Simulation of electron energy loss spectra of nanomaterials with linear-scaling density functional theory.

Experimental techniques for electron energy loss spectroscopy (EELS) combine high energy resolution with high spatial resolution. They are therefore powerful tools for investigating the local electronic structure of complex systems such as nanostructures, interfaces and even individual defects. Interpretation of experimental electron energy loss spectra is often challenging and can require theoretical modelling of candidate structures, which themselves may be large and complex, beyond the capabilities of traditional cubic-scaling density functional theory. In this work, we present functionality to compute electron energy loss spectra within the onetep linear-scaling density functional theory code. We first demonstrate that simulated spectra agree with those computed using conventional plane wave pseudopotential methods to a high degree of precision. The ability of onetep to tackle large problems is then exploited to investigate convergence of spectra with respect to supercell size. Finally, we apply the novel functionality to a study of the electron energy loss spectra of defects on the (1 0 1) surface of an anatase slab and determine concentrations of defects which might be experimentally detectable.

Development of a novel method for detection of Clostridium difficile using HS-SPME-GC-MS.

AIMS: A novel method has been developed that allows successful differentiation between Clostridium difficile culture-positive and culture-negative stool samples based on volatile organic compound (VOC) evolution and detection by headspace solid-phase microextraction coupled with gas chromatography mass spectrometry (HS-SPME-GC-MS). METHODS AND RESULTS: The method is based on the activation of p-hydroxyphenylacetate decarboxylase produced by Cl. difficile and the detection of a specific VOC, that is 2-fluoro-4-methylphenol from an enzyme substrate. In addition, other VOCs were good indicators for Cl. difficile, that is isocaproic acid and p-cresol, although they could not be used alone for identification purposes. One hundred stool samples were tested, of which 77 were positive by culture. Detection using HS-SPME-GC-MS allowed confirmation of the presence of Cl. difficile within 18 h with a sensitivity and specificity of 83·1 and 100%, respectively. CONCLUSIONS: It is recommended that this new approach could be used alongside conventional methods for Cl. difficile detection, including toxin detection methods, which would allow any false-negative results to be eliminated. SIGNIFICANCE AND IMPACT OF THE STUDY: The ability to identify Cl. difficile-positive stool samples by the analysis of VOCs could allow the development of a VOC detection device which could allow rapid diagnosis of disease and hence prompt treatment with appropriate antibiotics.

An international reference reagent for the detection of RHD and SRY DNA in plasma.

BACKGROUND AND OBJECTIVES: The determination of foetal RHD genotype using foetal DNA contained in the maternal circulation is increasingly used to manage pregnancies at risk of haemolytic disease of the foetus and newborn (HDFN) caused by maternal anti-D. The test is becoming increasingly reliable, and routine clinical services have been established in some centres. However, laboratories currently have no reference materials with which to determine the performance of their tests. This report describes the production and evaluation of a freeze-dried preparation of human plasma, code 07/222, containing RHD and SRY sequences which can be used as a minimum sensitivity reagent. MATERIALS AND METHODS: RhD-positive male plasma was diluted in an excess of RhD-negative female plasma, and 1 ml aliquots were freeze-dried in glass ampoules. To characterise the material, 19 laboratories took part in an international collaborative study. The participants evaluated dilutions of the material using their in-house routine assays and recorded the highest dilution where the genes could be detected. RESULTS: When diluted 1 in 2, most laboratories were able to detect the presence of RHD and SRY sequences in the material and the participants agreed that this was an appropriate level to set as the minimum sensitivity required. CONCLUSIONS: In October 2010, the WHO Expert Committee on Biological Standardization approved the material 07/222 as an International Reference Reagent for the detection of RHD and SRY DNA in plasma.

Clinical impact of computed tomography-based image-guided brachytherapy for cervix cancer using the tandem-ring applicator - the Addenbrooke's experience.

