Purification and electron cryomicroscopy of coronavirus particles.

Intact, enveloped coronavirus particles vary widely in size and contour, and are thus refractory to study by traditional structural means such as X-ray crystallography. Electron microscopy (EM) overcomes some problems associated with particle variability and has been an important tool for investigating coronavirus ultrastructure. However, EM sample preparation requires that the specimen be dried onto a carbon support film before imaging, collapsing internal particle structure in the case of coronaviruses. Moreover, conventional EM achieves image contrast by immersing the specimen briefly in heavy-metal-containing stain, which reveals some features while obscuring others. Electron cryomicroscopy (cryo-EM) instead employs a porous support film, to which the specimen is adsorbed and flash-frozen. Specimens preserved in vitreous ice over holes in the support film can then be imaged without additional staining. Cryo-EM, coupled with single-particle image analysis techniques, makes it possible to examine the size, structure and arrangement of coronavirus structural components in fully hydrated, native virions. Two virus purification procedures are described

The Changing Geography of Outpatient Procedures

Since the early 80s, many surgical procedures have moved from the inpatient to outpatient setting. Outpatient surgical visits now account for about two-thirds of all surgical visits in the U.S. Over the same period, freestanding ambulatory surgery centers (ASCs) have arisen as alternatives to traditional hospital-based outpatient surgical departments. The number of ASCs grew from 240 in 1983 to 5,174 in 2008. The growth of ASCs raises safety concerns about the risk of complications and adequate access to emergency care. This Issue Brief summarizes evidence from one state about the changing geography of outpatient procedures and the possible risks associated with these changes

Physician Division of Labor and Patient Selection for Outpatient Procedures

Little is known about the ability of incentives to influence decisions by physicians regarding choices of settings for care delivery. In the context of outpatient procedural care, the emergence of freestanding ambulatory surgery centers (ASCs) as alternatives to hospital-based outpatient departments (HOPDs) creates a unique opportunity to study this question. We advance a model where physicians’ division of labor between ASCs and HOPDs affects the medical complexity of patients treated in low-acuity settings (i.e. ASCs). Analyses of outpatient surgical procedure data show that physicians working exclusively in low-acuity settings (i.e. ASCs) treat patients of significantly higher medical complexity in these settings than do physicians who also practice in higher-acuity settings (i.e. HOPDs). This discrepancy shrinks with increasing procedural risk and with increasing distance between ASCs and acute care hospitals

Affording to Wait: Medicare Initiation and the Use of Health Care

Delays in receipt of necessary diagnostic and therapeutic medical procedures related to the timing of Medicare initiation at age 65 years have potentially broad welfare implications. We use 2005–2007 data from Florida and North Carolina to estimate the effect of initiation of Medicare benefits on healthcare utilization across procedures that differ in urgency and coverage. In particular, we study trends in the use of elective procedures covered by Medicare to treat conditions that vary in symptoms; these are compared with elective surgical procedures not eligible for Medicare reimbursement, and to a set of urgent and emergent procedures. We find large discontinuities in health services utilization at age 65 years concentrated among low urgency, Medicare‐reimbursable procedures, most pronounced among screening interventions and treatments for minimally symptomatic disease

Contrasting Evidence Within and Between Institutions that Provide Treatment in an Observational Study of Alternate Forms of Anesthesia

In a randomized trial, subjects are assigned to treatment or control by the flip of a fair coin. In many nonrandomized or observational studies, subjects find their way to treatment or control in two steps, either or both of which may lead to biased comparisons. By a vague process, perhaps affected by proximity or sociodemographic issues, subjects find their way to institutions that provide treatment. Once at such an institution, a second process, perhaps thoughtful and deliberate, assigns individuals to treatment or control. In the current article, the institutions are hospitals, and the treatment under study is the use of general anesthesia alone versus some use of regional anesthesia during surgery. For a specific operation, the use of regional anesthesia may be typical in one hospital and atypical in another. A new matched design is proposed for studies of this sort, one that creates two types of nonoverlapping matched pairs. Using a new extension of optimal matching with fine balance, pairs of the first type exactly balance treatment assignment across institutions, so each institution appears in the treated group with the same frequency that it appears in the control group; hence, differences between institutions that affect everyone in the same way cannot bias this comparison. Pairs of the second type compare institutions that assign most subjects to treatment and other institutions that assign most subjects to control, so each institution is represented in the treated group if it typically assigns subjects to treatment or, alternatively, in the control group if it typically assigns subjects to control, and no institution appears in both groups. By and large, in the second type of matched pair, subjects became treated subjects or controls by choosing an institution, not by a thoughtful and deliberate process of selecting subjects for treatment within institutions. The design provides two evidence factors, that is, two tests of the null hypothesis of no treatment effect that are independent when the null hypothesis is true, where each factor is largely unaffected by certain unmeasured biases that could readily invalidate the other factor. The two factors permit separate and combined sensitivity analyses, where the magnitude of bias affecting the two factors may differ. The case of knee surgery in the study of regional versus general anesthesia is considered in detail

