Improvement of transmission properties through two-bend resonance by holographic design for a two-dimensional photonic crystal waveguide

We have investigated the transmission properties of a photonic crystal waveguide (PCW) formed by holographic lithography for the first time with a two-dimensional (2D) triangular holographic photonic crystal (PhC) including a line defect with two 60 masculine bends. Calculations have shown that for this PCW high transmission (>90%) through sharp corners can be obtained in a wide frequency range from 0.298 to 0.310 (omega alpha/2pi c) with the relative band gap of 4% when the dielectric contrast is 7.6:1. As far as we know, this result should be the widest frequency range with high transmission (>90%) in the waveguide of similar 2D triangular PhCs ever reported. We have also found that the specific holographic designs of PhC have strong influence on the resonance between the two waveguide bends, and thus this fact can be used as an effective means to improve the transmission property of 2D holographic PCW. In addition to the simplicity and low cost of holographic fabrication of PhCs, these features may reveal the possibly better guiding ability of holographic PCW than the conventional waveguide and the promising potential of the former in the application of photonic integrated circuits.

Genome holography: deciphering function-form motifs from gene expression data

Background

DNA chips allow simultaneous measurements of genome-wide response of thousands of genes, i.e. system level monitoring of the gene-network activity. Advanced analysis methods have been developed to extract meaningful information from the vast amount of raw gene-expression data obtained from the microarray measurements. These methods usually aimed to distinguish between groups of subjects (e.g., cancer patients vs. healthy subjects) or identifying marker genes that help to distinguish between those groups. We assumed that motifs related to the internal structure of operons and gene-networks regulation are also embedded in microarray and can be deciphered by using proper analysis.

Methodology/Principal Findings

The analysis presented here is based on investigating the gene-gene correlations. We analyze a database of gene expression of Bacillus subtilis exposed to sub-lethal levels of 37 different antibiotics. Using unsupervised analysis (dendrogram) of the matrix of normalized gene-gene correlations, we identified the operons as they form distinct clusters of genes in the sorted correlation matrix. Applying dimension-reduction algorithm (Principal Component Analysis, PCA) to the matrices of normalized correlations reveals functional motifs. The genes are placed in a reduced 3-dimensional space of the three leading PCA eigen-vectors according to their corresponding eigen-values. We found that the organization of the genes in the reduced PCA space recovers motifs of the operon internal structure, such as the order of the genes along the genome, gene separation by non-coding segments, and translational start and end regions. In addition to the intra-operon structure, it is also possible to predict inter-operon relationships, operons sharing functional regulation factors, and more. In particular, we demonstrate the above in the context of the competence and sporulation pathways.

Conclusions/Significance

We demonstrated that by analyzing gene-gene correlation from gene-expression data it is possible to identify operons and to predict unknown internal structure of operons and gene-networks regulation.

An efficient method for the creation of tunable optical line traps via control of gradient and scattering forces

Interparticle interaction energies and other useful physical characteristics can be extracted from the statistical properties of the motion of particles confined by an optical line trap. In practice, however, the potential energy landscape, U(x), imposed by the line provides an extra, and in general unknown, influence on particle dynamics. We describe a new class of line traps in which both the optical gradient and scattering forces acting on a trapped particle are designed to be linear functions of the line coordinate and in which their magnitude can be counterbalanced to yield a flat U(x). These traps are formed using approximate solutions to general relations concerning non-conservative optical forces that have been the subject of recent investigations [Y. Roichman, B. Sun, Y. Roichman, J. Amato-Grill, and D. G. Grier, Phys. Rev. Lett. 100, 013602-4 (2008).]. We implement the lines using holographic optical trapping and measure the forces acting on silica microspheres, demonstrating the tunability of the confining potential energy landscape. Furthermore, we show that our approach efficiently directs available laser power to the trap, in contrast to other methods.

Autofocusing in digital holographic phase contrast microscopy on pure phase objects for live cell imaging

Digital holography enables a multifocus quantitative phase microscopy for the investigation of reflective surfaces and for marker-free live cell imaging. For digital holographic long-term investigations of living cells an automated (subsequent) robust and reliable numerical focus adjustment is of particular importance. Four numerical methods for the determination of the optimal focus position in the numerical reconstruction and propagation of the complex object waves of pure phase objects are characterized, compared, and adapted to the requirements of digital holographic microscopy. Results from investigations of an engineered surface and human pancreas tumor cells demonstrate the applicability of Fourier-weighting- and gradient-operator-based methods for robust and reliable automated subsequent numerical digital holographic focusing.

Three-dimensional optical disk data storage via the localized alteration of a format hologram

Three-dimensional optical data storage is demonstrated in an initially homogenous volume by first recording a reflection grating in a holographic photopolymer. This causes the entire volume to be weakly reflecting to a confocal read/write head. Superposition of two or three such gratings with slightly different k-vectors creates a track and layer structure that specialized servo detection optics can use to lock the focus to these deeply-buried tracks. Writing is accomplished by locally modifying the reflectivity of the preexisting hologram. This modification can take the form of ablation, inelastic deformation via heating at the focus, or erasure via linear or two-photon continued polymerization in the previously unexposed fringes of the hologram. Storage by each method is demonstrated with up to eight data layers separated by as little as 12 microns.

Out-of-phase mixed holographic gratings: a quantative analysis

We show, that by performing a simultaneous analysis of the angular dependencies of the +/- first and the zeroth diffraction orders of mixed holographic gratings, each of the relevant parameters can be obtained: the strength of the phase grating and the amplitude grating, respectively, as well as a potential phase between them. Experiments on a pure lithium niobate crystal are used to demonstrate the applicability of the analysis.

