after 6 weeks even though no degradation of GP in lung tissue was observed and large deposits of GP were evident in the lungs. Raman analysis of GP in tissue sections showed minimal oxidation, and in vitro examinations of enzymatic oxidation of GP via HRP and H2O2 showed only slight increases in ID/IG ratio and the appearance of the Raman D band at 1620 cm(-1) (surrogates of graphene oxidation). Our results showing non-inflammogenicity at medium time points have important implications in the hazard identification of GPs following inhalation exposure and for their use in biomedical applications. Additionally, the biopersistence of pristine GP in vivo with no associated inflammation could open the way to applications in tissue engineering and drug delivery.
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End-of-life care in neurodegenerative conditions: outcomes of a specialist palliative neurology service.
Int J Palliat Nurs
PUBLISHED: 08-24-2013
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People with advanced neurological conditions (ANCs) face complex problems and needs that are often unrecognised and undertreated.Their last year of life may be characterised by unplanned hospital admissions and an unexpected death. A National End-of-Life Care Programme (NEoLCP) 2010 framework made recommendations to aid timely and appropriate end-of-life care for people with ANCs.
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Period effects, cohort effects, and the narrowing gender wage gap.
Soc Sci Res
PUBLISHED: 07-11-2013
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Despite the abundance of sociological research on the gender wage gap, questions remain. In particular, the role of cohorts is under investigated. Using data from the Current Population Survey, we use age-period-cohort analysis to uniquely estimate age, period, and cohort effects on the gender wage gap. The narrowing of the gender wage gap that occurred between 1975 and 2009 is largely due to cohort effects. Since the mid-1990s, the gender wage gap has continued to close absent of period effects. While gains in female wages contributed to declines in the gender wage gap for cohorts born before 1950, for later cohorts the narrowing of the gender wage gap is primarily a result of declines in male wages.
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Cognitive flexibility among individuals with Down syndrome: assessing the influence of verbal and nonverbal abilities.
Am J Intellect Dev Disabil
PUBLISHED: 06-06-2013
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The influences of verbal mental age (VMA) and performance mental age (PMA) on cognitive flexibility were examined among a group of participants with Down syndrome (DS), in order to disentangle the relative contributions of each. The impaired cognitive flexibility typically observed among individuals with DS in combination with uneven VMA and PMA development suggests an opportunity to further understand the developmental relationship between VMA, PMA, and cognitive flexibility. We examined the performance of 22 participants with DS on the Flexible Item Selection Task (FIST), used for measuring cognitive flexibility among preschoolers. Partial correlations revealed that only VMA was related to the FIST after controlling for PMA, highlighting the role of verbal abilities in the development of cognitive flexibility.
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DNA-reactive protein monoepoxides induce cell death and mutagenesis in mammalian cells.
Biochemistry
PUBLISHED: 04-24-2013
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Although cytotoxic alkylating agents possessing two electrophilic reactive groups are thought to act by cross-linking cellular biomolecules, their exact mechanisms of action have not been established. In cells, these compounds form a mixture of DNA lesions, including nucleobase monoadducts, interstrand and intrastrand cross-links, and DNA-protein cross-links (DPCs). Interstrand DNA-DNA cross-links block replication and transcription by preventing DNA strand separation, contributing to toxicity and mutagenesis. In contrast, potential contributions of drug-induced DPCs are poorly understood. To gain insight into the biological consequences of DPC formation, we generated DNA-reactive protein reagents and examined their toxicity and mutagenesis in mammalian cells. Recombinant human O(6)-alkylguanine DNA alkyltransferase (AGT) protein or its variants (C145A and K125L) were treated with 1,2,3,4-diepoxybutane to yield proteins containing 2-hydroxy-3,4-epoxybutyl groups on cysteine residues. Gel shift and mass spectrometry experiments confirmed that epoxide-functionalized AGT proteins formed covalent DPC but no other types of nucleobase damage when incubated with duplex DNA. Introduction of purified AGT monoepoxides into mammalian cells via electroporation generated AGT-DNA cross-links and induced cell death and mutations at the hypoxanthine-guanine phosphoribosyltransferase gene. Smaller numbers of DPC lesions and reduced levels of cell death were observed when using protein monoepoxides generated from an AGT variant that fails to accumulate in the cell nucleus (K125L), suggesting that nuclear DNA damage is required for toxicity. Taken together, these results indicate that AGT protein monoepoxides produce cytotoxic and mutagenic DPC lesions within chromosomal DNA. More generally, these data suggest that covalent DPC lesions contribute to the cytotoxic and mutagenic effects of bis-electrophiles.
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1,2,3,4-Diepoxybutane-induced DNA-protein cross-linking in human fibrosarcoma (HT1080) cells.
J. Proteome Res.
PUBLISHED: 04-03-2013
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1,2,3,4-Diepoxybutane (DEB) is the key carcinogenic metabolite of 1,3-butadiene (BD), an important industrial and environmental chemical present in urban air and in cigarette smoke. DEB is a genotoxic bis-electrophile capable of cross-linking cellular biomolecules to form DNA-DNA and DNA-protein cross-links (DPCs). In the present work, mass spectrometry-based proteomics was employed to characterize DEB-mediated DNA-protein cross-linking in human fibrosarcoma (HT1080) cells. Over 150 proteins including histones, high mobility group proteins, transcription factors, splicing factors, and tubulins were found among those covalently cross-linked to chromosomal DNA in the presence of DEB. A large portion of the cross-linked proteins are known factors involved in DNA binding, transcriptional regulation, cell signaling, DNA repair, and DNA damage response. HPLC-ESI(+)-MS/MS analysis of total proteolytic digests revealed the presence of 1-(S-cysteinyl)-4-(guan-7-yl)-2,3-butanediol conjugates, confirming that DEB forms DPCs between cysteine thiols within proteins and the N-7 guanine positions within DNA. However, relatively high concentrations of DEB were required to achieve significant DPC formation, indicating that it is a poor cross-linking agent as compared to antitumor nitrogen mustards and platinum compounds.
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Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey.
Environ. Microbiol.
PUBLISHED: 03-18-2013
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The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different ammonia oxidizers, we used samples (n = 713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40-45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13-16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main ammonia oxidizers in acidic soils. However, for AOB, soil pH and substrate (ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning.
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Time-lapse ultrashort pulse microscopy of infection in three-dimensional versus two-dimensional culture environments reveals enhanced extra-chromosomal virus replication compartment formation.
