CHARIOT: a phase I study of berzosertib with chemoradiotherapy in oesophageal and other solid cancers using time to event continual reassessment method.

BACKGROUND: Berzosertib (M6620) is a highly potent (IC50 = 19 nM) and selective, first-in-class ataxia telangiectasia-mutated and Rad3-related protein kinase (ATR) inhibitor. This trial assessed the safety, preliminary efficacy, and tolerance of berzosertib in oesophageal cancer (A1 cohort) with RT and advanced solid tumours (A2 cohort) with cisplatin and capecitabine. METHODS: Single-arm, open-label dose-escalation (Time-to-Event Continual Reassessment Method) trial with 16 patients in A1 and 18 in A2. A1 tested six dose levels of berzosertib with RT (35 Gy over 15 fractions in 3 weeks). RESULTS: No dose-limiting toxicities (DLTs) in A1. Eight grade 3 treatment-related AEs occurred in five patients, with rash being the most common. The highest dose (240 mg/m2) was determined as the recommended phase II dose (RP2D) for A1. Seven DLTs in two patients in A2. The RP2D of berzosertib was 140 mg/m2 once weekly. The most common grade ≥3 treatment-related AEs were neutropenia and thrombocytopenia. No treatment-related deaths were reported. CONCLUSIONS: Berzosertib combined with RT is feasible and well tolerated in oesophageal cancer patients at high palliative doses. Berzosertib with cisplatin and capecitabine was well tolerated in advanced cancer. Further investigation is warranted in a phase 2 setting. CLINICAL TRIALS IDENTIFIER: EU Clinical Trials Register (EudraCT) - 2015-003965-27 ClinicalTrials.gov - NCT03641547.

Evaluating the effects of minimum unit pricing in Scotland on the prevalence of harmful drinking: a controlled interrupted time series analysis.

OBJECTIVES: In May 2018, the Scottish Government introduced a minimum unit price (MUP) for alcohol of £0.50 (1 UK unit = 8 g ethanol) to reduce alcohol consumption, particularly among people drinking at harmful levels. This study aimed to evaluate MUP's impact on the prevalence of harmful drinking among adults in Scotland. STUDY DESIGN: This was a controlled interrupted monthly time series analysis of repeat cross-sectional data collected via 1-week drinking diaries from adult drinkers in Scotland (N = 38,674) and Northern England (N = 71,687) between January 2009 and February 2020. METHODS: The primary outcome was the proportion of drinkers consuming at harmful levels (>50 [men] or >35 [women] units in diary week). The secondary outcomes included the proportion of drinkers consuming at hazardous (≥14-50 [men] or ≥14-35 [women] units) and moderate (<14 units) levels and measures of beverage preferences and drinking patterns. Analyses also examined the prevalence of harmful drinking in key subgroups. RESULTS: There was no significant change in the proportion of drinkers consuming at harmful levels (ß = +0.6 percentage points; 95% confidence interval [CI] = -1.1, +2.3) or moderate levels (ß = +1.4 percentage points; 95% confidence interval = -1.1, +3.8) after the introduction of MUP. The proportion consuming at hazardous levels fell significantly by 3.5 percentage points (95% CI = -5.4, -1.7). There were no significant changes in other secondary outcomes or in the subgroup analyses after correction for multiple testing. CONCLUSIONS: Introducing MUP in Scotland was not associated with reductions in the proportion of drinkers consuming at harmful levels but did reduce the prevalence of hazardous drinking. This adds to previous evidence that MUP reduced overall alcohol consumption in Scotland and consumption among those drinking above moderate levels.

Global Vertical Distribution of Water Vapor on Mars: Results From 3.5 Years of ExoMars-TGO/NOMAD Science Operations.

