Determining protein loop conformation using scaling-relaxation techniques

We recently developed a rapid loop closure algorithm in which bond lengths are scaled to constrain the ends of a segment to match a known distance and then gradually relaxed to their standard values, with boundary constraints maintained. Although the algorithm predicted the Zif286 zinc-finger loop to within approximately 2 A, it had a serious limitation that made its more general use tentative: it omitted the atomic environment of the loop. Here we report an extension of the algorithm to take into account the protein environment surrounding a given loop from the outset of the conformational search and show that it predicts structure with an efficiency and accuracy that could not be achieved without continuous environmental inclusion. The algorithm should be widely applicable to structure determination when complete experimental information is unavailable.     

Prophylactic effects of recombinant human superoxide dismutase in neonatal lung injury

To determine if recombinant human Cu-Zn superoxide dismutase (rhSOD) would prevent acute lung injury caused by hyperoxia and barotrauma, 26 newborn piglets were studied. Ten piglets were hyperventilated (arterial PCO2 15-20 Torr) with 100% O2 for 48 h. A second group received identical treatment for 4 h (n = 2) or 48 h (n = 8) but was given 5 mg/kg of rhSOD intratracheally at time 0. Six piglets were normally ventilated (arterial PCO2 40-45 Torr) for 48 h with 21% O2. Pulmonary function and tracheal aspirates were examined at time 0 and at 24 and 48 h, and bronchoalveolar lavage was performed at 48 h. In piglets treated with hyperoxia and hyperventilation, lung compliance decreased 42%, and tracheal aspirates showed an increase in neutrophil chemotactic activity (32%), total cell counts (135%), elastase activity (93%), and albumin concentration (339%) over 48 h (P < 0.05). All variables were significantly lower in rhSOD-treated piglets and comparable to normoxic control values. Surfactant remained active in all groups. Immunohistochemistry demonstrated that at 48 h significant rhSOD was distributed homogeneously in terminal airways. Adding rhSOD to tracheal aspirates of hyperoxic hyperventilated piglets did not alter neutrophil chemotaxis, suggesting that rhSOD protected the lung by reducing the production of chemotactic mediators. Results indicate that acute lung injury caused by 48 h of hyperoxia and hyperventilation is significantly ameliorated by prophylactic intratracheal administration of rhSOD.     

Activated partial thromboplastin time and outcome after thrombolytic therapy for acute myocardial infarction: results from the GUSTO-I trial

BACKGROUND: Although intravenous heparin is commonly used after thrombolytic therapy, few reports have addressed the relationship between the degree of anticoagulation and clinical outcomes. We examined the activated partial thromboplastin time (aPTT) in 29,656 patients in the Global Utilization of Streptokinase and t-PA for Occluded Coronary Arteries (GUSTO-I) trial and analyzed the relationship between the aPTT and both baseline patient characteristics and clinical outcomes. METHODS AND RESULTS: Intravenous heparin was administered as a 5000-U bolus followed by an initial infusion of 1000 U/h, with dose adjustment to achieve a target aPTT of 60 to 85 seconds. aPTTs were collected 6, 12, and 24 hours after thrombolytic administration. Higher aPTT at 24 hours was strongly related to lower patient weight (P < .00001) as well as older age, female sex, and lack of cigarette smoking (all PT< .0001). At 12 hours, the aPTT associated with the lowest 30-day mortality, stroke, and bleeding rates was 50 to 70 seconds. There was an unexpected direct relationship between the aPTT and the risk of subsequent reinfarction. There was a clustering of reinfarction in the first 10 hours after discontinuation of intravenous heparin. CONCLUSIONS: Although the relationship between aPTT and clinical outcome was confounded to some degree by the influence of baseline prognostic characteristics, aPTTs higher than 70 seconds were found to be associated with higher likelihood of mortality, stroke, bleeding, and reinfarction. These findings suggest that until proven otherwise, we should consider the aPTT range of 50 to 70 seconds as optimal with intravenous heparin after thrombolytic therapy.     

Two-dimensional phase unwrapping using a minimum spanning treealgorithm

Phase unwrapping refers to the determination of phase from modulo 2pi data, some of which may not be reliable. In 2D, this is equivalent to confining the support of the phase function to one or more arbitrarily shaped regions. A phase unwrapping algorithm is presented which works for 2D data known only within a set of nonconnected regions with possibly nonconvex boundaries. The algorithm includes the following steps: segmentation to identify connectivity, phase unwrapping within each segment using a Taylor series expansion, phase unwrapping between disconnected segments along an optimum path, and filling of phase information voids. The optimum path for intersegment unwrapping is determined by a minimum spanning tree algorithm. Although the algorithm is applicable to any 2D data, the main application addressed is magnetic resonance imaging (MRI) where phase maps are useful.     

Intermodality, retrospective image registration in the thorax

The purpose of this study was to develop an accurate, retrospectively applicable procedure for registering thoracic studies from different modalities in a short amount of time and with minimal operator intervention. METHODS: CT and PET studies were acquired from six patients. The pleural surfaces in both image sets were determined by segmenting based on 50% of the maximum soft-tissue value in the study. These surfaces were converted into three-dimensional volumes and used to register the CT and PET studies in three dimensions using a sum of least squares fitting approach. The registered PET study was then displayed in a hot metal scale overlayed on top of the gray scale CT study. The accuracy of the fit was evaluated through a phantom study and preliminary clinical evaluation. RESULTS: A phantom study was performed to determine the limits of this technique. The accuracy was determined to be less than 2.3 mm in the x and y direction and 3 mm in the z direction. Preliminary clinical evaluation was also performed with encouraging results. CONCLUSION: This technique accurately registers PET and CT images of the thorax, retrospectively, without the need for external fiducial markers or other a priori action.     

A prospective study of multiple needle biopsies versus a single open biopsy for testicular sperm extraction in men with non-obstructive azoospermia

To identify the predictive factors for testicular sperm extraction (TESE) and to understand the pathology associated with TESE, we carried out a prospective study in 40 consecutive men with azoospermia due to primary gonadal failure. The main outcome measure was the retrieval of at least one testicular spermatozoon. Endocrine and biophysical profiles, testicular histology, Johnsen score and testicular spermatids were used as predictors of sperm extraction. Spermatogenesis was quantified with the Johnsen score. A variable pattern of spermatogenesis was common, being present in 20 (50%) patients. Visualisation of testicular spermatids on testicular histology showed a strong association with TESE (P < 0.0001). Statistically significant differences were detected in plasma follicle stimulating hormone (FSH) and testicular volume between patients who had hypospermatogenesis and Sertoli cell-only or maturation arrest. There were no significant differences in Johnsen score, biophysical and endocrine profiles between the groups with successful and failed TESE. However, a statistically significant trend occurred with changes in histological pattern [chi2 for trend, P = 0.001; Pearson's coefficient (r) = 0.6], Johnsen score (P = 0.022; r = 0.5), testicular volume (P = 0.01; r = 0.5) and plasma FSH concentrations (P = 0.044; r = 0.4), albeit to a limited degree. Difference in the interpretation of histological patterns with different assessors was observed. The type of occupation or risk factors for azoospermia showed no association with testicular pathology or TESE. Variable histological patterns in different tubules in the same individual may explain the poor correlation of TESE with endocrine and biophysical profiles, Johnsen score and histological pattern. Differences in the amount of tissue used for TESE and histopathology, and misinterpretation of testicular histology rather than failure to quantify spermatogenesis may explain the poor correlation between histological patterns and TESE. Testicular spermatids predicted TESE. However, considerable overlap in values means that no single variable can provide a perfect discrimination between the groups with successful and failed TESE.