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Metabolic syndrome (MetS) is a global challenge for atherosclerosis. It was hypothesized that a four-week consumption of anthocyanin supplements by MetS patients who had three or more risk factors linked with metabolic syndrome would have a greater improvement in cardiometabolic biomarkers and would also reduce the risk of thrombosis. A total of 55 participants in two groups of Normal healthy and MetS (age 25-75y) were given 320 mg anthocyanin supplements twice daily for 4 weeks. Platelet coagulant activities, lipid profiles, fasting blood glucose, and inflammatory and oxidative stress biomarkers were measured before and after supplementation to evaluate the atheroprotective effects of anthocyanins in the study subjects. Four weeks of anthocyanin supplementation significantly decreased cardiometabolic risk factors including the average serum fasting blood glucose (FBG) (by 13.3%, P < .05) and lipid profiles by significant reduction in triglyceride (by 24.9%, P < .05) and LDL-C (by 33.1%, P < .05) in the MetS group. Anthocyanin supplementation also decreased high sensitivity C-reactive protein (hs-CRP) level (by 28%, P < .05) in females. However, no significant differences in serum UA (uric acid) and HDL-C were observed between anthocyanin pre- and post-treatment in both groups. Moreover, Anthocyanin supplements decreased ADP-induced platelet activation configuration expressed as P-selectin by 40% (P < .05). There was a positive correlation between decreased hs-CRP values and the levels of LDL-C and FBG in the MetS group (P < .05). These results support the hypothesis that anthocyanin supplementation exerts anti-atherogenicity effects by improving cardiometabolic risk factors and reducing thrombogenicity in the MetS population., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Metabolic syndrome (MetS) is a collection of pathological conditions associated with metabolic, pro-inflammatory, and prothrombotic states. MetS plays an essential role in the atherosclerotic process with associated clustering of risk factors which can increase the risk of atherogenic damage. There is an association between MetS components and the progression of atherosclerosis, which is the leading cause of cardiovascular deaths. This review was undertaken to assess the potential role of metabolic syndrome components, including oxidative stress, hypertension, hyperglycaemia and insulin resistance, obesity, dyslipidemia, chronic inflammation, physical inactivity, and atherogenic diet in the progression of atherosclerosis based on existing research.

An important element of radiation treatment planning for cancer therapy is the selection of beam angles (out of all possible coplanar and non-coplanar angles in relation to the patient) in order to maximize the delivery of radiation to the tumor site and minimize radiation damage to nearby organs-at-risk. This category of combinatorial optimization problem is particularly difficult because direct evaluation of the quality of treatment corresponding to any proposed selection of beams requires the solution of a large-scale dose optimization problem involving many thousands of variables that represent doses delivered to volume elements (voxels) in the patient. However, if the quality of angle sets can be accurately estimated without expensive computation, a large number of angle sets can be considered, increasing the likelihood of identifying a very high quality set. Using a computationally efficient surrogate beam set evaluation procedure based on single-beam data extracted from plans employing equallyspaced beams (eplans), we have developed a global search metaheuristic process based on the nested partitions framework for this combinatorial optimization problem. The surrogate scoring mechanism allows us to assess thousands of beam set samples within a clinically acceptable time frame. Tests on difficult clinical cases demonstrate that the beam sets obtained via our method are of superior quality.

The use of NextGen Sequencing clinically necessitates the need for informatics tools that support the complete workflow from sample accessioning to data analysis and reporting. To address this need we have developed Clinical Genomicist Workstation (CGW). CGW is a secure, n-tiered application where web browser submits requests to application servers that persist the data in a relational database. CGW is used by Washington University Genomic and Pathology Services for clinical genomic testing of many cancers. CGW has been used to accession, analyze and sign out over 409 cases since November, 2011. There are 22 ordering oncologists and 7 clinical genomicists that use the CGW. In summary, CGW a 'soup-to-nuts' solution to track, analyze, interpret, and report clinical genomic diagnostic tests.

IMRT treatment planning requires consideration of two competing objectives: achieving the required amount of radiation for the planning target volume and minimizing the amount of radiation delivered to all other tissues. It is important for planners to understand the tradeoff between competing factors so that the time-consuming human interaction loop (plan-evaluate-modify) can be eliminated. Treatment-plan-surface models have been proposed as a decision support tool to aid treatment planners and clinicians in choosing between rival treatment plans in a multi-plan environment. In this paper, an empirical approach is introduced to determine the minimum number of treatment plans (minimum knowledge base) required to build accurate representations of the IMRT plan surface in order to predict organ-at-risk (OAR) dose-volume (DV) levels and complications as a function of input DV constraint settings corresponding to all involved OARs in the plan. We have tested our approach on five head and neck patients and five whole pelvis/prostate patients. Our results suggest that approximately 30 plans were sufficient to predict DV levels with less than 3% relative error in both head and neck and whole pelvis/prostate cases. In addition, approximately 30-60 plans were sufficient to predict saliva flow rate with less than 2% relative error and to classify rectal bleeding with an accuracy of 90%.

The conventional IMRT planning process involves two stages in which the first stage consists of fast but approximate idealized pencil beam dose calculations and dose optimization and the second stage consists of discretization of the intensity maps followed by intensity map segmentation and a more accurate final dose calculation corresponding to physical beam apertures. Consequently, there can be differences between the presumed dose distribution corresponding to pencil beam calculations and optimization and a more accurately computed dose distribution corresponding to beam segments that takes into account collimator-specific effects. IMRT optimization is computationally expensive and has therefore led to the use of heuristic (e.g., simulated annealing and genetic algorithms) approaches that do not encompass a global view of the solution space. We modify the traditional two-stage IMRT optimization process by augmenting the second stage via an accurate Monte Carlo-based kernel-superposition dose calculations corresponding to beam apertures combined with an exact mathematical programming-based sequential optimization approach that uses linear programming (SLP). Our approach was tested on three challenging clinical test cases with multileaf collimator constraints corresponding to two vendors. We compared our approach to the conventional IMRT planning approach, a direct-aperture approach and a segment weight optimization approach. Our results in all three cases indicate that the SLP approach outperformed the other approaches, achieving superior critical structure sparing. Convergence of our approach is also demonstrated. Finally, our approach has also been integrated with a commercial treatment planning system and may be utilized clinically.

