Non-use of cancer information services among people experiencing cancer in Ireland.

PURPOSE: The purpose of this study was to explore the reasons for non-use of a national cancer society's cancer information services among people experiencing cancer. METHOD: This study used a qualitative design. Semi-structured interviews were conducted with a total of 17 participants who had not previously utilised the Cancer Society's information services. Data were analysed using Thematic Analysis. RESULTS: The key themes to emerge from the date were 'living in the here and now' and 'awareness of the Cancer Society'. For most participants, not utilising cancer information services was a means of coping with the initial diagnosis and the impact of treatment. Those who progressed to being ready to seek information identified the multi-disciplinary team as the primary source of trusted information, with particular mention of cancer nurse specialists. For participants with children, their role as a parent was central in how they managed their diagnosis. The majority of participants lacked awareness of the range of services provided by the Cancer Society. CONCLUSIONS: Reasons for non-use of cancer information services were identified as: readiness to seek information and a lack of knowledge of the Cancer Societies' services. Cancer information services need to continue make a concerted effort to enhance visibility and awareness of its services to optimise patient engagement.

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity.

BACKGROUND: Deregulated transcription is a major driver of diseases such as cancer. Bromodomain and extra-terminal (BET) proteins (BRD2, BRD3, BRD4 and BRDT) are chromatin readers essential for maintaining proper gene transcription by specifically binding acetylated lysine residues. Targeted displacement of BET proteins from chromatin, using BET inhibitors (I-BETs), is a promising therapy, especially for acute myeloid leukemia (AML), and evaluation of resistance mechanisms is necessary to optimize the clinical efficacy of these drugs. RESULTS: To uncover mechanisms of intrinsic I-BET resistance, we quantified chromatin binding and displacement for BRD2, BRD3 and BRD4 after dose response treatment with I-BET151, in sensitive and resistant in vitro models of leukemia, and mapped BET proteins/I-BET interactions genome wide using antibody- and compound-affinity capture methods followed by deep sequencing. The genome-wide map of BET proteins sensitivity to I-BET revealed a bimodal pattern of binding flanking transcription start sites (TSSs), in which drug-mediated displacement from chromatin primarily affects BRD4 downstream of the TSS and prolongs the pausing of RNA Pol II. Correlation of BRD4 binding and drug-mediated displacement at RNA Pol II pause sites with gene expression revealed a differential behavior of sensitive and resistant tumor cells to I-BET and identified a BRD4 signature at promoters of sensitive coding and non-coding genes. CONCLUSIONS: We provide evidence that I-BET-induced shift of Pol II pausing at promoters via displacement of BRD4 is a determinant of intrinsic I-BET sensitivity. This finding may guide pharmacological treatment to enhance the clinical utility of such targeted therapies in AML and potentially other BET proteins-driven diseases.

The symptom phenotype of oncology outpatients remains relatively stable from prior to through 1 week following chemotherapy.

Some oncology outpatients experience a higher number of and more severe symptoms during chemotherapy (CTX). However, little is known about whether this high risk phenotype persists over time. Latent transition analysis (LTA) was used to examine the probability that patients remained in the same symptom class when assessed prior to the administration of and following their next dose of CTX. For the patients whose class membership remained consistent, differences in demographic and clinical characteristics, and quality of life (QOL) were evaluated. The Memorial Symptom Assessment Scale (MSAS) was used to evaluate symptom burden. LTA was used to identify subgroups of patients with distinct symptom experiences based on the occurrence of the MSAS symptoms. Of the 906 patients evaluated, 83.9% were classified in the same symptom occurrence class at both assessments. Of these 760 patients, 25.0% were classified as Low-Low, 44.1% as Moderate-Moderate and 30.9% as High-High. Compared to the Low-Low class, the other two classes were younger, more likely to be women and to report child care responsibilities, and had a lower functional status and a higher comorbidity scores. The two higher classes reported lower QOL scores. The use of LTA could assist clinicians to identify higher risk patients and initiate more aggressive interventions.

Principal components analysis: an innovative approach to establish interferences in ochratoxin A detection.

This work aimed to establish an innovative approach to evaluate the effect of cereals composition on ochratoxin A extraction by multivariate analysis. Principal components analysis was applied to identify the effect of major matrix components on the recovery of ochratoxin A by QuEChERS method using HPTLC and HPLC, and to validate the method for ochratoxin A determination in wheat flour by HPLC. The matrices rice bran, wheat bran and wheat flour were characterized for their physical and chemical attributes. The ochratoxin A recovery in these matrices was highly influenced (R=0.99) by the sugar content of the matrix, while the lipids content showed a minor interference (R=0.29). From these data, the QuEChERS method was standardized for extracting ochratoxin A from flour using 1% ACN:water (2:1) as extraction solvent and dried magnesium sulfate and sodium chloride as salts. The recovery values ranged from 97.6% to 105%. The validated method was applied to evaluate natural occurrence of ochratoxin A in 20 wheat flour samples, which were contaminated with ochratoxin A levels in the range of 0.22-0.85 µg kg(-1).

