Automatic 3D Registration of Lung Surfaces in Computed Tomography Scans

We developed an automated system that registers chest CT scans temporally. Our registration method matches corresponding anatomical landmarks to obtain initial registration parameters. The initial point-to-point registration is then generalized to an iterative surface-to-surface registration method. Our "goodness-of-fit" measure is evaluated at each step in the iterative scheme until the registration performance is sufficient. We applied our method to register the 3D lung surfaces of 11 pairs of chest CT scans and report promising registration performance.

Computing a Uniform Scaling Parameter for 3D Registration of Lung Surfaces

A difficulty in lung image registration is accounting for changes in the size of the lungs due to inspiration. We propose two methods for computing a uniform scale parameter for use in lung image registration that account for size change. A scaled rigid-body transformation allows analysis of corresponding lung CT scans taken at different times and can serve as a good low-order transformation to initialize non-rigid registration approaches. Two different features are used to compute the scale parameter. The first method uses lung surfaces. The second uses lung volumes. Both approaches are computationally inexpensive and improve the alignment of lung images over rigid registration. The two methods produce different scale parameters and may highlight different functional information about the lungs.

A Laminar Cortical Model for 3D Perception of Slanted and Curved Surfaces and of 2D Images: Developement, attention, and Bistability

A model of laminar visual cortical dynamics proposes how 3D boundary and surface representations of slated and curved 3D objects and 2D images arise. The 3D boundary representations emerge from interactions between non-classical horizontal receptive field interactions with intracorticcal and intercortical feedback circuits. Such non-classical interactions contextually disambiguate classical receptive field responses to ambiguous visual cues using cells that are sensitive to angles and disparity gradients with cortical areas V1 and V2. These cells are all variants of bipole grouping cells. Model simulations show how horizontal connections can develop selectively to angles, how slanted surfaces can activate 3D boundary representations that are sensitive to angles and disparity gradients, how 3D filling-in occurs across slanted surfaces, how a 2D Necker cube image can be represented in 3D, and how bistable Necker cuber percepts occur. The model also explains data about slant aftereffects and 3D neon color spreading. It shows how habituative transmitters that help to control developement also help to trigger bistable 3D percepts and slant aftereffects, and how attention can influence which of these percepts is perceived by propogating along some object boundaries.

A Neural Theory of Visual Search: Recursive Attention to Segmentations and Surfaces

A neural theory is proposed in which visual search is accomplished by perceptual grouping and segregation, which occurs simultaneous across the visual field, and object recognition, which is restricted to a selected region of the field. The theory offers an alternative hypothesis to recently developed variations on Feature Integration Theory (Treisman, and Sato, 1991) and Guided Search Model (Wolfe, Cave, and Franzel, 1989). A neural architecture and search algorithm is specified that quantitatively explains a wide range of psychophysical search data (Wolfe, Cave, and Franzel, 1989; Cohen, and lvry, 1991; Mordkoff, Yantis, and Egeth, 1990; Treisman, and Sato, 1991).

Involvement of incipient hydrous oxide species in electrocatalysis at some metal electrode surfaces

In this thesis a novel theory of electrocatalysis at metal (especially noble metal)/solution interfaces was developed based on the assumption of metal adatom/incipient hydrous oxide cyclic redox transitions. Adatoms are considered as metastable, low coverage species that oxidise in-situ at potentials of often significantly cathodic to the regular metal/metal oxide transition. Because the adatom coverage is so low the electrochemical or spectroscopic response for oxidation is frequently overlooked; however, the product of such oxidation, referred to here as incipient hydrous oxide seems to be the important mediator in a wide variety of electrocatalytically demanding oxidation processes. Conversely, electrocatalytically demanding reductions apparently occur only at adatom sites at the metal/solution interface - such reactions generally occur only at potentials below, i.e. more cathodic than, the adatom/hydrous oxide transition. It was established that while silver in base oxidises in a regular manner (forming initially OHads species) at potentials above 1.0 V (RHE), there is a minor redox transition at much lower potentials, ca. o.35 v (RHE). The latter process is assumed to an adatom/hydrous oxide transition and the low coverage Ag(l) hydrous oxide (or hydroxide) species was shown to trigger or mediate the oxidation of aldehydes, e. g. HCHO. The results of a study of this system were shown to be in good agreement with a kinetic model based on the above assumptions; the similarity between this type of behaviour and enzyme-catalysed processes - both systems involve interfacial active sites - was pointed out. Similar behaviour was established for gold where both Au(l) and Au(lll) hydrous oxide mediators were shown to be the effective oxidants for different organic species. One of the most active electrocatalytic materials known at the present time is platinum. While the classical view of this high activity is based on the concept of activated chemisorption (and the important role of the latter is not discounted here) a vital role is attributed to the adatom/hydrous oxide transition. It was suggested that the well known intermediate (or anomalous) peak in the hydrogen region of the cyclic voltanmogram for platinum region is in fact due to an adatom/hydrous oxide transition. Using potential stepping procedures to minimise the effect of deactivating (COads) species, it was shown that the onset (anodic sweep) and termination (cathodic sweep) potential for the oxidation of a wide variety of organics coincided with the potential for the intermediate peak. The converse was also shown to apply; sluggish reduction reactions, that involve interaction with metal adatoms, occur at significant rates only in the region below the hydrous oxide/adatom transition.

