Monitoring river water quality with transplanted bryophytes: A methodological review

The aim of this literature review, which considers 47 articles published between 1989 and 2015, is to ascertain the current status of the active biomonitoring technique for assessing water quality and to evaluate the degree to which different aspects of the method have been standardized. Use of the tool is largely limited to Europe (83% of the articles reviewed). The technique has been used to biomonitor inorganic contaminants (in 96% of the studies) and, to a lesser extent, organic contaminants (4% of the studies). Only 25% of the articles concern methodological aspects of the technique. Moreover, most authors (78%) have only published one article on the topic, and many different protocols have been used in the various studies. As a result, the technique is not standardized, which hampers comparison of the results of different studies. We propose a protocol that would facilitate use of the technique for routine monitoring of the quality of river waters.     

Bioavailability of Soil-Borne Chemicals: Abiotic Assessment Tools

The abiotic tools that are available, or under development, for evaluating the oral and dermal bioavailability of contaminants from soils are described in this article. These tools generally rely on one of two approaches: (1) characterizing the form of the contaminant and the chemical binding of the contaminant to the soil matrix, and (2) chemical extractions intended to evaluate the fraction of the chemical that would be liberated in biological fluids (gastrointestinal fluid or sweat). For the purpose of human health risk assessment, abiotic methods to estimate the bioavailability of inorganic contaminants in soil are considered generally to be “screening” level tools at this time. Development work for physiologically based extraction tests (PBETs) is ongoing for many inorganic contaminants, and these methods hold great promise for eventual use in making quantitative bioavailability adjustments in risk assessment. The availability of abiotic tools to evaluate the bioavailability of organic contaminants from soils lags behind that for metals, due to the difficulty in conducting in vivo bioavailability studies with organic compounds and their complex interactions with soil. However, considerable research is being conducted in this field, and new assessment tools are being validated for use in human health risk assessment.     

Oxidative effects of inorganic and organic contaminants on haemolymph of mussels

We applied a newly-established method in haemolymph of mussels, Mytilus galloprovincialis, exposed to different concentrations of heavy metals, such as zinc and cadmium and organic pollutants, such as PAHs and lindane, for the detection of total antioxidant capacity (TAC). The susceptibility of exposed mussels was increased in relation to oxidative stress induced by contaminants tested. Oxidative modifications of proteins were estimated by measuring protein carbonyl content (PCC) and malondialdehyde levels (MDA). For PCC measurement, a highly sensitive and accurate ELISA method, which requires only 5 µg of protein, was used. The significant increase of PCC and MDA in haemolymph of exposed mussels reinforces its role as biomarkers of oxidative stress. Significant correlation of TAC assay, PCC and MDA was conducted in order to evaluate the utility of PCC and TAC assay, used in the present study, as tools for determining oxidative effects of pollutants in mussels. The results reinforce the application of PCC method as useful tool for the determination of PCC alterations in haemolymph of mussels exposed to different levels of contaminants. In addition, the TAC method gives encouraging results, concerning its ability to predict antioxidant efficiency in haemolymph of mussels exposed to inorganic and organic contaminants.     

Systematic review of cost effectiveness studies of telemedicine interventions

ObjectivesTo systematically review cost benefit studies of telemedicine.DesignSystematic review of English language, peer reviewed journal articles.Results557 articles without cost data categorised by topic. 55 articles with data initially categorised by cost variables employed in the study and conclusions. Only 24/55 (44%) studies met quality criteria justifying inclusion in a quality review. 20/24 (83%) restricted to simple cost comparisons. No study used cost utility analysis, the conventional means of establishing the “value for money” that a therapeutic intervention represents. Only 7/24 (29%) studies attempted to explore the level of utilisation that would be needed for telemedicine services to compare favourably with traditionally organised health care. None addressed this question in sufficient detail to adequately answer it. 15/24 (62.5%) of articles reviewed here provided no details of sensitivity analysis, a method all economic analyses should incorporate.ConclusionThere is no good evidence that telemedicine is a cost effective means of delivering health care.