Concentrations of hormones, pharmaceuticals and other micropollutants in groundwater affected by septic systems in New England and New York.

Septic-system discharges can be an important source of micropollutants (including pharmaceuticals and endocrine active compounds) to adjacent groundwater and surface water systems. Groundwater samples were collected from well networks tapping glacial till in New England (NE) and sandy surficial aquifer New York (NY) during one sampling round in 2011. The NE network assesses the effect of a single large septic system that receives discharge from an extended health care facility for the elderly. The NY network assesses the effect of many small septic systems used seasonally on a densely populated portion of Fire Island. The data collected from these two networks indicate that hydrogeologic and demographic factors affect micropollutant concentrations in these systems. The highest micropollutant concentrations from the NE network were present in samples collected from below the leach beds and in a well downgradient of the leach beds. Total concentrations for personal care/domestic use compounds, pharmaceutical compounds and plasticizer compounds generally ranged from 1 to over 20 µg/L in the NE network samples. High tris(2-butoxyethyl phosphate) plasticizer concentrations in wells beneath and downgradient of the leach beds (>20 µg/L) may reflect the presence of this compound in cleaning agents at the extended health-care facility. The highest micropollutant concentrations for the NY network were present in the shoreline wells and reflect groundwater that is most affected by septic system discharges. One of the shoreline wells had personal care/domestic use, pharmaceutical, and plasticizer concentrations ranging from 0.4 to 5.7 µg/L. Estradiol equivalency quotient concentrations were also highest in a shoreline well sample (3.1 ng/L). Most micropollutant concentrations increase with increasing specific conductance and total nitrogen concentrations for shoreline well samples. These findings suggest that septic systems serving institutional settings and densely populated areas in coastal settings may be locally important sources of micropollutants to adjacent aquifer and marine systems.

Reduction of aflatoxins by Rhizopus oryzae and Trichoderma reesei.

This study evaluated the ability of the microorganisms Rhizopus oryzae (CCT7560) and Trichoderma reesei (QM9414), producers of generally recognized as safe (GRAS) enzymes, to reduce the level of aflatoxins B1, B2, G1, G2, and M1. The variables considered to the screening were the initial number of spores in the inoculum and the culture time. The culture was conducted in contaminated 4 % potato dextrose agar (PDA) medium, and the residual mycotoxins were determined every 24 h by HPLC-FL. The fungus R. oryzae has reduced aflatoxins B1, B2, and G1 in the 96 h and aflatoxins M1 and G2 in the range of 120 h of culture by approximately 100 %. The fungus T. reesei has reduced aflatoxins B1, B2, and M1 in the 96 h and aflatoxin G1 in the range of 120 h of culture by approximately 100 %. The highest reduction occurred in the middle of R. oryzae culture.

Aflatoxin B1 and M1 in milk.

The aflatoxin M1 (AFLAM1) is a mycotoxin that results from the hydroxylation of the aflatoxin B1 (AFLAB1). It contaminates the milk of animals fed with a diet containing its precursor. In this work, we determined the occurrence of AFLAB1 and AFLAM1 in milk, as well as the chromatographic conditions to quantify these mycotoxins. The extraction and quantification of AFLAB1 and AFLAM1 in naturally contaminated and artificially spiked milk samples which are produced and marketed in the state of RS were performed using the AOAC official method and UHPLC with fluorescence detection. We obtained a separation factor of 2.3 for AFLAB1 and AFLAM1 using a mobile phase consisting of 1% acetic acid:acetonitrile:methanol (55:10:35). The analytical curves had a wide linearity range and the limit of quantification (LOQm) concentrations of AFLAB1 and AFLAM1 were equal to 0.5 and 0.25 µg L(-1), respectively. Samples of pasteurized and ultra-high-temperature processed (UHT) milk showed natural contamination, and the levels for both aflatoxins ranged from 0.7 to 1.5 µg L(-1). Raw and concentrated milk samples only contained AFLAM1, with a maximum average concentration of 1.7 µg L(-1). These concentrations, higher than permitted by legislation, confirm the existence of a health risk, as well as highlight the relevance of searching for alternatives to reduce this contamination.

