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Refinement of macromolecular atomic models versus experimental maps in crystallography and cryo-electron microscopy is a critical step in structure solution. For an appropriate comparison, model maps should mimic the imperfections in the experimental maps, mainly atomic disorder and limited resolution, which are often inhomogeneous over the molecular region. In the suggested method, these model maps are calculated as the sum of atomic contributions expressed through a specifically designed function describing a solitary spherical wave. Thanks to this function, atomic contributions are analytically expressed through their atomic displacement parameter and local resolution, a value now associated with each atom. Such a full analytic dependence of inhomogeneous-resolution map values on model parameters permits the refinement of all of these parameters together.

Cryo‐EM images have extremely low signal‐to‐noise levels because biological macromolecules are highly radiation‐sensitive, requiring low‐dose imaging, and because the molecules are poor in contrast. Confident recovery of the signal requires the averaging of many images, the iterative optimization of parameters and the introduction of much prior information. Poor parameter estimates, overfitting and variations in signal strength and resolution across the resulting reconstructions remain frequent issues. Because biological samples are real‐space phenomena, exhibiting local variations, real‐space measures can be both more reliable and more appropriate than Fourier‐space measures. Real‐space measures can be calculated separately over each differing region of an image or volume. Real‐space filters can be applied according to the local need. Powerful prior information, not available in Fourier space, can be introduced in real space. Priors can be applied in real space in ways that Fourier space precludes. The treatment of biological phenomena remains highly dependent on spatial frequency, however, which would normally be handled in Fourier space. We believe that measures and filters based around real‐space operations on extracted frequency bands, i.e. a series of band‐pass filtered real‐space volumes, and over real‐space densities of striding (sequentially increasing or decreasing) resolution through Fourier space are the best way to address this and will perform better than global Fourier‐space‐based approaches. Future developments in image processing within the field are generally expected to be based on a mixture of both rationally designed and deep‐learning approaches, and to incorporate novel prior information from developments such as AlphaFold. Regardless of approach, it is clear that 'locality', through real‐space measures, filters and processing, will become central to image processing. [ABSTRACT FROM AUTHOR]

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In this article, a method is presented to estimate a new local quality measure for 3D cryoEM maps that adopts the form of a `local resolution' type of information. The algorithm (DeepRes) is based on deep-learning 3D feature detection. DeepRes is fully automatic and parameter-free, and avoids the issues of most current methods, such as their insensitivity to enhancements owing to B-factor sharpening (unless the 3D mask is changed), among others, which is an issue that has been virtually neglected in the cryoEM field until now. In this way, DeepRes can be applied to any map, detecting subtle changes in local quality after applying enhancement processes such as isotropic filters or substantially more complex procedures, such as model-based local sharpening, non-model-based methods or denoising, that may be very difficult to follow using current methods. It performs as a human observer expects. The comparison with traditional local resolution indicators is also addressed.

Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.

Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces MonoTomo, a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to MonoRes, allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of MonoTomo are suggested for further exploration.

Confidence maps provide complementary information for interpreting cryo‐EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false‐discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP‐EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family‐wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • We propose an algorithm, LAFTER, that recovers features with more signal than noise from half maps. • LAFTER is shown to recover features over a wide range of FSCs and local signal-to-noise ratios. • We suggest effective local noise suppression be evaluated by comparing the filter-sum xFSC to C ref. Abstract We present LAFTER, an algorithm for de-noising single particle reconstructions from cryo-EM. Single particle analysis entails the reconstruction of high-resolution volumes from tens of thousands of particle images with low individual signal-to-noise. Imperfections in this process result in substantial variations in the local signal-to-noise ratio within the resulting reconstruction, complicating the interpretation of molecular structure. An effective local de-noising filter could therefore improve interpretability and maximise the amount of useful information obtained from cryo-EM maps. LAFTER is a local de-noising algorithm based on a pair of serial real-space filters. It compares independent half-set reconstructions to identify and retain shared features that have power greater than the noise. It is capable of recovering features across a wide range of signal-to-noise ratios, and we demonstrate recovery of the strongest features at Fourier shell correlation (FSC) values as low as 0.144 over a 2563-voxel cube. A fast and computationally efficient implementation of LAFTER is freely available. We also propose a new way to evaluate the effectiveness of real-space filters for noise suppression, based on the correspondence between two FSC curves: 1) the FSC between the filtered and unfiltered volumes, and 2) C ref , the FSC between the unfiltered volume and a hypothetical noiseless volume, which can readily be estimated from the FSC between two half-set reconstructions. [ABSTRACT FROM AUTHOR]