Optimization of multiplexed holographic gratings in PQ-PMMA for spectral-spatial imaging filters

Holographic gratings formed in thick phenanthrenquinone- (PQ-) doped poly(methyl methacrylate) (PMMA) can be made to have narrowband spectral and spatial transmittance filtering properties. We present the design and performance of angle-multiplexed holographic filters formed in PQ-PMMA at 488 nm and reconstructed with a LED operated at approximately 630 nm. The dark delay time between exposure and the preillumination exposure of the polymer prior to exposure of the holographic area are varied to optimize the diffraction efficiency of multiplexed holographic filters. The resultant holographic filters can enhance the performance of four-dimensional spatial-spectral imaging systems. The optimized filters are used to simultaneously sample spatial and spectral information at five different depths separated by 50 microm within biological tissue samples.

Sound field separation technique based on equivalent source method and its application in nearfield acoustic holography

A technique for separating sound fields using two closely spaced parallel measurement surfaces and based on equivalent source method is proposed. The method can separate wave components crossing two measurement surfaces in opposite directions, which makes nearfield acoustic holography (NAH) applications in a field where there exist sources on the two sides of the hologram surface, in a reverberant field or in a scattered field, possible. The method is flexible in applications, simple in computation, and very easy to implement. The measurement surfaces can be arbitrarily shaped, and they are not restricted to be regular as in the traditional field separation technique. And, because the method performs field separation calculations directly in the spatial domain-not in the wave number domain--it avoids the errors and limitations (the window effects, etc.) associated with the traditional field separation technique based on the spatial Fourier transform method. In the paper, a theoretical description is first given, and the performance of the proposed field separation technique and its application in NAH are then evaluated through experiments.

Introduction: materials research in an aberration-free environment

The last decade has witnessed a revolution in electron microscopy as online correction of spherical aberration has become a reality in both fixed-beam and scanning instruments. The combination of improved resolution and higher beam currents coupled with the prospect of simpler image interpretation has stimulated great interest and excitement across the entire field of microscopy. The Microscopy Society of America has an active Focused Interest Group on the topic of “Materials Research in an Aberration-Free Environment,” and its goal is to provide a forum for discussion and dissemination of the latest advances in instrumentation and novel applications of aberration-corrected electron microscopy. This special issue of Microscopy and Microanalysis contains contributions from the Pre-Meeting Congress on this topic held in Chicago, Illinois, in late July 2006, immediately preceding Microscopy & Microanalysis 2006.

A flux-preserving non-linear inline holography reconstruction algorithm for partially coherent electrons

Retrieving low spatial frequency components of the phase of the complex-valued exit-face wave function in a transmission electron microscope by reconstruction of a focal series of images requires a large defocus range to be used. In an aberration corrected TEM or at sufficiently low resolution the effect of spherical and higher order aberrations on the spatial coherence term in the transmission cross coefficient may be neglected for an appropriate choice of objective aperture. Applying this approximation, a computationally efficient and flux-preserving iterative computer algorithm has been designed which allows the reconstruction of focal series recorded over a large focal range and arbitrary degrees of spatial coherence. The reconstruction from an experimental data set will be presented. Since a flux-preserving description of image formation is consistent with the transport of intensity equation (TIE), I will also discuss the implications for the application of the TIE under the condition of partial spatial coherence. Finally, a comparison with off-axis holography will be made.

Electron holography study for two-dimensional dopant profile measurement with specimens prepared by backside ion milling

The visualization of two-dimensional dopant profiles and the quantitative analysis of the built-in potential across the p-n junction, DeltaV(p-n), by electron holography were carried out with specimens prepared from the backside ion milling method combined with the focused ion beam technique. It was possible to obtain dopant profiling of the large field of view with low surface damage and gradually changed thickness. From the quantitative analysis using the phase information of electron holography and the thickness information of electron energy-loss spectroscopy, DeltaV(p-n) was estimated to be about 0.78 V assuming that the thickness of the dead layer on both surfaces is 50 nm, which is to show the difference of within 12% from the calculated value. It demonstrates that the backside ion milling method is a very promising specimen preparation technique for the reliable and quantitative analysis of dopant profiling with electron holography.

Hologram QSAR model for the prediction of human oral bioavailability

A drug intended for use in humans should have an ideal balance of pharmacokinetics and safety, as well as potency and selectivity. Unfavorable pharmacokinetics can negatively affect the clinical development of many otherwise promising drug candidates. A variety of in silico ADME (absorption, distribution, metabolism, and excretion) models are receiving increased attention due to a better appreciation that pharmacokinetic properties should be considered in early phases of the drug discovery process. Human oral bioavailability is an important pharmacokinetic property, which is directly related to the amount of drug available in the systemic circulation to exert pharmacological and therapeutic effects. In the present work, hologram quantitative structure-activity relationships (HQSAR) were performed on a training set of 250 structurally diverse molecules with known human oral bioavailability. The most significant HQSAR model (q(2)=0.70, r(2)=0.93) was obtained using atoms, bond, connection, and chirality as fragment distinction. The predictive ability of the model was evaluated by an external test set containing 52 molecules not included in the training set, and the predicted values were in good agreement with the experimental values. The HQSAR model should be useful for the design of new drug candidates having increased bioavailability as well as in the process of chemical library design, virtual screening, and high-throughput screening.

Multifunctional and compact spectrometers based on cylindrical beam volume holograms

We propose a new class of slitless spectrometers using cylindrical beam volume holograms. These holograms disperse an input beam in one direction in an output plane while they do not affect the beam in the perpendicular direction. We show that the spectral mapping of the input beam can be obtained in one direction and the beam can be independently modified in the perpendicular direction. Using this unique property, we demonstrate a spectral wrapping technique to considerably increase the operation spectral range of the slitless spectrometers, without sacrificing their resolution.

