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.

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.

Database resources of the National Center for Biotechnology Information.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 38 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Labs and a new sequence database search. Resources that were updated in the past year include PubMed, PMC, Bookshelf, genome data viewer, Assembly, prokaryotic genomes, Genome, BioProject, dbSNP, dbVar, BLAST databases, igBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

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: improving access to variant interpretations and supporting evidence.

ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) is a freely available, public archive of human genetic variants and interpretations of their significance to disease, maintained at the National Institutes of Health. Interpretations of the clinical significance of variants are submitted by clinical testing laboratories, research laboratories, expert panels and other groups. ClinVar aggregates data by variant-disease pairs, and by variant (or set of variants). Data aggregated by variant are accessible on the website, in an improved set of variant call format files and as a new comprehensive XML report. ClinVar recently started accepting submissions that are focused primarily on providing phenotypic information for individuals who have had genetic testing. Submissions may come from clinical providers providing their own interpretation of the variant ('provider interpretation') or from groups such as patient registries that primarily provide phenotypic information from patients ('phenotyping only'). ClinVar continues to make improvements to its search and retrieval functions. Several new fields are now indexed for more precise searching, and filters allow the user to narrow down a large set of search results.

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.

Pathological ribonuclease H1 causes R-loop depletion and aberrant DNA segregation in mitochondria.

The genetic information in mammalian mitochondrial DNA is densely packed; there are no introns and only one sizeable noncoding, or control, region containing key cis-elements for its replication and expression. Many molecules of mitochondrial DNA bear a third strand of DNA, known as "7S DNA," which forms a displacement (D-) loop in the control region. Here we show that many other molecules contain RNA as a third strand. The RNA of these R-loops maps to the control region of the mitochondrial DNA and is complementary to 7S DNA. Ribonuclease H1 is essential for mitochondrial DNA replication; it degrades RNA hybridized to DNA, so the R-loop is a potential substrate. In cells with a pathological variant of ribonuclease H1 associated with mitochondrial disease, R-loops are of low abundance, and there is mitochondrial DNA aggregation. These findings implicate ribonuclease H1 and RNA in the physical segregation of mitochondrial DNA, perturbation of which represents a previously unidentified disease mechanism.

IFN-free therapy is associated with restoration of type I IFN response in HIV-1 patients with acute HCV infection who achieve SVR.

Interferon (IFN)-free direct-acting antiviral agents (DAAs) have revolutionized chronic hepatitis C virus (HCV) treatment; early studies suggest excellent efficacy in acute HCV. However, changes in innate immune responses during DAA therapy for acute HCV are unknown. We studied interferon-stimulated gene (ISG) expression and related cytokines/chemokines in HIV-infected patients with acute HCV receiving sofosbuvir plus ribavirin (SOF+RBV) as part of the A5327 clinical trial. ISG expression was determined from PBMCs, and circulating cytokines/chemokines were quantified from serum from study participants. The overall sustained virologic response (SVR) was 57%; all treatment failures were due to virologic relapse. Apart from NOS2a, baseline ISG/chemokine/cytokine levels were similar irrespective of treatment outcome. Downregulation of ISGs was observed at treatment week four and end of treatment (EOT), implicating HCV in establishing elevated ISGs early during HCV infection. Levels of many of these ISGs increased at post-treatment week 12 (PTW12) in relapsers only, coinciding with recurrent HCV RNA. Eleven ISGs were differentially expressed in responders vs relapsers. On-treatment viral suppression was also associated with a reduction in IP-10, CXCL11 and MIP-1ß levels. In contrast, circulating IFN-α levels were significantly higher at EOT and PTW12 in responders vs relapsers. Upregulation of peripheral ISG expression is established early in the course of HCV infection during acute HCV infection, but did not predict subsequent treatment outcome with SOF+RBV. ISGs were downregulated during therapy and increased post-therapy in relapsers. IFN-α levels were higher in responders at EOT/PTW12, suggesting that impaired type I IFN production/secretion may contribute to relapse.

Optical coherence tomography of basal cell carcinoma: influence of location, subtype, observer variability and image quality on diagnostic performance.