J Biomed Opt
PUBLISHED: 03-05-2013
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The mechanisms that enable viruses to harness cellular machinery for their own survival are primarily studied in cell lines cultured in two-dimensional (2-D) environments. However, there are increasing reports of biological differences between cells cultured in 2-D versus three-dimensional (3-D) environments. Here we report differences in host-virus interactions based on differences in culture environment. Using ultrashort pulse microscopy (UPM), a form of two-photon microscopy that utilizes sub-10-fs pulses to efficiently excite fluorophores, we have shown that de novo development of extra-chromosomal virus replication compartments (VRCs) upon murine cytomegalovirus (mCMV) infection is markedly enhanced when host cells are cultured in 3-D collagen gels versus 2-D monolayers. In addition, time-lapse imaging revealed that mCMV-induced VRCs have the capacity to grow by coalescence. This work supports the future potential of 3-D culture as a useful bridge between traditional monolayer cultures and animal models to study host-virus interactions in a more physiologically relevant environment for the development of effective anti-viral therapeutics. These advances will require broader adoption of modalities, such as UPM, to image deep within scattering tissues.
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Early-life residential exposure to soil components in rural areas and childhood respiratory health and allergy.
Sci. Total Environ.
PUBLISHED: 03-01-2013
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The increase in asthma and allergies has been attributed to declining exposure to environmental microorganisms. The main source of these is soil, the composition of which varies geographically and which is a major component (40-45%) of household dust. Our hypothesis-generating study aimed to investigate associations between soil components, respiratory health and allergy in a Scottish birth cohort. The cohort was recruited in utero in 1997/8, and followed up at one, two and five years for the development of wheezing, asthma and eczema. Lung function, exhaled nitric oxide and allergic sensitization were measured at age five in a subset. The Scottish Soils Database held at The James Hutton Institute was linked to the birth cohort data by the residential postcode at birth and five years. The soil database contained information on size separates, organic matter concentration, pH and a range of inorganic elements. Soil and clinical outcome data were available for 869, 790 and 727 children at one, two and five years. Three hundred and fifty nine (35%) of children had the same address at birth and five years. No associations were found between childhood outcomes and soil content in the residential area at age five. The soil silt content (2-20 ?m particle size) of the residential area at birth was associated with childhood wheeze (adjusted OR 1.20, 95% CI [1.05; 1.37]), wheeze without a cold (1.41 [1.18; 1.69]), doctor-diagnosed asthma (1.54 [1.04; 2.28]), lung function (FEV1: beta -0.025 [-0.047;-0.001]) and airway inflammation (FENO: beta 0.15 [0.03; 0.27]) at age five, but not with allergic status or eczema. Whilst residual confounding is the most likely explanation for the associations reported, the results of this study lead us to hypothesise that early life exposure to residential soil silt may adversely influence childhood respiratory health, possibly because of the organic components of silt.
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Harnessing clinical psychiatric data with an electronic assessment tool (OPCRIT+): the utility of symptom dimensions.
PLoS ONE
PUBLISHED: 02-06-2013
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Progress in personalised psychiatry is dependent on researchers having access to systematic and accurately acquired symptom data across clinical diagnoses. We have developed a structured psychiatric assessment tool, OPCRIT+, that is being introduced into the electronic medical records system of the South London and Maudsley NHS Foundation Trust which can help to achieve this. In this report we examine the utility of the symptom data being collected with the tool. Cross-sectional mental state data from a mixed-diagnostic cohort of 876 inpatients was subjected to a principal components analysis (PCA). Six components, explaining 46% of the variance in recorded symptoms, were extracted. The components represented dimensions of mania, depression, positive symptoms, anxiety, negative symptoms and disorganization. As indicated by component scores, different clinical diagnoses demonstrated distinct symptom profiles characterized by wide-ranging levels of severity. When comparing the predictive value of symptoms against diagnosis for a variety of clinical outcome measures (e.g. Overactive, aggressive behaviour), symptoms proved superior in five instances (R(2) range: 0.06-0.28) whereas diagnosis was best just once (R(2):0.25). This report demonstrates that symptom data being routinely gathered in an NHS trust, when documented on the appropriate tool, have considerable potential for onward use in a variety of clinical and research applications via representation as dimensions of psychopathology.
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Monitoring intracellular redox potential changes using SERS nanosensors.
ACS Nano
PUBLISHED: 12-13-2011
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Redox homeostasis and signaling are critically important in the regulation of cell function. There are significant challenges in quantitatively measuring intracellular redox potentials, and in this paper, we introduce a new approach. Our approach is based on the use of nanosensors which comprise molecules that sense the local redox potential, assembled on a gold nanoshell. Since the Raman spectrum of the sensor molecule changes depending on its oxidation state and since the nanoshell allows a huge enhancement of the Raman spectrum, intracellular potential can be calculated by a simple optical measurement. The nanosensors can be controllably delivered to the cytoplasm, without any toxic effects, allowing redox potential to be monitored in a reversible, non-invasive manner over a previously unattainable potential range encompassing both superphysiological and physiological oxidative stress.
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Decision-making for gastrostomy and ventilatory support for people with motor neurone disease: variations across UK hospices.
J Palliat Care
PUBLISHED: 10-01-2011
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Interventions, such as the use of percutaneous endoscopic gastrostomy (PEG) and non-invasive ventilation (NIV), are used in the management of people with motor neurone disease with the aim of improving quality of life and relieving symptoms. However, the number of people receiving these interventions varies across the UK. This study has looked at the involvement and knowledge of consultants, within specialist palliative care services, with these procedures, to ascertain if there were differences in attitudes to their use. Twenty-two consultants took part in a telephone audit. There appeared to be great variation in their involvement in and knowledge of the use of these interventions. The majority of services were involved in the care of people with MND, but often only in the terminal stages. There appears to be a need for the wider application of guidelines on the use of PEG and NIV, as well as the development of a collaborative approach with other services, including neurology and rehabilitation services.
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Discovery of a brain-penetrant S1P?-sparing direct agonist of the S1P? and S1P? receptors efficacious at low oral dose.
J. Med. Chem.
PUBLISHED: 09-09-2011
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2-Amino-2-(4-octylphenethyl)propane-1,3-diol 1 (fingolimod, FTY720) has been recently marketed in the United States for the treatment of patients with remitting relapsing multiple sclerosis (RRMS). Its efficacy has been primarily linked to the agonism on T cells of S1P(1), one of the five sphingosine 1-phosphate (S1P) G-protein-coupled receptors, while its cardiovascular side effects have been associated with activity at S1P(3). Emerging data suggest that the ability of this molecule to cross the blood-brain barrier and to interact with both S1P(1) and S1P(5) in the central nervous system (CNS) may contribute to its efficacy in treating patients with RRMS. We have recently disclosed the structure of an advanced, first generation S1P(3)-sparing S1P(1) agonist, a zwitterion with limited CNS exposure. In this Article, we highlight our strategy toward the identification of CNS-penetrant S1P(3)-sparing S1P(1) and S1P(5) agonists resulting in the discovery of 5-(3-{2-[2-hydroxy-1-(hydroxymethyl)ethyl]-5-methyl-1,2,3,4-tetrahydro-6-isoquinolinyl}-1,2,4-oxadiazol-5-yl)-2-[(1-methylethyl)oxy]benzonitrile 15. Its exceptional in vivo potency and good pharmacokinetic properties translate into a very low predicted therapeutic dose in human (<1 mg p.o. once daily).