Continuous blood glucose monitoring with a thin-film optical sensor

BACKGROUND

We recently described a holographic optical sensor with improved selectivity for glucose over fructose that was based on a thin-film polymer hydrogel containing phenylboronic acid receptors. The aim of the present work was to measure glucose in human blood plasma as opposed to simple buffers and track changes in concentration at a rate mimicking glucose changes in vivo.

METHODS

We used holographic sensors containing acrylamide, N,N'-methylenebisacrylamide, 3-acrylamidophenylboronic acid, and (3-acrylamidopropyl)trimethylammonium chloride to measure 7 human blood plasma samples at different glucose concentrations (3-33 mmol/L) in static mode. Separately, using a flow cell, the glucose concentration was varied at approximately 0.17-0.28 mmol(-1) x L(-1) x min(-1), and the sensor's ability to continuously monitor glucose was investigated over an extended period.

RESULTS

We subjected the results of the ex vivo static measurements to error grid analysis. Of 46 measurements, 42 (91.3%) fell in zone A of a Clarke error grid, and the remainder (8.7%) fell in zone B. The ex vivo flow experiments showed that the sensor is able to accurately track changes in concentration occurring in real time without lag or evidence of hysteresis.

CONCLUSIONS

We demonstrate the ability of a phenylboronic acid-based sensor to measure glucose in human blood plasma for the 1st time in vitro. Holographic glucose sensors can be used without recourse to recalibration. Their robust nature, coupled with their format flexibility, makes them an attractive alternative to conventional electrochemical enzyme-based methods of glucose monitoring for people with diabetes.

Biomimetic models of the actin cytoskeleton

The cytoskeleton is a complex polymer network that plays an essential role in the functionality of eukaryotic cells. It endows cells with mechanical stability, adaptability, and motility. To identify and understand the mechanisms underlying this large variety of capabilities and to possibly transfer them to engineered networks makes it necessary to have in vitro and in silico model systems of the cytoskeleton. These models must be realistic representatives of the cellular network and at the same time be controllable and reproducible. Here, an approach to design complementary experimental and numerical model systems of the actin cytoskeleton is presented and some of their properties discussed.

Violin f-hole contribution to far-field radiation via patch near-field acoustical holography

The violin radiates either from dual ports (f-holes) or via surface motion of the corpus (top+ribs+back), with no clear delineation between these sources. Combining "patch" near-field acoustical holography over just the f-hole region of a violin with far-field radiativity measurements over a sphere, it was possible to separate f-hole from surface motion contributions to the total radiation of the corpus below 2.6 kHz. A0, the Helmholtz-like lowest cavity resonance, radiated essentially entirely through the f-holes as expected while A1, the first longitudinal cavity mode with a node at the f-holes, had no significant f-hole radiation. The observed A1 radiation comes from an indirect radiation mechanism, induced corpus motion approximately mirroring the cavity pressure profile seen for violinlike bowed string instruments across a wide range of sizes. The first estimates of the fraction of radiation from the f-holes F(f) indicate that some low frequency corpus modes thought to radiate only via surface motion (notably the first corpus bending modes) had significant radiation through the f-holes, in agreement with net volume changes estimated from experimental modal analysis. F(f) generally trended lower with increasing frequency, following corpus mobility decreases. The f-hole directivity (top/back radiativity ratio) was generally higher than whole-violin directivity.

Visualization of Marginal Integrity of Resin-Enamel Interface by Holographic Interferometry

Holographic interferometry offers precise insight into both the frequency and location of cohesive fractures through its fringe information. If flowable composites are not used as a first layer, fringe distribution indicates cohesive fractures as a consequence of composite polymerization.

Dynamic Holography in Bacteriorhodopsin/Gelatin Films: Effects of Light-Dark Adaptation at Different Humidity†

This work examines the kinetics of dynamic holography responses in light-adapted and dark-adapted bacteriorhodopsin (BR) films at different humidity. We have demonstrated that the kinetics of the diffraction efficiency in wild type BR films is quite different in dark-adapted and light-adapted samples. The holographic recording kinetics, which depends on the duration of incubation in the dark after light adaptation at different humidity values, was studied in depth. A specially designed miniature cell containing a BR film was mounted inside the holographic set up to allow controlled humidity changes over a broad range. The diffraction efficiency kinetics at humidity values of 96-99% were quite different from the kinetics at 60-93% humidity. We found that humidity values of 90-93% were most optimal for dynamic holography recording using a gelatin film containing BR. In agreement with a calculation of the wavelength-dependent changes of the refractive index for dark-adapted and light-adapted BR samples using the Kramers-Kronig relation, the maximum difference in the refractive index and thus in the diffraction efficiency for dark-adapted and light-adapted BR films takes place at 630 nm, close to the wavelength of the He-Ne laser used.

Holographic interferometry method for assessment of static load stress distribution in dog mandible

This study compared the transmission of tensions in fresh, fixed and macerated dog mandibles in order to clarify the diversity of behavior of bone tissues under dry and moist conditions. Double-exposure holographic interferometry was applied and holograms were obtained from 12 fresh hemi-mandibles under static load (control group), which were randomly assigned to 2 groups: 6 were fixed in 10% formalin and 6 were macerated. The specimens were submitted to the same initial force and their respective holograms were obtained. Analysis of the holograms showed that the fresh specimens transmitted significantly less tension than the fixed and macerated ones (p<0.05), and the tension direction was different. An average two-fold tension increment was observed in the experimental conditions. The holographic interferometry method was efficient in quantifying and qualifying tension transmission. However, depending on the type of analysis, the anatomical specimens must be fresh because macerated specimens will produce different results.

