Inter-Bragg crystallographic phase retrieval from shape transforms, stacking faults and substitutional disorder.

One of the brilliant ideas of John Spence when he saw the first diffraction patterns from the Linac Coherent Light Source was that one could solve the crystallographic phase problem by utilising the intensities between Bragg peaks. Because these intensities are due to the Fourier transform of the shape of the crystal, the approach came to be known as "shape-transform phasing." Shape-transform phasing was developed over the next ten years and formed the basis for many other interesting ideas and pursuits. Here we describe the current best implementation of the original idea using a lattice occupancy formalism and show that certain types of crystal defects can also be modelled via this approach, allowing the molecular structure to be recovered from the additional information offered by the inter-Bragg intensities from these crystal defects.

Joint iterative reconstruction and 3D rigid alignment for X-ray tomography.

X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.

Shape transform phasing of edgy nanocrystals.

Diffraction patterns from small protein crystals illuminated by highly coherent X-rays often contain measurable interference signals between Bragg peaks. This coherent `shape transform' signal introduces enough additional information to allow the molecular densities to be determined from the diffracted intensities directly, without prior information or resolution restrictions. However, the various correlations amongst molecular occupancies/vacancies at the crystal surface result in a subtle yet critical problem in shape transform phasing whereby the sublattices of symmetry-related molecules exhibit a form of partial coherence amongst lattice sites when an average is taken over many crystal patterns. Here an iterative phase retrieval algorithm is developed which is capable of treating this problem; it is demonstrated on simulated data.

Prenatal maternal immune disruption and sex-dependent risk for psychoses.

BACKGROUND: Previous studies suggest that abnormalities in maternal immune activity during pregnancy alter the offspring's brain development and are associated with increased risk for schizophrenia (SCZ) dependent on sex. METHOD: Using a nested case-control design and prospectively collected prenatal maternal sera from which interleukin (IL)-1ß, IL-8, IL-6, tumor necrosis factor (TNF)-α and IL-10 were assayed, we investigated sex-dependent associations between these cytokines and 88 psychotic cases [SCZ = 44; affective psychoses (AP) = 44] and 100 healthy controls from a pregnancy cohort followed for > 40 years. Analyses included sex-stratified non-parametric tests adjusted for multiple comparisons to screen cytokines associated with SCZ risk, followed by deviant subgroup analyses using generalized estimating equation (GEE) models. RESULTS: There were higher prenatal IL-6 levels among male SCZ than male controls, and lower TNF-α levels among female SCZ than female controls. The results were supported by deviant subgroup analyses with significantly more SCZ males with high IL-6 levels (>highest quartile) compared with controls [odd ratio (OR)75 = 3.33, 95% confidence interval (CI) 1.13-9.82], and greater prevalence of low TNF-α levels (

In vitro and in vivo antibacterial activities of omadacycline, a novel aminomethylcycline.

Omadacycline is the first intravenous and oral 9-aminomethylcycline in clinical development for use against multiple infectious diseases including acute bacterial skin and skin structure infections (ABSSSI), community-acquired bacterial pneumonia (CABP), and urinary tract infections (UTI). The comparative in vitro activity of omadacycline was determined against a broad panel of Gram-positive clinical isolates, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), Lancefield groups A and B beta-hemolytic streptococci, penicillin-resistant Streptococcus pneumoniae (PRSP), and Haemophilus influenzae (H. influenzae). The omadacycline MIC90s for MRSA, VRE, and beta-hemolytic streptococci were 1.0 µg/ml, 0.25 µg/ml, and 0.5 µg/ml, respectively, and the omadacycline MIC90s for PRSP and H. influenzae were 0.25 µg/ml and 2.0 µg/ml, respectively. Omadacycline was active against organisms demonstrating the two major mechanisms of resistance, ribosomal protection and active tetracycline efflux. In vivo efficacy of omadacycline was demonstrated using an intraperitoneal infection model in mice. A single intravenous dose of omadacycline exhibited efficacy against Streptococcus pneumoniae, Escherichia coli, and Staphylococcus aureus, including tet(M) and tet(K) efflux-containing strains and MRSA strains. The 50% effective doses (ED50s) for Streptococcus pneumoniae obtained ranged from 0.45 mg/kg to 3.39 mg/kg, the ED50s for Staphylococcus aureus obtained ranged from 0.30 mg/kg to 1.74 mg/kg, and the ED50 for Escherichia coli was 2.02 mg/kg. These results demonstrate potent in vivo efficacy including activity against strains containing common resistance determinants. Omadacycline demonstrated in vitro activity against a broad range of Gram-positive and select Gram-negative pathogens, including resistance determinant-containing strains, and this activity translated to potent efficacy in vivo.

