This paper presents an overview of how to run the CCP4 programs for data reduction (SCALA, POINTLESS and CTRUNCATE) through the CCP4 graphical interface ccp4i and points out some issues that need to ...be considered, together with a few examples. It covers determination of the point‐group symmetry of the diffraction data (the Laue group), which is required for the subsequent scaling step, examination of systematic absences, which in many cases will allow inference of the space group, putting multiple data sets on a common indexing system when there are alternatives, the scaling step itself, which produces a large set of data‐quality indicators, estimation of |F| from intensity and finally examination of intensity statistics to detect crystal pathologies such as twinning. An appendix outlines the scoring schemes used by the program POINTLESS to assign probabilities to possible Laue and space groups.
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N.
Acta crystallographica. Section D, Biological crystallography.,
July 2013, Letnik:
69, Številka:
7
Journal Article
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Following integration of the observed diffraction spots, the process of `data reduction' initially aims to determine the point‐group symmetry of the data and the likely space group. This can be ...performed with the program POINTLESS. The scaling program then puts all the measurements on a common scale, averages measurements of symmetry‐related reflections (using the symmetry determined previously) and produces many statistics that provide the first important measures of data quality. A new scaling program, AIMLESS, implements scaling models similar to those in SCALA but adds some additional analyses. From the analyses, a number of decisions can be made about the quality of the data and whether some measurements should be discarded. The effective `resolution' of a data set is a difficult and possibly contentious question (particularly with referees of papers) and this is discussed in the light of tests comparing the data‐processing statistics with trials of refinement against observed and simulated data, and automated model‐building and comparison of maps calculated with different resolution limits. These trials show that adding weak high‐resolution data beyond the commonly used limits may make some improvement and does no harm.
To develop more efficient programmes for promoting dietary and/or physical activity change (in order to prevent type 2 diabetes) it is critical to ensure that the intervention components and ...characteristics most strongly associated with effectiveness are included. The aim of this systematic review of reviews was to identify intervention components that are associated with increased change in diet and/or physical activity in individuals at risk of type 2 diabetes.
MEDLINE, EMBASE, CINAHL, PsycInfo, and the Cochrane Library were searched for systematic reviews of interventions targeting diet and/or physical activity in adults at risk of developing type 2 diabetes from 1998 to 2008. Two reviewers independently selected reviews and rated methodological quality. Individual analyses from reviews relating effectiveness to intervention components were extracted, graded for evidence quality and summarised.
Of 3856 identified articles, 30 met the inclusion criteria and 129 analyses related intervention components to effectiveness. These included causal analyses (based on randomisation of participants to different intervention conditions) and associative analyses (e.g. meta-regression). Overall, interventions produced clinically meaningful weight loss (3-5 kg at 12 months; 2-3 kg at 36 months) and increased physical activity (30-60 mins/week of moderate activity at 12-18 months). Based on causal analyses, intervention effectiveness was increased by engaging social support, targeting both diet and physical activity, and using well-defined/established behaviour change techniques. Increased effectiveness was also associated with increased contact frequency and using a specific cluster of "self-regulatory" behaviour change techniques (e.g. goal-setting, self-monitoring). No clear relationships were found between effectiveness and intervention setting, delivery mode, study population or delivery provider. Evidence on long-term effectiveness suggested the need for greater consideration of behaviour maintenance strategies.
This comprehensive review of reviews identifies specific components which are associated with increased effectiveness in interventions to promote change in diet and/or physical activity. To maximise the efficiency of programmes for diabetes prevention, practitioners and commissioning organisations should consider including these components.
Improvement of glucose levels into the normal range can occur in some people living with diabetes, either spontaneously or after medical interventions, and in some cases can persist after withdrawal ...of glucose-lowering pharmacotherapy. Such sustained improvement may now be occurring more often due to newer forms of treatment. However, terminology for describing this process and objective measures for defining it are not well established, and the long-term risks versus benefits of its attainment are not well understood. To update prior discussions of this issue, an international expert group was convened by the American Diabetes Association to propose nomenclature and principles for data collection and analysis, with the goal of establishing a base of information to support future clinical guidance. This group proposed "remission" as the most appropriate descriptive term, and HbA1c <6.5% (48 mmol/mol) measured at least 3 months after cessation of glucose-lowering pharmacotherapy as the usual diagnostic criterion. The group also made suggestions for active observation of individuals experiencing a remission and discussed further questions and unmet needs regarding predictors and outcomes of remission.
