Comparison of the particulate organic carbon and permanganate oxidation methods for estimating labile soil organic carbon

Forty-four soils from under native vegetation and a range of management practices following clearing were analysed for ‘labile’ organic carbon (OC) using both the particulate organic carbon (POC) and the 333 mm KmnO4 (MnoxC) methods. Although there was some correlation between the 2 methods, the POC method was more sensitive by about a factor of 2 to rapid loss in OC as a result of management or land-use change. Unlike the POC method, the MnoxC method was insensitive to rapid gains in TOC following establishment of pasture on degraded soil. The MnoxC method was shown to be particularly sensitive to the presence of lignin or lignin-like compounds and therefore is likely to be very sensitive to the nature of the vegetation present at or near the time of sampling and explains the insensitivity of this method to OC gain under pasture. The presence of charcoal is an issue with both techniques, but whereas the charcoal contribution to the POC fraction can be assessed, the MnoxC method cannot distinguish between charcoal and most biomolecules found in soil. Because of these limitations, the MnoxC method should not be applied indiscriminately across different soil types and management practices.

A cost-effectiveness analysis of heroin detoxification methods in the Australian National Evaluation of Pharmacotherapies for Opioid Dependence (NEPOD)

This economic evaluation was part of the Australian National Evaluation of Pharmacotherapies for Opioid Dependence (NEPOD) project. Data from four trials of heroin detoxification methods, involving 365 participants, were pooled to enable a comprehensive comparison of the cost-effectiveness of five inpatient and outpatient detoxification methods. This study took the perspective of the treatment provider in assessing resource use and costs. Two short-term outcome measures were used-achievement of an initial 7-day period of abstinence, and entry into ongoing post-detoxification treatment. The mean costs of the various detoxification methods ranged widely, from AUD $491 (buprenorphine-based outpatient); to AUD $605 for conventional outpatient; AUD $1404 for conventional inpatient; AUD $1990 for rapid detoxification under sedation; and to AUD $2689 for anaesthesia per episode. An incremental cost-effectiveness analysis was carried out using conventional outpatient detoxification as the base comparator. The buprenorphine-based outpatient detoxification method was found to be the most cost-effective method overall, and rapid opioid detoxification under sedation was the most costeffective inpatient method.

Rapid Atrophy of the Lumbar Multifidus Follows Experimental Disc or Nerve Root Injury.

Study Design. Experimental study of muscle changes after lumbar spinal injury. Objectives. To investigate effects of intervertebral disc and nerve root lesions on cross-sectional area, histology and chemistry of porcine lumbar multifidus. Summary of Background Data. The multifidus cross-sectional area is reduced in acute and chronic low back pain. Although chronic changes are widespread, acute changes at 1 segment are identified within days of injury. It is uncertain whether changes precede or follow injury, or what is the mechanism. Methods. The multifidus cross-sectional area was measured in 21 pigs from L1 to S1 with ultrasound before and 3 or 6 days after lesions: incision into L3 - L4 disc, medial branch transection of the L3 dorsal ramus, and a sham procedure. Samples from L3 to L5 were studied histologically and chemically. Results. The multifidus cross-sectional area was reduced at L4 ipsilateral to disc lesion but at L4 - L6 after nerve lesion. There was no change after sham or on the opposite side. Water and lactate were reduced bilaterally after disc lesion and ipsilateral to nerve lesion. Histology revealed enlargement of adipocytes and clustering of myofibers at multiple levels after disc and nerve lesions. Conclusions. These data resolve the controversy that the multifidus cross-sectional area reduces rapidly after lumbar injury. Changes after disc lesion affect 1 level with a different distribution to denervation. Such changes may be due to disuse following reflex inhibitory mechanisms.

The rapid screen of concussion: An evaluation of the non-word repetition test for use in mTBI research

Primary objectives: (1) To investigate the Nonword Repetition test (NWR) as an index of sub-vocal rehearsal deficits after mild traumatic brain injury (mTBI); (2) to assess the reliability, validity and sensitivity of the NWR; and (3) to compare the NWR to more sensitive tests of verbal memory. Research design: An independent groups design. Methods and procedures: Study 1 administered the NWR to 46 mTBI and 61 uninjured controls with the Rapid Screen of Concussion (RSC). Study 2 compared mTBI, orthopaedic and uninjured participants on the NWR and the Hopkins Verbal Learning Test (HVLT-R). Main outcomes and results: The NWR did not improve the diagnostic accuracy of the RSC. However, it is reliable and indexes sub-vocal rehearsal speed. These findings provide evidence that although the current form of the NWR lacks sensitivity to the impact of mTBI, the development of a more sensitive test of sub-vocal rehearsal deficits following mTBI is warranted.

