Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5.

Geobacillus thermoleovorans CCB_US3_UF5 is a thermophilic bacterium isolated from a hot spring in Malaysia. Here, we report the complete genome of G. thermoleovorans CCB_US3_UF5, which shows high similarity to the genome of Geobacillus kaustophilus HTA 426 in terms of synteny and orthologous genes.

Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1.

Thermus sp. strain CCB_US3_UF1, a thermophilic bacterium, has been isolated from a hot spring in Malaysia. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1.

Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12.

We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India.

Long-term outcomes of augmentation ileocystoplasty in patients with spinal cord injury: a minimum of 10 years of follow-up.

OBJECTIVE: To report the long-term outcomes of augmentation ileocystoplasty (AIC) in patients with spinal cord injury (SCI), with a minimum follow-up period of 10 years. PATIENTS AND METHODS: We retrospectively analysed all operations performed by a single surgeon at a specialist spinal unit. Outcomes were measured by comparing preoperative and follow-up videocystometrograms (VCMGs). Complications were identified from case notes and the surgery database. Subjective assessment was through a previously validated questionnaire. RESULTS: The mean (range) follow-up was 14.7 (10.5-20.3) years. There were 19 patients (12 males) with a mean (range) age at time of surgery of 28.9 (12-52) years. The mean (range) period from injury to surgery was 4.5 (0.3-22) years. All had suprasacral injuries. The VCMGs showed a significant improvement in bladder capacity and a decrease in intravesical pressures (P < 0.001). Long-term complications included bladder stones (n= 4); urosepsis (n= 2); vesico-ureteric reflux ([VUR]n= 2), VUR requiring ureteric re-implantation (n= 1); neurogenic detrusor overactivity ([NDO]n= 1); and laparatomy for bowel obstruction (n= 1). Surveillance cystoscopies did not detect any bladder neoplasms. The response rate for the questionnaire survey was 14/17; 13/14 patients were satisfied with the operation such that they would consider it again or recommend it to a friend. No patient reported any significant changes in either bowel habit or sexual function. CONCLUSIONS: We found that AIC has excellent long-term outcomes in the definitive management of refractory NDO in patients with SCI. The complications of AIC appear to be more than counterbalanced by a high level of patient satisfaction with the procedure and by the achievement of the primary aim of ensuring continence and upper tract safety in these patients.

A Review of PRESAGE Radiochromic Polymer and the Compositions for Application in Radiotherapy Dosimetry.

Recent advances in radiotherapy technology and techniques have allowed a highly conformal radiation to be delivered to the tumour target inside the body for cancer treatment. A three-dimensional (3D) dosimetry system is required to verify the accuracy of the complex treatment delivery. A 3D dosimeter based on the radiochromic response of a polymer towards ionising radiation has been introduced as the PRESAGE dosimeter. The polyurethane dosimeter matrix is combined with a leuco-dye and a free radical initiator, whose colour changes in proportion to the radiation dose. In the previous decade, PRESAGE gained improvement and enhancement as a 3D dosimeter. Notably, PRESAGE overcomes the limitations of its predecessors, the Fricke gel and the polymer gel dosimeters, which are challenging to fabricate and read out, sensitive to oxygen, and sensitive to diffusion. This article aims to review the characteristics of the radiochromic dosimeter and its clinical applications. The formulation of PRESAGE shows a delicate balance between the number of radical initiators, metal compounds, and catalysts to achieve stability, optimal sensitivity, and water equivalency. The applications of PRESAGE in advanced radiotherapy treatment verifications are also discussed.

Construction of a microRNA-mRNA Regulatory Network in De Novo Cytogenetically Normal Acute Myeloid Leukemia Patients.

