Simultaneous detection and differentiation of human Polyomaviruses JC and BK by a rapid and sensitive PCR-ELAHA assay and a survey of the JCV subtypes within an Australian population

Human polyomaviruses JCV and BKV can cause several clinical manifestations in immunocompromised hosts, including progressive multifocal leukoencephalopathy (PML) and haemorrhagic cystitis. Molecular detection by polymerase chain reaction (PCR) is recognised as a sensitive and specific method for detecting human polyomaviruses in clinical samples. In this study, we developed a PCR assay using a single primer pair to amplify a segment of the VP1 gene of JCV and BKV. An enzyme linked amplicon hybridisation assay (ELAHA) using species-specific biotinylated oligonucleotide probes was used to differentiate between JCV and BKV. This assay (VP1-PCR-ELAHA) was evaluated and compared to a PCR assay targeting the human polyomavirus T antigen gene (pol-PCR). DNA sequencing was used to confirm the polyomavirus species identified by the VP1-PCR-ELAHA and to determine the subtype of each JCV isolate. A total of 297 urine specimens were tested and human polyomavirus was detected in 105 specimens (35.4%) by both PCR assays. The differentiation of JCV and BKV by the VP1-PCR-ELAHA showed good agreement with the results of DNA sequencing. Further, DNA sequencing of the JCV positive specimens showed the most prevalent JCV subtype in our cohort was 2a (27%) followed by 1b (20%), 1a (15%), 2c (14%), 4 (14%) and 2b (10%). The results of this study show that the VP1-PCR-ELAHA is a sensitive, specific and rapid method for detecting and differentiating human polyomaviruses JC and BK and is highly suitable for routine use in the clinical laboratory. (C) 2004 Wiley-Liss, Inc.

Eph/Ephrin memhrane proteins: A mammalian expression vector pTIg-BOS-Fc allowing rapid protein purification

There is an urgent need for high purity, single chain, fully functional Eph/ephrin membrane proteins. This report outlines the pTIg-BOS-Fc vector and purification approach resulting in rapid increased production of fully functional single chain extracellular proteins that were isolated with high purity and used in structure-function analysis and pre-clinical studies.

Measuring and predicting the dynamics of linear monodisperse entangled polymers in rapid flow through an abrupt contraction. A small angle neutron scattering study

Small-angle neutron scattering measurements on a series of monodisperse linear entangled polystyrene melts in nonlinear flow through an abrupt 4:1 contraction have been made. Clear signatures of melt deformation and subsequent relaxation can be observed in the scattering patterns, which were taken along the centerline. These data are compared with the predictions of a recently derived molecular theory. Two levels of molecular theory are used: a detailed equation describing the evolution of molecular structure over all length scales relevant to the scattering data and a simplified version of the model, which is suitable for finite element computations. The velocity field for the complex melt flow is computed using the simplified model and scattering predictions are made by feeding these flow histories into the detailed model. The modeling quantitatively captures the full scattering intensity patterns over a broad range of data with independent variation of position within the contraction geometry, bulk flow rate and melt molecular weight. The study provides a strong, quantitative validation of current theoretical ideas concerning the microscopic dynamics of entangled polymers which builds upon existing comparisons with nonlinear mechanical stress data. Furthermore, we are able to confirm the appreciable length scale dependence of relaxation in polymer melts and highlight some wider implications of this phenomenon.

Rapid testing for group B streptococcus during labour: a test accuracy study with evaluation of acceptability and cost-effectiveness

