Development of a device to measure adherence and pressure characteristics of positive expiratory pressure therapies used by adults with cystic fibrosis.

INTRODUCTION: Positive expiratory pressure (PEP) and oscillating positive expiratory pressure (OscPEP) therapies are often used by people with cystic fibrosis (CF) to facilitate airway clearance. However, suboptimal adherence and poor technique may reduce their effectiveness. OBJECTIVE: To develop a device (PEPtrac) to accurately measure and provide preliminary clinical data of adherence and technique characteristics when airway clearance is performed using PEP/OscPEP devices. METHODS: This study comprised two distinct phases: 1) a benchtop validation study; and 2) clinical study. Benchtop study: Accuracy of PEPtrac was measured by comparing it to video analysis for five different PEP/OscPEP devices. Clinical study: Clinical data were then collected for 18 adults with CF using one of three PEP/OscPEP devices (PariPEP S®, Acapella DH® or Aerobika®) unsupervised. RESULTS: There was 100% agreement between PEPtrac and video analysis data. Clinical data revealed significant variability in expiratory duration and pressure properties between the three PEP/OscPEP devices and between participants. For example, expiratory duration with PariPEP S® (mean [SD] = 4.8 [1.2] sec) was longer (p < .001) than Acapella DH® (3.7 [0.8] sec) and Aerobika® (2.9 [1.1] sec) and Aerobika® had a higher oscillation amplitude than Acapella DH® (6.4 [1.7] vs 5.3 [1.5] cmH2O, p < .001). DISCUSSION: Accurate measurement of PEP/OscPEP adherence and technique using a device such as PEPtrac was possible. Further research is required to investigate the clinical importance of the variability in technique seen in our clinical data.

Stochastic EM-based TFBS motif discovery with MITSU.

MOTIVATION: The Expectation-Maximization (EM) algorithm has been successfully applied to the problem of transcription factor binding site (TFBS) motif discovery and underlies the most widely used motif discovery algorithms. In the wider field of probabilistic modelling, the stochastic EM (sEM) algorithm has been used to overcome some of the limitations of the EM algorithm; however, the application of sEM to motif discovery has not been fully explored. RESULTS: We present MITSU (Motif discovery by ITerative Sampling and Updating), a novel algorithm for motif discovery, which combines sEM with an improved approximation to the likelihood function, which is unconstrained with regard to the distribution of motif occurrences within the input dataset. The algorithm is evaluated quantitatively on realistic synthetic data and several collections of characterized prokaryotic TFBS motifs and shown to outperform EM and an alternative sEM-based algorithm, particularly in terms of site-level positive predictive value. AVAILABILITY AND IMPLEMENTATION: Java executable available for download at http://www.sourceforge.net/p/mitsu-motif/, supported on Linux/OS X.

MCOIN: a novel heuristic for determining transcription factor binding site motif width.

BACKGROUND: In transcription factor binding site discovery, the true width of the motif to be discovered is generally not known a priori. The ability to compute the most likely width of a motif is therefore a highly desirable property for motif discovery algorithms. However, this is a challenging computational problem as a result of changing model dimensionality at changing motif widths. The complexity of the problem is increased as the discovered model at the true motif width need not be the most statistically significant in a set of candidate motif models. Further, the core motif discovery algorithm used cannot guarantee to return the best possible result at each candidate width. RESULTS: We present MCOIN, a novel heuristic for automatically determining transcription factor binding site motif width, based on motif containment and information content. Using realistic synthetic data and previously characterised prokaryotic data, we show that MCOIN outperforms the current most popular method (E-value of the resulting multiple alignment) as a predictor of motif width, based on mean absolute error. MCOIN is also shown to choose models which better match known sites at higher levels of motif conservation, based on ROC analysis. CONCLUSIONS: We demonstrate the performance of MCOIN as part of a deterministic motif discovery algorithm and conclude that MCOIN outperforms current methods for determining motif width.

Magnetovibrio blakemorei gen. nov., sp. nov., a magnetotactic bacterium (Alphaproteobacteria: Rhodospirillaceae) isolated from a salt marsh.