Patients with HPV-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) are significantly different with regard to sociodemographic and behavioral characteristics that clinicians may use to assume tumor HPV status. Machine learning methods were used to evaluate the predictive value of patient characteristics and laboratory biomarkers of HPV exposure for a diagnosis of HPV16-positive HNSCC compared to in situ hybridization, the current gold-standard. Models that used a combination of demographic characteristics such as age, tobacco use, gender, and race had only moderate predictive value for tumor HPV status among all patients with HNSCC (positive predictive value [PPV]=75%, negative predictive value [NPV]=68%) or when limited to oropharynx cancer patients (PPV=55%, NPV=65%) and thus included a sizeable number of false positive and false negative predictions. Prediction was not improved by the addition of other demographic or behavioral factors (sexual behavior, income, education) or biomarkers of HPV16 exposure (L1, E6/7 antibodies or DNA in oral exfoliated cells). Patient demographic and behavioral characteristics as well as HPV biomarkers are not an accurate substitute for clinical testing of tumor HPV status.

The island of Bioko is part of the Republic of Equatorial Guinea and is the only island in the World to have endemic onchocerciasis. The disease is hyperendemic and shows a forest-type epidemiology with low levels of blindness and high levels of skin disease, and the whole population of 68,000 is estimated to be at risk. Control of onchocerciasis began in 1990 using ivermectin and this yielded significant clinical benefits but transmission was not interrupted. Feasibility and preparatory studies carried out between 1995 and 2002 confirmed the probable isolation of the vector on the island, the high vectorial efficiency of the Bioko form of Simulium yahense, the seasonality of river flow, blackfly breeding and biting densities, and the distribution of the vector breeding sites. It was proposed that larviciding should be carried out from January to April, when most of the island's rivers were dry or too low to support Simulium damnosum s.l., and that most rivers would not need to be treated above 500 m altitude because they were too small to support the breeding of S. damnosum s.l. Larviciding (with temephos) would need to be carried out by helicopter (because of problems of access by land), supplemented by ground-based delivery. Insecticide susceptibility trials showed that the Bioko form was highly susceptible to temephos, and insecticide carry was tested in the rivers by assessing the length of river in which S. damnosum s.l. larvae were killed below a temephos dosing point. Regular fly catching points were established in 1999 to provide pre-control biting densities, and to act as monitoring points for control efforts. An environmental impact assessment concluded that the proposed control programme could be expected to do little damage, and a large-scale larviciding trial using ground-based applications of temephos (Abate 20EC) throughout the northern (accessible) part of the island was carried out for five weeks from 12 February 2001. Following this, a first attempt to eliminate the vectors was conducted using helicopter and ground-based applications of temephos from February to May 2003, but this was not successful because some vector populations persisted and subsequently spread throughout the island. A second attempt from January to May 2005 aimed to treat all flowing watercourses and greatly increased the number of treatment points. This led to the successful elimination of the vector. The last biting S. damnosum s.l. was caught in March 2005 and none have been found since then for more than 3 years.

Purpose: To predict organ-at-risk (OAR) complications as a function of dose-volume (DV) constraint settings without explicit plan computation in a multiplan intensity-modulated radiotherapy (IMRT) framework., Methods and Materials: Several plans were generated by varying the DV constraints (input features) on the OARs (multiplan framework), and the DV levels achieved by the OARs in the plans (plan properties) were modeled as a function of the imposed DV constraint settings. OAR complications were then predicted for each of the plans by using the imposed DV constraints alone (features) or in combination with modeled DV levels (plan properties) as input to machine learning (ML) algorithms. These ML approaches were used to model two OAR complications after head-and-neck and prostate IMRT: xerostomia, and Grade 2 rectal bleeding. Two-fold cross-validation was used for model verification and mean errors are reported., Results: Errors for modeling the achieved DV values as a function of constraint settings were 0-6%. In the head-and-neck case, the mean absolute prediction error of the saliva flow rate normalized to the pretreatment saliva flow rate was 0.42% with a 95% confidence interval of (0.41-0.43%). In the prostate case, an average prediction accuracy of 97.04% with a 95% confidence interval of (96.67-97.41%) was achieved for Grade 2 rectal bleeding complications., Conclusions: ML can be used for predicting OAR complications during treatment planning allowing for alternative DV constraint settings to be assessed within the planning framework.

Coupling beam angle optimization with dose optimization in intensity-modulated radiation therapy (IMRT) increases the size and complexity of an already large-scale combinatorial optimization problem. We have developed a novel algorithm, nested partitions (NP), that is capable of finding suitable beam angle sets by guiding the dose optimization process. NP is a metaheuristic that is flexible enough to guide the search of a heuristic or deterministic dose optimization algorithm. The NP method adaptively samples from the entire feasible region, or search space, and coordinates the sampling effort with a systematic partitioning of the feasible region at successive iterations, concentrating the search in promising subsets. We used a 'warm-start' approach by initiating NP with beam angle samples derived from an integer programming (IP) model. In this study, we describe our implementation of the NP framework with a commercial optimization algorithm. We compared the NP framework with equi-spaced beam angle selection, the IP method, greedy heuristic and random sampling heuristic methods. The results of the NP approach were evaluated using two clinical cases (head and neck and whole pelvis) involving the primary tumor and nodal volumes. Our results show that NP produces better quality solutions than the alternative considered methods.