BACKGROUND: We previously described the principal results from an observational, prospective, multicentre, clinical trial of the diagnostic value of optical coherence tomography (OCT) for basal cell carcinoma (BCC) in a clinical setting. In this trial, much additional useful information was gathered that warranted further analysis, presented here. OBJECTIVES: To investigate the influence of candidate diagnostic criteria, OCT image quality, lesion location, and observer confidence and interobserver variability on the diagnostic performance of OCT, and to assess its potential use for diagnosis of BCC subtypes. METHODS: A total of 234 clinically unclear 'pink lesions' were evaluated in three steps: after clinical examination, after adding dermoscopy and after adding OCT. In addition to the diagnoses (including lesion subtype), observers recorded which of 15 diagnostic criteria the OCT image contained, their confidence in the diagnoses, the OCT image quality and the anatomical location of the lesion. RESULTS: Diagnostic performance of OCT did not depend on the lesion's anatomical location. Good OCT image quality was correlated with improved diagnostic performance, but diagnostic performance for lesions with mediocre image quality was still better than by clinical and dermoscopic examination. The main reason for reduced image quality was superficial scales and crusting. Observer confidence in diagnosis was correlated with diagnostic performance. Interobserver diagnostic performance was consistently higher than clinical examination and dermoscopy across all sites. BCC subtype could be determined with moderate accuracy, but further independent image markers are required. CONCLUSION: OCT is useful in the diagnosis of BCC.

Optical coherence tomography for margin definition of basal cell carcinoma before micrographic surgery-recommendations regarding the marking and scanning technique.

BACKGROUND/PURPOSE: Mohs Micrographic Surgery (MMS) is the preferred therapeutic treatment for high-risk basal cell carcinoma (BCC). Optical Coherence Tomography (OCT) is a non-invasive imaging technique that enables the diagnosis of BCC. We thought to determine the margins of BCCs with OCT, prior to MMS, to reduce the number of surgical steps. METHODS: Different permanent markers were tested on the skin regarding line width, resistance against disinfection and brightness in the OCT image. The visible tumor margins of BCCs were defined by dermoscopy, adding a safety margin of 2 mm and labeled using the selected pen, causing a signal shadow in OCT. Scans of the center and of entire margin were performed. If parts of the BCC were visible outside the margin, another 2 mm were added and the scan was repeated until the tissue outside the labeling looked tumor free. RESULTS: Eight out of ten BCCs were totally excised in a single stage when margin delineation was done by OCT. Macroscopic margins were enlarged after OCT scanning in four patients, saving further stages of MMS. CONCLUSION: OCT may help to better define the microscopic dimensions of BCCs and therefore reduce the number of stages of MMS.

Dynamic optical coherence tomography of histamine induced wheals.

BACKGROUND: Dynamic optical coherence tomography (D-OCT) is a noninvasive imaging technique providing images of the skin and detecting movement in the tissue ie, measuring blood flow. The "attenuation coefficient" describes light absorption and scattering abilities of the tissue, while the dynamic signal provides a quantitative measure of the blood flow. AIM: The study objective is to describe the dynamic changes of the skin and skin vessels during histamine release using D-OCT. METHODS: Healthy volunteers had local histamine injections in the skin and D-OCT-scans performed at 2-minute intervals to detect changes in blood flow, attenuation and clinical symptoms. RESULTS: 9/10 participants showed clinical wheals. An increase in blood flow was shown at all depths (P < .001 at 2 minutes). The highest relative increase was seen at 300 µm. The signal at 500 µm decreased to insignificant values and remained low after 4 minutes. A decrease in visualization depth of up to 32.7% as well as a significant increase in the attenuation coefficient was shown (P < .001 at 12 minutes for both tests). CONCLUSION: Dynamic optical coherence tomography is able to reliably identify changes in blood flow of histamine induced wheals. Dermal oedema reduces visualization depth and increases the attenuation coefficient.

Interdisciplinary working in public health research: a proposed good practice checklist.