Rapid screening of 4000 individuals for germ-line variations in the BRAF gene

Background: The BRAF gene is frequently somatically altered in malignant melanoma. A majority of variations are at the valine 600 residue leading to a V600E substitution that constitutively activates the kinase. We screened 4000 patient and control DNAs for germ-line variations at the valine 600 residue. Methods: We developed a novel assay by adapting single-base variation assays and software for MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry to screen for all 5 reported variants at codon 600 of the BRAF gene. We screened a case-control collection comprising samples from 1082 melanoma patients and 154 of their unaffected relatives from 1278 families and from 2744 individuals from 659 unselected twin families with no history of melanoma. A panel of 66 melanoma cell lines was used for variation-positive controls. Results: All melanoma cell lines that we had found previously to carry a codon 600 variation were verified in this study. Three of the 4 possible variants (V600E n = 47, V600K n = 2, V600R n = 1) were detected, but no case of V600D was available. No germ-line variants were found in the samples from the 3980 melanoma patients or from the control individuals. Conclusions: This new assay is a high-throughput, automated alternative to standard sequencing and can be used as a rapid initial screen for somatic variants associated with melanoma. Germ-line variants at valine 600 are unlikely to exist and do not contribute to the reported role of the BRAF gene in melanoma predisposition. (c) 2006 American Association for Clinical Chemistry.

Rapid quantification of hepatitis B virus DNA by real-time PCR using efficient TaqMan probe and extraction of virus DNA

Aim: To rapidly quantify hepatitis B virus (HBV) DNA by real-time PCR using efficient TaqMan probe and extraction methods of virus DNA. Methods: Three standards were prepared by cloning PCR products which targeted S, C and X region of HBV genome into pGEM-T vector respectively. A pair of primers and matched TaqMan probe were selected by comparing the copy number and the Ct values of HBV serum samples derived from the three different standard curves using certain serum DNA. Then the efficiency of six HBV DNA extraction methods including guanidinium isothiocyanate, proteinase K, NaI, NaOH lysis, alkaline lysis and simple boiling was analyzed in sample A, B and C by real-time PCR. Meanwhile, 8 clinical HBV serum samples were quantified. Results: The copy number of the same HBV serum sample originated from the standard curve of S, C and X regions was 5.7 × 104/ mL, 6.3 × 102/mL and 1.6 × 103/mL respectively. The relative Ct value was 26.6, 31.8 and 29.5 respectively. Therefore, primers and matched probe from S region were chosen for further optimization of six extraction methods. The copy number of HBV serum samples A, B and C was 3.49 × 109/mL, 2.08 × 106/mL and 4.40 × 107/mL respectively, the relative Ct value was 19.9, 30 and 26.2 in the method of NaOH lysis, which was the efficientest among six methods. Simple boiling showed a slightly lower efficiency than NaOH lysis. Guanidinium isothiocyanate, proteinase K and NaI displayed that the copy number of HBV serum sample A, B and C was around 105/ mL, meanwhile the Ct value was about 30. Alkaline failed to quantify the copy number of three HBV serum samples, Standard deviation (SD) and coefficient variation (CV) were very low in all 8 clinical HBV serum samples, showing that quantification of HBV DNA in triplicate was reliable and accurate. Conclusion: Real-time PCR based on optimized primers and TaqMan probe from S region in combination with NaOH lysis is a simple, rapid and accurate method for quantification of HBV serum DNA. © 2006 The WJG Press. All rights reserved.