Recently, chemotherapy-induced peripheral neuropathy has received a great deal of attention. However, the interaction of diabetic neuropathy with potentially neurotoxic chemotherapy is far less understood. The incidence of type II diabetes has risen exponentially in the past two decades. In concert with the rise in type II diabetes, the number of individuals with diabetes who need chemotherapy for cancer also is expected to increase. Diabetic neuropathy and the neurotoxic effects of chemotherapy have a significant potential to cause functional disability. Diabetics may be most at risk for the effects of neurotoxic agents on peripheral nerve functioning, in addition to the other effects induced by chemotherapeutic agents. The purpose of this article is to review the evaluation, management, and clinical implications of peripheral neuropathy in patients with cancer and diabetes.

Purpose: To describe a multiplan intensity-modulated radiotherapy (IMRT) planning framework, and to describe a decision support system (DSS) for ranking multiple plans and modeling the planning surface., Methods and Materials: One hundred twenty-five plans were generated sequentially for a head-and-neck case and a pelvic case by varying the dose-volume constraints on each of the organs at risk (OARs). A DSS was used to rank plans according to dose-volume histogram (DVH) values, as well as equivalent uniform dose (EUD) values. Two methods for ranking treatment plans were evaluated: composite criteria and pre-emptive selection. The planning surface determined by the results was modeled using quadratic functions., Results: The DSS provided an easy-to-use interface for the comparison of multiple plan features. Plan ranking resulted in the identification of one to three "optimal" plans. The planning surface models had good predictive capability with respect to both DVH values and EUD values and generally, errors of <6%. Models generated by minimizing the maximum relative error had significantly lower relative errors than models obtained by minimizing the sum of squared errors. Using the quadratic model, plan properties for one OAR were determined as a function of the other OAR constraint settings. The modeled plan surface can then be used to understand the interdependence of competing planning objectives., Conclusion: The DSS can be used to aid the planner in the selection of the most desirable plan. The collection of quadratic models constructed from the plan data to predict DVH and EUD values generally showed excellent agreement with the actual plan values.

Background: Children may be agitated or even delirious especially when recovering from general anesthesia using volatile anesthetics. Many trials have focused on the newer agents sevoflurane and desflurane but for the widely used isoflurane little is known about its potential to generate agitation. We investigated the emergence characteristics of small children after sevoflurane or isoflurane with caudal anesthesia for postoperative pain control., Methods: After institutional approval and parental consent, anesthesia was randomly performed with sevoflurane (n = 30) or isoflurane (n = 29) in children at the age of 3.8 +/- 1.8 years during surgical interventions on the lower part of the body. After induction, all children received caudal anesthesia with bupivacaine (0.25%, 0.8 ml x kg(-1)). Postoperatively, the incidences of emergence agitation (EA) and emergence delirium (ED) were measured by a blinded observer using a ten point scale (TPS; EA = TPS > 5 ED = TPS > 7) as well as vigilance, nausea/vomiting and shivering., Results: The two groups were comparable with respect to demographic data, duration of surgery and duration of anesthesia. There were also no differences in the period of time from the end of surgery until extubation, duration of stay in the PACU, postoperative vigilance and vegetative parameters. Incidence of EA was 30% (9/30) for sevoflurane and 34% (10/29) for isoflurane during the first 60 min in the PACU (P = 0.785). Likewise, the incidence of ED was not different between the groups (20% and 24%, respectively)., Conclusions: In our randomized controlled study, we found no difference in the incidence of EA or ED between sevoflurane and isoflurane. Therefore, the decision to use one or the other should not be based upon the incidence of EA or ED.

Methods for accurate and automated determination of the coefficients of the wave aberration function are compared with particular emphasis on measurements of higher order coefficients in corrected instruments. Experimental applications of aberration measurement to the determination of illumination isoplanicity and high precision local refinement of restored exit waves are also described.

Using high resolution electron microscopy and first principles quantum mechanical calculations we have explored the fundamental physics and chemistry of the semiconductor, HgTe grown inside single wall carbon nanotubes. This material forms a low-dimensional structure based on a repeating Hg2Te2 motif in which both atom species adopt new coordination geometries not seen in the bulk. Density-functional theory calculations confirm the stability of this structure and demonstrate conclusively that it arises solely as a consequence of constrained low dimensionality. This change is directly correlated with a modified electronic structure in which the low-dimensional form of HgTe is transformed from a bulk semimetal to a semiconductor.

At an intermediate stage of radiation treatment planning for IMRT, most commercial treatment planning systems for IMRT generate intensity maps that describe the grid of beamlet intensities for each beam angle. Intensity map segmentation of the matrix of individual beamlet intensities into a set of MLC apertures and corresponding intensities is then required in order to produce an actual radiation delivery plan for clinical use. Mathematically, this is a very difficult combinatorial optimization problem, especially when mechanical limitations of the MLC lead to many constraints on aperture shape, and setup times for apertures make the number of apertures an important factor in overall treatment time. We have developed, implemented and tested on clinical cases a metaheuristic (that is, a method that provides a framework to guide the repeated application of another heuristic) that efficiently generates very high-quality (low aperture number) segmentations. Our computational results demonstrate that the number of beam apertures and monitor units in the treatment plans resulting from our approach is significantly smaller than the corresponding values for treatment plans generated by the heuristics embedded in a widely use commercial system. We also contrast the excellent results of our fast and robust metaheuristic with results from an 'exact' method, branch-and-cut, which attempts to construct optimal solutions, but, within clinically acceptable time limits, generally fails to produce good solutions, especially for intensity maps with more than five intensity levels. Finally, we show that in no instance is there a clinically significant change of quality associated with our more efficient plans.