Comparative safety of anesthetic type for hip fracture surgery in adults: retrospective cohort study

Objective: To evaluate the effect of anesthesia type on the risk of in-hospital mortality among adults undergoing hip fracture surgery in the United States. Design: Retrospective cohort study. Setting: Premier research database, United States. Participants: 73 284 adults undergoing hip fracture surgery on hospital day 2 or greater between 2007 and 2011. Of those, 61 554 (84.0%) received general anesthesia, 6939 (9.5%) regional anesthesia, and 4791 (6.5%) combined general and regional anesthesia. Main outcome measure In-hospital all cause mortality. Results: In-hospital deaths occurred in 1362 (2.2%) patients receiving general anesthesia, 144 (2.1%) receiving regional anesthesia, and 115 (2.4%) receiving combined anesthesia. In the multivariable adjusted analysis, when compared with general anesthesia the mortality risk did not differ significantly between regional anesthesia (risk ratio 0.93, 95% confidence interval 0.78 to 1.11) or combined anesthesia (1.00, 0.82 to 1.22). A mixed effects analysis accounting for differences between hospitals produced similar results: compared with general anesthesia the risk from regional anesthesia was 0.91 (0.75 to 1.10) and from combined anesthesia was 0.98 (0.79 to 1.21). Findings were also consistent in subgroup analyses. Conclusions: In this large nationwide sample of hospital admissions, mortality risk did not differ significantly by anesthesia type among patients undergoing hip fracture surgery. Our results suggest that if the previously posited beneficial effect of regional anesthesia on short term mortality exists, it is likely to be more modest than previously reported

Anesthesia Technique, Mortality, and Length of Stay After Hip Fracture Surgery

Importance: More than 300 000 hip fractures occur each year in the United States. Recent practice guidelines have advocated greater use of regional anesthesia for hip fracture surgery. Objective: To test the association of regional (ie, spinal or epidural) anesthesia vs general anesthesia with 30-day mortality and hospital length of stay after hip fracture

Structural basis of severe acute respiratory syndrome coronavirus ADP-ribose-1''-phosphate dephosphorylation by a conserved domain of nsP3.

The crystal structure of a conserved domain of nonstructural protein 3 (nsP3) from severe acute respiratory syndrome coronavirus (SARS-CoV) has been solved by single-wavelength anomalous dispersion to 1.4 A resolution. The structure of this "X" domain, seen in many single-stranded RNA viruses, reveals a three-layered alpha/beta/alpha core with a macro-H2A-like fold. The putative active site is a solvent-exposed cleft that is conserved in its three structural homologs, yeast Ymx7, Archeoglobus fulgidus AF1521, and Er58 from E. coli. Its sequence is similar to yeast YBR022W (also known as Poa1P), a known phosphatase that acts on ADP-ribose-1''-phosphate (Appr-1''-p). The SARS nsP3 domain readily removes the 1'' phosphate group from Appr-1''-p in in vitro assays, confirming its phosphatase activity. Sequence and structure comparison of all known macro-H2A domains combined with available functional data suggests that proteins of this superfamily form an emerging group of nucleotide phosphatases that dephosphorylate Appr-1''-p

Metaphor Identification in Large Texts Corpora

Identifying metaphorical language-use (e.g., sweet child) is one of the challenges facing natural language processing. This paper describes three novel algorithms for automatic metaphor identification. The algorithms are variations of the same core algorithm. We evaluate the algorithms on two corpora of Reuters and the New York Times articles. The paper presents the most comprehensive study of metaphor identification in terms of scope of metaphorical phrases and annotated corpora size. Algorithms’ performance in identifying linguistic phrases as metaphorical or literal has been compared to human judgment. Overall, the algorithms outperform the state-of-the-art algorithm with 71% precision and 27% averaged improvement in prediction over the base-rate of metaphors in the corpus.United States. Intelligence Advanced Research Projects Activity (IARPA)United States. Dept. of Defense (U.S. Army Research Laboratory Contract W911NF-12-C-0021