We present water vapor vertical distributions on Mars retrieved from 3.5 years of solar occultation measurements by Nadir and Occultation for Mars Discovery onboard the ExoMars Trace Gas Orbiter, which reveal a strong contrast between aphelion and perihelion water climates. In equinox periods, most of water vapor is confined into the low-middle latitudes. In aphelion periods, water vapor sublimated from the northern polar cap is confined into very low altitudes-water vapor mixing ratios observed at the 0-5 km lower boundary of measurement decrease by an order of magnitude at the approximate altitudes of 15 and 30 km for the latitudes higher than 50°N and 30-50°N, respectively. The vertical confinement of water vapor at northern middle latitudes around aphelion is more pronounced in the morning terminators than evening, perhaps controlled by the diurnal cycle of cloud formation. Water vapor is also observed over the low latitude regions in the aphelion southern hemisphere (0-30°S) mostly below 10-20 km, which suggests north-south transport of water still occurs. In perihelion periods, water vapor sublimated from the southern polar cap directly reaches high altitudes (>80 km) over high southern latitudes, suggesting more effective transport by the meridional circulation without condensation. We show that heating during perihelion, sporadic global dust storms, and regional dust storms occurring annually around 330° of solar longitude (L S) are the main events to supply water vapor to the upper atmosphere above 70 km.

Impacts of Heterogeneous Chemistry on Vertical Profiles of Martian Ozone.

We show a positive vertical correlation between ozone and water ice using a vertical cross-correlation analysis with observations from the ExoMars Trace Gas Orbiter's Nadir and Occultation for Mars Discovery instrument. This is particularly apparent during L S = 0°-180°, Mars Year 35 at high southern latitudes, when the water vapor abundance is low. Ozone and water vapor are anti-correlated on Mars; Clancy et al. (2016, https://doi.org/10.1016/j.icarus.2015.11.016) also discuss the anti-correlation between ozone and water ice. However, our simulations with gas-phase-only chemistry using a 1-D model show that ozone concentration is not influenced by water ice. Heterogeneous chemistry has been proposed as a mechanism to explain the underprediction of ozone in global climate models (GCMs) through the removal of HO x . We find improving the heterogeneous chemical scheme by creating a separate tracer for the HO x adsorbed state, causes ozone abundance to increase when water ice is present (30-50 km), better matching observed trends. When water vapor abundance is high, there is no consistent vertical correlation between observed ozone and water ice and, in simulated scenarios, the heterogeneous chemistry has a minor influence on ozone. HO x , which are by-products of water vapor, dominate ozone abundance, masking the effects of heterogeneous chemistry on ozone, and making adsorption of HO x have a negligible impact on ozone. This is consistent with gas-phase-only modeled ozone, showing good agreement with observations when water vapor is abundant. Overall, the inclusion of heterogeneous chemistry improves the ozone vertical structure in regions of low water vapor abundance, which may partially explain GCM ozone deficits.

Global Variations in Water Vapor and Saturation State Throughout the Mars Year 34 Dusty Season.

To understand the evolving martian water cycle, a global perspective of the combined vertical and horizontal distribution of water is needed in relation to supersaturation and water loss and how it varies spatially and temporally. The global vertical water vapor distribution is investigated through an analysis that unifies water, temperature and dust retrievals from several instruments on multiple spacecraft throughout Mars Year (MY) 34 with a global circulation model. During the dusty season of MY 34, northern polar latitudes are largely absent of water vapor below 20 km with variations above this altitude due to transport from mid-latitudes during a global dust storm, the downwelling branch of circulation during perihelion season and the intense MY 34 southern summer regional dust storm. Evidence is found of supersaturated water vapor breaking into the northern winter polar vortex. Supersaturation above around 60 km is found for most of the time period, with lower altitudes showing more diurnal variation in the saturation state of the atmosphere. Discrete layers of supersaturated water are found across all latitudes. The global dust storm and southern summer regional dust storm forced water vapor at all latitudes in a supersaturated state to 60-90 km where it is more likely to escape from the atmosphere. The reanalysis data set provides a constrained global perspective of the water cycle in which to investigate the horizontal and vertical transport of water throughout the atmosphere, of critical importance to understand how water is exchanged between different reservoirs and escapes the atmosphere.

Addressing COVID-19 health disparities through a regional community health response.