Escherichia coli is a model laboratory bacterium, a species that is widely distributed in the environment, as well as a mutualist and pathogen in its human hosts. As such, E. coli represents an attractive organism to study how environment impacts microbial genome structure and function. Uropathogenic E. coli (UPEC) must adapt to life in several microbial communities in the human body, and has a complex life cycle in the bladder when it causes acute or recurrent urinary tract infection (UTI). Several studies designed to identify virulence factors have focused on genes that are uniquely represented in UPEC strains, whereas the role of genes that are common to all E. coli has received much less attention. Here we describe the complete 5,065,741-bp genome sequence of a UPEC strain recovered from a patient with an acute bladder infection and compare it with six other finished E. coli genome sequences. We searched 3,470 ortholog sets for genes that are under positive selection only in UPEC strains. Our maximum likelihood-based analysis yielded 29 genes involved in various aspects of cell surface structure, DNA metabolism, nutrient acquisition, and UTI. These results were validated by resequencing a subset of the 29 genes in a panel of 50 urinary, periurethral, and rectal E. coli isolates from patients with UTI. These studies outline a computational approach that may be broadly applicable for studying strain-specific adaptation and pathogenesis in other bacteria.

Mixed phase Fe3O4-gamma-Fe2O3 (magnetite-maghemite) iron oxide nanoparticles have been fabricated by colloidal routes. HRTEM/HRSTEM images of the nanoparticles show the presence of [111] facets that terminate with enhanced contrast, which is shown to be caused by the presence of additional cations at the edges of the nanoparticles. HRTEM images were taken on a FEI CM200 FEGTEM, a JEOL 3100 with a LaB6 source, and a double aberration corrected JEOL-JEM 2200FS FEGTEM. The enhanced contrast effect was observed on the [111] surface atomic layers resolved using each machine. HRSTEM images, taken on an aberration corrected STEM, resolved enhanced contrast at specific surface sites. Exit wave reconstruction was also carried out on focal series taken on a double aberration corrected JEOL-JEM 2200FS and showed similar highly resolved enhanced contrast at specific surface cation sites. It is apparent that additional cations are occupying the [111] terminating layers of these nanoparticle surfaces. The use of different microscopes and techniques in this paper provides strong evidence that the enhanced contrast is a real effect and not an effect caused by microscope aberrations.

We have developed a numerical approach for the accurate and efficient calculation of HREM image intensity formed using a partially coherent source. The approach is based on Monte Carlo integration, and is suitable for use in general image restoration methods using a series of images. The accuracy of this approach is compared with calculations based on the transmission cross coefficient (TCC) for strong scattering objects, as a function of the number of sampling points, defocus, atomic number and specimen thickness. Its efficiency is compared with that of exact TCC calculations based on equally-spaced sampling of the beam divergence and focal spread distributions. The results indicate that the Monte Carlo approach is particularly advantageous for nonlinear image restoration algorithms.

The novel crystallization properties of nano-materials represent a great challenge to researchers across all disciplines of materials science. Simple binary solids can be found to adopt unprecedented structures, when confined into nanometer-sized cavities, such as the inner cylindrical bore of single-walled carbon nanotubes (SWNT). Lanthanum iodide was encapsulated within SWNTs and the resulting encapsulation composite was analyzed using energy-dispersive X-ray microanalysis (EDX) and high-resolution transmission electron microscopy (HRTEM) imaging techniques, to reveal a one-dimensional crystal fragment, with the stoichiometry of LaI2, crystallizing in the structure of LaI3 with one third of the iodine positions unoccupied. A complete characterization of the encapsulation composite was achieved using an enhanced image restoration technique, which restores the object wave from a focal series of HRTEM images, providing information about the precise structural data of both filling material and host SWNT, and thereby enabling the identification of the SWNT chirality.

Indirect high resolution electron microscopy using one of several possible data-set geometries offers advantages over conventional high-resolution imaging in enabling the recovery of the complex wavefunction at the specimen exit plane and simultaneously eliminating the aberrations present in the objective lens. This article discusses results obtained using this method from structures formed by inorganic materials confined within the bores of carbon nanotubes. Such materials are shown to be atomically regulated due to their confinement, leading to integral layer architectures that we have termed "Feynman crystals." These one-dimensional (1D) crystals also show a wide range of structural deviations from the bulk, including unexpected lattice distortions, and in some cases entirely new forms have been observed.

A case of spinal anesthesia in an extremely low birth weight male infant (body weight of 930 g at time of surgery) is presented. He was born prematurely at a gestational age of 27 weeks because of a placenta tumor and had to undergo inguinal herniotomy at 34 weeks postconceptional age. He had bronchopulmonary dysplasia and oxygen supply was still required because of frequent deterioration of oxygen saturation. Spinal anesthesia was performed successfully without any complications. Relevant aspects concerning the technique and management of spinal anesthesia in preterm infants are discussed.

The sequence of any genome becomes most useful for biological experimentation when a complete and accurate gene set is available. Gene prediction programs offer an efficient way to generate an automated gene set. Manual annotation, when performed by experienced annotators, is more accurate and complete than automated annotation. However, it is a laborious and expensive process, and by its nature, introduces a degree of variability not found with automated annotation. EAnnot (Electronic Annotation) is a program originally developed for manually annotating the human genome. It combines the latest bioinformatics tools to extract and analyze a wide range of publicly available data in order to achieve fast and reliable automatic gene prediction and annotation. EAnnot builds gene models based on mRNA, EST, and protein alignments to genomic sequence, attaches supporting evidence to the corresponding genes, identifies pseudogenes, and locates poly(A) sites and signals. Here, we compare manual annotation of human chromosome 6 with annotation performed by EAnnot in order to assess the latter's accuracy. EAnnot can readily be applied to manual annotation of other eukaryotic genomes and can be used to rapidly obtain an automated gene set.