Crystal habits and magnetic microstructures of magnetosomes in coccoid magnetotactic bacteria

We report on the application of off-axis electron holography and high-resolution TEM to study the crystal habits of magnetosomes and magnetic microstructure in two coccoid morphotypes of magnetotactic bacteria collected from a brackish lagoon at Itaipu, Brazil. Itaipu-1, the larger coccoid organism, contains two separated chains of unusually large magnetosomes; the magnetosome crystals have roughly square projections, lengths up to 250 nm and are slightly elongated along [111] (width/length ratio of about 0.9). Itaipu-3 magnetosome crystals have lengths up to 120 nm, greater elongation along [111] (width/length approximately 0.6), and prominent corner facets. The results show that Itaipu-1 and Itaipu-3 magnetosome crystal habits are related, differing only in the relative sizes of their crystal facets. In both cases, the crystals are aligned with their [111] elongation axes parallel to the chain direction. In Itaipu-1, but not Itaipu-3, crystallographic positioning perpendicular to [111] of successive crystals in the magnetosome chain appears to be under biological control. Whereas the large magnetosomes in Itaipu-1 are metastable, single-magnetic domains, magnetosomes in Itaipu-3 are permanent, single-magnetic domains, as in most magnetotactic bacteria.

Laser tweezer deformation of giant unilamellar vesicles

Two methods are presented for deforming giant unilamellar vesicles with holographic optical tweezers. The first allows ultrahigh spatial- and temporal-resolution optical tracking of membrane deformations, by using embedded silica microspheres in a giant unilamellar vesicle as tracers. The vesicles are stretched by moving several beads with multiple optical tweezers and then are released from an elongated shape. Time constants of relaxation can be extracted by tracking the beads with 0.5-ms time resolution and 10 nm or better spatial resolution. The second method allows for direct deformation of the membrane into complex shapes using two solutions with different indices of refraction and holographic optical tweezer. Vesicle shapes are extracted directly with an active contour algorithm. Fourier analysis of the relaxation of the vesicle shape back to an equilibrium shape demonstrates a possible application of this technique.

Representing word meaning and order information in a composite holographic lexicon

The authors present a computational model that builds a holographic lexicon representing both word meaning and word order from unsupervised experience with natural language. The model uses simple convolution and superposition mechanisms (cf. B. B. Murdock, 1982) to learn distributed holographic representations for words. The structure of the resulting lexicon can account for empirical data from classic experiments studying semantic typicality, categorization, priming, and semantic constraint in sentence completions. Furthermore, order information can be retrieved from the holographic representations, allowing the model to account for limited word transitions without the need for built-in transition rules. The model demonstrates that a broad range of psychological data can be accounted for directly from the structure of lexical representations learned in this way, without the need for complexity to be built into either the processing mechanisms or the representations. The holographic representations are an appropriate knowledge representation to be used by higher order models of language comprehension, relieving the complexity required at the higher level.

Sonoelastographic imaging of interference patterns for estimation of shear velocity distribution in biomaterials

The authors have recently demonstrated the shear wave interference patterns created by two coherent vibration sources imaged with the vibration sonoelastography technique. If the two sources vibrate at slightly different frequencies omega and omega+deltaomega, respectively, the interference patterns move at an apparent velocity of (deltaomega/2omega)upsilon(shear), where upsilon(shear) is the shear wave speed. We name the moving interference patterns "crawling waves." In this paper, we extend the techniques to inspect biomaterials with nonuniform stiffness distributions. A relationship between the local crawling wave speed and the local shear wave velocity is derived. In addition, a modified technique is proposed whereby only one shear wave source propagates shear waves into the medium at the frequency omega. The ultrasound probe is externally vibrated at the frequency omega-deltaomega. The resulting field estimated by the ultrasound (US) scanner is proven to be an exact representation of the propagating shear wave field. The authors name the apparent wave motion "holography waves." Real-time video sequences of both types of waves are acquired on various inhomogeneous elastic media. The distribution of the crawling/holographic wave speeds are estimated. The estimated wave speeds correlate with the stiffness distributions.

PACS storage technology update: holographic storage

This paper focuses on the emerging technology of holographic storage and its effect on picture archiving and communication systems (PACS). A review of the emerging technology is presented, which includes a high level description of holographic drives and the associated substrate media, the laser and optical technology, and the spatial light modulator. The potential advantages and disadvantages of holographic drive and storage technology are evaluated. PACS administrators face myriad complex and expensive storage solutions and selecting an appropriate system is time-consuming and costly. Storage technology may become obsolete quickly because of the exponential nature of the advances in digital storage media. Holographic storage may turn out to be a low cost, high speed, high volume storage solution of the future; however, data is inconclusive at this early stage of the technology lifecycle. Despite the current lack of quantitative data to support the hypothesis that holographic technology will have a significant effect on PACS and standards of practice, it seems likely from the current information that holographic technology will generate significant efficiencies. This paper assumes the reader has a fundamental understanding of PACS technology.

Functional holography analysis: simplifying the complexity of dynamical networks

We present a novel functional holography (FH) analysis devised to study the dynamics of task-performing dynamical networks. The latter term refers to networks composed of dynamical systems or elements, like gene networks or neural networks. The new approach is based on the realization that task-performing networks follow some underlying principles that are reflected in their activity. Therefore, the analysis is designed to decipher the existence of simple causal motives that are expected to be embedded in the observed complex activity of the networks under study. First we evaluate the matrix of similarities (correlations) between the activities of the network's components. We then perform collective normalization of the similarities (or affinity transformation) to construct a matrix of functional correlations. Using dimension reduction algorithms on the affinity matrix, the matrix is projected onto a principal three-dimensional space of the leading eigenvectors computed by the algorithm. To retrieve back information that is lost in the dimension reduction, we connect the nodes by colored lines that represent the level of the similarities to construct a holographic network in the principal space. Next we calculate the activity propagation in the network (temporal ordering) using different methods like temporal center of mass and cross correlations. The causal information is superimposed on the holographic network by coloring the nodes locations according to the temporal ordering of their activities. First, we illustrate the analysis for simple, artificially constructed examples. Then we demonstrate that by applying the FH analysis to modeled and real neural networks as well as recorded brain activity, hidden causal manifolds with simple yet characteristic geometrical and topological features are deciphered in the complex activity. The term "functional holography" is used to indicate that the goal of the analysis is to extract the maximum amount of functional information about the dynamical network as a whole unit.

