A prospective clinical trial of a real-time polymerase chain reaction assay for the diagnosis of candidemia in nonneutropenic, critically ill adults

Background. Invasive Candida infection among nonneutropenic, critically ill adults is a clinical problem that has received increasing attention in recent years. Poor performance of extant diagnostic modalities has promoted risk-based, preemptive prescribing in view of the poor outcomes associated with inadequate or delayed antifungal therapy; this risks unnecessary overtreatment. A rapid, reliable diagnostic test could have a substantial impact on therapeutic practice in this patient population.

Methods. Three TaqMan-based real-time polymerase chain reaction assays were developed that are capable of detecting the main medically important Candida species, categorized according to the likelihood of fluconazole susceptibility. Assay 1 detected Candida albicans, Candida parapsilosis, Candida tropicalis, and Candida dubliniensis. Assays 2 and 3 detected Candida glabrata and Candida krusei, respectively. The clinical performance of these assays, applied to serum, was evaluated in a prospective trial of nonneutropenic adults in a single intensive care unit.

Results. In all, 527 specimens were obtained from 157 participants. All 3 assays were run in parallel for each specimen; they could be completed within 1 working day. Of these, 23 specimens were obtained from 23 participants categorized as having proven Candida infection at the time of sampling. If a single episode of Candida famata candidemia was excluded, the estimated clinical sensitivity, specificity, and positive and negative predictive values of the assays in this trial were 90.9%, 100%, 100% and 99.8%, respectively.

Conclusions. These data suggest that the described assays perform well in this population for enhancing the diagnosis of candidemia. The extent to which they may affect clinical outcomes, prescribing practice, and cost-effectiveness of care remains to be ascertained.

Size Effects on Thin Film Ferroelectrics: Experiments on Isolated Single Crystal Sheets

Thin lamellae were cut from bulk single crystal BaTiO3 using a Focused Ion Beam Microscope. They were then removed and transferred onto single crystal MgO substrates, so that their functional properties could be measured independent of the original host bulk ferroelectric. The temperature dependence of the capacitance of these isolated single crystal films was found to be strongly bulk-like, demonstrating a sharp Curie anomaly, as well as Curie-Weiss behaviour. In addition, the sudden change in the remanent polarisation as a function of temperature at TC was characteristic of a first order phase change. The work represents a dramatic improvement on that previously published by M. M. Saad, P. Baxter, R. M. Bowman, J. M. Gregg, F. D. Morrison & J. F. Scott, J. Phys: Cond. Matt., 16 L451-L456 (2004), as critical shortcomings in the original specimen geometry, involving potential signal contributions from bulk BaTiO3, have now been obviated. That the functional properties of single crystal thin film lamellae are comparable to bulk, and not like those of conventionally deposited heteroegenous thin film systems, has therefore been confirmed.

A new method of measuring plastic limit of fine materials

Index properties such as the liquid limit and plastic limit are widely used to evaluate certain geotechnical parameters of fine-grained soils. Measurement of the liquid limit is a mechanical process, and the possibility of errors occurring during measurement is not significant. However, this is not the case for plastic limit testing, despite the fact that the current method of measurement is embraced by many standards around the world. The method in question relies on a fairly crude procedure known widely as the ‘thread rolling' test, though it has been the subject of much criticism in recent years. It is essential that a new, more reliable method of measuring the plastic limit is developed using a mechanical process that is both consistent and easily reproducible. The work reported in this paper concerns the development of a new device to measure the plastic limit, based on the existing falling cone apparatus. The force required for the test is equivalent to the application of a 54 N fast-static load acting on the existing cone used in liquid limit measurements. The test is complete when the relevant water content of the soil specimen allows the cone to achieve a penetration of 20 mm. The new technique was used to measure the plastic limit of 16 different clays from around the world. The plastic limit measured using the new method identified reasonably well the water content at which the soil phase changes from the plastic to the semi-solid state. Further evaluation was undertaken by conducting plastic limit tests using the new method on selected samples and comparing the results with values reported by local site investigation laboratories. Again, reasonable agreement was found.