While the process of IMRT planning involves optimization of the dose distribution, the procedure for selecting the beam inputs for this process continues to be largely trial-and-error. We have developed an integer programming (IP) optimization method to optimize beam orientation using mean organ-at-risk (MOD) data from single-beam plans. Two test cases were selected in which one organ-at-risk (OAR) and four OARs were simulated, respectively, along with a PTV. Beam orientation space was discretized in 10 degrees increments. For each beam orientation, a single-beam plan without intensity modulation and without constraints on OAR dose was generated and normalized to yield a mean PTV dose of 2 Gy and the corresponding MOD was calculated. The degree of OAR sparing was related to the average OAR MODs resulting from the beam orientations utilized with improvements of up to 10% at some dose levels. On the other hand, OAR DVHs in the IMRT plans were insensitive to beam numbers (in the 6-9 range) for similar average single-beam MODs. These MOD data were input to an IP optimization process, which then selected specified numbers of beam angles as inputs to a treatment planning system. Our results show that sets of beam angles with lower average single-beam MODs produce IMRT plans with better OAR sparing than manually selected beam angles. To optimize beam orientations, weights were assigned to each OAR following MOD input to the IP which was subsequently solved using the branch-and-cut algorithm. Seven-beam orientations obtained from solving the IP were applied to the test case with four OARs and the resulting plan with a dose prescription of 63 Gy was compared with an equi-spaced beam plan. The IP selected beams produced dose-volume improvements of up to 40% for OARs proximal to the PTV. Further improvement in the DVH can be obtained by increasing the weights assigned to these OARs but at the expense of the remaining OARs.

Improvements in instrumentation and image processing techniques mean that methods involving reconstruction of focal or beam-tilt series of images are now realizing the promise they have long offered. This indirect approach recovers both the phase and the modulus of the specimen exit plane wave function and can extend the interpretable resolution. However, such reconstructions require the a posteriori determination of the objective lens aberrations, including the actual beam tilt, defocus, and twofold and threefold astigmatism. In this review, we outline the theory behind exit plane wavefunction reconstruction and describe methods for the accurate and automated determination of the required coefficients of the wave aberration function. Finally, recent applications of indirect reconstruction in the structural analysis of complex oxides are presented.

A new method is presented for the determination of the antisymmetric coefficients of the wave aberration function from a tableau of tilted illumination images. The approach is based on measurements of the apparent defocus and two-fold astigmatism using a phase correlation function and phase contrast index calculated from a short focus series acquired at each tilt. This method is shown to be suitable for a wide range of specimens and is sufficiently accurate for exit plane wave restoration at 0.1 nm resolution. Experimental examples of this approach are provided and the method is compared to results obtained from measurements of conventional power spectra.

Single-walled carbon nanotubes (SWNTs) can be used as templates for the growth of low-dimensional inorganic materials whose structures and properties often differ greatly from those of the bulk. Here we describe the detailed crystallography of an entire helical one-dimensional cobalt diiodide nanostructure encapsulated within a SWNT. This material has an unprecedented twisted double tetrahedral chain structure arising from a rotation of Co(2)I(4) units along its length. The complete nanostructure comprises two distinct regions with oppositely handed helices separated by a short disordered region. The encapsulating SWNT shows a commensurate ovoid distortion reflecting an unexpectedly strong interaction between the nanostructure and the SWNT.

An approach to the unambiguous determination of the conformation of individual single walled nanotubes utilizing high-resolution transmission electron microscopy and digital image processing is described. The exit plane wave of single walled nanotubes restored from a focal series of images is used in a stepwise characterization procedure utilizing both the phase of the real space restoration and its Fourier transform. A combination of these complementary characterization steps yields an accurate measurement of the chiral vector for an individual nanotube.

Due to the special features of paediatric anatomy and physiology, the expected and unexpected difficult paediatric airway is one of the major challenges to every anaesthesiologist, paediatrician and emergency physician. During the last years, some new devices have been made available to improve airway management in children and infants, and several studies have advanced our understanding of the risks and benefits of our clinical practice. Certain risk factors for airway related problems during anaesthesia in children having a "cold" have been identified, and there are new aspects of the controversy concerning the use of cuffed endotracheal tube (ETT) in children. New video assisted systems have been introduced for the management of the difficult airway in paediatric patients, and new applications for well-known devices have been suggested, e.g. the laryngeal mask airway (LMA) serving as guidance for fibreoptic intubation. Recent studies have also demonstrated specific problems with the LMA in infants, as well as possible advantages of a new prototype LMA for children, similar to the ProSeal. Furthermore, the following review presents data about the use of the Cuffed Oropharyngeal Airway (COPA) and the Laryngeal Tube (LT) in paediatric patients.

A new method for the accurate determination of the symmetric coefficients of the wave aberration function has been developed. The relative defoci and displacements of images in a focus series are determined from an analysis of the phase correlation function between pairs of images, allowing the restoration of an image wave even when focus and specimen drift are present. Subsequently, the absolute coefficients of both defocus and 2-fold astigmatism are determined with a phase contrast index function. Overall this method allows a very accurate automated aberration determination even for largely crystalline samples with little amorphous contamination. Using experimental images of the complex oxide Nb16W18O94 we have demonstrated the new method and critically compared it with existing diffractogram based aberration determinations. A series of protocols for practical implementation is also given together with a detailed analysis of the accuracy achieved. Finally a focal series restoration of Nb16W18O94 with symmetric aberrations determined automatically using this method is presented.