OBJECTIVE: To determine the accuracy, acceptability and cost-effectiveness of polymerase chain reaction (PCR) and optical immunoassay (OIA) rapid tests for maternal group B streptococcal (GBS) colonisation at labour. DESIGN: A test accuracy study was used to determine the accuracy of rapid tests for GBS colonisation of women in labour. Acceptability of testing to participants was evaluated through a questionnaire administered after delivery, and acceptability to staff through focus groups. A decision-analytic model was constructed to assess the cost-effectiveness of various screening strategies. SETTING: Two large obstetric units in the UK. PARTICIPANTS: Women booked for delivery at the participating units other than those electing for a Caesarean delivery. INTERVENTIONS: Vaginal and rectal swabs were obtained at the onset of labour and the results of vaginal and rectal PCR and OIA (index) tests were compared with the reference standard of enriched culture of combined vaginal and rectal swabs. MAIN OUTCOME MEASURES: The accuracy of the index tests, the relative accuracies of tests on vaginal and rectal swabs and whether test accuracy varied according to the presence or absence of maternal risk factors. RESULTS: PCR was significantly more accurate than OIA for the detection of maternal GBS colonisation. Combined vaginal or rectal swab index tests were more sensitive than either test considered individually [combined swab sensitivity for PCR 84% (95% CI 79-88%); vaginal swab 58% (52-64%); rectal swab 71% (66-76%)]. The highest sensitivity for PCR came at the cost of lower specificity [combined specificity 87% (95% CI 85-89%); vaginal swab 92% (90-94%); rectal swab 92% (90-93%)]. The sensitivity and specificity of rapid tests varied according to the presence or absence of maternal risk factors, but not consistently. PCR results were determinants of neonatal GBS colonisation, but maternal risk factors were not. Overall levels of acceptability for rapid testing amongst participants were high. Vaginal swabs were more acceptable than rectal swabs. South Asian women were least likely to have participated in the study and were less happy with the sampling procedure and with the prospect of rapid testing as part of routine care. Midwives were generally positive towards rapid testing but had concerns that it might lead to overtreatment and unnecessary interference in births. Modelling analysis revealed that the most cost-effective strategy was to provide routine intravenous antibiotic prophylaxis (IAP) to all women without screening. Removing this strategy, which is unlikely to be acceptable to most women and midwives, resulted in screening, based on a culture test at 35-37 weeks' gestation, with the provision of antibiotics to all women who screened positive being most cost-effective, assuming that all women in premature labour would receive IAP. The results were sensitive to very small increases in costs and changes in other assumptions. Screening using a rapid test was not cost-effective based on its current sensitivity, specificity and cost. CONCLUSIONS: Neither rapid test was sufficiently accurate to recommend it for routine use in clinical practice. IAP directed by screening with enriched culture at 35-37 weeks' gestation is likely to be the most acceptable cost-effective strategy, although it is premature to suggest the implementation of this strategy at present.

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.

e-Business in supply chain management

E-business is concerned with the use of the Internet to link companies with their suppliers, customers and other trading partners. As a business concept, it has evolved significantly since its introduction in the 1990’s in parallel with the rapid rate of development of information technology (IT) during this period. Supply chain management (SCM) is fundamentally concerned with integration of activities both with and between organisations. IT plays a crucial role in SCM as a key enabler of supply chain integration (SCI). This chapter sets out the role of e-business concepts in the context of the supply chain challenges faced by firms. It specifically explores the role of e-procurement as an example of how e-business concepts have been applied to one key SCM activity, namely purchasing and procurement. In this context, the chapter examines the nature and evolution of e-marketplaces and goes on to identify key adoption drivers and benefits based on recent research. This research identifies key adoption drivers and benefits but also recognises that there are many barriers that ongoing research needs to address if the potential of e-business is to be fulfilled.

Supply chain innovation for competing in highly competitive markets:challenges and solutions

Rapid changes in technological development are forcing businesses to continuously innovate to improve their competitiveness, which is particularly evident in logistics and supply chain management (SCM), where innovation impacts both the strategic and operational levels. Supply Chain Innovation for Competing in Highly Dynamic Markets: Challenges and Solutions investigates the role of innovation in the management of supply chains of today. This book focuses on supply chain integration from both strategic and operational perspectives and the impact of information technology-related innovation in supply chain and logistics service industries. It also analyzes how environmental innovation affects logistical decisions throughout the supply chain and the strategies employed in managing logistics-related environmental impacts. Finally, the book explores theoretical and practical implications of innovation in the management of supply systems.