A magnetotactic bacterium, designated strain MV-1(T), was isolated from sulfide-rich sediments in a salt marsh near Boston, MA, USA. Cells of strain MV-1(T) were Gram-negative, and vibrioid to helicoid in morphology. Cells were motile by means of a single polar flagellum. The cells appeared to display a transitional state between axial and polar magnetotaxis: cells swam in both directions, but generally had longer excursions in one direction than the other. Cells possessed a single chain of magnetosomes containing truncated hexaoctahedral crystals of magnetite, positioned along the long axis of the cell. Strain MV-1(T) was a microaerophile that was also capable of anaerobic growth on some nitrogen oxides. Salinities greater than 10 % seawater were required for growth. Strain MV-1(T) exhibited chemolithoautotrophic growth on thiosulfate and sulfide with oxygen as the terminal electron acceptor (microaerobic growth) and on thiosulfate using nitrous oxide (N2O) as the terminal electron acceptor (anaerobic growth). Chemo-organoautotrophic and methylotrophic growth was supported by formate under microaerobic conditions. Autotrophic growth occurred via the Calvin-Benson-Bassham cycle. Chemo-organoheterotrophic growth was supported by various organic acids and amino acids, under microaerobic and anaerobic conditions. Optimal growth occurred at pH 7.0 and 26-28 °C. The genome of strain MV-1(T) consisted of a single, circular chromosome, about 3.7 Mb in size, with a G+C content of 52.9-53.5 mol%.Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MV-1(T) belongs to the family Rhodospirillaceae within the Alphaproteobacteria, but is not closely related to the genus Magnetospirillum. The name Magnetovibrio blakemorei gen. nov., sp. nov. is proposed for strain MV-1(T). The type strain of Magnetovibrio blakemorei is MV-1(T) ( = ATCC BAA-1436(T)  = DSM 18854(T)).

Quantitative proteomic analysis of the exoelectrogenic bacterium Arcobacter butzleri ED-1 reveals increased abundance of a flagellin protein under anaerobic growth on an insoluble electrode.

Exoelectrogens have the ability to generate electricity in mediator-less microbial fuel cells (MFCs) by extracellular electron transfer to the anode. We investigate the anode-specific responses of Arcobacter butzleri ED-1, the first identified exoelectrogenic Epsilonproteobacterium. iTRAQ and 2D-LC MS/MS driven proteomics were used to compare protein abundances in A. butzleri ED-1 when generating an electronegative potential (-225 mV) in an anaerobic half-cell - either growing as an electrogenic biofilm or suspended in the liquid medium - versus a microaerobic culture. This is the first quantitative proteomic study concentrating on growth of an exoelectrogen during current generation. From 720 proteins identified and quantified (soluble and insoluble sub-proteomes), statistical analysis reveals 75 differentially-expressed proteins. This dataset was enriched in proteins regulating energy and intermediary metabolism, electron and protein transport. Flagellin up-regulation was concomitant with electron transport in the anodic cells, while decreased abundance of a methyl-accepting chemotaxis protein suggested that flagella were involved in communication with the anode surface and electrogenesis, rather than motility. Two novel cytochromes potentially related to electron transport were up-regulated in anaerobic cultures. We demonstrate that employing an insoluble extracellular electron acceptor for anaerobic growth regulates multiple proteins involved in cell surface properties, electron transport and the methylcitrate cycle.

In situ measurement of coastal ocean movements and survival of juvenile Pacific salmon.

Many salmon populations in both the Pacific and Atlantic Oceans have experienced sharply decreasing returns and high ocean mortality in the past two decades, with some populations facing extirpation if current marine survival trends continue. Our inability to monitor the movements of marine fish or to directly measure their survival precludes experimental tests of theories concerning the factors regulating fish populations, and thus limits scientific advance in many aspects of fisheries management and conservation. Here we report a large-scale synthesis of survival and movement rates of free-ranging juvenile salmon across four species, 13 river watersheds, and 44 release groups of salmon smolts (>3,500 fish tagged in total) in rivers and coastal ocean waters, including an assessment of where mortality predominantly occurs during the juvenile migration. Of particular importance, our data indicate that, over the size range of smolts tagged, (i) smolt survival was not strongly related to size at release, (ii) tag burden did not appear to strongly reduce the survival of smaller animals, and (iii) for at least some populations, substantial mortality occurred much later in the migration and more distant from the river of origin than generally expected. Our findings thus have implications for determining where effort should be invested to improve the accuracy of salmon forecasting, to understand the mechanisms driving salmon declines, and to predict the impact of climate change on salmon stocks.

Fire regimes and tree growth in low rainfall jarrah forest of south-west Australia.

Regular fuel reduction burning is an important management strategy for reducing the scale and intensity of wildfires in south-west Australian native forests, but the long term effects of this on tree and stand growth are not well understood. Five fire treatments, including application of frequent and infrequent low intensity burns, and 25 years of fire exclusion, were applied to small (4 ha) experimental plots in a low rainfall mixed jarrah (Eucalyptus marginata) and marri (Corymbia calophylla) forest to investigate the effects of these treatments on tree stem diameter growth, stand basal area increment and tree mortality. Mean tree stem growth measured over 20 years was lowest in the long unburnt treatment compared with the burn treatments, although surface soil nutrient levels were generally higher in the unburnt treatment, suggesting these sites may be moisture limited. There was no clear pattern of the effects of the burn treatments, including the number of fires and the interval between fires, on tree stem growth, stand basal area increment, crown health or mortality. These factors were strongly influenced by dominance condition, with dominant and co-dominant trees growing most and suppressed trees growing least and experiencing the highest mortality levels. There was no evidence of deteriorating tree or stand health that could be attributed to either regular low intensity burning or to a long period (25 years) of fire exclusion.

