CO adsorption on Cu(111) and Cu(001) surfaces: improving site preference in DFT calculations

CO adsorption on Cu(111) and Cu(001) surfaces has been studied within ab-initio density functional theory (DFT). The structural, vibrational and thermodynamic properties of the adsorbate-substrate complex have been calculated. Calculations within the generalized gradient approximation (GGA) predict adsorption in the threefold hollow on Cu(111) and in the bridge-site on Cu(001), instead of on-top as found experimentally. It is demonstrated that the correct site preference is achieved if the underestimation of the HOMO-LUMO gap of CO characteristic for DFT is correct by applying a molecular DFT+U approach. The DFT+U approach also produces good agreement with the experimentally measured adsorption energies, while introducing only small changes in the calculated geometrical and vibrational properties further improving agreement with experiment which is fair already at the GGA level.Comment: 15 pages, 3 figures, submitted to Surf. Sci., WWW: http://cms.mpi.univie.ac.at/mgajdos

Comprehensive and Computable Molecular Diagnostic Panel (C2Dx) From Small Volume Specimens for Precision Oncology: Molecular Subtyping of Non-Small Cell Lung Cancer From Fine Needle Aspirates

The Comprehensive, Computable NanoString Diagnostic gene panel (C2Dx) is a promising solution to address the need for a molecular pathological research and diagnostic tool for precision oncology utilizing small volume tumor specimens. We translate subtyping-related gene expression patterns of Non-Small Cell Lung Cancer (NSCLC) derived from public transcriptomic data which establish a highly robust and accurate subtyping system. The C2Dx demonstrates supreme performance on the NanoString platform using microgram-level FNA samples and has excellent portability to frozen tissues and RNA-Seq transcriptomic data. This workflow shows great potential for research and the clinical practice of cancer molecular diagnosis

Achieving benchmarks for national quality indicators reduces recurrence and progression in non-muscle-invasive bladder cancer

Background Noncompliance with evidence-based interventions and guidelines contributes to significant and variable recurrence and progression in patients with non–muscle-invasive bladder cancer (NMIBC). The implementation of a quality performance indicator (QPI) programme in Scotland’s National Health Service (NHS) aimed to improve cancer outcomes and reduce nationwide variance. Objective To evaluate the effect of hospitals achieving benchmarks for two specific QPIs on time to recurrence and progression in NMIBC. Design, setting, and participants QPIs for bladder cancer (BC) were enforced nationally in April 2014. NHS health boards collected prospective data on all new BC patients. Prospectively recorded surveillance data were pooled from 12 collaborating centres. Intervention QPIs of interest were (1) hospitals achieving detrusor muscle (DM) sampling target at initial transurethral resection of bladder tumour (TURBT) and (2) use of single instillation of mitomycin C after TURBT (SI-MMC). Outcome measurements and statistical analysis The primary and secondary endpoints were time to recurrence and progression, respectively. Kaplan-Meier and Cox multivariable regression analyses were performed. Key findings and limitations Between April 1, 2014 and March 31, 2017, we diagnosed 3899 patients with new BC, of which 2688 were NMIBC . With a median follow up of 60.3 mo, hospitals achieving the DM sampling target had a 5.4% lower recurrence rate at 5 yr than hospitals not achieving this target (442/1136 [38.9%] vs 677/1528 [44.3%], 95% confidence interval [CI] = 1.6–9.2, p = 0.005). SI-MMC was associated with a 20.4% lower recurrence rate (634/1791 [35.4%] vs 469/840 [55.8%], 95% CI = 16.4–24.5, p < 0.001). On Cox multivariable regression, meeting the DM target and SI-MMC were associated with significant improvement in recurrence (hazard ratio [HR] 0.81, 95% CI = 0.73–0.91, p = 0.0002 and HR 0.66, 95% CI = 0.59–0.74, p < 0.004, respectively) as well as progression-free survival (HR 0.62, 95% CI = 0.45–0.84, p = 0.002 and HR 0.65, 95% CI = 0.49–0.87, p = 0.004, respectively). We did not have a national multicentre pre-QPI control. Conclusions Within a national QPI programme, meeting targets for sampling DM and SI-MMC in the real world were independently associated with delays to recurrence and progression in NMIBC patients. Patient summary Following the first 3 yr of implementing a novel quality performance indicator programme in Scotland, we evaluated compliance and outcomes in non–muscle-invasive bladder cancer. In 2688 patients followed up for 5 yr, we found that achieving targets for sampling detrusor muscle and the single instillation of mitomycin C during and after transurethral resection of bladder tumour, respectively, were associated with delays in cancer recurrence and progression

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Effect of Microwave Treatment on Ryegrass and Wild Radish Plants and Seeds

Annual ryegrass (Lolium rigidum) and wild radish (Raphanus raphanistrum) are significant weeds in Australian winter cropping systems. These species have developed significant herbicide resistance and new control strategies need to be developed. Microwave energy has been considered for weed control for some time. The research considered the effect of varying amounts of microwave energy on plants and their seeds for each species. Several experiments explored the interaction between microwave energy and seed depth in the soil. Plant responses to microwave energy were also determined for each species. Seed treatment requires higher energy applications than plant treatment and is conceptually similar to soil fumigation treatments. Soil treatment may have application in some high value horticultural crops, which already use soil fumigation. Microwave treatment of plants requires less energy, with wild radish requiring about 60 Jcm-2 to achieve 100% mortality, while ryegrass plants require about 370 Jcm-2 to achieve 100% mortality. Microwave treatment of growing plants can be compared to the application of herbicide. Therefore control of growing plants should be the focus of developing a commercially viable microwave weed control device for cropping systems