Design principles for developing an efficient clinical anatomy course

The exponential growth of medical knowledge presents a challenge for the medical school curriculum. Because anatomy is traditionally a long course, it is an attractive target to reduce course hours, yet designing courses that produce students with less understanding of human anatomy is not a viable option. Faced with the challenge of teaching more anatomy with less time, we set out to understand how students employ instructional media to learn anatomy inside and outside of the classroom. We developed a series of pilot programs to explore how students learn anatomy and, in particular, how they combine instructional technology with more traditional classroom and laboratory-based learning. We then integrated what we learned with principles of effective instruction to design a course that makes the most efficient use of students' in-class and out-of-class learning. Overall, we concluded that our new anatomy course needed to focus on transforming how medical students think, reason, and learn. We are currently testing the hypothesis that this novel approach will enhance the ability of students to recall and expand their base of anatomical knowledge throughout their medical school training and beyond.

A holographic collaborative medical visualization system

We report on our work on the development of a novel holographic display technology, capable of targeting multiple freely moving naked eye viewers, and of a demonstrator, exploiting this technology to provide medical specialists with a truly interactive collaborative 3D environment for diagnostic discussions and/or pre-operative planning.

Habits of magnetosome crystals in coccoid magnetotactic bacteria

High-resolution transmission electron microscopy and electron holography were used to study the habits of exceptionally large magnetite crystals in coccoid magnetotactic bacteria. In addition to the crystal habits, the crystallographic positioning of successive crystals in the magnetosome chain appears to be under strict biological control.

Efficiency of noncompliance simultaneous first and second upper molar distalization: a three-dimensional tooth movement analysis

Objective of this prospective study was the three-dimensional (3D) analysis of tooth movements after the noncompliance simultaneous distalization of the first and second maxillary molars. Ten patients (five girls and five boys; mean age: 13.2 years) with bilateral Class II molar relationships were treated with a noncompliance, fixed intraoral appliance. Upper second molars had already erupted in all cases. Dental casts and lateral cephalometric radiographs were taken immediately before placement and after removal of the appliance. The casts were 3D digitized and superimposed on a predefined area in the palate. The resulting holograms, as well as the cephalometric radiographs, were digitized and analyzed by means of customized cephalometric software. The whole procedure was repeated after a two- to four-week interval to estimate the error of both methods. The cast assessment of 3D sagittal and vertical tooth movements was more reliable than the cephalometric record. The average maxillary first molar distal movement was 2.8 mm. Anchorage loss was expressed by a 1.9-mm proclination of the central incisors. A substantial variation among patients and among the right and left side in the same patient was observed. Noncompliance simultaneous distalization of the first and second maxillary molars can be an efficient treatment option for the correction of Class II molar relationship. However, anchorage loss and individual variation have to be seriously considered. Bilaterally symmetrical effectiveness should not be relied upon.

[Hologram quantitative structure-activity relationship for predicting acute toxicity of benzene derivatives to the tadpoles (Rana japonica)]

Acute lethal toxicity, the negative logarithm of 12 h acute median lethal molar concentration (expressed as 12h-log1/LC50, mol/L) of a series of benzene derivatives to Rana japonica tadpoles was determined. The relationship between the structure of benzene derivatives and their acute lethal toxicity was investigated by using hologram quantitative structure-activity relationship (HQSAR). The influence of hologram length, fragment size and distinction parameters on the quality of HQSAR model was studied. The robustness and predictive ability of the model were also validated by Leave-One-Out cross-validation procedure. The tested 51 compounds revealed a range of acute median lethal toxicity (12h-log1/LC50, mol/L) from 2.07 to 4.56. As a result, the best model was generated using a fragment size of 6-7 from a hologram length of 83 with 6 components. The HQSAR model showed a conventional correlation coefficient r2 of 0.942 and a Leave-One-Out cross-validation r2(cv) equal to 0.849, indicating the model possess high statistical quality in the prediction of acute toxicity of novel benzene analogs.

A three-dimensional morphometric study of craniofacial shape in schizophrenia

BACKGROUND

Subtle dysmorphogenesis of the craniofacial region constitutes important corroborating evidence of the neurodevelopmental origins of schizophrenia. Advances in facial visualization now allow for three-dimensional anthropometric evaluations of potentially greater discriminatory power in examining the complex geometric relationships of facial topography.

METHOD

Sixty-five anthropometrically derived landmarks were identified from three-dimensional facial images collected from 14 patients with schizophrenia and 11 comparison subjects, imaged with a high-resolution, portable laser scanner.

RESULTS

Using the Procrustes morphometric approach for shape analysis, the difference in mean shapes was highly significant, with patients exhibiting superoinferior elongation of the face.

CONCLUSIONS

The topography of craniofacial anomalies in schizophrenia is not random and points to midline deformation.