During the last 2 years, some interesting new devices have been made available to improve airway management in children and infants, and several studies have advanced our understanding concerning risks and benefits of the current practice in the field. Certain risk factors for airway related problems during anaesthesia in children having a cold have been identified, and new aspects of the controversy concerning the use of cuffed endotracheal tubes in children presented. Novel video-assisted systems have been introduced for the management of the difficult airway in paediatric patients, and new applications for well known devices have been suggested, such as the laryngeal mask airway serving as guidance for fibreoptic intubation. Recent studies also demonstrated specific problems with the laryngeal mask airway in infants, as well as the advantages of a new prototypic laryngeal mask airway for children, similar to the ProSeal (LMA International S.A. Group, USA). Furthermore, the following review presents new data about the use of the cuffed oropharyngeal airway, the laryngeal tube, and the Arndt bronchus blocker in paediatric patients.

Purpose: In conventional treatment planning for permanent I-125 prostate implants, it has been suggested that lower seed activities result in more homogeneous dose distributions and also less overdose of the critical structures. We sought to determine if this hypothesis holds by analyzing treatment plans constructed using an automated optimized approach., Methods and Materials: We studied treatment plans for 10 patients using mixed-integer programming and the branch-and-bound method. Two mixed-integer models (that yielded somewhat different treatment plans) were developed: a "basic" model and a "dose homogeneity" model. For each resulting treatment plan, we examined dose homogeneity (by evaluating the dose non-uniformity ratio [DNR] and the full-width half-maximum [FWHM] of the differential dose-volume histogram [DVH]) as a function of three different source activities (0.35 mCi, 0.44 mCi, and 0.66 mCi). In addition, target coverage and critical structure dose distributions were evaluated. Plans using multiple source activities were also evaluated for resulting dose inhomogeneities., Results: The homogeneity model results in a more homogeneous dose distribution than the basic model. DNR is lowered by an average of 42% (standard deviation [SD] = 19%), 39% (SD = 21%), and 33% (SD = 21%) for the 0.35 mCi, 0.44 mCi, and 0.66 mCi seeds, respectively, when the homogeneity model is employed over the basic model. Corresponding average decreases in the FWHM of the DVH for 0.35 mCi, 0.44 mCi, and 0.66 mCi, respectively, are 29 Gy (SD = 28 Gy), 24 Gy (SD = 22 Gy), and 27 Gy (SD = 13 Gy). Seeds of 0.35 mCi and 0.44 mCi result in the lowest DNR and narrower FWHM of the DVH relative to 0.66 mCi seeds. In general, the 0.44 mCi seeds produce greater target coverage and require fewer seeds and needles than the 0.35 mCi seeds. Although 0.66 mCi seeds result in the greatest target coverage, they yield highest critical structure doses. They also yield solutions requiring the least number of seeds and needles. However, the dose distributions from 0.66 mCi seeds are highly inhomogeneous. Multiple source activities in the same treatment plan produce dose distributions that are comparable in homogeneity to 0.44 mCi seed implants., Conclusions: Even when an optimization model that seeks to minimize dose inhomogeneity is employed, all factors involved in seed implants make 0.44 mCi the best activity choice in comparison with 0.35 mCi and 0.66 mCi.

Conventional treatment planning for interstitial prostate brachytherapy is generally a 'trial and error' process in which improved treatment plans are generated by iteratively changing, via expert judgement, the configuration of sources within the target volume in order to achieve a satisfactory dose distribution. We have utilized linear mixed-integer programming (MIP) and the branch-and-bound method, a deterministic search algorithm, to generate treatment plans. The rapidity of dose falloff from an interstitial radioactive source requires fine sampling of the space in which dose is calculated. This leads to a large and complex model that is difficult to solve as a single 3D problem. We have therefore implemented an iterative sequential approach that optimizes pseudo-independent 2D slices to achieve a fine-grid 3D solution. Using our approach, treatment plans can be generated in 20-45 min on a 200 MHz processor. A comparison of our approach with the manual 'trial and error' approach shows that the optimized plans are generally superior. The dose to the urethra and rectum is usually maintained below harmful levels without sacrificing target coverage. In the event that the dose to the urethra is undesirably high, we present a refined optimization approach that lowers urethra dose without significant loss in target coverage. An analysis of the sensitivity of the optimized plans to seed misplacement during the implantation process is also presented that indicates remarkable stability of the dose distribution in comparison with manual treatment plans.

The modulation transfer function, noise transfer function and detection quantum efficiency of both 1k2 and 2k2 cameras attached to the same 300 kV FEGTEM have been measured. The results show that both the MTF and the DQE of the 2k2 camera are lower than for the 1k2 camera at frequencies above a third of the Nyquist limit. This lower per-pixel performance of the 2k2 camera is primarily a result of the use of a thicker phosphor scintillator. However, MTF and DQE of the 2k2 camera operated as an effective 1k2 camera by using 2 x 2 pixel binning are superior to the 1k2 camera in the medium spatial frequency range.

The complete crystallography of a one-dimensional crystal of potassium iodide encapsulated within a 1.6-nanometer-diameter single-walled carbon nanotube has been determined with high-resolution transmission electron microscopy. Individual atoms of potassium and iodine within the crystal were identified from a phase image that was reconstructed with a modified focal series restoration approach. The lattice spacings within the crystal are substantially different from those in bulk potassium iodide. This is attributed to the reduced coordination of the surface atoms of the crystal and the close proximity of the van der Waals surface of the confining nanotube.