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Development of immunosensors for direct detection of three wound infection biomarkers at point of care using electrochemical impedance spectroscopy.
Biosens Bioelectron
PUBLISHED: 07-19-2011
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A method for label-free, electrochemical impedance immunosensing for the detection and quantification of three infection biomarkers in both buffer and directly in the defined model matrix of mock wound fluid is demonstrated. Triggering Receptor-1 Expressed on Myeloid cells (TREM-1) and Matrix MetalloPeptidase 9 (MMP-9) are detected via direct assay and N-3-oxo-dodecanoyl-l-HomoSerineLactone (HSL), relevant in bacterial quorum sensing, is detected using a competition assay. Detection is performed with gold screen-printed electrodes modified with a specific thiolated antibody. Detection is achieved in less than 1h straight from mock wound fluid without any extensive sample preparation steps. The limits of detection of 3.3 pM for TREM-1, 1.1 nM for MMP-9 and 1.4 nM for HSL are either near or below the threshold required to indicate infection. A relatively large dynamic range for sensor response is also found, consistent with interaction between neighbouring antibody-antigen complexes in the close-packed surface layer. Together, these three novel electrochemical immunosensors demonstrate viable multi-parameter sensing with the required sensitivity for rapid wound infection detection directly from a clinically relevant specimen.
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Use of antiviral drugs to reduce household transmission of pandemic (H1N1) 2009, United Kingdom.
Emerging Infect. Dis.
PUBLISHED: 07-14-2011
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The United Kingdom implemented a containment strategy for pandemic (H1N1) 2009 through administering antiviral agents (AVs) to patients and their close contacts. This observational household cohort study describes the effect of AVs on household transmission. We followed 285 confirmed primary cases in 259 households with 761 contacts. At 2 weeks, the confirmed secondary attack rate (SAR) was 8.1% (62/761) and significantly higher in persons <16 years of age than in those >50 years of age (18.9% vs. 1.2%, p<0.001). Early (<48 hours) treatment of primary case-patients reduced SAR (4.5% vs. 10.6%, p = 0.003). The SAR in child contacts was 33.3% (10/30) when the primary contact was a woman and 2.9% (1/34) when the primary contact was a man (p = 0.010). Of 53 confirmed secondary case-patients, 45 had not received AV prophylaxis. The effectiveness of AV prophylaxis in preventing infection was 92%.
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Antibiotic resistance gene abundances correlate with metal and geochemical conditions in archived Scottish soils.
PLoS ONE
PUBLISHED: 06-21-2011
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The vast majority of antibiotic resistant genes (ARG) acquired by human pathogens have originated from the natural environment. Therefore, understanding factors that influence intrinsic levels of ARG in the environment could be epidemiologically significant. The selection for metal resistance often promotes AR in exposed organisms; however, the relationship between metal levels in nature and the intrinsic presence of ARG has not been fully assessed. Here, we quantified, using qPCR, the abundance of eleven ARG and compared their levels with geochemical conditions in randomly selected soils from a Scottish archive. Many ARG positively correlated with soil copper levels, with approximately half being highly significant (p<0.05); whereas chromium, nickel, lead, and iron also significantly correlated with specific ARG. Results show that geochemical metal conditions innately influence the potential for AR in soil. We suggest soil geochemical data might be used to estimate baseline gene presence on local, regional and global scales within epidemiological risk studies related to AR transmission from the environment.
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Fast DNA and protein microarray tests for the diagnosis of hepatitis C virus infection on a single platform.
Anal Bioanal Chem
PUBLISHED: 06-14-2011
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Hepatitis C virus (HCV) is a major cause of chronic liver disease and liver cancer, and remains a large health care burden to the world. In this study we developed a DNA microarray test to detect HCV RNA and a protein microarray to detect human anti-HCV antibodies on a single platform. A main focus of this study was to evaluate possibilities to reduce the assay time, as a short time-to-result (TTR) is a prerequisite for a point-of-care test. Significantly reducing hybridisation and washing times did not impair the assay performance. This was confirmed first using artificial targets and subsequently using clinical samples from an HCV seroconversion panel derived from a HCV-infected patient. We were able to reduce the time required for the detection of human anti-HCV antibodies to only 14 min, achieving nanomolar sensitivity. The protein microarray exhibited an analytical sensitivity comparable to that of commercial systems. Similar results were obtained with the DNA microarray using a universal probe which covered all different HCV genotypes. It was possible to reduce the assay time after PCR from 150 min to 16 min without any loss of sensitivity. Taken together, these results constitute a significant step forward in the design of rapid, microarray-based diagnostics for human infectious disease, and show that the protein microarray is currently the most favourable candidate to fill this role.
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Redox potential dependence of peptide structure studied using surface enhanced Raman spectroscopy.
Nano Lett.
PUBLISHED: 06-07-2011
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We describe a novel surface enhanced Raman spectroscopy (SERS) sensing approach utilizing modified gold nanoshells and demonstrate its application to analysis of critical redox-potential dependent changes in antigen structure that are implicated in the initiation of a human autoimmune disease. In Goodpastures disease, an autoimmune reaction is thought to arise from incomplete proteolysis of the autoantigen, ?3(IV)NC1(67-85) by proteases including Cathepsin D. We have used SERS to study conformational changes in the antigen that correlate with its oxidation state and to show that the antigen must be in the reduced state in order to undergo proteolysis. Our results demonstrate that a redox potential of ?-200 mV was sufficient for reduction and subsequent productive processing of the antigenic fragment ?3(IV)NC1(67-85). Moreover, we demonstrate that the peptide bonds subsequently cleaved by Cathepsisn D can be identified by comparison with a SERS library of short synthetic peptides.
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Links between ammonia oxidizer community structure, abundance, and nitrification potential in acidic soils.
Appl. Environ. Microbiol.
PUBLISHED: 05-13-2011
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Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.
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Neurocognitive signs in prodromal Huntington disease.
Neuropsychology
PUBLISHED: 05-04-2011
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PREDICT-HD is a large-scale international study of people with the Huntington disease (HD) CAG-repeat expansion who are not yet diagnosed with HD. The objective of this study was to determine the stage in the HD prodrome at which cognitive differences from CAG-normal controls can be reliably detected.
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Mechlorethamine-induced DNA-protein cross-linking in human fibrosarcoma (HT1080) cells.