What is already known on this topic

The use of telemedicine has garnered much attention in the past decadeHundreds of articles have been published claiming that telemedicine is cost effectiveHowever, missing from the literature is a synthesis or meta-analysis of these publications

What this study adds

A comprehensive literature search of cost related articles on telemedicine identified more than 600 articles, but only 9% contained any cost benefit dataOnly 4% of these articles met quality criteria justifying inclusion in a formalised quality review, and most of these were small scale, short term, pragmatic evaluations with few generalisable conclusionsThere is little published evidence to confirm whether or not telemedicine is a cost effective alternative to standard healthcare delivery     

Phytoremediation—An Overview

The use of plants (directly or indirectly) to remediate contaminated soil or water is known as phytoremediation. This technology has emerged as a more cost effective, noninvasive, and publicly acceptable way to address the removal of environmental contaminants. Plants can be used to accumulate inorganic and organic contaminants, metabolize organic contaminants, and encourage microbial degradation of organic contaminants in the root zone. Widespread utilization of phytoremediation can be limited by the small habitat range or size of plants expressing remediation potential, and insufficient abilities of native plants to tolerate, detoxify, and accumulate contaminants. A better understanding and appreciation of the potential mechanisms for removing contaminants from the root zone and the interaction between plants, microorganisms, and contaminants will be useful in extending the application of phytoremediation to additional contaminated sites.     

Individual patient data meta-analysis of acupuncture for chronic pain: protocol of the Acupuncture Trialists' Collaboration

Objectives

To evaluate the use and reporting of adjusted analysis in randomised controlled trials (RCTs) and compare the quality of reporting before and after the revision of the CONSORT Statement in 2001.

Design

Comparison of two cross sectional samples of published articles.

Data Sources

Journal articles indexed on PubMed in December 2000 and December 2006.

Study Selection

Parallel group RCTs with a full publication carried out in humans and published in English

Main outcome measures

Proportion of articles reported adjusted analysis; use of adjusted analysis; the reason for adjustment; the method of adjustment and the reporting of adjusted analysis results in the main text and abstract.

Results

In both cohorts, 25% of studies reported adjusted analysis (84/355 in 2000 vs 113/422 in 2006). Compared with articles reporting only unadjusted analyses, articles that reported adjusted analyses were more likely to specify primary outcomes, involve multiple centers, perform stratified randomization, be published in general medical journals, and recruit larger sample sizes. In both years a minority of articles explained why and how covariates were selected for adjustment (20% to 30%). Almost all articles specified the statistical methods used for adjustment (99% in 2000 vs 100% in 2006) but only 5% and 10%, respectively, reported both adjusted and unadjusted results as recommended in the CONSORT guidelines.

Conclusion

There was no evidence of change in the reporting of adjusted analysis results five years after the revision of the CONSORT Statement and only a few articles adhered fully to the CONSORT recommendations.     

Modified low‐salt CTAB extraction of high‐quality DNA from contaminant‐rich tissues

The increasing use of high‐throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that coprecipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often coprecipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low‐salt CTAB (MoLSC) extraction protocol to accommodate contaminant‐rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle. Comparisons of purity and molecular integrity showed that our in‐house protocol yielded genomic DNA generally free of contaminants and shearing, whereas the traditional CTAB method and some of the commercial kits yielded DNA unsuitable for some applications of massively parallel sequencing. Our open‐source MoLSC protocol provides a cost‐effective, scalable, alternative DNA extraction method that can be easily optimized and adapted for sequencing applications in other contaminant‐rich samples.     

Study Design and Quality of Reporting of Randomized Controlled Trials of Chronic Idiopathic or Autoimmune Urticaria: Review

Background

The recommended first-line therapy of chronic urticaria is second-generation antihistamines, but the modalities of treatment remains unclear. Numerous recommendations with heterogeneous conclusions have been published. We wondered whether such heterogeneous conclusions were linked to the quality of published studies and their reporting.

Objective

To review the study design and quality of reporting of randomized control trials investigating pharmacological treatment of autoimmune or idiopathic chronic urticaria.