Controlled cobalt doping of magnetosomes in vivo.

Magnetotactic bacteria biomineralize iron into magnetite (Fe3O4) nanoparticles that are surrounded by lipid vesicles. These 'magnetosomes' have considerable potential for use in bio- and nanotechnological applications because of their narrow size and shape distribution and inherent biocompatibility. The ability to tailor the magnetic properties of magnetosomes by chemical doping would greatly expand these applications; however, the controlled doping of magnetosomes has so far not been achieved. Here, we report controlled in vivo cobalt doping of magnetosomes in three strains of the bacterium Magnetospirillum. The presence of cobalt increases the coercive field of the magnetosomes--that is, the field necessary to reverse their magnetization--by 36-45%, depending on the strain and the cobalt content. With elemental analysis, X-ray absorption and magnetic circular dichroism, we estimate the cobalt content to be between 0.2 and 1.4%. These findings provide an important advance in designing biologically synthesized nanoparticles with useful highly tuned magnetic properties.

Rapid magnetosome formation shown by real-time x-ray magnetic circular dichroism.

Magnetosomes are magnetite nanoparticles formed by biomineralization within magnetotactic bacteria. Although there have been numerous genetic and proteomic studies of the magnetosome-formation process, there have been only limited and inconclusive studies of mineral-phase evolution during the formation process, and no real-time studies of such processes have yet been performed. Thus, suggested formation mechanisms still need substantiating with data. Here we report the examination of the magnetosome material throughout the formation process in a real-time in vivo study of Magnetospirillum gryphiswaldense, strain MSR-1. Transmission EM and x-ray absorption spectroscopy studies reveal that full-sized magnetosomes are seen 15 min after formation is initiated. These immature magnetosomes contain a surface layer of the nonmagnetic iron oxide-phase hematite. Mature magnetite is found after another 15 min, concurrent with a dramatic increase in magnetization. This rapid formation result is contrary to previously reported studies and discounts the previously proposed slow, multistep formation mechanisms. Thus, we conclude that the biomineralization of magnetite occurs rapidly in magnetotactic bacteria on a similar time scale to high-temperature chemical precipitation reactions, and we suggest that this finding is caused by a biological catalysis of the process.

The functional assessment of cancer-vulvar: reliability and validity.

OBJECTIVES: To assess the reliability and validity of the Functional Assessment of Cancer Therapy-Vulvar (FACT-V). METHODS: Seventy-seven patients treated between January 1996 and January 2001 for cancer of the vulva completed the FACT-V, the Eastern Cooperative Oncology Group Performance Status Rating (ECOG-PSR) and the Hospital Anxiety and Depression Scale (HADS) once, 20 consecutive patients treated between February 2001 and October 2001 completed the questionnaires twice, once before surgery and at 2 months follow-up. The FACT-V scores were compared by patients' performance status, FIGO stage, recurrence, and age, and correlated to the HADS scores. Changes in the FACT-V from baseline to 2 months follow-up were evaluated to establish FACT-V's responsiveness to change. RESULTS: The FACT-V's internal consistency was adequate (Chronbach's alpha range, 0.75 to 0.92). Patients with lower performance status, higher FIGO-stage or recurrent disease received lower FACT-V scores, indicating discriminant validity. The correlation between the FACT-V and the HADS were in the expected direction, indicating convergent and divergent validity. From pre- to post-surgery, scores in nine out of fifteen items of the vulvar cancer-specific subscale improved, while those of five items declined, indicating sensitivity of the vulvar cancer specific items to changes in patients' well-being. CONCLUSIONS: The newly developed FACT-V provides a reliable and valid assessment of the quality of life of women with vulvar cancer. It can be used as a short measure of quality of life within research studies, and to facilitate communication about quality of life issues in clinical practice.

United we stand? The effects of a couple-coping intervention on adjustment to early stage breast or gynecological cancer.

Cancer diagnosis affects the psychological well-being of both patients and their partners, and effective coping has been suggested to be a conjoint process of mutual support. Ninety-four married women with early stage cancer and their partners were randomly assigned to couples-based coping training (CanCOPE), individual coping training for the woman, or a medical education control. Couples' observed support communication and self-reported psychological distress, coping effort, and sexual adjustment were assessed at diagnosis, after cancer surgery, and at 6- and 12-month follow-ups. CanCOPE produced significant improvements in couples' supportive communication, reduced psychological distress and coping effort, and improved sexual adjustment. Training in couples rather than individual coping was more effective in facilitating adaptation to cancer.