[Display omitted] • CryoRes's design is based on learning resolution-aware patterns of the density map voxels from a single final cryo-EM density map; thus, there is no need for extra structural files and parameter tunning. • By supervised training on a large dataset of 1,174 experimental cryo-EM density maps, CryoRes achieves a much more accurate local resolution estimation performance than existing methods (e.g., blocres , ResMap, MonoRes, and DeepRes). • CryoRes is ultra-fast, fully automatic, and freely available at https://cryores.zhanglab.net. Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in different regions of a map. Currently available methods for local resolution estimation require manual adjustment of parameters and in some cases necessitate acquisition or de novo generation of so-called "half maps". Here, we developed CryoRes, a deep-learning algorithm to estimate local resolution directly from a single final cryo-EM density map, specifically by learning resolution-aware patterns of density map voxels through supervised training on a large dataset comprising 1,174 experimental cryo-EM density maps. CryoRes significantly outperforms all of the state-of-the-art competing resolution estimation methods, achieving an average RMSE of 2.26 Å for local resolution estimation relative to the currently most reliable FSC-based method blocres , yet requiring only the single final map as input. Further, CryoRes is able to generate a molecular mask for each map, with accuracy 12.12% higher than the masks generated by ResMap. CryoRes is ultra-fast, fully automatic, parameter-free, applicable to cryo-EM subtomogram data, and freely available at https://cryores.zhanglab.net. [ABSTRACT FROM AUTHOR]

This paper describes a service development in healthcare support workers (HCSWs) across departments in a large Scottish teaching hospital. In any healthcare setting, communication can be complex and challenging. Many healthcare support workers and ward clerks are often the first face seen by patient or family entering the ward. As junior members of the team, this task can appear daunting, particularly as there is limited access to formal training or support. There are also few chances to reflect on practice and develop skills, such as communication. The course was designed to fill this gap and give 15 support workers an opportunity to practise and reflect in a supported manner using patient, staff and family stories as a vehicle for deeper learning. Evaluation of this course, which was highly valued, showed that this was a successful method of encouraging reflection and self-awareness, as a way of improving their communication skills. [ABSTRACT FROM AUTHOR]

Julie Swann explores the development of reminiscence as an activity in the care home for patients with dementia. Ways that care staff can facilitate memory recall with their residents, by using person-centred methods, are also described. [ABSTRACT FROM AUTHOR]

Commentary is given on a paper [Urzhumtsev & Lunin (2022). IUCrJ , 9 , 728-734] proposing a new method for the analytic modelling of inhomogeneous resolution in electrostatic potential volumes and electron density maps for improved real-space refinement., (© Isabel Usón 2022.)

Refinement of macromolecular atomic models versus experimental maps in crystallography and cryo-electron microscopy is a critical step in structure solution. For an appropriate comparison, model maps should mimic the imperfections in the experimental maps, mainly atomic disorder and limited resolution, which are often inhomogeneous over the molecular region. In the suggested method, these model maps are calculated as the sum of atomic contributions expressed through a specifically designed function describing a solitary spherical wave. Thanks to this function, atomic contributions are analytically expressed through their atomic displacement parameter and local resolution, a value now associated with each atom. Such a full analytic dependence of inhomogeneous-resolution map values on model parameters permits the refinement of all of these parameters together., (© Urzhumtsev and Lunin 2022.)

