Raw diffraction data and reproducibility

In recent years, there has been a major expansion in digital storage capability for hosting raw diffraction datasets. Naturally, the question has now arisen as to the benefits and costs for the preservation of such raw, i.e., experimental diffraction datasets. We describe the consultations made of the global structural chemistry, i.e., chemical crystallography community from the points of view of the International Union of Crystallography (IUCr) Committee on Data, of which JRH was the Chair until very recently, and the IUCrData Raw Data Letters initiative, for which LKB is the Main Editor. The monitoring by the CCDC of CSD depositions which cite the digital object identifiers of raw diffraction datasets provides interesting statistics by probe (x-ray, neutron, or electron) and by home lab vs central facility. Clearly, a better understanding of the reproducibility of current analysis procedures is at hand. Policies for publication requiring raw data have been updated in IUCr Journals for macromolecular crystallography, namely, that raw data should be made available for a new crystal structure or a new method as well as the wwPDB deposition. For chemical crystallography, such a step requiring raw data archiving has not yet been recommended by the IUCr Commission on Structural Chemistry

Polymorphisms in the Estrogen Receptor 1 and Vitamin C and Matrix Metalloproteinase Gene Families Are Associated with Susceptibility to Lymphoma

BACKGROUND: Non-Hodgkin lymphoma (NHL) is the fifth most common cancer in the U.S. and few causes have been identified. Genetic association studies may help identify environmental risk factors and enhance our understanding of disease mechanisms. METHODOLOGY/PRINCIPAL FINDINGS: 768 coding and haplotype tagging SNPs in 146 genes were examined using Illumina GoldenGate technology in a large population-based case-control study of NHL in the San Francisco Bay Area (1,292 cases 1,375 controls are included here). Statistical analyses were restricted to HIV- participants of white non-Hispanic origin. Genes involved in steroidogenesis, immune function, cell signaling, sunlight exposure, xenobiotic metabolism/oxidative stress, energy balance, and uptake and metabolism of cholesterol, folate and vitamin C were investigated. Sixteen SNPs in eight pathways and nine haplotypes were associated with NHL after correction for multiple testing at the adjusted q<0.10 level. Eight SNPs were tested in an independent case-control study of lymphoma in Germany (494 NHL cases and 494 matched controls). Novel associations with common variants in estrogen receptor 1 (ESR1) and in the vitamin C receptor and matrix metalloproteinase gene families were observed. Four ESR1 SNPs were associated with follicular lymphoma (FL) in the U.S. study, with rs3020314 remaining associated with reduced risk of FL after multiple testing adjustments [odds ratio (OR) = 0.42, 95% confidence interval (CI) = 0.23-0.77) and replication in the German study (OR = 0.24, 95% CI = 0.06-0.94). Several SNPs and haplotypes in the matrix metalloproteinase-3 (MMP3) and MMP9 genes and in the vitamin C receptor genes, solute carrier family 23 member 1 (SLC23A1) and SLC23A2, showed associations with NHL risk. CONCLUSIONS/SIGNIFICANCE: Our findings suggest a role for estrogen, vitamin C and matrix metalloproteinases in the pathogenesis of NHL that will require further validation

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Deposition of Structure Factors: Trends 2011-2016

Analysis of how often structures deposited at the Cambridge Crystallographic Data Centre between January 2011 and June 2016 were accompanied by additional structure factor files

Hand hygiene monitoring technology: protocol for a systematic review

Abstract Background Healthcare worker hand hygiene is thought to be one of the most important strategies to prevent healthcare-associated infections, but compliance is generally poor. Hand hygiene improvement interventions must include audits of compliance (almost always with feedback), which are most often done by direct observation - a method that is expensive, subjective, and prone to bias. New technologies, including electronic and video hand hygiene monitoring systems, have the potential to provide continuous and objective monitoring of hand hygiene, regular feedback, and for some systems, real-time reminders. We propose a systematic review of the evidence supporting the effectiveness of these systems. The primary objective is to determine whether hand hygiene monitoring systems yield sustainable improvements in hand hygiene compliance when compared to usual care. Methods/Design MEDLINE, EMBASE, CINAHL, and other relevant databases will be searched for randomized control studies and quasi-experimental studies evaluating a video or electronic hand hygiene monitoring system. A standard data collection form will be used to abstract relevant information from included studies. Bias will be assessed using the Cochrane Effective Practice and Organization of Care Group Risk of Bias Assessment Tool. Studies will be reviewed independently by two reviewers, with disputes resolved by a third reviewer. The primary outcome is directly observed hand hygiene compliance. Secondary outcomes include healthcare-associated infection incidence and improvements in hand hygiene compliance as measured by alternative metrics. Results will be qualitatively summarized with comparisons made between study quality, the measured outcome, and study-specific factors that may be expected to affect outcome (for example, study duration, frequency of feedback, use of real-time reminders). Meta-analysis will be performed if there is more than one study of similar systems with comparable outcome definitions. Discussion Electronic and video monitoring systems have the potential to improve hand hygiene compliance and prevent healthcare-associated infection, but are expensive, difficult to install and maintain, and may not be accepted by all healthcare workers. This review will assess the current evidence of effectiveness of these systems before their widespread adoption. Study registration PROSPERO registration number: CRD4201300451

Raw diffraction data and reproducibility

In recent years, there has been a major expansion in digital storage capability for hosting raw diffraction datasets. Naturally, the question has now arisen as to the benefits and costs for the preservation of such raw, i.e., experimental diffraction datasets. We describe the consultations made of the global structural chemistry, i.e., chemical crystallography community from the points of view of the International Union of Crystallography (IUCr) Committee on Data, of which JRH was the Chair until very recently, and the IUCrData Raw Data Letters initiative, for which LKB is the Main Editor. The monitoring by the CCDC of CSD depositions which cite the digital object identifiers of raw diffraction datasets provides interesting statistics by probe (x-ray, neutron, or electron) and by home lab vs central facility. Clearly, a better understanding of the reproducibility of current analysis procedures is at hand. Policies for publication requiring raw data have been updated in IUCr Journals for macromolecular crystallography, namely, that raw data should be made available for a new crystal structure or a new method as well as the wwPDB deposition. For chemical crystallography, such a step requiring raw data archiving has not yet been recommended by the IUCr Commission on Structural Chemistry

Transformational grammar : a first course

Transformational Grammar A First Course is principally for students with little or no background in syntax who need a lively and up to date introduction to contemporary work on transformational grammar.xiI, 605 p.: ill.; 22,5 c

Transformational grammar : a first course

Transformational Grammar A First Course is principally for students with little or no background in syntax who need a lively and up to date introduction to contemporary work on transformational grammar.xiI, 605 p.: ill.; 22,5 c

Transformational grammar : a first course

Transformational Grammar A First Course is principally for students with little or no background in syntax who need a lively and up to date introduction to contemporary work on transformational grammar.xiI, 605 p.: ill.; 22,5 c