Scatter Signatures Research Articles

Sorting single-cell microcarriers using commercial flow cytometers.

The scale of biological discovery is driven by the vessels in which we can perform assays and analyze results, from multi-well plates to microfluidic compartments. We report on the compatibility of sub-nanoliter single-cell containers or "nanovials" with commercial fluorescence activated cell sorters (FACS). This recent lab on a particle approach utilizes 3D structured microparticles to isolate cells and perform single-cell assays at scale with existing lab equipment. Use of flow cytometry led to detection of fluorescently labeled protein with dynamic ranges spanning 2-3 log and detection limits down to ∼10,000 molecules per nanovial, which was the lowest amount tested. Detection limits were improved compared to fluorescence microscopy measurements using a 20X objective and a cooled CMOS camera. Nanovials with diameters between 35-85 µm could also be sorted with purity from 99-93% on different commercial instruments at throughputs up to 800 events/second. Cell-loaded nanovials were found to have unique forward and side (or back) scatter signatures that enabled gating of cell-containing nanovials using scatter metrics alone. The compatibility of nanovials with widely-available commercial FACS instruments promises to democratize single-cell assays used in discovery of antibodies and cell therapies, by enabling analysis of single cells based on secreted products and leveraging the unmatched analytical capabilities of flow cytometers to sort important clones.

Multicontrast investigation of in vivo wildtype zebrafish in three development stages using polarization-sensitive optical coherence tomography.

.Significance: The scattering and polarization characteristics of various organs of in vivo wildtype zebrafish in three development stages were investigated using a non-destructive and label-free approach. The presented results showed a promising first step for the usability of Jones-matrix optical coherence tomography (JM-OCT) in zebrafish-based research.Aim: We aim to visualize and quantify the scatter and polarization signatures of various zebrafish organs for larvae, juvenile, and young adult animals in vivo in a non-invasive and label-free way.Approach: A custom-built polarization-sensitive JM-OCT setup in combination with a motorized translation stage was utilized to investigate live zebrafish. Depth-resolved scattering (intensity and attenuation coefficient) and polarization (birefringence and degree of polarization uniformity) properties were analyzed. OCT angiography (OCT-A) was utilized to investigate the vasculature label-free and non-destructively.Results: The scatter and polarization signatures of the zebrafish organs such as the eye, gills, and muscles were investigated. The attenuation coefficient and birefringence changes between 1- and 2-month-old animals were evaluated in selected organs. OCT-A revealed the vasculature of in vivo larvae and juvenile zebrafish in a label-free manner.Conclusions: JM-OCT offers a rapid, label-free, non-invasive, tissue specific, and three-dimensional imaging tool to investigate in vivo processes in zebrafish in various development stages.

Small-Angle X-ray Scattering Signatures of Conformational Heterogeneity and Homogeneity of Disordered Protein Ensembles.

An accurate account of disordered protein conformations is of central importance to deciphering the physicochemical basis of biological functions of intrinsically disordered proteins and the folding-unfolding energetics of globular proteins. Physically, disordered ensembles of nonhomopolymeric polypeptides are expected to be heterogeneous, i.e., they should differ from those homogeneous ensembles of homopolymers that harbor an essentially unique relationship between average values of end-to-end distance REE and radius of gyration Rg. It was posited recently, however, that small-angle X-ray scattering (SAXS) data on conformational dimensions of disordered proteins can be rationalized almost exclusively by homopolymer ensembles. Assessing this perspective, chain-model simulations are used to evaluate the discriminatory power of SAXS-determined molecular form factors (MFFs) with regard to homogeneous versus heterogeneous ensembles. The general approach adopted here is not bound by any assumption about ensemble encodability, in that the postulated heterogeneous ensembles we evaluated are not restricted to those entailed by simple interaction schemes. Our analysis of MFFs for certain heterogeneous ensembles with more narrowly distributed REE and Rg indicates that while they deviate from MFFs of homogeneous ensembles, the differences can be rather small. Remarkably, some heterogeneous ensembles with asphericity and REE drastically different from those of homogeneous ensembles can nonetheless exhibit practically identical MFFs, demonstrating that SAXS MFFs do not afford unique characterizations of basic properties of conformational ensembles in general. In other words, the ensemble to MFF mapping is practically many-to-one and likely nonsmooth. Heteropolymeric variations of the REE-Rg relationship were further showcased using an analytical perturbation theory developed here for flexible heteropolymers. Ramifications of our findings for interpretation of experimental data are discussed.