Methodology/Principal Findings

MEDLINE and EMBASE were searched for pharmacological randomized controlled trials involving patients with chronic autoimmune or idiopathic urticaria, with the main outcome being treatment efficacy. Data were collected on general characteristics of the studies, internal validity, studied treatments, design of the trial, outcome measures and “spin” strategy in interpreting results. Spin was defined as use of specific reporting strategies to highlight that the experimental treatment is beneficial, despite statistically nonsignificant results. We evaluated 52 articles that met our criteria. Patients were reported as blinded in 42 articles (81%) and the outcome assessor was blinded in 37 (71%). A placebo was the only comparator in 13 (25%) studies. The study duration was <8 weeks in 39 articles (75%), with no follow-up after discontinuation of treatment in 37 (71%). In 4 articles (8%), blinding was clear because they described blinding of the outcome assessor, the treatment was not recognizable (identical or double-dummy) or had no major secondary effects, and computed randomization was centralized. The primary outcome was specified in 33 articles (63%) and was a score in 31. In total, 15 different scores were used. A spin strategy was used for 10 of 12 studies with a nonsignificant primary outcome.

Conclusion

For establishing guidelines in treatment of chronic urticaria, studies should focus on choosing clinically relevant and reproducible primary outcomes, long-term follow-up, limited use of placebo and avoiding spin strategies.     

Soil washing improves the recovery of total community DNA from polluted and high organic content sediments

Treatment of soil with surfactants and chelating agents is used in bioremediation studies to desorb and solubilize contaminants to increase their bioavalability to microorganisms. In the same way that pollutants are made more bioavailable to microorganisms, the procedure can be used to remove potential interfering materials from soil prior to cell lysis and extraction of DNA from indigenous microorganisms. The effect of soil washing was evaluated by extracting DNA from sediments of an intertidal freshwater wetland contaminated with hydrocarbons and from highly contaminated marine sediments from Sydney Harbour, Nova Scotia, Canada. Sediment samples had total organic carbon (TOC) contents that varied between 0.2% and 13%. The chemical lysis technique was also examined by comparison of an ammonium acetate precipitation of proteins and humic acids with a hexadecyltrimethylammonium bromide (CTAB) incubation and phenol:chloroform extraction. In this study, the incorporation of soil washing steps facilitated the desorption of contaminants from sediment surfaces and improved the recovery of DNA of amplifiable quality from both freshwater and marine sediments. CTAB contributed only slightly to the recovery of DNA of higher quality in the most contaminated sample from Sydney Harbour and was concomitant with a decrease in DNA yield in both sediment types. The incorporation of a soil washing step prior to the extraction of DNA from polluted environments may be important to solubilize and remove contaminants when high-quality DNA is required for subsequent analyses.     

Signal enhancement in DNA microarray using dye doped silica nanoparticles: application to human papilloma virus (HPV) detection

DNA microarray is a powerful tool for the parallel of nucleic acids and other biologically significant molecules. In this communication we report an easy and cheap synthesis route for incorporating organic dyes into monodisperse inorganic silica nanoparticles and their application on the detection of carcinogenic risky Human Papilloma Virus using DNA microarray technology. We correlate our system with conventional direct dyes and commercial quantum dots, with a promising increase in optical signal, and a related decrease of the limit of detection, thus giving a remarkable improvement in this technique towards early diagnosis of diseases and trace level detection of dangerous biological contaminants.     

Estimating the availability of polycyclic aromatic hydrocarbons for bioremediation of creosote contaminated soils

Bioremediation of soil contaminated by organic compounds can remove the contaminants to a large extent, but residual contamination levels may remain which are not or only slowly biodegraded. Residual levels often exceed existing clean-up guidelines and thereby limit the use of bioremediation in site clean-up. A method for estimating the expected residual levels would be a useful tool in the assessment of the feasability of bioremediation. In this study, three soil types from a creosote-contaminated field site, which had been subjected to 6 months of bioremediation in laboratory column studies, were used to characterize the residual contamination levels and assess their availability for biodegradation. The soils covered a wide range of organic carbon levels and particle size distributions. Results from the biodegradation studies were compared with desorption rate measurements and selective extractability using butanol. Residual levels of polycyclic aromatic hydrocarbons after bioremediation were found to be strongly dependent on soil type. The presence of both soil organic matter and asphaltic compounds in the soil was found to be associated with higher residual levels. Good agreement was found between the biodegradable fraction and the rapidly desorbable fraction in two of the three soils studied. Butanol extraction was found to be a useful method for roughly estimating the biodegradable fraction in the soil samples. The results indicate that both desorption and selective extraction measurements could aid the assessment of the feasability for bioremediation and identifying acceptable end-points. Received: 15 September 1999 / Received revision: 7 February 2000 / Accepted: 13 February 2000     