J. Proteome Res.
PUBLISHED: 04-29-2011
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Antitumor nitrogen mustards, such as bis(2-chloroethyl)methylamine (mechlorethamine), are useful chemotherapeutic agents with a long history of clinical application. The antitumor effects of nitrogen mustards are attributed to their ability to induce DNA-DNA and DNA-protein cross-links (DPCs) that block DNA replication. In the present work, a mass spectrometry-based methodology was employed to characterize in vivo DNA-protein cross-linking following treatment of human fibrosarcoma (HT1080) cells with cytotoxic concentrations of mechlorethamine. A combination of mass spectrometry-based proteomics and immunological detection was used to identify 38 nuclear proteins that were covalently cross-linked to chromosomal DNA following treatment with mechlorethamine. Isotope dilution HPLC-ESI(+)-MS/MS analysis of total proteolytic digests revealed a concentration-dependent formation of N-[2-(S-cysteinyl)ethyl]-N-[2-(guan-7-yl)ethyl]methylamine (Cys-N7G-EMA) conjugates, indicating that mechlorethamine cross-links cysteine thiols within proteins to N-7 positions of guanine in DNA.
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Network analysis reveals cross-links of the immune pathways activated by bacteria and allergen.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 04-26-2011
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Many biological networks are characterized by directed edges that represent either activating (positive) or inhibiting (negative) regulation. Most graph-theoretical methods used to study biological networks either disregard this important feature, or study the role of edge sign only in the context of small subgraphs called motifs. Here, we develop path-based measures which capture, on continuous scales spanning negative and positive values, both the long- and short-range regulatory relationships among node pairs. These measures also allow the quantification of each nodes overall influence on the whole network and its susceptibility to regulation by the rest of the network. We apply the measures to a network representation of the mammalian immune response to simultaneous attack by allergen and respiratory bacteria. Although allergen and bacteria elicit different immune pathways, there is significant overlap (cross-talk) and feedback between these pathways. We identify key immune components in this cross-talk; particularly revealing the importance of natural killer cells as a key regulatory target in the cross-talk.
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Why Do CD8+ T Cells become Indifferent to Tumors: A Dynamic Modeling Approach.
Front Physiol
PUBLISHED: 03-23-2011
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CD8+ T cells have the potential to influence the outcome of cancer pathogenesis, including complete tumor eradication or selection of malignant tumor escape variants. The Simian virus 40 large T-antigen (Tag) oncoprotein promotes tumor formation in Tag-transgenic mice and also provides multiple target determinants (sites) for responding CD8+ T cells in C57BL/6 (H-2(b)) mice. To understand the in vivo quantitative dynamics of CD8+ T cells after encountering Tag, we constructed a dynamic model from in vivo-generated data to simulate the interactions between Tag-expressing cells and CD8+ T cells in distinct scenarios including immunization of wild-type C57BL/6 mice and of Tag-transgenic mice that develop various tumors. In these scenarios the model successfully reproduces the dynamics of both the Tag-expressing cells and antigen-specific CD8+ T cell responses. The model predicts that the tolerance of the site-specific T cells is dependent on their apoptosis rates and that the net growth of CD8+ T cells is altered in transgenic mice. We experimentally validate both predictions. Our results indicate that site-specific CD8+ T cells have tissue-specific apoptosis rates affecting their tolerance to the tumor antigen. Moreover, the model highlights differences in apoptosis rates that contribute to compromised CD8+ T cell responses and tumor progression, knowledge of which is essential for development of cancer immunotherapy.
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Peptide-tags for enhanced DNA microarray performance.
Faraday Discuss.
PUBLISHED: 03-18-2011
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DNA microarrays are powerful tools for gene expression analysis and genotyping studies in research and diagnostic applications. A high sensitivity and short time-to-result are prerequisites for their practical application in the clinic. The hybridization efficiency of DNA microarrays depends on the probe density and the probe orientation and thus their accessibility for target molecules. In order to find an optimal probe immobilization procedure a set of different oligonucleotide modifications was tested on epoxy silane functionalized glass slides. It was found that histidine-tagged oligonucleotides resulted in the highest amount of bound probe and by far the best hybridization efficiencies. The detection limit obtained with histidine-tagged probes was up to two orders of magnitude lower compared to commonly used probe modifications. In order to further investigate the binding mechanism of histidine-tags towards functionalized glass substrates a set of different peptide-tags with and without free terminal amino-groups and with different amino acid compositions was tested. The results indicate an impact of the terminal amino group on the covalent surface binding and of aromatic amino acid residues on the enhanced hybridisation efficiency.
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Dielectrophoretic manipulation of ribosomal RNA.
Biomicrofluidics
PUBLISHED: 03-11-2011
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The manipulation of ribosomal RNA (rRNA) extracted from E. coli cells by dielectrophoresis (DEP) has been demonstrated over the range of 3 kHz-50 MHz using interdigitated microelectrodes. Quantitative measurement using total internal reflection fluorescence microscopy of the time dependent collection indicated a positive DEP response characterized by a plateau between 3 kHz and 1 MHz followed by a decrease in response at higher frequencies. Negative DEP was observed above 9 MHz. The positive DEP response below 1 MHz is described by the Clausius-Mossotti model and corresponds to an induced dipole moment of 3300 D with a polarizability of 7.8×10(-32) F m(2). The negative DEP response above 9 MHz indicates that the rRNA molecules exhibit a net moment of -250 D, to give an effective permittivity value of 78.5 ?(0), close to that of the aqueous suspending medium, and a relatively small surface conductance value of ?0.1 nS. This suggests that our rRNA samples have a fairly open structure accessible to the surrounding water molecules, with counterions strongly bound to the charged phosphate groups in the rRNA backbone. These results are the first demonstration of DEP for fast capture and release of rRNA units, opening new opportunities for rRNA-based biosensing devices.
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Formation of cyclophosphamide specific DNA adducts in hematological diseases.
Pediatr Blood Cancer
PUBLISHED: 03-03-2011
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Fanconi anemia (FA) patients are hypersensitive to DNA alkylating agents and require lower doses than non-FA patients to minimize serious toxicity. The mechanism by which hypersensitivity occurs is thought to be due to the inability of these individuals to effectively repair drug-induced interstrand DNA-DNA crosslinks. We recently developed a highly sensitive assay for cyclophosphamide specific interstrand DNA-DNA crosslinks (G-NOR-G) and are able to quantify and compare formation of these adducts in the blood of patients. Therefore we sought to determine whether FA patients have higher in vivo exposure to the cyclophosphamide specific interstrand DNA crosslink, G-NOR-G, relative to patients without FA.
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Risk assessment of the use of PAS100 green composts in sheep and cattle production in Scotland.
