Rearrangement processes and structural variations show evidence of selection in oesophageal adenocarcinomas.

Oesophageal adenocarcinoma (OAC) provides an ideal case study to characterize large-scale rearrangements. Using whole genome short-read sequencing of 383 cases, for which 214 had matched whole transcriptomes, we observed structural variations (SV) with a predominance of deletions, tandem duplications and inter-chromosome junctions that could be identified as LINE-1 mobile element (ME) insertions. Complex clusters of rearrangements resembling breakage-fusion-bridge cycles or extrachromosomal circular DNA accounted for 22% of complex SVs affecting known oncogenes. Counting SV events affecting known driver genes substantially increased the recurrence rates of these drivers. After excluding fragile sites, we identified 51 candidate new drivers in genomic regions disrupted by SVs, including ETV5, KAT6B and CLTC. RUNX1 was the most recurrently altered gene (24%), with many deletions inactivating the RUNT domain but preserved the reading frame, suggesting an altered protein product. These findings underscore the importance of identification of SV events in OAC with implications for targeted therapies.

Impact of hospital nephrectomy volume on intermediate- to long-term survival in renal cell carcinoma.

OBJECTIVE: To evaluate the relationship between hospital volume and intermediate- and long-term patient survival for patients undergoing nephrectomy for renal cell carcinoma (RCC). PATIENTS AND METHODS: Adult patients with RCC treated with nephrectomy between 2000 and 2010 were identified from the English Hospital Episode Statistics database and National Cancer Data Repository. Patients with nodal or metastatic disease were excluded. Hospitals were categorised into low- (LV; <20 cases/year), medium- (20-39 cases/year) and high-volume (HV; ≥40 cases/year), based on annual cases of RCC nephrectomy. Multivariable Cox regression analyses were used to calculate hazard ratios (HRs) for all-cause mortality by hospital volume, adjusting for patient, tumour and surgical characteristics. We assessed conditional survival over three follow-up periods: short (30 days to 1 year), intermediate (1-3 years) and long (3-5 years). We additionally explored whether associations between volume and outcomes varied by tumour stage. RESULTS: A total of 12 912 patients were included. Patients in HV hospitals had a 34% reduction in mortality risks up to 1 year compared to those in LV hospitals (HR 0.66, 95% confidence interval 0.53-0.83; P < 0.01). Assuming causality, treatment in HV hospitals was associated with one fewer death in every 71 patients treated. Benefit of nephrectomy centralisation did not change with higher T stage (P = 0.17). No significant association between hospital volume and survival was observed beyond the first year. CONCLUSIONS: Nephrectomy for RCC in HV hospitals was associated with improved survival for up to 1 year after treatment. Our results contribute new insights regarding the value of nephrectomy centralisation.

Time trends in service provision and survival outcomes for patients with renal cancer treated by nephrectomy in England 2000-2010.

OBJECTIVE: To describe the temporal trends in nephrectomy practice and outcomes for English patients with renal cell carcinoma (RCC). PATIENTS AND METHODS: Adult RCC nephrectomy patients treated between 2000 and 2010 were identified in the National Cancer Data Repository and Hospital Episode Statistics, and followed-up until date of death or 31 December 2015 (n = 30 763). We estimated the annual frequency for each nephrectomy type, the hospital and surgeon numbers and their case volumes. We analysed short-term surgical outcomes, as well as 1- and 5-year relative survivals. RESULTS: Annual RCC nephrectomy number increased by 66% during the study period. Hospital number decreased by 24%, whilst the median annual hospital volume increased from 10 to 23 (P < 0.01). Surgeon number increased by 27% (P < 0.01), doubling the median consultant number per hospital. The proportion of minimally invasive surgery (MIS) nephrectomies rose from 1% to 46%, whilst the proportion of nephron-sparing surgeries (NSS) increased from 5% to 16%, with 29% of all T1 disease treated with partial nephrectomy in 2010 (P < 0.01). The 30-day mortality rate halved from 2.4% to 1.1% and 90-day mortality decreased from 4.9% to 2.6% (P < 0.01). The 1-year relative survival rate increased from 86.9% to 93.4%, whilst the 5-year relative survival rate rose from 68.2% to 81.2% (P < 0.01). Improvements were most notable in patients aged ≥65 years and those with T3 and T4 disease. CONCLUSIONS: Surgical RCC management has changed considerably with nephrectomy centralisation and increased NSS and MIS. In parallel, we observed significant improvements in short- and long-term survival particularly for elderly patients and those with locally advanced disease.