Measurement of Oxygen Demand of Petroleum Hydrocarbon-Contaminated Groundwater

The standard biological oxygen demand (BOD) test was modified for application to petroleum hydrocarbon-contaminated groundwater. The goal was to assess the potential oxygen demand of plume constituents as part of a field trial investigating oxygen-enhanced in situ bioremediation. Modifications to standard BOD protocol included the use of an adapted microbial population developed from site groundwater and methods to minimize both the loss of volatile compounds and the exposure of samples to air. Results from this study indicated that the measured oxygen demand was significantly greater than the oxygen demand estimated solely by stoichiometric calculations from the concentrations of the analytes of typical regulatory concern, that is, benzene, toluene, ethylbenzene, and xylenes (BTEX). This is not surprising, because the petroleum hydrocarbon sources typically contain many organic contaminants other than BTEX, as well as potentially oxidizable natural dissolved organic matter and inorganic species typically present in hydrocarbon plumes. However, in practice, estimation of the total oxygen demand of a contaminated groundwater by exhaustive analyses of all oxidizable or aerobically degradable species typically will be infeasible. The modified BOD test may be a simple, low-cost, useful tool when assessing the potential for natural attenuation by aerobic biodegradation or designing methods to supply oxygen for enhanced aerobic bioremediation.     

Compound-Specific Stable Isotope Analysis: Implications in Hexachlorocyclohexane in-vitro and Field Assessment

Assessment of biotic and abiotic degradation reactions by studying the variation in stable isotopic compositions of organic contaminants in contaminated soil and aquifers is being increasingly considered during the last two decades with development of Compound specific stable isotope analysis (CSIA) technique. CSIA has been recognized as a potential tool for evaluating both qualitative and quantitative degradation with measurement of shifts in isotope ratios of contaminants and their degradation products as its basis. Amongst a wide variety of environmental pollutants including monoaromatics, chlorinated ethenes and benzenes etc., it is only recently that its efficacy is being tested for assessing biodegradation of a noxious pollutant namely hexachlorocyclohexane (HCH), by pure microbial cultures as well as directly at the field site. Anticipating the increase in demand of this technique for monitoring the microbial degradation along with natural attenuation, this review highlights the basic problems associated with HCH contamination emphasizing the applicability of emerging CSIA technique to absolve the major bottlenecks in assessment of HCH. To this end, the review also provides a brief overview of this technique with summarizing the recent revelations put forward by both in vitro and in situ studies by CSIA in monitoring HCH biodegradation.     

Health Reporting in Print Media in Lebanon: Evidence,Quality and Role in Informing Policymaking

Background

Media plays a vital role in shaping public policies and opinions through disseminating health-related information. This study aims at exploring the role of media in informing health policies in Lebanon, identifying the factors influencing health reporting and investigating the role of evidence in health journalism and the quality of health reporting. It also identifies strategies to enhance the use of evidence in health journalism and improve the quality of health reporting.

Methods

Media analysis was conducted to assess the way media reports on health-related issues and the quality of reporting using a quality assessment tool. Semi-structured interviews were also conducted with 27 journalists, researchers and policymakers to explore their perception on the role of media in health policymaking and the factors influencing health reporting. In addition, a validation workshop was conducted.

Results

Out of 1,279 health-related news articles identified, 318 articles used certain type of evidence to report health issues 39.8% of which relied on experts’ opinions as their source of evidence while only 5.9% referenced peer-reviewed research studies. The quality of health reporting was judged to be low based on a quality assessment tool consisting of a set of ten criteria. Journalists raised concerns about issues impeding them from referring to evidence. Journalists also reported difficulties with the investigative health journalism. Policymakers and researchers viewed media as an important tool for evidence-informed health policies, however, serious concerns were voiced in terms of the current practice and capacities.

Conclusion

Our study provides a structured reflection on the role of media and the factors that influence health reporting including context-specific strategies that would enhance the quality and promote the use of evidence in health reporting. In the light of the political changes in many Middle Eastern countries, findings from this study can contribute to redefining the role of media in strengthening health systems.     