Fabrication and performance evaluation of reflectorless refractive index fiber optic sensors using etched enhanced backscattering fibers

We propose and evaluate a technique for the fabrication and interrogation of fiber-optic refractive index (RI) sensors based on etched MgO-based nanoparticle doped fibers. The discussed method does not require to inscribe a reflective element into the fiber. Instead, light backscattered by the fiber can give sufficient information that is necessary for detection, by performing the cross-correlation of Rayleigh scatter signatures in the etched zones. The performance of the sensor is monitored using distributed sensing, which allows to interrogate several points along the length of the fiber. The sensitivities of several etched fibers are compared. The largest sensitivity that has been achieved is 45.95 nm/RIU (RI units), with the possibility of implementing temperature compensation.

Contrastive-Regulated CNN in the Complex Domain: A Method to Learn Physical Scattering Signatures From Flexible PolSAR Images

Single- and dual-polarimetric synthetic aperture radar (SAR) images provide very limited capabilities to interpret physical radar signatures. For generality and simplicity, we call single-polarimetric, dual-polarimetric, and fully polarimetric SAR (PolSAR) images flexible PolSAR images. In order to sufficiently extract physical scattering signatures from this kind of data and explore the potentials of different polarization modes on this task, this paper proposes a contrastive-regulated convolutional neural network (CNN) in the complex domain, attempting to learn a physically interpretable deep learning model directly from the original backscattered data. To achieve a better deep model containing physically interpretable parameters, the objective cost is compared to and selected from several commonly used loss functions in the complex form. The required ground-truth labels are generated automatically according to Cloude and Pottier’s H-alpha division plane, which significantly reduces intensive labor cost and transfers this method to an unsupervised learning mechanism. The boundaries between different scattering signatures, however, sometimes show an erroneous separation. With the aim of aggregating intra-class instances and alienating inter-class instances, meanwhile, a complex-valued contrastive regularization term is computed mathematically and is added to the objective cost by a tradeoff factor. Moreover, data augmentation is applied to relieve the side effects caused by data imbalance. Finally, we performed experiments on German Aerospace Center’s (DLR)’s L-band, high-resolution (HR), and airborne F-SAR data. Our results demonstrate the possibility of extracting physical scattering signatures from flexible PolSAR images. Physically interpretable potentials of SAR images with different polarization modes are analyzed, and we conclude with physical signature identification.

Developing focal construct technology for in vivo diagnosis of osteoporosis

Osteoporosis is a prevalent bone disease around the world, characterised by low bone mineral density and increased fracture risk. Currently, the gold standard for identifying osteoporosis and increased fracture risk is through quantification of bone mineral density (BMD), using dual energy X-ray absorption (DEXA). However, the use of BMD to diagnose osteoporosis is not without limitation and arguably the risk of osteoporotic fracture should be determined collectively by bone mass, architecture and physicochemistry of the mineral composite building blocks. Rather than depending exclusively on the ‘mass’ of bone, our previous research investigated predicting the risk of fracture using ‘bone quality’. The work highlighted that the material properties of OP tissue differ significantly to that of ‘normal’ bone and for the first time reported the clinical value of new biomarkers (obtained from X-ray scatter signatures) for fracture risk prediction. Thus, in order to improve fracture prediction models, diagnostic tools need to be developed which not only measure bone mineral density, but also bone quality.This pilot study builds on our previous work and aims to develop a new technology, Focal Construct Technology (FCT), which is hoped can measure XRD signatures in vivo. Our previous work was performed entirely with interrogating probes applied in transmission mode. This has some disadvantages that would be overcome were reflection mode employed. This study involves the creation of unique, high impact data with the potential to form the basis of a new generation of medical diagnostic instrumentation. A systematic series of conventional reflection mode ex vivo experiments were performed in which bone specimens were examined through increasing thicknesses of overlaying muscle/fat/skin. Further, we applied FCT to these geometries. This had not previously been attempted and required some initial modelling to ensure correct topologies of the hollow beams. The results from this study suggest it may be possible to obtain the parameters in vivo with the same precision as those obtained within the laboratory when using FCT.