ObjectiveContinuity of care is a long-standing feature of healthcare, especially of general practice. It is associated with increased patient satisfaction, increased take-up of health promotion, ...greater adherence to medical advice and decreased use of hospital services. This review aims to examine whether there is a relationship between the receipt of continuity of doctor care and mortality.DesignSystematic review without meta-analysis.Data sourcesMEDLINE, Embase and the Web of Science, from 1996 to 2017.Eligibility criteria for selecting studiesPeer-reviewed primary research articles, published in English which reported measured continuity of care received by patients from any kind of doctor, in any setting, in any country, related to measured mortality of those patients.ResultsOf the 726 articles identified in searches, 22 fulfilled the eligibility criteria. The studies were all cohort or cross-sectional and most adjusted for multiple potential confounding factors. These studies came from nine countries with very different cultures and health systems. We found such heterogeneity of continuity and mortality measurement methods and time frames that it was not possible to combine the results of studies. However, 18 (81.8%) high-quality studies reported statistically significant reductions in mortality, with increased continuity of care. 16 of these were with all-cause mortality. Three others showed no association and one demonstrated mixed results. These significant protective effects occurred with both generalist and specialist doctors.ConclusionsThis first systematic review reveals that increased continuity of care by doctors is associated with lower mortality rates. Although all the evidence is observational, patients across cultural boundaries appear to benefit from continuity of care with both generalist and specialist doctors. Many of these articles called for continuity to be given a higher priority in healthcare planning. Despite substantial, successive, technical advances in medicine, interpersonal factors remain important.PROSPERO registration numberCRD42016042091.
Mastering dynamic free-space spectral control and modulation in the near-infrared (NIR) and optical regimes remains a challenging task that is hindered by the available functional materials at high ...frequencies. In this work, we have realized an efficient metadevice capable of spectral control by minimizing the thermal mass of a vanadium dioxide phase-change material (PCM) and placing the PCM at the feed gap of a bow-tie field antenna. The device has an experimentally measured tuning range of up to 360 nm in the NIR and a modulation depth of 33% at the resonant wavelength. The metadevice is configured for integrated and local heating, leading to faster switching and more precise spatial control compared with devices based on phase-change thin films. We envisage that the combined advantages of this device will open new opportunities for signal processing, memory, security, and holography at optical frequencies.
High-energy radiation preferentially degrades cellulose and enriches lignin content at wood surfaces particularly in hardwoods. Accordingly, we hypothesize that a similar effect will occur at ...surfaces exposed to plasma. We test this hypothesis by plasma-treating pine and poplar veneers and assessing changes in the lignin and holocellulose-derived sugar-content of veneers; quantifying etching of pellets containing lignin and cellulose, and observing etching of different cell wall layers in pine and Homalium. The majority but not all of our results support our hypothesis. Lignin-rich regions of wood cell walls were easier to see after plasma treatment. We discuss the potential uses of plasma-etching for the study of wood ultrastructure and the creation of wood surfaces with self-bonding properties, and conclude that plasma-etching can be used as an alternative to chemical pretreatments for ultrastructural studies of the distribution of lignin in wood cell walls.
This paper gives an overview of recent developments in non-coplanar intensity modulated radiotherapy (IMRT) and volumetric modulated arc therapy (VMAT). Modern linear accelerators are capable of ...automating motion around multiple axes, allowing efficient delivery of highly non-coplanar radiotherapy techniques. Novel techniques developed for C-arm and non-standard linac geometries, methods of optimization, and clinical applications are reviewed. The additional degrees of freedom are shown to increase the therapeutic ratio, either through dose escalation to the target or dose reduction to functionally important organs at risk, by multiple research groups. Although significant work is still needed to translate these new non-coplanar radiotherapy techniques into the clinic, clinical implementation should be prioritized. Recent developments in non-coplanar radiotherapy demonstrate that it continues to have a place in modern cancer treatment.
Radical radiotherapy for prostate cancer is effective but dose limited because of the proximity of normal tissues. Comprehensive dose-volume analysis of the incidence of clinically relevant late ...rectal toxicities could indicate how the dose to the rectum should be constrained. Previous emphasis has been on constraining the mid-to-high dose range (>/=50 Gy). Evidence is emerging that lower doses could also be important.