To combat racial/ethnic and socioeconomic health disparities associated with COVID-19 in our surrounding communities, the Cleveland Clinic Community Health & Partnership team developed a comprehensive program focused on connecting and communicating with local officials, faith-based organizations, and individual community members. Since March of 2020, our team has donated resources (e.g., personal protective equipment) to local organizations, referred thousands of community members to community or clinical resources, and partnered with federally-qualified health centers to support community COVID-19 testing. Future work will include the use of these networks to deploy the COVID-19 vaccine.

Dynamic optical coherence tomography shows characteristic alterations of blood vessels in malignant melanoma.

BACKGROUND: Dynamic optical coherence tomography (D-OCT) allows in vivo visualization of blood vessels in the skin and in malignant tumours. Vessel patterns in malignant melanoma may be associated with tumour stage. OBJECTIVE: The aim of this study was to describe blood vessel patterns in melanomas and to correlate them with stage. METHODS: One hundred fifty-nine malignant melanomas were assessed in a multicentre study. Every tumour was imaged using D-OCT prior to surgery and histologic evaluation. The tumour data such as thickness and ulceration as well as the staging at primary diagnosis and a follow-up of at least 40 months resulted in a stage classification. The vessel patterns were assessed according to predefined categories, compared with healthy adjacent skin, and correlated to stage. RESULTS: Melanomas contained more blood vessels in different patterns compared with healthy adjacent skin. In particular, irregular vascular shapes such as blobs, coils, curves and serpiginous vessels were more common in melanomas. In addition, these patterns were significantly more often found in high-risk and metastatic melanomas than in low-risk lesions. CONCLUSION: In melanomas, the density of the blood vessels is increased, and irregular vascular patterns are more frequent. At higher stages, especially in metastatic melanomas, these atypical vessels are significantly more common.

ClinVar: improvements to accessing data.

ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH). Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.nlm.nih.gov/clinvar/), and as downloadable files via FTP and through programmatic tools such as NCBI's E-utilities. The default view on the ClinVar website, the Variation page, was recently redesigned. The new layout includes several new sections that make it easier to find submitted data as well as summary data such as all diseases and citations reported for the variant. The new design also better represents more complex data such as haplotypes and genotypes, as well as variants that are in ClinVar as part of a haplotype or genotype but have no interpretation for the single variant. ClinVar's variant-centric XML had its production release in April 2019. The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file. ClinVar's search engine has been fine-tuned for improved retrieval of search results.

SPDI: data model for variants and applications at NCBI.

MOTIVATION: Normalizing sequence variants on a reference, projecting them across congruent sequences and aggregating their diverse representations are critical to the elucidation of the genetic basis of disease and biological function. Inconsistent representation of variants among variant callers, local databases and tools result in discrepancies that complicate analysis. NCBI's genetic variation resources, dbSNP and ClinVar, require a robust, scalable set of principles to manage asserted sequence variants. RESULTS: The SPDI data model defines variants as a sequence of four attributes: sequence, position, deletion and insertion, and can be applied to nucleotide and protein variants. NCBI web services convert representations among HGVS, VCF and SPDI and provide two functions to aggregate variants. One, based on the NCBI Variant Overprecision Correction Algorithm, returns a unique, normalized representation termed the 'Contextual Allele'. The SPDI data model, with its four operations, defines exactly the reference subsequence affected by the variant, even in repeat regions, such as homopolymer and other sequence repeats. The second function projects variants across congruent sequences and depends on an alignment dataset of non-assembly NCBI RefSeq sequences (prefixed NM, NR and NG), as well as inter- and intra-assembly-associated genomic sequences (NCs, NTs and NWs), supporting robust projection of variants across congruent sequences and assembly versions. The variant is projected to all congruent Contextual Alleles. One of these Contextual Alleles, typically the allele based on the latest assembly version, represents the entire set, is designated the unique 'Canonical Allele' and is used directly to aggregate variants across congruent sequences. AVAILABILITY AND IMPLEMENTATION: The SPDI services are available for open access at: https://api.ncbi.nlm.nih.gov/variation/v0. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cardiovascular and renal outcomes following percutaneous coronary intervention in a population with renal disease: a case-control study.