Convective Boundary Layer Depth Estimation from S-Band Dual-Polarization Radar

AbstractThis study investigates Bragg scatter signatures in dual-polarization radar observations, which are defined by low differential reflectivity values, as a proxy for convective boundary layer (CBL) depth. Using data from the WSR-88D in Twin Lakes, Oklahoma (KTLX), local minima in quasi-vertical profiles of are found to provide a reasonable estimate of CBL depth when compared with depth estimates from upper-air soundings from Norman, Oklahoma (KOUN), during 2014. The 243 Bragg scatter and upper-air sounding CBL depth estimates have a correlation of 0.90 and an RMSE of 254 m. Using Bragg scatter as a proxy for CBL depth was expanded to other seasons and locations—performing well in Wilmington, Ohio; Fairbanks, Alaska; Tucson, Arizona; Minneapolis, Minnesota; Albany, New York; Portland, Oregon; and Tampa, Florida—showing its potential usefulness in monitoring CBL depth throughout the year in a variety of geographic locations and meteorological conditions.

Compact energy dispersive X-ray microdiffractometer for diagnosis of neoplastic tissues

An energy dispersive X-ray microdiffractometer with capillary optics has been developed for characterizing breast cancer. The employment of low divergence capillary optics helps to reduce the setup size to a few centimeters, while providing a lateral spatial resolution of 100µm. The system angular calibration and momentum transfer resolution were assessed by a detailed study of a polycrystalline reference material. The performance of the system was tested by means of the analysis of tissue-equivalent samples previously characterized by conventional X-ray diffraction. In addition, a simplified correction model for an appropriate comparison of the diffraction spectra was developed and validated. Finally, the system was employed to evaluate normal and neoplastic human breast samples, in order to determine their X-ray scatter signatures. The initial results indicate that the use of this compact energy dispersive X-ray microdiffractometer combined with a simplified correction procedure is able to provide additional information to breast cancer diagnosis.

Experimental characterization of nonlinear processes of whistler branch waves

Experiments in the Space Physics Simulation Chamber at the Naval Research Laboratory isolated and characterized important nonlinear wave-wave and wave-particle interactions that can occur in the Earth's Van Allen radiation belts by launching predominantly electrostatic waves in the intermediate frequency range with wave normal angle greater than 85° and measuring the nonlinearly generated electromagnetic scattered waves. The scattered waves have a perpendicular wavelength that is nearly an order of magnitude larger than that of the pump wave. Calculations of scattering efficiency from experimental measurements demonstrate that the scattering efficiency is inversely proportional to the damping rate and trends towards unity as the damping rate approaches zero. Signatures of both wave-wave and wave-particle scatterings are also observed in the triggered emission process in which a launched wave resonant with a counter-propagating electron beam generates a large amplitude chirped whistler wave. The possibility of nonlinear scattering or three wave decay as a saturation mechanism for the triggered emission is suggested. The laboratory experiment has inspired the search for scattering signatures in the in situ data of chorus emission in the radiation belts.

X-ray diffraction from bone employing annular and semi-annular beams

There is a compelling need for accurate, low cost diagnostics to identify osteo-tissues that are associated with a high risk of fracture within an individual. To satisfy this requirement the quantification of bone characteristics such as ‘bone quality’ need to exceed that provided currently by densitometry. Bone mineral chemistry and microstructure can be determined from coherent x-ray scatter signatures of bone specimens. Therefore, if these signatures can be measured, in vivo, to an appropriate accuracy it should be possible by extending terms within a fracture risk model to improve fracture risk prediction.In this preliminary study we present an examination of a new x-ray diffraction technique that employs hollow annular and semi-annular beams to measure aspects of ‘bone quality’. We present diffractograms obtained with our approach from ex vivo bone specimens at Mo Kα and W Kα energies. Primary data is parameterized to provide estimates of bone characteristics and to indicate the precision with which these can be determined.

Novel magnetic state ind4Mott insulators

We show that the interplay of strong Hubbard interaction $U$ and spin-orbit coupling $\lambda$ in systems with $d^4$ electronic configuration leads to several unusual magnetic phases. Most notably, we find that competition between superexchange and spin-orbit coupling leads to a phase transition from a non-magnetic state predicted by atomic physics to a novel magnetic state in the large $U$ limit. We show that the local moment changes dramatically across this phase transition, challenging the conventional wisdom that local moments are robust against small perturbations in a Mott insulator. The Hund's coupling plays an important role in determining the nature of the magnetism. We identify candidate materials and present predictions for Resonant X-ray Scattering (RXS) signatures of the unusual magnetism in $d^4$ Mott insulators.