Background: The association between dysregulated microRNAs (miRNAs) and acute myeloid leukemia (AML) is well known. However, our understanding of the regulatory role of miRNAs in the cytogenetically normal AML (CN-AML) subtype pathway is still poor. The current study integrated miRNA and mRNA profiles to explore novel miRNA-mRNA interactions that affect the regulatory patterns of de novo CN-AML. Methods: We utilized a multiplexed nanoString nCounter platform to profile both miRNAs and mRNAs using similar sets of patient samples (n = 24). Correlations were assessed, and an miRNA-mRNA network was constructed. The underlying biological functions of the mRNAs were predicted by gene enrichment. Finally, the interacting pairs were assessed using TargetScan and microT-CDS. We identified 637 significant negative correlations (false discovery rate <0.05). Results: Network analysis revealed a cluster of 12 miRNAs representing the majority of mRNA targets. Within the cluster, five miRNAs (miR-495-3p, miR-185-5p, let-7i-5p, miR-409-3p, and miR-127-3p) were posited to play a pivotal role in the regulation of CN-AML, as they are associated with the negative regulation of myeloid leukocyte differentiation, negative regulation of myeloid cell differentiation, and positive regulation of hematopoiesis. Conclusion: Three novel interactions in CN-AML were predicted as let-7i-5p:HOXA9, miR-495-3p:PIK3R1, and miR-495-3p:CDK6 may be responsible for regulating myeloid cell differentiation in CN-AML.

A 20-year follow-up of the mesh wallstent in the treatment of detrusor external sphincter dyssynergia in patients with spinal cord injury.

OBJECTIVE: To assess the long-term (20 years) effectiveness of the UroLume wallstent(TM) (Pfizer Inc., UK) in the treatment of detrusor external sphincter dyssynergia (DESD) in patients with spinal cord injury (SCI). PATIENTS AND METHODS: Twelve patients with quadriplegia secondary to SCI underwent external striated sphincter stenting with the UroLume wallstent in place of sphincterotomy for DESD ≈ 20 years ago. The mean (range) age was 41.8 (26-65) years. Eleven patients had cervical level injury whilst one had a thoracic injury. All the patients were shown to have high-pressure neurogenic detrusor overactivity and DESD with incomplete emptying on preoperative video-cystometrograms (VCMG). RESULTS: Six of the 12 patients have now been followed-up for a mean (range) of 20 (19-21) years. Of the remaining six, two were lost to follow-up at 1 and 3 years, but both remained free of complications during that time. Two patients developed encrustation causing obstruction, requiring stent removal within 1 year of insertion. Another patient with an adequately functioning stent died 7 years after stent insertion from a chest infection. The twelfth patient developed bladder cancer 14 years after stent insertion and underwent cystectomy with urinary diversion. VCMG follow-up of the six patients showed a significantly sustained reduction of maximum detrusor pressure and duration of detrusor contraction at the 20-year follow-up. Five of these six patients developed bladder neck dyssynergia of varying degrees as shown on VCMG within the first 9 years of follow-up. All were successfully treated with bladder neck incision (BNI) where the last BNI needed was at 12 years. We did not encounter any problem with stent migration, urethral erosion, erectile dysfunction or autonomic dysreflexia. CONCLUSION: Urethral stenting using the UroLume wallstent is effective in the management of DESD in patients with SCI and provides an acceptable long-term (20-year follow-up) alternative to sphincterotomy. The failures manifest within the first few years and can be managed easily with stent removal without any significant problems. Bladder neck dyssynergia was the long-term complication which was treated successfully with BNI. It has no significant interference with erectile function, being reversible, minimally invasive and has a shorter hospital stay.

Long-term outcome of tension-free vaginal tape for treating stress incontinence in women with neuropathic bladders.