Methods to characterise the performance of CCD cameras for electron detection are investigated with particular emphasis on the difference between the transfer of signal and noise. Similar to the Modulation Transfer Function MTF, which describes the spatial frequency dependent attenuation of contrast in the image, we introduce a Noise Transfer Function NTF that describes the transfer of the Poisson noise that is inevitably present in any electron image. A general model for signal and noise transfer by an image converter is provided. This allows the calculation of MTF and NTF from Monte-Carlo simulations of the trajectories of electrons and photons in the scintillator and the optical coupling of the camera. Furthermore, accurate methods to measure the modulation and noise transfer functions experimentally are presented. The spatial-frequency dependent Detection Quantum Efficiency DQE, an important figure of merit of the camera which has so far not been measured experimentally, can be obtained from the measured MTF and NTF. The experimental results are in good agreement with the simulations and show that the NTF at high spatial frequencies is in some cases by a factor of four higher than the MTF. This implies that the noise method, which is frequently used to measure the MTF, but in fact measures the NTF, gives over-optimistic results. Furthermore, the spatial frequency dependent DQE is lower than previously assumed., (Copyright 2000 Wiley-Liss, Inc.)

Fialuridine [FIAU, 1-(2'-deoxy-2'-fluoro-beta-D-arabinofuranosyl)-5- iodouridine] was used in clinical trials for chronic hepatitis B virus infection and was extremely toxic. Evidence suggested targets of FIAU toxicity included mitochondria, but toxic mechanisms were unclear. Since FIAU is a thymidine analog, we reasoned that triphosphorylated FIAU (FIAUTP) could be incorporated into mitochondrial DNA by DNA pol-gamma and into genomic DNA by DNA polymerases alpha, beta, delta, and epsilon. All five purified mammalian DNA polymerases incorporated FIAUMP into the nascent DNA chain during in vitro DNA synthesis. When FIAUTP was substituted for dTTP, oligonucleotide products were generated efficiently by DNA pol-gamma and were similar to those generated in the presence of the four normal dNTPs. In contrast, oligonucleotide products generated by the four nuclear DNA polymerases in the presence of FIAUTP were significantly reduced in length relative to those generated in the presence of dTTP. In parallel kinetic assays, FIAUTP competitively inhibited the accumulation of radiolabeled dTTP into DNA by DNA pol-gamma. The Ki with DNA pol-gamma was 0.04 microM, the lowest Ki among the mammalian DNA polymerases. Competition between FIAUTP and dTTP and the relative ease of accumulation of FIAUMP in mitochondrial DNA by DNA pol-gamma in vitro together may relate to clinical FIAU toxicity.

Zidovudine (azidothymidine [AZT]) inhibits human immunodeficiency virus replication and reduces the severity of acquired immunodeficiency syndrome. A limiting side effect of AZT is a mitochondrial cardiac and skeletal myopathy in which the pharmacologically active derivative of AZT (AZT triphosphate) plays a critical role. The present study determined biochemical mechanisms of AZT-induced mitochondrial toxicity and identified AZT triphosphate as an inhibitor of DNA polymerase-gamma in vitro. Inhibition kinetics were defined using purified bovine cardiac mitochondrial DNA polymerase-gamma and AZT triphosphate in vitro. The Km for deoxythymidine triphosphate was 0.8 +/- 0.3 mumol/L. AZT triphosphate incubation with DNA polymerase-gamma in vitro resulted in mixed kinetics with a competitive Ki of 1.8 +/- 0.2 mumol/L and a noncompetitive Ki' of 6.8 +/- 1.7 mumol/L. These Ki and Ki' values were strikingly higher than values for retroviral reverse transcriptase but lower than values for other cellular DNA polymerases. These data support previous molecular and morphological findings in clinical AZT mitochondrial myopathy and in models of AZT myopathy in vivo. Biochemical findings suggest that inhibition of mitochondrial DNA polymerase-gamma may be integral to the pathogenesis of AZT-induced myopathy.

DNA polymerase-beta was purified from Novikoff hepatoma and used as an antigen in an in vitro immunization system to produce monoclonal antibodies. These reagents surprisingly showed cross-reactivity to a number of proteins, including several DNA polymerases. Nearly all of these proteins possess nucleotide binding sites, which suggested the potential value of using the monoclonals to elucidate structure-function relationships within polymerase-beta. Furthermore, these antibodies were able to partially neutralize (40-50%) polymerase-beta activity, and this effect could be blocked by dNTP1 but not by dNMP or rNTP. The limited neutralization phenomenon is at least partially explained by the weak binding affinity of these antibodies. Scatchard analysis of immunoprecipitation data predicted a Kd of 1.8 x 10(-8) M. Epitope mapping studies showed that the region of polymerase-beta recognized by one of the monoclonal antibodies is within residues 235-335, and sequence homology studies indicated that the epitope is probably located in the region of amino acids 283-320. At least a portion of this area, namely residues 301-308 and 311-315, appears to be part of a nucleotide binding domain which has sequence homology with a portion of the highly conserved ATP binding site in adenylate kinase.

Previous studies from our laboratory have shown that an allele of the heat shock protein GroEL (groEL411) is able to specifically suppress some of the physiological defects of the single-stranded DNA-binding protein mutation ssb-1. A search for additional alleles of the groE genes which may act as suppressors for ssb mutations has led to the identification of groEL46 as a specific suppressor of ssb-113. It has very little or no effect on ssb-1 or ssb-3. All of the physiological defects of ssb-113, including temperature-sensitive growth, temperature-sensitive DNA synthesis, sensitivity to UV irradiation, methyl methanesulfonate, and bleomycin, and reduced recombinational capacity, are restored to wild-type levels. The ssb-113 allele, however, is unable to restore sensitivity of groEL46 cells to phage lambda. The mechanism of suppression of ssb-113 by groEL46 appears to differ from that of ssb-1 by groEL411. The data suggest that GroEL may interact with single-stranded DNA-binding protein in more than one domain.