Detection of hail through the three-body scattering signatures and its effects on radar algorithms observed in Romania

The Romanian National Meteorological Administration (NMA) radar network consists of five S-band and four C-band radars. Observation of convection in Romania through the Doppler radar network offered a new perspective in understanding the climatologic risk of certain regions and mesoscale environments. Highly organized convective systems, such as supercells, are better observed and their subsequent threat can be better anticipated during the nowcasting process using Doppler velocity fields and detection algorithms such as mesocyclones (MESO) and tornadic vortex signature (TVS). However, for warning purposes, these tools cannot be used without a subjective validation because of the associated errors and limitations of radar observations. In this paper several cases are presented where the presence of large hail inside the storm produced a radar artifact named three-body scatter signature (TBSS) that disturbed the Doppler velocity field. The cases presented were observed with S-band radars and were associated with hail reports on the ground. The first case shows a TBSS whose radial Doppler velocities are negative due to the falling hydrometeors. The second case is a less frequent event; there the Doppler velocities in the TBSS region are positive due to the updraft. The third case has both positive and negative values in the TBSS region; it ocurred in a supercell that affected the city of Varna in Bulgaria with large hail. The positive values were associated with the overhang region in the rotational updraft at upper heights, while the negative values in the regions outside the rotational updraft at lower heights, were associated with the downdrafts. Features produced by the TBSS have perturbed the output of the MESO and TVS algorithms by introducing false strong values of wind shear that have been interpreted as rotation. Thus false mesocyclonic and tornadic vortex signatures were generated. In some of the cases large hail and weak tornadoes were reported, so the presence of a TBSS was a challenge for the nowcasters. In the last part of the paper we analyze the link between the TBSS appearance with reports of large hail at the ground in 2009 within the coverage area of the Romanian S-band radars, which also cover parts of Hungary, Bulgaria, the Republic of Moldova and Serbia. The results show that the TBSS artifact is a strong indicator of large-size hail.

Classical Calculations of Scattering Signatures from a Gravitational Singularity or the Scattering and Absorption Cross-Sections of a Black Hole

Within the context of general relativity theory we calculate, analytically, scattering signatures around a gravitational singularity: angular and time distributions of scattered massive objects and photons and the time and space modulation of Doppler effects. Additionally, the scattering and absorption cross sections for the gravitational interactions are calculated. The results of numerical simulations of the trajectories are compared with the analytical results.

About the influence of Line Edge Roughness on measured effective–CD

Various reports state that Line Edge/Width Roughness (LER/LWR) has a significant impact on the integrated circuits fabricated by means of lithography, hence there is a need to determine the LER in-line so that it never exceeds certain specified limits. In our work we deal with the challenge of measuring LER on 50 nm resist gratings using scatterometry. We show by simulation that there is a difference between LER and no-LER scatter signatures which first: depends on the polarization and second: is proportional to the amount of LER. Moreover, we show that the mentioned difference is very specific, that is - a grating with LER acts like a grating without LER but showing another width (CD, Critical Dimension), which we refer-to as effective-CD.

Position determination of scatter signatures – A novel sensor geometry

A novel diffraction sensor geometry able to provide the diffraction pattern of a suspect material without prior knowledge of the samples location is introduced. The sensor geometry can also resolve diffraction patterns originating from multiple unknown materials overlapped along the primary X-ray beam path. This is achieved through tracking Bragg peak maxima that linearly propagate from the inspection volume at a series of X-ray detector positions. A series of simulations and experiments have been performed to verify this technique and provide an insight into its characteristics. Such a technique could have widespread appeal in the security industry. Areas of most relevance include the materials characterisation of volumes such as those prevalent in an airport screening environment or equally the rapid screening for illicit drugs trafficked through the postal system.

Flow Cytometry As a Novel Tool to Evaluate and Separate Vesicles Using Characteristic Scatter Signatures

Vesicles are usually characterized for their structure by microscopy or, less often, by the addition of fluorescent dyes in a flow cytometer. We present a new method of studying these structures and associated forms by forward and side scatter analysis on a flow cytometer which has the advantage of simultaneous handling of large population of vesicles to identify their shapes and lamellarities. The technique is suitable for several types of vesicular structures like Multivesicular vesicles (MVV), multilamellar and unilamellar vesicles. Characteristic signatures are given by tubular structures and fine features thereon allow detection of complex structures such as fused and ellipsoidal forms. Coexistence of tubular and spherical structures, such as those known to form when surfactants/salt solutions are diluted, can clearly be detected by the signature pattern, which separates into two distinctly identifiable populations. The population can be sorted or separated easily based on these signatures and such sorting has allowed us to confirm our findings by microscopic observations. This novel method can thus be used for concurrent observations of vesicle populations with dye or more advantageously without employing any fluorescent tag.