AIMS: We report our initial 3-year experience of chemoradiotherapy for cervical cancer with computed tomography-based image-guided high dose rate (HDR) brachytherapy using the tandem-ring applicator. MATERIALS AND METHODS: Twenty-eight patients were treated between February 2005 and December 2007. All patients received initial external beam radiotherapy (EBRT) followed by HDR brachytherapy (planned dose 21 Gy to point A in three fractions over 8 days). For each insertion, a computed tomography scan was obtained with the brachytherapy applicator in situ. The cervix, uterus and organs at risk (OAR) were contoured on the computed tomography images to create an individualised dosimetry plan. The D(90) (the dose delivered to 90% of the tumour target), V(100) (the percentage of tumour target volume receiving 100% of the prescribed dose) and the minimum dose in the most exposed 2 cm(3) volume (D(2 cc)) of rectum, bladder and bowel were recorded. The equivalent dose in 2 Gy fractions delivered by EBRT and brachytherapy was calculated. RESULTS: The 3-year cancer-specific survival was 81%, with a pelvic control rate of 96%. In 24 patients, a D(90)>or=74 Gy (alpha/beta10) was achieved. The only patient with local recurrence had a D(90) of 63.8 Gy(alpha/beta10). The overall actuarial risk of serious late morbidity was 14%. Seventeen patients had satisfactory OAR doses using the standard loading pattern. Seven patients had modifications to reduce the risk of toxicity, whereas two had modifications to improve the tumour dose. Comparison with a previous cohort of patients treated with chemoradiotherapy and a conventionally planned low dose rate triple source brachytherapy technique showed an improvement in local pelvic control of 20% (P=0.04). CONCLUSIONS: The implementation of a computed tomography-based tandem-ring HDR brachytherapy technique in conjunction with individual dose adaptation has resulted in a significant improvement in local control at Addenbrooke's without increasing the risk of serious toxicity, and with little effect on radiotherapy resources.

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies.

We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.

Prevalence of small inversions in yeast gene order evolution.

Gene order evolution in two eukaryotes was studied by comparing the Saccharomyces cerevisiae genome sequence to extensive new data from whole-genome shotgun and cosmid sequencing of Candida albicans. Gene order is substantially different between these two yeasts, with only 9% of gene pairs that are adjacent in one species being conserved as adjacent in the other. Inversion of small segments of DNA, less than 10 genes long, has been a major cause of rearrangement, which means that even where a pair of genes has been conserved as adjacent, the transcriptional orientations of the two genes relative to one another are often different. We estimate that about 1,100 single-gene inversions have occurred since the divergence between these species. Other genes that are adjacent in one species are in the same neighborhood in the other, but their precise arrangement has been disrupted, probably by multiple successive multigene inversions. We estimate that gene adjacencies have been broken as frequently by local rearrangements as by chromosomal translocations or long-distance transpositions. A bias toward small inversions has been suggested by other studies on animals and plants and may be general among eukaryotes.

From sequence to chromosome: the tip of the X chromosome of D. melanogaster.

One of the rewards of having a Drosophila melanogaster whole-genome sequence will be the potential to understand the molecular bases for structural features of chromosomes that have been a long-standing puzzle. Analysis of 2.6 megabases of sequence from the tip of the X chromosome of Drosophila identifies 273 genes. Cloned DNAs from the characteristic bulbous structure at the tip of the X chromosome in the region of the broad complex display an unusual pattern of in situ hybridization. Sequence analysis revealed that this region comprises 154 kilobases of DNA flanked by 1.2-kilobases of inverted repeats, each composed of a 350-base pair satellite related element. Thus, some aspects of chromosome structure appear to be revealed directly within the DNA sequence itself.

Thinking ahead--the importance of exit strategies to successful implementation of clinical effectiveness initiatives.

The Clinical Resource and Audit Group (CRAG) remains the focus for the development of clinical effectiveness with particular emphasis on strategic alignment and implementation. CRAG believes that early consideration and planning of exit strategies is essential to deliver successful dissemination and implementation of clinical effectiveness initiatives. Open sharing of results in encouraged, with due consideration of the challenges of presenting information fairly and clearly to avoid misinterpretation, particularly for the lay public. Valuable lessons from effectiveness initiatives should be shared widely and introduced quickly into normal clinical practice, releasing effectiveness resources for new challenges. CRAG will produce guidance to support the development of exit strategies later in the year; comments and contributions are welcome.