Mechanism of action of the novel aminomethylcycline antibiotic omadacycline.

Omadacycline is a novel first-in-class aminomethylcycline with potent activity against important skin and pneumonia pathogens, including community-acquired methicillin-resistant Staphylococcus aureus (MRSA), ß-hemolytic streptococci, penicillin-resistant Streptococcus pneumoniae, Haemophilus influenzae, and Legionella. In this work, the mechanism of action for omadacycline was further elucidated using a variety of models. Functional assays demonstrated that omadacycline is active against strains expressing the two main forms of tetracycline resistance (efflux and ribosomal protection). Macromolecular synthesis experiments confirmed that the primary effect of omadacycline is on bacterial protein synthesis, inhibiting protein synthesis with a potency greater than that of tetracycline. Biophysical studies with isolated ribosomes confirmed that the binding site for omadacycline is similar to that for tetracycline. In addition, unlike tetracycline, omadacycline is active in vitro in the presence of the ribosomal protection protein Tet(O).

Impact of genetic vulnerability and hypoxia on overall intelligence by age 7 in offspring at high risk for schizophrenia compared with affective psychoses.

Risk factors for schizophrenia, such as genetic vulnerability and obstetric complications, have been associated with cognitive deficits in schizophrenia. We tested the association of these risk factors with general intellectual ability in offspring at high risk for psychoses and normal control subjects. Offspring of 182 parents with DSM-IV schizophrenia or affective psychoses were recruited and diagnosed from the Boston and Providence cohorts of the National Collaborative Perinatal Project (NCPP). Control subjects from the NCPP were selected to be comparable with affected parents based on the parent's age, ethnicity, study site, number of offspring enrolled in the NCPP, and payment status, and on the offspring's age, sex, and history of obstetric complications. Based on data prospectively acquired from pregnancy and events of gestation, labor, delivery, and the neonatal period, we derived a measure of probable hypoxic-ischemic insult. We also report on standardized measures of general intelligence (intelligence quotient [IQ]) collected at age 7. General linear mixed models were used to test for the simultaneous effects of genetic vulnerability, defined as parental diagnosis, and probable hypoxic insult on age 7 IQ. Specificity of the effects for schizophrenia compared with affective psychoses and sex effects were also tested. Low IQ at age 7 was significantly associated with genetic vulnerability to psychoses, in particular with schizophrenia.

Rapid detection of group A streptococci: comparative performance by nurses and laboratory technologists in pediatric satellite laboratories using three test kits.

Rapid tests for detecting group A streptococci in throat swabs are often performed outside hospitals or commercial laboratories by individuals with little or no technical training. We compared the abilities of nurses and technologists to perform and interpret three commercial kits (Directigen 1-2-3, ICON Strep A, and Culturette Brand 10-Minute Strep A ID) in three hospital satellite locations (the emergency department, a walk-in emergency clinic, and a general pediatric clinic). When the three tests were compared with culture, the sensitivities of the tests as performed by nurses and technologists, respectively, were 39 versus 44% for Directigen, 55 versus 51% for Culturette, and 72 versus 39% for ICON. A significant difference in sensitivity was found only with ICON tests. This result was largely explained by the tendency of technologists to test moist swabs, while nurses generally processed dry swabs; ICON test sensitivity was significantly greater with dry swabs. The specificities of Directigen and ICON tests performed by nurses and technologists were high (97 to 100%). The difference in the specificities of the Culturette test as determined from results obtained by nurses and technologists (80 versus 98%) was due to the tendency of one nurse to overinterpret the latex agglutination reaction. Analysis of the accuracies of the tests during practice periods compared with the accuracies of the tests during the study periods revealed statistically significant improvement in test performance. We conclude that these tests are specific but not sensitive when performed by nurses and technologists in satellite laboratories. With one exception, nurses and technologists performed the tests with comparable accuracy after brief training periods.