Waste Manag
PUBLISHED: 02-07-2011
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A generalized quantitative risk assessment for the use of source-segregated green waste (SSGW) compost use in livestock production is presented. This assessment focussed on potential risks associated with a specific product, PAS100 compost that meets the UK publicly available specification 100 and represents the majority of compost available for use in extensive Scottish livestock systems. A hazard screening approach was used to identify all potentially hazardous agents present in compost. A total of 497 potentially hazardous agents were screened, with 147 finally put forward for quantitative risk assessment. Scenarios modelled in the assessment included surface application of compost to grazing land and also incorporation into soil and subsequent uptake by fodder crops. Risk estimates were compared to those associated with six comparator materials, including various sludges, slurries and farm yard manures. Overall, five potentially hazardous agents (PCB28, PCB138, PCB153, 1,2,3,4,6,7,8-HpCDD, Clopyralid) returned a hazard quotient >1 but within margins of uncertainty, indicating that further investigation may be required. Within the limitations of available information, SSGW compost was found to pose less risk to grazing livestock, or the environment, than other commonly-used soil amendments. While this assessment relates to a specific product/standard used in the UK, the methodology could easily be applied to other composts/products/situations. Therefore these results have wider applicability.
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A network model for plant-pollinator community assembly.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 12-20-2010
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Community assembly models, usually constructed for food webs, are an important component of our understanding of how ecological communities are formed. However, models for mutualistic community assembly are still needed, especially because these communities are experiencing significant anthropogenic disturbances that affect their biodiversity. Here, we present a unique network model that simulates the colonization and extinction process of mutualistic community assembly. We generate regional source pools of species interaction networks on the basis of statistical properties reported in the literature. We develop a dynamic synchronous Boolean framework to simulate, with few free parameters, the dynamics of new mutualistic community formation from the regional source pool. This approach allows us to deterministically map out every possible trajectory of community formation. This level of detail is rarely observed in other analytic approaches and allows for thorough analysis of the dynamical properties of community formation. As for food web assembly, we find that the number of stable communities is quite low, and the composition of the source pool influences the abundance and nature of community outcomes. However, in contrast to food web assembly, stable mutualistic communities form rapidly. Small communities with minor fluctuations in species presence/absence (self-similar limit cycles) are the most common community outcome. The unique application of this Boolean network approach to the study of mutualistic community assembly offers a great opportunity to improve our understanding of these critical communities.
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Effects of cis-regulatory variation differ across regions of the adult human brain.
Hum. Mol. Genet.
PUBLISHED: 09-09-2010
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Cis-regulatory variation is considered to be an important determinant of human phenotypic variability, including susceptibility to complex disease. Recent studies have shown that the effects of cis-regulatory polymorphism on gene expression can differ widely between tissues. In the present study, we tested whether the effects of cis-regulatory variation can also differ between regions of the adult human brain. We used relative allelic expression to measure cis-effects on the RNA expression of five candidate genes for neuropsychiatric illness (ZNF804A, NOS1, RGS4, AKT1 and TCF4) across multiple discrete brain regions within individual subjects. For all five genes, we observed significant differences in allelic expression between brain regions in several individual subjects, suggesting regional differences in the effects of cis-regulatory polymorphism to be a common phenomenon. As well as highlighting an important caveat for studies of regulatory polymorphism in the brain, our findings indicate that it is possible to delineate brain areas in which cis-regulatory variants are active. This may provide important insights into the fundamental biology of neuropsychiatric phenotypes with which such variants are associated.
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Rademacher chaos complexities for learning the kernel problem.
Neural Comput
PUBLISHED: 09-01-2010
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We develop a novel generalization bound for learning the kernel problem. First, we show that the generalization analysis of the kernel learning problem reduces to investigation of the suprema of the Rademacher chaos process of order 2 over candidate kernels, which we refer to as Rademacher chaos complexity. Next, we show how to estimate the empirical Rademacher chaos complexity by well-established metric entropy integrals and pseudo-dimension of the set of candidate kernels. Our new methodology mainly depends on the principal theory of U-processes and entropy integrals. Finally, we establish satisfactory excess generalization bounds and misclassification error rates for learning gaussian kernels and general radial basis kernels.
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Visuomotor integration deficits precede clinical onset in Huntingtons disease.
Neuropsychologia
PUBLISHED: 08-11-2010
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Visuomotor integration deficits have been documented in Huntington disease (HD), with disproportionately more impairment when direct visual feedback is unavailable. Visuomotor integration under direct and indirect visual feedback conditions has not been investigated in the stage before clinical onset (premanifest). However, given evidence of posterior cortical atrophy in premanifest HD, we predicted visuomotor integration would be adversely affected, with greater impairment under conditions of indirect visual feedback.
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DNA-protein cross-linking by 1,2,3,4-diepoxybutane.
J. Proteome Res.
PUBLISHED: 07-30-2010
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1,2,3,4-diepoxybutane (DEB) is a strongly genotoxic diepoxide hypothesized to be the ultimate carcinogenic metabolite of the common industrial chemical and environmental carcinogen 1,3-butadiene. DEB is a bis-electrophile capable of cross-linking cellular biomolecules to form DNA-DNA and DNA-protein cross-links (DPCs), which are thought to play a central role in its biological activity. Previous studies with recombinant proteins have shown that the biological outcomes of DEB-induced DPCs are strongly influenced by protein identities. The present work combines affinity capture methodology with mass spectrometry-based proteomics and immunological detection to identify the proteins that form DPCs in nuclear extracts from human cervical carcinoma (HeLa) cells. We identified 39 human proteins that form covalent DPCs in the presence of DEB. DNA-protein cross-linking efficiency following treatment with 25 mM DEB was 2-12%, depending on protein identity. High-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI+-MS/MS) analysis of the total proteolytic digests of cross-linked proteins revealed the presence of 1-(S-cysteinyl)-4-(guan-7-yl)-2,3-butanediol conjugates, suggesting that DEB forms DPCs between cysteine thiols within proteins and the N-7 guanine positions within DNA.
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Medication in the last days of life for motor neuron disease/amyotrophic lateral sclerosis.
Amyotroph Lateral Scler
PUBLISHED: 06-22-2010
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Our objective was to study the use of opioid and other medication at the end of life for patients with ALS/MND under specialist palliative care. A retrospective study looked at the medication received by 62 patients with MND/ALS in the last 72 h of life in six hospices in the UK and Ireland. Medication is widely used in the last 24 h of life, and use of the parenteral route increases as death approaches. We found that the doses of opioids and other medication do not increase appreciably during this period. The mean dose of opioid in the last 24 h of life was 80 mg oral morphine equivalent/24 h. These results are further evidence that opioids can be used both effectively and safely to manage symptoms at the end of life for people with MND/ALS.
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Systematic analysis of the IgG antibody immune response against varicella zoster virus (VZV) using a self-assembled protein microarray.