Background: Guidance on how different disciplines from the natural, behavioural and social sciences can collaborate to resolve complex public health problems is lacking. This article presents a checklist to support researchers and principle investigators to develop and implement interdisciplinary collaborations. Methods: Fourteen individuals, representing 10 disciplines, participated in in-depth interviews to explore the strengths and challenges of working together on an interdisciplinary project to identify the determinants of substance use and gambling disorders, and to make recommendations for future interdisciplinary teams. Data were analysed thematically and a checklist was derived from insights offered by participants during interview and discussion among the authors on the implications of findings. Results: Participants identified 18 scientific, interactional and structural strengths and challenges of interdisciplinary research. These findings were used to develop an 18-item BASICS checklist to support future interdisciplinary collaborations. The five domains of the checklist are: (i) Blueprint, (ii) Attitudes, (iii) Staffing, (iv) Interactions and (v) Core Science. Conclusion: Interdisciplinary work has the potential to advance public health science but the numerous challenges should not be underestimated. Use of a checklist, such as BASICS, when planning and managing projects may help future collaborations to avoid some of the common pitfalls of interdisciplinary research.

Dynamic optical coherence tomography of skin blood vessels - proposed terminology and practical guidelines.

BACKGROUND: Dynamic optical coherence tomography (D-OCT) has recently been introduced in dermatology. In contrast to 'Standard' OCT imaging, which exclusively relies on the morphological analysis of the tissue, D-OCT allows the in vivo visualization of blood flow. Preliminary D-OCT data showed differences in the vascularization of nevus to melanoma transition, suggesting that this technology may help to differentiate between benign and malignant lesions. OBJECTIVE: Several factors may influence the quality of D-OCT imaging. Therefore, standard operating procedures as well as a common terminology are required for better validation and comparison of the images. METHODS: Here, we present practical guidelines for optimal image acquisition and a proposed terminology on vascular patterns observed by D-OCT. RESULTS: Dynamic OCT allows the morphologic distinction of different vascular shapes (e.g. dots, blobs, curves, lines), their distribution and organization within skin lesions. CONCLUSION: D-OCT adds functional information on skin microvasculature and the vascular networks within lesions.

Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication.

Encoding ribonuclease H1 (RNase H1) degrades RNA hybridized to DNA, and its function is essential for mitochondrial DNA maintenance in the developing mouse. Here we define the role of RNase H1 in mitochondrial DNA replication. Analysis of replicating mitochondrial DNA in embryonic fibroblasts lacking RNase H1 reveals retention of three primers in the major noncoding region (NCR) and one at the prominent lagging-strand initiation site termed Ori-L. Primer retention does not lead immediately to depletion, as the persistent RNA is fully incorporated in mitochondrial DNA. However, the retained primers present an obstacle to the mitochondrial DNA polymerase γ in subsequent rounds of replication and lead to the catastrophic generation of a double-strand break at the origin when the resulting gapped molecules are copied. Hence, the essential role of RNase H1 in mitochondrial DNA replication is the removal of primers at the origin of replication.

Single arm two-stage studies: Improved designs for molecularly targeted agents.

Mechanistic understanding of cancers and their potential interactions with molecularly targeted agents is driving the need for stratified medicine to ensure each participant receives the best possible care. This understanding, backed by scientific research, should be used to guide the design of clinical trials for these agents. The mechanism of action of a molecularly targeted agent often suggests that a biomarker can be used as a predictor of activity of the agent on the targeted disease. A biomarker driven trial is needed to confirm that the molecularly targeted agent stratifies the participant population with disease into high and low responder groups. We assume that the biomarker of interest can be dichotomised and propose a balanced parallel two-stage single-arm phase II trial that builds on existing two-stage single-arm designs. A single-arm trial cannot distinguish between a marker being predictive in the population as a whole and the agent causing an increased response in the marker positive group, but it is a first step. We compare this approach to the existing single-arm approaches, sequential enrichment, tandem two-stage, and parallel two-stage designs, and discuss the advantages and disadvantages of each design. We show that our design compares favourably to existing designs in the Bayesian framework, making a more efficient use of collected data. We recommend using the parallel two-stage balanced or sequential enrichment designs when randomisation is not practical in a phase II trial.