Construction of cDNA libraries from trifluoroacetic acid-solvated amphibian skin secretions: molecular cloning of multiple bombinin-like peptide precursor transcripts from a library of yellow-bellied toad (Bombina variegata) secretion

Amphibian skin secretions are renowned as complex mixtures of bioactive peptides many of which are analogues of endogenous regulatory peptides. While skin secretions can be obtained non-invasively for peptidome analysis, parallel studies on the granular gland transcriptome required specimen sacrifice. The aim of the present study was to analyse archived skin secretions to determine the robustness of bioactive peptide precursor-encoding polyadenylated mRNAs in an attempt to extract maximum molecular information from rare samples. A range of solvated skin secretion samples were examined after lyophilisation for their potential to generate viable and comprehensive cDNA libraries based upon polyadenylated mRNA capture and amplification/cloning using appropriate commercial kits. Here we present unequivocal data that the granular gland transcriptome persists in a PCR amenable format even after storage for as long as 12 years in 0.1%(v/v) aqueous trifluoroacetic acid (TFA). We used a pooled skin secretion sample (2 ml) from the yellow-bellied toad, Bombina variegata (n = 14), containing the equivalent of 5 mg/ml of lyophilised skin secretion, that had been used in part for peptide isolation purposes in 1998 and had been stored at - 20 °C since that time. In the first cloning experiment, 12 different bombinin-like peptide precursor cDNAs were cloned encoding 17 different bombinins, the majority of which were novel. Subsequently, bombesin and bradykinin-related peptide precursor transcripts have been cloned successfully. These data illustrate the unexpected stability/longevity of the transcriptome in these secretions — a finding with implications for both this field of research and for the wider field of molecular biology.

Estimation of in situ stresses using anisotropic elasticity and suction measurements

Sampling and specimen preparation produce changes in mean effective stresses and pore water pressures, even with ‘perfect sampling’. The paper takes an existing simplified three-parameter cross-anisotropic elastic model and uses it to model these changes. The required ratio of cross-anisotropic parameters J/3G* can be obtained from standard CIU triaxial tests. If measurements are also made of suctions in unloaded specimens in the laboratory, then a combination of J/3G*, the measured suction, and the effective overburden pressure permits an estimation of the horizontal effective pressure and the K 0 ‘at rest’ coefficient. This can be helpful in numerical modelling that needs to start from in situ conditions, and in planning pressure levels for reconsolidation of clay specimens in the laboratory. Tests were done on Belfast Upper Boulder Clay from a depth of 28 m. Values of horizontal in situ effective stress estimated from these measurements compare favorably with conventional estimates of the ‘at rest’ coefficient K 0 and the overconsolidation ratio. Estimates of horizontal stress in London Clay were made using published data and the results compared with actual measurements. Again reasonable agreement was obtained.

Lack of horizontal gene transfer of methicillin-resitance genetic determinants from PBP2a-positive, coagulase-negative Staphylococci to methicillin-sensitive Staphylococcus aureus using transcutaneous electric nerve stimulation (TENS),

Previous research shows that approximately half of the coagulase-negative staphylococci (CNS) isolated from patients in the intensive care unit (ICU) at Belfast City Hospital were resistant to methicillin. The presence of this relatively high proportion of methicillin-resistance genetic material gives rise to speculation that these organisms may act as potential reservoirs of methicillinresistance genetic material to methicillin-sensitive Staphylococcus aureus (MSSA). Mechanisms of horizontal gene transfer from PBP2a-positive CNS to MSSA, potentially transforming MSSA to MRSA, aided by electroporation-type activities such as transcutaneous electrical nerve stimulation (TENS), should be considered. Methicillin-resistant CNS (MR-CNS) isolates are collected over a two-month period from a variety of clinical specimen types, particularly wound swabs. The species of all isolates are confirmed, as well as their resistance to oxacillin by standard disc diffusion assays. In addition, MSSA isolates are collected over the same period and confirmed as PBP2a-negative. Electroporation experiments are designed to mimic the time/voltage combinations used commonly in the clinical application of TENS. No transformed MRSA were isolated and all viable S. aureus cells remained susceptible to oxacillin and PBP2a-negative. Experiments using MSSA pre-exposed to sublethal concentrations of oxacillin (0.25 µg/mL) showed no evidence of methicillin gene transfer and the generation of an MRSA. The study showed no evidence of horizontal transfer of methicillin resistance genetic material from MR-CNS to MSSA. These data support the belief that TENS and the associated time/voltage combinations used do not increase conjugational transposons or facilitate horizontal gene transfer from MR-CNS to MSSA.