Mol Biosyst
PUBLISHED: 06-01-2010
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Varicella zoster virus (VZV) is a human herpesvirus encoding at least 69 distinct viral proteins which causes chickenpox after primary infection and shingles during reactivation and which is particularly important in pregnancy and immunocompromised patients. Current serodiagnostic tests are either based on whole cell lysates or glycoprotein preparations. In order to investigate the humoral immune response to VZV infection or vaccination in more detail, and to improve the currently available diagnostic assays, we developed a nucleic acid programmable protein array (NAPPA) containing all 69 VZV proteins and performed a detailed analysis of 68 sera from individuals with either no, a previous or an acute VZV infection. In addition to the known reactive glycoprotein antigens (ORF 5, ORF 14, ORF 31, ORF 37, ORF 68), we discovered IgG antibodies against a variety of other membrane (ORF 2, ORF 24), capsid (ORF 20, ORF 23, ORF 43) and tegument (ORF 53, ORF 9, ORF 11) proteins, as well as other proteins involved in virus replication and assembly (ORF 25, ORF 26, ORF 28) and the transactivator proteins ORF 12, ORF 62 and ORF 63. All of these antigens were only reactive in a subset of VZV-positive individuals. A subset of the newly identified VZV antigens was validated by western blot analysis. Using these seroreactive new VZV antigens, more sensitive assays and tests distinguishing between different clinical entities may be developed.
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The enigma of soil animal species diversity revisited: the role of small-scale heterogeneity.
PLoS ONE
PUBLISHED: 05-10-2010
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"The enigma of soil animal species diversity" was the title of a popular article by J. M. Anderson published in 1975. In that paper, Anderson provided insights on the great richness of species found in soils, but emphasized that the mechanisms contributing to the high species richness belowground were largely unknown. Yet, exploration of the mechanisms driving species richness has focused, almost exclusively, on above-ground plant and animal communities, and nearly 35 years later we have several new hypotheses but are not much closer to revealing why soils are so rich in species. One persistent but untested hypothesis is that species richness is promoted by small-scale environmental heterogeneity.
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Multi-factorial analysis of class prediction error: estimating optimal number of biomarkers for various classification rules.
J Bioinform Comput Biol
PUBLISHED: 04-14-2010
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Machine learning and statistical model based classifiers have increasingly been used with more complex and high dimensional biological data obtained from high-throughput technologies. Understanding the impact of various factors associated with large and complex microarray datasets on the predictive performance of classifiers is computationally intensive, under investigated, yet vital in determining the optimal number of biomarkers for various classification purposes aimed towards improved detection, diagnosis, and therapeutic monitoring of diseases. We investigate the impact of microarray based data characteristics on the predictive performance for various classification rules using simulation studies. Our investigation using Random Forest, Support Vector Machines, Linear Discriminant Analysis and k-Nearest Neighbour shows that the predictive performance of classifiers is strongly influenced by training set size, biological and technical variability, replication, fold change and correlation between biomarkers. Optimal number of biomarkers for a classification problem should therefore be estimated taking account of the impact of all these factors. A database of average generalization errors is built for various combinations of these factors. The database of generalization errors can be used for estimating the optimal number of biomarkers for given levels of predictive accuracy as a function of these factors. Examples show that curves from actual biological data resemble that of simulated data with corresponding levels of data characteristics. An R package optBiomarker implementing the method is freely available for academic use from the Comprehensive R Archive Network (http://www.cran.r-project.org/web/packages/optBiomarker/).
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Validation of a blood plasma separation system by biomarker detection.
Lab Chip
PUBLISHED: 03-31-2010
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A microfluidic system was developed for blood plasma separation at high flow rate. This system uses only hydrodynamic forces to separate plasma from whole blood. The microfluidic network features a series of constrictions and bifurcations to enhance the product yield and purity. A maximum purity efficiency of 100% is obtained on blood with entrance hematocrit level up to 30% with a flow rate of 2 mL h(-1). Flow cytometry was performed on the extracted plasma to evaluate the separation efficiency and to assess cell damage. A core target of this study was the detection of cell-free DNA from the on-chip extracted plasma. To this effect, PCR was successfully carried out off-chip on the cell-free DNA present in the plasma extracted on-chip. A house-keeping gene sequence (GAPDH) was amplified without the need for a purification after the separation, thereby showing the high quality of the plasma sample. The resulting data suggests that the system can be used as a preliminary module of a total analysis system for cell-free DNA detection in human plasma.
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Probing biomolecular interactions using surface enhanced Raman spectroscopy: label-free protein detection using a G-quadruplex DNA aptamer.
Chem. Commun. (Camb.)
PUBLISHED: 03-02-2010
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We demonstrate a strategy for label-free protein detection through monitoring the Surface Enhanced Raman Spectrum of an aptamer probe attached to a gold nanoshell. Low limit of detection and minimal non-specific binding show potential for in vitro and in vivo assays.
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Degradation of yew, ragwort and rhododendron toxins during composting.
Sci. Total Environ.
PUBLISHED: 01-19-2010
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Recent concerns have been raised that plants such as ragwort (Senecio jacobaea), yew (Taxus baccata) and rhododendron (Rhododendron ponticum) that are toxic to livestock may be included in compost windrows but may not be fully detoxified by the composting process. This study investigates the decomposition during composting of toxic pyrrolizidine alkaloids present in ragwort, taxines (A and B) present in yew, and grayanotoxins (GTX I, II, and III) present in rhododendron during composting. Plant samples were contained within microporous bags either towards the edge or within the centre of a pilot-scale compost heap. They were destructively harvested at regular intervals over 1200 degrees C cumulative temperature (about three months). Samples were analysed for levels of toxins by liquid chromatography time of flight mass spectrometry (LC-TOF-MS). Pyrrolizidine alkaloids and taxines were shown to degrade completely during the composting process. While GTX I showed significant reductions, concentrations of GTX III remained unchanged after 1200 degrees C cumulative temperature. However, estimates of exposure to grazing livestock coming into contact with source-segregated green waste compost containing up to 7% rhododendron suggest that GTX III poses no appreciable risk.
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Palliative care in multiple sclerosis and motor neurone disease.
Br J Hosp Med (Lond)
PUBLISHED: 01-19-2010
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The general physician can help patients and families living with advanced multiple sclerosis and motor neurone disease in a number of practical ways. The key areas requiring a palliative approach are the management of physical symptoms, psychosocial support, decisions around potentially life-prolonging treatments and end-of-life care.
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Detection of single nucleotide polymorphisms using a DNA Holliday junction nanoswitch--a high-throughput fluorescence lifetime assay.