Monitoring the condition of savanna riparian zones in Northern Australia using high spatial resolution imagery and a field based rapid assessment method

Government agencies responsible for riparian environments are assessing the combined utility of field survey and remote sensing for mapping and monitoring indicators of riparian zone condition. The objective of this work was to compare the Tropical Rapid Appraisal of Riparian Condition (TRARC) method to a satellite image based approach. TRARC was developed for rapid assessment of the environmental condition of savanna riparian zones. The comparison assessed mapping accuracy, representativeness of TRARC assessment, cost-effectiveness, and suitability for multi-temporal analysis. Two multi-spectral QuickBird images captured in 2004 and 2005 and coincident field data covering sections of the Daly River in the Northern Territory, Australia were used in this work. Both field and image data were processed to map riparian health indicators (RHIs) including percentage canopy cover, organic litter, canopy continuity, stream bank stability, and extent of tree clearing. Spectral vegetation indices, image segmentation and supervised classification were used to produce RHI maps. QuickBird image data were used to examine if the spatial distribution of TRARC transects provided a representative sample of ground based RHI measurements. Results showed that TRARC transects were required to cover at least 3% of the study area to obtain a representative sample. The mapping accuracy and costs of the image based approach were compared to those of the ground based TRARC approach. Results proved that TRARC was more cost-effective at smaller scales (1-100km), while image based assessment becomes more feasible at regional scales (100-1000km). Finally, the ability to use both the image and field based approaches for multi-temporal analysis of RHIs was assessed. Change detection analysis demonstrated that image data can provide detailed information on gradual change, while the TRARC method was only able to identify more gross scale changes. In conclusion, results from both methods were considered to complement each other if used at appropriate spatial scales.

Organohalogen contaminants in wildlife from the Yangtze River Delta : Development of methods and assessments of legacy and emerging persistent organic pollutants

Rapid economic development has occurred during the past few decades in China with the Yangtze River Delta (YRD) area as one of the most progressive areas. The urbanization, industrialization, agricultural and aquaculture activities result in extensive production and application of chemicals. Organohalogen contaminants (OHCs) have been widely used as i.e. pesticides, flame retardants and plasticizers. They are persistent, bioaccumulative and pose a potential threat to ecosystem and human health. However, limited research has been conducted in the YRD with respect to chemicals environmental exposure. The main objective of this thesis is to investigate the contamination level, distribution pattern and sources of OHCs in the YRD. Wildlife from different habitats are used to indicate the environmental pollution situation, and evaluate selected matrices for use in long term biomonitoring to determine the environmental stress the contamination may cause. In addition, a method is developed for dicofol analysis. Moreover, a specific effort is made to introduce statistic power analysis to assist in optimal sampling design. The thesis results show extensive contamination of OHCs in wildlife in the YRD. The occurrences of high concentrations of chlorinated paraffins (CPs) are reported in wildlife, in particular in terrestrial species, (i.e. short-tailed mamushi snake and peregrine falcon). Impurities and byproducts of pentachlorophenol products, i.e. polychlorinated diphenyl ethers (PCDEs) and hydroxylated polychlorinated diphenyl ethers (OH-PCDEs) are identified and reported for the first time in eggs from black-crowned night heron and whiskered tern. High concentrations of octachlorodibenzo-p-dioxin (OCDD) are determined in these samples. The toxic equivalents (TEQs) of polychlorinated dibenzo-p-dioxin (PCDDs) and polychlorinated dibenzofurans (PCDFs) are at mean levels of 300 and 520 pg TEQ g-1lw (WHO2005 TEQ) in eggs from the two bird species, respectively. This is two orders of magnitude higher than European Union (EU) regulation limit in chicken eggs. Also, a novel pattern of polychlorinated biphenyls (PCBs) with octa- to decaCBs, contributing to as much as 20% of total PCBs therein, are reported in birds. The legacy POPs shows a common characteristic with relatively high level of organochlorine pesticides (i.e. DDT, hexacyclohexanes (HCHs) and Mirex), indicating historic applications. In contrast, rather low concentrations are shown of industrial chemicals such as PCBs and polybrominated diphenyl ethers (PBDEs). A refined and improved analytical method is developed to separate dicofol from its major decomposition compound, 4,4’-dichlorobenzophenone. Hence dicofol is possible to assess as such. Statistic power analysis demonstrates that sampling of sedentary species should be consistently spread over a larger area to monitor temporal trends of contaminants in a robust manner. The results presented in this thesis show high CPs and OCDD concentrations in wildlife. The levels and patterns of OHCs in YRD differ from other well studied areas of the world. This is likely due to the extensive production and use of chemicals in the YRD. The results strongly signal the need of research biomonitoring programs that meet the current situation of the YRD. Such programs will contribute to the management of chemicals and environment in YRD, with the potential to grow into the human health sector, and to expand to China as a whole.