Polycyclic aromatic hydrocarbons in rice grain dried by different processes: evaluation of a quick, easy, cheap, effective, rugged and safe extraction method.

This study aims at developing a method for the determination of 16 polycyclic aromatic hydrocarbons (PAHs) in rice grain samples by combining the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method and determination by gas chromatography-mass spectrometry (GC-EI-MS). Quantification limits ranging from 1 to 5µgkg(-1) were obtained. Recoveries ranged from 70% to 106% for most of the 16 PAHs under analysis. The optimised methodology was applied to assess safety concerning the content of PAHs in white and parboiled rice samples, dried by gas and wood burning. Although benzo(a)pyrene, the marker used for evaluating the carcinogenic risk of PAHs in food, was not detected in the samples, naphthalene and phenanthrene were detected in all of them. Since cereals have been shown to be an important source of PAHs in the diet, methods that perform the evaluation of the quality of this food group become relevant.

Waste-indicator and pharmaceutical compounds in landfill-leachate-affected ground water near Elkhart, Indiana, 2000-2002.

Four wells downgradient from a landfill near Elkhart, Indiana were sampled during 2000-2002 to evaluate the presence of waste-indicator and pharmaceutical compounds in landfill-leachate-affected ground water. Compounds detected in leachate-affected ground water included detergent metabolites (p-nonylphenol, nonylphenol monoethoxylate, nonylphenol diethoxylate, and octylphenol monoethoxylate), plasticizers (ethanol-2-butoxy-phosphate and diethylphthalate), a plastic monomer (bisphenol A), disinfectants (1,4-dichlorobenzene and triclosan), an antioxidant (5-methyl-1H-benzotriazole), three fire-retardant compounds (tributylphosphate and tri(2-chloroethyl)phosphate, and tri(dichlorisopropyl)phosphate), and several pharmaceuticals and metabolites (acetaminophen, caffeine, cotinine, 1,7-dimethylxanthine, fluoxetine, and ibuprofen). Acetaminophen, caffeine, and cotinine detections confirm prior indications of pharmaceutical and nicotinate disposal in the landfill.

Raking it in: the impact of enculturation on chimpanzee tool use.

Recent evidence for different tool kits, proposed to be based upon culture-like transmission, have been observed across different chimpanzee communities across Western Africa. In light of these findings, the reported failures by seven captive juvenile chimpanzees tested with 27 tool use tasks (Povinelli 2000) seem enigmatic. Here we report successful performance by a group of nine captive, enculturated chimpanzees, and limited success by a group of six semi-enculturated chimpanzees, on two of the Povinelli tasks, the Flimsy Tool task, and the Hybrid Tool task. All chimpanzees were presented with a rake with a flimsy head and a second rake with a rigid head, either of which could be used to attempt to retrieve a food reward that was out of reach. The rigid rake was constructed such that it had the necessary functional features to permit successful retrieval, while the flimsy rake did not. Both chimpanzee groups in the present experiment selected the functional rigid tool correctly to use during the Flimsy Tool task. All animals were then presented with two "hybrid rakes" A and B, with one half of each rake head constructed from flimsy, non-functional fabric, and the other half of the head was made of wood. Food rewards were placed in front of the rigid side of Rake A and the flimsy side of Rake B. To be successful, the chimps needed to choose the rake that had the reward in front of the rigid side of the rake head. The fully enculturated animals were successful in selecting the functional rake, while the semi-enculturated subjects chose randomly between the two hybrid tools. Compared with findings from Povinelli, whose non-enculturated animals failed both tasks, our results demonstrate that chimpanzees reared under conditions of semi-enculturation could learn to discriminate correctly the necessary tool through trial-and-error during the Flimsy Tool task, but were unable to recognize the functional relationship necessary for retrieving the reward with the "hybrid" rake. In contrast, the enculturated chimpanzees were correct in their choices during both the Flimsy Tool and the Hybrid Tool tasks. These results provide the first empirical evidence for the differential effects of enculturation on subsequent tool use capacities in captive chimpanzees.

Comparison of a novel passive sampler to standard water-column sampling for organic contaminants associated with wastewater effluents entering a New Jersey stream.