Observation of manganese nodules and crusts recovered during the CHAIN 115 cruise from Nov 1973 until June 1974 in the Atlantic Ocean

Investigations of piston cores from the Vema Channel and lower flanks of the Rio Grande Rise suggest the presence of episodic flow of deep and bottom water during the Late Pleistocene. Cores from below the present-day foraminiferal lysocline (at ~4000 m) contain an incomplete depositional record consisting of Mn nodules and encrustations, hemipelagic clay, displaced high-latitude diatoms, and poorly preserved heterogeneous microfossil assemblages. Cores from the depth range between 2900 m and 4000 m contain an essentially complete Late Pleistocene record, and consist of well-defined carbonate dissolution cycles with periodicities of ~100,000 years. Low carbonate content and increased dissolution correspond to glacial episodes, as interpreted by oxygen isotopic analysis of bulk foraminiferal assemblages. The absence of diagnostic high-latitude indicators (Antarctic diatoms) within the dissolution cyclss, however, suggests that AABW may not have extended to significantly shallower elevations on the lower flanks of the Rio Grande Rise during the Late Pleistocene. Therefore episodic AABW flow may not necessarily be the mechanism responsible for producing these cyclic events. This interpretation is also supported by the presence of an apparently complete Brunhes depositional record in the same cores, suggesting current velocities insufficient for significant erosion. Fluctuations in the properties and flow characteristics of another water mass, such as NADW, may be involved. The geologic evidence in core-top samples near the present-day AABW/NADW transition zone is consistent with either of two possible interpretations of the upper limit of AABW on the east flank of the channel. The foraminiferal lysocline, at ~4000 m, is near the top of the benthic thermocline and nepheloid layer, and may therefore correspond to the upper limit of relatively corrosive AABW. On the other hand, the carbonate compensation depth (CDD) at ~4250 m, which corresponds to the maximum gradient in the benthic thermocline, is characterized by rapid deposition of relatively fine-grained sediment. Such a zone of convergence and preferential sediment accumulation would be expected near the level of no motion in the AABW/NADW transition zone as a consequence of Ekman-layer veering of the mean velocity vector in the bottom boundary layer. It is possible that both of these interpretations are in part correct. The "level of no motion'' may in fact correspond to the CCD, while at the same time relatively corrosive water of Antarctic origin may mix with overlying NADW and therefore elevate the foraminifera] lysocline to depths above the level of no motion. Closely spaced observations of the hydrography and flow characteristics within the benthic thermocline will be required in order to use sediment parameters as more precise indicators of paleo-circulation.

Supply Chain Adaptation of Finnish Companies in Chinese Institutional Environment

Within the last few decades of operations and supply chain management, the field has seen the rise of so called best practices, methods that will help supply chains obtain their business goals and gain a competitive edge. These methods were thought to be universal. This however is not always the case, as the surrounding business environment could have a significant impact on what will be effective in gaining competitive edge. Contingency theory states that the success of a supply chain is determined by both internal capabilities, as well as external context aligning. This creates a strategic fit, which is a major determinant of success. In order for supply chains to reach this strategic fit, they must adapt. As China has seen rapid growth and over the last few decades become one of the major economies of the world, Western companies have tried to establish themselves there, only to find that the Chinese market is extremely difficult to operate in. The aim of this thesis was to investigate from contingency theory perspective, what are the institutional factors that affect supply chain management of Finnish companies operating in China, and how do Finnish companies adapt their supply chains to better fit the Chinese institutional environment. A theoretical model was created for this thesis, in which supply chains possess resources, which can be combined in a meaningful manner to create capabilities. Both resources and capabilities are affected by the surrounding institutional environment, which forces supply chains to adapt in order to find a better strategic fit. A total of six Finnish managers from three large and three small companies operating in China were interviewed. The results indicated that the Chinese business environment is significantly different, than that of Finland or Western countries in general. Three institutional factors were identified: Confucian though, fast-paced business environment, and managing labor force. These three institutional factors made the relationship and delivery capabilities particularly important, as well as human resources, reputation, physical resources and technological resources. In conclusion, it was discovered that the Chinese institutional environment is heavily affected by Confucian thought, as well as the rapid market growth. These are the two most important institutional factors that shape the Chinese market. If supply chains wish to be successful in China, adaptation regarding these two institutional factors should yield good results.