Flat surfaces of finite type in the 3-sphere

We introduce the notion of flat surfaces of finite type in the 3- sphere, give the algebro-geometric description in terms of spectral curves and polynomial Killing fields, and show that finite type flat surfaces generated by curves on S2 with periodic curvature functions are dense in the space of all flat surfaces generated by curves on S2 with periodic curvature functions.

Identification and analysis of mechanisms involved in a broad-spectrum disease resistant mutant of the winter wheat cv. Guardian

M66 an X-ray induced mutant of winter wheat (Triticum aestivum) cv. Guardian exhibits broad-spectrum resistance to powdery mildew (Blumeria graminis f. sp. tritici), yellow rust (Puccinia striiformis f. sp. tritici), and leaf rust (Puccinia recondita f. sp. tritici), along with partial resistance to stagnonospora nodorum blotch (caused by the necrotroph Stagonosporum nodorum) and septoria tritici blotch (caused by the hemibiotroph Mycosphaerella graminicola) compared to the parent plant ‘Guardian’. Analysis revealed that M66 exhibited no symptoms of infection following artificial inoculation with Bgt in the glasshouse after adult growth stage (GS 45). Resistance in M66 was associated with widespread leaf flecking which developed during tillering. Flecking also occurred in M66 leaves without Bgt challenge; as a result grain yields were reduced by approximately 17% compared to ‘Guardian’ in the absence of disease. At the seedling stage, M66 exhibited partial resistance. M66, along with Tht mutants (Tht 12, Tht13), also exhibit increased tolerance to environmental stresses (abiotic), such as drought and heat stress at seedling and adult growth stages, However, adult M66 exhibited increased susceptibility to the aphid Schizaphis graminum compared to ‘Guardian’. Resistance to Bgt in M66 was characterized with increased and earlier H2O2 accumulation at the site of infection which resulted in increased papilla formation in epidermal cells, compared to ‘Guardian’. Papilla formation was associated with reduced pathogen ingress and haustorium formation, indicating that the primary cause of resistance in M66 was prevention of pathogen penetration. Heat treatment at 46º C prior to challenge with Bgt also induced partial disease resistance to Blumeria graminis f. sp. tritici in ‘Guardian’ and M66 seedlings. This was characterized by a delay in primary infection, due to increased production of ROS species, such as hydrogen peroxide, ROS-scavenging enzymes and Hsp70, resulting in cross-linking of cell wall components prior to inoculation. This actively prevented the fungus from penetrating the epidermal cell wall. Proteomics analysis using 2-D gel electrophoresis identified primary and secondary disease resistance effects in M66 including detection of ROS scavenging enzymes (4, 24 hai), such as ascorbate peroxidase and a superoxidase dismutase isoform (CuZnSOD) in M66 which were absent from ‘Guardian’. Chitinase (PR protein) was also upregulated (24 hai) in M66 compared to ‘Guardian’.Monosomic and ditelosomic analysis of M66 revealed that the mutation in M66 is located on the long arm of chromosome 2B (2BL). Chromosome 2BL is known to have key genes involved in resistance to pathogens such as those causing stripe rust and powdery mildew. The TaMloB1 gene, an orthologue of the barley Mlo gene, is also located on chromosome 2BL. Sanger sequencing of part of the coding sequence revealed no deletions in the TaMloB1 gene between ‘Guardian’ and M66.