Outpatient management of abnormal smears.

OBJECTIVES: To review the results of the first 403 women treated at the Abnormal Smear and Colposcopy Unit with special reference to the utility, efficacy, acceptability and economy of in-office treatment of cervical lesions by large loop or Fischer cone excision. DESIGN: Retrospective chart review of consecutive patients treated following, referral with an abnormal smear or abnormal cervical morphology, between 1 September 1996 and 1 August 2001. SETTING: Inner city private practice. SAMPLE: A total of 403 consecutive General Practitioner referred women. METHODS: Details of referral smear result, colposcopically directed biopsy result, subsequent treatment type and histological result including assessability, number of specimens submitted, complications and follow-up assessment were extracted at chart review. Costs of public hospital inpatient and outpatient care, supplied by the Casemix and Clinical Benchmarking Service, Mater Miseraecordae Public Hospitals (with permission to publish), were compared with Medicare rebates. MAIN OUTCOME MEASURES: A total of 187 women were treated by large loop excision of the transformation zone, and 216 by Fischer cone excision. The number of women who were treated as outpatients under local anaesthetic were 395, while eight patients were treated under general anaesthesia as inpatients. There was poor correlation between referring smear, biopsy and subsequent treatment results. Eight patients had abnormal cytology at follow-up, of whom two have been retreated. Three patients had primary or secondary bleeding requiring treatment and two developed cervical stenosis. Outpatient private practice treatment of women with abnormal smears allows significant savings to the public purse over public or private hospital care. CONCLUSIONS: Outpatient treatment of women with abnormal smears, using the Fischer cone technique, is safe, well accepted, effective and the most cost efficient solution to this public health problem.

The impact of positive peritoneal washings and serosal and adnexal involvement on survival in patients with stage IIIA uterine cancer.

OBJECTIVE: The aim of this study was to determine the prognostic significance of serosal involvement (SER), adnexal involvement (ADN), and positive peritoneal washings (PPW) in patients with Stage IIIA uterine cancer. We also sought to determine patterns of recurrence in patients with this disease. METHODS: The records of 136 patients with Stage IIIA uterine cancer treated at the Queensland Centre for Gynecological Cancer between March 1983 and August 2001 were reviewed. One hundred thirty-six patients underwent surgery and 58 (42.6%) had full surgical staging. Seventy-five patients (55.2%) had external beam radiotherapy and/or brachytherapy postoperatively. Overall survival was the primary statistical endpoint. Statistical analysis included univariate and multivariate Cox models. RESULTS: Forty-six patients (33.8%) had adnexal involvement, 23 (16.9%) had serosal involvement, and 40 (29.4%) had positive peritoneal washings. Median follow-up was 55.1 months (95% confidence interval, 36.9 to 73.4 months) after which time 71 patients (52.2%) remained alive. For patients with endometrioid adenocarcinoma, ADN and SER were associated with impaired survival on multivariate analysis (odds ratio 2.8 and 3.2, respectively). In the subgroup of patients with high-risk tumors (including papillary serous carcinomas, clear cell carcinomas, and uterine sarcomas), neither ADN, nor SER, nor PPW influenced survival. CONCLUSION: Patients with Stage IIIA uterine cancer constitute a heterogeneous group. For patients with endometrioid adenocarcinoma, both ADN and SER, but not PPW, were associated with impaired prognosis. For patients with high-risk histological types, prognosis is poor for all three factors.

Expression of MUC1 splice variants in benign and malignant ovarian tumours.

MUC1 is expressed on the surface of ovarian cancer cells. Nine different splice variants of MUC1 have been described, but no study has reported on the expression of MUC1 isoforms in human ovarian cancer. Our study compares patterns of expression of MUC1 splice variants of malignant and benign ovarian tumours. Ovarian tissue samples were taken from patients with benign ovarian tumours (n = 34) and from patients who had surgery for primary (n = 47) or recurrent (n = 8) ovarian cancer. RT-PCR for MUC1 splice variants A, B, C, D, X, Y, Z, REP and SEC was performed and their expression compared to clinical and histopathologic parameters. Variants A, D, X, Y and Z were more frequently expressed in malignant than in benign tumours. All primary ovarian cancer cases were positive for variant REP but negative for variant SEC. No significant association of the expression of MUC1 splice variants with the response to chemotherapy or patient survival could be demonstrated. Expression of MUC1 splice variants A, D, X, Y, Z and REP is associated with the presence of malignancy, whereas expression of MUC1/SEC is associated with the absence of malignancy.