Four water samples collected using standard depth and width water-column sampling methodology were compared to an innovative passive, in situ, sampler (the polar organic chemical integrative sampler or POCIS) for the detection of 96 organic wastewater-related contaminants (OWCs) in a stream that receives agricultural, municipal, and industrial wastewaters. Thirty-two OWCs were identified in POCIS extracts whereas 9-24 were identified in individual water-column samples demonstrating the utility of POCIS for identifying contaminants whose occurrence are transient or whose concentrations are below routine analytical detection limits. Overall, 10 OWCs were identified exclusively in the POCIS extracts and only six solely identified in the water-column samples, however, repetitive water samples taken using the standard method during the POCIS deployment period required multiple trips to the sampling site and an increased number of samples to store, process, and analyze. Due to the greater number of OWCs detected in the POCIS extracts as compared to individual water-column samples, the ease of performing a single deployment as compared to collecting and processing multiple water samples, the greater mass of chemical residues sequestered, and the ability to detect chemicals which dissipate quickly, the passive sampling technique offers an efficient and effective alternative for detecting OWCs in our waterways for wastewater contaminants.

Structural analysis of a set of proteins resulting from a bacterial genomics project.

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.

A holistic passive integrative sampling approach for assessing the presence and potential impacts of waterborne environmental contaminants.

As an integral part of our continuing research in environmental quality assessment approaches, we have developed a variety of passive integrative sampling devices widely applicable for use in defining the presence and potential impacts of a broad array of contaminants. The semipermeable membrane device has gained widespread use for sampling hydrophobic chemicals from water and air, the polar organic chemical integrative sampler is applicable for sequestering waterborne hydrophilic organic chemicals, the stabilized liquid membrane device is used to integratively sample waterborne ionic metals, and the passive integrative mercury sampler is applicable for sampling vapor phase or dissolved neutral mercury species. This suite of integrative samplers forms the basis for a new passive sampling approach for assessing the presence and potential toxicological significance of a broad spectrum of environmental contaminants. In a proof-of-concept study, three of our four passive integrative samplers were used to assess the presence of a wide variety of contaminants in the waters of a constructed wetland, and to determine the effectiveness of the constructed wetland in removing contaminants. The wetland is used for final polishing of secondary-treatment municipal wastewater and the effluent is used as a source of water for a state wildlife area. Numerous contaminants, including organochlorine pesticides, polycyclic aromatic hydrocarbons, organophosphate pesticides, and pharmaceutical chemicals (e.g., ibuprofen, oxindole, etc.) were detected in the wastewater. Herein we summarize the results of the analysis of the field-deployed samplers and demonstrate the utility of this holistic approach.

Fish Balistes capriscus skin extract-induced relaxation in mesenteric arterial bed of rat.

The vasorelaxing activity of the aqueous extract of fish Balistes capriscus skin (AEBc) on mesenteric arterial bed (MAB) of rats was studied. The bolus injections of AEBc (bolus of 5.1, 10.2, 20.5, and 41.1mg) significantly inhibited, in a concentration-dependent manner, the maximal contractile response induced by methoxamine (30 microM) in MAB. The vasodilatation action of AEBc is not mediated through beta-adrenoceptors or cyclo-oxigenase, since it was not affected by propranolol (20 microM) or diclofenac sodium (3 microM). The vasodilator response induced by subsequent addition of AEBc Balistes capriscus in bolus was significantly reduced in water infusion for endothelium removal. Treatment with an inhibitor of NO synthase (L-NAME, 10 microM) decreased AEBc effect. The guanylate cyclase inhibitor methylene blue (MB, 100 microM) had no significant effect on AEBc-induced vasodilatation. These results suggest that the vasorelaxing effect of AEBc is mediated by endothelium-dependent (NO/EDRF) and endothelium-independent neurally induced vasorelaxation from nonadrenergic and noncholinergic nerves (NO).

Patterns of gene expression during Drosophila mesoderm development.

The transcription factor Twist initiates Drosophila mesoderm development, resulting in the formation of heart, somatic muscle, and other cell types. Using a Drosophila embryo sorter, we isolated enough homozygous twist mutant embryos to perform DNA microarray experiments. Transcription profiles of twist loss-of-function embryos, embryos with ubiquitous twist expression, and wild-type embryos were compared at different developmental stages. The results implicate hundreds of genes, many with vertebrate homologs, in stage-specific processes in mesoderm development. One such gene, gleeful, related to the vertebrate Gli genes, is essential for somatic muscle development and sufficient to cause neural cells to express a muscle marker.

Identification of alkyl dimethylbenzylammonium surfactants in water samples by solid-phase extraction followed by ion trap LC/MS and LC/MS/MS.