Crinoids for lunch? An unexpected biotic interaction from the Upper Ordovician of Scotland

Specimens of the polyplacophoran mollusk 'Helminthochiton' thraivensis Reed from the Upper Ordovician of southwest Scotland provide rare examples of complete valve series preserved in near life position, albeit as external molds. Application of high-resolution X-ray microtomography to one such specimen has revealed the exceptional preservation of its last meal, which included elements of a crinoid column, in its intestine. The interaction was either predatory or scavenging; extant chitons are not known to be crinoidivorous. This is the earliest direct record of predation or scavenging on crinoids in the fossil record. It is also the first indication that the broad axial canal of primitive crinoids may have contained nutritious tissues. The predatory or scavenging habit of H. thraivensis is consistent with its inferred phylogenetic position as a stem-group aplacophoran and provides new data suggesting an origin of carnivory early in the evolution of this clade.

How long is a piece of Strix? Methods in measuring and measuring the measurers

An experiment to quantify intra- and interobserver error in anatomical measurements found that interobserver measurements can vary by over 14% of mean specimen length; disparity in measurement increases logarithmically with the number of contributors; instructions did not reduce variation or measurement disparity; scale of the specimen influenced the precision of measurement (relative error increasing with specimen size); different methods of taking a measurement yielded different results, although they did not differ in terms of precision, and topographical complexity of the elements being considered may potentially influence error (error increasing with complexity). These results highlight concerns about introduction of noise and potential bias that should be taken into account when compiling composite datasets and meta-analyses.

The last meal of the Late Ordovician mollusc ‘Helminthochiton’ thraivensis Reed, 1911, from the Lady Burn Starfish Beds, southwest Scotland.

An exceptional specimen of the Late Ordovician mollusc ‘Helminthochiton’ thraivensis Reed, from the Katian of the Lady Burn Starfish Beds, southwest Scotland, preserves gut contents that include nine pelmatozoan ossicles. These are interpreted as including two nodal and five intermodal columnals, and two radice ossicles from the attachment structure. The stem was cyclocyclic and heteromorphic, possibly N212. Radice ossicles were wider than the height of nodals, so radice scars must have encroached onto the latera of adjacent pluricolumnals. These features were compared with the 26 known pelmatozoan taxa from the Lady Burn Starfish Beds. Paracrinoids (one species) and glyptocystitid rhombiferans (six species) were discounted as prey because of their cemented attachment, and incorrect columnal morphology and lack of attachment, respectively. Of 19 species of crinoids, eight are discounted in which the column is pentagonal, tetragonal or unknown. Of the remaining eleven species, only the monobathrid camerate Macrostylocrinus cirrifer Ramsbottom satisfies all criteria for identification of the prey, including heteromorphy and radice scars encroaching adjacent internodals.

The Irish fossil Polyplacophora

Three species of fossil polyplacophoran molluscs are known from Ireland. Two species were originally described in the nineteenth century: Helminthochiton griffithi Salter in M‘Coy, 1846 and Pterochiton thomondiensis (Baily, 1859), and an articulated specimen representing a third indeterminate species, described here for the first time. Previous work on the evolutionary context of these species has relied on published illustrations and descriptions without examination of the type material. as chitons are considered rare in the fossil record, these specimens represent an interesting and important aspect of Irish palaeobiology.

Rare occurrence of a bigeye tuna Thunnus obesus in British waters, with notes on other occurrences of sub-tropical tunas

A freshly dead bigeye tuna Thunnus obesus was washed ashore near Burry Port, Wales (51 degrees 40' N; 4 degrees 15' W) in August, 2006. This is only the third occasion that the species has been observed in British waters, and is the largest and most northerly recorded specimen.