OBJECTIVE: To evaluate the long-term safety and efficacy of the tension-free vaginal tape (TVT) for the treatment of stress urinary incontinence (SUI) in women with neuropathic bladder dysfunction. PATIENTS AND METHODS: Twelve women (mean age 53.3 years, range 41-80) with neuropathic bladder dysfunction and SUI confirmed by video-cystometrography (VCMG) were treated with a TVT in one institution by an expert neuro-urologist between November 1997 and December 2000. The patient's notes, clinical annual follow-up and VCMG after the procedure, and the incontinence impact questionnaire (IIQ) forms (Urinary Distress Inventory, and IIQ-7) were assessed during the long-term clinical follow-up for SUI, in addition to a health-related quality of life assessment. The cure of SUI was defined as no loss of urine on physical exercise, confirmed VCMG after the procedure, and by clinical assessment. RESULTS: The mean (range) follow-up was 10 (8.5-12) years. Nine patients were using clean intermittent self-catheterization before the insertion of TVT and continued to do so afterward. At 10 years of follow-up, one patient had died (with failed TVT initially), and two were lost to follow-up at 5 years after surgery, but up to 5 years they did not complain of UI and VCMG did not show SUI. The remaining seven of the nine patients were completely dry, and two improved and were satisfied with using one or two pads/day. Two patients showed neurogenic detrusor overactivity confirmed on VCMG, with no evidence of SUI. One patient needed a transient urethral catheter for urinary retention after surgery, one had a bladder injury that required leaving the catheter for 5 days, but no urethral erosions were reported during the follow-up. CONCLUSIONS: In women with neuropathic bladder dysfunction secondary to a variety of spinal cord pathologies, and who have SUI necessitating a definitive intervention, insertion of TVT should be considered a desirable treatment, with very good long-term outcomes.

The index lesion and focal therapy: an analysis of the pathological characteristics of prostate cancer.

OBJECTIVE: To determine the pathological characteristics of radical prostatectomy specimens with respect to index and secondary lesions. METHODS: A total of 100 consecutive radical prostatectomy specimens examined at a single hospital were assessed. Patients undergoing salvage prostatectomy or those who had received neoadjuvant hormonal manipulation were excluded. Preoperative data and the number, volume and Gleason grade of each tumour focus were recorded. Criteria used to define a clinically significant lesion were tumour volume ≥0.5 mL and/or Gleason pattern 4 or 5 and/or extra-capsular disease. RESULTS: Overall, 374 foci were examined. The median number of tumours per patient was 3.5 (range 1-15). The overall median tumour volume was 1.4 mL (range 0.1-18.2), the median volume of the largest (index) tumour was 0.95 mL (range 0.1-18.2) and the median volume of the largest secondary tumour was 0.2 mL (range 0.05-1.7). There were no patients in whom the index lesion was insignificant and secondary tumours were significant (by grade or extra-capsular disease). Seventy-seven fulfilled the clinical parameters of low-to-intermediate-risk disease. If focal therapy can be delivered with the aim of ablating all clinically significant disease, with untreated areas harbouring no cancer or clinically insignificant disease, between 58.5 and 67.5% might have been suitable for such a strategy. CONCLUSIONS: The proportion of men with low-to-intermediate-risk prostate cancer who may potentially be suitable for a focal therapy approach is unknown. The key question is whether the volume of individual lesions points to clinically significant cancer and whether ablation of these lesions alone would lead to cancer control. This research question is currently undergoing evaluation within a prospective clinical trial.

The Validation of the Clinical Male Pelvic Trainer Mk 2-Advanced Models for Scrotal Examination Simulation.

OBJECTIVES: To validate the use of a novel physical model, the "Clinical Male Pelvic Trainer (CMPT) Mk 2-Advanced," for scrotal examination simulation and evaluate its use for surgical education. MATERIALS AND METHODS: A total of 7 CMPT Mk 2-Advanced scrotal models were used for teaching: normal, varicocele, testicular tumor, epididymal cyst, hydrocele, epididymo-orchitis, and indirect inguinoscrotal hernia. At 4 surgical courses in the West Yorkshire Foundation Deanery, UK, between 2015 and 2016, trainees were asked to assess their clinical experience, confidence levels in diagnosing scrotal pathology and simulation properties of the scrotal models on a 5-point Likert Scale. Expert responses were used to validate these findings. RESULTS: In total, 65 trainees and 12 experts (including 3 senior residents) participated in the study (n = 77). There was a positive-tailed distribution in responses from experts for realistic simulation of scrotal contents and pathology; only 1.5% and 14.4% of all responses by experts were scored as a "1" (strongly disagree) or "2" (disagree). The intraclass coefficient (κ) was 0.86 among experts. No significant differences between experts and trainees in assessment of simulation were observed. Following use of the models, there was a significant increase in confidence scores matched by trainee (p < 0.001). Approximately 92.9% and 100% of trainees and experts were in favor of using the models for assessment and future training respectively. CONCLUSIONS: Our study demonstrates that the CMPT MK 2-Advanced models have high "face validity" and may be a valuable tool for surgical education. The use of these models should be explored for use in the curriculum at medical school.