Supply Chain Adaptation of Finnish Companies in Chinese Institutional Environment

Within the last few decades of operations and supply chain management, the field has seen the rise of so called best practices, methods that will help supply chains obtain their business goals and gain a competitive edge. These methods were thought to be universal. This however is not always the case, as the surrounding business environment could have a significant impact on what will be effective in gaining competitive edge. Contingency theory states that the success of a supply chain is determined by both internal capabilities, as well as external context aligning. This creates a strategic fit, which is a major determinant of success. In order for supply chains to reach this strategic fit, they must adapt. As China has seen rapid growth and over the last few decades become one of the major economies of the world, Western companies have tried to establish themselves there, only to find that the Chinese market is extremely difficult to operate in. The aim of this thesis was to investigate from contingency theory perspective, what are the institutional factors that affect supply chain management of Finnish companies operating in China, and how do Finnish companies adapt their supply chains to better fit the Chinese institutional environment. A theoretical model was created for this thesis, in which supply chains possess resources, which can be combined in a meaningful manner to create capabilities. Both resources and capabilities are affected by the surrounding institutional environment, which forces supply chains to adapt in order to find a better strategic fit. A total of six Finnish managers from three large and three small companies operating in China were interviewed. The results indicated that the Chinese business environment is significantly different, than that of Finland or Western countries in general. Three institutional factors were identified: Confucian though, fast-paced business environment, and managing labor force. These three institutional factors made the relationship and delivery capabilities particularly important, as well as human resources, reputation, physical resources and technological resources. In conclusion, it was discovered that the Chinese institutional environment is heavily affected by Confucian thought, as well as the rapid market growth. These are the two most important institutional factors that shape the Chinese market. If supply chains wish to be successful in China, adaptation regarding these two institutional factors should yield good results.

A Putative Otu Domain-containing Protein 1 Deubiquitinating Enzyme Is Differentially Expressed In Thyroid Cancer And Identifies Less-aggressive Tumours.

This study aimed to identify novel biomarkers for thyroid carcinoma diagnosis and prognosis. We have constructed a human single-chain variable fragment (scFv) antibody library that was selected against tumour thyroid cells using the BRASIL method (biopanning and rapid analysis of selective interactive ligands) and phage display technology. One highly reactive clone, scFv-C1, with specific binding to papillary thyroid tumour proteins was confirmed by ELISA, which was further tested against a tissue microarray that comprised of 229 thyroid tissues, including: 110 carcinomas (38 papillary thyroid carcinomas (PTCs), 42 follicular carcinomas, 30 follicular variants of PTC), 18 normal thyroid tissues, 49 nodular goitres (NG) and 52 follicular adenomas. The scFv-C1 was able to distinguish carcinomas from benign lesions (P=0.0001) and reacted preferentially against T1 and T2 tumour stages (P=0.0108). We have further identified an OTU domain-containing protein 1, DUBA-7 deubiquitinating enzyme as the scFv-binding antigen using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry. The strategy of screening and identifying a cell-surface-binding antibody against thyroid tissues was highly effective and resulted in a useful biomarker that recognises malignancy among thyroid nodules and may help identify lower-risk cases that can benefit from less-aggressive management.

Quantitative Proteomic Analysis Reveals Metabolic Alterations, Calcium Dysregulation, And Increased Expression Of Extracellular Matrix Proteins In Laminin α2 Chain-deficient Muscle.