Data from a large multicenter randomized trial were used to investigate the correlation between seven clinically relevant rectal toxicity endpoints (including patient- and clinician-reported outcomes) and an absolute 5% increase in the volume of rectum receiving the specified doses. The results were quantified using odds ratios. Rectal dose-volume constraints were applied retrospectively to investigate the association of constraints with the incidence of late rectal toxicity.
A statistically significant dose-volume response was observed for six of the seven endpoints for at least one of the dose levels tested in the range of 30-70 Gy. Statistically significant reductions in the incidence of these late rectal toxicities were observed for the group of patients whose treatment plans met specific proposed dose-volume constraints. The incidence of moderate/severe toxicity (any endpoint) decreased incrementally for patients whose treatment plans met increasing numbers of dose-volume constraints from the set of V30<or=80%, V40<or=65%, V50<or=55%, V60<or=40%, V65<or=30%, V70<or=15%, and V75<or=3%.
Considering the entire dose distribution to the rectum by applying dose-volume constraints such as those tested here in the present will reduce the incidence of late rectal toxicity.
The goal of radiation therapy is to achieve maximal therapeutic benefit expressed in terms of a high probability of local control of disease with minimal side effects. Physically this often equates ...to the delivery of a high dose of radiation to the tumour or target region whilst maintaining an acceptably low dose to other tissues, particularly those adjacent to the target. Techniques such as intensity modulated radiotherapy (IMRT), stereotactic radiosurgery and computer planned brachytherapy provide the means to calculate the radiation dose delivery to achieve the desired dose distribution. Imaging is an essential tool in all state of the art planning and delivery techniques: (i) to enable planning of the desired treatment, (ii) to verify the treatment is delivered as planned and (iii) to follow-up treatment outcome to monitor that the treatment has had the desired effect. Clinical imaging techniques can be loosely classified into anatomic methods which measure the basic physical characteristics of tissue such as their density and biological imaging techniques which measure functional characteristics such as metabolism. In this review we consider anatomical imaging techniques. Biological imaging is considered in another article. Anatomical imaging is generally used for goals (i) and (ii) above. Computed tomography (CT) has been the mainstay of anatomical treatment planning for many years, enabling some delineation of soft tissue as well as radiation attenuation estimation for dose prediction. Magnetic resonance imaging is fast becoming widespread alongside CT, enabling superior soft-tissue visualization. Traditionally scanning for treatment planning has relied on the use of a single snapshot scan. Recent years have seen the development of techniques such as 4D CT and adaptive radiotherapy (ART). In 4D CT raw data are encoded with phase information and reconstructed to yield a set of scans detailing motion through the breathing, or cardiac, cycle. In ART a set of scans is taken on different days. Both allow planning to account for variability intrinsic to the patient. Treatment verification has been carried out using a variety of technologies including: MV portal imaging, kV portal/fluoroscopy, MVCT, conebeam kVCT, ultrasound and optical surface imaging. The various methods have their pros and cons. The four x-ray methods involve an extra radiation dose to normal tissue. The portal methods may not generally be used to visualize soft tissue, consequently they are often used in conjunction with implanted fiducial markers. The two CT-based methods allow measurement of inter-fraction variation only. Ultrasound allows soft-tissue measurement with zero dose but requires skilled interpretation, and there is evidence of systematic differences between ultrasound and other data sources, perhaps due to the effects of the probe pressure. Optical imaging also involves zero dose but requires good correlation between the target and the external measurement and thus is often used in conjunction with an x-ray method. The use of anatomical imaging in radiotherapy allows treatment uncertainties to be determined. These include errors between the mean position at treatment and that at planning (the systematic error) and the day-to-day variation in treatment set-up (the random error). Positional variations may also be categorized in terms of inter- and intra-fraction errors. Various empirical treatment margin formulae and intervention approaches exist to determine the optimum strategies for treatment in the presence of these known errors. Other methods exist to try to minimize error margins drastically including the currently available breath-hold techniques and the tracking methods which are largely in development. This paper will review anatomical imaging techniques in radiotherapy and how they are used to boost the therapeutic benefit of the treatment.
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