When do conservation planning methods deliver? Quantifying the consequences of uncertainty

The rapid global loss of biodiversity has led to a proliferation of systematic conservation planning methods. In spite of their utility and mathematical sophistication, these methods only provide approximate solutions to real-world problems where there is uncertainty and temporal change. The consequences of errors in these solutions are seldom characterized or addressed. We propose a conceptual structure for exploring the consequences of input uncertainty and oversimpli?ed approximations to real-world processes for any conservation planning tool or strategy. We then present a computational framework based on this structure to quantitatively model species representation and persistence outcomes across a range of uncertainties. These include factors such as land costs, landscape structure, species composition and distribution, and temporal changes in habitat. We demonstrate the utility of the framework using several reserve selection methods including simple rules of thumb and more sophisticated tools such as Marxan and Zonation. We present new results showing how outcomes can be strongly affected by variation in problem characteristics that are seldom compared across multiple studies. These characteristics include number of species prioritized, distribution of species richness and rarity, and uncertainties in the amount and quality of habitat patches. We also demonstrate how the framework allows comparisons between conservation planning strategies and their response to error under a range of conditions. Using the approach presented here will improve conservation outcomes and resource allocation by making it easier to predict and quantify the consequences of many different uncertainties and assumptions simultaneously. Our results show that without more rigorously generalizable results, it is very dif?cult to predict the amount of error in any conservation plan. These results imply the need for standard practice to include evaluating the effects of multiple real-world complications on the behavior of any conservation planning method.

Single-cell ELISA and flow cytometry as methods for highlighting potential neuronal and astrocytic toxicant specificity

The timeline imposed by recent worldwide chemical legislation is not amenable to conventional in vivo toxicity testing, requiring the development of rapid, economical in vitro screening strategies which have acceptable predictive capacities. When acquiring regulatory neurotoxicity data, distinction on whether a toxic agent affects neurons and/or astrocytes is essential. This study evaluated neurofilament (NF) and glial fibrillary acidic protein (GFAP) directed single-cell (S-C) ELISA and flow cytometry as methods for distinguishing cell-specific cytoskeletal responses, using the established human NT2 neuronal/astrocytic (NT2.N/A) co-culture model and a range of neurotoxic (acrylamide, atropine, caffeine, chloroquine, nicotine) and non-neurotoxic (chloramphenicol, rifampicin, verapamil) test chemicals. NF and GFAP directed flow cytometry was able to identify several of the test chemicals as being specifically neurotoxic (chloroquine, nicotine) or astrocytoxic (atropine, chloramphenicol) via quantification of cell death in the NT2.N/A model at cytotoxic concentrations using the resazurin cytotoxicity assay. Those neurotoxicants with low associated cytotoxicity are the most significant in terms of potential hazard to the human nervous system. The NF and GFAP directed S-C ELISA data predominantly demonstrated the known neurotoxicants only to affect the neuronal and/or astrocytic cytoskeleton in the NT2.N/A cell model at concentrations below those affecting cell viability. This report concluded that NF and GFAP directed S-C ELISA and flow cytometric methods may prove to be valuable additions to an in vitro screening strategy for differentiating cytotoxicity from specific neuronal and/or astrocytic toxicity. Further work using the NT2.N/A model and a broader array of toxicants is appropriate in order to confirm the applicability of these methods.

Rapid serodiagnosis of Staphylococcus aureus surgical site infection following median sternotomy

Objectives: To determine the sensitivity and specificity of a novel ELISA for the serodiagnosis of surgical site infection (SSI) due to staphylococci following median sternotomy. Methods: Twelve patients with a superficial sternal SSI and 19 with a deep sternal SSI due to Staphylococcus aureus were compared with 37 control patients who also underwent median sternotomy for cardiac surgery but exhibited no microbiological or clinical symptoms of infection. A further five patients with sternal SSI due to coagulase-negative (CoNS) staphylococci were studied. An ELISA incorporating a recently recognised exocellular short chain form of lipoteichoic acid (lipid S) recovered from CoNS, was used to determine serum levels of anti-lipid S IgG in all patient groups. Results: Serum anti-lipid S IgG titres of patients with sternal SSI due to S. aureus were significantly higher than the control patients (P<0.0001). In addition, patients with deep sternal SSI had significantly higher serum anti-lipid S IgG titres than patients with superficial sternal SSI (P=0.03). Serum anti-lipid S IgG titres of patients with sternal SSI due to CoNS were significantly higher than the control patients (P=0.001). Conclusion: The lipid S ELISA may facilitate the diagnosis of sternal SSI due to S. aureus and could also be of value with infection due to CoNS. © 2005 Published by Elsevier Ltd. on behalf of The Bristish Infection Society.