Dynamic holographic endoscopy--ex vivo investigations of malignant tumors in the human stomach

Laser holographic interferometry is based on the superimposition of the holograms of different motional states of an object on a single holographic storing medium. Using a combination of holographic interferometry and endoscopic imaging, we tried to detect areas of focally disturbed tissue elasticity in gastric cancer preparations. By connecting a mobile electronic speckle pattern interferometry (ESPI) camera system (light source: double frequency Nd:YAG laser, lambda = 532 nm) to different types of endoscopes, ex vivo experiments were performed on ten formalin fixed human stomachs, nine containing adenocarcinomas and one with a gastric lymphoma. Linking the endoscopic ESPI camera complex to a fast image processing system, the method of double pulse exposure image subtraction was applied at a video frame rate of 12.5 Hz. Speckle correlation patterns and corresponding phase difference distributions resulting from gastric wall deformation by gentle touch with a guide wire were analyzed. Tumor-free gastric areas showed high-contrast concentric fringes around the point of stimulation. In contrast, fringe patterns and filtered phase difference distributions corresponding to the areas of malignancy in all the cases were characterized by largely parallel lines, indicating that stimulation of rigid tumor tissue primarily led to tilting. Our ex vivo investigations of malignant gastric tumors show that the application of dynamic holographic endoscopy makes it possible to distinguish areas of malignancy from surrounding healthy tissue based on the differences in tissue elasticity.

Design and preparation of a particle dynamics space flight experiment, SHIVA

This paper describes the flight experiment, supporting ground science, and the design rationale for a project on spaceflight holography investigation in a virtual apparatus (SHIVA). SHIVA is a fundamental study of particle dynamics in fluids in microgravity. Gravitation effects and steady Stokes drag often dominate the equations of motion of a particle in a fluid and consequently microgravity provides an ideal environment in which to study the other forces, such as the pressure and viscous drag and especially the Basset history force. We have developed diagnostic recording methods using holography to save all of the particle field optical characteristics, essentially allowing the experiment to be transferred from space back to Earth in what we call the "virtual apparatus" for microgravity experiments on Earth. We can quantify precisely the three-dimensional motion of sets of particles, allowing us to test and apply new analytic solutions developed by members of the team. In addition to employing microgravity to augment the fundamental study of these forces, the resulting data will allow us to quantify and understand the ISS environment with great accuracy. This paper shows how we used both experiment and theory to identify and resolve critical issues and to produce an optimal experimental design that exploits microgravity for the study. We examined the response of particles of specific gravity from 0.1 to 20, with radii from 0.2 to 2 mm, to fluid oscillation at frequencies up to 80 Hz with amplitudes up to 200 microns. To observe some of the interesting effects predicted by the new solutions requires the precise location of the position of a particle in three dimensions. To this end we have developed digital holography algorithms that enable particle position location to a small fraction of a pixel in a CCD array. The spaceflight system will record holograms both on film and electronically. The electronic holograms can be downlinked providing real-time data, essentially acting like a remote window into the ISS experimental chamber. Ground experiments have provided input to a flight system design that can meet the requirements for a successful experiment on ISS. Moreover the ground experiments have provided a definitive, quantitative observation of the Basset history force over a wide range of conditions. Results of the ground experiments, the flight experiment design, preliminary flight hardware design, and data analysis procedures are reported.

Holographic QSAR of selected esters

The HQSAR (Holographic QSAR) method, which has been recently developed, can offer the ability to rapidly and easily generate QSAR models of high statistical quality and predictive value. HQSAR analysis requires selecting values for parameters that specify the size of the hologram that is to be used, and the size and type of fragment substructures that are to be encoded. The color coding is provided by HQSAR to reflect which molecular fragments may be important contributors to the biological activity. In this work, we studied the quantitative structure activity relationship of selected esters using the HQSAR method. A robust HQSAR model with r(2) (non-cross-validated regression coefficient) of 0.981 and q(2) (cross-validated regression coefficient) of 0.912, was developed after optimizing the fragment size and the hologram length. The color coding analysis, which has rarely been reported before, was done here to explain the outlier successfully.

On the transport of intensity technique for phase retrieval

The Transport of Intensity technique is becoming a viable alternative to electron holography for phase retrieval in Transmission Electron Microscopy. However, several issues are still to be clarified in order to ascertain the applicability of the technique; among them, the controversy regarding its geometrical or wave-optical nature, as related to the phase detection limit. We show here that the Transport of Intensity is a wave-optical technique that works in a special regime of small defocus where the image intensity is linear with the defocus parameter. By a simple analytical example we show that the Transport of Intensity correctly reconstructs the electron optical phase shift even when the phase is smaller than pi, a value defining the boundary between the geometrical and wave approaches. Another example is given, the reconstruction of a phase jump, accompanied with experimental support showing that phase retrieval by Electron Holography and Transport of Intensity techniques yields results in good agreement.

Experimental characterization and mitigation of specimen charging on thin films with one conducting layer

Specimen charging may be one of the most significant factors that contribute to the high variability and generally low quality of images in cryo-electron microscopy. Understanding the nature of specimen charging can help in devising methods to reduce or even avoid its effects and thus improve the rate of data collection as well as the quality of the data. We describe a series of experiments that help to characterize the charging phenomenon, which has been termed the Berriman effect. The pattern of buildup and disappearance of the charge pattern has led to several suggestions for how to alleviate the effect. Experiments are described that demonstrate the feasibility of such charge mitigation.

Simple, semiautomatic assay of cytostatic and cytotoxic effects of antitumor drugs by laser scanning cytometry: effects of the bis-intercalator WP631 on growth and cell cycle of T-24 cells

BACKGROUND

Common assays of drug-induced cytotoxicity on adherent cells rely on cell trypsinization followed by count of live and dead cells. To estimate the cell cycle effects, cellular DNA content is analyzed by flow cytometry. This procedure is laborious and time consuming. The alternative viability assays, e.g., based on reduction of 3-(4,5-dimethylthiazol-2-yl) 2,5-diphenyl tetrazolium bromide, although rapid and convenient, do not provide information about individual cells or cell cycle effects and may be biased by growth imbalance.