A comprehensive sediment dynamics study of a major mud belt system on the inner shelf along an energetic coast.

Globally mud areas on continental shelves are conduits for the dispersal of fluvial-sourced sediment. We address fundamental issues in sediment dynamics focusing on how mud is retained on the seabed on shallow inner shelves and what are the sources of mud. Through a process-based comprehensive study that integrates dynamics, provenance, and sedimentology, here we show that the key mechanism to keep mud on the seabed is the water-column stratification that forms a dynamic barrier in the vertical that restricts the upward mixing of suspended sediment. We studied the 1000 km-long mud belt that extends from the mouth of the Changjiang (Yangtze) River along the coast of Zhejiang and Fujian Provinces of China and ends on the west coast of Taiwan. This mud belt system is dynamically attached to the fluvial sources, of which the Changjiang River is the primary source. Winter is the constructive phase when active deposition takes place of fine-grained sediment carried mainly by the Changjiang plume driven by Zhe-Min Coastal Currents southwestward along the coast.

Influence of hospital volume on nephrectomy mortality and complications: a systematic review and meta-analysis stratified by surgical type.

OBJECTIVES: The provision of complex surgery is increasingly centralised to high-volume (HV) specialist hospitals. Evidence to support nephrectomy centralisation however has been inconsistent. We conducted a systematic review and meta-analysis to determine the association between hospital case volumes and perioperative outcomes in radical nephrectomy, partial nephrectomy and nephrectomy with venous thrombectomy. METHODS: Medline, Embase and the Cochrane Library were searched for relevant studies published between 1990 and 2016. Pooled effect estimates for nephrectomy mortality and complications were calculated for each nephrectomy type using the DerSimonian and Laird random-effects model. Sensitivity analyses were performed to examine the effects of heterogeneity on the pooled effect estimates by excluding studies with the heaviest weighting, lowest methodological score and most likely to introduce bias from misclassification of standardised hospital volume. RESULTS: Some 226 372 patients from 16 publications were included in our review and meta-analysis. Considerable between-study heterogeneity was noted and only a few reported volume-outcome relationships specifically in partial nephrectomy or nephrectomy with venous thrombectomy.HV hospitals were correlated with a 26% and 52% reduction in mortality for radical nephrectomy (OR 0.74, 95% CI 0.61 to 0.90, p<0.01) and nephrectomy with venous thrombectomy (OR 0.48, 95% CI 0.29 to 0.81, p<0.01), respectively. In addition, radical nephrectomy in HV hospitals was associated with an 18% reduction in complications (OR 0.82, 95% CI 0.73 to 0.92, p<0.01). No significant volume-outcome relationship in mortality (OR 0.84, 95% CI 0.31 to 2.26, p=0.73) or complications (OR 0.85, 95% CI 0.55 to 1.30, p=0.44) was observed for partial nephrectomy. CONCLUSIONS: Our findings suggest that patients undergoing radical nephrectomy have improved outcomes when treated by HV hospitals. Evidence of this in partial nephrectomy and nephrectomy with venous thrombectomy is however not yet clear and could be secondary to the low number of studies included and the small patient number in our analyses. Further investigation is warranted to establish the full potential of nephrectomy centralisation particularly as existing evidence is of low quality with significant heterogeneity.

Incorporating multiparametric MRI staging and the new histological Grade Group system improves risk-stratified detection of bone metastasis in prostate cancer.

BACKGROUND: There remains uncertainty on the need for bone staging in men with intermediate-risk prostate cancer. Current guidelines do not use mpMRI-staging information and rely on historic pathology grading. METHODS: We investigated the ability of mpMRI and the new Grade Group system to better predict bone metastasis status in a retrospective cohort study of 438 men with prostate cancer undergoing baseline mpMRI and isotope bone scintigraphy (BS). RESULTS: Including mpMRI-staging information significantly increased the specificity of bone metastasis detection from 3.0% to 24.2% (P<0.01) and sensitivity from 89.2% to 97.3%. The new Grade Group score demonstrated progressive increase in bone metastasis rates (P<0.001). A novel risk-stratification model combining Grade Groups, PSA and mpMRI staging shows promise in predicting bone metastasis and could potentially reduce BS usage by 22.4%-34.7%. CONCLUSIONS: Incorporating the new Grade Group system and mpMRI staging more accurately identified bone metastatic risk and suggests men with Grade Group ⩽2 and/or without radiological T3 disease could safely avoid routine bone staging.