Statistical controversies in clinical research: publication bias evaluations are not routinely conducted in clinical oncology systematic reviews.

Background: Publication bias is an over-representation of statistically significant results in the published literature and may exaggerate summary effect estimates in oncology systematic reviews. Omitting non-significant results in systematic reviews may therefore affect clinical decision-making. We investigate ways that systematic reviewers attempted to limit publication bias during the search process as well as the statistical methods used to evaluate it. For a subset of reviews not reporting publication bias evaluations, we carried out our own assessments for publication bias to determine its likelihood among these reviews. Design: We examined systematic reviews from the top five highest impact factor oncology journals published between 2007 and 2015. Systematic reviews were screened for eligibility and qualifying reviews (n = 182) were coded for relevant publication bias study characteristics by two authors. A re-analysis of reviews not initially evaluating for publication bias was carried out using Egger's regression, trim-and-fill, and selection models. Results: Of the 182 systematic reviews, roughly half carried out a hand search to locate additional studies. Conference abstracts were the most commonly reported form of gray literature, followed by clinical trials registries. Fifty-one reviews reported publication bias evaluations. The most common method was the funnel plot (80%, 41/51) followed by Egger's regression (59%, 30/51) and Begg's test (43%, 22/51). Our publication bias evaluations on non-reporting reviews suggest that the degree of publication bias depends on the method employed. Conclusion: Our study shows publication bias assessments are not frequently used in oncology systematic reviews. Furthermore, evidence of publication bias was found in a subset of non-reporting reviews. Systematic reviewers in oncology are encouraged to conduct such analyses when appropriate and to employ more robust methods for both mitigating and evaluating publication bias.

Temporal electronic phenotyping by mining careflows of breast cancer patients.

In this work we present a careflow mining approach designed to analyze heterogeneous longitudinal data and to identify phenotypes in a patient cohort. The main idea underlying our approach is to combine methods derived from sequential pattern mining and temporal data mining to derive frequent healthcare histories (careflows) in a population of patients. This approach was applied to an integrated data repository containing clinical and administrative data of more than 4000 breast cancer patients. We used the mined histories to identify sub-cohorts of patients grouped according to healthcare activities pathways, then we characterized these sub-cohorts with clinical data. In this way, we were able to perform temporal electronic phenotyping of electronic health records (EHR) data.

In vivo microvascular imaging of cutaneous actinic keratosis, Bowen's disease and squamous cell carcinoma using dynamic optical coherence tomography.

BACKGROUND: A clear distinction between actinic keratosis (AK), Bowen's disease (BD) and squamous cell carcinoma (SCC) cannot reliably be made by clinical and dermoscopic evaluation alone. Dynamic optical coherence tomography (D-OCT) is a novel angiographic variant of OCT that allows for non-invasive, in vivo evaluation of the cutaneous microvascular morphology. OBJECTIVE: To investigate the microvascular structures of AK, BD and invasive SCC using D-OCT in order to gain insights into the microvascular morphology of lesions in the spectrum of keratinocyte skin cancers. METHODS: Forty-seven patients with a total of 54 lesions (18 AK, 12 BD and 24 SCC) were included in the study. D-OCT still images of AK, BD and SCC at three predefined skin depths were prepared and randomized, creating a study set of 162 D-OCT images. Three observers performed blinded evaluations of the randomized study set assessing multiple parameters including the different types of vascular morphology. Non-blinded quantitative measurements of vascular diameter were also performed. RESULTS: The blinded observer analysis suggests that D-OCT evaluation of the vascular morphology may aid in distinguishing AK, BD and SCC lesions. We identified two vascular shapes that presented significantly differently across the lesion types, namely 'blobs' and 'curves'. A strong presence of blobs at 300 µm skin depth was characteristically seen in a third of BD cases, while not or only slightly present in AK and SCC lesions. Vascular curves were predominantly present in AK lesions. CONCLUSION: We identified various vascular D-OCT features that may aid in non-invasively differentiating subtypes within the keratinocyte skin cancer spectrum.