Limnonectins: A new class of antimicrobial peptides from the skin secretion of the Fujian large-headed frog (Limnonectes fujianensis)

Amphibian skin secretions are rich sources of biologically-active peptides with antimicrobial peptides predominating in many species. Several studies involving molecular cloning of biosynthetic precursor-encoding cDNAs from skin or skin secretions have revealed that these exhibit highly-conserved domain architectures with an unusually high degree of conserved nucleotide and resultant amino acid sequences within the signal peptides. This high degree of nucleotide sequence conservation has permitted the design of primers complementary to such sites facilitating “shotgun” cloning of skin or skin secretion-derived cDNA libraries from hitherto unstudied species. Here we have used such an approach using a skin secretion-derived cDNA library from an unstudied species of Chinese frog – the Fujian large-headed frog, Limnonectes fujianensis – and have discovered two 16-mer peptides of novel primary structures, named limnonectin-1Fa (SFPFFPPGICKRLKRC) and limnonectin-1Fb (SFHVFPPWMCKSLKKC), that represent the prototypes of a new class of amphibian skin antimicrobial peptide. Unusually these limnonectins display activity only against a Gram-negative bacterium (MICs of 35 and 70 µM) and are devoid of haemolytic activity at concentrations up to 160 µM. Thus the “shotgun” cloning approach described can exploit the unusually high degree of nucleotide conservation in signal peptide-encoding domains of amphibian defensive skin secretion peptide precursor-encoding cDNAs to rapidly expedite the discovery of novel and functional defensive peptides in a manner that circumvents specimen sacrifice without compromising robustness of data

Does pre-operative estimation of oesophageal tumour metabolic length using F-18-fluorodeoxyglucose PET/CT images compare with surgical pathology length?

PURPOSE:
The aim of the study was to compare the pre-operative metabolic tumour length on FDG PET/CT with the resected pathological specimen in patients with oesophageal cancer.

METHODS:
All patients diagnosed with oesophageal carcinoma who had undergone staging PET/CT imaging between the period of June 2002 and May 2008 who were then suitable for curative surgery, either with or without neo-adjuvant chemotherapy, were included in this study. Metabolic tumour length was assessed using both visual analysis and a maximum standardised uptake value (SUV(max)) cutoff of 2.5.

RESULTS:
Thirty-nine patients proceeded directly to curative surgical resection, whereas 48 patients received neo-adjuvant chemotherapy, followed by curative surgery. The 95% limits of agreement in the surgical arm were more accurate when the metabolic tumour length was visually assessed with a mean difference of -0.05 cm (SD 2.16 cm) compared to a mean difference of +2.42 cm (SD 3.46 cm) when assessed with an SUV(max) cutoff of 2.5. In the neo-adjuvant group, the 95% limits of agreement were once again more accurate when assessed visually with a mean difference of -0.6 cm (SD 1.84 cm) compared to a mean difference of +1.58 cm (SD 3.1 cm) when assessed with an SUV(max) cutoff of 2.5.

CONCLUSION:
This study confirms the high accuracy of PET/CT in measuring gross target volume (GTV) length. A visual method for GTV length measurement was demonstrated to be superior and more accurate than when using an SUV(max) cutoff of 2.5. This has the potential of reducing the planning target volume with dose escalation to the tumour with a corresponding reduction in normal tissue complication probability.

Impact of Sample Heterogeneity on Methylation Analysis

The recent emergence of high-throughput arrays for methylation analysis has made the influence of tumor content on the interpretation of methylation levels increasingly pertinent. However, to what degree does tumor content have an influence, and what degree of tumor content makes a specimen acceptable for accurate analysis remains unclear. Taking a systematic approach, we analyzed 98 unselected formalin-fixed and paraffin-embedded gastric tumors and matched normal tissue samples using the Illumina GoldenGate methylation assay. Unsupervised hierarchical clustering showed 2 separate clusters with a significant difference in average tumor content levels. The probes identified to be significantly differentially methylated between the tumors and normals also differed according to the tumor content of the samples included, with the sensitivity of identifying the

Recurrent lower gastrointestinal bleeding secondary to cytomegalovirus-associated colonic ulcer in a non human immunodeficiency virus infected patient:Timely diagnosis and treatment averted surgery

Mr C, a 68-year-old Chinese male with diabetes mellitus, previous stroke and ischaemic cardiomyopathy on clopidogrel, presented with haematochezia. Colonoscopy showed a sigmoid ulcer, which was treated endoscopically. Histology of the biopsy from the ulcer revealed non-specific changes. However, he presented with recurrent bleeding from this non-healing sigmoid ulcer. A review of the histologic specimen revealed CMV intranuclear inclusion bodies. He was treated with intravenous ganciclovir, with no further hematochezia.

Keywords Hematochezia, cytomegalovirus, ulcer