Assessing the Impact of Microwave Treatment on Soil Microbial Populations

Microwave soil treatment can kill weed plants and their seeds in the soil. It has also been demonstrated elsewhere that microwave soil treatment can kill nematodes in the soil; however few studies have considered the effect of microwave soil treatment on other key soil biota. This study explored the effect of microwave soil treatment on soil bacteria, fungi, and various protozoa. The research used a series of experiments using different techniques to verify the effect of varying degrees of microwave treatment on these soil biota. Microwave treatment reduces bacterial populations in the top layers of soil, but populations that are deeper in the soil are relatively unaffected. Bacterial populations increased significantly within a month of microwave treatment. E. coli populations experienced a 10-5 reduction in numbers in the top layer of soil by 500 J cm-2 of microwave energy; however other soil bacteria survived over 3000 J cm-2 of microwave energy applied to the soil surface, suggesting that some species are more susceptible to microwave treatment than others. No significant response of soil fungi, ciliates, amoeba and flagellates could be attributed to a microwave dose response

Groundwater residence time in a dissected and weathered sandstone plateau: Kulnura–Mangrove Mountain aquifer, NSW, Australia

Groundwater residence time in the Kulnura–Mangrove Mountain aquifer was assessed during a multi-year sampling programme using general hydrogeochemistry and isotopic tracers (H2O stable isotopes, δ13CDIC, 3H, 14C and 87Sr/86Sr). The study included whole-rock analysis from samples recovered during well construction at four sites to better characterise water–rock interactions. Based on hydrogeochemistry, isotopic tracers and mineral phase distribution from whole-rock XRD analysis, two main groundwater zones were differentiated (shallow and deep). The shallow zone contains oxidising Na–Cl-type waters, low pH, low SC and containing 3H and 14C activities consistent with modern groundwater and bomb pulse signatures (up to 116.9 pMC). In this shallow zone, the original Hawkesbury Sandstone has been deeply weathered, enhancing its storage capacity down to ∼50 m below ground surface in most areas and ∼90 m in the Peats Ridge area. The deeper groundwater zone was also relatively oxidised with a tendency towards Ca–HCO3-type waters, although with higher pH and SC, and no 3H and low 14C activities consistent with corrected residence times ranging from 11.8 to 0.9 ka BP. The original sandstone was found to be less weathered with depth, favouring the dissolution of dispersed carbonates and the transition from a semi-porous groundwater media flow in the shallow zone to fracture flow at depth, with both chemical and physical processes impacting on groundwater mean residence times. Detailed temporal and spatial sampling of groundwater revealed important inter-annual variations driven by groundwater extraction showing a progressive influx of modern groundwater found at >100 m in the Peats Ridge area. The progressive modernisation has exposed deeper parts of the aquifer to increased NO3− concentrations and evaporated irrigation waters. The change in chemistry of the groundwater, particularly the lowering of groundwater pH, has accelerated the dissolution of mineral phases that would generally be inactive within this sandstone aquifer triggering the mobilisation of elements such as aluminium in the aqueous phase. © 2020 Informa UK Limite

Enhanced Quality and Effectiveness of Transurethral Resection of Bladder Tumour in Non–muscle-invasive Bladder Cancer:A Multicentre Real-world Experience from Scotland's Quality Performance Indicators Programme

Background: Clinical outcomes from non–muscle-invasive bladder cancer (NMIBC) are partly determined by the quality of initial interventions. To improve and standardise treatment for cancer, Scotland implemented a national Quality Performance Indicator (QPI) programme for bladder cancer (BC). Objective: To evaluate compliance with specific quality indicators (QIs) related to transurethral resection of bladder tumour (TURBT) and to understand clinical outcomes from NMIBC following the introduction of the QPI programme. Design, setting, and participants: Within a robust governance framework, 12 mandatory evidence-based QPIs were implemented nationally in April 2014. We report prospectively collected data for all new BC patients (between April 2014 and March 2017). We include follow-up data for 2689 patients. Intervention: The TURBT-related QPIs were (1) using a bladder diagram, (2) single post-TURBT instillation of mitomycin C (SPI-MMC), (3) detrusor muscle (DM) in the specimen, and (4) early re-TURBT in high-risk NMIBC. Outcome measurements and statistical analysis: We measured compliance with these QPIs and (1) recurrence rate at first follow-up cystoscopy (RRFFC), (2) rates of residual cancer, and (3) pT2 cancer at re-TURBT. Associations between QPI compliance, tumour features, and outcomes were assessed with multivariable logistic regression models. Results and limitations: Among 4246 new BC patients, SPI-MMC was used in 67% (2029/3023) NMIBC patients. In 1860 NMIBC patients undergoing TURBT, RRFFC, rate of residual cancer, and rate of pT2 at re-TURBT were 13% (116/888), 33% (212/653), and 2.9% (19/653), respectively. SPI-MMC was associated with lower RRFFC, independent of all variables including hospital volume and surgeon. Presence of DM in the specimen halved the likelihood of residual disease in pT1 cancers. The main limitation is the lack of a pre-QPI introduction cohort for comparison. Conclusions: The implementation of a QI programme in Scotland appears to facilitate high-quality TURBT, which in a real-world setting is associated with low early recurrence/residual cancer and accurate pathological staging. Patient summary: Following the first 3 yr of implementing a novel Quality Performance Indicator (QPI) programme in Scotland, we assessed compliance and outcomes in non–muscle-invasive bladder cancer. Evaluating over 4000 new bladder cancer patients, we found that the QPI programme was associated with low recurrence and accurate staging following the initial transurethral resection of bladder tumour