Analysis of protein carbonylation - pitfalls and promise in commonly used methods

Abstract Oxidation of proteins has received a lot of attention in the last decades due to the fact that they have been shown to accumulate and to be implicated in the progression and the patho-physiology of several diseases such as Alzheimer, coronary heart diseases, etc. This has also resulted in the fact that research scientist became more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases. Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods.

Methods in mind

The evolution of cognitive neuroscience has been spurred by the development of increasingly sophisticated investigative techniques to study human cognition. In Methods in Mind, experts examine the wide variety of tools available to cognitive neuroscientists, paying particular attention to the ways in which different methods can be integrated to strengthen empirical findings and how innovative uses for established techniques can be developed. The book will be a uniquely valuable resource for the researcher seeking to expand his or her repertoire of investigative techniques. Each chapter explores a different approach. These include transcranial magnetic stimulation, cognitive neuropsychiatry, lesion studies in nonhuman primates, computational modeling, psychophysiology, single neurons and primate behavior, grid computing, eye movements, fMRI, electroencephalography, imaging genetics, magnetoencephalography, neuropharmacology, and neuroendocrinology. As mandated, authors focus on convergence and innovation in their fields; chapters highlight such cross-method innovations as the use of the fMRI signal to constrain magnetoencephalography, the use of electroencephalography (EEG) to guide rapid transcranial magnetic stimulation at a specific frequency, and the successful integration of neuroimaging and genetic analysis. Computational approaches depend on increased computing power, and one chapter describes the use of distributed or grid computing to analyze massive datasets in cyberspace. Each chapter author is a leading authority in the technique discussed.

A rapid ELISA for the diagnosis of intravascular catheter related sepsis caused by coagulase negative staphylococci

Aim: To develop and evaluate a rapid enzyme linked immunosorbent assay (ELISA) for the diagnosis of intravascular catheter related sepsis caused by coagulase negative staphylococci. Methods: Forty patients with a clinical and microbiological diagnosis of intravascular catheter related sepsis and positive blood cultures, caused by coagulase negative staphylococci, and 40 control patients requiring a central venous catheter as part of their clinical management were recruited into the study. Serum IgG responses to a previously undetected exocellular antigen produced by coagulase negative staphylococci, termed lipid S, were determined in the patient groups by a rapid ELISA. Results: There was a significant difference (p = < 0.0001) in serum IgG to lipid S between patients with catheter related sepsis and controls. The mean antibody titre in patients with sepsis caused by coagulase negative staphylococci was 10 429 (range, no detectable serum IgG antibody to 99 939), whereas serum IgG was not detected in the control group of patients. Conclusions: The rapid ELISA offers a simple, economical, and rapid diagnostic test for suspected intravascular catheter related sepsis caused by coagulase negative staphylococci, which can be difficult to diagnose clinically. This may facilitate treatment with appropriate antimicrobials and may help prevent the unnecessary removal of intravascular catheters.

Rapid machine tool verification

This paper describes work carried out to develop methods of verifying that machine tools are capable of machining parts to within specification, immediately before carrying out critical material removal operations, and with negligible impact on process times. A review of machine tool calibration and verification technologies identified that current techniques were not suitable due to requirements for significant time and skilled human intervention. A 'solution toolkit' is presented consisting of a selection circular tests and artefact probing which are able to rapidly verify the kinematic errors and in some cases also dynamic errors for different types of machine tool, as well as supplementary methods for tool and spindle error detection. A novel artefact probing process is introduced which simplifies data processing so that the process can be readily automated using only the native machine tool controller. Laboratory testing and industrial case studies are described which demonstrate the effectiveness of this approach.