Expression of Transforming Growth Factor-beta Receptors and Related Cell-Cycle Components in Transitional-Cell Carcinoma of the Bladder.

Exogenous transforming growth factor-beta (TGF-beta) is a potent inhibitor of normal epithelial cell growth but does not generally inhibit the growth of cell lines of transitional-cell carcinoma (TCC) of the bladder. In addition, a lack of the TGF-beta2 transcript and a marked reduction of the TGF-beta1 transcript have been reported in some high-stage TCCs. The purpose of this investigation was to examine the steady-state expression of TGF-beta receptor I and TGF-beta receptor II and a downstream target, p27(KIP1), as well as cyclin E in normal bladder and superficial and invasive TCC in order to better understand the role of TGF-beta downstream targets in TCC insensitivity to TGF-beta. Quantitative RT-PCR was employed to study the expression of TGF-beta receptor I and receptor II. p27(KIP1), and cyclin E in normal bladder and superficial and invasive TCC lesions. Steady-state levels of p27(KIP1), TGF-beta receptors, and cyclin E mRNAs were similar in superficial TCC samples and normal bladder mucosa. There was a significant decrease in p27(KIP1) and TGF-beta receptor II mRNA expression in invasive lesions compared with superficial tumors (P < 0.004; P < 0.02). In contrast, there was no significant difference in the expression of TGF-beta receptor I mRNA between normal bladder and superficial and invasive TCC. There was a significant increase in the expression of cyclin E mRNA in invasive TCC compared with superficial TCC or normal bladder (P < 0.015). These results suggest that aberrant expression of these genes contributes to the phenotype of invasive bladder cancer.

A Candida albicans genome project: cosmid contigs, physical mapping, and gene isolation.

A new project to map the genome of the pathogenic fungus, Candida albicans, has been started. The entire genome was cloned as 5088 cosmids, stored in individual microtiter plate wells. DNA was prepared and fingerprinted using restriction digestion, fluorescent labeling, and analysis on an ABI sequencer. These data are being used to construct contigs of the genome. Simultaneously, a DNA pooling system has been set up, suitable for PCR-based isolation of cosmids containing any known gene. Ultimately, these approaches will lead to the creation of a physically based map of the C. albicans genome, providing the means to localize precisely all the genes, act as a substrate for genome sequencing projects, and provide probes for future studies of genome rearrangement and comparative genomics.

Nomenclature of health care organisations: the extent of public understanding.

Health care systems in many parts of the world are undergoing organisational change. In Britain, the establishment of new organisations following the National health Service (NHS) reforms of 1990 has led to a change and a greater diversity in the nomenclature of health bodies. An important but often overlooked consequence of such change is the extent to which the public, as consumers of services, can recognise health organisations by their names. We investigated this in a study in the North east of England in early 1994. Eleven hundred respondents were asked to identify their local health authority, acute hospital and community health service provider. Mean scores for correct identification were: health authorities (or consortia of health authorities) 32%; acute hospitals 36%; community units 19%. Worst performing organisations scored very high 'don't know' responses: worst performing health authority 52%; acute hospitals 59%; community unit 48%. This survey demonstrates that the names chosen for themselves by health care organisations can convey little meaning to the public. This is an area which needs attention if health care systems are to create a culture in which they regard their patients as informed consumers.

Effects of a televised smoking cessation intervention among low-income and minority smokers.

In November 1985, a television smoking cessation program was broadcast for 20 days on the noon and 9 p.m. news. Smokers in West Garfield Park, an inner-city impoverished area of Chicago, were randomly assigned either to a comprehensive intervention or to a no-intervention control condition. Although 100,000 self-help manuals had been distributed throughout Chicago, none of the controls in this low-income area had obtained a manual. The intervention consisted of providing the smokers a self-help manual, the televised broadcast, weekly support meetings, and supportive phone calls. At a 4-month follow-up, 20% of treatment participants were abstinent compared to 9% of controls. The results indicated that intensive supplementary opportunities enhanced participation by low-income smokers in a media smoking cessation program.