Mol Biosyst
PUBLISHED: 10-19-2009
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We report a simple DNA sensor device, using a combination of binding and conformational switching, capable of rapid detection of specific single nucleotide polymorphisms in an unlabelled nucleic acid target sequence. The detection is demonstrated using fluorescence lifetime measurements in a high-throughput micro plate reader instrument based on the time-correlated single-photon counting technique. The sensor design and instrumental architecture are capable of detecting perturbations in the molecular structure of the probe-target complex (which is similar to that of a Holliday junction), due to a single base pair mismatch in a synthetic target. Structural information, including fluorophore separations, is obtained using time-resolved Förster resonance energy transfer between two fluorophores covalently bound to the probe molecule. The two probes required are designed to detect a single nucleotide polymorphism from a sequence present on each of the two copies of human chromosome 11.
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Nanoshells for surface-enhanced Raman spectroscopy in eukaryotic cells: cellular response and sensor development.
ACS Nano
PUBLISHED: 10-08-2009
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The application of gold nanoshells (NS) as a surface-enhanced Raman (SER) platform for intracellular sensing in NIH-3T3 fibroblast cells was studied by using a near-infrared Raman system. To show the feasibility of using these 151 +/- 5 nm sized solution-stable nanoparticles inside living cells, we investigated the uptake, cellular response, and the health of the cell population. We show that NS are taken up voluntarily and can be found in the cytosol by transmission electron microscopy (TEM), which also provides detailed information about location and immediate surrounding of the NS. The internalization into cells has been found to be independent of active cellular mechanisms, such as endocytosis, and can be suggested to be of passive nature. Uptake of NS into cells can be controlled, and cells show no increase in necrosis or apoptosis as a result; we show that NS-based intracytosolic SER spectra can be measured on biological samples using short acquisition times and low laser powers. We demonstrate its application using 4-mercaptobenzoic acid (4-MBA)-functionalized nanoshells as a pH sensor.
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A DNA nanoswitch incorporating the fluorescent base analogue 2-aminopurine detects single nucleotide mismatches in unlabelled targets.
Analyst
PUBLISHED: 07-13-2009
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DNA nanoswitches can be designed to detect unlabelled nucleic acid targets and have been shown to discriminate between targets which differ in the identity of only one base. This paper demonstrates that the fluorescent base analogue 2-aminopurine (AP) can be used to discriminate between nanoswitches with and without targets and to discriminate between matched and mismatched targets. In particular, we have used both steady-state and time-resolved fluorescence spectroscopy to determine differences in AP environment at the branchpoint of nanoswitches assembled using complementary targets and targets which incorporate single base mismatches.
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Lactic acidosis in a newborn with adrenal calcifications.
Pediatr. Res.
PUBLISHED: 07-08-2009
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A patient is reported who presented in the newborn period with an unusual combination of congenital lactic acidosis and bilateral calcifications in the adrenal medulla, visible on standard abdominal x-ray and ultrasound examination. At birth, the proband was hypotonic and dystrophic. She developed respiratory insufficiency, cardiomegaly, and hepatomegaly and died at the age of 38 d. Examination of postmortem heart muscle revealed multiple areas of myocardial infarction with dystrophic calcifications. In the medulla of the adrenal glands, foci of necrosis and calcifications, and in the liver, multiple zones of necrosis and iron deposition were detected. Biochemical analysis in heart muscle revealed a decreased activity of complex IV of the oxidative phosphorylation (OXPHOS) and in liver a combined deficiency involving the complexes I, III, IV, and V. The findings were suggestive of a defect in biosynthesis of the mitochondrially encoded subunits of the OXPHOS complexes. Extensive analysis of the probands mitochondrial DNA revealed neither pathogenic deletions and point mutations nor copy number alterations. Relative amounts of mitochondrial transcripts for the ribosomal mitochondrial 12S rRNA (12S) and mitochondrial 16S rRNA (16S) were significantly increased suggesting a compensatory mechanism involving the transcription machinery to low levels of translation. The underlying molecular defect has not been identified yet.
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Bayesian unsupervised learning with multiple data types.
Stat Appl Genet Mol Biol
PUBLISHED: 06-05-2009
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We propose Bayesian generative models for unsupervised learning with two types of data and an assumed dependency of one type of data on the other. We consider two algorithmic approaches, based on a correspondence model, where latent variables are shared across datasets. These models indicate the appropriate number of clusters in addition to indicating relevant features in both types of data. We evaluate the model on artificially created data. We then apply the method to a breast cancer dataset consisting of gene expression and microRNA array data derived from the same patients. We assume partial dependence of gene expression on microRNA expression in this study. The method ranks genes within subtypes which have statistically significant abnormal expression and ranks associated abnormally expressing microRNA. We report a genetic signature for the basal-like subtype of breast cancer found across a number of previous gene expression array studies. Using the two algorithmic approaches we find that this signature also arises from clustering on the microRNA expression data and appears derivative from this data.
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Proteomic analysis of DNA-protein cross-linking by antitumor nitrogen mustards.
Chem. Res. Toxicol.
PUBLISHED: 06-02-2009
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Nitrogen mustards are antitumor agents used clinically for the treatment of a variety of neoplastic conditions. The biological activity of these compounds is typically attributed to their ability to induce DNA-DNA cross-links. However, nitrogen mustards are able to produce a variety of other lesions, including DNA-protein cross-links (DPCs). DPCs induced by nitrogen mustards are not well-characterized because of their structural complexity and the insufficient specificity and sensitivity of previously available experimental methodologies. In the present work, affinity capture methodology in combination with mass spectrometry-based proteomics was employed to identify mammalian proteins that form covalent cross-links to DNA in the presence of a simple nitrogen mustard, mechlorethamine. Following incubation of 5-biotinylated DNA duplexes with nuclear protein extracts, DPCs were isolated by affinity capture on streptavidin beads, and the cross-linked proteins were identified by high-performance liquid chromatography-electrospray tandem mass spectrometry of tryptic peptides. Mechlorethamine treatment resulted in the formation of DPCs with nuclear proteins involved in chromatin regulation, DNA replication and repair, cell cycle control, transcriptional regulation, and cell architecture. Western blot analysis was employed to confirm protein identification and to quantify the extent of drug-mediated cross-linking. Mass spectrometry of amino acid-nucleobase conjugates found in total proteolytic digests revealed that mechlorethamine-induced DPCs are formed via alkylation of the N7 position of guanine in duplex DNA and cysteine thiols within the proteins to give N-[2-[S-cysteinyl]ethyl]-N-[2-(guan-7-yl)ethyl]methylamine lesions. The results described herein suggest that cellular exposure to nitrogen mustards leads to cross-linking of a large spectrum of nuclear proteins to chromosomal DNA, potentially contributing to the cytotoxic and mutagenic effects of these drugs.
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Enhanced protein fold recognition through a novel data integration approach.