METHODS

The bladder carcinoma T-24 cells were seeded onto eight-chamber microscope slide-based tissue culture vessels. The novel antitumor drug, the bis-intercalating anthracycline WP631, was administered at various concentrations to different chamber cultures on the same slide; the control cultures were left untreated. After 24, 48, and 72 h, the cultures were fixed, and cellular DNA was stained with 4,6-diamidino-2-phenyl indole (DAPI). The slides were scanned by laser scanning cytometry (LSC) to obtain the number of attached cells per culture chamber and reveal their cell cycle distribution.

RESULTS

The cell growth and viability plots in the absence and presence of WP621 were constructed from the frequency of the attached cells per chamber. A 50% reduction in cell number was observed at the 75 nM concentration of WP321. Mitotic and postmitotic cells were identified based on high intensity of maximal pixel of DAPI fluorescence. An increase in proportion of cells in G2 was seen at 75-300 nM of WP631. Relatively few (<12%) apoptotic cells, identified by the presence of DNA strand breaks, remained attached in the WP631-treated cultures.

CONCLUSIONS

Because late apoptotic cells detach during culturing, the cells that remain attached in the multi-chamber cultures represent predominantly live cells; the deficit in their number compared with the untreated cultures, recorded by LSC during scanning, provides information about the degree of cytostatic and cytotoxic effects of the studied drug. The possibility to demonstrate the cell cycle distribution, including a distinction between G2 and M cells, provides an additional advantage of this assay. Other parameters that may be associated with the cell cycle perturbation or with induction of apoptosis also can be measured in the same cultures by using the multiparameter capabilities of LSC. Each measured cell can be relocated for imaging or measurement after subsequent staining with other probes.

Holographic face models as planning tool in maxillofacial surgery

The holographic facial profile scan is a new technique for creation of high-resolution, three-dimensional, realistic facial computer models which can be used for surgical planning and documentation in maxillofacial surgery. First, a holographic image of the patient is recorded using a pulsed laser system. In a second step, called holographic tomography, the real image of the patient's hologram is reconstructed by means of a continuous-wave laser. By moving a screen through the real three-dimensional image, it is sliced into a series of two-dimensional projections which are captured with a digital camera. The slices containing the specific two-dimensional information are superimposed to a three-dimensional surface model using special software. The extremely short exposure time of 35 nanoseconds for taking a holographic image is separated from the time-consuming rendering process of the surface model; thus, the obtained models are not affected by the movements of the patient.

Holographic optical coherence imaging of rat osteogenic sarcoma tumor spheroids

Holographic optical coherence imaging is a full-frame variant of coherence-domain imaging. An optoelectronic semiconductor holographic film functions as a coherence filter placed before a conventional digital video camera that passes coherent (structure-bearing) light to the camera during holographic readout while preferentially rejecting scattered light. The data are acquired as a succession of en face images at increasing depth inside the sample in a fly-through acquisition. The samples of living tissue were rat osteogenic sarcoma multicellular tumor spheroids that were grown from a single osteoblast cell line in a bioreactor. Tumor spheroids are nearly spherical and have radial symmetry, presenting a simple geometry for analysis. The tumors investigated ranged in diameter from several hundred micrometers to over 1 mm. Holographic features from the tumors were observed in reflection to depths of 500-600 microm with a total tissue path length of approximately 14 mean free paths. The volumetric data from the tumor spheroids reveal heterogeneous structure, presumably caused by necrosis and microcalcifications characteristic of some human avascular tumors.

Metabolite-sensitive holographic biosensors

A new type of biosensor that combines the inexpensiveness and mass-produceability of reflection holograms with the selectivity and specificity of enzymes is described. pH-sensitive holographic sensors were fabricated from ionizable monomers incorporated into thin, polymeric, hydrogel films which were transformed into volume holograms using a diffusion method coupled with holographic recording, using a frequency-doubled Nd:YAG laser (532 nm). These holograms were used as transducer systems to monitor the pH changes associated with specific enzymatic reactions to construct prototype urea- and penicillin-sensitive biosensors. The diffraction wavelength (color) of the holographic biosensors was used to characterize their shrinkage and swelling behavior as a function of analyte concentration. The potential of these sensors for the measurement of the clinically and industrially important metabolites urea and penicillin G is demonstrated.

X-ray omni microscopy

The science of wave-field phase retrieval and phase measurement is sufficiently mature to permit the routine reconstruction, over a given plane, of the complex wave-function associated with certain coherent forward-propagating scalar wave-fields. This reconstruction gives total knowledge of the information that has been encoded in the complex wave-field by passage through a sample of interest. Such total knowledge is powerful, because it permits the emulation in software of the subsequent action of an infinite variety of coherent imaging systems. Such 'virtual optics', in which software forms a natural extension of the 'hardware optics' in an imaging system, may be useful in contexts such as quantitative atom and X-ray imaging, in which optical elements such as beam-splitters and lenses can be realized in software rather than optical hardware. Here, we develop the requisite theory to describe such hybrid virtual-physical imaging systems, which we term 'omni optics' because of their infinite flexibility. We then give an experimental demonstration of these ideas by showing that a lensless X-ray point projection microscope can, when equipped with the appropriate software, emulate an infinite variety of optical imaging systems including those which yield interferograms, Zernike phase contrast, Schlieren imaging and diffraction-enhanced imaging.