Precursor adsorption on copper surfaces as the first step during the deposition of copper: a density functional study with van der Waals correction

Copper dimethylamino-2-propoxide [Cu(dmap)2] is used as a precursor for low-temperature atomic layer deposition (ALD) of copper thin films. Chemisorption of the precursor is the necessary first step of ALD, but it is not known in this case whether there is selectivity for adsorption sites, defects, or islands on the substrate. Therefore, we study the adsorption of the Cu(dmap)2 molecule on the different sites on flat and rough Cu surfaces using PBE, PBE-D3, optB88-vdW, and vdW-DF2 methods. We found the relative order of adsorption energies for Cu(dmap)2 on Cu surfaces is Eads (PBE-D3) > Eads (optB88-vdW) > Eads (vdW-DF2) > Eads (PBE). The PBE and vdW-DF2 methods predict one chemisorption structure, while optB88-vdW predicts three chemisorption structures for Cu(dmap)2 adsorption among four possible adsorption configurations, whereas PBE-D3 predicts a chemisorbed structure for all the adsorption sites on Cu(111). All the methods with and without van der Waals corrections yield a chemisorbed molecule on the Cu(332) step and Cu(643) kink because of less steric hindrance on the vicinal surfaces. Strong distortion of the molecule and significant elongation of Cu–N bonds are predicted in the chemisorbed structures, indicating that the ligand–Cu bonds break during the ALD of Cu from Cu(dmap)2. The molecule loses its initial square-planar structure and gains linear O–Cu–O bonding as these atoms attach to the surface. As a result, the ligands become unstable and the precursor becomes more reactive to the coreagent. Charge redistribution mainly occurs between the adsorbate O–Cu–O bond and the surface. Bader charge analysis shows that electrons are donated from the surface to the molecule in the chemisorbed structures, so that the Cu center in the molecule is partially reduced.

A microscopic study of structural and electronic properties of functionalized silicon surfaces based on first-principles

Surface modification of silicon with organic monolayers tethered to the surface by different linkers is an important process in realizing future (opto-)electronic devices. Understanding the role played by the nature of the linking group and the chain length on the adsorption structures and electronic properties of these assemblies is vital to advance this technology. This Thesis is a study of such properties and contributes in particular to a microscopic understanding of induced changes in the work function of experimentally studied functionalized silicon surfaces. Using first-principles density functional theory (DFT), at the first step, we provide predictions for chemical trends in the work function of hydrogenated silicon (111) surfaces modified with various terminations. For nonpolar terminating atomic species such as F, Cl, Br, and I, the change in the work function is directly proportional to the amount of charge transferred from the surface, thus relating to the difference in electronegativity of the adsorbate and silicon atoms. The change is a monotonic function of coverage in this case, and the work function increases with increasing electronegativity. Polar species such as −TeH, −SeH, −SH, −OH, −NH2, −CH3, and −BH2 do not follow this trend due to the interaction of their dipole with the induced electric field at the surface. In this case, the magnitude and sign of the surface dipole moment need to be considered in addition to the bond dipole to generally describe the change in work function. Compared to hydrogenated surfaces, there is slight increase in the work function of H:Si(111)-XH, where X = Te, Se, and S, whereas reduction is observed for surfaces covered with −OH, −CH3, and −NH2. Next, we study the hydrogen passivated Si(111) surface modified with alkyl chains of the general formula H:Si–(CH2)n–CH2 and H:Si–X–(CH2)n–CH3, where X = NH, O, S and n = (0, 1, 3, 5, 7, 9, 11), at half coverage. For (X)–Hexyl and (X)–Dodecyl functionalization, we also examined various coverages up to full monolayer grafting in order to validate the result of half covered surface and the linker effect on the coverage. We find that it is necessary to take into account the van der Waals interaction between the alkyl chains. The strongest binding is for the oxygen linker, followed by S, N, and C, irrespective of chain length. The result revealed that the sequence of the stability is independent of coverage; however, linkers other than carbon can shift the optimum coverage considerably and allow further packing density. For all linkers apart from sulfur, structural properties, in particular, surface-linker-chain angles, saturate to a single value once n > 3. For sulfur, we identify three regimes, namely, n = 0–3, n = 5–7, and n = 9–11, each with its own characteristic adsorption structures. Where possible, our computational results are shown to be consistent with the available experimental data and show how the fundamental structural properties of modified Si surfaces can be controlled by the choice of linking group and chain length. Later we continue by examining the work function tuning of H:Si(111) over a range of 1.73 eV through adsorption of alkyl monolayers with general formula -[Xhead-group]-(CnH2n)-[Xtail-group], X = O(H), S(H), NH(2). The work function is practically converged at 4 carbons (8 for oxygen), for head-group functionalization. For tail-group functionalization and with both head- and tail-groups, there is an odd-even effect in the behavior of the work function, with peak-to-peak amplitudes of up to 1.7 eV in the oscillations. This behavior is explained through the orientation of the terminal-group's dipole. The shift in the work function is largest for NH2-linked and smallest for SH-linked chains and is rationalized in terms of interface dipoles. Our study reveals that the choice of the head- and/or tail-groups effectively changes the impact of the alkyl chain length on the work function tuning using self-assembled monolayers and this is an important advance in utilizing hybrid functionalized Si surfaces. Bringing together the understanding gained from studying single type functionalization of H:Si(111) with different alkyl chains and bearing in mind how to utilize head-group, tail-group or both as well as monolayer coverage, in the final part of this Thesis we study functionalized H:Si(111) with binary SAMs. Aiming at enhancing work function adjustment together with SAM stability and coverage we choose a range of terminations and linker-chains denoted as –X–(Alkyl) with X = CH3, O(H), S(H), NH(2) and investigate the stability and work function of various binary components grafted onto H:Si(111) surface. Using binary functionalization with -[NH(2)/O(H)/S(H)]-[Hexyl/Dodecyl] we show that work function can be tuned within the interval of 3.65-4.94 eV and furthermore, enhance the SAM’s stability. Although direct Si-C grafted SAMs are less favourable compared to their counterparts with O, N or S linkage, regardless of the ratio, binary functionalized alkyl monolayers with X-alkyl (X = NH, O) is always more stable than single type alkyl functionalization with the same coverage. Our results indicate that it is possible to go beyond the optimum coverage of pure alkyl functionalized SAMs (50%) by adding a linker with the correct choice of the linker. This is very important since dense packed monolayers have fewer defects and deliver higher efficiency. Our results indicate that binary anchoring can modify the charge injection and therefore bond stability while preserving the interface electronic structure.