Efficiency optimisation of proteins on a chip.

This study elucidates that the protein reorientation on a chip can be changed by an external electric field (EEF) and optimised for achieving strong effective binding between proteins. Protein A and its binding protein immunoglobulin G (IgG) were used as an example, in addition to an anticancer peptide (CB1a) and its antibody (anti-CB1a). The binding forces (BFs) were measured by atomic force microscopy (AFM) with EEFs applied at different angles (EEF°). The optimal angle (OA) of the EEF (OAEEF°) corresponding to the maximum binding force (BFmax) was obtained. The results showed that the BFmax values between IgG/Protein A and anti-CB1a/CB1a were 6424.2 ± 195.3 pN (OAEEF° = 45°) and 729.1 ± 33.2 pN (OAEEF° = 22.5°), respectively. Without an EEF, the BF values were only 730.0 ± 113.9 pN and 337.3 ± 35.0 pN, respectively. Based on these observations, we concluded that the efficient optimisation of protein-protein interaction on a chip is essential. This finding is applicable to the industrial fabrication of all protein chips.

Fast incorporation of primary amine group into polylactide surface for improving C2C12 cell proliferation using nitrogen-based atmospheric-pressure plasma jets.

In this article, we report the development of the fast incorporation of primary amine functional groups into a polylactide (PLA) surface using the post-discharge jet region of an atmospheric-pressure nitrogen-based dielectric barrier discharge (DBD). Plasma treatments were carried out in two sequential steps: (1) nitrogen with 0.1% oxygen addition, and (2) nitrogen with 5% ammonia addition. The analyses show that the concentration of N/C ratio, surface energy, contact angle, and surface roughness of the treated PLA surface can reach 19.1%, 70.5 mJ/m(2), 38° and 73.22 nm, respectively. In addition, the proposed two-step plasma treatment procedure can produce a PLA surface exhibiting almost the same C2C12 cell attachment and proliferation performance as that of the conventional gelatin coating method. Most importantly, the processing/preparation time is reduced from 13-15 h (gelatin coating method) to 5-15 min (two-step plasma treatment), which is very useful in practical applications.

Efficacy verification and microscopic observations of an anticancer peptide, CB1a, on single lung cancer cell.

In this work, we introduce a new customized anti-lung cancer peptide, CB1a, with IC50 of about 25.0 ± 1.6 µM on NCI-H460 lung cancer cells. Using a multi-cellular tumor spheroid (MCTS) model, results show that CB1a is potent in preventing the growth of lung cancer tumor-like growths in vitro. Additionally, atomic force microscopy (AFM) was used to examine cell surface damage of a single cancer. The mechanism for cell death under CB1a toxicity was verified as being largely due to cell surface damage. Moreover, with a treatment dosage of CB1a at 25 µM, Young's module (E) shows that the elasticity and stiffness of cancer cell decreased with time such that the interaction time for a 50% reduction of E (IT50) was about 7.0min. This new single-cell toxicity investigation using IT50 under AFM assay can be used to separately verify drug efficacy in support of the traditional IC50 measurement in bulk solution. These results could be of special interest to researchers engaged in new drug development.

Chip-based protein-protein interaction studied by atomic force microscopy.

In this article, a technique for accurate direct measurement of protein-to-protein interactions before and after the introduction of a drug candidate is developed using atomic force microscopy (AFM). The method is applied to known immunosuppressant drug candidate Echinacea purpurea derived cynarin. T-cell/CD28 is on-chip immobilized and B-cell/CD80 is immobilized on an AFM tip. The difference in unbinding force between these two proteins before and after the introduction of cynarin is measured. The method is described in detail including determination of the loading rates, maximum probability of bindings, and average unbinding forces. At an AFM loading rate of 1.44 × 10(4) pN/s, binding events were largely reduced from 61 ± 5% to 47 ± 6% after cynarin introduction. Similarly, maximum probability of bindings reduced from 70% to 35% with a blocking effect of about 35% for a fixed contact time of 0.5 s or greater. Furthermore, average unbinding forces were reduced from 61.4 to 38.9 pN with a blocking effect of ≈ 37% as compared with ≈ 9% by SPR. AFM, which can provide accurate quantitative measures, is shown to be a good method for drug screening. The method could be applied to a wider variety of drug candidates with advances in bio-chip technology and a more comprehensive AFM database of protein-to-protein interactions.

Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2)) and D lineages.

UNLABELLED: Chlamydia trachomatis is an obligate intracellular bacterium that causes a diversity of severe and debilitating diseases worldwide. Sporadic and ongoing outbreaks of lymphogranuloma venereum (LGV) strains among men who have sex with men (MSM) support the need for research on virulence factors associated with these organisms. Previous analyses have been limited to single genes or genomes of laboratory-adapted reference strain L(2)/434 and outbreak strain L(2)b/UCH-1/proctitis. We characterized an unusual LGV strain, termed L(2)c, isolated from an MSM with severe hemorrhagic proctitis. L(2)c developed nonfusing, grape-like inclusions and a cytotoxic phenotype in culture, unlike the LGV strains described to date. Deep genome sequencing revealed that L(2)c was a recombinant of L(2) and D strains with conserved clustered regions of genetic exchange, including a 78-kb region and a partial, yet functional, toxin gene that was lost with prolonged culture. Indels (insertions/deletions) were discovered in an ftsK gene promoter and in the tarp and hctB genes, which encode key proteins involved in replication, inclusion formation, and histone H1-like protein activity, respectively. Analyses suggest that these indels affect gene and/or protein function, supporting the in vitro and disease phenotypes. While recombination has been known to occur for C. trachomatis based on gene sequence analyses, we provide the first whole-genome evidence for recombination between a virulent, invasive LGV strain and a noninvasive common urogenital strain. Given the lack of a genetic system for producing stable C. trachomatis mutants, identifying naturally occurring recombinants can clarify gene function and provide opportunities for discovering avenues for genomic manipulation. IMPORTANCE: Lymphogranuloma venereum (LGV) is a prevalent and debilitating sexually transmitted disease in developing countries, although there are significant ongoing outbreaks in Australia, Europe, and the United States among men who have sex with men (MSM). Relatively little is known about LGV virulence factors, and only two LGV genomes have been sequenced to date. We isolated an LGV strain from an MSM with severe hemorrhagic proctitis that was morphologically unique in tissue culture compared with other LGV strains. Bioinformatic and statistical analyses identified the strain as a recombinant of L(2) and D strains with highly conserved clustered regions of genetic exchange. The unique culture morphology and, more importantly, disease phenotype could be traced to the genes involved in recombination. The findings have implications for bacterial species evolution and, in the case of ongoing LGV outbreaks, suggest that recombination is a mechanism for strain emergence that results in significant disease pathology.

Study of release speeds and bacteria inhibiting capabilities of drug delivery membranes fabricated via electrospinning by observing bacteria growth curves.

The study found that biodegradable drug delivery membranes that were fabricated from Poly(a-L-alanine) (PLLA) and chlorhexidine (CHX)-gluconate via electrospinning could steadily and continuously inhibit the growth of bacteria. Bacterial growth curves were used to evaluate on a real-time basis the relationship between drug delivery speeds of the membranes and growth rates of bacteria in different phases. The results showed that PLLA/CHX (50:50 in terms of volume) drug delivery membranes could do what drug delivery systems can normally do. SEM morphology observations, FTIR, and Raman spectra analyses were conducted on the drug delivery membranes. This is the first study that confirms that biodegradable CHX delivery membranes fabricated via electrospinning are a rate-preprogrammed drug delivery system by comparing the growth curves of competent cell and plasmid inserted competent cell, bacteria that are of the same strain but grow at different speeds due to the insertion.

Morphology and optical properties of single- and multi-layer InAs quantum dots.

An understanding of the structural and optical properties of quantum dots (QDs) is critical for their use in optical communication devices. In this study, single- and multi-layer self-organized InAs QDs grown on (001) GaAs substrates by molecular beam epitaxy (MBE) were investigated. High-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) images show that the lateral size of multi-layer InAs QDs are larger and flatter than single-layer InAs QDs, which are oval-shaped. The change in shape and size may be attributed to the presence of InGaAs spacer layers in multi-layer InAs QDs. Reciprocal spacer mapping and fast Fourier transformation images clearly show that InGaAs spacer layers present in the multi-layer InAs QDs structures help to release the strain originally existing in the QDs. In addition, the photoluminescence peak of the multi-layer InAs QDs is broader than QD in the single-layer one, which implies that the multi-layer InAs QDs size variation is more random than the single-layer one and this corresponds with the HAADF-STEM images. These results prove that spacer layers release strain influencing the morphology and optical properties of the QDs.