Every year, 150 000 people in the UK suffer a stroke. This works out at one every five minutes (Townsend et al, 2012). Stroke is the single largest cause of disability and the third largest cause of deaths in England. Stroke costs the NHS over £2.8 billion and can lead to death or severe disability (Mant et al, 2004). The National Stroke Strategy launched in 2007 outlined a 10-point strategy to develop stroke services, reduce death and disability and to improve care (Department of Health (DH), 2007; 2008). One of the most important aspects of stroke care is ensuring that stroke is recognised and that everyone acts quickly to preserve brain function and minimise disability. Healthcare professionals and the public need to be able to recognise stroke and to act appropriately when stroke occurs. This article aims to enable readers to recognise acute stroke and to act quickly and appropriately when stroke occurs INSET: ROSIER test: ROSIER¿Recognition Of Stroke in the Emergency Room. [ABSTRACT FROM AUTHOR]

The characteristics of the measured total impedance spectra of polymer electrolyte membrane fuel cells are often not representative of the performance of the cell. This is due in part mainly to two reasons; total impedance measurements are not representative of local phenomena and perturbation of the cell around the steady-state polarization can result in oscillations of the gas concentrations downstream the flow channels that can affect the trend of the local spectrum. In this study, we overcome these two challenges by measuring the spectra of a segmented cell using local excitation of the segments. With these capabilities, we experimentally investigate the explanation given in works found in literature in regards to the oxygen oscillation in the channel and its effect on the spectra of locally perturbed segments. We further investigate the characteristics of the low frequency arc, measuring for the first time a loop in the spectrum around the transition frequency between the high and low frequency arcs. The characteristics of the spectra are investigated by varying the flow properties with a focus on the effect of air stoichiometry. [ABSTRACT FROM AUTHOR]

This article discusses the ramifications of the Government's response to the Francis report, in which secretary of state for health, Jeremy Hunt, argues that every undergraduate nursing student seeking NHS funding should first serve up to a year as a healthcare assistant (HCA). It questions if the role of the nurse mentor is pivotal in the preparation of nursing students. [ABSTRACT FROM AUTHOR]

This study examines the experience of Healthcare Assistants (HCAs) working on medical and surgical wards of a general hospital. The purpose of the research was to provide an insight into the organisation's nursing 'culture' and healthcare workers' perceptions as to what constitutes HCA work. Data was collected using a qualitative approach, in which in-depth interviews were conducted, transcribed and analysed. The emerging descriptions of the HCA role informed the development of four themes. These themes suggest that with due consideration the HCA role may be advanced through a process of regulation and a comprehensive programme of training and supervision. INSETS: Box 1. Potential for confusion;Box 2. How research findings will inform. [ABSTRACT FROM AUTHOR]

This article looks at the many religious and cultural considerations that patients present healthcare workers with. Through case studies, it examines 12 different areas. [ABSTRACT FROM AUTHOR]

Healthcare assistants (HCAs) and assistant practitioners (APs) can be using technology for much of the time during their working day, without really thinking about the technology itself. This article looks at some of the ways in which technologies will be part of the new care provision as well as technologies that can be used to assist caring for someone. [ABSTRACT FROM AUTHOR]

Abstract: A self-modeling curve resolution (SMCR) method is proposed to calculate concentration and spectral profiles for the two-way spectral data from an equilibrium containing several chemical components. The proposed method has three main distinctive steps: (i) fixed size moving window evolving factor analysis (FSMWEFA) is used to identify the selective and zero concentration regions for a desired component, (ii) orthogonal projection resolution (OPR) is used to calculate its concentration profile and (iii) the component striping is done directly to resolve other components. The results of simulated and real polyprotic acid dissociation equilibria showed that the proposed combined method performs well even in situation when the successive stepwise equilibrium constants are close to each other. The applicability of method for resolving the triprotic acid system with rank deficiency due full spectral overlapping of two involved chemical species also is shown. [Copyright &y& Elsevier]