Congenital muscular dystrophy with laminin α2 chain deficiency (MDC1A) is one of the most severe forms of muscular disease and is characterized by severe muscle weakness and delayed motor milestones. The genetic basis of MDC1A is well known, yet the secondary mechanisms ultimately leading to muscle degeneration and subsequent connective tissue infiltration are not fully understood. In order to obtain new insights into the molecular mechanisms underlying MDC1A, we performed a comparative proteomic analysis of affected muscles (diaphragm and gastrocnemius) from laminin α2 chain-deficient dy(3K)/dy(3K) mice, using multidimensional protein identification technology combined with tandem mass tags. Out of the approximately 700 identified proteins, 113 and 101 proteins, respectively, were differentially expressed in the diseased gastrocnemius and diaphragm muscles compared with normal muscles. A large portion of these proteins are involved in different metabolic processes, bind calcium, or are expressed in the extracellular matrix. Our findings suggest that metabolic alterations and calcium dysregulation could be novel mechanisms that underlie MDC1A and might be targets that should be explored for therapy. Also, detailed knowledge of the composition of fibrotic tissue, rich in extracellular matrix proteins, in laminin α2 chain-deficient muscle might help in the design of future anti-fibrotic treatments. All MS data have been deposited in the ProteomeXchange with identifier PXD000978 (http://proteomecentral.proteomexchange.org/dataset/PXD000978).

Improvement Of The Physical Performance Is Associated With Activation Of No/pgc-1α/mttfa Signaling Pathway And Increased Protein Expressions Of Electron Transport Chain In Gastrocnemius Muscle From Rats Supplemented With L-arginine.

To examine the influence of l-arginine supplementation in combination with physical training on mitochondrial biomarkers from gastrocnemius muscle and its relationship with physical performance. Male Wistar rats were divided into four groups: control sedentary (SD), sedentary supplemented with l-arginine (SDLA), trained (TR) and trained supplemented with l-arginine (TRLA). Supplementation of l-arginine was administered by gavage (62.5mg/ml/day/rat). Physical training consisted of 60min/day, 5days/week, 0% grade, speed of 1.2km/h. The study lasted 8weeks. Skeletal muscle mitochondrial enriched fraction as well as cytoplasmic fractions were obtained for Western blotting and biochemical analyses. Protein expressions of transcriptor coactivator (PGC-1α), transcriptor factors (mtTFA), ATP synthase subunit c, cytochrome oxidase (COXIV), constitutive nitric oxide synthases (eNOS and nNOS), Cu/Zn-superoxide dismutase (SOD) and manganese-SOD (Mn-SOD) were evaluated. We also assessed in plasma: lipid profile, glycemia and malondialdehyde (MDA) levels. The nitrite/nitrate (NOx(-)) levels were measured in both plasma and cytosol fraction of the gastrocnemius muscle. 8-week l-arginine supplementation associated with physical training was effective in promoting greater tolerance to exercise that was accompanied by up-regulation of the protein expressions of mtTFA, PGC-1α, ATP synthase subunit c, COXIV, Cu/Zn-SOD and Mn-SOD. The upstream pathway was associated with improvement of NO bioavailability, but not in NO production since no changes in nNOS or eNOS protein expressions were observed. This combination would be an alternative approach for preventing cardiometabolic diseases given that in overt diseases a profound impairment in the physical performance of the patients is observed.

A Rapid And Simple Capillary Electrophoresis Method For Indirect Determination Of The Biocide 2,2-dibromo-3-nitrilo-propionamide (dbnpa) In Cooling Waters.

A capillary zone electrophoresis (CE) method was developed for the determination of the biocide 2,2-dibromo-3-nitrilo-propionamide (DBNPA) in water used in cooling systems. The biocide is indirectly determined by CE measurement of the concentration of bromide ions produced by the reaction between the DBNPA and bisulfite. The relationship between the bromide peak areas and the DBNPA concentrations showed a good linearity and a coefficient of determination (R(2)) of 0.9997 in the evaluated concentration range of 0-75 μmol L(-1). The detection and quantification limits for DBNPA were 0.23 and 0.75 μmol L(-1), respectively. The proposed CE method was successfully applied for the analysis of samples of tap water and cooling water spiked with DBNPA. The intra-day and inter-day (intermediary) precisions were lower than 2.8 and 6.2%, respectively. The DBNPA concentrations measured by the CE method were compared to the values obtained by a spectrophotometric method and were found to agree well.