Prevalence and type distribution of human papillomavirus in 5,000 British Columbia women--implications for vaccination.

BACKGROUND: Human papilloma virus (HPV) prevalence studies performed in different regions and population groups across Canada would inform public health decisions regarding implementation of anti-HPV vaccines. METHODS: A total of 8,700 liquid-based specimens from 8,660 women aged 13-86 from throughout British Columbia were collected. DNA was isolated from 4,980 of these samples and assessed for HPV prevalence and type distribution. HPV was detected by PCR analysis using tagged GP5+/6+ consensus primers to amplify the L1 region of HPV; typing was done by bi-directional sequencing of PCR products. RESULTS: Overall HPV prevalence was 16.8% (age adjusted 15.5%). Prevalence of high-risk HPV was 13.9, and 10.7% of samples contained HPV16. HPV prevalence was highest in the youngest group of women (<20 years). One-third of HPV positive samples contained more than one HPV type. Percentages of low-grade (LGIL) and high-grade intraepithelial lesions (HGIL) containing high-risk HPV are 52.3 and 79.4%, respectively. CONCLUSIONS: Overall HPV prevalence in this study is within the range of estimates from other studies. The prevalence of HPV16 is higher than what is found in other Canadian and international studies. HPV16 and HPV18 compose a majority of the high-risk virus in this study. Use of current HPV vaccines could considerably reduce HPV-related conditions including cervical cancer and procedures such as colposcopy.

Analysis of InAsN quantum dots by transmission electron microscopy and photoluminescence.

Quantum dots (QDs) have great potential in optical fiber communication applications were widely recognized. The structure of molecular beam epitaxy (MBE) grew InAsN QDs were investigated by transmission electron microscopy (TEM) and measured their optical properties by photoluminescence (PL). TEM images show that the InAsN QDs are irregular or oval shaped. Some of the InAsN QDs are observed to have defects, such as dislocations at or near the surface in contrast to InAs QDs, which appear to be defect free. PL results for InAsN QDs showed a red-shifted emission peak. In addition, the InAsN emission peak is broader than InAs QDs, which supports the TEM observation that the size distribution of the InAsN QDs is more random than InAs QDs. The results show that the addition of nitrogen to InAs QDs leads to a decrease in the average size of the QDs, bring changes in the QD's shape, compositional distribution, and optical properties.

NADPH oxidase mediates hypersomnolence and brain oxidative injury in a murine model of sleep apnea.

RATIONALE: Persons with obstructive sleep apnea may have significant residual hypersomnolence, despite therapy. Long-term hypoxia/reoxygenation events in adult mice, simulating oxygenation patterns of moderate-severe sleep apnea, result in lasting hypersomnolence, oxidative injury, and proinflammatory responses in wake-active brain regions. We hypothesized that long-term intermittent hypoxia activates brain NADPH oxidase and that this enzyme serves as a critical source of superoxide in the oxidation injury and in hypersomnolence. OBJECTIVES: We sought to determine whether long-term hypoxia/reoxygenation events in mice result in NADPH oxidase activation and whether NADPH oxidase is essential for the proinflammatory response and hypersomnolence. METHODS: NADPH oxidase gene and protein responses were measured in wake-active brain regions in wild-type mice exposed to long-term hypoxia/reoxygenation. Sleep and oxidative and proinflammatory responses were measured in adult mice either devoid of NADPH oxidase activity (gp91phox-null mice) or in which NADPH oxidase activity was systemically inhibited with apocynin osmotic pumps throughout hypoxia/reoxygenation. MAIN RESULTS: Long-term intermittent hypoxia increased NADPH oxidase gene and protein responses in wake-active brain regions. Both transgenic absence and pharmacologic inhibition of NADPH oxidase activity throughout long-term hypoxia/reoxygenation conferred resistance to not only long-term hypoxia/reoxygenation hypersomnolence but also to carbonylation, lipid peroxidation injury, and the proinflammatory response, including inducible nitric oxide synthase activity in wake-active brain regions. CONCLUSIONS: Collectively, these findings strongly support a critical role for NADPH oxidase in the lasting hypersomnolence and oxidative and proinflammatory responses after hypoxia/reoxygenation patterns simulating severe obstructive sleep apnea oxygenation, highlighting the potential of inhibiting NADPH oxidase to prevent oxidation-mediated morbidities in obstructive sleep apnea.