BACKGROUND: Patients with renal disease are less likely to undergo percutaneous coronary intervention (PCI) due to concerns about poor outcomes. AIM: We describe outcomes following PCI in individuals with chronic kidney disease (CKD), as compared with matched controls with comparable CKD who did not undergo PCI. We also identified factors predictive of poor outcomes following PCI amongst patients with CKD. DESIGN: Retrospective observational case-control study. METHODS: Cases were individuals with CKD (stages 1-5) undergoing PCI between 2008 and 2014. Controls were age, gender and creatinine-matched individuals not requiring PCI. We compared mortality between groups using Kaplan-Meier curves and Cox regression modelling. We assessed changes in serum creatinine using Wilcoxon Rank testing. We explored the relationship between biochemical and haematological measures (baseline creatinine, calcium, phosphate, calcium-phosphate product, parathyroid hormone, white cell count, haemoglobin, platelet count, c-reactive protein and total cholesterol) and post-PCI mortality, using logistic regression. RESULTS: We identified 144 cases and 144 controls. Mortality was significantly lower amongst cases compared with controls [hazard ratio 0.46 (95% confidence intervals 0.31, 0.69)]. PCI did not result in a significant change in renal function (P=0.52). Amongst cases, serum creatinine and calcium-phosphate product were predictors of mortality following PCI. CONCLUSION: Cases undergoing PCI had lower mortality, and PCI was not associated with accelerated CKD progression. On this data, PCI should not be deferred as a treatment option in patients with CKD. Serum creatinine and calcium-phosphate product predict mortality following PCI in this cohort, and may be useful in risk-stratifying patients with CKD being considered for PCI.

GRAF-pop: A Fast Distance-Based Method To Infer Subject Ancestry from Multiple Genotype Datasets Without Principal Components Analysis.

Inferring subject ancestry using genetic data is an important step in genetic association studies, required for dealing with population stratification. It has become more challenging to infer subject ancestry quickly and accurately since large amounts of genotype data, collected from millions of subjects by thousands of studies using different methods, are accessible to researchers from repositories such as the database of Genotypes and Phenotypes (dbGaP) at the National Center for Biotechnology Information (NCBI). Study-reported populations submitted to dbGaP are often not harmonized across studies or may be missing. Widely-used methods for ancestry prediction assume that most markers are genotyped in all subjects, but this assumption is unrealistic if one wants to combine studies that used different genotyping platforms. To provide ancestry inference and visualization across studies, we developed a new method, GRAF-pop, of ancestry prediction that is robust to missing genotypes and allows researchers to visualize predicted population structure in color and in three dimensions. When genotypes are dense, GRAF-pop is comparable in quality and running time to existing ancestry inference methods EIGENSTRAT, FastPCA, and FlashPCA2, all of which rely on principal components analysis (PCA). When genotypes are not dense, GRAF-pop gives much better ancestry predictions than the PCA-based methods. GRAF-pop employs basic geometric and probabilistic methods; the visualized ancestry predictions have a natural geometric interpretation, which is lacking in PCA-based methods. Since February 2018, GRAF-pop has been successfully incorporated into the dbGaP quality control process to identify inconsistencies between study-reported and computationally predicted populations and to provide harmonized population values in all new dbGaP submissions amenable to population prediction, based on marker genotypes. Plots, produced by GRAF-pop, of summary population predictions are available on dbGaP study pages, and the software, is available at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/Software.cgi.

Resonance assisted jump-in voltage reduction for electrostatically actuated nanobeam-based gateless NEM switches.

Electrostatically actuated nanobeam-based electromechanical switches have shown promise for versatile novel applications, such as low power devices. However, their widespread use is restricted due to poor reliability resulting from high jump-in voltages. This article reports a new method for lowering the jump-in voltage by inducing mechanical oscillations in the active element during the switching ON process, reducing the jump-in voltage by more than three times. Ge0.91Sn0.09 alloy and Bi2Se3 nanowire-based nanoelectromechanical switches were constructed in situ to demonstrate the operation principles and advantages of the proposed method.

20 years of national wildlife disease surveillance.

The need for wildlife surveillance is as great now as it ever has been. Here, members of the APHA's Diseases of Wildlife Scheme explain why their work is important.