An EORTC-IDBBC phase I study of gemcitabine and continuous infusion 5-fluorouracil in patients with metastatic breast cancer resistant to anthracyclines or pre-treated with both anthracyclines and taxanes.

The aim of this study was to determine the maximum tolerated dose (MTD), dose-limiting toxicities (DLT), and potential activity of combined gemcitabine and continuous infusion 5-fluorouracil (5-FU) in metastatic breast cancer (MBC) patients that are resistant to anthracyclines or have been pretreated with both anthracyclines and taxanes. 15 patients with MBC were studied at three European Organization for Research and Treatment of Cancer centres. 13 patients had received both anthracylines and taxanes. Gemcitabine was given intravenously (i.v.) on days 1 and 8, and 5-FU as a continuous i.v. infusion on days 1 through to 14, both drugs given in a 21-day schedule at four different dose levels. Both were given at doses commonly used for the single agents for the last dose level (dose level 4). One of 6 patients at level 4 (gemcitabine 1200 mg/m2 and 5-FU 250 mg/m2/day) had a DLT, a grade 3 stomatitis and skin toxicity. One DLT, a grade 3 transaminase rise and thrombosis, occurred in a patient at level 2 (gemcitabine 1000 mg/m2 and 5-FU 200 mg/m2/day). Thus, the MTD was not reached. One partial response and four disease stabilisations were observed. Only 1 patient withdrew from the treatment due to toxicity. The MTD was not reached in the phase I study. The combination of gemcitabine and 5-FU is well tolerated at doses up to 1200 mg/m2 given on days 1 and 8 and 250 mg/m2/day given on days 1 through to 14, respectively, every 21 days. The clinical benefit rate (responses plus no change of at least 6 months) was 33% with one partial response, suggesting that MBC patients with prior anthracycline and taxane therapy may derive significant benefit from this combination with minimal toxicity.

Gold nanoparticles on polarizable surfaces as Raman scattering antennas.

Surface plasmons supported by metal nanoparticles are perturbed by coupling to a surface that is polarizable. Coupling results in enhancement of near fields and may increase the scattering efficiency of radiative modes. In this study, we investigate the Rayleigh and Raman scattering properties of gold nanoparticles functionalized with cyanine deposited on silicon and quartz wafers and on gold thin films. Dark-field scattering images display red shifting of the gold nanoparticle plasmon resonance and doughnut-shaped scattering patterns when particles are deposited on silicon or on a gold film. The imaged radiation patterns and individual particle spectra reveal that the polarizable substrates control both the orientation and brightness of the radiative modes. Comparison with simulation indicates that, in a particle-surface system with a fixed junction width, plasmon band shifts are controlled quantitatively by the permittivity of the wafer or the film. Surface-enhanced resonance Raman scattering (SERRS) spectra and images are collected from cyanine on particles on gold films. SERRS images of the particles on gold films are doughnut-shaped as are their Rayleigh images, indicating that the SERRS is controlled by the polarization of plasmons in the antenna nanostructures. Near-field enhancement and radiative efficiency of the antenna are sufficient to enable Raman scattering cyanines to function as gap field probes. Through collective interpretation of individual particle Rayleigh spectra and spectral simulations, the geometric basis for small observed variations in the wavelength and intensity of plasmon resonant scattering from individual antenna on the three surfaces is explained.