A direct quantitative determination by EPR of the nucleic acid binding affinity relationship of the single-stranded DNA-binding protein (SSB) from Escherichia coli at close to physiological NaCl concentration is reported. Titrations of (DUAP, dT)n, an enzymatically spin-labeled (dT)n, with SSB in 20 mM Tris-HCl (pH 8.1), 1 mM sodium EDTA, 0.1 mM dithiothreitol, 10% (w/v) glycerol, 0.05% Triton with either low (5 mM), intermediate (125 mM) or high 200 mM) NaCl content, reveal the formation of a high nucleic acid density complex with a binding stoichiometry (s) of 60 to 75 nucleotides per SSB tetramer. Reverse titrations, achieved by adding (DUAP, dT)n to SSB-containing solutions, form a low nucleic acid density complex with an s = 25 to 35 in the buffer with low NaCl content (5 mM NaCl). The complex with an s = 25 to 35 is converted to the high nucleic acid density complex by increasing the NaCl content to 200 mM. It is, therefore, metastable and forms only under reverse titration conditions in low NaCl. The relative apparent affinity constant Kapp of SSB for various unlabeled single-stranded nucleic acids was determined by EPR competition experiments with spin-labeled nucleic acids as macromolecular probes in the presence of the high nucleic acid density complex. The Kapp of SSB exhibits the greatest affinity for (dT)n as was previously found for T4 gene 32 protein (Bobst, A.M., Langemeier, P.W., Warwick-Koochaki, P.E., Bobst, E.V. and Ireland, J.C. (1982) J. Biol. Chem. 257, 6184) and gene 5 protein (Bobst, A.M., Ireland, J.C. and Bobst, E.V. (1984) J. Biol. Chem. 259, 2130) by EPR competition assays. In contrast, however, SSB does not display several orders of magnitude greater affinity for (dT)n than for other single stranded DNAs as is the case with both gene 5 and T4 gene 32 protein. The relative Kapp values for SSB in the above buffer with 125 mM NaCl are: Kapp(dT)n = 4KappfdDNA = 40Kapp(dA)n = 200Kapp(A)n.

The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.

Rabbit rheumatoid factor produced in animals by hyperimmunized with group C streptococcal vaccine activated guinea pig complement. Anti-streptococcal serum was fractionated by Sephacryl S-200 chromatography into excluded (19S) and included (7S) material and examined for hemolytic activity in a sensitive homologous hemolytic assay system. In the presence of complement, both 19S and 7S antistreptococcal serum fractions induced lysis of bovine (ox) erythrocytes coated with mildly reduced and carboxymethylated rabbit anti-erythrocyte immunoglobulin G. That rabbit rheumatoid factor was responsible for the observed hemolytic activity was substantiated by hemolytic inhibition assays. Significant inhibition of hemolysis was effected when antistreptococcal serum fractions were incubated in the presence of human immunoglobulin G, rabbit immunoglobulin G, and Fc, whereas, no inhibition was detected when the same fractions were tested in the presence of rabbit Fab or F(ab')2 fragments. Deaggregation of inhibitor preparations revealed a preferential reactivity of rheumatoid factor for rabbit immunoglobulin G. In addition to the rheumatoid factor-dependent hemolytic activity observed in humoral preparations, immunoglobulin G-specific antibody-forming cells in spleen and peripheral blood lymphocyte isolates were enumerated by plaque-forming cell assay.

An Escherichia coli mutant, temperature-sensitive for DNA synthesis in vivo and in vitro, is defective in single-strand binding protein (SSB; DNA-binding protein). Conversion of phage G4 single strands to the duplex form is defective in crude enzyme fractions of the mutant and is complemented by pure wild-type SSB. Radioimmunoassays of mutant extracts show normal levels of material crossreacting with anti-SSB antibody. SSB purified to homogeneity from the mutant is active, with lower specific activity, in the reconstituted G4 replication assay at 30 degrees C, but virtually inactive at 42 degrees C. Surprisingly, the mutant protein, like the wild-type protein, survives heating at 100 degrees C. Thus, mutant SSB is structurally heat-resistant but is functionally thermosensitive in vitro and in vivo. Both the in vivo and in vitro defects are tightly linked in transductions by phage P1. The mutation in the binding protein, designated ssb-1, is located between 90 and 91 min on the E. coli genetic map.

Extracts of Novikoff hepatoma cells contain factors capable of stimulating in vitro DNA synthesis several fold. The activity can be resolved into three separate protein peaks on DEAE-Sephadex. Two of these, factors II and III, have been purified and partially characterized. Both factors increase the initial rate of DNA synthesis and allow synthesis to proceed much longer. If either factor is added after synthesis by the DNA polymerase has reached a plateau, resumption of synthesis occurs. The factors appear to have different modes of action or sites of action since they show an additive effect even when a single one is used at saturating conditions. These factors are present in normal rat liver but at a concentration less than 5% of that found in the tumor cells. When tested with several highly purified DNA polymerases (DNA nucleotidyltransferase, EC 2.7.7.7), the factors show a much greater stimulation of homologous, non-mitochondrial enzymes (rat liver nuclear-, rat liver cytoplasmic-, or Novikoff-DNA polymerases) when compared with rat liver or calf liver mitochondrial-, Escherichia coli I-, or sea urchin nuclear-DNA polymerases. The mechanism of action of these factors is not known at present. No enzymatic activity has been associated with factor III. Highly purified, but not homogeneous, preparations of factor II contain low levels of endonuclease; it has not been established whether endonuclease is a contaminant or is responsible for the stimulating activity.