Influence of the elliptical illumination on acquisition and correction of coherent aberrations in high-resolution electron holography

In high-resolution off-axis electron holography, the interpretable lateral resolution is extended up to the information limit of the electron microscope by means of a correcting phase plate in Fourier space. A plane illuminating electron wave is generally assumed. However, in order to improve spatial coherence, which is essential for holography, the object under investigation is illuminated with an elliptically shaped electron source. This special illumination imposes a variation of beam directions over the field of view. Therefore, due to the interaction of beam tilt and coherent wave aberration, the effective aberrations vary over the field of view yielding a loss of isoplanicity. Consequently, in the past the aberrations were only corrected successfully for a small part of the field of view. However, a thorough analysis of the holographic imaging process shows that the imaging artifacts introduced by the elliptical illumination can be corrected under reconstruction by means of a phase curvature, which models the illuminating wave front. Applied in real space, this phase curvature is seamlessly incorporated into the correction process for coherent wave aberration resulting in an improvement of interpretable lateral resolution up to the information limit for the whole field of view.

Quantitative characterization of edge enhancement in phase contrast x-ray imaging

The aim of this study was to model the edge enhancement effect in in-line holography phase contrast imaging. A simple analytical approach was used to quantify refraction and interference contrasts in terms of beam energy and imaging geometry. The model was applied to predict the peak intensity and frequency of the edge enhancement for images of cylindrical fibers. The calculations were compared with measurements, and the relationship between the spatial resolution of the detector and the amplitude of the phase contrast signal was investigated. Calculations using the analytical model were in good agreement with experimental results for nylon, aluminum and copper wires of 50 to 240 microm diameter, and with numerical simulations based on Fresnel-Kirchhoff theory. A relationship between the defocusing distance and the pixel size of the image detector was established. This analytical model is a useful tool for optimizing imaging parameters in phase contrast in-line holography, including defocusing distance, detector resolution and beam energy.

Holography does not account for goodness: a critique of van der Helm and Leeuwenberg (1996)

P. A. van der Helm and E. L. J. Leeuwenberg (1996) outlined a holographic account of figural goodness of a perceptual stimulus. The theory is mathematically precise and can be applied to a broad spectrum of empirical data. The authors argue, however, that the account is inadequate on both theoretical and empirical grounds. The theoretical difficulties concern the internal consistency of the account and its reliance on unspecified auxiliary assumptions. The account also makes counterintuitive empirical predictions, which do not fit past data or the results of a series of new experimental studies.

Off-axis STEM or TEM holography combined with four-dimensional diffraction imaging

Ultrahigh-resolution imaging may be achieved using modifications of the off-axis holography scheme in a scanning transmission electron microscopy (STEM) instrument equipped with one or more electrostatic biprisms in the illuminating system. The resolution is governed by the diameter of a reference beam, reduced by channeling through a line of atoms in an atomic-focuser crystal. Alternatively, the off-axis holography may be combined with the Rodenburg method in which a four-dimensional data set is obtained by recording a nanodiffraction pattern from each point of the specimen as the incident beams are scanned. An ultrahigh-resolution image is derived by computer processing to give a particular two-dimensional section of this data set. The large amount of data recording and data processing involved with this method may be avoided if the two-dimensional section is derived by recording the hologram while the four beams produced by two perpendicular biprisms are scanned in opposing directions across the specimen by varying the voltages on the biprisms. An equivalent scheme for conventional TEM is also possible. In each case, the complex transmission function of the specimen may be derived and resolutions of about 0.05 nm may be expected.

Transmission electron microscopy on thin film of high density magnetic composite prepared by FIB method

A thin specimen of a high density magnetic composite (HDMC), which is a type of powder magnetic cores was prepared for transmission electron microscopy (TEM) using a focused ion beam (FIB) method. A homogeneous thin film containing an insulator boundary between the constituent Fe powders was obtained successfully. Using this thin film, detailed flow of magnetic flux was visualized by electron holography, and the magnetic flux density was estimated to be 1.73 +/- 0.09 T being consistent with that of a bulk HDMC (1.70 T). Moreover, through Lorentz microscopy, the characteristic magnetization process of HDMC was observed by applying the magnetic field up to approximately 8 kA/m.

Time-dependent speckle in holographic optical coherence imaging and the health of tumor tissue

Holographic optical coherence imaging acquires en face images from successive depths inside scattering tissue. In a study of multicellular tumor spheroids the holographic features recorded from a fixed depth are observed to be time dependent, and they may be classified as variable or persistent. The ratio of variable to persistent features, as well as speckle correlation times, provides quantitative measures of the health of the tissue. Studies of rat osteogenic sarcoma tumor spheroids that have been subjected to metabolic and cross-polymerizing poisons provide quantitative differentiation among healthy, necrotic, and poisoned tissue. Organelle motility in healthy tissue appears as super-Brownian laser speckle, whereas chemically fixed tissue exhibits static speckle.

Side-milling technique of preparing device cross-sections for electron holography based on a focused ion beam micro-sampling system

A new milling technique based on a focused ion beam (FIB) microsampling system is proposed to avoid the curtaining effect, commonly occurring in other FIB milling methods, in order to obtain a crosssectional device specimen with uniform thickness can be obtained for electron holographic observation.

Electron holography on remanent magnetization distribution of melt-spun Nd-Fe-B magnets

Microstructures and magnetic domain structures of melt-spun Nd-Fe-B permanent magnets were investigated in detail by analytical electron microscopy and electron holography. While the crystal orientation of matrix Nd2Fe14B grains was analyzed by nanobeam electron diffraction, precipitates of a few tens of nanometers at grain boundaries were identified to be alpha-Fe by energy-dispersive X-ray spectroscopy. The detailed magnetization distribution in Nd2Fe14B grains and at their boundaries was visualized by electron holography. Ex situ experimentation with an electromagnet revealed that the domain walls in the demagnetized state and remanent states were pinned at grain boundaries, and Fe precipitates at the grain boundary were situated at the center of the closure domain.