In many jurisdictions it is increasingly recognized that police complaints systems should contain a mixture of formal and less formal procedures, as well as allow for a variety of outcomes including remedial and punitive ones. Recent changes to the system for handling complaints against the police in England and Wales envisage an expanded role for local (informal) resolution, with a new range of options including restorative justice conferences. Yet little is known about whether complainants would welcome the option of a restorative justice conference or whether restorative processes would constitute an improvement on conventional practices. This article presents the results of a Nuffield Foundation funded study of these issues carried out in 2002-3 in two police force areas. The findings suggest that restorative processes can achieve moderately better results than conventional processes. While widespread implementation of this new approach is likely to prove problematic for many police services, a flexible approach to introducing changes, drawing on the experience of restorative practitioners in related areas, is likely to benefit complainants without creating dissatisfaction among police officers. [ABSTRACT FROM AUTHOR]

In many jurisdictions it is increasingly recognized that police complaints systems should contain a mixture of formal and less formal procedures, as well as allow for a variety of outcomes including remedial and punitive ones. Recent changes to the system for handling complaints against the police in England and Wales envisage an expanded role for local (informal) resolution, with a new range of options including restorative justice conferences. Yet little is known about whether complainants would welcome the option of a restorative justice conference or whether restorative processes would constitute an improvement on conventional practices. This article presents the results of a Nuffield Foundation funded study of these issues carried out in 2002-3 in two police force areas. The findings suggest that restorative processes can achieve moderately better results than conventional processes. While widespread implementation of this new approach is likely to prove problematic for many police services, a flexible approach to introducing changes, drawing on the experience of restorative practitioners in related areas, is likely to benefit complainants without creating dissatisfaction among police officers. [ABSTRACT FROM PUBLISHER]

Wound infection continues to be a challenging problem for clinicians and is the result of complex interactions between micro-organisms and the host environment (World Union of Wound Healing Societies (WUWHS), 2008; Patel, 2009). Wound infection results in a huge financial burden for both the NHS and the patient. It is therefore important, where possible, to prevent wound infection. Where this is not possible, it is essential to diagnose the infection and commence appropriate treatment as soon as possible (Patel, 2009). In the third of our analyses of best practice statements, we look at a powerful introduction to this important subject. [ABSTRACT FROM AUTHOR]

A crucial element of the work of healthcare assistants and assistant practitioners is the ability to listen effectively to patients using clear communication to aid interactions so that high quality person-centred care can be achieved. This article looks at how, as individuals, we bring our own uniqueness (beliefs, emotions and processes) to the way we interact (and respond) to patients, and how with this awareness we can build on and improve our listening skills. [ABSTRACT FROM AUTHOR]

• Over-fitting occurs in regions of low local signal-to-noise despite independent half-set refinement. • We show that real space filtering according to SNR during refinement prevents overfitting. • We describe an algorithm, SIDESPLITTER, that achieves this while maintaining independence between half-sets. • SIDESPLITTER can also improve the final resolution in cases of severe over-fitting. Single particle analysis has become a key structural biology technique. Experimental images are extremely noisy, and during iterative refinement it is possible to stably incorporate noise into the reconstruction. Such "over-fitting" can lead to misinterpretation of the structure and flawed biological results. Several strategies are routinely used to prevent over-fitting, the most common being independent refinement of two sides of a split dataset. In this study, we show that over-fitting remains an issue within regions of low local signal-to-noise, despite independent refinement of half datasets. We propose a modification of the refinement process through the application of a local signal-to-noise filter: SIDESPLITTER. We show that our approach can reduce over-fitting for both idealised and experimental data while maintaining independence between the two sides of a split refinement. SIDESPLITTER refinement leads to improved density, and can also lead to improvement of the final resolution in extreme cases where datasets are prone to severe over-fitting, such as small membrane proteins. [ABSTRACT FROM AUTHOR]

Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces MonoTomo , a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to MonoRes , allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of MonoTomo are suggested for further exploration., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2019 Published by Elsevier Inc.)