Transcriptome analysis of Pseudomonas aeruginosa PAO1 grown at both body and elevated temperatures.

Functional genomics research can give us valuable insights into bacterial gene function. RNA Sequencing (RNA-seq) can generate information on transcript abundance in bacteria following abiotic stress treatments. In this study, we used the RNA-seq technique to study the transcriptomes of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 following heat shock. Samples were grown at both the human body temperature (37 °C) and an arbitrarily-selected temperature of 46 °C. In this work using RNA-seq, we identified 133 genes that are differentially expressed at 46 °C compared to the human body temperature. Our work identifies some key P. aeruginosa PAO1 genes whose products have importance in both environmental adaptation as well as in vivo infection in febrile hosts. More importantly, our transcriptomic results show that many genes are only expressed when subjected to heat shock. Because the RNA-seq can generate high throughput gene expression profiles, our work reveals many unanticipated genes with further work to be done exploring such genes products.

Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia.

Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus, a member of the family Thermaceae. Members of the genus Thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot spring in Malaysia, which is the fifth member of the genus Thermus with a completely sequenced and publicly available genome (Genbank date of release: December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In addition, its genome revealed potential pathways for the synthesis of secondary metabolites (isoprenoid) and pigments (carotenoid).

Xylanase Superproducer: Genome Sequence of a Compost-Loving Thermophilic Fungus, Thermomyces lanuginosus Strain SSBP.

We report here the draft genome sequence of Thermomyces lanuginosus strain SSBP, which was isolated from soil in South Africa. This fungus produces the largest amount of xylanase ever reported in the literature.

Review of doped silica glass optical fibre: their TL properties and potential applications in radiation therapy dosimetry.

Review is made of dosimetric studies of Ge-doped SiO(2) telecommunication fibre as a 1-D thermoluminescence (TL) system for therapeutic applications. To-date, the response of these fibres has been investigated for UV sources, superficial X-ray beam therapy facilities, a synchrotron microbeam facility, electron linear accelerators, protons, neutrons and alpha particles, covering the energy range from a few eV to several MeV. Dosimetric characteristics include, reproducibility, fading, dose response, reciprocity between TL yield and dose-rate and energy dependence. The fibres produce a flat response to fixed photon and electron doses to within better than 3% of the mean TL distribution. Irradiated Ge-doped SiO(2) optical fibres show limited signal fading, with an average loss of TL signal of ~0.4% per day. In terms of dose response, Ge-doped SiO(2) optical fibres have been shown to provide linearity to x and electron doses, from a fraction of 1 Gy up to 2 kGy. The dosimeters have also been used in measuring photoelectron generation from iodinated contrast media; TL yields being some 60% greater in the presence of iodine than in its absence. The review is accompanied by previously unpublished data.

Urodynamic studies in the evaluation of the older man with lower urinary tract symptoms: when, which ones, and what to do with the results.

Lower urinary tract dysfunction is a major cause of morbidity and decreased quality of life in older men. Most urinary dysfunctions in the elderly are multifactorial in origin and associated with a broad spectrum of mental and physical conditions. In this population, it is essential to have a comprehensive assessment of the lower urinary tract, functional impairments and concurrent medical diseases. A holistic and individualized approach to management is important. Urodynamic studies (UDS) are objective tests which provide a major contribution to our understanding of the pathophysiology of lower urinary tract symptoms (LUTS). Urodynamic findings in older men may include common diagnoses such as bladder outlet obstruction and urinary incontinence. However, coexisting conditions such as detrusor overactivity and impaired detrusor contractility are common in older men. The identification of these conditions is necessary to appropriately counsel patients regarding treatment options. Simple urodynamic tests should be used whenever possible such as uroflowmetry and residual volume estimation. However, in complicated cases more invasive tests such as pressure flow studies are important to help choose the best treatment.