Hand hygiene noncompliance and the cost of hospital-acquired methicillin-resistant Staphylococcus aureus infection.

BACKGROUND: Hand hygiene noncompliance is a major cause of nosocomial infection. Nosocomial infection cost data exist, but the effect of hand hygiene noncompliance is unknown. OBJECTIVE: To estimate methicillin-resistant Staphylococcus aureus (MRSA)-related cost of an incident of hand hygiene noncompliance by a healthcare worker during patient care. DESIGN: Two models were created to simulate sequential patient contacts by a hand hygiene-noncompliant healthcare worker. Model 1 involved encounters with patients of unknown MRSA status. Model 2 involved an encounter with an MRSA-colonized patient followed by an encounter with a patient of unknown MRSA status. The probability of new MRSA infection for the second patient was calculated using published data. A simulation of 1 million noncompliant events was performed. Total costs of resulting infections were aggregated and amortized over all events. SETTING: Duke University Medical Center, a 750-bed tertiary medical center in Durham, North Carolina. RESULTS: Model 1 was associated with 42 MRSA infections (infection rate, 0.0042%). Mean infection cost was $47,092 (95% confidence interval [CI], $26,040-$68,146); mean cost per noncompliant event was $1.98 (95% CI, $0.91-$3.04). Model 2 was associated with 980 MRSA infections (0.098%). Mean infection cost was $53,598 (95% CI, $50,098-$57,097); mean cost per noncompliant event was $52.53 (95% CI, $47.73-$57.32). A 200-bed hospital incurs $1,779,283 in annual MRSA infection-related expenses attributable to hand hygiene noncompliance. A 1.0% increase in hand hygiene compliance resulted in annual savings of $39,650 to a 200-bed hospital. CONCLUSIONS: Hand hygiene noncompliance is associated with significant attributable hospital costs. Minimal improvements in compliance lead to substantial savings.

Apparent treatment-resistant hypertension and chronic kidney disease: another cardiovascular-renal syndrome?

To identify patients at increased risk of cardiovascular (CV) outcomes, apparent treatment-resistant hypertension (aTRH) is defined as having a blood pressure above goal despite the use of 3 or more antihypertensive therapies of different classes at maximally tolerated doses, ideally including a diuretic. Recent epidemiologic studies in selected populations estimated the prevalence of aTRH as 10% to 15% among patients with hypertension and that aTRH is associated with elevated risk of CV and renal outcomes. Additionally, aTRH and CKD are associated. Although the pathogenesis of aTRH is multifactorial, the kidney is believed to play a significant role. Increased volume expansion, aldosterone concentration, mineralocorticoid receptor activity, arterial stiffness, and sympathetic nervous system activity are central to the pathogenesis of aTRH and are targets of therapies. Although diuretics form the basis of therapy in aTRH, pathophysiologic and clinical data suggest an important role for aldosterone antagonism. Interventional techniques, such as renal denervation and carotid baroreceptor activation, modulate the sympathetic nervous system and are currently in phase III trials for the treatment of aTRH. These technologies are as yet unproven and have not been investigated in relationship to CV outcomes or in patients with CKD.

The F4 fimbrial chaperone FaeE is stable as a monomer that does not require self-capping of its pilin-interactive surfaces.

Many Gram-negative bacteria use the chaperone-usher pathway to express adhesive surface structures, such as fimbriae, in order to mediate attachment to host cells. Periplasmic chaperones are required to shuttle fimbrial subunits or pilins through the periplasmic space in an assembly-competent form. The chaperones cap the hydrophobic surface of the pilins through a donor-strand complementation mechanism. FaeE is the periplasmic chaperone required for the assembly of the F4 fimbriae of enterotoxigenic Escherichia coli. The FaeE crystal structure shows a dimer formed by interaction between the pilin-binding interfaces of the two monomers. Dimerization and tetramerization have been observed previously in crystal structures of fimbrial chaperones and have been suggested to serve as a self-capping mechanism that protects the pilin-interactive surfaces in solution in the absence of the pilins. However, thermodynamic and biochemical data show that FaeE occurs as a stable monomer in solution. Other lines of evidence indicate that self-capping of the pilin-interactive interfaces is not a mechanism that is conservedly applied by all periplasmic chaperones, but is rather a case-specific solution to cap aggregation-prone surfaces.