Three-Dimensional Crystallographic Reconstruction for Atomic Resolution

Three-dimensional structures have recently been determined by electron crystallography at a resolution high enough to determine atomic arrangements in both protein and mineral specimens. The different nature of these two types of specimens produces some very significant differences in the way data is obtained and processed, although the principles are the same. The sensitivity of proteins to damage by the electron beam limits the signal-to-noise ratio in the image and the resolution to which data can be extracted from the image. A number of constraints, such as the amino acid sequence and the connectivity of atoms within amino acids, can be used in interpreting the limited image data. In materials samples, the relative insensitivity to damage allows obtaining resolution limited only by the microscope. In many samples, dynamical scattering and other non-linear effects limit the information in the image, but this limit can be circumvented by working in very thin areas of the specimen

Cognitive therapy and spirituality: the battleground and the blend

Includes bibliographical references

A CCD Camera with Electron Decelerator for Intermediate Voltage Electron Microscopy

Electron microscopists are increasingly turning to Intermediate Voltage Electron Microscopes (IVEMs) operating at 300 - 400 kV for a wide range of studies. They are also increasingly taking advantage of slow-scan charge coupled device (CCD) cameras, which have become widely used on electron microscopes. Under some conditions CCDs provide an improvement in data quality over photographic film, as well as the many advantages of direct digital readout. However, CCD performance is seriously degraded on IVEMs compared to the more conventional 100 kV microscopes. In order to increase the efficiency and quality of data recording on IVEMs, we have developed a CCD camera system in which the electrons are decelerated to below 100 kV before impacting the camera, resulting in greatly improved performance in both signal quality and resolution compared to other CCDs used in electron microscopy. These improvements will allow high-quality image and diffraction data to be collected directly with the CCD, enabling improvements in data collection for applications including high-resolution electron crystallography, single-particle reconstruction of protein structures, tomographic studies of cell ultrastructure and remote microscope operation. This approach will enable us to use even larger format CCD chips that are being developed with smaller pixels

Improving Palliative Care with Deep Learning

Improving the quality of end-of-life care for hospitalized patients is a priority for healthcare organizations. Studies have shown that physicians tend to over-estimate prognoses, which in combination with treatment inertia results in a mismatch between patients wishes and actual care at the end of life. We describe a method to address this problem using Deep Learning and Electronic Health Record (EHR) data, which is currently being piloted, with Institutional Review Board approval, at an academic medical center. The EHR data of admitted patients are automatically evaluated by an algorithm, which brings patients who are likely to benefit from palliative care services to the attention of the Palliative Care team. The algorithm is a Deep Neural Network trained on the EHR data from previous years, to predict all-cause 3-12 month mortality of patients as a proxy for patients that could benefit from palliative care. Our predictions enable the Palliative Care team to take a proactive approach in reaching out to such patients, rather than relying on referrals from treating physicians, or conduct time consuming chart reviews of all patients. We also present a novel interpretation technique which we use to provide explanations of the model's predictions.Comment: IEEE International Conference on Bioinformatics and Biomedicine 201

Structural insights into microtubule doublet interactions inaxonemes

Coordinated sliding of microtubule doublets, driven by dynein motors, produces periodic beating of the axoneme. Recent structural studies of the axoneme have used cryo-electron tomography to reveal new details of the interactions among some of the multitude of proteins that form the axoneme and regulate its movement. Connections among the several sets of dyneins, in particular, suggest ways in which their actions may be coordinated. Study of the molecular architecture of isolated doublets has provided a structural basis for understanding the doublet's mechanical properties that are related to the bending of the axoneme, and has also offered insight into its potential role in the mechanism of dynein activity regulation

Restoration of Weak Phase-Contrast Images Recorded With a High Degree of Defocus: The "Twin Image" Problem Associated With CTF Correction

Relatively large values of objective-lens defocus must normally be used to produce detectable levels of image contrast for unstained biological specimens, which are generally weak phase objects. As a result, a subsequent restoration operation must be used to correct for oscillations in the contrast transfer function (CTF) at higher resolution. Currently used methods of CTF-correction assume the ideal case in which Friedel mates in the scattered wave have contributed pairs of Fourier components that overlap with one another in the image plane. This"ideal" situation may be only poorly satisfied, or not satisfied at all, as the particle size gets smaller, the defocus value gets larger, and the resolution gets higher. We have therefore investigated whether currently used methods of CTF correction are also effective in restoring the single-sideband image information that becomes displaced (delocalized) by half (or more) the diameter of a particle of finite size. Computer simulations are used to show that restoration either by"phase flipping" or by multiplying by the CTF recovers only about half of the delocalized information. The other half of the delocalized information goes into a doubly defocused"twin" image of the type produced during optical reconstruction of an in-line hologram. Restoration with a Wiener filter is effective in recovering the delocalized information only when the signal-to-noise ratio (S/N) is orders of magnitude higher than that which exists in low-dose images of biological specimens, in which case the Wiener filter approaches division by the CTF (i.e. the formal inverse). For realistic values of the S/N, however, the"twin image" problem seenwith a Wiener filter is very similar to that seen when either phase flipping or multiplying by the CTF are used for restoration. The results of these simulations suggest that CTF correction is a poor alternative to using a Zernike-type phase plate when imaging biological specimens, in which case the images can be recorded in a close-to-focus condition, and delocalization of high-resolution information is thus minimized

Production of Heparin-Binding Epidermal Growth Factor–like Growth Factor (HB-EGF) at Sites of Thermal Injury in Pediatric Patients

Fluids that accumulate at wound sites may be an important reservoir of growth factors that promote the normal wound healing response. The presence of heparin-binding growth factors was studied in burn wound fluid (BWF) from 45 pediatric patients who had sustained partial thickness burns. One of the growth factors present was similar to platelet-derived growth factor (PDGF) based on its heparin affinity, inhibition of bioactivity by a PDGF antiserum, and detection in a PDGF-AB enzyme-linked iminunosorbent assay. A second growth factor was identified as heparin-binding epidermal growth factor–like growth factor (HB-EGF) based on its heparin affinity, competition with 125I-labeled epidermal growth factor (EGF) for EGF receptor binding, and recognition in biological assays and Western blots by two HB-EGF antisera. Amino acid sequence analysis of one form of this second growth factor verified its identity as an N-terminally truncated form of HB-EGF. Immunohistochemical analysis of partial thickness burns demonstrated the presence of HB-EGF in the advancing epithelial margin, islands of regenerating epithelium within the burn wound, and in the duct and proximal tubules of eccrine sweat glands. HB-EGF in the surface epithelium of burn wounds was uniformally distributed, whereas it was restricted to the basal epithelium in nonburned skin. These data support a role for PDGF and HB-EGF in burn wound healing and suggest that the response to injury includes deposition of HB-EGF and PDGF into blister fluid and a redistribution of HB-EGF in the surface epithelium near the wound site