An active pixel sensor x-ray diffraction (APXRD) system for breast cancer diagnosis

This paper describes the potential application of an active pixel sensor-based x-ray diffraction (APXRD) system in the field of breast cancer diagnosis. The design and initial testing of the system was reported previously (Bohndiek et al 2008b Phys. Med. Biol. 53 655–72). The system has potential both as a ‘diffraction enhanced breast imager’ (DEBI) and as a probe for quantitative analysis of breast biopsy samples. The resolution of the system in a DEBI arrangement is 1 mm and the contrast available using a material-specific x-ray diffraction image was found to be up to seven times greater than that of a transmission image. Scatter signatures from a series of biopsy-equivalent samples, ranging in composition from 100% fat to 100% fibrous tissue, were acquired with the APXRD system. Multivariate data analysis was used to produce a partial least squares (PLS) model sensitive to sample fat content. The final model is able to accurately predict the fat content of a series of unknown samples and is robust to significant added noise. This suggests that the APXRD system could provide a simple, semi-automated, quantitative measurement system for analysis of breast biopsy samples. Training on a range of scatter signatures from real breast biopsy samples covering various stages of disease is now needed to test this hypothesis.

Aspect sensitive E- and F-region SPEAR-enhanced incoherent backscatter observed by the EISCAT Svalbard radar

Abstract. Previous studies of the aspect sensitivity of heater-enhanced incoherent radar backscatter in the high-latitude ionosphere have demonstrated the directional dependence of incoherent scatter signatures corresponding to artificially excited electrostatic waves, together with consistent field-aligned signatures that may be related to the presence of artificial field-aligned irregularities. These earlier high-latitude results have provided motivation for repeating the investigation in the different geophysical conditions that obtain in the polar cap ionosphere. The Space Plasma Exploration by Active Radar (SPEAR) facility is located within the polar cap and has provided observations of RF-enhanced ion and plasma line spectra recorded by the EISCAT Svalbard UHF incoherent scatter radar system (ESR), which is collocated with SPEAR. In this paper, we present observations of aspect sensitive E- and F-region SPEAR-induced ion and plasma line enhancements that indicate excitation of both the purely growing mode and the parametric decay instability, together with sporadic E-layer results that may indicate the presence of cavitons. We note consistent enhancements from field-aligned, vertical and also from 5° south of field-aligned. We attribute the prevalence of vertical scatter to the importance of the Spitze region, and of that from field-aligned to possible wave/irregularity coupling.

Automated identification of tumor microscopic morphology based on macroscopically measured scatter signatures

An automated algorithm and methodology is presented to identify tumor-tissue morphologies based on broadband scatter data measured by raster scan imaging of the samples. A quasi-confocal reflectance imaging system was used to directly measure the tissue scatter reflectance in situ, and the spectrum was used to identify the scattering power, amplitude, and total wavelength-integrated intensity. Pancreatic tumor and normal samples were characterized using the instrument, and subtle changes in the scatter signal were encountered within regions of each sample. Discrimination between normal versus tumor tissue was readily performed using a K-nearest neighbor classifier algorithm. A similar approach worked for regions of tumor morphology when statistical preprocessing of the scattering parameters was included to create additional data features. This type of automated interpretation methodology can provide a tool for guiding surgical resection in areas where microscopy imaging cannot be realized efficiently by the surgeon. In addition, the results indicate important design changes for future systems.

Label-free detection of multiple bacterial pathogens using light-scattering sensor

Technologies for rapid detection and classification of bacterial pathogens are crucial for securing the food supply. This report describes a light-scattering sensor capable of real-time detection and identification of colonies of multiple pathogens without the need for a labeling reagent or biochemical processing. Bacterial colonies consisting of the progeny of a single parent cell scatter light at 635 nm to produce unique forward-scatter signatures. Zernike moment invariants and Haralick descriptors aid in feature extraction and construction of the scatter-signature image library. The method is able to distinguish bacterial cultures at the genus and species level for Listeria, Staphylococcus, Salmonella, Vibrio, and Escherichia with an accuracy of 90–99% for samples derived from food or experimentally infected animal. Varied amounts of exopolysaccharide produced by the bacteria causes changes in phase modulation distributions, resulting in strikingly different scatter signatures. With the aid of a robust database the method can potentially detect and identify any bacteria colony essentially instantaneously. Unlike other methods, it does not destroy the sample, but leaves it intact for other confirmatory testing, if needed, for forensic or outbreak investigations.