A novel methodology was developed for the determination of alkyl (C12, C14, and C16) dimethylbenzylammonium chloride (benzalkonium chloride or BAC, Chemical Abstract Service number: 8001-54-5) in water samples. This method is based on solid-phase extraction (SPE) using polymeric cartridges, followed by high-performance liquid chromatography/ion trap mass spectrometry (LC/MS) and tandem mass spectrometry(MS/MS) detection, equipped with an electrospray interface in positive ion mode. Chromatographic separation was achieved for three BAC homologues by using a C18 column and a gradient of acetonitrile/10 millimolar aqueous ammonium formate. Total method recoveries were higher than 71% in different water matrices. The main ions observed by LC/MS were at mass-to-charge ratios (m/z) of 304, 332, and 360, which correspond to the molecular ions of the C12, C14, and C16 alkyl BAC, respectively. The unequivocal structural identification of these compounds in water samples was performed by LC/MS/MS after isolation and subsequent fragmentation of each molecular ion. The main fragmentation observed for the three different homologues corresponded to the loss of the toluyl group in the chemical structure, which leads to the fragment ions at m/z 212, 240, and 268 and a tropylium ion, characteristic of all homologues, at m/z 91. Detection limits for the methodology developed in this work were in the low nanogram-per-liter range. Concentration levels of BAC--ranging from 1.2 to 36.6 micrograms per liter--were found in surface-water samples collected downstream from different wastewater-treatment discharges, thus indicating its input and persistence through the wastewater-treatment process.

A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs.

BACKGROUND: Quorum sensing is the mechanism by which bacteria control gene expression in response to cell density. Two major quorum-sensing systems have been identified, system 1 and system 2, each with a characteristic signaling molecule (autoinducer-1, or AI-1, in the case of system 1, and AI-2 in system 2). The luxS gene is required for the AI-2 system of quorum sensing. LuxS and AI-2 have been described in both Gram-negative and Gram-positive bacterial species and have been shown to be involved in the expression of virulence genes in several pathogens. RESULTS: The structure of the LuxS protein from three different bacterial species with resolutions ranging from 1.8 A to 2.4 A has been solved using an X-ray crystallographic structural genomics approach. The structure of LuxS reported here is seen to have a new alpha-beta fold. In all structures, an equivalent homodimer is observed. A metal ion identified as zinc was seen bound to a Cys-His-His triad. Methionine was found bound to the protein near the metal and at the dimer interface. CONCLUSIONS: These structures provide support for a hypothesis that explains the in vivo action of LuxS. Specifically, acting as a homodimer, the protein binds a methionine analog, S-ribosylhomocysteine (SRH). The zinc atom is in position to cleave the ribose ring in a step along the synthesis pathway of AI-2.

Detection of bacteria from biological mixtures using immunomagnetic separation combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

A rapid method for identifying specific bacteria from complex biological mixtures using immunomagnetic separation coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been developed. The technique employs commercially available magnetic beads coated with polycolonal antibodies raised against specific bacteria and whole cell analysis by MALDI-MS. A suspension of a bacterial mixture is mixed with the immunomagnetic beads specific for the target microorganism. After a short incubation period (20 mins) the bacteria captured by the beads are washed, resuspended in deionized H(2)O and directly applied onto a MALDI probe. Liquid suspensions containing bacterial mixtures can be screened within 1 h total analysis time. Positive tests result in the production of a fingerprint mass spectrum primarily consisting of protein biomarkers characteristic of the targeted microorganism. Using this procedure, Salmonella choleraesuis was isolated and detected from standard bacterial mixtures and spiked samples of river water, human urine, and chicken blood.

Occurrence and potential adverse effects of semivolatile organic compounds in streambed sediment, United States, 1992-1995.

The occurrence and potential adverse effects of select semivolatile organic compounds (SVOCs) in streambed sediment were assessed at 536 sites in 20 major river basins across the United States from 1992 to 1995. Fifty-six SVOCs were detected at one or more sites, and one or more SVOCs were detected at 71% of sites. The northeastern and Great Lakes regions and large metropolitan areas have the highest SVOC concentrations. Polycyclic aromatic hydrocarbons (PAHs) were detected most frequently and at the highest concentrations. Concentrations of PAHs and phthalates were about 10 times higher at sites influenced by urban activities than at sites in other land-use areas. Semivolatile organic compounds were significantly (alpha = 0.05) correlated with land use and population density, and PAHs also correlated with physical/chemical properties. On the basis of sediment-quality guidelines, adverse effects are probable at 7.5% and possible at 16.2% of the sites. Most of the potential for adverse effects is due to PAHs. The median percentage of urban land use was 8% at sites with possible adverse effects and 16% at sites with probable adverse effects. Urbanization profoundly affects sediment quality, even though it comprised a small percentage of most drainage basins.