BMC Bioinformatics
PUBLISHED: 04-16-2009
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Protein fold recognition is a key step in protein three-dimensional (3D) structure discovery. There are multiple fold discriminatory data sources which use physicochemical and structural properties as well as further data sources derived from local sequence alignments. This raises the issue of finding the most efficient method for combining these different informative data sources and exploring their relative significance for protein fold classification. Kernel methods have been extensively used for biological data analysis. They can incorporate separate fold discriminatory features into kernel matrices which encode the similarity between samples in their respective data sources.
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Palliative sedation therapy.
Br J Hosp Med (Lond)
PUBLISHED: 04-10-2009
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It is sometimes not possible to relieve symptoms adequately in dying patients. When all other remedies have failed, sedation can be a useful means to relieve terminal suffering. When used appropriately, palliative sedation does not, and should not, shorten life.
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Fluorescence lifetime imaging of quantum dot labeled DNA microarrays.
Int J Mol Sci
PUBLISHED: 03-04-2009
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Quantum dot (QD) labeling combined with fluorescence lifetime imaging microscopy is proposed as a powerful transduction technique for the detection of DNA hybridization events. Fluorescence lifetime analysis of DNA microarray spots of hybridized QD labeled target indicated a characteristic lifetime value of 18.8 ns, compared to 13.3 ns obtained for spots of free QD solution, revealing that QD labels are sensitive to the spot microenvironment. Additionally, time gated detection was shown to improve the microarray image contrast ratio by 1.8, achieving femtomolar target sensitivity. Finally, lifetime multiplexing based on Qdot525 and Alexa430 was demonstrated using a single excitation-detection readout channel.
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Long term repeated prescribed burning increases evenness in the basidiomycete laccase gene pool in forest soils.
FEMS Microbiol. Ecol.
PUBLISHED: 01-28-2009
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Repeated prescribed burning alters the biologically labile fraction of nutrients and carbon of soil organic matter (SOM). Using a long-term (30 years) repeated burning experiment where burning has been carried out at a 2- or 4-year frequency, we analysed the effect of prescribed burning on gross potential C turnover rates and phenol oxidase activity in relation to shifts in SOM composition as observed using Fourier-transform infrared spectroscopy. In tandem, we assessed the genetic diversity of basidiomycete laccases. While the overall effect of burning was a decline in phenol oxidase activity, Shannon diversity and evenness of laccases was significantly higher in burned sites. Co-correspondence analysis of SOM composition and laccase operational taxonomic unit frequency data also suggested a strong correlation. While this correlation could indicate that the observed increase in laccase genetic diversity due to burning is due to increased resource diversity, a temporal replacement of the most abundant members of the assembly by an otherwise dormant pool of fungi cannot be excluded. As such, our results fit the intermediate disturbance hypothesis. Effects were stronger in plots burned in 2-year rotations, suggesting that the 4-year burn frequency may be a more sustainable practice to ensure the long-term stability of C cycling in such ecosystems.
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Topology of plant-pollinator networks that are vulnerable to collapse from species extinction.
Phys Rev E Stat Nonlin Soft Matter Phys
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The ability to predict the collapse of ecological communities is of significant concern in light of global patterns of rapid species extinctions. Here, we use a recently developed dynamic Boolean network-based model of mutualistic plant-pollinator community formation to investigate the stability of simulated ecological communities in the face of sequential species extinctions. We assess communities in terms of the relative change in biodiversity after species loss, and find that communities that experience a significant loss of biodiversity differ from more robust communities according to a number of topological characteristics. Notably, we show that high nestedness, a property commonly believed to promote community stability, may in extreme circumstances promote a critical over-reliance on individual species. Furthermore, the species important to the survival of the rest of the ecosystem occupy different positions in the network than less important species. Our results suggest that network measures may be applied to real ecosystems to yield insight into both their stability and the identity of potentially critical species.
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Multiplex T-RFLP allows for increased target number and specificity: detection of Salmonella enterica and six species of Listeria in a single test.
PLoS ONE
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A multiplex T-RFLP test was developed to detect and identify Salmonella enterica and all six species of Listeria inoculated into milk at minimal levels. Extensive in silico analysis was used to design a fifteen-primer, six-amplimer methodology and in vitro application showed target organism DNA, when amplified individually, yielded the predicted terminal restriction fragments (TRFs) following digestion. Non-target organisms were either not-amplified or yielded TRFs which did not interfere with target identification. Multiple target DNA analysis gave over 86% detection of total TRFs predicted, and this was improved to over 90% detection of total TRFs predicted when only two target DNA extracts were combined analysed. Co-inoculation of milk with five strains each of the target species of S. enterica and L. monocytogenes, along with five strains of the non-target species E. coli was followed by enrichment in SEL medium for M-TRFLP analysis. This allowed for detection of both target species in all samples, with detection of one S. enterica and two Listeria TRFs in all cases, and detection of a second S. enterica TRF in 91% of cases. This was from an initial inoculum of <5 cfu per 25 ml milk with a background of competing E. coli present, and gave a result from sampling of under 20 hours. The ability to increase target species number without loss of sensitivity means that extensive screening can be performed at reduced cost due to a reduction in the number of tests required.
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Prevalence and survival of potential pathogens in source-segregated green waste compost.
Sci. Total Environ.
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Composting of source-separated green waste (SSGW) is essential to meet the EU Landfill Directive target and agricultural land is considered a significant market for the resulting composts. A critical review of the literature was performed to evaluate the potential for pathogens to enter the composting process via SSGW feedstocks and the likelihood of their survival of the composting process and subsequent application to land. This is discussed in the context of application of other organic wastes to land. It was concluded that zoonoses such as verotoxigenic Escherichia coli and Salmonella spp. are unlikely to survive and effective composting process, whereas spore forming organisms are more resistant to composting but are also ubiquitous in the environment. Adherence to existing guidelines, such as those for farm yard manures, is likely to provide a rational degree of health protection for humans and livestock.
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Cellular redox potential and the biomolecular electrochemical series: a systems hypothesis.
Free Radic. Biol. Med.
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The role of cellular redox potential in the regulation of protein activity is becoming increasingly appreciated and characterized. In this paper we put forward a new hypothesis relating to redox regulation of cellular physiology. We have exemplified our hypothesis using apoptosis since its redox phenomenology is well established, but believe that it is equally applicable to several other pathways. Our hypothesis is that since multiple proteins in the apoptosis pathway are thought to be regulated via oxidation/reduction reactions and since cellular redox potentials have been shown to become progressively more oxidative during apoptosis, that the proteins could be arranged in an electrochemical series where the proteins standard potential correlates with its position in the pathway. Since the most stable oxidation state of the protein is determined by its standard potential and the redox potential of its environment (in a way predictable by the Nernst equation), a quantitative model of the redox regulation of the pathway could be developed. We have outlined our hypothesis, illustrating it using a pathway map which assembles a selection of the literature on apoptosis into a readable graphical format. We have also outlined experimental approaches suitable for testing our hypothesis.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.