A Simple and Rapid Computer-assisted Technique for the Identification of some Selected Bacillus Species using Biochemical Tests

A computer-assisted probabilistic identification technique was developed to identify species of the genus Bacillus known to be potentially pathogenic and/or frequently found as contaminants in pharmaceutical preparations. An identification matrix on 18 species of the genus Bacillus was constructed. Twenty-four biochemical tests were used. The reaction profile of each species was quantified in probability terms and called up on a computer. The computer method was used on 30 test cultures. In each case, the most likely identification, according to the computer method, was the species to which the strain had already been assigned. In 29 of the 30 cases, the identification was with a probability level of one; in seven of these, however, more than one species tied for first choice. Only one strain was identified with a lower level of probability. The technique developed is comparatively easy to use and would seem to constitute a useful diagnostic tool within the pharmaceutical field.     

Methodological Deficits in Diagnostic Research Using ‘-Omics’ Technologies: Evaluation of the QUADOMICS Tool and Quality of Recently Published Studies

Background

QUADOMICS is an adaptation of QUADAS (a quality assessment tool for use in systematic reviews of diagnostic accuracy studies), which takes into account the particular challenges presented by ‘-omics’ based technologies. Our primary objective was to evaluate the applicability and consistency of QUADOMICS. Subsequently we evaluated and describe the methodological quality of a sample of recently published studies using the tool.

Methodology/Principal Findings

45‘-omics’- based diagnostic studies were identified by systematic search of Pubmed using suitable MeSH terms (“Genomics”, “Sensitivity and specificity”, “Diagnosis”). Three investigators independently assessed the quality of the articles using QUADOMICS and met to compare observations and generate a consensus. Consistency and applicability was assessed by comparing each reviewer''s original rating with the consensus. Methodological quality was described using the consensus rating. Agreement was above 80% for all three reviewers. Four items presented difficulties with application, mostly due to the lack of a clearly defined gold standard. Methodological quality of our sample was poor; studies met roughly half of the applied criteria (mean ± sd, 54.7±18.4%). Few studies were carried out in a population that mirrored the clinical situation in which the test would be used in practice, (6, 13.3%); none described patient recruitment sufficiently; and less than half described clinical and physiological factors that might influence the biomarker profile (20, 44.4%).

Conclusions

The QUADOMICS tool can consistently be applied to diagnostic ‘-omics’ studies presently published in biomedical journals. A substantial proportion of reports in this research field fail to address design issues that are fundamental to make inferences relevant for patient care.     

Structural determination of complex natural products by quantum mechanical calculations of <Superscript>13</Superscript>C NMR chemical shifts: development of a parameterized protocol for terpenes

Nuclear magnetic resonance (NMR) spectroscopy is one of the most important tools for determining the structures of organic molecules. Despite the advances made in this technique, revisions of erroneously established structures for natural products are still commonly published in the literature. In this context, the prediction of chemical shifts through ab initio and density functional theory (DFT) calculations has become a very powerful tool for assisting with the structural determination of complex organic molecules. In this work, we present the development of a protocol for ¹³C chemical shift calculations of terpenes, a class of natural products that are widely distributed among plant species and are very important due to their biological and pharmacological activities. This protocol consists of GIAO-DFT calculations of chemical shifts and the application of a parameterized scaling factor in order to ensure accurate structural determination of this class of natural products. The application of this protocol to a set of five terpenes yielded accurate calculated chemical shifts, showing that this is a very attractive tool for the calculation of complex organic structures such as terpenes.     

Extraction of genomic DNA from the lipid-, polysaccharide-, and polyphenol-rich coconut (Cocos nucifera L.)

One prerequisite to reliable molecular biology work is that the genomic DNA of a sample be of good quality. Coconut is quite difficult to work on because of the high lipid and polysaccharide content of its endosperm and the high polyphenol content of its leaves. This study aimed to determine which protocol to use and which part of the coconut tree is most appropriate to extract good-quality genomic DNA. Genomic DNA from the solid endosperm was found to be of poor quality because of high levels of lipid and galactomannan contaminants. By using a modified protocol by Cheung et al. (1993) as modified by Rogers et al. (1996) and by Dellaporta et al. (1983) as modified by Datta et al. (1997), genomic DNA extracted from the young leaves of the first emergent frond provided enzyme-digestible, good-quality DNA. The modification involved the use of a higher salt concentration (2 M instead of 0.5 M) in the extraction buffer and the use of polyvinylpolypyrrolidone. Moreover, this modified protocol did not involve the use of organic solvents.